Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014981.1 Kokia drynarioides strain JFW-HI SEQ_130025, 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: 189539
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Warning! 126 characters in sequence are not A, C, G, or T
Found at i:16028 original size:2 final size:2
Alignment explanation
Indices: 16021--16045 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
16011 AATAATAATA
16021 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
16046 ATTTATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:21279 original size:22 final size:22
Alignment explanation
Indices: 21252--21295 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
21242 ATATTACTAT
21252 ATTAATATAGAATATACTAATA
1 ATTAATATAGAATATACTAATA
*
21274 ATTAATATAGAATCTACTAATA
1 ATTAATATAGAATATACTAATA
21296 GAATATAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.52, C:0.07, G:0.05, T:0.36
Consensus pattern (22 bp):
ATTAATATAGAATATACTAATA
Found at i:34448 original size:48 final size:49
Alignment explanation
Indices: 34396--34494 Score: 182
Period size: 48 Copynumber: 2.0 Consensus size: 49
34386 TTAATAACAA
*
34396 TACGATTCGAATTTAAATCACATCTG-AAAAATATTGAGTATTTTTAAT
1 TACGATTCGAATTTAAATCACATCTGAAAAAATATCGAGTATTTTTAAT
34444 TACGATTCGAATTTAAATCACATCTGAAAAAATATCGAGTATTTTTAAT
1 TACGATTCGAATTTAAATCACATCTGAAAAAATATCGAGTATTTTTAAT
34493 TA
1 TA
34495 TCAAATCAAC
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
48 26 0.53
49 23 0.47
ACGTcount: A:0.40, C:0.11, G:0.10, T:0.38
Consensus pattern (49 bp):
TACGATTCGAATTTAAATCACATCTGAAAAAATATCGAGTATTTTTAAT
Found at i:35945 original size:31 final size:31
Alignment explanation
Indices: 35910--35977 Score: 136
Period size: 31 Copynumber: 2.2 Consensus size: 31
35900 TGAAACAAGG
35910 AAAACTGAACAATAAAGAAGAAACCTATAGA
1 AAAACTGAACAATAAAGAAGAAACCTATAGA
35941 AAAACTGAACAATAAAGAAGAAACCTATAGA
1 AAAACTGAACAATAAAGAAGAAACCTATAGA
35972 AAAACT
1 AAAACT
35978 TTTTCCTATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.62, C:0.13, G:0.12, T:0.13
Consensus pattern (31 bp):
AAAACTGAACAATAAAGAAGAAACCTATAGA
Found at i:39035 original size:2 final size:2
Alignment explanation
Indices: 39030--39061 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
39020 AAAAAAAAAA
39030 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39062 TTGATCCTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:47892 original size:470 final size:470
Alignment explanation
Indices: 46964--48671 Score: 1682
Period size: 516 Copynumber: 3.5 Consensus size: 470
46954 ATCTACAAAT
* * *
46964 ATAAACAAGGGAACAA-AAAGTAACGTTTCTACTTAAGTTTAACATTCAAAAGCGTTAGAAAATG
1 ATAAACAAGGGAACAAGAAA-TAACATTTCTACTTAAGTATAACATTCAAAAGCTTTAGAAAATG
* * * *
47028 AGATAGTTGGCCAATGCTAAATTGCAACAGTACTTTCAAC-AAA-TCCACTTTCAGAATCTTTTG
65 AGATGGTTGGCCAATGCTAGATTGCATCAGAACTTTCAACAAAATTCCACTTTCAGAATCTTTTG
* ** * *
47091 ACATTAAATACAGTGGTTGATTGTTAATGCAATGATTTGCAATAAACCAACACAATCTAATTATT
130 ACATTAAATACAGTGGTTTATTGTTAATGCAATGATTCACAAAAAACCAACAGAATCTAATTATT
* *
47156 ATACATCATAACAAACTAACCAAATTTGCCAAAAGAACTTATCAACTACATGTGGCAAGTTACAC
195 ATACATCATAACAAACTAACCAAATTTGCCAAAAGAACTTATCAACTACATGTGGCAAGTGACAA
* *
47221 AAAAAGGATTCCATTTTTGTTAATAGCTACAAAATCTAGAATCGAATTGTGCCAATGGAATATAA
260 AAAAAGGATTCC--------T-ATAGCTACAAAATCTAGAATCGAATTGTGCAAATGGAAGATAA
* * * ** *
47286 AAAGTCATCGAAAATTGTAAAACCCAAAAATCTTCATTCACTTGGGTTTCACAAGTAGCCAAAGG
316 AAAGTCAACG-AAATCGAAAAACCCAAAAATCTTCATTCACTCAGGTTTCACAAGAAGCCAAAGG
*
47351 GCACTTCTTACGACTTCTCGTGACATTGACTGGAGAAAATTCCTTAAACAATAACCATATAAGGA
380 GCACTTCTTACGACTTCTCGTGACATTAACTGGAGAAAATTCCTTAAACAATAACCATATAAGGA
*
47416 ACATGTTACTTGTAG-TCAACACTCTA
445 ACATGTTACTTGTAGCTC-ACACCCTA
*
47442 ATAAACAAGGGAACAAGAAATAACATTTCTACTTAAGTATAACATTCAAAAGCTTTAG-AATTGA
1 ATAAACAAGGGAACAAGAAATAACATTTCTACTTAAGTATAACATTCAAAAGCTTTAGAAAATGA
*
47506 GATGGTTGGCCAATGCTAGATTGCATCCA-AACTTTCAACAAAATTCCACTTTCAAAATCTTTTG
66 GATGGTTGGCCAATGCTAGATTGCAT-CAGAACTTTCAACAAAATTCCACTTTCAGAATCTTTTG
* * * *
47570 ACATTAAATACAGTAGTTTATTGTTAATGCAATGATTCACGACAAACCAACAGAATCTATTTATT
130 ACATTAAATACAGTGGTTTATTGTTAATGCAATGATTCACAAAAAACCAACAGAATCTAATTATT
*
47635 ATACATCATAACAAACTAACCAACTTTGCCAAAAGAACTTATCAACTACATGTGGCAAGTGACAA
195 ATACATCATAACAAACTAACCAAATTTGCCAAAAGAACTTATCAACTACATGTGGCAAGTGACAA
*
47700 AGAAAAGGATTCC-ATAGCTACAAAATCTAGAATCTAATTGTGCAAATGGAAAGATAAAAAAGTC
260 A-AAAAGGATTCCTATAGCTACAAAATCTAGAATCGAATTGTGCAAATGG-AAGAT-AAAAAGTC
* * * *
47764 AACG-AATCGAAAAACCCAGAAATCTTCGTTCACTCAGGTTTCACGAGAAGCCAAAGGGCAGTTC
322 AACGAAATCGAAAAACCCAAAAATCTTCATTCACTCAGGTTTCACAAGAAGCCAAAGGGCACTTC
* * * * *
47828 TTATGATTTTTCGTGACATTAACTGGAGAAAATTCCTTAAATAATAACCATATAAGGCACATGTT
387 TTACGACTTCTCGTGACATTAACTGGAGAAAATTCCTTAAACAATAACCATATAAGGAACATGTT
47893 ACTTGTAGCTCACACCCTA
452 ACTTGTAGCTCACACCCTA
* *
47912 ATAAACAAGGGAACAAGAAATAACATTTCTACTAAAGTATAACATTCAAAAGTTTTAGAAAATGA
1 ATAAACAAGGGAACAAGAAATAACATTTCTACTTAAGTATAACATTCAAAAGCTTTAGAAAATGA
* * * * *
47977 GATGGCTGCCCAATGCTAGACTGCATCAGAACTTTCAAAAAAATTCCACTTTCAGAATCATTTGA
66 GATGGTTGGCCAATGCTAGATTGCATCAGAACTTTCAACAAAATTCCACTTTCAGAATCTTTTGA
* * * * *
48042 CATTAGATACAATGGTTTATTGTTAATGCAATGAGTCTCAAAAAACTAACAGAATCTAATTATTA
131 CATTAAATACAGTGGTTTATTGTTAATGCAATGATTCACAAAAAACCAACAGAATCTAATTATTA
* * * * * *
48107 TATATCATAACAAACCAACAAAATTTTCCAAAAGAAGTTATCAACTACAGGTGGCAAGTTTGGAA
196 TACATCATAACAAACTAACCAAATTTGCCAAAAGAACTTATCAACTACATGTGGCAAG--T-G-A
* ** * * * * * * * * * **
48172 CTCAGAATCAGGCATGAGCTAACTAAACTGGTACAACGAA-ATGGATTCCATTTTTGTTAAT---
257 --CAAAAAAAGG-AT----T-CCTATA--GCTACAA--AATCTAGAATCGAATTGTGCAAATGGA
* * * * *** * * *
48233 AGCTACAAAA-TCTAGAATCTAATTGTGCCAATGGAAAGATAAAAAGTCATCGAATCGTAAAACC
310 AGATA-AAAAGTC---AA-CGAA--AT-CGAA---AAACCCAAAAA-TCTTC--AT--T--CACT
* * *
48297 CAGAAATCTTCATTCACTTAGGTTTAACAGTAGCCAAAGGGCACTTCTTACGACTTTTCGTGATA
357 CAG--GT-TTCA--CA---A-G------A--AGCCAAAGGGCACTTCTTACGACTTCTCGTGACA
* * * * * * * * *
48362 CTGACTGGAGAAAATTCCTTAAAGAGTAATCA-AGTAAGGTACATGTTACTAGTA-ATCAACCCC
405 TTAACTGGAGAAAATTCCTTAAACAATAACCATA-TAAGGAACATGTTACTTGTAGCTC-ACACC
48425 CTA
468 CTA
* *
48428 ATAAACAAGAGAACAAGAAATAGCATTTCTACTTAAGTATAACATTCAAAAGCTTTAGAAAATGA
1 ATAAACAAGGGAACAAGAAATAACATTTCTACTTAAGTATAACATTCAAAAGCTTTAGAAAATGA
* *** ** *
48493 GATGGTTGCCCAATGCTAGATTGCATCAGAACTTTCAATGTAGGTCCACTTCCAGAATCTTTTGA
66 GATGGTTGGCCAATGCTAGATTGCATCAGAACTTTCAACAAAATTCCACTTTCAGAATCTTTTGA
* * * * **
48558 CATTAAATACAGCGGTTGATTGTTAATGCAATGATTCACGATAAACTGACAGAATCTAATTATTA
131 CATTAAATACAGTGGTTTATTGTTAATGCAATGATTCACAAAAAACCAACAGAATCTAATTATTA
* *
48623 TACATCCTAACGAACTAACCAAATTTGCCAAAAGAACTTATCAACTACA
196 TACATCATAACAAACTAACCAAATTTGCCAAAAGAACTTATCAACTACA
48672 CGTGACAGGT
Statistics
Matches: 1030, Mismatches: 135, Indels: 92
0.82 0.11 0.07
Matches are distributed among these distances:
470 217 0.21
471 174 0.17
472 11 0.01
473 1 0.00
474 1 0.00
475 1 0.00
476 4 0.00
477 42 0.04
478 56 0.05
479 142 0.14
480 11 0.01
481 4 0.00
482 8 0.01
483 2 0.00
484 2 0.00
485 7 0.01
486 14 0.01
487 2 0.00
488 1 0.00
489 3 0.00
492 7 0.01
493 4 0.00
495 1 0.00
497 1 0.00
499 5 0.00
501 1 0.00
502 4 0.00
504 1 0.00
507 1 0.00
508 1 0.00
514 1 0.00
515 3 0.00
516 297 0.29
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28
Consensus pattern (470 bp):
ATAAACAAGGGAACAAGAAATAACATTTCTACTTAAGTATAACATTCAAAAGCTTTAGAAAATGA
GATGGTTGGCCAATGCTAGATTGCATCAGAACTTTCAACAAAATTCCACTTTCAGAATCTTTTGA
CATTAAATACAGTGGTTTATTGTTAATGCAATGATTCACAAAAAACCAACAGAATCTAATTATTA
TACATCATAACAAACTAACCAAATTTGCCAAAAGAACTTATCAACTACATGTGGCAAGTGACAAA
AAAAGGATTCCTATAGCTACAAAATCTAGAATCGAATTGTGCAAATGGAAGATAAAAAGTCAACG
AAATCGAAAAACCCAAAAATCTTCATTCACTCAGGTTTCACAAGAAGCCAAAGGGCACTTCTTAC
GACTTCTCGTGACATTAACTGGAGAAAATTCCTTAAACAATAACCATATAAGGAACATGTTACTT
GTAGCTCACACCCTA
Found at i:48766 original size:516 final size:517
Alignment explanation
Indices: 47713--48793 Score: 1549
Period size: 516 Copynumber: 2.1 Consensus size: 517
47703 AAAGGATTCC
*
47713 ATAGCTACAAAATCTAGAATCTAATTGTGCAAATGGAAAGATAAAAAAGTCAACGAATCGAAAAA
1 ATAGCTACAAAATCTAGAATCTAATTGTGCCAATGGAAAGAT-AAAAAGTCAACGAATCGAAAAA
* * * * *
47778 CCCAGAAATCTTCGTTCACTCAGGTTTCACGAGAAGCCAAAGGGCAGTTCTTATGATTTTTCGTG
65 CCCAGAAATCTTCATTCACTCAGGTTTAACGAGAAGCCAAAGGGCACTTCTTACGACTTTTCGTG
* * * *
47843 ACATTAACTGGAGAAAATTCCTTAAATAATAACCATATAAGGCACATGTTACTTGTAGCTCACAC
130 ACACTAACTGGAGAAAATTCCTTAAAGAATAACCATATAAGGCACATGTTACTAGTAGATCACAC
* *
47908 CCTAATAAACAAGGGAACAAGAAATAACATTTCTACTAAAGTATAACATTCAAAAGTTTTAGAAA
195 CCTAATAAACAAGAGAACAAGAAATAACATTTCTACTAAAGTATAACATTCAAAAGCTTTAGAAA
* *
47973 ATGAGATGGCTGCCCAATGCTAGACTGCATCAGAACTTTCAAAAAAATTCCACTTTCAGAATCAT
260 ATGAGATGGCTGCCCAATGCTAGACTGCATCAGAACTTTCAAAAAAAGTCCACTTCCAGAATCAT
* * * *
48038 TTGACATTAGATACAATGGTTTATTGTTAATGCAATGAGTCTCAAAAAACTAACAGAATCTAATT
325 TTGACATTAAATACAACGGTTGATTGTTAATGCAATGAGTCACAAAAAACTAACAGAATCTAATT
* * * * *
48103 ATTATATATCATAACAAACCAACAAAATTTTCCAAAAGAAGTTATCAACTACAGGTGGCAAGTTT
390 ATTATACATCATAACAAACCAACAAAATTTGCCAAAAGAACTTATCAACTACACGTGACAAGTTT
* * * *
48168 GGAACTCAGAATCAGGCATGAGCTAACTAAACTGGTACAACGAAATGGATTCCATTTTTGTTA
455 GCAACTCAGAATCAGGCAAGAGCTAACTAAACTGGTACAAAGAAACGGATTCCATTTTTGTTA
* *
48231 ATAGCTACAAAATCTAGAATCTAATTGTGCCAATGGAAAGATAAAAAGTCATCGAATCGTAAAAC
1 ATAGCTACAAAATCTAGAATCTAATTGTGCCAATGGAAAGATAAAAAGTCAACGAATCGAAAAAC
* *
48296 CCAGAAATCTTCATTCACTTAGGTTTAAC-AGTAGCCAAAGGGCACTTCTTACGACTTTTCGTGA
66 CCAGAAATCTTCATTCACTCAGGTTTAACGAGAAGCCAAAGGGCACTTCTTACGACTTTTCGTGA
* * * * * *
48360 TACTGACTGGAGAAAATTCCTTAAAGAGTAATCA-AGTAAGGTACATGTTACTAGTA-ATCAACC
131 CACTAACTGGAGAAAATTCCTTAAAGAATAACCATA-TAAGGCACATGTTACTAGTAGATC-ACA
* *
48423 CCCTAATAAACAAGAGAACAAGAAATAGCATTTCTACTTAAGTATAACATTCAAAAGCTTTAGAA
194 CCCTAATAAACAAGAGAACAAGAAATAACATTTCTACTAAAGTATAACATTCAAAAGCTTTAGAA
* * *** * *
48488 AATGAGATGGTTGCCCAATGCTAGATTGCATCAGAACTTTCAATGTAGGTCCACTTCCAGAATCT
259 AATGAGATGGCTGCCCAATGCTAGACTGCATCAGAACTTTCAAAAAAAGTCCACTTCCAGAATCA
* * * * *
48553 TTTGACATTAAATACAGCGGTTGATTGTTAATGCAATGATTCACGATAAACTGACAGAATCTAAT
324 TTTGACATTAAATACAACGGTTGATTGTTAATGCAATGAGTCACAAAAAACTAACAGAATCTAAT
* * * * *
48618 TATTATACATCCTAACGAACTAACCAAATTTGCCAAAAGAACTTATCAACTACACGTGACAGGTT
389 TATTATACATCATAACAAACCAACAAAATTTGCCAAAAGAACTTATCAACTACACGTGACAAGTT
* * * *
48683 TGCCAAGTTAGAATCTGGCAAGAGCTAACTAAACTGGTACAAAGAAACGGTTTCCATTTTTGTTA
454 TG-CAACTCAGAATCAGGCAAGAGCTAACTAAACTGGTACAAAGAAACGGATTCCATTTTTGTTA
*
48748 ATAGCTACAAAA-CTAGAATCTAATTGTGTCAATGGAAAGATAAAAA
1 ATAGCTACAAAATCTAGAATCTAATTGTGCCAATGGAAAGATAAAAA
48794 AAGAAACAGA
Statistics
Matches: 499, Mismatches: 61, Indels: 8
0.88 0.11 0.01
Matches are distributed among these distances:
515 3 0.01
516 342 0.69
517 113 0.23
518 41 0.08
ACGTcount: A:0.40, C:0.18, G:0.16, T:0.27
Consensus pattern (517 bp):
ATAGCTACAAAATCTAGAATCTAATTGTGCCAATGGAAAGATAAAAAGTCAACGAATCGAAAAAC
CCAGAAATCTTCATTCACTCAGGTTTAACGAGAAGCCAAAGGGCACTTCTTACGACTTTTCGTGA
CACTAACTGGAGAAAATTCCTTAAAGAATAACCATATAAGGCACATGTTACTAGTAGATCACACC
CTAATAAACAAGAGAACAAGAAATAACATTTCTACTAAAGTATAACATTCAAAAGCTTTAGAAAA
TGAGATGGCTGCCCAATGCTAGACTGCATCAGAACTTTCAAAAAAAGTCCACTTCCAGAATCATT
TGACATTAAATACAACGGTTGATTGTTAATGCAATGAGTCACAAAAAACTAACAGAATCTAATTA
TTATACATCATAACAAACCAACAAAATTTGCCAAAAGAACTTATCAACTACACGTGACAAGTTTG
CAACTCAGAATCAGGCAAGAGCTAACTAAACTGGTACAAAGAAACGGATTCCATTTTTGTTA
Found at i:48834 original size:70 final size:70
Alignment explanation
Indices: 48723--48859 Score: 213
Period size: 70 Copynumber: 2.0 Consensus size: 70
48713 AAACTGGTAC
* * * * *
48723 AAAGAAACGGTTTCCATTTTTGTTAATAGCTACAAAACTAGAATCTAATTGTGTCAATGGAAAGA
1 AAAGAAACAGATTCCATCTTTGTTAATAGCTACAAAACTAGAATCGAATTGTGCCAATGGAAAGA
48788 TAAAA
66 TAAAA
48793 AAAGAAACAGATTCCA-CTTTGTTAATAGCTACAAAATCTAGAATCGAATTGTGCCAATGGAAAG
1 AAAGAAACAGATTCCATCTTTGTTAATAGCTACAAAA-CTAGAATCGAATTGTGCCAATGGAAAG
48857 ATA
65 ATA
48860 CAAAGTCATC
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
69 19 0.31
70 42 0.69
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.28
Consensus pattern (70 bp):
AAAGAAACAGATTCCATCTTTGTTAATAGCTACAAAACTAGAATCGAATTGTGCCAATGGAAAGA
TAAAA
Found at i:49355 original size:127 final size:132
Alignment explanation
Indices: 49100--49355 Score: 344
Period size: 127 Copynumber: 2.0 Consensus size: 132
49090 GAAAGAAAGC
* **
49100 CAATGAATGTAGTGATAAAGAAATCGATGTGCCAAGCTCTCGGGTTCATAGTTTCCGTTTAGGGG
1 CAATGAATGTAGTGATAAAGAAATCGATGTGCCAAGCCCTCGGGTTCATAGTTTCCGTCAAGGGG
*
49165 ATCAATTCCAGATTTAGTCATACCGAATGTAACTACCGAAATGCCAAGGGTTTTAGTAAAAAACC
66 ATCAATT-C--ATTTAGTCATACCGAATGTAACAACCGAAATGCCAAGGGTTTTAGTAAAAAACC
49230 CTTGG
128 CTTGG
*
49235 CAATGAATGTAG-GA-AATA-AAA-CGATGTGCCAAGCCCTTGGGTTCATAGTTTCCGTCAAGGG
1 CAATGAATGTAGTGATAA-AGAAATCGATGTGCCAAGCCCTCGGGTTCATAGTTTCCGTCAAGGG
* ** * *
49296 GCTCAA-T-ATTTAGTCATATTGAATGTAACAACCGAATTGCCAAGGGTTTTAGTCAAAAAC
65 GATCAATTCATTTAGTCATACCGAATGTAACAACCGAAATGCCAAGGGTTTTAGTAAAAAAC
49356 ACTATGAAAA
Statistics
Matches: 110, Mismatches: 10, Indels: 10
0.85 0.08 0.08
Matches are distributed among these distances:
127 48 0.44
131 1 0.01
132 41 0.37
133 5 0.05
134 3 0.03
135 12 0.11
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.28
Consensus pattern (132 bp):
CAATGAATGTAGTGATAAAGAAATCGATGTGCCAAGCCCTCGGGTTCATAGTTTCCGTCAAGGGG
ATCAATTCATTTAGTCATACCGAATGTAACAACCGAAATGCCAAGGGTTTTAGTAAAAAACCCTT
GG
Found at i:50691 original size:2 final size:2
Alignment explanation
Indices: 50684--50718 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
50674 TCAAATCATC
50684 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
50719 AAAGATAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:54489 original size:19 final size:19
Alignment explanation
Indices: 54467--54511 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
54457 TTATATTAGG
54467 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
54486 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
54505 ATTTAAT
1 ATTTAAT
54512 TTATATTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:55327 original size:15 final size:16
Alignment explanation
Indices: 55309--55338 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
55299 CTTCCCCATT
55309 TTCTA-TTTCTTTTAA
1 TTCTATTTTCTTTTAA
55324 TTCTATTTTCTTTTA
1 TTCTATTTTCTTTTA
55339 TTTTTAATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.17, C:0.13, G:0.00, T:0.70
Consensus pattern (16 bp):
TTCTATTTTCTTTTAA
Found at i:55333 original size:22 final size:22
Alignment explanation
Indices: 55306--55364 Score: 68
Period size: 21 Copynumber: 2.7 Consensus size: 22
55296 CGACTTCCCC
55306 ATTTTCTATTT-CTTTTAATTCT
1 ATTTTCT-TTTACTTTTAATTCT
*
55328 ATTTTCTTTTATTTTTAATTCT
1 ATTTTCTTTTACTTTTAATTCT
* *
55350 -GTTTCTTTTATTTTT
1 ATTTTCTTTTACTTTT
55365 CCTTAGATCA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
21 17 0.50
22 17 0.50
ACGTcount: A:0.15, C:0.10, G:0.02, T:0.73
Consensus pattern (22 bp):
ATTTTCTTTTACTTTTAATTCT
Found at i:55354 original size:21 final size:22
Alignment explanation
Indices: 55318--55364 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
55308 TTTCTATTTC
*
55318 TTTTAATTCTATTTTCTTTTAT
1 TTTTAATTCTAGTTTCTTTTAT
55340 TTTTAATTCT-GTTTCTTTTAT
1 TTTTAATTCTAGTTTCTTTTAT
55361 TTTT
1 TTTT
55365 CCTTAGATCA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.15, C:0.09, G:0.02, T:0.74
Consensus pattern (22 bp):
TTTTAATTCTAGTTTCTTTTAT
Found at i:62091 original size:24 final size:24
Alignment explanation
Indices: 62063--62137 Score: 123
Period size: 24 Copynumber: 3.1 Consensus size: 24
62053 AGAAATAATC
62063 TTTCAGTTAAACTCAGTTTAATTG
1 TTTCAGTTAAACTCAGTTTAATTG
62087 TTTCAGTTAAACTCAGTTTAATTG
1 TTTCAGTTAAACTCAGTTTAATTG
* * *
62111 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAGTTAAACTCAGTTTAATTG
62135 TTT
1 TTT
62138 GACTCAAACT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.27, C:0.12, G:0.11, T:0.51
Consensus pattern (24 bp):
TTTCAGTTAAACTCAGTTTAATTG
Found at i:62147 original size:48 final size:48
Alignment explanation
Indices: 62063--62154 Score: 121
Period size: 48 Copynumber: 1.9 Consensus size: 48
62053 AGAAATAATC
* * *
62063 TTTCAGTTAAACTCAGTTTAATTGTTTCAGTTAAACTCAGTTTAATTG
1 TTTCAATTAAACTCAGTTTAATTGTTTCACTCAAACTCAGTTTAATTG
* * * *
62111 TTTCAATTAAACTCTGTTTATTTGTTTGACTCAAACTCTGTTTA
1 TTTCAATTAAACTCAGTTTAATTGTTTCACTCAAACTCAGTTTA
62155 TTCTAGATTA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 37 1.00
ACGTcount: A:0.27, C:0.14, G:0.11, T:0.48
Consensus pattern (48 bp):
TTTCAATTAAACTCAGTTTAATTGTTTCACTCAAACTCAGTTTAATTG
Found at i:66731 original size:3 final size:3
Alignment explanation
Indices: 66723--66763 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
66713 TCTTCGGCAA
* * *
66723 CAT CAT CAT CAT CAT CAT CTT CAT AAT CAT CAT CTT CAT CA
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CA
66764 GCTTCTGTAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.37
Consensus pattern (3 bp):
CAT
Found at i:67180 original size:20 final size:20
Alignment explanation
Indices: 67157--67196 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
67147 TTCATTTACT
67157 GTCATAAACCCCAACAAAGG
1 GTCATAAACCCCAACAAAGG
67177 GTCATAAACCCCAACAAAGG
1 GTCATAAACCCCAACAAAGG
67197 ATCACAAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.30, G:0.15, T:0.10
Consensus pattern (20 bp):
GTCATAAACCCCAACAAAGG
Found at i:69757 original size:15 final size:14
Alignment explanation
Indices: 69735--69767 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
69725 ATAAAATTTT
69735 AAAT-TTTAAAACTA
1 AAATATTTAAAA-TA
69749 AAATATTTAAAATA
1 AAATATTTAAAATA
69763 AAATA
1 AAATA
69768 AATATTTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (14 bp):
AAATATTTAAAATA
Found at i:73181 original size:6 final size:6
Alignment explanation
Indices: 73170--73205 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
73160 AAAATAAGGA
*
73170 GGGAAG GGGAAG AGGAAG GGGAAGG GGGAAG GGGAA
1 GGGAAG GGGAAG GGGAAG GGGAA-G GGGAAG GGGAA
73206 CAGAAAAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
6 21 0.78
7 6 0.22
ACGTcount: A:0.36, C:0.00, G:0.64, T:0.00
Consensus pattern (6 bp):
GGGAAG
Found at i:73199 original size:13 final size:13
Alignment explanation
Indices: 73165--73205 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
73155 AAGGCAAAAT
73165 AAGGAGGGAAGGGG
1 AAGG-GGGAAGGGG
*
73179 AA-GAGGAAGGGG
1 AAGGGGGAAGGGG
73191 AAGGGGGAAGGGG
1 AAGGGGGAAGGGG
73204 AA
1 AA
73206 CAGAAAAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 10 0.42
13 12 0.50
14 2 0.08
ACGTcount: A:0.39, C:0.00, G:0.61, T:0.00
Consensus pattern (13 bp):
AAGGGGGAAGGGG
Found at i:73278 original size:13 final size:13
Alignment explanation
Indices: 73260--73308 Score: 53
Period size: 13 Copynumber: 3.5 Consensus size: 13
73250 ATACTTATAT
73260 ATTTTAAAAAATA
1 ATTTTAAAAAATA
**
73273 ATTTTAATAATTTTA
1 ATTTTAA-AA-AATA
73288 TATTTTAAAAAATA
1 -ATTTTAAAAAATA
73302 ATTTTAA
1 ATTTTAA
73309 TAATTTTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
13 14 0.48
14 4 0.14
15 4 0.14
16 7 0.24
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
ATTTTAAAAAATA
Found at i:73289 original size:29 final size:29
Alignment explanation
Indices: 73244--73316 Score: 128
Period size: 29 Copynumber: 2.5 Consensus size: 29
73234 GATGACGATG
* *
73244 ATTTTAATACTTATATATTTTAAAAAATA
1 ATTTTAATAATTTTATATTTTAAAAAATA
73273 ATTTTAATAATTTTATATTTTAAAAAATA
1 ATTTTAATAATTTTATATTTTAAAAAATA
73302 ATTTTAATAATTTTA
1 ATTTTAATAATTTTA
73317 AAATCATTTG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (29 bp):
ATTTTAATAATTTTATATTTTAAAAAATA
Found at i:73303 original size:20 final size:22
Alignment explanation
Indices: 73278--73319 Score: 70
Period size: 20 Copynumber: 2.0 Consensus size: 22
73268 AAATAATTTT
73278 AATAATTTT-AT-ATTTTAAAA
1 AATAATTTTAATAATTTTAAAA
73298 AATAATTTTAATAATTTTAAAA
1 AATAATTTTAATAATTTTAAAA
73320 TCATTTGCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 9 0.45
21 2 0.10
22 9 0.45
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AATAATTTTAATAATTTTAAAA
Found at i:73320 original size:20 final size:20
Alignment explanation
Indices: 73269--73325 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
73259 TATTTTAAAA
73269 AATAATTTT--AATAATTTT
1 AATAATTTTAAAATAATTTT
73287 -AT-ATTTTAAAAAATAATTTT
1 AATAATTTT--AAAATAATTTT
*
73307 AATAATTTTAAAATCATTT
1 AATAATTTTAAAATAATTT
73326 GCTGACGTGA
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
16 5 0.16
17 2 0.06
20 18 0.56
21 2 0.06
22 5 0.16
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (20 bp):
AATAATTTTAAAATAATTTT
Found at i:75307 original size:18 final size:19
Alignment explanation
Indices: 75275--75313 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
75265 CGTTTCTTTT
75275 TTATTAATTTAAAATT-TA
1 TTATTAATTTAAAATTATA
75293 TTATTAAATTT-AAATTATA
1 TTATT-AATTTAAAATTATA
75312 TT
1 TT
75314 TATATTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TTATTAATTTAAAATTATA
Found at i:77393 original size:57 final size:56
Alignment explanation
Indices: 77308--77514 Score: 154
Period size: 60 Copynumber: 3.5 Consensus size: 56
77298 TTTTTGGCTC
77308 CTTTTTGAGAAAAAAAAATT-CAAAATTTTTTGGTGTTAGCCATGCAATGATCGACACCCT
1 CTTTTTGAG-AAAAAAAATTGC--AATTTTTTGGTGTT-GCCAT-CAATGATCGACACCCT
* * *
77368 CTTTTTGAGAAAAAAAATTGC-A-TTTTTGAGTGTTGACCATTACAT-AGCCGACACCTT
1 CTTTTTGAGAAAAAAAATTGCAATTTTTTG-GTGTTG-CCATCA-ATGA-TCGACACCCT
* * ** *
77425 CTTTTTTAGGAAAAAAAAAATTTCAAAATTTTTTTATGTTGGTCATACAATGATCGACACCCT
1 C-TTTTT--GAGAAAAAAAATTGC--AATTTTTTGGTGTT-GCCAT-CAATGATCGACACCCT
*
77488 CTATTTGAGAAAAAAAATTGC-ATTTTT
1 CTTTTTGAGAAAAAAAATTGCAATTTTT
77515 GGATGCACGG
Statistics
Matches: 118, Mismatches: 14, Indels: 33
0.72 0.08 0.20
Matches are distributed among these distances:
56 9 0.08
57 27 0.23
58 5 0.04
59 10 0.08
60 36 0.31
62 4 0.03
63 19 0.16
64 8 0.07
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
Consensus pattern (56 bp):
CTTTTTGAGAAAAAAAATTGCAATTTTTTGGTGTTGCCATCAATGATCGACACCCT
Found at i:77585 original size:45 final size:46
Alignment explanation
Indices: 77491--77599 Score: 123
Period size: 45 Copynumber: 2.4 Consensus size: 46
77481 ACACCCTCTA
* * *
77491 TTTGAG-AAAAAAAATTGCATTTTTGGATGCACGGCCAACACCCCCTT
1 TTTGAGAAAAAAAAATTGAATTTTTGCA--CACGGCCAACACCCCATT
* * *
77538 TTTGAGAAAAAAAAATTGAATTTTTGCA-ATGGCCGACACCTCATT
1 TTTGAGAAAAAAAAATTGAATTTTTGCACACGGCCAACACCCCATT
*
77583 TTTCAGAAAAAAAAATT
1 TTTGAGAAAAAAAAATT
77600 TCAAAATTTT
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
45 29 0.54
47 6 0.11
48 19 0.35
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.29
Consensus pattern (46 bp):
TTTGAGAAAAAAAAATTGAATTTTTGCACACGGCCAACACCCCATT
Found at i:77678 original size:62 final size:61
Alignment explanation
Indices: 77562--77685 Score: 178
Period size: 62 Copynumber: 2.0 Consensus size: 61
77552 ATTGAATTTT
* *
77562 TGCAATGGCCGACACCTCATTTTTCAGAAAAAAAAATTTCAAAATTTTTTGGTGTTGACCA
1 TGCAATGGCCGACACCCCATTTTTCAGAAAAAAAAATTACAAAATTTTTTGGTGTTGACCA
* * *
77623 TGCAATGGCCGACACCCCTTTTTTTC-GAATAAAAAAATTACAAATTTTTTTGGTGTTGGCCA
1 TGCAATGGCCGACACCCC-ATTTTTCAGAA-AAAAAAATTACAAAATTTTTTGGTGTTGACCA
77685 T
1 T
77686 TGCCTTTTTC
Statistics
Matches: 56, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
61 20 0.36
62 36 0.64
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (61 bp):
TGCAATGGCCGACACCCCATTTTTCAGAAAAAAAAATTACAAAATTTTTTGGTGTTGACCA
Found at i:77704 original size:109 final size:109
Alignment explanation
Indices: 77581--77781 Score: 312
Period size: 109 Copynumber: 1.8 Consensus size: 109
77571 CGACACCTCA
* * * *
77581 TTTTTCAGAAAAAAAAATTTCAAAATTTTTTGGTGTTGACCATGCAATGGCCGACACCCCTTTTT
1 TTTTTCACAAAAAAAAATTTCAAAATTTTTTGGTATTGACCATGCAATGACCGACACCCCCTTTT
*
77646 TTCGAATAAAAAAATTACAAATTTTTTTGGTGTTGGCCATTGCC
66 CTCGAATAAAAAAATTACAAATTTTTTTGGTGTTGGCCATTGCC
* ** *
77690 TTTTTCACATAAAAAAATTTCAAAATTTTTTGGTATTGGTCATGCAATGATCGACACCCCCTTTT
1 TTTTTCACAAAAAAAAATTTCAAAATTTTTTGGTATTGACCATGCAATGACCGACACCCCCTTTT
*
77755 CTCGAATAAAAAAATTGCAAATTTTTT
66 CTCGAATAAAAAAATTACAAATTTTTT
77782 ATGTGAAAAA
Statistics
Matches: 82, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
109 82 1.00
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.38
Consensus pattern (109 bp):
TTTTTCACAAAAAAAAATTTCAAAATTTTTTGGTATTGACCATGCAATGACCGACACCCCCTTTT
CTCGAATAAAAAAATTACAAATTTTTTTGGTGTTGGCCATTGCC
Found at i:77827 original size:61 final size:62
Alignment explanation
Indices: 77762--78001 Score: 242
Period size: 61 Copynumber: 3.9 Consensus size: 62
77752 TTTCTCGAAT
* * * *
77762 AAAAAAATTGCAAATTTTTTATGTG-AAAAAGGGGGTGTCGGCCATTGTATGGCTAACACTA
1 AAAAAAATTGCAAATTTTTTATGTGAAAAAAGGGGGTGTCGACCATTGCATGACCAACACTA
* * * ** *
77823 AAAAAATTTGTAATTTTTTTATCCGAAAAAAGGGGGTGTC-AGCCATTGCATGACCAACAC-C
1 AAAAAAATTGCAAATTTTTTATGTGAAAAAAGGGGGTGTCGA-CCATTGCATGACCAACACTA
* ** * *
77884 AAAAAATTTTAAAATTTTTTTACGTG-AAAAAGAGGGTGTCGACCATTGCATGACCAACA-TA
1 AAAAAAATTGCAAA-TTTTTTATGTGAAAAAAGGGGGTGTCGACCATTGCATGACCAACACTA
*
77945 AAAAAAATTTGC-AATTTTTT-TGTCCGAAAAAAAGGGGTGTCGACCATTGCATGACCA
1 AAAAAAA-TTGCAAATTTTTTATGT--GAAAAAAGGGGGTGTCGACCATTGCATGACCA
78002 GTACCCAAAA
Statistics
Matches: 146, Mismatches: 24, Indels: 17
0.78 0.13 0.09
Matches are distributed among these distances:
59 2 0.01
60 6 0.04
61 70 0.48
62 68 0.47
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.29
Consensus pattern (62 bp):
AAAAAAATTGCAAATTTTTTATGTGAAAAAAGGGGGTGTCGACCATTGCATGACCAACACTA
Found at i:77828 original size:62 final size:62
Alignment explanation
Indices: 77761--78001 Score: 255
Period size: 62 Copynumber: 3.9 Consensus size: 62
77751 TTTTCTCGAA
* * * *
77761 TAAAAAAA-TTGCAAATTTTTTATGTG-AAAAAGGGGGTGTCGGCCATTGTATGGCTAACAC
1 TAAAAAAATTTGCAAATTTTTTATGTGAAAAAAGGGGGTGTCGACCATTGCATGACCAACAC
* * **
77821 TAAAAAAATTTGTAATTTTTTTATCCGAAAAAAGGGGGTGTC-AGCCATTGCATGACCAACAC
1 TAAAAAAATTTGCAAATTTTTTATGTGAAAAAAGGGGGTGTCGA-CCATTGCATGACCAACAC
* ** * *
77883 -CAAAAAATTTTAAAATTTTTTTACGTG-AAAAAGAGGGTGTCGACCATTGCATGACCAACA-
1 TAAAAAAATTTGCAAA-TTTTTTATGTGAAAAAAGGGGGTGTCGACCATTGCATGACCAACAC
*
77943 TAAAAAAAATTTGC-AATTTTTT-TGTCCGAAAAAAAGGGGTGTCGACCATTGCATGACCA
1 T-AAAAAAATTTGCAAATTTTTTATGT--GAAAAAAGGGGGTGTCGACCATTGCATGACCA
78002 GTACCCAAAA
Statistics
Matches: 149, Mismatches: 22, Indels: 18
0.79 0.12 0.10
Matches are distributed among these distances:
59 2 0.01
60 14 0.09
61 58 0.39
62 75 0.50
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.29
Consensus pattern (62 bp):
TAAAAAAATTTGCAAATTTTTTATGTGAAAAAAGGGGGTGTCGACCATTGCATGACCAACAC
Found at i:78013 original size:123 final size:123
Alignment explanation
Indices: 77776--78001 Score: 339
Period size: 123 Copynumber: 1.8 Consensus size: 123
77766 AAATTGCAAA
* * * * * * *
77776 TTTTTTATGTGAAAAAGGGGGTGTCGGCCATTGTATGGCTAACACTAAAAAAATTTGTAATTTTT
1 TTTTTTACGTGAAAAAGAGGGTGTCGACCATTGCATGACCAACACTAAAAAAATTTGCAATTTTT
*
77841 TTATCCGAAAAAAGGGGGTGTCAGCCATTGCATGACCAACACCAAAAAATTTTAAAAT
66 TTATCCGAAAAAAAGGGGTGTCAGCCATTGCATGACCAACACCAAAAAATTTTAAAAT
77899 TTTTTTACGTGAAAAAGAGGGTGTCGACCATTGCATGACCAACA-TAAAAAAAATTTGCAATTTT
1 TTTTTTACGTGAAAAAGAGGGTGTCGACCATTGCATGACCAACACT-AAAAAAATTTGCAATTTT
*
77963 TTTGTCCGAAAAAAAGGGGTGTC-GACCATTGCATGACCA
65 TTTATCCGAAAAAAAGGGGTGTCAG-CCATTGCATGACCA
78002 GTACCCAAAA
Statistics
Matches: 92, Mismatches: 9, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
122 2 0.02
123 90 0.98
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (123 bp):
TTTTTTACGTGAAAAAGAGGGTGTCGACCATTGCATGACCAACACTAAAAAAATTTGCAATTTTT
TTATCCGAAAAAAAGGGGTGTCAGCCATTGCATGACCAACACCAAAAAATTTTAAAAT
Found at i:78048 original size:56 final size:56
Alignment explanation
Indices: 77858--78097 Score: 176
Period size: 56 Copynumber: 4.1 Consensus size: 56
77848 AAAAAAGGGG
* * ** * *
77858 GTGTCAGCCATTGCATGACCAACACCAAAAAATTTTAAAATTTTTTTACGTGAAA-AAGAGG
1 GTGTCAACCATTGCATGACCAACACCCAAAAA---TGCAATTTTTTT-C-TCAAATAA-AGA
* *** * * *
77919 GTGTCGACCATTGCATGACCAACATAAAAAAAATTTGCAATTTTTTTGTCCGAAAAAAAGGG
1 GTGTCAACCATTGCATGACCAACA-CCCAAAAA--TGCAATTTTTTTCT-C-AAATAAA-GA
* ** * *
77981 GTGTCGACCATTGCATGACCAGTACCCAAAAATGCACTTTTTTTCTCAAATAGAGA
1 GTGTCAACCATTGCATGACCAACACCCAAAAATGCAATTTTTTTCTCAAATAAAGA
* * *
78037 GTGTCAACCATTGCATGGCCAACATCCAAAAATGTAATTTTTTTCTCAAATAAAGA
1 GTGTCAACCATTGCATGACCAACACCCAAAAATGCAATTTTTTTCTCAAATAAAGA
78093 GTGTC
1 GTGTC
78098 GGCCATTACA
Statistics
Matches: 148, Mismatches: 26, Indels: 15
0.78 0.14 0.08
Matches are distributed among these distances:
56 54 0.36
57 5 0.03
58 1 0.01
59 13 0.09
61 43 0.29
62 32 0.22
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.29
Consensus pattern (56 bp):
GTGTCAACCATTGCATGACCAACACCCAAAAATGCAATTTTTTTCTCAAATAAAGA
Found at i:78104 original size:56 final size:56
Alignment explanation
Indices: 77919--78235 Score: 208
Period size: 56 Copynumber: 5.4 Consensus size: 56
77909 GAAAAAGAGG
* *** * * *
77919 GTGTCGACCATTGCATGACCAACATAAAAAAAATTTGCAATTTTTTTGTCCGAAAAAAAGGG
1 GTGTCGACCATTGCATGGCCAACA-CCCAAAAA--TGCAATTTTTTTCT-C-AAATAAA-GA
* ** * *
77981 GTGTCGACCATTGCATGACCAGTACCCAAAAATGCACTTTTTTTCTCAAATAGAGA
1 GTGTCGACCATTGCATGGCCAACACCCAAAAATGCAATTTTTTTCTCAAATAAAGA
* * *
78037 GTGTCAACCATTGCATGGCCAACATCCAAAAATGTAATTTTTTTCTCAAATAAAGA
1 GTGTCGACCATTGCATGGCCAACACCCAAAAATGCAATTTTTTTCTCAAATAAAGA
* * ** *** * *
78093 GTGTCGGCCATTACATGGGAAACATAAAAAAATTTTGAAATTTTTTTTTCTCAAAAAAAGA
1 GTGTCGACCATTGCATGGCCAACACCCAAAAA---TGCAA--TTTTTTTCTCAAATAAAGA
* * * * *
78154 -TGTCGGCCA-TGCAATGGTCAATACCCAAAAATACAATTTTTTTCTTCAAA-AAAGGGG
1 GTGTCGACCATTGC-ATGGCCAACACCCAAAAATGCAATTTTTTTC-TCAAATAAA--GA
*
78211 GTGTCGATCATTGCATGGCCAACAC
1 GTGTCGACCATTGCATGGCCAACAC
78236 AAAAAAAATT
Statistics
Matches: 203, Mismatches: 41, Indels: 26
0.75 0.15 0.10
Matches are distributed among these distances:
55 11 0.05
56 79 0.39
57 9 0.04
58 17 0.08
59 21 0.10
60 21 0.10
61 23 0.11
62 22 0.11
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.29
Consensus pattern (56 bp):
GTGTCGACCATTGCATGGCCAACACCCAAAAATGCAATTTTTTTCTCAAATAAAGA
Found at i:85957 original size:18 final size:18
Alignment explanation
Indices: 85934--85971 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
85924 TAGATTAATA
*
85934 AAATTAACTAATAATTAT
1 AAATTAAATAATAATTAT
*
85952 AAATTAAATTATAATTAT
1 AAATTAAATAATAATTAT
85970 AA
1 AA
85972 TTACACATTT
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:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (18 bp):
AAATTAAATAATAATTAT
Found at i:86082 original size:21 final size:24
Alignment explanation
Indices: 86048--86102 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 24
86038 GCATAATATT
86048 TTAACTAATAA-TTTT-AAATTAAA
1 TTAA-TAATAATTTTTAAAATTAAA
* *
86071 TT-ATAATTATTTTTAAAATTAAT
1 TTAATAATAATTTTTAAAATTAAA
86094 TTAATAATA
1 TTAATAATA
86103 TGATAAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
21 5 0.19
22 5 0.19
23 11 0.42
24 5 0.19
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (24 bp):
TTAATAATAATTTTTAAAATTAAA
Found at i:90732 original size:3 final size:3
Alignment explanation
Indices: 90724--90749 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
90714 TGCAAAATTG
90724 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
90750 GATTTAGCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:92011 original size:22 final size:21
Alignment explanation
Indices: 91985--92026 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
91975 TAATTAATTT
*
91985 TAAATTTTTTATGATGTAAAAA
1 TAAATATTTTAT-ATGTAAAAA
*
92007 TAAATATTTTATATTTAAAA
1 TAAATATTTTATATGTAAAA
92027 TAATAAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (21 bp):
TAAATATTTTATATGTAAAAA
Found at i:92082 original size:26 final size:27
Alignment explanation
Indices: 92053--92106 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
92043 AAATTTTTAT
* *
92053 ATAAAATTT-ATATTTTAAAAAATAAA
1 ATAAAATTTGAAAATTTAAAAAATAAA
*
92079 ATAAAATTTGAAAATTTAAAAATTAAA
1 ATAAAATTTGAAAATTTAAAAAATAAA
92106 A
1 A
92107 AGACTAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 9 0.38
27 15 0.62
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (27 bp):
ATAAAATTTGAAAATTTAAAAAATAAA
Found at i:99678 original size:305 final size:306
Alignment explanation
Indices: 99119--99729 Score: 1188
Period size: 305 Copynumber: 2.0 Consensus size: 306
99109 AATACATGAA
99119 CTTGAGCTACTGACTCGCTATTTTGTTACATATAAATTGGTGGATTAATCTTTTTACTAGTTTTT
1 CTTGAGCTACTGACTCGCTATTTTGTTACATATAAATTGGTGGATTAATCTTTTTACTAGTTTTT
99184 TTTTGCATATAAATTATTGCACTACTAATTTTTAAGTCACTGATTAATGTATCTAATTAGATAAC
66 TTTTGCATATAAATTATTGCACTACTAATTTTTAAGTCACTGATTAATGTATCTAATTAGATAAC
*
99249 TTTTTCAATTTTCGTAAAGTATAAGAATCAAATTATGATAAGCTTCTCAATATTCATAAAACAGT
131 TTTTTCAATTTTCGTAAAGTATAAGAATCAAATTATGATAAGCTTCTCAAAATTCATAAAACAGT
*
99314 AAGAATGAAATTTTTAATTAGAGTGTCTAAAGAAAACCTTAGGCTCTTTCTCGAAGTGTGAATGT
196 AAGAATGAAATTTTTAATTAGAGTGTCTAAAGAAAACCTTAGGCTCTTTCTCAAAGTGTGAATGT
99379 CGAATATGAATATATATTCAATATAAGAATGTTTATATACAAATAT
261 CGAATATGAATATATATTCAATATAAGAATGTTTATATACAAATAT
99425 CTTGAGCTACTGACTCGCTATTTTGTTACATATAAATTGGTGGATTAATCTTTTTACTAG-TTTT
1 CTTGAGCTACTGACTCGCTATTTTGTTACATATAAATTGGTGGATTAATCTTTTTACTAGTTTTT
*
99489 TTTTGCATATAAATTATTGCACTGCTAATTTTTAAGTCACTGATTAATGTATCTAATTAGATAAC
66 TTTTGCATATAAATTATTGCACTACTAATTTTTAAGTCACTGATTAATGTATCTAATTAGATAAC
99554 TTTTTCAATTTTCGTAAAGTATAAGAATCAAATTATGATAAGCTTCTCAAAATTCATAAAACAGT
131 TTTTTCAATTTTCGTAAAGTATAAGAATCAAATTATGATAAGCTTCTCAAAATTCATAAAACAGT
99619 AAGAATGAAATTTTTAATTAGAGTGTCTAAAGAAAACCTTAGGCTCTTTCTCAAAGTGTGAATGT
196 AAGAATGAAATTTTTAATTAGAGTGTCTAAAGAAAACCTTAGGCTCTTTCTCAAAGTGTGAATGT
99684 CGAATATGAATATATATTCAATATAAGAATGTTTATATACAAATAT
261 CGAATATGAATATATATTCAATATAAGAATGTTTATATACAAATAT
99730 TTTTAAAATT
Statistics
Matches: 302, Mismatches: 3, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
305 242 0.80
306 60 0.20
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.40
Consensus pattern (306 bp):
CTTGAGCTACTGACTCGCTATTTTGTTACATATAAATTGGTGGATTAATCTTTTTACTAGTTTTT
TTTTGCATATAAATTATTGCACTACTAATTTTTAAGTCACTGATTAATGTATCTAATTAGATAAC
TTTTTCAATTTTCGTAAAGTATAAGAATCAAATTATGATAAGCTTCTCAAAATTCATAAAACAGT
AAGAATGAAATTTTTAATTAGAGTGTCTAAAGAAAACCTTAGGCTCTTTCTCAAAGTGTGAATGT
CGAATATGAATATATATTCAATATAAGAATGTTTATATACAAATAT
Found at i:102291 original size:47 final size:47
Alignment explanation
Indices: 102240--102336 Score: 176
Period size: 47 Copynumber: 2.1 Consensus size: 47
102230 ATTCTTATCA
102240 AATAATCCAACAAGGCACAGGTTATTGATTTAACTGATGTCCAAACC
1 AATAATCCAACAAGGCACAGGTTATTGATTTAACTGATGTCCAAACC
* *
102287 AATAATCCAACAAGTCACAGGTTATTTATTTAACTGATGTCCAAACC
1 AATAATCCAACAAGGCACAGGTTATTGATTTAACTGATGTCCAAACC
102334 AAT
1 AAT
102337 TAGTGTTTCT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.39, C:0.21, G:0.12, T:0.28
Consensus pattern (47 bp):
AATAATCCAACAAGGCACAGGTTATTGATTTAACTGATGTCCAAACC
Found at i:106135 original size:19 final size:19
Alignment explanation
Indices: 106111--106149 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
106101 TATTAGTATT
106111 AGTTAATTATAATTAATTA
1 AGTTAATTATAATTAATTA
*
106130 AGTTAATTTTAATTAATTA
1 AGTTAATTATAATTAATTA
106149 A
1 A
106150 TAAACTAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (19 bp):
AGTTAATTATAATTAATTA
Found at i:107142 original size:19 final size:21
Alignment explanation
Indices: 107103--107144 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
107093 ATGCCATTAG
*
107103 GGTTCAAACAGAAAAGGAAAT
1 GGTTCAAACAGAAAAGAAAAT
107124 GGTTCAAACA-AAAA-AAAAT
1 GGTTCAAACAGAAAAGAAAAT
107143 GG
1 GG
107145 GTGTTTGATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 6 0.30
20 4 0.20
21 10 0.50
ACGTcount: A:0.55, C:0.10, G:0.21, T:0.14
Consensus pattern (21 bp):
GGTTCAAACAGAAAAGAAAAT
Found at i:115673 original size:9 final size:9
Alignment explanation
Indices: 115659--115804 Score: 70
Period size: 9 Copynumber: 16.0 Consensus size: 9
115649 TTTTGGTGCG
115659 ATAATTTTT
1 ATAATTTTT
115668 ATAATTTTTT
1 ATAA-TTTTT
*
115678 ACAATTTTT
1 ATAATTTTT
*
115687 ATATTTTTT
1 ATAATTTTT
115696 AT-ATTTTGT
1 ATAATTTT-T
* *
115705 GTATTTTCTT
1 ATAATTT-TT
* *
115715 ATGA-CTTT
1 ATAATTTTT
**
115723 ATAAAAATTT
1 AT-AATTTTT
*
115733 ATATTTTTT
1 ATAATTTTT
*
115742 AT-ATTTCT
1 ATAATTTTT
115750 AT-ATATTTT
1 ATAAT-TTTT
115759 ATAATTTTT
1 ATAATTTTT
115768 -TACGATTTTT
1 ATA--ATTTTT
*
115778 ATAAAATTTT
1 AT-AATTTTT
*
115788 ACAATTTTT
1 ATAATTTTT
115797 AT-ATTTTT
1 ATAATTTTT
115805 TTTCTAATTT
Statistics
Matches: 103, Mismatches: 22, Indels: 25
0.69 0.15 0.17
Matches are distributed among these distances:
8 24 0.23
9 44 0.43
10 32 0.31
11 2 0.02
12 1 0.01
ACGTcount: A:0.30, C:0.04, G:0.03, T:0.63
Consensus pattern (9 bp):
ATAATTTTT
Found at i:115683 original size:19 final size:19
Alignment explanation
Indices: 115661--115825 Score: 78
Period size: 19 Copynumber: 8.9 Consensus size: 19
115651 TTGGTGCGAT
115661 AATTTTTATAATTTTTTAC
1 AATTTTTATAATTTTTTAC
115680 AATTTTTAT-ATTTTTTA-
1 AATTTTTATAATTTTTTAC
* * *
115697 TATTTTGTGT-ATTTTCTTAT
1 AATTTT-TATAATTTT-TTAC
* * *** *
115717 GA-CTTTATAAAAATTTAT
1 AATTTTTATAATTTTTTAC
* *
115735 ATTTTTTAT-A-TTTCTA-
1 AATTTTTATAATTTTTTAC
*
115751 TATATTTTATAATTTTTTAC
1 AAT-TTTTATAATTTTTTAC
* **
115771 GATTTTTATAAAATTTTAC
1 AATTTTTATAATTTTTTAC
* *
115790 AATTTTTATATTTTTTTTC
1 AATTTTTATAATTTTTTAC
115809 TAA-TTTT-TAATTTTTTA
1 -AATTTTTATAATTTTTTA
115826 TTAAAATTTA
Statistics
Matches: 109, Mismatches: 27, Indels: 21
0.69 0.17 0.13
Matches are distributed among these distances:
16 1 0.01
17 14 0.13
18 31 0.28
19 58 0.53
20 5 0.05
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.64
Consensus pattern (19 bp):
AATTTTTATAATTTTTTAC
Found at i:115726 original size:55 final size:54
Alignment explanation
Indices: 115665--115805 Score: 158
Period size: 55 Copynumber: 2.6 Consensus size: 54
115655 TGCGATAATT
** * * *
115665 TTTATAATTTTTTACAATTTTTATATTTTTTATATTTTGTGTATTTTCTTATGA-C
1 TTTATAAAATTTTACAATTTTTATATTTTTTATATTTTAT-AATTTT-TTACGATC
* * * * *
115720 TTTATAAAAATTTATATTTTTTATATTTCTATATATTTTATAATTTTTTACGATT
1 TTTATAAAATTTTACAATTTTTATATTT-TTTATATTTTATAATTTTTTACGATC
115775 TTTATAAAATTTTACAATTTTTATATTTTTT
1 TTTATAAAATTTTACAATTTTTATATTTTTT
115806 TTCTAATTTT
Statistics
Matches: 70, Mismatches: 14, Indels: 5
0.79 0.16 0.06
Matches are distributed among these distances:
54 7 0.10
55 53 0.76
56 10 0.14
ACGTcount: A:0.29, C:0.04, G:0.03, T:0.64
Consensus pattern (54 bp):
TTTATAAAATTTTACAATTTTTATATTTTTTATATTTTATAATTTTTTACGATC
Found at i:115807 original size:20 final size:19
Alignment explanation
Indices: 115784--115834 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
115774 TTTTATAAAA
115784 TTTTACAATTTTTATATTTT
1 TTTTACAATTTTTA-ATTTT
115804 TTTT-CTAATTTTTAATTTT
1 TTTTAC-AATTTTTAATTTT
*
115823 TTATTAAAATTT
1 TT-TTACAATTT
115835 AATAATATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 8 0.30
20 19 0.70
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTTACAATTTTTAATTTT
Found at i:115823 original size:55 final size:55
Alignment explanation
Indices: 115662--115823 Score: 143
Period size: 55 Copynumber: 2.9 Consensus size: 55
115652 TGGTGCGATA
** * * * *
115662 ATTTTTATAATTTTTTACAATTTTTATA-TTTTTTATATTTTGTGTATTTTCTTATG
1 ATTTTTATAAAATTTTACAATTTTTATATTTTTTTATAATTT-TATAATTT-TTACG
* * * * * *
115718 A-CTTTATAAAAATTTATATTTTTTATATTTCTATAT-ATTTTATAATTTTTTACG
1 ATTTTTATAAAATTTTACAATTTTTATATTTTTTTATAATTTTATAA-TTTTTACG
*
115772 ATTTTTATAAAATTTTACAATTTTTATATTTTTTTTCTAATTTT-TAATTTTT
1 ATTTTTATAAAATTTTACAATTTTTATA-TTTTTTTATAATTTTATAATTTTT
115824 TATTAAAATT
Statistics
Matches: 82, Mismatches: 19, Indels: 11
0.73 0.17 0.10
Matches are distributed among these distances:
54 8 0.10
55 53 0.65
56 16 0.20
57 5 0.06
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.65
Consensus pattern (55 bp):
ATTTTTATAAAATTTTACAATTTTTATATTTTTTTATAATTTTATAATTTTTACG
Found at i:116048 original size:87 final size:86
Alignment explanation
Indices: 115893--116117 Score: 245
Period size: 87 Copynumber: 2.6 Consensus size: 86
115883 TTTTTTTAAT
* * * *
115893 AAAAGTAGGGGTTTAATTACTTTTTTTTTGAAAAAGTTTGAGAGTTTTTTTTTATGCATTTTAAA
1 AAAAGTAGGGGCTTAATTAC--TTTTTTTG-AAAAGTTTGAG-GGTCTTTTTGATGCATTTTAAA
* *
115958 AGTTCAAGTACCCAATTGAGTACAA
62 AGTTCAAGTACCCAAATAAGTACAA
*
115983 AAAAGTAGGGGCTTAATTACTTTTTTTGAAAAGGTTTGAGGGTCTTTTTGATGCATTTTGAAAGT
1 AAAAGTAGGGGCTTAATTACTTTTTTTGAAAA-GTTTGAGGGTCTTTTTGATGCATTTTAAAAGT
* **
116048 TGAAGTACCCAAATAAGTGTAA
65 TCAAGTACCCAAATAAGTACAA
** ** * *
116070 AAAAAAAGGGGCTTAATTGGTTTTTTTCAGAAAGTTTGAGAG-CTTTTT
1 AAAAGTAGGGGCTTAATTACTTTTTTTGA-AAAGTTTGAGGGTCTTTTT
116118 ATACTCTTAA
Statistics
Matches: 117, Mismatches: 16, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
86 6 0.05
87 74 0.63
88 18 0.15
90 19 0.16
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.40
Consensus pattern (86 bp):
AAAAGTAGGGGCTTAATTACTTTTTTTGAAAAGTTTGAGGGTCTTTTTGATGCATTTTAAAAGTT
CAAGTACCCAAATAAGTACAA
Found at i:118496 original size:24 final size:24
Alignment explanation
Indices: 118426--118726 Score: 345
Period size: 24 Copynumber: 12.3 Consensus size: 24
118416 GACGAAGCTC
* *
118426 CTGCTGCCGCTGATGTTCCAACTG
1 CTGCTGCCGCTGAAGCTCCAACTG
* *
118450 CCGTTGATGCTGCTGAA-CTTCCAACTG
1 -C--TGCTGCCGCTGAAGC-TCCAACTG
*
118477 CTGCTGCCGCTGAAGCTCCAACAG
1 CTGCTGCCGCTGAAGCTCCAACTG
* *
118501 AC-GATGCTGCTGAAGCTCCAACTG
1 -CTGCTGCCGCTGAAGCTCCAACTG
*
118525 CTGCTGCCGCTGAAGCTCCAATTG
1 CTGCTGCCGCTGAAGCTCCAACTG
*
118549 CTGCTGCCGCTGAAGCTCCAATTG
1 CTGCTGCCGCTGAAGCTCCAACTG
* *
118573 CTGCTGCCGCTGAAGCTCTAATTG
1 CTGCTGCCGCTGAAGCTCCAACTG
* *
118597 CTGCTGTCGCTGAAGCTCCAATTG
1 CTGCTGCCGCTGAAGCTCCAACTG
118621 CTGCTGCCGCTGAAGCTCCAACTG
1 CTGCTGCCGCTGAAGCTCCAACTG
118645 CTGCTGCCGCTGAAGCTCCAACTG
1 CTGCTGCCGCTGAAGCTCCAACTG
* *
118669 CTGCTGCCGCTGAAACTCAAACTGATG
1 CTGCTGCCGCTGAAGCTCCAAC---TG
* * *
118696 CTGCTGCCGTTGTAGTTCCAACTG
1 CTGCTGCCGCTGAAGCTCCAACTG
*
118720 CCGCTGC
1 CTGCTGC
118727 TGCTCAAATT
Statistics
Matches: 241, Mismatches: 26, Indels: 19
0.84 0.09 0.07
Matches are distributed among these distances:
23 1 0.00
24 199 0.83
25 3 0.01
26 1 0.00
27 37 0.15
ACGTcount: A:0.18, C:0.33, G:0.25, T:0.25
Consensus pattern (24 bp):
CTGCTGCCGCTGAAGCTCCAACTG
Found at i:138436 original size:2 final size:2
Alignment explanation
Indices: 138429--138460 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
138419 ATTAACCGAA
138429 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
138461 TTACCTTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:139122 original size:25 final size:25
Alignment explanation
Indices: 139059--139122 Score: 60
Period size: 25 Copynumber: 2.5 Consensus size: 25
139049 TAAATATTTT
* *
139059 TATATTTATAATTTCATTTTTATAAA
1 TATATTTAT-ATTACATTATTATAAA
*
139085 TATATCTCA-ATTACATTCATT-TAAA
1 TATAT-TTATATTACATT-ATTATAAA
139110 TATATTTATATTA
1 TATATTTATATTA
139123 TATGAAAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
24 2 0.06
25 20 0.65
26 7 0.23
27 2 0.06
ACGTcount: A:0.39, C:0.08, G:0.00, T:0.53
Consensus pattern (25 bp):
TATATTTATATTACATTATTATAAA
Found at i:145773 original size:15 final size:15
Alignment explanation
Indices: 145753--145783 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
145743 TTTGAATTTT
145753 TCAAATCGAATCGAG
1 TCAAATCGAATCGAG
*
145768 TCAAATCGAGTCGAG
1 TCAAATCGAATCGAG
145783 T
1 T
145784 TAACGAATTC
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:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (15 bp):
TCAAATCGAATCGAG
Found at i:154118 original size:21 final size:21
Alignment explanation
Indices: 154089--154136 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
154079 ATTACATAAA
* * *
154089 TAATATAATGGTTTTGTCTTT
1 TAATTTAATAGTTTTGACTTT
154110 TAATTTAATAGTTTTGACTTT
1 TAATTTAATAGTTTTGACTTT
154131 TAATTT
1 TAATTT
154137 TTGAAAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.27, C:0.04, G:0.10, T:0.58
Consensus pattern (21 bp):
TAATTTAATAGTTTTGACTTT
Found at i:155409 original size:44 final size:44
Alignment explanation
Indices: 155324--155409 Score: 109
Period size: 44 Copynumber: 2.0 Consensus size: 44
155314 GTCTTTTTAA
* *
155324 AATTTGTCGAGAAACATTTGTTTCAATGTTTTCAATTTATTTTC
1 AATTTGTCGAGAAACATATGTTTCAATGTTTTCAATGTATTTTC
* * * * *
155368 AATTTGTTGGGAAACATATGTTTTAATGTTTTTAGTGTATTT
1 AATTTGTCGAGAAACATATGTTTCAATGTTTTCAATGTATTT
155410 GATATATTAT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
44 35 1.00
ACGTcount: A:0.27, C:0.07, G:0.15, T:0.51
Consensus pattern (44 bp):
AATTTGTCGAGAAACATATGTTTCAATGTTTTCAATGTATTTTC
Found at i:158952 original size:7 final size:7
Alignment explanation
Indices: 158940--158968 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
158930 AAGATTAATA
158940 TTAAAAT
1 TTAAAAT
158947 TTAAAAT
1 TTAAAAT
158954 TTAAAAT
1 TTAAAAT
158961 TTAAAAT
1 TTAAAAT
158968 T
1 T
158969 CGAAGTAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (7 bp):
TTAAAAT
Found at i:160036 original size:30 final size:30
Alignment explanation
Indices: 159980--160038 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
159970 ATACATAATT
* *
159980 TATATTTATTATGAAGCTTATGATTGAGTC
1 TATATTTATTATAAAGCTTATAATTGAGTC
*
160010 TATATTTATTATAAATCATT-TAATTGAGT
1 TATATTTATTATAAAGC-TTATAATTGAGT
160039 TGATGTTATG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 23 0.92
31 2 0.08
ACGTcount: A:0.34, C:0.05, G:0.12, T:0.49
Consensus pattern (30 bp):
TATATTTATTATAAAGCTTATAATTGAGTC
Found at i:165818 original size:25 final size:27
Alignment explanation
Indices: 165790--165843 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
165780 CATATTATAA
165790 TATTAA-T-GTGTAATAAAAATAAATT
1 TATTAAGTAGTGTAATAAAAATAAATT
* *
165815 TATTAAGTTATTGTAATAAAAATTAATT
1 TATTAAG-TAGTGTAATAAAAATAAATT
165843 T
1 T
165844 TATAAGAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 6 0.25
27 1 0.04
28 17 0.71
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.44
Consensus pattern (27 bp):
TATTAAGTAGTGTAATAAAAATAAATT
Found at i:169910 original size:31 final size:30
Alignment explanation
Indices: 169875--169932 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
169865 TAAATTGACA
*
169875 CTAATTGAAACTCATATAAATTTAAAATATC
1 CTAATTGAAA-TCATATAAATGTAAAATATC
* *
169906 CTAATTTAAATTATATAAATGTAAAAT
1 CTAATTGAAATCATATAAATGTAAAAT
169933 TTTCTATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 15 0.62
31 9 0.38
ACGTcount: A:0.50, C:0.09, G:0.03, T:0.38
Consensus pattern (30 bp):
CTAATTGAAATCATATAAATGTAAAATATC
Found at i:175784 original size:17 final size:17
Alignment explanation
Indices: 175762--175795 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
175752 AGTTCAATTA
175762 ATGCTATAGACCATGAT
1 ATGCTATAGACCATGAT
175779 ATGCTATAGACCATGAT
1 ATGCTATAGACCATGAT
175796 CCGGAAACTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (17 bp):
ATGCTATAGACCATGAT
Found at i:176897 original size:44 final size:44
Alignment explanation
Indices: 176834--176922 Score: 169
Period size: 44 Copynumber: 2.0 Consensus size: 44
176824 GCCGTGATGG
176834 CATGGATGTTGATGATTCTAGACCCCCATCCCTGAAACGATCCA
1 CATGGATGTTGATGATTCTAGACCCCCATCCCTGAAACGATCCA
*
176878 CATGGATGTTGATGATTCTAGCCCCCCATCCCTGAAACGATCCA
1 CATGGATGTTGATGATTCTAGACCCCCATCCCTGAAACGATCCA
176922 C
1 C
176923 TGTGCTTTTG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.25
Consensus pattern (44 bp):
CATGGATGTTGATGATTCTAGACCCCCATCCCTGAAACGATCCA
Found at i:185379 original size:19 final size:17
Alignment explanation
Indices: 185355--185399 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 17
185345 AATTTTTTCC
185355 TTTATTTTCATAATATCTA
1 TTTATTTTCATAAT-T-TA
185374 TTTATTCCTTCATAATTTA
1 TTTATT--TTCATAATTTA
185393 TTTATTT
1 TTTATTT
185400 ATTTTTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
17 1 0.04
19 14 0.58
20 1 0.04
21 8 0.33
ACGTcount: A:0.27, C:0.11, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTATTTTCATAATTTA
Found at i:187358 original size:22 final size:24
Alignment explanation
Indices: 187325--187372 Score: 73
Period size: 22 Copynumber: 2.1 Consensus size: 24
187315 GATATACGAA
*
187325 TTAATTTTTATAATATAAT-TTTT
1 TTAATTTTTATAATACAATATTTT
187348 TTAA-TTTTATAATACAATATTTT
1 TTAATTTTTATAATACAATATTTT
187371 TT
1 TT
187373 GTCATAACCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 13 0.57
23 10 0.43
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62
Consensus pattern (24 bp):
TTAATTTTTATAATACAATATTTT
Found at i:187877 original size:26 final size:27
Alignment explanation
Indices: 187825--187877 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 27
187815 TAATAGACGA
**
187825 AATTATATTTTTAATATAAAATTAAAT
1 AATTATATTTTTAATATAAAAACAAAT
187852 AATT-TATTTTTAA-ATAAAAAACAAAT
1 AATTATATTTTTAATAT-AAAAACAAAT
187878 TTTAATTTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 2 0.09
26 17 0.74
27 4 0.17
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (27 bp):
AATTATATTTTTAATATAAAAACAAAT
Done.