Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007802.1 Hibiscus syriacus cultivar Beakdansim tig00110120_pilon, whole genome shotgun sequence
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: 449556
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 3 of 3
Found at i:356725 original size:13 final size:13
Alignment explanation
Indices: 356686--356729 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
356676 GTCATAAATC
*
356686 TATGACGCGCATT
1 TATGACGCACATT
* *
356699 TATGA-ACTCATT
1 TATGACGCACATT
356711 TATGACGCACATT
1 TATGACGCACATT
356724 TATGAC
1 TATGAC
356730 ACTCATTTAG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
12 10 0.38
13 16 0.62
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (13 bp):
TATGACGCACATT
Found at i:356736 original size:13 final size:13
Alignment explanation
Indices: 356695--356738 Score: 63
Period size: 13 Copynumber: 3.5 Consensus size: 13
356685 CTATGACGCG
356695 CATTTATGA-ACT
1 CATTTATGACACT
* *
356707 CATTTATGACGCA
1 CATTTATGACACT
356720 CATTTATGACACT
1 CATTTATGACACT
356733 CATTTA
1 CATTTA
356739 GCATCATTGA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
12 9 0.33
13 18 0.67
ACGTcount: A:0.32, C:0.20, G:0.09, T:0.39
Consensus pattern (13 bp):
CATTTATGACACT
Found at i:356814 original size:85 final size:85
Alignment explanation
Indices: 356708--356939 Score: 261
Period size: 85 Copynumber: 2.7 Consensus size: 85
356698 TTATGAACTC
* * * *
356708 ATTTATGACGCACATTTATGACACT-CATTTAGCATCATTGAAGCCCCCGTCATAAATAAAGATG
1 ATTTATGACACGCATGTATGAC-CTACATTGAGCATCATTGAAGCCCCCGTCATAAATAAAGATG
356772 ACACACATTTGTGTGTCATAA
65 ACACACATTTGTGTGTCATAA
* * * ** * * *
356793 ATTTATGACCCGCATGTATGACTTACATTGCGTGTCATTGAAGCCCCTGTCATAAATAAAGTTTA
1 ATTTATGACACGCATGTATGACCTACATTGAGCATCATTGAAGCCCCCGTCATAAATAAAGATGA
356858 CACACATTTGTGTGTCATAA
66 CACACATTTGTGTGTCATAA
* * * ** * *
356878 ATTTATGACATGCATGTATGACTTACATTGCGTGTCATTGAAGCACACGTCATTAAA-AAAGA
1 ATTTATGACACGCATGTATGACCTACATTGAGCATCATTGAAGCCCCCGTCA-TAAATAAAGA
356940 CTGTTGAGTT
Statistics
Matches: 128, Mismatches: 17, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
84 1 0.01
85 123 0.96
86 4 0.03
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (85 bp):
ATTTATGACACGCATGTATGACCTACATTGAGCATCATTGAAGCCCCCGTCATAAATAAAGATGA
CACACATTTGTGTGTCATAA
Found at i:357732 original size:28 final size:28
Alignment explanation
Indices: 357701--357758 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 28
357691 AATAGCCAGA
*
357701 GTGCATCGATGCATCAAATTCATTCGAT
1 GTGCATCGATGCATCAAATGCATTCGAT
* *
357729 GTGCATTGATGCATGAAATGCATTCGAT
1 GTGCATCGATGCATCAAATGCATTCGAT
357757 GT
1 GT
357759 TCAATTTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (28 bp):
GTGCATCGATGCATCAAATGCATTCGAT
Found at i:357751 original size:45 final size:45
Alignment explanation
Indices: 357702--357788 Score: 106
Period size: 45 Copynumber: 1.9 Consensus size: 45
357692 ATAGCCAGAG
* *
357702 TGCA-TCGATGCATCAAATTCATTCGAT-GTGCATTGATGCATGAAA
1 TGCATTCGATG-ATCAAATTAATTC-ATGGTGCATCGATGCATGAAA
* *
357747 TGCATTCGATGTTCAATTTAATTCATGGTGCATCGATGCATG
1 TGCATTCGATGATCAAATTAATTCATGGTGCATCGATGCATG
357789 GATTGGTGCA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
44 2 0.06
45 28 0.78
46 6 0.17
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (45 bp):
TGCATTCGATGATCAAATTAATTCATGGTGCATCGATGCATGAAA
Found at i:369158 original size:15 final size:15
Alignment explanation
Indices: 369128--369169 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
369118 GATGCTTTCT
*
369128 TTTTCATTCTTTGACG
1 TTTTC-TTCTTAGACG
369144 TTTTCTTCTTAGACG
1 TTTTCTTCTTAGACG
*
369159 TTGTCTTCTTA
1 TTTTCTTCTTA
369170 CCCCATGAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 19 0.79
16 5 0.21
ACGTcount: A:0.12, C:0.19, G:0.12, T:0.57
Consensus pattern (15 bp):
TTTTCTTCTTAGACG
Found at i:375378 original size:38 final size:38
Alignment explanation
Indices: 375315--375436 Score: 140
Period size: 39 Copynumber: 3.2 Consensus size: 38
375305 TGCAGTAGGT
*
375315 ACTTACCCT-ATGCACGAA-GCAGAGGAGCCTGCGTAAGG
1 ACTTACCCTGA-GCACAAAGGC-GAGGAGCCTGCGTAAGG
**
375353 ACTTACCCTGAGCACAAAGGCGAGGAATCTGCGGTAAGG
1 ACTTACCCTGAGCACAAAGGCGAGGAGCCTGC-GTAAGG
* * *
375392 ACTTACACTGAGCACAAAGTCGAGGAGCCTGTGGTAAGG
1 ACTTACCCTGAGCACAAAGGCGAGGAGCCTG-CGTAAGG
375431 ACTTAC
1 ACTTAC
375437 AAGTCATAGG
Statistics
Matches: 72, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
38 24 0.33
39 48 0.67
ACGTcount: A:0.30, C:0.24, G:0.29, T:0.17
Consensus pattern (38 bp):
ACTTACCCTGAGCACAAAGGCGAGGAGCCTGCGTAAGG
Found at i:375403 original size:39 final size:39
Alignment explanation
Indices: 375336--375437 Score: 143
Period size: 39 Copynumber: 2.6 Consensus size: 39
375326 GCACGAAGCA
* *
375336 GAGGAGCCTGC-GTAAGGACTTACCCTGAGCACAAAGGC
1 GAGGAACCTGCGGTAAGGACTTACACTGAGCACAAAGGC
* *
375374 GAGGAATCTGCGGTAAGGACTTACACTGAGCACAAAGTC
1 GAGGAACCTGCGGTAAGGACTTACACTGAGCACAAAGGC
* *
375413 GAGGAGCCTGTGGTAAGGACTTACA
1 GAGGAACCTGCGGTAAGGACTTACA
375438 AGTCATAGGC
Statistics
Matches: 56, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
38 9 0.16
39 47 0.84
ACGTcount: A:0.30, C:0.22, G:0.31, T:0.17
Consensus pattern (39 bp):
GAGGAACCTGCGGTAAGGACTTACACTGAGCACAAAGGC
Found at i:381193 original size:16 final size:16
Alignment explanation
Indices: 381172--381210 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
381162 GGTTCATACG
381172 ATAAATCCATATATCA
1 ATAAATCCATATATCA
*
381188 ATAAATACATATATCA
1 ATAAATCCATATATCA
*
381204 AAAAATC
1 ATAAATC
381211 GTATAAAACA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.28
Consensus pattern (16 bp):
ATAAATCCATATATCA
Found at i:381703 original size:39 final size:41
Alignment explanation
Indices: 381604--381709 Score: 123
Period size: 39 Copynumber: 2.7 Consensus size: 41
381594 AGACCCGAGG
* * * * *
381604 TAAGGACTTACCTTGCGCACAAAG--TAGAGGATCATGCGG
1 TAAGGACTTACCCTGAGCACAAAGCCGAGAAGATCATGCGA
*
381643 TAAGGACTTA-TCTGAGCACAAAGCCGAGAAGA-C-TGCGA
1 TAAGGACTTACCCTGAGCACAAAGCCGAGAAGATCATGCGA
381681 TAAGGACTTACCCTGAGCACAAAGCCGAG
1 TAAGGACTTACCCTGAGCACAAAGCCGAG
381710 GAGCCTGTAG
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
38 24 0.42
39 28 0.49
40 5 0.09
ACGTcount: A:0.34, C:0.23, G:0.26, T:0.17
Consensus pattern (41 bp):
TAAGGACTTACCCTGAGCACAAAGCCGAGAAGATCATGCGA
Found at i:381724 original size:39 final size:38
Alignment explanation
Indices: 381603--381730 Score: 114
Period size: 39 Copynumber: 3.3 Consensus size: 38
381593 AAGACCCGAG
* * ** * * *
381603 GTAAGGACTTACCTTGCGCACAAAGTAGAGGATCATGCG
1 GTAAGGACTTACCCTGAGCACAAAGCCGAGGAGCCTG-A
* * * *
381642 GTAAGGACTTA-TCTGAGCACAAAGCCGAGAAGACTGC
1 GTAAGGACTTACCCTGAGCACAAAGCCGAGGAGCCTGA
381679 GATAAGGACTTACCCTGAGCACAAAGCCGAGGAGCCTGTA
1 G-TAAGGACTTACCCTGAGCACAAAGCCGAGGAGCCTG-A
*
381719 GTAAGGAGTTAC
1 GTAAGGACTTAC
381731 AAGTCATAGA
Statistics
Matches: 71, Mismatches: 15, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
37 1 0.01
38 26 0.37
39 43 0.61
40 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.28, T:0.18
Consensus pattern (38 bp):
GTAAGGACTTACCCTGAGCACAAAGCCGAGGAGCCTGA
Found at i:383378 original size:53 final size:51
Alignment explanation
Indices: 383309--383505 Score: 214
Period size: 53 Copynumber: 3.8 Consensus size: 51
383299 ACAATAAGGG
* * * *
383309 TTAGGGTAAGAGAAGATAAACAAAGATAGAAGATGAAGAGCCTCGATTTGGGT
1 TTAGGGTTAGAGAAGATAAACAGAGACAAAAGATGAAGAG-CT-GATTTGGGT
* * * * *
383362 TTAGGGTTAGATAAGATGAATAGAGGCAAAAGATGAAGAAGCTAATTTGGGT
1 TTAGGGTTAGAGAAGATAAACAGAGACAAAAGATGAAG-AGCTGATTTGGGT
* * *
383414 TTAGGATTAGAGAATATGAACAGAGACAAAAGATGAAGAGGCTTGATTTGGGT
1 TTAGGGTTAGAGAAGATAAACAGAGACAAAAGATGAAGA-GC-TGATTTGGGT
* * *
383467 TTAGGGTTAGAGAATATAAATAGAGATAAAAGATGAAGA
1 TTAGGGTTAGAGAAGATAAACAGAGACAAAAGATGAAGA
383506 TACTAGGTTA
Statistics
Matches: 122, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
51 1 0.01
52 43 0.35
53 76 0.62
54 2 0.02
ACGTcount: A:0.43, C:0.05, G:0.29, T:0.23
Consensus pattern (51 bp):
TTAGGGTTAGAGAAGATAAACAGAGACAAAAGATGAAGAGCTGATTTGGGT
Found at i:383424 original size:52 final size:53
Alignment explanation
Indices: 383354--383505 Score: 216
Period size: 52 Copynumber: 2.9 Consensus size: 53
383344 AAGAGCCTCG
* * *
383354 ATTTGGGTTTAGGGTTAGATAAGATGAATAGAGGCAAAAGATGAAGAAGC-TA
1 ATTTGGGTTTAGGGTTAGAGAATATGAATAGAGACAAAAGATGAAGAAGCTTA
* * * *
383406 ATTTGGGTTTAGGATTAGAGAATATGAACAGAGACAAAAGATGAAGAGGCTTG
1 ATTTGGGTTTAGGGTTAGAGAATATGAATAGAGACAAAAGATGAAGAAGCTTA
* *
383459 ATTTGGGTTTAGGGTTAGAGAATATAAATAGAGATAAAAGATGAAGA
1 ATTTGGGTTTAGGGTTAGAGAATATGAATAGAGACAAAAGATGAAGA
383506 TACTAGGTTA
Statistics
Matches: 88, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
52 44 0.50
53 44 0.50
ACGTcount: A:0.41, C:0.03, G:0.30, T:0.26
Consensus pattern (53 bp):
ATTTGGGTTTAGGGTTAGAGAATATGAATAGAGACAAAAGATGAAGAAGCTTA
Found at i:383426 original size:105 final size:105
Alignment explanation
Indices: 383317--383505 Score: 270
Period size: 105 Copynumber: 1.8 Consensus size: 105
383307 GGTTAGGGTA
* * * *
383317 AGAGAAGATAAACAAAGATAGAAGATGAAGAGCCTCGATTTGGGTTTAGGGTTAGATAAGATGAA
1 AGAGAAGATAAACAAAGACAAAAGATGAAGAGCCTCGATTTGGGTTTAGGGTTAGAGAAGATAAA
*
383382 TAGAGGCAAAAGATGAAGAAGCTAATTTGGGTTTAGGATT
66 TAGAGACAAAAGATGAAGAAGCTAATTTGGGTTTAGGATT
* * * * * *
383422 AGAGAATATGAACAGAGACAAAAGATGAAGAGGCTTGATTTGGGTTTAGGGTTAGAGAATATAAA
1 AGAGAAGATAAACAAAGACAAAAGATGAAGAGCCTCGATTTGGGTTTAGGGTTAGAGAAGATAAA
*
383487 TAGAGATAAAAGATGAAGA
66 TAGAGACAAAAGATGAAGA
383506 TACTAGGTTA
Statistics
Matches: 72, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
105 72 1.00
ACGTcount: A:0.43, C:0.05, G:0.29, T:0.23
Consensus pattern (105 bp):
AGAGAAGATAAACAAAGACAAAAGATGAAGAGCCTCGATTTGGGTTTAGGGTTAGAGAAGATAAA
TAGAGACAAAAGATGAAGAAGCTAATTTGGGTTTAGGATT
Found at i:383530 original size:53 final size:53
Alignment explanation
Indices: 383317--383559 Score: 168
Period size: 53 Copynumber: 4.6 Consensus size: 53
383307 GGTTAGGGTA
* * * * * * * * * *
383317 AGAGAAGATAAACAAAGATAGAAGATGAAGAGCCTCGATTTGGGTTTAGGGTT
1 AGAGAATATAAACAGAGACAAAAGATGAAGAGACTAGATTAGGGTATAAGATT
* * * * * * * *
383370 AGATAAGATGAATAGAGGCAAAAGATGAAGA-AGCTA-ATTTGGGTTTAGGATT
1 AGAGAATATAAACAGAGACAAAAGATGAAGAGA-CTAGATTAGGGTATAAGATT
* * * * * * *
383422 AGAGAATATGAACAGAGACAAAAGATGAAGAGGCTTGATTTGGGTTTAGGGTT
1 AGAGAATATAAACAGAGACAAAAGATGAAGAGACTAGATTAGGGTATAAGATT
* * * *
383475 AGAGAATATAAATAGAGATAAAAGATGAAGATACTAGGTTAGGGTATAAGATT
1 AGAGAATATAAACAGAGACAAAAGATGAAGAGACTAGATTAGGGTATAAGATT
* *
383528 AGAGAATATGAACAGAAACAAAA-AGTGAAGAG
1 AGAGAATATAAACAGAGACAAAAGA-TGAAGAG
383560 GCTCAGTTAA
Statistics
Matches: 153, Mismatches: 33, Indels: 8
0.79 0.17 0.04
Matches are distributed among these distances:
52 45 0.29
53 108 0.71
ACGTcount: A:0.44, C:0.05, G:0.28, T:0.22
Consensus pattern (53 bp):
AGAGAATATAAACAGAGACAAAAGATGAAGAGACTAGATTAGGGTATAAGATT
Found at i:383579 original size:105 final size:105
Alignment explanation
Indices: 383338--383579 Score: 267
Period size: 105 Copynumber: 2.3 Consensus size: 105
383328 ACAAAGATAG
* * ** * * *
383338 AAGATGAAGAGCCTCGATTTGGGTTTAGGGTTAGATAAGATGAATAGAGGCAAAAGATGAAGAAG
1 AAGATGAAGAGGCTAGATTAAGGTTTAGGGTTAGAGAAGATAAATAGAGACAAAAGATGAAGAAG
* * * *
383403 CTAATTTGGGTTTAGGATTAGAGAATATGAACAGAGACAA
66 CTAATTAGGGTATAAGATTAGAGAATATGAACAGAAACAA
* ** * *
383443 AAGATGAAGAGGCTTGATTTGGGTTTAGGGTTAGAGAATATAAATAGAGATAAAAGATGAAGATA
1 AAGATGAAGAGGCTAGATTAAGGTTTAGGGTTAGAGAAGATAAATAGAGACAAAAGATGAAGA-A
*
383508 -CTAGGTTAGGGTATAAGATTAGAGAATATGAACAGAAACAA
65 GCTA-ATTAGGGTATAAGATTAGAGAATATGAACAGAAACAA
383549 AA-AGTGAAGAGGCTCAG-TTAAGGTTT-GGGTT
1 AAGA-TGAAGAGGCT-AGATTAAGGTTTAGGGTT
383580 TTAGTTAGAG
Statistics
Matches: 118, Mismatches: 15, Indels: 8
0.84 0.11 0.06
Matches are distributed among these distances:
105 65 0.55
106 52 0.44
107 1 0.01
ACGTcount: A:0.40, C:0.05, G:0.29, T:0.25
Consensus pattern (105 bp):
AAGATGAAGAGGCTAGATTAAGGTTTAGGGTTAGAGAAGATAAATAGAGACAAAAGATGAAGAAG
CTAATTAGGGTATAAGATTAGAGAATATGAACAGAAACAA
Found at i:383938 original size:100 final size:97
Alignment explanation
Indices: 383769--383973 Score: 270
Period size: 100 Copynumber: 2.1 Consensus size: 97
383759 GAATGGTTTG
* * * *
383769 GGATGAACAAGGGTTGAATTTTTGGGTGTTTGATAAAAAAGGAATGGTTTGGGTTTTGGTGTTTT
1 GGATGAACAACGGTTGAAATTTTGGGTGTTTGATAAAAAAGAAATGGTTTGGGTTTTGGTGTTTG
*
383834 TGAAGATCAAAT-AGGGTTTTGGGATGAACAC
66 TGAAGATCAAATAAGGATTTTGGGATGAACAC
* *
383865 GGATGAACAACGGTTTAAATTTTGGG-GTTTGATCGAAAAAACAAGAAATGGTTTGGGTTTTTGT
1 GGATGAACAACGGTTGAAATTTTGGGTGTTTGAT----AAAA-AAGAAATGGTTTGGGTTTTGGT
*
383929 GTTTGTGAAGATCAAATGAAGGATTTTGGGATGAACGC
61 GTTTGTGAAGATCAAAT-AAGGATTTTGGGATGAACAC
383967 GGATGAA
1 GGATGAA
383974 TTTCTTGTGA
Statistics
Matches: 94, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
95 7 0.07
96 23 0.24
99 4 0.04
100 36 0.38
102 24 0.26
ACGTcount: A:0.30, C:0.05, G:0.31, T:0.33
Consensus pattern (97 bp):
GGATGAACAACGGTTGAAATTTTGGGTGTTTGATAAAAAAGAAATGGTTTGGGTTTTGGTGTTTG
TGAAGATCAAATAAGGATTTTGGGATGAACAC
Found at i:384301 original size:22 final size:22
Alignment explanation
Indices: 384271--384379 Score: 62
Period size: 22 Copynumber: 4.8 Consensus size: 22
384261 TATATTTCAA
*
384271 TTATTTTAATTAATATATATGT
1 TTATATTAATTAATATATATGT
*
384293 TTATATTAATAAATTAATATATAGT
1 TTATATTAATTAA-T-ATATAT-GT
* *
384318 TTATA-TATACT-ATATAGTTTGT
1 TTATATTA-ATTAATATA-TATGT
* * *
384340 TTATACTAATGAACTATATA-CT
1 TTATATTAATTAA-TATATATGT
*
384362 TTATAGTTTATTAATATA
1 TTATA-TTAATTAATATA
384380 AACTATATAT
Statistics
Matches: 66, Mismatches: 12, Indels: 18
0.69 0.12 0.19
Matches are distributed among these distances:
22 32 0.48
23 13 0.20
24 13 0.20
25 8 0.12
ACGTcount: A:0.39, C:0.04, G:0.06, T:0.51
Consensus pattern (22 bp):
TTATATTAATTAATATATATGT
Found at i:384331 original size:18 final size:18
Alignment explanation
Indices: 384310--384347 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
384300 AATAAATTAA
384310 TATATAGTTTATATATAC
1 TATATAGTTTATATATAC
* *
384328 TATATAGTTTGTTTATAC
1 TATATAGTTTATATATAC
384346 TA
1 TA
384348 ATGAACTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.34, C:0.05, G:0.08, T:0.53
Consensus pattern (18 bp):
TATATAGTTTATATATAC
Found at i:384448 original size:16 final size:18
Alignment explanation
Indices: 384412--384445 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
384402 AAAATGAATC
*
384412 ATATAATTTATATTTATT
1 ATATAATATATATTTATT
384430 ATATAATATAT-TTTAT
1 ATATAATATATATTTAT
384446 ATAGTTCATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
ATATAATATATATTTATT
Found at i:388618 original size:21 final size:22
Alignment explanation
Indices: 388592--388633 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
388582 TTGCAAATGA
*
388592 TAAATAA-AATATTTACAATAT
1 TAAATAAGAACATTTACAATAT
388613 TAAATAAGAACATTTACAATA
1 TAAATAAGAACATTTACAATA
388634 CATGCATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.33
Consensus pattern (22 bp):
TAAATAAGAACATTTACAATAT
Found at i:389234 original size:14 final size:15
Alignment explanation
Indices: 389215--389248 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
389205 TCAGTGACGA
389215 AAACATAAGTAC-CG
1 AAACATAAGTACTCG
*
389229 AAACATAAGTGCTCG
1 AAACATAAGTACTCG
389244 AAACA
1 AAACA
389249 AAATAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.50, C:0.21, G:0.15, T:0.15
Consensus pattern (15 bp):
AAACATAAGTACTCG
Found at i:390284 original size:3 final size:3
Alignment explanation
Indices: 390272--390301 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
390262 CAAAAATTTG
390272 TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
390302 TAAATGAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:390720 original size:134 final size:133
Alignment explanation
Indices: 390497--390853 Score: 473
Period size: 134 Copynumber: 2.7 Consensus size: 133
390487 AGTTCGGGTC
* * * *
390497 ATCTAAGGGTGACACGGTTCCTACGTGATGAGGAAATCTGGTCGAGCGATGACACGCTCATACGT
1 ATCTAAGGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCGGGGGATGACACGCTCATACGT
* * * *
390562 GATGACGAGTTCTTGGCCATCTTTAAGAAGGGTGATAACTCGGTTCCTAAGCGATGAGGATGGCT
66 GATGAAGAGTTC-TGGCCATCTTTAAGAAGGGTGATAACACGGTTCCTAAGCGATGAGGACGACT
390627 GGTT
130 GGTT
* * * * *
390631 ATCTAGGGGTGACATGGCTCATACGTGATGAAGTGATCTGGTCGGGGGATGACACGACTCATACG
1 ATCTAAGGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCGGGGGATGACACG-CTCATACG
* ** * *
390696 TGATAAAGAGTTCTGATCATCTTTAGGAAGGGTGATAACACGGTTCCTACGCGATGAGGACGACT
65 TGATGAAGAGTTCTGGCCATCTTTAAGAAGGGTGATAACACGGTTCCTAAGCGATGAGGACGACT
390761 GGTT
130 GGTT
* * * * *
390765 ATC-AAGGTTTACACGGCTCCTACGTGATGAGGAGGTCTGGTCGGGGAATGACACGGCTCATACA
1 ATCTAAGGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCGGGGGATGACAC-GCTCATACG
390829 TGATGAAGAGTTCTGGCCATCTTTA
65 TGATGAAGAGTTCTGGCCATCTTTA
390854 GGGATACTGG
Statistics
Matches: 190, Mismatches: 31, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
133 71 0.37
134 100 0.53
135 19 0.10
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.26
Consensus pattern (133 bp):
ATCTAAGGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCGGGGGATGACACGCTCATACGT
GATGAAGAGTTCTGGCCATCTTTAAGAAGGGTGATAACACGGTTCCTAAGCGATGAGGACGACTG
GTT
Found at i:390921 original size:27 final size:28
Alignment explanation
Indices: 390863--390943 Score: 94
Period size: 28 Copynumber: 2.9 Consensus size: 28
390853 AGGGATACTG
**
390863 GTTTCAAAAGAAACTGACTCAAAGATAA
1 GTTTCAAAAGAAACAAACTCAAAGATAA
**
390891 GTTTCAAAAGAAAC-AACTCAAAGATTT
1 GTTTCAAAAGAAACAAACTCAAAGATAA
*
390918 GTTTCAAGAA-AAACAAATTCAAAGAT
1 GTTTCAA-AAGAAACAAACTCAAAGAT
390944 GCTTTGTTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
27 21 0.45
28 26 0.55
ACGTcount: A:0.51, C:0.14, G:0.12, T:0.23
Consensus pattern (28 bp):
GTTTCAAAAGAAACAAACTCAAAGATAA
Found at i:391179 original size:30 final size:31
Alignment explanation
Indices: 391123--391182 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
391113 AGAGACAAAA
* *
391123 TTTTGTTTTAAAAGAAAAATACTCAAATATC
1 TTTTGTTTCAAAAGAAAAAGACTCAAATATC
*
391154 TTTTGTTTCAAAAG-AAACGACTCAAATAT
1 TTTTGTTTCAAAAGAAAAAGACTCAAATAT
391183 GATGTTCAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 13 0.50
31 13 0.50
ACGTcount: A:0.43, C:0.12, G:0.08, T:0.37
Consensus pattern (31 bp):
TTTTGTTTCAAAAGAAAAAGACTCAAATATC
Found at i:391696 original size:66 final size:66
Alignment explanation
Indices: 391620--391744 Score: 171
Period size: 67 Copynumber: 1.9 Consensus size: 66
391610 GTGGGTATTT
* * * *
391620 TCAAAAGAAATTGTC-TCGAGAGGCAAACTTTTGTTTCAAAGGAAACAAACTCAAAGATTTTTTT
1 TCAAAAGAAATTGTCTTCAAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATTTTTTT
391684 C
66 C
* * *
391685 TCAAAAGGAAATTGTCTTTAAGAGATAAAATTTTGTTTCAAAAGAAACAGACTCAAAGAT
1 TCAAAA-GAAATTGTCTTCAAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGAT
391745 GGATTACATC
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
65 6 0.12
66 9 0.18
67 36 0.71
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.30
Consensus pattern (66 bp):
TCAAAAGAAATTGTCTTCAAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATTTTTTT
C
Found at i:391794 original size:121 final size:122
Alignment explanation
Indices: 391643--391865 Score: 292
Period size: 120 Copynumber: 1.8 Consensus size: 122
391633 TCTCGAGAGG
* *
391643 CAAACTTTTGTTTCAAAGGAAACAAACTCAAAGATT-TTTTTCTCAAAAGGAAATTGTCTTTAAG
1 CAAACTTTTGTTTCAAAGGAAACAAACTCAAAGATTGGTTTT-TC-AAAGGAAATTGTC-TCAAG
*
391707 AGATAAAAT-TTTGTTTCAAAAGAAACAGACTCAAAGATGGATTACATCTTAAGTGAGAC
63 AGAGAAAATATTTGTTTCAAAAGAAACAGACTCAAAGATGGATTACATCTTAAGTGAGAC
* * * *
391766 CAAA-TTTT-TTTCAAAGGAAACAATCTCAAAGGTTGGTTTTTCAATGGGAATTGTCTCAAGAGA
1 CAAACTTTTGTTTCAAAGGAAACAAACTCAAAGATTGGTTTTTCAAAGGAAATTGTCTCAAGAGA
* * * *
391829 GACAATATTTGTTTTAATAGAAATAGACTCAAAGATG
66 GAAAATATTTGTTTCAAAAGAAACAGACTCAAAGATG
391866 ATTTTGTTAA
Statistics
Matches: 87, Mismatches: 11, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
119 11 0.13
120 38 0.44
121 26 0.30
122 8 0.09
123 4 0.05
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.32
Consensus pattern (122 bp):
CAAACTTTTGTTTCAAAGGAAACAAACTCAAAGATTGGTTTTTCAAAGGAAATTGTCTCAAGAGA
GAAAATATTTGTTTCAAAAGAAACAGACTCAAAGATGGATTACATCTTAAGTGAGAC
Found at i:392660 original size:35 final size:35
Alignment explanation
Indices: 392577--392719 Score: 178
Period size: 36 Copynumber: 4.0 Consensus size: 35
392567 CATTTCAAAG
* * *
392577 GAAAAATGTCTCAAGTGAGACGAAATTTGTTTTGAA
1 GAAAATTGTCTCAAGCGAGACAAAATTTGTTTT-AA
* * *
392613 AAAAATTGTCTCAAACGAGACAAAATTTGTTTTTA
1 GAAAATTGTCTCAAGCGAGACAAAATTTGTTTTAA
* *
392648 GAAAATTTTCTCAAGCGAGACAAAATTTGTTTTGA
1 GAAAATTGTCTCAAGCGAGACAAAATTTGTTTTAA
*
392683 GAGAAATTGTCTCAAGCAAGACAAAAATTTGTTTTAA
1 GA-AAATTGTCTCAAGCGAGAC-AAAATTTGTTTTAA
392720 AATTCTCAAA
Statistics
Matches: 92, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
35 34 0.37
36 45 0.49
37 13 0.14
ACGTcount: A:0.41, C:0.10, G:0.17, T:0.32
Consensus pattern (35 bp):
GAAAATTGTCTCAAGCGAGACAAAATTTGTTTTAA
Found at i:392662 original size:71 final size:72
Alignment explanation
Indices: 392585--392717 Score: 205
Period size: 71 Copynumber: 1.9 Consensus size: 72
392575 AGGAAAAATG
* * *
392585 TCTCAAGTGAGACGAAATTTGTTTTGAAAAAAATTGTCTCAAACGAGAC-AAAATTTGTTTTTAG
1 TCTCAAGCGAGACAAAATTTGTTTTGAAAAAAATTGTCTCAAACAAGACAAAAATTTGTTTTTAG
392649 AAAATTT
66 AAAATTT
* * *
392656 TCTCAAGCGAGACAAAATTTGTTTTGAGAGAAATTGTCTCAAGCAAGACAAAAATTTGTTTT
1 TCTCAAGCGAGACAAAATTTGTTTTGAAAAAAATTGTCTCAAACAAGACAAAAATTTGTTTT
392718 AAAATTCTCA
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
71 43 0.78
72 12 0.22
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.34
Consensus pattern (72 bp):
TCTCAAGCGAGACAAAATTTGTTTTGAAAAAAATTGTCTCAAACAAGACAAAAATTTGTTTTTAG
AAAATTT
Found at i:393120 original size:16 final size:16
Alignment explanation
Indices: 393087--393121 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
393077 TATATGTATG
*
393087 TGTATGTATGTAATTA
1 TGTATGTATGTAAGTA
*
393103 TGTATGTATGTACGTA
1 TGTATGTATGTAAGTA
393119 TGT
1 TGT
393122 GTTGATGTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.26, C:0.03, G:0.23, T:0.49
Consensus pattern (16 bp):
TGTATGTATGTAAGTA
Found at i:398568 original size:21 final size:22
Alignment explanation
Indices: 398542--398583 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
398532 TTGCAAATGA
*
398542 TAAATAA-AATATTTACAATAT
1 TAAATAAGAACATTTACAATAT
398563 TAAATAAGAACATTTACAATA
1 TAAATAAGAACATTTACAATA
398584 CATGCATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.33
Consensus pattern (22 bp):
TAAATAAGAACATTTACAATAT
Found at i:400230 original size:3 final size:3
Alignment explanation
Indices: 400216--400256 Score: 73
Period size: 3 Copynumber: 13.3 Consensus size: 3
400206 CAAAAATTTG
400216 TAA TATA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
400257 TAAATGACAA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:402639 original size:31 final size:30
Alignment explanation
Indices: 402604--402683 Score: 83
Period size: 32 Copynumber: 2.6 Consensus size: 30
402594 TAACCTTACA
402604 ACTCTATTTTTTCAATGGATAAGA-TAGAATC
1 ACTCTATTTTTTCAA-GGATAA-ACTAGAATC
* *
402635 ACTCTAGTTTTTTTTAAGGCTAAACTAGAATC
1 ACTCTA--TTTTTTCAAGGATAAACTAGAATC
402667 ACTCTCA-TTTTTCAAGG
1 ACTCT-ATTTTTTCAAGG
402684 TTTGATATGG
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
30 9 0.21
31 7 0.17
32 17 0.40
33 9 0.21
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.40
Consensus pattern (30 bp):
ACTCTATTTTTTCAAGGATAAACTAGAATC
Found at i:403036 original size:20 final size:20
Alignment explanation
Indices: 403013--403076 Score: 76
Period size: 20 Copynumber: 3.2 Consensus size: 20
403003 GAATATTTCT
*
403013 AAACTCTTATGATAGTTTTG
1 AAACTCTTATGAAAGTTTTG
* *
403033 AAACTCTAATGACAGTTTTG
1 AAACTCTTATGAAAGTTTTG
* *
403053 AAACT-TTGTGAAAGTATTG
1 AAACTCTTATGAAAGTTTTG
403072 AAACT
1 AAACT
403077 TTTAAACACA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
19 15 0.39
20 23 0.61
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.38
Consensus pattern (20 bp):
AAACTCTTATGAAAGTTTTG
Found at i:403582 original size:123 final size:124
Alignment explanation
Indices: 403342--403587 Score: 449
Period size: 124 Copynumber: 2.0 Consensus size: 124
403332 AATTTCAATA
* *
403342 TAATAGAAGTATTTTTTTAATTTGTGTTAAAATTTAATTAGGTATTAATAATTTAACGAGTCTAG
1 TAATAGAAGTATTTTTTTAATTTGGGTTAAAATTTAATTAAGTATTAATAATTTAACGAGTCTAG
403407 TGTGGTTAAAAAATAATTGAGTCTTAATTCTTAATGGTTTTGAGCTTAAAATATGTATT
66 TGTGGTTAAAAAATAATTGAGTCTTAATTCTTAATGGTTTTGAGCTTAAAATATGTATT
*
403466 TAATAGAAGTATTTTTTTAATTTGGGTTAAAATTTAATTAAGTATTAATAATTTAATGAGTCTAG
1 TAATAGAAGTATTTTTTTAATTTGGGTTAAAATTTAATTAAGTATTAATAATTTAACGAGTCTAG
*
403531 TGTGGTT-AAAAATAATTGAGTCTTTATTCTTAATGGTTTTGAGCTTAAAATATGTAT
66 TGTGGTTAAAAAATAATTGAGTCTTAATTCTTAATGGTTTTGAGCTTAAAATATGTAT
403588 ATATTATATA
Statistics
Matches: 118, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
123 49 0.42
124 69 0.58
ACGTcount: A:0.35, C:0.04, G:0.15, T:0.46
Consensus pattern (124 bp):
TAATAGAAGTATTTTTTTAATTTGGGTTAAAATTTAATTAAGTATTAATAATTTAACGAGTCTAG
TGTGGTTAAAAAATAATTGAGTCTTAATTCTTAATGGTTTTGAGCTTAAAATATGTATT
Found at i:403960 original size:20 final size:19
Alignment explanation
Indices: 403935--404001 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 19
403925 TTTAAAAGCC
403935 TTAAACACATTATAATCACT
1 TTAAACACATTATAA-CACT
** * * *
403955 TTAAACATGTTTTAAAAGCC
1 TTAAACACATTATAACA-CT
403975 TTAAACACATTATAAACACT
1 TTAAACACATTAT-AACACT
403995 TTAAACA
1 TTAAACA
404002 TGTTTTAATT
Statistics
Matches: 35, Mismatches: 10, Indels: 4
0.71 0.20 0.08
Matches are distributed among these distances:
19 1 0.03
20 31 0.89
21 3 0.09
ACGTcount: A:0.46, C:0.18, G:0.03, T:0.33
Consensus pattern (19 bp):
TTAAACACATTATAACACT
Found at i:403979 original size:40 final size:40
Alignment explanation
Indices: 403924--404009 Score: 163
Period size: 40 Copynumber: 2.1 Consensus size: 40
403914 GTTTTTCATA
*
403924 TTTTAAAAGCCTTAAACACATTATAATCACTTTAAACATG
1 TTTTAAAAGCCTTAAACACATTATAAACACTTTAAACATG
403964 TTTTAAAAGCCTTAAACACATTATAAACACTTTAAACATG
1 TTTTAAAAGCCTTAAACACATTATAAACACTTTAAACATG
404004 TTTTAA
1 TTTTAA
404010 TTAACTCAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.43, C:0.16, G:0.05, T:0.36
Consensus pattern (40 bp):
TTTTAAAAGCCTTAAACACATTATAAACACTTTAAACATG
Found at i:404025 original size:40 final size:39
Alignment explanation
Indices: 403924--404025 Score: 116
Period size: 40 Copynumber: 2.5 Consensus size: 39
403914 GTTTTTCATA
* * *
403924 TTTTAAAAGCCTTAAACACATTATAATCACTTTAAACATG
1 TTTTAAAA-CCTCAAAAACATTATAAACACTTTAAACATG
* *
403964 TTTTAAAAGCCTTAAACACATTATAAACACTTTAAACATG
1 TTTTAAAA-CCTCAAAAACATTATAAACACTTTAAACATG
404004 TTTTAATTAA-CTCAAAAACATT
1 TTTTAA--AACCTCAAAAACATT
404026 TCACATATAT
Statistics
Matches: 57, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
40 55 0.96
42 2 0.04
ACGTcount: A:0.44, C:0.17, G:0.04, T:0.35
Consensus pattern (39 bp):
TTTTAAAACCTCAAAAACATTATAAACACTTTAAACATG
Found at i:404999 original size:24 final size:25
Alignment explanation
Indices: 404972--405018 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
404962 AAACCAATGT
*
404972 AAAAAAATAAAAT-AAAAATAAATA
1 AAAAAAACAAAATAAAAAATAAATA
**
404996 AAAAATGCAAAATAAAAAATAAA
1 AAAAAAACAAAATAAAAAATAAA
405019 AACGGTCAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 10 0.53
25 9 0.47
ACGTcount: A:0.81, C:0.02, G:0.02, T:0.15
Consensus pattern (25 bp):
AAAAAAACAAAATAAAAAATAAATA
Found at i:405001 original size:7 final size:7
Alignment explanation
Indices: 404973--405020 Score: 53
Period size: 7 Copynumber: 6.7 Consensus size: 7
404963 AACCAATGTA
404973 AAAAAAT
1 AAAAAAT
404980 AAAATAA-
1 AAAA-AAT
404987 AAATAAAT
1 AAA-AAAT
404995 AAAAAAT
1 AAAAAAT
**
405002 GCAAAAT
1 AAAAAAT
405009 AAAAAAT
1 AAAAAAT
405016 AAAAA
1 AAAAA
405021 CGGTCAATGT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
7 28 0.82
8 6 0.18
ACGTcount: A:0.81, C:0.02, G:0.02, T:0.15
Consensus pattern (7 bp):
AAAAAAT
Found at i:409089 original size:28 final size:28
Alignment explanation
Indices: 409036--409089 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
409026 ACTAAATTGT
*
409036 AAAATAATAAAACTATAGTCTCTAATTC
1 AAAATAATAAAACTATAGTATCTAATTC
* *
409064 AAAATATTATAACTATAAGTAT-TAAT
1 AAAATAATAAAACTAT-AGTATCTAAT
409090 AATAATTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
28 18 0.82
29 4 0.18
ACGTcount: A:0.52, C:0.09, G:0.04, T:0.35
Consensus pattern (28 bp):
AAAATAATAAAACTATAGTATCTAATTC
Found at i:410344 original size:3 final size:3
Alignment explanation
Indices: 410331--410404 Score: 57
Period size: 3 Copynumber: 24.3 Consensus size: 3
410321 ATTTGTAAAT
*
410331 ATA AT- ATA ATA ATA TATT ATA TATA ATA A-A TATGA A-A GATA ATA
1 ATA ATA ATA ATA ATA -ATA ATA -ATA ATA ATA -AT-A ATA -ATA ATA
*
410375 ATA ATA ATA ATA ATA AT- ATG ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
410405 CATATATAAC
Statistics
Matches: 59, Mismatches: 3, Indels: 18
0.74 0.04 0.22
Matches are distributed among these distances:
2 6 0.10
3 45 0.76
4 7 0.12
5 1 0.02
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:426462 original size:16 final size:16
Alignment explanation
Indices: 426441--426479 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
426431 AATATTCAAG
426441 AAGAAAACAAAATGAA
1 AAGAAAACAAAATGAA
* * *
426457 AAGAAAATAAATTGCA
1 AAGAAAACAAAATGAA
426473 AAGAAAA
1 AAGAAAA
426480 AGAAGTTGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.72, C:0.05, G:0.13, T:0.10
Consensus pattern (16 bp):
AAGAAAACAAAATGAA
Found at i:434661 original size:32 final size:32
Alignment explanation
Indices: 434625--434686 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
434615 CTTTTAGAGA
*
434625 GTTATAAATTATCTAAATGTGACACTGACTCT
1 GTTATAAATTATCTAAATGTCACACTGACTCT
** * *
434657 GTTATGCATTATTTGAATGTCACACTGACT
1 GTTATAAATTATCTAAATGTCACACTGACT
434687 AGTATCTGGT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.39
Consensus pattern (32 bp):
GTTATAAATTATCTAAATGTCACACTGACTCT
Found at i:441629 original size:13 final size:13
Alignment explanation
Indices: 441578--441623 Score: 74
Period size: 13 Copynumber: 3.5 Consensus size: 13
441568 GTCATAAATC
441578 TATGACGCACATT
1 TATGACGCACATT
**
441591 TATGAAACACATT
1 TATGACGCACATT
441604 TATGACGCACATT
1 TATGACGCACATT
441617 TATGACG
1 TATGACG
441624 TTCATTGAGC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (13 bp):
TATGACGCACATT
Found at i:448603 original size:17 final size:17
Alignment explanation
Indices: 448581--448623 Score: 70
Period size: 17 Copynumber: 2.5 Consensus size: 17
448571 TAAAGCCCTG
448581 ATTACAAGCC-GAAGCCC
1 ATTACAA-CCTGAAGCCC
448598 ATTACAACCTGAAGCCC
1 ATTACAACCTGAAGCCC
448615 ATTACAACC
1 ATTACAACC
448624 AACTCCCAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 2 0.08
17 23 0.92
ACGTcount: A:0.37, C:0.35, G:0.12, T:0.16
Consensus pattern (17 bp):
ATTACAACCTGAAGCCC
Done.