Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold142
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1252394
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.30
Warning! 144568 characters in sequence are not A, C, G, or T
File 3 of 4
Found at i:365964 original size:7 final size:7
Alignment explanation
Indices: 365949--366015 Score: 89
Period size: 7 Copynumber: 9.6 Consensus size: 7
365939 TTTAGATATT
365949 GAATCTC
1 GAATCTC
*
365956 GAATTTC
1 GAATCTC
365963 GAATCTC
1 GAATCTC
365970 GAATCTC
1 GAATCTC
* *
365977 GTATTTC
1 GAATCTC
365984 GAATCTC
1 GAATCTC
* *
365991 GTATTTC
1 GAATCTC
365998 GAATCTC
1 GAATCTC
366005 GAATCTC
1 GAATCTC
366012 GAAT
1 GAAT
366016 GATCCTTCTC
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
7 50 1.00
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (7 bp):
GAATCTC
Found at i:365974 original size:21 final size:21
Alignment explanation
Indices: 365949--366015 Score: 98
Period size: 21 Copynumber: 3.2 Consensus size: 21
365939 TTTAGATATT
365949 GAATCTCGAATTTCGAATCTC
1 GAATCTCGAATTTCGAATCTC
*
365970 GAATCTCGTATTTCGAATCTC
1 GAATCTCGAATTTCGAATCTC
* * *
365991 GTATTTCGAATCTCGAATCTC
1 GAATCTCGAATTTCGAATCTC
366012 GAAT
1 GAAT
366016 GATCCTTCTC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (21 bp):
GAATCTCGAATTTCGAATCTC
Found at i:366491 original size:2 final size:2
Alignment explanation
Indices: 366484--366523 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
366474 ATGTTTAAAA
*
366484 CT CT CT CT CT CT CT CT CT CT CC CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
366524 AATCTAGTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
CT
Found at i:369108 original size:21 final size:21
Alignment explanation
Indices: 369084--369145 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
369074 GTTATCTCTA
369084 TTGTTGTTGTTGGTTTTGTTC
1 TTGTTGTTGTTGGTTTTGTTC
* *
369105 TTGTTGTTGTT-ATCTTTGTTG
1 TTGTTGTTGTTGGT-TTTGTTC
* *
369126 TTGTCGTCGTTGGTTTTGTT
1 TTGTTGTTGTTGGTTTTGTT
369146 ATAGTTGTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 1 0.03
21 32 0.94
22 1 0.03
ACGTcount: A:0.02, C:0.06, G:0.27, T:0.65
Consensus pattern (21 bp):
TTGTTGTTGTTGGTTTTGTTC
Found at i:377579 original size:20 final size:20
Alignment explanation
Indices: 377554--377597 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
377544 AAAGTTTACA
*
377554 GACGGACAGACAGACAGACG
1 GACGGACAAACAGACAGACG
*
377574 GACGGACAAACGGACAGACG
1 GACGGACAAACAGACAGACG
377594 GACG
1 GACG
377598 ACGGACAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.39, C:0.25, G:0.36, T:0.00
Consensus pattern (20 bp):
GACGGACAAACAGACAGACG
Found at i:377602 original size:7 final size:8
Alignment explanation
Indices: 377551--377604 Score: 55
Period size: 8 Copynumber: 7.4 Consensus size: 8
377541 TAAAAAGTTT
377551 ACAGACGG
1 ACAGACGG
*
377559 ACAGACAG
1 ACAGACGG
377567 ACAGAC-G
1 ACAGACGG
377574 ---GACGG
1 ACAGACGG
*
377579 ACAAACGG
1 ACAGACGG
377587 ACAGACGG
1 ACAGACGG
377595 AC-GACGG
1 ACAGACGG
377602 ACA
1 ACA
377605 AAATGTGATC
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
4 3 0.08
5 1 0.03
7 8 0.21
8 26 0.68
ACGTcount: A:0.41, C:0.26, G:0.33, T:0.00
Consensus pattern (8 bp):
ACAGACGG
Found at i:381393 original size:17 final size:18
Alignment explanation
Indices: 381371--381408 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
381361 TTTTTTTTTT
381371 TTTGGT-GTGTTTGTT-TG
1 TTTGGTGGT-TTTGTTGTG
381388 TTTGGTGGTTTTGTTGTG
1 TTTGGTGGTTTTGTTGTG
381406 TTT
1 TTT
381409 TTTTTTGGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.00, C:0.00, G:0.34, T:0.66
Consensus pattern (18 bp):
TTTGGTGGTTTTGTTGTG
Found at i:381406 original size:26 final size:24
Alignment explanation
Indices: 381370--381417 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
381360 GTTTTTTTTT
381370 TTTTGGTGTGTTTGTTTGTTTGGTGG
1 TTTTGGTGTGTTT-TTT-TTTGGTGG
*
381396 TTTTGTTGTGTTTTTTTTTGGT
1 TTTTGGTGTGTTTTTTTTTGGT
381418 TTTTTTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 6 0.29
25 3 0.14
26 12 0.57
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (24 bp):
TTTTGGTGTGTTTTTTTTTGGTGG
Found at i:386984 original size:11 final size:12
Alignment explanation
Indices: 386946--386991 Score: 58
Period size: 11 Copynumber: 3.8 Consensus size: 12
386936 TTATAGGCCT
*
386946 ATTTATATTTCA
1 ATTTATATTTTA
*
386958 ATTTATTATATTA
1 ATTTA-TATTTTA
386971 ATTTA-ATTTTA
1 ATTTATATTTTA
386982 ATTTATATTT
1 ATTTATATTT
386992 ATATGAATCT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 10 0.34
12 9 0.31
13 10 0.34
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (12 bp):
ATTTATATTTTA
Found at i:390455 original size:59 final size:60
Alignment explanation
Indices: 390363--390483 Score: 208
Period size: 59 Copynumber: 2.0 Consensus size: 60
390353 ATTAGCTAAT
*
390363 ACGAGTAGTAAGCTTTGAAACATGTTAAAATGCACA-TGTTTATCGAATGATGTTTGAGC
1 ACGAGTAGTAAGCTTTAAAACATGTTAAAATGCACATTGTTTATCGAATGATGTTTGAGC
390422 ACGAGTAGTAAGCTTTAAAACATGTTAAAATGCACATGTTGTTTATCGAATGATGTTTGAGC
1 ACGAGTAGTAAGCTTTAAAACATGTTAAAATGCACA--TTGTTTATCGAATGATGTTTGAGC
390484 GGAAGATACA
Statistics
Matches: 58, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
59 35 0.60
62 23 0.40
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (60 bp):
ACGAGTAGTAAGCTTTAAAACATGTTAAAATGCACATTGTTTATCGAATGATGTTTGAGC
Found at i:393166 original size:2 final size:2
Alignment explanation
Indices: 393159--393283 Score: 196
Period size: 2 Copynumber: 62.5 Consensus size: 2
393149 TTTCAAACAA
**
393159 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC NN
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
** **
393201 NN NN TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
393243 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
393284 TTTAAGTTCG
Statistics
Matches: 119, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 119 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.48
Consensus pattern (2 bp):
TC
Found at i:400268 original size:7 final size:7
Alignment explanation
Indices: 400256--400322 Score: 89
Period size: 7 Copynumber: 9.6 Consensus size: 7
400246 GAGAAGGATC
400256 ATTCGAG
1 ATTCGAG
400263 ATTCGAG
1 ATTCGAG
*
400270 ATTCGAA
1 ATTCGAG
*
400277 ATACGAG
1 ATTCGAG
*
400284 ATTCGAA
1 ATTCGAG
*
400291 ATACGAG
1 ATTCGAG
400298 ATTCGAG
1 ATTCGAG
*
400305 ATTCGAA
1 ATTCGAG
400312 ATTCGAG
1 ATTCGAG
400319 ATTC
1 ATTC
400323 AATATCTAAA
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
7 50 1.00
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.27
Consensus pattern (7 bp):
ATTCGAG
Found at i:402719 original size:2 final size:2
Alignment explanation
Indices: 402712--402762 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
402702 GCTAGGTGAT
*
402712 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA AA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
402754 GA GA GA GA G
1 GA GA GA GA G
402763 TCGATGTAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
GA
Found at i:402982 original size:2 final size:2
Alignment explanation
Indices: 402968--403010 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
402958 TGTCTGTCTG
* *
402968 TC TC TC T- TT TC TC TC TC TC TC TA TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
403009 TC
1 TC
403011 ATATCGACAA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.02, C:0.44, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:403520 original size:7 final size:7
Alignment explanation
Indices: 403505--403567 Score: 81
Period size: 7 Copynumber: 9.0 Consensus size: 7
403495 TTTAGATATT
403505 GAATCTC
1 GAATCTC
*
403512 GAATTTC
1 GAATCTC
403519 GAATCTC
1 GAATCTC
403526 GAATCTC
1 GAATCTC
* *
403533 GTATTTC
1 GAATCTC
403540 GAATCTC
1 GAATCTC
* *
403547 GTATTTC
1 GAATCTC
403554 GAATCTC
1 GAATCTC
403561 GAATCTC
1 GAATCTC
403568 AAATGATCCT
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
7 46 1.00
ACGTcount: A:0.25, C:0.24, G:0.14, T:0.37
Consensus pattern (7 bp):
GAATCTC
Found at i:403530 original size:21 final size:21
Alignment explanation
Indices: 403505--403567 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
403495 TTTAGATATT
403505 GAATCTCGAATTTCGAATCTC
1 GAATCTCGAATTTCGAATCTC
*
403526 GAATCTCGTATTTCGAATCTC
1 GAATCTCGAATTTCGAATCTC
* * *
403547 GTATTTCGAATCTCGAATCTC
1 GAATCTCGAATTTCGAATCTC
403568 AAATGATCCT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.25, C:0.24, G:0.14, T:0.37
Consensus pattern (21 bp):
GAATCTCGAATTTCGAATCTC
Found at i:408041 original size:32 final size:31
Alignment explanation
Indices: 407999--408070 Score: 135
Period size: 32 Copynumber: 2.3 Consensus size: 31
407989 CCTAGCCATC
407999 TTTCCCCCCGGAAAAATGGCTATATAGCAGT
1 TTTCCCCCCGGAAAAATGGCTATATAGCAGT
408030 TCTTCCCCCCGGAAAAATGGCTATATAGCAGT
1 T-TTCCCCCCGGAAAAATGGCTATATAGCAGT
408062 TTTCCCCCC
1 TTTCCCCCC
408071 ACGGAAAGCT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
31 9 0.22
32 31 0.77
ACGTcount: A:0.25, C:0.32, G:0.17, T:0.26
Consensus pattern (31 bp):
TTTCCCCCCGGAAAAATGGCTATATAGCAGT
Found at i:408087 original size:33 final size:32
Alignment explanation
Indices: 408000--408090 Score: 121
Period size: 32 Copynumber: 2.8 Consensus size: 32
407990 CTAGCCATCT
*
408000 TTCCCCCCGGAAAAATGGCTATATAGCAGTTC
1 TTCCCCCCGGAAAAATGACTATATAGCAGTTC
*
408032 TTCCCCCCGGAAAAATGGCTATATAGCAGTT-
1 TTCCCCCCGGAAAAATGACTATATAGCAGTTC
**
408063 TTCCCCCCACGGAAAGCTGACTATATAG
1 TT-CCCCC-CGGAAAAATGACTATATAG
408091 TGGGCTTTCC
Statistics
Matches: 54, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
31 2 0.04
32 36 0.67
33 16 0.30
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.24
Consensus pattern (32 bp):
TTCCCCCCGGAAAAATGACTATATAGCAGTTC
Found at i:410492 original size:32 final size:33
Alignment explanation
Indices: 410418--410502 Score: 118
Period size: 36 Copynumber: 2.5 Consensus size: 33
410408 ACCCTACTAT
410418 GGGGGAAAAGCTACTATATAGTAGCTTTTCCCCCCG
1 GGGGGAAAAGCTACTATATAGTAGCTTTT---CCCG
* *
410454 GGGGGAAAGGCTACTATATAGTAGGTTTT-CCG
1 GGGGGAAAAGCTACTATATAGTAGCTTTTCCCG
410486 GGGGGAAAAGCTACTAT
1 GGGGGAAAAGCTACTAT
410503 GGGGGAAAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
32 19 0.41
36 27 0.59
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.25
Consensus pattern (33 bp):
GGGGGAAAAGCTACTATATAGTAGCTTTTCCCG
Found at i:410519 original size:17 final size:17
Alignment explanation
Indices: 410486--410519 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
410476 AGGTTTTCCG
*
410486 GGGGGAAAAGCTACTAT
1 GGGGGAAAAACTACTAT
*
410503 GGGGGAAAAACTGCTAT
1 GGGGGAAAAACTACTAT
410520 ACAACACCGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.12, G:0.35, T:0.18
Consensus pattern (17 bp):
GGGGGAAAAACTACTAT
Found at i:412716 original size:17 final size:17
Alignment explanation
Indices: 412694--412727 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
412684 TTAAATAATT
412694 TATTTCAATAGTGGTTG
1 TATTTCAATAGTGGTTG
412711 TATTTCAATAGTGGTTG
1 TATTTCAATAGTGGTTG
412728 CAAAGTGAAT
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:0.24, C:0.06, G:0.24, T:0.47
Consensus pattern (17 bp):
TATTTCAATAGTGGTTG
Found at i:412798 original size:17 final size:17
Alignment explanation
Indices: 412776--412810 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
412766 ATTGAAATAA
*
412776 TTTATTTCAATAGTGGT
1 TTTATTTCAATAGCGGT
*
412793 TTTATTTTAATAGCGGT
1 TTTATTTCAATAGCGGT
412810 T
1 T
412811 GCAAGGTGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.23, C:0.06, G:0.17, T:0.54
Consensus pattern (17 bp):
TTTATTTCAATAGCGGT
Found at i:412805 original size:84 final size:84
Alignment explanation
Indices: 412659--412861 Score: 273
Period size: 84 Copynumber: 2.4 Consensus size: 84
412649 TGATTTTCAA
* * * * *
412659 AATGGAATACATCCCGGAA-CACTATTTAAATAATTTATTTCAATAGTGGTTGTATTTCAATAGT
1 AATGAAATACATCCC-CAACCACAATTGAAATAATTTATTTCAATAGTGGTTGTATTTCAATAGC
412723 GGTTGCAAAGTGAATCTTCT
65 GGTTGCAAAGTGAATCTTCT
* * *
412743 AATGAAATACGTCCCCAACCACAATTGAAATAATTTATTTCAATAGTGGTTTTATTTTAATAGCG
1 AATGAAATACATCCCCAACCACAATTGAAATAATTTATTTCAATAGTGGTTGTATTTCAATAGCG
* * *
412808 GTTGCAAGGTGATTTTTCT
66 GTTGCAAAGTGAATCTTCT
* *
412827 AATGAAATACATTCCCAACCACTATTGAAATAATT
1 AATGAAATACATCCCCAACCACAATTGAAATAATT
412862 AATCGCCGAA
Statistics
Matches: 104, Mismatches: 14, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
83 2 0.02
84 102 0.98
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
Consensus pattern (84 bp):
AATGAAATACATCCCCAACCACAATTGAAATAATTTATTTCAATAGTGGTTGTATTTCAATAGCG
GTTGCAAAGTGAATCTTCT
Found at i:413429 original size:19 final size:19
Alignment explanation
Indices: 413405--413456 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
413395 CCCCCCCCCT
*
413405 CCTTCTCAACTTTTGCTGC
1 CCTTCTCCACTTTTGCTGC
*
413424 CCTTCTCCACATTTGCTGC
1 CCTTCTCCACTTTTGCTGC
413443 CCTTCTCCACTTTT
1 CCTTCTCCACTTTT
413457 ACTGAAGCAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.10, C:0.40, G:0.08, T:0.42
Consensus pattern (19 bp):
CCTTCTCCACTTTTGCTGC
Found at i:421479 original size:2 final size:2
Alignment explanation
Indices: 421472--421548 Score: 154
Period size: 2 Copynumber: 38.5 Consensus size: 2
421462 TTTACCTTTA
421472 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
421514 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
421549 AGAGTTGTGT
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 75 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:425350 original size:167 final size:171
Alignment explanation
Indices: 425134--425491 Score: 496
Period size: 167 Copynumber: 2.1 Consensus size: 171
425124 TAATCGGCAG
* *
425134 AGAAAGCTGAAACTTGTGTGGAAGCATTCTCATGTATTAAAGATTCAAAGTTGTGAATATCATGA
1 AGAAAGCTGAAACTTGTGTGGAAGCATTCTCATGTAGTAAAGATTCAAAGTTGTGAAAATCATGA
* * * *
425199 GCCCTGGGGGTAGGGTCTGG-CCACAAT-GGGGGGGG-GTCAAAATTTTACATAGGAATATATTT
66 CCCCCGGGGGTAGGGT-GGGACCACAATGGGGGGGGGTGTCAAAATTTTACATAGGAATATATTG
* *
425261 AGTAAATCTTT-AAAAATCTTCTTCTCA-GAAACTAA-CAGTC
130 AGTAAATCTTTAAAAAATCTTCTCCTCATGAAAC-AATCAGCC
* **
425301 AGAAAGCTGAAAATTGTGTGGAAGCATTCTCA-GTTAGTGTAGATTCAAAGTTGTGAAAATCATG
1 AGAAAGCTGAAACTTGTGTGGAAGCATTCTCATG-TAGTAAAGATTCAAAGTTGTGAAAATCATG
* *
425365 ACCCCCGGGGGTAGGGTGGGACCACAATGGGGGGGGGTGTCGAAGTTTTACATAGGAATATATTG
65 ACCCCCGGGGGTAGGGTGGGACCACAATGGGGGGGGGTGTCAAAATTTTACATAGGAATATATTG
* *
425430 AGTTAATCTTTAAAAAATCTTCTCCTCATGATACAATCAGCC
130 AGTAAATCTTTAAAAAATCTTCTCCTCATGAAACAATCAGCC
425472 AGGAAAGCTGAAACTTGTGT
1 A-GAAAGCTGAAACTTGTGT
425492 AAAGGCATAC
Statistics
Matches: 167, Mismatches: 16, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
166 3 0.02
167 79 0.47
168 8 0.05
169 34 0.20
170 17 0.10
171 9 0.05
172 17 0.10
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.28
Consensus pattern (171 bp):
AGAAAGCTGAAACTTGTGTGGAAGCATTCTCATGTAGTAAAGATTCAAAGTTGTGAAAATCATGA
CCCCCGGGGGTAGGGTGGGACCACAATGGGGGGGGGTGTCAAAATTTTACATAGGAATATATTGA
GTAAATCTTTAAAAAATCTTCTCCTCATGAAACAATCAGCC
Found at i:428741 original size:12 final size:12
Alignment explanation
Indices: 428724--428767 Score: 72
Period size: 12 Copynumber: 3.8 Consensus size: 12
428714 TTAATGATCC
428724 TTATATATTATG
1 TTATATATTATG
*
428736 TTATATAATATG
1 TTATATATTATG
428748 TTATATA-TATG
1 TTATATATTATG
428759 TTATATATT
1 TTATATATT
428768 TATTTATTAC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
11 11 0.37
12 19 0.63
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (12 bp):
TTATATATTATG
Found at i:432348 original size:25 final size:25
Alignment explanation
Indices: 432314--432363 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
432304 TTTTTATCAA
432314 ACGGGCGATAAGCTATCAAATTCTT
1 ACGGGCGATAAGCTATCAAATTCTT
**
432339 ACGGGCGATAATTTATCAAATTCTT
1 ACGGGCGATAAGCTATCAAATTCTT
432364 CAGGTCAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (25 bp):
ACGGGCGATAAGCTATCAAATTCTT
Found at i:434802 original size:86 final size:86
Alignment explanation
Indices: 434657--434927 Score: 515
Period size: 86 Copynumber: 3.2 Consensus size: 86
434647 TACTACAGGT
* * *
434657 ATTCAAAATTTAGAATTCATATGTGGGGCCCGCTTGCCTTATATGTAACTGAATAGTGAACTGCG
1 ATTCAAAATTTAGAATTCATATTTGGGGCCCGCTTGCCTTATATGCAATTGAATAGTGAACTGCG
434722 TTCTATAGAACGCAGTTCGCA
66 TTCTATAGAACGCAGTTCGCA
434743 ATTCAAAATTTAGAATTCATATTTGGGGCCCGCTTGCCTTATATGCAATTGAATAGTGAACTGCG
1 ATTCAAAATTTAGAATTCATATTTGGGGCCCGCTTGCCTTATATGCAATTGAATAGTGAACTGCG
434808 TTCTATAGAACGCAGTTCGCA
66 TTCTATAGAACGCAGTTCGCA
434829 ATTCAAAATTTAGAATTCATATTTGGGGCCCGCTTGCCTTATATGCAATTGAATAGTGAACTGCG
1 ATTCAAAATTTAGAATTCATATTTGGGGCCCGCTTGCCTTATATGCAATTGAATAGTGAACTGCG
434894 TTCTATAGAACGCAGTTCGCA
66 TTCTATAGAACGCAGTTCGCA
434915 ATTCAAAATTTAG
1 ATTCAAAATTTAG
434928 TGCGATTGAA
Statistics
Matches: 182, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
86 182 1.00
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (86 bp):
ATTCAAAATTTAGAATTCATATTTGGGGCCCGCTTGCCTTATATGCAATTGAATAGTGAACTGCG
TTCTATAGAACGCAGTTCGCA
Found at i:434943 original size:56 final size:57
Alignment explanation
Indices: 434876--434985 Score: 204
Period size: 58 Copynumber: 1.9 Consensus size: 57
434866 CTTATATGCA
434876 ATTGAATAGTGAACTGCGTTCTA-TAGAACGCAGTTCGCAATTCAAAATTTAGTGCG
1 ATTGAATAGTGAACTGCGTTCTACTAGAACGCAGTTCGCAATTCAAAATTTAGTGCG
434932 ATTGAATAGTGAACTGCGTTCTATCTAGAACGCAGTTCGCAATTCAAAATTTAG
1 ATTGAATAGTGAACTGCGTTCTA-CTAGAACGCAGTTCGCAATTCAAAATTTAG
434986 AAATAATATT
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
56 23 0.44
58 29 0.56
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (57 bp):
ATTGAATAGTGAACTGCGTTCTACTAGAACGCAGTTCGCAATTCAAAATTTAGTGCG
Found at i:435083 original size:88 final size:88
Alignment explanation
Indices: 434932--435149 Score: 354
Period size: 88 Copynumber: 2.5 Consensus size: 88
434922 ATTTAGTGCG
434932 ATTGAATAGTGAACTGCGTTCTATCTAGAACGCAGTTCGCAATTCAAAATTTAGAAATAATATTT
1 ATTGAATAGTGAACTGCGTTCTATCTAGAACGCAGTTCGCAATTCAAAATTTAGAAATAATATTT
*
434997 GGGGCCCGATTGCCTTATTTGCA
66 GGGGCCCGATTGCCTTATATGCA
* * * *
435020 ATTGAATAGTGAACTGCGTTCTATCTAGAATGCAGTTCGCGATTCAAAATTTAGAATTTATATTT
1 ATTGAATAGTGAACTGCGTTCTATCTAGAACGCAGTTCGCAATTCAAAATTTAGAAATAATATTT
*
435085 GGGGCCCGCTTGCCTTATATGCA
66 GGGGCCCGATTGCCTTATATGCA
435108 ATTGAATAGTGAACTGCGTTC-A---AGAACGCAGTTCGCAATTCA
1 ATTGAATAGTGAACTGCGTTCTATCTAGAACGCAGTTCGCAATTCA
435150 TTTTTGGGGC
Statistics
Matches: 122, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
84 18 0.15
87 1 0.01
88 103 0.84
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (88 bp):
ATTGAATAGTGAACTGCGTTCTATCTAGAACGCAGTTCGCAATTCAAAATTTAGAAATAATATTT
GGGGCCCGATTGCCTTATATGCA
Found at i:435136 original size:230 final size:228
Alignment explanation
Indices: 434706--435149 Score: 775
Period size: 230 Copynumber: 1.9 Consensus size: 228
434696 TATATGTAAC
* *
434706 TGAATAGTGAACTGCGTTCTATAGAACGCAGTTCGCAATTCAAAATTTAGAATTCATATTTGGGG
1 TGAATAGTGAACTGCGTTCTATAGAACGCAGTTCGCAATTCAAAATTTAGAAATAATATTTGGGG
*
434771 CCCGCTTGCCTTATATGCAATTGAATAGTGAACTGCGTTCTATAGAACGCAGTTCGCAATTCAAA
66 CCCGATTGCCTTATATGCAATTGAATAGTGAACTGCGTTCTATAGAACGCAGTTCGCAATTCAAA
434836 ATTTAGAATTCATATTTGGGGCCCGCTTGCCTTATATGCAATTGAATAGTGAACTGCGTTCTATA
131 ATTTAGAATTCATATTTGGGGCCCGCTTGCCTTATATGCAATTGAATAGTGAACTGCGTTCTATA
434901 GAACGCAGTTCGCAATTCAAAATTTAGTGCGAT
196 GAACGCAGTTCGCAATTCAAAATTTAGTGCGAT
434934 TGAATAGTGAACTGCGTTCTATCTAGAACGCAGTTCGCAATTCAAAATTTAGAAATAATATTTGG
1 TGAATAGTGAACTGCGTTCTA--TAGAACGCAGTTCGCAATTCAAAATTTAGAAATAATATTTGG
* * *
434999 GGCCCGATTGCCTTATTTGCAATTGAATAGTGAACTGCGTTCTATCTAGAATGCAGTTCGCGATT
64 GGCCCGATTGCCTTATATGCAATTGAATAGTGAACTGCGTTCTA--TAGAACGCAGTTCGCAATT
*
435064 CAAAATTTAGAATTTATATTTGGGGCCCGCTTGCCTTATATGCAATTGAATAGTGAACTGCGTTC
127 CAAAATTTAGAATTCATATTTGGGGCCCGCTTGCCTTATATGCAATTGAATAGTGAACTGCGTTC
435129 -A-AGAACGCAGTTCGCAATTCA
192 TATAGAACGCAGTTCGCAATTCA
435150 TTTTTGGGGC
Statistics
Matches: 205, Mismatches: 7, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
228 21 0.10
230 102 0.50
231 1 0.00
232 81 0.40
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (228 bp):
TGAATAGTGAACTGCGTTCTATAGAACGCAGTTCGCAATTCAAAATTTAGAAATAATATTTGGGG
CCCGATTGCCTTATATGCAATTGAATAGTGAACTGCGTTCTATAGAACGCAGTTCGCAATTCAAA
ATTTAGAATTCATATTTGGGGCCCGCTTGCCTTATATGCAATTGAATAGTGAACTGCGTTCTATA
GAACGCAGTTCGCAATTCAAAATTTAGTGCGAT
Found at i:435361 original size:31 final size:31
Alignment explanation
Indices: 435323--435448 Score: 198
Period size: 31 Copynumber: 4.1 Consensus size: 31
435313 AACACATGTA
* *
435323 CACAACACACCGTCGCGCTAACGCAACTTTG
1 CACAACACGCCGTCGCGCTAACACAACTTTG
435354 CACAACACGCCGTCGCGCTAACACAACTTTG
1 CACAACACGCCGTCGCGCTAACACAACTTTG
*
435385 CACAACACGCCGTCGCGCTAACAAAACTTTG
1 CACAACACGCCGTCGCGCTAACACAACTTTG
** *
435416 CTTAACACGCCGTCGCGCTAACGCAACTTTG
1 CACAACACGCCGTCGCGCTAACACAACTTTG
435447 CA
1 CA
435449 AGTTTCACAG
Statistics
Matches: 87, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 87 1.00
ACGTcount: A:0.29, C:0.37, G:0.17, T:0.17
Consensus pattern (31 bp):
CACAACACGCCGTCGCGCTAACACAACTTTG
Found at i:435762 original size:2 final size:2
Alignment explanation
Indices: 435755--435808 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
435745 CCCCCTTCCC
435755 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
435797 AG AG AG AG AG AG
1 AG AG AG AG AG AG
435809 TCCGGTACCT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:440333 original size:10 final size:10
Alignment explanation
Indices: 440320--440352 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
440310 ATTGATATGA
440320 TATGATACAT
1 TATGATACAT
440330 TATGATA-AT
1 TATGATACAT
440339 ATATGATACAT
1 -TATGATACAT
440350 TAT
1 TAT
440353 TATGCCTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
9 2 0.10
10 17 0.81
11 2 0.10
ACGTcount: A:0.42, C:0.06, G:0.09, T:0.42
Consensus pattern (10 bp):
TATGATACAT
Found at i:458308 original size:2 final size:2
Alignment explanation
Indices: 458301--458391 Score: 103
Period size: 2 Copynumber: 45.5 Consensus size: 2
458291 AAAATAACAT
* * *
458301 TC TC TC TC TC TC TG TC TG TC TC TC TC TC -C TAC TT TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T-C TC TC TC TC TC
* * * *
458343 TC TC TC TC TC TC TG TC TC TG TC TC TG TG TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
458385 TC TC TC T
1 TC TC TC T
458392 TATATAATTT
Statistics
Matches: 75, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
1 1 0.01
2 72 0.96
3 2 0.03
ACGTcount: A:0.01, C:0.42, G:0.07, T:0.51
Consensus pattern (2 bp):
TC
Found at i:462712 original size:20 final size:20
Alignment explanation
Indices: 462608--462761 Score: 92
Period size: 21 Copynumber: 7.5 Consensus size: 20
462598 CTATACTGAG
* *
462608 AAATGAAAAATAATATAATAC
1 AAATG-AAAATTATACAATAC
* ** * *
462629 ATATGAAGTTTATACTATGC
1 AAATGAAAATTATACAATAC
* *
462649 AAATGAACTATTATATAATAC
1 AAATGAA-AATTATACAATAC
* * *** *
462670 AAATGAAAATGAGAGTTTTC
1 AAATGAAAATTATACAATAC
*
462690 AAATGAAAATTATACGATAC
1 AAATGAAAATTATACAATAC
* *
462710 AAATAAAAAAATATACAATAC
1 AAAT-GAAAATTATACAATAC
*
462731 AAATGAAAATTATTAAAATAC
1 AAATGAAAATTA-TACAATAC
462752 AAATGGAAAA
1 AAAT-GAAAA
462762 GATCGAATAT
Statistics
Matches: 97, Mismatches: 32, Indels: 7
0.71 0.24 0.05
Matches are distributed among these distances:
20 45 0.46
21 47 0.48
22 5 0.05
ACGTcount: A:0.56, C:0.07, G:0.09, T:0.27
Consensus pattern (20 bp):
AAATGAAAATTATACAATAC
Found at i:463217 original size:4 final size:4
Alignment explanation
Indices: 463210--463242 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
463200 AATTATTTAT
463210 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG A
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG A
463243 TAGATAGATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:463247 original size:4 final size:4
Alignment explanation
Indices: 463240--463307 Score: 136
Period size: 4 Copynumber: 17.0 Consensus size: 4
463230 AAAGAAAGAA
463240 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT
1 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT
463288 AGAT AGAT AGAT AGAT AGAT
1 AGAT AGAT AGAT AGAT AGAT
463308 TATTTGGGTA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.25, T:0.25
Consensus pattern (4 bp):
AGAT
Found at i:466618 original size:2 final size:2
Alignment explanation
Indices: 466611--466694 Score: 132
Period size: 2 Copynumber: 42.0 Consensus size: 2
466601 TTTCCAATAA
466611 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
* * * *
466653 CT CT TT CT CT CT CT GT CT CT CT GT CT CT CT CT GT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
466695 GAAAGAATGT
Statistics
Matches: 74, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.00, C:0.45, G:0.04, T:0.51
Consensus pattern (2 bp):
CT
Found at i:480551 original size:2 final size:2
Alignment explanation
Indices: 480544--480571 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
480534 AATTTCATGT
480544 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
480572 TAATTTACTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:497433 original size:4 final size:4
Alignment explanation
Indices: 497420--497471 Score: 97
Period size: 4 Copynumber: 13.2 Consensus size: 4
497410 TGTTATGTGC
497420 GATT -ATT GATT GATT GATT GATT GATT GATT GATT GATT GATT GATT
1 GATT GATT GATT GATT GATT GATT GATT GATT GATT GATT GATT GATT
497467 GATT G
1 GATT G
497472 GTTTTAAGAC
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 3 0.06
4 44 0.94
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
GATT
Found at i:503242 original size:21 final size:21
Alignment explanation
Indices: 503208--503287 Score: 99
Period size: 21 Copynumber: 3.8 Consensus size: 21
503198 AATTTAATGC
* * *
503208 TATGCTATGGTATGCGATTT-
1 TATGATATGCTATGAGATTTG
503228 TAATGATATGCTATGAGATTTG
1 T-ATGATATGCTATGAGATTTG
*
503250 TATGGTATGCTATGAGATTTG
1 TATGATATGCTATGAGATTTG
*
503271 TATGCTATGCTATGAGA
1 TATGATATGCTATGAGA
503288 AATTGAAATG
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
20 1 0.02
21 51 0.96
22 1 0.02
ACGTcount: A:0.26, C:0.07, G:0.25, T:0.41
Consensus pattern (21 bp):
TATGATATGCTATGAGATTTG
Found at i:503556 original size:21 final size:21
Alignment explanation
Indices: 503530--503584 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
503520 ATGAGATTGT
*
503530 ATGCTATGGTATGAGATTCCA
1 ATGCTATGCTATGAGATTCCA
*
503551 ATGCTATGCTATGAGATTTCA
1 ATGCTATGCTATGAGATTCCA
*
503572 ATTCTATGCTATG
1 ATGCTATGCTATG
503585 CTATGGTGTA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.38
Consensus pattern (21 bp):
ATGCTATGCTATGAGATTCCA
Found at i:503723 original size:21 final size:21
Alignment explanation
Indices: 503699--503754 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
503689 CAAATATGCC
*
503699 GACATGCAAGATAATTATGAT
1 GACATGCAACATAATTATGAT
503720 GACATGCAACATAATTATG-T
1 GACATGCAACATAATTATGAT
*
503740 CAACATGCAACATAA
1 -GACATGCAACATAA
503755 CTACATGTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 1 0.03
21 31 0.97
ACGTcount: A:0.45, C:0.16, G:0.14, T:0.25
Consensus pattern (21 bp):
GACATGCAACATAATTATGAT
Found at i:503957 original size:42 final size:42
Alignment explanation
Indices: 503911--504010 Score: 128
Period size: 42 Copynumber: 2.4 Consensus size: 42
503901 GCGAGATAAA
503911 TATGTTGACATGCAAGTTATTTACATCAACATGCAACTTAGT
1 TATGTTGACATGCAAGTTATTTACATCAACATGCAACTTAGT
* * * ** * *
503953 TATGTTTACATGCTACTTATTTATGTCGACATGCAACTTCGT
1 TATGTTGACATGCAAGTTATTTACATCAACATGCAACTTAGT
*
503995 TATGTCGACATGCAAG
1 TATGTTGACATGCAAG
504011 ATAAATATGT
Statistics
Matches: 47, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.37
Consensus pattern (42 bp):
TATGTTGACATGCAAGTTATTTACATCAACATGCAACTTAGT
Found at i:503963 original size:21 final size:21
Alignment explanation
Indices: 503911--504071 Score: 108
Period size: 21 Copynumber: 7.7 Consensus size: 21
503901 GCGAGATAAA
* *
503911 TATGTTGACATGCAAGTTATT
1 TATGTTGACATGCAACTTAGT
** **
503932 TACATCAACATGCAACTTAGT
1 TATGTTGACATGCAACTTAGT
* * *
503953 TATGTTTACATGCTACTTATT
1 TATGTTGACATGCAACTTAGT
* *
503974 TATGTCGACATGCAACTTCGT
1 TATGTTGACATGCAACTTAGT
* ** **
503995 TATGTCGACATGCAAGATAAA
1 TATGTTGACATGCAACTTAGT
*
504016 TATGTTGACATGCAACATA-T
1 TATGTTGACATGCAACTTAGT
* * * *
504036 TCATCTTGAAACGCAACTTATT
1 T-ATGTTGACATGCAACTTAGT
*
504058 TATGTTAACATGCA
1 TATGTTGACATGCA
504072 CCATATATAT
Statistics
Matches: 105, Mismatches: 33, Indels: 4
0.74 0.23 0.03
Matches are distributed among these distances:
20 1 0.01
21 102 0.97
22 2 0.02
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.36
Consensus pattern (21 bp):
TATGTTGACATGCAACTTAGT
Found at i:504170 original size:21 final size:21
Alignment explanation
Indices: 504140--504268 Score: 71
Period size: 21 Copynumber: 6.1 Consensus size: 21
504130 TCAACATATT
* *
504140 CATGTGAACATAATTAAGTTG
1 CATGTCAACATAAATAAGTTG
** ** *
504161 CATGTCAACATATTTATCTCG
1 CATGTCAACATAAATAAGTTG
504182 CATGTCAACATAACA-AAGTTG
1 CATGTCAACATAA-ATAAGTTG
* ** **
504203 CACGTTGACATAAATAAGAAG
1 CATGTCAACATAAATAAGTTG
*** **
504224 CATAAGAACATACCTAAGTTG
1 CATGTCAACATAAATAAGTTG
* *
504245 CATGTCGACATAAATAAGTAG
1 CATGTCAACATAAATAAGTTG
504266 CAT
1 CAT
504269 TTAGTATCTT
Statistics
Matches: 75, Mismatches: 31, Indels: 4
0.68 0.28 0.04
Matches are distributed among these distances:
20 1 0.01
21 74 0.99
ACGTcount: A:0.40, C:0.17, G:0.16, T:0.27
Consensus pattern (21 bp):
CATGTCAACATAAATAAGTTG
Found at i:504234 original size:42 final size:42
Alignment explanation
Indices: 504188--504268 Score: 117
Period size: 42 Copynumber: 1.9 Consensus size: 42
504178 CTCGCATGTC
*
504188 AACATAACAAAGTTGCACGTTGACATAAATAAGAAGCATAAG
1 AACATAACAAAGTTGCACGTCGACATAAATAAGAAGCATAAG
* * * *
504230 AACATACCTAAGTTGCATGTCGACATAAATAAGTAGCAT
1 AACATAACAAAGTTGCACGTCGACATAAATAAGAAGCAT
504269 TTAGTATCTT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.46, C:0.16, G:0.16, T:0.22
Consensus pattern (42 bp):
AACATAACAAAGTTGCACGTCGACATAAATAAGAAGCATAAG
Found at i:504391 original size:21 final size:21
Alignment explanation
Indices: 504365--504420 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
504355 GTAGTTATGC
* *
504365 TGCATGTTAACATAGCTATTT
1 TGCATGTCAACATAGCTATCT
**
504386 TGCATGTCAACATATTTATCT
1 TGCATGTCAACATAGCTATCT
*
504407 TGCATGTCGACATA
1 TGCATGTCAACATA
504421 TTTGATGGAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (21 bp):
TGCATGTCAACATAGCTATCT
Found at i:507042 original size:17 final size:17
Alignment explanation
Indices: 507022--507054 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
507012 AACCCTCAGT
507022 TTAGCCGATAACTGGTC
1 TTAGCCGATAACTGGTC
507039 TTAGCCGATAACTGGT
1 TTAGCCGATAACTGGT
507055 ACAGTACCAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.30
Consensus pattern (17 bp):
TTAGCCGATAACTGGTC
Found at i:508006 original size:17 final size:17
Alignment explanation
Indices: 507963--508040 Score: 72
Period size: 17 Copynumber: 4.6 Consensus size: 17
507953 GTCGCAATTG
*
507963 TATTGTATTATTTA-TT
1 TATTTTATTATTTATTT
*
507979 TA-TCTATTTATTTATTT
1 TATTTTA-TTATTTATTT
*
507996 TATTTTATTATTTTTTT
1 TATTTTATTATTTATTT
*
508013 TATTTTTATTACTT-TTT
1 TA-TTTTATTATTTATTT
508030 TATTTTTATTA
1 TA-TTTTATTA
508041 AAGTGAGCTT
Statistics
Matches: 54, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
15 3 0.06
16 9 0.17
17 29 0.54
18 13 0.24
ACGTcount: A:0.22, C:0.03, G:0.01, T:0.74
Consensus pattern (17 bp):
TATTTTATTATTTATTT
Found at i:508014 original size:26 final size:26
Alignment explanation
Indices: 507985--508036 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
507975 TATTTATCTA
507985 TTTATTTATT-TTA-TTTTATTATTTTT
1 TTTATTT-TTATTACTTTT-TTATTTTT
508011 TTTATTTTTATTACTTTTTTATTTTT
1 TTTATTTTTATTACTTTTTTATTTTT
508037 ATTAAAGTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 2 0.08
26 18 0.75
27 4 0.17
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.81
Consensus pattern (26 bp):
TTTATTTTTATTACTTTTTTATTTTT
Found at i:524492 original size:4 final size:4
Alignment explanation
Indices: 524483--524568 Score: 145
Period size: 4 Copynumber: 21.5 Consensus size: 4
524473 TTGTTTACTA
* *
524483 TATC TATC TATA TATC TATC TATC TATT TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
*
524531 TATT TATC TATC TATC TATC TATC TATC TATC TATC TA
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TA
524569 CAGTAAGATG
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 76 1.00
ACGTcount: A:0.27, C:0.21, G:0.00, T:0.52
Consensus pattern (4 bp):
TATC
Found at i:531281 original size:11 final size:11
Alignment explanation
Indices: 531265--531290 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
531255 CAAAGTCATA
531265 AACACTTATGT
1 AACACTTATGT
531276 AACACTTATGT
1 AACACTTATGT
531287 AACA
1 AACA
531291 TATTGATTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.42, C:0.19, G:0.08, T:0.31
Consensus pattern (11 bp):
AACACTTATGT
Found at i:532144 original size:2 final size:2
Alignment explanation
Indices: 532084--532132 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
532074 GCTTTTCATA
532084 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
532126 CT CT CT C
1 CT CT CT C
532133 CATGATCTCT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:532264 original size:2 final size:2
Alignment explanation
Indices: 532259--532317 Score: 73
Period size: 2 Copynumber: 29.5 Consensus size: 2
532249 TAATTACACA
* **
532259 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT TT CT GA
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
* *
532301 GT CT TT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT C
532318 AAACTCTCAA
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.02, C:0.44, G:0.03, T:0.51
Consensus pattern (2 bp):
CT
Found at i:539801 original size:21 final size:21
Alignment explanation
Indices: 539777--539910 Score: 117
Period size: 21 Copynumber: 6.4 Consensus size: 21
539767 CGATAAACCT
539777 GATAGGATTAACGCACGATAG
1 GATAGGATTAACGCACGATAG
*
539798 GATAGCATTAACGCACGATAG
1 GATAGGATTAACGCACGATAG
* * * **
539819 AACAGTATCCACGCACGATAG
1 GATAGGATTAACGCACGATAG
*
539840 GATAGGATTAACGCACGTTAG
1 GATAGGATTAACGCACGATAG
* * * *
539861 AACAGTA-TACACGCACGATAC
1 GATAGGATTA-ACGCACGATAG
* ** *
539882 GATAGGATTGATACACGATAC
1 GATAGGATTAACGCACGATAG
539903 GATAGGAT
1 GATAGGAT
539911 AGGATAGGAT
Statistics
Matches: 88, Mismatches: 23, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
20 2 0.02
21 85 0.97
22 1 0.01
ACGTcount: A:0.38, C:0.19, G:0.24, T:0.19
Consensus pattern (21 bp):
GATAGGATTAACGCACGATAG
Found at i:539887 original size:42 final size:42
Alignment explanation
Indices: 539787--539890 Score: 172
Period size: 42 Copynumber: 2.5 Consensus size: 42
539777 GATAGGATTA
* *
539787 ACGCACGATAGGATAGCATTAACGCACGATAGAACAGTATCC
1 ACGCACGATAGGATAGGATTAACGCACGATAGAACAGTATAC
*
539829 ACGCACGATAGGATAGGATTAACGCACGTTAGAACAGTATAC
1 ACGCACGATAGGATAGGATTAACGCACGATAGAACAGTATAC
*
539871 ACGCACGATACGATAGGATT
1 ACGCACGATAGGATAGGATT
539891 GATACACGAT
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 58 1.00
ACGTcount: A:0.38, C:0.21, G:0.23, T:0.18
Consensus pattern (42 bp):
ACGCACGATAGGATAGGATTAACGCACGATAGAACAGTATAC
Found at i:539964 original size:14 final size:14
Alignment explanation
Indices: 539945--539971 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
539935 TTGCGGGTAC
539945 TGTATATATATATG
1 TGTATATATATATG
539959 TGTATATATATAT
1 TGTATATATATAT
539972 ATATATTAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.52
Consensus pattern (14 bp):
TGTATATATATATG
Found at i:550487 original size:2 final size:2
Alignment explanation
Indices: 550480--550519 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
550470 TGACTAGAGA
550480 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
550520 GCATGAATCG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:566946 original size:20 final size:20
Alignment explanation
Indices: 566919--566970 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
566909 CTTTCCTCTG
*
566919 CGTCTGTCTGTCTGTCCATC
1 CGTCTGTCTGTCAGTCCATC
566939 TC-TCTGTCTGTCAGTCCATC
1 -CGTCTGTCTGTCAGTCCATC
566959 CGTCTGTCTGTC
1 CGTCTGTCTGTC
566971 CCACTTTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 1 0.03
20 27 0.93
21 1 0.03
ACGTcount: A:0.06, C:0.35, G:0.19, T:0.40
Consensus pattern (20 bp):
CGTCTGTCTGTCAGTCCATC
Found at i:570550 original size:24 final size:22
Alignment explanation
Indices: 570523--570649 Score: 87
Period size: 24 Copynumber: 5.5 Consensus size: 22
570513 CTAGATTTAT
570523 GGTTAAGGTTGGTATTGAAGTTAG
1 GGTTAAGGTTGG--TTGAAGTTAG
* *
570547 GGTTAAGGTGGGGGTTGAAGTTAA
1 GGTTAAGGT--TGGTTGAAGTTAG
* *
570571 GGTTATGGTAGGTTGAAGTTAG
1 GGTTAAGGTTGGTTGAAGTTAG
* *
570593 GGTTAGGGTTGAAG-TGAGGGTTAG
1 GGTTAAGGTTG--GTTGA-AGTTAG
* *
570617 GGTTATGG-TGAGTTGAAGTTGG
1 GGTTAAGGTTG-GTTGAAGTTAG
*
570639 GGTTAGGGTTG
1 GGTTAAGGTTG
570650 AAGTGAGGGT
Statistics
Matches: 84, Mismatches: 12, Indels: 15
0.76 0.11 0.14
Matches are distributed among these distances:
22 33 0.39
23 10 0.12
24 39 0.46
26 2 0.02
ACGTcount: A:0.21, C:0.00, G:0.45, T:0.34
Consensus pattern (22 bp):
GGTTAAGGTTGGTTGAAGTTAG
Found at i:570604 original size:18 final size:18
Alignment explanation
Indices: 570558--570666 Score: 81
Period size: 18 Copynumber: 6.3 Consensus size: 18
570548 GTTAAGGTGG
*
570558 GGGTTGAAGTTAAGGTTA
1 GGGTTGAAGTTAGGGTTA
570576 TGGTAGGTTGAAGTTAGGGTTA
1 --G--GGTTGAAGTTAGGGTTA
*
570598 GGGTTGAAGTGAGGGTTA
1 GGGTTGAAGTTAGGGTTA
570616 GGGTT--A--T--GG-T-
1 GGGTTGAAGTTAGGGTTA
* *
570626 GAGTTGAAGTTGGGGTTA
1 GGGTTGAAGTTAGGGTTA
*
570644 GGGTTGAAGTGAGGGTTA
1 GGGTTGAAGTTAGGGTTA
570662 GGGTT
1 GGGTT
570667 ATGGTGAGAG
Statistics
Matches: 72, Mismatches: 7, Indels: 22
0.71 0.07 0.22
Matches are distributed among these distances:
10 4 0.06
11 1 0.01
12 3 0.04
14 1 0.01
16 3 0.04
17 1 0.01
18 41 0.57
20 2 0.03
22 16 0.22
ACGTcount: A:0.21, C:0.00, G:0.46, T:0.33
Consensus pattern (18 bp):
GGGTTGAAGTTAGGGTTA
Found at i:570621 original size:46 final size:47
Alignment explanation
Indices: 570566--570693 Score: 206
Period size: 46 Copynumber: 2.7 Consensus size: 47
570556 GGGGGTTGAA
*
570566 GTTAAGGTTATGGTAG-GTTGAAGTTAGGGTTAGGGTTGAAGTGAGG
1 GTTAGGGTTATGGTAGAGTTGAAGTTAGGGTTAGGGTTGAAGTGAGG
*
570612 GTTAGGGTTATGGT-GAGTTGAAGTTGGGGTTAGGGTTGAAGTGAGG
1 GTTAGGGTTATGGTAGAGTTGAAGTTAGGGTTAGGGTTGAAGTGAGG
*
570658 GTTAGGGTTATGGTGAGAGTTGAAGCTAGGGTTAGG
1 GTTAGGGTTATGGT-AGAGTTGAAGTTAGGGTTAGG
570694 ATTATGGCTG
Statistics
Matches: 75, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
45 1 0.01
46 56 0.75
48 18 0.24
ACGTcount: A:0.22, C:0.01, G:0.45, T:0.32
Consensus pattern (47 bp):
GTTAGGGTTATGGTAGAGTTGAAGTTAGGGTTAGGGTTGAAGTGAGG
Found at i:570655 original size:28 final size:28
Alignment explanation
Indices: 570600--570656 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 28
570590 TAGGGTTAGG
*
570600 GTTGAAGTGAGGGTTAGGGTTATGGTGA
1 GTTGAAGTGAGGGTTAGGGTTATAGTGA
570628 GTTGAAGTTG-GGGTTAGGGTTGA-AGTGA
1 GTTGAAG-TGAGGGTTAGGGTT-ATAGTGA
570656 G
1 G
570657 GGTTAGGGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
28 23 0.88
29 3 0.12
ACGTcount: A:0.21, C:0.00, G:0.47, T:0.32
Consensus pattern (28 bp):
GTTGAAGTGAGGGTTAGGGTTATAGTGA
Found at i:570674 original size:18 final size:18
Alignment explanation
Indices: 570581--570666 Score: 82
Period size: 18 Copynumber: 5.2 Consensus size: 18
570571 GGTTATGGTA
*
570581 GGTTGAAGTTAGGGTTAG
1 GGTTGAAGTGAGGGTTAG
570599 GGTTGAAGTGAGGGTTAG
1 GGTTGAAGTGAGGGTTAG
570617 GGTT--A-T---GG-T-G
1 GGTTGAAGTGAGGGTTAG
*
570627 AGTTGAAGTTG-GGGTTAG
1 GGTTGAAG-TGAGGGTTAG
570645 GGTTGAAGTGAGGGTTAG
1 GGTTGAAGTGAGGGTTAG
570663 GGTT
1 GGTT
570667 ATGGTGAGAG
Statistics
Matches: 56, Mismatches: 3, Indels: 18
0.73 0.04 0.23
Matches are distributed among these distances:
10 4 0.07
11 1 0.02
12 3 0.05
14 1 0.02
15 1 0.02
16 3 0.05
17 3 0.05
18 40 0.71
ACGTcount: A:0.20, C:0.00, G:0.48, T:0.33
Consensus pattern (18 bp):
GGTTGAAGTGAGGGTTAG
Found at i:570763 original size:24 final size:23
Alignment explanation
Indices: 570726--570771 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
570716 TTTGGTTTAA
*
570726 GGTACGGGTTAAGTTAGGGTTAT
1 GGTAAGGGTTAAGTTAGGGTTAT
570749 GGTAAGGGTTGAAGTTAGGGTTA
1 GGTAAGGGTT-AAGTTAGGGTTA
570772 GGGTTGAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.24, C:0.02, G:0.41, T:0.33
Consensus pattern (23 bp):
GGTAAGGGTTAAGTTAGGGTTAT
Found at i:570802 original size:18 final size:18
Alignment explanation
Indices: 570753--570794 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
570743 GGTTATGGTA
*
570753 AGGGTTGAAGTTAGGGTT
1 AGGGTTGAAGTGAGGGTT
570771 AGGGTTGAAGTGAGGGTT
1 AGGGTTGAAGTGAGGGTT
570789 AGGGTT
1 AGGGTT
570795 ATGGTGAGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.21, C:0.00, G:0.48, T:0.31
Consensus pattern (18 bp):
AGGGTTGAAGTGAGGGTT
Found at i:570844 original size:99 final size:98
Alignment explanation
Indices: 570712--570892 Score: 299
Period size: 99 Copynumber: 1.8 Consensus size: 98
570702 TGAATTTTGG
* *
570712 GGGGTTTGGTTTAAGGTACGGGTTAAGTTAGGGTTATGGTAAGGGTTGAAGTTAGGGTTAGGGTT
1 GGGGTTTGGTGTAAGGTACGGGTTAACTTAGGGTTATGGTAAGGGTTGAAGTTAGGGTTAGGGTT
570777 GAAGTGAGGGTTAGGGTTATGGTGAGTTGAAGAT
66 GAA-TGAGGGTTAGGGTTATGGTGAGTTGAAGAT
** *
570811 GGGGTTTGGTGTAAGGTTGGGGTTAACTTAGGGTTATGGTGAGGGTTGAAGTTAGGGTTAGGGTT
1 GGGGTTTGGTGTAAGGTACGGGTTAACTTAGGGTTATGGTAAGGGTTGAAGTTAGGGTTAGGGTT
*
570876 GAATTAGGGTTAGGGTT
66 GAATGAGGGTTAGGGTT
570893 GAAGTTAGGC
Statistics
Matches: 76, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
98 13 0.17
99 63 0.83
ACGTcount: A:0.20, C:0.01, G:0.44, T:0.34
Consensus pattern (98 bp):
GGGGTTTGGTGTAAGGTACGGGTTAACTTAGGGTTATGGTAAGGGTTGAAGTTAGGGTTAGGGTT
GAATGAGGGTTAGGGTTATGGTGAGTTGAAGAT
Found at i:570873 original size:18 final size:18
Alignment explanation
Indices: 570852--570911 Score: 95
Period size: 18 Copynumber: 3.4 Consensus size: 18
570842 GGTTATGGTG
570852 AGGGTTGAAGTTAGGGTT
1 AGGGTTGAAGTTAGGGTT
570870 AGGGTTGAA-TTAGGGTT
1 AGGGTTGAAGTTAGGGTT
* *
570887 AGGGTTGAAGTTAGGCTC
1 AGGGTTGAAGTTAGGGTT
570905 AGGGTTG
1 AGGGTTG
570912 CTGTAAGGAT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
17 17 0.44
18 22 0.56
ACGTcount: A:0.22, C:0.03, G:0.43, T:0.32
Consensus pattern (18 bp):
AGGGTTGAAGTTAGGGTT
Found at i:571963 original size:2 final size:2
Alignment explanation
Indices: 571956--572001 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
571946 CATACTAAAC
571956 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
571998 AG AG
1 AG AG
572002 NNNNNNNNNN
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:580914 original size:2 final size:2
Alignment explanation
Indices: 580907--580946 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
580897 CTCTAATACA
580907 TC TC TC TC TC TC TC -C TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
580947 GTAAAATAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:582634 original size:2 final size:2
Alignment explanation
Indices: 582627--582680 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
582617 AAACCCACAT
582627 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
582669 TC TC TC TC TC TC
1 TC TC TC TC TC TC
582681 NCTCATTACC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:585878 original size:21 final size:20
Alignment explanation
Indices: 585854--585964 Score: 123
Period size: 21 Copynumber: 5.3 Consensus size: 20
585844 GGTATTTCAT
* *
585854 TTATATGCAATAGTAATATCA
1 TTATATGCAGT-GTAACATCA
585875 TTATATGCAGTGGTAACATCA
1 TTATATGCAGT-GTAACATCA
*
585896 TTACATGCAGTGATAACATCA
1 TTATATGCAGTG-TAACATCA
585917 TTATATGCAGTGATAACATCA
1 TTATATGCAGTG-TAACATCA
* * *
585938 TTTTTTGTAGTGCTAACATCA
1 TTATATGCAGTG-TAACATCA
585959 TTATAT
1 TTATAT
585965 ACTATTATTT
Statistics
Matches: 78, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
20 1 0.01
21 77 0.99
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.38
Consensus pattern (20 bp):
TTATATGCAGTGTAACATCA
Found at i:586316 original size:21 final size:21
Alignment explanation
Indices: 586265--586317 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
586255 TATGGTGTAT
*
586265 TAAAACCATTATGTATGGTGG
1 TAAAACCTTTATGTATGGTGG
*
586286 TAAAACCTTTATGTATTGTGG
1 TAAAACCTTTATGTATGGTGG
* *
586307 TGAAAGCTTTA
1 TAAAACCTTTA
586318 CATGCAATTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.32, C:0.09, G:0.21, T:0.38
Consensus pattern (21 bp):
TAAAACCTTTATGTATGGTGG
Found at i:586477 original size:21 final size:21
Alignment explanation
Indices: 586422--586464 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
586412 TCATTTCATG
* *
586422 ATATGGAGTGGTAACTTCTTT
1 ATATGCAGTCGTAACTTCTTT
586443 ATATGCAGTCGTAAC-TCTTT
1 ATATGCAGTCGTAACTTCTTT
586463 AT
1 AT
586465 GATGAGGTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.26, C:0.14, G:0.19, T:0.42
Consensus pattern (21 bp):
ATATGCAGTCGTAACTTCTTT
Found at i:588322 original size:2 final size:2
Alignment explanation
Indices: 588315--588358 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
588305 GACAGATAAA
588315 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
588357 CT
1 CT
588359 TCAAAACAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:588681 original size:21 final size:21
Alignment explanation
Indices: 588632--588684 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
588622 CAGTTGCATG
* *
588632 TAAAGCTTTCACCACAATACA
1 TAAAGGTTTTACCACAATACA
*
588653 TAAAGGTTTTACCACCATACA
1 TAAAGGTTTTACCACAATACA
*
588674 TAATGGTTTTA
1 TAAAGGTTTTA
588685 ATACACCATA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.38, C:0.21, G:0.09, T:0.32
Consensus pattern (21 bp):
TAAAGGTTTTACCACAATACA
Found at i:588971 original size:42 final size:42
Alignment explanation
Indices: 588925--589137 Score: 198
Period size: 42 Copynumber: 5.1 Consensus size: 42
588915 CGACATAACG
* * * *
588925 TAATGATGTTACCACTTCATATAAAGATTTTACCCCTGAATA
1 TAATGATGTTACCACTTCATATAATGATGTTACCACTGCATA
* * ** * *
588967 TAATGGTGAAATAATA-GT-ATATAATGATGTTAGCACTGCATA
1 TAATGATG--TTACCACTTCATATAATGATGTTACCACTGCATA
* * *
589009 TAATGATGTTAGCACTGCATATAATGATGTTAGCACTGCATA
1 TAATGATGTTACCACTTCATATAATGATGTTACCACTGCATA
* * *
589051 TAATGATATTACCA-TTGCATGTAATGATGTTACCACTGCATG
1 TAATGATGTTACCACTT-CATATAATGATGTTACCACTGCATA
* * * *
589093 TAATGATGTTACCACTGCATATAATGATATTACTATTGCATA
1 TAATGATGTTACCACTTCATATAATGATGTTACCACTGCATA
589135 TAA
1 TAA
589138 ATGAAATACC
Statistics
Matches: 136, Mismatches: 29, Indels: 12
0.77 0.16 0.07
Matches are distributed among these distances:
40 3 0.02
41 1 0.01
42 127 0.93
43 2 0.01
44 3 0.02
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Consensus pattern (42 bp):
TAATGATGTTACCACTTCATATAATGATGTTACCACTGCATA
Found at i:589009 original size:21 final size:21
Alignment explanation
Indices: 588985--589137 Score: 216
Period size: 21 Copynumber: 7.3 Consensus size: 21
588975 AAATAATAGT
*
588985 ATATAATGATGTTAGCACTGC
1 ATATAATGATGTTACCACTGC
*
589006 ATATAATGATGTTAGCACTGC
1 ATATAATGATGTTACCACTGC
*
589027 ATATAATGATGTTAGCACTGC
1 ATATAATGATGTTACCACTGC
* *
589048 ATATAATGATATTACCATTGC
1 ATATAATGATGTTACCACTGC
*
589069 ATGTAATGATGTTACCACTGC
1 ATATAATGATGTTACCACTGC
*
589090 ATGTAATGATGTTACCACTGC
1 ATATAATGATGTTACCACTGC
* * *
589111 ATATAATGATATTACTATTGC
1 ATATAATGATGTTACCACTGC
589132 ATATAA
1 ATATAA
589138 ATGAAATACC
Statistics
Matches: 122, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 122 1.00
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (21 bp):
ATATAATGATGTTACCACTGC
Found at i:590964 original size:2 final size:2
Alignment explanation
Indices: 590959--590997 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
590949 TATAGGTAAA
* *
590959 TC TC TC TT TC TC TT TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
590998 GATATACGAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (2 bp):
TC
Found at i:591502 original size:2 final size:2
Alignment explanation
Indices: 591495--591555 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
591485 GGATAGTGCC
591495 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
591537 AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG A
591556 CTGAGTTTGC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:595654 original size:63 final size:59
Alignment explanation
Indices: 595543--595720 Score: 217
Period size: 53 Copynumber: 3.1 Consensus size: 59
595533 GCATTTCTAG
* * *
595543 TTAAGGTCTTCCGTTTCCAACGGAAGACCTTATTGTTATTGCT-TTGTTTCTTTTCCTCTATTA
1 TTAAGGTCTTCCGTTTCCAACGGAAGACCTTATAGTGATTG-TAATGTTTCTTTT--TC--TTA
595606 TTAAGGTCTTCCGTTTCCAACGGAAGACCTTATAGTGATTGTAATG------TTTCTTA
1 TTAAGGTCTTCCGTTTCCAACGGAAGACCTTATAGTGATTGTAATGTTTCTTTTTCTTA
* *
595659 TTAAGGTCTTCCGTTTCCAACGGAAGACCTTATAGTGATTGTAATGTTTCTTATTATTA
1 TTAAGGTCTTCCGTTTCCAACGGAAGACCTTATAGTGATTGTAATGTTTCTTTTTCTTA
595718 TTA
1 TTA
595721 TTCTTATTTT
Statistics
Matches: 103, Mismatches: 5, Indels: 18
0.82 0.04 0.14
Matches are distributed among these distances:
53 49 0.48
55 2 0.02
57 2 0.02
59 8 0.08
62 1 0.01
63 41 0.40
ACGTcount: A:0.22, C:0.17, G:0.16, T:0.44
Consensus pattern (59 bp):
TTAAGGTCTTCCGTTTCCAACGGAAGACCTTATAGTGATTGTAATGTTTCTTTTTCTTA
Found at i:595683 original size:53 final size:53
Alignment explanation
Indices: 595603--595714 Score: 224
Period size: 53 Copynumber: 2.1 Consensus size: 53
595593 TTTTCCTCTA
595603 TTATTAAGGTCTTCCGTTTCCAACGGAAGACCTTATAGTGATTGTAATGTTTC
1 TTATTAAGGTCTTCCGTTTCCAACGGAAGACCTTATAGTGATTGTAATGTTTC
595656 TTATTAAGGTCTTCCGTTTCCAACGGAAGACCTTATAGTGATTGTAATGTTTC
1 TTATTAAGGTCTTCCGTTTCCAACGGAAGACCTTATAGTGATTGTAATGTTTC
595709 TTATTA
1 TTATTA
595715 TTATTATTCT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 59 1.00
ACGTcount: A:0.25, C:0.16, G:0.18, T:0.41
Consensus pattern (53 bp):
TTATTAAGGTCTTCCGTTTCCAACGGAAGACCTTATAGTGATTGTAATGTTTC
Found at i:598891 original size:16 final size:18
Alignment explanation
Indices: 598859--598894 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
598849 CTTCAAAAAT
598859 AACTCCTTTTTCGCATAA
1 AACTCCTTTTTCGCATAA
598877 AACTCC-TTTTC-CATAA
1 AACTCCTTTTTCGCATAA
598893 AA
1 AA
598895 TAGATATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.39
17 5 0.28
18 6 0.33
ACGTcount: A:0.33, C:0.28, G:0.03, T:0.36
Consensus pattern (18 bp):
AACTCCTTTTTCGCATAA
Found at i:601983 original size:63 final size:63
Alignment explanation
Indices: 601903--602034 Score: 237
Period size: 63 Copynumber: 2.1 Consensus size: 63
601893 AAGAGTCTAG
* *
601903 TTATTAAGGTCTTCCGTTTCCAACGGAAGACCTTATTGTTATTGCTTTGTTTCTTTTTCACTA
1 TTATTAAGGTCTTCCGTTTCCAACGGAAGACCTTATTGTTATTGCTTTGATTCTTTTCCACTA
*
601966 TTATTAAGGTCTTCCGTTTCCAACGGAAGACCTTATTGTTATTGCTTTGATTCTTTTCCTCTA
1 TTATTAAGGTCTTCCGTTTCCAACGGAAGACCTTATTGTTATTGCTTTGATTCTTTTCCACTA
602029 TTATTA
1 TTATTA
602035 TTATTATTCT
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
63 66 1.00
ACGTcount: A:0.20, C:0.19, G:0.14, T:0.48
Consensus pattern (63 bp):
TTATTAAGGTCTTCCGTTTCCAACGGAAGACCTTATTGTTATTGCTTTGATTCTTTTCCACTA
Found at i:603013 original size:2 final size:2
Alignment explanation
Indices: 603006--603063 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
602996 CACTATGAAA
603006 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
603048 TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC
603064 ACCCTGACAA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:603358 original size:2 final size:2
Alignment explanation
Indices: 603351--603400 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
603341 GTTCAATAAT
603351 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
603393 TC TC TC TC
1 TC TC TC TC
603401 ATTATAGCTA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:604029 original size:1 final size:1
Alignment explanation
Indices: 604023--604047 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
604013 CACCGACCAA
604023 CCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCC
604048 ATTCATAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:605636 original size:2 final size:2
Alignment explanation
Indices: 605629--605684 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
605619 CGCATTAAAA
605629 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
605671 CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT
605685 GAATTGCAAT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:616304 original size:21 final size:22
Alignment explanation
Indices: 616266--616323 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 22
616256 GGCATTGAAG
* **
616266 TCTCATACAATAGAATTGGA-A
1 TCTCATACCATATCATTGGAGA
616287 TCTCATACCATATCATTGGAGA
1 TCTCATACCATATCATTGGAGA
*
616309 -GTCATACCATATCAT
1 TCTCATACCATATCAT
616324 ATAATCTCAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 31 0.97
22 1 0.03
ACGTcount: A:0.36, C:0.21, G:0.12, T:0.31
Consensus pattern (22 bp):
TCTCATACCATATCATTGGAGA
Found at i:616661 original size:42 final size:42
Alignment explanation
Indices: 616602--616690 Score: 160
Period size: 42 Copynumber: 2.1 Consensus size: 42
616592 AAATAGCATA
*
616602 CAAATCTCATAGCATTGCATTCAAATCTCATATCATATCATT
1 CAAATCTCATAGCATTGCATTCAAATCTCATAGCATATCATT
616644 CAAATCTCATAGCATTGCATTCAAATCTCATAGCATATCATT
1 CAAATCTCATAGCATTGCATTCAAATCTCATAGCATATCATT
*
616686 AAAAT
1 CAAAT
616691 TGCATACCAT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.38, C:0.22, G:0.06, T:0.34
Consensus pattern (42 bp):
CAAATCTCATAGCATTGCATTCAAATCTCATAGCATATCATT
Found at i:616696 original size:21 final size:22
Alignment explanation
Indices: 616597--616690 Score: 133
Period size: 21 Copynumber: 4.5 Consensus size: 22
616587 TTATAAAATA
*
616597 GCATACAAATCTCATAGCAT-T
1 GCATTCAAATCTCATAGCATAT
*
616618 GCATTCAAATCTCATATCATAT
1 GCATTCAAATCTCATAGCATAT
616640 -CATTCAAATCTCATAGCAT-T
1 GCATTCAAATCTCATAGCATAT
616660 GCATTCAAATCTCATAGCATAT
1 GCATTCAAATCTCATAGCATAT
*
616682 -CATTAAAAT
1 GCATTCAAAT
616691 TGCATACCAT
Statistics
Matches: 66, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
20 1 0.02
21 63 0.95
22 2 0.03
ACGTcount: A:0.38, C:0.22, G:0.06, T:0.33
Consensus pattern (22 bp):
GCATTCAAATCTCATAGCATAT
Found at i:619281 original size:331 final size:332
Alignment explanation
Indices: 617654--619370 Score: 2263
Period size: 331 Copynumber: 5.2 Consensus size: 332
617644 CATAATACAT
* * * *
617654 ACTTTGTATCTACACTACCTGACGATGCTT-CACAGAAGTTTCAACTTTCCTGGCTGATTAGGTT
1 ACTTTGTATCTACACTACCTGAGGATGCTTCCACACAAGTGTCAGCTTTCCTGGCTGATTA-GTT
* * * *
617718 CTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTTAAATTTTGA---CACCCCTT
65 -TTAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTTAAACTTTGACCCCCCCCCAT
* *
617780 TGTGGCCTTACCCTACCCCCGGGGGTCTTGATTTTCACAACTTTGAATTTACACTACCTGAGGAT
129 TGTGGCCCTACCCTACCCCC-GGGGTCATGATTTTCACAACTTTGAATTTACACTACCTGAGGAT
* * *
617845 GCTTCAACACAAGTGTCAGCTTTGCC-GGCTGAATAGTTTCTGAGAAGAGGATTTTTAAAGATTT
193 GCTTCCACACAAGTGTCAGCTTT-CCTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTT
* * *
617909 ACTCTATATATTCCTAGGTAAAACTTCTATCCCCCATTGTGGCCCCACCCTACACCC-GGGGTCA
257 ACTCTATATATTCCTATGTAAAACTTCGACCCCCCATTGTGGCCCCACCCTACACCCGGGGGTCA
617973 TGATTTTCACA
322 TGATTTTCACA
*
617984 ACTTTGTATCTACACTACCTGGGGATGCTTCCACACAAGTGTCAGCTTTCCTGGCTGATTAGTTT
1 ACTTTGTATCTACACTACCTGAGGATGCTTCCACACAAGTGTCAGCTTTCCTGGCTGATTAGTTT
* **
618049 CTGAGAAGAAGATTTTTAAAGATATACTCTATATATTTATATGTTAAACTTTGACCCCCCCCCCC
66 -T-AGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTTAAACTTTGA--CCCCCCCCC
* * ** * *
618114 ATTGCGGTCCTACCCTAAACCCGGGGTCATGATTTTCACAACTTTGAATCTACACTACCTGTGGA
127 ATTGTGGCCCTACCCTACCCCCGGGGTCATGATTTTCACAACTTTGAATTTACACTACCTGAGGA
* *
618179 TGCTTCCACACAAGTGTCAACTTTCCTCGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTT
192 TGCTTCCACACAAGTGTCAGCTTTCCTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTT
** * *
618244 ACTCTATATATTCCTATGTAAAACTTCGA-TACCCATTGTGGCCCCACCCTTCACCCGGGGATCA
257 ACTCTATATATTCCTATGTAAAACTTCGACCCCCCATTGTGGCCCCACCCTACACCCGGGGGTCA
618308 TGATTTTCACA
322 TGATTTTCACA
* * *
618319 ACTTCGTATCTACTCTACCTGAGGATGCTTCCACACAAGTGTCAGCTTTCCTTGCTGATTAGTTT
1 ACTTTGTATCTACACTACCTGAGGATGCTTCCACACAAGTGTCAGCTTTCCTGGCTGATTAGTTT
* * * *
618384 CTGAGTAGAAGTTTTTTAAAAGATTTACTCTATATATTCCTATGTAAAAC-TT--CCACCCCCCA
66 -T-AGAAGAAGATTTTT-AAAGATTTACTCTATATATTCCTATGTTAAACTTTGACCCCCCCCCA
618446 TTGTGGCCCTACCCTACCCCCGGGGATCATGATTTTCACAACTTTGAATTTACACTACCTGAGGA
128 TTGTGGCCCTACCCTACCCCCGGGG-TCATGATTTTCACAACTTTGAATTTACACTACCTGAGGA
* * * * * * *
618511 TGCTCCCACACAAGTTTAAGCTTTCCTTG-T-AATATGGTTCATGAGAAAAAGATTTTTAAAGAT
192 TGCTTCCACACAAGTGTCAGCTTTCCTGGCTGATTA-GTTTC-TGAGAAGAAGATTTTTAAAGAT
* * *
618574 TTACTCTGTATATTCCTATGTAAAATTTCGACCCCCTCCCATTGTGGCCCCACCCTACCCCCGGG
255 TTACTCTATATATTCCTATGTAAAACTTCGA--CCC-CCCATTGTGGCCCCACCCTACACCCGGG
*
618639 GGTCATGATTTTCTCA
317 GGTCATGATTTTCACA
* * *
618655 ACTTTGTATCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTCTCCTGGCTGATTTGTTT
1 ACTTTGTATCTACACTACCTGAGGATGCTTCCACACAAGTGTCAGCTTTCCTGGCTGATTAG-TT
*
618720 TTGAGAAGAAGATTTTTAAAGATTTACTCAATATATT--TATGTTAAACTTTGA--CCCCCCCAT
65 TT-AGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTTAAACTTTGACCCCCCCCCAT
* * * *
618781 TGTGGCCCCAGCCTACCCCCAGGGGTCATGATTTTCACAACTTAGAATTTACACTACCTGAGAAT
129 TGTGGCCCTACCCTACCCCC-GGGGTCATGATTTTCACAACTTTGAATTTACACTACCTGAGGAT
* *
618846 GTTTCCACACAAGTTTCAGCTTTGCCAT--CTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATT
193 GCTTCCACACAAGTGTCAGCTTT-CC-TGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATT
* **
618909 TACTCTATATATTCCTATGTTAAACTTCGATTCCCCATTGTGGCCCCACCCTACACCCGGGGGTC
256 TACTCTATATATTCCTATGTAAAACTTCGACCCCCCATTGTGGCCCCACCCTACACCCGGGGGTC
*
618974 ATGATTTTGACA
321 ATGATTTTCACA
* * * * * *
618986 ACTTTGAATCTACACTACCTCATGATGCTTTCATACAAGTGTCATCTTTCCTGGCTGATTAGTTT
1 ACTTTGTATCTACACTACCTGAGGATGCTTCCACACAAGTGTCAGCTTTCCTGGCTGATTAGTTT
* * *
619051 TTG-AGAAGA-TTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTCGACCCCCCCCCCATT
66 TAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTTAAACTTTGA-CCCCCCCCCATT
* * * * * *
619114 GTGACCCAACCCTACCCCCGGGGATCATGATTTTTACAACTGTGAATCTACACTACCTGAGAATG
130 GTGGCCCTACCCTACCCCCGGGG-TCATGATTTTCACAACTTTGAATTTACACTACCTGAGGATG
* * **
619179 CTTCAACACAAGTGTCAGCTTTCCTGGCCGATTAGTTTCTGAGAAGAAGATTTTTAAAGAAATAC
194 CTTCCACACAAGTGTCAGCTTTCCTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTAC
* *
619244 TCTATATATTCATATGTTAAACTTCGA-CCCCCATTGTGGCCCCACCCTAC-CCTCGGGGGTCAT
259 TCTATATATTCCTATGTAAAACTTCGACCCCCCATTGTGGCCCCACCCTACACC-CGGGGGTCAT
619307 GATTTTCACA
323 GATTTTCACA
* * *
619317 ACGTTCTATCTACATTACCTGAGGATGCTTCCACACAAGTGTCAGCTTTCCTGG
1 ACTTTGTATCTACACTACCTGAGGATGCTTCCACACAAGTGTCAGCTTTCCTGG
619371 TCTTATGGTC
Statistics
Matches: 1220, Mismatches: 131, Indels: 71
0.86 0.09 0.05
Matches are distributed among these distances:
327 23 0.02
328 6 0.00
329 15 0.01
330 41 0.03
331 295 0.24
332 255 0.21
333 9 0.01
334 161 0.13
335 249 0.20
336 163 0.13
337 3 0.00
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.33
Consensus pattern (332 bp):
ACTTTGTATCTACACTACCTGAGGATGCTTCCACACAAGTGTCAGCTTTCCTGGCTGATTAGTTT
TAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTTAAACTTTGACCCCCCCCCATTG
TGGCCCTACCCTACCCCCGGGGTCATGATTTTCACAACTTTGAATTTACACTACCTGAGGATGCT
TCCACACAAGTGTCAGCTTTCCTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTC
TATATATTCCTATGTAAAACTTCGACCCCCCATTGTGGCCCCACCCTACACCCGGGGGTCATGAT
TTTCACA
Found at i:619398 original size:165 final size:166
Alignment explanation
Indices: 617654--619370 Score: 2206
Period size: 165 Copynumber: 10.3 Consensus size: 166
617644 CATAATACAT
* * * * * *
617654 ACTTTGTATCTACACTACCTGACGATGCTT-CACAGAAGTTTCAACTTTCCTGGCTGATTAGGTT
1 ACTTTGAATCTACACTACCTGAGGATGCTTCCACACAAGTGTCAGCTTTCCTGGCTGATTAGTTT
* * * * *
617718 CTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTTAAATTTTGACACCCCTTTGT
66 CTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTCGACCCCCCATTGT
** *
617783 GGCCTTACCCTACCCCCGGGGGTCTTGATTTTCACA
131 GGCCCCACCCTACCCCCGGGGGTCATGATTTTCACA
* * *
617819 ACTTTGAATTTACACTACCTGAGGATGCTTCAACACAAGTGTCAGCTTTGCC-GGCTGAATAGTT
1 ACTTTGAATCTACACTACCTGAGGATGCTTCCACACAAGTGTCAGCTTT-CCTGGCTGATTAGTT
* * * *
617883 TCTGAGAAGAGGATTTTTAAAGATTTACTCTATATATTCCTAGGTAAAACTTCTATCCCCCATTG
65 TCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTCGACCCCCCATTG
*
617948 TGGCCCCACCCTACACCC-GGGGTCATGATTTTCACA
130 TGGCCCCACCCTACCCCCGGGGGTCATGATTTTCACA
* *
617984 ACTTTGTATCTACACTACCTGGGGATGCTTCCACACAAGTGTCAGCTTTCCTGGCTGATTAGTTT
1 ACTTTGAATCTACACTACCTGAGGATGCTTCCACACAAGTGTCAGCTTTCCTGGCTGATTAGTTT
* ** * *
618049 CTGAGAAGAAGATTTTTAAAGATATACTCTATATATTTATATGTTAAACTTTGACCCCCCCCCCC
66 CTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTCGA-----CCCCCC
* * * **
618114 ATTGCGGTCCTACCCTAAACCC-GGGGTCATGATTTTCACA
126 ATTGTGGCCCCACCCTACCCCCGGGGGTCATGATTTTCACA
* * *
618154 ACTTTGAATCTACACTACCTGTGGATGCTTCCACACAAGTGTCAACTTTCCTCGCTGATTAGTTT
1 ACTTTGAATCTACACTACCTGAGGATGCTTCCACACAAGTGTCAGCTTTCCTGGCTGATTAGTTT
**
618219 CTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTCGA-TACCCATTGT
66 CTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTCGACCCCCCATTGT
* * *
618283 GGCCCCACCCTTCACCCGGGGATCATGATTTTCACA
131 GGCCCCACCCTACCCCCGGGGGTCATGATTTTCACA
* * * *
618319 ACTTCGTATCTACTCTACCTGAGGATGCTTCCACACAAGTGTCAGCTTTCCTTGCTGATTAGTTT
1 ACTTTGAATCTACACTACCTGAGGATGCTTCCACACAAGTGTCAGCTTTCCTGGCTGATTAGTTT
* * *
618384 CTGAGTAGAAGTTTTTTAAAAGATTTACTCTATATATTCCTATGTAAAACTTCCACCCCCCATTG
66 CTGAGAAGAAGATTTTT-AAAGATTTACTCTATATATTCCTATGTAAAACTTCGACCCCCCATTG
* *
618449 TGGCCCTACCCTACCCCCGGGGATCATGATTTTCACA
130 TGGCCCCACCCTACCCCCGGGGGTCATGATTTTCACA
* * * * * * *
618486 ACTTTGAATTTACACTACCTGAGGATGCTCCCACACAAGTTTAAGCTTTCCTTG-T-AATATGGT
1 ACTTTGAATCTACACTACCTGAGGATGCTTCCACACAAGTGTCAGCTTTCCTGGCTGATTA-GTT
* * *
618549 TCATGAGAAAAAGATTTTTAAAGATTTACTCTGTATATTCCTATGTAAAATTTCGACCCCCTCCC
65 TC-TGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTCGA--CCC-CCC
*
618614 ATTGTGGCCCCACCCTACCCCCGGGGGTCATGATTTTCTCA
126 ATTGTGGCCCCACCCTACCCCCGGGGGTCATGATTTTCACA
* * * *
618655 ACTTTGTATCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTCTCCTGGCTGATTTGTTT
1 ACTTTGAATCTACACTACCTGAGGATGCTTCCACACAAGTGTCAGCTTTCCTGGCTGATTAGTTT
* * * *
618720 TTGAGAAGAAGATTTTTAAAGATTTACTCAATATATT--TATGTTAAACTTTGACCCCCCCATTG
66 CTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTCGA-CCCCCCATTG
* *
618783 TGGCCCCAGCCTACCCCCAGGGGTCATGATTTTCACA
130 TGGCCCCACCCTACCCCCGGGGGTCATGATTTTCACA
* * * * *
618820 ACTTAGAATTTACACTACCTGAGAATGTTTCCACACAAGTTTCAGCTTTGCCAT--CTGATTAGT
1 ACTTTGAATCTACACTACCTGAGGATGCTTCCACACAAGTGTCAGCTTT-CC-TGGCTGATTAGT
* **
618883 TTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTTAAACTTCGATTCCCCATT
64 TTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTCGACCCCCCATT
* *
618948 GTGGCCCCACCCTACACCCGGGGGTCATGATTTTGACA
129 GTGGCCCCACCCTACCCCCGGGGGTCATGATTTTCACA
* * * * *
618986 ACTTTGAATCTACACTACCTCATGATGCTTTCATACAAGTGTCATCTTTCCTGGCTGATTAGTTT
1 ACTTTGAATCTACACTACCTGAGGATGCTTCCACACAAGTGTCAGCTTTCCTGGCTGATTAGTTT
*
619051 -T-TG-AGAAGA-TTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTCGACCCCCCCCCCA
66 CTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTCGA----CCCCCCA
* * * *
619112 TTGTGACCCAACCCTACCCCCGGGGATCATGATTTTTACA
127 TTGTGGCCCCACCCTACCCCCGGGGGTCATGATTTTCACA
* * * *
619152 ACTGTGAATCTACACTACCTGAGAATGCTTCAACACAAGTGTCAGCTTTCCTGGCCGATTAGTTT
1 ACTTTGAATCTACACTACCTGAGGATGCTTCCACACAAGTGTCAGCTTTCCTGGCTGATTAGTTT
** * *
619217 CTGAGAAGAAGATTTTTAAAGAAATACTCTATATATTCATATGTTAAACTTCGA-CCCCCATTGT
66 CTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTCGACCCCCCATTGT
*
619281 GGCCCCACCCTACCCTCGGGGGTCATGATTTTCACA
131 GGCCCCACCCTACCCCCGGGGGTCATGATTTTCACA
* ** *
619317 ACGTTCTATCTACATTACCTGAGGATGCTTCCACACAAGTGTCAGCTTTCCTGG
1 ACTTTGAATCTACACTACCTGAGGATGCTTCCACACAAGTGTCAGCTTTCCTGG
619371 TCTTATGGTC
Statistics
Matches: 1351, Mismatches: 169, Indels: 64
0.85 0.11 0.04
Matches are distributed among these distances:
162 40 0.03
163 6 0.00
164 24 0.02
165 461 0.34
166 363 0.27
167 131 0.10
168 4 0.00
169 128 0.09
170 192 0.14
171 2 0.00
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.33
Consensus pattern (166 bp):
ACTTTGAATCTACACTACCTGAGGATGCTTCCACACAAGTGTCAGCTTTCCTGGCTGATTAGTTT
CTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTCGACCCCCCATTGT
GGCCCCACCCTACCCCCGGGGGTCATGATTTTCACA
Found at i:619577 original size:4 final size:4
Alignment explanation
Indices: 619568--619609 Score: 50
Period size: 4 Copynumber: 10.8 Consensus size: 4
619558 TGAAAAGTTT
* * *
619568 ACAG ACAG ACGG ACAG ACGG ACAG ACAG ACGG AC-G ACAG ACA
1 ACAG ACAG ACAG ACAG ACAG ACAG ACAG ACAG ACAG ACAG ACA
619610 AAATGTGATC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
3 3 0.09
4 29 0.91
ACGTcount: A:0.43, C:0.26, G:0.31, T:0.00
Consensus pattern (4 bp):
ACAG
Found at i:621954 original size:48 final size:46
Alignment explanation
Indices: 621815--622087 Score: 376
Period size: 46 Copynumber: 6.0 Consensus size: 46
621805 CACATATATA
621815 GGAAGAAATATTGTTATTATATATAGTTACTGTATACAGGGCTATT
1 GGAAGAAATATTGTTATTATATATAGTTACTGTATACAGGGCTATT
* *
621861 GGAAGTAATATTGTTATTATATATAGTTACTGTATACAGGACTATT
1 GGAAGAAATATTGTTATTATATATAGTTACTGTATACAGGGCTATT
*
621907 GGAAGTAATATTGTTATTAAATATATAGTTACTGTATACAGGGCTATT
1 GGAAGAAATATTGTTATT--ATATATAGTTACTGTATACAGGGCTATT
*
621955 GGAAGAAATATTGTTATTATATATAGTTACTGTATATAGGGCTATT
1 GGAAGAAATATTGTTATTATATATAGTTACTGTATACAGGGCTATT
*** * *
622001 -TTTGAAATATTTTTATTATATAAAGTTACTGTATACAGGGCTATT
1 GGAAGAAATATTGTTATTATATATAGTTACTGTATACAGGGCTATT
*** *
622046 -TTTGAAATA---TTATTATATATAGTTACTGTATACAGGACTATT
1 GGAAGAAATATTGTTATTATATATAGTTACTGTATACAGGGCTATT
622088 TTTGTCCCGT
Statistics
Matches: 212, Mismatches: 13, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
42 31 0.15
45 48 0.23
46 89 0.42
48 44 0.21
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (46 bp):
GGAAGAAATATTGTTATTATATATAGTTACTGTATACAGGGCTATT
Found at i:621974 original size:94 final size:92
Alignment explanation
Indices: 621815--622087 Score: 385
Period size: 94 Copynumber: 3.0 Consensus size: 92
621805 CACATATATA
*
621815 GGAAGAAATATTGTTATTATATATAGTTACTGTATACAGGGCTATTGGAAGTAATATTGTTATTA
1 GGAAGAAATATTGTTATTATATATAGTTACTGTATACAGGGCTATTGGAAGAAATATTGTTATTA
621880 TATATAGTTACTGTATACAGGACTATT
66 TATATAGTTACTGTATACAGGACTATT
*
621907 GGAAGTAATATTGTTATTAAATATATAGTTACTGTATACAGGGCTATTGGAAGAAATATTGTTAT
1 GGAAGAAATATTGTTATT--ATATATAGTTACTGTATACAGGGCTATTGGAAGAAATATTGTTAT
* *
621972 TATATATAGTTACTGTATATAGGGCTATT
64 TATATATAGTTACTGTATACAGGACTATT
*** * * ***
622001 -TTTGAAATATTTTTATTATATAAAGTTACTGTATACAGGGCTATT-TTTGAAATA---TTATTA
1 GGAAGAAATATTGTTATTATATATAGTTACTGTATACAGGGCTATTGGAAGAAATATTGTTATTA
622061 TATATAGTTACTGTATACAGGACTATT
66 TATATAGTTACTGTATACAGGACTATT
622088 TTTGTCCCGT
Statistics
Matches: 164, Mismatches: 15, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
87 31 0.19
90 6 0.04
91 27 0.16
92 17 0.10
93 12 0.07
94 71 0.43
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (92 bp):
GGAAGAAATATTGTTATTATATATAGTTACTGTATACAGGGCTATTGGAAGAAATATTGTTATTA
TATATAGTTACTGTATACAGGACTATT
Found at i:622047 original size:34 final size:37
Alignment explanation
Indices: 622013--622090 Score: 93
Period size: 42 Copynumber: 2.0 Consensus size: 37
622003 TGAAATATTT
* *
622013 TTATTATATAAAGTTACTGTATACAGGGCTATTTTTGAAATA
1 TTATTATATATAGTTACTGTATACAGGACTA-TTTT----TA
622055 TTATTATATATAGTTACTGTATACAGGACTATTTTT
1 TTATTATATATAGTTACTGTATACAGGACTATTTTT
622091 GTCCCGTGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
37 1 0.03
41 4 0.12
42 29 0.85
ACGTcount: A:0.33, C:0.08, G:0.13, T:0.46
Consensus pattern (37 bp):
TTATTATATATAGTTACTGTATACAGGACTATTTTTA
Found at i:628053 original size:47 final size:47
Alignment explanation
Indices: 627981--628728 Score: 1000
Period size: 47 Copynumber: 16.0 Consensus size: 47
627971 CCCAAAACAA
* *
627981 TATACATACTATAACATTATCAACATAATTAACTATTCATATTACAG
1 TATACATACTATAACATTATTAACATAATTAACTAGTCATATTACAG
* * * *
628028 AATACATCCTATATCATTATTAACATAAGTAACTAGTCATATTACAG
1 TATACATACTATAACATTATTAACATAATTAACTAGTCATATTACAG
* * *
628075 TATACATACTATAACATTATTAACATAATCAACTATTCATATCACAG
1 TATACATACTATAACATTATTAACATAATTAACTAGTCATATTACAG
* * * *
628122 TATTCATCCTATAACATTATTAACATAATTAACTATTCATATAACAG
1 TATACATACTATAACATTATTAACATAATTAACTAGTCATATTACAG
* * * *
628169 TATACATACTGTAACATTATAAACATAATTAACTATTCATATTGCAG
1 TATACATACTATAACATTATTAACATAATTAACTAGTCATATTACAG
* * *
628216 TATACATCCTATAACATTATTAAC--AATTAACTAGTCATATTAAAT
1 TATACATACTATAACATTATTAACATAATTAACTAGTCATATTACAG
* * *
628261 TATACGTACTATAACATTGTTAACATAATTAACTAGTCACATTA-AG
1 TATACATACTATAACATTATTAACATAATTAACTAGTCATATTACAG
628307 TATACATACTATAACATTATTAACATAATTAAC-ATGTCATATTACAG
1 TATACATACTATAACATTATTAACATAATTAACTA-GTCATATTACAG
** * * * * *
628354 TATACATGTTATAACATCATTAATATAATCAATTATTCATATTACAG
1 TATACATACTATAACATTATTAACATAATTAACTAGTCATATTACAG
*
628401 AATACATACTATAACATTATTAACATAATTAACTAGTCATATTACAG
1 TATACATACTATAACATTATTAACATAATTAACTAGTCATATTACAG
** * * * *
628448 TATACATGTTATAACATCATTAACATAATCAATTATTCATATTACAG
1 TATACATACTATAACATTATTAACATAATTAACTAGTCATATTACAG
* * *
628495 AATACATACTATAACATTATTAACATGATCAACTAGTCATATTACAG
1 TATACATACTATAACATTATTAACATAATTAACTAGTCATATTACAG
* *
628542 TATATATACTATAACATTATTAACATAATCAACTAGTCATATTACAG
1 TATACATACTATAACATTATTAACATAATTAACTAGTCATATTACAG
* *
628589 TATACATACTATAACATTATTAGCATAGTTAACTAGTCATATTACAG
1 TATACATACTATAACATTATTAACATAATTAACTAGTCATATTACAG
* * * * *
628636 TATACATGCTATTACATTAATAACATAATCAACTATTCATATTACAG
1 TATACATACTATAACATTATTAACATAATTAACTAGTCATATTACAG
* *
628683 TATACATGCTATAACATTATTACCATAATTAACTAGTCATATTACA
1 TATACATACTATAACATTATTAACATAATTAACTAGTCATATTACA
628729 TTTCTTTCTT
Statistics
Matches: 610, Mismatches: 86, Indels: 10
0.86 0.12 0.01
Matches are distributed among these distances:
45 39 0.06
46 40 0.07
47 530 0.87
48 1 0.00
ACGTcount: A:0.43, C:0.16, G:0.05, T:0.36
Consensus pattern (47 bp):
TATACATACTATAACATTATTAACATAATTAACTAGTCATATTACAG
Found at i:630221 original size:4 final size:4
Alignment explanation
Indices: 630199--630240 Score: 50
Period size: 4 Copynumber: 10.8 Consensus size: 4
630189 ATCACATTTT
* * *
630199 GTCC GT-C GTCC GTCT GTCC GTCC GTCC GTCT GTCT GTCC GTC
1 GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTC
630241 TGTAAACATT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
3 3 0.09
4 30 0.91
ACGTcount: A:0.00, C:0.40, G:0.26, T:0.33
Consensus pattern (4 bp):
GTCC
Found at i:630222 original size:12 final size:12
Alignment explanation
Indices: 630199--630243 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
630189 ATCACATTTT
630199 GTCCGTC-GTCC
1 GTCCGTCTGTCC
* *
630210 GTCTGTCCGTCC
1 GTCCGTCTGTCC
*
630222 GTCCGTCTGTCT
1 GTCCGTCTGTCC
630234 GTCCGTCTGT
1 GTCCGTCTGT
630244 AAACATTTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
11 6 0.21
12 23 0.79
ACGTcount: A:0.00, C:0.38, G:0.27, T:0.36
Consensus pattern (12 bp):
GTCCGTCTGTCC
Found at i:630226 original size:16 final size:16
Alignment explanation
Indices: 630198--630240 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
630188 GATCACATTT
630198 TGTCCGT-CGTCCGTC
1 TGTCCGTCCGTCCGTC
630213 TGTCCGTCCGTCCGTC
1 TGTCCGTCCGTCCGTC
*
630229 TGTCTGTCCGTC
1 TGTCCGTCCGTC
630241 TGTAAACATT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 7 0.27
16 19 0.73
ACGTcount: A:0.00, C:0.40, G:0.26, T:0.35
Consensus pattern (16 bp):
TGTCCGTCCGTCCGTC
Found at i:633961 original size:2 final size:2
Alignment explanation
Indices: 633956--634002 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
633946 GAAACCCCCC
633956 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
633998 CT CT C
1 CT CT C
634003 ATGCTTTTAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:640614 original size:41 final size:41
Alignment explanation
Indices: 640553--641424 Score: 1239
Period size: 41 Copynumber: 21.5 Consensus size: 41
640543 CATAGTACAT
* * *
640553 ATGTGTATCAGTGACAGATAAATACACAACAACAAAGTGCC
1 ATGTGTATCAGTGACTGATAAATACACAACAACACAGTACC
* *
640594 ATGTGTATCAGTGACTGATAAATACACAACAACACAGAACT
1 ATGTGTATCAGTGACTGATAAATACACAACAACACAGTACC
* * **
640635 ATGTGCATCATTGACTGATAAATACACAACAACATTGTACC
1 ATGTGTATCAGTGACTGATAAATACACAACAACACAGTACC
* *
640676 ATGTGTATCAGTGACTGAAAAATATACAACAACACAGTACC
1 ATGTGTATCAGTGACTGATAAATACACAACAACACAGTACC
*
640717 ATGTGTATCAGTGACTGAAAAATACACAACAACACAGTACC
1 ATGTGTATCAGTGACTGATAAATACACAACAACACAGTACC
* *
640758 ATGTGTATCAGTGACTGAAAAATACACAAC-A-A-TGTACCC
1 ATGTGTATCAGTGACTGATAAATACACAACAACACAGTA-CC
* *
640797 ATGTGTTTGAGTGACTGATAAATACACAACAACACAGTACC
1 ATGTGTATCAGTGACTGATAAATACACAACAACACAGTACC
* * *
640838 ATGTGTATTAGTGACTGATTAATACTCAACAACACAGTACC
1 ATGTGTATCAGTGACTGATAAATACACAACAACACAGTACC
*
640879 ATGTGTATCAGTGACTGATCAATACACAACAACACAGTACC
1 ATGTGTATCAGTGACTGATAAATACACAACAACACAGTACC
**
640920 ATGTGTATCAGTGACTGATAAATACACAACAACATTGTACC
1 ATGTGTATCAGTGACTGATAAATACACAACAACACAGTACC
* **
640961 TATGTGTATCAGTGACTGATAAAT--A-GACAACATTGTACC
1 -ATGTGTATCAGTGACTGATAAATACACAACAACACAGTACC
*
641000 TATGTGTATCATTGACTGATAAATACACAACAACACAGTACC
1 -ATGTGTATCAGTGACTGATAAATACACAACAACACAGTACC
* *
641042 ATGTGTATCATTGACTAATAAAT--AC-ACAACACAGTACC
1 ATGTGTATCAGTGACTGATAAATACACAACAACACAGTACC
* *
641080 ATGTGTATTAGTGACTGATAAATACACAAC-ACACAGAACC
1 ATGTGTATCAGTGACTGATAAATACACAACAACACAGTACC
* *
641120 ATGTGTATCATTAACTGATAAATACACAACAAC-CAGTACC
1 ATGTGTATCAGTGACTGATAAATACACAACAACACAGTACC
* *
641160 ATGTGTATCAGTGACTGATTAATACACAACAACACAGTGCC
1 ATGTGTATCAGTGACTGATAAATACACAACAACACAGTACC
641201 ATGTGTATCAGTGACTGATAAATACACAACAACACAGTACC
1 ATGTGTATCAGTGACTGATAAATACACAACAACACAGTACC
* * *
641242 TTATGTATCAGTGACTGGTAAATACACAACAACACAGTACC
1 ATGTGTATCAGTGACTGATAAATACACAACAACACAGTACC
*
641283 ATGTGTATCAGTGACTGATCAATACACAACAACACAGTAACC
1 ATGTGTATCAGTGACTGATAAATACACAACAACACAGT-ACC
* *
641325 -TGTGTATCAGTGACTGATAAATTCA-AACAACACAGTATC
1 ATGTGTATCAGTGACTGATAAATACACAACAACACAGTACC
*
641364 ATGTGTATCAGTGACTGATGAATACACAACAACACAGTACC
1 ATGTGTATCAGTGACTGATAAATACACAACAACACAGTACC
*
641405 ATGTGTATCATTGACTGATA
1 ATGTGTATCAGTGACTGATA
641425 NNNNNNNNNN
Statistics
Matches: 747, Mismatches: 68, Indels: 32
0.88 0.08 0.04
Matches are distributed among these distances:
38 36 0.05
39 70 0.09
40 111 0.15
41 490 0.66
42 40 0.05
ACGTcount: A:0.40, C:0.21, G:0.15, T:0.25
Consensus pattern (41 bp):
ATGTGTATCAGTGACTGATAAATACACAACAACACAGTACC
Found at i:641301 original size:363 final size:366
Alignment explanation
Indices: 640553--641422 Score: 1290
Period size: 363 Copynumber: 2.4 Consensus size: 366
640543 CATAGTACAT
* *
640553 ATGTGTATCAGTGACAGATAAATACACAACAACAAAGTGCCATGTGTATCAGTGACTGATAAATA
1 ATGTGTATCAGTGACTGATAAATACACAACAACAAAGTACCATGTGTATCAGTGACTGATAAAT-
* **
640618 CACAACAACACAG-AACTATGTGCATCATTGACTGATAAATACACAACAACATTGTACCATGTGT
65 CA-AACAACACAGTAACTATGTGTATCATTGACTGATAAATACACAACAACACAGTACCATGTGT
*
640682 ATCAGTGACTGAAAAATATACAACAACACAGTACCATGTGTATCAGTGACTGAAAAATACACAAC
129 ATCATTGACTGAAAAATATACAACAACACAGTACCATGTGTATCAGTGACTGAAAAATACACAAC
* * * * *
640747 AACACAGTACCATGTGTATCAGTGACTGAAAAATACACAACAATGTACCCATGTGTTTGAGTGAC
194 AACACAGAACCATGTGTATCAGTAACTGAAAAATACACAACAAAGTACCCATGTGTATCAGTGAC
* * *
640812 TGATAAATACACAACAACACAGTACCATGTGTATTAGTGACTGATTAATACTCAACAACACAGTA
259 TGATAAATACACAACAACACAGTACCATGTGTATCAGTGACTGATAAATACACAACAACACAGTA
* *
640877 CCATGTGTATCAGTGACTGATCAATACACAACAACACAGTACC
324 CCATATGTATCAGTGACTGATAAATACACAACAACACAGTACC
**
640920 ATGTGTATCAGTGACTGATAAATACACAACAACATTGTACCTATGTGTATCAGTGACTGATAAAT
1 ATGTGTATCAGTGACTGATAAATACACAACAACAAAGTACC-ATGTGTATCAGTGACTGATAAAT
* ** *
640985 -AGACAACATTGTACCTATGTGTATCATTGACTGATAAATACACAACAACACAGTACCATGTGTA
65 CAAACAACACAGTAACTATGTGTATCATTGACTGATAAATACACAACAACACAGTACCATGTGTA
* * *
641049 TCATTGACT-AATAA-ATAC-ACAACACAGTACCATGTGTATTAGTGACTGATAAATACACAAC-
130 TCATTGACTGAAAAATATACAACAACACAGTACCATGTGTATCAGTGACTGAAAAATACACAACA
* *
641110 ACACAGAACCATGTGTATCATTAACTGATAAATACACAACAACCAGTA-CCATGTGTATCAGTGA
195 ACACAGAACCATGTGTATCAGTAACTGAAAAATACACAACAA--AGTACCCATGTGTATCAGTGA
* *
641174 CTGATTAATACACAACAACACAGTGCCATGTGTATCAGTGACTGATAAATACACAACAACACAGT
258 CTGATAAATACACAACAACACAGTACCATGTGTATCAGTGACTGATAAATACACAACAACACAGT
* *
641239 ACCTTATGTATCAGTGACTGGTAAATACACAACAACACAGTACC
323 ACCATATGTATCAGTGACTGATAAATACACAACAACACAGTACC
* *
641283 ATGTGTATCAGTGACTGATCAATACACAACAACACAGTAACC-TGTGTATCAGTGACTGATAAAT
1 ATGTGTATCAGTGACTGATAAATACACAACAACAAAGT-ACCATGTGTATCAGTGACTGATAAA-
* * *
641347 TCAAACAACACAGTATC-ATGTGTATCAGTGACTGATGAATACACAACAACACAGTACCATGTGT
64 TCAAACAACACAGTAACTATGTGTATCATTGACTGATAAATACACAACAACACAGTACCATGTGT
641411 ATCATTGACTGA
129 ATCATTGACTGA
641423 TANNNNNNNN
Statistics
Matches: 455, Mismatches: 40, Indels: 19
0.89 0.08 0.04
Matches are distributed among these distances:
362 59 0.13
363 246 0.54
364 22 0.05
365 11 0.02
366 57 0.13
367 37 0.08
368 23 0.05
ACGTcount: A:0.40, C:0.21, G:0.15, T:0.24
Consensus pattern (366 bp):
ATGTGTATCAGTGACTGATAAATACACAACAACAAAGTACCATGTGTATCAGTGACTGATAAATC
AAACAACACAGTAACTATGTGTATCATTGACTGATAAATACACAACAACACAGTACCATGTGTAT
CATTGACTGAAAAATATACAACAACACAGTACCATGTGTATCAGTGACTGAAAAATACACAACAA
CACAGAACCATGTGTATCAGTAACTGAAAAATACACAACAAAGTACCCATGTGTATCAGTGACTG
ATAAATACACAACAACACAGTACCATGTGTATCAGTGACTGATAAATACACAACAACACAGTACC
ATATGTATCAGTGACTGATAAATACACAACAACACAGTACC
Found at i:649224 original size:41 final size:41
Alignment explanation
Indices: 649165--649480 Score: 406
Period size: 41 Copynumber: 7.6 Consensus size: 41
649155 NNNNNNNNNN
* *
649165 AACAACACAGT-ATCATGTGTATCAGTGACTGATTAATACAC
1 AACAACACAGTGCT-ATGTGTATCAGTGACTGATAAATACAC
*
649206 AACAACACAGTGCTATGTGTATCATTGACTGATAAATACAC
1 AACAACACAGTGCTATGTGTATCAGTGACTGATAAATACAC
*
649247 AACAACACAGTGCCATGTGTATCAGTGACTGATAAATACAC
1 AACAACACAGTGCTATGTGTATCAGTGACTGATAAATACAC
* * * *
649288 AGCAACACAG-GACCTATGTGTATCAATGATTGATAAACACAC
1 AACAACACAGTG--CTATGTGTATCAGTGACTGATAAATACAC
*
649330 AACAACACAGTGCCATGTGTATCAGTGACTGATAAATACAC
1 AACAACACAGTGCTATGTGTATCAGTGACTGATAAATACAC
* * * *
649371 AGCAACACAG-GACCTATGTGTATCAATGATTGATAAACACAC
1 AACAACACAGTG--CTATGTGTATCAGTGACTGATAAATACAC
*
649413 AACAACACAGTGCCATGTGTATCAGTGACTGATAAATACAC
1 AACAACACAGTGCTATGTGTATCAGTGACTGATAAATACAC
*
649454 AGCAACACAG-GACCTATGTGTATCAGT
1 AACAACACAGTG--CTATGTGTATCAGT
649481 CTATTCCTTA
Statistics
Matches: 239, Mismatches: 27, Indels: 17
0.84 0.10 0.06
Matches are distributed among these distances:
40 3 0.01
41 152 0.64
42 82 0.34
43 2 0.01
ACGTcount: A:0.39, C:0.21, G:0.17, T:0.23
Consensus pattern (41 bp):
AACAACACAGTGCTATGTGTATCAGTGACTGATAAATACAC
Found at i:649342 original size:83 final size:83
Alignment explanation
Indices: 649165--649478 Score: 542
Period size: 83 Copynumber: 3.8 Consensus size: 83
649155 NNNNNNNNNN
** * *
649165 AACAACACAGTATCATGTGTATCAGTGACTGATTAATACACAACAACACAGTG--CTATGTGTAT
1 AACAACACAGTGCCATGTGTATCAGTGACTGATAAATACACAGCAACACAG-GACCTATGTGTAT
* * *
649228 CATTGACTGATAAATACAC
65 CAATGATTGATAAACACAC
649247 AACAACACAGTGCCATGTGTATCAGTGACTGATAAATACACAGCAACACAGGACCTATGTGTATC
1 AACAACACAGTGCCATGTGTATCAGTGACTGATAAATACACAGCAACACAGGACCTATGTGTATC
649312 AATGATTGATAAACACAC
66 AATGATTGATAAACACAC
649330 AACAACACAGTGCCATGTGTATCAGTGACTGATAAATACACAGCAACACAGGACCTATGTGTATC
1 AACAACACAGTGCCATGTGTATCAGTGACTGATAAATACACAGCAACACAGGACCTATGTGTATC
649395 AATGATTGATAAACACAC
66 AATGATTGATAAACACAC
649413 AACAACACAGTGCCATGTGTATCAGTGACTGATAAATACACAGCAACACAGGACCTATGTGTATC
1 AACAACACAGTGCCATGTGTATCAGTGACTGATAAATACACAGCAACACAGGACCTATGTGTATC
649478 A
66 A
649479 GTCTATTCCT
Statistics
Matches: 223, Mismatches: 7, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
81 1 0.00
82 47 0.21
83 175 0.78
ACGTcount: A:0.39, C:0.21, G:0.17, T:0.23
Consensus pattern (83 bp):
AACAACACAGTGCCATGTGTATCAGTGACTGATAAATACACAGCAACACAGGACCTATGTGTATC
AATGATTGATAAACACAC
Found at i:649431 original size:124 final size:123
Alignment explanation
Indices: 649165--649480 Score: 431
Period size: 124 Copynumber: 2.5 Consensus size: 123
649155 NNNNNNNNNN
** * *
649165 AACAACACAGTATCATGTGTATCAGTGACTGATTAATACACAACAACACAGTGCTATGTGTATCA
1 AACAACACAGTGCCATGTGTATCAGTGACTGATAAATACACAACAACACAGTGCCATGTGTATCA
* * *
649230 TTGACTGATAAATACACAACAACACAGTGCCATGTGTATCAGTGACTGATAAATACAC
66 GTGACTGATAAATACACAACAACACAGTGCCATGTGTATCAATGACTGATAAACACAC
* * * *
649288 AGCAACACAG-GACCTATGTGTATCAATGATTGATAAACACACAACAACACAGTGCCATGTGTAT
1 AACAACACAGTG-CC-ATGTGTATCAGTGACTGATAAATACACAACAACACAGTGCCATGTGTAT
* *
649352 CAGTGACTGATAAATACACAGCAACACAG-GACCTATGTGTATCAATGATTGATAAACACAC
64 CAGTGACTGATAAATACACAACAACACAGTG-CC-ATGTGTATCAATGACTGATAAACACAC
*
649413 AACAACACAGTGCCATGTGTATCAGTGACTGATAAATACACAGCAACACAG-GACCTATGTGTAT
1 AACAACACAGTGCCATGTGTATCAGTGACTGATAAATACACAACAACACAGTG-CC-ATGTGTAT
649477 CAGT
64 CAGT
649481 CTATTCCTTA
Statistics
Matches: 168, Mismatches: 18, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
123 12 0.07
124 108 0.64
125 47 0.28
126 1 0.01
ACGTcount: A:0.39, C:0.21, G:0.17, T:0.23
Consensus pattern (123 bp):
AACAACACAGTGCCATGTGTATCAGTGACTGATAAATACACAACAACACAGTGCCATGTGTATCA
GTGACTGATAAATACACAACAACACAGTGCCATGTGTATCAATGACTGATAAACACAC
Found at i:653935 original size:37 final size:36
Alignment explanation
Indices: 653885--653954 Score: 122
Period size: 37 Copynumber: 1.9 Consensus size: 36
653875 CATGTTAATG
*
653885 TATAACTAAGACAGTGTGATTTAGTAGTCAATAGCTT
1 TATAACAAAGACAGTGTGATTTA-TAGTCAATAGCTT
653922 TATAACAAAGACAGTGTGATTTATAGTCAATAG
1 TATAACAAAGACAGTGTGATTTATAGTCAATAG
653955 ATGTATTGTG
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
36 10 0.31
37 22 0.69
ACGTcount: A:0.39, C:0.10, G:0.19, T:0.33
Consensus pattern (36 bp):
TATAACAAAGACAGTGTGATTTATAGTCAATAGCTT
Found at i:656315 original size:36 final size:36
Alignment explanation
Indices: 656211--656968 Score: 1026
Period size: 36 Copynumber: 21.1 Consensus size: 36
656201 TCAGCAGAGG
* *
656211 ATGCTCACTCATCCATGGCACCTGATGCTGCTTCTA
1 ATGCTCACTCACCCATGGCACCTGATGCTGCCTCTA
* * * ** ** * *
656247 TTACTCATTCAATCATACCGCCTAATGCTGCCTCTA
1 ATGCTCACTCACCCATGGCACCTGATGCTGCCTCTA
* * *
656283 ATGCTCACTCACCCAAGGCACCTGACGTTGCCTCTA
1 ATGCTCACTCACCCATGGCACCTGATGCTGCCTCTA
* * * * *
656319 ATGCCCACTCATCCATGGCACCTGACGTTGCCTCCA
1 ATGCTCACTCACCCATGGCACCTGATGCTGCCTCTA
*
656355 ATGC-CGACTCATCCATGGCACCTGATGCTGCCTCTA
1 ATGCTC-ACTCACCCATGGCACCTGATGCTGCCTCTA
656391 ATGCTCACTCACCCATGGCACCTGATGCTGCCTCTA
1 ATGCTCACTCACCCATGGCACCTGATGCTGCCTCTA
* * * *
656427 ATGCCCACTCATCCATGGCGCCTAATGCTGCCTCTA
1 ATGCTCACTCACCCATGGCACCTGATGCTGCCTCTA
*
656463 ATGCTCACTCACCCATGGCACCTAATGCTGCCTCTA
1 ATGCTCACTCACCCATGGCACCTGATGCTGCCTCTA
656499 ATGCTCACTC-CTCCATGGCACCTGATGCTGCCTCTA
1 ATGCTCACTCAC-CCATGGCACCTGATGCTGCCTCTA
656535 ATGCTCACTC-CTCCATGGCACCTGATGCTGCCTCTA
1 ATGCTCACTCAC-CCATGGCACCTGATGCTGCCTCTA
* * *
656571 ATGCTCACTC-CTCCATAGTACCAGATGCTGCCTCTA
1 ATGCTCACTCAC-CCATGGCACCTGATGCTGCCTCTA
656607 ATGCTCACTCACCCATGGCACCTGATGCTGCCTCTA
1 ATGCTCACTCACCCATGGCACCTGATGCTGCCTCTA
656643 ATGCTCACTCACCCATGGCACCTGATGCTGCCTCTA
1 ATGCTCACTCACCCATGGCACCTGATGCTGCCTCTA
* *
656679 ATGCTCACTCACCCATGGCACCTAATGCTGCCTCCA
1 ATGCTCACTCACCCATGGCACCTGATGCTGCCTCTA
* * * *
656715 ATGCCCACTCATCCATGGCACCTTATGCTGCCTCTT
1 ATGCTCACTCACCCATGGCACCTGATGCTGCCTCTA
* *
656751 ATGCCCACTCATCCATGGCACCTGATGCTGCCTCTA
1 ATGCTCACTCACCCATGGCACCTGATGCTGCCTCTA
*
656787 ATGCTCATTC-CTCCATGGCACCTGATGCTGCCTCTA
1 ATGCTCACTCAC-CCATGGCACCTGATGCTGCCTCTA
*
656823 ATGCTCACTC-CTCCATGGTACCTGATGCTGCCTCTA
1 ATGCTCACTCAC-CCATGGCACCTGATGCTGCCTCTA
* *
656859 ATGCCCACTCATCCATGGCACCTGATGCTGCCTCTA
1 ATGCTCACTCACCCATGGCACCTGATGCTGCCTCTA
656895 ATGCTCACTCACCCATGGCACCTGATGCTGCCTCTA
1 ATGCTCACTCACCCATGGCACCTGATGCTGCCTCTA
* *
656931 ATGCTCACTC-CTCCATGGCACGTGATGCTACCTCTA
1 ATGCTCACTCAC-CCATGGCACCTGATGCTGCCTCTA
656967 AT
1 AT
656969 TTTTGTAGAG
Statistics
Matches: 650, Mismatches: 65, Indels: 14
0.89 0.09 0.02
Matches are distributed among these distances:
35 3 0.00
36 645 0.99
37 2 0.00
ACGTcount: A:0.20, C:0.38, G:0.16, T:0.27
Consensus pattern (36 bp):
ATGCTCACTCACCCATGGCACCTGATGCTGCCTCTA
Found at i:657986 original size:21 final size:20
Alignment explanation
Indices: 657957--658162 Score: 288
Period size: 21 Copynumber: 9.9 Consensus size: 20
657947 ATATTCGATC
*
657957 TTTTCCATTTGTATTATATAAA
1 TTTT-CATTTGTATTGTAT-AA
*
657979 TATTCATTTGTATTGTATAA
1 TTTTCATTTGTATTGTATAA
657999 TTTTCTATTTGTATTGTATAA
1 TTTTC-ATTTGTATTGTATAA
*
658020 TTTTCCATTTGTATTCTATAA
1 TTTT-CATTTGTATTGTATAA
658041 TTTTTCATTTGTATTGTATAAA
1 -TTTTCATTTGTATTGTAT-AA
658063 TTTT-ATTTGTATTGTATAA
1 TTTTCATTTGTATTGTATAA
658082 TTTTCAATTTGTATTGTATAA
1 TTTTC-ATTTGTATTGTATAA
658103 TTTTCCATTTGTATTGTATAA
1 TTTT-CATTTGTATTGTATAA
*
658124 TTTTCATTTGTATTCTATAA
1 TTTTCATTTGTATTGTATAA
658144 TTTTCAATTTGTATTGTAT
1 TTTTC-ATTTGTATTGTAT
658163 CCGAGGGATT
Statistics
Matches: 169, Mismatches: 7, Indels: 17
0.88 0.04 0.09
Matches are distributed among these distances:
19 6 0.04
20 39 0.23
21 113 0.67
22 11 0.07
ACGTcount: A:0.26, C:0.07, G:0.08, T:0.59
Consensus pattern (20 bp):
TTTTCATTTGTATTGTATAA
Found at i:658092 original size:83 final size:83
Alignment explanation
Indices: 657957--658162 Score: 317
Period size: 83 Copynumber: 2.5 Consensus size: 83
657947 ATATTCGATC
* * *
657957 TTTTCCATTTGTATTATATAAATATTCATTTGTATTGTATAATTTTCTATTTGTATTGTATAATT
1 TTTTTCATTTGTATTATATAAAT-TTTATTTGTATTGTATAATTTTCAATTTGTATTGTATAATT
658022 TTCCATTTGTATTCTATAA
65 TTCCATTTGTATTCTATAA
*
658041 TTTTTCATTTGTATTGTATAAATTTTATTTGTATTGTATAATTTTCAATTTGTATTGTATAATTT
1 TTTTTCATTTGTATTATATAAATTTTATTTGTATTGTATAATTTTCAATTTGTATTGTATAATTT
*
658106 TCCATTTGTATTGTATAA
66 TCCATTTGTATTCTATAA
*
658124 -TTTTCATTTGTATTCTAT-AATTTTCAATTTGTATTGTAT
1 TTTTTCATTTGTATTATATAAATTTT--ATTTGTATTGTAT
658163 CCGAGGGATT
Statistics
Matches: 114, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
81 6 0.05
82 17 0.15
83 70 0.61
84 21 0.18
ACGTcount: A:0.26, C:0.07, G:0.08, T:0.59
Consensus pattern (83 bp):
TTTTTCATTTGTATTATATAAATTTTATTTGTATTGTATAATTTTCAATTTGTATTGTATAATTT
TCCATTTGTATTCTATAA
Found at i:658102 original size:62 final size:62
Alignment explanation
Indices: 657957--658162 Score: 306
Period size: 62 Copynumber: 3.3 Consensus size: 62
657947 ATATTCGATC
* * * * *
657957 TTTTCCATTTGTATTATATAAATATTCATTTGTATTGTATAATTTTCTATTTGTATTGTATAA
1 TTTTCAATTTGTATTGTATAATTTTTCATTTGTATTGTATAAATTT-TATTTGTATTGTATAA
* *
658020 TTTTCCATTTGTATTCTATAATTTTTCATTTGTATTGTATAAATTTTATTTGTATTGTATAA
1 TTTTCAATTTGTATTGTATAATTTTTCATTTGTATTGTATAAATTTTATTTGTATTGTATAA
* *
658082 TTTTCAATTTGTATTGTATAATTTTCCATTTGTATTGTAT-AATTTTCATTTGTATTCTATAA
1 TTTTCAATTTGTATTGTATAATTTTTCATTTGTATTGTATAAATTTT-ATTTGTATTGTATAA
658144 TTTTCAATTTGTATTGTAT
1 TTTTCAATTTGTATTGTAT
658163 CCGAGGGATT
Statistics
Matches: 134, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
61 6 0.04
62 86 0.64
63 42 0.31
ACGTcount: A:0.26, C:0.07, G:0.08, T:0.59
Consensus pattern (62 bp):
TTTTCAATTTGTATTGTATAATTTTTCATTTGTATTGTATAAATTTTATTTGTATTGTATAA
Found at i:658339 original size:21 final size:20
Alignment explanation
Indices: 658310--658638 Score: 478
Period size: 21 Copynumber: 15.8 Consensus size: 20
658300 CACAGGCGTN
658310 TACAATACAAATGAAACATTA
1 TACAATACAAATGAAA-ATTA
*
658331 TAGAATACAAATTGAAAATTA
1 TACAATACAAA-TGAAAATTA
658352 TACAATACAAATTGAAAATTA
1 TACAATACAAA-TGAAAATTA
658373 TACAATACAAATGGAAAATTA
1 TACAATACAAAT-GAAAATTA
658394 TACAATACAAATTGAAAATTA
1 TACAATACAAA-TGAAAATTA
*
658415 TACAATACAAATGGAAATTA
1 TACAATACAAATGAAAATTA
658435 TACAATACAAATGAAAATTTA
1 TACAATACAAATGAAAA-TTA
* *
658456 TAGAATACAAATGAAATTTA
1 TACAATACAAATGAAAATTA
658476 TACAATACAAATGGAAAATTA
1 TACAATACAAAT-GAAAATTA
658497 TACAATACAAATAGAAAATTA
1 TACAATACAAAT-GAAAATTA
* *
658518 TAGAATACAAATGAAATTTA
1 TACAATACAAATGAAAATTA
658538 TACAATACAAATGAAAAATTA
1 TACAATACAAATG-AAAATTA
*
658559 TAGAATACAAATGGAAAATTA
1 TACAATACAAAT-GAAAATTA
658580 TACAATACAAATAGAAAATTA
1 TACAATACAAAT-GAAAATTA
658601 TACAATACAAATAGAAAATTA
1 TACAATACAAAT-GAAAATTA
*
658622 TACAATAAAAATGAAAA
1 TACAATACAAATGAAAA
658639 AGATCGAATA
Statistics
Matches: 284, Mismatches: 17, Indels: 15
0.90 0.05 0.05
Matches are distributed among these distances:
20 63 0.22
21 214 0.75
22 7 0.02
ACGTcount: A:0.59, C:0.09, G:0.07, T:0.26
Consensus pattern (20 bp):
TACAATACAAATGAAAATTA
Found at i:658464 original size:62 final size:62
Alignment explanation
Indices: 658310--658639 Score: 488
Period size: 62 Copynumber: 5.3 Consensus size: 62
658300 CACAGGCGTN
658310 TACAATACAAAT-GAAACATTATAGAATACAAATTGAAAATTATACAATACAAATTGAAAATTA
1 TACAATACAAATGGAAA-ATTATAGAATACAAATTGAAAATTATACAATACAAA-TGAAAATTA
* *
658373 TACAATACAAATGGAAAATTATACAATACAAATTGAAAATTATACAATACAAATGGAAATTA
1 TACAATACAAATGGAAAATTATAGAATACAAATTGAAAATTATACAATACAAATGAAAATTA
*
658435 TACAATACAAAT-GAAAATTTATAGAATACAAA-TGAAATTTATACAATACAAATGGAAAATTA
1 TACAATACAAATGGAAAA-TTATAGAATACAAATTGAAAATTATACAATACAAAT-GAAAATTA
* *
658497 TACAATACAAATAGAAAATTATAGAATACAAA-TGAAATTTATACAATACAAATGAAAAATTA
1 TACAATACAAATGGAAAATTATAGAATACAAATTGAAAATTATACAATACAAATG-AAAATTA
* * *
658559 TAGAATACAAATGGAAAATTATACAATACAAATAGAAAATTATACAATACAAATAGAAAATTA
1 TACAATACAAATGGAAAATTATAGAATACAAATTGAAAATTATACAATACAAAT-GAAAATTA
* *
658622 TACAATAAAAATGAAAAA
1 TACAATACAAATGGAAAA
658640 GATCGAATAT
Statistics
Matches: 247, Mismatches: 13, Indels: 14
0.90 0.05 0.05
Matches are distributed among these distances:
61 26 0.11
62 123 0.50
63 93 0.38
64 5 0.02
ACGTcount: A:0.59, C:0.08, G:0.07, T:0.25
Consensus pattern (62 bp):
TACAATACAAATGGAAAATTATAGAATACAAATTGAAAATTATACAATACAAATGAAAATTA
Found at i:659297 original size:13 final size:13
Alignment explanation
Indices: 659279--659303 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
659269 ATAATAAAGA
659279 TTTTAACATAATG
1 TTTTAACATAATG
659292 TTTTAACATAAT
1 TTTTAACATAAT
659304 ATTTCCTCTT
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:0.40, C:0.08, G:0.04, T:0.48
Consensus pattern (13 bp):
TTTTAACATAATG
Found at i:663979 original size:2 final size:2
Alignment explanation
Indices: 663972--664035 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
663962 GTCGTCCACA
663972 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
664014 TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC
664036 ATTATCATCA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:664479 original size:2 final size:2
Alignment explanation
Indices: 664472--664515 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
664462 TGATATTTTG
664472 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
664514 CT
1 CT
664516 GTTTTATCTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Done.