Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032254.1 Gossypioides kirkii chromosome KI_12
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: 43711324
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 2 of 135
Found at i:502349 original size:20 final size:20
Alignment explanation
Indices: 502311--502348 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
502301 TAGTAGTTTA
*
502311 TTTTTATCTGTAGATTTTTC
1 TTTTTATCTGTACATTTTTC
502331 TTTTTAT-TGTACATTTTT
1 TTTTTATCTGTACATTTTT
502349 TTTCTAATGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.16, C:0.08, G:0.08, T:0.68
Consensus pattern (20 bp):
TTTTTATCTGTACATTTTTC
Found at i:511082 original size:21 final size:20
Alignment explanation
Indices: 511058--511096 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
511048 TTTCACAAGA
511058 ATTTTAGATTTTTTTAATACG
1 ATTTT-GATTTTTTTAATACG
*
511079 ATTTTTATTTTTTTAATA
1 ATTTTGATTTTTTTAATA
511097 GTTTAAAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.28, C:0.03, G:0.05, T:0.64
Consensus pattern (20 bp):
ATTTTGATTTTTTTAATACG
Found at i:512700 original size:18 final size:19
Alignment explanation
Indices: 512679--512728 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
512669 GAGAAAAATT
512679 TAAATATTAAATTGAA-TA
1 TAAATATTAAATTGAAGTA
* *
512697 TAAAAATTAAATTTAAGTA
1 TAAATATTAAATTGAAGTA
*
512716 TCAAATATGAAAT
1 T-AAATATTAAAT
512729 AAAAAATAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
18 14 0.54
19 3 0.12
20 9 0.35
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.36
Consensus pattern (19 bp):
TAAATATTAAATTGAAGTA
Found at i:512709 original size:31 final size:31
Alignment explanation
Indices: 512674--512738 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
512664 TTATTGAGAA
* *
512674 AAATTTAAATATTAAAT-TGAATATAAAAATT
1 AAATTTAAATATCAAATATGAA-ATAAAAAAT
*
512705 AAATTTAAGTATCAAATATGAAATAAAAAAT
1 AAATTTAAATATCAAATATGAAATAAAAAAT
512736 AAA
1 AAA
512739 AAGAAAAACA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
31 26 0.87
32 4 0.13
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.32
Consensus pattern (31 bp):
AAATTTAAATATCAAATATGAAATAAAAAAT
Found at i:518390 original size:22 final size:21
Alignment explanation
Indices: 518355--518395 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
518345 TAAAAAATAA
518355 TATATTTTAATATACTTAAATT
1 TATATTTTAATATA-TTAAATT
**
518377 TATATTTTTTTATATTAAA
1 TATATTTTAATATATTAAA
518396 ATAATATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (21 bp):
TATATTTTAATATATTAAATT
Found at i:519540 original size:31 final size:31
Alignment explanation
Indices: 519505--519563 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
519495 AATAATTCTG
*
519505 TGATTTAAATAAAAACT-TTTAAATAATTAAA
1 TGATTTAAATAAAAA-TATTCAAATAATTAAA
*
519536 TGATTTCAATAAAAATATTCAAATAATT
1 TGATTTAAATAAAAATATTCAAATAATT
519564 TAATAATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 1 0.04
31 24 0.96
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.39
Consensus pattern (31 bp):
TGATTTAAATAAAAATATTCAAATAATTAAA
Found at i:519559 original size:23 final size:22
Alignment explanation
Indices: 519525--519569 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
519515 AAAAACTTTT
*
519525 AAATAATTAAATGATTTCAATAA
1 AAATAATTAAATAATTT-AATAA
519548 AAAT-ATTCAAATAATTTAATAA
1 AAATAATT-AAATAATTTAATAA
519570 TTATTTTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (22 bp):
AAATAATTAAATAATTTAATAA
Found at i:531128 original size:12 final size:14
Alignment explanation
Indices: 531103--531165 Score: 51
Period size: 14 Copynumber: 4.5 Consensus size: 14
531093 GACACAATCA
531103 ATATATTATGAAAT
1 ATATATTATGAAAT
531117 ATATATT-T-AAAT
1 ATATATTATGAAAT
* *
531129 ATAAACTTAT-AAAGA
1 ATATA-TTATGAAA-T
*
531144 ATTATACTATGAAAT
1 A-TATATTATGAAAT
531159 ATATATT
1 ATATATT
531166 TATATATAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
12 8 0.21
13 3 0.08
14 16 0.42
15 5 0.13
16 6 0.16
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (14 bp):
ATATATTATGAAAT
Found at i:531155 original size:42 final size:41
Alignment explanation
Indices: 531104--531188 Score: 127
Period size: 42 Copynumber: 2.0 Consensus size: 41
531094 ACACAATCAA
*
531104 TATATTATGAAATATATATTTAAATATAA-ACTTATAAAGAAT
1 TATACTATGAAATATATATTTAAATATAATA--TATAAAGAAT
*
531146 TATACTATGAAATATATATTTATATATAATATATAAAGAAT
1 TATACTATGAAATATATATTTAAATATAATATATAAAGAAT
531187 TA
1 TA
531189 AAGTTTTCCT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
41 12 0.30
42 27 0.68
43 1 0.03
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.41
Consensus pattern (41 bp):
TATACTATGAAATATATATTTAAATATAATATATAAAGAAT
Found at i:532468 original size:31 final size:31
Alignment explanation
Indices: 532440--532521 Score: 119
Period size: 33 Copynumber: 2.6 Consensus size: 31
532430 CTTAATAGCC
532440 AAGTGACTTAAATAAAAATATTCAAATAGTT
1 AAGTGACTTAAATAAAAATATTCAAATAGTT
**
532471 AAGTGAAGTAAATAAAAAAATATTCAAATAGTT
1 AAGTGACTTAAAT--AAAAATATTCAAATAGTT
*
532504 TAGTGACTTAAATAAAAA
1 AAGTGACTTAAATAAAAA
532522 CTTATGAATA
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
31 16 0.36
33 28 0.64
ACGTcount: A:0.55, C:0.05, G:0.11, T:0.29
Consensus pattern (31 bp):
AAGTGACTTAAATAAAAATATTCAAATAGTT
Found at i:532599 original size:30 final size:30
Alignment explanation
Indices: 532565--532632 Score: 91
Period size: 33 Copynumber: 2.2 Consensus size: 30
532555 TTTGAAGTTG
**
532565 AGTGACCAAATTTAAACTTATTAATAATTT
1 AGTGACCAAAAGTAAACTTATTAATAATTT
532595 AGTGAACACCAAAAGTAAACTTATTAATAATTT
1 AGTG---ACCAAAAGTAAACTTATTAATAATTT
532628 AGTGA
1 AGTGA
532633 ACTTGAGTGT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
30 5 0.15
33 28 0.85
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.34
Consensus pattern (30 bp):
AGTGACCAAAAGTAAACTTATTAATAATTT
Found at i:537559 original size:20 final size:20
Alignment explanation
Indices: 537534--537573 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
537524 TGAGAAATTT
*
537534 AAAGAAGAAATATTTTGAAC
1 AAAGAAGAAACATTTTGAAC
537554 AAAGAAGAAACATTTTGAAC
1 AAAGAAGAAACATTTTGAAC
537574 CCTAGTAGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.55, C:0.07, G:0.15, T:0.23
Consensus pattern (20 bp):
AAAGAAGAAACATTTTGAAC
Found at i:549643 original size:24 final size:27
Alignment explanation
Indices: 549592--549647 Score: 73
Period size: 24 Copynumber: 2.2 Consensus size: 27
549582 ATAAATCTCT
*
549592 TTCATATTTTTTTTAGAAATTCCTAAA
1 TTCATATTTTTTTTAGAAATTCCAAAA
*
549619 TTCAT-TTTTTTTTTG-AA-TCCAAAA
1 TTCATATTTTTTTTAGAAATTCCAAAA
549643 TTCAT
1 TTCAT
549648 GCTTTAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 11 0.41
25 2 0.07
26 9 0.33
27 5 0.19
ACGTcount: A:0.30, C:0.12, G:0.04, T:0.54
Consensus pattern (27 bp):
TTCATATTTTTTTTAGAAATTCCAAAA
Found at i:550279 original size:262 final size:257
Alignment explanation
Indices: 549636--550338 Score: 1034
Period size: 262 Copynumber: 2.7 Consensus size: 257
549626 TTTTTTTGAA
*
549636 TCCAAAATTCATGCTTTAATATAAAAATAATTGTT-AAATTTA-AAATTAATTTAGA-AAAAAAA
1 TCCAAAATTCATGCTTTAATATAAAAATAATT-TTCAAATTTAGGAATTAATTTAGATAAAAAAA
* * * * * * *
549698 TCAAATCTCAATATAAAAATAATTATTAAATTCAGTATCTAAATAGAGAGTCAATCTTTAATTAT
65 TTAAATATCAATATAAAAATAATTATTAAATTCAGTATCCAAATAGTGATTTAATCTTTAATTAA
* * * *
549763 ATAATAATTTTATTACATGATATAGTTAACTTTTTTATATATAGAATTGCAGAATTTTTCTACAA
130 ATAATGATTTTATTACATGATATAATTAACTTTTTTATATATAGAATTGCAGAATTTCTCGACAA
*
549828 ACAAAGCGTCATTCACCACCTATTTCTTAGTTTACTAATAAATTATTCATATTTTTTAAAAAT
195 ACAAAGCGTCACTCACCACCTATTTCTTAGTTTACTAATAAATTATTCATATTTTTTAAAAAT
* * * *
549891 TCCAAAATTCATGCTTTAATGTAAAAATAATTATCAAATTTAGGAATTAATTTAAATAAAAAATT
1 TCCAAAATTCATGCTTTAATATAAAAATAATTTTCAAATTTAGGAATTAATTTAGATAAAAAAAT
* * *
549956 TAAATTTCAATATAAAAATAATTATTAAATTCAGTATCCAAATAGTGATTTAATATTTAATTACA
66 TAAATATCAATATAAAAATAATTATTAAATTCAGTATCCAAATAGTGATTTAATCTTTAATTAAA
** *
550021 TAATGATTTTATTACATGATATTCTTAACTTTTTTATATATAGATTTGCAGAATTTCTCGACAAA
131 TAATGATTTTATTACATGATATAATTAACTTTTTTATATATAGAATTGCAGAATTTCTCGACAAA
** * *
550086 CAAAGCGTCACTCACGGCCTATTTCTTAGTTTACTAATAAATTATCTTTTATATTTTTCTTAGAA
196 CAAAGCGTCACTCACCACCTATTTCTTAGTTTACTAATAAATTA---TTCATA-TTTT-TTAAAA
550151 AT
256 AT
* * * *
550153 TCTAAAATTCATGATTTAATATAAAAATTATTTTCAAATTTAGGGATTAATTTAGATAAAAAAAT
1 TCCAAAATTCATGCTTTAATATAAAAATAATTTTCAAATTTAGGAATTAATTTAGATAAAAAAAT
550218 TAAATATCAATATAAAAATAATTATTAAATTCAGTATCCAAATAGTGATTTAATCTTTAATTAAA
66 TAAATATCAATATAAAAATAATTATTAAATTCAGTATCCAAATAGTGATTTAATCTTTAATTAAA
* *
550283 TAATGATTTTATTACATGATATAATTAACTTTTTTATATATAGAATCGTAGAATTT
131 TAATGATTTTATTACATGATATAATTAACTTTTTTATATATAGAATTGCAGAATTT
550339 TTTAGTTTAC
Statistics
Matches: 400, Mismatches: 40, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
254 1 0.00
255 38 0.09
256 11 0.03
257 164 0.41
260 5 0.01
261 4 0.01
262 177 0.44
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.41
Consensus pattern (257 bp):
TCCAAAATTCATGCTTTAATATAAAAATAATTTTCAAATTTAGGAATTAATTTAGATAAAAAAAT
TAAATATCAATATAAAAATAATTATTAAATTCAGTATCCAAATAGTGATTTAATCTTTAATTAAA
TAATGATTTTATTACATGATATAATTAACTTTTTTATATATAGAATTGCAGAATTTCTCGACAAA
CAAAGCGTCACTCACCACCTATTTCTTAGTTTACTAATAAATTATTCATATTTTTTAAAAAT
Found at i:550513 original size:229 final size:229
Alignment explanation
Indices: 550106--550569 Score: 741
Period size: 229 Copynumber: 2.0 Consensus size: 229
550096 CTCACGGCCT
* * * *
550106 ATTTCTTAGTTTACTAATAAATTATCTTTTATATTTTTCTTAGAAATTCTAAAATTCATGATTTA
1 ATTTCTTAGTTTACTAATAAATTATCCTTCATATTATTCTTAGAAATTCCAAAATTCATGATTTA
* * *
550171 ATATAAAAATTATTTTCAAATTTAGGGATTAATTTAGATAAAAAAATTAAATATCAATATAAAAA
66 ATATAAAAATAATTGTCAAATTTAGGAATTAATTTAGATAAAAAAATTAAATATCAATATAAAAA
*
550236 TAATTATTAAATTCAGTATCCAAATAGTGATTTAATCTTTAATTAAATAATGATTTTATTACATG
131 TAATTATTAAATTCAATATCCAAATAGTGATTTAATCTTTAATTAAATAATGATTTTATTACATG
*
550301 ATATAATTAACTTTTTTATATATAGAATCGTAGA
196 ATATAATTAACTTTTTTATATATAGAATCGCAGA
* * * *
550335 ATTTTTTAGTTTACTAATAAATTCTCCTTCATATTATT-TTAGAAATTCCAAATTTCATGCTTTA
1 ATTTCTTAGTTTACTAATAAATTATCCTTCATATTATTCTTAGAAATTCCAAAATTCATGATTTA
* *
550399 ATATAAAAATAATTGTCAAATTTAGGAATTAATTTAGATTAAAAAATTCAAATCTCAATATAAAA
66 ATATAAAAATAATTGTCAAATTTAGGAATTAATTTAGATAAAAAAATT-AAATATCAATATAAAA
* *
550464 ATAATTATTAAATTCAATATCTAAATAGTGATTTAATCTTTATTTAAATAATGATTTTATTACAT
130 ATAATTATTAAATTCAATATCCAAATAGTGATTTAATCTTTAATTAAATAATGATTTTATTACAT
* *
550529 GATATATTTAACTTTTTTATATATAGAATTGCAGA
195 GATATAATTAACTTTTTTATATATAGAATCGCAGA
550564 ATTTCT
1 ATTTCT
550570 GGACAAACAA
Statistics
Matches: 214, Mismatches: 20, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
228 67 0.31
229 147 0.69
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.44
Consensus pattern (229 bp):
ATTTCTTAGTTTACTAATAAATTATCCTTCATATTATTCTTAGAAATTCCAAAATTCATGATTTA
ATATAAAAATAATTGTCAAATTTAGGAATTAATTTAGATAAAAAAATTAAATATCAATATAAAAA
TAATTATTAAATTCAATATCCAAATAGTGATTTAATCTTTAATTAAATAATGATTTTATTACATG
ATATAATTAACTTTTTTATATATAGAATCGCAGA
Found at i:550517 original size:491 final size:483
Alignment explanation
Indices: 549849--550814 Score: 1439
Period size: 491 Copynumber: 2.0 Consensus size: 483
549839 TTCACCACCT
*
549849 ATTTCTTAGTTTACTAATAAATTATTCATATTTTTTAAAAATTCCAAAATTCATGCTTTAATGTA
1 ATTTCTTAGTTTACTAATAAATTATTCATATTTTTTAAAAATTCCAAAATTCATGCTTTAATATA
* *
549914 AAAATAATTATCAAATTTAGGAATTAATTTAAATAAAAAATTTAAATTTCAATATAAAAATAATT
66 AAAATAATTATCAAATTTAGGAATTAATTTAAATAAAAAATTCAAATCTCAATATAAAAATAATT
* *
549979 ATTAAATTCAGTATCCAAATAGTGATTTAATATTTAATTACATAATGATTTTATTACATGATAT-
131 ATTAAATTCAATATCCAAATAGTGATTTAATATTTAATTAAATAATGATTTTATTACATGATATA
* * * *
550043 TCTTAACTTTTTTATATATAGATTTGCAGAATTTCTCGACAAACAAAGCGTCACTCACGGCCTAT
196 T-TTAACTTTTTTATATATAGAATTGCAGAATTTCTCGACAAACAAAACGTAACTCACAGCCTAT
* * * * * *
550108 TTCTTAGTTTACTAATAAATTATCTTTTATATTTTTCTTAGAAATTCTAAAATTCATGATTTAAT
260 TTCCTAGTTAACTAATAAATTATCCTTCATACTTTT-TTAAAAATTCTAAAATTCATGATTTAAT
* * ** *
550173 ATAAAAATTATTTTCAAATTTAGGGATTAATTTAGATAAAAAAATTAAATATCAATATAAAAATA
324 ATAAAAATAATTGTCAAATTTAAAGATTAATTTAGA-AAAAAAATCAAATATCAATATAAAAATA
* * * * * * *
550238 ATTATTAAATTCAGTATCCAAATAGTGATTTAATCTTTAATTAAATAATGATTTTATTACATGAT
388 ATTATTAAAATCAGTATCCAAATAGTAATTTAATATTTAATTAAATAATAAATATATTACATAAT
550303 ATAATTAACTTTTTTATATATAGAATCGTAGA
453 ATAATTAACTTTTTT-TATATAGAATCGTAGA
* * * *
550335 ATTTTTTAGTTTACTAATAAATTCTCCTTCATATTATTTTAGAAATTCCAAATTTCATGCTTTAA
1 ATTTCTTAGTTTACTAATAAA-T-T-ATTCATATT-TTTTAAAAATTCCAAAATTCATGCTTTAA
* *
550400 TATAAAAATAATTGTCAAATTTAGGAATTAATTTAGATTAAAAAATTCAAATCTCAATATAAAAA
62 TATAAAAATAATTATCAAATTTAGGAATTAATTTA-AATAAAAAATTCAAATCTCAATATAAAAA
* * *
550465 TAATTATTAAATTCAATATCTAAATAGTGATTTAATCTTTATTTAAATAATGATTTTATTACATG
126 TAATTATTAAATTCAATATCCAAATAGTGATTTAATATTTAATTAAATAATGATTTTATTACATG
* *
550530 ATATATTTAACTTTTTTATATATAGAATTGCAGAATTTCTGGACAAACAAAACGTAATTCACAGC
191 ATATATTTAACTTTTTTATATATAGAATTGCAGAATTTCTCGACAAACAAAACGTAACTCACAGC
* * * *
550595 CTATTTCCTAGTTAAGTAATAAATTCTCCTTCATACTTTTTTAAAAATTCTAAATTTCATGCTTT
256 CTATTTCCTAGTTAACTAATAAATTATCCTTCATACTTTTTTAAAAATTCTAAAATTCATGATTT
* *
550660 AATATAAAAATAATTGTCAAATTTAAAGATTGATTTAGAAAAAAAATCAAATCTCAATATAAAAA
321 AATATAAAAATAATTGTCAAATTTAAAGATTAATTTAGAAAAAAAATCAAATATCAATATAAAAA
550725 TAATTATTAAAATCAGTATCCAAATAGTAATTTAATATTTAATTAAATAATAAATATATTACATA
386 TAATTATTAAAATCAGTATCCAAATAGTAATTTAATATTTAATTAAATAATAAATATATTACATA
*
550790 ATATAATTGACTTTTTTTATATAGA
451 ATATAATTAACTTTTTTTATATAGA
550815 GAATATAATT
Statistics
Matches: 429, Mismatches: 45, Indels: 10
0.89 0.09 0.02
Matches are distributed among these distances:
486 20 0.05
487 1 0.00
488 9 0.02
489 106 0.25
490 116 0.27
491 176 0.41
492 1 0.00
ACGTcount: A:0.43, C:0.09, G:0.06, T:0.42
Consensus pattern (483 bp):
ATTTCTTAGTTTACTAATAAATTATTCATATTTTTTAAAAATTCCAAAATTCATGCTTTAATATA
AAAATAATTATCAAATTTAGGAATTAATTTAAATAAAAAATTCAAATCTCAATATAAAAATAATT
ATTAAATTCAATATCCAAATAGTGATTTAATATTTAATTAAATAATGATTTTATTACATGATATA
TTTAACTTTTTTATATATAGAATTGCAGAATTTCTCGACAAACAAAACGTAACTCACAGCCTATT
TCCTAGTTAACTAATAAATTATCCTTCATACTTTTTTAAAAATTCTAAAATTCATGATTTAATAT
AAAAATAATTGTCAAATTTAAAGATTAATTTAGAAAAAAAATCAAATATCAATATAAAAATAATT
ATTAAAATCAGTATCCAAATAGTAATTTAATATTTAATTAAATAATAAATATATTACATAATATA
ATTAACTTTTTTTATATAGAATCGTAGA
Found at i:575030 original size:20 final size:20
Alignment explanation
Indices: 574990--575030 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
574980 ATGCTCTTAA
*
574990 AATATTTTAAAAATATGATT
1 AATATTTTAAAAATATAATT
* *
575010 AATATTTTAACAATTTAATT
1 AATATTTTAAAAATATAATT
575030 A
1 A
575031 TTAAAATTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.46
Consensus pattern (20 bp):
AATATTTTAAAAATATAATT
Found at i:575171 original size:26 final size:29
Alignment explanation
Indices: 575108--575163 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
575098 TTGTAAAGAT
* *
575108 TAAATTAAAT-TAATTCTTCTATTATTATA
1 TAAATT-AATCTAATTCTTATACTATTATA
575137 TAAATTAATCTAATTCTTATACTATTA
1 TAAATTAATCTAATTCTTATACTATTA
575164 AAAATAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 3 0.12
29 21 0.88
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (29 bp):
TAAATTAATCTAATTCTTATACTATTATA
Found at i:575522 original size:21 final size:22
Alignment explanation
Indices: 575498--575541 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
575488 TTAATATTGT
575498 ATTAATAAA-TAAA-ATAAAATA
1 ATTAATAAATTAAACA-AAAATA
575519 ATTAATAAATTAAACAAAAATA
1 ATTAATAAATTAAACAAAAATA
575541 A
1 A
575542 AAGAATAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 9 0.43
22 11 0.52
23 1 0.05
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.27
Consensus pattern (22 bp):
ATTAATAAATTAAACAAAAATA
Found at i:579551 original size:24 final size:24
Alignment explanation
Indices: 579502--579552 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
579492 ATTGATGTAC
* * *
579502 ATAAATTAAATTTTAATAGTAGAA
1 ATAAATAAAATTTTAACAGTAAAA
579526 ATAAATAAAATTATTAACAG-AAAA
1 ATAAATAAAATT-TTAACAGTAAAA
579550 ATA
1 ATA
579553 GATTTACTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.61, C:0.02, G:0.06, T:0.31
Consensus pattern (24 bp):
ATAAATAAAATTTTAACAGTAAAA
Found at i:579571 original size:5 final size:5
Alignment explanation
Indices: 579561--579592 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
579551 TAGATTTACT
579561 ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA AT
1 ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA AT
579593 GTATAAGGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
ATTTA
Found at i:590520 original size:13 final size:13
Alignment explanation
Indices: 590504--590528 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
590494 AGGTACATGA
590504 ACAAAAAAAAAAG
1 ACAAAAAAAAAAG
590517 ACAAAAAAAAAA
1 ACAAAAAAAAAA
590529 CATAAAATAC
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:0.88, C:0.08, G:0.04, T:0.00
Consensus pattern (13 bp):
ACAAAAAAAAAAG
Found at i:605990 original size:42 final size:43
Alignment explanation
Indices: 605914--606000 Score: 108
Period size: 44 Copynumber: 2.0 Consensus size: 43
605904 ATTTGATGTT
*
605914 GTTTAATTTAGAGTTTTTTTTAAGAAGAGAAAATTGAT-TTTGA
1 GTTTAATTTAGAGTTTTTTGTAAGAAGAGAAAATT-ATATTTGA
* *
605957 GTTTAGTTTATGAGTTTTTTGTAAGAA-CG-AAATTATATTTGA
1 GTTTAATTTA-GAGTTTTTTGTAAGAAGAGAAAATTATATTTGA
605999 GT
1 GT
606001 AAGATAAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
41 2 0.05
42 12 0.31
43 10 0.26
44 15 0.38
ACGTcount: A:0.32, C:0.01, G:0.20, T:0.47
Consensus pattern (43 bp):
GTTTAATTTAGAGTTTTTTGTAAGAAGAGAAAATTATATTTGA
Found at i:608948 original size:42 final size:41
Alignment explanation
Indices: 608858--608992 Score: 112
Period size: 43 Copynumber: 3.2 Consensus size: 41
608848 CCAAATGCTT
* * ***
608858 TTAAACTCAAATATAATTTCATTCTTAAAAAAATATTCATAAA
1 TTAAACCCAAATATAATTTTATTCTTAAAAAAACCCTC--AAA
*
608901 CTAAACCCAAATATAATTTTATTCTTAAAAAACACCCTCAAA
1 TTAAACCCAAATATAATTTTATTCTTAAAAAA-ACCCTCAAA
* * * *
608943 TTAAACTCAAA-ATCAATTTTTTTATCCTAAAGAAACCCT-AAA
1 TTAAACCCAAATAT-AA-TTTTAT-TCTTAAAAAAACCCTCAAA
608985 TTAAACCC
1 TTAAACCC
608993 CCCTTTACCT
Statistics
Matches: 76, Mismatches: 12, Indels: 9
0.78 0.12 0.09
Matches are distributed among these distances:
41 2 0.03
42 24 0.32
43 39 0.51
44 11 0.14
ACGTcount: A:0.47, C:0.19, G:0.01, T:0.33
Consensus pattern (41 bp):
TTAAACCCAAATATAATTTTATTCTTAAAAAAACCCTCAAA
Found at i:614979 original size:22 final size:22
Alignment explanation
Indices: 614937--614979 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
614927 TATCTTAACT
*
614937 ATTTTAATTTATCAATAATTAC
1 ATTTTAATTAATCAATAATTAC
*
614959 ATTTTAAATTAAT-AATTATTA
1 ATTTT-AATTAATCAATAATTA
614980 AATTATCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (22 bp):
ATTTTAATTAATCAATAATTAC
Found at i:616897 original size:26 final size:26
Alignment explanation
Indices: 616868--616923 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
616858 TAGAATTTTT
616868 TTTTATTT-GCAATTTATTTTTGTGTG
1 TTTTATTTGGCAA-TTATTTTTGTGTG
* *
616894 TTTTTTTTGGTAATTATTTTTGTGTG
1 TTTTATTTGGCAATTATTTTTGTGTG
616920 TTTT
1 TTTT
616924 TTAATTCCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
26 24 0.89
27 3 0.11
ACGTcount: A:0.12, C:0.02, G:0.16, T:0.70
Consensus pattern (26 bp):
TTTTATTTGGCAATTATTTTTGTGTG
Found at i:616900 original size:13 final size:13
Alignment explanation
Indices: 616884--616925 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
616874 TTGCAATTTA
616884 TTTTTGTGTGTTT
1 TTTTTGTGTGTTT
* *
616897 TTTTTG-GTAATTA
1 TTTTTGTGT-GTTT
616910 TTTTTGTGTGTTT
1 TTTTTGTGTGTTT
616923 TTT
1 TTT
616926 AATTCCTAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
12 2 0.09
13 19 0.83
14 2 0.09
ACGTcount: A:0.07, C:0.00, G:0.19, T:0.74
Consensus pattern (13 bp):
TTTTTGTGTGTTT
Found at i:616935 original size:28 final size:26
Alignment explanation
Indices: 616881--616939 Score: 82
Period size: 26 Copynumber: 2.2 Consensus size: 26
616871 TATTTGCAAT
**
616881 TTATTTTTGTGTGTTTTTTTTGGTAA
1 TTATTTTTGTGTGTTTTTTTTCCTAA
616907 TTATTTTTGTGTGTTTTTTAATTCCTAA
1 TTATTTTTGTGTGTTTTTT--TTCCTAA
616935 TTATT
1 TTATT
616940 GTTTTATCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 19 0.66
28 10 0.34
ACGTcount: A:0.15, C:0.03, G:0.14, T:0.68
Consensus pattern (26 bp):
TTATTTTTGTGTGTTTTTTTTCCTAA
Found at i:617181 original size:15 final size:15
Alignment explanation
Indices: 617161--617198 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
617151 GACTAAATAA
*
617161 TTAATAAATTTATTT
1 TTAATAAATTTAATT
617176 TTAAT-AATTTAATT
1 TTAATAAATTTAATT
617190 TTAA-AAATT
1 TTAATAAATT
617199 ATAAAATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 16 0.76
15 5 0.24
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TTAATAAATTTAATT
Found at i:632585 original size:3 final size:3
Alignment explanation
Indices: 632577--632617 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
632567 TAATGATTTG
*
632577 TTA TTA TTA CTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
632618 CTCAGGGCTA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:634896 original size:20 final size:21
Alignment explanation
Indices: 634858--634897 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
634848 CAGAACTTTC
**
634858 TTTTCTTTTCTTTTTTTGTCT
1 TTTTCTTTTCTTTCCTTGTCT
634879 TTTTCTTTT-TTTCCTTGTC
1 TTTTCTTTTCTTTCCTTGTC
634898 GTGGAATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.00, C:0.17, G:0.05, T:0.78
Consensus pattern (21 bp):
TTTTCTTTTCTTTCCTTGTCT
Found at i:637381 original size:28 final size:29
Alignment explanation
Indices: 637319--637374 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
637309 ATTATTATAT
*
637319 TAATT-ATTTATATATTTATAATTTTAAA
1 TAATTAATTTAAATATTTATAATTTTAAA
*
637347 TAATTAATTTAAATTTTTAT-ATTTTAAA
1 TAATTAATTTAAATATTTATAATTTTAAA
637375 ATATTAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 13 0.52
29 12 0.48
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (29 bp):
TAATTAATTTAAATATTTATAATTTTAAA
Found at i:639866 original size:17 final size:17
Alignment explanation
Indices: 639844--639877 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
639834 ACAAAATTAA
639844 ACCATAGAAAAGGGAAT
1 ACCATAGAAAAGGGAAT
639861 ACCATAGAAAAGGGAAT
1 ACCATAGAAAAGGGAAT
639878 GAGGTGGTGT
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:0.53, C:0.12, G:0.24, T:0.12
Consensus pattern (17 bp):
ACCATAGAAAAGGGAAT
Found at i:652489 original size:3 final size:3
Alignment explanation
Indices: 652481--652511 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
652471 CTTTCTTTGT
652481 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
652512 CGAGGTTCTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:665831 original size:16 final size:17
Alignment explanation
Indices: 665812--665854 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
665802 ATATTTATTT
*
665812 CATATA-ATATAAATGA
1 CATATATATATAAAGGA
665828 CATA-ATATATAAAGGA
1 CATATATATATAAAGGA
665844 -ATATATATATA
1 CATATATATATA
665855 TATATATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 4 0.17
16 20 0.83
ACGTcount: A:0.56, C:0.05, G:0.07, T:0.33
Consensus pattern (17 bp):
CATATATATATAAAGGA
Found at i:667324 original size:13 final size:13
Alignment explanation
Indices: 667306--667330 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
667296 AATTAGACTT
667306 TTATTATTATTTA
1 TTATTATTATTTA
667319 TTATTATTATTT
1 TTATTATTATTT
667331 TGATCTATTA
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:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TTATTATTATTTA
Found at i:671527 original size:29 final size:29
Alignment explanation
Indices: 671476--671531 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
671466 CTCTATACCT
*
671476 GATCAAATTAGTCCCTCTACTATTAAATG
1 GATCAAATTAGTCCCTCGACTATTAAATG
* * *
671505 GATCAATTTAGTCCCTGGGCTATTAAA
1 GATCAAATTAGTCCCTCGACTATTAAA
671532 AAGAATCCGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Consensus pattern (29 bp):
GATCAAATTAGTCCCTCGACTATTAAATG
Found at i:681120 original size:41 final size:41
Alignment explanation
Indices: 681075--681157 Score: 105
Period size: 41 Copynumber: 2.0 Consensus size: 41
681065 TCCAAATCCA
*
681075 TCATTATCCTTCTTC-AACAATCCCTAAATTAAACCCTAAAT
1 TCATTATCCTTCTTCGAA-AAACCCTAAATTAAACCCTAAAT
* * * *
681116 TCATTTTTCTTCTTCGAAAAACCTTAAATTAAACCCTCAAT
1 TCATTATCCTTCTTCGAAAAACCCTAAATTAAACCCTAAAT
681157 T
1 T
681158 ATTCGTCAGC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
41 34 0.94
42 2 0.06
ACGTcount: A:0.35, C:0.27, G:0.01, T:0.37
Consensus pattern (41 bp):
TCATTATCCTTCTTCGAAAAACCCTAAATTAAACCCTAAAT
Found at i:688043 original size:2 final size:2
Alignment explanation
Indices: 688038--688063 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
688028 ACCTTATTTG
688038 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
688064 GTAAGGCTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:693991 original size:12 final size:12
Alignment explanation
Indices: 693976--694009 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
693966 ATAAAAGCCT
693976 GAAAAAAAAAAG
1 GAAAAAAAAAAG
*
693988 GAAAAAAAAAAT
1 GAAAAAAAAAAG
694000 GAAAGAAAAA
1 GAAA-AAAAA
694010 TGGTAGCCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 15 0.75
13 5 0.25
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (12 bp):
GAAAAAAAAAAG
Found at i:711922 original size:10 final size:10
Alignment explanation
Indices: 711892--711930 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
711882 ATGGTAATGT
*
711892 TTTTTTTCTTG
1 TTTTTTT-TTC
711903 TTTCTTTTTTC
1 TTT-TTTTTTC
711914 TTTTTTTTTC
1 TTTTTTTTTC
711924 TTTTTTT
1 TTTTTTT
711931 GCAGACTTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 14 0.54
11 8 0.31
12 4 0.15
ACGTcount: A:0.00, C:0.10, G:0.03, T:0.87
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:719795 original size:221 final size:221
Alignment explanation
Indices: 719412--720075 Score: 1274
Period size: 221 Copynumber: 3.0 Consensus size: 221
719402 TTTGGACAGG
719412 ATAGAGGATTAACTTCAAAAATTCACCATAAATTGTATATAATGAGTTAAGGGTCGAATTATATA
1 ATAGAGGATTAACTTCAAAAATTCACCATAAATTGTATATAATGAGTTAAGGGTCGAATTATATA
* * *
719477 TGTAATTAAATCTTATTGAGTGTAGTTTCATATGGAAGAAACAGTGATGGAAATGGATCTGTATA
66 TTTAATTAAATCTTATTGAGTTTAGTTTCATATGGAAGAAACGGTGATGGAAATGGATCTGTATA
719542 TTCTGAGATATAACTGATTTTGTGTAACAAGGTCAGAGTAGATTTGAGTTCCCTTGTTCTGACTT
131 TTCTGAGATATAACTGATTTTGTGTAACAAGGTCAGAGTAGATTTGAGTTCCCTTGTTCTGACTT
719607 TGAAAAATCATAGAAAAATGTATAAA
196 TGAAAAATCATAGAAAAATGTATAAA
719633 ATAGAGGATTAACTTCAAAAATTCACCATAAATTGTATATAATGAGTTAAGGGTCGAATTATATA
1 ATAGAGGATTAACTTCAAAAATTCACCATAAATTGTATATAATGAGTTAAGGGTCGAATTATATA
719698 TTTAATTAAATCTTATTGAGTTTAGTTTCATATGGAAGAAACGGTGATGGAAATGGATCTGTATA
66 TTTAATTAAATCTTATTGAGTTTAGTTTCATATGGAAGAAACGGTGATGGAAATGGATCTGTATA
*
719763 CTCTGAGATATAACTGATTTTGTGTAACAAGGTCAGAGTAGATTTGAGTTCCCTTGTTCTGACTT
131 TTCTGAGATATAACTGATTTTGTGTAACAAGGTCAGAGTAGATTTGAGTTCCCTTGTTCTGACTT
719828 TGAAAAATCATAGAAAAATGTATAAA
196 TGAAAAATCATAGAAAAATGTATAAA
*
719854 ATAGAGGATTAGCTTCAAAAATTCACCATAAATTGTATATAATGAGTTAAGGGTCGAATTATATA
1 ATAGAGGATTAACTTCAAAAATTCACCATAAATTGTATATAATGAGTTAAGGGTCGAATTATATA
719919 TTTAATTAAATCTTATTGAGTTTAGTTTCATATGGAAGAAACGGTGATGGAAATGGATCTGTATA
66 TTTAATTAAATCTTATTGAGTTTAGTTTCATATGGAAGAAACGGTGATGGAAATGGATCTGTATA
*
719984 TTCTGAGATATAACTGATTTTGTATAACAAGGTCAGAGTAGATTTGAGTTCCCTTGTTCTGACTT
131 TTCTGAGATATAACTGATTTTGTGTAACAAGGTCAGAGTAGATTTGAGTTCCCTTGTTCTGACTT
720049 TGAAAAATCATAGAAAAATGTATAAA
196 TGAAAAATCATAGAAAAATGTATAAA
720075 A
1 A
720076 ATTATTAGAG
Statistics
Matches: 436, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
221 436 1.00
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.35
Consensus pattern (221 bp):
ATAGAGGATTAACTTCAAAAATTCACCATAAATTGTATATAATGAGTTAAGGGTCGAATTATATA
TTTAATTAAATCTTATTGAGTTTAGTTTCATATGGAAGAAACGGTGATGGAAATGGATCTGTATA
TTCTGAGATATAACTGATTTTGTGTAACAAGGTCAGAGTAGATTTGAGTTCCCTTGTTCTGACTT
TGAAAAATCATAGAAAAATGTATAAA
Found at i:720594 original size:23 final size:22
Alignment explanation
Indices: 720566--720679 Score: 102
Period size: 25 Copynumber: 4.8 Consensus size: 22
720556 ACACTGGCAC
720566 GCTCTCTGTTTAGCACTGTGTGT
1 GCTCTCTGTTTAGCACT-TGTGT
*
720589 ACTCTCTGTTATTAGCACTTCGTGT
1 GCTCTCTG-T-TTAGCACTT-GTGT
* *
720614 GCTCTCTGATTAGCACTTTATGT
1 GCTCTCTGTTTAGCAC-TTGTGT
* *
720637 GCTCTCTGTTACTCAGTACTTATGT
1 GCTCTCTGTT--T-AGCACTTGTGT
*
720662 GCTCTCTGTTTAGTACTT
1 GCTCTCTGTTTAGCACTT
720680 CGGTACTCTC
Statistics
Matches: 78, Mismatches: 6, Indels: 15
0.79 0.06 0.15
Matches are distributed among these distances:
22 7 0.09
23 27 0.35
24 4 0.05
25 36 0.46
26 4 0.05
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (22 bp):
GCTCTCTGTTTAGCACTTGTGT
Found at i:720642 original size:48 final size:48
Alignment explanation
Indices: 720566--720679 Score: 140
Period size: 48 Copynumber: 2.4 Consensus size: 48
720556 ACACTGGCAC
* * * *
720566 GCTCTCTGTTTAGCACTGTGTGTACTCTCTGTTA-TTAGCACTTCGTGT
1 GCTCTCTGTTTAGCACTTTATGTACTCTCTGTTACTCAGCACTT-ATGT
* * *
720614 GCTCTCTGATTAGCACTTTATGTGCTCTCTGTTACTCAGTACTTATGT
1 GCTCTCTGTTTAGCACTTTATGTACTCTCTGTTACTCAGCACTTATGT
*
720662 GCTCTCTGTTTAGTACTT
1 GCTCTCTGTTTAGCACTT
720680 CGGTACTCTC
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
48 49 0.88
49 7 0.12
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (48 bp):
GCTCTCTGTTTAGCACTTTATGTACTCTCTGTTACTCAGCACTTATGT
Found at i:731434 original size:65 final size:65
Alignment explanation
Indices: 731294--731425 Score: 219
Period size: 65 Copynumber: 2.0 Consensus size: 65
731284 TTTAAATTAG
* * *
731294 TCCTTATATTTCAAAATATTTTAATTGAATGCTCACAAGTTCAGTTATCGTATCAATTAAGTCTT
1 TCCTTATATTTCAAAACATTTTAATTGAACGCTCACAAGTTCAATTATCGTATCAATTAAGTCTT
* *
731359 TCCTTATATTTCAAAACATTTTAATTGAACGCTCACGAGTTCAATTATCTTATCAATTAAGTCTT
1 TCCTTATATTTCAAAACATTTTAATTGAACGCTCACAAGTTCAATTATCGTATCAATTAAGTCTT
731424 TC
1 TC
731426 TGTCTATTTA
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
65 62 1.00
ACGTcount: A:0.32, C:0.17, G:0.08, T:0.42
Consensus pattern (65 bp):
TCCTTATATTTCAAAACATTTTAATTGAACGCTCACAAGTTCAATTATCGTATCAATTAAGTCTT
Found at i:738806 original size:18 final size:18
Alignment explanation
Indices: 738783--738818 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
738773 CTATTTTTTT
*
738783 AATAATATCATCTTTAAA
1 AATAATATCATCTCTAAA
738801 AATAATATCATCTCTAAA
1 AATAATATCATCTCTAAA
738819 GTTTAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (18 bp):
AATAATATCATCTCTAAA
Found at i:742561 original size:2 final size:2
Alignment explanation
Indices: 742554--742603 Score: 82
Period size: 2 Copynumber: 25.0 Consensus size: 2
742544 AAATTAATAC
* *
742554 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
742596 AT AT AT AT
1 AT AT AT AT
742604 GTATGAAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:743066 original size:25 final size:25
Alignment explanation
Indices: 743019--743066 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
743009 GTTGATATGG
* **
743019 TTTACAATTTTTTTTATTTTTTAGT
1 TTTACAATTTTTTTAATAATTTAGT
*
743044 TTTATAATTTTTTTAATAATTTA
1 TTTACAATTTTTTTAATAATTTA
743067 TTTAATTGAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (25 bp):
TTTACAATTTTTTTAATAATTTAGT
Found at i:749388 original size:39 final size:39
Alignment explanation
Indices: 749163--749374 Score: 257
Period size: 39 Copynumber: 5.4 Consensus size: 39
749153 AATAGCATCA
* * * **
749163 CAGTGTTTACAGTATCACTGCCAGTTCAATATAGCTA-CA
1 CAGTGTTTACAGTGTCACTGCCAGTTCAGTATTG-TATTG
* * * *
749202 CTA-TGTTTACAGTGTCACCGTCAATTCAGTGTTGTATTG
1 C-AGTGTTTACAGTGTCACTGCCAGTTCAGTATTGTATTG
749241 CAGTGTTTACAGTGTCACTGCCAGTTCAGTATTGTATTG
1 CAGTGTTTACAGTGTCACTGCCAGTTCAGTATTGTATTG
* *
749280 CGGTGTTTATAGTGTCACTGCCAGTTCAGTATTGTATTG
1 CAGTGTTTACAGTGTCACTGCCAGTTCAGTATTGTATTG
* *
749319 CAGTGTTCACAGTGTCACTGCTAGTTCAGTATTGTATTG
1 CAGTGTTTACAGTGTCACTGCCAGTTCAGTATTGTATTG
* *
749358 CAATGTTTACATTGTCA
1 CAGTGTTTACAGTGTCA
749375 TTATCAATTC
Statistics
Matches: 148, Mismatches: 22, Indels: 6
0.84 0.12 0.03
Matches are distributed among these distances:
38 3 0.02
39 144 0.97
40 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.21, T:0.38
Consensus pattern (39 bp):
CAGTGTTTACAGTGTCACTGCCAGTTCAGTATTGTATTG
Found at i:749660 original size:72 final size:72
Alignment explanation
Indices: 749478--749676 Score: 238
Period size: 72 Copynumber: 2.7 Consensus size: 72
749468 CCGTGTGTGT
* * * *
749478 CACACGGTCTGACACACGCTCGTGTGTCCAAGCCGTGTAACTCACTATTTTTGTTTGCACAAAAC
1 CACACGGTCTGGCACACGCTCGTGTGTCC-AGCTGTGTAACTCACTATTTTTGATTCCACAAAAC
* * * *
749543 GGTATGGG
65 AGAATAGC
* * * *
749551 CACACGATCTAGCACACGCCCGTGTGTCCAGCTTGTGTAACTCACTGTTTTTGATTCCAC-AAAC
1 CACACGGTCTGGCACACGCTCGTGTGTCCAGC-TGTGTAACTCACTATTTTTGATTCCACAAAAC
*
749615 AGAATATC
65 AGAATAGC
*
749623 CACATGGTCTGGCACACGCTCGTGTGTCCAGGCTGTGTAACTCACTATTTTTGA
1 CACACGGTCTGGCACACGCTCGTGTGTCCA-GCTGTGTAACTCACTATTTTTGA
749677 ACTTTCAAAA
Statistics
Matches: 106, Mismatches: 18, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
72 56 0.53
73 50 0.47
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.29
Consensus pattern (72 bp):
CACACGGTCTGGCACACGCTCGTGTGTCCAGCTGTGTAACTCACTATTTTTGATTCCACAAAACA
GAATAGC
Found at i:762982 original size:29 final size:30
Alignment explanation
Indices: 762937--762996 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 30
762927 TTCAAATTTT
762937 AATTTAACTTATGTATTTTT-AATTTTAAA
1 AATTTAACTTATGTATTTTTAAATTTTAAA
*
762966 AATTTAATCTT-TTTATTTTTCAAATTTTAAA
1 AATTTAA-CTTATGTATTTTT-AAATTTTAAA
762997 GTTTAAATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
29 15 0.56
30 3 0.11
31 9 0.33
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.57
Consensus pattern (30 bp):
AATTTAACTTATGTATTTTTAAATTTTAAA
Found at i:762985 original size:23 final size:23
Alignment explanation
Indices: 762952--762995 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
762942 AACTTATGTA
762952 TTTTTAATTTTAAAAATTTAATC
1 TTTTTAATTTTAAAAATTTAATC
* * *
762975 TTTTTATTTTTCAAATTTTAA
1 TTTTTAATTTTAAAAATTTAA
762996 AGTTTAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (23 bp):
TTTTTAATTTTAAAAATTTAATC
Found at i:763047 original size:18 final size:17
Alignment explanation
Indices: 763007--763040 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
762997 GTTTAAATTT
763007 AACTAATTAATTTCAAC
1 AACTAATTAATTTCAAC
763024 AACTAATTCAA-TTCAAC
1 AACTAATT-AATTTCAAC
763041 CAGCTAACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.88
18 2 0.12
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.32
Consensus pattern (17 bp):
AACTAATTAATTTCAAC
Found at i:763806 original size:13 final size:14
Alignment explanation
Indices: 763778--763811 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
763768 CATTTTAATC
763778 ATATTTATATTTTA
1 ATATTTATATTTTA
*
763792 ATATTTTTA-TTTA
1 ATATTTATATTTTA
763805 ATATTTA
1 ATATTTA
763812 ACTGTTATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
ATATTTATATTTTA
Found at i:764759 original size:4 final size:4
Alignment explanation
Indices: 764750--764780 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
764740 GCTAGAGCTT
764750 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
764781 TTTTGTTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTC
Found at i:767897 original size:16 final size:16
Alignment explanation
Indices: 767873--767903 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
767863 TATTTTAATA
767873 TTTTATTTAATTTTTC
1 TTTTATTTAATTTTTC
*
767889 TTTTTTTTAATTTTT
1 TTTTATTTAATTTTT
767904 AATTTGCATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTTATTTAATTTTTC
Found at i:774557 original size:1 final size:1
Alignment explanation
Indices: 774551--774577 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
774541 CTAGCAGCGG
774551 CCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCC
774578 AAAAAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:778325 original size:26 final size:26
Alignment explanation
Indices: 778278--778327 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
778268 TTTAAGAATA
* *
778278 TCTTATTTAATATTTAAAAAAAAATC
1 TCTTATTTAAAAATTAAAAAAAAATC
* *
778304 TCTTATTTAAAAATTGAGAAAAAA
1 TCTTATTTAAAAATTAAAAAAAAA
778328 CTATATTAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.52, C:0.06, G:0.04, T:0.38
Consensus pattern (26 bp):
TCTTATTTAAAAATTAAAAAAAAATC
Found at i:789799 original size:19 final size:19
Alignment explanation
Indices: 789775--789811 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
789765 GAGTAATGTA
789775 GTTCGAGATTATGTTATTG
1 GTTCGAGATTATGTTATTG
* *
789794 GTTCGAGTTTTTGTTATT
1 GTTCGAGATTATGTTATT
789812 CATGCATGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.16, C:0.05, G:0.24, T:0.54
Consensus pattern (19 bp):
GTTCGAGATTATGTTATTG
Found at i:794062 original size:33 final size:33
Alignment explanation
Indices: 794020--794095 Score: 116
Period size: 33 Copynumber: 2.3 Consensus size: 33
794010 TTTGATGACT
794020 ATGAAGATGATAGCGAATTCGTTGACGACCACG
1 ATGAAGATGATAGCGAATTCGTTGACGACCACG
* * **
794053 ATGAAGATGATAGCGAATTTGTTGATGATGACG
1 ATGAAGATGATAGCGAATTCGTTGACGACCACG
794086 ATGAAGATGA
1 ATGAAGATGA
794096 GGCTGACAAC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.36, C:0.11, G:0.29, T:0.25
Consensus pattern (33 bp):
ATGAAGATGATAGCGAATTCGTTGACGACCACG
Found at i:806999 original size:22 final size:23
Alignment explanation
Indices: 806954--806999 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
806944 ATAATAAATT
*
806954 ATTTTTAAAAATTTAATATATTC
1 ATTTTTAAAAATTTAAAATATTC
806977 ATTTTT-AAAATTTCAAAAT-TTC
1 ATTTTTAAAAATTT-AAAATATTC
806999 A
1 A
807000 CTATAACCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (23 bp):
ATTTTTAAAAATTTAAAATATTC
Found at i:810785 original size:23 final size:24
Alignment explanation
Indices: 810742--810787 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
810732 TCTTTCTCTT
810742 ATATTTTATTATATTAAATAATAAA
1 ATATTTTATTATATT-AATAATAAA
810767 ATATTATTATT-TATT-ATAATA
1 ATATT-TTATTATATTAATAATA
810788 TTGTTTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 6 0.30
25 9 0.45
26 5 0.25
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
ATATTTTATTATATTAATAATAAA
Found at i:812163 original size:19 final size:21
Alignment explanation
Indices: 812130--812181 Score: 65
Period size: 19 Copynumber: 2.6 Consensus size: 21
812120 TTAAAATGTC
*
812130 ATATCAATAAATTTAATAA-AA
1 ATAT-AATAATTTTAATAATAA
812151 AT-TAATAATTTTAATAATAA
1 ATATAATAATTTTAATAATAA
812171 ATATAA-AATTT
1 ATATAATAATTT
812182 GAAATATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 13 0.46
20 10 0.36
21 5 0.18
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (21 bp):
ATATAATAATTTTAATAATAA
Found at i:812198 original size:31 final size:30
Alignment explanation
Indices: 812163--812231 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 30
812153 TAATAATTTT
*
812163 AATAATAAATATAAAAT-TTGAAATATAAAAA
1 AATAAAAAAT-TAAAATCTTGAAA-ATAAAAA
*
812194 AATAAAAAATTAAATTCTTGAAAAT-AAAA
1 AATAAAAAATTAAAATCTTGAAAATAAAAA
812223 AATAAAAAA
1 AATAAAAAA
812232 ATTTCAATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 13 0.37
30 7 0.20
31 15 0.43
ACGTcount: A:0.70, C:0.01, G:0.03, T:0.26
Consensus pattern (30 bp):
AATAAAAAATTAAAATCTTGAAAATAAAAA
Found at i:812779 original size:68 final size:68
Alignment explanation
Indices: 812701--812835 Score: 218
Period size: 68 Copynumber: 2.0 Consensus size: 68
812691 TACAAATCTA
* *
812701 TCTCAAAGCTTGAATATTTGAAA-CTCATTAACCCAAAGATTCAATATCTTTAATTCCAATATCT
1 TCTCAAAGCTTGAATATTT-AAAGCTCATTAACCCAAAAATTCAATATCTTTAATTCCAATATAT
812765 TTTG
65 TTTG
* *
812769 TCTCAAAGCTTGAATCTTTAAAGCTCATTAACCCAAAAATTCAATATCTTTGATTCCAATATATT
1 TCTCAAAGCTTGAATATTTAAAGCTCATTAACCCAAAAATTCAATATCTTTAATTCCAATATATT
812834 TT
66 TT
812836 TCCCGTTAAG
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
67 3 0.05
68 59 0.95
ACGTcount: A:0.36, C:0.19, G:0.07, T:0.39
Consensus pattern (68 bp):
TCTCAAAGCTTGAATATTTAAAGCTCATTAACCCAAAAATTCAATATCTTTAATTCCAATATATT
TTG
Found at i:813213 original size:29 final size:29
Alignment explanation
Indices: 813152--813213 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
813142 AAATACTAAT
* * *
813152 ATAAGTTATTAAAACGTAATATTACAAAC
1 ATAAGTAACTAAAACGTAATATTACAAAA
*
813181 ATAAGTAACTAAAATGTAATATTA-AACAA
1 ATAAGTAACTAAAACGTAATATTACAA-AA
813210 ATAA
1 ATAA
813214 AAATGATTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 2 0.07
29 26 0.93
ACGTcount: A:0.56, C:0.08, G:0.06, T:0.29
Consensus pattern (29 bp):
ATAAGTAACTAAAACGTAATATTACAAAA
Found at i:815210 original size:24 final size:23
Alignment explanation
Indices: 815179--815229 Score: 75
Period size: 24 Copynumber: 2.2 Consensus size: 23
815169 ACATCTAAAC
*
815179 AAAAAATAACCAAAACAACAACA
1 AAAAAATAACAAAAACAACAACA
*
815202 AAAAGAATAGCAAAAACAACAACA
1 AAAA-AATAACAAAAACAACAACA
815226 AAAA
1 AAAA
815230 TAGCAGCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 4 0.16
24 21 0.84
ACGTcount: A:0.75, C:0.18, G:0.04, T:0.04
Consensus pattern (23 bp):
AAAAAATAACAAAAACAACAACA
Found at i:815227 original size:12 final size:12
Alignment explanation
Indices: 815190--815229 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
815180 AAAAATAACC
815190 AAAACAACAACA
1 AAAACAACAACA
* * *
815202 AAAAGAATAGCA
1 AAAACAACAACA
815214 AAAACAACAACA
1 AAAACAACAACA
815226 AAAA
1 AAAA
815230 TAGCAGCAAA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.75, C:0.17, G:0.05, T:0.03
Consensus pattern (12 bp):
AAAACAACAACA
Found at i:815237 original size:24 final size:24
Alignment explanation
Indices: 815190--815246 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
815180 AAAAATAACC
*
815190 AAAACAACAACAAAAAGAATAGCA
1 AAAACAACAACAAAAAGAACAGCA
* *
815214 AAAACAACAACAAAAATAGCAGCA
1 AAAACAACAACAAAAAGAACAGCA
*
815238 AAAGCAACA
1 AAAACAACA
815247 CTAAAACAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.68, C:0.19, G:0.09, T:0.04
Consensus pattern (24 bp):
AAAACAACAACAAAAAGAACAGCA
Found at i:815239 original size:12 final size:12
Alignment explanation
Indices: 815190--815246 Score: 51
Period size: 12 Copynumber: 4.8 Consensus size: 12
815180 AAAAATAACC
*
815190 AAAACAACAACA
1 AAAACAACAGCA
* *
815202 AAAAGAATAGCA
1 AAAACAACAGCA
*
815214 AAAACAACAACA
1 AAAACAACAGCA
* *
815226 AAAATAGCAGCA
1 AAAACAACAGCA
*
815238 AAAGCAACA
1 AAAACAACA
815247 CTAAAACAGT
Statistics
Matches: 33, Mismatches: 12, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.68, C:0.19, G:0.09, T:0.04
Consensus pattern (12 bp):
AAAACAACAGCA
Found at i:816173 original size:31 final size:31
Alignment explanation
Indices: 816138--816206 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 31
816128 AACTTTTAGG
* * * *
816138 TTAATATATGATTTGATATTTGAGTTTAGTT
1 TTAATATATAATTTAATATTTAAGTTTAGCT
* *
816169 TTAATTTTTAATTTAATATTTAAGTTTAGCT
1 TTAATATATAATTTAATATTTAAGTTTAGCT
*
816200 TCAATAT
1 TTAATAT
816207 TCAATTTGAT
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.32, C:0.03, G:0.10, T:0.55
Consensus pattern (31 bp):
TTAATATATAATTTAATATTTAAGTTTAGCT
Found at i:816213 original size:31 final size:31
Alignment explanation
Indices: 816148--816218 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
816138 TTAATATATG
* * * * *
816148 ATTTGATATTTGAGTTTAGTTTTAATTTTTA
1 ATTTGATATTTAAGTTTAGCTTCAATATTCA
*
816179 ATTTAATATTTAAGTTTAGCTTCAATATTCA
1 ATTTGATATTTAAGTTTAGCTTCAATATTCA
816210 ATTTGATAT
1 ATTTGATAT
816219 CCATATTAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.31, C:0.04, G:0.10, T:0.55
Consensus pattern (31 bp):
ATTTGATATTTAAGTTTAGCTTCAATATTCA
Found at i:821169 original size:3 final size:3
Alignment explanation
Indices: 821161--821187 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
821151 GATATTATCG
821161 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
821188 GAAGGGAAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:835571 original size:30 final size:31
Alignment explanation
Indices: 835519--835577 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
835509 AACAATTGAA
*
835519 GCTAAATTTTGAAATAT-AAAAAATTATAAG
1 GCTAAATTCTGAAATATAAAAAAATTATAAG
*
835549 GCTAAATTCT-AAATTTACAAAAAATTATA
1 GCTAAATTCTGAAATATA-AAAAAATTATA
835578 GGTATTTAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 5 0.20
30 9 0.36
31 11 0.44
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.34
Consensus pattern (31 bp):
GCTAAATTCTGAAATATAAAAAAATTATAAG
Found at i:836838 original size:205 final size:204
Alignment explanation
Indices: 836480--837096 Score: 923
Period size: 205 Copynumber: 3.0 Consensus size: 204
836470 AGAAATTAGA
* * * * * *
836480 AAGTTGAATGCCTTAATAAGGATGCATGGTATGGTGTTTCTATCTTGTAATGCTTGAAAACTGTG
1 AAGTTGATTG-CTTAATATGGATGCATGATATAGTGTTTCCATCTTGTAATGCTCGAAAAC--TG
* * *
836545 TATAAACCAGAATGGATGAAAGTATAATTGCATCTTGTGTTTTGTGTTTTAAAATTAGTAATATT
63 TATAAACCAGAGTGGATGAAAGTATAATTGCATCTTGTGTTTTGTGTTTCAAAATTAGCAATATT
* * *
836610 TCTGTCATTAACTGCTGATTTGCATGTTCTGCTGCTCTGCCTTGTTTTCATTTGGATGATTTTAC
128 TCTGTCATTAACTGCTAATTTGCATGTTCTGCTGCTCTGCCTTGTTTTCATTTGGATAATTGTAC
836675 CATATATAATGT
193 CATATATAATGT
*
836687 AAGTTGATTGCATTAATATGGATGCATGATATAGTGTTTCCATCTTGTAATGCTCAAAAACTGTA
1 AAGTTGATTGC-TTAATATGGATGCATGATATAGTGTTTCCATCTTGTAATGCTCGAAAACTGTA
*
836752 TAAACCAGAGTGAATTG-AAGTATAATTGCATCTTGTGTTTTGTGTTTCAAAATTAGCAATATTT
65 TAAACCAGAGTGGA-TGAAAGTATAATTGCATCTTGTGTTTTGTGTTTCAAAATTAGCAATATTT
*
836816 CTGTCATTAACTGCTAATTTGCATGTTCTGCTGCTCTGCCTTGTTTTCTTTTGGATAATTGTACC
129 CTGTCATTAACTGCTAATTTGCATGTTCTGCTGCTCTGCCTTGTTTTCATTTGGATAATTGTACC
* * *
836881 ATGTAAAATGC
194 ATATATAATGT
* * *
836892 GAGTTGAATGGCTTAATATGGATGCATGATATAGTGTTTCCATCTTGTAATGCTCGGAAACTGTA
1 AAGTTG-ATTGCTTAATATGGATGCATGATATAGTGTTTCCATCTTGTAATGCTCGAAAACTGTA
* *
836957 TAAACCAGAGTGGATGAAAGTATAATTGCATCTTGTGTTTTGTGTTTCAAAATTAGCATTATTTT
65 TAAACCAGAGTGGATGAAAGTATAATTGCATCTTGTGTTTTGTGTTTCAAAATTAGCAATATTTC
* * *
837022 TGTCATTAACTGCTGATTTTG-TTGTTCTGCTGCCCTGCCTTGTTTTCATTTGGATAATTGTACC
130 TGTCATTAACTGCT-AATTTGCATGTTCTGCTGCTCTGCCTTGTTTTCATTTGGATAATTGTACC
837086 ATATATAATGT
194 ATATATAATGT
837097 GATAATTCCT
Statistics
Matches: 373, Mismatches: 32, Indels: 12
0.89 0.08 0.03
Matches are distributed among these distances:
204 2 0.01
205 307 0.82
206 12 0.03
207 52 0.14
ACGTcount: A:0.27, C:0.13, G:0.19, T:0.41
Consensus pattern (204 bp):
AAGTTGATTGCTTAATATGGATGCATGATATAGTGTTTCCATCTTGTAATGCTCGAAAACTGTAT
AAACCAGAGTGGATGAAAGTATAATTGCATCTTGTGTTTTGTGTTTCAAAATTAGCAATATTTCT
GTCATTAACTGCTAATTTGCATGTTCTGCTGCTCTGCCTTGTTTTCATTTGGATAATTGTACCAT
ATATAATGT
Found at i:843042 original size:24 final size:24
Alignment explanation
Indices: 842998--843045 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
842988 TTAAGTAGAT
*
842998 TTAAATTTTAAAATCTAAAAAAAA
1 TTAAATTTTAAAATATAAAAAAAA
*
843022 TTAAATTTT-AAATATACAAAAAA
1 TTAAATTTTAAAATATAAAAAAAA
843045 T
1 T
843046 ACAAATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 13 0.59
24 9 0.41
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.35
Consensus pattern (24 bp):
TTAAATTTTAAAATATAAAAAAAA
Found at i:843051 original size:24 final size:24
Alignment explanation
Indices: 843000--843051 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
842990 AAGTAGATTT
* *
843000 AAATTTTAAAATCTAAAAAAAATT
1 AAATTTTAAAATATAAAAAAAATC
*
843024 AAATTTT-AAATATACAAAAAATAC
1 AAATTTTAAAATATAAAAAAAAT-C
843048 AAAT
1 AAAT
843052 ATATTTAACC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 13 0.54
24 11 0.46
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (24 bp):
AAATTTTAAAATATAAAAAAAATC
Found at i:845575 original size:33 final size:33
Alignment explanation
Indices: 845533--845600 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
845523 GACTCTTGAA
845533 GAGCGGAACTCCCAATTAGAGCAACAGGTTTGC
1 GAGCGGAACTCCCAATTAGAGCAACAGGTTTGC
845566 GAGCGGAACTCCCAATTAGAGCAACAGGTTTGC
1 GAGCGGAACTCCCAATTAGAGCAACAGGTTTGC
845599 GA
1 GA
845601 TGCTTAGTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.31, C:0.24, G:0.28, T:0.18
Consensus pattern (33 bp):
GAGCGGAACTCCCAATTAGAGCAACAGGTTTGC
Found at i:858057 original size:23 final size:24
Alignment explanation
Indices: 858022--858083 Score: 63
Period size: 23 Copynumber: 2.6 Consensus size: 24
858012 AATTCGTATA
* *
858022 TTTTAGATAAAAAAATAAATTAAT
1 TTTTATATTAAAAAATAAATTAAT
* * *
858046 TTTT-TATTAAAAATTACATTTAT
1 TTTTATATTAAAAAATAAATTAAT
858069 TTTTACTATTAAAAA
1 TTTTA-TATTAAAAA
858084 TTGATTTTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
23 18 0.58
24 4 0.13
25 9 0.29
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (24 bp):
TTTTATATTAAAAAATAAATTAAT
Found at i:859099 original size:19 final size:19
Alignment explanation
Indices: 859075--859113 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
859065 TTTATTTTTT
859075 AGATTAAATTTTTGAGTTC
1 AGATTAAATTTTTGAGTTC
859094 AGATTAAATTTTTGAGTTC
1 AGATTAAATTTTTGAGTTC
859113 A
1 A
859114 AATCAGACAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.05, G:0.15, T:0.46
Consensus pattern (19 bp):
AGATTAAATTTTTGAGTTC
Found at i:859642 original size:26 final size:27
Alignment explanation
Indices: 859613--859664 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
859603 TTTAAACTAA
* *
859613 ACTTTTCAAAAGTACTT-TACAAAATC
1 ACTTTTCAAAAGCACTTCTAAAAAATC
*
859639 ACTTTTCCAAAGCACTTCTAAAAAAT
1 ACTTTTCAAAAGCACTTCTAAAAAAT
859665 AATGCTAAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 15 0.68
27 7 0.32
ACGTcount: A:0.42, C:0.21, G:0.04, T:0.33
Consensus pattern (27 bp):
ACTTTTCAAAAGCACTTCTAAAAAATC
Found at i:861447 original size:78 final size:78
Alignment explanation
Indices: 861318--861699 Score: 621
Period size: 78 Copynumber: 5.0 Consensus size: 78
861308 TTAAAAATCA
* * **
861318 TTAAAATTCCGGCCATAATTTTAATTGAGAGTAAATAACTCCGTTTAAACAAAGTAGTTGAAACT
1 TTAAAATTCCGGCCATCATTTTAATTGAGAGTAAATTACTCCCCTTAAACAAAGTAGTTGAAACT
861383 TCCATTATTTATC
66 TCCATTATTTATC
* *
861396 TTAAAATTCCAGCCATCATTTTAATTGAGAGTAAATTGCTCCCCTTAAACAAAGTAGTTG--A--
1 TTAAAATTCCGGCCATCATTTTAATTGAGAGTAAATTACTCCCCTTAAACAAAGTAGTTGAAACT
861457 -CCATTATTTATC
66 TCCATTATTTATC
* * *
861469 TTAAAATTCCGGCCATCATTTTATTTGAAAGTAAATTACTCCCCTTAAACAAAGTAGTTTAAACT
1 TTAAAATTCCGGCCATCATTTTAATTGAGAGTAAATTACTCCCCTTAAACAAAGTAGTTGAAACT
861534 TCCATTATTTATC
66 TCCATTATTTATC
* * *
861547 TTAAAATTCCGGCCATCATTTTAATTGAGAGTAAATTACACCCCTTAAACAAAATAGTTGAAAAT
1 TTAAAATTCCGGCCATCATTTTAATTGAGAGTAAATTACTCCCCTTAAACAAAGTAGTTGAAACT
861612 TCCATTATTTATC
66 TCCATTATTTATC
861625 TTAAAATTCCGGCCATCATTTTAATTGAGAGTAAATTACTCCCCTTAAACAAAGTAGTTGAAACT
1 TTAAAATTCCGGCCATCATTTTAATTGAGAGTAAATTACTCCCCTTAAACAAAGTAGTTGAAACT
861690 TCCATTATTT
66 TCCATTATTT
861700 TTTAGTAGTA
Statistics
Matches: 279, Mismatches: 20, Indels: 10
0.90 0.06 0.03
Matches are distributed among these distances:
73 67 0.24
75 1 0.00
76 1 0.00
78 210 0.75
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.36
Consensus pattern (78 bp):
TTAAAATTCCGGCCATCATTTTAATTGAGAGTAAATTACTCCCCTTAAACAAAGTAGTTGAAACT
TCCATTATTTATC
Found at i:861524 original size:151 final size:153
Alignment explanation
Indices: 861318--861699 Score: 624
Period size: 151 Copynumber: 2.5 Consensus size: 153
861308 TTAAAAATCA
* * **
861318 TTAAAATTCCGGCCATAATTTTAATTGAGAGTAAATAACTCCGTTTAAACAAAGTAGTTGAAACT
1 TTAAAATTCCGGCCATCATTTTAATTGAGAGTAAATTACTCCCCTTAAACAAAGTAGTTGAAACT
* *
861383 TCCATTATTTATCTTAAAATTCCAGCCATCATTTTAATTGAGAGTAAATTGCTCCCCTTAAACAA
66 TCCATTATTTATCTTAAAATTCCAGCCATCATTTTAATTGAGAGTAAATTACACCCCTTAAACAA
*
861448 AGTAGTTG-A-CCATTATTTATC
131 AATAGTTGAATCCATTATTTATC
* * *
861469 TTAAAATTCCGGCCATCATTTTATTTGAAAGTAAATTACTCCCCTTAAACAAAGTAGTTTAAACT
1 TTAAAATTCCGGCCATCATTTTAATTGAGAGTAAATTACTCCCCTTAAACAAAGTAGTTGAAACT
*
861534 TCCATTATTTATCTTAAAATTCCGGCCATCATTTTAATTGAGAGTAAATTACACCCCTTAAACAA
66 TCCATTATTTATCTTAAAATTCCAGCCATCATTTTAATTGAGAGTAAATTACACCCCTTAAACAA
861599 AATAGTTGAAAATTCCATTATTTATC
131 AATAGTTG--AA-TCCATTATTTATC
861625 TTAAAATTCCGGCCATCATTTTAATTGAGAGTAAATTACTCCCCTTAAACAAAGTAGTTGAAACT
1 TTAAAATTCCGGCCATCATTTTAATTGAGAGTAAATTACTCCCCTTAAACAAAGTAGTTGAAACT
861690 TCCATTATTT
66 TCCATTATTT
861700 TTTAGTAGTA
Statistics
Matches: 212, Mismatches: 14, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
151 127 0.60
154 1 0.00
156 84 0.40
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.36
Consensus pattern (153 bp):
TTAAAATTCCGGCCATCATTTTAATTGAGAGTAAATTACTCCCCTTAAACAAAGTAGTTGAAACT
TCCATTATTTATCTTAAAATTCCAGCCATCATTTTAATTGAGAGTAAATTACACCCCTTAAACAA
AATAGTTGAATCCATTATTTATC
Found at i:868021 original size:20 final size:20
Alignment explanation
Indices: 867987--868034 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
867977 ATCCCAAAAG
* * *
867987 AAAATAAATATTAATTAC-A
1 AAAACAAATACTAATCACTA
868006 AACAACAAATACTAATCACTA
1 AA-AACAAATACTAATCACTA
868027 AAAACAAA
1 AAAACAAA
868035 AAATAATAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.65, C:0.15, G:0.00, T:0.21
Consensus pattern (20 bp):
AAAACAAATACTAATCACTA
Found at i:868038 original size:23 final size:23
Alignment explanation
Indices: 868005--868056 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
867995 TATTAATTAC
* *
868005 AAACAACAAATACTAATCACTAA
1 AAACAAAAAATAATAATCACTAA
*
868028 AAACAAAAAATAATAATTACTAA
1 AAACAAAAAATAATAATCACTAA
868051 AAACAA
1 AAACAA
868057 CGCCCAATCC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.67, C:0.15, G:0.00, T:0.17
Consensus pattern (23 bp):
AAACAAAAAATAATAATCACTAA
Found at i:878812 original size:31 final size:30
Alignment explanation
Indices: 878775--878859 Score: 86
Period size: 31 Copynumber: 2.8 Consensus size: 30
878765 CAATTAGACT
878775 CTTCAAAAGCTTTTGTAAAATTTTATT-AAAC
1 CTTCAAAA--TTTTGTAAAATTTTATTAAAAC
*
878806 CTTCAAAATTTT-TGAAAATTATCATTAAAAC
1 CTTCAAAATTTTGT-AAAATT-TTATTAAAAC
*
878837 CCTCAAAATATTT-TAAAATTTTA
1 CTTCAAAAT-TTTGTAAAATTTTA
878860 GTTTGACTCT
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
28 1 0.02
29 10 0.21
30 6 0.13
31 26 0.55
32 4 0.09
ACGTcount: A:0.42, C:0.13, G:0.04, T:0.41
Consensus pattern (30 bp):
CTTCAAAATTTTGTAAAATTTTATTAAAAC
Found at i:878876 original size:94 final size:94
Alignment explanation
Indices: 878686--878876 Score: 210
Period size: 93 Copynumber: 2.0 Consensus size: 94
878676 ATTAAGACCC
** * * * *
878686 AAAGCTTTTGTAAATTTTAATTAGGCCTCCCAAAAATTTTGAAATTTCTCATTAAACCTTTGAAA
1 AAAGCTTTTGTAAATTTTAATTAAACCTCCCAAAAATTTTGAAAATTATCATTAAACCTCTCAAA
*
878751 ATTTTTAAAAATTTCAATTAGACTCTTCA
66 ATTTTTAAAAATTTCAATTAGACTCTCCA
* *
878780 AAAGCTTTTGTAAAATTTT-ATTAAACCT-TCAAAATTTTTGAAAATTATCATTAAAACC-CTCA
1 AAAGCTTTTGT-AAATTTTAATTAAACCTCCCAAAAATTTTGAAAATTATCATT-AAACCTCTCA
* * *
878842 AAATATTTT-AAAATTTTAGTTTGACTCTCCCA
64 AAAT-TTTTAAAAATTTCAATTAGACTCT-CCA
878874 AAA
1 AAA
878877 TTTAATGCCA
Statistics
Matches: 81, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
93 42 0.52
94 32 0.40
95 7 0.09
ACGTcount: A:0.39, C:0.15, G:0.06, T:0.40
Consensus pattern (94 bp):
AAAGCTTTTGTAAATTTTAATTAAACCTCCCAAAAATTTTGAAAATTATCATTAAACCTCTCAAA
ATTTTTAAAAATTTCAATTAGACTCTCCA
Found at i:884075 original size:18 final size:18
Alignment explanation
Indices: 884052--884095 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
884042 ATTATTTTTT
*
884052 AAAAGTATTTTTGGGACA
1 AAAAGTATTTTTGAGACA
* *
884070 AAAAGTAATTTTGAGATA
1 AAAAGTATTTTTGAGACA
884088 AAAA-TATT
1 AAAAGTATT
884096 ATTAAATAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 3 0.14
18 19 0.86
ACGTcount: A:0.48, C:0.02, G:0.16, T:0.34
Consensus pattern (18 bp):
AAAAGTATTTTTGAGACA
Found at i:887301 original size:32 final size:31
Alignment explanation
Indices: 887255--887343 Score: 103
Period size: 32 Copynumber: 2.9 Consensus size: 31
887245 TGGTATCTGA
887255 ATTTTTTTTCAATTTGATA-CTCAAACTTGAC
1 ATTTTTTTTCAATTTGATACCT-AAACTTGAC
*
887286 ATTTTTTTTCTAATTTGGTACCTAAACTTGAC
1 ATTTTTTTTC-AATTTGATACCTAAACTTGAC
* * *
887318 A-CTTTTTT-AAGTTGATACTTAAACTT
1 ATTTTTTTTCAATTTGATACCTAAACTT
887344 TTTGAGATCC
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
29 15 0.29
31 16 0.31
32 18 0.35
33 2 0.04
ACGTcount: A:0.28, C:0.15, G:0.08, T:0.49
Consensus pattern (31 bp):
ATTTTTTTTCAATTTGATACCTAAACTTGAC
Found at i:887324 original size:31 final size:30
Alignment explanation
Indices: 887211--887397 Score: 101
Period size: 32 Copynumber: 6.4 Consensus size: 30
887201 TTAATAAAAT
* *
887211 ATTTGGTACCTGAACTTGACATATTTTTTTA
1 ATTTGGTACCTAAACTTGACAT-TTTTTCTA
* *
887242 ATTTGGTATCTGAA-TT----TTTTTTC-A
1 ATTTGGTACCTAAACTTGACATTTTTTCTA
*
887266 ATTTGATA-CTCAAACTTGACATTTTTTTTCTA
1 ATTTGGTACCT-AAACTTGACA--TTTTTTCTA
*
887298 ATTTGGTACCTAAACTTGACACTTTTT-TA
1 ATTTGGTACCTAAACTTGACATTTTTTCTA
* * * ** *
887327 AGTTGATACTTAAACTT----TTTGAGATCCA
1 ATTTGGTACCTAAACTTGACATTT--TTTCTA
* * *
887355 ATTTGGTACTTGAACTTGACATTTTTTTTA
1 ATTTGGTACCTAAACTTGACATTTTTTCTA
887385 ATTTGGTACCTAA
1 ATTTGGTACCTAA
887398 TATTTTTTAA
Statistics
Matches: 117, Mismatches: 22, Indels: 35
0.67 0.13 0.20
Matches are distributed among these distances:
23 2 0.02
24 10 0.09
25 9 0.08
26 1 0.01
27 1 0.01
28 15 0.13
29 16 0.14
30 20 0.17
31 20 0.17
32 21 0.18
33 2 0.02
ACGTcount: A:0.27, C:0.13, G:0.12, T:0.48
Consensus pattern (30 bp):
ATTTGGTACCTAAACTTGACATTTTTTCTA
Found at i:887416 original size:58 final size:57
Alignment explanation
Indices: 887294--887417 Score: 133
Period size: 58 Copynumber: 2.2 Consensus size: 57
887284 ACATTTTTTT
* *
887294 TCTAATTTGGTACCTAAACTTGACACTTTTTTAAGTTGATACTTAAACTTTTTGAGA
1 TCTAATTTGGTACCTAAACTTGACACTTTTTTAAGTTGATACCTAAACTTTTTAAGA
* * * * * * * *
887351 TCCAATTTGGTACTTGAACTTGACATTTTTTTTAATTTGGTACCTAATATTTTTTAATA
1 TCTAATTTGGTACCTAAACTTGACA-CTTTTTTAAGTTGATACCTAA-ACTTTTTAAGA
887410 T-TAATTTG
1 TCTAATTTG
887418 TTAAGCATAG
Statistics
Matches: 54, Mismatches: 11, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
57 22 0.41
58 23 0.43
59 9 0.17
ACGTcount: A:0.28, C:0.12, G:0.11, T:0.48
Consensus pattern (57 bp):
TCTAATTTGGTACCTAAACTTGACACTTTTTTAAGTTGATACCTAAACTTTTTAAGA
Found at i:889007 original size:19 final size:19
Alignment explanation
Indices: 888983--889022 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
888973 ACTAAAAGAA
888983 ACCAAAATTCAAAAAGGAG
1 ACCAAAATTCAAAAAGGAG
889002 ACCAAAATTCAAAAAGGAG
1 ACCAAAATTCAAAAAGGAG
889021 AC
1 AC
889023 TGTTATCTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.57, C:0.17, G:0.15, T:0.10
Consensus pattern (19 bp):
ACCAAAATTCAAAAAGGAG
Found at i:896328 original size:31 final size:31
Alignment explanation
Indices: 896292--896352 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
896282 AAAATGGTCA
* *
896292 CTGAACTATTCGAAAGT-TTTCATTTAAGTCG
1 CTGAACTATTCAAAAGTAGTT-ATTTAAGTCG
896323 CTGAACTATTCAAAAGTAGTTATTTAAGTC
1 CTGAACTATTCAAAAGTAGTTATTTAAGTC
896353 ACTAGGTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 25 0.93
32 2 0.07
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.38
Consensus pattern (31 bp):
CTGAACTATTCAAAAGTAGTTATTTAAGTCG
Found at i:897706 original size:15 final size:16
Alignment explanation
Indices: 897686--897718 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
897676 TCAAAAAACA
897686 TAATTTATAATTT-AT
1 TAATTTATAATTTCAT
*
897701 TAATTTATGATTTCAT
1 TAATTTATAATTTCAT
897717 TA
1 TA
897719 TTTTTGAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (16 bp):
TAATTTATAATTTCAT
Found at i:898779 original size:29 final size:28
Alignment explanation
Indices: 898729--898783 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
898719 TTCCCATGAA
* *
898729 TTTAGAATTTAGTTTATATATTTTTATT
1 TTTAGAATTTAATCTATATATTTTTATT
*
898757 TTTAGAAATTTAATCTATTTATTTTTA
1 TTTAG-AATTTAATCTATATATTTTTA
898784 AACTTTTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 5 0.22
29 18 0.78
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.62
Consensus pattern (28 bp):
TTTAGAATTTAATCTATATATTTTTATT
Found at i:907080 original size:29 final size:29
Alignment explanation
Indices: 907048--907120 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 29
907038 AAATTAGATC
* * **
907048 AAATCAAAATTTATGTATGAAATTACACA
1 AAATCAAAATTCATATAAAAAATTACACA
907077 AAATCAAAATTCATATAAAAAATTACACA
1 AAATCAAAATTCATATAAAAAATTACACA
*
907106 TTAAACCAAAATTCA
1 --AAATCAAAATTCA
907121 CATATAATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 25 0.68
31 12 0.32
ACGTcount: A:0.56, C:0.14, G:0.03, T:0.27
Consensus pattern (29 bp):
AAATCAAAATTCATATAAAAAATTACACA
Found at i:920598 original size:21 final size:19
Alignment explanation
Indices: 920556--920602 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 19
920546 ATTTTAAAAA
*
920556 TAAAAATAATTAAAAATTT
1 TAAAAATAATTAAAAATAT
*
920575 TAAAAATATATTTAGAAATAT
1 TAAAAATA-A-TTAAAAATAT
920596 TAAAAAT
1 TAAAAAT
920603 TAAAAAAGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 8 0.33
20 1 0.04
21 15 0.62
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (19 bp):
TAAAAATAATTAAAAATAT
Found at i:928690 original size:2 final size:2
Alignment explanation
Indices: 928685--928713 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
928675 AAAAAAATGT
928685 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
928714 CTTAAATTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:929834 original size:5 final size:5
Alignment explanation
Indices: 929826--929854 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
929816 TAAAGAGACC
929826 AAATT AAATT AAATT AAATT AAATT AAAT
1 AAATT AAATT AAATT AAATT AAATT AAAT
929855 AACATAATAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
AAATT
Found at i:932231 original size:31 final size:32
Alignment explanation
Indices: 932170--932233 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
932160 TTCGTTTCAC
*
932170 GTTCTATGAAGATTAGTTTTTTTCGAGATTTAT
1 GTTCTATGAAAATTAG-TTTTTTCGAGATTTAT
*
932203 GTTCTATGAAAATTAG-TTTTTCGGGATTTAT
1 GTTCTATGAAAATTAGTTTTTTCGAGATTTAT
932234 AACTGCCCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 14 0.48
33 15 0.52
ACGTcount: A:0.25, C:0.06, G:0.19, T:0.50
Consensus pattern (32 bp):
GTTCTATGAAAATTAGTTTTTTCGAGATTTAT
Found at i:932403 original size:16 final size:18
Alignment explanation
Indices: 932372--932406 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
932362 CCAGTCCAAT
932372 TAAATAAATCATTAAAAA
1 TAAATAAATCATTAAAAA
932390 TAAA-AAAT-ATTAAAAA
1 TAAATAAATCATTAAAAA
932406 T
1 T
932407 TTAGTTCAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
17 4 0.24
18 4 0.24
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (18 bp):
TAAATAAATCATTAAAAA
Found at i:941696 original size:22 final size:22
Alignment explanation
Indices: 941652--941714 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 22
941642 GACGGCGGAT
*
941652 TGAACGAG-GAGA-AAAGA-AG
1 TGAAAGAGCGAGAGAAAGAGAG
941671 TGAAATG-GCGAG-GAAAGGAGAG
1 TGAAA-GAGCGAGAGAAA-GAGAG
941693 TGAAAGAGCGAGAGAAAGAGAG
1 TGAAAGAGCGAGAGAAAGAGAG
941715 GAGGGCCATG
Statistics
Matches: 36, Mismatches: 1, Indels: 11
0.75 0.02 0.23
Matches are distributed among these distances:
19 5 0.14
20 7 0.19
21 3 0.08
22 17 0.47
23 4 0.11
ACGTcount: A:0.48, C:0.05, G:0.41, T:0.06
Consensus pattern (22 bp):
TGAAAGAGCGAGAGAAAGAGAG
Found at i:945979 original size:59 final size:59
Alignment explanation
Indices: 945866--945985 Score: 152
Period size: 59 Copynumber: 2.0 Consensus size: 59
945856 TGAATATTAA
*
945866 TTATGTACTAATCATTTTAAAATTATGATTAAAATTCGTAATTATTCTTCTTAATAATG
1 TTATGTACTAATCATTTTAAAATTATGATTAAAATTCGTAATTAATCTTCTTAATAATG
** ** ** *
945925 TTATGTACTAATCATTTTAATGTTCATGATTATTATTTTTAA-TAATCTTTTTAATAATG
1 TTATGTACTAATCATTTTAAAATT-ATGATTAAAATTCGTAATTAATCTTCTTAATAATG
945984 TT
1 TT
945986 TGAAACATTA
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
59 39 0.75
60 13 0.25
ACGTcount: A:0.34, C:0.07, G:0.07, T:0.52
Consensus pattern (59 bp):
TTATGTACTAATCATTTTAAAATTATGATTAAAATTCGTAATTAATCTTCTTAATAATG
Found at i:946272 original size:3 final size:3
Alignment explanation
Indices: 946266--946292 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
946256 AAATTATTAA
946266 CAC CAC CAC CAC CAC CAC CAC CAC CAC
1 CAC CAC CAC CAC CAC CAC CAC CAC CAC
946293 ATTGAGTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.67, G:0.00, T:0.00
Consensus pattern (3 bp):
CAC
Found at i:952396 original size:20 final size:20
Alignment explanation
Indices: 952371--952409 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
952361 ATATATATTT
*
952371 TTTAAAAAAATGGAAAATGC
1 TTTAAAAAAATGAAAAATGC
952391 TTTAAAAAAATGAAAAATG
1 TTTAAAAAAATGAAAAATG
952410 AAATAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.59, C:0.03, G:0.13, T:0.26
Consensus pattern (20 bp):
TTTAAAAAAATGAAAAATGC
Found at i:952416 original size:20 final size:20
Alignment explanation
Indices: 952373--952417 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
952363 ATATATTTTT
* ***
952373 TAAAAAAATGGAAAATGCTT
1 TAAAAAAATGAAAAATGAAA
952393 TAAAAAAATGAAAAATGAAA
1 TAAAAAAATGAAAAATGAAA
952413 TAAAA
1 TAAAA
952418 TTGGAATGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.67, C:0.02, G:0.11, T:0.20
Consensus pattern (20 bp):
TAAAAAAATGAAAAATGAAA
Found at i:960318 original size:61 final size:61
Alignment explanation
Indices: 960221--960379 Score: 187
Period size: 61 Copynumber: 2.6 Consensus size: 61
960211 GCCATTGCCC
* * ** **
960221 TTTTCTCGAGAAAAAAATTCAAATTTTTTTGGTGTTGGTCATCAAATGGTCAACACC-CAT
1 TTTTCTCGAGAAAAAATTTCAAATTTTTTTTGTGTTGACCATCAAATGACCAACACCTCAT
* *
960281 TTTTCTCGAGAAAAAATTTGCAAATTTTTTTTGTGTTGACCATCAAATGACCGACACCTCCT
1 TTTTCTCGAGAAAAAATTT-CAAATTTTTTTTGTGTTGACCATCAAATGACCAACACCTCAT
* *
960343 TTTTTTTGAGAAAAAAATTT-AAATTTTTTTTGGTGTT
1 TTTTCTCGAG-AAAAAATTTCAAATTTTTTTT-GTGTT
960380 TTGGTGTCGG
Statistics
Matches: 85, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
60 18 0.21
61 43 0.51
62 15 0.18
63 9 0.11
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (61 bp):
TTTTCTCGAGAAAAAATTTCAAATTTTTTTTGTGTTGACCATCAAATGACCAACACCTCAT
Found at i:960496 original size:75 final size:77
Alignment explanation
Indices: 960401--960546 Score: 206
Period size: 77 Copynumber: 1.9 Consensus size: 77
960391 CATCAAATGG
* * *
960401 CCGACACCTCCTATTATTGAG-AAAAAA-TTCAAATTTTTTTAGTGTTGGCCATCAAATGGCCGA
1 CCGACACCCCCTATTATTGAGAAAAAAATTTCAAATTTTCTTAGTGTTGACCATCAAATGGCCGA
960464 CACCCCCCTTTT
66 CACCCCCCTTTT
* * * * *
960476 CCGACACCCCCTGTTCTTGAGAAAAAAATTTTAAATTTTCTTGGTGTTGACCATCAAATGGCTGA
1 CCGACACCCCCTATTATTGAGAAAAAAATTTCAAATTTTCTTAGTGTTGACCATCAAATGGCCGA
960541 CACCCC
66 CACCCC
960547 TTTTCACGGT
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
75 18 0.30
76 6 0.10
77 37 0.61
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.31
Consensus pattern (77 bp):
CCGACACCCCCTATTATTGAGAAAAAAATTTCAAATTTTCTTAGTGTTGACCATCAAATGGCCGA
CACCCCCCTTTT
Found at i:964351 original size:12 final size:12
Alignment explanation
Indices: 964309--964356 Score: 51
Period size: 12 Copynumber: 3.7 Consensus size: 12
964299 ATTTGTGTAA
*
964309 AAATTAATTTGA
1 AAATTAATTTGG
964321 AAATTAATTTAAGTTG
1 AAATTAATTT--G--G
964337 AAATTAATTTGG
1 AAATTAATTTGG
964349 AAATTAAT
1 AAATTAAT
964357 GAACATGTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
12 19 0.61
14 2 0.06
16 10 0.32
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (12 bp):
AAATTAATTTGG
Found at i:964431 original size:25 final size:29
Alignment explanation
Indices: 964377--964441 Score: 84
Period size: 25 Copynumber: 2.4 Consensus size: 29
964367 AAATTTAAAT
*
964377 AATTTAAACTTCATAATTATATAAGTTTG
1 AATTTAAAATTCATAATTATATAAGTTTG
964406 AATTTAAAATTC-TAATT-TA-AA-TTTG
1 AATTTAAAATTCATAATTATATAAGTTTG
*
964431 AAGTTAAAATT
1 AATTTAAAATT
964442 TAAAATACAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
25 14 0.41
26 2 0.06
27 2 0.06
28 5 0.15
29 11 0.32
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.45
Consensus pattern (29 bp):
AATTTAAAATTCATAATTATATAAGTTTG
Found at i:964479 original size:11 final size:11
Alignment explanation
Indices: 964439--964478 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
964429 TGAAGTTAAA
**
964439 ATTTAAAATAC
1 ATTTAAAATGT
964450 ATTTAAAATGT
1 ATTTAAAATGT
964461 ATTTAAAAT-T
1 ATTTAAAATGT
964471 ATTTAAAA
1 ATTTAAAA
964479 AAGATAGTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
10 9 0.33
11 18 0.67
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (11 bp):
ATTTAAAATGT
Found at i:964692 original size:83 final size:83
Alignment explanation
Indices: 964486--965086 Score: 796
Period size: 83 Copynumber: 7.3 Consensus size: 83
964476 AAAAAGATAG
* * * * * *
964486 TTATTATATTACAATTTATATCAAATATTGTATTAATTTGACAATACATTATTTATCAAATTTTC
1 TTATTATATTACAATTTTTATCATATAATGTATTGATTTGACAATACAATATTTAT-TAATTTT-
*
964551 ATA--TTTAAAGTACAAA-TTA
64 ATATCTTTAAA-TA-AAATTTT
* * * *
964570 TTATTATATTATAATTTTTATCATATAGTGTATTAATTTGACAATACAATATTTATTAATTTTGT
1 TTATTATATTACAATTTTTATCATATAATGTATTGATTTGACAATACAATATTTATTAATTTTAT
*
964635 ATCTTTAAATAAATTTTT
66 ATCTTTAAATAAAATTTT
* *
964653 TTATTATATTACAATTTTTATCATATAATGTGTTGATTTGATAATACAATATTTATTAATTTTAT
1 TTATTATATTACAATTTTTATCATATAATGTATTGATTTGACAATACAATATTTATTAATTTTAT
*
964718 GTCTTTAAATAAAATTTTT
66 ATCTTTAAATAAAA-TTTT
* *
964737 TTATTATATTATAATTTTTATAATATAATGTATTGATTTGACAATACAATATTTATTAATTTTAT
1 TTATTATATTACAATTTTTATCATATAATGTATTGATTTGACAATACAATATTTATTAATTTTAT
***
964802 ATCTTTAAATAAAAAAAT
66 ATCTTTAAATAAAATTTT
* * * *
964820 TTATTTAAAGATACAATTTTTATCATATAATGTGTTGATTTGATAATACAATATTTATTAATTTT
1 TTA-TTATA-TTACAATTTTTATCATATAATGTATTGATTTGACAATACAATATTTATTAATTTT
*
964885 ATATCTTTAAATAAATTTTT
64 ATATCTTTAAATAAAATTTT
*
964905 TTATTATATTACAATTTTTATAATATAATGTATTGATTTGACAATACAATATTTATTAATTTTAT
1 TTATTATATTACAATTTTTATCATATAATGTATTGATTTGACAATACAATATTTATTAATTTTAT
964970 ATCTTTAAATAAAATTTT
66 ATCTTTAAATAAAATTTT
*
964988 TTA-T-TA-T---A---TTAT-ATATAATGTGTTGATTTGACAATACAATATTTATTAATTTTAT
1 TTATTATATTACAATTTTTATCATATAATGTATTGATTTGACAATACAATATTTATTAATTTTAT
*
965043 ATCTTTAAATAAAAATTT
66 ATCTTTAAATAAAATTTT
965061 TTATTATATTACAATTTTTATCATAT
1 TTATTATATTACAATTTTTATCATAT
965087 TTTATATTTA
Statistics
Matches: 458, Mismatches: 43, Indels: 33
0.86 0.08 0.06
Matches are distributed among these distances:
73 62 0.14
74 5 0.01
75 2 0.00
76 1 0.00
77 1 0.00
79 1 0.00
80 1 0.00
81 2 0.00
82 9 0.02
83 162 0.35
84 143 0.31
85 69 0.15
ACGTcount: A:0.39, C:0.05, G:0.04, T:0.51
Consensus pattern (83 bp):
TTATTATATTACAATTTTTATCATATAATGTATTGATTTGACAATACAATATTTATTAATTTTAT
ATCTTTAAATAAAATTTT
Found at i:964933 original size:252 final size:246
Alignment explanation
Indices: 964486--965086 Score: 828
Period size: 252 Copynumber: 2.4 Consensus size: 246
964476 AAAAAGATAG
* * * * * *
964486 TTATTATATTACAATTTATATCAA-ATATTGTATTAATTTGACAATACATTATTTATCAAATTTT
1 TTATTATATTATAATTTTTAT-AATATAATGTATTGATTTGACAATACAATATTTAT-TAATTTT
* * *
964550 CATA--TTTAAAGT-ACAAATTATTATTATATTATAATTTTTATCATATAGTGTATTAATTTGAC
64 -ATATCTTTAAA-TAAAAAATT-TTATTATATTACAATTTTTATCATATAATGTATTAATTTGAC
* *
964612 AATACAATATTTATTAATTTTGTATCTTTAAATAAATTTTTTTATTATATTACAATTTTTATCAT
126 AATACAATATTTATTAATTTTATATCTTTAAATAAATTTTTTTATTATATTACAATTTTTATAAT
* * *
964677 ATAATGTGTTGATTTGATAATACAATATTTATTAATTTTATGTCTTTAAATAAAATTTTT
191 ATAATGTATTGATTTGACAATACAATATTTATTAATTTTATATCTTTAAATAAAA----T
964737 TTATTATATTATAATTTTTATAATATAATGTATTGATTTGACAATACAATATTTATTAATTTTAT
1 TTATTATATTATAATTTTTATAATATAATGTATTGATTTGACAATACAATATTTATTAATTTTAT
* * * * * *
964802 ATCTTTAAATAAAAAAATTTATTTAAAGATACAATTTTTATCATATAATGTGTTGATTTGATAAT
66 ATCTTTAAATAAAAAATTTTA-TTATA-TTACAATTTTTATCATATAATGTATTAATTTGACAAT
964867 ACAATATTTATTAATTTTATATCTTTAAATAAATTTTTTTATTATATTACAATTTTTATAATATA
129 ACAATATTTATTAATTTTATATCTTTAAATAAATTTTTTTATTATATTACAATTTTTATAATATA
964932 ATGTATTGATTTGACAATACAATATTTATTAATTTTATATCTTTAAATAAAAT
194 ATGTATTGATTTGACAATACAATATTTATTAATTTTATATCTTTAAATAAAAT
*
964985 TT-TT-TATTAT-A---TTAT-ATATAATGTGTTGATTTGACAATACAATATTTATTAATTTTAT
1 TTATTATATTATAATTTTTATAATATAATGTATTGATTTGACAATACAATATTTATTAATTTTAT
*
965043 ATCTTTAAATAAAAATTTTTATTATATTACAATTTTTATCATAT
66 ATCTTTAAATAAAAAATTTTATTATATTACAATTTTTATCATAT
965087 TTTATATTTA
Statistics
Matches: 319, Mismatches: 25, Indels: 24
0.87 0.07 0.07
Matches are distributed among these distances:
239 17 0.05
240 4 0.01
241 61 0.19
242 4 0.01
245 1 0.00
246 6 0.02
247 2 0.01
248 3 0.01
249 3 0.01
250 12 0.04
251 63 0.20
252 143 0.45
ACGTcount: A:0.39, C:0.05, G:0.04, T:0.51
Consensus pattern (246 bp):
TTATTATATTATAATTTTTATAATATAATGTATTGATTTGACAATACAATATTTATTAATTTTAT
ATCTTTAAATAAAAAATTTTATTATATTACAATTTTTATCATATAATGTATTAATTTGACAATAC
AATATTTATTAATTTTATATCTTTAAATAAATTTTTTTATTATATTACAATTTTTATAATATAAT
GTATTGATTTGACAATACAATATTTATTAATTTTATATCTTTAAATAAAAT
Found at i:965019 original size:73 final size:74
Alignment explanation
Indices: 964922--965071 Score: 275
Period size: 73 Copynumber: 2.0 Consensus size: 74
964912 ATTACAATTT
*
964922 TTATAATATAATGTATTGATTTGACAATACAATATTTATTAATTTTATATCTTTAAATAAAATTT
1 TTATAATATAATGTATTGATTTGACAATACAATATTTATTAATTTTATATCTTTAAATAAAAATT
964987 TTTATTATA
66 TTTATTATA
*
964996 TTAT-ATATAATGTGTTGATTTGACAATACAATATTTATTAATTTTATATCTTTAAATAAAAATT
1 TTATAATATAATGTATTGATTTGACAATACAATATTTATTAATTTTATATCTTTAAATAAAAATT
965060 TTTATTATA
66 TTTATTATA
965069 TTA
1 TTA
965072 CAATTTTTAT
Statistics
Matches: 74, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
73 70 0.95
74 4 0.05
ACGTcount: A:0.40, C:0.04, G:0.05, T:0.51
Consensus pattern (74 bp):
TTATAATATAATGTATTGATTTGACAATACAATATTTATTAATTTTATATCTTTAAATAAAAATT
TTTATTATA
Found at i:967013 original size:24 final size:24
Alignment explanation
Indices: 966969--967015 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
966959 CCAAGCCCAA
*
966969 GGATGAGCCCAATGTCGAGCCCGC
1 GGATGAGCCCAATGTCCAGCCCGC
*
966993 GGATGAGCCCGAT-TACCAGCCCG
1 GGATGAGCCCAATGT-CCAGCCCG
967016 ATTACGAGCC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 19 0.95
ACGTcount: A:0.21, C:0.34, G:0.32, T:0.13
Consensus pattern (24 bp):
GGATGAGCCCAATGTCCAGCCCGC
Found at i:968588 original size:59 final size:58
Alignment explanation
Indices: 968461--968622 Score: 179
Period size: 61 Copynumber: 2.8 Consensus size: 58
968451 ATCCTAGGAA
* * *
968461 AATGGCCAACACCAAAAAAATTTGAATTTTTTTCTCGAGAAAAAAGGGGTGTCGGCCATTGC
1 AATGGCCAACACCAAAAAAATTTGAATTTTTTT-T--TG-AAAAAGGGGTGTCGACCATTAC
*
968523 -ATGGCCAACACCAAAAAAATTTGAAATTTTTTTTTGAAATAGGAGGTGTCGACCA-TAC
1 AATGGCCAACACCAAAAAAATTTG-AATTTTTTTTTGAAAAAGG-GGTGTCGACCATTAC
* * *
968581 AATGGCCAACACC-GAAAAATGT-AATTTTTTTTTGAAACAGGG
1 AATGGCCAACACCAAAAAAATTTGAATTTTTTTTTGAAAAAGGG
968623 CATTGCCAAC
Statistics
Matches: 90, Mismatches: 7, Indels: 13
0.82 0.06 0.12
Matches are distributed among these distances:
55 1 0.01
56 18 0.20
58 15 0.17
59 23 0.26
61 24 0.27
62 9 0.10
ACGTcount: A:0.37, C:0.16, G:0.19, T:0.28
Consensus pattern (58 bp):
AATGGCCAACACCAAAAAAATTTGAATTTTTTTTTGAAAAAGGGGTGTCGACCATTAC
Found at i:970971 original size:5 final size:5
Alignment explanation
Indices: 970961--970985 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
970951 TCAACATTTT
970961 AAATA AAATA AAATA AAATA AAATA
1 AAATA AAATA AAATA AAATA AAATA
970986 TTTAGACTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAATA
Found at i:976245 original size:29 final size:30
Alignment explanation
Indices: 976203--976268 Score: 116
Period size: 29 Copynumber: 2.2 Consensus size: 30
976193 AAGGTCTCTG
*
976203 AACTTTCTAAAAATCATATTTTGGCCT-CA
1 AACTTTCTAAAAATCATATTTTGACCTCCA
976232 AACTTTCTAAAAATCATATTTTGACCTCCA
1 AACTTTCTAAAAATCATATTTTGACCTCCA
976262 AACTTTC
1 AACTTTC
976269 CAAGATTACA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
29 26 0.74
30 9 0.26
ACGTcount: A:0.35, C:0.23, G:0.05, T:0.38
Consensus pattern (30 bp):
AACTTTCTAAAAATCATATTTTGACCTCCA
Found at i:976281 original size:29 final size:28
Alignment explanation
Indices: 976220--976463 Score: 179
Period size: 29 Copynumber: 8.4 Consensus size: 28
976210 TAAAAATCAT
* * * * *
976220 ATTTTGGCCTCAAACTTTCTAAAAATCAT
1 ATTTTGACCCCAAACTTTC-CAAAATTAC
*
976249 ATTTTGACCTCCAAACTTTCCAAGATTAC
1 ATTTTGACC-CCAAACTTTCCAAAATTAC
* **
976278 A-TTTAATCCTTAAACTTCTCCAAAATTAC
1 ATTTTGA-CCCCAAACTT-TCCAAAATTAC
* ** * *
976307 ACTTT-AGCCTTAAATTATTCAAAAATTAC
1 ATTTTGA-CCCCAAACT-TTCCAAAATTAC
976336 A-TTTGACCCCAAAACTTTTCCAAAATTAC
1 ATTTTGACCCC-AAAC-TTTCCAAAATTAC
*
976365 ATTTTGACCCTCAAACTTTTCCAAAATTTC
1 ATTTTGACCC-CAAAC-TTTCCAAAATTAC
* * *
976395 ATTTTGCCCCCTAAACTTCCCAAAAGTCAC
1 ATTTTGACCCC-AAACTTTCCAAAA-TTAC
*
976425 ATTTTGACCCCAAACTCTTCCAAAATTGC
1 ATTTTGACCCCAAACT-TTCCAAAATTAC
976454 ATTTTGACCC
1 ATTTTGACCC
976464 AAAATTCTTT
Statistics
Matches: 176, Mismatches: 26, Indels: 26
0.77 0.11 0.11
Matches are distributed among these distances:
28 15 0.09
29 89 0.51
30 71 0.40
31 1 0.01
ACGTcount: A:0.34, C:0.27, G:0.05, T:0.35
Consensus pattern (28 bp):
ATTTTGACCCCAAACTTTCCAAAATTAC
Found at i:976303 original size:58 final size:58
Alignment explanation
Indices: 976241--976463 Score: 200
Period size: 58 Copynumber: 3.8 Consensus size: 58
976231 AAACTTTCTA
* * * * *
976241 AAAATCATATTTTGACCTCCAAACT-TTCCAAGATTACATTTAATCCTTAAACTTCTCC
1 AAAATCACATTTTGACC-CCAAACTATTCCAAAATTACATTTGACCCCTAAACTTCTCC
* * ** * * * *
976299 AAAATTACACTTT-AGCCTTAAATTATTCAAAAATTACATTTGACCCCAAAACTTTTCC
1 AAAATCACATTTTGA-CCCCAAACTATTCCAAAATTACATTTGACCCCTAAACTTCTCC
* * * *
976357 AAAATTACATTTTGACCCTCAAACTTTTCCAAAATTTCATTTTGCCCCCTAAACTTC-CC
1 AAAATCACATTTTGACCC-CAAACTATTCCAAAATTACA-TTTGACCCCTAAACTTCTCC
* *
976416 AAAAGTCACATTTTGACCCCAAACTCTTCCAAAATTGCATTTTGACCC
1 AAAA-TCACATTTTGACCCCAAACTATTCCAAAATTACA-TTTGACCC
976464 AAAATTCTTT
Statistics
Matches: 132, Mismatches: 27, Indels: 11
0.78 0.16 0.06
Matches are distributed among these distances:
57 5 0.04
58 52 0.39
59 48 0.36
60 27 0.20
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.34
Consensus pattern (58 bp):
AAAATCACATTTTGACCCCAAACTATTCCAAAATTACATTTGACCCCTAAACTTCTCC
Done.