Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold313
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 790584
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
File 6 of 6
Found at i:720894 original size:20 final size:20
Alignment explanation
Indices: 720871--720923 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
720861 ATTAAGCAAA
720871 ATGTATCGATACATCTGGGT
1 ATGTATCGATACATCTGGGT
720891 ATGTATCGATACATCTGGGT
1 ATGTATCGATACATCTGGGT
720911 ATGTATCGATACA
1 ATGTATCGATACA
720924 ATTAAGGGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (20 bp):
ATGTATCGATACATCTGGGT
Found at i:726395 original size:26 final size:26
Alignment explanation
Indices: 726357--726411 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
726347 AAAGAAATTT
* * *
726357 AAAATAGGTGGAGAAATTATTTTGTA
1 AAAAAAGGAGGAGAAATTATTTTATA
*
726383 AAAAAAGGAGGAGAAATTGTTTTATA
1 AAAAAAGGAGGAGAAATTATTTTATA
726409 AAA
1 AAA
726412 GAGATTATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.49, C:0.00, G:0.22, T:0.29
Consensus pattern (26 bp):
AAAAAAGGAGGAGAAATTATTTTATA
Found at i:729326 original size:27 final size:27
Alignment explanation
Indices: 729295--729352 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 27
729285 ATTTGACATA
*
729295 TAAAGCCTTGCCTCAATTGGACATCTT
1 TAAAGCCTTGCCTCAATCGGACATCTT
*
729322 TAAAGCCTTGCCTTAATCGGACATCTT
1 TAAAGCCTTGCCTCAATCGGACATCTT
729349 TAAA
1 TAAA
729353 AGTGCAAATG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (27 bp):
TAAAGCCTTGCCTCAATCGGACATCTT
Found at i:731755 original size:19 final size:20
Alignment explanation
Indices: 731731--731781 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
731721 TAATTGAGTG
*
731731 TGTATCGATACAATG-A-ACA
1 TGTATCGATACAAAGCATA-A
731750 TGTATCGATACAAAGCATAA
1 TGTATCGATACAAAGCATAA
731770 TGTATCGATACA
1 TGTATCGATACA
731782 TCTGGATGTG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 14 0.48
20 14 0.48
21 1 0.03
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (20 bp):
TGTATCGATACAAAGCATAA
Found at i:732561 original size:40 final size:40
Alignment explanation
Indices: 732507--732611 Score: 192
Period size: 40 Copynumber: 2.6 Consensus size: 40
732497 TTATAAAATA
*
732507 ATTTCTCAATAATTTCTCCCCCTTTGTCAAATGTCAAATTT
1 ATTT-TCAAAAATTTCTCCCCCTTTGTCAAATGTCAAATTT
732548 ATTTTCAAAAATTTCTCCCCCTTTGTCAAATGTCAAATTT
1 ATTTTCAAAAATTTCTCCCCCTTTGTCAAATGTCAAATTT
732588 ATTTTCAAAAATTTCTCCCCCTTT
1 ATTTTCAAAAATTTCTCCCCCTTT
732612 TTGTTATAGC
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
40 59 0.94
41 4 0.06
ACGTcount: A:0.28, C:0.25, G:0.04, T:0.44
Consensus pattern (40 bp):
ATTTTCAAAAATTTCTCCCCCTTTGTCAAATGTCAAATTT
Found at i:732963 original size:19 final size:19
Alignment explanation
Indices: 732936--732990 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 19
732926 GTATCGATAT
732936 ATTGTATCGATACATGCTC
1 ATTGTATCGATACATGCTC
* *
732955 ATTGCATCGATACATACTC
1 ATTGTATCGATACATGCTC
*
732974 ATTTGTATCAATACATG
1 A-TTGTATCGATACATG
732991 AAACTGGCAG
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 18 0.60
20 12 0.40
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (19 bp):
ATTGTATCGATACATGCTC
Found at i:740765 original size:19 final size:20
Alignment explanation
Indices: 740728--740768 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
740718 AATTTTTGGC
740728 ATTTGACAAAGGAGGAGAAA
1 ATTTGACAAAGGAGGAGAAA
740748 ATTTGACAAAGG-GGAGAAA
1 ATTTGACAAAGGAGGAGAAA
740767 AT
1 AT
740769 CATTTTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.49, C:0.05, G:0.29, T:0.17
Consensus pattern (20 bp):
ATTTGACAAAGGAGGAGAAA
Found at i:740836 original size:20 final size:21
Alignment explanation
Indices: 740789--740830 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
740779 AGAGAGCTTT
*
740789 AATTAGTTTATCAAGGGGGAG
1 AATTATTTTATCAAGGGGGAG
*
740810 AATTATTTTATTAAGGGGGAG
1 AATTATTTTATCAAGGGGGAG
740831 TTTATTGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.02, G:0.31, T:0.33
Consensus pattern (21 bp):
AATTATTTTATCAAGGGGGAG
Found at i:750176 original size:19 final size:19
Alignment explanation
Indices: 750130--750187 Score: 62
Period size: 19 Copynumber: 3.0 Consensus size: 19
750120 CTGCCAGTTT
*
750130 CATGTATCGATACAATTGAG
1 CATGTATCGATACAA-TGAA
**
750150 TGTGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
* *
750169 CATGTATCAATACATTGAA
1 CATGTATCGATACAATGAA
750188 TCGATATAAA
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
19 18 0.58
20 13 0.42
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:750713 original size:20 final size:20
Alignment explanation
Indices: 750690--750727 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
750680 AAGTCAATTA
* *
750690 TCAATGATCAATGTTCAAAG
1 TCAACGATCAATGGTCAAAG
750710 TCAACGATCAATGGTCAA
1 TCAACGATCAATGGTCAA
750728 CATCAATTAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.26
Consensus pattern (20 bp):
TCAACGATCAATGGTCAAAG
Found at i:750733 original size:20 final size:19
Alignment explanation
Indices: 750689--750733 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
750679 AAAGTCAATT
* *
750689 ATCAATGATCAATGTTCAA
1 ATCAACGATCAATGGTCAA
750708 AGTCAACGATCAATGGTCAA
1 A-TCAACGATCAATGGTCAA
750728 CATCAA
1 -ATCAA
750734 TTAGGGTCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 1 0.05
20 20 0.91
21 1 0.05
ACGTcount: A:0.42, C:0.20, G:0.13, T:0.24
Consensus pattern (19 bp):
ATCAACGATCAATGGTCAA
Found at i:752699 original size:31 final size:31
Alignment explanation
Indices: 752646--752747 Score: 134
Period size: 31 Copynumber: 3.2 Consensus size: 31
752636 CCTTACAACA
*
752646 CTATCTTTT-AAAGGCTAAGATAGAACTTCC
1 CTATCTTTTCACAGGCTAAGATAGAACTTCC
* *
752676 CTATCTTTTCACAGGATAAGATAGAACCTCC
1 CTATCTTTTCACAGGCTAAGATAGAACTTCC
*
752707 CTATCTTTTCACAGGCTAACATAGAACCTCTTCC
1 CTATCTTTTCACAGGCTAAGATAGAA---CTTCC
752741 CTATCTT
1 CTATCTT
752748 GGGTGTTTTA
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
30 9 0.15
31 42 0.68
34 11 0.18
ACGTcount: A:0.29, C:0.26, G:0.11, T:0.33
Consensus pattern (31 bp):
CTATCTTTTCACAGGCTAAGATAGAACTTCC
Found at i:757308 original size:154 final size:154
Alignment explanation
Indices: 756996--757371 Score: 465
Period size: 154 Copynumber: 2.4 Consensus size: 154
756986 AGCATTATCC
* * * *
756996 TAAGTCCTTTAGGGGTACTAGGTACTTTTACGTCAAAGGTATCCCTTA-GGGTATTTTTGTAATT
1 TAAGTCCTTTAGGGGTATTGGGTACTTTTACGTCAAAGGTATCCCCTAGGGGTATTTTCGTAATT
* * * * * * * * *
757060 TTTCAAAACCAAGTGATAGGTTGTCATCGGGTCTGCTTTTCTGCAAAGGTAGATATTTAGGATAG
66 TTTCAAAACAAACTCATAGGTTGTCACCGAGTCCGCTTTTATCCAAAGGTAGATATTTAAGATAG
* *
757125 GTTCATCCCATCTATTATCCTTTT
131 GTTCATCCCATCTATAAACCTTTT
*
757149 TAAGTCCTTTAGGGGTATTGGGTACTTTTACGTTAAAGGTATCCCCTAGGGGTATTTTCGTAATT
1 TAAGTCCTTTAGGGGTATTGGGTACTTTTACGTCAAAGGTATCCCCTAGGGGTATTTTCGTAATT
*
757214 TTT-AAGAACAAACTCTTAGGTTGTCACCGAGTCCGCTTTTATACCAAAGGTAG-TCATTTAAGA
66 TTTCAA-AACAAACTCATAGGTTGTCACCGAGTCCGCTTTTAT-CCAAAGGTAGAT-ATTTAAGA
*
757277 TAGTTTCATCCCAT-T-TCAAACCTTTT
128 TAGGTTCATCCCATCTAT-AAACCTTTT
* * * * * *
757303 TAAGTCCTTTAGGGGTATCGAGTACTTTTACGCCAAAAGTATCCCCTAGGGGCATTTTCATAATT
1 TAAGTCCTTTAGGGGTATTGGGTACTTTTACGTCAAAGGTATCCCCTAGGGGTATTTTCGTAATT
757368 TTTC
66 TTTC
757372 TACAAAACCG
Statistics
Matches: 192, Mismatches: 25, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
153 47 0.24
154 116 0.60
155 29 0.15
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.38
Consensus pattern (154 bp):
TAAGTCCTTTAGGGGTATTGGGTACTTTTACGTCAAAGGTATCCCCTAGGGGTATTTTCGTAATT
TTTCAAAACAAACTCATAGGTTGTCACCGAGTCCGCTTTTATCCAAAGGTAGATATTTAAGATAG
GTTCATCCCATCTATAAACCTTTT
Found at i:760356 original size:13 final size:13
Alignment explanation
Indices: 760338--760362 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
760328 CATAAAGTGT
760338 TGTATCGATACAA
1 TGTATCGATACAA
760351 TGTATCGATACA
1 TGTATCGATACA
760363 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:760360 original size:33 final size:33
Alignment explanation
Indices: 760318--760384 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
760308 TTCAACGATT
760318 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*** *
760351 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
760384 T
1 T
760385 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:760443 original size:13 final size:13
Alignment explanation
Indices: 760425--760449 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
760415 ATCACTTAAA
760425 TGTATCGATACAT
1 TGTATCGATACAT
760438 TGTATCGATACA
1 TGTATCGATACA
760450 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:760502 original size:52 final size:51
Alignment explanation
Indices: 760438--760586 Score: 244
Period size: 52 Copynumber: 2.9 Consensus size: 51
760428 ATCGATACAT
**
760438 TGTATCGATACACTGATCTTTGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACT-ATCAATGTATCGATACATGCAGGCAAATTTGCCCAGA
*
760490 TGTATCGATACACTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACTAT-CAATGTATCGATACATGCAGGCAAATTTGCCCAGA
760542 TGTATCGATACACTATTCAATGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACACTA-TCAATGTATCGATACATGCAGGCAAATTT
760587 TCATATTTCG
Statistics
Matches: 91, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
51 2 0.02
52 88 0.97
53 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.30
Consensus pattern (51 bp):
TGTATCGATACACTATCAATGTATCGATACATGCAGGCAAATTTGCCCAGA
Found at i:767240 original size:20 final size:19
Alignment explanation
Indices: 767191--767250 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 19
767181 ATACAATAAG
767191 AAATGTATTGATACAATTGTA
1 AAATGTATTGATAC-ATT-TA
767212 AACATGTATTGATACATTTA
1 AA-ATGTATTGATACATTTA
* **
767232 TTAATGTATCAATACATTT
1 -AAATGTATTGATACATTT
767251 CCTTGGCAGT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
20 16 0.47
21 6 0.18
22 12 0.35
ACGTcount: A:0.40, C:0.08, G:0.10, T:0.42
Consensus pattern (19 bp):
AAATGTATTGATACATTTA
Found at i:772642 original size:21 final size:20
Alignment explanation
Indices: 772618--772672 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
772608 TCCACATGGT
772618 CATGTATCGATACATTTCAAA
1 CATGTATCGATACA-TTCAAA
* **
772639 CATGTATCCATACATTCACT
1 CATGTATCGATACATTCAAA
*
772659 TATGTATCGATACA
1 CATGTATCGATACA
772673 AATTATTAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 16 0.55
21 13 0.45
ACGTcount: A:0.35, C:0.22, G:0.09, T:0.35
Consensus pattern (20 bp):
CATGTATCGATACATTCAAA
Found at i:773566 original size:21 final size:19
Alignment explanation
Indices: 773517--773574 Score: 80
Period size: 19 Copynumber: 2.9 Consensus size: 19
773507 TTGTATTGAT
*
773517 ACAATGTATCGATACATGT
1 ACAATGTATCGATACATGG
*
773536 TCAATGTATCGATACATGG
1 ACAATGTATCGATACATGG
773555 ACAAATTGTATCGATACATG
1 AC-AA-TGTATCGATACATG
773575 AAATTGGTAG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 18 0.53
20 2 0.06
21 14 0.41
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (19 bp):
ACAATGTATCGATACATGG
Found at i:775359 original size:13 final size:13
Alignment explanation
Indices: 775308--775361 Score: 90
Period size: 13 Copynumber: 4.2 Consensus size: 13
775298 AAAACCCAGA
*
775308 TGTATCGATACAA
1 TGTATCGATACAT
775321 TGTATCGATACAT
1 TGTATCGATACAT
*
775334 TGTATCTATACAT
1 TGTATCGATACAT
775347 TGTATCGATACAT
1 TGTATCGATACAT
775360 TG
1 TG
775362 GGTACTAGTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 38 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:775525 original size:20 final size:22
Alignment explanation
Indices: 775485--775525 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
775475 TTCCATAAAT
775485 TTTCTATTTTTCACTTCAAAAAC
1 TTTCTATTTTTCAC-TCAAAAAC
775508 TTTC-ATTTTTCA-TCAAAA
1 TTTCTATTTTTCACTCAAAA
775526 TCATCAACAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
22 8 0.44
23 4 0.22
ACGTcount: A:0.32, C:0.20, G:0.00, T:0.49
Consensus pattern (22 bp):
TTTCTATTTTTCACTCAAAAAC
Found at i:777242 original size:19 final size:19
Alignment explanation
Indices: 777218--777276 Score: 75
Period size: 19 Copynumber: 3.1 Consensus size: 19
777208 TACATAAGGG
777218 GGAGAAGATAACTGTTTAA
1 GGAGAAGATAACTGTTTAA
*
777237 GGAGAAGATAACTATTTAA
1 GGAGAAGATAACTGTTTAA
* *
777256 GGGGGAGATAA-TCGTTTAA
1 GGAGAAGATAACT-GTTTAA
777275 GG
1 GG
777277 GGGAGAATTG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
18 1 0.03
19 34 0.97
ACGTcount: A:0.39, C:0.05, G:0.31, T:0.25
Consensus pattern (19 bp):
GGAGAAGATAACTGTTTAA
Found at i:779545 original size:31 final size:31
Alignment explanation
Indices: 779510--779572 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
779500 TATCTTAATA
779510 AACCTAAAAGACTAAAAAATTATATGAAATG
1 AACCTAAAAGACTAAAAAATTATATGAAATG
779541 AACCTAAAAGACTAAAAAATTATATGAAATG
1 AACCTAAAAGACTAAAAAATTATATGAAATG
779572 A
1 A
779573 TATTTTTACT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.22
Consensus pattern (31 bp):
AACCTAAAAGACTAAAAAATTATATGAAATG
Found at i:781143 original size:13 final size:13
Alignment explanation
Indices: 781125--781150 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
781115 TACAGCAAGT
781125 ATGTATCGATACA
1 ATGTATCGATACA
781138 ATGTATCGATACA
1 ATGTATCGATACA
781151 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:783411 original size:21 final size:22
Alignment explanation
Indices: 783365--783409 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
783355 TTGCAAGTTG
783365 AAATAAAGAAGTTAGCTAATGA
1 AAATAAAGAAGTTAGCTAATGA
*
783387 AAATAATG-AGTTAGCTAA-GA
1 AAATAAAGAAGTTAGCTAATGA
783407 AAA
1 AAA
783410 ATGAAAACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.23
21 10 0.45
22 7 0.32
ACGTcount: A:0.56, C:0.04, G:0.18, T:0.22
Consensus pattern (22 bp):
AAATAAAGAAGTTAGCTAATGA
Found at i:785232 original size:15 final size:15
Alignment explanation
Indices: 785212--785242 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
785202 TAAAAATGTC
*
785212 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
785227 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
785242 C
1 C
785243 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:787339 original size:13 final size:13
Alignment explanation
Indices: 787321--787346 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
787311 ACATTTTTCT
787321 TTGTATCGATACA
1 TTGTATCGATACA
787334 TTGTATCGATACA
1 TTGTATCGATACA
787347 GGGTGATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:787510 original size:20 final size:20
Alignment explanation
Indices: 787467--787512 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
787457 AAATCTTTTG
787467 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
787488 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
787508 CAAAA
1 CAAAA
787513 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:789914 original size:13 final size:13
Alignment explanation
Indices: 789896--789921 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
789886 TACAGCAAGT
789896 ATGTATCGATACA
1 ATGTATCGATACA
789909 ATGTATCGATACA
1 ATGTATCGATACA
789922 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Done.