Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold226
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: 1170647
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 5 of 8
Found at i:476711 original size:29 final size:29
Alignment explanation
Indices: 476669--476726 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
476659 TAAGGCCATC
476669 ATTGTGATCTTTGCATGAAATTTCTTAAA
1 ATTGTGATCTTTGCATGAAATTTCTTAAA
476698 ATTGTGATCTTTGCATGAAATTTCTTAAA
1 ATTGTGATCTTTGCATGAAATTTCTTAAA
476727 GCACTCATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.31, C:0.10, G:0.14, T:0.45
Consensus pattern (29 bp):
ATTGTGATCTTTGCATGAAATTTCTTAAA
Found at i:481758 original size:23 final size:23
Alignment explanation
Indices: 481707--481769 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 23
481697 AACACCTTTG
481707 ATATATATTT-ATATTTAAAATT
1 ATATATATTTAATATTTAAAATT
* *
481729 TTAATATATTTAATAATTT-ATATT
1 AT-ATATATTTAAT-ATTTAAAATT
481753 ATATATATTTAAATATT
1 ATATATATTT-AATATT
481770 ATCAAAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
22 1 0.03
23 19 0.56
24 10 0.29
25 4 0.12
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
ATATATATTTAATATTTAAAATT
Found at i:482232 original size:3 final size:3
Alignment explanation
Indices: 482224--482262 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
482214 TTTTTTGTAA
*
482224 AAT AAT AAT AAT AAT AAT AAT AAG AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
482263 TTTGGAATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:483437 original size:26 final size:28
Alignment explanation
Indices: 483408--483468 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
483398 ATTTTAAATT
483408 TAATATAAAAATAA-TAA-ATAATAAAA
1 TAATATAAAAATAATTAATATAATAAAA
* * *
483434 TAATTTAAATATAATTAATATAATAATA
1 TAATATAAAAATAATTAATATAATAAAA
483462 TAATATA
1 TAATATA
483469 TATTATATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 12 0.41
27 3 0.10
28 14 0.48
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (28 bp):
TAATATAAAAATAATTAATATAATAAAA
Found at i:483473 original size:23 final size:23
Alignment explanation
Indices: 483407--483473 Score: 65
Period size: 23 Copynumber: 3.1 Consensus size: 23
483397 AATTTTAAAT
483407 TTAATATAA-AA-ATAATA-A-A
1 TTAATATAATAATATAATATATA
* *
483426 -TAATAAAATAATTTAA-ATATAA
1 TTAATATAATAATATAATATAT-A
483448 TTAATATAATAATATAATATATA
1 TTAATATAATAATATAATATATA
483471 TTA
1 TTA
483474 TATTTATATT
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
18 7 0.19
19 3 0.08
20 4 0.11
22 1 0.03
23 18 0.49
24 4 0.11
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (23 bp):
TTAATATAATAATATAATATATA
Found at i:483492 original size:35 final size:32
Alignment explanation
Indices: 483447--483526 Score: 97
Period size: 35 Copynumber: 2.3 Consensus size: 32
483437 TTTAAATATA
483447 ATTAATATAATAATATAATATATATTATATTTAT
1 ATTAATATAATAA-AT-ATATATATTATATTTAT
* *
483481 ATTTAAAATAATTTAAATATATTTATTATATTTAT
1 A-TTAATATAA--TAAATATATATATTATATTTAT
483516 ATTAATATAAT
1 ATTAATATAAT
483527 TAACAAATAC
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
32 1 0.03
34 9 0.22
35 25 0.62
36 2 0.05
37 3 0.08
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (32 bp):
ATTAATATAATAAATATATATATTATATTTAT
Found at i:483519 original size:11 final size:11
Alignment explanation
Indices: 483460--483516 Score: 50
Period size: 9 Copynumber: 5.4 Consensus size: 11
483450 AATATAATAA
483460 TATAATATATAT
1 TATAATATAT-T
*
483472 TATATTTATATT
1 TATA-ATATATT
*
483484 TAAAATA-ATT
1 TATAATATATT
483494 TA-AATATATT
1 TATAATATATT
483504 TAT--TATATT
1 TATAATATATT
483513 TATA
1 TATA
483517 TTAATATAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
9 13 0.34
10 10 0.26
11 2 0.05
12 8 0.21
13 5 0.13
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (11 bp):
TATAATATATT
Found at i:483521 original size:29 final size:32
Alignment explanation
Indices: 483452--483526 Score: 102
Period size: 29 Copynumber: 2.4 Consensus size: 32
483442 ATATAATTAA
483452 TATAATAATATAATATATATTATATTTATATT
1 TATAATAATATAATATATATTATATTTATATT
* *
483484 TAAAATAATTTAA-ATATATT-TA-TTATATT
1 TATAATAATATAATATATATTATATTTATATT
*
483513 TATATTAATATAAT
1 TATAATAATATAAT
483527 TAACAAATAC
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
29 17 0.46
30 2 0.05
31 7 0.19
32 11 0.30
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (32 bp):
TATAATAATATAATATATATTATATTTATATT
Found at i:484446 original size:20 final size:19
Alignment explanation
Indices: 484423--484476 Score: 58
Period size: 18 Copynumber: 2.8 Consensus size: 19
484413 TAAAATCCTA
484423 ATTTTTTATTAAAAATTTAT
1 ATTTTTTATTAAAAATTT-T
484443 ATTTTTTA--AAATAATTTT
1 ATTTTTTATTAAA-AATTTT
* *
484461 ATATTTTATTCAAAAT
1 ATTTTTTATTAAAAAT
484477 AAAAATAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
18 11 0.38
19 8 0.28
20 10 0.34
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (19 bp):
ATTTTTTATTAAAAATTTT
Found at i:484478 original size:22 final size:20
Alignment explanation
Indices: 484438--484478 Score: 64
Period size: 20 Copynumber: 1.9 Consensus size: 20
484428 TTATTAAAAA
484438 TTTATATTTTTTAAAATAAT
1 TTTATATTTTTTAAAATAAT
484458 TTTATATTTTATTCAAAATAA
1 TTTATATTTT-TT-AAAATAA
484479 AAATAATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.53
21 2 0.11
22 7 0.37
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (20 bp):
TTTATATTTTTTAAAATAAT
Found at i:484827 original size:19 final size:17
Alignment explanation
Indices: 484793--484829 Score: 56
Period size: 19 Copynumber: 2.1 Consensus size: 17
484783 GATCAGATAT
484793 ATTTTTATAATATTTTA
1 ATTTTTATAATATTTTA
484810 ATTTTATATAAGTATTTTA
1 ATTTT-TATAA-TATTTTA
484829 A
1 A
484830 AATTTAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 5 0.28
18 5 0.28
19 8 0.44
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (17 bp):
ATTTTTATAATATTTTA
Found at i:485114 original size:18 final size:18
Alignment explanation
Indices: 485091--485126 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
485081 ACAGTATTTA
*
485091 AATTATTAAAAATTAAAT
1 AATTATGAAAAATTAAAT
*
485109 AATTATGAATAATTAAAT
1 AATTATGAAAAATTAAAT
485127 TCATATTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (18 bp):
AATTATGAAAAATTAAAT
Found at i:487972 original size:28 final size:28
Alignment explanation
Indices: 487895--487973 Score: 83
Period size: 28 Copynumber: 2.8 Consensus size: 28
487885 TTTAAGTTAA
487895 ATTTAATAA-TTTATATATTTAT-ATTAT
1 ATTTAA-AATTTTATATATTTATAATTAT
* *
487922 ATTTATATATTTTGTA-ATATTATAATTAT
1 ATTTA-AAATTTTATATAT-TTATAATTAT
*
487951 ATTTAAAATTTTTTATATTTATA
1 ATTTAAAATTTTATATATTTATA
487974 TAAATTTTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
27 8 0.19
28 23 0.53
29 12 0.28
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59
Consensus pattern (28 bp):
ATTTAAAATTTTATATATTTATAATTAT
Found at i:487986 original size:18 final size:17
Alignment explanation
Indices: 487961--488009 Score: 52
Period size: 17 Copynumber: 3.0 Consensus size: 17
487951 ATTTAAAATT
487961 TTTTATATTTATATAAA
1 TTTTATATTTATATAAA
487978 TTTTAATATATTA-AT-AA
1 TTTT-ATAT-TTATATAAA
487995 -TTTATA-TTATATAAA
1 TTTTATATTTATATAAA
488010 ATAATGAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
13 3 0.11
14 2 0.07
15 5 0.18
16 3 0.11
17 6 0.21
18 6 0.21
19 3 0.11
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTTATATTTATATAAA
Found at i:487987 original size:20 final size:20
Alignment explanation
Indices: 487892--487989 Score: 55
Period size: 19 Copynumber: 4.8 Consensus size: 20
487882 GTATTTAAGT
487892 TAAA-TTTAATA-ATTTATA
1 TAAATTTTAATATATTTATA
*
487910 T--ATTTATATTATATTTATA
1 TAAATTT-TAATATATTTATA
*
487929 T-ATTTTGTAATATTATAATTATA
1 TAAATTT-TAATA-TAT--TTATA
*
487952 TTTAAAATTTT-TTATATTTATA
1 --T-AAATTTTAATATATTTATA
487974 TAAATTTTAATATATT
1 TAAATTTTAATATATT
487990 AATAATTTAT
Statistics
Matches: 61, Mismatches: 7, Indels: 22
0.68 0.08 0.24
Matches are distributed among these distances:
16 1 0.02
17 2 0.03
18 5 0.08
19 15 0.25
20 14 0.23
21 3 0.05
22 5 0.08
23 5 0.08
24 3 0.05
25 3 0.05
26 1 0.02
27 4 0.07
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (20 bp):
TAAATTTTAATATATTTATA
Found at i:491310 original size:20 final size:20
Alignment explanation
Indices: 491272--491310 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
491262 AAAAATATAA
* *
491272 TTTTTTAAATACATGAAATT
1 TTTTTTAAAAAAATGAAATT
*
491292 TTTTTTAAAAAAATTAAAT
1 TTTTTTAAAAAAATGAAAT
491311 ATATCTGTAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (20 bp):
TTTTTTAAAAAAATGAAATT
Found at i:492858 original size:40 final size:38
Alignment explanation
Indices: 492775--492868 Score: 97
Period size: 36 Copynumber: 2.5 Consensus size: 38
492765 TTTATTAGTT
* * *
492775 TTAAATATAAA-ATAATAAAACATAAATATTATTAATTA
1 TTAATTATAAATA-AATAAAACATAAATATAATAAATTA
492813 -T-ATTATAAATAAATAAAACATAAATAATAATAATATTA
1 TTAATTATAAATAAATAAAACATAAAT-ATAATAA-ATTA
492851 TTAATTAT-AATCAAATAA
1 TTAATTATAAAT-AAATAA
492869 TAAATTAACT
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
36 21 0.45
37 7 0.15
38 4 0.09
39 4 0.09
40 11 0.23
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (38 bp):
TTAATTATAAATAAATAAAACATAAATATAATAAATTA
Found at i:494161 original size:21 final size:20
Alignment explanation
Indices: 494136--494186 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
494126 GATTTTTAAT
494136 TTTTTAAATATTTTTTATAA
1 TTTTTAAATATTTTTTATAA
*
494156 TATTTTAAA-GTTTTTTATTAA
1 T-TTTTAAATATTTTTTA-TAA
*
494177 TTTATAAATA
1 TTTTTAAATA
494187 AAATATTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (20 bp):
TTTTTAAATATTTTTTATAA
Found at i:494608 original size:32 final size:30
Alignment explanation
Indices: 494572--494638 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 30
494562 TATATTTTTT
494572 AAAAATTCTATAAAAATAATTATTTT-AAT-ATA
1 AAAAATT-T-TAAAAA-AA-TATTTTAAATGATA
494604 AAAAATTTTAAAAAAATATTTTAAATGATA
1 AAAAATTTTAAAAAAATATTTTAAATGATA
494634 AAAAA
1 AAAAA
494639 ATATCAATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
28 6 0.18
29 5 0.15
30 14 0.42
31 1 0.03
32 7 0.21
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.36
Consensus pattern (30 bp):
AAAAATTTTAAAAAAATATTTTAAATGATA
Found at i:494744 original size:51 final size:51
Alignment explanation
Indices: 494683--494785 Score: 188
Period size: 51 Copynumber: 2.0 Consensus size: 51
494673 AATCATCAAA
*
494683 ATCATACATTATCCCAATAGTGGAAGGAGAATAATGATTTGTCAAAGCATT
1 ATCATACATTATCCCAATAGTGGAAGGAGAATAATAATTTGTCAAAGCATT
*
494734 ATCATTCATTATCCCAATAGTGGAAGGAGAATAATAATTTGTCAAAGCATT
1 ATCATACATTATCCCAATAGTGGAAGGAGAATAATAATTTGTCAAAGCATT
494785 A
1 A
494786 CAAACATCAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.30
Consensus pattern (51 bp):
ATCATACATTATCCCAATAGTGGAAGGAGAATAATAATTTGTCAAAGCATT
Found at i:504880 original size:2 final size:2
Alignment explanation
Indices: 504873--504907 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
504863 TTAGCTTTTA
504873 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
504908 ATTGGGTTAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:505109 original size:2 final size:2
Alignment explanation
Indices: 505104--505142 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
505094 AACTAGATAA
505104 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
505143 AAAGAAATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:512772 original size:2 final size:2
Alignment explanation
Indices: 512765--512795 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
512755 GAATTTAAAA
512765 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
512796 TTGATCGCTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:512982 original size:2 final size:2
Alignment explanation
Indices: 512975--513011 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
512965 TCGACATTGC
*
512975 GA GA GA GA GA GA GA GA GA GA GA GA GA GC GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
513012 GGGGAAGTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.03, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:513476 original size:12 final size:12
Alignment explanation
Indices: 513461--513513 Score: 54
Period size: 12 Copynumber: 4.2 Consensus size: 12
513451 TTTGAATTGT
*
513461 AATATTAATTTC
1 AATATTAATTTA
513473 AATATTAATTTA
1 AATATTAATTTA
*
513485 AATAATT-ATTAA
1 AAT-ATTAATTTA
513497 ATATATTTAATTTA
1 A-ATA-TTAATTTA
513511 AAT
1 AAT
513514 TTGGCTAATG
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
12 20 0.59
13 9 0.26
14 5 0.15
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (12 bp):
AATATTAATTTA
Found at i:514069 original size:23 final size:23
Alignment explanation
Indices: 514014--514069 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
514004 TAAAAATAAC
*
514014 TTAAAAATAA-AAATTTTAAATT
1 TTAAAAATAATAAATATTAAATT
** *
514036 TTAAATTTAATAAATATTATATT
1 TTAAAAATAATAAATATTAAATT
514059 TTAAAAATAAT
1 TTAAAAATAAT
514070 TATATGATTT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
22 8 0.30
23 19 0.70
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TTAAAAATAATAAATATTAAATT
Found at i:514071 original size:17 final size:17
Alignment explanation
Indices: 514041--514097 Score: 55
Period size: 17 Copynumber: 3.3 Consensus size: 17
514031 AAATTTTAAA
514041 TTTAATAAATATTATAT
1 TTTAATAAATATTATAT
514058 TTTAA-AAATAATTATAT
1 TTTAATAAAT-ATTATAT
* *
514075 GATTTAATTAA-ATTAAAT
1 --TTTAATAAATATTATAT
514093 TTTAA
1 TTTAA
514098 ATTTAATTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
16 9 0.26
17 12 0.35
18 6 0.18
19 5 0.15
20 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (17 bp):
TTTAATAAATATTATAT
Found at i:514277 original size:24 final size:25
Alignment explanation
Indices: 514243--514322 Score: 83
Period size: 24 Copynumber: 3.1 Consensus size: 25
514233 AACCTTGTTT
*
514243 TAATATATAAAAAATAATTAAAATA
1 TAATTTATAAAAAATAATTAAAATA
*
514268 TAATTT-TAAAAAATAA-TATAAATT
1 TAATTTATAAAAAATAATTA-AAATA
514292 TAATTTAAATATAAAAATATATTAAAATA
1 TAATTT--ATA-AAAAATA-ATTAAAATA
514321 TA
1 TA
514323 TATTATGAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
23 2 0.04
24 20 0.44
25 5 0.11
27 2 0.04
28 7 0.16
29 7 0.16
30 2 0.04
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (25 bp):
TAATTTATAAAAAATAATTAAAATA
Found at i:515862 original size:14 final size:14
Alignment explanation
Indices: 515840--515908 Score: 61
Period size: 13 Copynumber: 4.9 Consensus size: 14
515830 AATAATATTT
515840 TTATTTAAATTTAA
1 TTATTTAAATTTAA
* *
515854 TTATATAAA-ATAA
1 TTATTTAAATTTAA
*
515867 TTTTTTAAATTTAA
1 TTATTTAAATTTAA
515881 TTTAAGTTTAAATTTAA
1 -TT-A-TTTAAATTTAA
*
515898 AT-TTTAAATTT
1 TTATTTAAATTT
515909 TAAAAATTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
13 19 0.43
14 11 0.25
15 2 0.05
16 1 0.02
17 11 0.25
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (14 bp):
TTATTTAAATTTAA
Found at i:515890 original size:6 final size:6
Alignment explanation
Indices: 515870--515908 Score: 53
Period size: 6 Copynumber: 6.5 Consensus size: 6
515860 AAAATAATTT
*
515870 TTTAAA TTT-AA TTTAAG TTTAAA TTTAAA TTTTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA -TTTAAA TTT
515909 TAAAAATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
5 5 0.17
6 18 0.62
7 6 0.21
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:516332 original size:27 final size:26
Alignment explanation
Indices: 516302--516366 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 26
516292 GAGCAGTATG
*
516302 AATTAATTTGATAT-ATTTAATTGATTA
1 AATTAATTT-ATATGATTTAATT-ATAA
* *
516329 AATTAAATTTATTTGATTTGATTATAA
1 AATT-AATTTATATGATTTAATTATAA
516356 AATTAATTTAT
1 AATTAATTTAT
516367 TAATTTTTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
26 7 0.21
27 14 0.42
28 12 0.36
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (26 bp):
AATTAATTTATATGATTTAATTATAA
Found at i:516439 original size:7 final size:7
Alignment explanation
Indices: 516429--516512 Score: 52
Period size: 7 Copynumber: 12.3 Consensus size: 7
516419 AATTATATTT
516429 TATATAA
1 TATATAA
516436 TATA-AA
1 TATATAA
516442 TA-A-AA
1 TATATAA
*
516447 TATAT-T
1 TATATAA
516453 TATATAA
1 TATATAA
*
516460 TAATTTAA
1 T-ATATAA
*
516468 AAT-TATA
1 TATATA-A
516475 TAATATAA
1 T-ATATAA
*
516483 TATATTA
1 TATATAA
* *
516490 TTTATAT
1 TATATAA
516497 TATATAA
1 TATATAA
516504 TATATAA
1 TATATAA
516511 TA
1 TA
516513 ATATTTCGTT
Statistics
Matches: 59, Mismatches: 11, Indels: 14
0.70 0.13 0.17
Matches are distributed among these distances:
5 5 0.08
6 12 0.20
7 31 0.53
8 9 0.15
9 2 0.03
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (7 bp):
TATATAA
Found at i:516475 original size:26 final size:24
Alignment explanation
Indices: 516412--516514 Score: 82
Period size: 24 Copynumber: 4.2 Consensus size: 24
516402 AATTATTTTT
* **
516412 TAATTTTAATTATATTTTATATAA
1 TAATTTAAATTATATAATATATAA
** * *
516436 TATAAATAAAATATAT-TTATATAA
1 TA-ATTTAAATTATATAATATATAA
516460 TAATTTAAAATTATATAATATAATATA
1 TAATTT-AAATTATATAATAT-ATA-A
* *
516487 TTATTTATATTATATAATATATAA
1 TAATTTAAATTATATAATATATAA
516511 TAAT
1 TAAT
516515 ATTTCGTTTT
Statistics
Matches: 63, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
23 2 0.03
24 24 0.38
25 15 0.24
26 16 0.25
27 6 0.10
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
TAATTTAAATTATATAATATATAA
Found at i:516514 original size:36 final size:36
Alignment explanation
Indices: 516428--516516 Score: 91
Period size: 34 Copynumber: 2.6 Consensus size: 36
516418 TAATTATATT
*
516428 TTATATAATATA-AATAAAATATATTTATATAATAA
1 TTATATAATATATAATAATATATATTTATATAATAA
* *
516463 TT-TAAAAT-TAT-ATAATATAATATATTAT-TTAT-A
1 TTATATAATATATAATAATAT-ATAT-TTATATAATAA
516496 TTATATAATATATAATAATAT
1 TTATATAATATATAATAATAT
516517 TTCGTTTTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
33 11 0.25
34 17 0.39
35 9 0.20
36 7 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (36 bp):
TTATATAATATATAATAATATATATTTATATAATAA
Found at i:516517 original size:26 final size:26
Alignment explanation
Indices: 516414--516518 Score: 83
Period size: 26 Copynumber: 4.2 Consensus size: 26
516404 TTATTTTTTA
* **
516414 ATTTTAATTATATTTTATATAAT-AT
1 ATTTAAATTATATAATATATAATAAT
** * *
516439 AAATAAAATATAT-TTATATAATAAT
1 ATTTAAATTATATAATATATAATAAT
* *
516464 -TTAAAATTATATAATATA-ATATATT
1 ATTTAAATTATATAATATATA-ATAAT
*
516489 ATTTATATTATATAATATATAATAAT
1 ATTTAAATTATATAATATATAATAAT
516515 ATTT
1 ATTT
516519 CGTTTTTATT
Statistics
Matches: 62, Mismatches: 13, Indels: 9
0.74 0.15 0.11
Matches are distributed among these distances:
24 18 0.29
25 19 0.31
26 24 0.39
27 1 0.02
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (26 bp):
ATTTAAATTATATAATATATAATAAT
Found at i:516881 original size:2 final size:2
Alignment explanation
Indices: 516874--516898 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
516864 CTTTCCTTCA
516874 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
516899 CAACAAAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:520388 original size:14 final size:15
Alignment explanation
Indices: 520369--520397 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
520359 AAAAGAGTGA
520369 GAAATTG-AATTAAT
1 GAAATTGAAATTAAT
520383 GAAATTGAAATTAAT
1 GAAATTGAAATTAAT
520398 CGAGTTGGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.52, C:0.00, G:0.14, T:0.34
Consensus pattern (15 bp):
GAAATTGAAATTAAT
Found at i:520579 original size:30 final size:30
Alignment explanation
Indices: 520545--520606 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
520535 GAGTATATTA
520545 AAAATAATATAA-ATAA-ATAAATAAATAAAT
1 AAAAT-ATATAACA-AACATAAATAAATAAAT
* *
520575 AAAATTTTTAACAAACATAAATAAATAAAT
1 AAAATATATAACAAACATAAATAAATAAAT
520605 AA
1 AA
520607 TAATCATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 6 0.21
30 22 0.79
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.27
Consensus pattern (30 bp):
AAAATATATAACAAACATAAATAAATAAAT
Found at i:520599 original size:4 final size:4
Alignment explanation
Indices: 520546--520577 Score: 55
Period size: 4 Copynumber: 7.8 Consensus size: 4
520536 AGTATATTAA
520546 AAAT AATAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AA-AT AAAT AAAT AAAT AAAT AAAT AAA
520578 ATTTTTAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:520970 original size:2 final size:2
Alignment explanation
Indices: 520965--520991 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
520955 ACACACACAC
520965 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
520992 AAATATAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:521107 original size:2 final size:2
Alignment explanation
Indices: 521100--521128 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
521090 ATCATAAGTT
521100 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
521129 GGCAAATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:528034 original size:28 final size:28
Alignment explanation
Indices: 528002--528056 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
527992 ACATTCATGA
528002 AGATGTTCCATTTGAAAACAACTTATAT
1 AGATGTTCCATTTGAAAACAACTTATAT
528030 AGATGTTCCATTTGAAAACAACTTATA
1 AGATGTTCCATTTGAAAACAACTTATA
528057 ATGGTTGCAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.35
Consensus pattern (28 bp):
AGATGTTCCATTTGAAAACAACTTATAT
Found at i:528859 original size:15 final size:15
Alignment explanation
Indices: 528821--528865 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
528811 TAAAATATTA
528821 TATATTAATATAAATT
1 TATATT-ATATAAATT
528837 T-T-TTATATAAATT
1 TATATTATATAAATT
528850 TATATTATATAAATT
1 TATATTATATAAATT
528865 T
1 T
528866 TAATACGTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
13 10 0.37
14 3 0.11
15 13 0.48
16 1 0.04
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TATATTATATAAATT
Found at i:529532 original size:16 final size:18
Alignment explanation
Indices: 529501--529536 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
529491 AAAAATTAAA
529501 AAAAAGTAATATAATAAT
1 AAAAAGTAATATAATAAT
529519 AAAAA-TAA-ATAATAAT
1 AAAAAGTAATATAATAAT
529535 AA
1 AA
529537 TAATTTGGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.56
17 3 0.17
18 5 0.28
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (18 bp):
AAAAAGTAATATAATAAT
Found at i:533295 original size:12 final size:12
Alignment explanation
Indices: 533274--533304 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
533264 ACAGTGCGAG
533274 AGAGAAAGAGAC
1 AGAGAAAGAGAC
*
533286 AGAGACAGAGAC
1 AGAGAAAGAGAC
533298 AGAGAAA
1 AGAGAAA
533305 TTGATAGACC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.58, C:0.10, G:0.32, T:0.00
Consensus pattern (12 bp):
AGAGAAAGAGAC
Found at i:533429 original size:18 final size:18
Alignment explanation
Indices: 533406--533450 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
533396 AAGTAATTAA
533406 GAACAGTGTAGGAAGATG
1 GAACAGTGTAGGAAGATG
533424 GAACAGTGTAGGAAGATG
1 GAACAGTGTAGGAAGATG
533442 GAACAGTGT
1 GAACAGTGT
533451 TGTCTAAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.38, C:0.07, G:0.38, T:0.18
Consensus pattern (18 bp):
GAACAGTGTAGGAAGATG
Found at i:533717 original size:20 final size:19
Alignment explanation
Indices: 533681--533720 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
533671 AAAAATAATT
533681 TAAATTTAATTATAAAATA
1 TAAATTTAATTATAAAATA
533700 TAAATATTAA-TATAAAA-A
1 TAAAT-TTAATTATAAAATA
533718 TAA
1 TAA
533721 TTCAGACTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 4 0.20
19 12 0.60
20 4 0.20
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TAAATTTAATTATAAAATA
Found at i:535294 original size:28 final size:26
Alignment explanation
Indices: 535249--535303 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 26
535239 AAGCACATTC
**
535249 ATATTTTTTTAAAATTTATTAATTTA
1 ATATTTTTTTAAAATTTAAAAATTTA
*
535275 ATATTTTTTTATTAAGTTTAAAAATTTA
1 ATATTTTTTTA--AAATTTAAAAATTTA
535303 A
1 A
535304 ATAACTTAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 11 0.46
28 13 0.54
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (26 bp):
ATATTTTTTTAAAATTTAAAAATTTA
Found at i:535986 original size:18 final size:19
Alignment explanation
Indices: 535955--535996 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
535945 ATATACACTT
*
535955 TAAATATTATTATAA-TACA
1 TAAA-ATTAATATAAGTACA
535974 TAAAATTAATATAAGTACA
1 TAAAATTAATATAAGTACA
535993 -AAAA
1 TAAAA
535997 GATTACATGC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (19 bp):
TAAAATTAATATAAGTACA
Found at i:536763 original size:24 final size:23
Alignment explanation
Indices: 536708--536771 Score: 71
Period size: 24 Copynumber: 2.8 Consensus size: 23
536698 AAAAATATTT
536708 TATTTAAAT-TTAATAATAAAAA
1 TATTTAAATATTAATAATAAAAA
*
536730 TATATAAATATTAAT-ATAAAATAA
1 TATTTAAATATTAATAAT-AAA-AA
*
536754 TTTTTAAATATT-ATAATA
1 TATTTAAATATTAATAATA
536772 TTATTTAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
22 10 0.29
23 11 0.31
24 14 0.40
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
TATTTAAATATTAATAATAAAAA
Found at i:537343 original size:65 final size:67
Alignment explanation
Indices: 537211--537345 Score: 150
Period size: 65 Copynumber: 2.0 Consensus size: 67
537201 TATGATACAC
* * *
537211 TCTCTCATTTGTTCAATCTGCCTGTCACCCCAAAACCCCAGCTTAAACCTCAATCAATTGTCCCC
1 TCTCTCATTTGTTCAATCT-CCTGTCACCCCAAAACCCCAGCTTAAACCTCAATCAAATATACCC
537276 CTT
65 CTT
* * ** * *
537279 TCTCTCATTTGTTCAATCT-TTTTCA-CCCAAAACCTTAG-TGTAAATCTCAATCAAATATATCC
1 TCTCTCATTTGTTCAATCTCCTGTCACCCCAAAACCCCAGCT-TAAACCTCAATCAAATATACCC
537341 CTT
65 CTT
537344 TC
1 TC
537346 CCGTTGTTTC
Statistics
Matches: 57, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
64 1 0.02
65 33 0.58
66 4 0.07
68 19 0.33
ACGTcount: A:0.26, C:0.33, G:0.06, T:0.36
Consensus pattern (67 bp):
TCTCTCATTTGTTCAATCTCCTGTCACCCCAAAACCCCAGCTTAAACCTCAATCAAATATACCCC
TT
Found at i:539763 original size:2 final size:2
Alignment explanation
Indices: 539756--539795 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
539746 ATTTGGCCAC
539756 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
539796 CAAACTTGTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:546978 original size:19 final size:19
Alignment explanation
Indices: 546957--547021 Score: 64
Period size: 19 Copynumber: 3.5 Consensus size: 19
546947 TATCAAAATT
*
546957 TATATAAATATAAAATATT
1 TATATAAATATAAAATATA
546976 TAT-TATAATATAATAA-A-A
1 TATATA-AATATAA-AATATA
* *
546994 TATACAAATATAAAATAAA
1 TATATAAATATAAAATATA
547013 TATATAAAT
1 TATATAAAT
547022 GGCTAAGTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
17 2 0.05
18 13 0.34
19 21 0.55
20 2 0.05
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (19 bp):
TATATAAATATAAAATATA
Found at i:547002 original size:8 final size:7
Alignment explanation
Indices: 546925--547020 Score: 50
Period size: 7 Copynumber: 12.9 Consensus size: 7
546915 TTTTAAAATT
*
546925 TATATAA
1 TATAAAA
*
546932 TATAAAT
1 TATAAAA
*
546939 TATTAACA
1 TA-TAAAA
546947 TATCAAAA
1 TAT-AAAA
546955 TTTATATAAA
1 --TATA-AAA
546965 TATAAAA
1 TATAAAA
** *
546972 TATTTAT
1 TATAAAA
*
546979 TATAATA
1 TATAAAA
546986 TAATAAAA
1 T-ATAAAA
546994 TATACAAA
1 TATA-AAA
547002 TATAAAA
1 TATAAAA
*
547009 TA-AATA
1 TATAAAA
547015 TATAAA
1 TATAAA
547021 TGGCTAAGTT
Statistics
Matches: 66, Mismatches: 15, Indels: 16
0.68 0.15 0.16
Matches are distributed among these distances:
6 5 0.08
7 29 0.44
8 25 0.38
9 1 0.02
10 6 0.09
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (7 bp):
TATAAAA
Found at i:547017 original size:13 final size:14
Alignment explanation
Indices: 546957--547020 Score: 51
Period size: 15 Copynumber: 4.6 Consensus size: 14
546947 TATCAAAATT
546957 TATAT-AAATATAA
1 TATATAAAATATAA
* ** *
546970 AATATTTATTATAA
1 TATATAAAATATAA
546984 TATAATAAAATATACA
1 TAT-ATAAAATATA-A
*
547000 AATATAAAATA-AA
1 TATATAAAATATAA
547013 TATATAAA
1 TATATAAA
547021 TGGCTAAGTT
Statistics
Matches: 39, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
13 12 0.31
14 9 0.23
15 15 0.38
16 3 0.08
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (14 bp):
TATATAAAATATAA
Found at i:547574 original size:2 final size:2
Alignment explanation
Indices: 547556--547637 Score: 83
Period size: 2 Copynumber: 41.0 Consensus size: 2
547546 TATCATCATA
* * * * *
547556 AT AT AC AT AT TT AT AT AT AT TT AT AT GT GT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
547598 AT AT AT AT AT CT AT AT GT GT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
547638 TCTTTTCACG
Statistics
Matches: 66, Mismatches: 14, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.52
Consensus pattern (2 bp):
AT
Found at i:547603 original size:32 final size:32
Alignment explanation
Indices: 547556--547637 Score: 128
Period size: 32 Copynumber: 2.6 Consensus size: 32
547546 TATCATCATA
* * *
547556 ATATACATATTTATATATATTTATATGTGTAT
1 ATATATATATATATATATATCTATATGTGTAT
547588 ATATATATATATATATATATCTATATGTGTAT
1 ATATATATATATATATATATCTATATGTGTAT
*
547620 ATATATATATATTTATAT
1 ATATATATATATATATAT
547638 TCTTTTCACG
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 46 1.00
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.52
Consensus pattern (32 bp):
ATATATATATATATATATATCTATATGTGTAT
Found at i:547984 original size:2 final size:2
Alignment explanation
Indices: 547944--547970 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
547934 TCAGACCAGA
547944 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
547971 ATCAAATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:548965 original size:22 final size:23
Alignment explanation
Indices: 548940--548987 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 23
548930 TTATTTTAAC
*
548940 ATATTA-TTATTATTATATATAT
1 ATATTATTTATTATTATAGATAT
* *
548962 ATA-TATTTTTTTTTATAGATAT
1 ATATTATTTATTATTATAGATAT
548984 ATAT
1 ATAT
548988 ATATCTAGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
21 2 0.10
22 19 0.90
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (23 bp):
ATATTATTTATTATTATAGATAT
Found at i:551527 original size:2 final size:2
Alignment explanation
Indices: 551515--551549 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
551505 ATAAATATGT
*
551515 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
551550 CGATTAAACA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:553712 original size:23 final size:24
Alignment explanation
Indices: 553667--553715 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
553657 AATTCGAATG
*
553667 TTTAATTATTATTTAAAATAAAAT
1 TTTAATTATAATTTAAAATAAAAT
*
553691 TTTAATT-TAATTTAATAAAAAAAT
1 TTTAATTATAATTTAA-AATAAAAT
553715 T
1 T
553716 AAATCCAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
TTTAATTATAATTTAAAATAAAAT
Found at i:555533 original size:6 final size:6
Alignment explanation
Indices: 555524--555548 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
555514 GAAAAAGAAA
555524 GGAAGG GGAAGG GGAAGG GGAAGG G
1 GGAAGG GGAAGG GGAAGG GGAAGG G
555549 AGAGTACCTT
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:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (6 bp):
GGAAGG
Found at i:556587 original size:22 final size:23
Alignment explanation
Indices: 556559--556607 Score: 82
Period size: 22 Copynumber: 2.2 Consensus size: 23
556549 GCAAATGAAT
556559 AAAAGTAAGTCAAAAATTGATA-
1 AAAAGTAAGTCAAAAATTGATAG
*
556581 AAAAGTAAGTCAAAATTTGATAG
1 AAAAGTAAGTCAAAAATTGATAG
556604 AAAA
1 AAAA
556608 CCTGTTTGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 21 0.84
23 4 0.16
ACGTcount: A:0.59, C:0.04, G:0.14, T:0.22
Consensus pattern (23 bp):
AAAAGTAAGTCAAAAATTGATAG
Found at i:559430 original size:20 final size:20
Alignment explanation
Indices: 559406--559477 Score: 63
Period size: 20 Copynumber: 3.5 Consensus size: 20
559396 TTTTAAGATT
559406 AATTTAAAATTTTATTTTAA
1 AATTTAAAATTTTATTTTAA
* ** **
559426 TATTTAAAATAATATTAAAA
1 AATTTAAAATTTTATTTTAA
*
559446 AATTTTAAAATTTTATATTAA
1 AA-TTTAAAATTTTATTTTAA
* *
559467 CATTTATAATT
1 AATTTAAAATT
559478 AAAATTAAAT
Statistics
Matches: 38, Mismatches: 13, Indels: 2
0.72 0.25 0.04
Matches are distributed among these distances:
20 24 0.63
21 14 0.37
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (20 bp):
AATTTAAAATTTTATTTTAA
Found at i:559453 original size:41 final size:42
Alignment explanation
Indices: 559408--559493 Score: 120
Period size: 41 Copynumber: 2.1 Consensus size: 42
559398 TTAAGATTAA
* * *
559408 TTTAAAATTTTATTTTAATATTTA-AAATAATATTAAAAAAT
1 TTTAAAATTTTATATTAACATTTATAAATAAAATTAAAAAAT
* *
559449 TTTAAAATTTTATATTAACATTTATAATTAAAATTAAATAAT
1 TTTAAAATTTTATATTAACATTTATAAATAAAATTAAAAAAT
559491 TTT
1 TTT
559494 TATATGATAA
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
41 22 0.56
42 17 0.44
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (42 bp):
TTTAAAATTTTATATTAACATTTATAAATAAAATTAAAAAAT
Found at i:559946 original size:146 final size:147
Alignment explanation
Indices: 559771--560213 Score: 782
Period size: 146 Copynumber: 3.0 Consensus size: 147
559761 ATTCGATTTA
*
559771 GTATTTGAAAAAAAATATATTATTAATATACAATATTTTGATTTA-TAAGAATAAAGCAAGATTA
1 GTATTTGAAAAAAAAT-TATCATTAATATACAATATTTTGATTTATTAAGAATAAAGCAAGATTA
* * *
559835 AATTAAATAACTTTTATAACAAACTAATTCGAACTAAATTTAACAAAAATCAAATAGATCTGAAT
65 AATCAAATAACTTTTATAACAAACTAATTCGAACTAAATTTAATAAAAATCAAATAGAACTGAAT
*
559900 ATACGGTTTAAATCAATT
130 ATACAGTTTAAATCAATT
*
559918 GTATTTGAAAAAAAATTATCATTAATATACAATATTTTAATTTATTAAGAATAAAGCAAGATTAA
1 GTATTTGAAAAAAAATTATCATTAATATACAATATTTTGATTTATTAAGAATAAAGCAAGATTAA
559983 ATCAAATAACTTTTATAACAAACTAATTCGAACTAAA-TTAATAAAAATCAAATAGAACTGAATA
66 ATCAAATAACTTTTATAACAAACTAATTCGAACTAAATTTAATAAAAATCAAATAGAACTGAATA
560047 TACAGTTTAAATCAATT
131 TACAGTTTAAATCAATT
560064 GTATTTGAAAAAAAATTATCATTAATATACAATATTTTGATTTATTAAGAATAAAGCAAGATTAA
1 GTATTTGAAAAAAAATTATCATTAATATACAATATTTTGATTTATTAAGAATAAAGCAAGATTAA
*
560129 ATCAAATAACTTTTATAACAAACTAATTCGAACTAAATTTAATAAAAATCAAATAGAACTTAATA
66 ATCAAATAACTTTTATAACAAACTAATTCGAACTAAATTTAATAAAAATCAAATAGAACTGAATA
* *
560194 TCCAGTTCAAATCAATT
131 TACAGTTTAAATCAATT
560211 GTA
1 GTA
560214 AGTTTTCTCT
Statistics
Matches: 284, Mismatches: 10, Indels: 4
0.95 0.03 0.01
Matches are distributed among these distances:
146 168 0.59
147 116 0.41
ACGTcount: A:0.50, C:0.09, G:0.07, T:0.34
Consensus pattern (147 bp):
GTATTTGAAAAAAAATTATCATTAATATACAATATTTTGATTTATTAAGAATAAAGCAAGATTAA
ATCAAATAACTTTTATAACAAACTAATTCGAACTAAATTTAATAAAAATCAAATAGAACTGAATA
TACAGTTTAAATCAATT
Found at i:567431 original size:21 final size:24
Alignment explanation
Indices: 567405--567459 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 24
567395 TTATAATTAA
567405 AATTAAATAAA-AAT-TTT-AATT
1 AATTAAATAAATAATATTTAAATT
567426 AATTAAATAAATAATAATTTAAATT
1 AATTAAATAAATAAT-ATTTAAATT
567451 ATATTAAAT
1 A-ATTAAAT
567460 TAACTTAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
21 11 0.38
22 3 0.10
24 3 0.10
25 5 0.17
26 7 0.24
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (24 bp):
AATTAAATAAATAATATTTAAATT
Found at i:567436 original size:25 final size:25
Alignment explanation
Indices: 567398--567459 Score: 79
Period size: 25 Copynumber: 2.4 Consensus size: 25
567388 TATATTTTTA
*
567398 TAATTAAAATTAAATAAAAATTTTAAT
1 TAATT-AAA-TAAATAAAAATTTAAAT
*
567425 TAATTAAATAAATAATAATTTAAAT
1 TAATTAAATAAATAAAAATTTAAAT
567450 TATATTAAAT
1 TA-ATTAAAT
567460 TAACTTAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
25 17 0.53
26 10 0.31
27 5 0.16
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (25 bp):
TAATTAAATAAATAAAAATTTAAAT
Found at i:567481 original size:20 final size:21
Alignment explanation
Indices: 567426--567490 Score: 62
Period size: 20 Copynumber: 3.1 Consensus size: 21
567416 AATTTTAATT
* * *
567426 AATTAAATAAATAATAATTTA
1 AATTATATAAATATTAACTTA
*
567447 AATTATATTAA-ATTAACTTA
1 AATTATATAAATATTAACTTA
*
567467 AATTATA-AAATATTATATTTA
1 AATTATATAAATATTA-ACTTA
567488 AAT
1 AAT
567491 CAACGGAAGA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
19 2 0.06
20 18 0.50
21 16 0.44
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
AATTATATAAATATTAACTTA
Found at i:570487 original size:27 final size:27
Alignment explanation
Indices: 570456--570509 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
570446 TAACTGATAC
570456 ACACTTGTGGCTGCATAGCAACTGTGG
1 ACACTTGTGGCTGCATAGCAACTGTGG
570483 ACACTTGTGGCTGCATAGCAACTGTGG
1 ACACTTGTGGCTGCATAGCAACTGTGG
570510 GTTGGCCCAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.22, C:0.22, G:0.30, T:0.26
Consensus pattern (27 bp):
ACACTTGTGGCTGCATAGCAACTGTGG
Found at i:572838 original size:15 final size:15
Alignment explanation
Indices: 572818--572847 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
572808 TCTTTTGTTT
572818 AAAAAAAGAAAAAAG
1 AAAAAAAGAAAAAAG
*
572833 AAAAAAAGTAAAAAG
1 AAAAAAAGAAAAAAG
572848 GGAATTGAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.83, C:0.00, G:0.13, T:0.03
Consensus pattern (15 bp):
AAAAAAAGAAAAAAG
Found at i:573490 original size:2 final size:2
Alignment explanation
Indices: 573485--573532 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
573475 ACACACACAC
*
573485 AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
573527 AT AT AT
1 AT AT AT
573533 CAATCAAACA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:574520 original size:17 final size:16
Alignment explanation
Indices: 574477--574522 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
574467 ATAACTTTGA
*
574477 TTTAAAATTTAAATTT
1 TTTAATATTTAAATTT
574493 TTTAATATTTATAATTT
1 TTTAATATTTA-AATTT
* *
574510 TTTTATTTTTAAA
1 TTTAATATTTAAA
574523 ATTGCCACAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
16 12 0.46
17 14 0.54
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TTTAATATTTAAATTT
Found at i:576734 original size:34 final size:34
Alignment explanation
Indices: 576688--576872 Score: 248
Period size: 34 Copynumber: 5.5 Consensus size: 34
576678 GTAAAAACCA
*
576688 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
576722 TCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
* *
576756 CCATTTAATCAATAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
576790 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
576824 CCATTTAGTCAACAATGGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
576857 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
576873 TCTCCCACTT
Statistics
Matches: 133, Mismatches: 16, Indels: 5
0.86 0.10 0.03
Matches are distributed among these distances:
33 18 0.14
34 111 0.83
35 4 0.03
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.26
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:580965 original size:18 final size:18
Alignment explanation
Indices: 580930--580999 Score: 77
Period size: 19 Copynumber: 3.8 Consensus size: 18
580920 CCACTATTTC
*
580930 ACGTGTACAGTAACCGTAT
1 ACGTGAACAGT-ACCGTAT
*
580949 ACTTGAACAGTACCGTAT
1 ACGTGAACAGTACCGTAT
* *
580967 ACGTGAATAGTACCTATAT
1 ACGTGAACAGTACC-GTAT
*
580986 ACGTGAATAGTACC
1 ACGTGAACAGTACC
581000 TCGACAACCA
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
18 19 0.42
19 26 0.58
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (18 bp):
ACGTGAACAGTACCGTAT
Found at i:581350 original size:34 final size:34
Alignment explanation
Indices: 581304--581486 Score: 244
Period size: 34 Copynumber: 5.4 Consensus size: 34
581294 GTAAAAACCA
*
581304 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
581338 TCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
* *
581372 CCATTTAATCAATAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
581406 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
581440 CCATTTAGTCAACAATGGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
581473 CCATTTAATCAACA
1 CCATTTAATCAACA
581487 GGATTCATCT
Statistics
Matches: 131, Mismatches: 16, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
33 16 0.12
34 111 0.85
35 4 0.03
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.26
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:583250 original size:28 final size:30
Alignment explanation
Indices: 583218--583280 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 30
583208 ATGTATTTAT
* *
583218 ATATTTTTATA-TCAT-AATTATTTTTAAA
1 ATATTTTTATATTCATAAATAAATTTTAAA
*
583246 ATA-TTTTATATTTATAAATAAATTTTAAA
1 ATATTTTTATATTCATAAATAAATTTTAAA
583275 ATATTT
1 ATATTT
583281 ACGATTTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
27 7 0.24
28 6 0.21
29 14 0.48
30 2 0.07
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (30 bp):
ATATTTTTATATTCATAAATAAATTTTAAA
Found at i:583294 original size:28 final size:29
Alignment explanation
Indices: 583239--583296 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
583229 TCATAATTAT
*
583239 TTTTAAAATATTTTATATTTATAAATAAA
1 TTTTAAAATATTTTAGATTTATAAATAAA
583268 TTTTAAAATA-TTTACGATTTAT-AATAAA
1 TTTTAAAATATTTTA-GATTTATAAATAAA
583296 T
1 T
583297 AGATTTTATG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 11 0.41
29 16 0.59
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (29 bp):
TTTTAAAATATTTTAGATTTATAAATAAA
Found at i:583347 original size:17 final size:18
Alignment explanation
Indices: 583317--583377 Score: 61
Period size: 17 Copynumber: 3.3 Consensus size: 18
583307 GTAATTTTAC
* *
583317 TATATTTATTTTATTTTT
1 TATATTTATATTATATTT
583335 TATA-TTATATTATATTT
1 TATATTTATATTATATTT
*
583352 TAATTTTTATATTTATATTT
1 T-ATATTTATA-TTATATTT
583372 ATATAT
1 -TATAT
583378 AAATTTAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
17 12 0.34
18 6 0.17
19 5 0.14
20 11 0.31
21 1 0.03
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
TATATTTATATTATATTT
Found at i:583376 original size:14 final size:14
Alignment explanation
Indices: 583312--583377 Score: 57
Period size: 14 Copynumber: 4.6 Consensus size: 14
583302 TTATGGTAAT
583312 TTTACTATATTTAT-
1 TTTA-TATATTTATA
*
583326 TTTAT-TTTTTATA
1 TTTATATATTTATA
583339 TTATATTATATTT-TAA
1 TT-TA-TATATTTAT-A
*
583355 TTTTTATATTTATA
1 TTTATATATTTATA
583369 TTTATATAT
1 TTTATATAT
583378 AAATTTAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
12 6 0.14
13 3 0.07
14 22 0.52
15 4 0.10
16 7 0.17
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (14 bp):
TTTATATATTTATA
Found at i:583386 original size:6 final size:6
Alignment explanation
Indices: 583317--583375 Score: 52
Period size: 6 Copynumber: 9.8 Consensus size: 6
583307 GTAATTTTAC
* *
583317 TATATT TAT-TT TAT-TT TTTATAT TATA-T TATATTT TAATTTT TATATT
1 TATATT TATATT TATATT TATAT-T TATATT TATA-TT T-ATATT TATATT
583365 TATATT TATAT
1 TATATT TATAT
583376 ATAAATTTAA
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
5 14 0.32
6 19 0.43
7 9 0.20
8 2 0.05
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TATATT
Found at i:584144 original size:9 final size:9
Alignment explanation
Indices: 584119--584152 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
584109 AATAAAATAT
584119 TAATTACAAA
1 TAATTA-AAA
*
584129 TACTTAAAA
1 TAATTAAAA
584138 TAATTAAAA
1 TAATTAAAA
584147 TAATTA
1 TAATTA
584153 TACTTTTCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 17 0.77
10 5 0.23
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (9 bp):
TAATTAAAA
Found at i:584214 original size:15 final size:15
Alignment explanation
Indices: 584193--584240 Score: 69
Period size: 15 Copynumber: 3.2 Consensus size: 15
584183 CAAAAATCGA
584193 ATTTAAACTTAAATT
1 ATTTAAACTTAAATT
* *
584208 TTTTAAATTTAAATT
1 ATTTAAACTTAAATT
*
584223 AATTAAACTTAAATT
1 ATTTAAACTTAAATT
584238 ATT
1 ATT
584241 ATTTATTAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTTAAACTTAAATT
Found at i:584503 original size:2 final size:2
Alignment explanation
Indices: 584496--584542 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
584486 TTAGTTATCT
584496 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
584538 TC TC T
1 TC TC T
584543 ATATATATAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:584547 original size:2 final size:2
Alignment explanation
Indices: 584542--584574 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
584532 TCTCTCTCTC
584542 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
584575 GAGATAAGCG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:595184 original size:6 final size:6
Alignment explanation
Indices: 595163--595300 Score: 66
Period size: 6 Copynumber: 24.7 Consensus size: 6
595153 TTACTCTCTC
* * * * *
595163 TATA-A TATAAA TATATA TATATCA -AAATT TATTTA AATATA -AT-TA
1 TATATA TATATA TATATA TATAT-A TATATA TATATA TATATA TATATA
* * * *
595208 TA-ATA TATAAA TATATA TAAATA -ATATA AATATA TATCATT TATAT-
1 TATATA TATATA TATATA TATATA TATATA TATATA TAT-ATA TATATA
* * *
595254 TATATA AATATA -ATAT- TA-ATA TATA-A T-TATA AATATA TAAATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
595297 TATA
1 TATA
595301 AATTTATTTT
Statistics
Matches: 100, Mismatches: 19, Indels: 27
0.68 0.13 0.18
Matches are distributed among these distances:
4 6 0.06
5 30 0.30
6 58 0.58
7 6 0.06
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (6 bp):
TATATA
Found at i:595262 original size:24 final size:24
Alignment explanation
Indices: 595173--595300 Score: 95
Period size: 24 Copynumber: 5.2 Consensus size: 24
595163 TATAATATAA
*
595173 ATATATATATATCAAA-ATTTAT-TT
1 ATATATA-ATAT-AAATATATATATT
* *
595197 AAATATAATTATAATATATAAATATAT
1 ATATATAA-TATAA-ATATATATAT-T
*
595224 ATAAATAATATAAATATATATCATT
1 ATATATAATATAAATATATAT-ATT
*
595249 -TATATTATATAAATATA-ATATT
1 ATATATAATATAAATATATATATT
*
595271 AATATATAATTATAAATATATA-AAT
1 -ATATATAA-TATAAATATATATATT
595296 ATATA
1 ATATA
595301 AATTTATTTT
Statistics
Matches: 84, Mismatches: 10, Indels: 20
0.74 0.09 0.18
Matches are distributed among these distances:
22 3 0.04
23 5 0.06
24 36 0.43
25 24 0.29
26 9 0.11
27 7 0.08
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (24 bp):
ATATATAATATAAATATATATATT
Found at i:595263 original size:33 final size:31
Alignment explanation
Indices: 595199--595301 Score: 68
Period size: 33 Copynumber: 3.2 Consensus size: 31
595189 ATTTATTTAA
595199 ATATAATTAT-AATATATAAATATATATAAAT
1 ATATAATTATAAATATATAAATA-ATATAAAT
* * * * *
595230 AATATAAATATATATCATTTATATTATATAAAT
1 -ATATAATTATAAAT-ATATAAATAATATAAAT
*
595263 ATA-ATATTAATATATAATTATAAAT-ATATAAAT
1 ATATA-ATT-ATAAAT-A-TATAAATAATATAAAT
595296 ATATAA
1 ATATAA
595302 ATTTATTTTA
Statistics
Matches: 56, Mismatches: 9, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
31 1 0.02
32 14 0.25
33 29 0.52
34 12 0.21
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (31 bp):
ATATAATTATAAATATATAAATAATATAAAT
Found at i:595266 original size:62 final size:60
Alignment explanation
Indices: 595164--595300 Score: 163
Period size: 62 Copynumber: 2.3 Consensus size: 60
595154 TACTCTCTCT
* * *
595164 ATAATATAAATATATATATATCAAAATTTATTTAAATATAAT-TATAATATATAAATATAT
1 ATAATATAAATATATATATATCAAAATTTATATAAATATAATAT-TAATATATAATTATAA
* **
595224 ATAA-ATAATATAAATATATATCATTTATATTATATAAATATAATATTAATATATAATTATAA
1 ATAATATAA-ATATATATATATCA-AAAT-TTATATAAATATAATATTAATATATAATTATAA
595286 AT-ATATAAATATATA
1 ATAATATAAATATATA
595301 AATTTATTTT
Statistics
Matches: 65, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
59 4 0.06
60 17 0.26
61 9 0.14
62 34 0.52
63 1 0.02
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (60 bp):
ATAATATAAATATATATATATCAAAATTTATATAAATATAATATTAATATATAATTATAA
Found at i:595267 original size:35 final size:33
Alignment explanation
Indices: 595163--595298 Score: 115
Period size: 35 Copynumber: 4.1 Consensus size: 33
595153 TTACTCTCTC
* **
595163 TATAATATAAATATAT-ATATATCAAA-ATTTATT
1 TATAATATAAATATATAAT-TAT-AAATATATAAA
595196 TA-AATAT-AAT-TATAATATATAAATATATATAA
1 TATAATATAAATATATAAT-TATAAATATATA-AA
*
595228 -ATAATATAAATATATATCATT-TATATTATATAAA
1 TATAATATAAATATATA--ATTATA-AATATATAAA
*
595262 TATAATATTAATATATAATTATAAATATATAAA
1 TATAATATAAATATATAATTATAAATATATAAA
595295 TATA
1 TATA
595299 TAAATTTATT
Statistics
Matches: 86, Mismatches: 6, Indels: 22
0.75 0.05 0.19
Matches are distributed among these distances:
30 6 0.07
31 14 0.16
32 10 0.12
33 21 0.24
34 10 0.12
35 23 0.27
36 2 0.02
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (33 bp):
TATAATATAAATATATAATTATAAATATATAAA
Found at i:598425 original size:21 final size:22
Alignment explanation
Indices: 598360--598426 Score: 64
Period size: 24 Copynumber: 3.0 Consensus size: 22
598350 TTTGAATTAC
*
598360 TATTTAATAATAAAAATAATATTT
1 TATTTAAT-ATAAAAATAATA-TA
* **
598384 TATTTAAATTTAATTATAATATA
1 TATTT-AATATAAAAATAATATA
598407 TA-TTAATATAAAAATAATAT
1 TATTTAATATAAAAATAATAT
598427 TTTGAAAATA
Statistics
Matches: 35, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
21 13 0.37
22 2 0.06
23 3 0.09
24 14 0.40
25 3 0.09
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
TATTTAATATAAAAATAATATA
Found at i:601534 original size:16 final size:16
Alignment explanation
Indices: 601512--601544 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
601502 ATGAATATTT
*
601512 TAAAAAAAATA-AGAG
1 TAAAAAAAATATAAAG
601527 TAAAAAAAATATAAAG
1 TAAAAAAAATATAAAG
601543 TA
1 TA
601545 TGGTTATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.73, C:0.00, G:0.09, T:0.18
Consensus pattern (16 bp):
TAAAAAAAATATAAAG
Found at i:608163 original size:18 final size:20
Alignment explanation
Indices: 608140--608180 Score: 68
Period size: 18 Copynumber: 2.1 Consensus size: 20
608130 GATTTAGTTA
608140 AAAATAATATT-TTTAA-AT
1 AAAATAATATTATTTAATAT
608158 AAAATAATATTATTTAATAT
1 AAAATAATATTATTTAATAT
608178 AAA
1 AAA
608181 TTTAATTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 11 0.52
19 5 0.24
20 5 0.24
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
AAAATAATATTATTTAATAT
Found at i:608186 original size:21 final size:21
Alignment explanation
Indices: 608144--608207 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 21
608134 TAGTTAAAAA
*
608144 TAATATT-TTTAA-ATAAA-A
1 TAATATTATTTAATATAAATT
608162 TAATATTATTTAATATAAATT
1 TAATATTATTTAATATAAATT
608183 T-A-ATTATATT-ATATAAATAT
1 TAATATTAT-TTAATATAAAT-T
608203 TAATA
1 TAATA
608208 AAAAATTTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
18 7 0.18
19 18 0.47
20 10 0.26
21 2 0.05
22 1 0.03
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
TAATATTATTTAATATAAATT
Found at i:608223 original size:21 final size:20
Alignment explanation
Indices: 608198--608237 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
608188 ATATTATATA
*
608198 AATATTAATAAAAAATTTAAT
1 AATATAAAT-AAAAATTTAAT
*
608219 AATATAAATAATAATTTAA
1 AATATAAATAAAAATTTAA
608238 ACTTAAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
AATATAAATAAAAATTTAAT
Found at i:608246 original size:18 final size:18
Alignment explanation
Indices: 608223--608263 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
608213 TTTAATAATA
*
608223 TAAAT-AATAATTTAAACT
1 TAAATAAATAAATTAAA-T
608241 TAAATAAATAAATTAAAT
1 TAAATAAATAAATTAAAT
608259 TAAAT
1 TAAAT
608264 CCTATTTAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 11 0.52
19 10 0.48
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (18 bp):
TAAATAAATAAATTAAAT
Found at i:608246 original size:27 final size:27
Alignment explanation
Indices: 608184--608253 Score: 70
Period size: 27 Copynumber: 2.6 Consensus size: 27
608174 ATATAAATTT
* * *
608184 AATTATATTATATAAATATTAATAAAA
1 AATTAAATAATATAAATAATAATAAAA
* **
608211 AATTTAATAATATAAATAATAATTTAA
1 AATTAAATAATATAAATAATAATAAAA
*
608238 ACTTAAATAA-ATAAAT
1 AATTAAATAATATAAAT
608254 TAAATTAAAT
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
26 6 0.17
27 29 0.83
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (27 bp):
AATTAAATAATATAAATAATAATAAAA
Found at i:608599 original size:148 final size:149
Alignment explanation
Indices: 608346--608635 Score: 415
Period size: 148 Copynumber: 2.0 Consensus size: 149
608336 ATAATGCTTT
* * ** *
608346 TAATTTTTTTAATTATTTTATTTCAATTTGAGTTAAGTTTATTTATAATAAAATTTGTTCAAGAG
1 TAATTTTTTTAATTATTTTATTTCAATTTGAGTCAAGTTCATCCATAATAAAATTTGTTCAAAAG
* * * *
608411 TCGAATTATTCGTTTAAGCTTAAAAATTAATTAGATATTTAGTA-GAGTTTTAATAAAAATATTA
66 TCAAATTATTCATTTAAGCTTAAAAATTAATTAGATATTTAATAGGA-TTTAAATAAAAATATTA
*
608475 AATTTAAAAAATAATGACTC
130 AATTAAAAAAATAATGACTC
* *
608495 TAATTTTTTTAATTATTTTATTTCAATTTGAGTCAAGTTCATCCATAAT-AAATTTTTTTAAAAG
1 TAATTTTTTTAATTATTTTATTTCAATTTGAGTCAAGTTCATCCATAATAAAATTTGTTCAAAAG
*
608559 TCAAATTATTCATTTAAGCTTAAAAATTAATTCA-ATATTTAATAGGATTTAAATAAAATTATTA
66 TCAAATTATTCATTTAAGCTTAAAAATTAATT-AGATATTTAATAGGATTTAAATAAAAATATTA
*
608623 GATTAAAAAAATA
130 AATTAAAAAAATA
608636 GATTTAAATA
Statistics
Matches: 125, Mismatches: 14, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
148 77 0.62
149 48 0.38
ACGTcount: A:0.42, C:0.06, G:0.08, T:0.45
Consensus pattern (149 bp):
TAATTTTTTTAATTATTTTATTTCAATTTGAGTCAAGTTCATCCATAATAAAATTTGTTCAAAAG
TCAAATTATTCATTTAAGCTTAAAAATTAATTAGATATTTAATAGGATTTAAATAAAAATATTAA
ATTAAAAAAATAATGACTC
Found at i:608761 original size:21 final size:21
Alignment explanation
Indices: 608718--608757 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
608708 TTTTATTATA
* *
608718 AAATTTATATTCTTATAATAT
1 AAATATATATTCTTAAAATAT
608739 AAATATATATT-TTAAAATA
1 AAATATATATTCTTAAAATA
608758 ATAATTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (21 bp):
AAATATATATTCTTAAAATAT
Found at i:608830 original size:27 final size:27
Alignment explanation
Indices: 608799--608857 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
608789 TTTGTTAAAT
* *
608799 TTTTTTATAATAAAAGTCATACAATATA
1 TTTTTTA-AATAAAAGTAATAAAATATA
* *
608827 TTTTTTAAATAATATTAATAAAATATA
1 TTTTTTAAATAAAAGTAATAAAATATA
608854 TTTT
1 TTTT
608858 AATTATTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
27 20 0.74
28 7 0.26
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.49
Consensus pattern (27 bp):
TTTTTTAAATAAAAGTAATAAAATATA
Found at i:608901 original size:21 final size:20
Alignment explanation
Indices: 608863--608901 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
608853 ATTTTAATTA
* *
608863 TTAAAAATTAAATTAATATT
1 TTAAAAAATAAATGAATATT
608883 TTAAAAAATAACATGAATA
1 TTAAAAAATAA-ATGAATA
608902 AATATAAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.36
Consensus pattern (20 bp):
TTAAAAAATAAATGAATATT
Found at i:609095 original size:16 final size:16
Alignment explanation
Indices: 609074--609195 Score: 68
Period size: 16 Copynumber: 7.2 Consensus size: 16
609064 TTTTATGGTA
609074 TAAATTTAAAATAATT
1 TAAATTTAAAATAATT
*
609090 TAAATTT-AATTAATT
1 TAAATTTAAAATAATT
* * *
609105 TATATATTGAACTAAATT
1 TAAAT-TTAAAAT-AATT
*
609123 AATACGAATATAAAATAATT
1 --TA--AATTTAAAATAATT
* *
609143 AAAATCTAAAATAATT
1 TAAATTTAAAATAATT
* *
609159 AAAATATAAAAATAATT
1 TAAAT-TTAAAATAATT
609176 TAAAATTTAATAA-AATT
1 T-AAATTTAA-AATAATT
609193 TAA
1 TAA
609196 TCGCCCAAGG
Statistics
Matches: 83, Mismatches: 13, Indels: 20
0.72 0.11 0.17
Matches are distributed among these distances:
15 11 0.13
16 29 0.35
17 20 0.24
18 11 0.13
20 6 0.07
21 4 0.05
22 2 0.02
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (16 bp):
TAAATTTAAAATAATT
Found at i:609147 original size:9 final size:9
Alignment explanation
Indices: 609133--609181 Score: 50
Period size: 9 Copynumber: 5.7 Consensus size: 9
609123 AATACGAATA
609133 TAAAATAAT
1 TAAAATAAT
*
609142 TAAAAT--C
1 TAAAATAAT
609149 TAAAATAAT
1 TAAAATAAT
609158 TAAAAT-AT
1 TAAAATAAT
*
609166 AAAAATAATT
1 TAAAATAA-T
609176 TAAAAT
1 TAAAAT
609182 TTAATAAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
7 6 0.19
8 7 0.22
9 13 0.41
10 6 0.19
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (9 bp):
TAAAATAAT
Found at i:609192 original size:17 final size:18
Alignment explanation
Indices: 609129--609195 Score: 72
Period size: 16 Copynumber: 4.0 Consensus size: 18
609119 AATTAATACG
609129 AATAT-AAAATAA-TTAA
1 AATATAAAAATAATTTAA
*
609145 AATCT-AAAATAA-TTAA
1 AATATAAAAATAATTTAA
609161 AATATAAAAATAATTTAA
1 AATATAAAAATAATTTAA
* *
609179 AATTTAATAA-AATTTAA
1 AATATAAAAATAATTTAA
609196 TCGCCCAAGG
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
16 19 0.42
17 14 0.31
18 12 0.27
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.34
Consensus pattern (18 bp):
AATATAAAAATAATTTAA
Found at i:609287 original size:16 final size:16
Alignment explanation
Indices: 609266--609298 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
609256 ATATAATAGG
609266 CTGAGACGGTAAAGAT
1 CTGAGACGGTAAAGAT
609282 CTGAGACGGTAAAGAT
1 CTGAGACGGTAAAGAT
609298 C
1 C
609299 GGTGGAGAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.15, G:0.30, T:0.18
Consensus pattern (16 bp):
CTGAGACGGTAAAGAT
Found at i:612320 original size:12 final size:13
Alignment explanation
Indices: 612303--612333 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
612293 ATAAATAACG
612303 AAAAAAGAACC-A
1 AAAAAAGAACCGA
612315 AAAAAAGAACCGA
1 AAAAAAGAACCGA
612328 AAAAAA
1 AAAAAA
612334 AAAAAAACTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.77, C:0.13, G:0.10, T:0.00
Consensus pattern (13 bp):
AAAAAAGAACCGA
Found at i:616090 original size:12 final size:12
Alignment explanation
Indices: 616073--616116 Score: 54
Period size: 12 Copynumber: 3.6 Consensus size: 12
616063 AAATTTTAAT
616073 TTTATATTAAAA
1 TTTATATTAAAA
616085 TTTATATTAAAAA
1 TTTATATT-AAAA
*
616098 TATTA-AATAAAA
1 T-TTATATTAAAA
616110 TTTATAT
1 TTTATAT
616117 ATTAATATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
11 3 0.11
12 14 0.52
13 7 0.26
14 3 0.11
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
TTTATATTAAAA
Found at i:616169 original size:2 final size:2
Alignment explanation
Indices: 616162--616198 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
616152 ATAAGTGATA
616162 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
616199 CACACACTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:616627 original size:14 final size:13
Alignment explanation
Indices: 616598--616624 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
616588 ATAAATATAT
616598 ATTTTATTTTTTA
1 ATTTTATTTTTTA
616611 ATTTTATTTTTTA
1 ATTTTATTTTTTA
616624 A
1 A
616625 ATTATATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (13 bp):
ATTTTATTTTTTA
Found at i:616682 original size:18 final size:17
Alignment explanation
Indices: 616647--616685 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
616637 TATTCATATT
616647 TAAATATTTATTAAAAA
1 TAAATATTTATTAAAAA
616664 TAAATA-TTATTCAAAAAA
1 TAAATATTTATT--AAAAA
616682 TAAA
1 TAAA
616686 ATCTAAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 5 0.25
17 6 0.30
18 9 0.45
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (17 bp):
TAAATATTTATTAAAAA
Found at i:617396 original size:28 final size:28
Alignment explanation
Indices: 617365--617420 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
617355 TTATTTATTA
* * * *
617365 ATAAATATATTTTTATTTAAAATTAATT
1 ATAAATATATATTAATATAAAAATAATT
617393 ATAAATATATATTAATATAAAAATAATT
1 ATAAATATATATTAATATAAAAATAATT
617421 TTTTAAAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (28 bp):
ATAAATATATATTAATATAAAAATAATT
Found at i:623736 original size:17 final size:19
Alignment explanation
Indices: 623688--623736 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 19
623678 TTTAAAAATA
*
623688 TTAATATAAAAATATATCT
1 TTAATATAATAATATATCT
**
623707 TTAATATTTTAATATAT-T
1 TTAATATAATAATATATCT
623725 TTAA-ATAATAAT
1 TTAATATAATAAT
623737 TTAAATTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
17 6 0.24
18 5 0.20
19 14 0.56
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (19 bp):
TTAATATAATAATATATCT
Found at i:625409 original size:10 final size:10
Alignment explanation
Indices: 625391--625466 Score: 54
Period size: 10 Copynumber: 7.9 Consensus size: 10
625381 TATATTATAA
*
625391 TATTAAAATT
1 TATTTAAATT
625401 TATTTAAATT
1 TATTTAAATT
* *
625411 AAATTAAATTT
1 TATTTAAA-TT
625422 TATTT---TT
1 TATTTAAATT
625429 TAATTT-AATT
1 T-ATTTAAATT
625439 TATTTAAA-T
1 TATTTAAATT
*
625448 TAATTAAATT
1 TATTTAAATT
*
625458 TAATTAAAT
1 TATTTAAAT
625467 AAATTTAGTA
Statistics
Matches: 54, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
7 3 0.06
8 4 0.07
9 12 0.22
10 30 0.56
11 5 0.09
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (10 bp):
TATTTAAATT
Found at i:625426 original size:47 final size:46
Alignment explanation
Indices: 625372--625466 Score: 111
Period size: 47 Copynumber: 2.0 Consensus size: 46
625362 TCGAATCGAG
*
625372 TTATATTTTTATATTATAA-TATTAAAATTTATTTAAATTAAATTAAATT
1 TTAT-TTTTTA-ATT-TAATTATTAAAA-TTAATTAAATTAAATTAAATT
* *
625421 TTATTTTTTAATTTAATTTATTTAAATTAATTAAATTTAATTAAAT
1 TTATTTTTTAATTTAA-TTATTAAAATTAATTAAATTAAATTAAAT
625467 AAATTTAGTA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
46 3 0.07
47 21 0.51
48 13 0.32
49 4 0.10
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (46 bp):
TTATTTTTTAATTTAATTATTAAAATTAATTAAATTAAATTAAATT
Found at i:625435 original size:5 final size:5
Alignment explanation
Indices: 625397--625462 Score: 50
Period size: 5 Copynumber: 13.8 Consensus size: 5
625387 ATAATATTAA
* * *
625397 AATTT -ATTT AAATTA AATTA AATTT TATTT --TTT AATTT AATTT -ATTT
1 AATTT AATTT -AATTT AATTT AATTT AATTT AATTT AATTT AATTT AATTT
* *
625444 AAATT AATTA AATTT AATT
1 AATTT AATTT AATTT AATT
625463 AAATAAATTT
Statistics
Matches: 49, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
3 3 0.06
4 8 0.16
5 35 0.71
6 3 0.06
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
AATTT
Found at i:625463 original size:14 final size:14
Alignment explanation
Indices: 625427--625473 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
625417 AATTTTATTT
*
625427 TTTAATTTAATT-TA
1 TTTAA-TTAATTAAA
625441 TTTAAATTAATTAAA
1 TTT-AATTAATTAAA
*
625456 TTTAATTAAATAAA
1 TTTAATTAATTAAA
625470 TTTA
1 TTTA
625474 GTAAGATAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 23 0.79
15 6 0.21
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TTTAATTAATTAAA
Found at i:625577 original size:38 final size:34
Alignment explanation
Indices: 625524--625611 Score: 92
Period size: 39 Copynumber: 2.5 Consensus size: 34
625514 ATTAATTAAA
625524 ATTATTTAATTATT-AATTTAAAATAATTTATATTTAATAT
1 ATTATTT--TTATTAAATTTAAAA-AA--TATA-TTAAT-T
625564 ATTATTTTTATTAAATTTAAAAAATATATTAATT
1 ATTATTTTTATTAAATTTAAAAAATATATTAATT
625598 A-TATTTTTA-TAAAT
1 ATTATTTTTATTAAAT
625612 ATTTTCTTGA
Statistics
Matches: 47, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
32 5 0.11
33 8 0.17
34 2 0.04
35 5 0.11
36 4 0.09
38 7 0.15
39 9 0.19
40 7 0.15
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (34 bp):
ATTATTTTTATTAAATTTAAAAAATATATTAATT
Found at i:625637 original size:21 final size:21
Alignment explanation
Indices: 625612--625652 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
625602 TTTTATAAAT
625612 ATTTTCTTGATATTAATTGAC
1 ATTTTCTTGATATTAATTGAC
*
625633 ATTTTCTTTATATTAATTGA
1 ATTTTCTTGATATTAATTGA
625653 AATGAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.07, G:0.07, T:0.56
Consensus pattern (21 bp):
ATTTTCTTGATATTAATTGAC
Found at i:625968 original size:21 final size:21
Alignment explanation
Indices: 625939--625979 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
625929 AATTTAAATA
*
625939 TTAATATTAATATTTTTTATTT
1 TTAATATT-ATAATTTTTATTT
625961 TTAA-ATTATAATTTTTATT
1 TTAATATTATAATTTTTATT
625980 GTATAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 11 0.61
21 3 0.17
22 4 0.22
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (21 bp):
TTAATATTATAATTTTTATTT
Found at i:627090 original size:103 final size:100
Alignment explanation
Indices: 626894--627208 Score: 371
Period size: 103 Copynumber: 3.2 Consensus size: 100
626884 ATTAAATAAA
* * ** *
626894 TAAATAAAATTAAAAAAATAAAGATAAAAATAATTTGAAGTAAATATGGTAAAATACTTTTTCTT
1 TAAAT-AAA-TAAATAAAT-AA-ATAAAAATACTTTGAAGTAAATATCATAAAATACTTTTACTT
626959 TCCAAAAATAGAAAAAAACCTATTTTTTATTTTAATTAAG-TT
62 TCCAAAAATAGAAAAAAA-C---TTTTTATTTTAATTAAGTTT
* *
627001 TAAATAAATAAATAAATAAATAAAAATACTTTGAAGTAATTATCATAAAATACTTTTAATTTCCA
1 TAAATAAATAAATAAATAAATAAAAATACTTTGAAGTAAATATCATAAAATACTTTTACTTTCCA
*
627066 AAAATA-AAAAACTA-TTTTTATTTTAATTAAGTTT
66 AAAATAGAAAAA-AACTTTTTATTTTAATTAAGTTT
* *
627100 TAAA-AAATAAAT-AA-AAATAAAAATACTTTGAAGTAAGTATCATAAAATAC-TTTACTTTACA
1 TAAATAAATAAATAAATAAATAAAAATACTTTGAAGTAAATATCATAAAATACTTTTACTTTCCA
*
627161 AAAATAGAAAAAAA--ATTTATTTTAATTAA-TTT
66 AAAATAGAAAAAAACTTTTTATTTTAATTAAGTTT
*
627193 TCAATAAATAAATAAA
1 TAAATAAATAAATAAA
627209 ATGAACTTGT
Statistics
Matches: 189, Mismatches: 14, Indels: 22
0.84 0.06 0.10
Matches are distributed among these distances:
93 6 0.03
94 22 0.12
95 18 0.10
96 40 0.21
97 2 0.01
98 25 0.13
99 6 0.03
102 5 0.03
103 47 0.25
104 2 0.01
105 8 0.04
106 3 0.02
107 5 0.03
ACGTcount: A:0.54, C:0.06, G:0.04, T:0.36
Consensus pattern (100 bp):
TAAATAAATAAATAAATAAATAAAAATACTTTGAAGTAAATATCATAAAATACTTTTACTTTCCA
AAAATAGAAAAAAACTTTTTATTTTAATTAAGTTT
Done.