Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold353
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: 851076
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.32
Warning! 45297 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:421526 original size:14 final size:15
Alignment explanation
Indices: 421509--421537 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
421499 ACATAATATT
421509 TTAAATATAA-ATGA
1 TTAAATATAATATGA
421523 TTAAATATAATATGA
1 TTAAATATAATATGA
421538 GACAAGTGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (15 bp):
TTAAATATAATATGA
Found at i:426409 original size:16 final size:16
Alignment explanation
Indices: 426360--426412 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 16
426350 GAAAAATTAT
426360 ATTTTTCAT-TTATCTA
1 ATTTTTCATCTT-TCTA
* *
426376 TTTTTTCATCCCTT-TA
1 ATTTTTCAT-CTTTCTA
426392 ATTTTTCATCTTTCTA
1 ATTTTTCATCTTTCTA
426408 ATTTT
1 ATTTT
426413 CTTTTCACTT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
15 3 0.10
16 25 0.83
17 1 0.03
18 1 0.03
ACGTcount: A:0.19, C:0.17, G:0.00, T:0.64
Consensus pattern (16 bp):
ATTTTTCATCTTTCTA
Found at i:429434 original size:24 final size:24
Alignment explanation
Indices: 429402--429453 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 24
429392 TAATTTATAT
*
429402 TTTATATATCATTGT-ATTAAATTA
1 TTTAAATATCATT-TAATTAAATTA
429426 TTTAAATATCATTTAAATTAAATTA
1 TTTAAATATCATTT-AATTAAATTA
429451 TTT
1 TTT
429454 TTATTTTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 1 0.04
24 12 0.48
25 12 0.48
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (24 bp):
TTTAAATATCATTTAATTAAATTA
Found at i:431320 original size:19 final size:19
Alignment explanation
Indices: 431253--431319 Score: 64
Period size: 18 Copynumber: 3.3 Consensus size: 19
431243 TTTCCCCCTA
431253 TTTATTCCCCCCCTAAA-T
1 TTTATTCCCCCCCTAAATT
*
431271 TTTACTCCCCATCCCTCCAAACTT
1 TTTATTCCCC--CCCT--AAA-TT
*
431295 TTTATTTCCCCCCTAAATT
1 TTTATTCCCCCCCTAAATT
431314 TTTATT
1 TTTATT
431320 TTTCATCCTT
Statistics
Matches: 40, Mismatches: 3, Indels: 11
0.74 0.06 0.20
Matches are distributed among these distances:
18 9 0.22
19 8 0.20
20 7 0.17
22 7 0.17
24 9 0.22
ACGTcount: A:0.21, C:0.36, G:0.00, T:0.43
Consensus pattern (19 bp):
TTTATTCCCCCCCTAAATT
Found at i:438023 original size:22 final size:22
Alignment explanation
Indices: 437995--438037 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
437985 ATATAAAAAT
437995 AAAAATACCTTCAAAATAATAG
1 AAAAATACCTTCAAAATAATAG
** *
438017 AAAAATATTTTTAAAATAATA
1 AAAAATACCTTCAAAATAATA
438038 TTTGTTACAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.60, C:0.07, G:0.02, T:0.30
Consensus pattern (22 bp):
AAAAATACCTTCAAAATAATAG
Found at i:447786 original size:26 final size:26
Alignment explanation
Indices: 447750--447802 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
447740 CCCATAGACA
447750 ACACCTATTATTATAACAATTAAGTT
1 ACACCTATTATTATAACAATTAAGTT
447776 ACACCTATTATTATAACAATTAAGTT
1 ACACCTATTATTATAACAATTAAGTT
447802 A
1 A
447803 TACAAAGTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.43, C:0.15, G:0.04, T:0.38
Consensus pattern (26 bp):
ACACCTATTATTATAACAATTAAGTT
Found at i:452529 original size:20 final size:20
Alignment explanation
Indices: 452500--452558 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
452490 ATTTTATCTT
*
452500 GAACCCTGAACCTTAAACTC
1 GAACACTGAACCTTAAACTC
* * *
452520 GAACATTGAATCTTGAACTC
1 GAACACTGAACCTTAAACTC
* *
452540 GAACCCTAAACCTTAAACT
1 GAACACTGAACCTTAAACT
452559 TTAAACTTTA
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.37, C:0.29, G:0.10, T:0.24
Consensus pattern (20 bp):
GAACACTGAACCTTAAACTC
Found at i:452570 original size:21 final size:21
Alignment explanation
Indices: 452546--452585 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
452536 ACTCGAACCC
*
452546 TAAACCTTAAA-CTTTAAACTT
1 TAAACCCTAAATC-TTAAACTT
452567 TAAACCCTAAATCTTAAAC
1 TAAACCCTAAATCTTAAAC
452586 ACCAAACCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.45, C:0.23, G:0.00, T:0.33
Consensus pattern (21 bp):
TAAACCCTAAATCTTAAACTT
Found at i:452577 original size:14 final size:14
Alignment explanation
Indices: 452541--452594 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
452531 CTTGAACTCG
452541 AACCCTAAACCTTA
1 AACCCTAAACCTTA
** *
452555 AACTTTAAACTTTA
1 AACCCTAAACCTTA
*
452569 AACCCTAAATCTTA
1 AACCCTAAACCTTA
452583 AACACC-AAACCT
1 AAC-CCTAAACCT
452595 CGAGCTCGAA
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
14 29 0.94
15 2 0.06
ACGTcount: A:0.44, C:0.30, G:0.00, T:0.26
Consensus pattern (14 bp):
AACCCTAAACCTTA
Found at i:454911 original size:12 final size:12
Alignment explanation
Indices: 454894--454924 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
454884 ATTTAGCCTT
454894 AAGTGAATATTG
1 AAGTGAATATTG
454906 AAGTGAATATTG
1 AAGTGAATATTG
454918 AAGTGAA
1 AAGTGAA
454925 ATAAATTGGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.00, G:0.26, T:0.29
Consensus pattern (12 bp):
AAGTGAATATTG
Found at i:467430 original size:30 final size:29
Alignment explanation
Indices: 467396--467555 Score: 230
Period size: 30 Copynumber: 5.3 Consensus size: 29
467386 TATATTTCCA
*
467396 AATTGATTTGTATATAGATATACATTGTCG
1 AATTGATTTGTATAT-GATATACATTGCCG
467426 AATTGATTTGTATATGGATATACATTGCCG
1 AATTGATTTGTATAT-GATATACATTGCCG
*
467456 AATTGATTTGTATATAGATACACATTGCCG
1 AATTGATTTGTATAT-GATATACATTGCCG
* *
467486 AATTGATTTGTATATGTATATATATTGCTG
1 AATTGATTTGTATATG-ATATACATTGCCG
*
467516 AATTGATTTGTATATGTATATATATTGCCG
1 AATTGATTTGTATATG-ATATACATTGCCG
467546 AATTGATTTG
1 AATTGATTTG
467556 AGCATTGGAT
Statistics
Matches: 121, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
29 1 0.01
30 120 0.99
ACGTcount: A:0.31, C:0.07, G:0.17, T:0.44
Consensus pattern (29 bp):
AATTGATTTGTATATGATATACATTGCCG
Found at i:479180 original size:26 final size:25
Alignment explanation
Indices: 479151--479208 Score: 89
Period size: 25 Copynumber: 2.3 Consensus size: 25
479141 TAAGCTTTTC
479151 CGAGCTAAATAACTGGGAAGCTCATG
1 CGAGCTAAATAAC-GGGAAGCTCATG
**
479177 CGAGCTGTATAACGGGAAGCTCATG
1 CGAGCTAAATAACGGGAAGCTCATG
479202 CGAGCTA
1 CGAGCTA
479209 TGGTGTGTCT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 18 0.62
26 11 0.38
ACGTcount: A:0.31, C:0.21, G:0.29, T:0.19
Consensus pattern (25 bp):
CGAGCTAAATAACGGGAAGCTCATG
Found at i:479199 original size:25 final size:26
Alignment explanation
Indices: 479159--479207 Score: 91
Period size: 25 Copynumber: 1.9 Consensus size: 26
479149 TCCGAGCTAA
479159 ATAACTGGGAAGCTCATGCGAGCTGT
1 ATAACTGGGAAGCTCATGCGAGCTGT
479185 ATAAC-GGGAAGCTCATGCGAGCT
1 ATAACTGGGAAGCTCATGCGAGCT
479208 ATGGTGTGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 18 0.78
26 5 0.22
ACGTcount: A:0.29, C:0.20, G:0.31, T:0.20
Consensus pattern (26 bp):
ATAACTGGGAAGCTCATGCGAGCTGT
Found at i:494197 original size:39 final size:39
Alignment explanation
Indices: 494143--494221 Score: 131
Period size: 39 Copynumber: 2.0 Consensus size: 39
494133 AAGTAGATTC
* *
494143 CATAACTATGCACCTATTACTCTACCATGTTCTGAAACA
1 CATAACTATCCACCTATTACTCTACCATGTTCAGAAACA
*
494182 CATAACTATCCACCTATTACTCTTCCATGTTCAGAAACA
1 CATAACTATCCACCTATTACTCTACCATGTTCAGAAACA
494221 C
1 C
494222 TTAGCACTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.33, C:0.30, G:0.06, T:0.30
Consensus pattern (39 bp):
CATAACTATCCACCTATTACTCTACCATGTTCAGAAACA
Found at i:495008 original size:21 final size:21
Alignment explanation
Indices: 494984--495029 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
494974 GCGTCGGGGG
* *
494984 TTTGGGTA-GAAGGAGTGTCGT
1 TTTGGGGAGGAAGG-GTATCGT
495005 TTTGGGGAGGAAGGGTATCGT
1 TTTGGGGAGGAAGGGTATCGT
495026 TTTG
1 TTTG
495030 AGGTGGGTCG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.17, C:0.04, G:0.43, T:0.35
Consensus pattern (21 bp):
TTTGGGGAGGAAGGGTATCGT
Found at i:495588 original size:3 final size:3
Alignment explanation
Indices: 495580--495604 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
495570 TTTAATTTAA
495580 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
495605 ATTCCAACAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:495824 original size:13 final size:11
Alignment explanation
Indices: 495797--495831 Score: 52
Period size: 11 Copynumber: 3.0 Consensus size: 11
495787 CATTTTCCTT
495797 ATTTTAAAAAA
1 ATTTTAAAAAA
495808 ATTTTAAAACCAA
1 ATTTTAAAA--AA
495821 ATTTTAAAAAA
1 ATTTTAAAAAA
495832 TCAAGCCTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 11 0.50
13 11 0.50
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (11 bp):
ATTTTAAAAAA
Found at i:496239 original size:19 final size:18
Alignment explanation
Indices: 496217--496256 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
496207 ACTCAAATTC
496217 AAATTAAAATTCAAGTTTG
1 AAATTAAAATTCAAG-TTG
* *
496236 AAATTAAATTTGAAGTTG
1 AAATTAAAATTCAAGTTG
496254 AAA
1 AAA
496257 CTCAATTCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.50, C:0.03, G:0.12, T:0.35
Consensus pattern (18 bp):
AAATTAAAATTCAAGTTG
Found at i:503714 original size:24 final size:24
Alignment explanation
Indices: 503678--503788 Score: 102
Period size: 24 Copynumber: 4.5 Consensus size: 24
503668 AACACACCAC
503678 AGCTCGTATGAGCTTACCGATTTT
1 AGCTCGTATGAGCTTACCGATTTT
*
503702 AGCTCGTGA-GAGCTTACCGATTTAC
1 AGCTCGT-ATGAGCTTACCGATTT-T
* *
503727 AACTCGTATGAGCTTACTG-TTATT
1 AGCTCGTATGAGCTTACCGATT-TT
* *
503751 CAGCTCGGAGGAGCTTACCG-TTTAT
1 -AGCTCGTATGAGCTTACCGATTT-T
*
503776 CGCTCGTATGAGC
1 AGCTCGTATGAGC
503789 ATACATGTAC
Statistics
Matches: 70, Mismatches: 11, Indels: 12
0.75 0.12 0.13
Matches are distributed among these distances:
24 35 0.50
25 35 0.50
ACGTcount: A:0.22, C:0.23, G:0.23, T:0.32
Consensus pattern (24 bp):
AGCTCGTATGAGCTTACCGATTTT
Found at i:503739 original size:25 final size:24
Alignment explanation
Indices: 503680--503788 Score: 87
Period size: 25 Copynumber: 4.5 Consensus size: 24
503670 CACACCACAG
* *
503680 CTCGTATGAGCTTACCGATTTTAG
1 CTCGTATGAGCTTACCGATTTCAA
503704 CTCGTGA-GAGCTTACCGATTTACAA
1 CTCGT-ATGAGCTTACCGATTT-CAA
* * *
503729 CTCGTATGAGCTTACTGTTATTCAG
1 CTCGTATGAGCTTACCGAT-TTCAA
* * * *
503754 CTCGGAGGAGCTTACCGTTTATC-G
1 CTCGTATGAGCTTACCGATT-TCAA
503778 CTCGTATGAGC
1 CTCGTATGAGC
503789 ATACATGTAC
Statistics
Matches: 70, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
24 31 0.44
25 37 0.53
26 2 0.03
ACGTcount: A:0.21, C:0.23, G:0.23, T:0.33
Consensus pattern (24 bp):
CTCGTATGAGCTTACCGATTTCAA
Found at i:503782 original size:49 final size:49
Alignment explanation
Indices: 503676--503788 Score: 144
Period size: 49 Copynumber: 2.3 Consensus size: 49
503666 CGAACACACC
503676 ACAGCTCGTATGAGCTTACCGATTTTAGCTCGTGAGAGCTTACCGATTT
1 ACAGCTCGTATGAGCTTACCGATTTTAGCTCGTGAGAGCTTACCGATTT
* *
503725 ACAACTCGTATGAGCTTACTG-TTATTCAGCTCG-GAGGAGCTTACCG-TTT
1 ACAGCTCGTATGAGCTTACCGATT-TT-AGCTCGTGA-GAGCTTACCGATTT
503774 ATC-GCTCGTATGAGC
1 A-CAGCTCGTATGAGC
503789 ATACATGTAC
Statistics
Matches: 57, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
48 2 0.04
49 38 0.67
50 17 0.30
ACGTcount: A:0.22, C:0.23, G:0.23, T:0.32
Consensus pattern (49 bp):
ACAGCTCGTATGAGCTTACCGATTTTAGCTCGTGAGAGCTTACCGATTT
Found at i:509576 original size:39 final size:39
Alignment explanation
Indices: 509532--509686 Score: 188
Period size: 39 Copynumber: 4.0 Consensus size: 39
509522 AGTGCTAATA
*
509532 ATTATTCGGGCTATGTGCCTAGCAGGCTGTGTGCCGGTG
1 ATTATTCAGGCTATGTGCCTAGCAGGCTGTGTGCCGGTG
* * * * *
509571 ATTATTCAGGCTATGTGCCTAGTAGGATGTGTACCGATA
1 ATTATTCAGGCTATGTGCCTAGCAGGCTGTGTGCCGGTG
* *
509610 ATTATTC-GAGCTATGTGCCTAGTAGGCTTTGTGCCGGT-
1 ATTATTCAG-GCTATGTGCCTAGCAGGCTGTGTGCCGGTG
* * *
509648 ATTATTCAGGCCATGTGCCTAGCAGGCTCTGTGTCGGTG
1 ATTATTCAGGCTATGTGCCTAGCAGGCTGTGTGCCGGTG
509687 TATTGAAAAT
Statistics
Matches: 99, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
38 33 0.33
39 66 0.67
ACGTcount: A:0.17, C:0.19, G:0.30, T:0.33
Consensus pattern (39 bp):
ATTATTCAGGCTATGTGCCTAGCAGGCTGTGTGCCGGTG
Found at i:515727 original size:21 final size:23
Alignment explanation
Indices: 515685--515729 Score: 58
Period size: 21 Copynumber: 2.0 Consensus size: 23
515675 ATTTTTTCCA
*
515685 AATATGTGTATTGGACTGAATTG
1 AATATGTGTATTGGACTAAATTG
*
515708 AATATG-G-ATTGTACTAAATTG
1 AATATGTGTATTGGACTAAATTG
515729 A
1 A
515730 GCTAAATTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 13 0.65
22 1 0.05
23 6 0.30
ACGTcount: A:0.36, C:0.04, G:0.22, T:0.38
Consensus pattern (23 bp):
AATATGTGTATTGGACTAAATTG
Found at i:515957 original size:20 final size:20
Alignment explanation
Indices: 515915--515956 Score: 77
Period size: 19 Copynumber: 2.1 Consensus size: 20
515905 TGAAAAATAA
515915 TTTCTGGAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
515935 TTTCTGG-AAATGATTTACT
1 TTTCTGGAAAATGATTTACT
515954 TTT
1 TTT
515957 TTGGTGTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.26, C:0.10, G:0.14, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:520287 original size:25 final size:26
Alignment explanation
Indices: 520271--520361 Score: 77
Period size: 25 Copynumber: 3.7 Consensus size: 26
520261 TTTCTGTTAT
520271 TTGGCTCTCACGAGC-TTCTTGATAA
1 TTGGCTCTCACGAGCTTTCTTGATAA
* *
520296 TTGGCTCTCATGAGC-TTCTCGATTAA
1 TTGGCTCTCACGAGCTTTCTTGA-TAA
*
520322 -TGGCTCTCTA-GAGC-TTCCTGAT-A
1 TTGGCTCTC-ACGAGCTTTCTTGATAA
* *
520345 TTGGCTCGCATGAGCTT
1 TTGGCTCTCACGAGCTT
520362 CCCGTTACAT
Statistics
Matches: 56, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
23 2 0.04
24 12 0.21
25 38 0.68
26 4 0.07
ACGTcount: A:0.18, C:0.24, G:0.22, T:0.36
Consensus pattern (26 bp):
TTGGCTCTCACGAGCTTTCTTGATAA
Found at i:520374 original size:49 final size:50
Alignment explanation
Indices: 520272--520376 Score: 144
Period size: 49 Copynumber: 2.1 Consensus size: 50
520262 TTCTGTTATT
* * *
520272 TGGCTCTCACGAGCTTCTTGATAATTGGCTCTCATGAGCTTCTCGATTAA
1 TGGCTCTCACGAGCTTCCTGATAATTGGCTCGCATGAGCTTCCCGATTAA
520322 TGGCTCTCTA-GAGCTTCCTGAT-ATTGGCTCGCATGAGCTTCCCG-TTACA
1 TGGCTCTC-ACGAGCTTCCTGATAATTGGCTCGCATGAGCTTCCCGATTA-A
520371 TGGCTC
1 TGGCTC
520377 GGAATAGCTT
Statistics
Matches: 50, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
48 3 0.06
49 27 0.54
50 19 0.38
51 1 0.02
ACGTcount: A:0.17, C:0.27, G:0.22, T:0.34
Consensus pattern (50 bp):
TGGCTCTCACGAGCTTCCTGATAATTGGCTCGCATGAGCTTCCCGATTAA
Found at i:520912 original size:2 final size:2
Alignment explanation
Indices: 520905--520933 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
520895 GCCCATTTCG
520905 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
520934 GTAAATCAAT
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:522001 original size:17 final size:17
Alignment explanation
Indices: 521979--522013 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
521969 AGTAAGATTC
*
521979 AGACTGTGACAAGCACA
1 AGACTGTCACAAGCACA
*
521996 AGACTGTCACTAGCACA
1 AGACTGTCACAAGCACA
522013 A
1 A
522014 TGCATATATA
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:0.40, C:0.26, G:0.20, T:0.14
Consensus pattern (17 bp):
AGACTGTCACAAGCACA
Found at i:524731 original size:40 final size:40
Alignment explanation
Indices: 524687--524815 Score: 138
Period size: 40 Copynumber: 3.2 Consensus size: 40
524677 TCCACGTCAG
524687 CGCGCTTTGCTCACGTGGACACAAATTGCGCTTTTCAGGC
1 CGCGCTTTGCTCACGTGGACACAAATTGCGCTTTTCAGGC
* * * * * ***
524727 CGCGCTTTGTTCCCAT-GTCAGCAAATCGCGTCCACGTCA-G-
1 CGCGCTTTGCTCACGTGGACA-CAAATTGCG--CTTTTCAGGC
524767 CGCGCTTTGCTCACGTGGACACAAATTGCGCTTTTCAGGC
1 CGCGCTTTGCTCACGTGGACACAAATTGCGCTTTTCAGGC
524807 CGCGCTTTG
1 CGCGCTTTG
524816 TTCCCATGTC
Statistics
Matches: 67, Mismatches: 16, Indels: 12
0.71 0.17 0.13
Matches are distributed among these distances:
38 4 0.06
39 4 0.06
40 51 0.76
41 4 0.06
42 4 0.06
ACGTcount: A:0.16, C:0.32, G:0.25, T:0.27
Consensus pattern (40 bp):
CGCGCTTTGCTCACGTGGACACAAATTGCGCTTTTCAGGC
Found at i:524832 original size:40 final size:40
Alignment explanation
Indices: 524708--524832 Score: 130
Period size: 40 Copynumber: 3.1 Consensus size: 40
524698 CACGTGGACA
524708 CAAATTGCGCTTTTCAGGCCGCGCTTTGTTCCCATGTCAG
1 CAAATTGCGCTTTTCAGGCCGCGCTTTGTTCCCATGTCAG
* *** * * * *
524748 CAAATCGCGTCCACGTCA-G-CGCGCTTTGCTCACGTGGACA-
1 CAAATTGCG--CTTTTCAGGCCGCGCTTTGTTCCCAT-GTCAG
524788 CAAATTGCGCTTTTCAGGCCGCGCTTTGTTCCCATGTCAG
1 CAAATTGCGCTTTTCAGGCCGCGCTTTGTTCCCATGTCAG
524828 CAAAT
1 CAAAT
524833 CGCGTCCACG
Statistics
Matches: 63, Mismatches: 16, Indels: 12
0.69 0.18 0.13
Matches are distributed among these distances:
38 4 0.06
39 4 0.06
40 47 0.75
41 4 0.06
42 4 0.06
ACGTcount: A:0.18, C:0.31, G:0.22, T:0.28
Consensus pattern (40 bp):
CAAATTGCGCTTTTCAGGCCGCGCTTTGTTCCCATGTCAG
Found at i:524896 original size:80 final size:80
Alignment explanation
Indices: 524661--524857 Score: 376
Period size: 80 Copynumber: 2.5 Consensus size: 80
524651 GTCAGGGGAT
524661 ATGTCAGCAAATCGCGTCCACGTCAGCGCGCTTTGCTCACGTGGACACAAATTGCGCTTTTCAGG
1 ATGTCAGCAAATCGCGTCCACGTCAGCGCGCTTTGCTCACGTGGACACAAATTGCGCTTTTCAGG
524726 CCGCGCTTTGTTCCC
66 CCGCGCTTTGTTCCC
524741 ATGTCAGCAAATCGCGTCCACGTCAGCGCGCTTTGCTCACGTGGACACAAATTGCGCTTTTCAGG
1 ATGTCAGCAAATCGCGTCCACGTCAGCGCGCTTTGCTCACGTGGACACAAATTGCGCTTTTCAGG
524806 CCGCGCTTTGTTCCC
66 CCGCGCTTTGTTCCC
* *
524821 ATGTCAGCAAATCGCGTCCACGGCAGCGCGATTTGCT
1 ATGTCAGCAAATCGCGTCCACGTCAGCGCGCTTTGCT
524858 GACATGGGAA
Statistics
Matches: 115, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
80 115 1.00
ACGTcount: A:0.18, C:0.32, G:0.24, T:0.25
Consensus pattern (80 bp):
ATGTCAGCAAATCGCGTCCACGTCAGCGCGCTTTGCTCACGTGGACACAAATTGCGCTTTTCAGG
CCGCGCTTTGTTCCC
Found at i:525266 original size:125 final size:125
Alignment explanation
Indices: 525040--525459 Score: 583
Period size: 125 Copynumber: 3.4 Consensus size: 125
525030 GGACGTCAAT
* * * * *
525040 AATTTGTGAAATCGCGCCCCCCTGGATGCGCTTTTGCTACAGTTGGTCCTGGAAGAAATAATTTT
1 AATTTGTGAAATCACGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGGAAGAAATAATTTT
*
525105 GAGTTGACATTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTTTATGAGAAG
66 GAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTTTATGAGAAG
* * * *
525165 AATTTGTTAAATCACGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCT-GAAAAAATTATTTC
1 AATTTGTGAAATCACGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGGAAGAAATAATTTT
* * * * * *
525229 GAGTTGACGTTTCTGAGCAAATAGTACAAAAAACGCTTCAAGCAGGCTACTATT-TGAGAAG
66 GAGTTGACGTTTCTGAGCAAATAGTA-TAAAATCGCTTCTACCAGGATGCT-TTATGAGAAG
* * * *
525290 AATTTCTGAAATCACGCCCTCGTGGACGCGCTTTTGCTATAGTTGGTCCTGGAAGAAATAATTTT
1 AATTTGTGAAATCACGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGGAAGAAATAATTTT
525355 GAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTTTATGAGAAG
66 GAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTTTATGAGAAG
* * * * *
525415 AATTTGTGAAATCGCGTCCACATGGACGCGCTTTTACCACAGTAG
1 AATTTGTGAAATCACGCCCACGTGGACGCGCTTTTGCTACAGTAG
525460 CATGTTTGGG
Statistics
Matches: 252, Mismatches: 39, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
124 38 0.15
125 175 0.69
126 39 0.15
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.30
Consensus pattern (125 bp):
AATTTGTGAAATCACGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGGAAGAAATAATTTT
GAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTTTATGAGAAG
Found at i:528617 original size:70 final size:70
Alignment explanation
Indices: 528537--528667 Score: 228
Period size: 70 Copynumber: 1.9 Consensus size: 70
528527 TACTTACATG
* *
528537 TTATTACATCAAATAATATCAAAATAACTCG-AAAAAATTTCTATTTTATTACATCAAATAAACT
1 TTATTACATCAAAAAATATCAAAATAACT-GAAAAAAATTTCTATTTTATTACATAAAATAAACT
528601 TCTATT
65 TCTATT
528607 TTATTACATCAAAAAATATCAAAATAACTGAAAAAAATTTCTATTTTATTACATAAAATAA
1 TTATTACATCAAAAAATATCAAAATAACTGAAAAAAATTTCTATTTTATTACATAAAATAA
528668 TATCAAAATA
Statistics
Matches: 58, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
69 1 0.02
70 57 0.98
ACGTcount: A:0.50, C:0.12, G:0.02, T:0.37
Consensus pattern (70 bp):
TTATTACATCAAAAAATATCAAAATAACTGAAAAAAATTTCTATTTTATTACATAAAATAAACTT
CTATT
Found at i:529119 original size:18 final size:18
Alignment explanation
Indices: 529096--529135 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
529086 GACTCGAAAA
*
529096 AGGATACATATAAGGGTT
1 AGGATACATATAAGGGCT
529114 AGGATACATATAAGGGCT
1 AGGATACATATAAGGGCT
529132 AGGA
1 AGGA
529136 AACGCACCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.40, C:0.07, G:0.30, T:0.23
Consensus pattern (18 bp):
AGGATACATATAAGGGCT
Found at i:531009 original size:51 final size:51
Alignment explanation
Indices: 530938--531035 Score: 135
Period size: 51 Copynumber: 1.9 Consensus size: 51
530928 AATTATTTAA
* *
530938 AAATAGGGATTTAAGCGAAA-TTTAAGAAGAACTTGAGAGCAAATTGAAATT
1 AAATACGGATTTAAGAGAAATTTTAA-AAGAACTTGAGAGCAAATTGAAATT
* * *
530989 AAATACGGATTTGAGAGAAATTTTAAAGGAATTTGAGAGCAAATTGA
1 AAATACGGATTTAAGAGAAATTTTAAAAGAACTTGAGAGCAAATTGA
531036 GAGGAAATTT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
51 36 0.88
52 5 0.12
ACGTcount: A:0.46, C:0.05, G:0.22, T:0.27
Consensus pattern (51 bp):
AAATACGGATTTAAGAGAAATTTTAAAAGAACTTGAGAGCAAATTGAAATT
Found at i:531040 original size:22 final size:23
Alignment explanation
Indices: 530997--531051 Score: 60
Period size: 22 Copynumber: 2.4 Consensus size: 23
530987 TTAAATACGG
*
530997 ATTTGAGAGAAATTTTAAAGG-A
1 ATTTGAGAGAAATTTGAAAGGAA
*
531019 ATTTGAGAGCAAA-TTGAGAGGAA
1 ATTTGAGAG-AAATTTGAAAGGAA
*
531042 ATTTAAGAGA
1 ATTTGAGAGA
531052 GGATTAGTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
22 16 0.57
23 12 0.43
ACGTcount: A:0.45, C:0.02, G:0.25, T:0.27
Consensus pattern (23 bp):
ATTTGAGAGAAATTTGAAAGGAA
Found at i:534556 original size:13 final size:13
Alignment explanation
Indices: 534538--534562 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
534528 AACGAATATC
534538 AAATAAAATAAAT
1 AAATAAAATAAAT
534551 AAATAAAATAAA
1 AAATAAAATAAA
534563 ATTAGTAACC
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):
AAATAAAATAAAT
Found at i:538478 original size:3 final size:3
Alignment explanation
Indices: 538470--538495 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
538460 AATATTTTAA
538470 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
538496 CAAAAAGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:555007 original size:23 final size:23
Alignment explanation
Indices: 554981--555054 Score: 78
Period size: 23 Copynumber: 3.2 Consensus size: 23
554971 ATCTCGAATG
554981 CATACATAAATAATTATCAAACA
1 CATACATAAATAATTATCAAACA
* * * **
555004 CATA-GTATATATATATCTCAAATG
1 CATACATAAATA-AT-TATCAAACA
555028 CATACATAAATAATTATCAAACA
1 CATACATAAATAATTATCAAACA
555051 CATA
1 CATA
555055 GACTCAACAT
Statistics
Matches: 38, Mismatches: 10, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
22 5 0.13
23 16 0.42
24 12 0.32
25 5 0.13
ACGTcount: A:0.51, C:0.16, G:0.03, T:0.30
Consensus pattern (23 bp):
CATACATAAATAATTATCAAACA
Found at i:555015 original size:47 final size:47
Alignment explanation
Indices: 554962--555055 Score: 179
Period size: 47 Copynumber: 2.0 Consensus size: 47
554952 TGAGTACATT
*
554962 TATATATATATCTCGAATGCATACATAAATAATTATCAAACACATAG
1 TATATATATATCTCAAATGCATACATAAATAATTATCAAACACATAG
555009 TATATATATATCTCAAATGCATACATAAATAATTATCAAACACATAG
1 TATATATATATCTCAAATGCATACATAAATAATTATCAAACACATAG
555056 ACTCAACATA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.48, C:0.15, G:0.05, T:0.32
Consensus pattern (47 bp):
TATATATATATCTCAAATGCATACATAAATAATTATCAAACACATAG
Found at i:555416 original size:41 final size:41
Alignment explanation
Indices: 555356--555470 Score: 131
Period size: 41 Copynumber: 2.8 Consensus size: 41
555346 TGATTCGGTA
* * * * * *
555356 CACCGGCCTTTAGCTTGCTAGACCTATAGTCTGAAATGTAT
1 CACCGGCATTAAGCCTGCTAGACGTAAAGTCTGAAATATAT
* * *
555397 CACCGGCATTAAGCCTGCTAGACGTAAAGTCTGTATTATTT
1 CACCGGCATTAAGCCTGCTAGACGTAAAGTCTGAAATATAT
* *
555438 CACCGGTATCAAGCCTGCTAGACGTAAAGTCTG
1 CACCGGCATTAAGCCTGCTAGACGTAAAGTCTG
555471 TATTACATTC
Statistics
Matches: 63, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 63 1.00
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (41 bp):
CACCGGCATTAAGCCTGCTAGACGTAAAGTCTGAAATATAT
Found at i:555471 original size:41 final size:41
Alignment explanation
Indices: 555396--555475 Score: 142
Period size: 41 Copynumber: 2.0 Consensus size: 41
555386 CTGAAATGTA
*
555396 TCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGTATTATT
1 TCACCGGCATCAAGCCTGCTAGACGTAAAGTCTGTATTATT
*
555437 TCACCGGTATCAAGCCTGCTAGACGTAAAGTCTGTATTA
1 TCACCGGCATCAAGCCTGCTAGACGTAAAGTCTGTATTA
555476 CATTCGATCA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.30
Consensus pattern (41 bp):
TCACCGGCATCAAGCCTGCTAGACGTAAAGTCTGTATTATT
Found at i:557629 original size:16 final size:17
Alignment explanation
Indices: 557606--557644 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
557596 TTTTTATAGA
*
557606 ATTTTTTTATA-AATTT
1 ATTTTTTTACATAATTT
557622 ATTTTTTTACATAATTT
1 ATTTTTTTACATAATTT
557639 -TTTTTT
1 ATTTTTT
557645 CACTCAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 16 0.76
17 5 0.24
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.72
Consensus pattern (17 bp):
ATTTTTTTACATAATTT
Found at i:564845 original size:53 final size:51
Alignment explanation
Indices: 564765--564866 Score: 177
Period size: 53 Copynumber: 2.0 Consensus size: 51
564755 AAACTGATGC
*
564765 AATTTATATTATCTTTTTTCATGACAGTCGAAGGGCCCATCACAACCTAACTT
1 AATTTATATTATCTTTTTTCATGACAGT-GAAGAGCCC-TCACAACCTAACTT
564818 AATTTATATTATCTTTTTTCATGACAGTGAAGAGCCCTCACAACCTAAC
1 AATTTATATTATCTTTTTTCATGACAGTGAAGAGCCCTCACAACCTAAC
564867 ATCAATTTGA
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
51 12 0.25
52 8 0.17
53 28 0.58
ACGTcount: A:0.31, C:0.23, G:0.11, T:0.35
Consensus pattern (51 bp):
AATTTATATTATCTTTTTTCATGACAGTGAAGAGCCCTCACAACCTAACTT
Found at i:566698 original size:25 final size:25
Alignment explanation
Indices: 566670--566772 Score: 93
Period size: 25 Copynumber: 4.1 Consensus size: 25
566660 ATGTAAACCA
* *
566670 GAAGCTCTTCCGAGCCATATAACGG
1 GAAGCTCTTACGAGCCATATATCGG
* ** *
566695 GAAGCTCATACGAGCTGTATATTGG
1 GAAGCTCTTACGAGCCATATATCGG
* * *
566720 GAAGCTCTTGCGAGCCAAATATCGA
1 GAAGCTCTTACGAGCCATATATCGG
566745 GAAGCTCATTA-GAGCCA-AGTATCGG
1 GAAGCTC-TTACGAGCCATA-TATCGG
566770 GAA
1 GAA
566773 ACTCAAGAGA
Statistics
Matches: 61, Mismatches: 15, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
24 1 0.02
25 58 0.95
26 2 0.03
ACGTcount: A:0.31, C:0.21, G:0.26, T:0.21
Consensus pattern (25 bp):
GAAGCTCTTACGAGCCATATATCGG
Found at i:566772 original size:50 final size:50
Alignment explanation
Indices: 566670--566772 Score: 111
Period size: 50 Copynumber: 2.1 Consensus size: 50
566660 ATGTAAACCA
* * ** *
566670 GAAGCTCTTCCGAGCCATATAACGGGAAGCTCATACGAGCTGTATATTGG
1 GAAGCTCTTCCGAGCCAAATAACGAGAAGCTCATACGAGCTCAATATCGG
* *
566720 GAAGCTCTTGCGAGCCAAATATCGAGAAGCTCATTA-GAGC-CAAGTATCGG
1 GAAGCTCTTCCGAGCCAAATAACGAGAAGCTCA-TACGAGCTCAA-TATCGG
566770 GAA
1 GAA
566773 ACTCAAGAGA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
49 1 0.02
50 41 0.93
51 2 0.05
ACGTcount: A:0.31, C:0.21, G:0.26, T:0.21
Consensus pattern (50 bp):
GAAGCTCTTCCGAGCCAAATAACGAGAAGCTCATACGAGCTCAATATCGG
Found at i:566783 original size:25 final size:25
Alignment explanation
Indices: 566731--566784 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
566721 AAGCTCTTGC
* **
566731 GAGCCAAATATCGAGAAGCTCATTA
1 GAGCCAAATATCGAGAAACTCAAGA
* *
566756 GAGCCAAGTATCGGGAAACTCAAGA
1 GAGCCAAATATCGAGAAACTCAAGA
566781 GAGC
1 GAGC
566785 TGTGGTGTGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.20, G:0.26, T:0.15
Consensus pattern (25 bp):
GAGCCAAATATCGAGAAACTCAAGA
Found at i:567132 original size:16 final size:15
Alignment explanation
Indices: 567092--567134 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
567082 TATACGAATG
* *
567092 AATTTAACTCAATTT
1 AATTTAATTCAATTC
*
567107 AATATAATTCATATTC
1 AATTTAATTCA-ATTC
567123 AATTTAATTCAA
1 AATTTAATTCAA
567135 CACACATCTT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTTAATTCAATTC
Found at i:571125 original size:2 final size:2
Alignment explanation
Indices: 571118--571145 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
571108 CAAACAAATG
571118 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
571146 TATNNNNNNN
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:571793 original size:2 final size:2
Alignment explanation
Indices: 571786--571817 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
571776 GAAACAAATG
571786 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
571818 ATCCGTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:577707 original size:19 final size:21
Alignment explanation
Indices: 577667--577705 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
577657 AAAATATGAG
*
577667 AAAAGATATTTTAAATTAAAT
1 AAAAGATATTTAAAATTAAAT
577688 AAAA-ATATTTAAAATTAA
1 AAAAGATATTTAAAATTAA
577706 TATTGTTTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (21 bp):
AAAAGATATTTAAAATTAAAT
Found at i:579703 original size:40 final size:40
Alignment explanation
Indices: 579595--579769 Score: 197
Period size: 40 Copynumber: 4.3 Consensus size: 40
579585 ACCTAAGCCC
* * *
579595 AAAGCGCCGCTAATGCTCGGGGATTTTGCGGTATTTTTGAA
1 AAAGCGCCGCTAATGCTCGGGGATTTAGCAGCATTTTTG-A
* * * * * *
579636 AAAGTGCCTCTAATACTTGGGGCTTTAGCAGCGTTTTTGA
1 AAAGCGCCGCTAATGCTCGGGGATTTAGCAGCATTTTTGA
*
579676 AAAGCGCCGCTAATGCTCGGGGATTTAGCGGCATTTTTGA
1 AAAGCGCCGCTAATGCTCGGGGATTTAGCAGCATTTTTGA
* * * * *
579716 ACAGCGCCGCTAATGTTCGGGGCTTTAGCAGCGTTTTTAAA
1 AAAGCGCCGCTAATGCTCGGGGATTTAGCAGCATTTTT-GA
579757 AAAGCGCCGCTAA
1 AAAGCGCCGCTAA
579770 AAACATTTTA
Statistics
Matches: 110, Mismatches: 23, Indels: 2
0.81 0.17 0.01
Matches are distributed among these distances:
40 67 0.61
41 43 0.39
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.29
Consensus pattern (40 bp):
AAAGCGCCGCTAATGCTCGGGGATTTAGCAGCATTTTTGA
Found at i:579760 original size:81 final size:81
Alignment explanation
Indices: 579595--579769 Score: 255
Period size: 81 Copynumber: 2.2 Consensus size: 81
579585 ACCTAAGCCC
* * * *
579595 AAAGCGCCGCTAATGCTCGGGGATTTTGCGGTATTTTTGAAAAAGTGCCTCTAATACTTGGGGCT
1 AAAGCGCCGCTAATGCTCGGGGATTTAGCGGCATTTTTGAAAAAGCGCCGCTAATACTTGGGGCT
*
579660 TTAGCAGCGTTTTTGA
66 TTAGCAGCGTTTTTAA
* *
579676 AAAGCGCCGCTAATGCTCGGGGATTTAGCGGCATTTTTG-AACAGCGCCGCTAAT-GTTCGGGGC
1 AAAGCGCCGCTAATGCTCGGGGATTTAGCGGCATTTTTGAAAAAGCGCCGCTAATACTT-GGGGC
579739 TTTAGCAGCGTTTTTAAA
65 TTTAGCAGCGTTTTT-AA
579757 AAAGCGCCGCTAA
1 AAAGCGCCGCTAA
579770 AAACATTTTA
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
79 2 0.02
80 32 0.38
81 51 0.60
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.29
Consensus pattern (81 bp):
AAAGCGCCGCTAATGCTCGGGGATTTAGCGGCATTTTTGAAAAAGCGCCGCTAATACTTGGGGCT
TTAGCAGCGTTTTTAA
Found at i:580158 original size:14 final size:15
Alignment explanation
Indices: 580129--580162 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
580119 GTTTAAGGAG
580129 TATGGATTTAGAGAT
1 TATGGATTTAGAGAT
*
580144 TATGGA-TTAGGGAT
1 TATGGATTTAGAGAT
580158 TATGG
1 TATGG
580163 TTCAAAGGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.29, C:0.00, G:0.32, T:0.38
Consensus pattern (15 bp):
TATGGATTTAGAGAT
Found at i:580382 original size:7 final size:7
Alignment explanation
Indices: 580370--580418 Score: 53
Period size: 7 Copynumber: 7.0 Consensus size: 7
580360 TATAATTATA
580370 GTTTAAG
1 GTTTAAG
580377 GTTTAAG
1 GTTTAAG
*
580384 GTTTAGG
1 GTTTAAG
* *
580391 GTATATG
1 GTTTAAG
* *
580398 GTGTAGG
1 GTTTAAG
580405 GTTTAAG
1 GTTTAAG
580412 GTTTAAG
1 GTTTAAG
580419 AGTTACTATT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
7 35 1.00
ACGTcount: A:0.24, C:0.00, G:0.35, T:0.41
Consensus pattern (7 bp):
GTTTAAG
Found at i:580679 original size:18 final size:18
Alignment explanation
Indices: 580653--580697 Score: 72
Period size: 18 Copynumber: 2.4 Consensus size: 18
580643 GGATCAAATT
*
580653 ATAACAAATAAAAATGAA
1 ATAAAAAATAAAAATGAA
580671 ATAAAAAATAAAAATGAA
1 ATAAAAAATAAAAATGAA
580689 ATACAAAAA
1 ATA-AAAAA
580698 CTATAAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 20 0.80
19 5 0.20
ACGTcount: A:0.76, C:0.04, G:0.04, T:0.16
Consensus pattern (18 bp):
ATAAAAAATAAAAATGAA
Found at i:587730 original size:15 final size:16
Alignment explanation
Indices: 587710--587743 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
587700 ATATGTGAAG
*
587710 AATATTATTTAAA-AA
1 AATATTATTAAAATAA
587725 AATATTATTAAAATAA
1 AATATTATTAAAATAA
587741 AAT
1 AAT
587744 TGAAATATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AATATTATTAAAATAA
Found at i:588996 original size:107 final size:108
Alignment explanation
Indices: 588879--589097 Score: 424
Period size: 107 Copynumber: 2.0 Consensus size: 108
588869 TAACAAAATC
588879 ATTTAAGCCCAAATTAAATTAAGAAGTTAAGATACCGAATTTGCCAAAGATTAACTTGTTATTTC
1 ATTTAAGCCCAAATTAAATTAAGAAGTTAAGATACCGAATTTGCCAAAGATTAACTTGTTATTTC
588944 ATTAAAAGCTCATTGATTTTTATATAA-TTTTTATAAATATAT
66 ATTAAAAGCTCATTGATTTTTATATAATTTTTTATAAATATAT
588986 ATTTAAGCCCAAATTAAATTAAGAAGTTAAGATACCGAATTTGCCAAAGATTAACTTGTTATTTC
1 ATTTAAGCCCAAATTAAATTAAGAAGTTAAGATACCGAATTTGCCAAAGATTAACTTGTTATTTC
589051 ATTAAAAGCTCATTGATTTTTATATAATTTTTTATAAATATAT
66 ATTAAAAGCTCATTGATTTTTATATAATTTTTTATAAATATAT
589094 -TTTA
1 ATTTA
589098 TTTATTTTTG
Statistics
Matches: 111, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
107 96 0.86
108 15 0.14
ACGTcount: A:0.40, C:0.10, G:0.09, T:0.41
Consensus pattern (108 bp):
ATTTAAGCCCAAATTAAATTAAGAAGTTAAGATACCGAATTTGCCAAAGATTAACTTGTTATTTC
ATTAAAAGCTCATTGATTTTTATATAATTTTTTATAAATATAT
Found at i:606558 original size:51 final size:51
Alignment explanation
Indices: 606494--606632 Score: 158
Period size: 51 Copynumber: 2.7 Consensus size: 51
606484 TGTTCGGTTT
* * * *
606494 ACATACTAGCCTGCACATAGTATTACACATGTGACCATTACCATCC-GATAC
1 ACATAGTAGCCTGCACATAGTACTACACACGTGACCATAACCATCCAG-TAC
* * * *
606545 ACGTAGTAGCCTGCACATAGTACTATACACGTGATCGA-AACTATCCAGTAC
1 ACATAGTAGCCTGCACATAGTACTACACACGTGA-CCATAACCATCCAGTAC
*
606596 GCATAGTAG-CTGCACATAGTACTACACACGTGACCAT
1 ACATAGTAGCCTGCACATAGTACTACACACGTGACCAT
606633 CACTTTCACT
Statistics
Matches: 73, Mismatches: 12, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
49 2 0.03
50 23 0.32
51 45 0.62
52 3 0.04
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.24
Consensus pattern (51 bp):
ACATAGTAGCCTGCACATAGTACTACACACGTGACCATAACCATCCAGTAC
Found at i:608321 original size:2 final size:2
Alignment explanation
Indices: 608281--608312 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
608271 TAAAATTTGG
*
608281 AT AT AT AT TT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
608313 GCGTATATAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:611427 original size:3 final size:3
Alignment explanation
Indices: 611419--611444 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
611409 CTTTTTGTTT
611419 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
611445 GTAAACTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:614719 original size:18 final size:17
Alignment explanation
Indices: 614678--614732 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 17
614668 GACTAAATCA
* *
614678 TTATTAGAAAATAATATC
1 TTATTATAAAATAA-ATT
614696 TTATTATAAAATAAATT
1 TTATTATAAAATAAATT
614713 TTGATTATCAAAATGAAATT
1 TT-ATTAT-AAAAT-AAATT
614733 GTACTATAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
17 4 0.12
18 18 0.56
19 5 0.16
20 5 0.16
ACGTcount: A:0.49, C:0.04, G:0.05, T:0.42
Consensus pattern (17 bp):
TTATTATAAAATAAATT
Found at i:619801 original size:12 final size:11
Alignment explanation
Indices: 619766--619792 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
619756 AACAGAAGGG
619766 GAAAAAGGAAA
1 GAAAAAGGAAA
619777 GAAAAAGGAAA
1 GAAAAAGGAAA
619788 GAAAA
1 GAAAA
619793 GGAGAAAGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (11 bp):
GAAAAAGGAAA
Found at i:620488 original size:24 final size:24
Alignment explanation
Indices: 620461--620507 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
620451 ATTGAAATGG
620461 ATTG-ATTTAGTATGTGA-TGAATTT
1 ATTGAATTTA-TAT-TGATTGAATTT
620485 ATTGAATTTATATTGATTGAATT
1 ATTGAATTTATATTGATTGAATT
620508 GGTATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 3 0.14
24 13 0.62
25 5 0.24
ACGTcount: A:0.32, C:0.00, G:0.17, T:0.51
Consensus pattern (24 bp):
ATTGAATTTATATTGATTGAATTT
Found at i:633575 original size:86 final size:86
Alignment explanation
Indices: 633476--633663 Score: 376
Period size: 86 Copynumber: 2.2 Consensus size: 86
633466 ATTATTTTAG
633476 TAAATATAACATTGATAGAGTTGTGTATTAAGATAGTTTTGGTAGTGTATGTTGATTTTATTTTT
1 TAAATATAACATTGATAGAGTTGTGTATTAAGATAGTTTTGGTAGTGTATGTTGATTTTATTTTT
633541 TAATGATAATTTGTATAGTTT
66 TAATGATAATTTGTATAGTTT
633562 TAAATATAACATTGATAGAGTTGTGTATTAAGATAGTTTTGGTAGTGTATGTTGATTTTATTTTT
1 TAAATATAACATTGATAGAGTTGTGTATTAAGATAGTTTTGGTAGTGTATGTTGATTTTATTTTT
633627 TAATGATAATTTGTATAGTTT
66 TAATGATAATTTGTATAGTTT
633648 TAAATATAACATTGAT
1 TAAATATAACATTGAT
633664 CATTATATTT
Statistics
Matches: 102, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
86 102 1.00
ACGTcount: A:0.32, C:0.02, G:0.18, T:0.49
Consensus pattern (86 bp):
TAAATATAACATTGATAGAGTTGTGTATTAAGATAGTTTTGGTAGTGTATGTTGATTTTATTTTT
TAATGATAATTTGTATAGTTT
Found at i:637023 original size:5 final size:5
Alignment explanation
Indices: 637015--637072 Score: 57
Period size: 5 Copynumber: 12.0 Consensus size: 5
637005 TATTTAATTT
* * * * *
637015 ATATA ATATA ATACA ATATA ATATA TTATA TTATT ATATT ATATA ATA-A
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
637064 A-ATA ATATA
1 ATATA ATATA
637073 TAAAAAACAT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
3 1 0.02
4 4 0.09
5 40 0.89
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (5 bp):
ATATA
Found at i:637733 original size:9 final size:9
Alignment explanation
Indices: 637719--637749 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
637709 TTTGGTTAAA
637719 AATTAACCG
1 AATTAACCG
637728 AATTAACCG
1 AATTAACCG
*
637737 AATTAACCA
1 AATTAACCG
637746 AATT
1 AATT
637750 GAATCACTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.48, C:0.19, G:0.06, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:644114 original size:15 final size:15
Alignment explanation
Indices: 644062--644115 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 15
644052 GAAAATTTAT
644062 GTTTTCCATCCTTCTA
1 GTTTT-CATCCTTCTA
*
644078 GTTTTCTACGCCTTCTA
1 GTTTTC-A-TCCTTCTA
* *
644095 TTTTTCATCCTTCTG
1 GTTTTCATCCTTCTA
644110 GTTTTC
1 GTTTTC
644116 TTTCCACTCT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
15 12 0.39
16 7 0.23
17 12 0.39
ACGTcount: A:0.09, C:0.28, G:0.09, T:0.54
Consensus pattern (15 bp):
GTTTTCATCCTTCTA
Found at i:655074 original size:31 final size:31
Alignment explanation
Indices: 654986--655075 Score: 153
Period size: 31 Copynumber: 2.9 Consensus size: 31
654976 ATTAAGAACA
* *
654986 AAATCTTTTCAAAAGTGCTCAAATAAGGACT
1 AAATCTTTTTAAAAGTGCTCAAATAATGACT
*
655017 AAATTTTTTTAAAAGTGCTCAAATAATGACT
1 AAATCTTTTTAAAAGTGCTCAAATAATGACT
655048 AAATCTTTTTAAAAGTGCTCAAATAATG
1 AAATCTTTTTAAAAGTGCTCAAATAATG
655076 GCTTCTAAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 55 1.00
ACGTcount: A:0.42, C:0.12, G:0.11, T:0.34
Consensus pattern (31 bp):
AAATCTTTTTAAAAGTGCTCAAATAATGACT
Found at i:658470 original size:22 final size:22
Alignment explanation
Indices: 658445--658491 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
658435 TTAAAATAAT
* *
658445 TAATATATAAAATAACTTAAAA
1 TAATATACAAAACAACTTAAAA
* *
658467 TAATATACAAAGCAACTTAACA
1 TAATATACAAAACAACTTAAAA
658489 TAA
1 TAA
658492 ATAATTTACA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.60, C:0.11, G:0.02, T:0.28
Consensus pattern (22 bp):
TAATATACAAAACAACTTAAAA
Found at i:679560 original size:18 final size:17
Alignment explanation
Indices: 679523--679574 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
679513 CTAAATGACG
* *
679523 ACAAATAATCGATAAAT
1 ACAAATAAGCAATAAAT
679540 ACAAATAAGCAATACAAT
1 ACAAATAAGCAATA-AAT
*
679558 ACACATGAGAGCAATAA
1 ACAAAT-A-AGCAATAA
679575 TCTTACATCA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 12 0.41
18 8 0.28
19 2 0.07
20 7 0.24
ACGTcount: A:0.58, C:0.15, G:0.10, T:0.17
Consensus pattern (17 bp):
ACAAATAAGCAATAAAT
Found at i:680124 original size:61 final size:60
Alignment explanation
Indices: 680019--680147 Score: 138
Period size: 61 Copynumber: 2.1 Consensus size: 60
680009 AGTTTTTTAA
*
680019 GGAAATAAATTATATATATATATATATGAAAATAGGTAAAAAAAAGATAT-ATATAATAGCAT
1 GGAAATAAATTATATATATATATATATGAAAAT--GTAAAAAAAAGATATAAAATAATAG-AT
* * * *
680081 -GAAATATATTATATATGTATATATGATTGAAAAT-TACATAAAAATATATAAAATAATAGAT
1 GGAAATAAATTATATATATATATAT-A-TGAAAATGTA-AAAAAAAGATATAAAATAATAGAT
680142 GGAAAT
1 GGAAAT
680148 TAAAACAATA
Statistics
Matches: 57, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
60 2 0.04
61 34 0.60
62 14 0.25
63 7 0.12
ACGTcount: A:0.55, C:0.02, G:0.11, T:0.33
Consensus pattern (60 bp):
GGAAATAAATTATATATATATATATATGAAAATGTAAAAAAAAGATATAAAATAATAGAT
Found at i:682450 original size:46 final size:46
Alignment explanation
Indices: 682383--682643 Score: 411
Period size: 46 Copynumber: 5.7 Consensus size: 46
682373 GTGATCATGA
* *
682383 ACACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGTT
1 ACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCT
** *
682429 ACACTTATCTGATCAAAAGACAAAGTGATAAGTGGTAGCTTTATCT
1 ACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCT
* *
682475 ACACTTATCTGATCCAGTGACAAAGTGATAAGTGATAGCTTTAGCT
1 ACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCT
682521 ACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCT
1 ACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCT
* *
682567 ACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGC-CTCGCT
1 ACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCT
*
682612 ACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 ACACTTATCTGATCAAGTGACAAAGTGATAAGTG
682644 ATCATACGTA
Statistics
Matches: 202, Mismatches: 13, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
43 12 0.06
44 5 0.02
45 18 0.09
46 167 0.83
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (46 bp):
ACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCT
Found at i:690060 original size:27 final size:28
Alignment explanation
Indices: 690006--690078 Score: 69
Period size: 27 Copynumber: 2.7 Consensus size: 28
689996 ATAACTATTA
* * *
690006 AATT-TATATATGAATTTTTATTTAGTG
1 AATTATATATATGAAATTTGAATTAGTG
690033 AATTATATATATGAAATTTGAATT-GTG
1 AATTATATATATGAAATTTGAATTAGTG
* * * *
690060 ATTTACATACATAAAATTT
1 AATTATATATATGAAATTT
690079 TGATTTTAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
27 22 0.58
28 16 0.42
ACGTcount: A:0.40, C:0.03, G:0.10, T:0.48
Consensus pattern (28 bp):
AATTATATATATGAAATTTGAATTAGTG
Found at i:700590 original size:19 final size:20
Alignment explanation
Indices: 700566--700609 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
700556 AATATATTAA
*
700566 TATTAATA-TTAAATTTTTT
1 TATTAATAGCTAAATTTTTT
700585 TATTAA-AGCTAAATTTTTT
1 TATTAATAGCTAAATTTTTT
700604 T-TTAAT
1 TATTAAT
700610 TTTTTCTGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 5 0.23
19 17 0.77
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.59
Consensus pattern (20 bp):
TATTAATAGCTAAATTTTTT
Found at i:705242 original size:20 final size:20
Alignment explanation
Indices: 705226--705264 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
705216 ACCAAAAATT
705226 TATTTTAAAAATTAAAAAAG
1 TATTTTAAAAATTAAAAAAG
*
705246 TATTTTAAAATTTAAAAAA
1 TATTTTAAAAATTAAAAAA
705265 ATTTAAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (20 bp):
TATTTTAAAAATTAAAAAAG
Found at i:708623 original size:36 final size:37
Alignment explanation
Indices: 708578--708653 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 37
708568 TTCCCTTTTC
* * *
708578 TTTTCTAAATTCAAATTAAAAATTTATTAATATC-AT
1 TTTTATAAATTCAAATTAAAAACTTACTAATATCTAT
** *
708614 TTTTATAAATTTTAATTAAAAACTTACTAATTTCTAT
1 TTTTATAAATTCAAATTAAAAACTTACTAATATCTAT
708651 TTT
1 TTT
708654 ATTTCCTTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
36 28 0.85
37 5 0.15
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.51
Consensus pattern (37 bp):
TTTTATAAATTCAAATTAAAAACTTACTAATATCTAT
Found at i:716843 original size:38 final size:38
Alignment explanation
Indices: 716792--716868 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
716782 CTGGAAGTAT
716792 ATTCTTTCAATCTCTAAAGATTCATTATTATTCATTTA
1 ATTCTTTCAATCTCTAAAGATTCATTATTATTCATTTA
716830 ATTCTTTCAATCTCTAAAGATTCATTATTATTCATTTA
1 ATTCTTTCAATCTCTAAAGATTCATTATTATTCATTTA
716868 A
1 A
716869 ACTGACCATC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.32, C:0.16, G:0.03, T:0.49
Consensus pattern (38 bp):
ATTCTTTCAATCTCTAAAGATTCATTATTATTCATTTA
Found at i:726544 original size:16 final size:16
Alignment explanation
Indices: 726523--726562 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
726513 CTCAACACCA
726523 TACCTATCAATATTTC
1 TACCTATCAATATTTC
*
726539 TACCTATCGATATTTC
1 TACCTATCAATATTTC
726555 TACCTATC
1 TACCTATC
726563 CCACACACCC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.28, C:0.28, G:0.03, T:0.42
Consensus pattern (16 bp):
TACCTATCAATATTTC
Found at i:726736 original size:63 final size:63
Alignment explanation
Indices: 726628--726752 Score: 214
Period size: 63 Copynumber: 2.0 Consensus size: 63
726618 TTGAAACCGG
*
726628 ACTACAAGCACCATCGATATTCAATTTAATGAATCCCGAAAGAGGTGGAACCCACATTCGATC
1 ACTACAAGCACCATCGATATTCAATTTAATGAATCCCGAAAGAGGTGAAACCCACATTCGATC
* * *
726691 ACTACAAGTACCATCGATATTCAATTTAATGAATCCGGAAGGAGGTGAAACCCACATTCGAT
1 ACTACAAGCACCATCGATATTCAATTTAATGAATCCCGAAAGAGGTGAAACCCACATTCGAT
726753 TCCCATGGTA
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
63 58 1.00
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.23
Consensus pattern (63 bp):
ACTACAAGCACCATCGATATTCAATTTAATGAATCCCGAAAGAGGTGAAACCCACATTCGATC
Found at i:726951 original size:21 final size:21
Alignment explanation
Indices: 726927--726967 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
726917 GATAATTTTA
*
726927 AATACAATATAATTA-AAAAAC
1 AATACAA-AAAATTATAAAAAC
726948 AATACAAAAAATTATAAAAA
1 AATACAAAAAATTATAAAAA
726968 TATAAATACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.71, C:0.07, G:0.00, T:0.22
Consensus pattern (21 bp):
AATACAAAAAATTATAAAAAC
Found at i:726989 original size:26 final size:24
Alignment explanation
Indices: 726948--726995 Score: 60
Period size: 26 Copynumber: 1.9 Consensus size: 24
726938 ATTAAAAAAC
*
726948 AATACAAAAAATTATAAAAATATA
1 AATACAAAAAAATATAAAAATATA
*
726972 AATACAGAACAAAATATACAAATA
1 AATACA-AA-AAAATATAAAAATA
726996 ATTATATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 6 0.30
25 2 0.10
26 12 0.60
ACGTcount: A:0.69, C:0.08, G:0.02, T:0.21
Consensus pattern (24 bp):
AATACAAAAAAATATAAAAATATA
Found at i:733128 original size:13 final size:13
Alignment explanation
Indices: 733091--733122 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
733081 TCTTTTTACA
733091 TTTTTAT-AATTT
1 TTTTTATAAATTT
733103 TTTTTATAAATTT
1 TTTTTATAAATTT
733116 TTTTTAT
1 TTTTTAT
733123 TTATTTACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (13 bp):
TTTTTATAAATTT
Found at i:734727 original size:21 final size:20
Alignment explanation
Indices: 734701--734738 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
734691 AAATAGAAGT
734701 ATTTCTCTTGTATTTTTTTAG
1 ATTTCTCTT-TATTTTTTTAG
734722 ATTTCTCTTT-TTTTTTT
1 ATTTCTCTTTATTTTTTT
734739 TGCATGCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 7 0.41
20 1 0.06
21 9 0.53
ACGTcount: A:0.11, C:0.11, G:0.05, T:0.74
Consensus pattern (20 bp):
ATTTCTCTTTATTTTTTTAG
Found at i:737468 original size:31 final size:29
Alignment explanation
Indices: 737430--737507 Score: 93
Period size: 29 Copynumber: 2.6 Consensus size: 29
737420 CTAACGGCTC
* *
737430 AGTGACTAAAATGTTACAACGTGATAACATA
1 AGTGACTAAAATGTAAC-ACGTCA-AACATA
* **
737461 AGTGACTAAAACGTAACATTTCAAACATA
1 AGTGACTAAAATGTAACACGTCAAACATA
737490 AGTGACTAAAATGTAACA
1 AGTGACTAAAATGTAACA
737508 TGAGCCAAAC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
29 23 0.56
30 3 0.07
31 15 0.37
ACGTcount: A:0.47, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AGTGACTAAAATGTAACACGTCAAACATA
Found at i:742321 original size:16 final size:17
Alignment explanation
Indices: 742288--742322 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
742278 AACAATTCTA
*
742288 ATAATTTTAAATACAAT
1 ATAATTATAAATACAAT
742305 ATAATTATAAA-ACAAT
1 ATAATTATAAATACAAT
742321 AT
1 AT
742323 GAAAATTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (17 bp):
ATAATTATAAATACAAT
Found at i:745349 original size:13 final size:14
Alignment explanation
Indices: 745321--745352 Score: 50
Period size: 12 Copynumber: 2.4 Consensus size: 14
745311 GTTCATTTAA
745321 TTTTAATATAAATT
1 TTTTAATATAAATT
745335 TTTTAAT-T-AATT
1 TTTTAATATAAATT
745347 TTTTAA
1 TTTTAA
745353 AATTTTTAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 10 0.56
13 1 0.06
14 7 0.39
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TTTTAATATAAATT
Found at i:745567 original size:14 final size:14
Alignment explanation
Indices: 745548--745578 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
745538 TTAAATGATT
745548 TTTAATTAATTAAA
1 TTTAATTAATTAAA
745562 TTTAATTAATTAAA
1 TTTAATTAATTAAA
745576 TTT
1 TTT
745579 TCTAAATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TTTAATTAATTAAA
Found at i:747440 original size:41 final size:40
Alignment explanation
Indices: 747368--747446 Score: 106
Period size: 41 Copynumber: 1.9 Consensus size: 40
747358 AAGTCAACGC
**
747368 TTTTTTTTATTTTATTTTAAAAATATATTATTTTAGTTGT
1 TTTTTTTTATTTTAAATTAAAAATATATTATTTTAGTTGT
*
747408 TTTTTTTTACTTTTTAAATTAAAAA-ATGTTATTTTAGTT
1 TTTTTTTTA--TTTTAAATTAAAAATATATTATTTTAGTT
747447 TAAGAATAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
40 9 0.26
41 13 0.38
42 12 0.35
ACGTcount: A:0.29, C:0.01, G:0.05, T:0.65
Consensus pattern (40 bp):
TTTTTTTTATTTTAAATTAAAAATATATTATTTTAGTTGT
Found at i:749810 original size:32 final size:31
Alignment explanation
Indices: 749771--749863 Score: 159
Period size: 32 Copynumber: 2.9 Consensus size: 31
749761 ATAGATATTG
749771 ATTATGTTTTAAGCTTGTTAGATATTGAATTT
1 ATTATGTTTTAAGCTTGTT-GATATTGAATTT
749803 ATTATGTTTTAAGCTTGTTGAATATTGAATTT
1 ATTATGTTTTAAGCTTGTTG-ATATTGAATTT
749835 ATTATGTTTTAAGCTTGTTGGATATTGAA
1 ATTATGTTTTAAGCTTGTT-GATATTGAA
749864 ATAATTGACA
Statistics
Matches: 59, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
31 1 0.02
32 57 0.97
33 1 0.02
ACGTcount: A:0.28, C:0.03, G:0.17, T:0.52
Consensus pattern (31 bp):
ATTATGTTTTAAGCTTGTTGATATTGAATTT
Found at i:751270 original size:14 final size:14
Alignment explanation
Indices: 751246--751283 Score: 60
Period size: 14 Copynumber: 2.7 Consensus size: 14
751236 CCAGAAAAGT
751246 AAAATATTTTCCA-
1 AAAATATTTTCCAG
751259 AAAATCATTTTCCAG
1 AAAAT-ATTTTCCAG
751274 AAAATATTTT
1 AAAATATTTT
751284 ACTGGAAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 5 0.22
14 13 0.57
15 5 0.22
ACGTcount: A:0.45, C:0.13, G:0.03, T:0.39
Consensus pattern (14 bp):
AAAATATTTTCCAG
Found at i:758449 original size:40 final size:40
Alignment explanation
Indices: 758397--758480 Score: 159
Period size: 40 Copynumber: 2.1 Consensus size: 40
758387 GTCTCAGAGA
758397 ACATGCACAATGTCCTTAGTATCATGACCACATAATGAGC
1 ACATGCACAATGTCCTTAGTATCATGACCACATAATGAGC
*
758437 ACATGCATAATGTCCTTAGTATCATGACCACATAATGAGC
1 ACATGCACAATGTCCTTAGTATCATGACCACATAATGAGC
758477 ACAT
1 ACAT
758481 ATTGTTTTGC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (40 bp):
ACATGCACAATGTCCTTAGTATCATGACCACATAATGAGC
Found at i:763217 original size:14 final size:14
Alignment explanation
Indices: 763198--763228 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
763188 AAGCTTATGG
763198 TTTCTTTTTCTTTT
1 TTTCTTTTTCTTTT
*
763212 TTTCTTTTTGTTTT
1 TTTCTTTTTCTTTT
763226 TTT
1 TTT
763229 ATTGAATTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.00, C:0.10, G:0.03, T:0.87
Consensus pattern (14 bp):
TTTCTTTTTCTTTT
Found at i:763885 original size:25 final size:25
Alignment explanation
Indices: 763857--763906 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
763847 TATGTGAATT
763857 GATGCATTTCCTATAAAAATTATTC
1 GATGCATTTCCTATAAAAATTATTC
763882 GATGCATTTCCTATAAAAATTATTC
1 GATGCATTTCCTATAAAAATTATTC
763907 TCTCTCTCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (25 bp):
GATGCATTTCCTATAAAAATTATTC
Found at i:765944 original size:14 final size:14
Alignment explanation
Indices: 765925--765955 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
765915 TAAATGATTT
765925 TTTAATTAATTAAA
1 TTTAATTAATTAAA
765939 TTTAATTAATTAAA
1 TTTAATTAATTAAA
765953 TTT
1 TTT
765956 TCTAAATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TTTAATTAATTAAA
Found at i:767817 original size:41 final size:40
Alignment explanation
Indices: 767745--767823 Score: 106
Period size: 41 Copynumber: 1.9 Consensus size: 40
767735 AAGTCAACGC
**
767745 TTTTTTTTATTTTATTTTAAAAATATATTATTTTAGTTGT
1 TTTTTTTTATTTTAAATTAAAAATATATTATTTTAGTTGT
*
767785 TTTTTTTTACTTTTTAAATTAAAAA-ATGTTATTTTAGTT
1 TTTTTTTTA--TTTTAAATTAAAAATATATTATTTTAGTT
767824 TAAGAATAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
40 9 0.26
41 13 0.38
42 12 0.35
ACGTcount: A:0.29, C:0.01, G:0.05, T:0.65
Consensus pattern (40 bp):
TTTTTTTTATTTTAAATTAAAAATATATTATTTTAGTTGT
Found at i:769536 original size:3 final size:3
Alignment explanation
Indices: 769528--769552 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
769518 ATTGATTTTC
769528 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
769553 TTGTTTTTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:774554 original size:19 final size:18
Alignment explanation
Indices: 774501--774562 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 18
774491 GCCTGAATTA
774501 TTTATTAAATATATATTT
1 TTTATTAAATATATATTT
* *
774519 TATTTTTAATCAAATATACTTT
1 T-TTATTAA--ATATATA-TTT
*
774541 TTTATTAAATATATATAT
1 TTTATTAAATATATATTT
774559 TTTA
1 TTTA
774563 AACTTTTAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
18 7 0.20
19 12 0.34
21 12 0.34
22 4 0.11
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (18 bp):
TTTATTAAATATATATTT
Found at i:774556 original size:21 final size:20
Alignment explanation
Indices: 774501--774561 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 20
774491 GCCTGAATTA
774501 TTTATTAAATATATAT-TTT
1 TTTATTAAATATATATATTT
*
774520 ATTT-TT-AATCAAATATACTTT
1 -TTTATTAAAT-ATATATA-TTT
774541 TTTATTAAATATATATATTT
1 TTTATTAAATATATATATTT
774561 T
1 T
774562 AAACTTTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
18 3 0.09
19 7 0.21
20 10 0.29
21 11 0.32
22 3 0.09
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTATTAAATATATATATTT
Found at i:776581 original size:21 final size:21
Alignment explanation
Indices: 776555--776605 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
776545 TTTCCCTAAG
* *
776555 ATGTAACTTGGATTGAATTGA
1 ATGTAAATTGGATTAAATTGA
*
776576 ATGTAAATTGTATTAAATTG-
1 ATGTAAATTGGATTAAATTGA
776596 ATGTTAAATT
1 ATG-TAAATT
776606 TACTCGTATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.37, C:0.02, G:0.18, T:0.43
Consensus pattern (21 bp):
ATGTAAATTGGATTAAATTGA
Found at i:777097 original size:24 final size:24
Alignment explanation
Indices: 777060--777119 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
777050 TATATGGCTA
* *
777060 TTCGGTGCTTCCCGTTAAGTGCTC
1 TTCGGAGCTACCCGTTAAGTGCTC
*
777084 TTCGGAGCTACCCGTTAATTGCTC
1 TTCGGAGCTACCCGTTAAGTGCTC
*
777108 TTCGGAGATACC
1 TTCGGAGCTACC
777120 AATTATAGGC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.15, C:0.28, G:0.23, T:0.33
Consensus pattern (24 bp):
TTCGGAGCTACCCGTTAAGTGCTC
Found at i:778419 original size:17 final size:17
Alignment explanation
Indices: 778378--778425 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 17
778368 GAATTTAGAA
*
778378 GAATTTT-TGAATTAGT
1 GAATTTTGTGATTTAGT
* *
778394 GACTTTTGTGATTTATT
1 GAATTTTGTGATTTAGT
778411 GAATTTTGTGATTTA
1 GAATTTTGTGATTTA
778426 AAAAGAATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
16 6 0.22
17 21 0.78
ACGTcount: A:0.25, C:0.02, G:0.19, T:0.54
Consensus pattern (17 bp):
GAATTTTGTGATTTAGT
Found at i:779778 original size:46 final size:46
Alignment explanation
Indices: 779641--779779 Score: 224
Period size: 46 Copynumber: 3.0 Consensus size: 46
779631 TGGCAAAGTG
* * *
779641 TGAAACGTAGGTATCGTATTTCAGTGAAGAAAACCATACTGAGTTG
1 TGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGTTA
*
779687 TGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGTTA
1 TGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGTTA
* *
779733 TGCAAAGTAGGTATGGTATTTCCGTGAAGAAAACCATACTGAGTTA
1 TGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGTTA
779779 T
1 T
779780 AGCAGTGTGA
Statistics
Matches: 86, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 86 1.00
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.29
Consensus pattern (46 bp):
TGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGTTA
Found at i:780423 original size:5 final size:5
Alignment explanation
Indices: 780413--780437 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
780403 ATTTTTTTTA
780413 AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT
780438 TGCAATGGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:787819 original size:24 final size:24
Alignment explanation
Indices: 787786--787846 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
787776 GGTGCTTCCT
787786 GTTAAGTGCTCTTCAGAGCTACCC
1 GTTAAGTGCTCTTCAGAGCTACCC
* * *
787810 GTTAATTGCTCTTCGGAGCTACTC
1 GTTAAGTGCTCTTCAGAGCTACCC
* *
787834 GTTATGGGCTCTT
1 GTTAAGTGCTCTT
787847 TGTGAACTTC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.16, C:0.25, G:0.23, T:0.36
Consensus pattern (24 bp):
GTTAAGTGCTCTTCAGAGCTACCC
Found at i:789014 original size:49 final size:48
Alignment explanation
Indices: 788924--789020 Score: 140
Period size: 49 Copynumber: 2.0 Consensus size: 48
788914 TTTCTTTGCT
* *
788924 TAAAAACGCCTAAGTCAGCCTAACTCACAATGATAACGGATTCAACAG
1 TAAAAACACCTAAGTCAGCCTAACTCACAATGATAAAGGATTCAACAG
* * *
788972 TAAAAACACCTAAGTTAGCTTAATCTCGCAATGATAAAGGATTCAACAG
1 TAAAAACACCTAAGTCAGCCTAA-CTCACAATGATAAAGGATTCAACAG
789021 AATCCCCTCA
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
48 20 0.47
49 23 0.53
ACGTcount: A:0.42, C:0.22, G:0.14, T:0.22
Consensus pattern (48 bp):
TAAAAACACCTAAGTCAGCCTAACTCACAATGATAAAGGATTCAACAG
Found at i:792854 original size:23 final size:24
Alignment explanation
Indices: 792813--792858 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
792803 AAATTGAAAG
*
792813 TTAAATACCAAAATGATAAAAAAA
1 TTAAATACCAAAATAATAAAAAAA
*
792837 TTAAAT-CTAAAATAATAAAAAA
1 TTAAATACCAAAATAATAAAAAA
792859 TAAATATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.67, C:0.07, G:0.02, T:0.24
Consensus pattern (24 bp):
TTAAATACCAAAATAATAAAAAAA
Found at i:793228 original size:32 final size:29
Alignment explanation
Indices: 793192--793259 Score: 57
Period size: 32 Copynumber: 2.2 Consensus size: 29
793182 AATTAGTAAA
* *
793192 GATAAAATTAT-ACTTTAATTCACTTTAAAAAT
1 GATAAAATT-TGA-TTTAATTC-TTTAAAAA-T
793224 GATAAAAATTTGATTTAATTCTTTAAAAAT
1 GATA-AAATTTGATTTAATTCTTTAAAAAT
*
793254 TATAAA
1 GATAAA
793260 GATAGATGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
29 2 0.06
30 4 0.13
31 6 0.19
32 13 0.42
33 6 0.19
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.41
Consensus pattern (29 bp):
GATAAAATTTGATTTAATTCTTTAAAAAT
Found at i:805015 original size:2 final size:2
Alignment explanation
Indices: 805008--805032 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
804998 AAAACAAACA
805008 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
805033 AAACTTAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:813521 original size:13 final size:13
Alignment explanation
Indices: 813503--813581 Score: 68
Period size: 13 Copynumber: 5.6 Consensus size: 13
813493 AAGTAATCGT
813503 AAATGGGAATGGG
1 AAATGGGAATGGG
*
813516 AAATGGGAATGAG
1 AAATGGGAATGGG
*
813529 AAATGGGAGGAGGGG
1 AAATGGGA--ATGGG
* *
813544 AATCGATGGAAGAGGGG
1 AA---ATGGGA-ATGGG
813561 AAATGGGAATGGG
1 AAATGGGAATGGG
813574 AAATGGGA
1 AAATGGGA
813582 GGAGGGCACG
Statistics
Matches: 55, Mismatches: 6, Indels: 10
0.77 0.08 0.14
Matches are distributed among these distances:
13 32 0.58
14 5 0.09
15 5 0.09
17 8 0.15
18 5 0.09
ACGTcount: A:0.39, C:0.01, G:0.47, T:0.13
Consensus pattern (13 bp):
AAATGGGAATGGG
Found at i:813613 original size:43 final size:43
Alignment explanation
Indices: 813513--813648 Score: 218
Period size: 43 Copynumber: 3.1 Consensus size: 43
813503 AAATGGGAAT
* * *
813513 GGGAAATGGGAATGAGAAATGGGAGGAGGGGAATCGATGGAAGAG
1 GGGAAATGGGAATGGGAAATGGGAGGA-GGGCA-CGGTGGAAGAG
*
813558 GGGAAATGGGAATGGGAAATGGGAGGAGGGCACGGTCGAAGAG
1 GGGAAATGGGAATGGGAAATGGGAGGAGGGCACGGTGGAAGAG
813601 GGGAAATGGGAATGGGAAATGGGAGGAGGGCACGGTGGAAGAG
1 GGGAAATGGGAATGGGAAATGGGAGGAGGGCACGGTGGAAGAG
813644 GGGAA
1 GGGAA
813649 TCGATGGAAA
Statistics
Matches: 86, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
43 56 0.65
44 4 0.05
45 26 0.30
ACGTcount: A:0.35, C:0.04, G:0.51, T:0.10
Consensus pattern (43 bp):
GGGAAATGGGAATGGGAAATGGGAGGAGGGCACGGTGGAAGAG
Found at i:813729 original size:30 final size:30
Alignment explanation
Indices: 813694--813807 Score: 203
Period size: 30 Copynumber: 3.8 Consensus size: 30
813684 CATTGTATTT
813694 GTGTATTTTAAAAATAAAAAAATATATGTA
1 GTGTATTTTAAAAATAAAAAAATATATGTA
* *
813724 ATGTATTTTAAAAATAAAGAAATATATGTA
1 GTGTATTTTAAAAATAAAAAAATATATGTA
813754 GTGTATTTTAAAAATAAAAAAA-ATATGTA
1 GTGTATTTTAAAAATAAAAAAATATATGTA
813783 GTGTATTTTAAAAATAAAAAAATAT
1 GTGTATTTTAAAAATAAAAAAATAT
813808 TTATCATTGT
Statistics
Matches: 79, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
29 29 0.37
30 50 0.63
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.36
Consensus pattern (30 bp):
GTGTATTTTAAAAATAAAAAAATATATGTA
Found at i:813792 original size:59 final size:60
Alignment explanation
Indices: 813694--813807 Score: 203
Period size: 59 Copynumber: 1.9 Consensus size: 60
813684 CATTGTATTT
*
813694 GTGTATTTTAAAAATAAAAAAATATATGTAATGTATTTTAAAAATAAAGAAATATATGTA
1 GTGTATTTTAAAAATAAAAAAATATATGTAATGTATTTTAAAAATAAAAAAATATATGTA
*
813754 GTGTATTTTAAAAATAAAAAAA-ATATGTAGTGTATTTTAAAAATAAAAAAATAT
1 GTGTATTTTAAAAATAAAAAAATATATGTAATGTATTTTAAAAATAAAAAAATAT
813808 TTATCATTGT
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
59 30 0.58
60 22 0.42
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.36
Consensus pattern (60 bp):
GTGTATTTTAAAAATAAAAAAATATATGTAATGTATTTTAAAAATAAAAAAATATATGTA
Found at i:813826 original size:59 final size:60
Alignment explanation
Indices: 813694--813826 Score: 162
Period size: 59 Copynumber: 2.2 Consensus size: 60
813684 CATTGTATTT
* * * *
813694 GTGTATTTTAAAAATAAAAAAATATATGTAATGTATTTTAAAAATAAAGAAATATATGTA
1 GTGTATATAAAAAATAAAAAAATATATGTAATGTATTTTAAAAATAAAAAAATATATATA
* * * *
813754 GTGTATTTTAAAAATAAAAAAA-ATATGTAGTGTATTTTAAAAATAAAAAAATATTTATCA
1 GTGTATATAAAAAATAAAAAAATATATGTAATGTATTTTAAAAATAAAAAAATATATAT-A
*
813814 TTGT-TATAAAAAA
1 GTGTATATAAAAAA
813827 ATATTTAATT
Statistics
Matches: 65, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
59 39 0.60
60 26 0.40
ACGTcount: A:0.53, C:0.01, G:0.09, T:0.37
Consensus pattern (60 bp):
GTGTATATAAAAAATAAAAAAATATATGTAATGTATTTTAAAAATAAAAAAATATATATA
Found at i:813845 original size:24 final size:23
Alignment explanation
Indices: 813796--813850 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
813786 TATTTTAAAA
***
813796 ATAAAAAAATATTTATCATTGTT
1 ATAAAAAAATATTTATCATAACT
*
813819 ATAAAAAAATATTTAATTATAACT
1 ATAAAAAAATATTT-ATCATAACT
813843 ATAAAAAA
1 ATAAAAAA
813851 GTTAAAAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
23 14 0.52
24 13 0.48
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (23 bp):
ATAAAAAAATATTTATCATAACT
Found at i:814129 original size:21 final size:21
Alignment explanation
Indices: 814103--814155 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
814093 CATTGTTTCT
*
814103 AATCTCACCGCTACAGTACCC
1 AATCTCACCGCTACAGTAACC
* *
814124 AATCTCACTGCTACAGTAACT
1 AATCTCACCGCTACAGTAACC
814145 AATCTCACCGC
1 AATCTCACCGC
814156 CACCGCTGTT
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:0.30, C:0.38, G:0.09, T:0.23
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:814480 original size:37 final size:39
Alignment explanation
Indices: 814416--814496 Score: 112
Period size: 37 Copynumber: 2.1 Consensus size: 39
814406 TTGCAGAAAG
814416 AAAACTAAACTAGAGAAGAAGGAACTAAAACCAGAATACA
1 AAAACTAAACTA-AGAAGAAGGAACTAAAACCAGAATACA
* * *
814456 AAAACTAAACT-A-AAGAATGAACTAAAATCAGAATGCA
1 AAAACTAAACTAAGAAGAAGGAACTAAAACCAGAATACA
814493 AAAA
1 AAAA
814497 GTAGTCTGCT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
37 26 0.68
38 1 0.03
40 11 0.29
ACGTcount: A:0.62, C:0.14, G:0.12, T:0.12
Consensus pattern (39 bp):
AAAACTAAACTAAGAAGAAGGAACTAAAACCAGAATACA
Found at i:817051 original size:11 final size:11
Alignment explanation
Indices: 817035--817061 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
817025 TAGGCAACTT
817035 TTTTTTTGCGG
1 TTTTTTTGCGG
817046 TTTTTTTGCGG
1 TTTTTTTGCGG
817057 TTTTT
1 TTTTT
817062 GCTTCTTCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.00, C:0.07, G:0.22, T:0.70
Consensus pattern (11 bp):
TTTTTTTGCGG
Found at i:817105 original size:19 final size:19
Alignment explanation
Indices: 817048--817105 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 19
817038 TTTTGCGGTT
*
817048 TTTTTGCGGTTTTTGCTTCTTC
1 TTTTTGCTGTTTTT--TT-TTC
*
817070 TTTTTTCT-TTTTCTTTTTC
1 TTTTTGCTGTTTT-TTTTTC
817089 TTTTTGCTGTTTTTTTT
1 TTTTTGCTGTTTTTTTT
817106 AAAGAACAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
19 14 0.45
20 6 0.19
21 4 0.13
22 7 0.23
ACGTcount: A:0.00, C:0.14, G:0.10, T:0.76
Consensus pattern (19 bp):
TTTTTGCTGTTTTTTTTTC
Found at i:817702 original size:31 final size:32
Alignment explanation
Indices: 817643--817707 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
817633 GGCAAATTAC
817643 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
817675 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
817706 AA
1 AA
817708 ATTATCTAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.39
32 20 0.61
ACGTcount: A:0.48, C:0.12, G:0.09, T:0.31
Consensus pattern (32 bp):
AAGAGTAATTGAATCCTAATAAAAACTCTTTA
Done.