Initiator element gene transcriptions

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Editor-In-Chief: Henry A. Hoff

In the biosynthesis of any human protein, the gene that contains the nucleotide sequence which is translated into that protein must be transcribed. For RNA polymerase II holoenzyme to transcribe the gene, the gene's promoter must be located. After the promoter is located, the transcription start site (TSS) is pinpointed by using nucleotide sequences that include the TSS. Within the promoter, most human genes lack a TATA box and have an initiator element (Inr) or downstream promoter element instead.

On the basis of descriptions available, various Inrs are located to test whether the known TSS is located.

Notations

Main article: Notations

Notation: let the symbol Inr denote an initiator element.

Notation: let the symbol +1 designate the nucleotide that is the transcription start site (TSS).

Genetics

Main article: Genetics

Inr in humans was first explained and sequenced in 1989.[1]

The Inr element for core promoters was found to be more prevalent than the TATA box in eukaryotic promoter domains.[2] In a study of 1800+ distinct human promoter sequences it was found that 49% contain the Inr element while 21.8% contain the TATA box.[2]

Gene transcriptions

Main article: Gene transcriptions

Two subunits, TAF1 and TAF2, of the TFIID recognize the Inr sequence and bring the complex together.[3]

The interaction between TFIID and Inr is believed to be most imperative in initiating transcription due to the Inr sequence overlapping the start site.[4]

The Inr element is also believed to interact with the activator Sp1 transcription factor (Sp1), specificity protein 1 transcription factor, which is then able to regulate the activation and initiation of transcription[5]

Promoters with a functional Inr are more likely to lack a TATA box or to possess a degenerate TATA sequence because a gene with an active Inr is less dependent on a functional TATA box or additional promoters.[6] Although Inr element varies between promoters, the sequence is highly conserved between humans and yeast.[6] An analysis of 7670 transcription start sites showed that roughly 40% had an exact match to the BBCA+1BW Inr sequence, while 16% contained only one mismatch [7] TFIID and subunits are very sensitive to the Inr sequence and nucleotide changes have been shown to drastically change the binding affinity, where the +1 and -3 positions have been identified as the most critical for transcription efficiency and Inr function.[6] A replacement of the Adenosine (A) nucleotide at the +1 to G or T changes transcription activity by 10% and a replacement of Thymine (T) at the +3 position changes transcription activity levels by 22%.[8]

Theoretical initiator elements

Here's a theoretical definition:

Def. a series of nucleotides including a transcription start site on one DNA strand whose presence in a gene promoter eventually leads to a chain reaction or polymerization such as transcription is called an initiator element.

Consensus sequence for an Inr-like/TCT is 5'-TTCTCT-3'.[9]

RNA polymerase IIs

Main articles: RNA polymerase II gene transcriptions and RNA polymerase IIs

"RNA pol II itself recognizes features of the Inr which might assist the correct positioning of the polymerase on the promoter (Carcamo et al., 1991; Weis and Reinberg, 1997)."[10][11][12]

RNA polymerase II may form a stable complex on TATA-less promoters that contain Inr elements and possess a weak, intrinsic preference for Inr-like sequences.[11]

RNA polymerase II holoenzyme complexes

Main articles: RNA polymerase II holoenzyme complex gene transcriptions and RNA polymerase II holoenzyme complexes

Gene ID: 672 is BRCA1 BRCA1, DNA repair associated. "This gene encodes a nuclear phosphoprotein that plays a role in maintaining genomic stability, and it also acts as a tumor suppressor. The encoded protein combines with other tumor suppressors, DNA damage sensors, and signal transducers to form a large multi-subunit protein complex known as the BRCA1-associated genome surveillance complex (BASC). This gene product associates with RNA polymerase II, and through the C-terminal domain, also interacts with histone deacetylase complexes. This protein thus plays a role in transcription, DNA repair of double-stranded breaks, and recombination. Mutations in this gene are responsible for approximately 40% of inherited breast cancers and more than 80% of inherited breast and ovarian cancers. Alternative splicing plays a role in modulating the subcellular localization and physiological function of this gene. Many alternatively spliced transcript variants, some of which are disease-associated mutations, have been described for this gene, but the full-length natures of only some of these variants has been described. A related pseudogene, which is also located on chromosome 17, has been identified."[13]

Gene ID: 1660 is DHX9 DExH-box helicase 9 (aka LKP; RHA; DDX9; NDH2; NDHII). "This gene encodes a member of the DEAH-containing family of RNA helicases. The encoded protein is an enzyme that catalyzes the ATP-dependent unwinding of double-stranded RNA and DNA-RNA complexes. This protein localizes to both the nucleus and the cytoplasm and functions as a transcriptional regulator. This protein may also be involved in the expression and nuclear export of retroviral RNAs. Alternate splicing results in multiple transcript variants. Pseudogenes of this gene are found on chromosomes 11 and 13."[14]

BRCA1 has been shown to interact with DHX9; i.e., overexpression of a protein fragment of RNA helicase A causes inhibition of endogenous BRCA1 function and defects in ploidy and cytokinesis in mammary epithelial cells[15] and the BRCA1 protein is linked to the RNA polymerase II holoenzyme complex via RNA helicase A.[16]

ATP-dependent RNA helicase A (RHA; also known as DHX9, LKP, and NDHI) is an enzyme that in humans is encoded by the DHX9 gene.[17][18][14]

RNA polymerase II subunit A C-terminal domain phosphatase is an enzyme that in humans is encoded by the CTDP1 gene.[19][20][21]

Gene ID: 9150 is CTDP1 CTD phosphatase subunit 1. "This gene encodes a protein which interacts with the carboxy-terminus of the RAP74 subunit of transcription initiation factor TFIIF, and functions as a phosphatase that processively dephosphorylates the C-terminus of POLR2A (a subunit of RNA polymerase II), making it available for initiation of gene expression. Mutations in this gene are associated with congenital cataracts, facial dysmorphism and neuropathy syndrome (CCFDN). Alternatively spliced transcript variants encoding different isoforms have been described for this gene."[22]

"This gene encodes a protein which interacts with the carboxy-terminus of transcription initiation factor TFIIF, a transcription factor which regulates elongation as well as initiation by RNA polymerase II. The protein may also represent a component of an RNA polymerase II holoenzyme complex. Alternative splicing of this gene results in two transcript variants encoding 2 different isoforms."[21]

CTDP1 has been shown to interact with WD repeat-containing protein 77,[23] GTF2F1[20] and POLR2A.[24]

Gene ID: 168400 is DDX53 DEAD-box helicase 53. "This intronless gene encodes a protein which contains several domains found in members of the DEAD-box helicase protein family. Other members of this protein family participate in ATP-dependent RNA unwinding."[25]

"DEAD/DEAH box helicases are proteins, and are putative RNA helicases. They are implicated in a number of cellular processes involving alteration of RNA secondary structure such as translation initiation, nuclear and mitochondrial splicing, and ribosome and spliceosome assembly. Based on their distribution patterns, some members of this family are believed to be involved in embryogenesis, spermatogenesis, and cellular growth and division. This gene encodes a DEAD box protein with RNA helicase activity. It may participate in melting of DNA:RNA hybrids, such as those that occur during transcription, and may play a role in X-linked gene expression. It contains 2 copies of a double-stranded RNA-binding domain, a DEXH core domain and an RGG box. The RNA-binding domains and RGG box influence and regulate RNA helicase activity."[25]

Consensus sequences

Main articles: Consensus sequence gene transcriptions and Consensus sequences

As in other metazoans, for genes lacking a TATA box, the Inr is functionally analogous, with a base pair (bp) consensus 5'-YYA+1NWYY-3', to direct transcription initiation.[26] Using the degenerate nucleotide code, the consensus sequence is 5'-C/T-C/T-A-A/C/G/T-A/T-C/T-C/T-3', or in the direction of transcription on the template strand: 3'-C/T-C/T-A-A/C/G/T-A/T-C/T-C/T-5'.

"TATA-less core promoters that lack AT-rich sequences in the -30 region and do not stably bind TBP are likely to assemble PICs via alternative pathways and to be regulated by distinct mechanisms (Smale and Kadonaga, 2003). However, the number of such bona fide TATA-less genes remains unclear in eukaryotic genomes."[27]

In Entamoeba histolytica, the consensus sequence is AAAAATTCA.[28]

The Inr has the consensus sequence YYANWYY.[29] Similarly to the TATA box, the Inr element facilitates the binding of transcription Factor II D (TATA binding protein TAF).[29]

Enhancers

Main article: Enhancer gene transcriptions

An Inr for mammalian RNA polymerase II can be defined as a DNA sequence element that overlaps a TSS and is sufficient for

  1. determining the start site location in a promoter that lacks a TATA box and
  2. enhancing the strength of a promoter that contains a TATA box.[30]

TATA binding protein associated factors

Main articles: TATA binding protein ssociated factor gene transcriptions and TATA binding protein associated factors

"Although any isolated TAF may not exhibit sequence-specific interactions at the Inr element in the absence of a TATA-box, a combination of TAFs may bind sequence specifically to the Inr element regardless of the TATA-box and/or DPE (Chalkley and Verrijzer, 1999)."[31] Bold added.

TAF1 "binds to core promoter sequences encompassing the transcription start site. It also binds to activators and other transcriptional regulators, and these interactions affect the rate of transcription initiation."[32]

Prior to transcription, stable binding to an Inr occurs by a complex consisting of TAF1 and TAF2.[10]

TATA box-likes

The Inr is the only element in metazoan protein-encoding genes known to be a functional analog of the TATA box, in that it is sufficient for directing accurate transcription initiation in genes that lack TATA boxes.[33]

General transcription factor II As

Main articles: General factor II A gene transcriptions and General transcription factor II As

General transcription factor II A is critical for the cooperative binding of TFIID to the Inr.[34]

General transcription factor II Ds

Main articles: General factors II D gene transcriptions and General transcription factor II Ds

The general transcription factor II D (TFIID) is one of several general transcription factors that make up the RNA polymerase II preinitiation complex.[35] Before the start of transcription, the transcription factor II D (TFIID) complex, binds to the core promoter of the gene.[35]

TFIID is the first protein to bind to DNA during the formation of the pre-initiation transcription complex of RNA polymerase II (RNA Pol II).[35]

General transcription factor II Is

Main articles: General factor II I gene transcriptions and General transcription factor II Is

General transcription factor II I, or TFII-I, is a factor capable of binding the Inr element.[36][37]

Transcription start sites

Main articles: Start site gene transcriptions and Transcription start sites

Usually the Inr contains the TSS.

"[T]he initiator (INR) element located at, or immediately adjacent to, the TSS, ... is recognized by the TBP-associated factors TAF1 and TAF2 of the TFIID complex".[27]

"[T]ranscription does not need to begin at the +1 nucleotide for the Inr to function. RNA polymerase II has been redirected to alternative start sites by reducing ATP concentrations within a nuclear extract, by altering the spacing between the TATA and Inr in a promoter containing both elements, and by dinucleotide initiation strategies".[38]

Hypotheses

Main article: Hypotheses
  1. A1BG is not transcribed by an initiator element.
  2. A1BG is not transcribed by a TATA box.

Samplings

Main article: A1BG gene transcription core promoters

5'-YYRNWYY-3'

The wider consensus sequence of 3'-YYRNWYY-5' allows a G at the TSS but at most only allows two Gs in a row.[39]

For the Basic programs (starting with SuccessablesInr.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:

  1. negative strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesInr--.bas, looking for 3'-C/T-C/T-A/G-A/C/G/T-A/T-C/T-C/T-5', 121, 3'-TTGTTCC-5', 71, 3'-CTATACC-5', 77, 3'-CCGTTTC-5', 93, 3'-CCGTACT-5', 124, 3'-CCATATT-5', 181, 3'-CTACATT-5', 247, 3'-TTGGTCC-5', 262, 3'-TTATACT-5', 274, 3'-TCACTCT-5', 301, 3'-CTGCTTT-5', 312, 3'-CCGGTTC-5', 419, 3'-CCAGTCC-5', 441, 3'-TCGGACC-5', 459, 3'-TTGTATC-5', 468, 3'-TCACTTT-5', 473, 3'-TCGGACC-5', 508, 3'-CCGGTTC-5', 556, 3'-CCAGTCC-5', 578, 3'-TTATACC-5', 605, 3'-CCGGTCC-5', 648, 3'-CCGGTTC-5', 692, 3'-CCAGTCC-5', 714, 3'-TCGGACT-5', 732, 3'-TCGCACC-5', 741, 3'-CTACACC-5', 787, 3'-TCGGTTC-5', 874, 3'-TCGGACC-5', 899, 3'-TCGCTCT-5', 913, 3'-TCGGTCC-5', 948, 3'-CCGTACC-5', 953, 3'-TTAGTCC-5', 984, 3'-TTGGACC-5', 1015, 3'-TCACTCT-5', 1079, 3'-TCGGACC-5', 1198, 3'-TTGTACC-5', 1207, 3'-CCACTTT-5', 1212, 3'-CCGCACC-5', 1244, 3'-TTGGATC-5', 1306, 3'-TCAGACC-5', 1356, 3'-TTATTCT-5', 1365, 3'-TCGTTTT-5', 1371, 3'-TTGTTTT-5', 1394, 3'-CCACACT-5', 1479, 3'-TTGCTTC-5', 1555, 3'-CCGTTTT-5', 1561, 3'-TTACTTT-5', 1582, 3'-TTGGATT-5', 1591, 3'-TTAATTT-5', 1697, 3'-TTATACC-5', 1742, 3'-CCGCACC-5', 1897, 3'-CCGTACT-5', 1953, 3'-TTGGACC-5', 1959, 3'-TCGGACC-5', 2009, 3'-TCGTTCT-5', 2023, 3'-TTACACC-5', 2065, 3'-CCGGTCC-5', 2077, 3'-TCACATT-5', 2087, 3'-TCAAACT-5', 2141, 3'-TTGTACC-5', 2152, 3'-CCGCTTT-5', 2157, 3'-CCAGTCC-5', 2250, 3'-TCAAACT-5', 2257, 3'-TCGGACC-5', 2268, 3'-TCGTACC-5', 2277, 3'-CCACTTT-5', 2282, 3'-TTGGACC-5', 2385, 3'-TCGGACC-5', 2435, 3'-TCACTCT-5', 2449, 3'-TCGTTTT-5', 2476, 3'-TTGTTTT-5', 2490, 3'-TCATTCT-5', 2503, 3'-CCGGTCC-5', 2519, 3'-CCAGTCC-5', 2587, 3'-TCACACC-5', 2605, 3'-TTGTACC-5', 2614, 3'-CCACTTT-5', 2619, 3'-TCACACC-5', 2658, 3'-TTGGACC-5', 2720, 3'-TCGGACC-5', 2770, 3'-TCGTACT-5', 2784, 3'-TTGATTC-5', 2914, 3'-CCGATTT-5', 3009, 3'-TTGATTC-5', 3031, 3'-CCGCACC-5', 3047, 3'-TCGGACC-5', 3128, 3'-TTGTTCC-5', 3141, 3'-CCACTTT-5', 3146, 3'-TTGTATT-5', 3169, 3'-CCACACC-5', 3186, 3'-TCGGTTC-5', 3273, 3'-TCGGACC-5', 3298, 3'-TTGTTCT-5', 3307, 3'-TCGTTTT-5', 3313, 3'-TTGTTCT-5', 3340, 3'-TCGTTCT-5', 3374, 3'-CCGAACT-5', 3401, 3'-CCGTATC-5', 3446, 3'-TTGATCT-5', 3463, 3'-TTGGTCT-5', 3486, 3'-CTGTTCT-5', 3759, 3'-CTACACC-5', 3810, 3'-CTGGTCC-5', 3871, 3'-TCATTCT-5', 3893, 3'-CTACTTT-5', 3922, 3'-CCGGTCC-5', 3951, 3'-TCGGACC-5', 4037, 3'-TTGTATC-5', 4046, 3'-TCACTCT-5', 4051, 3'-TTACACT-5', 4092, 3'-CCGGTCC-5', 4102, 3'-CCGTACC-5', 4107, 3'-CCGGTCC-5', 4170, 3'-TCGAACC-5', 4188, 3'-TCACTCT-5', 4202, 3'-TCGGTCT-5', 4233, 3'-CTGCACC-5', 4238, 3'-TCGGACC-5', 4300, 3'-CCAGTTT-5', 4309, 3'-TCGGACC-5', 4349, 3'-TCACACT-5', 4361, 3'-TTACTCC-5', 4557,
  2. negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesInr-+.bas, looking for 3'-C/T-C/T-A/G-A/C/G/T-A/T-C/T-C/T-5', 45, 5'-TTGTATT-3' at 115, 5'-CTGTTTT-3' at 147, 5'-CCACACT-3' at 345, 5'-CCGGACT-3' at 746, 5'-CTGCACT-3' at 1372, 5'-CTGCACT-3' at 1472, 5'-CCAGACT-3' at 1744, 5'-CCACTTC-3' at 1914, 5'-CTATTTC-3' at 1978, 5'-CCAGTCC-3' at 2026, 5'-TCGCTTC-3' at 2095, 5'-TCATATT-3' at 2178, 5'-CTGCATT-3' at 2206, 5'-CCAGATC-3' at 2230, 5'-TCAATCT-3' at 2235, 5'-CTGTTTC-3' at 2263, 5'-TCACTCT-3' at 2306, 5'-CTACACC-3' at 2430, 5'-CTAATTT-3' at 2440, 5'-CCGCACC-3' at 2566, 5'-TTATACC-3' at 2590, 5'-CCACACC-3' at 2602, 5'-CCACACT-3' at 2636, 5'-TCAGATT-3' at 2868, 5'-CTGCTCC-3' at 2978, 5'-CCAGTCC-3' at 2998, 5'-CCAGTCC-3' at 3084, 5'-CTGGTCT-3' at 3245, 5'-TCGCTCT-3' at 3276, 5'-CTGGTCT-3' at 3299, 5'-CTGCTCC-3' at 3309, 5'-CTGCACC-3' at 3322, 5'-CCGCATC-3' at 3328, 5'-TTGCACT-3' at 3343, 5'-CTGTTCC-3' at 3352, 5'-TTGCATC-3' at 3402, 5'-TCACACT-3' at 3507, 5'-CCAGACC-3' at 3550, 5'-CTGTTCC-3' at 3625, 5'-TCACACC-3' at 3824, 5'-TCATTTT-3' at 4120, 5'-TCACTCT-3' at 4128, 5'-TTGATTT-3' at 4134, 5'-TTAGTTT-3' at 4139, 5'-CTGCACC-3' at 4343.
  3. positive strand in the negative direction is SuccessablesInr+-.bas, looking for 3'-C/T-C/T-A/G-A/C/G/T-A/T-C/T-C/T-5', 40, 3'-CTGAATT-5', 20, 3'-TTGGACC-5', 32, 3'-CTGCATT-5', 152, 3'-TTGAACC-5', 846, 3'-TCACACC-5', 882, 3'-TTGAACC-5', 1012, 3'-TCACTCC-5', 1058, 3'-TCACACC-5', 1128, 3'-TTGAACC-5', 1303, 3'-TTGCACC-5', 1339, 3'-TTGCACT-5', 1347, 3'-CCAGTCT-5', 1354, 3'-CCATTTC-5', 1380, 3'-TCGCTCT-5', 1450, 3'-CTATATC-5', 1528, 3'-TTATTTT-5', 1727, 3'-CTGCACT-5', 2000, 3'-CTACTCC-5', 2352, 3'-TTGAACC-5', 2382, 3'-TCACACC-5', 2418, 3'-CTGCACT-5', 2426, 3'-TTGAATC-5', 2708, 3'-TTGAACC-5', 2717, 3'-CTGCACC-5', 2761, 3'-TTGAACC-5', 3245, 3'-TTGCACT-5', 3289, 3'-CCAGATC-5', 3488, 3'-CTGCTCC-5', 3582, 3'-CCATTTC-5', 3688, 3'-CTGGACT-5', 3747, 3'-CTGAACC-5', 3784, 3'-CCATACC-5', 3858, 3'-TCACACC-5', 3967, 3'-CCGGACT-5', 4327, 3'-CTGCACT-5', 4340, 3'-CCAGTTC-5', 4417, 3'-CCACTCC-5', 4425, 3'-CCACTTT-5', 4461, 3'-TCACATT-5', 4533, 3'-TTAATTC-5', 4542,
  4. positive strand in the positive direction is SuccessablesInr++.bas, looking for 3'-C/T-C/T-A/G-A/C/G/T-A/T-C/T-C/T-5', 75, 5'-CTGGACC-3' at 40, 5'-CCGGTCC-3' at 215, 5'-TTACACT-3' at 230, 5'-CCGGACC-3' at 286, 5'-CCGTTCC-3' at 503, 5'-TCGGTCC-3' at 515, 5'-CCGCTCT-3' at 557, 5'-CCGTTCC-3' at 587, 5'-CCGCTCT-3' at 641, 5'-CCGTTCC-3' at 671, 5'-CCGGACT-3' at 725, 5'-CCGTTCC-3' at 823, 5'-TCGGTCT-3' at 835, 5'-TTGGACC-3' at 847, 5'-CCGTTCC-3' at 923, 5'-TCGGTCT-3' at 935, 5'-TTGGACC-3' at 947, 5'-CCGTTCC-3' at 1007, 5'-TCGCTCT-3' at 1061, 5'-CCGGTCC-3' at 1175, 5'-CCGCTCT-3' at 1229, 5'-CCGTTCC-3' at 1259, 5'-CCGTTCC-3' at 1327, 5'-CCGCTCT-3' at 1381, 5'-CCGTTCC-3' at 1427, 5'-CCGCTCT-3' at 1481, 5'-TCGTTCC-3' at 1511, 5'-CCGCTCT-3' at 1565, 5'-CCGCACT-3' at 1720, 5'-CCACACC-3' at 1805, 5'-CCGCTCT-3' at 1921, 5'-CCGTTCT-3' at 1948, 5'-CCACACC-3' at 1971, 5'-TCAATTT-3' at 2136, 5'-TTGTACT-3' at 2141, 5'-CTACTTT-3' at 2146, 5'-CCGTTCT-3' at 2190, 5'-CCAGTCT-3' at 2222, 5'-TTGGTCT-3' at 2228, 5'-CCGCACT-3' at 2555, 5'-CCGGTCC-3' at 2574, 5'-TCAGTCT-3' at 2609, 5'-TCAGTTC-3' at 2615, 5'-TCAGTCC-3' at 2620, 5'-CTATATT-3' at 2662, 5'-TCAATCC-3' at 2668, 5'-TCGTTTT-3' at 2707, 5'-TCGATTC-3' at 2789, 5'-TTGCTCC-3' at 2806, 5'-CTAAACT-3' at 2871, 5'-CTGGTCC-3' at 2876, 5'-CCAGACT-3' at 2943, 5'-CCGGACC-3' at 2988, 5'-CCAGACC-3' at 3021, 5'-TTATACC-3' at 3162, 5'-CTGGTTT-3' at 3175, 5'-TCGGTCT-3' at 3221, 5'-CTACTCC-3' at 3478, 5'-CCGATCC-3' at 3484, 5'-TCGATCC-3' at 3522, 5'-CTGGTCT-3' at 3548, 5'-TCACACT-3' at 3594, 5'-CCACTCC-3' at 3647, 5'-CCGGACC-3' at 3679, 5'-CCGGACC-3' at 3758, 5'-CTGGACC-3' at 3787, 5'-TCACTCC-3' at 3878, 5'-TCAGACT-3' at 3924, 5'-TCACACC-3' at 3966, 5'-CCACACT-3' at 3971, 5'-TTACTCC-3' at 4096, 5'-CTACTCC-3' at 4102, 5'-CTAAATC-3' at 4136, 5'-CCACTCC-3' at 4401, 5'-CCAGACC-3' at 4416.
  5. complement, negative strand, negative direction is SuccessablesInrc--.bas, looking for 3'-A/G-A/G-C/T-A/C/G/T-A/T-A/G-A/G-5', 40, 3'-GACTTAA-5', 20, 3'-AACCTGG-5', 32, 3'-GACGTAA-5', 152, 3'-AACTTGG-5', 846, 3'-AGTGTGG-5', 882, 3'-AACTTGG-5', 1012, 3'-AGTGAGG-5', 1058, 3'-AGTGTGG-5', 1128, 3'-AACTTGG-5', 1303, 3'-AACGTGG-5', 1339, 3'-AACGTGA-5', 1347, 3'-GGTCAGA-5', 1354, 3'-GGTAAAG-5', 1380, 3'-AGCGAGA-5', 1450, 3'-GATATAG-5', 1528, 3'-AATAAAA-5', 1727, 3'-GACGTGA-5', 2000, 3'-GATGAGG-5', 2352, 3'-AACTTGG-5', 2382, 3'-AGTGTGG-5', 2418, 3'-GACGTGA-5', 2426, 3'-AACTTAG-5', 2708, 3'-AACTTGG-5', 2717, 3'-GACGTGG-5', 2761, 3'-AACTTGG-5', 3245, 3'-AACGTGA-5', 3289, 3'-GGTCTAG-5', 3488, 3'-GACGAGG-5', 3582, 3'-GGTAAAG-5', 3688, 3'-GACCTGA-5', 3747, 3'-GACTTGG-5', 3784, 3'-GGTATGG-5', 3858, 3'-AGTGTGG-5', 3967, 3'-GGCCTGA-5', 4327, 3'-GACGTGA-5', 4340, 3'-GGTCAAG-5', 4417, 3'-GGTGAGG-5', 4425, 3'-GGTGAAA-5', 4461, 3'-AGTGTAA-5', 4533, 3'-AATTAAG-5', 4542,
  6. complement, negative strand, positive direction is SuccessablesInrc-+.bas, looking for 3'-A/G-A/G-C/T-A/C/G/T-A/T-A/G-A/G-5', 75, 5'-GACCTGG-3' at 40, 5'-GGCCAGG-3' at 215, 5'-AATGTGA-3' at 230, 5'-GGCCTGG-3' at 286, 5'-GGCAAGG-3' at 503, 5'-AGCCAGG-3' at 515, 5'-GGCGAGA-3' at 557, 5'-GGCAAGG-3' at 587, 5'-GGCGAGA-3' at 641, 5'-GGCAAGG-3' at 671, 5'-GGCCTGA-3' at 725, 5'-GGCAAGG-3' at 823, 5'-AGCCAGA-3' at 835, 5'-AACCTGG-3' at 847, 5'-GGCAAGG-3' at 923, 5'-AGCCAGA-3' at 935, 5'-AACCTGG-3' at 947, 5'-GGCAAGG-3' at 1007, 5'-AGCGAGA-3' at 1061, 5'-GGCCAGG-3' at 1175, 5'-GGCGAGA-3' at 1229, 5'-GGCAAGG-3' at 1259, 5'-GGCAAGG-3' at 1327, 5'-GGCGAGA-3' at 1381, 5'-GGCAAGG-3' at 1427, 5'-GGCGAGA-3' at 1481, 5'-AGCAAGG-3' at 1511, 5'-GGCGAGA-3' at 1565, 5'-GGCGTGA-3' at 1720, 5'-GGTGTGG-3' at 1805, 5'-GGCGAGA-3' at 1921, 5'-GGCAAGA-3' at 1948, 5'-GGTGTGG-3' at 1971, 5'-AGTTAAA-3' at 2136, 5'-AACATGA-3' at 2141, 5'-GATGAAA-3' at 2146, 5'-GGCAAGA-3' at 2190, 5'-GGTCAGA-3' at 2222, 5'-AACCAGA-3' at 2228, 5'-GGCGTGA-3' at 2555, 5'-GGCCAGG-3' at 2574, 5'-AGTCAGA-3' at 2609, 5'-AGTCAAG-3' at 2615, 5'-AGTCAGG-3' at 2620, 5'-GATATAA-3' at 2662, 5'-AGTTAGG-3' at 2668, 5'-AGCAAAA-3' at 2707, 5'-AGCTAAG-3' at 2789, 5'-AACGAGG-3' at 2806, 5'-GATTTGA-3' at 2871, 5'-GACCAGG-3' at 2876, 5'-GGTCTGA-3' at 2943, 5'-GGCCTGG-3' at 2988, 5'-GGTCTGG-3' at 3021, 5'-AATATGG-3' at 3162, 5'-GACCAAA-3' at 3175, 5'-AGCCAGA-3' at 3221, 5'-GATGAGG-3' at 3478, 5'-GGCTAGG-3' at 3484, 5'-AGCTAGG-3' at 3522, 5'-GACCAGA-3' at 3548, 5'-AGTGTGA-3' at 3594, 5'-GGTGAGG-3' at 3647, 5'-GGCCTGG-3' at 3679, 5'-GGCCTGG-3' at 3758, 5'-GACCTGG-3' at 3787, 5'-AGTGAGG-3' at 3878, 5'-AGTCTGA-3' at 3924, 5'-AGTGTGG-3' at 3966, 5'-GGTGTGA-3' at 3971, 5'-AATGAGG-3' at 4096, 5'-GATGAGG-3' at 4102, 5'-GATTTAG-3' at 4136, 5'-GGTGAGG-3' at 4401, 5'-GGTCTGG-3' at 4416.
  7. complement, positive strand, negative direction is SuccessablesInrc+-.bas, looking for 3'-A/G-A/G-C/T-A/C/G/T-A/T-A/G-A/G-5', 121, 3'-AACAAGG-5', 71, 3'-GATATGG-5', 77, 3'-GGCAAAG-5', 93, 3'-GGCATGA-5', 124, 3'-GGTATAA-5', 181, 3'-GATGTAA-5', 247, 3'-AACCAGG-5', 262, 3'-AATATGA-5', 274, 3'-AGTGAGA-5', 301, 3'-GACGAAA-5', 312, 3'-GGCCAAG-5', 419, 3'-GGTCAGG-5', 441, 3'-AGCCTGG-5', 459, 3'-AACATAG-5', 468, 3'-AGTGAAA-5', 473, 3'-AGCCTGG-5', 508, 3'-GGCCAAG-5', 556, 3'-GGTCAGG-5', 578, 3'-AATATGG-5', 605, 3'-GGCCAGG-5', 648, 3'-GGCCAAG-5', 692, 3'-GGTCAGG-5', 714, 3'-AGCCTGA-5', 732, 3'-AGCGTGG-5', 741, 3'-GATGTGG-5', 787, 3'-AGCCAAG-5', 874, 3'-AGCCTGG-5', 899, 3'-AGCGAGA-5', 913, 3'-AGCCAGG-5', 948, 3'-GGCATGG-5', 953, 3'-AATCAGG-5', 984, 3'-AACCTGG-5', 1015, 3'-AGTGAGA-5', 1079, 3'-AGCCTGG-5', 1198, 3'-AACATGG-5', 1207, 3'-GGTGAAA-5', 1212, 3'-GGCGTGG-5', 1244, 3'-AACCTAG-5', 1306, 3'-AGTCTGG-5', 1356, 3'-AATAAGA-5', 1365, 3'-AGCAAAA-5', 1371, 3'-AACAAAA-5', 1394, 3'-GGTGTGA-5', 1479, 3'-AACGAAG-5', 1555, 3'-GGCAAAA-5', 1561, 3'-AATGAAA-5', 1582, 3'-AACCTAA-5', 1591, 3'-AATTAAA-5', 1697, 3'-AATATGG-5', 1742, 3'-GGCGTGG-5', 1897, 3'-GGCATGA-5', 1953, 3'-AACCTGG-5', 1959, 3'-AGCCTGG-5', 2009, 3'-AGCAAGA-5', 2023, 3'-AATGTGG-5', 2065, 3'-GGCCAGG-5', 2077, 3'-AGTGTAA-5', 2087, 3'-AGTTTGA-5', 2141, 3'-AACATGG-5', 2152, 3'-GGCGAAA-5', 2157, 3'-GGTCAGG-5', 2250, 3'-AGTTTGA-5', 2257, 3'-AGCCTGG-5', 2268, 3'-AGCATGG-5', 2277, 3'-GGTGAAA-5', 2282, 3'-AACCTGG-5', 2385, 3'-AGCCTGG-5', 2435, 3'-AGTGAGA-5', 2449, 3'-AGCAAAA-5', 2476, 3'-AACAAAA-5', 2490, 3'-AGTAAGA-5', 2503, 3'-GGCCAGG-5', 2519, 3'-GGTCAGG-5', 2587, 3'-AGTGTGG-5', 2605, 3'-AACATGG-5', 2614, 3'-GGTGAAA-5', 2619, 3'-AGTGTGG-5', 2658, 3'-AACCTGG-5', 2720, 3'-AGCCTGG-5', 2770, 3'-AGCATGA-5', 2784, 3'-AACTAAG-5', 2914, 3'-GGCTAAA-5', 3009, 3'-AACTAAG-5', 3031, 3'-GGCGTGG-5', 3047, 3'-AGCCTGG-5', 3128, 3'-AACAAGG-5', 3141, 3'-GGTGAAA-5', 3146, 3'-AACATAA-5', 3169, 3'-GGTGTGG-5', 3186, 3'-AGCCAAG-5', 3273, 3'-AGCCTGG-5', 3298, 3'-AACAAGA-5', 3307, 3'-AGCAAAA-5', 3313, 3'-AACAAGA-5', 3340, 3'-AGCAAGA-5', 3374, 3'-GGCTTGA-5', 3401, 3'-GGCATAG-5', 3446, 3'-AACTAGA-5', 3463, 3'-AACCAGA-5', 3486, 3'-GACAAGA-5', 3759, 3'-GATGTGG-5', 3810, 3'-GACCAGG-5', 3871, 3'-AGTAAGA-5', 3893, 3'-GATGAAA-5', 3922, 3'-GGCCAGG-5', 3951, 3'-AGCCTGG-5', 4037, 3'-AACATAG-5', 4046, 3'-AGTGAGA-5', 4051, 3'-AATGTGA-5', 4092, 3'-GGCCAGG-5', 4102, 3'-GGCATGG-5', 4107, 3'-GGCCAGG-5', 4170, 3'-AGCTTGG-5', 4188, 3'-AGTGAGA-5', 4202, 3'-AGCCAGA-5', 4233, 3'-GACGTGG-5', 4238, 3'-AGCCTGG-5', 4300, 3'-GGTCAAA-5', 4309, 3'-AGCCTGG-5', 4349, 3'-AGTGTGA-5', 4361, 3'-AATGAGG-5', 4557,
  8. complement, positive strand, positive direction is SuccessablesInrc++.bas, looking for 3'-A/G-A/G-C/T-A/C/G/T-A/T-A/G-A/G-5', 45, 5'-AACATAA-3' at 115, 5'-GACAAAA-3' at 147, 5'-GGTGTGA-3' at 345, 5'-GGCCTGA-3' at 746, 5'-GACGTGA-3' at 1372, 5'-GACGTGA-3' at 1472, 5'-GGTCTGA-3' at 1744, 5'-GGTGAAG-3' at 1914, 5'-GATAAAG-3' at 1978, 5'-GGTCAGG-3' at 2026, 5'-AGCGAAG-3' at 2095, 5'-AGTATAA-3' at 2178, 5'-GACGTAA-3' at 2206, 5'-GGTCTAG-3' at 2230, 5'-AGTTAGA-3' at 2235, 5'-GACAAAG-3' at 2263, 5'-AGTGAGA-3' at 2306, 5'-GATGTGG-3' at 2430, 5'-GATTAAA-3' at 2440, 5'-GGCGTGG-3' at 2566, 5'-AATATGG-3' at 2590, 5'-GGTGTGG-3' at 2602, 5'-GGTGTGA-3' at 2636, 5'-AGTCTAA-3' at 2868, 5'-GACGAGG-3' at 2978, 5'-GGTCAGG-3' at 2998, 5'-GGTCAGG-3' at 3084, 5'-GACCAGA-3' at 3245, 5'-AGCGAGA-3' at 3276, 5'-GACCAGA-3' at 3299, 5'-GACGAGG-3' at 3309, 5'-GACGTGG-3' at 3322, 5'-GGCGTAG-3' at 3328, 5'-AACGTGA-3' at 3343, 5'-GACAAGG-3' at 3352, 5'-AACGTAG-3' at 3402, 5'-AGTGTGA-3' at 3507, 5'-GGTCTGG-3' at 3550, 5'-GACAAGG-3' at 3625, 5'-AGTGTGG-3' at 3824, 5'-AGTAAAA-3' at 4120, 5'-AGTGAGA-3' at 4128, 5'-AACTAAA-3' at 4134, 5'-AATCAAA-3' at 4139, 5'-GACGTGG-3' at 4343.
  9. inverse complement, negative strand, negative direction is SuccessablesInrci--.bas, looking for 3'-A/G-A/G-A/T-A/C/G/T-C/T-A/G-A/G-5', 32, 3'-GATACAA-5', 213, 3'-GGACCGA-5', 598, 3'-AGTGCGG-5', 664, 3'-GGACTGG-5', 734, 3'-AGTGTGG-5', 882, 3'-GAAGTGA-5', 1056, 3'-AGTGTGG-5', 1128, 3'-GGACCGG-5', 1200, 3'-AGAGCGA-5', 1448, 3'-GGTCCGA-5', 1462, 3'-GATATAG-5', 1528, 3'-AGAACGG-5', 1608, 3'-AAAATAG-5', 1730, 3'-AGTGCAG-5', 1773, 3'-GGACCGA-5', 1843, 3'-AGTGCGG-5', 1992, 3'-AGTGCGG-5', 2208, 3'-AGTGTGG-5', 2418, 3'-AGTACGG-5', 2535, 3'-AGTACGG-5', 2753, 3'-AAAGTAG-5', 2887, 3'-GATTCGA-5', 3033, 3'-GGACCGG-5', 3130, 3'-AGTGCGG-5', 3281, 3'-AGTCCGA-5', 3398, 3'-GGTCTAG-5', 3488, 3'-GGTATGG-5', 3858, 3'-GGTCCGG-5', 3873, 3'-AGTGTGG-5', 3967, 3'-AGTACGG-5', 4118, 3'-GGTCCGA-5', 4255, 3'-AGTGTAA-5', 4533,
  10. inverse complement, negative strand, positive direction is SuccessablesInrci-+.bas, looking for 3'-A/G-A/G-A/T-A/C/G/T-C/T-A/G-A/G-5', 61, 5'-AGAGTGG-3' at 53, 5'-AATGTGA-3' at 230, 5'-GGAGCGA-3' at 429, 5'-AGACCGG-3' at 442, 5'-GGTGCGG-3' at 489, 5'-AGTGCGG-3' at 498, 5'-AGTGCGG-3' at 582, 5'-AGTGCGG-3' at 666, 5'-GGTGCAG-3' at 784, 5'-AGTGCGG-3' at 1086, 5'-AGTGCGG-3' at 1170, 5'-AGTGCGG-3' at 1254, 5'-AATGCGG-3' at 1322, 5'-AATGCGG-3' at 1422, 5'-AGTGCGG-3' at 1590, 5'-GAAGCGG-3' at 1636, 5'-GGTGCGG-3' at 1764, 5'-AGTGCAG-3' at 1787, 5'-GGTGTGG-3' at 1805, 5'-GAACTGG-3' at 1953, 5'-GGTGTGG-3' at 1971, 5'-AAAGCAG-3' at 2007, 5'-AGTGCAG-3' at 2064, 5'-GAACCAG-3' at 2227, 5'-AGATCAA-3' at 2232, 5'-AGTGCAG-3' at 2327, 5'-GGTGCAA-3' at 2335, 5'-GAAATAG-3' at 2626, 5'-GATATAA-3' at 2662, 5'-GGACTGA-3' at 2674, 5'-AGAGCAA-3' at 2705, 5'-AAAGTGG-3' at 2711, 5'-GGTGCAA-3' at 2801, 5'-AGAATGA-3' at 2841, 5'-GATTTGA-3' at 2871, 5'-GGTCTGA-3' at 2943, 5'-GGTCTGG-3' at 3021, 5'-AATATGG-3' at 3162, 5'-GAAATGG-3' at 3168, 5'-GGACCAA-3' at 3174, 5'-GGAATGA-3' at 3441, 5'-GATGCAG-3' at 3460, 5'-AGTGCAG-3' at 3465, 5'-GGACCAG-3' at 3547, 5'-GGAATGA-3' at 3567, 5'-AGTGTGA-3' at 3594, 5'-GAAGCGG-3' at 3670, 5'-AATCCGA-3' at 3799, 5'-AGAATGA-3' at 3835, 5'-GAACCAG-3' at 3840, 5'-AGAGTGA-3' at 3876, 5'-AGTCTGA-3' at 3924, 5'-AGTGTGG-3' at 3966, 5'-GGTGTGA-3' at 3971, 5'-AGAGTGG-3' at 4040, 5'-AGAACAG-3' at 4069, 5'-GAAATGA-3' at 4094, 5'-GATTTAG-3' at 4136, 5'-GGAGTGA-3' at 4350, 5'-GGTCTGG-3' at 4416, 5'-GGAACAA-3' at 4445.
  11. inverse complement, positive strand, negative direction is SuccessablesInrci+-.bas, looking for 3'-A/G-A/G-A/T-A/C/G/T-C/T-A/G-A/G-5', 100, 3'-AGACTGA-5', 17, 3'-GGACCAG-5', 34, 3'-AAAACAA-5', 69, 3'-GATATGG-5', 77, 3'-AAACTGA-5', 130, 3'-AAAACAG-5', 167, 3'-GGTATAA-5', 181, 3'-GAAACAA-5', 229, 3'-GATGTAA-5', 247, 3'-AGTTCAA-5', 255, 3'-AAACCAG-5', 261, 3'-AATATGA-5', 274, 3'-AGAACAG-5', 288, 3'-AAACTGA-5', 307, 3'-GGTGCGG-5', 380, 3'-AGTGCGA-5', 448, 3'-AATACGA-5', 492, 3'-AAATTAG-5', 499, 3'-AGATTGA-5', 585, 3'-AATATGG-5', 605, 3'-AATACAA-5', 635, 3'-AAATTGG-5', 643, 3'-AGTTCGA-5', 721, 3'-AGACCAG-5', 727, 3'-AATACAA-5', 769, 3'-AAATTAG-5', 777, 3'-GATGTGG-5', 787, 3'-AGAGCGA-5', 911, 3'-GATCCAG-5', 975, 3'-AGATTGG-5', 1045, 3'-AGAGTGA-5', 1077, 3'-AAATTAG-5', 1234, 3'-AGTCTGG-5', 1356, 3'-AGAGCAA-5', 1369, 3'-AAAACAA-5', 1388, 3'-AGTGCAG-5', 1471, 3'-GGTGTGA-5', 1479, 3'-AGTGCAA-5', 1536, 3'-AGAACGA-5', 1553, 3'-AATACAG-5', 1566, 3'-GAAACAA-5', 1585, 3'-GAAATGA-5', 1663, 3'-AAAGCGG-5', 1680, 3'-GAATTAA-5', 1696, 3'-AATATGG-5', 1742, 3'-AATACAA-5', 1878, 3'-AAATTAG-5', 1887, 3'-AGACTGA-5', 1935, 3'-AGAATGG-5', 1948, 3'-AGAGCAA-5', 2021, 3'-AATGTGG-5', 2065, 3'-GGTGCAG-5', 2082, 3'-AGTGTAA-5', 2087, 3'-AGTTTGA-5', 2141, 3'-AGACCAA-5', 2147, 3'-GATACAA-5', 2180, 3'-AAAATGA-5', 2187, 3'-GGTGCGG-5', 2197, 3'-AGTTTGA-5', 2257, 3'-AGACCAG-5', 2263, 3'-AATACAA-5', 2305, 3'-AAACTAG-5', 2313, 3'-AGAGTGA-5', 2447, 3'-GATTCGG-5', 2454, 3'-AAAGCAA-5', 2474, 3'-AAAGCAA-5', 2480, 3'-AAAACAA-5', 2509, 3'-AGACCAG-5', 2600, 3'-AGTGTGG-5', 2605, 3'-AAATCAG-5', 2649, 3'-AGTGTGG-5', 2658, 3'-AAAACAA-5', 2842, 3'-AGAATGG-5', 3004, 3'-AAAATAA-5', 3013, 3'-AAACTAA-5', 3030, 3'-AGACCAG-5', 3123, 3'-AAATTAG-5', 3176, 3'-GGTGTGG-5', 3186, 3'-AGAGCAA-5', 3311, 3'-AAAACAA-5', 3330, 3'-AAATTGA-5', 3358, 3'-GAAGTGA-5', 3410, 3'-GAACTAG-5', 3462, 3'-AAACCAG-5', 3485, 3'-AATCCAG-5', 3681, 3'-GGAACAG-5', 3725, 3'-GGACTGG-5', 3749, 3'-AATGCAG-5', 3772, 3'-GATGTGG-5', 3810, 3'-GGACCAG-5', 3870, 3'-GGAGTAA-5', 3891, 3'-AGTTCAA-5', 4026, 3'-AGACCAG-5', 4032, 3'-AAAATAA-5', 4071, 3'-AATGTGA-5', 4092, 3'-AGTTCAA-5', 4177, 3'-AAAATAA-5', 4221, 3'-AGTGTGA-5', 4361, 3'-AGTCCAA-5', 4502, 3'-GGAATGA-5', 4555,
  12. inverse complement, positive strand, positive direction is SuccessablesInrci++.bas, looking for 3'-A/G-A/G-A/T-A/C/G/T-C/T-A/G-A/G-5', 75, 5'-GGTCCGA-3' at 10, 5'-AGTCCGG-3' at 92, 5'-AATCCAG-3' at 152, 5'-GGTCCAG-3' at 217, 5'-GGTGTGA-3' at 345, 5'-GAAGCGG-3' at 459, 5'-AGAATGA-3' at 524, 5'-GAAGCGG-3' at 595, 5'-GATGCGA-3' at 652, 5'-GGTGCGA-3' at 777, 5'-GGACCGG-3' at 849, 5'-GGACCGG-3' at 949, 5'-GGTCCGA-3' at 1177, 5'-AAAGCAG-3' at 1183, 5'-GAAGCGG-3' at 1308, 5'-GAAGCGG-3' at 1408, 5'-AATTCGG-3' at 1541, 5'-GATGCGA-3' at 1576, 5'-GGACTGG-3' at 1662, 5'-GGTCTGA-3' at 1744, 5'-GGACCGA-3' at 1817, 5'-GGTCCGG-3' at 1857, 5'-AGAATGG-3' at 1888, 5'-GAAGTAG-3' at 2110, 5'-AGTATAA-3' at 2178, 5'-GGACTGG-3' at 2213, 5'-GGTCTAG-3' at 2230, 5'-AGAGTGG-3' at 2247, 5'-AAAGTGA-3' at 2304, 5'-GGTCCGA-3' at 2318, 5'-AATCCGA-3' at 2368, 5'-GATGTGG-3' at 2430, 5'-GGACCGA-3' at 2435, 5'-AGAGTGG-3' at 2470, 5'-GGTACAA-3' at 2475, 5'-GGACCGG-3' at 2571, 5'-AATATGG-3' at 2590, 5'-GGTGTGG-3' at 2602, 5'-AGTTCAG-3' at 2617, 5'-GGTGTGA-3' at 2636, 5'-AGTCTAA-3' at 2868, 5'-AAACTGG-3' at 2873, 5'-GGTCCGG-3' at 2878, 5'-AGACCGA-3' at 2885, 5'-GGAGTAA-3' at 2902, 5'-AGACTGA-3' at 2945, 5'-AGACCGG-3' at 2985, 5'-GGACCGG-3' at 2990, 5'-GGAACAG-3' at 3003, 5'-GGTCCAG-3' at 3018, 5'-AGACCAA-3' at 3023, 5'-AGTCCGG-3' at 3036, 5'-GGACCAA-3' at 3049, 5'-GAAGTAG-3' at 3250, 5'-AGTGCAG-3' at 3255, 5'-GGACCAG-3' at 3298, 5'-AGAGTGA-3' at 3317, 5'-GGTACAA-3' at 3337, 5'-GGAACGG-3' at 3375, 5'-AGTGTGA-3' at 3507, 5'-GATCCGA-3' at 3524, 5'-GGTCTGG-3' at 3550, 5'-AGAGTGG-3' at 3612, 5'-GGACCGG-3' at 3681, 5'-AGTGTGG-3' at 3824, 5'-GAACTGG-3' at 4018, 5'-AAAATAG-3' at 4123, 5'-GAACTAA-3' at 4133, 5'-AAATCAA-3' at 4138, 5'-GAAACGG-3' at 4210, 5'-GGACTGG-3' at 4216, 5'-GGAGTAA-3' at 4309, 5'-AGTACAG-3' at 4366, 5'-GGTACGA-3' at 4372, 5'-AGAACGA-3' at 4390.
  13. inverse, negative strand, negative direction, is SuccessablesInri--.bas, looking for 3'-C/T-C/T-A/T-A/C/G/T-A/G-C/T-C/T-5', 100, 3'-TCTGACT-5', 17, 3'-CCTGGTC-5', 34, 3'-TTTTGTT-5', 69, 3'-CTATACC-5', 77, 3'-TTTGACT-5', 130, 3'-TTTTGTC-5', 167, 3'-CCATATT-5', 181, 3'-CTTTGTT-5', 229, 3'-CTACATT-5', 247, 3'-TCAAGTT-5', 255, 3'-TTTGGTC-5', 261, 3'-TTATACT-5', 274, 3'-TCTTGTC-5', 288, 3'-TTTGACT-5', 307, 3'-CCACGCC-5', 380, 3'-TCACGCT-5', 448, 3'-TTATGCT-5', 492, 3'-TTTAATC-5', 499, 3'-TCTAACT-5', 585, 3'-TTATACC-5', 605, 3'-TTATGTT-5', 635, 3'-TTTAACC-5', 643, 3'-TCAAGCT-5', 721, 3'-TCTGGTC-5', 727, 3'-TTATGTT-5', 769, 3'-TTTAATC-5', 777, 3'-CTACACC-5', 787, 3'-TCTCGCT-5', 911, 3'-CTAGGTC-5', 975, 3'-TCTAACC-5', 1045, 3'-TCTCACT-5', 1077, 3'-TTTAATC-5', 1234, 3'-TCAGACC-5', 1356, 3'-TCTCGTT-5', 1369, 3'-TTTTGTT-5', 1388, 3'-TCACGTC-5', 1471, 3'-CCACACT-5', 1479, 3'-TCACGTT-5', 1536, 3'-TCTTGCT-5', 1553, 3'-TTATGTC-5', 1566, 3'-CTTTGTT-5', 1585, 3'-CTTTACT-5', 1663, 3'-TTTCGCC-5', 1680, 3'-CTTAATT-5', 1696, 3'-TTATACC-5', 1742, 3'-TTATGTT-5', 1878, 3'-TTTAATC-5', 1887, 3'-TCTGACT-5', 1935, 3'-TCTTACC-5', 1948, 3'-TCTCGTT-5', 2021, 3'-TTACACC-5', 2065, 3'-CCACGTC-5', 2082, 3'-TCACATT-5', 2087, 3'-TCAAACT-5', 2141, 3'-TCTGGTT-5', 2147, 3'-CTATGTT-5', 2180, 3'-TTTTACT-5', 2187, 3'-CCACGCC-5', 2197, 3'-TCAAACT-5', 2257, 3'-TCTGGTC-5', 2263, 3'-TTATGTT-5', 2305, 3'-TTTGATC-5', 2313, 3'-TCTCACT-5', 2447, 3'-CTAAGCC-5', 2454, 3'-TTTCGTT-5', 2474, 3'-TTTCGTT-5', 2480, 3'-TTTTGTT-5', 2509, 3'-TCTGGTC-5', 2600, 3'-TCACACC-5', 2605, 3'-TTTAGTC-5', 2649, 3'-TCACACC-5', 2658, 3'-TTTTGTT-5', 2842, 3'-TCTTACC-5', 3004, 3'-TTTTATT-5', 3013, 3'-TTTGATT-5', 3030, 3'-TCTGGTC-5', 3123, 3'-TTTAATC-5', 3176, 3'-CCACACC-5', 3186, 3'-TCTCGTT-5', 3311, 3'-TTTTGTT-5', 3330, 3'-TTTAACT-5', 3358, 3'-CTTCACT-5', 3410, 3'-CTTGATC-5', 3462, 3'-TTTGGTC-5', 3485, 3'-TTAGGTC-5', 3681, 3'-CCTTGTC-5', 3725, 3'-CCTGACC-5', 3749, 3'-TTACGTC-5', 3772, 3'-CTACACC-5', 3810, 3'-CCTGGTC-5', 3870, 3'-CCTCATT-5', 3891, 3'-TCAAGTT-5', 4026, 3'-TCTGGTC-5', 4032, 3'-TTTTATT-5', 4071, 3'-TTACACT-5', 4092, 3'-TCAAGTT-5', 4177, 3'-TTTTATT-5', 4221, 3'-TCACACT-5', 4361, 3'-TCAGGTT-5', 4502, 3'-CCTTACT-5', 4555,
  14. inverse, negative strand, positive direction, is SuccessablesInri-+.bas, looking for 3'-C/T-C/T-A/T-A/C/G/T-A/G-C/T-C/T-5', 75, 5'-CCAGGCT-3' at 10, 5'-TCAGGCC-3' at 92, 5'-TTAGGTC-3' at 152, 5'-CCAGGTC-3' at 217, 5'-CCACACT-3' at 345, 5'-CTTCGCC-3' at 459, 5'-TCTTACT-3' at 524, 5'-CTTCGCC-3' at 595, 5'-CTACGCT-3' at 652, 5'-CCACGCT-3' at 777, 5'-CCTGGCC-3' at 849, 5'-CCTGGCC-3' at 949, 5'-CCAGGCT-3' at 1177, 5'-TTTCGTC-3' at 1183, 5'-CTTCGCC-3' at 1308, 5'-CTTCGCC-3' at 1408, 5'-TTAAGCC-3' at 1541, 5'-CTACGCT-3' at 1576, 5'-CCTGACC-3' at 1662, 5'-CCAGACT-3' at 1744, 5'-CCTGGCT-3' at 1817, 5'-CCAGGCC-3' at 1857, 5'-TCTTACC-3' at 1888, 5'-CTTCATC-3' at 2110, 5'-TCATATT-3' at 2178, 5'-CCTGACC-3' at 2213, 5'-CCAGATC-3' at 2230, 5'-TCTCACC-3' at 2247, 5'-TTTCACT-3' at 2304, 5'-CCAGGCT-3' at 2318, 5'-TTAGGCT-3' at 2368, 5'-CTACACC-3' at 2430, 5'-CCTGGCT-3' at 2435, 5'-TCTCACC-3' at 2470, 5'-CCATGTT-3' at 2475, 5'-CCTGGCC-3' at 2571, 5'-TTATACC-3' at 2590, 5'-CCACACC-3' at 2602, 5'-TCAAGTC-3' at 2617, 5'-CCACACT-3' at 2636, 5'-TCAGATT-3' at 2868, 5'-TTTGACC-3' at 2873, 5'-CCAGGCC-3' at 2878, 5'-TCTGGCT-3' at 2885, 5'-CCTCATT-3' at 2902, 5'-TCTGACT-3' at 2945, 5'-TCTGGCC-3' at 2985, 5'-CCTGGCC-3' at 2990, 5'-CCTTGTC-3' at 3003, 5'-CCAGGTC-3' at 3018, 5'-TCTGGTT-3' at 3023, 5'-TCAGGCC-3' at 3036, 5'-CCTGGTT-3' at 3049, 5'-CTTCATC-3' at 3250, 5'-TCACGTC-3' at 3255, 5'-CCTGGTC-3' at 3298, 5'-TCTCACT-3' at 3317, 5'-CCATGTT-3' at 3337, 5'-CCTTGCC-3' at 3375, 5'-TCACACT-3' at 3507, 5'-CTAGGCT-3' at 3524, 5'-CCAGACC-3' at 3550, 5'-TCTCACC-3' at 3612, 5'-CCTGGCC-3' at 3681, 5'-TCACACC-3' at 3824, 5'-CTTGACC-3' at 4018, 5'-TTTTATC-3' at 4123, 5'-CTTGATT-3' at 4133, 5'-TTTAGTT-3' at 4138, 5'-CTTTGCC-3' at 4210, 5'-CCTGACC-3' at 4216, 5'-CCTCATT-3' at 4309, 5'-TCATGTC-3' at 4366, 5'-CCATGCT-3' at 4372, 5'-TCTTGCT-3' at 4390.
  15. inverse, positive strand, negative direction, is SuccessablesInri+-.bas, looking for 3'-C/T-C/T-A/T-A/C/G/T-A/G-C/T-C/T-5', 32, 3'-CTATGTT-5', 213, 3'-CCTGGCT-5', 598, 3'-TCACGCC-5', 664, 3'-CCTGACC-5', 734, 3'-TCACACC-5', 882, 3'-CTTCACT-5', 1056, 3'-TCACACC-5', 1128, 3'-CCTGGCC-5', 1200, 3'-TCTCGCT-5', 1448, 3'-CCAGGCT-5', 1462, 3'-CTATATC-5', 1528, 3'-TCTTGCC-5', 1608, 3'-TTTTATC-5', 1730, 3'-TCACGTC-5', 1773, 3'-CCTGGCT-5', 1843, 3'-TCACGCC-5', 1992, 3'-TCACGCC-5', 2208, 3'-TCACACC-5', 2418, 3'-TCATGCC-5', 2535, 3'-TCATGCC-5', 2753, 3'-TTTCATC-5', 2887, 3'-CTAAGCT-5', 3033, 3'-CCTGGCC-5', 3130, 3'-TCACGCC-5', 3281, 3'-TCAGGCT-5', 3398, 3'-CCAGATC-5', 3488, 3'-CCATACC-5', 3858, 3'-CCAGGCC-5', 3873, 3'-TCACACC-5', 3967, 3'-TCATGCC-5', 4118, 3'-CCAGGCT-5', 4255, 3'-TCACATT-5', 4533,
  16. inverse, positive strand, positive direction, is SuccessablesInri++.bas, looking for 3'-C/T-C/T-A/T-A/C/G/T-A/G-C/T-C/T-5', 61, 5'-TCTCACC-3' at 53, 5'-TTACACT-3' at 230, 5'-CCTCGCT-3' at 429, 5'-TCTGGCC-3' at 442, 5'-CCACGCC-3' at 489, 5'-TCACGCC-3' at 498, 5'-TCACGCC-3' at 582, 5'-TCACGCC-3' at 666, 5'-CCACGTC-3' at 784, 5'-TCACGCC-3' at 1086, 5'-TCACGCC-3' at 1170, 5'-TCACGCC-3' at 1254, 5'-TTACGCC-3' at 1322, 5'-TTACGCC-3' at 1422, 5'-TCACGCC-3' at 1590, 5'-CTTCGCC-3' at 1636, 5'-CCACGCC-3' at 1764, 5'-TCACGTC-3' at 1787, 5'-CCACACC-3' at 1805, 5'-CTTGACC-3' at 1953, 5'-CCACACC-3' at 1971, 5'-TTTCGTC-3' at 2007, 5'-TCACGTC-3' at 2064, 5'-CTTGGTC-3' at 2227, 5'-TCTAGTT-3' at 2232, 5'-TCACGTC-3' at 2327, 5'-CCACGTT-3' at 2335, 5'-CTTTATC-3' at 2626, 5'-CTATATT-3' at 2662, 5'-CCTGACT-3' at 2674, 5'-TCTCGTT-3' at 2705, 5'-TTTCACC-3' at 2711, 5'-CCACGTT-3' at 2801, 5'-TCTTACT-3' at 2841, 5'-CTAAACT-3' at 2871, 5'-CCAGACT-3' at 2943, 5'-CCAGACC-3' at 3021, 5'-TTATACC-3' at 3162, 5'-CTTTACC-3' at 3168, 5'-CCTGGTT-3' at 3174, 5'-CCTTACT-3' at 3441, 5'-CTACGTC-3' at 3460, 5'-TCACGTC-3' at 3465, 5'-CCTGGTC-3' at 3547, 5'-CCTTACT-3' at 3567, 5'-TCACACT-3' at 3594, 5'-CTTCGCC-3' at 3670, 5'-TTAGGCT-3' at 3799, 5'-TCTTACT-3' at 3835, 5'-CTTGGTC-3' at 3840, 5'-TCTCACT-3' at 3876, 5'-TCAGACT-3' at 3924, 5'-TCACACC-3' at 3966, 5'-CCACACT-3' at 3971, 5'-TCTCACC-3' at 4040, 5'-TCTTGTC-3' at 4069, 5'-CTTTACT-3' at 4094, 5'-CTAAATC-3' at 4136, 5'-CCTCACT-3' at 4350, 5'-CCAGACC-3' at 4416, 5'-CCTTGTT-3' at 4445.

5'-BBCABW-3'

For the Basic programs (starting with SuccessablesInr2.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:

  1. negative strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesInr2--.bas, looking for 5'-C/G/T-C/G/T-C-A-C/G/T-A/T-3', 44, 3'-TCCATA-5', 179, 3'-CCCAGT-5', 206, 3'-CTCAGA-5', 278, 3'-GTCACT-5', 299, 3'-TTCACA-5', 322, 3'-TCCAGT-5', 439, 3'-TGCATT-5', 533, 3'-TCCAGT-5', 568, 3'-TCCAGT-5', 576, 3'-TCCAGT-5', 712, 3'-GGCAGA-5', 754, 3'-GCCACT-5', 868, 3'-GTCACT-5', 1034, 3'-CCCACT-5', 1049, 3'-CTCACT-5', 1077, 3'-GGCACA-5', 1220, 3'-GTCACT-5', 1325, 3'-GTCAGA-5', 1354, 3'-CTCAGA-5', 1444, 3'-GGCAGT-5', 1511, 3'-TGCAGA-5', 1774, 3'-GTCACT-5', 1978, 3'-GTCACA-5', 2085, 3'-TCCAGT-5', 2248, 3'-GTCACT-5', 2404, 3'-CTCACT-5', 2447, 3'-TCCAGT-5', 2585, 3'-GTCACA-5', 2603, 3'-GTCACA-5', 2656, 3'-GTCACT-5', 2739, 3'-TTCACA-5', 2860, 3'-TCCACT-5', 3144, 3'-CCCACA-5', 3184, 3'-TTCACT-5', 3410, 3'-GTCATT-5', 3480, 3'-TCCACT-5', 3825, 3'-CTCATA-5', 3829, 3'-CTCATT-5', 3891, 3'-TTCACA-5', 3939, 3'-GTCACT-5', 4200, 3'-TCCAGT-5', 4307, 3'-GTCACT-5', 4319, 3'-CCCACT-5', 4353, 3'-GTCACA-5', 4359.
  2. negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesInr2-+.bas, looking for 5'-C/G/T-C/G/T-C-A-C/G/T-A/T-3', 87, 3'-TCCAGA-5', 15, 3'-GGCATT-5', 22, 3'-GTCACA-5', 155, 3'-CCCAGA-5', 204, 3'-GCCACA-5', 343, 3'-CGCAGA-5', 396, 3'-TGCAGA-5', 438, 3'-CCCAGA-5', 468, 3'-TGCACA-5', 548, 3'-TCCACA-5', 632, 3'-CGCACT-5', 686, 3'-CGCACA-5', 800, 3'-GCCAGA-5', 835, 3'-GCCACA-5', 884, 3'-GCCAGA-5', 935, 3'-GCCACA-5', 984, 3'-CGCACA-5', 1052, 3'-CGCACA-5', 1136, 3'-TGCACA-5', 1220, 3'-CCCAGT-5', 1250, 3'-CGCAGA-5', 1316, 3'-TGCACT-5', 1372, 3'-CGCAGA-5', 1416, 3'-TGCACT-5', 1472, 3'-CCCACT-5', 1502, 3'-CGCACA-5', 1556, 3'-GGCATT-5', 1702, 3'-CCCAGA-5', 1742, 3'-TGCACA-5', 1822, 3'-TCCACT-5', 1912, 3'-TGCAGA-5', 1937, 3'-GGCACT-5', 1996, 3'-CCCAGT-5', 2024, 3'-TCCACA-5', 2029, 3'-CTCAGT-5', 2060, 3'-TGCAGT-5', 2065, 3'-GCCACT-5', 2072, 3'-TTCAGT-5', 2098, 3'-CTCATA-5', 2176, 3'-TGCATT-5', 2206, 3'-GTCAGA-5', 2222, 3'-CTCAGA-5', 2239, 3'-TTCACT-5', 2304, 3'-TGCAGT-5', 2328, 3'-GTCACT-5', 2425, 3'-GTCAGA-5', 2609, 3'-CTCAGA-5', 2699, 3'-TGCAGA-5', 2721, 3'-CTCAGA-5', 2729, 3'-TGCAGA-5', 2859, 3'-CTCAGA-5', 2866, 3'-CTCATT-5', 2902, 3'-GTCACT-5', 2929, 3'-TTCAGT-5', 2936, 3'-TGCACA-5', 2962, 3'-TGCATT-5', 3072, 3'-CCCAGT-5', 3082, 3'-CCCAGA-5', 3091, 3'-TCCACA-5', 3192, 3'-CTCACA-5', 3209, 3'-GCCAGA-5', 3221, 3'-TGCAGT-5', 3232, 3'-TGCAGT-5', 3281, 3'-CTCACT-5', 3317, 3'-TGCACT-5', 3343, 3'-CCCAGT-5', 3379, 3'-CCCACT-5', 3388, 3'-GGCACA-5', 3409, 3'-TGCAGT-5', 3461, 3'-GGCAGA-5', 3473, 3'-CTCACA-5', 3505, 3'-GCCACA-5', 3705, 3'-TCCAGA-5', 3806, 3'-GTCACA-5', 3822, 3'-TGCAGA-5', 3831, 3'-TCCAGA-5', 3891, 3'-CGCAGA-5', 3916, 3'-GTCACA-5', 3954, 3'-TGCAGT-5', 3962, 3'-GGCACT-5', 4006, 3'-TCCACT-5', 4013, 3'-CTCAGA-5', 4195, 3'-GTCAGT-5', 4271, 3'-CTCATT-5', 4309, 3'-TGCAGA-5', 4317, 3'-CCCAGA-5', 4330, 3'-CTCACT-5', 4338.
  3. positive strand in the negative direction is SuccessablesInr2+-.bas, looking for 5'-C/G/T-C/G/T-C-A-C/G/T-A/T-3', 59, 3'-GCCATA-5', 39, 3'-TGCATT-5', 152, 3'-GTCACT-5', 208, 3'-GGCACA-5', 266, 3'-GGCACA-5', 518, 3'-GGCACA-5', 960, 3'-GGCAGA-5', 1023, 3'-TGCAGT-5', 1032, 3'-TTCACT-5', 1056, 3'-GGCACA-5', 1116, 3'-CTCACA-5', 1126, 3'-GGCAGA-5', 1314, 3'-TGCAGT-5', 1323, 3'-TGCACT-5', 1347, 3'-TCCAGT-5', 1352, 3'-TCCATT-5', 1378, 3'-CCCAGA-5', 1411, 3'-TGCAGT-5', 1472, 3'-CTCACT-5', 1491, 3'-CCCAGA-5', 1518, 3'-TCCAGT-5', 1532, 3'-TGCACA-5', 1719, 3'-GGCAGA-5', 1967, 3'-TGCAGT-5', 1976, 3'-GCCACT-5', 1995, 3'-TGCACT-5', 2000, 3'-TGCAGT-5', 2083, 3'-GCCAGT-5', 2211, 3'-TGCAGT-5', 2402, 3'-TGCACT-5', 2426, 3'-TCCACT-5', 2632, 3'-GCCAGT-5', 2654, 3'-GGCACA-5', 2665, 3'-TGCAGT-5', 2737, 3'-GCCACT-5', 2756, 3'-GCCATT-5', 3284, 3'-TGCACT-5', 3289, 3'-TGCAGA-5', 3431, 3'-GGCATA-5', 3445, 3'-GGCATA-5', 3451, 3'-GGCAGT-5', 3478, 3'-GGCAGA-5', 3589, 3'-GGCAGT-5', 3600, 3'-GTCAGA-5', 3625, 3'-GGCACA-5', 3632, 3'-CTCAGA-5', 3644, 3'-GCCATT-5', 3686, 3'-TCCACA-5', 3692, 3'-CCCATA-5', 3856, 3'-CTCACA-5', 3965, 3'-GCCAGA-5', 4233, 3'-TGCAGT-5', 4317, 3'-TGCACT-5', 4340, 3'-GCCAGT-5', 4415, 3'-TCCACT-5', 4423, 3'-CCCAGA-5', 4448, 3'-TCCACT-5', 4459, 3'-CCCACT-5', 4485, 3'-TTCACA-5', 4531.
  4. positive strand in the positive direction is SuccessablesInr2++.bas, looking for 5'-C/G/T-C/G/T-C-A-C/G/T-A/T-3', 40, 3'-TCCAGT-5', 153, 3'-CGCACA-5', 1020, 3'-CCCAGA-5', 1711, 3'-CGCACT-5', 1720, 3'-CCCACA-5', 1803, 3'-CCCAGA-5', 1958, 3'-TCCACA-5', 1969, 3'-GTCAGT-5', 2100, 3'-TCCACT-5', 2128, 3'-TCCAGT-5', 2220, 3'-TCCAGA-5', 2258, 3'-TCCACT-5', 2375, 3'-CGCAGT-5', 2423, 3'-GTCACA-5', 2464, 3'-CCCAGA-5', 2489, 3'-TTCACT-5', 2511, 3'-CGCACT-5', 2555, 3'-GTCAGT-5', 2607, 3'-CTCAGT-5', 2613, 3'-TTCAGT-5', 2618, 3'-TCCATA-5', 2642, 3'-TCCAGA-5', 3019, 3'-CTCAGA-5', 3187, 3'-TGCAGA-5', 3256, 3'-CTCACA-5', 3592, 3'-GCCAGA-5', 3608, 3'-CTCACT-5', 3712, 3'-TCCATT-5', 3731, 3'-TCCAGA-5', 3771, 3'-CCCAGT-5', 3820, 3'-GTCACT-5', 3843, 3'-CTCACT-5', 3876, 3'-TTCAGA-5', 3922, 3'-TCCACT-5', 3934, 3'-GTCACA-5', 3964, 3'-CGCAGA-5', 4056, 3'-TCCAGT-5', 4269, 3'-CTCACT-5', 4350, 3'-CCCACT-5', 4399, 3'-CCCAGA-5', 4414.
  5. complement, negative strand, negative direction is SuccessablesInr2c--.bas, looking for 5'-A/C/G-A/C/G-G-T-A/C/G-A/T-3', 59, 3'-CGGTAT-5', 39, 3'-ACGTAA-5', 152, 3'-CAGTGA-5', 208, 3'-CCGTGT-5', 266, 3'-CCGTGT-5', 518, 3'-CCGTGT-5', 960, 3'-CCGTCT-5', 1023, 3'-ACGTCA-5', 1032, 3'-AAGTGA-5', 1056, 3'-CCGTGT-5', 1116, 3'-GAGTGT-5', 1126, 3'-CCGTCT-5', 1314, 3'-ACGTCA-5', 1323, 3'-ACGTGA-5', 1347, 3'-AGGTCA-5', 1352, 3'-AGGTAA-5', 1378, 3'-GGGTCT-5', 1411, 3'-ACGTCA-5', 1472, 3'-GAGTGA-5', 1491, 3'-GGGTCT-5', 1518, 3'-AGGTCA-5', 1532, 3'-ACGTGT-5', 1719, 3'-CCGTCT-5', 1967, 3'-ACGTCA-5', 1976, 3'-CGGTGA-5', 1995, 3'-ACGTGA-5', 2000, 3'-ACGTCA-5', 2083, 3'-CGGTCA-5', 2211, 3'-ACGTCA-5', 2402, 3'-ACGTGA-5', 2426, 3'-AGGTGA-5', 2632, 3'-CGGTCA-5', 2654, 3'-CCGTGT-5', 2665, 3'-ACGTCA-5', 2737, 3'-CGGTGA-5', 2756, 3'-CGGTAA-5', 3284, 3'-ACGTGA-5', 3289, 3'-ACGTCT-5', 3431, 3'-CCGTAT-5', 3445, 3'-CCGTAT-5', 3451, 3'-CCGTCA-5', 3478, 3'-CCGTCT-5', 3589, 3'-CCGTCA-5', 3600, 3'-CAGTCT-5', 3625, 3'-CCGTGT-5', 3632, 3'-GAGTCT-5', 3644, 3'-CGGTAA-5', 3686, 3'-AGGTGT-5', 3692, 3'-GGGTAT-5', 3856, 3'-GAGTGT-5', 3965, 3'-CGGTCT-5', 4233, 3'-ACGTCA-5', 4317, 3'-ACGTGA-5', 4340, 3'-CGGTCA-5', 4415, 3'-AGGTGA-5', 4423, 3'-GGGTCT-5', 4448, 3'-AGGTGA-5', 4459, 3'-GGGTGA-5', 4485, 3'-AAGTGT-5', 4531.
  6. complement, negative strand, positive direction is SuccessablesInr2c-+.bas, looking for 5'-A/C/G-A/C/G-G-T-A/C/G-A/T-3', 40 , 3'-AGGTCA-5', 153 , 3'-GCGTGT-5', 1020 , 3'-GGGTCT-5', 1711 , 3'-GCGTGA-5', 1720 , 3'-GGGTGT-5', 1803 , 3'-GGGTCT-5', 1958 , 3'-AGGTGT-5', 1969 , 3'-CAGTCA-5', 2100 , 3'-AGGTGA-5', 2128 , 3'-AGGTCA-5', 2220 , 3'-AGGTCT-5', 2258 , 3'-AGGTGA-5', 2375 , 3'-GCGTCA-5', 2423 , 3'-CAGTGT-5', 2464 , 3'-GGGTCT-5', 2489 , 3'-AAGTGA-5', 2511 , 3'-GCGTGA-5', 2555 , 3'-CAGTCA-5', 2607 , 3'-GAGTCA-5', 2613 , 3'-AAGTCA-5', 2618 , 3'-AGGTAT-5', 2642 , 3'-AGGTCT-5', 3019 , 3'-GAGTCT-5', 3187 , 3'-ACGTCT-5', 3256 , 3'-GAGTGT-5', 3592 , 3'-CGGTCT-5', 3608 , 3'-GAGTGA-5', 3712 , 3'-AGGTAA-5', 3731 , 3'-AGGTCT-5', 3771 , 3'-GGGTCA-5', 3820 , 3'-CAGTGA-5', 3843 , 3'-GAGTGA-5', 3876 , 3'-AAGTCT-5', 3922 , 3'-AGGTGA-5', 3934 , 3'-CAGTGT-5', 3964 , 3'-GCGTCT-5', 4056 , 3'-AGGTCA-5', 4269 , 3'-GAGTGA-5', 4350 , 3'-GGGTGA-5', 4399 , 3'-GGGTCT-5', 4414.
  7. complement, positive strand, negative direction is SuccessablesInr2c+-.bas, looking for 5'-A/C/G-A/C/G-G-T-A/C/G-A/T-3', 44, 3'-AGGTAT-5', 179, 3'-GGGTCA-5', 206, 3'-GAGTCT-5', 278, 3'-CAGTGA-5', 299, 3'-AAGTGT-5', 322, 3'-AGGTCA-5', 439, 3'-ACGTAA-5', 533, 3'-AGGTCA-5', 568, 3'-AGGTCA-5', 576, 3'-AGGTCA-5', 712, 3'-CCGTCT-5', 754, 3'-CGGTGA-5', 868, 3'-CAGTGA-5', 1034, 3'-GGGTGA-5', 1049, 3'-GAGTGA-5', 1077, 3'-CCGTGT-5', 1220, 3'-CAGTGA-5', 1325, 3'-CAGTCT-5', 1354, 3'-GAGTCT-5', 1444, 3'-CCGTCA-5', 1511, 3'-ACGTCT-5', 1774, 3'-CAGTGA-5', 1978, 3'-CAGTGT-5', 2085, 3'-AGGTCA-5', 2248, 3'-CAGTGA-5', 2404, 3'-GAGTGA-5', 2447, 3'-AGGTCA-5', 2585, 3'-CAGTGT-5', 2603, 3'-CAGTGT-5', 2656, 3'-CAGTGA-5', 2739, 3'-AAGTGT-5', 2860, 3'-AGGTGA-5', 3144, 3'-GGGTGT-5', 3184, 3'-AAGTGA-5', 3410, 3'-CAGTAA-5', 3480, 3'-AGGTGA-5', 3825, 3'-GAGTAT-5', 3829, 3'-GAGTAA-5', 3891, 3'-AAGTGT-5', 3939, 3'-CAGTGA-5', 4200, 3'-AGGTCA-5', 4307, 3'-CAGTGA-5', 4319, 3'-GGGTGA-5', 4353, 3'-CAGTGT-5', 4359.
  8. complement, positive strand, positive direction is SuccessablesInr2c++.bas, looking for 5'-A/C/G-A/C/G-G-T-A/C/G-A/T-3', 87, 3'-AGGTCT-5', 15, 3'-CCGTAA-5', 22, 3'-CAGTGT-5', 155, 3'-GGGTCT-5', 204, 3'-CGGTGT-5', 343, 3'-GCGTCT-5', 396, 3'-ACGTCT-5', 438, 3'-GGGTCT-5', 468, 3'-ACGTGT-5', 548, 3'-AGGTGT-5', 632, 3'-GCGTGA-5', 686, 3'-GCGTGT-5', 800, 3'-CGGTCT-5', 835, 3'-CGGTGT-5', 884, 3'-CGGTCT-5', 935, 3'-CGGTGT-5', 984, 3'-GCGTGT-5', 1052, 3'-GCGTGT-5', 1136, 3'-ACGTGT-5', 1220, 3'-GGGTCA-5', 1250, 3'-GCGTCT-5', 1316, 3'-ACGTGA-5', 1372, 3'-GCGTCT-5', 1416, 3'-ACGTGA-5', 1472, 3'-GGGTGA-5', 1502, 3'-GCGTGT-5', 1556, 3'-CCGTAA-5', 1702, 3'-GGGTCT-5', 1742, 3'-ACGTGT-5', 1822, 3'-AGGTGA-5', 1912, 3'-ACGTCT-5', 1937, 3'-CCGTGA-5', 1996, 3'-GGGTCA-5', 2024, 3'-AGGTGT-5', 2029, 3'-GAGTCA-5', 2060, 3'-ACGTCA-5', 2065, 3'-CGGTGA-5', 2072, 3'-AAGTCA-5', 2098, 3'-GAGTAT-5', 2176, 3'-ACGTAA-5', 2206, 3'-CAGTCT-5', 2222, 3'-GAGTCT-5', 2239, 3'-AAGTGA-5', 2304, 3'-ACGTCA-5', 2328, 3'-CAGTGA-5', 2425, 3'-CAGTCT-5', 2609, 3'-GAGTCT-5', 2699, 3'-ACGTCT-5', 2721, 3'-GAGTCT-5', 2729, 3'-ACGTCT-5', 2859, 3'-GAGTCT-5', 2866, 3'-GAGTAA-5', 2902, 3'-CAGTGA-5', 2929, 3'-AAGTCA-5', 2936, 3'-ACGTGT-5', 2962, 3'-ACGTAA-5', 3072, 3'-GGGTCA-5', 3082, 3'-GGGTCT-5', 3091, 3'-AGGTGT-5', 3192, 3'-GAGTGT-5', 3209, 3'-CGGTCT-5', 3221, 3'-ACGTCA-5', 3232, 3'-ACGTCA-5', 3281, 3'-GAGTGA-5', 3317, 3'-ACGTGA-5', 3343, 3'-GGGTCA-5', 3379, 3'-GGGTGA-5', 3388, 3'-CCGTGT-5', 3409, 3'-ACGTCA-5', 3461, 3'-CCGTCT-5', 3473, 3'-GAGTGT-5', 3505, 3'-CGGTGT-5', 3705, 3'-AGGTCT-5', 3806, 3'-CAGTGT-5', 3822, 3'-ACGTCT-5', 3831, 3'-AGGTCT-5', 3891, 3'-GCGTCT-5', 3916, 3'-CAGTGT-5', 3954, 3'-ACGTCA-5', 3962, 3'-CCGTGA-5', 4006, 3'-AGGTGA-5', 4013, 3'-GAGTCT-5', 4195, 3'-CAGTCA-5', 4271, 3'-GAGTAA-5', 4309, 3'-ACGTCT-5', 4317, 3'-GGGTCT-5', 4330, 3'-GAGTGA-5', 4338.
  9. inverse complement, negative strand, negative direction is SuccessablesInr2ci--.bas, looking for 5'-A/T-A/C/G-T-G-A/C/G-A/C/G-3', 46, 3'-TCTGAC-5', 16, 3'-TGTGGA-5', 62, 3'-TGTGCA-5', 342, 3'-TGTGCA-5', 531, 3'-AGTGCG-5', 663, 3'-TGTGGG-5', 749, 3'-TCTGAG-5', 916, 3'-TGTGCG-5', 963, 3'-ACTGAA-5', 1052, 3'-AGTGAG-5', 1057, 3'-TCTGAG-5', 1082, 3'-TGTGGA-5', 1129, 3'-AGTGGA-5', 1171, 3'-AATGAA-5', 1298, 3'-TCTGAG-5', 1403, 3'-AGTGAC-5', 1492, 3'-TGTGAA-5', 1544, 3'-TCTGAA-5', 1617, 3'-AGTGCA-5', 1772, 3'-TCTGAC-5', 1934, 3'-AGTGCG-5', 1991, 3'-TCTGAG-5', 2026, 3'-TATGAC-5', 2162, 3'-ACTGGC-5', 2190, 3'-AGTGCG-5', 2207, 3'-TGTGAA-5', 2551, 3'-AGTGAA-5', 2578, 3'-ACTGAG-5', 2787, 3'-TATGGA-5', 2994, 3'-AGTGGG-5', 3057, 3'-AGTGAA-5', 3101, 3'-AGTGAA-5', 3240, 3'-AGTGCG-5', 3280, 3'-TCTGAC-5', 3425, 3'-TATGAC-5', 3541, 3'-TATGCG-5', 3547, 3'-TATGGA-5', 3859, 3'-TGTGGA-5', 3968, 3'-TGTGAA-5', 3983, 3'-AGTGAA-5', 4010, 3'-TCTGAG-5', 4054, 3'-AGTGAA-5', 4161, 3'-TCTGGG-5', 4205, 3'-TCTGCA-5', 4236, 3'-TGTGAC-5', 4336, 3'-TCTGGG-5', 4366.
  10. inverse complement, negative strand, positive direction is SuccessablesInr2ci-+.bas, looking for 5'-A/T-A/C/G-T-G-A/C/G-A/C/G-3', 94, 3'-AGTGGG-5', 54, 3'-TCTGCA-5', 224, 3'-TGTGAA-5', 231, 3'-ACTGCC-5', 238, 3'-TCTGAG-5', 256, 3'-TCTGGA-5', 271, 3'-ACTGGG-5', 348, 3'-AGTGCG-5', 497, 3'-AGTGCG-5', 581, 3'-AGTGCG-5', 665, 3'-ACTGCG-5', 749, 3'-TGTGGC-5', 819, 3'-ACTGCC-5', 901, 3'-TGTGGC-5', 919, 3'-ACTGCG-5', 1001, 3'-TGTGGC-5', 1023, 3'-AGTGCG-5', 1085, 3'-AGTGCG-5', 1160, 3'-AGTGCG-5', 1169, 3'-AGTGCG-5', 1253, 3'-ACTGAG-5', 1287, 3'-AATGCG-5', 1321, 3'-TCTGGC-5', 1377, 3'-TCTGCG-5', 1396, 3'-AATGCG-5', 1421, 3'-TCTGGC-5', 1477, 3'-TCTGCG-5', 1496, 3'-ACTGCA-5', 1505, 3'-AGTGCG-5', 1589, 3'-AGTGCG-5', 1725, 3'-AGTGCA-5', 1786, 3'-TGTGGA-5', 1806, 3'-TCTGGG-5', 1865, 3'-ACTGGG-5', 1954, 3'-TGTGGC-5', 1972, 3'-TCTGGC-5', 1993, 3'-AGTGCA-5', 2063, 3'-AGTGGC-5', 2068, 3'-TATGGC-5', 2160, 3'-ACTGCA-5', 2204, 3'-AGTGCA-5', 2326, 3'-TGTGCA-5', 2681, 3'-AGTGGA-5', 2712, 3'-ACTGCC-5', 2823, 3'-AATGAC-5', 2842, 3'-TCTGCA-5', 2857, 3'-TCTGGC-5', 2884, 3'-AATGGG-5', 2911, 3'-TCTGAC-5', 2944, 3'-TCTGAG-5', 2951, 3'-TGTGCA-5', 2960, 3'-TCTGGC-5', 2984, 3'-TCTGAG-5', 3007, 3'-AGTGCC-5', 3011, 3'-TATGAC-5', 3028, 3'-TCTGCA-5', 3061, 3'-AATGCA-5', 3070, 3'-ACTGGC-5', 3118, 3'-TCTGAG-5', 3124, 3'-TATGGA-5', 3163, 3'-AATGGG-5', 3169, 3'-AGTGCC-5', 3235, 3'-TATGAG-5', 3261, 3'-TCTGCA-5', 3268, 3'-TCTGCA-5', 3279, 3'-ACTGCA-5', 3320, 3'-ACTGGC-5', 3346, 3'-TCTGCC-5', 3359, 3'-TCTGGC-5', 3406, 3'-AATGCC-5', 3431, 3'-TGTGGA-5', 3437, 3'-AATGAA-5', 3442, 3'-AATGAG-5', 3446, 3'-AGTGGG-5', 3450, 3'-AGTGCA-5', 3464, 3'-AATGAC-5', 3568, 3'-TGTGAA-5', 3595, 3'-AGTGAC-5', 3713, 3'-ACTGAG-5', 3736, 3'-AATGAC-5', 3783, 3'-AATGAA-5', 3836, 3'-AGTGAG-5', 3877, 3'-TGTGAG-5', 3904, 3'-TCTGAA-5', 3925, 3'-TGTGCA-5', 3960, 3'-TGTGAC-5', 3972, 3'-AGTGGG-5', 4041, 3'-ACTGAA-5', 4090, 3'-AATGAG-5', 4095, 3'-AGTGCC-5', 4274, 3'-ACTGCA-5', 4341, 3'-AGTGAG-5', 4351, 3'-TGTGGG-5', 4395, 3'-TCTGGG-5', 4417.
  11. inverse complement, positive strand, negative direction is SuccessablesInr2ci+-.bas, looking for 5'-A/T-A/C/G-T-G-A/C/G-A/C/G-3', 54, 3'-ACTGAA-5', 18, 3'-TATGGG-5', 78, 3'-ACTGAA-5', 131, 3'-TATGAG-5', 275, 3'-AGTGAG-5', 300, 3'-ACTGAC-5', 308, 3'-AGTGCG-5', 447, 3'-AGTGAA-5', 472, 3'-AGTGGA-5', 523, 3'-AGTGAG-5', 1035, 3'-AGTGAG-5', 1078, 3'-AGTGGC-5', 1121, 3'-AGTGAG-5', 1326, 3'-TCTGGG-5', 1357, 3'-AGTGCA-5', 1470, 3'-ACTGCA-5', 1494, 3'-AGTGCA-5', 1535, 3'-AATGAA-5', 1581, 3'-AATGCC-5', 1634, 3'-TATGGC-5', 1743, 3'-ACTGAG-5', 1936, 3'-AATGGC-5', 1949, 3'-AGTGAG-5', 1979, 3'-ACTGCA-5', 1998, 3'-TGTGGC-5', 2066, 3'-AATGAC-5', 2188, 3'-AGTGAG-5', 2405, 3'-ACTGCA-5', 2424, 3'-AGTGAG-5', 2448, 3'-TGTGGC-5', 2606, 3'-AGTGAG-5', 2740, 3'-ACTGCA-5', 2759, 3'-TGTGCA-5', 2863, 3'-AATGGC-5', 3005, 3'-TGTGAG-5', 3268, 3'-AGTGAC-5', 3411, 3'-TGTGCA-5', 3429, 3'-TGTGCC-5', 3561, 3'-AATGGG-5', 3660, 3'-TGTGGG-5', 3712, 3'-ACTGGG-5', 3750, 3'-AATGCA-5', 3771, 3'-TCTGGA-5', 3836, 3'-ACTGCC-5', 3852, 3'-TGTGGC-5', 3960, 3'-AGTGAG-5', 4050, 3'-TGTGAG-5', 4093, 3'-AGTGAG-5', 4201, 3'-ACTGCA-5', 4315, 3'-AGTGAG-5', 4320, 3'-ACTGCA-5', 4330, 3'-ACTGCA-5', 4338, 3'-TGTGAG-5', 4362, 3'-AATGAG-5', 4556.
  12. inverse complement, positive strand, positive direction is SuccessablesInr2ci++.bas, looking for 5'-A/T-A/C/G-T-G-A/C/G-A/C/G-3', 47, 3'-TCTGAC-5', 236, 3'-TGTGAC-5', 346, 3'-TCTGCC-5', 399, 3'-TCTGGC-5', 441, 3'-AATGAA-5', 525, 3'-TGTGCA-5', 569, 3'-TGTGCG-5', 803, 3'-TGTGCG-5', 887, 3'-TGTGCG-5', 987, 3'-TGTGAC-5', 1139, 3'-TGTGCC-5', 1223, 3'-TGTGCC-5', 1559, 3'-ACTGGG-5', 1663, 3'-TGTGCC-5', 1698, 3'-TCTGAA-5', 1745, 3'-AATGGG-5', 1889, 3'-ACTGGC-5', 2214, 3'-AGTGGA-5', 2248, 3'-AGTGAG-5', 2305, 3'-AGTGGG-5', 2313, 3'-AGTGAC-5', 2341, 3'-TCTGAA-5', 2417, 3'-TGTGGA-5', 2431, 3'-TATGAA-5', 2740, 3'-TCTGGA-5', 2862, 3'-AGTGAC-5', 2930, 3'-ACTGAA-5', 2946, 3'-TGTGGG-5', 2965, 3'-ACTGAA-5', 3030, 3'-AGTGCA-5', 3254, 3'-AGTGAC-5', 3318, 3'-TGTGAG-5', 3508, 3'-TGTGGG-5', 3533, 3'-TCTGGA-5', 3551, 3'-AGTGGG-5', 3613, 3'-AGTGCC-5', 3748, 3'-ACTGGA-5', 3785, 3'-ACTGGA-5', 4019, 3'-AGTGAC-5', 4088, 3'-AGTGAG-5', 4127, 3'-AGTGGG-5', 4204, 3'-ACTGGG-5', 4217, 3'-TGTGCC-5', 4259, 3'-TCTGCG-5', 4320, 3'-AGTGGG-5', 4326, 3'-TGTGAG-5', 4335, 3'-AGTGAC-5', 4339.
  13. inverse, negative strand, negative direction, is SuccessablesInr2i--.bas, looking for 5'-A/T-C/G/T-A-C-C/G/T-C/G/T-3', 54, 3'-TGACTT-5', 18, 3'-ATACCC-5', 78, 3'-TGACTT-5', 131, 3'-ATACTC-5', 275, 3'-TCACTC-5', 300, 3'-TGACTG-5', 308, 3'-TCACGC-5', 447, 3'-TCACTT-5', 472, 3'-TCACCT-5', 523, 3'-TCACTC-5', 1035, 3'-TCACTC-5', 1078, 3'-TCACCG-5', 1121, 3'-TCACTC-5', 1326, 3'-AGACCC-5', 1357, 3'-TCACGT-5', 1470, 3'-TGACGT-5', 1494, 3'-TCACGT-5', 1535, 3'-TTACTT-5', 1581, 3'-TTACGG-5', 1634, 3'-ATACCG-5', 1743, 3'-TGACTC-5', 1936, 3'-TTACCG-5', 1949, 3'-TCACTC-5', 1979, 3'-TGACGT-5', 1998, 3'-ACACCG-5', 2066, 3'-TTACTG-5', 2188, 3'-TCACTC-5', 2405, 3'-TGACGT-5', 2424, 3'-TCACTC-5', 2448, 3'-ACACCG-5', 2606, 3'-TCACTC-5', 2740, 3'-TGACGT-5', 2759, 3'-ACACGT-5', 2863, 3'-TTACCG-5', 3005, 3'-ACACTC-5', 3268, 3'-TCACTG-5', 3411, 3'-ACACGT-5', 3429, 3'-ACACGG-5', 3561, 3'-TTACCC-5', 3660, 3'-ACACCC-5', 3712, 3'-TGACCC-5', 3750, 3'-TTACGT-5', 3771, 3'-AGACCT-5', 3836, 3'-TGACGG-5', 3852, 3'-ACACCG-5', 3960, 3'-TCACTC-5', 4050, 3'-ACACTC-5', 4093, 3'-TCACTC-5', 4201, 3'-TGACGT-5', 4315, 3'-TCACTC-5', 4320, 3'-TGACGT-5', 4330, 3'-TGACGT-5', 4338, 3'-ACACTC-5', 4362, 3'-TTACTC-5', 4556.
  14. inverse, negative strand, positive direction, is SuccessablesInr2i-+.bas, looking for 5'-A/T-C/G/T-A-C-C/G/T-C/G/T-3', 47, 3'-AGACTG-5', 236, 3'-ACACTG-5', 346, 3'-AGACGG-5', 399, 3'-AGACCG-5', 441, 3'-TTACTT-5', 525, 3'-ACACGT-5', 569, 3'-ACACGC-5', 803, 3'-ACACGC-5', 887, 3'-ACACGC-5', 987, 3'-ACACTG-5', 1139, 3'-ACACGG-5', 1223, 3'-ACACGG-5', 1559, 3'-TGACCC-5', 1663, 3'-ACACGG-5', 1698, 3'-AGACTT-5', 1745, 3'-TTACCC-5', 1889, 3'-TGACCG-5', 2214, 3'-TCACCT-5', 2248, 3'-TCACTC-5', 2305, 3'-TCACCC-5', 2313, 3'-TCACTG-5', 2341, 3'-AGACTT-5', 2417, 3'-ACACCT-5', 2431, 3'-ATACTT-5', 2740, 3'-AGACCT-5', 2862, 3'-TCACTG-5', 2930, 3'-TGACTT-5', 2946, 3'-ACACCC-5', 2965, 3'-TGACTT-5', 3030, 3'-TCACGT-5', 3254, 3'-TCACTG-5', 3318, 3'-ACACTC-5', 3508, 3'-ACACCC-5', 3533, 3'-AGACCT-5', 3551, 3'-TCACCC-5', 3613, 3'-TCACGG-5', 3748, 3'-TGACCT-5', 3785, 3'-TGACCT-5', 4019, 3'-TCACTG-5', 4088, 3'-TCACTC-5', 4127, 3'-TCACCC-5', 4204, 3'-TGACCC-5', 4217, 3'-ACACGG-5', 4259, 3'-AGACGC-5', 4320, 3'-TCACCC-5', 4326, 3'-ACACTC-5', 4335, 3'-TCACTG-5', 4339.
  15. inverse, positive strand, negative direction, is SuccessablesInr2i+-.bas, looking for 5'-A/T-C/G/T-A-C-C/G/T-C/G/T-3', 46, 3'-AGACTG-5', 16, 3'-ACACCT-5', 62, 3'-ACACGT-5', 342, 3'-ACACGT-5', 531, 3'-TCACGC-5', 663, 3'-ACACCC-5', 749, 3'-AGACTC-5', 916, 3'-ACACGC-5', 963, 3'-TGACTT-5', 1052, 3'-TCACTC-5', 1057, 3'-AGACTC-5', 1082, 3'-ACACCT-5', 1129, 3'-TCACCT-5', 1171, 3'-TTACTT-5', 1298, 3'-AGACTC-5', 1403, 3'-TCACTG-5', 1492, 3'-ACACTT-5', 1544, 3'-AGACTT-5', 1617, 3'-TCACGT-5', 1772, 3'-AGACTG-5', 1934, 3'-TCACGC-5', 1991, 3'-AGACTC-5', 2026, 3'-ATACTG-5', 2162, 3'-TGACCG-5', 2190, 3'-TCACGC-5', 2207, 3'-ACACTT-5', 2551, 3'-TCACTT-5', 2578, 3'-TGACTC-5', 2787, 3'-ATACCT-5', 2994, 3'-TCACCC-5', 3057, 3'-TCACTT-5', 3101, 3'-TCACTT-5', 3240, 3'-TCACGC-5', 3280, 3'-AGACTG-5', 3425, 3'-ATACTG-5', 3541, 3'-ATACGC-5', 3547, 3'-ATACCT-5', 3859, 3'-ACACCT-5', 3968, 3'-ACACTT-5', 3983, 3'-TCACTT-5', 4010, 3'-AGACTC-5', 4054, 3'-TCACTT-5', 4161, 3'-AGACCC-5', 4205, 3'-AGACGT-5', 4236, 3'-ACACTG-5', 4336, 3'-AGACCC-5', 4366.
  16. inverse, positive strand, positive direction, is SuccessablesInr2i++.bas, looking for 5'-A/T-C/G/T-A-C-C/G/T-C/G/T-3', 94, 3'-TCACCC-5', 54, 3'-AGACGT-5', 224, 3'-ACACTT-5', 231, 3'-TGACGG-5', 238, 3'-AGACTC-5', 256, 3'-AGACCT-5', 271, 3'-TGACCC-5', 348, 3'-TCACGC-5', 497, 3'-TCACGC-5', 581, 3'-TCACGC-5', 665, 3'-TGACGC-5', 749, 3'-ACACCG-5', 819, 3'-TGACGG-5', 901, 3'-ACACCG-5', 919, 3'-TGACGC-5', 1001, 3'-ACACCG-5', 1023, 3'-TCACGC-5', 1085, 3'-TCACGC-5', 1160, 3'-TCACGC-5', 1169, 3'-TCACGC-5', 1253, 3'-TGACTC-5', 1287, 3'-TTACGC-5', 1321, 3'-AGACCG-5', 1377, 3'-AGACGC-5', 1396, 3'-TTACGC-5', 1421, 3'-AGACCG-5', 1477, 3'-AGACGC-5', 1496, 3'-TGACGT-5', 1505, 3'-TCACGC-5', 1589, 3'-TCACGC-5', 1725, 3'-TCACGT-5', 1786, 3'-ACACCT-5', 1806, 3'-AGACCC-5', 1865, 3'-TGACCC-5', 1954, 3'-ACACCG-5', 1972, 3'-AGACCG-5', 1993, 3'-TCACGT-5', 2063, 3'-TCACCG-5', 2068, 3'-ATACCG-5', 2160, 3'-TGACGT-5', 2204, 3'-TCACGT-5', 2326, 3'-ACACGT-5', 2681, 3'-TCACCT-5', 2712, 3'-TGACGG-5', 2823, 3'-TTACTG-5', 2842, 3'-AGACGT-5', 2857, 3'-AGACCG-5', 2884, 3'-TTACCC-5', 2911, 3'-AGACTG-5', 2944, 3'-AGACTC-5', 2951, 3'-ACACGT-5', 2960, 3'-AGACCG-5', 2984, 3'-AGACTC-5', 3007, 3'-TCACGG-5', 3011, 3'-ATACTG-5', 3028, 3'-AGACGT-5', 3061, 3'-TTACGT-5', 3070, 3'-TGACCG-5', 3118, 3'-AGACTC-5', 3124, 3'-ATACCT-5', 3163, 3'-TTACCC-5', 3169, 3'-TCACGG-5', 3235, 3'-ATACTC-5', 3261, 3'-AGACGT-5', 3268, 3'-AGACGT-5', 3279, 3'-TGACGT-5', 3320, 3'-TGACCG-5', 3346, 3'-AGACGG-5', 3359, 3'-AGACCG-5', 3406, 3'-TTACGG-5', 3431, 3'-ACACCT-5', 3437, 3'-TTACTT-5', 3442, 3'-TTACTC-5', 3446, 3'-TCACCC-5', 3450, 3'-TCACGT-5', 3464, 3'-TTACTG-5', 3568, 3'-ACACTT-5', 3595, 3'-TCACTG-5', 3713, 3'-TGACTC-5', 3736, 3'-TTACTG-5', 3783, 3'-TTACTT-5', 3836, 3'-TCACTC-5', 3877, 3'-ACACTC-5', 3904, 3'-AGACTT-5', 3925, 3'-ACACGT-5', 3960, 3'-ACACTG-5', 3972, 3'-TCACCC-5', 4041, 3'-TGACTT-5', 4090, 3'-TTACTC-5', 4095, 3'-TCACGG-5', 4274, 3'-TGACGT-5', 4341, 3'-TCACTC-5', 4351, 3'-ACACCC-5', 4395, 3'-AGACCC-5', 4417.

Inr-like, TCTs samplings

Copying TTCTCT in "⌘F" yields three between ZSCAN22 and A1BG and three between ZNF497 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence TTCTCT (starting with SuccessablesTCT.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:

  1. negative strand, negative direction, looking for TTCTCT, 3, TTCTCT at 3380, TTCTCT at 2826, TTCTCT at 2809.
  2. negative strand, positive direction, looking for TTCTCT, 4, TTCTCT at 4386, TTCTCT at 1990, TTCTCT at 139, TTCTCT at 119.
  3. positive strand, negative direction, looking for TTCTCT, 1, TTCTCT at 622.
  4. positive strand, positive direction, looking for TTCTCT, 0.
  5. complement, negative strand, negative direction, looking for AAGAGA, 1, AAGAGA at 622.
  6. complement, negative strand, positive direction, looking for AAGAGA, 0.
  7. complement, positive strand, negative direction, looking for AAGAGA, 3, AAGAGA at 3380, AAGAGA at 2826, AAGAGA at 2809.
  8. complement, positive strand, positive direction, looking for AAGAGA, 4, AAGAGA at 4386, AAGAGA at 1990, AAGAGA at 139, AAGAGA at 119.
  9. inverse complement, negative strand, negative direction, looking for AGAGAA, 1, AGAGAA at 4527.
  10. inverse complement, negative strand, positive direction, looking for AGAGAA, 0.
  11. inverse complement, positive strand, negative direction, looking for AGAGAA, 3, AGAGAA at 3406, AGAGAA at 2827, AGAGAA at 2810.
  12. inverse complement, positive strand, positive direction, looking for AGAGAA, 2, AGAGAA at 4387, AGAGAA at 3056.
  13. inverse negative strand, negative direction, looking for TCTCTT, 3, TCTCTT at 3406, TCTCTT at 2827, TCTCTT at 2810.
  14. inverse negative strand, positive direction, looking for TCTCTT, 2, TCTCTT at 4387, TCTCTT at 3056.
  15. inverse positive strand, negative direction, looking for TCTCTT, 1, TCTCTT at 4527.
  16. inverse positive strand, positive direction, looking for TCTCTT, 0.

TCT core promoters

Main article: Core promoter gene transcriptions

Negative strand, negative direction: AGAGAA at 4527, and complement.

Negative strand, positive direction: TTCTCT at 4386, and complement.

Positive strand, positive direction: AGAGAA at 4387, and complement.

TCT distal promoters

Main article: Distal promoter gene transcriptions

Negative strand, negative direction: TTCTCT at 3380, TTCTCT at 2826, TTCTCT at 2809, and complements.

Positive strand, negative direction: AGAGAA at 3406, AGAGAA at 2827, AGAGAA at 2810, TTCTCT at 622, and complements.

Negative strand, positive direction: TTCTCT at 1990, TTCTCT at 139, TTCTCT at 119, and complements.

Positive strand, positive direction: AGAGAA at 3056, and complement.

Acknowledgements

The content on this page was first contributed by: Henry A. Hoff.

Initial content for this page in some instances came from Wikiversity.

See also

References

  1. ↑ Smale, Stephen T.; Baltimore, David (1989-04-07). "The "initiator" as a transcription control element". Cell. 57 (1): 103–113. doi:10.1016/0092-8674(89)90176-1. ISSN 0092-8674. PMID 2467742.
  2. ↑ 2.0 2.1 Gershenzon, Naum I.; Ioshikhes, Ilya P. (2005-04-15). "Synergy of human Pol II core promoter elements revealed by statistical sequence analysis". Bioinformatics. 21 (8): 1295–1300. doi:10.1093/bioinformatics/bti172. ISSN 1367-4803.
  3. ↑ Lim, Chin Yan; Santoso, Buyung; Boulay, Thomas; Dong, Emily; Ohler, Uwe; Kadonaga, James T. (2004-07-01). "The MTE, a new core promoter element for transcription by RNA polymerase II". Genes & Development. 18 (13): 1606–1617. doi:10.1101/gad.1193404. ISSN 0890-9369. PMC 443522. PMID 15231738.
  4. ↑ Kaufmann, J.; Smale, S. T. (1994-04-01). "Direct recognition of initiator elements by a component of the transcription factor IID complex". Genes & Development. 8 (7): 821–829. doi:10.1101/gad.8.7.821. ISSN 0890-9369. PMID 7926770.
  5. ↑ O'Shea-Greenfield, A.; Smale, S. T. (1992-01-15). "Roles of TATA and initiator elements in determining the start site location and direction of RNA polymerase II transcription". The Journal of Biological Chemistry. 267 (2): 1391–1402. ISSN 0021-9258. PMID 1730658.
  6. ↑ 6.0 6.1 6.2 Yang, Chuhu; Bolotin, Eugene; Jiang, Tao; Sladek, Frances M.; Martinez, Ernest (2007-03-01). "Prevalence of the Initiator over the TATA box in human and yeast genes and identification of DNA motifs enriched in human TATA-less core promoters". Gene. 389 (1): 52–65. doi:10.1016/j.gene.2006.09.029. ISSN 0378-1119. PMC 1955227. PMID 17123746.
  7. ↑ Ngoc, Long Vo; Cassidy, California Jack; Huang, Cassidy Yunjing; Duttke, Sascha H. C.; Kadonaga, James T. (2017-01-20). "The human initiator is a distinct and abundant element that is precisely positioned in focused core promoters". Genes & Development. doi:10.1101/gad.293837.116. ISSN 0890-9369. PMC 5287114. PMID 28108474.
  8. ↑ Javahery, R; Khachi, A; Lo, K; Zenzie-Gregory, B; Smale, S T (1994-01-01). "DNA sequence requirements for transcriptional initiator activity in mammalian cells". Molecular and Cellular Biology. 14 (1): 116–127. doi:10.1128/mcb.14.1.116. ISSN 0270-7306. PMC 358362. PMID 8264580.
  9. ↑ Takuya Matsumoto, Saemi Kitajima, Chisato Yamamoto, Mitsuru Aoyagi, Yoshiharu Mitoma, Hiroyuki Harada and Yuji Nagashima (9 August 2020). "Cloning and tissue distribution of the ATP-binding cassette subfamily G member 2 gene in the marine pufferfish Takifugu rubripes" (PDF). Fisheries Science. 86: 873–887. doi:10.1007/s12562-020-01451-z. Retrieved 27 September 2020.
  10. ↑ 10.0 10.1 Gillian E. Chalkley and C. Peter Verrijzer (September 1, 1999). "DNA binding site selection by RNA polymerase II TAFs: a TAFII250-TAFII150 complex recognizes the Initiator" (PDF). The EMBO Journal. 18 (17): 4835–45. PMID 10469661. Retrieved 2012-04-26.
  11. ↑ 11.0 11.1 J. Carcamo, L. Buckbinder, D. Reinberg (1991). Proceedings of the National Academy of Sciences USA. 88: 8052–6. Missing or empty |title= (help); |access-date= requires |url= (help)
  12. ↑ L. Weis and D. Reinberg (1997). "Accurate positioning of RNA polymerase II on a natural TATA-less promoter is independent of TATA-binding protein associated factors and initiator-binding proteins". Mol. Cell. Biol. 17: 2973–84. |access-date= requires |url= (help)
  13. ↑ RefSeq (May 2009). "BRCA1 BRCA1, DNA repair associated [ Homo sapiens (human) ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 22 December 2018.
  14. ↑ 14.0 14.1 RefSeq (February 2010). "BRCA1 BRCA1, DNA repair associated [ Homo sapiens (human) ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 22 December 2018.
  15. ↑ Schlegel BP, Starita LM, Parvin JD (February 2003). "Overexpression of a protein fragment of RNA helicase A causes inhibition of endogenous BRCA1 function and defects in ploidy and cytokinesis in mammary epithelial cells". Oncogene. 22 (7): 983–91. doi:10.1038/sj.onc.1206195. PMID 12592385.
  16. ↑ Anderson SF, Schlegel BP, Nakajima T, Wolpin ES, Parvin JD (July 1998). "BRCA1 protein is linked to the RNA polymerase II holoenzyme complex via RNA helicase A". Nat. Genet. 19 (3): 254–6. doi:10.1038/930. PMID 9662397.
  17. ↑ Lee CG, Hurwitz J (Aug 1993). "Human RNA helicase A is homologous to the maleless protein of Drosophila". The Journal of Biological Chemistry. 268 (22): 16822–30. PMID 8344961.
  18. ↑ Zhang S, Grosse F (April 1997). "Domain structure of human nuclear DNA helicase II (RNA helicase A)". The Journal of Biological Chemistry. 272 (17): 11487–94. doi:10.1074/jbc.272.17.11487. PMID 9111062.
  19. ↑ Archambault J, Chambers RS, Kobor MS, Ho Y, Cartier M, Bolotin D, Andrews B, Kane CM, Greenblatt J (February 1998). "An essential component of a C-terminal domain phosphatase that interacts with transcription factor IIF in Saccharomyces cerevisiae". Proc Natl Acad Sci U S A. 94 (26): 14300–5. Bibcode:1997PNAS...9414300A. doi:10.1073/pnas.94.26.14300. PMC 24951. PMID 9405607.
  20. ↑ 20.0 20.1 Archambault J, Pan G, Dahmus GK, Cartier M, Marshall N, Zhang S, Dahmus ME, Greenblatt J (November 1998). "FCP1, the RAP74-interacting subunit of a human protein phosphatase that dephosphorylates the carboxyl-terminal domain of RNA polymerase IIO". J Biol Chem. 273 (42): 27593–601. doi:10.1074/jbc.273.42.27593. PMID 9765293.
  21. ↑ 21.0 21.1 "Entrez Gene: CTDP1 CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) phosphatase, subunit 1".
  22. ↑ RefSeq (February 2011). "CTDP1 CTD phosphatase subunit 1 [ Homo sapiens (human) ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 22 December 2018.
  23. ↑ Licciardo, Paolo; Amente Stefano; Ruggiero Luca; Monti Maria; Pucci Piero; Lania Luigi; Majello Barbara (Feb 2003). "The FCP1 phosphatase interacts with RNA polymerase II and with MEP50 a component of the methylosome complex involved in the assembly of snRNP". Nucleic Acids Res. England. 31 (3): 999–1005. doi:10.1093/nar/gkg197. PMC 149217. PMID 12560496.
  24. ↑ Scully, R; Anderson S F; Chao D M; Wei W; Ye L; Young R A; Livingston D M; Parvin J D (May 1997). "BRCA1 is a component of the RNA polymerase II holoenzyme". Proc. Natl. Acad. Sci. U.S.A. UNITED STATES. 94 (11): 5605–10. Bibcode:1997PNAS...94.5605S. doi:10.1073/pnas.94.11.5605. ISSN 0027-8424. PMC 20825. PMID 9159119.
  25. ↑ 25.0 25.1 RefSeq (September 2011). "DDX53 DEAD-box helicase 53 [ Homo sapiens (human)". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 22 December 2018.
  26. ↑ DR Liston, PJ Johnson (March 1999). "Analysis of a Ubiquitous Promoter Element in a Primitive Eukaryote: Early Evolution of the Initiator Element". Molecular and Cellular Biology. 19 (3): 2380–8. PMID 10022924. |access-date= requires |url= (help)
  27. ↑ 27.0 27.1 C Yang, E Bolotin, T Jiang, FM Sladek, E Martinez (March 2007). "Prevalence of the initiator over the TATA box in human and yeast genes and identification of DNA motifs enriched in human TATA-less core promoters". Gene. 389 (1): 52–65. doi:10.1016/j.gene.2006.09.029. PMC 1955227. PMID 17123746.
  28. ↑ JE Purdy, BJ Mann, LT Pho, WA Petri Jr (July 19, 1994). "Transient transfection of the enteric parasite Entamoeba histolytica and expression of firefly luciferase". Proceedings of the National Academy of Science USA. 91 (15): 7099–103. PMID 8041752. Retrieved 2012-06-10.
  29. ↑ 29.0 29.1 Hualin Xi, Yong Yu, Yutao Fu, Jonathan Foley, Anason Halees, and Zhiping Weng (June 2007). "Analysis of overrepresented motifs in human core promoters reveals dual regulatory roles of YY1". Genome Research. 17 (6): 798–806. doi:10.1101/gr.5754707. PMC 1891339. PMID 17567998.
  30. ↑ R. Javahery, A. Khachi, K. Lo, B. Zenzie-Gregory, S. T. Smale (January 1994). "DNA Sequence Requirements for Transcriptional Initiator Activity in Mammalian Cells". Molecular and Cellular Biology. 14 (1): 116–27. PMID 8264580. |access-date= requires |url= (help)
  31. ↑ Ananda L. Roy (August 2001). "Biochemistry and biology of the inducible multifunctional transcription factor TFII-I" (PDF). Gene. 274 (1–2): 1–13. doi:10.1016/S0378-1119(01)00625-4. Retrieved 2012-04-06.
  32. ↑ HGNC:11535 (March 24, 2012). "TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa". Bethesda, Maryland: NCBI. Retrieved 2012-04-09.
  33. ↑ ST Smale (March 1997). "Transcription initiation from TATA-less promoters within eukaryotic protein-coding genes". Biochimica & Biophysica Acta. 1351 (1–2): 73–88. doi:10.1016/S0167-4781(96)00206-0. PMID 9116046. |access-date= requires |url= (help)
  34. ↑ KH Emami, A Jain, ST Smale (1997). Genes Development. 11: 3007–19. Missing or empty |title= (help); |access-date= requires |url= (help)
  35. ↑ 35.0 35.1 35.2 Benjamin Lewin (2004). Genes VIII. Upper Saddle River, NJ: Pearson Prentice Hall. pp. 636–637. ISBN 0-13-144946-X.
  36. ↑ AL Roy, M Meisterernst, P. Pognonec, RG Roeder (1991). Nature. 354: 245–8. Missing or empty |title= (help); |access-date= requires |url= (help)
  37. ↑ AL Roy, S. Malik, M. Meisterernst, RG Roeder (1993). 365: 355–9. Missing or empty |title= (help); |access-date= requires |url= (help)
  38. ↑ Stephen T. Smale and James T. Kadonaga (July 2003). "The RNA Polymerase II Core Promoter" (PDF). Annual Review of Biochemistry. 72 (1): 449–79. doi:10.1146/annurev.biochem.72.121801.161520. PMID 12651739. Retrieved 2012-05-07.
  39. ↑ Tamar Juven-Gershon, Jer-Yuan Hsu, Joshua W. M. Theisen, and James T. Kadonaga (June 2008). "The RNA Polymerase II Core Promoter – the Gateway to Transcription". Current Opinion in Cell Biology. 20 (3): 253–9. doi:10.1016/j.ceb.2008.03.003. Retrieved 2013-02-13.

Further reading

External links

{{Chemistry resources}}

{{Phosphate biochemistry}}Template:Sisterlinks

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