Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A05
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 102776486
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2328156 characters in sequence are not A, C, G, or T
File 4 of 325
Found at i:1019804 original size:13 final size:12
Alignment explanation
Indices: 1019746--1019808 Score: 51
Period size: 13 Copynumber: 5.2 Consensus size: 12
1019736 TAAACAATTC
1019746 AATAATATAAAT
1 AATAATATAAAT
1019758 AAT-ATA-AAATTT
1 AATAATATAAA--T
* *
1019770 AA-AATTTAATTT
1 AATAATATAA-AT
1019782 AATAATATAAAT
1 AATAATATAAAT
1019794 AATAGATATAAAT
1 AATA-ATATAAAT
1019807 AA
1 AA
1019809 AATTATTACT
Statistics
Matches: 40, Mismatches: 4, Indels: 13
0.70 0.07 0.23
Matches are distributed among these distances:
10 3 0.08
11 3 0.08
12 16 0.40
13 18 0.45
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (12 bp):
AATAATATAAAT
Found at i:1020300 original size:9 final size:9
Alignment explanation
Indices: 1020283--1020319 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
1020273 TATAGTTTGA
*
1020283 TATTTGAAT
1 TATTCGAAT
1020292 TATTCGAAT
1 TATTCGAAT
*
1020301 TATTCGAGT
1 TATTCGAAT
1020310 TATTCGAAT
1 TATTCGAAT
1020319 T
1 T
1020320 CGAAAACTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.30, C:0.08, G:0.14, T:0.49
Consensus pattern (9 bp):
TATTCGAAT
Found at i:1023390 original size:22 final size:22
Alignment explanation
Indices: 1023361--1023428 Score: 84
Period size: 22 Copynumber: 3.0 Consensus size: 22
1023351 TGCACAAACG
1023361 AACAGAGAGCACTAAAGTGCTA
1 AACAGAGAGCACTAAAGTGCTA
* *
1023383 TACAGAGAGCAC-AGATGTGCTA
1 AACAGAGAGCACTA-AAGTGCTA
*
1023405 AACAGAGAGCACTTAACGTGCTA
1 AACAGAGAGCAC-TAAAGTGCTA
1023428 A
1 A
1023429 TAATAGTACA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
21 1 0.03
22 29 0.74
23 8 0.21
24 1 0.03
ACGTcount: A:0.41, C:0.19, G:0.24, T:0.16
Consensus pattern (22 bp):
AACAGAGAGCACTAAAGTGCTA
Found at i:1024635 original size:20 final size:20
Alignment explanation
Indices: 1024610--1024652 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1024600 ATATTATACT
1024610 ATATATAATATAATATAATA
1 ATATATAATATAATATAATA
* * *
1024630 ATATATTATATTATATATTA
1 ATATATAATATAATATAATA
1024650 ATA
1 ATA
1024653 CTTAAATATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
ATATATAATATAATATAATA
Found at i:1031968 original size:46 final size:46
Alignment explanation
Indices: 1031901--1032029 Score: 231
Period size: 46 Copynumber: 2.8 Consensus size: 46
1031891 TGTAACCCGC
* *
1031901 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
1031947 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGAACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
1031993 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
1032030 TGCCCAAATA
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 79 1.00
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.19
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
Found at i:1035560 original size:9 final size:9
Alignment explanation
Indices: 1035543--1035576 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
1035533 AAAAAATTTA
1035543 TTTATAAAAT
1 TTTA-AAAAT
1035553 TTTAAAAAT
1 TTTAAAAAT
1035562 TTTAAAAAT
1 TTTAAAAAT
*
1035571 ATTAAA
1 TTTAAA
1035577 TCTCGTAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 19 0.83
10 4 0.17
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
TTTAAAAAT
Found at i:1043648 original size:29 final size:29
Alignment explanation
Indices: 1043616--1043676 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
1043606 TAAATTTATT
1043616 ATTATGTCAAAATTAAAAATTATCACGCC
1 ATTATGTCAAAATTAAAAATTATCACGCC
* *
1043645 ATTATGTCAAATTTAAAAATTATCACGTC
1 ATTATGTCAAAATTAAAAATTATCACGCC
1043674 ATT
1 ATT
1043677 TTTTCATCTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.43, C:0.15, G:0.07, T:0.36
Consensus pattern (29 bp):
ATTATGTCAAAATTAAAAATTATCACGCC
Found at i:1051220 original size:2 final size:2
Alignment explanation
Indices: 1051213--1051241 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1051203 AATGAAGCAA
1051213 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1051242 ATCTTTAAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1055568 original size:15 final size:15
Alignment explanation
Indices: 1055548--1055604 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
1055538 ATTCAATATT
1055548 AATATTTTAATAATA
1 AATATTTTAATAATA
*
1055563 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
*
1055582 AATATATTAATAATA
1 AATATTTTAATAATA
*
1055597 AATGTTTT
1 AATATTTT
1055605 GTAATATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 16 0.48
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.30
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:1056081 original size:14 final size:14
Alignment explanation
Indices: 1056062--1056100 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
1056052 CCAGAAAAGT
1056062 AAATCATTTTCCAG
1 AAATCATTTTCCAG
*
1056076 AAATCATTTT-CTG
1 AAATCATTTTCCAG
1056089 AAAGTCATTTTC
1 AAA-TCATTTTC
1056101 AATAAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 5 0.23
14 17 0.77
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.41
Consensus pattern (14 bp):
AAATCATTTTCCAG
Found at i:1064625 original size:124 final size:124
Alignment explanation
Indices: 1064409--1065128 Score: 888
Period size: 124 Copynumber: 5.9 Consensus size: 124
1064399 AACACTAAAC
* * * *
1064409 ATGAACTATAAAATAGACAT---G-A-AAAAAATTTGAATGAGCTAATTGTATTAATCGAATCTG
1 ATGAACTATAAAATAGACATGAAGAATAAAAAAATTGAATGAGTTAATTGTATTAATCGGATCCG
* * *
1064469 ATGTGTAATTACTTTAAAAAGAAAATGTCTTTTAAAAAATTTGACTTGAAACCTTGAAT
66 ATATGTAATTACTTAAAAAAGAAAATGCCTTTTAAAAAATTTGACTTGAAACCTTGAAT
* *
1064528 ATGAACTACAAAATAGACATGAAGAATCAAAAAATTGAATGAGTTAATTGTATTAATCGGATCCG
1 ATGAACTATAAAATAGACATGAAGAATAAAAAAATTGAATGAGTTAATTGTATTAATCGGATCCG
* *
1064593 ATATGTAATTACTTAAAAAAGAAAATGCCTTTTAAAAAAGTTGAATTGAAACCTTGAAT
66 ATATGTAATTACTTAAAAAAGAAAATGCCTTTTAAAAAATTTGACTTGAAACCTTGAAT
** * *
1064652 ATGAACTATAAAATAGACATGAAGAATGTAAAAATTGAATGAGTTAATTATATTAATCAGATCCG
1 ATGAACTATAAAATAGACATGAAGAATAAAAAAATTGAATGAGTTAATTGTATTAATCGGATCCG
* * * *
1064717 ATATGTAATTACTTGAAAAAGAAAATGCCTTCTAAAAAAATTGAATTGAAACCTTGAAT
66 ATATGTAATTACTTAAAAAAGAAAATGCCTTTTAAAAAATTTGACTTGAAACCTTGAAT
* * * * *
1064776 ATAAACTATAAAATAGACATGAATAA-AAAAAAATTGAATAAGTTAATTGTATTAATGGGATTCG
1 ATGAACTATAAAATAGACATGAAGAATAAAAAAATTGAATGAGTTAATTGTATTAATCGGATCCG
* * *
1064840 ATATGTAATTAC-TAAAAAAGAAAATACC-TTTAAAAAAATTGACTTGAAACCTTGAAC
66 ATATGTAATTACTTAAAAAAGAAAATGCCTTTTAAAAAATTTGACTTGAAACCTTGAAT
* * * * *
1064897 ATAAACTATAAAATAGACATAAAGAATAAAAAAAATTAAATGAGTTAATTGTATTAATCAGATCT
1 ATGAACTATAAAATAGACATGAAGAAT-AAAAAAATTGAATGAGTTAATTGTATTAATCGGATCC
* * * * *
1064962 GATATGTAATTACTT-AAAAAGAAAATGTCTTTT-AAAAATTTGACTTAAAAAACTTTAAA
65 GATATGTAATTACTTAAAAAAGAAAATGCCTTTTAAAAAATTTGACTT-GAAACCTTGAAT
* * * * * * *
1065021 AAGAACTATAAAATAAATATGAAGAATAAAAAAAATTAAATAAGTTAATTATATTAATCGAATCC
1 ATGAACTATAAAATAGACATGAAGAAT-AAAAAAATTGAATGAGTTAATTGTATTAATCGGATCC
* * *
1065086 GATATGAAAATT-CCTAAAAAAGAAAATG-CTTTTGGAAAAATTT
65 GATATG-TAATTACTTAAAAAAGAAAATGCCTTTT-AAAAAATTT
1065129 ACTGTATTCA
Statistics
Matches: 527, Mismatches: 60, Indels: 21
0.87 0.10 0.03
Matches are distributed among these distances:
119 19 0.04
121 50 0.09
122 15 0.03
123 112 0.21
124 307 0.58
125 16 0.03
126 8 0.02
ACGTcount: A:0.49, C:0.08, G:0.12, T:0.30
Consensus pattern (124 bp):
ATGAACTATAAAATAGACATGAAGAATAAAAAAATTGAATGAGTTAATTGTATTAATCGGATCCG
ATATGTAATTACTTAAAAAAGAAAATGCCTTTTAAAAAATTTGACTTGAAACCTTGAAT
Found at i:1064932 original size:370 final size:367
Alignment explanation
Indices: 1064412--1065114 Score: 952
Period size: 370 Copynumber: 1.9 Consensus size: 367
1064402 ACTAAACATG
* * *
1064412 AACTATAAAATAGACATGAAAAAAATTTGAATGAGCTAATTGTATTAATCGAATCTGATGTGTAA
1 AACTATAAAATAGACATGAAAAAAAATTGAATAAGCTAATTGTATTAATCGAATCTGATATGTAA
* * * * * *
1064477 TTACTTTAAAAAGAAAATGTCTTTTAAAAAATTTGACTTGAAACCTTGAATATGAACTACAAAAT
66 TTACTTAAAAAAGAAAATGACCTTTAAAAAAATTGACTTGAAACCTTGAACATAAACTACAAAAT
* * * *
1064542 AGACATGAAGAATCAAAAAATTGAATGAGTTAATTGTATTAATCGGATCCGATATGTAATTACTT
131 AGACATAAAGAATAAAAAAATTAAATGAGTTAATTGTATTAATCAGATCCGATATGTAATTACTT
* * * * *
1064607 AAAAAAGAAAATGCCTTTTAAAAAAGTTGAATT-GAAACCTTGAATATGAACTATAAAATAGACA
196 -AAAAAGAAAATGCCTTTT-AAAAAGTTGAATTAAAAAACTTGAAAAAGAACTATAAAATAAACA
** * * * * *
1064671 TGAAGAAT-GTAAAAATTGAATGAGTTAATTATATTAATC-AGATCCGATATG-TAATTACTTGA
259 TGAAGAATAAAAAAAATTAAATAAGTTAATTATATTAATCGA-ATCCGATATGAAAATT-CCTAA
1064733 AAAAGAAAATGCCTTCTAAAAAAATTGAATTGAAACCTTGAATATA
322 AAAAGAAAATGCCTTCTAAAAAAATTGAATTGAAACCTTGAATATA
* * *
1064779 AACTATAAAATAGACATGAATAAAAAAAAATTGAATAAGTTAATTGTATTAATGGGAT-TCGATA
1 AACTATAAAATAGACATG----AAAAAAAATTGAATAAGCTAATTGTATTAATCGAATCT-GATA
*
1064843 TGTAATTAC-TAAAAAAGAAAAT-ACCTTTAAAAAAATTGACTTGAAACCTTGAACATAAACTAT
61 TGTAATTACTTAAAAAAGAAAATGACCTTTAAAAAAATTGACTTGAAACCTTGAACATAAACTAC
*
1064906 AAAATAGACATAAAGAATAAAAAAAATTAAATGAGTTAATTGTATTAATCAGATCTGATATGTAA
126 AAAATAGACATAAAGAAT-AAAAAAATTAAATGAGTTAATTGTATTAATCAGATCCGATATGTAA
* * * *
1064971 TTACTTAAAAAGAAAATGTCTTTTAAAAATTTGACTTAAAAAACTTTAAAAAGAACTATAAAATA
190 TTACTTAAAAAGAAAATGCCTTTTAAAAAGTTGAATTAAAAAACTTGAAAAAGAACTATAAAATA
*
1065036 AATATGAAGAATAAAAAAAATTAAATAAGTTAATTATATTAATCGAATCCGATATGAAAATTCCT
255 AACATGAAGAATAAAAAAAATTAAATAAGTTAATTATATTAATCGAATCCGATATGAAAATTCCT
1065101 AAAAAAGAAAATGC
320 AAAAAAGAAAATGC
1065115 TTTTGGAAAA
Statistics
Matches: 291, Mismatches: 35, Indels: 17
0.85 0.10 0.05
Matches are distributed among these distances:
367 18 0.06
368 11 0.04
369 101 0.35
370 113 0.39
371 48 0.16
ACGTcount: A:0.50, C:0.08, G:0.12, T:0.30
Consensus pattern (367 bp):
AACTATAAAATAGACATGAAAAAAAATTGAATAAGCTAATTGTATTAATCGAATCTGATATGTAA
TTACTTAAAAAAGAAAATGACCTTTAAAAAAATTGACTTGAAACCTTGAACATAAACTACAAAAT
AGACATAAAGAATAAAAAAATTAAATGAGTTAATTGTATTAATCAGATCCGATATGTAATTACTT
AAAAAGAAAATGCCTTTTAAAAAGTTGAATTAAAAAACTTGAAAAAGAACTATAAAATAAACATG
AAGAATAAAAAAAATTAAATAAGTTAATTATATTAATCGAATCCGATATGAAAATTCCTAAAAAA
GAAAATGCCTTCTAAAAAAATTGAATTGAAACCTTGAATATA
Found at i:1071249 original size:15 final size:16
Alignment explanation
Indices: 1071200--1071249 Score: 50
Period size: 15 Copynumber: 3.1 Consensus size: 16
1071190 GGCTGGCTCG
1071200 ATTTTAAAATTTATAATT
1 ATTTTAAAA-TT-TAATT
**
1071218 -TTTTAAAATTTTTTT
1 ATTTTAAAATTTAATT
1071233 ATTTT-AAATTTAATT
1 ATTTTAAAATTTAATT
1071248 AT
1 AT
1071250 AAAATATATG
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
15 13 0.48
16 6 0.22
17 8 0.30
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
ATTTTAAAATTTAATT
Found at i:1074272 original size:16 final size:16
Alignment explanation
Indices: 1074253--1074301 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
1074243 TTTAAATTTA
1074253 AAAAAATATAAAAATT
1 AAAAAATATAAAAATT
1074269 AAAAAATA-AATAAATT
1 AAAAAATATAA-AAATT
*
1074285 --AAAGTATAAAAATT
1 AAAAAATATAAAAATT
1074299 AAA
1 AAA
1074302 TTCATAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
14 10 0.36
15 4 0.14
16 14 0.50
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (16 bp):
AAAAAATATAAAAATT
Found at i:1074478 original size:18 final size:19
Alignment explanation
Indices: 1074446--1074481 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1074436 TAAAAAAGAC
*
1074446 AAGAGAAATACAAAAGTTG
1 AAGAGAAATAAAAAAGTTG
1074465 AAGAGAAA-AAAAAAGTT
1 AAGAGAAATAAAAAAGTT
1074482 AAAATATGAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.64, C:0.03, G:0.19, T:0.14
Consensus pattern (19 bp):
AAGAGAAATAAAAAAGTTG
Found at i:1078440 original size:6 final size:6
Alignment explanation
Indices: 1078429--1078461 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
1078419 AACGGTTATA
1078429 CCAGCT CCAGCT CCAGCT CCAGCT CCAGCT CCA
1 CCAGCT CCAGCT CCAGCT CCAGCT CCAGCT CCA
1078462 TGTTTTAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.18, C:0.52, G:0.15, T:0.15
Consensus pattern (6 bp):
CCAGCT
Found at i:1081504 original size:51 final size:51
Alignment explanation
Indices: 1081425--1081679 Score: 359
Period size: 51 Copynumber: 5.0 Consensus size: 51
1081415 GATGCCGAAC
* * *
1081425 CAGCAAGGCGGAAACATTGAATCTCAAACATACACTCAGCTACCACAACAG
1 CAGCAAGGTGGAAACATTGAATCCCAAACATATACTCAGCTACCACAACAG
* ** *
1081476 CAGCAAGGTGGTAACATCAAATCCCAAACATATACTCAACTACCACAACAG
1 CAGCAAGGTGGAAACATTGAATCCCAAACATATACTCAGCTACCACAACAG
* * * *
1081527 CAGCAAGGTGGAAACGTTGAATACCAAACATATACTCAGCTGCCACAACAA
1 CAGCAAGGTGGAAACATTGAATCCCAAACATATACTCAGCTACCACAACAG
* * *
1081578 CAGCAAGGAGGAAACATTGAATCCCAAACTTATACTCAGCTACAACAACAG
1 CAGCAAGGTGGAAACATTGAATCCCAAACATATACTCAGCTACCACAACAG
*
1081629 GAGCAAGGTGGAAACATTGAATCCCAAACATATACTCAGCCT-CCACAACAG
1 CAGCAAGGTGGAAACATTGAATCCCAAACATATACTCAG-CTACCACAACAG
1081680 TACTTAATGG
Statistics
Matches: 177, Mismatches: 26, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
51 175 0.99
52 2 0.01
ACGTcount: A:0.42, C:0.27, G:0.16, T:0.15
Consensus pattern (51 bp):
CAGCAAGGTGGAAACATTGAATCCCAAACATATACTCAGCTACCACAACAG
Found at i:1089475 original size:2 final size:2
Alignment explanation
Indices: 1089468--1089494 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1089458 AAGAAAGAAA
1089468 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1089495 ATGGTGGAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1114529 original size:20 final size:21
Alignment explanation
Indices: 1114497--1114535 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
1114487 ACTAAAGATA
1114497 TTTAAAAATTTTAC-TATTAT
1 TTTAAAAATTTTACATATTAT
1114517 TTTAATAAA-TTTACATATT
1 TTTAA-AAATTTTACATATT
1114536 TAAATATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (21 bp):
TTTAAAAATTTTACATATTAT
Found at i:1115672 original size:26 final size:26
Alignment explanation
Indices: 1115640--1115696 Score: 105
Period size: 26 Copynumber: 2.2 Consensus size: 26
1115630 TTGACTAAGT
1115640 GTATATGGATTATTTCAAGGATTGTA
1 GTATATGGATTATTTCAAGGATTGTA
1115666 GTATATGGATTATTTCAAGGATTGTA
1 GTATATGGATTATTTCAAGGATTGTA
*
1115692 CTATA
1 GTATA
1115697 AGAGTGAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.32, C:0.05, G:0.21, T:0.42
Consensus pattern (26 bp):
GTATATGGATTATTTCAAGGATTGTA
Found at i:1116011 original size:33 final size:33
Alignment explanation
Indices: 1115973--1116074 Score: 145
Period size: 33 Copynumber: 3.2 Consensus size: 33
1115963 AGATTAATTT
* *
1115973 ATATTTTATGTATCATTATATTAAATTATTTAA
1 ATATTTCATGTATCATTCTATTAAATTATTTAA
1116006 ATATTTCATGTATCATTCTATTAAATTATTTAA
1 ATATTTCATGTATCATTCTATTAAATTATTTAA
* * *
1116039 ATA--TCATTTACCATTCCATTAAATTATTTAA
1 ATATTTCATGTATCATTCTATTAAATTATTTAA
1116070 ATATT
1 ATATT
1116075 ATATAACTTA
Statistics
Matches: 62, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
31 28 0.45
33 34 0.55
ACGTcount: A:0.38, C:0.09, G:0.02, T:0.51
Consensus pattern (33 bp):
ATATTTCATGTATCATTCTATTAAATTATTTAA
Found at i:1116060 original size:31 final size:31
Alignment explanation
Indices: 1115992--1116073 Score: 119
Period size: 31 Copynumber: 2.6 Consensus size: 31
1115982 GTATCATTAT
* *
1115992 ATTAAATTATTTAAATATTTCATGTATCATTCT
1 ATTAAATTATTTAAATA--TCATGTACCATTCC
*
1116025 ATTAAATTATTTAAATATCATTTACCATTCC
1 ATTAAATTATTTAAATATCATGTACCATTCC
1116056 ATTAAATTATTTAAATAT
1 ATTAAATTATTTAAATAT
1116074 TATATAACTT
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
31 29 0.63
33 17 0.37
ACGTcount: A:0.40, C:0.10, G:0.01, T:0.49
Consensus pattern (31 bp):
ATTAAATTATTTAAATATCATGTACCATTCC
Found at i:1125560 original size:50 final size:50
Alignment explanation
Indices: 1125485--1125661 Score: 248
Period size: 50 Copynumber: 3.5 Consensus size: 50
1125475 CCATGGAAAC
1125485 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* * * *
1125535 AAGTGATAAGTAATAACTTCGGCTACACTTATCTGATTAAGGACAAGTGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
*
1125585 AAGTGATAAATGATAGCTTCGGCTACACTTATCTGATCAATGG-CAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAA-GGACAAATGA
* * * *
1125635 CAACTGAAAAGTGGTAGCTTCAGCTAC
1 -AAGTGATAAGTGATAGCTTCGGCTAC
1125662 CTGATCAGTG
Statistics
Matches: 111, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
50 88 0.79
51 23 0.21
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.27
Consensus pattern (50 bp):
AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
Found at i:1125847 original size:31 final size:31
Alignment explanation
Indices: 1125639--1125840 Score: 314
Period size: 31 Copynumber: 6.5 Consensus size: 31
1125629 AAATGACAAC
1125639 TGAAAAGTGGTAGCTTCAGCTACCTGATCAG
1 TGAAAAGTGGTAGCTTCAGCTACCTGATCAG
*
1125670 TGAAAAGTGGTAGTTTCAGCTACCTGATCAG
1 TGAAAAGTGGTAGCTTCAGCTACCTGATCAG
* *
1125701 TGAAAAGTGGTAGCTTCTGCTACCTAATCAG
1 TGAAAAGTGGTAGCTTCAGCTACCTGATCAG
*
1125732 TGAAAAGTGGTAGCTTCGGCTACCTGATCAG
1 TGAAAAGTGGTAGCTTCAGCTACCTGATCAG
* *
1125763 TGAAAAGTGGTAGCTCCGGCTACCTGATCAG
1 TGAAAAGTGGTAGCTTCAGCTACCTGATCAG
* **
1125794 TGAAAAATGGTAGCACCAGCTACCTGATCAG
1 TGAAAAGTGGTAGCTTCAGCTACCTGATCAG
*
1125825 TGAATAGTGGTAGCTT
1 TGAAAAGTGGTAGCTT
1125841 TGGCTACAAG
Statistics
Matches: 157, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 157 1.00
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (31 bp):
TGAAAAGTGGTAGCTTCAGCTACCTGATCAG
Found at i:1125858 original size:7 final size:7
Alignment explanation
Indices: 1125846--1125874 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
1125836 AGCTTTGGCT
1125846 ACAAGTG
1 ACAAGTG
1125853 ACAAGTG
1 ACAAGTG
1125860 ACAAGTG
1 ACAAGTG
1125867 ACAAGTG
1 ACAAGTG
1125874 A
1 A
1125875 TTTCTGTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.45, C:0.14, G:0.28, T:0.14
Consensus pattern (7 bp):
ACAAGTG
Found at i:1130037 original size:48 final size:48
Alignment explanation
Indices: 1129966--1130063 Score: 178
Period size: 48 Copynumber: 2.0 Consensus size: 48
1129956 AGGCCTTTAC
*
1129966 CTTCAAACTCTCTTCACTTTCATTCTCCATAACCCCCAGCTCTTTGTT
1 CTTCAAACTCTCTTCACTTTCATTCTCCATAACCCCCAACTCTTTGTT
*
1130014 CTTCAAACTCTCTTCACTTTCATTCTCCATAGCCCCCAACTCTTTGTT
1 CTTCAAACTCTCTTCACTTTCATTCTCCATAACCCCCAACTCTTTGTT
1130062 CT
1 CT
1130064 AGCTGGGTGA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.18, C:0.38, G:0.04, T:0.40
Consensus pattern (48 bp):
CTTCAAACTCTCTTCACTTTCATTCTCCATAACCCCCAACTCTTTGTT
Found at i:1130039 original size:24 final size:24
Alignment explanation
Indices: 1129966--1130039 Score: 69
Period size: 24 Copynumber: 3.1 Consensus size: 24
1129956 AGGCCTTTAC
1129966 CTTCAAACTCTCTTCACTTTCATT
1 CTTCAAACTCTCTTCACTTTCATT
* * * ** * *
1129990 CTCCATAACCCCCAGCTCTTT-GTT
1 CTTCA-AACTCTCTTCACTTTCATT
1130014 CTTCAAACTCTCTTCACTTTCATT
1 CTTCAAACTCTCTTCACTTTCATT
1130038 CT
1 CT
1130040 CCATAGCCCC
Statistics
Matches: 34, Mismatches: 14, Indels: 4
0.65 0.27 0.08
Matches are distributed among these distances:
23 10 0.29
24 14 0.41
25 10 0.29
ACGTcount: A:0.19, C:0.36, G:0.03, T:0.42
Consensus pattern (24 bp):
CTTCAAACTCTCTTCACTTTCATT
Found at i:1132672 original size:20 final size:20
Alignment explanation
Indices: 1132629--1132672 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1132619 AAAATATTTT
* *
1132629 AAAATTTAAAAATAACATAT
1 AAAACTTAAAAATAACATAA
1132649 AAAACTTAAAATATAA-ATAA
1 AAAACTTAAAA-ATAACATAA
1132669 AAAA
1 AAAA
1132673 ATACATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (20 bp):
AAAACTTAAAAATAACATAA
Found at i:1141502 original size:22 final size:23
Alignment explanation
Indices: 1141472--1141515 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
1141462 TTTTTACTTC
1141472 TTTAAACTTATATCCTG-ATTTT
1 TTTAAACTTATATCCTGTATTTT
*
1141494 TTTATACTTATATCCTGTATTT
1 TTTAAACTTATATCCTGTATTT
1141516 ATTACCATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.25, C:0.14, G:0.05, T:0.57
Consensus pattern (23 bp):
TTTAAACTTATATCCTGTATTTT
Found at i:1149965 original size:17 final size:18
Alignment explanation
Indices: 1149943--1149976 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1149933 TAAAAGGAAT
*
1149943 AATTATGAATT-TAAAAA
1 AATTATAAATTATAAAAA
1149960 AATTATAAATTATAAAA
1 AATTATAAATTATAAAA
1149977 CGAATCTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (18 bp):
AATTATAAATTATAAAAA
Found at i:1165189 original size:22 final size:20
Alignment explanation
Indices: 1165163--1165221 Score: 57
Period size: 22 Copynumber: 2.8 Consensus size: 20
1165153 AGTTTATACA
*
1165163 TAATTTATATATTACAAATTT
1 TAATTTATATATTA-AAATCT
*
1165184 TCAATTTAAAATATTAAAATCT
1 T-AATTT-ATATATTAAAATCT
1165206 TAATTT-TATAGTTAAA
1 TAATTTATATA-TTAAA
1165222 TTATAATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
19 3 0.09
20 5 0.16
21 6 0.19
22 11 0.34
23 7 0.22
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.47
Consensus pattern (20 bp):
TAATTTATATATTAAAATCT
Found at i:1168576 original size:19 final size:19
Alignment explanation
Indices: 1168552--1168592 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
1168542 TGGAAACCAG
1168552 AATCTAAATTGAATTAACA
1 AATCTAAATTGAATTAACA
1168571 AATCTAAATTGAATTAACA
1 AATCTAAATTGAATTAACA
1168590 AAT
1 AAT
1168593 ATAATGAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.54, C:0.10, G:0.05, T:0.32
Consensus pattern (19 bp):
AATCTAAATTGAATTAACA
Found at i:1168664 original size:24 final size:25
Alignment explanation
Indices: 1168614--1168667 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 25
1168604 ATTATATACA
* *
1168614 AATAAATTTAACAAAAATAAAACAC
1 AATAAATTCAACAAAAAGAAAACAC
*
1168639 AATAAATTCAAC-ATAAGAAAACAC
1 AATAAATTCAACAAAAAGAAAACAC
1168663 AATAA
1 AATAA
1168668 CCAATCAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 15 0.58
25 11 0.42
ACGTcount: A:0.67, C:0.13, G:0.02, T:0.19
Consensus pattern (25 bp):
AATAAATTCAACAAAAAGAAAACAC
Found at i:1170186 original size:16 final size:18
Alignment explanation
Indices: 1170167--1170199 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
1170157 TTATACTAAA
1170167 ATAAATA-AT-TAAAAAT
1 ATAAATATATCTAAAAAT
1170183 ATAAATATATCTAAAAA
1 ATAAATATATCTAAAAA
1170200 AAAGCTTTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 2 0.13
18 6 0.40
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (18 bp):
ATAAATATATCTAAAAAT
Found at i:1171616 original size:3 final size:3
Alignment explanation
Indices: 1171608--1171647 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
1171598 TTATATTGAT
1171608 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A
1171648 GTAGTTATGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.35, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:1175422 original size:16 final size:16
Alignment explanation
Indices: 1175403--1175439 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
1175393 TGGAAAGATG
1175403 GAAAACT-GAAGGGATA
1 GAAAACTAGAA-GGATA
1175419 GAAAACTAGAAGGATA
1 GAAAACTAGAAGGATA
1175435 GAAAA
1 GAAAA
1175440 TATAACTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 17 0.85
17 3 0.15
ACGTcount: A:0.57, C:0.05, G:0.27, T:0.11
Consensus pattern (16 bp):
GAAAACTAGAAGGATA
Found at i:1179789 original size:75 final size:75
Alignment explanation
Indices: 1179668--1179808 Score: 196
Period size: 75 Copynumber: 1.9 Consensus size: 75
1179658 CCAGGCTATG
* *
1179668 CTCCTCCAAGGCCAAGTCCTCAAGCGCCACCACCAGGACCTCGTCATCCTCC-GAGTCCACCACA
1 CTCCTCCAAGGCCAAGTCCTCAAGCGCCACCACCAAGACCACGTCATCCTCCAG-GTCCACCACA
1179732 TGCTGAGCATC
65 TGCTGAGCATC
* * * *
1179743 CTCCTCCAAGGCCAAGT-CTCTATGTGCCACCACCAAGACCAGGTCATCCTCCAGGTCCACTACA
1 CTCCTCCAAGGCCAAGTCCTC-AAGCGCCACCACCAAGACCACGTCATCCTCCAGGTCCACCACA
1179807 TG
65 TG
1179809 AGCATCCTCC
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
74 3 0.05
75 54 0.93
76 1 0.02
ACGTcount: A:0.23, C:0.42, G:0.17, T:0.18
Consensus pattern (75 bp):
CTCCTCCAAGGCCAAGTCCTCAAGCGCCACCACCAAGACCACGTCATCCTCCAGGTCCACCACAT
GCTGAGCATC
Found at i:1179829 original size:99 final size:99
Alignment explanation
Indices: 1179712--1179906 Score: 284
Period size: 99 Copynumber: 2.0 Consensus size: 99
1179702 AGGACCTCGT
* * * *
1179712 CATCCTCCGAGTCCACCACATGCTGAGCATCCTCCTCCAAGGCCA-AGTCTCTATGTGCCACCAC
1 CATCCTCCAAGTCCACCACATGCTGAGCATCCTCCTCCAAGGCCAGA-TCCCCATGCGCCACCAC
*
1179776 CAAGACCAGGTCATCCTCCAGGTCCACTACATGAG
65 CAAGACCAGGTCATCCTCCAAGTCCACTACATGAG
* ***
1179811 CATCCTCCAAGTCCACCACATGTTGAGCATCCTCCTCCAAGGCCAGATCCCCATGCGCCACCGTT
1 CATCCTCCAAGTCCACCACATGCTGAGCATCCTCCTCCAAGGCCAGATCCCCATGCGCCACCACC
*
1179876 AGGACCAGGTCATCCTCCAAGTCCACTACAT
66 AAGACCAGGTCATCCTCCAAGTCCACTACAT
1179907 AATAATCATC
Statistics
Matches: 85, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
99 84 0.99
100 1 0.01
ACGTcount: A:0.24, C:0.40, G:0.16, T:0.19
Consensus pattern (99 bp):
CATCCTCCAAGTCCACCACATGCTGAGCATCCTCCTCCAAGGCCAGATCCCCATGCGCCACCACC
AAGACCAGGTCATCCTCCAAGTCCACTACATGAG
Found at i:1179845 original size:27 final size:24
Alignment explanation
Indices: 1179787--1179832 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
1179777 AAGACCAGGT
* *
1179787 CATCCTCCAGGTCCACTACATGAG
1 CATCCTCCAAGTCCACCACATGAG
1179811 CATCCTCCAAGTCCACCACATG
1 CATCCTCCAAGTCCACCACATG
1179833 TTGAGCATCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.26, C:0.41, G:0.13, T:0.20
Consensus pattern (24 bp):
CATCCTCCAAGTCCACCACATGAG
Found at i:1179983 original size:93 final size:93
Alignment explanation
Indices: 1179741--1180144 Score: 313
Period size: 93 Copynumber: 4.3 Consensus size: 93
1179731 ATGCTGAGCA
* * * *
1179741 TCCTCCTCCAAGGCCAAGTCTCTATGTGCCACCACCAAGACCAGGTCATCCTCCAGGTCCACTAC
1 TCCTCCTCCAAGGCCAGGTCCCCATGTGCCACCACCAAGACCAGGTCATCCTCCAAGTCCACTAC
* * *
1179806 ---ATGAGCATCCTCCAAGTCCA-CCACATGTTGAGC
66 ATAATGATCAT-CTTC-A-TCCAGGC-CA---T--GC
* * *** *
1179839 ATCCTCCTCCAAGGCCAGATCCCCATGCGCCACCGTTAGGACCAGGTCATCCTCCAAGTCCACTA
1 -TCCTCCTCCAAGGCCAGGTCCCCATGTGCCACCACCAAGACCAGGTCATCCTCCAAGTCCACTA
* *
1179904 CATAATAATCATCTTCATCCAGACCATGC
65 CATAATGATCATCTTCATCCAGGCCATGC
* * * *
1179933 TCCTCCTCCAGGGCCAGGTCCCCATGTGCCACCACCAAGACCTGGACATCCTCCAAGTGCA-TCA
1 TCCTCCTCCAAGGCCAGGTCCCCATGTGCCACCACCAAGACCAGGTCATCCTCCAAGTCCACT-A
** *
1179997 CATGCTGAGCAT-TCTCATCCAGGCCATGC
65 CATAATGATCATCT-TCATCCAGGCCATGC
* * *
1180026 TCCTCCTCC-AGGACCAAGTCCCCATGCT-CCACCACC-AGAACCAGGTCATCTTCCAAGTCAAC
1 TCCTCCTCCAAGG-CCAGGTCCCCATG-TGCCACCACCAAG-ACCAGGTCATCCTCCAAGTCCAC
* ** * * * *
1180088 CACATCTTGGTCATCCTCATCCAGGCCACGG
63 TACATAATGATCATCTTCATCCAGGCCATGC
*
1180119 TCCCCCTCCAAGGCCAGGTCCCCATG
1 TCCTCCTCCAAGGCCAGGTCCCCATG
1180145 CACCACTACC
Statistics
Matches: 247, Mismatches: 46, Indels: 30
0.76 0.14 0.09
Matches are distributed among these distances:
92 6 0.02
93 162 0.66
94 6 0.02
96 1 0.00
99 61 0.25
100 2 0.01
101 3 0.01
102 6 0.02
ACGTcount: A:0.24, C:0.40, G:0.16, T:0.20
Consensus pattern (93 bp):
TCCTCCTCCAAGGCCAGGTCCCCATGTGCCACCACCAAGACCAGGTCATCCTCCAAGTCCACTAC
ATAATGATCATCTTCATCCAGGCCATGC
Found at i:1183854 original size:14 final size:14
Alignment explanation
Indices: 1183835--1183867 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1183825 TTGGAAATAG
1183835 CTTTTACTTTCT-TT
1 CTTTTACTTT-TATT
1183849 CTTTTACTTTTATT
1 CTTTTACTTTTATT
1183863 CTTTT
1 CTTTT
1183868 TAACTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 1 0.06
14 17 0.94
ACGTcount: A:0.09, C:0.18, G:0.00, T:0.73
Consensus pattern (14 bp):
CTTTTACTTTTATT
Found at i:1191405 original size:17 final size:19
Alignment explanation
Indices: 1191380--1191420 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 19
1191370 GCTAATAATT
*
1191380 TATTGTAATATT-ATA-TA
1 TATTTTAATATTAATAGTA
*
1191397 TATTTTAATTTTAATAGTA
1 TATTTTAATATTAATAGTA
1191416 TATTT
1 TATTT
1191421 AATTTGTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 10 0.50
18 3 0.15
19 7 0.35
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.59
Consensus pattern (19 bp):
TATTTTAATATTAATAGTA
Found at i:1211779 original size:24 final size:24
Alignment explanation
Indices: 1211731--1211780 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1211721 TTTAAATTAA
* *
1211731 TAAAAATAAATTTATATTTTGATT
1 TAAAAATAAATTTAGATTTTAATT
1211755 TAAAAATAAAATTTAGA-TTTAATT
1 TAAAAAT-AAATTTAGATTTTAATT
1211779 TA
1 TA
1211781 TTAAATTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 15 0.65
25 8 0.35
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (24 bp):
TAAAAATAAATTTAGATTTTAATT
Found at i:1220857 original size:19 final size:19
Alignment explanation
Indices: 1220805--1220868 Score: 53
Period size: 19 Copynumber: 3.4 Consensus size: 19
1220795 CTTTTAAAAA
*
1220805 TTATAAAAATTGT-AGAATT
1 TTATAAAAA-TGTAAGAAAT
* *
1220824 TTAT-AAAGTCATAAGAAAT
1 TTATAAAAAT-GTAAGAAAT
1220843 TTATAAAAATGTAAGGAAAT
1 TTATAAAAATGTAA-GAAAT
1220863 TT-TAAA
1 TTATAAA
1220869 TTTGTAAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
17 1 0.03
18 4 0.11
19 20 0.56
20 11 0.31
ACGTcount: A:0.52, C:0.02, G:0.11, T:0.36
Consensus pattern (19 bp):
TTATAAAAATGTAAGAAAT
Found at i:1221153 original size:21 final size:21
Alignment explanation
Indices: 1221111--1221152 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
1221101 TCTCTCTCTC
*
1221111 TCTATAAATTTTTAATATTTT
1 TCTATAAATTATTAATATTTT
*
1221132 TCTAT-AATTATTATTATTTT
1 TCTATAAATTATTAATATTTT
1221152 T
1 T
1221153 TATTATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (21 bp):
TCTATAAATTATTAATATTTT
Found at i:1221315 original size:9 final size:10
Alignment explanation
Indices: 1221277--1221313 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
1221267 TTTTGATGCA
1221277 TTTTATAAAT
1 TTTTATAAAT
1221287 TTTTACT--AT
1 TTTTA-TAAAT
1221296 TTTTATAAAT
1 TTTTATAAAT
1221306 TTTTATAA
1 TTTTATAA
1221314 TTCTTAATAC
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
8 1 0.04
9 7 0.29
10 15 0.62
11 1 0.04
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (10 bp):
TTTTATAAAT
Found at i:1224538 original size:25 final size:25
Alignment explanation
Indices: 1224510--1224557 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
1224500 AACAAATTAA
1224510 AAAATACA-AAAAAAAAATCAATGTG
1 AAAATA-AGAAAAAAAAATCAATGTG
* *
1224535 AAAATAAGGAAAAATAATCAATG
1 AAAATAAGAAAAAAAAATCAATG
1224558 AGTTGTATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 19 0.95
ACGTcount: A:0.67, C:0.06, G:0.10, T:0.17
Consensus pattern (25 bp):
AAAATAAGAAAAAAAAATCAATGTG
Found at i:1230371 original size:26 final size:22
Alignment explanation
Indices: 1230341--1230395 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 22
1230331 ATTGTGTAAA
*
1230341 TTTTAAAGTTTATATGTTATTTGATT
1 TTTTAAA-TTT-TAT-TTACTT-ATT
1230367 TTTTAAATTTTATTTACTTATT
1 TTTTAAATTTTATTTACTTATT
1230389 TTTTAAA
1 TTTTAAA
1230396 AAAAAAAGAG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 10 0.36
23 5 0.18
24 3 0.11
25 3 0.11
26 7 0.25
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.64
Consensus pattern (22 bp):
TTTTAAATTTTATTTACTTATT
Found at i:1236316 original size:19 final size:17
Alignment explanation
Indices: 1236292--1236326 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
1236282 TTTGATTTAA
1236292 AATTTTTATACTTTTAAAT
1 AATTTTTA-A-TTTTAAAT
1236311 AATTTTTAATTTTAAA
1 AATTTTTAATTTTAAA
1236327 AGAATTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 1 0.06
19 8 0.50
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (17 bp):
AATTTTTAATTTTAAAT
Found at i:1236332 original size:18 final size:19
Alignment explanation
Indices: 1236292--1236332 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
1236282 TTTGATTTAA
*
1236292 AATTTTTATACTTTTAAAT
1 AATTTTTATACTTTTAAAG
1236311 AATTTTTA-A-TTTTAAAAG
1 AATTTTTATACTTTT-AAAG
1236329 AATT
1 AATT
1236333 AATTAATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 4 0.20
18 8 0.40
19 8 0.40
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (19 bp):
AATTTTTATACTTTTAAAG
Found at i:1239200 original size:18 final size:17
Alignment explanation
Indices: 1239179--1239213 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1239169 AAAGCATTTT
1239179 AAATTCAAAATATTTATA
1 AAATTCAAAAT-TTTATA
*
1239197 AAATTCCAAATTTTATA
1 AAATTCAAAATTTTATA
1239214 TTTTTTGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (17 bp):
AAATTCAAAATTTTATA
Found at i:1241326 original size:22 final size:23
Alignment explanation
Indices: 1241296--1241338 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1241286 ATAGATACGC
*
1241296 GAATTTCC-ACCCAAACACACTA
1 GAATATCCAACCCAAACACACTA
1241318 GAATATCCAACCCAAACACAC
1 GAATATCCAACCCAAACACAC
1241339 CCGGAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.44, C:0.37, G:0.05, T:0.14
Consensus pattern (23 bp):
GAATATCCAACCCAAACACACTA
Found at i:1242488 original size:18 final size:17
Alignment explanation
Indices: 1242453--1242485 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1242443 CTTTTTATTC
1242453 TTTTATTATTTCATTTA
1 TTTTATTATTTCATTTA
1242470 TTTTACTTATTT-ATTT
1 TTTTA-TTATTTCATTT
1242486 TATCATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTATTATTTCATTTA
Found at i:1243474 original size:14 final size:13
Alignment explanation
Indices: 1243450--1243483 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
1243440 ACCGTTTTAC
1243450 TATTATGTTGTTAT
1 TATT-TGTTGTTAT
1243464 TAGTTTGTTGTTAT
1 TA-TTTGTTGTTAT
1243478 TATTTG
1 TATTTG
1243484 GATATTGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 4 0.21
14 13 0.68
15 2 0.11
ACGTcount: A:0.18, C:0.00, G:0.18, T:0.65
Consensus pattern (13 bp):
TATTTGTTGTTAT
Found at i:1243643 original size:18 final size:20
Alignment explanation
Indices: 1243622--1243662 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
1243612 GAAATATTTA
*
1243622 TTTTGATGT-TTTTA-GTAT
1 TTTTGATGTATTATATGTAT
1243640 TTTTGATGTATTATATGTAT
1 TTTTGATGTATTATATGTAT
1243660 TTT
1 TTT
1243663 AAAATTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 9 0.45
19 4 0.20
20 7 0.35
ACGTcount: A:0.20, C:0.00, G:0.15, T:0.66
Consensus pattern (20 bp):
TTTTGATGTATTATATGTAT
Found at i:1243880 original size:23 final size:24
Alignment explanation
Indices: 1243837--1243881 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
1243827 AACAATAATT
1243837 TTTTGATAATTATTTTCTTTTTTC
1 TTTTGATAATTATTTTCTTTTTTC
*
1243861 TTTTG-TAA-TATTTTATTTTTT
1 TTTTGATAATTATTTTCTTTTTT
1243882 GTCGTGATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 12 0.60
23 3 0.15
24 5 0.25
ACGTcount: A:0.18, C:0.04, G:0.04, T:0.73
Consensus pattern (24 bp):
TTTTGATAATTATTTTCTTTTTTC
Found at i:1247161 original size:2 final size:2
Alignment explanation
Indices: 1247154--1247179 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1247144 TTCTAAAAAG
1247154 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
1247180 AATCTTGTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1263152 original size:18 final size:18
Alignment explanation
Indices: 1263121--1263201 Score: 72
Period size: 18 Copynumber: 4.5 Consensus size: 18
1263111 ATGGTGGGAG
* *
1263121 TGACGAAGAAGATGACGA
1 TGACGAAGATGATGATGA
* *
1263139 TGACGATGATGATGATGG
1 TGACGAAGATGATGATGA
*
1263157 GGACGAAGATGATGATGA
1 TGACGAAGATGATGATGA
* * * *
1263175 CGACGATGATGGTGAGGA
1 TGACGAAGATGATGATGA
*
1263193 TGAAGAAGA
1 TGACGAAGA
1263202 GGAGGACGAA
Statistics
Matches: 49, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 49 1.00
ACGTcount: A:0.37, C:0.07, G:0.38, T:0.17
Consensus pattern (18 bp):
TGACGAAGATGATGATGA
Found at i:1263155 original size:15 final size:15
Alignment explanation
Indices: 1263131--1263195 Score: 58
Period size: 15 Copynumber: 4.1 Consensus size: 15
1263121 TGACGAAGAA
*
1263131 GATGACGATGACGAT
1 GATGATGATGACGAT
*
1263146 GATGATGATGGGGACGAA
1 GATGATGAT---GACGAT
*
1263164 GATGATGATGACGAC
1 GATGATGATGACGAT
* *
1263179 GATGATGGTGAGGAT
1 GATGATGATGACGAT
1263194 GA
1 GA
1263196 AGAAGAGGAG
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
15 27 0.66
18 14 0.34
ACGTcount: A:0.32, C:0.08, G:0.40, T:0.20
Consensus pattern (15 bp):
GATGATGATGACGAT
Found at i:1263212 original size:15 final size:15
Alignment explanation
Indices: 1263188--1263222 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1263178 CGATGATGGT
*
1263188 GAGGATGAAGAAGAG
1 GAGGACGAAGAAGAG
*
1263203 GAGGACGAAGAAGAT
1 GAGGACGAAGAAGAG
1263218 GAGGA
1 GAGGA
1263223 TGATGAGGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.46, C:0.03, G:0.46, T:0.06
Consensus pattern (15 bp):
GAGGACGAAGAAGAG
Found at i:1290919 original size:23 final size:20
Alignment explanation
Indices: 1290893--1290942 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
1290883 ATTTTGATTA
1290893 TTAAATTATTTAAATTTTTTTAT
1 TTAAATTA-TTAAA-TTTTTT-T
* *
1290916 TTAAGTTATTAGATTTTTTT
1 TTAAATTATTAAATTTTTTT
1290936 TTAAATT
1 TTAAATT
1290943 TGGTTAACAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 7 0.29
21 6 0.25
22 4 0.17
23 7 0.29
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (20 bp):
TTAAATTATTAAATTTTTTT
Found at i:1297258 original size:22 final size:21
Alignment explanation
Indices: 1297209--1297259 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
1297199 TTTGAAATTC
1297209 ATTTTAAATATATATCATTAT
1 ATTTTAAATATATATCATTAT
* **
1297230 ATGTTTAAATTTATAATTGTTAT
1 AT-TTTAAATATAT-ATCATTAT
1297253 ATTTTAA
1 ATTTTAA
1297260 TGATATTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 2 0.08
22 15 0.60
23 8 0.32
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (21 bp):
ATTTTAAATATATATCATTAT
Found at i:1297276 original size:31 final size:32
Alignment explanation
Indices: 1297241--1297308 Score: 83
Period size: 31 Copynumber: 2.2 Consensus size: 32
1297231 TGTTTAAATT
1297241 TATAATTGTTATAT-TTTAATGAT-A-TTTAAAA
1 TATAATT-TTATATATTTAAT-ATAATTTTAAAA
1297272 TATAA-TTTATATATTTAATATAATTTTAAAA
1 TATAATTTTATATATTTAATATAATTTTAAAA
1297303 -ATAATT
1 TATAATT
1297309 AATATTTATA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
29 8 0.24
30 12 0.36
31 13 0.39
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (32 bp):
TATAATTTTATATATTTAATATAATTTTAAAA
Found at i:1297307 original size:30 final size:29
Alignment explanation
Indices: 1297249--1297316 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
1297239 TTTATAATTG
1297249 TTATAT-TTTAATGATATTTAAAATATAA
1 TTATATATTTAATGATATTTAAAATATAA
1297277 TTTATATATTTAAT-ATAATTTTAAAA-ATAA
1 -TTATATATTTAATGAT-A-TTTAAAATATAA
1297307 TTA-ATATTTA
1 TTATATATTTA
1297317 TATCCATCTA
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
28 7 0.19
29 11 0.31
30 11 0.31
31 7 0.19
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (29 bp):
TTATATATTTAATGATATTTAAAATATAA
Found at i:1312283 original size:61 final size:62
Alignment explanation
Indices: 1312201--1312331 Score: 167
Period size: 62 Copynumber: 2.1 Consensus size: 62
1312191 ACATATTCTA
* * *
1312201 TCAATTT-GATCCAAATATAAAAAAAT-CAACAAATTTAGCCCTTAATATTTACAGAATTTG
1 TCAATTTAGATCCAAATATAAAAAAATAAAAAAAATTTAGCCCTTAATATTTACAAAATTTG
* * * * * *
1312261 TCATTTTAGATCCAATTCTAAAAAAATAAAAAAAATTTGGCTCTTGATATTTACAAAATTTG
1 TCAATTTAGATCCAAATATAAAAAAATAAAAAAAATTTAGCCCTTAATATTTACAAAATTTG
1312323 TCAATTTAG
1 TCAATTTAG
1312332 TCTTTAACTC
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
60 6 0.10
61 17 0.29
62 36 0.61
ACGTcount: A:0.44, C:0.13, G:0.08, T:0.36
Consensus pattern (62 bp):
TCAATTTAGATCCAAATATAAAAAAATAAAAAAAATTTAGCCCTTAATATTTACAAAATTTG
Found at i:1313474 original size:34 final size:34
Alignment explanation
Indices: 1313426--1313499 Score: 121
Period size: 34 Copynumber: 2.2 Consensus size: 34
1313416 TGAGTACGTC
*
1313426 GTTTACTCAGTGCCACAATTCACAACTCAGTATG
1 GTTTTCTCAGTGCCACAATTCACAACTCAGTATG
*
1313460 GTTTTCTCAGTGCCACGATTCACAACTCAGTATG
1 GTTTTCTCAGTGCCACAATTCACAACTCAGTATG
*
1313494 ATTTTC
1 GTTTTC
1313500 CTCGTGAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.34
Consensus pattern (34 bp):
GTTTTCTCAGTGCCACAATTCACAACTCAGTATG
Found at i:1313586 original size:34 final size:34
Alignment explanation
Indices: 1313514--1313660 Score: 215
Period size: 34 Copynumber: 4.3 Consensus size: 34
1313504 TGAAAAATGT
* *
1313514 CATACCTACGTTTCATAACTCAGTATGGAAAATAC
1 CATACCTACGTATCATAACTCGGTATGG-AAATAC
1313549 CATACCTACGTATCATAACTCGGTATGGAAATAC
1 CATACCTACGTATCATAACTCGGTATGGAAATAC
* * *
1313583 CATACCTACG-ATCATAGCTCGGTATAGAATTAC
1 CATACCTACGTATCATAACTCGGTATGGAAATAC
* *
1313616 CATACCTACATATCATAGCTCGGTATGGAAATAC
1 CATACCTACGTATCATAACTCGGTATGGAAATAC
1313650 CATACCTACGT
1 CATACCTACGT
1313661 TTCGCATTTT
Statistics
Matches: 102, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
33 29 0.28
34 47 0.46
35 26 0.25
ACGTcount: A:0.35, C:0.24, G:0.14, T:0.27
Consensus pattern (34 bp):
CATACCTACGTATCATAACTCGGTATGGAAATAC
Found at i:1313622 original size:67 final size:69
Alignment explanation
Indices: 1313514--1313660 Score: 217
Period size: 67 Copynumber: 2.2 Consensus size: 69
1313504 TGAAAAATGT
* * *
1313514 CATACCTACGTTTCATAACTCAGTATGGAAAATACCATACCTACGTATCATAACTCGGTATGGAA
1 CATACCTACGTATCATAACTCAGTATAGAAAATACCATACCTACATATCATAACTCGGTATGGAA
1313579 ATAC
66 ATAC
* * * *
1313583 CATACCTACG-ATCATAGCTCGGTATAG-AATTACCATACCTACATATCATAGCTCGGTATGGAA
1 CATACCTACGTATCATAACTCAGTATAGAAAATACCATACCTACATATCATAACTCGGTATGGAA
1313646 ATAC
66 ATAC
1313650 CATACCTACGT
1 CATACCTACGT
1313661 TTCGCATTTT
Statistics
Matches: 70, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
67 47 0.67
68 13 0.19
69 10 0.14
ACGTcount: A:0.35, C:0.24, G:0.14, T:0.27
Consensus pattern (69 bp):
CATACCTACGTATCATAACTCAGTATAGAAAATACCATACCTACATATCATAACTCGGTATGGAA
ATAC
Found at i:1314688 original size:37 final size:37
Alignment explanation
Indices: 1314627--1314772 Score: 242
Period size: 37 Copynumber: 4.0 Consensus size: 37
1314617 TACGTATGAT
* *
1314627 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
1314662 CACCTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1314699 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
1314736 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1314773 TAAAGCTATC
Statistics
Matches: 104, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
35 9 0.09
36 3 0.03
37 92 0.88
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (37 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:1314789 original size:46 final size:46
Alignment explanation
Indices: 1314736--1314958 Score: 248
Period size: 52 Copynumber: 4.6 Consensus size: 46
1314726 TAAGTGTAGC
* *
1314736 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTAT
* * *
1314782 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTAT
* *
1314828 CACTTTTCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCCAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCCAAAGCTAT
* *
1314880 CACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCAAAGCTAT
*
1314932 CACTTATCACTTTATCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
1314959 AGTACTCAAA
Statistics
Matches: 158, Mismatches: 12, Indels: 14
0.86 0.07 0.08
Matches are distributed among these distances:
46 67 0.42
49 1 0.01
50 1 0.01
51 3 0.02
52 86 0.54
ACGTcount: A:0.28, C:0.23, G:0.13, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTAT
Found at i:1314855 original size:52 final size:52
Alignment explanation
Indices: 1314779--1314952 Score: 249
Period size: 52 Copynumber: 3.3 Consensus size: 52
1314769 TAGCTAAAGC
* * * *
1314779 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACT
* *
1314832 TTTCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCCAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACT
* * *
1314884 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACT
1314936 TATCACTTTATCACTTG
1 TATCACTTT-TCACTTG
1314953 ATCAGAAGTA
Statistics
Matches: 109, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
52 92 0.84
53 17 0.16
ACGTcount: A:0.27, C:0.24, G:0.13, T:0.36
Consensus pattern (52 bp):
TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACT
Found at i:1318593 original size:7 final size:7
Alignment explanation
Indices: 1318581--1318613 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
1318571 GTGAGATATT
1318581 AAAAAAG
1 AAAAAAG
1318588 AAAAAAG
1 AAAAAAG
1318595 AAAAAAG
1 AAAAAAG
1318602 AAAAAAG
1 AAAAAAG
1318609 AAAAA
1 AAAAA
1318614 TAGTGTCCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:1325265 original size:15 final size:15
Alignment explanation
Indices: 1325245--1325274 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1325235 CCGTAAGTAA
1325245 CTTAGCCATTTCTAT
1 CTTAGCCATTTCTAT
1325260 CTTAGCCATTTCTAT
1 CTTAGCCATTTCTAT
1325275 TTTCCTTAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.27, G:0.07, T:0.47
Consensus pattern (15 bp):
CTTAGCCATTTCTAT
Found at i:1329517 original size:26 final size:28
Alignment explanation
Indices: 1329488--1329539 Score: 72
Period size: 26 Copynumber: 1.9 Consensus size: 28
1329478 CTTAAAAATG
1329488 TAAAATAAATAATT-A-AATATATGATT
1 TAAAATAAATAATTAATAATATATGATT
* *
1329514 TAAAATTAATTATTAATAATATATGA
1 TAAAATAAATAATTAATAATATATGA
1329540 AATATATATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 12 0.55
27 1 0.05
28 9 0.41
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (28 bp):
TAAAATAAATAATTAATAATATATGATT
Found at i:1330651 original size:14 final size:13
Alignment explanation
Indices: 1330626--1330650 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1330616 ATTCAATGAG
1330626 AATTAAAAAAAAT
1 AATTAAAAAAAAT
1330639 AATTAAAAAAAA
1 AATTAAAAAAAA
1330651 AACAGGCGCT
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:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
AATTAAAAAAAAT
Found at i:1337889 original size:22 final size:22
Alignment explanation
Indices: 1337853--1337919 Score: 66
Period size: 22 Copynumber: 3.0 Consensus size: 22
1337843 TGGTTGTACT
* * *
1337853 TTTTTGTATATTTAAAATTTAG
1 TTTTTCTATTTTTAAAATTTAA
1337875 TATTTT-TATTTTTAAAAATTTAA
1 T-TTTTCTATTTTT-AAAATTTAA
1337898 TTTTTCTAATTTTT-AAATTTAA
1 TTTTTCT-ATTTTTAAAATTTAA
1337920 AATTTCAGAT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
22 19 0.49
23 14 0.36
24 6 0.15
ACGTcount: A:0.34, C:0.01, G:0.03, T:0.61
Consensus pattern (22 bp):
TTTTTCTATTTTTAAAATTTAA
Found at i:1344648 original size:17 final size:17
Alignment explanation
Indices: 1344604--1344651 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
1344594 AAATAATTTA
*
1344604 AAAATTATAAAAATATTC
1 AAAATT-TAAAAAAATTC
**
1344622 AAAAAATAAAAAAATTC
1 AAAATTTAAAAAAATTC
1344639 AAAATTTAAAAAA
1 AAAATTTAAAAAA
1344652 TTAAAAGTCC
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
17 21 0.84
18 4 0.16
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.25
Consensus pattern (17 bp):
AAAATTTAAAAAAATTC
Found at i:1344657 original size:7 final size:8
Alignment explanation
Indices: 1344601--1344657 Score: 51
Period size: 8 Copynumber: 6.8 Consensus size: 8
1344591 GTCAAATAAT
*
1344601 TTAAAAAT
1 TTAAAAAA
1344609 TATAAAAATA
1 T-TAAAAA-A
1344619 TTCAAAAAA
1 TT-AAAAAA
*
1344628 TAAAAAAA
1 TTAAAAAA
* *
1344636 TTCAAAAT
1 TTAAAAAA
1344644 TTAAAAAA
1 TTAAAAAA
1344652 TTAAAA
1 TTAAAA
1344658 GTCCATAAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
8 24 0.62
9 9 0.23
10 6 0.15
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (8 bp):
TTAAAAAA
Found at i:1349734 original size:31 final size:31
Alignment explanation
Indices: 1349699--1349760 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
1349689 TACAATTTGA
* *
1349699 TCACTAAATTATTCAAAA-TTTTTCATTTAAG
1 TCACTAAACTATTAAAAAGTTTTT-ATTTAAG
1349730 TCACTAAACTATTAAAAAGTTTTTATTTAAG
1 TCACTAAACTATTAAAAAGTTTTTATTTAAG
1349761 CCATTGGACT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 23 0.82
32 5 0.18
ACGTcount: A:0.40, C:0.11, G:0.05, T:0.44
Consensus pattern (31 bp):
TCACTAAACTATTAAAAAGTTTTTATTTAAG
Found at i:1352413 original size:39 final size:40
Alignment explanation
Indices: 1352370--1352481 Score: 113
Period size: 39 Copynumber: 2.8 Consensus size: 40
1352360 TCAGATAGTT
*
1352370 CGAAGTAATAGTTGACACCCAGTGTCTCATCG-GCCTAGC
1 CGAAGTAATAGTTGACACCCAGTGTCTCATCGAACCTAGC
** ** * *
1352409 CGAAGTAA-AGTTGGTACCCAGTACCTCATCGAATCTATC
1 CGAAGTAATAGTTGACACCCAGTGTCTCATCGAACCTAGC
*
1352448 CGAAGAAATA-TAGTGACACCCAGTGTCTCATCGA
1 CGAAGTAATAGT--TGACACCCAGTGTCTCATCGA
1352482 CTCGAGGTCG
Statistics
Matches: 57, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
38 19 0.33
39 20 0.35
40 1 0.02
41 17 0.30
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (40 bp):
CGAAGTAATAGTTGACACCCAGTGTCTCATCGAACCTAGC
Found at i:1354060 original size:5 final size:5
Alignment explanation
Indices: 1354050--1354082 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
1354040 TTTATATATA
1354050 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATA
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATA
1354083 CTTAATTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATAAT
Found at i:1354914 original size:50 final size:51
Alignment explanation
Indices: 1354837--1354965 Score: 199
Period size: 50 Copynumber: 2.5 Consensus size: 51
1354827 GACCATGGCA
1354837 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGA-AAAGTG
1 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAA-TG
*
1354888 A-AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAATGACAAATG
1 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATG
* * *
1354938 ACAAGTGAAAAGTGGTAGCTTCAGCTAC
1 ACAAGTGATAAGTGATAGCTTCGGCTAC
1354966 CTGATCAGTG
Statistics
Matches: 72, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
50 45 0.62
51 27 0.38
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26
Consensus pattern (51 bp):
ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATG
Found at i:1354979 original size:31 final size:31
Alignment explanation
Indices: 1354941--1355058 Score: 184
Period size: 31 Copynumber: 3.8 Consensus size: 31
1354931 ACAAATGACA
*
1354941 AGTGAAAAGTGGTAGCTTCAGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
1354972 AGTGAAAAGTGGTAG-TTCTGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTC-GGCTACCTGATC
* *
1355003 AGTGAAAAATGGTAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
1355034 AGTGAATAGTGGTAGCTTCGGCTAC
1 AGTGAAAAGTGGTAGCTTCGGCTAC
1355059 AAGTAACAAG
Statistics
Matches: 79, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
30 3 0.04
31 74 0.94
32 2 0.03
ACGTcount: A:0.27, C:0.19, G:0.28, T:0.26
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
Found at i:1355169 original size:47 final size:46
Alignment explanation
Indices: 1355084--1355204 Score: 127
Period size: 47 Copynumber: 2.6 Consensus size: 46
1355074 AGTGATTTCC
* * ** *
1355084 GTATAAGACCATATTTGGGATATGACATCGGTGTGATATATG-CTA
1 GTATAAGACCATATCTGGGATATGGCATAAGTGAGATATATGACTA
* *
1355129 CTGTATAAGACCATATCTGGGATATGGCATAAGTGAGATATGTGATTA
1 --GTATAAGACCATATCTGGGATATGGCATAAGTGAGATATATGACTA
* * *
1355177 GTGTAAGACCATAGCTGGGTTATGGCAT
1 GTATAAGACCATATCTGGGATATGGCAT
1355205 CGATATATGA
Statistics
Matches: 63, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
46 25 0.40
47 36 0.57
48 2 0.03
ACGTcount: A:0.31, C:0.12, G:0.26, T:0.31
Consensus pattern (46 bp):
GTATAAGACCATATCTGGGATATGGCATAAGTGAGATATATGACTA
Found at i:1355195 original size:46 final size:44
Alignment explanation
Indices: 1355134--1355274 Score: 132
Period size: 42 Copynumber: 3.2 Consensus size: 44
1355124 TGCTACTGTA
* * *
1355134 TAAGACCATATCTGGGATATGGCATAAGTGAGATATGTGATTA-GTG
1 TAAGACCATAGCTGGGATATGGCAT-A-T-AGATATATGAATATGTG
* *
1355180 TAAGACCATAGCTGGGTTATGGC--ATCGATATATGAATATGTG
1 TAAGACCATAGCTGGGATATGGCATATAGATATATGAATATGTG
* * *
1355222 TAAGACCATAGCTGGGCTATGGCATCAT---TATGTGAAGATGTG
1 TAAGACCATAGCTGGGATATGGCAT-ATAGATATATGAATATGTG
1355264 TAAGACCATAG
1 TAAGACCATAG
1355275 TTGAACTATG
Statistics
Matches: 83, Mismatches: 8, Indels: 12
0.81 0.08 0.12
Matches are distributed among these distances:
41 10 0.12
42 49 0.59
43 1 0.01
45 2 0.02
46 21 0.25
ACGTcount: A:0.32, C:0.12, G:0.27, T:0.29
Consensus pattern (44 bp):
TAAGACCATAGCTGGGATATGGCATATAGATATATGAATATGTG
Found at i:1355235 original size:42 final size:42
Alignment explanation
Indices: 1355177--1355289 Score: 156
Period size: 42 Copynumber: 2.7 Consensus size: 42
1355167 TATGTGATTA
* *
1355177 GTGTAAGACCATAGCTGGGTTATGGCATCGA-TATATGAATAT
1 GTGTAAGACCATAGCTGGGCTATGGCATC-ATTATATGAAGAT
*
1355219 GTGTAAGACCATAGCTGGGCTATGGCATCATTATGTGAAGAT
1 GTGTAAGACCATAGCTGGGCTATGGCATCATTATATGAAGAT
* **
1355261 GTGTAAGACCATAGTTGAACTATGGCATC
1 GTGTAAGACCATAGCTGGGCTATGGCATC
1355290 GAGAAAACGA
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
41 1 0.02
42 63 0.98
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.29
Consensus pattern (42 bp):
GTGTAAGACCATAGCTGGGCTATGGCATCATTATATGAAGAT
Found at i:1356265 original size:24 final size:24
Alignment explanation
Indices: 1356233--1356282 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
1356223 TGTTGAGTAG
*
1356233 AAGAACATACTTTAGGTCCAAGTC
1 AAGAACATACATTAGGTCCAAGTC
1356257 AAGAACATACATTAGGTCCAAGTC
1 AAGAACATACATTAGGTCCAAGTC
1356281 AA
1 AA
1356283 TTTGACTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.42, C:0.20, G:0.16, T:0.22
Consensus pattern (24 bp):
AAGAACATACATTAGGTCCAAGTC
Found at i:1365686 original size:31 final size:30
Alignment explanation
Indices: 1365655--1365714 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
1365645 AAGATTTATA
* *
1365655 AATAAAATATTAA-TAATTTTATTTAAATAT
1 AATAAAATAATAATTAA-TTTAATTAAATAT
*
1365685 AATTAAATAATAATTAATTTAATTAAATAT
1 AATAAAATAATAATTAATTTAATTAAATAT
1365715 TAAAATCTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 23 0.88
31 3 0.12
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (30 bp):
AATAAAATAATAATTAATTTAATTAAATAT
Found at i:1366195 original size:29 final size:29
Alignment explanation
Indices: 1366152--1366220 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
1366142 ATTTTAAATT
* *
1366152 AATAATGATAAAATTGTACTTT-ATTCTTTTA
1 AATAAT-A-AAAATT-TAATTTAATTCTTTAA
1366183 AATAATAAAAATTTAATTTAATTCTTTAA
1 AATAATAAAAATTTAATTTAATTCTTTAA
*
1366212 AATTATAAA
1 AATAATAAA
1366221 GATATAAGAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 5 0.15
29 22 0.65
30 1 0.03
31 6 0.18
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (29 bp):
AATAATAAAAATTTAATTTAATTCTTTAA
Found at i:1374093 original size:19 final size:18
Alignment explanation
Indices: 1374044--1374096 Score: 56
Period size: 19 Copynumber: 2.9 Consensus size: 18
1374034 AATATTTAGC
*
1374044 TTTTATTTTATTT-TTCAT
1 TTTTA-TTTATTTATTAAT
*
1374062 TGTT-TTTATTTATTAAT
1 TTTTATTTATTTATTAAT
1374079 TTTTATTTAATTTATTAA
1 TTTTATTT-ATTTATTAA
1374097 GCTATTAACT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
16 7 0.24
17 7 0.24
18 6 0.21
19 9 0.31
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.72
Consensus pattern (18 bp):
TTTTATTTATTTATTAAT
Found at i:1383901 original size:13 final size:13
Alignment explanation
Indices: 1383883--1383907 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1383873 AATTAAAGAA
1383883 ATTTTAGATTTAG
1 ATTTTAGATTTAG
1383896 ATTTTAGATTTA
1 ATTTTAGATTTA
1383908 TTTTTATTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
ATTTTAGATTTAG
Found at i:1384381 original size:16 final size:16
Alignment explanation
Indices: 1384356--1384386 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1384346 TTCATTAAAA
*
1384356 TTTATCTGAATAATTG
1 TTTATATGAATAATTG
1384372 TTTATATGAATAATT
1 TTTATATGAATAATT
1384387 CTAACATCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.03, G:0.10, T:0.52
Consensus pattern (16 bp):
TTTATATGAATAATTG
Found at i:1386861 original size:17 final size:17
Alignment explanation
Indices: 1386826--1386857 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1386816 TCCCAAGTTT
1386826 TATTTTAATATTTTATA
1 TATTTTAATATTTTATA
1386843 TATTTTAAT-TTTTAT
1 TATTTTAATATTTTAT
1386858 TATACACACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TATTTTAATATTTTATA
Found at i:1401348 original size:21 final size:18
Alignment explanation
Indices: 1401334--1401369 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1401324 CAAAGCTTGG
1401334 ACCCACTTCACCAAATGTT
1 ACCCACTTCACCAAA-GTT
*
1401353 ACCTACTTCACCAAAGT
1 ACCCACTTCACCAAAGT
1401370 ATATTTATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 2 0.12
19 14 0.88
ACGTcount: A:0.33, C:0.36, G:0.06, T:0.25
Consensus pattern (18 bp):
ACCCACTTCACCAAAGTT
Found at i:1404132 original size:20 final size:20
Alignment explanation
Indices: 1404095--1404133 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1404085 TCTTAAACAC
* *
1404095 TTAAATCTTAAATCAACCTT
1 TTAAAACTTAAATAAACCTT
*
1404115 TTAAAACTTAAGTAAACCT
1 TTAAAACTTAAATAAACCT
1404134 GAGCCATCAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.44, C:0.18, G:0.03, T:0.36
Consensus pattern (20 bp):
TTAAAACTTAAATAAACCTT
Found at i:1408575 original size:17 final size:17
Alignment explanation
Indices: 1408555--1408587 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1408545 TAAATTTACT
1408555 TATA-ATAACTTTTTATA
1 TATATATAA-TTTTTATA
1408572 TATATATAATTTTTAT
1 TATATATAATTTTTAT
1408588 TGAAATACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (17 bp):
TATATATAATTTTTATA
Found at i:1409891 original size:15 final size:15
Alignment explanation
Indices: 1409871--1409901 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1409861 GAAGTCGAAT
*
1409871 AGGTTCCAGCGTTTA
1 AGGTTCCAGAGTTTA
1409886 AGGTTCCAGAGTTTA
1 AGGTTCCAGAGTTTA
1409901 A
1 A
1409902 TTTTCTTCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (15 bp):
AGGTTCCAGAGTTTA
Found at i:1417791 original size:23 final size:24
Alignment explanation
Indices: 1417763--1417810 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
1417753 CACCAACCTT
1417763 TAATATAAATCGTAAA-AATAAAA
1 TAATATAAATCGTAAATAATAAAA
* *
1417786 TAATATTAATCTTAAATAATAAAA
1 TAATATAAATCGTAAATAATAAAA
1417810 T
1 T
1417811 TGATAATGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 14 0.64
24 8 0.36
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.33
Consensus pattern (24 bp):
TAATATAAATCGTAAATAATAAAA
Found at i:1418200 original size:26 final size:26
Alignment explanation
Indices: 1418171--1418220 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
1418161 ATCGATATAG
1418171 AAATTAATT-TTTAAATTTAAATTTAA
1 AAATTAATTATTT-AATTTAAATTTAA
* *
1418197 AAATTTATTATTTATTTTAAATTT
1 AAATTAATTATTTAATTTAAATTT
1418221 GTTTAATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 18 0.86
27 3 0.14
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (26 bp):
AAATTAATTATTTAATTTAAATTTAA
Found at i:1427510 original size:6 final size:5
Alignment explanation
Indices: 1427459--1427509 Score: 77
Period size: 5 Copynumber: 10.0 Consensus size: 5
1427449 TTAATACCAC
1427459 CTTTT CTTTT CTTTT CTTTT CTTTT CTTCTT CTTCTT CTTTT -TTTT CTTTT
1 CTTTT CTTTT CTTTT CTTTT CTTTT CTT-TT CTT-TT CTTTT CTTTT CTTTT
1427510 TACATCATTA
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 11 0.25
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (5 bp):
CTTTT
Found at i:1437879 original size:12 final size:12
Alignment explanation
Indices: 1437862--1437894 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
1437852 CAGTCTACCC
1437862 ATATTAATTTTT
1 ATATTAATTTTT
1437874 ATATT-ATTTTT
1 ATATTAATTTTT
1437885 ATA-TAATTTT
1 ATATTAATTTT
1437895 AAAATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 14 0.70
12 5 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:1438057 original size:30 final size:30
Alignment explanation
Indices: 1438016--1438077 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
1438006 CTTAACAAGT
*
1438016 AAATGTCTTTAAAATAATAACAAAATTAAC
1 AAATATCTTTAAAATAATAACAAAATTAAC
1438046 AAATATCTTTAAAATAATAACAAAATTAAC
1 AAATATCTTTAAAATAATAACAAAATTAAC
1438076 AA
1 AA
1438078 TAAAATAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.60, C:0.10, G:0.02, T:0.29
Consensus pattern (30 bp):
AAATATCTTTAAAATAATAACAAAATTAAC
Found at i:1448855 original size:13 final size:14
Alignment explanation
Indices: 1448832--1448860 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1448822 AACCAGTGCA
1448832 CTTTTTCTTTTTTT
1 CTTTTTCTTTTTTT
1448846 CTTTTT-TTTTTTT
1 CTTTTTCTTTTTTT
1448859 CT
1 CT
1448861 GCTGCCATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (14 bp):
CTTTTTCTTTTTTT
Found at i:1449087 original size:16 final size:16
Alignment explanation
Indices: 1449066--1449098 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1449056 TTCGCTGTAT
1449066 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
*
1449082 TGGAATAGAGGTGTAA
1 TGGAATAGAGGCGTAA
1449098 T
1 T
1449099 AGCAAATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.36, C:0.03, G:0.36, T:0.24
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:1449143 original size:45 final size:44
Alignment explanation
Indices: 1449078--1449167 Score: 119
Period size: 45 Copynumber: 2.0 Consensus size: 44
1449068 GAATAGAGGC
* *
1449078 GTAATGGAATAGAGGTGTAATAGCAAATCAAT-TGTTTGGTTGAAT
1 GTAATGCAATAGAGGCGTAATAG-AAATC-ATGTGTTTGGTTGAAT
* *
1449123 GTAATGCAATAGAGGCGTAATAGTATTCATGTGTTTGGTTGAAT
1 GTAATGCAATAGAGGCGTAATAGAAATCATGTGTTTGGTTGAAT
1449167 G
1 G
1449168 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
43 2 0.05
44 17 0.43
45 21 0.52
ACGTcount: A:0.32, C:0.06, G:0.28, T:0.34
Consensus pattern (44 bp):
GTAATGCAATAGAGGCGTAATAGAAATCATGTGTTTGGTTGAAT
Found at i:1449184 original size:39 final size:40
Alignment explanation
Indices: 1449080--1449186 Score: 119
Period size: 44 Copynumber: 2.6 Consensus size: 40
1449070 ATAGAGGCGT
1449080 AATGGAATAGAGGTGTAATAGCAAATCAATTGTTTGGTTG
1 AATGGAATAGAGGTGTAATAGCAAATCAATTGTTTGGTTG
* * *
1449120 AATGTAATGCAATAGAGGCGTAATAG-TATTC-ATGTGTTTGGTTG
1 AATG----G-AATAGAGGTGTAATAGCAAATCAAT-TGTTTGGTTG
1449164 AATGGAATAGAGGTGTAATAGCA
1 AATGGAATAGAGGTGTAATAGCA
1449187 TAATAGAAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
39 15 0.27
40 5 0.09
43 2 0.04
44 18 0.33
45 15 0.27
ACGTcount: A:0.35, C:0.06, G:0.28, T:0.32
Consensus pattern (40 bp):
AATGGAATAGAGGTGTAATAGCAAATCAATTGTTTGGTTG
Found at i:1449350 original size:16 final size:16
Alignment explanation
Indices: 1449313--1449354 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
1449303 TTAATCATAT
*
1449313 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
1449329 TT-AAATATATTATAA
1 TTAAAATATATTATAA
1449344 TTAAAATATAT
1 TTAAAATATAT
1449355 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:1449361 original size:14 final size:15
Alignment explanation
Indices: 1449322--1449363 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
1449312 TTTAAACATA
*
1449322 ATTATTATTAAATAT
1 ATTATAATTAAATAT
1449337 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
1449351 A-TATAATTTAATA
1 ATTATAATTAAATA
1449364 AAATTCTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:1449413 original size:61 final size:61
Alignment explanation
Indices: 1449342--1449535 Score: 193
Period size: 61 Copynumber: 3.2 Consensus size: 61
1449332 AATATATTAT
*
1449342 AATTAAAATATATAATTTAATAAAATTCTTTATAATCAATATTCTTATATGAATTTACTCA
1 AATTATAATATATAATTTAATAAAATTCTTTATAATCAATATTCTTATATGAATTTACTCA
* * * ** * * * *
1449403 AATCATAATATATGATACT-ATAAAATATAATT-TAA-C-ATGATTATTAT-TAAATATA-TTA
1 AATTATAATATATAAT-TTAATAAAAT-TCTTTATAATCAAT-ATTCTTATATGAATTTACTCA
* * *
1449461 TAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCA
1 -AATTATAATATATAATTTAATAAAATTCTTTATAATCAATATTCTTATATGAATTTACTCA
1449523 AATTATAATATAT
1 AATTATAATATAT
1449536 GATACTATAA
Statistics
Matches: 100, Mismatches: 23, Indels: 20
0.70 0.16 0.14
Matches are distributed among these distances:
58 5 0.05
59 31 0.31
60 15 0.15
61 43 0.43
62 6 0.06
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (61 bp):
AATTATAATATATAATTTAATAAAATTCTTTATAATCAATATTCTTATATGAATTTACTCA
Found at i:1449456 original size:120 final size:120
Alignment explanation
Indices: 1449311--1449568 Score: 462
Period size: 120 Copynumber: 2.1 Consensus size: 120
1449301 ATTTAATCAT
*
1449311 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTTATA
1 ATTT-AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
*
1449376 ATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATA
65 ATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
*
1449432 ATTTAACATGATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
1 ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
* *
1449497 TTAATATTCTTATATGAATTTACTCAAATTATAATATATGATACTATAAAAGATA
66 TCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
1449552 ATTTAACATAATTATTA
1 ATTTAACATAATTATTA
1449569 GACAACTGCC
Statistics
Matches: 131, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
120 127 0.97
121 4 0.03
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.43
Consensus pattern (120 bp):
ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
TCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
Found at i:1449472 original size:16 final size:15
Alignment explanation
Indices: 1449428--1449483 Score: 53
Period size: 15 Copynumber: 3.8 Consensus size: 15
1449418 TACTATAAAA
* *
1449428 TATAATTTAACATGAT
1 TATAATTAAATAT-AT
*
1449444 TATTATTAAATATAT
1 TATAATTAAATATAT
1449459 TATAATTAAA-ATA-
1 TATAATTAAATATAT
*
1449472 TATAATTTAATA
1 TATAATTAAATA
1449484 AAATTCTTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
13 9 0.26
14 4 0.12
15 11 0.32
16 10 0.29
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (15 bp):
TATAATTAAATATAT
Found at i:1452731 original size:23 final size:20
Alignment explanation
Indices: 1452714--1452751 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1452704 AAGAAACAGA
1452714 GGGAGCAAATCGGCAGAAAC
1 GGGAGCAAATCGGCAGAAAC
*
1452734 TGGAGCAAATCGGCAGAA
1 GGGAGCAAATCGGCAGAA
1452752 GCAAAAGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.18, G:0.34, T:0.08
Consensus pattern (20 bp):
GGGAGCAAATCGGCAGAAAC
Found at i:1460465 original size:21 final size:21
Alignment explanation
Indices: 1460439--1460478 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1460429 TATTATATGT
1460439 ATTTTA-ATTTAATTAAATTAA
1 ATTTTATATTT-ATTAAATTAA
*
1460460 ATTTTATATTTTTTAAATT
1 ATTTTATATTTATTAAATT
1460479 TTAAAATTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTTATATTTATTAAATTAA
Found at i:1462859 original size:20 final size:20
Alignment explanation
Indices: 1462823--1462860 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1462813 GTGAAATTTG
*
1462823 TATAAAAATATAGAATTAAT
1 TATAAAAATATAAAATTAAT
1462843 TATAAAGAATA-AAAATTA
1 TATAAA-AATATAAAATTA
1462861 GTCTCGGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (20 bp):
TATAAAAATATAAAATTAAT
Found at i:1466168 original size:52 final size:52
Alignment explanation
Indices: 1466090--1466221 Score: 219
Period size: 52 Copynumber: 2.5 Consensus size: 52
1466080 ACCAATGCCA
* * *
1466090 ATGGTCTTATACGAGAGTACATATCACAATGCACCGATGCCATAGCCCAGCT
1 ATGGTCTTATACGGGCGCACATATCACAATGCACCGATGCCATAGCCCAGCT
*
1466142 ATGGTCTTATACGGGCGCACATATCACAATGCACCGATGTCATAGCCCAGCT
1 ATGGTCTTATACGGGCGCACATATCACAATGCACCGATGCCATAGCCCAGCT
*
1466194 ATGGTCTTATACAGGCGCACATATCACA
1 ATGGTCTTATACGGGCGCACATATCACA
1466222 TCTATTCTGT
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 75 1.00
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (52 bp):
ATGGTCTTATACGGGCGCACATATCACAATGCACCGATGCCATAGCCCAGCT
Found at i:1466380 original size:22 final size:22
Alignment explanation
Indices: 1466355--1466398 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
1466345 TAAGATAACT
1466355 TAGTAATCATAATATTTTCATA
1 TAGTAATCATAATATTTTCATA
1466377 TAGTAATCATAATATTTTCATA
1 TAGTAATCATAATATTTTCATA
1466399 ATAAAACATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.41, C:0.09, G:0.05, T:0.45
Consensus pattern (22 bp):
TAGTAATCATAATATTTTCATA
Found at i:1469623 original size:46 final size:44
Alignment explanation
Indices: 1469540--1469654 Score: 126
Period size: 46 Copynumber: 2.5 Consensus size: 44
1469530 GACGAGTACT
*
1469540 AGTGTAAGACATGTCTGGGACATGCTTCGGCCTCGAGACGTAAGCC
1 AGTGTAAGACATGTCTGGGACATGCTTCAGCCTCGAGACGT--GCC
* * *
1469586 AGTGTAAGACATGTTTGGGACATGCATT-AG-CTACGAGATGTGTC
1 AGTGTAAGACATGTCTGGGACATGC-TTCAGCCT-CGAGACGTGCC
*
1469630 AGTGTAAGACCATGTCTAGGACATG
1 AGTGTAAGA-CATGTCTGGGACATG
1469655 ATGTAATACC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
44 11 0.18
45 15 0.25
46 32 0.53
47 2 0.03
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.25
Consensus pattern (44 bp):
AGTGTAAGACATGTCTGGGACATGCTTCAGCCTCGAGACGTGCC
Found at i:1471773 original size:15 final size:16
Alignment explanation
Indices: 1471764--1471801 Score: 51
Period size: 18 Copynumber: 2.3 Consensus size: 16
1471754 TAAAGTAAAT
1471764 GAAAT-AAAAGAAAAA
1 GAAATGAAAAGAAAAA
1471779 GAAATGAAAAGAAGGAAA
1 GAAATGAAAAGAA--AAA
1471797 GAAAT
1 GAAAT
1471802 ATAATAGCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 5 0.25
16 7 0.35
18 8 0.40
ACGTcount: A:0.71, C:0.00, G:0.21, T:0.08
Consensus pattern (16 bp):
GAAATGAAAAGAAAAA
Found at i:1473068 original size:44 final size:44
Alignment explanation
Indices: 1472988--1473079 Score: 114
Period size: 44 Copynumber: 2.1 Consensus size: 44
1472978 TGTTTAGGGA
* * *
1472988 TACTTCGACCTTGAGTTGATGAGGCACTATAAGTGTCGTACTAT
1 TACTTCGACCTTAAGTCGATGAGGCACTATAAGTGTCATACTAT
* * *
1473032 TACTTCGACTTTAAGTCGATGAGGCACCT-TATGTGTCATACTGT
1 TACTTCGACCTTAAGTCGATGAGGCA-CTATAAGTGTCATACTAT
1473076 TACT
1 TACT
1473080 ATTACTTCAG
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
44 39 0.95
45 2 0.05
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.36
Consensus pattern (44 bp):
TACTTCGACCTTAAGTCGATGAGGCACTATAAGTGTCATACTAT
Found at i:1473276 original size:18 final size:18
Alignment explanation
Indices: 1473244--1473355 Score: 98
Period size: 18 Copynumber: 6.2 Consensus size: 18
1473234 TAAATAAAAG
* *
1473244 TACTGAATGACTGATTGT
1 TACTGAATAATTGATTGT
* *
1473262 TACTAAATAATTGATCGT
1 TACTGAATAATTGATTGT
* * *
1473280 TACTGAATAACTAATTGC
1 TACTGAATAATTGATTGT
** *
1473298 TACTGAGCAAATGATTGT
1 TACTGAATAATTGATTGT
* * *
1473316 TATTGAATAATTAATTGC
1 TACTGAATAATTGATTGT
*
1473334 TACTGAATAATTGAATGT
1 TACTGAATAATTGATTGT
1473352 TACT
1 TACT
1473356 AAATGAAATT
Statistics
Matches: 70, Mismatches: 24, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
18 70 1.00
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (18 bp):
TACTGAATAATTGATTGT
Done.