Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D13
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: 64892201
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 205 of 221
Found at i:60212691 original size:25 final size:25
Alignment explanation
Indices: 60212657--60212726 Score: 122
Period size: 25 Copynumber: 2.8 Consensus size: 25
60212647 TCGAATTTTA
*
60212657 AAAAAAAATCGAACATTTTTTTATT
1 AAAAAAAATCCAACATTTTTTTATT
60212682 AAAAAAAATCCAACATTTTTTTATT
1 AAAAAAAATCCAACATTTTTTTATT
*
60212707 CAAAAAAATCCAACATTTTT
1 AAAAAAAATCCAACATTTTT
60212727 CGACCGAAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 43 1.00
ACGTcount: A:0.49, C:0.13, G:0.01, T:0.37
Consensus pattern (25 bp):
AAAAAAAATCCAACATTTTTTTATT
Found at i:60213142 original size:16 final size:16
Alignment explanation
Indices: 60213097--60213147 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
60213087 TAACTCAAAC
60213097 TAATATTATTTTAATTTT
1 TAATATTATTTTAA--TT
*
60213115 TTATATTATTTTAATT
1 TAATATTATTTTAATT
* *
60213131 TAATATTTTTTTCATT
1 TAATATTATTTTAATT
60213147 T
1 T
60213148 TATTAAAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
16 16 0.55
18 13 0.45
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (16 bp):
TAATATTATTTTAATT
Found at i:60213664 original size:3 final size:3
Alignment explanation
Indices: 60213656--60213686 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
60213646 AGAAAAATGC
60213656 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
60213687 CAATATAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:60214548 original size:3 final size:3
Alignment explanation
Indices: 60214542--60214598 Score: 98
Period size: 3 Copynumber: 19.0 Consensus size: 3
60214532 ATCTTCTTCT
60214542 TCC TCC TCC TCC TCC T-C TCC TCC TCC TCTC TCC TCC TCC TCC TCC
1 TCC TCC TCC TCC TCC TCC TCC TCC TCC TC-C TCC TCC TCC TCC TCC
60214587 TCC TCC TCC TCC
1 TCC TCC TCC TCC
60214599 CTTCTCTCGC
Statistics
Matches: 52, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.04
3 47 0.90
4 3 0.06
ACGTcount: A:0.00, C:0.65, G:0.00, T:0.35
Consensus pattern (3 bp):
TCC
Found at i:60217038 original size:20 final size:18
Alignment explanation
Indices: 60217003--60217039 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 18
60216993 ATGTAAATTG
60217003 TATATATGTATAAAATGA
1 TATATATGTATAAAATGA
60217021 TATATATCGTATATAAATG
1 TATATAT-GTATA-AAATG
60217040 TTAACACTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
19 5 0.29
20 5 0.29
ACGTcount: A:0.46, C:0.03, G:0.11, T:0.41
Consensus pattern (18 bp):
TATATATGTATAAAATGA
Found at i:60221066 original size:23 final size:24
Alignment explanation
Indices: 60221040--60221089 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
60221030 CCGTTACTTG
*
60221040 TTAAGCTC-AATGAGCTTCATGTT
1 TTAAACTCTAATGAGCTTCATGTT
* * *
60221063 TTAAACTCTTATGAGTTTCCTGTT
1 TTAAACTCTAATGAGCTTCATGTT
60221087 TTA
1 TTA
60221090 GCCCGGATAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.24, C:0.16, G:0.14, T:0.46
Consensus pattern (24 bp):
TTAAACTCTAATGAGCTTCATGTT
Found at i:60229474 original size:55 final size:55
Alignment explanation
Indices: 60229385--60229493 Score: 191
Period size: 55 Copynumber: 2.0 Consensus size: 55
60229375 AGATAAACCG
*
60229385 TTCATGGGTTGAGTTATTTTTTCAAGCTTGAAGGTCTGTCTGAAATTTGAAAGGA
1 TTCATGGGTTGAGTTATTTTTTCAAGCTTAAAGGTCTGTCTGAAATTTGAAAGGA
* *
60229440 TTCATGGGTTGAGTTATTTTTTTAAGCTTAAAGGTCTGTTTGAAATTTGAAAGG
1 TTCATGGGTTGAGTTATTTTTTCAAGCTTAAAGGTCTGTCTGAAATTTGAAAGG
60229494 GTGTGGACAA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
55 51 1.00
ACGTcount: A:0.26, C:0.07, G:0.25, T:0.42
Consensus pattern (55 bp):
TTCATGGGTTGAGTTATTTTTTCAAGCTTAAAGGTCTGTCTGAAATTTGAAAGGA
Found at i:60229695 original size:17 final size:16
Alignment explanation
Indices: 60229640--60229790 Score: 55
Period size: 17 Copynumber: 9.3 Consensus size: 16
60229630 AATATATTAA
**
60229640 TAAAATAAATTTATAT
1 TAAAATAAATAAATAT
*
60229656 T-AAATATAT-AATAT
1 TAAAATAAATAAATAT
***
60229670 TACTCTAATATAAATAT
1 TAAAATAA-ATAAATAT
60229687 TAAAATAATATTAAGATGAT
1 TAAAATAA-A-TAA-AT-AT
* *
60229707 T-ATATAAA-AAATTT
1 TAAAATAAATAAATAT
*
60229721 TAATAAATAAA-AAATGT
1 T-A-AAATAAATAAATAT
* *
60229738 GTAAAATTATTAAATAT
1 -TAAAATAAATAAATAT
60229755 TAAAATAAGATAAA-A-
1 TAAAATAA-ATAAATAT
**
60229770 TAAAATAAATATTTAT
1 TAAAATAAATAAATAT
60229786 TAAAA
1 TAAAA
60229791 ATTTTAAAAA
Statistics
Matches: 101, Mismatches: 20, Indels: 28
0.68 0.13 0.19
Matches are distributed among these distances:
14 10 0.10
15 20 0.20
16 23 0.23
17 33 0.33
18 5 0.05
19 7 0.07
20 3 0.03
ACGTcount: A:0.58, C:0.01, G:0.03, T:0.37
Consensus pattern (16 bp):
TAAAATAAATAAATAT
Found at i:60231807 original size:31 final size:29
Alignment explanation
Indices: 60231765--60231833 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
60231755 AAATATTAAA
*
60231765 ATTATATATGAACTTTCG-TTTAATGTACAAT
1 ATTATACATGAA-TTTCGATTT--TGTACAAT
*
60231796 ATTATACATGAATTTTGATTTTGTACAAT
1 ATTATACATGAATTTCGATTTTGTACAAT
*
60231825 TTTATACAT
1 ATTATACAT
60231834 TAAATTTTCG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 16 0.47
30 4 0.12
31 14 0.41
ACGTcount: A:0.35, C:0.09, G:0.09, T:0.48
Consensus pattern (29 bp):
ATTATACATGAATTTCGATTTTGTACAAT
Found at i:60237385 original size:23 final size:22
Alignment explanation
Indices: 60237351--60237411 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 22
60237341 TTTTTTGCGC
*
60237351 TTTTTGCTTTTTTTTTC-CTTTT
1 TTTTTGCCTTTTTTTTCAC-TTT
**
60237373 TTTTTGCACTTTTTACTCACTTT
1 TTTTTGC-CTTTTTTTTCACTTT
60237396 TTTTTGCGCTTTTTTT
1 TTTTTGC-CTTTTTTT
60237412 GTTTTTTTAA
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
22 7 0.23
23 23 0.74
24 1 0.03
ACGTcount: A:0.05, C:0.16, G:0.07, T:0.72
Consensus pattern (22 bp):
TTTTTGCCTTTTTTTTCACTTT
Found at i:60237397 original size:31 final size:31
Alignment explanation
Indices: 60237337--60237397 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
60237327 AGGTAGGCAA
* * ***
60237337 CTTTTTTTTTGCGCTTTTTGCTTTTTTTTTC
1 CTTTTTTTTTGCACTTTTTACTCACTTTTTC
60237368 CTTTTTTTTTGCACTTTTTACTCACTTTTT
1 CTTTTTTTTTGCACTTTTTACTCACTTTTT
60237398 TTTGCGCTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.05, C:0.18, G:0.07, T:0.70
Consensus pattern (31 bp):
CTTTTTTTTTGCACTTTTTACTCACTTTTTC
Found at i:60238069 original size:25 final size:24
Alignment explanation
Indices: 60238020--60238070 Score: 75
Period size: 25 Copynumber: 2.1 Consensus size: 24
60238010 CTTTAAAATT
60238020 ATCTAAGAAAATAAATAAATAATA
1 ATCTAAGAAAATAAATAAATAATA
* *
60238044 ATCTAATAAAATTAACTAAATAATA
1 ATCTAAGAAAA-TAAATAAATAATA
60238069 AT
1 AT
60238071 AATAAGATAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 10 0.42
25 14 0.58
ACGTcount: A:0.63, C:0.06, G:0.02, T:0.29
Consensus pattern (24 bp):
ATCTAAGAAAATAAATAAATAATA
Found at i:60242082 original size:31 final size:31
Alignment explanation
Indices: 60242039--60242099 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
60242029 TTGCAAGATC
*
60242039 AACGGCTCTGATATCCTT-GTGATGGACATCT
1 AACGGCTCTGATAT-CTTCATGATGGACATCT
*
60242070 AACGGCTTTGATATCTTCATGATGGACATC
1 AACGGCTCTGATATCTTCATGATGGACATC
60242100 ACACGGGTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 3 0.11
31 24 0.89
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (31 bp):
AACGGCTCTGATATCTTCATGATGGACATCT
Found at i:60245151 original size:3 final size:3
Alignment explanation
Indices: 60245139--60245169 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
60245129 AGATCTACAA
60245139 ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
60245170 CAAACTCATT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:60258068 original size:30 final size:31
Alignment explanation
Indices: 60258034--60258092 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
60258024 AGAAGAACTT
60258034 AATAGCCCAGTGATTTAAAT-AAAACTTTTG
1 AATAGCCCAGTGATTTAAATAAAAACTTTTG
**
60258064 AATAGTTCAGTGATTTAAATAAAAACTTT
1 AATAGCCCAGTGATTTAAATAAAAACTTT
60258093 CAAATAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 18 0.69
31 8 0.31
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.36
Consensus pattern (31 bp):
AATAGCCCAGTGATTTAAATAAAAACTTTTG
Found at i:60258385 original size:22 final size:23
Alignment explanation
Indices: 60258360--60258403 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
60258350 AATTTAAATC
*
60258360 ATTAATACA-ATTAAAATTTTTT
1 ATTAAGACACATTAAAATTTTTT
*
60258382 ATTAAGACACATTATAATTTTT
1 ATTAAGACACATTAAAATTTTT
60258404 AGAGGAGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (23 bp):
ATTAAGACACATTAAAATTTTTT
Found at i:60262521 original size:17 final size:17
Alignment explanation
Indices: 60262495--60262528 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
60262485 CAAAGTTTGA
* *
60262495 ATTATTATTTGTATTCC
1 ATTATAATTTATATTCC
60262512 ATTATAATTTATATTCC
1 ATTATAATTTATATTCC
60262529 CAATTTTTCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.29, C:0.12, G:0.03, T:0.56
Consensus pattern (17 bp):
ATTATAATTTATATTCC
Found at i:60274433 original size:23 final size:23
Alignment explanation
Indices: 60274407--60274456 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
60274397 TAAACAAATT
60274407 CAATTTCCAGCAGAC-AATCAA-AA
1 CAATTTCCAG-A-ACAAATCAAGAA
60274430 CAATTTCCAGAACAAATCAAGAA
1 CAATTTCCAGAACAAATCAAGAA
60274453 CAAT
1 CAAT
60274457 ATCAAAACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 2 0.08
22 7 0.28
23 16 0.64
ACGTcount: A:0.50, C:0.24, G:0.08, T:0.18
Consensus pattern (23 bp):
CAATTTCCAGAACAAATCAAGAA
Found at i:60274465 original size:22 final size:22
Alignment explanation
Indices: 60274422--60274468 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
60274412 TCCAGCAGAC
* *
60274422 AATCAAAACAATTTCCAGAACA
1 AATCAAAACAATATCCAAAACA
60274444 AATCAAGAACAATAT-CAAAACA
1 AATCAA-AACAATATCCAAAACA
60274466 AAT
1 AAT
60274469 GCAACAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.60, C:0.19, G:0.04, T:0.17
Consensus pattern (22 bp):
AATCAAAACAATATCCAAAACA
Found at i:60276684 original size:27 final size:27
Alignment explanation
Indices: 60276618--60276684 Score: 98
Period size: 27 Copynumber: 2.5 Consensus size: 27
60276608 TAGGTTGTGG
* *
60276618 CTATTTGATAGGCGCGACTAGTTGAGC
1 CTATCTGACAGGCGCGACTAGTTGAGC
* *
60276645 CTATCTCAGAGGCGCGACTAGTTGAGC
1 CTATCTGACAGGCGCGACTAGTTGAGC
60276672 CTATCTGACAGGC
1 CTATCTGACAGGC
60276685 ACAACTAACT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.22, C:0.24, G:0.28, T:0.25
Consensus pattern (27 bp):
CTATCTGACAGGCGCGACTAGTTGAGC
Found at i:60276691 original size:27 final size:27
Alignment explanation
Indices: 60276634--60276691 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
60276624 GATAGGCGCG
* * *
60276634 ACTAGTTGAGCCTATCTCAGAGGCGCG
1 ACTAGTTGAGCCTATCTCACAGGCACA
*
60276661 ACTAGTTGAGCCTATCTGACAGGCACA
1 ACTAGTTGAGCCTATCTCACAGGCACA
60276688 ACTA
1 ACTA
60276692 ACTGAGAGGC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.28, C:0.26, G:0.24, T:0.22
Consensus pattern (27 bp):
ACTAGTTGAGCCTATCTCACAGGCACA
Found at i:60276697 original size:27 final size:27
Alignment explanation
Indices: 60276640--60276697 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
60276630 CGCGACTAGT
* * * **
60276640 TGAGCCTATCTCAGAGGCGCGACTAGT
1 TGAGCCTATCTCACAGGCACAACTAAC
*
60276667 TGAGCCTATCTGACAGGCACAACTAAC
1 TGAGCCTATCTCACAGGCACAACTAAC
60276694 TGAG
1 TGAG
60276698 AGGCGCGAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.21
Consensus pattern (27 bp):
TGAGCCTATCTCACAGGCACAACTAAC
Found at i:60277543 original size:7 final size:7
Alignment explanation
Indices: 60277533--60277570 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
60277523 TCTTTTCTTT
*
60277533 TTTTTTG
1 TTTTCTG
60277540 TTTTCTG
1 TTTTCTG
60277547 TTTTCTG
1 TTTTCTG
*
60277554 TTTGCTG
1 TTTTCTG
60277561 TTTTCT-
1 TTTTCTG
60277567 TTTT
1 TTTT
60277571 ATTCTTTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
6 4 0.14
7 24 0.86
ACGTcount: A:0.00, C:0.11, G:0.13, T:0.76
Consensus pattern (7 bp):
TTTTCTG
Found at i:60280591 original size:62 final size:62
Alignment explanation
Indices: 60280525--60280707 Score: 323
Period size: 62 Copynumber: 3.0 Consensus size: 62
60280515 CACGTATCTC
*
60280525 TTCATTCATTAACATTACATTTCATTACATACAATAAATTTCCTAAAATCCAAAAATACGCG
1 TTCATGCATTAACATTACATTTCATTACATACAATAAATTTCCTAAAATCCAAAAATACGCG
60280587 TTCATGCATTAACATTACATTTCATTACATACAATAAATTTCCTAAAATCCAAAAATACGCG
1 TTCATGCATTAACATTACATTTCATTACATACAATAAATTTCCTAAAATCCAAAAATACGCG
* * *
60280649 TTCATGCATCAACATTACATTTCATTGCATACAATAAATTT-CTAAAATCCAAAAGTACG
1 TTCATGCATTAACATTACATTTCATTACATACAATAAATTTCCTAAAATCCAAAAATACG
60280708 TCGAGTTTAG
Statistics
Matches: 117, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
61 17 0.15
62 100 0.85
ACGTcount: A:0.42, C:0.21, G:0.05, T:0.33
Consensus pattern (62 bp):
TTCATGCATTAACATTACATTTCATTACATACAATAAATTTCCTAAAATCCAAAAATACGCG
Found at i:60281918 original size:14 final size:15
Alignment explanation
Indices: 60281899--60281927 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
60281889 AGTTCAGTAG
60281899 GCAAAAAA-AAAAAA
1 GCAAAAAAGAAAAAA
60281913 GCAAAAAAGAAAAAA
1 GCAAAAAAGAAAAAA
60281928 AAAAAAGTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.83, C:0.07, G:0.10, T:0.00
Consensus pattern (15 bp):
GCAAAAAAGAAAAAA
Found at i:60281941 original size:23 final size:21
Alignment explanation
Indices: 60281901--60281944 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
60281891 TTCAGTAGGC
*
60281901 AAAAAAAAAAAAGCAAAAAAG
1 AAAAAAAAAAAAGAAAAAAAG
60281922 AAAAAAAAAAAAGTTAAAAAAAG
1 AAAAAAAAAAAAG--AAAAAAAG
60281945 GATAACATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 13 0.65
23 7 0.35
ACGTcount: A:0.84, C:0.02, G:0.09, T:0.05
Consensus pattern (21 bp):
AAAAAAAAAAAAGAAAAAAAG
Found at i:60282259 original size:13 final size:12
Alignment explanation
Indices: 60282241--60282287 Score: 58
Period size: 13 Copynumber: 3.7 Consensus size: 12
60282231 ACTTCACTCG
60282241 AAAAAAAGAAACA
1 AAAAAAAGAAA-A
60282254 AAAAAAAGAAAA
1 AAAAAAAGAAAA
*
60282266 AAAAAGAACAAAA
1 AAAAA-AAGAAAA
60282279 AAGAAAAAG
1 AA-AAAAAG
60282288 GAGGGCCAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 6 0.20
13 21 0.70
14 3 0.10
ACGTcount: A:0.85, C:0.04, G:0.11, T:0.00
Consensus pattern (12 bp):
AAAAAAAGAAAA
Found at i:60282266 original size:10 final size:10
Alignment explanation
Indices: 60282240--60282286 Score: 60
Period size: 10 Copynumber: 4.6 Consensus size: 10
60282230 TACTTCACTC
60282240 GAAAAAAAGAA
1 GAAAAAAA-AA
60282251 -ACAAAAAAAA
1 GA-AAAAAAAA
60282261 GAAAAAAAAA
1 GAAAAAAAAA
*
60282271 GAACAAAAAA
1 GAAAAAAAAA
60282281 GAAAAA
1 GAAAAA
60282287 GGAGGGCCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
10 25 0.78
11 7 0.22
ACGTcount: A:0.85, C:0.04, G:0.11, T:0.00
Consensus pattern (10 bp):
GAAAAAAAAA
Found at i:60283366 original size:45 final size:44
Alignment explanation
Indices: 60283315--60283452 Score: 124
Period size: 45 Copynumber: 3.2 Consensus size: 44
60283305 GGAGCTGGTT
60283315 GAAGACAATAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGATC
1 GAAGACAA-AGATCTTGCCTTCCTGTATTGACAGCGAAGCAGATC
* * * * * * * *
60283360 GAAGAC-AA-ACCTTGCC-TCTCTCG-GTTG-TAGTGGAGCTGGTT
1 GAAGACAAAGATCTTGCCTTC-CT-GTATTGACAGCGAAGCAGATC
*
60283401 GAAGACAACAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATC
1 GAAGACAA-AGATCTTGCCTTCCTGTATTGACAGCGAAGCAGATC
60283446 GAAGACA
1 GAAGACA
60283453 CAAGCCTTGC
Statistics
Matches: 68, Mismatches: 17, Indels: 16
0.67 0.17 0.16
Matches are distributed among these distances:
41 16 0.24
42 13 0.19
43 4 0.06
44 12 0.18
45 23 0.34
ACGTcount: A:0.29, C:0.23, G:0.25, T:0.23
Consensus pattern (44 bp):
GAAGACAAAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGATC
Found at i:60283408 original size:41 final size:41
Alignment explanation
Indices: 60283279--60283408 Score: 104
Period size: 41 Copynumber: 3.1 Consensus size: 41
60283269 CAGATCGAAA
*
60283279 ACAAACCTTG-CTCTCTCGGTTGTGGTGGAGCTGGTTGAAG
1 ACAAACCTTGCCTCTCTCGGTTGTAGTGGAGCTGGTTGAAG
* * * * * * * *
60283319 ACAATAGATCTTGCCT-TC-CTGTATTGACAGCGAAGCAGATCGAAG
1 AC-A-A-ACCTTGCCTCTCTC-G-GTTG-TAGTGGAGCTGGTTGAAG
60283364 ACAAACCTTGCCTCTCTCGGTTGTAGTGGAGCTGGTTGAAG
1 ACAAACCTTGCCTCTCTCGGTTGTAGTGGAGCTGGTTGAAG
60283405 ACAA
1 ACAA
60283409 CAGATCTTGC
Statistics
Matches: 64, Mismatches: 17, Indels: 17
0.65 0.17 0.17
Matches are distributed among these distances:
40 2 0.03
41 17 0.27
42 13 0.20
43 12 0.19
44 7 0.11
45 13 0.20
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.27
Consensus pattern (41 bp):
ACAAACCTTGCCTCTCTCGGTTGTAGTGGAGCTGGTTGAAG
Found at i:60283416 original size:86 final size:86
Alignment explanation
Indices: 60283238--60283536 Score: 386
Period size: 86 Copynumber: 3.5 Consensus size: 86
60283228 TCAAAGATAG
* * * * * *
60283238 CAGATCTTGCCTTCCTGCATTAATAGTGAAGCAGATCGAAAACAAACCTTG-CTCTCTCGGTTGT
1 CAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACAAACCTTGCCTCTCTCGGTTGT
*
60283302 GGTGGAGCTGGTTGAAGACAA
66 AGTGGAGCTGGTTGAAGACAA
* *
60283323 TAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGATCGAAGACAAACCTTGCCTCTCTCGGTTGT
1 CAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACAAACCTTGCCTCTCTCGGTTGT
60283388 AGTGGAGCTGGTTGAAGACAA
66 AGTGGAGCTGGTTGAAGACAA
*
60283409 CAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACAAGCCTTGCCTCCCTCGGTT
1 CAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACA-AA-CCTTGCCTCTCTCGGTT
* * * ***
60283474 GTAGTGGAGCAGG-TCAGCGATTG
64 GTAGTGGAGCTGGTTGA-AGACAA
* * *
60283497 CAAATCTTGCCTTCCTGTACTGACGGCAAAGCAGATCGAA
1 CAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAA
60283537 AAGCAAGTCT
Statistics
Matches: 191, Mismatches: 19, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
85 45 0.24
86 75 0.39
87 4 0.02
88 67 0.35
ACGTcount: A:0.26, C:0.24, G:0.25, T:0.25
Consensus pattern (86 bp):
CAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACAAACCTTGCCTCTCTCGGTTGT
AGTGGAGCTGGTTGAAGACAA
Found at i:60283462 original size:44 final size:42
Alignment explanation
Indices: 60283328--60283464 Score: 118
Period size: 44 Copynumber: 3.2 Consensus size: 42
60283318 GACAATAGAT
60283328 CTTGCCTTCCTGTATTGACAGCGAAGCAGATCGAAGACAAA-C
1 CTTGCCTTCCTGTA-TGACAGCGAAGCAGATCGAAGACAAAGC
* * * * * * * *
60283370 CTTGCCTCTCTCGGT-TG-TAGTGGAGCTGGTTGAAGACAACAGAT
1 CTTGCCT-TC-CTGTATGACAGCGAAGCAGATCGAAGACAA-AG-C
60283414 CTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACAAGC
1 CTTGCCTTCCTGTA-TGACAGCGAAGCAGATCGAAGACA-AAGC
60283458 CTTGCCT
1 CTTGCCT
60283465 CCCTCGGTTG
Statistics
Matches: 70, Mismatches: 16, Indels: 16
0.69 0.16 0.16
Matches are distributed among these distances:
41 16 0.23
42 13 0.19
43 4 0.06
44 19 0.27
45 17 0.24
46 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.24, T:0.24
Consensus pattern (42 bp):
CTTGCCTTCCTGTATGACAGCGAAGCAGATCGAAGACAAAGC
Found at i:60283573 original size:43 final size:43
Alignment explanation
Indices: 60283413--60283574 Score: 116
Period size: 43 Copynumber: 3.7 Consensus size: 43
60283403 AGACAACAGA
60283413 TCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACA-CAAG
1 TCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAA-A-AGCAAG
* * * * * * * ** *
60283457 CCTTGCCTCCCTCGGT--TG-TAGTGGAGCAGGTCAGCGATTGCAAA
1 TCTTGCCTTCCT--GTACTGACAGCGAAGCAGATC-G-AAAAGCAAG
* *
60283501 TCTTGCCTTCCTGTACTGACGGCAAAGCAGATCGAAAAGCAAG
1 TCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAAAGCAAG
* *
60283544 TCTTGCCTTCCTGTACTGACAGTGGAGCAGA
1 TCTTGCCTTCCTGTACTGACAGCGAAGCAGA
60283575 CTAAAGATAG
Statistics
Matches: 84, Mismatches: 26, Indels: 17
0.66 0.20 0.13
Matches are distributed among these distances:
42 2 0.02
43 42 0.50
44 29 0.35
45 9 0.11
46 2 0.02
ACGTcount: A:0.25, C:0.27, G:0.25, T:0.23
Consensus pattern (43 bp):
TCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAAAGCAAG
Found at i:60283592 original size:88 final size:87
Alignment explanation
Indices: 60283200--60283620 Score: 284
Period size: 88 Copynumber: 4.8 Consensus size: 87
60283190 AAACAGATCA
* * * * * * * * *
60283200 TTGCCTCCATCAGTTGCAGTGGAACTGGTCAAAGATAGCAGATCTTGCCTTCCTGCATTAATAGT
1 TTGCCTCCCTC-GTTGCAGTGGAGCAGCTCAAAGATAGCAGATCTTGCCTTCCTGTACTGACAGC
* *
60283265 GAAGCAGATCGAA-A-ACAAACC
65 AAAGCAGATCGAAGACACAAGCC
* ** * * ** * ** *
60283286 TTG-CTCTCTCGGTTGTGGTGGAGCTGGTTGAAGACAATAGATCTTGCCTTCCTGTATTGACAGC
1 TTGCCTCCCTC-GTTGCAGTGGAGCAGCTCAAAGATAGCAGATCTTGCCTTCCTGTACTGACAGC
*
60283350 GAAGCAGATCGAAGACA-AA-CC
65 AAAGCAGATCGAAGACACAAGCC
* * * * ** * *
60283371 TTGCCTCTCTCGGTTGTAGTGGAGCTGGTTGAAGACAACAGATCTTGCCTTCCTGTACTGACAGC
1 TTGCCTCCCTC-GTTGCAGTGGAGCAGCTCAAAGATAGCAGATCTTGCCTTCCTGTACTGACAGC
*
60283436 GAAGCAGATCGAAGACACAAGCC
65 AAAGCAGATCGAAGACACAAGCC
* * ** * * *
60283459 TTGCCTCCCTCGGTTGTAGTGGAGCAGGTCAGCGATTGCAAATCTTGCCTTCCTGTACTGACGGC
1 TTGCCTCCCTC-GTTGCAGTGGAGCAGCTCAAAGATAGCAGATCTTGCCTTCCTGTACTGACAGC
*
60283524 AAAGCAGATCGAA-A-AGCAAGTC
65 AAAGCAGATCGAAGACA-CAAGCC
* * * * *
60283546 TTGCCTTCCT-GTACTGACAGTGGAGCAGACT-AAAGATAGCAGATCTTACCTTACTGCATTGAC
1 TTGCCTCCCTCGT--TG-CAGTGGAGCAG-CTCAAAGATAGCAGATCTTGCCTTCCTGTACTGAC
*
60283609 AGCAAAGTAGAT
62 AGCAAAGCAGAT
60283621 AGCAGATCAA
Statistics
Matches: 281, Mismatches: 44, Indels: 18
0.82 0.13 0.05
Matches are distributed among these distances:
85 66 0.23
86 82 0.29
87 20 0.07
88 112 0.40
89 1 0.00
ACGTcount: A:0.27, C:0.23, G:0.24, T:0.25
Consensus pattern (87 bp):
TTGCCTCCCTCGTTGCAGTGGAGCAGCTCAAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCA
AAGCAGATCGAAGACACAAGCC
Found at i:60283822 original size:127 final size:124
Alignment explanation
Indices: 60283680--60284092 Score: 532
Period size: 127 Copynumber: 3.3 Consensus size: 124
60283670 CATTGAAGCC
* *
60283680 AACAGTCTTATCTCCCTAAGCAGTAGTGGAACAGATCACATCAAGTCTTATCTCCCTAAGAAGTA
1 AACAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTA
*
60283745 GTGGAGCAGACGAAAGAAACCA-TTCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CGAAAGA
66 GTGGAGCAGACGAAAGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC--AA-A
* *
60283805 AACCAGATCTTATCTCCCTAAGTAGTAGTGGAGCAGATCACATTAAGTCTTATCTCCCTAAGCAG
1 AA-CAG-TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAG
* *
60283870 TAGTGGAGCAGATGAAA-AAACCCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC-AC
64 TAGTGGAGCAGACGAAAGAAA-CCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAA
* * * * *
60283930 ATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CGAAAGAAACCAGTCTGATCTCCCTAAG
1 AAC-AGTCTTATCTCCCTAAGCAGTAGTGGAGCAGATC---A-CATCAAGTCTTATCTCCCTAAG
* * *
60283994 CAGTAGTGGAGCAGACAAAAGAAACTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACAT
61 CAGTAGTGGAGCAGACGAAAGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCA-AA
*
60284059 TA-AGTCTTATCTCCCTAAGCAGTAGTGGAGCAGA
1 AACAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGA
60284093 CGAAAGAAAC
Statistics
Matches: 255, Mismatches: 20, Indels: 24
0.85 0.07 0.08
Matches are distributed among these distances:
123 1 0.00
124 30 0.12
125 5 0.02
126 8 0.03
127 176 0.69
128 33 0.13
129 2 0.01
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.23
Consensus pattern (124 bp):
AACAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTA
GTGGAGCAGACGAAAGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAA
Found at i:60283873 original size:84 final size:84
Alignment explanation
Indices: 60283680--60284117 Score: 479
Period size: 84 Copynumber: 5.2 Consensus size: 84
60283670 CATTGAAGCC
* * * * *
60283680 AACAGTCTTATCTCCCTAAGCAGTAGTGGAACAGATC---ACATCAAGTCTTATCTCCCTAAGAA
1 AACAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CGAAAAAACCAGTCTTATCTCCCTAAGCA
*
60283742 GTAGTGGAGCAGACGAAAGA
65 GTAGTGGAGCAGACAAAAGA
*
60283762 AACCATTCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACCAGATCTTATCTCCCTAAG
1 AA-CAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAA-AAACCAG-TCTTATCTCCCTAAG
* * *
60283827 TAGTAGTGGAGCAGATC-ACA-T
63 CAGTAGTGGAGCAGA-CAAAAGA
* *
60283848 TA-AGTCTTATCTCCCTAAGCAGTAGTGGAGCAGATGAAAAAACCCAGATCTTATCTCCCTAAGC
1 AACAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAAAA-CCAG-TCTTATCTCCCTAAGC
* *
60283912 AGTAGTGGAGCAGATC-ACA-T
64 AGTAGTGGAGCAGA-CAAAAGA
* *
60283932 CA-AGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACCAGTCTGATCTCCCTAAGCA
1 AACAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAA-AAACCAGTCTTATCTCCCTAAGCA
60283996 GTAGTGGAGCAGACAAAAGA
65 GTAGTGGAGCAGACAAAAGA
* **
60284016 AACTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC-ACATTA--AGTCTTATCTCCCTAAG
1 AAC-AG-TCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CGAAAAAACCAGTCTTATCTCCCTAAG
*
60284078 CAGTAGTGGAGCAGACGAAAGA
63 CAGTAGTGGAGCAGACAAAAGA
60284100 AACCAGT-TCTATCTCCCT
1 AA-CAGTCT-TATCTCCCT
60284118 GAAATTGCAG
Statistics
Matches: 316, Mismatches: 23, Indels: 33
0.85 0.06 0.09
Matches are distributed among these distances:
82 5 0.02
83 75 0.24
84 158 0.50
85 5 0.02
86 8 0.03
87 63 0.20
88 2 0.01
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.23
Consensus pattern (84 bp):
AACAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAAAACCAGTCTTATCTCCCTAAGCAG
TAGTGGAGCAGACAAAAGA
Found at i:60284049 original size:211 final size:211
Alignment explanation
Indices: 60283685--60284117 Score: 762
Period size: 211 Copynumber: 2.1 Consensus size: 211
60283675 AAGCCAACAG
60283685 TCTTATCTCCCTAAGCAGTAGTGGAACAGATCACATCAAGTCTTATCTCCCTAAGAAGTAGTGGA
1 TCTTATCTCCCTAAGCAGTAGTGGAACAGATCACATCAAGTCTTATCTCCCTAAGAAGTAGTGGA
* * *
60283750 GCAGACGAAAGAAACCATTCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACCAGATCT
66 GCAGACGAAAGAAACCAGTCTGATCTCCCTAAGCAGTAGTGGAGCAGACAAAAGAAACCAGATCT
*
60283815 TATCTCCCTAAGTAGTAGTGGAGCAGATCACATTAAGTCTTATCTCCCTAAGCAGTAGTGGAGCA
131 TATCTCCCTAAGCAGTAGTGGAGCAGATCACATTAAGTCTTATCTCCCTAAGCAGTAGTGGAGCA
*
60283880 GATGAAA-AAACCCAGA
196 GACGAAAGAAA-CCAGA
* *
60283896 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAGTGGA
1 TCTTATCTCCCTAAGCAGTAGTGGAACAGATCACATCAAGTCTTATCTCCCTAAGAAGTAGTGGA
*
60283961 GCAGACGAAAGAAACCAGTCTGATCTCCCTAAGCAGTAGTGGAGCAGACAAAAGAAACTAGATCT
66 GCAGACGAAAGAAACCAGTCTGATCTCCCTAAGCAGTAGTGGAGCAGACAAAAGAAACCAGATCT
60284026 TATCTCCCTAAGCAGTAGTGGAGCAGATCACATTAAGTCTTATCTCCCTAAGCAGTAGTGGAGCA
131 TATCTCCCTAAGCAGTAGTGGAGCAGATCACATTAAGTCTTATCTCCCTAAGCAGTAGTGGAGCA
*
60284091 GACGAAAGAAACCAGT
196 GACGAAAGAAACCAGA
60284107 TC-TATCTCCCT
1 TCTTATCTCCCT
60284118 GAAATTGCAG
Statistics
Matches: 212, Mismatches: 9, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
210 9 0.04
211 200 0.94
212 3 0.01
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.23
Consensus pattern (211 bp):
TCTTATCTCCCTAAGCAGTAGTGGAACAGATCACATCAAGTCTTATCTCCCTAAGAAGTAGTGGA
GCAGACGAAAGAAACCAGTCTGATCTCCCTAAGCAGTAGTGGAGCAGACAAAAGAAACCAGATCT
TATCTCCCTAAGCAGTAGTGGAGCAGATCACATTAAGTCTTATCTCCCTAAGCAGTAGTGGAGCA
GACGAAAGAAACCAGA
Found at i:60286080 original size:24 final size:22
Alignment explanation
Indices: 60286035--60286078 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
60286025 ATATACACAC
60286035 ATACTTACATTTTTATTTTATA
1 ATACTTACATTTTTATTTTATA
*
60286057 ATACTTACAGATTTT-TTTTATA
1 ATACTTACA-TTTTTATTTTATA
60286079 TATGTATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.32, C:0.09, G:0.02, T:0.57
Consensus pattern (22 bp):
ATACTTACATTTTTATTTTATA
Found at i:60295936 original size:29 final size:29
Alignment explanation
Indices: 60295902--60295963 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 29
60295892 CCATATAAAT
60295902 AAAAATAATTTTT-TTCACTATTTTTATTA
1 AAAAATAATTTTTATT-ACTATTTTTATTA
**
60295931 AAAAATAATTTTTATTTTTATTTTTATTA
1 AAAAATAATTTTTATTACTATTTTTATTA
60295960 AAAA
1 AAAA
60295964 TTTAAATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 28 0.93
30 2 0.07
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (29 bp):
AAAAATAATTTTTATTACTATTTTTATTA
Found at i:60295979 original size:29 final size:29
Alignment explanation
Indices: 60295920--60295979 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
60295910 TTTTTTTCAC
* **
60295920 TATTTTTATTAAAAAATAATTTTTATTTT
1 TATTTTTATTAAAAAATAATATTTAAATT
*
60295949 TATTTTTATTAAAAATTTAA-ATTTAAATT
1 TATTTTTATTAAAAA-ATAATATTTAAATT
60295978 TA
1 TA
60295980 ATTAAATCTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
29 23 0.88
30 3 0.12
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (29 bp):
TATTTTTATTAAAAAATAATATTTAAATT
Found at i:60296093 original size:21 final size:22
Alignment explanation
Indices: 60296056--60296098 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
60296046 ATTAAATCTT
*
60296056 TATATATGTACTAA-TTTATAA
1 TATATATGTAATAATTTTATAA
60296077 TATATATGTAA-ATATTTTATAA
1 TATATATGTAATA-ATTTTATAA
60296099 ATACAAATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 1 0.05
21 11 0.58
22 7 0.37
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (22 bp):
TATATATGTAATAATTTTATAA
Found at i:60302493 original size:9 final size:9
Alignment explanation
Indices: 60302471--60302555 Score: 61
Period size: 9 Copynumber: 9.7 Consensus size: 9
60302461 TAAATGTGCG
*
60302471 TTTTTATTAT
1 TTTTTA-TAA
60302481 TTTTTATAA
1 TTTTTATAA
*
60302490 TTTTTATTA
1 TTTTTATAA
*
60302499 TTTTT-TTA
1 TTTTTATAA
*
60302507 TTTTTTTAA
1 TTTTTATAA
*
60302516 TCTTTTA-CA
1 T-TTTTATAA
*
60302525 TATTTA-AA
1 TTTTTATAA
60302533 -TTTTATAA
1 TTTTTATAA
*
60302541 TCTTTATAA
1 TTTTTATAA
60302550 TTTTTA
1 TTTTTA
60302556 ATTTTTTTAT
Statistics
Matches: 61, Mismatches: 10, Indels: 9
0.76 0.12 0.11
Matches are distributed among these distances:
7 4 0.07
8 15 0.25
9 32 0.52
10 10 0.16
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (9 bp):
TTTTTATAA
Found at i:60303619 original size:1 final size:1
Alignment explanation
Indices: 60303613--60303658 Score: 74
Period size: 1 Copynumber: 46.0 Consensus size: 1
60303603 TCTATCTAGG
* *
60303613 AAAAAAAAAAAAGAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
60303659 TGATTTACCA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
1 41 1.00
ACGTcount: A:0.96, C:0.02, G:0.02, T:0.00
Consensus pattern (1 bp):
A
Found at i:60303639 original size:21 final size:21
Alignment explanation
Indices: 60303613--60303658 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
60303603 TCTATCTAGG
*
60303613 AAAAAAAAAAAAGAAAAAAAA
1 AAAAAAAAAAAACAAAAAAAA
60303634 AAAAAAAAAAAACAAAAAAAA
1 AAAAAAAAAAAACAAAAAAAA
60303655 AAAA
1 AAAA
60303659 TGATTTACCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.96, C:0.02, G:0.02, T:0.00
Consensus pattern (21 bp):
AAAAAAAAAAAACAAAAAAAA
Found at i:60318691 original size:31 final size:31
Alignment explanation
Indices: 60318633--60318691 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 31
60318623 GGTAGGCAAC
* * ***
60318633 TTTTTTTTGCGCTTTTTGCTTTTTTTTTCCT
1 TTTTTTTTGCACTTTTTACTCACTTTTTCCT
60318664 TTTTTTTTGCACTTTTTACTCACTTTTT
1 TTTTTTTTGCACTTTTTACTCACTTTTT
60318692 TTGCGCTTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 23 1.00
ACGTcount: A:0.05, C:0.17, G:0.07, T:0.71
Consensus pattern (31 bp):
TTTTTTTTGCACTTTTTACTCACTTTTTCCT
Found at i:60319361 original size:25 final size:24
Alignment explanation
Indices: 60319312--60319362 Score: 75
Period size: 25 Copynumber: 2.1 Consensus size: 24
60319302 CTTTAAAATT
60319312 ATCTAAGAAAATAAATAAATAATA
1 ATCTAAGAAAATAAATAAATAATA
* *
60319336 ATCTAATAAAATTAACTAAATAATA
1 ATCTAAGAAAA-TAAATAAATAATA
60319361 AT
1 AT
60319363 AATAAGATAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 10 0.42
25 14 0.58
ACGTcount: A:0.63, C:0.06, G:0.02, T:0.29
Consensus pattern (24 bp):
ATCTAAGAAAATAAATAAATAATA
Found at i:60323380 original size:31 final size:31
Alignment explanation
Indices: 60323337--60323397 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
60323327 TTGCAAGATC
*
60323337 AACGGCTCTGATATCCTT-GTGATGGACATCT
1 AACGGCTCTGATAT-CTTCATGATGGACATCT
*
60323368 AACGGCTTTGATATCTTCATGATGGACATC
1 AACGGCTCTGATATCTTCATGATGGACATC
60323398 ACACGGGTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 3 0.11
31 24 0.89
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (31 bp):
AACGGCTCTGATATCTTCATGATGGACATCT
Found at i:60326460 original size:3 final size:3
Alignment explanation
Indices: 60326448--60326481 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
60326438 AGATCTACAA
60326448 ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
60326482 CAAACTCATT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:60339419 original size:30 final size:31
Alignment explanation
Indices: 60339385--60339443 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
60339375 AGAAGAACTT
60339385 AATAGCCCAGTGATTTAAAT-AAAACTTTTG
1 AATAGCCCAGTGATTTAAATAAAAACTTTTG
**
60339415 AATAGTTCAGTGATTTAAATAAAAACTTT
1 AATAGCCCAGTGATTTAAATAAAAACTTT
60339444 CAAATAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 18 0.69
31 8 0.31
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.36
Consensus pattern (31 bp):
AATAGCCCAGTGATTTAAATAAAAACTTTTG
Found at i:60339736 original size:22 final size:23
Alignment explanation
Indices: 60339711--60339754 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
60339701 AATTTAAATC
*
60339711 ATTAATACA-ATTAAAATTTTTT
1 ATTAAGACACATTAAAATTTTTT
*
60339733 ATTAAGACACATTATAATTTTT
1 ATTAAGACACATTAAAATTTTT
60339755 AGAGGAGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (23 bp):
ATTAAGACACATTAAAATTTTTT
Found at i:60344081 original size:17 final size:17
Alignment explanation
Indices: 60344055--60344088 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
60344045 CAAAGTTTGA
* *
60344055 ATTATTATTTGTATTCC
1 ATTATAATTTATATTCC
60344072 ATTATAATTTATATTCC
1 ATTATAATTTATATTCC
60344089 CAATTTTTCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.29, C:0.12, G:0.03, T:0.56
Consensus pattern (17 bp):
ATTATAATTTATATTCC
Found at i:60346708 original size:31 final size:29
Alignment explanation
Indices: 60346639--60346712 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 29
60346629 ACAAAATAAT
**
60346639 AACATAAGTGACTAAAATGTAACATTTCA
1 AACATAAGTGACTAAAATGTAACATGGCA
*
60346668 AACATAAGTGACTAAAATGTAACCTGAGGCA
1 AACATAAGTGACTAAAATGTAACAT--GGCA
*
60346699 AACAAAAGTGACTA
1 AACATAAGTGACTA
60346713 TTTTTGTAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 24 0.62
31 15 0.38
ACGTcount: A:0.49, C:0.15, G:0.15, T:0.22
Consensus pattern (29 bp):
AACATAAGTGACTAAAATGTAACATGGCA
Found at i:60349042 original size:16 final size:16
Alignment explanation
Indices: 60349023--60349064 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
60349013 GTTTGAGTTG
60349023 TTTCAAGTTCAGATCA
1 TTTCAAGTTCAGATCA
* *
60349039 TTTCAAATTCAGGTCA
1 TTTCAAGTTCAGATCA
*
60349055 TTCCAAGTTC
1 TTTCAAGTTC
60349065 GGGTATGGGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (16 bp):
TTTCAAGTTCAGATCA
Found at i:60351108 original size:18 final size:20
Alignment explanation
Indices: 60351071--60351111 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
60351061 AAATACTAAC
60351071 AAAAGCTAAAAATTTAATTTA
1 AAAAGCTAAAAA-TTAATTTA
60351092 AAAAG-TAAAAA-TAATTTA
1 AAAAGCTAAAAATTAATTTA
60351110 AA
1 AA
60351112 TTTCAACTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 9 0.45
20 6 0.30
21 5 0.25
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (20 bp):
AAAAGCTAAAAATTAATTTA
Found at i:60352467 original size:15 final size:17
Alignment explanation
Indices: 60352449--60352480 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
60352439 AATTTTACCA
60352449 TTTATAA-TT-TAAAAT
1 TTTATAAGTTATAAAAT
60352464 TTTATAAGTTATAAAAT
1 TTTATAAGTTATAAAAT
60352481 GCCTAAATGG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 2 0.13
17 6 0.40
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (17 bp):
TTTATAAGTTATAAAAT
Found at i:60353784 original size:37 final size:38
Alignment explanation
Indices: 60353734--60353811 Score: 97
Period size: 37 Copynumber: 2.1 Consensus size: 38
60353724 TTCGAAGTAA
*
60353734 TAAATTGACACCCAATGTC-TCATCG-GTTAAACCGAAG
1 TAAATTGACACCCAATG-CATCATCGAATTAAACCGAAG
* * *
60353771 TAAATTGGCACCCAGTGCATCATCGAATTAATCCGAAG
1 TAAATTGACACCCAATGCATCATCGAATTAAACCGAAG
60353809 TAA
1 TAA
60353812 TAAATTGACA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
36 1 0.03
37 21 0.60
38 13 0.37
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.24
Consensus pattern (38 bp):
TAAATTGACACCCAATGCATCATCGAATTAAACCGAAG
Found at i:60353835 original size:41 final size:41
Alignment explanation
Indices: 60353702--60353837 Score: 140
Period size: 40 Copynumber: 3.4 Consensus size: 41
60353692 ACCAGTTTGG
* * * *
60353702 CACCCGGTGCCTCATCGGA-TAATTCGAAGTAATAAATTGA
1 CACCCAGTGTCTCATCGAATTAATCCGAAGTAATAAATTGA
* * * *
60353742 CACCCAATGTCTCATCG-GTTAAACCGAAG---TAAATTGG
1 CACCCAGTGTCTCATCGAATTAATCCGAAGTAATAAATTGA
60353779 CACCCAGTG-CATCATCGAATTAATCCGAAGTAATAAATTGA
1 CACCCAGTGTC-TCATCGAATTAATCCGAAGTAATAAATTGA
*
60353820 CACCTAGTGTCTCATCGA
1 CACCCAGTGTCTCATCGA
60353838 CTCGAAGTCG
Statistics
Matches: 77, Mismatches: 12, Indels: 13
0.75 0.12 0.13
Matches are distributed among these distances:
36 1 0.01
37 21 0.27
38 10 0.13
40 22 0.29
41 22 0.29
42 1 0.01
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (41 bp):
CACCCAGTGTCTCATCGAATTAATCCGAAGTAATAAATTGA
Found at i:60354038 original size:24 final size:24
Alignment explanation
Indices: 60353993--60354039 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
60353983 TATATATACC
60353993 AATTCAATCAATATAAATTCAATA
1 AATTCAATCAATATAAATTCAATA
60354017 AATTC-ATCACATACTAAA-TCAAT
1 AATTCAATCA-ATA-TAAATTCAAT
60354040 CCATTTCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 13 0.62
25 4 0.19
ACGTcount: A:0.51, C:0.17, G:0.00, T:0.32
Consensus pattern (24 bp):
AATTCAATCAATATAAATTCAATA
Found at i:60354386 original size:18 final size:19
Alignment explanation
Indices: 60354360--60354395 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
60354350 TAAACTAAAT
*
60354360 TTAACTCCCT-AATTTCAC
1 TTAAATCCCTAAATTTCAC
60354378 TTAAATCCCTAAATTTCA
1 TTAAATCCCTAAATTTCA
60354396 ATTTTTTTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.33, C:0.28, G:0.00, T:0.39
Consensus pattern (19 bp):
TTAAATCCCTAAATTTCAC
Found at i:60356426 original size:42 final size:42
Alignment explanation
Indices: 60356372--60356557 Score: 198
Period size: 42 Copynumber: 4.4 Consensus size: 42
60356362 TTTTAGAAAT
60356372 AAACGCCGCTAAAGAACAAGACCTTTAGCGGCGCTTTTCCAC
1 AAACGCCGCTAAAGAACAAGACCTTTAGCGGCGCTTTTCCAC
* * * *
60356414 AAACGCCACTAAAGACCAAGACCTTTAGCGGCGCTTATCAAC
1 AAACGCCGCTAAAGAACAAGACCTTTAGCGGCGCTTTTCCAC
* * * *
60356456 AATCGCCGCTAAAG-ACTATGACCTTTAGCAGCGCTTTTATCAC
1 AAACGCCGCTAAAGAAC-AAGACCTTTAGCGGCGCTTTT-CCAC
* * * * * *
60356499 AAACGCCGCTATAGATCAA-ACCTTTAGTGACGCTTCTTGCAA
1 AAACGCCGCTAAAGAACAAGACCTTTAGCGGCGCTT-TTCCAC
60356541 AAACGCCGCTAAA-AACA
1 AAACGCCGCTAAAGAACA
60356558 TAACTTAAAA
Statistics
Matches: 117, Mismatches: 23, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
41 4 0.03
42 95 0.81
43 17 0.15
44 1 0.01
ACGTcount: A:0.33, C:0.29, G:0.17, T:0.21
Consensus pattern (42 bp):
AAACGCCGCTAAAGAACAAGACCTTTAGCGGCGCTTTTCCAC
Found at i:60358468 original size:21 final size:20
Alignment explanation
Indices: 60358440--60358478 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
60358430 GTTTGCAAAG
*
60358440 TTAGGGTTTCAGTGGGAAAA
1 TTAGGGTTTCAGGGGGAAAA
60358460 TTAGAGGTTTCAGGGGGAA
1 TTAG-GGTTTCAGGGGGAA
60358479 TTTGGAGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.28, C:0.05, G:0.38, T:0.28
Consensus pattern (20 bp):
TTAGGGTTTCAGGGGGAAAA
Found at i:60359474 original size:15 final size:15
Alignment explanation
Indices: 60359454--60359529 Score: 54
Period size: 15 Copynumber: 5.3 Consensus size: 15
60359444 CCGACCCCTG
60359454 AATCCCTAAACCTTA
1 AATCCCTAAACCTTA
60359469 AATCCCT-AACTCTTA
1 AATCCCTAAAC-CTTA
* *
60359484 AA--CCTTAACATCT-
1 AATCCCTAAACCT-TA
* *
60359497 AACCCCTAAACCCT-
1 AATCCCTAAACCTTA
*
60359511 AACCCCTAAACCTTA
1 AATCCCTAAACCTTA
60359526 AATC
1 AATC
60359530 TCAACCCTTA
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
13 6 0.12
14 21 0.43
15 22 0.45
ACGTcount: A:0.38, C:0.37, G:0.00, T:0.25
Consensus pattern (15 bp):
AATCCCTAAACCTTA
Found at i:60359514 original size:14 final size:14
Alignment explanation
Indices: 60359495--60359522 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
60359485 ACCTTAACAT
60359495 CTAACCCCTAAACC
1 CTAACCCCTAAACC
60359509 CTAACCCCTAAACC
1 CTAACCCCTAAACC
60359523 TTAAATCTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.50, G:0.00, T:0.14
Consensus pattern (14 bp):
CTAACCCCTAAACC
Found at i:60359527 original size:21 final size:21
Alignment explanation
Indices: 60359472--60359527 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
60359462 AACCTTAAAT
*
60359472 CCCT-AACTCTTAAACCTTAAC
1 CCCTAAAC-CTTAAACCCTAAC
** * *
60359493 ATCTAACCCCTAAACCCTAAC
1 CCCTAAACCTTAAACCCTAAC
60359514 CCCTAAACCTTAAA
1 CCCTAAACCTTAAA
60359528 TCTCAACCCT
Statistics
Matches: 25, Mismatches: 9, Indels: 2
0.69 0.25 0.06
Matches are distributed among these distances:
21 23 0.92
22 2 0.08
ACGTcount: A:0.38, C:0.39, G:0.00, T:0.23
Consensus pattern (21 bp):
CCCTAAACCTTAAACCCTAAC
Found at i:60359790 original size:15 final size:15
Alignment explanation
Indices: 60359770--60359798 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
60359760 AACACGTCGA
60359770 CTAACCCCTAAACCC
1 CTAACCCCTAAACCC
60359785 CTAACCCCTAAACC
1 CTAACCCCTAAACC
60359799 TTAAATCCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.52, G:0.00, T:0.14
Consensus pattern (15 bp):
CTAACCCCTAAACCC
Found at i:60359817 original size:21 final size:22
Alignment explanation
Indices: 60359778--60359830 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
60359768 GACTAACCCC
* *
60359778 TAAACCCCTAACCCCTAAACCT
1 TAAATCCCTAACCCCTAAACCA
*
60359800 TAAATCCC-AACCCTTAAACCA
1 TAAATCCCTAACCCCTAAACCA
60359821 T-AATCCCTAA
1 TAAATCCCTAA
60359831 ACCCAACTCC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 6 0.22
21 14 0.52
22 7 0.26
ACGTcount: A:0.40, C:0.40, G:0.00, T:0.21
Consensus pattern (22 bp):
TAAATCCCTAACCCCTAAACCA
Found at i:60359845 original size:14 final size:14
Alignment explanation
Indices: 60359797--60359846 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
60359787 AACCCCTAAA
60359797 CCTTAAATCCCAAC-
1 CCTTAAA-CCCAACT
*
60359811 CCTTAAA-CCATAAT
1 CCTTAAACCCA-ACT
*
60359825 CCCTAAACCCAACT
1 CCTTAAACCCAACT
60359839 CCTTAAAC
1 CCTTAAAC
60359847 TAAAAACCCT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
12 3 0.10
13 1 0.03
14 22 0.76
15 3 0.10
ACGTcount: A:0.38, C:0.40, G:0.00, T:0.22
Consensus pattern (14 bp):
CCTTAAACCCAACT
Found at i:60359856 original size:28 final size:27
Alignment explanation
Indices: 60359794--60359860 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 27
60359784 CCTAACCCCT
* *
60359794 AAACCTTAAATCCCAACCCTTAAACCAT
1 AAACCCTAAA-CCCAACCCTTAAACCAA
* *
60359822 AATCCCTAAACCCAACTCCTTAAACTAA
1 AAACCCTAAACCCAAC-CCTTAAACCAA
60359850 AAACCCTAAAC
1 AAACCCTAAAC
60359861 TATAGTGATA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
27 6 0.18
28 27 0.82
ACGTcount: A:0.45, C:0.36, G:0.00, T:0.19
Consensus pattern (27 bp):
AAACCCTAAACCCAACCCTTAAACCAA
Found at i:60360188 original size:41 final size:41
Alignment explanation
Indices: 60360130--60360324 Score: 327
Period size: 41 Copynumber: 4.8 Consensus size: 41
60360120 TAAAATGTTT
* *
60360130 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGACCAGAGCA
1 TTAGCGGCGCTTCTTCAAAAGCGCCGCTAAAGACCAGAGCA
* *
60360171 TTAGCGGCTCTTCTTCAAAAGCGCCGCTAAAGACCAGAGTA
1 TTAGCGGCGCTTCTTCAAAAGCGCCGCTAAAGACCAGAGCA
* *
60360212 TTAGCGGCGTTTCTTCAAAAGCGCCGCTAAAGACCAGAGTA
1 TTAGCGGCGCTTCTTCAAAAGCGCCGCTAAAGACCAGAGCA
*
60360253 TTAGCGGCGCTTCTTCAAAAGCGCCGCTAAAGAACAGAGCA
1 TTAGCGGCGCTTCTTCAAAAGCGCCGCTAAAGACCAGAGCA
60360294 TTAGCGGCGCTTCTTCAAAAGCGCCGCTAAA
1 TTAGCGGCGCTTCTTCAAAAGCGCCGCTAAA
60360325 TCCCCAAAAA
Statistics
Matches: 145, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 145 1.00
ACGTcount: A:0.30, C:0.27, G:0.23, T:0.21
Consensus pattern (41 bp):
TTAGCGGCGCTTCTTCAAAAGCGCCGCTAAAGACCAGAGCA
Found at i:60360488 original size:40 final size:41
Alignment explanation
Indices: 60360364--60360500 Score: 140
Period size: 40 Copynumber: 3.4 Consensus size: 41
60360354 TAGGTTTAGG
* * * *
60360364 TTTTAGCGGCGCTTTTTGGAAAA-CGCCGCTAATTCTC-AT
1 TTTTAGAGGCGTTTTTTAGAAAAGCGCCGCTAATACTCGAT
*
60360403 TTTTAGTGGCG-TTTTTAGAAAAGCGCCGCTAATACTCGAT
1 TTTTAGAGGCGTTTTTTAGAAAAGCGCCGCTAATACTCGAT
* * *
60360443 CTTTAGAGGCGTTTTTTAG-ATAGCGCCGCTAATGA-TTGAT
1 TTTTAGAGGCGTTTTTTAGAAAAGCGCCGCTAAT-ACTCGAT
* *
60360483 TTTTAGCGGTGTTTTTTA
1 TTTTAGAGGCGTTTTTTA
60360501 TCCAAACGCC
Statistics
Matches: 84, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
38 10 0.12
39 23 0.27
40 43 0.51
41 8 0.10
ACGTcount: A:0.21, C:0.17, G:0.23, T:0.39
Consensus pattern (41 bp):
TTTTAGAGGCGTTTTTTAGAAAAGCGCCGCTAATACTCGAT
Found at i:60360697 original size:13 final size:13
Alignment explanation
Indices: 60360681--60360706 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
60360671 TTTATAAATT
60360681 ATAAAAATAAAAA
1 ATAAAAATAAAAA
60360694 ATAAAAATAAAAA
1 ATAAAAATAAAAA
60360707 TCTATTTTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (13 bp):
ATAAAAATAAAAA
Found at i:60363452 original size:16 final size:15
Alignment explanation
Indices: 60363424--60363465 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 15
60363414 AGGAAAAAAT
60363424 TAAAAAACA-ATATGA
1 TAAAAAACATATAT-A
60363439 TAAAAAACATATATA
1 TAAAAAACATATATA
60363454 TAAAAAAACATA
1 T-AAAAAACATA
60363466 AAATACAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 11 0.44
16 14 0.56
ACGTcount: A:0.69, C:0.07, G:0.02, T:0.21
Consensus pattern (15 bp):
TAAAAAACATATATA
Found at i:60370960 original size:17 final size:17
Alignment explanation
Indices: 60370928--60370961 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
60370918 ACTAATTTAA
*
60370928 GAAAAAAATATCAAATT
1 GAAAAAAAAATCAAATT
*
60370945 GAAAAAAAAATTAAATT
1 GAAAAAAAAATCAAATT
60370962 CAAATATCAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.68, C:0.03, G:0.06, T:0.24
Consensus pattern (17 bp):
GAAAAAAAAATCAAATT
Found at i:60377497 original size:18 final size:18
Alignment explanation
Indices: 60377474--60377508 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
60377464 CCTCACTTCT
60377474 TGCATTATAATTAACTTG
1 TGCATTATAATTAACTTG
*
60377492 TGCATTATAGTTAACTT
1 TGCATTATAATTAACTT
60377509 TTTGTAGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.11, G:0.11, T:0.46
Consensus pattern (18 bp):
TGCATTATAATTAACTTG
Found at i:60377815 original size:23 final size:22
Alignment explanation
Indices: 60377781--60377855 Score: 70
Period size: 23 Copynumber: 3.5 Consensus size: 22
60377771 GTAAACTTGT
60377781 TTGTGATCTAAAAGTATGTTAAC
1 TTGTGATCTAAAA-TATGTTAAC
* *
60377804 TTGTGATGT-AAATTTG-T---
1 TTGTGATCTAAAATATGTTAAC
60377821 TTGTGATCTAAAAATATGTTAAC
1 TTGTGATCT-AAAATATGTTAAC
*
60377844 TTGTGATGTAAA
1 TTGTGATCTAAA
60377856 TTTGTTTGTG
Statistics
Matches: 41, Mismatches: 5, Indels: 13
0.69 0.08 0.22
Matches are distributed among these distances:
17 8 0.20
19 6 0.15
20 2 0.05
21 3 0.07
22 6 0.15
23 16 0.39
ACGTcount: A:0.33, C:0.05, G:0.19, T:0.43
Consensus pattern (22 bp):
TTGTGATCTAAAATATGTTAAC
Found at i:60377822 original size:40 final size:40
Alignment explanation
Indices: 60377767--60377885 Score: 202
Period size: 40 Copynumber: 3.0 Consensus size: 40
60377757 ATGCCTAGTT
* *
60377767 TGATGTAAACTTGTTTGTGATCTAAAAGTATGTTAACTTG
1 TGATGTAAATTTGTTTGTGATCTAAAAATATGTTAACTTG
60377807 TGATGTAAATTTGTTTGTGATCTAAAAATATGTTAACTTG
1 TGATGTAAATTTGTTTGTGATCTAAAAATATGTTAACTTG
* *
60377847 TGATGTAAATTTGTTTGTGATTTAAAAATATGTTTACTT
1 TGATGTAAATTTGTTTGTGATCTAAAAATATGTTAACTT
60377886 CCTACTTAGA
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 75 1.00
ACGTcount: A:0.31, C:0.05, G:0.18, T:0.46
Consensus pattern (40 bp):
TGATGTAAATTTGTTTGTGATCTAAAAATATGTTAACTTG
Found at i:60377826 original size:17 final size:17
Alignment explanation
Indices: 60377804--60377872 Score: 57
Period size: 17 Copynumber: 3.7 Consensus size: 17
60377794 GTATGTTAAC
60377804 TTGTGATGTAAATTTGT
1 TTGTGATGTAAATTTGT
* *
60377821 TTGTGATCTAAAAATATGTT
1 TTGTGATGT--AAATTTG-T
60377841 AACTTGTGATGTAAATTTGT
1 ---TTGTGATGTAAATTTGT
*
60377861 TTGTGATTTAAA
1 TTGTGATGTAAA
60377873 AATATGTTTA
Statistics
Matches: 41, Mismatches: 5, Indels: 12
0.71 0.09 0.21
Matches are distributed among these distances:
17 19 0.46
19 6 0.15
20 2 0.05
21 6 0.15
23 8 0.20
ACGTcount: A:0.30, C:0.03, G:0.19, T:0.48
Consensus pattern (17 bp):
TTGTGATGTAAATTTGT
Found at i:60379937 original size:33 final size:33
Alignment explanation
Indices: 60379898--60379984 Score: 165
Period size: 33 Copynumber: 2.6 Consensus size: 33
60379888 TTTAAAGGAG
60379898 ATAGTCTCCGCTCAGACAGTGGTAAGCAAAGTA
1 ATAGTCTCCGCTCAGACAGTGGTAAGCAAAGTA
*
60379931 ATAGTCTCCGCTCAGACAGCGGTAAGCAAAGTA
1 ATAGTCTCCGCTCAGACAGTGGTAAGCAAAGTA
60379964 ATAGTCTCCGCTCAGACAGTG
1 ATAGTCTCCGCTCAGACAGTG
60379985 CGAAACGTAT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 52 1.00
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.21
Consensus pattern (33 bp):
ATAGTCTCCGCTCAGACAGTGGTAAGCAAAGTA
Found at i:60389554 original size:16 final size:16
Alignment explanation
Indices: 60389533--60389567 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
60389523 GATTGGCTAG
*
60389533 CATACAAATATGCATA
1 CATACAAATATACATA
*
60389549 CATACATATATACATA
1 CATACAAATATACATA
60389565 CAT
1 CAT
60389568 CATACATGGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.49, C:0.20, G:0.03, T:0.29
Consensus pattern (16 bp):
CATACAAATATACATA
Found at i:60408099 original size:43 final size:43
Alignment explanation
Indices: 60408038--60408203 Score: 178
Period size: 43 Copynumber: 3.9 Consensus size: 43
60408028 TTTCCGATAA
*
60408038 GTGTTTTCGTGTAAGACCACGT-TTGAGACGTTGGCATCGACTT
1 GTGTTTTCGTGTAAGACCACGTCTAG-GACGTTGGCATCGACTT
60408081 GTGTTTTCGTGTAAGACCACGTCTAGGACGTTGGCATCGACTT
1 GTGTTTTCGTGTAAGACCACGTCTAGGACGTTGGCATCGACTT
* * * * *
60408124 GTGTTTTCGTATAAGACC-CTGCCTGGGATAG-TCGCATCGA-TCT
1 GTGTTTTCGTGTAAGACCAC-GTCTAGGA-CGTTGGCATCGACT-T
* * * *
60408167 GTGATTACATGTAAGACCACGTTTAGGACGTTGGCAT
1 GTGTTTTCGTGTAAGACCACGTCTAGGACGTTGGCAT
60408204 TGTACGAGCC
Statistics
Matches: 102, Mismatches: 15, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
42 3 0.03
43 95 0.93
44 4 0.04
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.33
Consensus pattern (43 bp):
GTGTTTTCGTGTAAGACCACGTCTAGGACGTTGGCATCGACTT
Found at i:60412658 original size:20 final size:20
Alignment explanation
Indices: 60412635--60412741 Score: 89
Period size: 20 Copynumber: 5.3 Consensus size: 20
60412625 TTCATATAAA
*
60412635 TTATAATATTTTATTAATTT
1 TTATAATATTTTATAAATTT
60412655 TTATAATATTTTA-ATAATTT
1 TTATAATATTTTATA-AATTT
* *
60412675 TAAT-ATATTTTTATAAAATT
1 TTATAATA-TTTTATAAATTT
60412695 TTA-AATATTTTA-AACATGTT
1 TTATAATATTTTATAA-AT-TT
* *
60412715 TT-TATTAATTTTATGAATTT
1 TTATAAT-ATTTTATAAATTT
60412735 TTATAAT
1 TTATAAT
60412742 TTATTAAATT
Statistics
Matches: 69, Mismatches: 8, Indels: 19
0.72 0.08 0.20
Matches are distributed among these distances:
18 2 0.03
19 9 0.13
20 45 0.65
21 12 0.17
22 1 0.01
ACGTcount: A:0.38, C:0.01, G:0.02, T:0.59
Consensus pattern (20 bp):
TTATAATATTTTATAAATTT
Found at i:60412661 original size:9 final size:9
Alignment explanation
Indices: 60412635--60412752 Score: 71
Period size: 10 Copynumber: 12.0 Consensus size: 9
60412625 TTCATATAAA
60412635 TTATAATATT
1 TTATAAT-TT
60412645 TTATTAATTT
1 TTA-TAATTT
60412655 TTATAATATT
1 TTATAAT-TT
60412665 TTAATAATTT
1 TT-ATAATTT
*
60412675 TAATATATTT
1 TTATA-ATTT
*
60412685 TTATAAAATT
1 TTAT-AATTT
60412695 TTA-AATATT
1 TTATAAT-TT
*
60412704 TTAAACATGTTT
1 TTATA-A--TTT
60412716 TTATTAA-TT
1 TTA-TAATTT
60412725 TTATGAATTT
1 TTAT-AATTT
60412735 TTATAATTT
1 TTATAATTT
60412744 ATTA-AATTT
1 -TTATAATTT
60412753 ATGAAGTTTA
Statistics
Matches: 89, Mismatches: 5, Indels: 29
0.72 0.04 0.24
Matches are distributed among these distances:
8 3 0.03
9 29 0.33
10 38 0.43
11 11 0.12
12 6 0.07
13 2 0.02
ACGTcount: A:0.38, C:0.01, G:0.02, T:0.59
Consensus pattern (9 bp):
TTATAATTT
Found at i:60412699 original size:8 final size:9
Alignment explanation
Indices: 60412639--60412708 Score: 54
Period size: 9 Copynumber: 7.2 Consensus size: 9
60412629 TATAAATTAT
60412639 AATATTTTA
1 AATATTTTA
60412648 TTAAT-TTTTA
1 --AATATTTTA
60412658 TAATATTTT-
1 -AATATTTTA
60412667 AATAATTTTA
1 AAT-ATTTTA
60412677 ATATATTTTTA
1 A-ATA-TTTTA
*
60412688 TAAAATTTTA
1 -AATATTTTA
60412698 AATATTTTA
1 AATATTTTA
60412707 AA
1 AA
60412709 CATGTTTTTA
Statistics
Matches: 51, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
8 3 0.06
9 19 0.37
10 16 0.31
11 12 0.24
12 1 0.02
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (9 bp):
AATATTTTA
Found at i:60412744 original size:26 final size:28
Alignment explanation
Indices: 60412715--60412769 Score: 87
Period size: 26 Copynumber: 2.0 Consensus size: 28
60412705 TAAACATGTT
*
60412715 TTTATTAATTTTATGAA-TTT-TTATAA
1 TTTATTAAATTTATGAAGTTTATTATAA
60412741 TTTATTAAATTTATGAAGTTTATTATAA
1 TTTATTAAATTTATGAAGTTTATTATAA
60412769 T
1 T
60412770 ATTTACAAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 16 0.62
27 3 0.12
28 7 0.27
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.58
Consensus pattern (28 bp):
TTTATTAAATTTATGAAGTTTATTATAA
Found at i:60413751 original size:17 final size:17
Alignment explanation
Indices: 60413730--60413767 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
60413720 ATGAAGATAT
*
60413730 TTATA-AAATT-TAAAG
1 TTATATAAATTATAAAA
60413745 TTATATAAATTATAAAA
1 TTATATAAATTATAAAA
60413762 TTATAT
1 TTATAT
60413768 CTTAATGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 5 0.25
16 5 0.25
17 10 0.50
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (17 bp):
TTATATAAATTATAAAA
Found at i:60414569 original size:24 final size:24
Alignment explanation
Indices: 60414542--60414588 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
60414532 ATTGAAATGG
60414542 ATTG-ATTTAGTATGTGA-TGAATTT
1 ATTGAATTTA-TAT-TGATTGAATTT
60414566 ATTGAATTTATATTGATTGAATT
1 ATTGAATTTATATTGATTGAATT
60414589 GGTATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 3 0.14
24 13 0.62
25 5 0.24
ACGTcount: A:0.32, C:0.00, G:0.17, T:0.51
Consensus pattern (24 bp):
ATTGAATTTATATTGATTGAATTT
Found at i:60420306 original size:19 final size:19
Alignment explanation
Indices: 60420282--60420319 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
60420272 AATTTTAAAA
60420282 TATTTTAAAAATATTTTTT
1 TATTTTAAAAATATTTTTT
60420301 TATTTTAAAAATATTTTTT
1 TATTTTAAAAATATTTTTT
60420320 GTGTTTATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
TATTTTAAAAATATTTTTT
Found at i:60435107 original size:27 final size:27
Alignment explanation
Indices: 60435076--60435253 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
60435066 TAAATTGTAC
60435076 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
60435103 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
60435129 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
60435157 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
60435185 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
60435212 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
60435239 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
60435254 GGCTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:60435190 original size:82 final size:81
Alignment explanation
Indices: 60435077--60435232 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
60435067 AAATTGTACA
* *
60435077 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
60435141 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
60435158 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
60435223 TGCGAGTTGA
65 TGCGAATTGA
60435233 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:60435244 original size:82 final size:81
Alignment explanation
Indices: 60435073--60435253 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
60435063 GATTAAATTG
* *
60435073 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
60435138 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
60435154 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
60435218 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
60435236 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
60435254 GGCTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:60435264 original size:27 final size:27
Alignment explanation
Indices: 60435158--60435264 Score: 70
Period size: 27 Copynumber: 3.9 Consensus size: 27
60435148 TGACCATGCG
* * * *
60435158 GCACTAAGTGTGCGAGTTTGACTATGTA
1 GCACTAAGTGTGCGAG-CTCAATATATA
** * * **
60435186 GCACTAAGTGTGCGATTTGATTACGTA
1 GCACTAAGTGTGCGAGCTCAATATATA
* * *
60435213 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGAGCTCAATATATA
* *
60435240 GCACTGAGTGTGCGGGCTCAATATA
1 GCACTAAGTGTGCGAGCTCAATATA
60435265 CATTCGTGAA
Statistics
Matches: 68, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
27 53 0.78
28 15 0.22
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (27 bp):
GCACTAAGTGTGCGAGCTCAATATATA
Found at i:60437060 original size:18 final size:18
Alignment explanation
Indices: 60437037--60437077 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
60437027 TCTCAGATCT
60437037 TCGACACTGATCGTTAGA
1 TCGACACTGATCGTTAGA
60437055 TCGACACTGATCGTTAGA
1 TCGACACTGATCGTTAGA
60437073 TCGAC
1 TCGAC
60437078 TTGAATATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (18 bp):
TCGACACTGATCGTTAGA
Found at i:60439331 original size:16 final size:16
Alignment explanation
Indices: 60439286--60439331 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 16
60439276 GCGCTTTTTT
60439286 ACTTAAATAATATA-A
1 ACTTAAATAATATATA
* * *
60439301 A-ATAAACAATTTATA
1 ACTTAAATAATATATA
60439316 ACTTAAATAATATATA
1 ACTTAAATAATATATA
60439332 CCCAATATCA
Statistics
Matches: 23, Mismatches: 6, Indels: 3
0.72 0.19 0.09
Matches are distributed among these distances:
14 9 0.39
15 3 0.13
16 11 0.48
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.35
Consensus pattern (16 bp):
ACTTAAATAATATATA
Found at i:60439869 original size:22 final size:22
Alignment explanation
Indices: 60439838--60439921 Score: 96
Period size: 22 Copynumber: 3.8 Consensus size: 22
60439828 ATATCCAAAC
60439838 AATAACAATAAAACAATAGCAA
1 AATAACAATAAAACAATAGCAA
* * **
60439860 TATAATAATAAAATGATAGCAA
1 AATAACAATAAAACAATAGCAA
* **
60439882 AATGACAATAAAACAATAATAA
1 AATAACAATAAAACAATAGCAA
*
60439904 AATAACAACAAAACAATA
1 AATAACAATAAAACAATA
60439922 TATGAGAAAA
Statistics
Matches: 49, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 49 1.00
ACGTcount: A:0.67, C:0.11, G:0.05, T:0.18
Consensus pattern (22 bp):
AATAACAATAAAACAATAGCAA
Found at i:60441389 original size:28 final size:29
Alignment explanation
Indices: 60441335--60441393 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
60441325 TATTCTTATA
* *
60441335 TTAATTTTATAATTATTTATGACATATATT
1 TTAATTTTATAAATATGTAT-ACATATATT
*
60441365 TTAATTTTATAAATATGTAT-TATATATT
1 TTAATTTTATAAATATGTATACATATATT
60441393 T
1 T
60441394 CATTATAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 8 0.31
30 18 0.69
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.58
Consensus pattern (29 bp):
TTAATTTTATAAATATGTATACATATATT
Found at i:60441890 original size:7 final size:7
Alignment explanation
Indices: 60441878--60441909 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
60441868 ACAAATTTAC
60441878 TAAATAT
1 TAAATAT
60441885 TAAATAT
1 TAAATAT
60441892 TAAATAT
1 TAAATAT
60441899 TAAATAT
1 TAAATAT
60441906 TAAA
1 TAAA
60441910 CAAAAATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (7 bp):
TAAATAT
Found at i:60449957 original size:3 final size:3
Alignment explanation
Indices: 60449949--60449973 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
60449939 ACAAAATTAG
60449949 GCT GCT GCT GCT GCT GCT GCT GCT G
1 GCT GCT GCT GCT GCT GCT GCT GCT G
60449974 GCATTGATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.36, T:0.32
Consensus pattern (3 bp):
GCT
Found at i:60456089 original size:17 final size:17
Alignment explanation
Indices: 60456069--60456120 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
60456059 AATAAATATA
60456069 TTTATTTTTTAAATTTT
1 TTTATTTTTTAAATTTT
* * *
60456086 TTTAATTTTAAAATATT
1 TTTATTTTTTAAATTTT
*
60456103 TTTATTATTTTTAATTTT
1 TTTATT-TTTTAAATTTT
60456121 AAAATATTTT
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
17 19 0.70
18 8 0.30
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTATTTTTTAAATTTT
Found at i:60456152 original size:38 final size:38
Alignment explanation
Indices: 60456091--60456190 Score: 157
Period size: 38 Copynumber: 2.6 Consensus size: 38
60456081 ATTTTTTTAA
* *
60456091 TTTTAAAATA-TTTTTATTATTTTTAATTTTAAAATAT
1 TTTTAAAATACTTTTTAATTTTTTTAATTTTAAAATAT
60456128 TTTTAAAATACTTTTTAATTTTTTTAATTTTAAAATAT
1 TTTTAAAATACTTTTTAATTTTTTTAATTTTAAAATAT
60456166 TTTTAAAATACTTTTTTTAATTTTT
1 TTTTAAAATAC--TTTTTAATTTTT
60456191 AAAATAAATT
Statistics
Matches: 58, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
37 10 0.17
38 36 0.62
40 12 0.21
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (38 bp):
TTTTAAAATACTTTTTAATTTTTTTAATTTTAAAATAT
Found at i:60456202 original size:21 final size:21
Alignment explanation
Indices: 60456164--60456203 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
60456154 ATTTTAAAAT
**
60456164 ATTTTTAAAATACTTTTTTTA
1 ATTTTTAAAATAAATTTTTTA
60456185 ATTTTTAAAATAAATTTTT
1 ATTTTTAAAATAAATTTTT
60456204 GGTATTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTTTAAAATAAATTTTTTA
Found at i:60456210 original size:22 final size:20
Alignment explanation
Indices: 60456163--60456217 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 20
60456153 AATTTTAAAA
* *
60456163 TATTTTTAAAATACTTTTTT
1 TATTTTTAAAATAATTTTTG
60456183 TAATTTTTAAAATAAATTTTTGG
1 T-ATTTTTAAAAT-AATTTTT-G
60456206 TATTTATTAAAA
1 TATTT-TTAAAA
60456218 ATGGGCCGGG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
20 1 0.03
21 11 0.38
22 10 0.34
23 7 0.24
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (20 bp):
TATTTTTAAAATAATTTTTG
Found at i:60461470 original size:12 final size:11
Alignment explanation
Indices: 60461449--60461478 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
60461439 ATTAAATAAT
60461449 AAAAAAGGAAA
1 AAAAAAGGAAA
*
60461460 AAAAAAGGGAA
1 AAAAAAGGAAA
60461471 AAAAAAGG
1 AAAAAAGG
60461479 CCGACAGATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (11 bp):
AAAAAAGGAAA
Found at i:60471333 original size:6 final size:6
Alignment explanation
Indices: 60471322--60471353 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
60471312 CTTCTTCTCA
*
60471322 GCTTTG GCTTTG GCTTTG GCTGTG GCTTTG GC
1 GCTTTG GCTTTG GCTTTG GCTTTG GCTTTG GC
60471354 AGGAGGATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.19, G:0.38, T:0.44
Consensus pattern (6 bp):
GCTTTG
Found at i:60476238 original size:20 final size:24
Alignment explanation
Indices: 60476192--60476240 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
60476182 TTTGTCTGTC
60476192 AATTTTTAATTATATAAATAGATT
1 AATTTTTAATTATATAAATAGATT
60476216 AATTTTTAA-TA-A-AAATA-ATT
1 AATTTTTAATTATATAAATAGATT
60476236 AATTT
1 AATTT
60476241 ATTATTTAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.32
21 5 0.20
22 1 0.04
23 2 0.08
24 9 0.36
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (24 bp):
AATTTTTAATTATATAAATAGATT
Found at i:60476266 original size:30 final size:30
Alignment explanation
Indices: 60476222--60476279 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
60476212 GATTAATTTT
60476222 TAATAAAAATAATTAATTTATTATTTAAGA
1 TAATAAAAATAATTAATTTATTATTTAAGA
*
60476252 TAATATAAAA-AATTAATTTATTTTTTAA
1 TAATA-AAAATAATTAATTTATTATTTAA
60476280 TAGAGTAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (30 bp):
TAATAAAAATAATTAATTTATTATTTAAGA
Found at i:60477672 original size:3 final size:3
Alignment explanation
Indices: 60477664--60477709 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
60477654 TTATCCAAAA
60477664 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
60477710 GGTAATAAAG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:60478167 original size:19 final size:19
Alignment explanation
Indices: 60478143--60478180 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
60478133 AAGGGATGAC
60478143 AGTATGACAAATGGCTATT
1 AGTATGACAAATGGCTATT
60478162 AGTATGACAAATGGCTATT
1 AGTATGACAAATGGCTATT
60478181 CTTATTGAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.32
Consensus pattern (19 bp):
AGTATGACAAATGGCTATT
Found at i:60482970 original size:2 final size:2
Alignment explanation
Indices: 60482963--60482988 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
60482953 AGTAACTTTG
60482963 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
60482989 TTGTATTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:60498998 original size:15 final size:16
Alignment explanation
Indices: 60498967--60498999 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
60498957 GGAATTCACA
*
60498967 TATTTTTCAATATTAT
1 TATTTTTAAATATTAT
60498983 TATTTTTAAATA-TAT
1 TATTTTTAAATATTAT
60498998 TA
1 TA
60499000 CATTTATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (16 bp):
TATTTTTAAATATTAT
Found at i:60499443 original size:22 final size:25
Alignment explanation
Indices: 60499418--60499465 Score: 66
Period size: 23 Copynumber: 2.0 Consensus size: 25
60499408 GTAGATATGA
*
60499418 TCAAA-ATCTATA-ATGAG-ATTAT
1 TCAAATATATATATATGAGAATTAT
60499440 TCAAATATATATATATGAGAATTAT
1 TCAAATATATATATATGAGAATTAT
60499465 T
1 T
60499466 TGATATACCG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 5 0.23
23 6 0.27
24 5 0.23
25 6 0.27
ACGTcount: A:0.46, C:0.06, G:0.08, T:0.40
Consensus pattern (25 bp):
TCAAATATATATATATGAGAATTAT
Found at i:60502654 original size:17 final size:19
Alignment explanation
Indices: 60502622--60502659 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
60502612 GACTAAGATG
*
60502622 TTGAGACTTATATATTTTC
1 TTGAGACTTATATATTCTC
60502641 TTGAG-CTT-TATATTCTC
1 TTGAGACTTATATATTCTC
60502658 TT
1 TT
60502660 AGCCTCAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 10 0.56
18 3 0.17
19 5 0.28
ACGTcount: A:0.21, C:0.13, G:0.11, T:0.55
Consensus pattern (19 bp):
TTGAGACTTATATATTCTC
Found at i:60517762 original size:19 final size:18
Alignment explanation
Indices: 60517727--60517769 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
60517717 AAAATTATGC
60517727 TTTTTAAAATTAATTTATA
1 TTTTTAAAATTAATTTA-A
*
60517746 TTTTTAAAA-TATTTTTAA
1 TTTTTAAAATTA-ATTTAA
60517764 TTTTTA
1 TTTTTA
60517770 TTTTAGGTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 9 0.41
19 13 0.59
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTTTAAAATTAATTTAA
Found at i:60523209 original size:15 final size:15
Alignment explanation
Indices: 60523189--60523228 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
60523179 CACCAACGCC
60523189 GCCGCGGCACACACG
1 GCCGCGGCACACACG
60523204 GCCGCGGCACACACG
1 GCCGCGGCACACACG
*
60523219 GCCGCCGCAC
1 GCCGCGGCAC
60523229 CCACCGCTAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.17, C:0.50, G:0.33, T:0.00
Consensus pattern (15 bp):
GCCGCGGCACACACG
Found at i:60523225 original size:18 final size:17
Alignment explanation
Indices: 60523184--60523226 Score: 63
Period size: 15 Copynumber: 2.6 Consensus size: 17
60523174 TGTACCACCA
60523184 ACGCCGCCGCGGCACAC
1 ACGCCGCCGCGGCACAC
60523201 ACG--GCCGCGGCACAC
1 ACGCCGCCGCGGCACAC
60523216 ACGGCCGCCGC
1 AC-GCCGCCGC
60523227 ACCCACCGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 14 0.61
16 1 0.04
17 3 0.13
18 5 0.22
ACGTcount: A:0.16, C:0.51, G:0.33, T:0.00
Consensus pattern (17 bp):
ACGCCGCCGCGGCACAC
Found at i:60530497 original size:16 final size:16
Alignment explanation
Indices: 60530462--60530502 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
60530452 CATCAATATT
*
60530462 AATAATCAAATAAACT
1 AATAATCAAATAAACA
60530478 AATAATCAAACT-AACA
1 AATAATCAAA-TAAACA
60530494 AATAA-CAAA
1 AATAATCAAA
60530503 ATAAGAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 4 0.17
16 18 0.78
17 1 0.04
ACGTcount: A:0.66, C:0.15, G:0.00, T:0.20
Consensus pattern (16 bp):
AATAATCAAATAAACA
Found at i:60538783 original size:10 final size:10
Alignment explanation
Indices: 60538768--60538796 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
60538758 TATGATTATG
60538768 GGCTCGGCTT
1 GGCTCGGCTT
60538778 GGCTCGGCTT
1 GGCTCGGCTT
60538788 GGCTCGGCT
1 GGCTCGGCT
60538797 CTTGCGCAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.00, C:0.31, G:0.41, T:0.28
Consensus pattern (10 bp):
GGCTCGGCTT
Found at i:60544468 original size:14 final size:15
Alignment explanation
Indices: 60544449--60544477 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
60544439 CTCTCTCAAC
60544449 AAAAA-TTAAAATAA
1 AAAAATTTAAAATAA
60544463 AAAAATTTAAAATAA
1 AAAAATTTAAAATAA
60544478 TTTTCAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
AAAAATTTAAAATAA
Found at i:60553748 original size:39 final size:39
Alignment explanation
Indices: 60553692--60553770 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
60553682 TCAAACAATG
60553692 ATTAAAGCTAAAAAAGCTAAAATATTCGATCGAAAAACA
1 ATTAAAGCTAAAAAAGCTAAAATATTCGATCGAAAAACA
* *
60553731 ATTAAAGCTGAACAAGCTAAAATATTCGATCGAAAAACA
1 ATTAAAGCTAAAAAAGCTAAAATATTCGATCGAAAAACA
60553770 A
1 A
60553771 AGTTCAAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.54, C:0.14, G:0.11, T:0.20
Consensus pattern (39 bp):
ATTAAAGCTAAAAAAGCTAAAATATTCGATCGAAAAACA
Found at i:60554732 original size:31 final size:31
Alignment explanation
Indices: 60554668--60554732 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
60554658 TCTTAACAAC
* *
60554668 TCAGTAACTTAAATAAAAGCTTTCAAATTAT
1 TCAGTAACTTAAATAAAAACTTTCAAATAAT
* * **
60554699 TCAGTGACTTAAATAAAAATTTTTGAATAAT
1 TCAGTAACTTAAATAAAAACTTTCAAATAAT
60554730 TCA
1 TCA
60554733 ATGATCATTT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.45, C:0.11, G:0.08, T:0.37
Consensus pattern (31 bp):
TCAGTAACTTAAATAAAAACTTTCAAATAAT
Found at i:60554895 original size:19 final size:20
Alignment explanation
Indices: 60554858--60554895 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
60554848 ATCATCAATG
* *
60554858 AAAATTTTAAAATCTTATAT
1 AAAATTTAAAAATCATATAT
60554878 AAAATTTAAAAAT-ATATA
1 AAAATTTAAAAATCATATA
60554896 CATAATTGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (20 bp):
AAAATTTAAAAATCATATAT
Done.