Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D01
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: 64473564
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1880000 characters in sequence are not A, C, G, or T
File 2 of 213
Found at i:407590 original size:1 final size:1
Alignment explanation
Indices: 407552--407582 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
407542 TTAACATTTG
407552 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
407583 AAATTTTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:413623 original size:27 final size:29
Alignment explanation
Indices: 413592--413646 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
413582 AGAACACATT
413592 AAGAAA-GATAGAAAT-ATGAGAATAAGA
1 AAGAAAGGATAGAAATGATGAGAATAAGA
*
413619 AAGAAAGTGATAGAAATGGTGAGAATAA
1 AAGAAAG-GATAGAAATGATGAGAATAA
413647 TGGCTCTTGC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 6 0.25
29 9 0.38
30 9 0.38
ACGTcount: A:0.58, C:0.00, G:0.25, T:0.16
Consensus pattern (29 bp):
AAGAAAGGATAGAAATGATGAGAATAAGA
Found at i:414532 original size:2 final size:2
Alignment explanation
Indices: 414525--414567 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
414515 CTGATCAGGT
414525 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
414567 T
1 T
414568 TTATATATAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:417605 original size:30 final size:29
Alignment explanation
Indices: 417569--417633 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 29
417559 AAATTTTTTG
* *
417569 AAAATTGGATCAAATCAAAATTTCATATAT
1 AAAATTGCATAAAATCAAAATTT-ATATAT
* *
417599 AAAATTGCATAAAATCAAAGTTTATGTAT
1 AAAATTGCATAAAATCAAAATTTATATAT
417628 AAAATT
1 AAAATT
417634 ACACATCGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 11 0.35
30 20 0.65
ACGTcount: A:0.51, C:0.08, G:0.08, T:0.34
Consensus pattern (29 bp):
AAAATTGCATAAAATCAAAATTTATATAT
Found at i:420467 original size:17 final size:18
Alignment explanation
Indices: 420445--420478 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
420435 TATTTCATAG
*
420445 TAAAAA-TAAAATAATTT
1 TAAAAATTAAAAAAATTT
420462 TAAAAATTAAAAAAATT
1 TAAAAATTAAAAAAATT
420479 AACAGTACAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
TAAAAATTAAAAAAATTT
Found at i:421966 original size:4 final size:4
Alignment explanation
Indices: 421957--422008 Score: 104
Period size: 4 Copynumber: 13.0 Consensus size: 4
421947 TCAAACATCA
421957 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
422005 ACAT
1 ACAT
422009 TTGAATTGAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 48 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:429211 original size:20 final size:20
Alignment explanation
Indices: 429186--429236 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
429176 AATTATAAAC
*
429186 TTTTTTAAACTTTTGTTGAA-
1 TTTTTTAAACTTTTATT-AAT
*
429206 TTTTTTAATATTTTTATTAAT
1 TTTTTTAA-ACTTTTATTAAT
429227 TTTTTTAAAC
1 TTTTTTAAAC
429237 CTTATAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.65
Consensus pattern (20 bp):
TTTTTTAAACTTTTATTAAT
Found at i:432110 original size:24 final size:24
Alignment explanation
Indices: 432081--432132 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
432071 TTATTTTATT
*
432081 TTTATAATTTTA-TATTTTTAATA
1 TTTATAATTATACTATTTTTAATA
*
432104 GTTTATAATTATACTTTTTTTAATA
1 -TTTATAATTATACTATTTTTAATA
432129 TTTA
1 TTTA
432133 GAATAATGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 15 0.60
25 10 0.40
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (24 bp):
TTTATAATTATACTATTTTTAATA
Found at i:434419 original size:22 final size:22
Alignment explanation
Indices: 434391--434433 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
434381 GTAAAAAATA
*
434391 AAAATTGATTTTGCTTTTATTC
1 AAAATTGATTTTGATTTTATTC
* *
434413 AAAATTGTTTTTTATTTTATT
1 AAAATTGATTTTGATTTTATT
434434 AATTTATTTT
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:0.28, C:0.05, G:0.07, T:0.60
Consensus pattern (22 bp):
AAAATTGATTTTGATTTTATTC
Found at i:437421 original size:16 final size:16
Alignment explanation
Indices: 437399--437467 Score: 111
Period size: 16 Copynumber: 4.2 Consensus size: 16
437389 TTTGGTTCGC
437399 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
437415 CGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
437431 TGTATTGGGATTAGAAG
1 TGTATT-GGATTAGAGG
437448 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
437464 TGTA
1 TGTA
437468 ATAGCTAATC
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
16 33 0.69
17 15 0.31
ACGTcount: A:0.26, C:0.01, G:0.36, T:0.36
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:437445 original size:33 final size:32
Alignment explanation
Indices: 437399--437467 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 32
437389 TTTGGTTCGC
*
437399 TGTATTGGATTAGAGGCGTATTGGATTAGAGG
1 TGTATTGGATTAGAAGCGTATTGGATTAGAGG
*
437431 TGTATTGGGATTAGAAGTGTATTGGATTAGAGG
1 TGTATT-GGATTAGAAGCGTATTGGATTAGAGG
437464 TGTA
1 TGTA
437468 ATAGCTAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
32 6 0.18
33 28 0.82
ACGTcount: A:0.26, C:0.01, G:0.36, T:0.36
Consensus pattern (32 bp):
TGTATTGGATTAGAAGCGTATTGGATTAGAGG
Found at i:437532 original size:44 final size:45
Alignment explanation
Indices: 437448--437538 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
437438 GGATTAGAAG
* * *
437448 TGTATTGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
***
437493 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
437537 TG
1 TG
437539 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.27, C:0.07, G:0.29, T:0.37
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
Found at i:437724 original size:18 final size:17
Alignment explanation
Indices: 437703--437737 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
437693 TTATTATTAA
*
437703 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
437721 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
437738 TCTTAATAAT
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:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:437899 original size:120 final size:120
Alignment explanation
Indices: 437686--438428 Score: 1405
Period size: 120 Copynumber: 6.2 Consensus size: 120
437676 ATCATATTTA
437686 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
437751 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
*
437806 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
437871 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
*
437926 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATGAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
437991 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTGAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
*
438046 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
438111 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
*
438166 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATGAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
438231 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
* *
438286 AACATAATTATTATTAAATATATTTTAATTAAACTATAAAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
438351 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
438406 AACATAATTATTATTAAATATAT
1 AACATAATTATTATTAAATATAT
438429 AACTTGAAAA
Statistics
Matches: 608, Mismatches: 15, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
120 608 1.00
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.44
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
Found at i:441496 original size:33 final size:33
Alignment explanation
Indices: 441457--441566 Score: 127
Period size: 33 Copynumber: 3.3 Consensus size: 33
441447 ATTATAAAGC
441457 ATGTATAATTGACCTAAAATTAATTGTTGGTGT
1 ATGTATAATTGACCTAAAATTAATTGTTGGTGT
* *
441490 ATGTATAATTGACCTAAAATTACTTGTTGGTTT
1 ATGTATAATTGACCTAAAATTAATTGTTGGTGT
* * *
441523 AATGT-T-ATTGTCCCTAAAA-AACATTGCTGGTGT
1 -ATGTATAATTG-ACCTAAAATTA-ATTGTTGGTGT
441556 ATGTATAATTG
1 ATGTATAATTG
441567 TTGGTTTAAT
Statistics
Matches: 65, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
32 9 0.14
33 48 0.74
34 8 0.12
ACGTcount: A:0.32, C:0.09, G:0.17, T:0.42
Consensus pattern (33 bp):
ATGTATAATTGACCTAAAATTAATTGTTGGTGT
Found at i:441573 original size:51 final size:51
Alignment explanation
Indices: 441513--441666 Score: 283
Period size: 51 Copynumber: 3.0 Consensus size: 51
441503 CTAAAATTAC
*
441513 TTGTTGGTTTAATGTTATTGT-CCCTAAAAAACATTGCTGGTGTATGTATAA
1 TTGTTGGTTTAATGTTATT-TACCCTAAAAAACATTGTTGGTGTATGTATAA
441564 TTGTTGGTTTAATGTTATTTACCCTAAAAAACATTGTTGGTGTATGTATAA
1 TTGTTGGTTTAATGTTATTTACCCTAAAAAACATTGTTGGTGTATGTATAA
441615 TTGTTGGTTTAATGTTATTTACCCTAAAAAACATTGTTGGTGTATGTATAA
1 TTGTTGGTTTAATGTTATTTACCCTAAAAAACATTGTTGGTGTATGTATAA
441666 T
1 T
441667 CTTTTAATTT
Statistics
Matches: 101, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
50 1 0.01
51 100 0.99
ACGTcount: A:0.29, C:0.08, G:0.18, T:0.45
Consensus pattern (51 bp):
TTGTTGGTTTAATGTTATTTACCCTAAAAAACATTGTTGGTGTATGTATAA
Found at i:441844 original size:86 final size:86
Alignment explanation
Indices: 441741--441921 Score: 355
Period size: 86 Copynumber: 2.1 Consensus size: 86
441731 TTCTCTCCAC
441741 ATAA-AATTATATCAACATTAATACTTAACAAACAGGTTTCATGTTTATTATTAATTTCAAATTA
1 ATAATAATTATATCAACATTAATACTTAACAAACAGGTTTCATGTTTATTATTAATTTCAAATTA
441805 TTAATATTAAAGATAAAAATT
66 TTAATATTAAAGATAAAAATT
441826 ATAATAATTATATCAACATTAATACTTAACAAACAGGTTTCATGTTTATTATTAATTTCAAATTA
1 ATAATAATTATATCAACATTAATACTTAACAAACAGGTTTCATGTTTATTATTAATTTCAAATTA
441891 TTAATATTAAAGATAAAAATT
66 TTAATATTAAAGATAAAAATT
441912 ATAATAATTA
1 ATAATAATTA
441922 CAATTATATT
Statistics
Matches: 95, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
85 4 0.04
86 91 0.96
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.40
Consensus pattern (86 bp):
ATAATAATTATATCAACATTAATACTTAACAAACAGGTTTCATGTTTATTATTAATTTCAAATTA
TTAATATTAAAGATAAAAATT
Found at i:465578 original size:32 final size:32
Alignment explanation
Indices: 465537--465605 Score: 120
Period size: 32 Copynumber: 2.2 Consensus size: 32
465527 ATATAGAAAA
465537 ATATGCTTTTAGTATGTTTCAGCTACGTGATT
1 ATATGCTTTTAGTATGTTTCAGCTACGTGATT
**
465569 ATATGCTTTTAGTATGTTTTGGCTACGTGATT
1 ATATGCTTTTAGTATGTTTCAGCTACGTGATT
465601 ATATG
1 ATATG
465606 TAAGATTTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.22, C:0.10, G:0.20, T:0.48
Consensus pattern (32 bp):
ATATGCTTTTAGTATGTTTCAGCTACGTGATT
Found at i:470110 original size:31 final size:31
Alignment explanation
Indices: 470043--470101 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
470033 ACAAAATGGT
470043 CATTGAACTATTCAAAAGTTTTCATTTAAGA
1 CATTGAACTATTCAAAAGTTTTCATTTAAGA
*
470074 CATTGAACTATTCAAAAGTTTTTATTTA
1 CATTGAACTATTCAAAAGTTTTCATTTA
470102 GGTTATTGAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.37, C:0.12, G:0.08, T:0.42
Consensus pattern (31 bp):
CATTGAACTATTCAAAAGTTTTCATTTAAGA
Found at i:476124 original size:12 final size:12
Alignment explanation
Indices: 476107--476131 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
476097 AAACAAGTTA
476107 TGTTTATTTATT
1 TGTTTATTTATT
476119 TGTTTATTTATT
1 TGTTTATTTATT
476131 T
1 T
476132 TCACCTTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (12 bp):
TGTTTATTTATT
Found at i:477319 original size:10 final size:10
Alignment explanation
Indices: 477300--477354 Score: 51
Period size: 9 Copynumber: 5.5 Consensus size: 10
477290 TCTTTTTAAT
*
477300 TTTTTTTGAA
1 TTTTTATGAA
477310 TTTTTATGAA
1 TTTTTATGAA
*
477320 CTTTTTAT-AT
1 -TTTTTATGAA
*
477330 TTTTTA-AAA
1 TTTTTATGAA
477339 TTTTTATGAA
1 TTTTTATGAA
477349 TATTTT
1 T-TTTT
477355 TATAACTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
9 13 0.35
10 13 0.35
11 11 0.30
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.65
Consensus pattern (10 bp):
TTTTTATGAA
Found at i:477333 original size:29 final size:31
Alignment explanation
Indices: 477290--477358 Score: 90
Period size: 29 Copynumber: 2.3 Consensus size: 31
477280 TCATACTTCT
**
477290 TCTTTTTA-ATTTTTTTTGAATTTTTATGAA
1 TCTTTTTATATTTTTTTAAAATTTTTATGAA
477320 -CTTTTTATA-TTTTTTAAAATTTTTATGAA
1 TCTTTTTATATTTTTTTAAAATTTTTATGAA
*
477349 TATTTTTATA
1 TCTTTTTATA
477359 ACTTTTAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 25 0.74
30 9 0.26
ACGTcount: A:0.28, C:0.03, G:0.04, T:0.65
Consensus pattern (31 bp):
TCTTTTTATATTTTTTTAAAATTTTTATGAA
Found at i:477368 original size:29 final size:28
Alignment explanation
Indices: 477303--477375 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 28
477293 TTTTAATTTT
* * **
477303 TTTTGAATTTTTATGAACTTTTTATATT
1 TTTTAAATTTTTATGAAATTTTTATAAC
477331 TTTTAAAATTTTTATGAATATTTTTATAAC
1 TTTT-AAATTTTTATGAA-ATTTTTATAAC
477361 TTTTAAATTATTTAT
1 TTTTAAATT-TTTAT
477376 TAATTTGGTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
28 4 0.11
29 17 0.45
30 17 0.45
ACGTcount: A:0.32, C:0.03, G:0.04, T:0.62
Consensus pattern (28 bp):
TTTTAAATTTTTATGAAATTTTTATAAC
Found at i:479441 original size:30 final size:30
Alignment explanation
Indices: 479402--479471 Score: 72
Period size: 30 Copynumber: 2.3 Consensus size: 30
479392 AAAAGAAAGA
* *
479402 TTTGGAAATTCCT-ATTAAGCCCCT-AAATC
1 TTTGAAAATT-CTAATTAACCCCCTAAAATC
* *
479431 TTTTGAAAATTTTAATTATCCCCCTAAAATC
1 -TTTGAAAATTCTAATTAACCCCCTAAAATC
479462 TTTGAAAATT
1 TTTGAAAATT
479472 TTAAGTACCC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
29 1 0.03
30 28 0.82
31 5 0.15
ACGTcount: A:0.34, C:0.19, G:0.07, T:0.40
Consensus pattern (30 bp):
TTTGAAAATTCTAATTAACCCCCTAAAATC
Found at i:481810 original size:9 final size:9
Alignment explanation
Indices: 481796--481820 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
481786 ATAAATCGAG
481796 ACTAGTATT
1 ACTAGTATT
481805 ACTAGTATT
1 ACTAGTATT
481814 ACTAGTA
1 ACTAGTA
481821 ACTTCTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (9 bp):
ACTAGTATT
Found at i:488761 original size:31 final size:31
Alignment explanation
Indices: 488719--488777 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
488709 GGTTAGACTA
488719 AAATTTCAAAAGTACAAGGACTAAAATTAAC
1 AAATTTCAAAAGTACAAGGACTAAAATTAAC
* **
488750 AAATTTGAAAAGTACTGGGACTAAAATT
1 AAATTTCAAAAGTACAAGGACTAAAATT
488778 GATCAAATGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.51, C:0.10, G:0.14, T:0.25
Consensus pattern (31 bp):
AAATTTCAAAAGTACAAGGACTAAAATTAAC
Found at i:489434 original size:19 final size:19
Alignment explanation
Indices: 489410--489448 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
489400 AAATGCCCCG
489410 CCGTTCATATATATATTCA
1 CCGTTCATATATATATTCA
489429 CCGTTCATATATATATTCA
1 CCGTTCATATATATATTCA
489448 C
1 C
489449 GAGTTTTCGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.31, C:0.23, G:0.05, T:0.41
Consensus pattern (19 bp):
CCGTTCATATATATATTCA
Found at i:489875 original size:16 final size:17
Alignment explanation
Indices: 489849--489882 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
489839 GAATTTAATA
489849 AAAATATTTTTTATTTT
1 AAAATATTTTTTATTTT
489866 AAAATA-TTTTTATTTT
1 AAAATATTTTTTATTTT
489882 A
1 A
489883 TTTTTATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
AAAATATTTTTTATTTT
Found at i:489879 original size:6 final size:6
Alignment explanation
Indices: 489870--489907 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
489860 TATTTTAAAA
*
489870 TATTTT TA-TTT TATTTT TATTTT ATTTTTT TATTTT TA
1 TATTTT TATTTT TATTTT TATTTT -TATTTT TATTTT TA
489908 AAATTATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
5 5 0.18
6 18 0.64
7 5 0.18
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (6 bp):
TATTTT
Found at i:489884 original size:11 final size:11
Alignment explanation
Indices: 489870--489898 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
489860 TATTTTAAAA
489870 TATTTTTATTT
1 TATTTTTATTT
489881 TATTTTTATTT
1 TATTTTTATTT
489892 TATTTTT
1 TATTTTT
489899 TTATTTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (11 bp):
TATTTTTATTT
Found at i:497072 original size:24 final size:24
Alignment explanation
Indices: 497030--497076 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
497020 CTTCTTCTTC
497030 TTTTTATCACTCAACTATTTAATTT
1 TTTTTATCACTCAACTA-TTAATTT
* *
497055 TTTTTGTCACT-AATTATTAATT
1 TTTTTATCACTCAACTATTAATT
497077 ATCAACGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 6 0.30
24 4 0.20
25 10 0.50
ACGTcount: A:0.28, C:0.13, G:0.02, T:0.57
Consensus pattern (24 bp):
TTTTTATCACTCAACTATTAATTT
Found at i:505420 original size:37 final size:37
Alignment explanation
Indices: 505379--505460 Score: 128
Period size: 37 Copynumber: 2.2 Consensus size: 37
505369 TTGAATAAGA
*
505379 TTGAATCGAATACTTAGAATGATTTTAGAGAAGGGTT
1 TTGAATCGAATACTTAGAATGATTCTAGAGAAGGGTT
* * *
505416 TTGAATCGAATATTTTGATTGATTCTAGAGAAGGGTT
1 TTGAATCGAATACTTAGAATGATTCTAGAGAAGGGTT
505453 TTGAATCG
1 TTGAATCG
505461 GTTGATTTTG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.32, C:0.06, G:0.24, T:0.38
Consensus pattern (37 bp):
TTGAATCGAATACTTAGAATGATTCTAGAGAAGGGTT
Found at i:505557 original size:19 final size:22
Alignment explanation
Indices: 505533--505574 Score: 63
Period size: 19 Copynumber: 2.0 Consensus size: 22
505523 TAAATAATAC
505533 TTTTAAT-ATTT-TTT-ATCAA
1 TTTTAATGATTTATTTAATCAA
505552 TTTTAATGATTTATTTAATCAA
1 TTTTAATGATTTATTTAATCAA
505574 T
1 T
505575 CTAGTTGAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 7 0.35
20 4 0.20
21 3 0.15
22 6 0.30
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (22 bp):
TTTTAATGATTTATTTAATCAA
Found at i:516368 original size:137 final size:137
Alignment explanation
Indices: 516045--517552 Score: 1258
Period size: 146 Copynumber: 10.8 Consensus size: 137
516035 ATGACAAAAT
* * *
516045 TATATATTTTGTTGTTTGGTTAGTTAGAAAGTAAGTTGA-AGTGGATTAAGCTTAACTTAGCTAC
1 TATATATTTTGTTGTTTGGTTACTTAGAAAGTAAATT-ATAGTGGATTAAGCTTAATTTAGCTAC
* *
516109 TTTAATTGTCTAAATTTGGTCATTTAGGTG-AAAATTTTAGTGTTCTTTTGTTATTAATAAGTTT
65 TTTAATTGTCTAAATTTCGTCATTTAGGTGAAAAATTTTAGTGTTC---T-TT-TTAAT--GGTT
516173 CTTTATGAATATATG
123 CTTTATGAATATATG
* * * * *
516188 TATATATTTTGTTGTTTGGTTACGTAGAAAGTAAATTGA-AGTGGATTAAGTTTAATTTAACCAT
1 TATATATTTTGTTGTTTGGTTACTTAGAAAGTAAATT-ATAGTGGATTAAGCTTAATTTAGCTAC
* * * **
516252 TTTAATTGTCTCAATTTCGTAATTTAGGTGAAAAAATTTAGTGTTCTTTTTGGTGGTTCTTTATG
65 TTTAATTGTCTAAATTTCGTCATTTAGGTGAAAAATTTTAGTGTTCTTTTTAATGGTTCTTTATG
* *
516317 AATGTAAG
130 AATATATG
* *
516325 TATATATTTTGTTCTTTGGTTACTTAGAAAGTAAATTATAGTGGATTAAGCTTAATATAGCTACT
1 TATATATTTTGTTGTTTGGTTACTTAGAAAGTAAATTATAGTGGATTAAGCTTAATTTAGCTACT
* * * ** * *
516390 TTAGTTGTCGTGAAA------AATTTTGGTG-TTATTTTTGGTGGTTC--TTT-A----------
66 TTAATTGTC-T-AAATTTCGTCATTTAGGTGAAAAATTTTAGT-GTTCTTTTTAATGGTTCTTTA
*
516435 TGAATATAAG
128 TGAATATATG
516445 TATATATTTTGTTGTTTGGTTACTTAGAAAGTAAATT-TGAGTGGATTAAGCTTAATTTAGCTAC
1 TATATATTTTGTTGTTTGGTTACTTAGAAAGTAAATTAT-AGTGGATTAAGCTTAATTTAGCTAC
* * **
516509 TTTAATTGTCTCAATTTCGTCATTTAGGTGAAAAATTTTAGTGTTCATTTTGGTGGTTCTTTATG
65 TTTAATTGTCTAAATTTCGTCATTTAGGTGAAAAATTTTAGTGTTCTTTTTAATGGTTCTTTATG
*
516574 AATATAAG
130 AATATATG
* * *
516582 TATATATTTTGTTGTTGGGTTACTTAGAAAGTAAATTATAGTGGAATAAGCTTAAGTTAGCTACT
1 TATATATTTTGTTGTTTGGTTACTTAGAAAGTAAATTATAGTGGATTAAGCTTAATTTAGCTACT
* * * **
516647 TTAATT-TCTAAGTTTGGTCATTCAGGTGAAAAACATTAGTGTTCTTTTGCTATTTTTTTGATGG
66 TTAATTGTCTAAATTTCGTCATTTAGGTGAAAAATTTTAGTGTTCTTTT--TA--------ATGG
516711 TTCTTTATGAATATATG
121 TTCTTTATGAATATATG
* * *
516728 TATATAATTTGTTGTTTGTTTACTTAGAAAGTAAATTATAGTGGGA-TAAGCTTAATTTACACTA
1 TATATATTTTGTTGTTTGGTTACTTAGAAAGTAAATTATAGT-GGATTAAGCTTAATTTA-GCTA
* * ** *
516792 CTTTAATTGTCTAAATTTCGTCATTTAGGTGAAAAA----ATTGTTATTAGTAA-GTTTCTTTAT
64 CTTTAATTGTCTAAATTTCGTCATTTAGGTGAAAAATTTTAGTGTTCTTTTTAATGGTTCTTTAT
* *
516852 GAATATGTC
129 GAATATATG
* ** ** *
516861 TATATGTTTTGTTGTTTGGTTACTTAGAAAGTAAATGGTAGTGGGGTAAGCTTAA-GTATGCTAC
1 TATATATTTTGTTGTTTGGTTACTTAGAAAGTAAATTATAGTGGATTAAGCTTAATTTA-GCTAC
* * * *
516925 TTTAGTTTTCTAAATTTCGTCACTTAGGTGAAAAAATTTAGTGTTCTTTTGCTATTTTTTATGGT
65 TTTAATTGTCTAAATTTCGTCATTTAGGTGAAAAATTTTAGTGTTCTTTT--TA------ATGGT
*
516990 TCATTATGAATATATG
122 TCTTTATGAATATATG
* * * * * *
517006 TATATAATTTATTGTTTGGTTACCTACAAAGTAAATTACAGTGGGA-TAACCTTAATTTAGCTAC
1 TATATATTTTGTTGTTTGGTTACTTAGAAAGTAAATTATAGT-GGATTAAGCTTAATTTAGCTAC
* * ** * ** *
517070 TTTACTTGTCTAAATGTATTCGTTTAGGTGAAAAGCTTTAGTG-TCTTTTGTTATTTTTTTTATA
65 TTTAATTGTCTAAATTTCGTCATTTAGGTGAAAAATTTTAGTGTTC-TTT-TTA--------ATG
* *
517134 GTTCTTTATGAATATCTT
120 GTTCTTTATGAATATATG
* * *
517152 TATATATTTTGTTGTTTGGTCACTTAGAAAGCAAATTATCA-TGGATTGAGCTTAATTTAGCTAC
1 TATATATTTTGTTGTTTGGTTACTTAGAAAGTAAATTAT-AGTGGATTAAGCTTAATTTAGCTAC
* * * * *
517216 TTTCATTGTCTAAAATTCGTCATTTAGGTGAAAATTTTTTGTGTTCTTTTGTTATTAGCAAGTTT
65 TTTAATTGTCTAAATTTCGTCATTTAGGTGAAAAATTTTAGTGTTC-TTT-TTAAT-G---G-TT
* *
517281 CTTTATGAATTTGTG
123 CTTTATGAATATATG
* *
517296 TATATATTTTGTTGTTTGGTTTCTTAGAAAGTAAATTGTAGTGGGA-TAAGCTTAATTTAGCTAC
1 TATATATTTTGTTGTTTGGTTACTTAGAAAGTAAATTATAGT-GGATTAAGCTTAATTTAGCTAC
* * * * * **
517360 TTTAATTGTCTAAAATTCGTCATTTAGGTGAAAAACTTTCGTGTTTCTTTTGTTATTAGTAAGTT
65 TTTAATTGTCTAAATTTCGTCATTTAGGTGAAAAATTTTAGTG-TTC-TTT-TTAATGGT-TCTT
*
517425 TATGCACAAGCATATG
126 TATG---AA-TATATG
* * *
517441 TATATA--TTGCTT-TTTGGTTGCTTAGAAAGTAAATTATGGTGGAATAAGCTTAATTTAGCTAC
1 TATATATTTTG-TTGTTTGGTTACTTAGAAAGTAAATTATAGTGGATTAAGCTTAATTTAGCTAC
* *
517503 TTTAATTGTCCAAATTTCGTCATTTAGGTGAAAAATTTTAATGTTCTTTT
65 TTTAATTGTCTAAATTTCGTCATTTAGGTGAAAAATTTTAGTGTTCTTTT
517553 GGTTTTTTGG
Statistics
Matches: 1123, Mismatches: 164, Indels: 159
0.78 0.11 0.11
Matches are distributed among these distances:
118 2 0.00
119 2 0.00
120 78 0.07
124 12 0.01
125 7 0.01
126 3 0.00
131 3 0.00
132 46 0.04
133 75 0.07
134 1 0.00
136 43 0.04
137 156 0.14
138 5 0.00
139 6 0.01
140 4 0.00
141 11 0.01
142 8 0.01
143 169 0.15
144 136 0.12
145 127 0.11
146 180 0.16
147 25 0.02
148 24 0.02
ACGTcount: A:0.28, C:0.08, G:0.18, T:0.46
Consensus pattern (137 bp):
TATATATTTTGTTGTTTGGTTACTTAGAAAGTAAATTATAGTGGATTAAGCTTAATTTAGCTACT
TTAATTGTCTAAATTTCGTCATTTAGGTGAAAAATTTTAGTGTTCTTTTTAATGGTTCTTTATGA
ATATATG
Found at i:516492 original size:120 final size:122
Alignment explanation
Indices: 516279--516649 Score: 473
Period size: 137 Copynumber: 2.9 Consensus size: 122
516269 CGTAATTTAG
* * * *
516279 GTGAAAAAATTTAGTGTTCTTTTTGGTGGTTCTTTATGAATGTAAGTATATATTTTGTTCTTTGG
1 GTGAAAAATTTTAGTGTTATTTTTGGTGGTTCTTTATGAATATAAGTATATATTTTGTTGTTTGG
516344 TTACTTAGAAAGTAAATTATAGTGGATTAAGCTTAATATAGCTACTTTA-G-T-TGTC
66 TTACTTAGAAAGTAAATTATAGTGGATTAAGCTTAAT-TAGCTACTTTATGCTATGTC
*
516399 GTGAAAAATTTTGGTGTTATTTTTGGTGGTTCTTTATGAATATAAGTATATATTTTGTTGTTTGG
1 GTGAAAAATTTTAGTGTTATTTTTGGTGGTTCTTTATGAATATAAGTATATATTTTGTTGTTTGG
516464 TTACTTAGAAAGTAAATT-TGAGTGGATTAAGCTTAATTTAGCTACTTTAATTGTCTCAATTTCG
66 TTACTTAGAAAGTAAATTAT-AGTGGATTAAGCTTAA-TTAGCTACTTT-A-TG-CT--A--T-G
516528 TC
121 TC
516530 ATTTAGGTGAAAAATTTTAGTGTTCA-TTTTGGTGGTTCTTTATGAATATAAGTATATATTTTGT
1 ------GTGAAAAATTTTAGTGTT-ATTTTTGGTGGTTCTTTATGAATATAAGTATATATTTTGT
* *
516594 TGTTGGGTTACTTAGAAAGTAAATTATAGTGGAATAAGCTTAAGTTAGCTACTTTA
59 TGTTTGGTTACTTAGAAAGTAAATTATAGTGGATTAAGCTTAA-TTAGCTACTTTA
516650 ATTTCTAAGT
Statistics
Matches: 221, Mismatches: 9, Indels: 26
0.86 0.04 0.10
Matches are distributed among these distances:
119 1 0.00
120 104 0.47
121 2 0.01
123 1 0.00
125 1 0.00
130 1 0.00
131 3 0.01
136 1 0.00
137 105 0.48
138 2 0.01
ACGTcount: A:0.29, C:0.06, G:0.19, T:0.46
Consensus pattern (122 bp):
GTGAAAAATTTTAGTGTTATTTTTGGTGGTTCTTTATGAATATAAGTATATATTTTGTTGTTTGG
TTACTTAGAAAGTAAATTATAGTGGATTAAGCTTAATTAGCTACTTTATGCTATGTC
Found at i:516634 original size:257 final size:268
Alignment explanation
Indices: 516171--516931 Score: 884
Period size: 257 Copynumber: 2.8 Consensus size: 268
516161 ATTAATAAGT
*
516171 TTCTTTATGAATATATGTATATATTTTGTTGTTTGGTTACGTAGAAAGTAAA-TTGAAGTGGATT
1 TTCTTTATGAATATATGTATATATTTTGTTGTTTGGTTACTTAGAAAGTAAATTTG-AGTGGATT
* * * * *
516235 AAGTTTAATTTAACCATTTTAATTGTCTCAATTTCGTAATTTAGGTGAAAAAATTTAGTGTTCTT
65 AAGCTTAATTTAACTACTTTAATTGTCTCAATTTCGTCATTTAGGTG-AAAAATTTAGTGTTCAT
* *
516300 TTTGGTGGTTCTTTATGAATGTAAGTATATATTTTGTTCTTTGGTTACTTAGAAAGTAAATTATA
129 TTTGGTGGTTCTTTATGAATATAAGTATATATTTTGTTGTTTGGTTACTTAGAAAGTAAATTATA
*
516365 GTGGATTAAGCTTAA-TATAGCTACTTTAGTT-G-TC-GTG-AAAA-A-T-T-TT-GGTG-T-TA
194 GTGGAATAAGCTTAAGTATAGCTACTTTAGTTGGTTCAGTGAAAAACATTATGTTCGGTGCTATA
*
516418 TTTTTGGTGG
259 TTTTTGATGG
*
516428 TTCTTTATGAATATAAGTATATATTTTGTTGTTTGGTTACTTAGAAAGTAAATTTGAGTGGATTA
1 TTCTTTATGAATATATGTATATATTTTGTTGTTTGGTTACTTAGAAAGTAAATTTGAGTGGATTA
*
516493 AGCTTAATTTAGCTACTTTAATTGTCTCAATTTCGTCATTTAGGTGAAAAATTTTAGTGTTCATT
66 AGCTTAATTTAACTACTTTAATTGTCTCAATTTCGTCATTTAGGTGAAAAA-TTTAGTGTTCATT
*
516558 TTGGTGGTTCTTTATGAATATAAGTATATATTTTGTTGTTGGGTTACTTAGAAAGTAAATTATAG
130 TTGGTGGTTCTTTATGAATATAAGTATATATTTTGTTGTTTGGTTACTTAGAAAGTAAATTATAG
516623 TGGAATAAGCTTAAGT-TAGCTACTTTAATTTCTAAGTTTGGTCATTCAGGTGAAAAACATTAGT
195 TGGAATAAGCTTAAGTATAGCTAC------TT-T-AG-TTGG---TTCA-GTGAAAAACATTA-T
** *
516687 GTTCTTTTGCTATTTTTTTGATGG
246 GTTC-GGTGCTATATTTTTGATGG
* *
516711 TTCTTTATGAATATATGTATATAATTTGTTGTTTGTTTACTTAGAAAGTAAATTAT-AGTGGGA-
1 TTCTTTATGAATATATGTATATATTTTGTTGTTTGGTTACTTAGAAAGTAAATT-TGAGT-GGAT
* *
516774 TAAGCTTAATTTACACTACTTTAATTGTCTAAATTTCGTCATTTAGGTGAAAAA---ATTGTT-A
64 TAAGCTTAATTTA-ACTACTTTAATTGTCTCAATTTCGTCATTTAGGTGAAAAATTTAGTGTTCA
* * *** * *
516835 --TTAGTAAGTTTCTTTATGAATATGTCTATATGTTTTGTTGTTTGGTTACTTAGAAAGTAAATG
128 TTTTGGT--GGTTCTTTATGAATATAAGTATATATTTTGTTGTTTGGTTACTTAGAAAGTAAATT
* **
516898 GTAGTGGGGTAAGCTTAAGTAT-GCTACTTTAGTT
191 ATAGTGGAATAAGCTTAAGTATAGCTACTTTAGTT
516932 TTCTAAATTT
Statistics
Matches: 436, Mismatches: 33, Indels: 57
0.83 0.06 0.11
Matches are distributed among these distances:
256 5 0.01
257 194 0.44
258 4 0.01
263 2 0.00
264 1 0.00
265 2 0.00
266 2 0.00
267 1 0.00
270 2 0.00
271 4 0.01
272 1 0.00
273 5 0.01
274 4 0.01
275 1 0.00
276 1 0.00
277 4 0.01
278 1 0.00
279 74 0.17
280 6 0.01
281 2 0.00
282 1 0.00
283 77 0.18
284 42 0.10
ACGTcount: A:0.29, C:0.07, G:0.19, T:0.46
Consensus pattern (268 bp):
TTCTTTATGAATATATGTATATATTTTGTTGTTTGGTTACTTAGAAAGTAAATTTGAGTGGATTA
AGCTTAATTTAACTACTTTAATTGTCTCAATTTCGTCATTTAGGTGAAAAATTTAGTGTTCATTT
TGGTGGTTCTTTATGAATATAAGTATATATTTTGTTGTTTGGTTACTTAGAAAGTAAATTATAGT
GGAATAAGCTTAAGTATAGCTACTTTAGTTGGTTCAGTGAAAAACATTATGTTCGGTGCTATATT
TTTGATGG
Found at i:516960 original size:133 final size:133
Alignment explanation
Indices: 516711--517394 Score: 385
Period size: 144 Copynumber: 4.9 Consensus size: 133
516701 TTTTTGATGG
* * *
516711 TTCTTTATGAATATATGTATATAATTTGTTGTTTGTTTACTTAGAAAGTAAATTATAGTGGGATA
1 TTCTTTATGAATATATCTATATAATTTGTTGTTTGGTTACTTAGAAAGTAAATGATAGTGGGATA
* *
516776 AGCTTAATTTACACTACTTTAATTGTCTAAATTTCGTCATTTAGGTGAAAAAATTGTTATTAGTA
66 AGCTTAATGTACACTACTTTAATTGTCTAAATTTCGTCACTTAGGTGAAAAAATTGTTATTAGTA
516841 AGT
131 AGT
* ** * *
516844 TTCTTTATGAATATGTCTATATGTTTTGTTGTTTGGTTACTTAGAAAGTAAATGGTAGTGGGGTA
1 TTCTTTATGAATATATCTATATAATTTGTTGTTTGGTTACTTAGAAAGTAAATGATAGTGGGATA
** * * *
516909 AGCTTAA-GTATGCTACTTTAGTTTTCTAAATTTCGTCACTTAGGTGAAAAAATTTAGTGTTCTT
66 AGCTTAATGTACACTACTTTAATTGTCTAAATTTCGTCACTTAGGTGAAAAAA--T--TGTT-AT
* *
516973 TTGCTATTTTTTATGG
126 TAG-TA------A-GT
* * * * * * *
516989 TTCATTATGAATATATGTATATAATTTATTGTTTGGTTACCTACAAAGTAAATTACAGTGGGATA
1 TTCTTTATGAATATATCTATATAATTTGTTGTTTGGTTACTTAGAAAGTAAATGATAGTGGGATA
* * * * * ** ** *
517054 ACCTTAATTTA-GCTACTTTACTTGTCTAAATGTATTCGTTTAGGTGAAAAGCTTTAGTGTCTTT
66 AGCTTAATGTACACTACTTTAATTGTCTAAATTTCGTCACTTAGGTGAAAA-----A------AT
**
517118 TGTTATTTTTTTTATAG-
120 TGTTA---TTAGTA-AGT
* * * * * *
517135 TTCTTTATGAATATCTTTATATATTTTGTTGTTTGGTCACTTAGAAAGCAAATTATCA-T-GGAT
1 TTCTTTATGAATATATCTATATAATTTGTTGTTTGGTTACTTAGAAAGTAAATGAT-AGTGGGA-
* * * * * *
517198 TGAGCTTAATTTA-GCTACTTTCATTGTCTAAAATTCGTCATTTAGGTGAAAATTTTTTGTGTTC
64 TAAGCTTAATGTACACTACTTTAATTGTCTAAATTTCGTCACTTAGGTGAAAA------------
** *
517262 TTTTGTTATTAGCAAGT
117 AATTGTTATTAGTAAGT
* * * * *
517279 TTCTTTATGAATTTGTGTATATATTTTGTTGTTTGGTTTCTTAGAAAGTAAATTG-TAGTGGGAT
1 TTCTTTATGAATATATCTATATAATTTGTTGTTTGGTTACTTAGAAAGTAAA-TGATAGTGGGAT
* * * *
517343 AAGCTTAATTTA-GCTACTTTAATTGTCTAAAATTCGTCATTTAGGTGAAAAA
65 AAGCTTAATGTACACTACTTTAATTGTCTAAATTTCGTCACTTAGGTGAAAAA
517395 CTTTCGTGTT
Statistics
Matches: 433, Mismatches: 77, Indels: 83
0.73 0.13 0.14
Matches are distributed among these distances:
132 39 0.09
133 64 0.15
134 1 0.00
136 4 0.01
137 3 0.01
138 2 0.00
143 3 0.01
144 102 0.24
145 99 0.23
146 92 0.21
147 9 0.02
148 2 0.00
150 1 0.00
152 4 0.01
153 4 0.01
154 4 0.01
ACGTcount: A:0.28, C:0.08, G:0.17, T:0.46
Consensus pattern (133 bp):
TTCTTTATGAATATATCTATATAATTTGTTGTTTGGTTACTTAGAAAGTAAATGATAGTGGGATA
AGCTTAATGTACACTACTTTAATTGTCTAAATTTCGTCACTTAGGTGAAAAAATTGTTATTAGTA
AGT
Found at i:517208 original size:424 final size:423
Alignment explanation
Indices: 516428--517416 Score: 1187
Period size: 424 Copynumber: 2.3 Consensus size: 423
516418 TTTTTGGTGG
** *
516428 TTCTTTATGAATATAAGTATATATTTTGTTGTTTGGTTACTTAGAAAGTAAATTTGAGT-GGATT
1 TTCTTTATGAATATGTGTATATATTTTGTTGTTTGGTTACTTAGAAAGTAAATGT-AGTGGGA-T
* *
516492 AAGCTTAATTTAGCTACTTTAATTGTCTCAATTTCGTCATTTAGGTGAAAAATTTTAGTG-----
64 AAGCTTAATTTAGCTACTTTAATTGTCTAAATTTCGTCATTTAGGTGAAAAAATTTAGTGTTCTT
* * * * * *
516552 TT-C-A-TTTTGGTGGTTCTTTATGAATATAAGTATATATTTTGTTGTTGGGTTACTTAGAAAGT
129 TTGCTATTTTTGATGGTTCATTATGAATATAAGTATATAATTTATTGTTGGGTTACCTACAAAGT
* * * * *
516614 AAATTATAGTGGAATAAGCTTAAGTTAGCTACTTTAATTTCTAAGTTTGGTCATTCAGGTGAAAA
194 AAATTACAGTGGAATAACCTTAAGTTAGCTACTTTAATTTCTAAATGTAGTCATTCAGGTGAAAA
*
516679 ACATTAGTGTTCTTTTGCTATTTTTTTGATGGTTCTTTATGAATATATGTATATAATTTGTTGTT
259 ACATTAGTGTTCTTTTGCTATTTTTTTGATAGTTCTTTATGAATATATGTATATAATTTGTTGTT
* * * *
516744 TGTTTACTTAGAAAGTAAATTATAGTGGGATAAGCTTAATTTACACTACTTTAATTGTCTAAATT
324 TGGTCACTTAGAAAGCAAATTATAGTGGGATAAGCTTAATTTA-ACTACTTTAATTGTCTAAAAT
*
516809 TCGTCATTTAGGTGAAAA-AATTGTTATTAGTAAGT
388 TCGTCATTTAGGTGAAAATAATTGTTATTAGCAAGT
* * *
516844 TTCTTTATGAATATGTCTATATGTTTTGTTGTTTGGTTACTTAGAAAGTAAATGGTAGTGGGGTA
1 TTCTTTATGAATATGTGTATATATTTTGTTGTTTGGTTACTTAGAAAGTAAAT-GTAGTGGGATA
* * * *
516909 AGCTTAA-GTATGCTACTTTAGTTTTCTAAATTTCGTCACTTAGGTGAAAAAATTTAGTGTTCTT
65 AGCTTAATTTA-GCTACTTTAATTGTCTAAATTTCGTCATTTAGGTGAAAAAATTTAGTGTTCTT
* * *
516973 TTGCTATTTTTTATGGTTCATTATGAATATATGTATATAATTTATTGTTTGGTTACCTACAAAGT
129 TTGCTATTTTTGATGGTTCATTATGAATATAAGTATATAATTTATTGTTGGGTTACCTACAAAGT
* * * * * *
517038 AAATTACAGTGGGATAACCTTAATTTAGCTACTTTACTTGTCTAAATGTATTCGTTTAGGTGAAA
194 AAATTACAGTGGAATAACCTTAAGTTAGCTACTTTAATT-TCTAAATGTAGTCATTCAGGTGAAA
* * * * * * *
517103 AGCTTTAGTG-TCTTTTGTTATTTTTTTTATAGTTCTTTATGAATATCTTTATATATTTTGTTGT
258 AACATTAGTGTTCTTTTGCTATTTTTTTGATAGTTCTTTATGAATATATGTATATAATTTGTTGT
* * *
517167 TTGGTCACTTAGAAAGCAAATTATCA-T-GGATTGAGCTTAATTTAGCTACTTTCATTGTCTAAA
323 TTGGTCACTTAGAAAGCAAATTAT-AGTGGGA-TAAGCTTAATTTAACTACTTTAATTGTCTAAA
**
517230 ATTCGTCATTTAGGTGAAAATTTTTTGTGTTCTTTTGTTATTAGCAAGT
386 ATTCGTCATTTAGGTGAAAA----------T-AATTGTTATTAGCAAGT
* *
517279 TTCTTTATGAATTTGTGTATATATTTTGTTGTTTGGTTTCTTAGAAAGTAAATTGTAGTGGGATA
1 TTCTTTATGAATATGTGTATATATTTTGTTGTTTGGTTACTTAGAAAGTAAA-TGTAGTGGGATA
* * *
517344 AGCTTAATTTAGCTACTTTAATTGTCTAAAATTCGTCATTTAGGTGAAAAACTTTCGTGTTTCTT
65 AGCTTAATTTAGCTACTTTAATTGTCTAAATTTCGTCATTTAGGTGAAAAAATTTAGTG-TTCTT
*
517409 TTGTTATT
129 TTGCTATT
517417 AGTAAGTTTA
Statistics
Matches: 481, Mismatches: 63, Indels: 38
0.83 0.11 0.07
Matches are distributed among these distances:
415 2 0.00
416 104 0.22
417 3 0.01
421 2 0.00
422 1 0.00
423 40 0.08
424 165 0.34
425 28 0.06
435 121 0.25
436 15 0.03
ACGTcount: A:0.28, C:0.08, G:0.17, T:0.47
Consensus pattern (423 bp):
TTCTTTATGAATATGTGTATATATTTTGTTGTTTGGTTACTTAGAAAGTAAATGTAGTGGGATAA
GCTTAATTTAGCTACTTTAATTGTCTAAATTTCGTCATTTAGGTGAAAAAATTTAGTGTTCTTTT
GCTATTTTTGATGGTTCATTATGAATATAAGTATATAATTTATTGTTGGGTTACCTACAAAGTAA
ATTACAGTGGAATAACCTTAAGTTAGCTACTTTAATTTCTAAATGTAGTCATTCAGGTGAAAAAC
ATTAGTGTTCTTTTGCTATTTTTTTGATAGTTCTTTATGAATATATGTATATAATTTGTTGTTTG
GTCACTTAGAAAGCAAATTATAGTGGGATAAGCTTAATTTAACTACTTTAATTGTCTAAAATTCG
TCATTTAGGTGAAAATAATTGTTATTAGCAAGT
Found at i:517404 original size:144 final size:144
Alignment explanation
Indices: 516428--516827 Score: 453
Period size: 137 Copynumber: 2.8 Consensus size: 144
516418 TTTTTGGTGG
*
516428 TTCTTTATGAATATAAGTATATATTTTGTTGTTTGGTTACTTAGAAAGTAAATT-TGAGT-GGAT
1 TTCTTTATGAATATATGTATATATTTTGTTGTTTGGTTACTTAGAAAGTAAATTAT-AGTGGGA-
* * *
516491 TAAGCTTAATTTAGCTACTTTAATTGTCTCAATTTCGTCATTTAGGTGAAAAATTTTAGTGTTCA
64 TAAGCTTAATTTAGCTACTTTAATTGTCTAAAATTCGTCATTTAGGTGAAAAACTTTAGTGTTC-
*
516556 TTTTG------GT--GG
128 TTTTGTTATTAGTAAGT
* * *
516565 TTCTTTATGAATATAAGTATATATTTTGTTGTTGGGTTACTTAGAAAGTAAATTATAGTGGAATA
1 TTCTTTATGAATATATGTATATATTTTGTTGTTTGGTTACTTAGAAAGTAAATTATAGTGGGATA
* ** * * *
516630 AGCTTAAGTTAGCTACTTTAATT-TCTAAGTTTGGTCATTCAGGTGAAAAACATTAGTGTTCTTT
66 AGCTTAATTTAGCTACTTTAATTGTCTAAAATTCGTCATTTAGGTGAAAAACTTTAGTGTTCTTT
* ** * *
516694 TGCTATTTTTTTGATGG
131 TG-T-TATTAGT-AAGT
* *
516711 TTCTTTATGAATATATGTATATAATTTGTTGTTTGTTTACTTAGAAAGTAAATTATAGTGGGATA
1 TTCTTTATGAATATATGTATATATTTTGTTGTTTGGTTACTTAGAAAGTAAATTATAGTGGGATA
* *
516776 AGCTTAATTTACACTACTTTAATTGTCTAAATTTCGTCATTTAGGTGAAAAA
66 AGCTTAATTTA-GCTACTTTAATTGTCTAAAATTCGTCATTTAGGTGAAAAA
516828 ATTGTTATTA
Statistics
Matches: 228, Mismatches: 20, Indels: 19
0.85 0.07 0.07
Matches are distributed among these distances:
135 5 0.02
136 32 0.14
137 80 0.35
138 3 0.01
143 1 0.00
146 72 0.32
147 11 0.05
148 24 0.11
ACGTcount: A:0.30, C:0.07, G:0.17, T:0.46
Consensus pattern (144 bp):
TTCTTTATGAATATATGTATATATTTTGTTGTTTGGTTACTTAGAAAGTAAATTATAGTGGGATA
AGCTTAATTTAGCTACTTTAATTGTCTAAAATTCGTCATTTAGGTGAAAAACTTTAGTGTTCTTT
TGTTATTAGTAAGT
Found at i:517595 original size:143 final size:141
Alignment explanation
Indices: 516868--517583 Score: 471
Period size: 144 Copynumber: 5.0 Consensus size: 141
516858 GTCTATATGT
* ** ** * *
516868 TTTG-TTGTTTGGTTACTTAGAAAGTAAATGGTAGTGGGGTAAGCTTAA-GTATGCTACTTTAGT
1 TTTGCTTGTTTGGTTGCTTAGAAAGTAAATTATAGTGGAATAAGCTTAATTTA-GCTACTTTAAT
* * * * *
516931 TTTCTAAATTTCGTCACTTAGGTGAAAAAATTTAGTGTTCTTTTGCTATTTTTTA-TGGTTCATT
65 TGTCTAAAATTCGTCATTTAGGTGAAAAATTTTAGTGTTCTTTTG-T-TTTTTGAGTGGTTC-TT
*
516995 ATGAA-TATATGTATATAA
127 -TTAATTATA-G-ATAT-A
* * * * * * * *
517013 TTT-ATTGTTTGGTTACCTACAAAGTAAATTACAGTGGGATAACCTTAATTTAGCTACTTTACTT
1 TTTGCTTGTTTGGTTGCTTAGAAAGTAAATTATAGTGGAATAAGCTTAATTTAGCTACTTTAATT
** * ** * *
517077 GTCT-AAATGTATTCGTTTAGGTGAAAAGCTTTAGTG-TCTTTTGTTATTTTTTTTA-TAGTTCT
66 GTCTAAAAT-TCGTCATTTAGGTGAAAAATTTTAGTGTTCTTTTG----TTTTTTGAGTGGTTCT
* **
517139 TTATGAATATCTTTATATA
126 TT-T-AAT-TATAGATATA
** * * * *
517158 TTTTG-TTGTTTGGTCACTTAGAAAGCAAATTATCA-TGGATTGAGCTTAATTTAGCTACTTTCA
1 -TTTGCTTGTTTGGTTGCTTAGAAAGTAAATTAT-AGTGGAATAAGCTTAATTTAGCTACTTTAA
* * * *
517221 TTGTCTAAAATTCGTCATTTAGGTGAAAATTTTTTGTGTTCTTTTGTTATTAGCAAGT--TTCTT
64 TTGTCTAAAATTCGTCATTTAGGTGAAAAATTTTAGTGTTCTTTTGTTTTTTG--AGTGGTTCTT
*
517284 TATGAATT-TGTGTATATA
127 T-T-AATTAT-AG-ATATA
* * *
517302 TTTTG-TTGTTTGGTTTCTTAGAAAGTAAATTGTAGTGGGATAAGCTTAATTTAGCTACTTTAAT
1 -TTTGCTTGTTTGGTTGCTTAGAAAGTAAATTATAGTGGAATAAGCTTAATTTAGCTACTTTAAT
* * * *
517366 TGTCTAAAATTCGTCATTTAGGTGAAAAACTTTCGTGTTTCTTTTG-TTATT-AGTAAGTT-TAT
65 TGTCTAAAATTCGTCATTTAGGTGAAAAATTTTAGTG-TTCTTTTGTTTTTTGAGT-GGTTCT-T
** **
517428 GCACAAGCATATG-TATA
127 --TTAATTATA-GATATA
*
517445 TATTGCTT-TTTGGTTGCTTAGAAAGTAAATTATGGTGGAATAAGCTTAATTTAGCTACTTTAAT
1 T-TTGCTTGTTTGGTTGCTTAGAAAGTAAATTATAGTGGAATAAGCTTAATTTAGCTACTTTAAT
* * * *
517509 TGTCCAAATTTCGTCATTTAGGTGAAAAATTTTAATGTTCTTTTGGTTTTTTGGGTGGTTCTTTT
65 TGTCTAAAATTCGTCATTTAGGTGAAAAATTTTAGTGTTCTTTT-GTTTTTTGAGTGGTTCTTTT
*
517574 TATTATAGAT
129 AATTATAGAT
517584 TAGCTTGTGC
Statistics
Matches: 454, Mismatches: 80, Indels: 77
0.74 0.13 0.13
Matches are distributed among these distances:
141 4 0.01
142 14 0.03
143 100 0.22
144 133 0.29
145 92 0.20
146 96 0.21
147 13 0.03
148 2 0.00
ACGTcount: A:0.27, C:0.09, G:0.17, T:0.47
Consensus pattern (141 bp):
TTTGCTTGTTTGGTTGCTTAGAAAGTAAATTATAGTGGAATAAGCTTAATTTAGCTACTTTAATT
GTCTAAAATTCGTCATTTAGGTGAAAAATTTTAGTGTTCTTTTGTTTTTTGAGTGGTTCTTTTAA
TTATAGATATA
Found at i:523050 original size:6 final size:6
Alignment explanation
Indices: 523039--523063 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
523029 AATCTGAACA
523039 AAATTT AAATTT AAATTT AAATTT A
1 AAATTT AAATTT AAATTT AAATTT A
523064 GGTTGAGGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
AAATTT
Found at i:523591 original size:15 final size:15
Alignment explanation
Indices: 523571--523611 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
523561 TCTTTTTTCT
*
523571 TATATACATTCATCA
1 TATATACATACATCA
523586 TATATACATACATCA
1 TATATACATACATCA
*
523601 CATAATACATA
1 TAT-ATACATA
523612 AGCATCATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 16 0.70
16 7 0.30
ACGTcount: A:0.46, C:0.20, G:0.00, T:0.34
Consensus pattern (15 bp):
TATATACATACATCA
Found at i:523886 original size:4 final size:4
Alignment explanation
Indices: 523877--523901 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
523867 CCTCTTTTAC
523877 ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT A
523902 AGCATCATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:524211 original size:29 final size:29
Alignment explanation
Indices: 524164--524222 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
524154 TCTCAGCAAC
*
524164 AGTACGGAGGGTACTCGAGCTCGGGTGTA
1 AGTACGGAAGGTACTCGAGCTCGGGTGTA
*
524193 AGTACGGAAAGGTAC-CGAGCTCGTGTGTA
1 AGTACGG-AAGGTACTCGAGCTCGGGTGTA
524222 A
1 A
524223 ATTTCGGATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 21 0.78
30 6 0.22
ACGTcount: A:0.25, C:0.17, G:0.37, T:0.20
Consensus pattern (29 bp):
AGTACGGAAGGTACTCGAGCTCGGGTGTA
Found at i:528041 original size:31 final size:31
Alignment explanation
Indices: 528006--528068 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
527996 ATACATTGGT
528006 TGGAAAACCAGCAAAGTAGAATAGACTAGAC
1 TGGAAAACCAGCAAAGTAGAATAGACTAGAC
528037 TGGAAAACCAGCAAAGTAGAATAGACTAGAC
1 TGGAAAACCAGCAAAGTAGAATAGACTAGAC
528068 T
1 T
528069 TTCTCATACT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.48, C:0.16, G:0.22, T:0.14
Consensus pattern (31 bp):
TGGAAAACCAGCAAAGTAGAATAGACTAGAC
Found at i:533818 original size:31 final size:31
Alignment explanation
Indices: 533780--533877 Score: 78
Period size: 31 Copynumber: 3.2 Consensus size: 31
533770 TTAATTTTAA
*
533780 AAAATTTTAATTAGGCCCCTTAAATTTTTTG
1 AAAATTTTAATTAGGCCCATTAAATTTTTTG
* * * * *
533811 AAAATTTTCATT--TCTCCTTTGAAGTTATTT-
1 AAAATTTTAATTAGGC-CCATT-AAATTTTTTG
*
533841 AAAATTTTTAATTAGGCCCATTTAA-TTTTTG
1 AAAA-TTTTAATTAGGCCCATTAAATTTTTTG
533872 AAAATT
1 AAAATT
533878 CTCATTATTC
Statistics
Matches: 50, Mismatches: 11, Indels: 13
0.68 0.15 0.18
Matches are distributed among these distances:
29 1 0.02
30 14 0.28
31 30 0.60
32 4 0.08
33 1 0.02
ACGTcount: A:0.33, C:0.11, G:0.08, T:0.48
Consensus pattern (31 bp):
AAAATTTTAATTAGGCCCATTAAATTTTTTG
Found at i:533848 original size:61 final size:59
Alignment explanation
Indices: 533780--533913 Score: 162
Period size: 61 Copynumber: 2.2 Consensus size: 59
533770 TTAATTTTAA
* *
533780 AAAATTTTAATTAGGCCCCTTAAATTTTTTGAAAATTTTCATT-TCTCCTTTGAAGTTATTT
1 AAAATTTTAATTAGGCCCATTAAA-TTTTTGAAAATTCTCATTAT-TCCTTTGAA-TTATTT
* * * *
533841 AAAATTTTTAATTAGGCCCATTTAATTTTTGAAAATTCTCATTATTCTTTTTAATTTTTT
1 AAAA-TTTTAATTAGGCCCATTAAATTTTTGAAAATTCTCATTATTCCTTTGAATTATTT
*
533901 TAAATTTTAATTA
1 AAAATTTTAATTA
533914 AGCTCTCTTT
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
59 9 0.14
60 8 0.12
61 28 0.44
62 19 0.30
ACGTcount: A:0.31, C:0.10, G:0.06, T:0.52
Consensus pattern (59 bp):
AAAATTTTAATTAGGCCCATTAAATTTTTGAAAATTCTCATTATTCCTTTGAATTATTT
Found at i:534281 original size:23 final size:23
Alignment explanation
Indices: 534255--534299 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
534245 CAAAAACTAT
534255 ATTA-TCCCTAAAAAATAGGTTTC
1 ATTATTCCCTAAAAAA-AGGTTTC
* *
534278 ATTATTCTCTATAAAAAGGTTT
1 ATTATTCCCTAAAAAAAGGTTT
534300 AATTTTGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40
Consensus pattern (23 bp):
ATTATTCCCTAAAAAAAGGTTTC
Found at i:536973 original size:22 final size:22
Alignment explanation
Indices: 536948--536990 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
536938 TGCTGCTGTT
536948 TTGCTAACATTTTGTTATTATA
1 TTGCTAACATTTTGTTATTATA
** *
536970 TTGCTAATTTTTTGTTGTTAT
1 TTGCTAACATTTTGTTATTAT
536991 CATTTGAATA
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:0.21, C:0.07, G:0.12, T:0.60
Consensus pattern (22 bp):
TTGCTAACATTTTGTTATTATA
Found at i:537023 original size:19 final size:17
Alignment explanation
Indices: 536999--537033 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 17
536989 ATCATTTGAA
536999 TATTGTATAATCTTTGTTT
1 TATTGT-TAAT-TTTGTTT
537018 TATTGTTAATTTTGTT
1 TATTGTTAATTTTGTT
537034 ACTATTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 4 0.25
19 6 0.38
ACGTcount: A:0.20, C:0.03, G:0.11, T:0.66
Consensus pattern (17 bp):
TATTGTTAATTTTGTTT
Found at i:544408 original size:28 final size:28
Alignment explanation
Indices: 544377--544436 Score: 120
Period size: 28 Copynumber: 2.1 Consensus size: 28
544367 AGTATCTAAT
544377 AAGAGTTTTAACCATCTTCATTCAAGTC
1 AAGAGTTTTAACCATCTTCATTCAAGTC
544405 AAGAGTTTTAACCATCTTCATTCAAGTC
1 AAGAGTTTTAACCATCTTCATTCAAGTC
544433 AAGA
1 AAGA
544437 TAAATTTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.33
Consensus pattern (28 bp):
AAGAGTTTTAACCATCTTCATTCAAGTC
Found at i:547594 original size:31 final size:31
Alignment explanation
Indices: 547549--547665 Score: 93
Period size: 31 Copynumber: 3.9 Consensus size: 31
547539 TTAAACATTG
* * *
547549 TTAATATACTATTTGGTATCTGATTTTAATT
1 TTAATATTCAATTTGGTATCTGAGTTTAATT
*
547580 TTAATATTCAATTTGATA-CTAGAAGTTT--TT
1 TTAATATTCAATTTGGTATCT-G-AGTTTAATT
* *
547610 TT-AT-CTCAATTTGGTACCTGAGTTTAGA-T
1 TTAATATTCAATTTGGTATCTGAGTTTA-ATT
**
547639 TTAATATTCAAAATGGTATCTGAGTTT
1 TTAATATTCAATTTGGTATCTGAGTTT
547666 TTTTTTTCCC
Statistics
Matches: 68, Mismatches: 10, Indels: 16
0.72 0.11 0.17
Matches are distributed among these distances:
27 5 0.07
28 11 0.16
29 7 0.10
30 8 0.12
31 33 0.49
32 4 0.06
ACGTcount: A:0.30, C:0.09, G:0.13, T:0.49
Consensus pattern (31 bp):
TTAATATTCAATTTGGTATCTGAGTTTAATT
Found at i:548575 original size:5 final size:5
Alignment explanation
Indices: 548565--548590 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
548555 TGAGCATTCG
548565 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
548591 AATTTTCAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:549035 original size:25 final size:25
Alignment explanation
Indices: 549014--549067 Score: 72
Period size: 27 Copynumber: 2.1 Consensus size: 25
549004 AATATTTTAT
*
549014 GGCATAATATTAAAAAAAATTTGGA
1 GGCAAAATATTAAAAAAAATTTGGA
*
549039 GGGAAAATATTAAAAAAAAAATTTGGA
1 GGCAAAATATT--AAAAAAAATTTGGA
549066 GG
1 GG
549068 GGGGAGGGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 9 0.36
27 16 0.64
ACGTcount: A:0.54, C:0.02, G:0.20, T:0.24
Consensus pattern (25 bp):
GGCAAAATATTAAAAAAAATTTGGA
Found at i:549138 original size:30 final size:31
Alignment explanation
Indices: 549099--549158 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
549089 GGAGGTGGGA
*
549099 TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
* *
549130 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAA
549159 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
Found at i:555844 original size:46 final size:46
Alignment explanation
Indices: 555760--556028 Score: 244
Period size: 46 Copynumber: 5.6 Consensus size: 46
555750 TTTGAGTACT
* *
555760 TCTGATCAAGTGACAAAGTGATAAGTGGT-AGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGATAAG-TATAGCTACACTTA
*
555806 TCTGATCAAGTGAC-AAGTGGA-AAGTGATAAGTAATAGCTTCGGCTATACTTA
1 TCTGATCAAGTGACAAAGT-GATAAGTGATAAGT-ATA------GCTACACTTA
* *
555858 TCTGATCAAGTGACAAAGTGATAAGTGATAACT-TCGGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGATAAGTAT-AGCTACACTTA
* *
555904 TCTGATCAAGTGAC-AAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGATAAGT-ATA------GCTACACTTA
* *
555956 TCTGATCAAGAGACAAAGTGATAAGTGAT-AGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGATAAG-TATAGCTACACTTA
*
556002 TCTGATCAAGAGACAAAGTGATAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTG
556029 GCTACACTTA
Statistics
Matches: 187, Mismatches: 14, Indels: 44
0.76 0.06 0.18
Matches are distributed among these distances:
45 27 0.14
46 79 0.42
47 1 0.01
51 1 0.01
52 51 0.27
53 28 0.15
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.28
Consensus pattern (46 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAAGTATAGCTACACTTA
Found at i:555845 original size:52 final size:48
Alignment explanation
Indices: 555826--556028 Score: 256
Period size: 46 Copynumber: 4.3 Consensus size: 48
555816 TGACAAGTGG
* *
555826 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
*
555872 AAAGTGATAAGTGATAACTTCGGCTACACTTATCTGATCAAGTGACAAGTGA
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC-A---A
* *
555924 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
** *
555970 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
556016 AAAGTGATAAGTG
1 AAAGTGATAAGTG
556029 GCTACACTTA
Statistics
Matches: 142, Mismatches: 9, Indels: 12
0.87 0.06 0.07
Matches are distributed among these distances:
46 99 0.70
52 43 0.30
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.28
Consensus pattern (48 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
Found at i:555880 original size:98 final size:98
Alignment explanation
Indices: 555760--556028 Score: 448
Period size: 98 Copynumber: 2.7 Consensus size: 98
555750 TTTGAGTACT
*
555760 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
555825 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
* **
555858 TCTGATCAAGTGACAAAGTGATAAGTGATAACTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
555923 AAAAGTGATAAGTGATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
* *
555956 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGAC-AAGT
*
556021 GATAAGTG
65 GAAAAGTG
556029 GCTACACTTA
Statistics
Matches: 158, Mismatches: 12, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
98 147 0.93
99 11 0.07
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.28
Consensus pattern (98 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
Found at i:556036 original size:37 final size:37
Alignment explanation
Indices: 555992--556137 Score: 235
Period size: 37 Copynumber: 4.0 Consensus size: 37
555982 GATAGCTTTA
*
555992 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
556029 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
556066 GCTACACTTATCTGATCAAGAAACAAAGTGAT-AGTTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAG-TG
**
556103 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
556138 ATCATACGTA
Statistics
Matches: 104, Mismatches: 3, Indels: 6
0.92 0.03 0.05
Matches are distributed among these distances:
35 9 0.09
36 8 0.08
37 87 0.84
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:557453 original size:49 final size:49
Alignment explanation
Indices: 557392--557535 Score: 216
Period size: 49 Copynumber: 2.9 Consensus size: 49
557382 ATGTGAACAT
* *
557392 GTGATTATGTGATTCCGTGTAAGACCATAGCTGGGCTGTGGCATCGGTAA
1 GTGA-TATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
* *
557442 GTGATATGTGATTTCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAT
1 GTGATATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
* * *
557491 GTGATTTGTGATTACGTGTAAGACCATAGTTGGACTATGGCATCG
1 GTGATATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATCG
557536 AGAAAACGAA
Statistics
Matches: 87, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
49 83 0.95
50 4 0.05
ACGTcount: A:0.23, C:0.15, G:0.31, T:0.32
Consensus pattern (49 bp):
GTGATATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
Found at i:560742 original size:46 final size:46
Alignment explanation
Indices: 560658--560926 Score: 244
Period size: 46 Copynumber: 5.6 Consensus size: 46
560648 TTTGAGTACT
* *
560658 TCTGATCAAGTGACAAAGTGATAAGTGGT-AGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGATAAG-TATAGCTACACTTA
*
560704 TCTGATCAAGTGAC-AAGTGGA-AAGTGATAAGTAATAGCTTCGGCTATACTTA
1 TCTGATCAAGTGACAAAGT-GATAAGTGATAAGT-ATA------GCTACACTTA
* *
560756 TCTGATCAAGTGACAAAGTGATAAGTGATAACT-TCGGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGATAAGTAT-AGCTACACTTA
* *
560802 TCTGATCAAGTGAC-AAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGATAAGT-ATA------GCTACACTTA
* *
560854 TCTGATCAAGAGACAAAGTGATAAGTGAT-AGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGATAAG-TATAGCTACACTTA
*
560900 TCTGATCAAGAGACAAAGTGATAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTG
560927 GCTACACTTA
Statistics
Matches: 187, Mismatches: 14, Indels: 44
0.76 0.06 0.18
Matches are distributed among these distances:
45 27 0.14
46 79 0.42
47 1 0.01
51 1 0.01
52 51 0.27
53 28 0.15
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.28
Consensus pattern (46 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAAGTATAGCTACACTTA
Found at i:560743 original size:52 final size:48
Alignment explanation
Indices: 560724--560926 Score: 256
Period size: 46 Copynumber: 4.3 Consensus size: 48
560714 TGACAAGTGG
* *
560724 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
*
560770 AAAGTGATAAGTGATAACTTCGGCTACACTTATCTGATCAAGTGACAAGTGA
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC-A---A
* *
560822 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
** *
560868 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
560914 AAAGTGATAAGTG
1 AAAGTGATAAGTG
560927 GCTACACTTA
Statistics
Matches: 142, Mismatches: 9, Indels: 12
0.87 0.06 0.07
Matches are distributed among these distances:
46 99 0.70
52 43 0.30
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.28
Consensus pattern (48 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
Found at i:560778 original size:98 final size:98
Alignment explanation
Indices: 560658--560926 Score: 448
Period size: 98 Copynumber: 2.7 Consensus size: 98
560648 TTTGAGTACT
*
560658 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
560723 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
* **
560756 TCTGATCAAGTGACAAAGTGATAAGTGATAACTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
560821 AAAAGTGATAAGTGATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
* *
560854 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGAC-AAGT
*
560919 GATAAGTG
65 GAAAAGTG
560927 GCTACACTTA
Statistics
Matches: 158, Mismatches: 12, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
98 147 0.93
99 11 0.07
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.28
Consensus pattern (98 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
Found at i:560934 original size:37 final size:37
Alignment explanation
Indices: 560890--561035 Score: 235
Period size: 37 Copynumber: 4.0 Consensus size: 37
560880 GATAGCTTTA
*
560890 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
560927 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
560964 GCTACACTTATCTGATCAAGAAACAAAGTGAT-AGTTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAG-TG
**
561001 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
561036 ATCATACGTA
Statistics
Matches: 104, Mismatches: 3, Indels: 6
0.92 0.03 0.05
Matches are distributed among these distances:
35 9 0.09
36 8 0.08
37 87 0.84
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:562350 original size:49 final size:49
Alignment explanation
Indices: 562289--562432 Score: 216
Period size: 49 Copynumber: 2.9 Consensus size: 49
562279 ATGTGAACAT
* *
562289 GTGATTATGTGATTCCGTGTAAGACCATAGCTGGGCTGTGGCATCGGTAA
1 GTGA-TATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
* *
562339 GTGATATGTGATTTCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAT
1 GTGATATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
* * *
562388 GTGATTTGTGATTACGTGTAAGACCATAGTTGGACTATGGCATCG
1 GTGATATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATCG
562433 AGAAAACGAA
Statistics
Matches: 87, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
49 83 0.95
50 4 0.05
ACGTcount: A:0.23, C:0.15, G:0.31, T:0.32
Consensus pattern (49 bp):
GTGATATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
Found at i:565637 original size:46 final size:46
Alignment explanation
Indices: 565553--565821 Score: 244
Period size: 46 Copynumber: 5.6 Consensus size: 46
565543 TTTGAGTACT
* *
565553 TCTGATCAAGTGACAAAGTGATAAGTGGT-AGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGATAAG-TATAGCTACACTTA
*
565599 TCTGATCAAGTGAC-AAGTGGA-AAGTGATAAGTAATAGCTTCGGCTATACTTA
1 TCTGATCAAGTGACAAAGT-GATAAGTGATAAGT-ATA------GCTACACTTA
* *
565651 TCTGATCAAGTGACAAAGTGATAAGTGATAACT-TCGGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGATAAGTAT-AGCTACACTTA
* *
565697 TCTGATCAAGTGAC-AAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGATAAGT-ATA------GCTACACTTA
* *
565749 TCTGATCAAGAGACAAAGTGATAAGTGAT-AGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGATAAG-TATAGCTACACTTA
*
565795 TCTGATCAAGAGACAAAGTGATAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTG
565822 GCTACACTTA
Statistics
Matches: 187, Mismatches: 14, Indels: 44
0.76 0.06 0.18
Matches are distributed among these distances:
45 27 0.14
46 79 0.42
47 1 0.01
51 1 0.01
52 51 0.27
53 28 0.15
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.28
Consensus pattern (46 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAAGTATAGCTACACTTA
Found at i:565638 original size:52 final size:48
Alignment explanation
Indices: 565619--565821 Score: 256
Period size: 46 Copynumber: 4.3 Consensus size: 48
565609 TGACAAGTGG
* *
565619 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
*
565665 AAAGTGATAAGTGATAACTTCGGCTACACTTATCTGATCAAGTGACAAGTGA
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC-A---A
* *
565717 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
** *
565763 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
565809 AAAGTGATAAGTG
1 AAAGTGATAAGTG
565822 GCTACACTTA
Statistics
Matches: 142, Mismatches: 9, Indels: 12
0.87 0.06 0.07
Matches are distributed among these distances:
46 99 0.70
52 43 0.30
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.28
Consensus pattern (48 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
Found at i:565673 original size:98 final size:98
Alignment explanation
Indices: 565553--565821 Score: 448
Period size: 98 Copynumber: 2.7 Consensus size: 98
565543 TTTGAGTACT
*
565553 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
565618 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
* **
565651 TCTGATCAAGTGACAAAGTGATAAGTGATAACTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
565716 AAAAGTGATAAGTGATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
* *
565749 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGAC-AAGT
*
565814 GATAAGTG
65 GAAAAGTG
565822 GCTACACTTA
Statistics
Matches: 158, Mismatches: 12, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
98 147 0.93
99 11 0.07
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.28
Consensus pattern (98 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
Found at i:565829 original size:37 final size:37
Alignment explanation
Indices: 565785--565930 Score: 235
Period size: 37 Copynumber: 4.0 Consensus size: 37
565775 GATAGCTTTA
*
565785 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
565822 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
565859 GCTACACTTATCTGATCAAGAAACAAAGTGAT-AGTTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAG-TG
**
565896 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
565931 ATCATACGTA
Statistics
Matches: 104, Mismatches: 3, Indels: 6
0.92 0.03 0.05
Matches are distributed among these distances:
35 9 0.09
36 8 0.08
37 87 0.84
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:576846 original size:16 final size:17
Alignment explanation
Indices: 576823--576864 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
576813 ATCAAGCTAC
576823 TCAAGCTCGAATTCA-AT
1 TCAAGCTCG-ATTCATAT
576840 T-AAGCTCG-TTCATAT
1 TCAAGCTCGATTCATAT
576855 TCAAGCTCGA
1 TCAAGCTCGA
576865 GCGTATTCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 4 0.18
15 3 0.14
16 14 0.64
17 1 0.05
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.31
Consensus pattern (17 bp):
TCAAGCTCGATTCATAT
Found at i:577234 original size:80 final size:80
Alignment explanation
Indices: 577140--577301 Score: 324
Period size: 80 Copynumber: 2.0 Consensus size: 80
577130 GAGCTAAATG
577140 TTGGTTATGTATGTGTACCTATAACATGGAGGACTTGACTATGGCAAAGACAGTGTTGATAAATT
1 TTGGTTATGTATGTGTACCTATAACATGGAGGACTTGACTATGGCAAAGACAGTGTTGATAAATT
577205 AGTAGTAGTGTTATT
66 AGTAGTAGTGTTATT
577220 TTGGTTATGTATGTGTACCTATAACATGGAGGACTTGACTATGGCAAAGACAGTGTTGATAAATT
1 TTGGTTATGTATGTGTACCTATAACATGGAGGACTTGACTATGGCAAAGACAGTGTTGATAAATT
577285 AGTAGTAGTGTTATT
66 AGTAGTAGTGTTATT
577300 TT
1 TT
577302 TTTAACGCGT
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
80 82 1.00
ACGTcount: A:0.30, C:0.09, G:0.25, T:0.37
Consensus pattern (80 bp):
TTGGTTATGTATGTGTACCTATAACATGGAGGACTTGACTATGGCAAAGACAGTGTTGATAAATT
AGTAGTAGTGTTATT
Found at i:581969 original size:30 final size:30
Alignment explanation
Indices: 581943--582017 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 30
581933 ATAATAATTT
581943 AGTAATATT-ATT-ATATGATAGTAATAAA
1 AGTAATATTAATTAATATGATAGTAATAAA
* *
581971 AGTAATGTTAATTAATATGATAGTATATTAA
1 AGTAATATTAATTAATATGATAGTA-ATAAA
*
582002 TGTGAA-ATTAATTAAT
1 AGT-AATATTAATTAAT
582018 TTAGTTATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
28 8 0.21
29 3 0.08
30 11 0.28
31 15 0.38
32 2 0.05
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.41
Consensus pattern (30 bp):
AGTAATATTAATTAATATGATAGTAATAAA
Found at i:582078 original size:15 final size:16
Alignment explanation
Indices: 582055--582087 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
582045 TAAATAAAAT
582055 ATTATTAATTTATAAA
1 ATTATTAATTTATAAA
582071 ATTA-TAATTTATAAA
1 ATTATTAATTTATAAA
582086 AT
1 AT
582088 CATTTAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
ATTATTAATTTATAAA
Found at i:582897 original size:11 final size:9
Alignment explanation
Indices: 582870--582914 Score: 58
Period size: 8 Copynumber: 5.0 Consensus size: 9
582860 TGATTGATAT
582870 AATATTTT-
1 AATATTTTA
582878 AATATTTTA
1 AATATTTTA
582887 AATTAATTTTA
1 AA-T-ATTTTA
582898 AATATTTTA
1 AATATTTTA
582907 AA-ATTTTA
1 AATATTTTA
582915 TAGTTGCATA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
8 14 0.41
9 10 0.29
10 2 0.06
11 8 0.24
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
AATATTTTA
Found at i:585831 original size:238 final size:239
Alignment explanation
Indices: 585409--585962 Score: 740
Period size: 239 Copynumber: 2.3 Consensus size: 239
585399 TTTTACACCA
* * * * *
585409 ATATTCAATAGTTCGATGGGGGAATATCAGGTTCATTCATACCAAACATGTCCAAAAGAAAAGCA
1 ATATTCAACAGTTTGAAGGGGGAATATCAGGTTCATTTATACCAAACATATCCAAAAGAAAAGCA
* * *
585474 CATTAGAAGTATGTGTTAAATCTCATAACGGTCAAGCCATGTCAACGAGCCTAGATGCTTGGAAC
66 CATTAGAAGTATGCGTTAAATCTCATAACGGTAAAGCCATGTCAACGAGCCTAGATGCTCGGAAC
* * * * *
585539 ATGTTTTCGTTGAAGCATCACATTGAGTTTATTGTCCATAGATTATAGCTTCTAAGGGTAA-TCA
131 AAGTTTTCGTTGAAGCATCACATCGAGTTTATTGTCCATAGATCATACCTTCTAAGAGTAATTCA
*
585603 CAACAAATATCACATTTAACTAGAACCCACGTCAGATTA-TGAAC
196 CAACAAATATCACATTTAACTAGAACCCACGTCAGACTAGT-AAC
* * ** * *
585647 ATATTCAACAGTTTGAAGGGGGAATATCAGGTTCATTTATTCCGAACATATCTGAAAGAGAAGTA
1 ATATTCAACAGTTTGAAGGGGGAATATCAGGTTCATTTATACCAAACATATCCAAAAGAAAAGCA
* *
585712 CATTAGAAGTATGCGTTAGAATCTTATAACGGTAAAGCCATGTCAATGAGCCTAGATGCTCGGAA
66 CATTAGAAGTATGCGTTA-AATCTCATAACGGTAAAGCCATGTCAACGAGCCTAGATGCTCGG-A
*
585777 ACAAGTTGTT-GTTGAAGCA-C-CATCGAGTTTATTGTCCATGGATCATACCTTCTAAGAGTAAT
129 ACAAGTT-TTCGTTGAAGCATCACATCGAGTTTATTGTCCATAGATCATACCTTCTAAGAGTAAT
** * * *
585839 TCACAGGAAATATCGCATTTAACTAGAACCCACTTCGGACTAGTAAC
193 TCACAACAAATATCACATTTAACTAGAACCCACGTCAGACTAGTAAC
* * * * *
585886 ATATTCAACGGTTTGAAGTGGGAATATCGGGTTCATTTATACCTAACATATCCAAAAGATAAGCA
1 ATATTCAACAGTTTGAAGGGGGAATATCAGGTTCATTTATACCAAACATATCCAAAAGAAAAGCA
585951 CATTAGAAGTAT
66 CATTAGAAGTAT
585963 AATGGTAAAG
Statistics
Matches: 274, Mismatches: 37, Indels: 9
0.86 0.12 0.03
Matches are distributed among these distances:
238 107 0.39
239 148 0.54
240 17 0.06
241 2 0.01
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.29
Consensus pattern (239 bp):
ATATTCAACAGTTTGAAGGGGGAATATCAGGTTCATTTATACCAAACATATCCAAAAGAAAAGCA
CATTAGAAGTATGCGTTAAATCTCATAACGGTAAAGCCATGTCAACGAGCCTAGATGCTCGGAAC
AAGTTTTCGTTGAAGCATCACATCGAGTTTATTGTCCATAGATCATACCTTCTAAGAGTAATTCA
CAACAAATATCACATTTAACTAGAACCCACGTCAGACTAGTAAC
Found at i:586814 original size:30 final size:32
Alignment explanation
Indices: 586759--586834 Score: 102
Period size: 30 Copynumber: 2.4 Consensus size: 32
586749 ATGAAGACAT
*
586759 ATATATATTATATAGACAATGTCTAGGATAAAC
1 ATATATA-TATATAGACAATCTCTAGGATAAAC
*
586792 ATATATATATA-AGA-AATCTCTAGGATTAAC
1 ATATATATATATAGACAATCTCTAGGATAAAC
*
586822 CTATATATATATA
1 ATATATATATATA
586835 TGCATGTAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
30 24 0.62
31 4 0.10
32 4 0.10
33 7 0.18
ACGTcount: A:0.46, C:0.09, G:0.09, T:0.36
Consensus pattern (32 bp):
ATATATATATATAGACAATCTCTAGGATAAAC
Found at i:587155 original size:8 final size:8
Alignment explanation
Indices: 587142--587184 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
587132 AAGATACATA
*
587142 CATGCATG
1 CATGCATC
*
587150 CATGCATA
1 CATGCATC
*
587158 CATCCATC
1 CATGCATC
*
587166 CATTCATC
1 CATGCATC
587174 CATGCATC
1 CATGCATC
587182 CAT
1 CAT
587185 CCATTCATAC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
8 30 1.00
ACGTcount: A:0.28, C:0.35, G:0.09, T:0.28
Consensus pattern (8 bp):
CATGCATC
Found at i:589128 original size:12 final size:12
Alignment explanation
Indices: 589113--589138 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
589103 AGAATGCAAG
589113 TTAGGTATAAAA
1 TTAGGTATAAAA
589125 TTAGGTATAAAA
1 TTAGGTATAAAA
589137 TT
1 TT
589139 GCAGCGCAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.00, G:0.15, T:0.38
Consensus pattern (12 bp):
TTAGGTATAAAA
Found at i:600592 original size:96 final size:95
Alignment explanation
Indices: 600468--600674 Score: 281
Period size: 96 Copynumber: 2.2 Consensus size: 95
600458 GGTTTCACCT
* * *
600468 CCTTCAAAAGCGGTGGTCTCGATGTTCGAAGCAACTGTGGAACTTAGAACATTGATTT-GATCAT
1 CCTTCAAAAGCGGT-GACTCGATGTTCGAAGCAACTGTAGAACTTAGAACACT-ATTTAGATCAT
*
600532 AAAAATTTTCCTCCTGCGTGAAGAACTGACCA
64 AAAAATCTTCCTCCTGCGTGAAGAACTGACCA
* * *
600564 CCTTCAAAAGCGGTGACGTCGATGTTCGAAGCAACTGTAGAATTTAGAACACTATTTAGGTTATA
1 CCTTCAAAAGCGGTGAC-TCGATGTTCGAAGCAACTGTAGAACTTAGAACACTATTTAGATCATA
* *
600629 AATATCTTCCTCCTGCGTGAAGAATTGACCA
65 AAAATCTTCCTCCTGCGTGAAGAACTGACCA
* *
600660 ACTTCATAAGCGGTG
1 CCTTCAAAAGCGGTG
600675 GCGCCGCCAT
Statistics
Matches: 98, Mismatches: 11, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
95 6 0.06
96 92 0.94
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (95 bp):
CCTTCAAAAGCGGTGACTCGATGTTCGAAGCAACTGTAGAACTTAGAACACTATTTAGATCATAA
AAATCTTCCTCCTGCGTGAAGAACTGACCA
Found at i:601441 original size:19 final size:20
Alignment explanation
Indices: 601414--601464 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
601404 TAAGATCATA
* *
601414 TATTAATATAAATATTTA-T
1 TATTTATATAAATATTAATT
601433 TATTTATATAAAATATTAATT
1 TATTTATAT-AAATATTAATT
*
601454 TTTTTATATAA
1 TATTTATATAA
601465 TAAATATTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 8 0.30
20 10 0.37
21 9 0.33
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TATTTATATAAATATTAATT
Found at i:601466 original size:19 final size:20
Alignment explanation
Indices: 601414--601481 Score: 57
Period size: 19 Copynumber: 3.3 Consensus size: 20
601404 TAAGATCATA
* *
601414 TATTAATATA-AATATTTAT
1 TATTTATATATAATATTAAT
*
601433 TATTTATATAAAATATTAATT
1 TATTTATATATAATATTAA-T
*
601454 TTTTTATATAATAAATATTAAT
1 TATTTATAT-AT-AATATTAAT
*
601476 TCTTTA
1 TATTTA
601482 ATAAAAATTT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
19 9 0.22
20 7 0.17
21 9 0.22
22 7 0.17
23 8 0.20
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.54
Consensus pattern (20 bp):
TATTTATATATAATATTAAT
Found at i:601469 original size:23 final size:22
Alignment explanation
Indices: 601419--601476 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 22
601409 TCATATATTA
*
601419 ATATAAATATTTA-TTATTTAT
1 ATATAAATATTAATTTATTTAT
*
601440 ATA-AAATATTAATTTTTTTAT
1 ATATAAATATTAATTTATTTAT
601461 ATAATAAATATTAATT
1 AT-ATAAATATTAATT
601477 CTTTAATAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 8 0.25
21 12 0.38
22 1 0.03
23 11 0.34
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
ATATAAATATTAATTTATTTAT
Found at i:601561 original size:40 final size:41
Alignment explanation
Indices: 601520--601599 Score: 124
Period size: 43 Copynumber: 1.9 Consensus size: 41
601510 TTGAAGTGAA
601520 TTTTTTATTTAGGAGGAATCCCTATAACACTAGGAGAGAATTT
1 TTTTTTATTTAGGAGGAATCCCTATAACACTAGGAGAGAA--T
* *
601563 TTTTTTATTTAGGATGAATCCCTATAATACTAGGAGA
1 TTTTTTATTTAGGAGGAATCCCTATAACACTAGGAGA
601600 TAATATACAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (41 bp):
TTTTTTATTTAGGAGGAATCCCTATAACACTAGGAGAGAAT
Found at i:604270 original size:12 final size:12
Alignment explanation
Indices: 604253--604300 Score: 69
Period size: 12 Copynumber: 4.0 Consensus size: 12
604243 CACATTTCGA
*
604253 CGGTGGTCTTGG
1 CGGTGGTTTTGG
604265 CGGTGGTTTTGG
1 CGGTGGTTTTGG
604277 CGGTGGTTTTGG
1 CGGTGGTTTTGG
* *
604289 TGTTGGTTTTGG
1 CGGTGGTTTTGG
604301 TTTTGGTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.00, C:0.08, G:0.48, T:0.44
Consensus pattern (12 bp):
CGGTGGTTTTGG
Found at i:604301 original size:12 final size:12
Alignment explanation
Indices: 604280--604334 Score: 101
Period size: 12 Copynumber: 4.6 Consensus size: 12
604270 GTTTTGGCGG
*
604280 TGGTTTTGGTGT
1 TGGTTTTGGTTT
604292 TGGTTTTGGTTT
1 TGGTTTTGGTTT
604304 TGGTTTTGGTTT
1 TGGTTTTGGTTT
604316 TGGTTTTGGTTT
1 TGGTTTTGGTTT
604328 TGGTTTT
1 TGGTTTT
604335 CGTATTTGTG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
12 42 1.00
ACGTcount: A:0.00, C:0.00, G:0.35, T:0.65
Consensus pattern (12 bp):
TGGTTTTGGTTT
Found at i:604301 original size:18 final size:18
Alignment explanation
Indices: 604280--604334 Score: 101
Period size: 18 Copynumber: 3.1 Consensus size: 18
604270 GTTTTGGCGG
*
604280 TGGTTTTGGTGTTGGTTT
1 TGGTTTTGGTTTTGGTTT
604298 TGGTTTTGGTTTTGGTTT
1 TGGTTTTGGTTTTGGTTT
604316 TGGTTTTGGTTTTGGTTT
1 TGGTTTTGGTTTTGGTTT
604334 T
1 T
604335 CGTATTTGTG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.00, C:0.00, G:0.35, T:0.65
Consensus pattern (18 bp):
TGGTTTTGGTTTTGGTTT
Found at i:604350 original size:3 final size:3
Alignment explanation
Indices: 604342--604381 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
604332 TTTCGTATTT
604342 GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG G
1 GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG G
604382 AGATGCTGGA
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:0.00, C:0.00, G:0.68, T:0.33
Consensus pattern (3 bp):
GTG
Found at i:605137 original size:19 final size:19
Alignment explanation
Indices: 605093--605139 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 19
605083 TTAAATATTT
605093 TTTATAAAAGTACAAAAGA
1 TTTATAAAAGTACAAAAGA
605112 TTGTATAAAA-TACATACAA-A
1 TT-TATAAAAGTACA-A-AAGA
605132 TTTATAAA
1 TTTATAAA
605140 TGAATGAGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
19 12 0.48
20 11 0.44
21 2 0.08
ACGTcount: A:0.55, C:0.06, G:0.06, T:0.32
Consensus pattern (19 bp):
TTTATAAAAGTACAAAAGA
Found at i:608067 original size:27 final size:27
Alignment explanation
Indices: 608030--608101 Score: 110
Period size: 27 Copynumber: 2.7 Consensus size: 27
608020 AAAAATAAAA
608030 ATTTATCAAAATATTATAA-CTTTTTTT
1 ATTTATCAAAATA-TATAATCTTTTTTT
* *
608057 ATTTACCAAAATATATAATTTTTTTTT
1 ATTTATCAAAATATATAATCTTTTTTT
608084 ATTTATCAAAATATATAA
1 ATTTATCAAAATATATAA
608102 AAAAACCAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
26 5 0.12
27 36 0.88
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (27 bp):
ATTTATCAAAATATATAATCTTTTTTT
Found at i:608394 original size:19 final size:21
Alignment explanation
Indices: 608356--608394 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
608346 AATAATTGAT
*
608356 TATATTGTTGTTATTATTTTG
1 TATATTGTTGTTAATATTTTG
608377 TATATT-TTG-TAATATTTT
1 TATATTGTTGTTAATATTTT
608395 TTGTTTTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 3 0.18
21 6 0.35
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.67
Consensus pattern (21 bp):
TATATTGTTGTTAATATTTTG
Found at i:608473 original size:3 final size:3
Alignment explanation
Indices: 608467--608495 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
608457 ATTATTATTA
608467 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
608496 AGTATTAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:608713 original size:26 final size:26
Alignment explanation
Indices: 608684--608736 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
608674 TTTTAGTGTG
*
608684 TATTATTTTGAGTATAAAATTATTAA
1 TATTATTTTGAGTATAAAATTAATAA
608710 TATTATTTTGAGTATAAAATTAATAA
1 TATTATTTTGAGTATAAAATTAATAA
608736 T
1 T
608737 TTTAGTGTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49
Consensus pattern (26 bp):
TATTATTTTGAGTATAAAATTAATAA
Found at i:609984 original size:11 final size:11
Alignment explanation
Indices: 609965--610056 Score: 63
Period size: 11 Copynumber: 8.9 Consensus size: 11
609955 ACTTTTTTAA
*
609965 TTTTAAAATAT
1 TTTTTAAATAT
*
609976 TTTTTAAATAC
1 TTTTTAAATAT
*
609987 TTTTTAAAAAT
1 TTTTTAAATAT
609998 TTTTT--A-A-
1 TTTTTAAATAT
*
610005 TTTTAAAATAT
1 TTTTTAAATAT
*
610016 TTTTAAAATACT
1 TTTTTAAATA-T
*
610028 TTTTT-TA-AT
1 TTTTTAAATAT
610037 TTTTTAAA-AT
1 TTTTTAAATAT
*
610047 TTTTAAAATA
1 TTTTTAAATA
610057 AAAATGGGCC
Statistics
Matches: 65, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
7 4 0.06
8 1 0.02
9 8 0.12
10 12 0.18
11 35 0.54
12 5 0.08
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (11 bp):
TTTTTAAATAT
Found at i:610035 original size:31 final size:30
Alignment explanation
Indices: 609974--610056 Score: 109
Period size: 31 Copynumber: 2.8 Consensus size: 30
609964 ATTTTAAAAT
609974 ATTTTTTAAATACTTTTTAAAA-ATTTTTTA
1 ATTTTTTAAATA-TTTTTAAAATATTTTTTA
*
610004 A-TTTTAAAATATTTTTAAAATACTTTTTTTA
1 ATTTTTTAAATATTTTTAAAATA--TTTTTTA
610035 ATTTTTTAAA-ATTTTTAAAATA
1 ATTTTTTAAATATTTTTAAAATA
610057 AAAATGGGCC
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
28 9 0.19
29 10 0.21
30 1 0.02
31 20 0.43
32 7 0.15
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (30 bp):
ATTTTTTAAATATTTTTAAAATATTTTTTA
Found at i:614671 original size:158 final size:160
Alignment explanation
Indices: 614226--614674 Score: 393
Period size: 160 Copynumber: 2.8 Consensus size: 160
614216 AAGTTGAAAA
* *
614226 AAAAGTTAGTAAATAAATCTTACTTCGGCCATTTATTCGTATTTTTTTCTTCGCATTTTATTACT
1 AAAAGTTAGT-AATAACTCTTACTTCTGCCATTTATTCGTATTTTTTTC-TCGCATTTTATTACT
**
614291 TTAAAAAAAATCAT-AATTTCTAATTTTATAATTTTACATTATTTCAGTGCATAATGTTTGAAAT
64 TTAAAAAAAATCATAAATTAGT-ATTTTATAATTTTACATTATTTCAGTGCATAATGTTTGAAA-
* * *
614355 TTATTACTCTAGTGTGTTATTTAAATTAATTTGGTGT
127 -TATTACTCTAGTGTATTATTT-AATGAATTT-GTAT
* ** * * *
614392 AAAA---A--AATAACCCTTACACCTGCCCTTTACTCGTATTATTTTCTCG-ATTTTTATTACTT
1 AAAAGTTAGTAATAACTCTTACTTCTGCCATTTATTCGTATTTTTTTCTCGCA-TTTTATTACTT
* * * * ** * * ** *
614451 TAAATAAAATTATATTATTCTCGTATTTTATTGTTTTATATTATTTCAGTACATTTTCTTTGAAA
65 TAAAAAAAATCATA--AAT-TAGTATTTTATAATTTTACATTATTTCAGTGCATAATGTTTGAAA
* * *
614516 TATT-TTGTA-T-TAATTATTT-CTGAATTT-TAT
127 TATTACTCTAGTGT-ATTATTTAATGAATTTGTAT
* *
614546 AAAAGTTAGTAGTACACTCTTACTTCTGCCATTTGTTCGTATTTTTTTCTCCGCATTTTATTAC-
1 AAAAGTTAGTAATA-ACTCTTACTTCTGCCATTTATTCGTATTTTTTTCT-CGCATTTTATTACT
* *
614610 TTAAAAAAAATCATAAACTTAGTCTTTTATAATTTTACATTATTTCAGTGCATCATGTTTGAAAT
64 TTAAAAAAAATCATAAA-TTAGTATTTTATAATTTTACATTATTTCAGTGCATAATGTTTGAAAT
614675 TTATTAATTT
Statistics
Matches: 222, Mismatches: 46, Indels: 38
0.73 0.15 0.12
Matches are distributed among these distances:
154 6 0.03
156 6 0.03
157 2 0.01
158 46 0.21
159 32 0.14
160 75 0.34
161 11 0.05
162 37 0.17
163 3 0.01
166 4 0.02
ACGTcount: A:0.31, C:0.13, G:0.08, T:0.48
Consensus pattern (160 bp):
AAAAGTTAGTAATAACTCTTACTTCTGCCATTTATTCGTATTTTTTTCTCGCATTTTATTACTTT
AAAAAAAATCATAAATTAGTATTTTATAATTTTACATTATTTCAGTGCATAATGTTTGAAATATT
ACTCTAGTGTATTATTTAATGAATTTGTAT
Found at i:615479 original size:17 final size:17
Alignment explanation
Indices: 615423--615480 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
615413 AACTATAATG
*
615423 AAATAACATAAATTT-T
1 AAATAAAATAAATTTAT
* * *
615439 AAAT-ACACAAATATTAC
1 AAATAAAATAAAT-TTAT
615456 AAA-AAAATAAATTTAT
1 AAATAAAATAAATTTAT
615472 AAATAAAAT
1 AAATAAAAT
615481 TACCTTTTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
15 7 0.21
16 12 0.36
17 14 0.42
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (17 bp):
AAATAAAATAAATTTAT
Found at i:615544 original size:29 final size:28
Alignment explanation
Indices: 615512--615630 Score: 102
Period size: 29 Copynumber: 4.1 Consensus size: 28
615502 CCTTCCTTCC
615512 CTCTTCTTCTTCTTCTTTTTTTTTCTCTT
1 CTCTTCTTCTT-TTCTTTTTTTTTCTCTT
* *
615541 CTCTTCTCCTTTCCTTTTCTTTCCTTCT-TT
1 CTCTTCTTCTTTTCTTTT-TTT--TTCTCTT
* *
615571 CT-TTCTT-TTTTCTTCTCTTTTC-CTT
1 CTCTTCTTCTTTTCTTTTTTTTTCTCTT
615596 CTCTTCTTCTTCTTTCTTTCTTTTTTTCTCTT
1 CTCTTCTTC-T-TTTC-TT-TTTTTTTCTCTT
615628 CTC
1 CTC
615631 CTTTCCCTTT
Statistics
Matches: 71, Mismatches: 8, Indels: 19
0.72 0.08 0.19
Matches are distributed among these distances:
25 7 0.10
26 5 0.07
27 2 0.03
28 14 0.20
29 21 0.30
30 6 0.08
31 10 0.14
32 6 0.08
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (28 bp):
CTCTTCTTCTTTTCTTTTTTTTTCTCTT
Found at i:615568 original size:44 final size:43
Alignment explanation
Indices: 615520--615651 Score: 150
Period size: 44 Copynumber: 3.1 Consensus size: 43
615510 CCCTCTTCTT
615520 CTTCTTCTTTTTTTTTCTCTTCTCTTCTCCTTTCCTTTTCTTTC
1 CTTCTTCTTTTTTTTT-TCTTCTCTTCTCCTTTCCTTTTCTTTC
* * *
615564 CTTCTTTCTTTCTTTTTTCTTCTCTTTTCC-TT-CTCTTC-TT-
1 CTTC-TTCTTTTTTTTTTCTTCTCTTCTCCTTTCCTTTTCTTTC
* *
615604 CTTCTT-TCTTTCTTTTT-TTCTCTTCTCCTTTCCCTTTCTTTC
1 CTTCTTCT-TTTTTTTTTCTTCTCTTCTCCTTTCCTTTTCTTTC
615646 CTTCTT
1 CTTCTT
615652 TTTCTTTCTT
Statistics
Matches: 74, Mismatches: 8, Indels: 14
0.77 0.08 0.15
Matches are distributed among these distances:
38 11 0.15
39 11 0.15
40 8 0.11
41 4 0.05
42 11 0.15
43 2 0.03
44 16 0.22
45 11 0.15
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (43 bp):
CTTCTTCTTTTTTTTTTCTTCTCTTCTCCTTTCCTTTTCTTTC
Found at i:615572 original size:4 final size:4
Alignment explanation
Indices: 615556--615705 Score: 105
Period size: 4 Copynumber: 37.0 Consensus size: 4
615546 CTCCTTTCCT
* *
615556 TTTC TTTC CTTC TTTC TTTC TTT- TTTC TTCTC TTTTC CTTC TCTTC -TTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT-TC -TTTC TTTC T-TTC TTTC
* * *
615605 -TTC TTTC TTTC TTTT TTTC TCTTC -TCC TTTCCC TTTC TTTC CTTC -TT-
1 TTTC TTTC TTTC TTTC TTTC T-TTC TTTC TTT--C TTTC TTTC TTTC TTTC
* * * *
615652 TTTC TTTC TTCCC TCTCC TTTC TTCC TTTC TTTC TCTC TTTC TTTC TTTC
1 TTTC TTTC TT-TC T-TTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
615702 TTTC
1 TTTC
615706 CCTTTCCTTC
Statistics
Matches: 118, Mismatches: 15, Indels: 26
0.74 0.09 0.16
Matches are distributed among these distances:
3 15 0.13
4 81 0.69
5 15 0.13
6 7 0.06
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (4 bp):
TTTC
Found at i:615642 original size:82 final size:80
Alignment explanation
Indices: 615516--615714 Score: 237
Period size: 82 Copynumber: 2.5 Consensus size: 80
615506 CCTTCCCTCT
* *
615516 TCTTCTTCTTCTTT-TTT-TTTCTCTTCTCTTCTCCTTTCCTTTTCTTTCCTTCTTTCTTTCTTT
1 TCTTCTTCTTCTTTCTTTCTTT-TTTTCTCTTCTCCTTTCCCTTTCTTTCCTTC-TT-TTTCTTT
* * *
615579 -TTTCTTCTCTTTTCCTTC
63 CTTCCCTCTCCTTT-CTTC
615597 TCTTCTTCTTCTTTCTTTCTTTTTTTCTCTTCTCCTTTCCCTTTCTTTCCTTCTTTTTCTTTCTT
1 TCTTCTTCTTCTTTCTTTCTTTTTTTCTCTTCTCCTTTCCCTTTCTTTCCTTCTTTTTCTTTCTT
615662 CCCTCTCCTTTCTTC
66 CCCTCTCCTTTCTTC
* *
615677 -CTTTCTTTCTCTCTTTCTTTCTTTCTTTCCCTT-TCCTT
1 TC-TTC-TTCT-TCTTTCTTTCTTTTTTTCTCTTCTCCTT
615715 CTGCCTCCCC
Statistics
Matches: 105, Mismatches: 7, Indels: 12
0.85 0.06 0.10
Matches are distributed among these distances:
79 1 0.01
80 14 0.13
81 35 0.33
82 52 0.50
83 3 0.03
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (80 bp):
TCTTCTTCTTCTTTCTTTCTTTTTTTCTCTTCTCCTTTCCCTTTCTTTCCTTCTTTTTCTTTCTT
CCCTCTCCTTTCTTC
Found at i:615645 original size:70 final size:69
Alignment explanation
Indices: 615567--615716 Score: 171
Period size: 70 Copynumber: 2.1 Consensus size: 69
615557 TTCTTTCCTT
* * * * *
615567 CTTTCTTTCTTTTTTCTTCTCTT-TTCCTTCTCTTCTTCTT-CTTTCTTTCTTTTTTTCTCTTC-
1 CTTTCTTTCTTCTTT-TTCT-TTCTTCCCTCTCCT-TTCTTCCTTTCTTTCTCTCTTTCT-TTCT
615629 TCCTTTCC
62 TCCTTTCC
*
615637 CTTTCTTTCCTTCTTTTTCTTTCTTCCCTCTCCTTTCTTCCTTTCTTTCTCTCTTTCTTTCTTTC
1 CTTTCTTT-CTTCTTTTTCTTTCTTCCCTCTCCTTTCTTCCTTTCTTTCTCTCTTTCTTTCTTCC
615702 TTTCC
65 TTTCC
*
615707 CTTTCCTTCT
1 CTTTCTTTCT
615717 GCCTCCCCCA
Statistics
Matches: 69, Mismatches: 7, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
69 12 0.17
70 51 0.74
71 6 0.09
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (69 bp):
CTTTCTTTCTTCTTTTTCTTTCTTCCCTCTCCTTTCTTCCTTTCTTTCTCTCTTTCTTTCTTCCT
TTCC
Found at i:615656 original size:44 final size:42
Alignment explanation
Indices: 615484--615661 Score: 146
Period size: 40 Copynumber: 4.3 Consensus size: 42
615474 ATAAAATTAC
* *
615484 CTTTTT-TTCCTTTTTTTTCCT-TCC-TTCCCTCTTC-TTCTT
1 CTTTTTCTTTCTTTTTTTTCTTCTCCTTTCCCT-TTCTTTCTT
* *
615523 CTTCTTT-TTT-TTTCTCTTCTCTTCTCCTTTCCTTTTCTTTC--
1 CTT-TTTCTTTCTTT-T-TTTTCTTCTCCTTTCCCTTTCTTTCTT
*
615564 CTTCTTTCTTTC--TTTTTTCTTCT-CTTTTCC-TTCTCTTCTT
1 CTT-TTTCTTTCTTTTTTTTCTTCTCCTTTCCCTTTCT-TTCTT
615604 CTTCTTTCTTTCTTTTTTTCTCTTCTCCTTTCCCTTTCTTTCCTT
1 CTT-TTTCTTTCTTTTTTT-TCTTCTCCTTTCCCTTTCTTT-CTT
615649 CTTTTTCTTTCTT
1 CTTTTTCTTTCTT
615662 CCCTCTCCTT
Statistics
Matches: 114, Mismatches: 8, Indels: 29
0.75 0.05 0.19
Matches are distributed among these distances:
37 4 0.04
38 8 0.07
39 14 0.12
40 19 0.17
41 13 0.11
42 14 0.12
43 14 0.12
44 18 0.16
45 10 0.09
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (42 bp):
CTTTTTCTTTCTTTTTTTTCTTCTCCTTTCCCTTTCTTTCTT
Found at i:615657 original size:48 final size:47
Alignment explanation
Indices: 615502--615661 Score: 110
Period size: 44 Copynumber: 3.5 Consensus size: 47
615492 CCTTTTTTTT
* * * *
615502 CCTTCCTTCCCTCTTCTTC-TTC-TTCTTTTTTTTTCTCTTCTC-TT-
1 CCTTCTTTCCTTCTTTTTCTTTCTTTC-TTTCTTTTCTCTTCTCTTTC
* * * *
615546 -CTCCTTTCCTT-TTCTTTCCTTCTTTCTTTCTTTTTTCTTCTCTTTT
1 CCTTCTTTCCTTCTT-TTTCTTTCTTTCTTTCTTTTCTCTTCTCTTTC
615592 CCTTCTCTT-CTTCTTCTTTCTTTC--T--TT-TTTTCTCTTCTCCTTTC
1 CCTTCT-TTCCTTCTT-TTTCTTTCTTTCTTTCTTTTCTCTTCT-CTTTC
615636 CCTTTCTTTCCTTCTTTTTCTTTCTT
1 CC-TTCTTTCCTTCTTTTTCTTTCTT
615662 CCCTCTCCTT
Statistics
Matches: 93, Mismatches: 10, Indels: 24
0.73 0.08 0.19
Matches are distributed among these distances:
42 2 0.02
43 21 0.23
44 35 0.38
45 15 0.16
46 1 0.01
47 7 0.08
48 12 0.13
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (47 bp):
CCTTCTTTCCTTCTTTTTCTTTCTTTCTTTCTTTTCTCTTCTCTTTC
Found at i:615831 original size:25 final size:27
Alignment explanation
Indices: 615802--615870 Score: 115
Period size: 25 Copynumber: 2.6 Consensus size: 27
615792 GATTTTTTTG
615802 ATATATTTTGGTAAAT-AAAAAAA-TT
1 ATATATTTTGGTAAATAAAAAAAAGTT
615827 ATATATTTTGGTAAATAAAAAAAAGTT
1 ATATATTTTGGTAAATAAAAAAAAGTT
615854 ATAATATTTTGGTAAAT
1 AT-ATATTTTGGTAAAT
615871 TTTTATTTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
25 16 0.39
26 7 0.17
27 4 0.10
28 14 0.34
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (27 bp):
ATATATTTTGGTAAATAAAAAAAAGTT
Found at i:617023 original size:6 final size:6
Alignment explanation
Indices: 617014--617042 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
617004 AAATAAAATT
617014 CTAAAA CTAAAA CTAAAA CTAAAA CTAAA
1 CTAAAA CTAAAA CTAAAA CTAAAA CTAAA
617043 GTCTAAAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.66, C:0.17, G:0.00, T:0.17
Consensus pattern (6 bp):
CTAAAA
Found at i:617115 original size:18 final size:18
Alignment explanation
Indices: 617090--617139 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
617080 GTAGTGATTC
*
617090 AATTCGGTTAATTTGGGT
1 AATTCGGTTAATTTGGAT
* *
617108 AGTTCGGTTAATTCGGAT
1 AATTCGGTTAATTTGGAT
*
617126 AATTTGGTTAATTT
1 AATTCGGTTAATTT
617140 TTAACTAAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.24, C:0.06, G:0.24, T:0.46
Consensus pattern (18 bp):
AATTCGGTTAATTTGGAT
Found at i:617139 original size:9 final size:9
Alignment explanation
Indices: 617090--617138 Score: 53
Period size: 9 Copynumber: 5.4 Consensus size: 9
617080 GTAGTGATTC
617090 AATTCGGTT
1 AATTCGGTT
* *
617099 AATTTGGGT
1 AATTCGGTT
*
617108 AGTTCGGTT
1 AATTCGGTT
*
617117 AATTCGGAT
1 AATTCGGTT
*
617126 AATTTGGTT
1 AATTCGGTT
617135 AATT
1 AATT
617139 TTTAACTAAA
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
9 31 1.00
ACGTcount: A:0.24, C:0.06, G:0.24, T:0.45
Consensus pattern (9 bp):
AATTCGGTT
Found at i:617248 original size:29 final size:29
Alignment explanation
Indices: 617200--617279 Score: 124
Period size: 29 Copynumber: 2.8 Consensus size: 29
617190 GAATTAACCG
*
617200 AAAAAATTTCGGTTCAGTTAATTTTTTTA
1 AAAAAATTTCGGTTCGGTTAATTTTTTTA
* * *
617229 AAAAAATTTTGGCTCGGTTAATTTTTTTG
1 AAAAAATTTCGGTTCGGTTAATTTTTTTA
617258 AAAAAATTTCGGTTCGGTTAAT
1 AAAAAATTTCGGTTCGGTTAAT
617280 GGTTAAAATT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.33, C:0.07, G:0.15, T:0.45
Consensus pattern (29 bp):
AAAAAATTTCGGTTCGGTTAATTTTTTTA
Found at i:619933 original size:100 final size:100
Alignment explanation
Indices: 619752--619937 Score: 248
Period size: 100 Copynumber: 1.9 Consensus size: 100
619742 ATTTATTACG
* * * * *
619752 AATTCAATGTAGGCTTTTGATTTTTAGATTGAAAAATCAGTGATTATTACTTTTTAATTAGCTAA
1 AATTCAATGTAGGCTTTTGATCTCTAGAGTGAAAAATCAGTGACTATCACTTTTTAATTAGCTAA
* *
619817 TAATCAGAGTAATAAGCAGATTTTGTTTATTCGAC
66 CAATCAAAGTAATAAGCAGATTTTGTTTATTCGAC
* *
619852 AATTGAATGTAGTCTTTTGATCTCTAGAGTGAAAAATCAGTGACTATCA-TTTGTTAATTAGCTA
1 AATTCAATGTAGGCTTTTGATCTCTAGAGTGAAAAATCAGTGACTATCACTTT-TTAATTAGCTA
* **
619916 CCAATCAAAGTGTTAAGCAGAT
65 ACAATCAAAGTAATAAGCAGAT
619938 AATTTTGTTA
Statistics
Matches: 73, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
99 3 0.04
100 70 0.96
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.39
Consensus pattern (100 bp):
AATTCAATGTAGGCTTTTGATCTCTAGAGTGAAAAATCAGTGACTATCACTTTTTAATTAGCTAA
CAATCAAAGTAATAAGCAGATTTTGTTTATTCGAC
Found at i:619951 original size:237 final size:239
Alignment explanation
Indices: 619492--619964 Score: 700
Period size: 237 Copynumber: 2.0 Consensus size: 239
619482 TCGGATTTTG
* * * *
619492 TTAATGGTAAATTTATTAGCAATTGAATGTATGTTTTTGATATTTTAGAGCGACAAATCAGTGAT
1 TTAATGGTAAATTTATTAGCAATTCAATGTAGGCTTTTGATATTTTAGAGCGAAAAATCAGTGAT
* * * *
619557 TATTACTCGTTAATTTGCCAGTAATCAAAGTGATAAGCAGATAATTTGTTTATTCCACGATTGAA
66 TATTACTCGTTAATTAGCCAATAATCAAAGTAATAAGCAGAT-ATTTGTTTATTCCACAATTGAA
* * * *
619622 TTTAGTCTTTTGATCTCTAGAGTGAAGAATCAGTGACTGTAACTTGTTAATTAGCTACCAATCAG
130 TGTAGTCTTTTGATCTCTAGAGTGAAAAATCAGTGACTATAACTTGTTAATTAGCTACCAATCAA
619687 AGTGCTAAGCAGATAATTTTGTTATTTGGGAGCTAAATTTGTGAT
195 AGTGCTAAGCAGATAATTTTGTTATTTGGGAGCTAAATTTGTGAT
* **
619732 TTAATTGTAAATTTATTA-CGAATTCAATGTAGGCTTTTGAT-TTTTAGATTGAAAAATCAGTGA
1 TTAATGGTAAATTTATTAGC-AATTCAATGTAGGCTTTTGATATTTTAGAGCGAAAAATCAGTGA
** * * *
619795 TTATTACTTTTTAATTAGCTAATAATCAGAGTAATAAGCAGAT-TTTGTTTATTCGACAATTGAA
65 TTATTACTCGTTAATTAGCCAATAATCAAAGTAATAAGCAGATATTTGTTTATTCCACAATTGAA
* *
619859 TGTAGTCTTTTGATCTCTAGAGTGAAAAATCAGTGACTATCATTTGTTAATTAGCTACCAATCAA
130 TGTAGTCTTTTGATCTCTAGAGTGAAAAATCAGTGACTATAACTTGTTAATTAGCTACCAATCAA
*
619924 AGTGTTAAGCAGATAATTTTGTTATTTGGGAGCTAAATTTG
195 AGTGCTAAGCAGATAATTTTGTTATTTGGGAGCTAAATTTG
619965 GAATTTGATT
Statistics
Matches: 209, Mismatches: 23, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
237 118 0.56
239 56 0.27
240 35 0.17
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.40
Consensus pattern (239 bp):
TTAATGGTAAATTTATTAGCAATTCAATGTAGGCTTTTGATATTTTAGAGCGAAAAATCAGTGAT
TATTACTCGTTAATTAGCCAATAATCAAAGTAATAAGCAGATATTTGTTTATTCCACAATTGAAT
GTAGTCTTTTGATCTCTAGAGTGAAAAATCAGTGACTATAACTTGTTAATTAGCTACCAATCAAA
GTGCTAAGCAGATAATTTTGTTATTTGGGAGCTAAATTTGTGAT
Found at i:620610 original size:15 final size:15
Alignment explanation
Indices: 620590--620620 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
620580 GAAGAACCAC
620590 AACTTCGATTTTCTT
1 AACTTCGATTTTCTT
620605 AACTTCGATTTTCTT
1 AACTTCGATTTTCTT
620620 A
1 A
620621 TTGCAGTCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.23, C:0.19, G:0.06, T:0.52
Consensus pattern (15 bp):
AACTTCGATTTTCTT
Found at i:629263 original size:69 final size:69
Alignment explanation
Indices: 629151--629287 Score: 202
Period size: 69 Copynumber: 2.0 Consensus size: 69
629141 GAAGGTAAAA
** * * *
629151 AAATCGAAAACTGAAATTGAATTGTCACTTTTTGCATGCACTAGGGTAAGATATGTTTTGATGAA
1 AAATCGAAAACCAAAATCGAATTGTCACTTTTTGCATGCACTAGGATAAGATATGTTTCGATGAA
629216 TAAC
66 TAAC
* * *
629220 AAATCGAAAACCAAAATCGAATTGTCATTTTTTGCATGTACTAGGATGAGATATGTTTCGATGAA
1 AAATCGAAAACCAAAATCGAATTGTCACTTTTTGCATGCACTAGGATAAGATATGTTTCGATGAA
629285 TAA
66 TAA
629288 TCTCTAGCGG
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
69 60 1.00
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (69 bp):
AAATCGAAAACCAAAATCGAATTGTCACTTTTTGCATGCACTAGGATAAGATATGTTTCGATGAA
TAAC
Found at i:630325 original size:21 final size:21
Alignment explanation
Indices: 630292--630371 Score: 106
Period size: 21 Copynumber: 3.8 Consensus size: 21
630282 TTCATCTGCA
*
630292 TACCCTCCTCCACCTTCGGCT
1 TACCCTCCACCACCTTCGGCT
* *
630313 TATCCTCCACCACATTCGGCT
1 TACCCTCCACCACCTTCGGCT
* *
630334 TACCCTCCACCACCTTCCGCA
1 TACCCTCCACCACCTTCGGCT
*
630355 TACCCTCCGCCACCTTC
1 TACCCTCCACCACCTTC
630372 ATCGTATCCC
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 51 1.00
ACGTcount: A:0.15, C:0.53, G:0.07, T:0.25
Consensus pattern (21 bp):
TACCCTCCACCACCTTCGGCT
Found at i:634887 original size:13 final size:13
Alignment explanation
Indices: 634869--634896 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
634859 TGATAGCGCC
634869 GCCAGCCGCGGTT
1 GCCAGCCGCGGTT
634882 GCCAGCCGCGGTT
1 GCCAGCCGCGGTT
634895 GC
1 GC
634897 TGAAAGCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.07, C:0.39, G:0.39, T:0.14
Consensus pattern (13 bp):
GCCAGCCGCGGTT
Found at i:643830 original size:21 final size:20
Alignment explanation
Indices: 643789--643848 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 20
643779 AATTATTGTT
643789 TTAAAATATTTAT-AA-AAAA
1 TTAAAA-ATTTATAAATAAAA
643808 TTAAAAATTTATCAAATAAAA
1 TTAAAAATTTAT-AAATAAAA
* * *
643829 TTTAAAAGTCATAAATAAAA
1 TTAAAAATTTATAAATAAAA
643849 AATTATTTCA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
18 6 0.17
19 6 0.17
20 10 0.29
21 13 0.37
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (20 bp):
TTAAAAATTTATAAATAAAA
Found at i:643833 original size:22 final size:20
Alignment explanation
Indices: 643788--643835 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 20
643778 AAATTATTGT
643788 TTTAAAATATTTATAAAAAA
1 TTTAAAATATTTATAAAAAA
643808 -TTAAAA-ATTTATCAAATAAAA
1 TTTAAAATATTTAT--AA-AAAA
643829 TTTAAAA
1 TTTAAAA
643836 GTCATAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
18 6 0.25
19 6 0.25
20 2 0.08
21 4 0.17
22 6 0.25
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (20 bp):
TTTAAAATATTTATAAAAAA
Found at i:645384 original size:19 final size:17
Alignment explanation
Indices: 645360--645403 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 17
645350 AATAAATTAT
645360 AAATATTAAAAAGTCAAAA
1 AAATATTAAAAA-T-AAAA
*
645379 AAATATTCAAAATAAAA
1 AAATATTAAAAATAAAA
645396 AAA-ATTAA
1 AAATATTAA
645404 CATAAAGTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 4 0.17
17 7 0.30
18 1 0.04
19 11 0.48
ACGTcount: A:0.70, C:0.05, G:0.02, T:0.23
Consensus pattern (17 bp):
AAATATTAAAAATAAAA
Found at i:652243 original size:21 final size:21
Alignment explanation
Indices: 652217--652257 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
652207 ATCTGCTCAA
* *
652217 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
652238 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
652258 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:662265 original size:46 final size:46
Alignment explanation
Indices: 662208--662391 Score: 287
Period size: 46 Copynumber: 4.0 Consensus size: 46
662198 ATAGCAAAGC
* *
662208 GTGAAACGTAGGTATGGTATTTCAATAAAGAAAACCATACTGAGTT
1 GTGAAAAGTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGTT
*
662254 GTGAAAAGTAGGTATGATATTTCAGTAAAGAAAACCATACTGAGTT
1 GTGAAAAGTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGTT
* * * *
662300 GTGAGAAGTGGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGTT
1 GTGAAAAGTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGTT
* *
662346 GTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAATCATACTGAGTT
1 GTGAAAAGTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGTT
662392 ACAGCATTGT
Statistics
Matches: 126, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 126 1.00
ACGTcount: A:0.37, C:0.09, G:0.26, T:0.29
Consensus pattern (46 bp):
GTGAAAAGTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGTT
Found at i:664476 original size:29 final size:30
Alignment explanation
Indices: 664416--664476 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
664406 GGAGGGGAGG
* * *
664416 GGAGTAAAAGTTTTGGGGGGAAAGTGAGAA
1 GGAGTAAAAGTTTTGAGGGAAAAGTGAAAA
664446 GGAGTAAAAGTTTTGAGGGAAAAGT-AAAA
1 GGAGTAAAAGTTTTGAGGGAAAAGTGAAAA
664475 GG
1 GG
664477 GTTTGGGAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 5 0.18
30 23 0.82
ACGTcount: A:0.41, C:0.00, G:0.39, T:0.20
Consensus pattern (30 bp):
GGAGTAAAAGTTTTGAGGGAAAAGTGAAAA
Done.