Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D12
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: 63843421
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1690000 characters in sequence are not A, C, G, or T
File 182 of 214
Found at i:53437164 original size:20 final size:20
Alignment explanation
Indices: 53437117--53437164 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
53437107 AATGTGCTAC
*
53437117 ATTTGAAAAAGAAAATTTTG
1 ATTTGAAGAAGAAAATTTTG
53437137 ATTTGAAGAAGAAAATTTTG
1 ATTTGAAGAAGAAAATTTTG
*
53437157 GTTTGAAG
1 ATTTGAAG
53437165 TTAAAACTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.44, C:0.00, G:0.21, T:0.35
Consensus pattern (20 bp):
ATTTGAAGAAGAAAATTTTG
Found at i:53437422 original size:22 final size:23
Alignment explanation
Indices: 53437397--53437453 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
53437387 TTGTATATTA
53437397 TTTTAAATTTTA-AATTATA-GAT
1 TTTTAAATTTTACAATTATATG-T
* *
53437419 TTTTAAAATTTACATTTATATGT
1 TTTTAAATTTTACAATTATATGT
*
53437442 TTTAAAATTTTA
1 TTTTAAATTTTA
53437454 TTTAAAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 11 0.38
23 17 0.59
24 1 0.03
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.56
Consensus pattern (23 bp):
TTTTAAATTTTACAATTATATGT
Found at i:53437453 original size:23 final size:23
Alignment explanation
Indices: 53437397--53437453 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 23
53437387 TTGTATATTA
53437397 TTTT-AAATTTTAAATTATAGAT
1 TTTTAAAATTTTAAATTATAGAT
* *
53437419 TTTTAAAA-TTTACATT-TATAT
1 TTTTAAAATTTTAAATTATAGAT
53437440 GTTTTAAAATTTTA
1 -TTTTAAAATTTTA
53437454 TTTAAAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
21 4 0.13
22 19 0.63
23 7 0.23
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.56
Consensus pattern (23 bp):
TTTTAAAATTTTAAATTATAGAT
Found at i:53439692 original size:9 final size:9
Alignment explanation
Indices: 53439678--53439714 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
53439668 TATAGTTTGA
53439678 TATTCGAAT
1 TATTCGAAT
53439687 TATTCGAAT
1 TATTCGAAT
*
53439696 TATTCGAGT
1 TATTCGAAT
53439705 TATTCGAAT
1 TATTCGAAT
53439714 T
1 T
53439715 CAAAAACTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:53439785 original size:9 final size:9
Alignment explanation
Indices: 53439768--53439798 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
53439758 TTGAGTTGAT
53439768 TCGAATAAC
1 TCGAATAAC
*
53439777 TCGATTAAC
1 TCGAATAAC
53439786 TCGAATAAC
1 TCGAATAAC
53439795 TCGA
1 TCGA
53439799 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:53449078 original size:29 final size:29
Alignment explanation
Indices: 53449028--53449084 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
53449018 GTGAATGATA
*
53449028 AATGTAATAAAAATATTTATAAAAAAATT
1 AATGTAATAAAAATATTAATAAAAAAATT
* *
53449057 AATGTGATAAATAA-ATTAATAAATAAAT
1 AATGTAATAAA-AATATTAATAAAAAAAT
53449085 AAACTTTGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 22 0.92
30 2 0.08
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.33
Consensus pattern (29 bp):
AATGTAATAAAAATATTAATAAAAAAATT
Found at i:53454186 original size:22 final size:21
Alignment explanation
Indices: 53454142--53454182 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
53454132 ATGTCATTAG
*
53454142 GGTTTAAACAAAAAAGGAAAT
1 GGTTCAAACAAAAAAGGAAAT
*
53454163 GGTTCAAACGAAAAAGGAAA
1 GGTTCAAACAAAAAAGGAAA
53454183 ATGGGTGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.56, C:0.07, G:0.22, T:0.15
Consensus pattern (21 bp):
GGTTCAAACAAAAAAGGAAAT
Found at i:53456871 original size:12 final size:12
Alignment explanation
Indices: 53456826--53456872 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
53456816 CGATGATTGC
*
53456826 ATATTAAAATA-
1 ATATTTAAATAT
*
53456837 ATTATTTAAAAAT
1 A-TATTTAAATAT
*
53456850 ATATTTAAATTT
1 ATATTTAAATAT
53456862 ATATTTAAATA
1 ATATTTAAATA
53456873 AAATTCTAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
11 1 0.03
12 27 0.93
13 1 0.03
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
ATATTTAAATAT
Found at i:53467000 original size:26 final size:25
Alignment explanation
Indices: 53466963--53467044 Score: 60
Period size: 26 Copynumber: 3.2 Consensus size: 25
53466953 TATTTGATAA
*
53466963 ATTTTT-AGAATAATTTTTATAGAT
1 ATTTTTAAAAATAATTTTTATAGAT
* *
53466987 ATTTTTGAAAAATAAAATTTCA-AGAT
1 ATTTTT-AAAAAT-AATTTTTATAGAT
* * *
53467013 ATATTTAAAAAAATATTTTTATATAGT
1 ATTTTTAAAAATA-ATTTTTATAGA-T
53467040 ATTTT
1 ATTTT
53467045 AATTTACTTT
Statistics
Matches: 43, Mismatches: 9, Indels: 9
0.70 0.15 0.15
Matches are distributed among these distances:
24 7 0.16
25 10 0.23
26 15 0.35
27 11 0.26
ACGTcount: A:0.44, C:0.01, G:0.06, T:0.49
Consensus pattern (25 bp):
ATTTTTAAAAATAATTTTTATAGAT
Found at i:53469461 original size:13 final size:13
Alignment explanation
Indices: 53469443--53469468 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
53469433 TTGGATCTGT
53469443 ACCAAAACAATCA
1 ACCAAAACAATCA
53469456 ACCAAAACAATCA
1 ACCAAAACAATCA
53469469 TAAAACATAT
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:0.62, C:0.31, G:0.00, T:0.08
Consensus pattern (13 bp):
ACCAAAACAATCA
Found at i:53473586 original size:7 final size:7
Alignment explanation
Indices: 53473548--53473577 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
53473538 ACCCAACAAT
53473548 AACCTTA
1 AACCTTA
53473555 AACCTTA
1 AACCTTA
53473562 AACCTTA
1 AACCTTA
*
53473569 AACCCTA
1 AACCTTA
53473576 AA
1 AA
53473578 ACCCTAAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.47, C:0.30, G:0.00, T:0.23
Consensus pattern (7 bp):
AACCTTA
Found at i:53479831 original size:6 final size:6
Alignment explanation
Indices: 53479820--53479844 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
53479810 GCCTTGCGTC
53479820 TTTCTT TTTCTT TTTCTT TTTCTT T
1 TTTCTT TTTCTT TTTCTT TTTCTT T
53479845 CTTTCCTTTC
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:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTCTT
Found at i:53482791 original size:20 final size:21
Alignment explanation
Indices: 53482761--53482804 Score: 65
Period size: 19 Copynumber: 2.1 Consensus size: 21
53482751 GTCAGAAGTT
53482761 AATTAATTTTTTAAAAA-TTAA
1 AATTAA-TTTTTAAAAATTTAA
53482782 AATT-ATTTTTAAAAATTTAA
1 AATTAATTTTTAAAAATTTAA
53482802 AAT
1 AAT
53482805 CTTTAAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 10 0.45
20 8 0.36
21 4 0.18
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
AATTAATTTTTAAAAATTTAA
Found at i:53482870 original size:57 final size:57
Alignment explanation
Indices: 53482772--53482879 Score: 141
Period size: 57 Copynumber: 1.9 Consensus size: 57
53482762 ATTAATTTTT
53482772 TAAAAATTAAAATTATTTTTAAAAATTTAAAATCTTTAAAATT-ATTAAATAAATTA
1 TAAAAATTAAAATTATTTTTAAAAATTTAAAATCTTTAAAATTAATTAAATAAATTA
* * *
53482828 TAAAAATTTAAAA-TATTTTTTAATATTTTAATAT-TTTAAAAATTAATTAAAT
1 TAAAAA-TTAAAATTA-TTTTTAAAAATTTAAAATCTTT-AAAATTAATTAAAT
53482880 TTTTATGTGT
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
56 11 0.24
57 27 0.60
58 7 0.16
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (57 bp):
TAAAAATTAAAATTATTTTTAAAAATTTAAAATCTTTAAAATTAATTAAATAAATTA
Found at i:53482883 original size:19 final size:19
Alignment explanation
Indices: 53482759--53482884 Score: 56
Period size: 19 Copynumber: 6.8 Consensus size: 19
53482749 ACGTCAGAAG
*
53482759 TTAATTAATTTTTTAAAAA
1 TTAATTAAATTTTTAAAAA
53482778 TTAA--AATTATTTTTAAAAA
1 TTAATTAA--ATTTTTAAAAA
* *
53482797 TT--TAAAATCTTTAAAATTA
1 TTAATTAAATTTTTAAAA--A
* *
53482816 TTAAATAAA-TTATAAAAA
1 TTAATTAAATTTTTAAAAA
* *
53482834 TTTAA--AATATTTTTTAATA
1 -TTAATTAA-ATTTTTAAAAA
53482853 TT--TT-AATATTTTAAAAA
1 TTAATTAAAT-TTTTAAAAA
53482870 TTAATTAAATTTTTA
1 TTAATTAAATTTTTA
53482885 TGTGTTATTT
Statistics
Matches: 79, Mismatches: 11, Indels: 34
0.64 0.09 0.27
Matches are distributed among these distances:
16 2 0.03
17 23 0.29
18 4 0.05
19 38 0.48
20 9 0.11
21 3 0.04
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (19 bp):
TTAATTAAATTTTTAAAAA
Found at i:53484715 original size:21 final size:21
Alignment explanation
Indices: 53484691--53484745 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
53484681 TAGGGATCCT
**
53484691 ACACGGGCGTGTGTTTTGGAC
1 ACACGGGCGTGTGTGGTGGAC
** * *
53484712 ACACGTCCGTGTCTGGTGGGC
1 ACACGGGCGTGTGTGGTGGAC
53484733 ACACGGGCGTGTG
1 ACACGGGCGTGTG
53484746 AGACCCGCAC
Statistics
Matches: 25, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.13, C:0.24, G:0.40, T:0.24
Consensus pattern (21 bp):
ACACGGGCGTGTGTGGTGGAC
Found at i:53484914 original size:22 final size:22
Alignment explanation
Indices: 53484870--53484914 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
53484860 CACATGGTCA
*
53484870 TGTGACTCTCCTCACACTAGCG
1 TGTGACTCTCCTCACACGAGCG
* * *
53484892 TGTGCCTCTCTTCACACGGGCG
1 TGTGACTCTCCTCACACGAGCG
53484914 T
1 T
53484915 TTAGACCCCT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.13, C:0.36, G:0.22, T:0.29
Consensus pattern (22 bp):
TGTGACTCTCCTCACACGAGCG
Found at i:53488089 original size:20 final size:20
Alignment explanation
Indices: 53488064--53488103 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
53488054 CGTAAAATGA
*
53488064 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
53488084 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
53488104 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:53488093 original size:34 final size:35
Alignment explanation
Indices: 53488049--53488115 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
53488039 CAGTAAAATA
*
53488049 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
53488083 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
53488116 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:53488119 original size:14 final size:15
Alignment explanation
Indices: 53488043--53488119 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
53488033 GATTGCCAGT
* *
53488043 AAAAT-ATTTTCCGT
1 AAAATGATTTTCTGG
53488057 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
53488071 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
53488091 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
53488106 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
53488120 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 24 0.48
15 12 0.24
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:53488877 original size:47 final size:47
Alignment explanation
Indices: 53488819--53488953 Score: 137
Period size: 48 Copynumber: 2.8 Consensus size: 47
53488809 AAAATCTGCT
* * * *
53488819 AATACATTGTGGATGAACCACTAGTCGAGCAGAT-GACTGTCAACTAA
1 AATACGTTGTGGAT-AACCACTAGTCGAGTAGATAAACTGACAACTAA
* * * *
53488866 AATACGTTGTGGATAAAACATTGGTCGAGTAGATAAACTGACGACTAA
1 AATACGTTGTGGAT-AACCACTAGTCGAGTAGATAAACTGACAACTAA
* * *
53488914 AACATGTTATGGATAATCCACTAGTCGAGTAGATAAACTG
1 AATACGTTGTGGATAA-CCACTAGTCGAGTAGATAAACTG
53488954 TTGACTACTT
Statistics
Matches: 71, Mismatches: 15, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
47 30 0.42
48 41 0.58
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.25
Consensus pattern (47 bp):
AATACGTTGTGGATAACCACTAGTCGAGTAGATAAACTGACAACTAA
Found at i:53496604 original size:7 final size:7
Alignment explanation
Indices: 53496592--53496625 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
53496582 TTTCTAGATA
53496592 TATTTTT
1 TATTTTT
53496599 TATTTTT
1 TATTTTT
*
53496606 TATTTTA
1 TATTTTT
53496613 TAGTTTTT
1 TA-TTTTT
53496621 TATTT
1 TATTT
53496626 AAAATATGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 18 0.75
8 6 0.25
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (7 bp):
TATTTTT
Found at i:53496609 original size:14 final size:15
Alignment explanation
Indices: 53496592--53496625 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
53496582 TTTCTAGATA
*
53496592 TATTTTTTA-TTTTT
1 TATTTTATAGTTTTT
53496606 TATTTTATAGTTTTT
1 TATTTTATAGTTTTT
53496621 TATTT
1 TATTT
53496626 AAAATATGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (15 bp):
TATTTTATAGTTTTT
Found at i:53498251 original size:19 final size:18
Alignment explanation
Indices: 53498223--53498269 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 18
53498213 ACTTTATGCT
53498223 TTTTTAAATTTTCATTAA
1 TTTTTAAATTTTCATTAA
**
53498241 TTTTTATAATTTTTTTTAA
1 TTTTTA-AATTTTCATTAA
*
53498260 TTTTGAAATT
1 TTTTTAAATT
53498270 CTTTTTTTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 10 0.40
19 15 0.60
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (18 bp):
TTTTTAAATTTTCATTAA
Found at i:53498274 original size:18 final size:19
Alignment explanation
Indices: 53498237--53498275 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
53498227 TAAATTTTCA
* *
53498237 TTAATTTTTATAATTTTTT
1 TTAATTTTGATAATTCTTT
53498256 TTAATTTTGA-AATTCTTT
1 TTAATTTTGATAATTCTTT
53498274 TT
1 TT
53498276 TTGAATATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.69
Consensus pattern (19 bp):
TTAATTTTGATAATTCTTT
Found at i:53498274 original size:19 final size:19
Alignment explanation
Indices: 53498237--53498276 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
53498227 TAAATTTTCA
*
53498237 TTAATTTTTATAATTTTTT
1 TTAATTTTGATAATTTTTT
53498256 TTAATTTTGA-AATTCTTTT
1 TTAATTTTGATAATT-TTTT
53498275 TT
1 TT
53498277 TGAATATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.70
Consensus pattern (19 bp):
TTAATTTTGATAATTTTTT
Found at i:53500391 original size:5 final size:5
Alignment explanation
Indices: 53500381--53500411 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
53500371 TATATATAAA
53500381 CAAAC CAAAC CAAAC CAAAC CAAAC CAAAC C
1 CAAAC CAAAC CAAAC CAAAC CAAAC CAAAC C
53500412 CTTGCCTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.58, C:0.42, G:0.00, T:0.00
Consensus pattern (5 bp):
CAAAC
Found at i:53506278 original size:28 final size:28
Alignment explanation
Indices: 53506239--53506296 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
53506229 TGGTCAACAG
53506239 AAAATAACTTAGATGACAACGAAAAATA
1 AAAATAACTTAGATGACAACGAAAAATA
53506267 AAAATAACTTAGATGACAACGAAAAATA
1 AAAATAACTTAGATGACAACGAAAAATA
53506295 AA
1 AA
53506297 CATTTTTTCG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.62, C:0.10, G:0.10, T:0.17
Consensus pattern (28 bp):
AAAATAACTTAGATGACAACGAAAAATA
Found at i:53506636 original size:26 final size:25
Alignment explanation
Indices: 53506607--53506661 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 25
53506597 AATGATATTC
53506607 TTAATATATTACTAA-AAATAATTATA
1 TTAATATATTACTAATAAAT-A-TATA
* *
53506633 TTAATATTTTAGTAATAAATATATA
1 TTAATATATTACTAATAAATATATA
53506658 TTAA
1 TTAA
53506662 AATTTATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 8 0.31
26 14 0.54
27 4 0.15
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (25 bp):
TTAATATATTACTAATAAATATATA
Found at i:53514151 original size:27 final size:28
Alignment explanation
Indices: 53514121--53514204 Score: 91
Period size: 27 Copynumber: 3.0 Consensus size: 28
53514111 AATTTTTTTT
*
53514121 TTTTATTTTTGTTA-TTATTATTTATTA
1 TTTTATTTTTATTATTTATTATTTATTA
*
53514148 TTTTATTTTATTTTATTTACTTTATTTATTA
1 TTTTATTTT-TATTATTTA--TTATTTATTA
* *
53514179 CTTTA-TTTTATTATTTATTACTTATT
1 TTTTATTTTTATTATTTATTATTTATT
53514205 TGGATATTAA
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
27 17 0.35
28 4 0.08
29 11 0.22
30 3 0.06
31 14 0.29
ACGTcount: A:0.23, C:0.04, G:0.01, T:0.73
Consensus pattern (28 bp):
TTTTATTTTTATTATTTATTATTTATTA
Found at i:53514155 original size:5 final size:5
Alignment explanation
Indices: 53514112--53514190 Score: 58
Period size: 5 Copynumber: 15.6 Consensus size: 5
53514102 AGGCAACCCA
*
53514112 ATTTT -TTTT -TTTT ATTTT -TGTT ATTATT ATTTATT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATT-TT A-TT-TT ATTTT ATTTT
* *
53514157 ATTTT A-TTT ACTTT ATTTATT ACTTT ATTTT ATT
1 ATTTT ATTTT ATTTT A-TT-TT ATTTT ATTTT ATT
53514191 ATTTATTACT
Statistics
Matches: 62, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
4 15 0.24
5 31 0.50
6 7 0.11
7 9 0.15
ACGTcount: A:0.20, C:0.03, G:0.01, T:0.76
Consensus pattern (5 bp):
ATTTT
Found at i:53514176 original size:31 final size:32
Alignment explanation
Indices: 53514116--53514200 Score: 102
Period size: 32 Copynumber: 2.7 Consensus size: 32
53514106 AACCCAATTT
* *
53514116 TTTTTTTTTATTTTTGTTATTATTATTTATTA
1 TTTTATTTTATTTTTGTTACTATTATTTATTA
53514148 TTTTATTTTATTTTAT-TTACT-TTATTTATTA
1 TTTTATTTTATTTT-TGTTACTATTATTTATTA
* *
53514179 CTTTATTTTATTATTTATTACT
1 TTTTATTTTATT-TTTGTTACT
53514201 TATTTGGATA
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
31 22 0.47
32 24 0.51
33 1 0.02
ACGTcount: A:0.21, C:0.04, G:0.01, T:0.74
Consensus pattern (32 bp):
TTTTATTTTATTTTTGTTACTATTATTTATTA
Found at i:53515521 original size:101 final size:100
Alignment explanation
Indices: 53515327--53515519 Score: 280
Period size: 101 Copynumber: 1.9 Consensus size: 100
53515317 TTTTAAGAAC
*
53515327 ATGTTGGGCTGAGTAACCGGGGTGAGGTGCTTGGCTGTCATCTCTCTTCGTGTCAAAAGGTTCGA
1 ATGTTGGGCTGAGTAACCGGGGTGAGGTGCTTGGCTGTCATCTCTCTTCGCGTCAAAAGGTTCGA
* *
53515392 TGTGTTCTTAAGAAAAAATTATAATAAATTAGGAGT
66 TATGTTCTAAAGAAAAAA-TATAATAAATTAGGAGT
* *
53515428 ATGTTGGGCTGAGTAACCGGGGTGGGGTGCTTGGTTGTCATCTCTCTTCGCGTCAAAAGGTTCAG
1 ATGTTGGGCTGAGTAACCGGGGTGAGGTGCTTGGCTGTCATCTCTCTTCGCGTCAAAAGGTTC-G
53515493 TATAT-TTCTAAAGCATAAAAAATATAA
65 -ATATGTTCTAAAG---AAAAAATATAA
53515520 ATAATAAATA
Statistics
Matches: 82, Mismatches: 5, Indels: 7
0.87 0.05 0.07
Matches are distributed among these distances:
101 60 0.73
102 8 0.10
103 3 0.04
104 5 0.06
105 6 0.07
ACGTcount: A:0.27, C:0.14, G:0.27, T:0.32
Consensus pattern (100 bp):
ATGTTGGGCTGAGTAACCGGGGTGAGGTGCTTGGCTGTCATCTCTCTTCGCGTCAAAAGGTTCGA
TATGTTCTAAAGAAAAAATATAATAAATTAGGAGT
Found at i:53516117 original size:15 final size:15
Alignment explanation
Indices: 53516092--53516126 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
53516082 GACTCTATTT
*
53516092 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
53516106 TAATTAATATTAAGA
1 TAATTAATATTAAGA
53516121 TAATTA
1 TAATTA
53516127 TTAAGAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:53518349 original size:25 final size:26
Alignment explanation
Indices: 53518291--53518351 Score: 88
Period size: 26 Copynumber: 2.4 Consensus size: 26
53518281 TACCCCCAAC
* *
53518291 AAAATTTTGATGATTTTACCCTTGGT
1 AAAATTTTGACGATTTTACCCTTAGT
*
53518317 AAAATTTTGACGATTTTTCCC-TAGT
1 AAAATTTTGACGATTTTACCCTTAGT
53518342 AAAATTTTGA
1 AAAATTTTGA
53518352 GAAAATATGT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
25 13 0.41
26 19 0.59
ACGTcount: A:0.31, C:0.11, G:0.13, T:0.44
Consensus pattern (26 bp):
AAAATTTTGACGATTTTACCCTTAGT
Found at i:53518643 original size:9 final size:10
Alignment explanation
Indices: 53518624--53518652 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
53518614 ATTCAATTTT
53518624 TTTCTATTCA
1 TTTCTATTCA
53518634 TTTC-ATTCA
1 TTTCTATTCA
53518643 TTTCTATTCA
1 TTTCTATTCA
53518653 AAACAAGCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.21, C:0.21, G:0.00, T:0.59
Consensus pattern (10 bp):
TTTCTATTCA
Found at i:53520690 original size:19 final size:20
Alignment explanation
Indices: 53520653--53520704 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
53520643 AGGTCGCTCC
*
53520653 TACTATAATTTTATTTATAT-
1 TACTTTAATTTT-TTTATATA
53520673 TACTTTAATTTTTTTATATA
1 TACTTTAATTTTTTTATATA
*
53520693 TA-ATTAATTTTT
1 TACTTTAATTTTT
53520705 ATGATTCATG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (20 bp):
TACTTTAATTTTTTTATATA
Found at i:53522232 original size:22 final size:22
Alignment explanation
Indices: 53522184--53522232 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
53522174 ATTTGAAATT
*
53522184 TAATTTTTATTTTAATTTGATA
1 TAATTTTTATTTTAATTTCATA
* *
53522206 TAATTTATTTTTTTATTTTCATA
1 TAATTT-TTATTTTAATTTCATA
53522229 -AATT
1 TAATT
53522233 AGTCCGGTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 10 0.43
23 13 0.57
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (22 bp):
TAATTTTTATTTTAATTTCATA
Found at i:53522909 original size:22 final size:23
Alignment explanation
Indices: 53522883--53522925 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
53522873 ATCTAAATTT
53522883 TTAAATT-TAAAAAATAAAAAAA
1 TTAAATTCTAAAAAATAAAAAAA
**
53522905 TTAAATTCTTGAAAATAAAAA
1 TTAAATTCTAAAAAATAAAAA
53522926 TGAGTAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (23 bp):
TTAAATTCTAAAAAATAAAAAAA
Found at i:53530688 original size:90 final size:92
Alignment explanation
Indices: 53530521--53530696 Score: 239
Period size: 90 Copynumber: 1.9 Consensus size: 92
53530511 TCGCACTTGA
* * * **
53530521 TATAAATAAGTGTCAATTTCTTAACTATTTTCATTAAAAAGTTCATTTTAATCTCACATTGACTA
1 TATAAATAAGTGACAATTTC-T-ACTATTTTCATTAAAAAGTTAATTTTAATCACACATCAACTA
* *
53530586 GAGAACATTCTCATATCTCACATTGACCT
64 GAGAACACTCTCATAGCTCACATTGACCT
*
53530615 TATAAATAAGTGACAATTTC-ACTATTTTCATTAAAAA-TTAATTTTAATCACACGTCAACTAGA
1 TATAAATAAGTGACAATTTCTACTATTTTCATTAAAAAGTTAATTTTAATCACACATCAACTAGA
*
53530678 GAAGACTCTCATAGCTCAC
66 GAACACTCTCATAGCTCAC
53530697 TTCTTCACTA
Statistics
Matches: 73, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
90 37 0.51
91 17 0.23
94 19 0.26
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.36
Consensus pattern (92 bp):
TATAAATAAGTGACAATTTCTACTATTTTCATTAAAAAGTTAATTTTAATCACACATCAACTAGA
GAACACTCTCATAGCTCACATTGACCT
Found at i:53530763 original size:68 final size:68
Alignment explanation
Indices: 53530632--53530764 Score: 169
Period size: 69 Copynumber: 2.0 Consensus size: 68
53530622 AAGTGACAAT
* * *
53530632 TTCACTATTTTCATTAAAAATTAATTTTAATCACACGTCAACTAGAGAAGACTCTCATAGCTCAC
1 TTCACTATTTTCATTAAAAATTAATTTTAATCACACATCAACTAGAGAACAATCTCATAGCTCAC
53530697 TTC
66 TTC
* * ****
53530700 TTCACTATTTTCATTAAAACGTTAATTTTAATCCCACATTGGTTAGAGAACAATCTCAT-GCTCA
1 TTCACTATTTTCATTAAAA-ATTAATTTTAATCACACATCAACTAGAGAACAATCTCATAGCTCA
53530764 C
65 C
53530765 ACTTACACTA
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
68 25 0.45
69 30 0.55
ACGTcount: A:0.34, C:0.22, G:0.08, T:0.36
Consensus pattern (68 bp):
TTCACTATTTTCATTAAAAATTAATTTTAATCACACATCAACTAGAGAACAATCTCATAGCTCAC
TTC
Found at i:53530774 original size:68 final size:68
Alignment explanation
Indices: 53530632--53530775 Score: 166
Period size: 68 Copynumber: 2.1 Consensus size: 68
53530622 AAGTGACAAT
* * *
53530632 TTCACTATTTTCATTAAAAATTAATTTTAATCACACGTCAACTAGAGAAGACTCTCATAGCTCAC
1 TTCACTATTTTCATTAAAAATTAATTTTAATCACACATCAACTAGAGAACAATCTCATAGCTCAC
*
53530697 TTC
66 TAC
* * ****
53530700 TTCACTATTTTCATTAAAACGTTAATTTTAATCCCACATTGGTTAGAGAACAATCTCAT-GCTCA
1 TTCACTATTTTCATTAAAA-ATTAATTTTAATCACACATCAACTAGAGAACAATCTCATAGCTCA
53530764 C-AC
65 CTAC
53530767 TTACACTAT
1 TT-CACTAT
53530776 AAATAAGTGT
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
67 3 0.05
68 31 0.48
69 30 0.47
ACGTcount: A:0.34, C:0.22, G:0.08, T:0.36
Consensus pattern (68 bp):
TTCACTATTTTCATTAAAAATTAATTTTAATCACACATCAACTAGAGAACAATCTCATAGCTCAC
TAC
Found at i:53530825 original size:252 final size:254
Alignment explanation
Indices: 53530381--53531079 Score: 979
Period size: 257 Copynumber: 2.8 Consensus size: 254
53530371 CATAGCTCAC
* *
53530381 TTCTTCACTATTTTTATTAAAAAAATTAATTTTAATCCCACATTAACTAGAGAATACT-TCCATA
1 TTCTTCACTATTTTCATT-AAAAAATTAATTTTAATCCCACATTAACTAGAGAAAACTCT-CATA
** * * ** *
53530445 GCTTGCTTCTTCACTACTGTT-ATTAAAA-GTTAATTTTAA-CTTAAAAAGTTA-AGAACACTCC
64 GCTCACTTCTTCACTA-TTTTCATTAAAACGTTAATTTTAATCCTAATTAGTTAGAGAACACTCT
* * *
53530506 CATACTCGCACTT-GA-TATAAATAAGTGTCAATTTCTTAACTATTTTCATTAAAAAGTTCATTT
128 CATGCTCACACTTACACTATAAATAAGTGTCAATTTCTTAACTATTTTCATTAAAAAGTTCATTT
53530569 TAATCTCACATTGACTAGAGAACATTCTCATATCTCACATTGACCTTATAAATAAGTGACAA
193 TAATCTCACATTGACTAGAGAACATTCTCATATCTCACATTGACCTTATAAATAAGTGACAA
* * * *
53530631 -T-TTCACTATTTTCATT-AAAAATTAATTTTAATCACACGTCAACTAGAGAAGACTCTCATAGC
1 TTCTTCACTATTTTCATTAAAAAATTAATTTTAATCCCACATTAACTAGAGAAAACTCTCATAGC
* * *
53530693 TCACTTCTTCACTATTTTCATTAAAACGTTAATTTTAATCCCACATTGGTTAGAGAACAATCTCA
66 TCACTTCTTCACTATTTTCATTAAAACGTTAATTTTAATCCTA-ATTAGTTAGAGAACACTCTCA
53530758 TGCTCACACTTACACTATAAATAAGTGTCAATTTCTTAACTATTTTCATTAAAAAGTTCATTTTA
130 TGCTCACACTTACACTATAAATAAGTGTCAATTTCTTAACTATTTTCATTAAAAAGTTCATTTTA
*
53530823 ATCTCACATTGACTAGAGAACATTCTCATATCTCATATTGACCTTATAAATAAGTGACAA
195 ATCTCACATTGACTAGAGAACATTCTCATATCTCACATTGACCTTATAAATAAGTGACAA
*
53530883 TTTCTTCACTATTTTCATTAAAAAATTTAATTTTAATCCCACATTAACTAGGGAAAACTCTCATA
1 -TTCTTCACTATTTTCATTAAAAAA-TTAATTTTAATCCCACATTAACTAGAGAAAACTCTCATA
* *
53530948 GCTCTCTTCTTCACTATTTTCATTAAAACGTTAATTTTAATCCTATATTAGTTAGAGAACTCTCT
64 GCTCACTTCTTCACTATTTTCATTAAAACGTTAATTTTAATCCTA-ATTAGTTAGAGAACACTCT
* * * * * * * *
53531013 CATGCTCATACTTACACTGTAAATAGGTGTCAATTTCTT-CCTTTTTTTATTAAAAAGATAATTT
128 CATGCTCACACTTACACTATAAATAAGTGTCAATTTCTTAACTATTTTCATTAAAAAGTTCATTT
53531077 TAA
193 TAA
53531080 ATTTAAATAA
Statistics
Matches: 398, Mismatches: 38, Indels: 20
0.87 0.08 0.04
Matches are distributed among these distances:
245 3 0.01
246 59 0.15
247 12 0.03
248 16 0.04
249 6 0.02
250 19 0.05
251 1 0.00
252 109 0.27
254 1 0.00
255 15 0.04
256 28 0.07
257 129 0.32
ACGTcount: A:0.35, C:0.18, G:0.08, T:0.39
Consensus pattern (254 bp):
TTCTTCACTATTTTCATTAAAAAATTAATTTTAATCCCACATTAACTAGAGAAAACTCTCATAGC
TCACTTCTTCACTATTTTCATTAAAACGTTAATTTTAATCCTAATTAGTTAGAGAACACTCTCAT
GCTCACACTTACACTATAAATAAGTGTCAATTTCTTAACTATTTTCATTAAAAAGTTCATTTTAA
TCTCACATTGACTAGAGAACATTCTCATATCTCACATTGACCTTATAAATAAGTGACAA
Found at i:53530904 original size:94 final size:94
Alignment explanation
Indices: 53530697--53530951 Score: 329
Period size: 93 Copynumber: 2.7 Consensus size: 94
53530687 CATAGCTCAC
* **
53530697 TTCTTCACTATTTTCATTAAAACGTTAATTTTAATCCCACATTGGTTAGAGAACAATCTCAT-GC
1 TTCTTCACTATTTTCATTAAAAAGTTAATTTTAATCCCACATTGACTAGAGAACAATCTCATAGC
*
53530761 TCACACTTACACTATAAATAAGTGTCAAT
66 TCACACTTACACTATAAATAAGTGACAAT
* * * * *
53530790 TTCTTAACTATTTTCATTAAAAAGTTCATTTTAATCTCACATTGACTAGAGAACATTCTCATATC
1 TTCTTCACTATTTTCATTAAAAAGTTAATTTTAATCCCACATTGACTAGAGAACAATCTCATAGC
*
53530855 TCATA-TTGAC-CTTATAAATAAGTGACAAT
66 TCACACTT-ACAC-TATAAATAAGTGACAAT
* * *
53530884 TTCTTCACTATTTTCATTAAAAAATTTAATTTTAATCCCACATTAACTAGGGAA-AACTCTCATA
1 TTCTTCACTATTTTCATT-AAAAAGTTAATTTTAATCCCACATTGACTAGAGAACAA-TCTCATA
53530948 GCTC
64 GCTC
53530952 TCTTCTTCAC
Statistics
Matches: 139, Mismatches: 18, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
93 58 0.42
94 41 0.29
95 40 0.29
ACGTcount: A:0.35, C:0.19, G:0.07, T:0.38
Consensus pattern (94 bp):
TTCTTCACTATTTTCATTAAAAAGTTAATTTTAATCCCACATTGACTAGAGAACAATCTCATAGC
TCACACTTACACTATAAATAAGTGACAAT
Found at i:53531512 original size:19 final size:20
Alignment explanation
Indices: 53531490--53531529 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
53531480 GTTTTTATAA
53531490 TAAAAT-TATCATTTATTTT
1 TAAAATGTATCATTTATTTT
**
53531509 TAAAATGTATTTTTTATTTT
1 TAAAATGTATCATTTATTTT
53531529 T
1 T
53531530 TTATTTCACC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (20 bp):
TAAAATGTATCATTTATTTT
Found at i:53531713 original size:35 final size:35
Alignment explanation
Indices: 53531662--53531742 Score: 135
Period size: 35 Copynumber: 2.3 Consensus size: 35
53531652 CAAATTGCTT
*
53531662 TTTTTGTCACCTAACTATGAAAAATAACAAAATGA
1 TTTTAGTCACCTAACTATGAAAAATAACAAAATGA
* *
53531697 TTTTAGTCACTTAACTATGAAAAGTAACAAAATGA
1 TTTTAGTCACCTAACTATGAAAAATAACAAAATGA
53531732 TTTTAGTCACC
1 TTTTAGTCACC
53531743 AGCTAGCTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.33
Consensus pattern (35 bp):
TTTTAGTCACCTAACTATGAAAAATAACAAAATGA
Found at i:53531855 original size:10 final size:11
Alignment explanation
Indices: 53531828--53531857 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
53531818 TTGGTCTCTC
53531828 TCTTTTTTCTT
1 TCTTTTTTCTT
53531839 TCTTTTTTCTT
1 TCTTTTTTCTT
53531850 TCTTTTTT
1 TCTTTTTT
53531858 GCAAATTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (11 bp):
TCTTTTTTCTT
Found at i:53532265 original size:31 final size:29
Alignment explanation
Indices: 53532202--53532265 Score: 76
Period size: 29 Copynumber: 2.1 Consensus size: 29
53532192 GACGAAGTTA
*
53532202 AATAGTTGAATGACCATAAAAAATGTATT
1 AATAGTTGAATGACCAAAAAAAATGTATT
*
53532231 AATAGTT-AGATGACCAAAAAAGAAATTTATT
1 AATAGTTGA-ATGACC-AAAAA-AAATGTATT
53532262 AATA
1 AATA
53532266 ATTAAATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 1 0.03
29 13 0.43
30 4 0.13
31 12 0.40
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.30
Consensus pattern (29 bp):
AATAGTTGAATGACCAAAAAAAATGTATT
Found at i:53541770 original size:21 final size:22
Alignment explanation
Indices: 53541731--53541771 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
53541721 TATTTTTTAT
*
53541731 TTTTAAGAATTTAATTTTAAAA
1 TTTTAAGAATTTAAGTTTAAAA
*
53541753 TTTTAA-AATTTAGGTTTAA
1 TTTTAAGAATTTAAGTTTAA
53541772 TGGTTAAACC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.51
Consensus pattern (22 bp):
TTTTAAGAATTTAAGTTTAAAA
Found at i:53544373 original size:16 final size:16
Alignment explanation
Indices: 53544352--53544396 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
53544342 GTTTGGTTCA
53544352 CTGTAATAGAATAGAG
1 CTGTAATAGAATAGAG
*
53544368 CTGTAATTGAATAGAG
1 CTGTAATAGAATAGAG
* *
53544384 TTGTAATGGAATA
1 CTGTAATAGAATA
53544397 ATGATGTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.40, C:0.04, G:0.24, T:0.31
Consensus pattern (16 bp):
CTGTAATAGAATAGAG
Found at i:53561353 original size:16 final size:17
Alignment explanation
Indices: 53561317--53561353 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
53561307 AATTTTATTT
*
53561317 TAATAGTAAGTTTTAAA
1 TAATAATAAGTTTTAAA
53561334 -AATAATAA-TTTTAAA
1 TAATAATAAGTTTTAAA
53561349 TAATA
1 TAATA
53561354 TTATTCATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (17 bp):
TAATAATAAGTTTTAAA
Found at i:53561403 original size:15 final size:15
Alignment explanation
Indices: 53561385--53561441 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
53561375 TATCAATATT
53561385 AATATTTTAATAATA
1 AATATTTTAATAATA
*
53561400 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
*
53561419 AATATATTAATAATA
1 AATATTTTAATAATA
*
53561434 AATGTTTT
1 AATATTTT
53561442 GTAGTATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 16 0.48
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.30
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:53564850 original size:5 final size:5
Alignment explanation
Indices: 53564840--53564871 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
53564830 AAGCATGAAG
53564840 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TT
53564872 ATCTTTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:53564878 original size:15 final size:15
Alignment explanation
Indices: 53564843--53564878 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
53564833 CATGAAGTTT
*
53564843 TATTTTATTTTATTT
1 TATTTTATTTTATTA
53564858 TATTTTATTTTATTA
1 TATTTTATTTTATTA
*
53564873 TCTTTT
1 TATTTT
53564879 TTACAGGATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (15 bp):
TATTTTATTTTATTA
Found at i:53570482 original size:25 final size:25
Alignment explanation
Indices: 53570454--53570534 Score: 69
Period size: 25 Copynumber: 3.2 Consensus size: 25
53570444 ATATAAAAAC
53570454 TTGAACAATGACATGGAAAACTCAA
1 TTGAACAATGACATGGAAAACTCAA
** * *
53570479 TTGAA-AGATTGA-ATATATATA-TAAA
1 TTGAACA-A-TGACATGGA-AAACTCAA
53570504 CTTGAACAATGACATGGAAAACTCAA
1 -TTGAACAATGACATGGAAAACTCAA
53570530 TTGAA
1 TTGAA
53570535 AGATTGAATT
Statistics
Matches: 41, Mismatches: 8, Indels: 14
0.65 0.13 0.22
Matches are distributed among these distances:
24 1 0.02
25 22 0.54
26 17 0.41
27 1 0.02
ACGTcount: A:0.48, C:0.11, G:0.15, T:0.26
Consensus pattern (25 bp):
TTGAACAATGACATGGAAAACTCAA
Found at i:53570505 original size:51 final size:51
Alignment explanation
Indices: 53570440--53570543 Score: 199
Period size: 51 Copynumber: 2.0 Consensus size: 51
53570430 ATATACATAT
53570440 ATATATATAAAAACTTGAACAATGACATGGAAAACTCAATTGAAAGATTGA
1 ATATATATAAAAACTTGAACAATGACATGGAAAACTCAATTGAAAGATTGA
*
53570491 ATATATATATAAACTTGAACAATGACATGGAAAACTCAATTGAAAGATTGA
1 ATATATATAAAAACTTGAACAATGACATGGAAAACTCAATTGAAAGATTGA
53570542 AT
1 AT
53570544 TCTGAAAAAC
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.50, C:0.10, G:0.13, T:0.27
Consensus pattern (51 bp):
ATATATATAAAAACTTGAACAATGACATGGAAAACTCAATTGAAAGATTGA
Found at i:53581483 original size:31 final size:31
Alignment explanation
Indices: 53581445--53581503 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
53581435 AGGAGGAAAA
53581445 AAGAGAGAAATAGTCTTAAAGTCAAAAAGTC
1 AAGAGAGAAATAGTCTTAAAGTCAAAAAGTC
* *
53581476 AAGAGAGAAATAGTGTTAAAGTGAAAAA
1 AAGAGAGAAATAGTCTTAAAGTCAAAAA
53581504 CTTATTATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.54, C:0.05, G:0.22, T:0.19
Consensus pattern (31 bp):
AAGAGAGAAATAGTCTTAAAGTCAAAAAGTC
Found at i:53582921 original size:28 final size:29
Alignment explanation
Indices: 53582879--53582938 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 29
53582869 GTATTTTCGT
53582879 AAAATCGATCTAATCAT-ATAAATTTTCAA
1 AAAATCGATCTAATC-TGATAAATTTTCAA
* * *
53582908 AAAAT-GATTTAATCTGATAATTTTTTAA
1 AAAATCGATCTAATCTGATAAATTTTCAA
53582936 AAA
1 AAA
53582939 TTGACATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 1 0.04
28 21 0.78
29 5 0.19
ACGTcount: A:0.48, C:0.08, G:0.05, T:0.38
Consensus pattern (29 bp):
AAAATCGATCTAATCTGATAAATTTTCAA
Found at i:53585351 original size:22 final size:22
Alignment explanation
Indices: 53585295--53585358 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
53585285 GGGCCGAAAT
53585295 TTAATTATAATTTTATCATATA
1 TTAATTATAATTTTATCATATA
* * *
53585317 TCAAAATATAATTTTAT-ATGTA
1 T-TAATTATAATTTTATCATATA
*
53585339 TTAATTTATAATTTCATCAT
1 TTAA-TTATAATTTTATCAT
53585359 TTTTTAAGGG
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
21 2 0.06
22 16 0.48
23 15 0.45
ACGTcount: A:0.41, C:0.06, G:0.02, T:0.52
Consensus pattern (22 bp):
TTAATTATAATTTTATCATATA
Found at i:53586683 original size:41 final size:41
Alignment explanation
Indices: 53586621--53586795 Score: 287
Period size: 41 Copynumber: 4.3 Consensus size: 41
53586611 AATTTAACAT
* **
53586621 ATTCAGATCACCGGCACTTAGCCTGCTAGGTTTATAATCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
* * *
53586662 ATTCATATCACCGGCATTTAGCCTACTAGGCTTATAGCCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
*
53586703 ATTCAGATCACCGGCACTTAGCCTGCGAGGCTTATAGCCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
53586744 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
53586785 ATTCAGATCAC
1 ATTCAGATCAC
53586796 AAATTTTAAT
Statistics
Matches: 123, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 123 1.00
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.29
Consensus pattern (41 bp):
ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
Found at i:53588768 original size:23 final size:23
Alignment explanation
Indices: 53588742--53588840 Score: 155
Period size: 23 Copynumber: 4.3 Consensus size: 23
53588732 ATAAGTGCAA
53588742 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
53588765 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
53588788 CACT-ATTATGTAGCCGAAGCTAC
1 CACTGA-TATGTAGCCGAAGCTAC
* *
53588811 CACTGAAACGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
53588834 CACTGAT
1 CACTGAT
53588841 CAATAACACT
Statistics
Matches: 69, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
22 1 0.01
23 67 0.97
24 1 0.01
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.20
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:53588815 original size:46 final size:46
Alignment explanation
Indices: 53588748--53588837 Score: 171
Period size: 46 Copynumber: 2.0 Consensus size: 46
53588738 GCAACACTGA
*
53588748 TATGTAGCCGAAGCTACCACTGAAATGTAGCCGAAGCTACCACTAT
1 TATGTAGCCGAAGCTACCACTGAAACGTAGCCGAAGCTACCACTAT
53588794 TATGTAGCCGAAGCTACCACTGAAACGTAGCCGAAGCTACCACT
1 TATGTAGCCGAAGCTACCACTGAAACGTAGCCGAAGCTACCACT
53588838 GATCAATAAC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.32, C:0.28, G:0.20, T:0.20
Consensus pattern (46 bp):
TATGTAGCCGAAGCTACCACTGAAACGTAGCCGAAGCTACCACTAT
Found at i:53589479 original size:17 final size:18
Alignment explanation
Indices: 53589454--53589490 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
53589444 CAACTTTATG
*
53589454 CACACTTTA-CCATTTTT
1 CACAATTTAGCCATTTTT
53589471 CACAATTTAGCCATTTTT
1 CACAATTTAGCCATTTTT
53589489 CA
1 CA
53589491 ACATTTTCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.27, C:0.27, G:0.03, T:0.43
Consensus pattern (18 bp):
CACAATTTAGCCATTTTT
Found at i:53590119 original size:510 final size:510
Alignment explanation
Indices: 53589155--53590175 Score: 2006
Period size: 510 Copynumber: 2.0 Consensus size: 510
53589145 CGGATGCAAA
*
53589155 ACGACTATTTTTTTTGTAATTTAGTCGATAACTTTCTCTTTTCCCTGATCACTTCCACTATTTCT
1 ACGACTATTTTTTTTGTAATTTAGTCGATAACTTTCTCTTTTCCCCGATCACTTCCACTATTTCT
*
53589220 TCTTTCTTGATCTATATTAACACAATTTAATATATTTTATCAACATTTCATTCAAATACAATTCA
66 TCTTTCTTGATCTATATTAACACAATTTAATACATTTTATCAACATTTCATTCAAATACAATTCA
53589285 TACACAACATTTTGGCAAATTTATATTTTTCCCCATAACTTTTCAAAAATTCCACTTTTGTCCCA
131 TACACAACATTTTGGCAAATTTATATTTTTCCCCATAACTTTTCAAAAATTCCACTTTTGTCCCA
53589350 AAGCTCGTAAAAATAAAATTCACTAAATTCTTAAATTTCAAACTTCACTAAATCATATTTCATGC
196 AAGCTCGTAAAAATAAAATTCACTAAATTCTTAAATTTCAAACTTCACTAAATCATATTTCATGC
53589415 TCATAACAGCCCTCAATTTCACAAAATCACAACTTTATGCACACTTTACCATTTTTCACAATTTA
261 TCATAACAGCCCTCAATTTCACAAAATCACAACTTTATGCACACTTTACCATTTTTCACAATTTA
53589480 GCCATTTTTCAACATTTTCATTGAAATTGATCTAGTAAAACTTGTAATTAACACTTCAAACATTC
326 GCCATTTTTCAACATTTTCATTGAAATTGATCTAGTAAAACTTGTAATTAACACTTCAAACATTC
53589545 ATTATCTAACATCACTAATCAATTTACAATTATATCATGAATGGGTCAATTTTTAAAATTTAATT
391 ATTATCTAACATCACTAATCAATTTACAATTATATCATGAATGGGTCAATTTTTAAAATTTAATT
53589610 TCATTTAAATTAAATGGTAGAAACATAAAATTCAAGCATCAATAAGCATAAAAAT
456 TCATTTAAATTAAATGGTAGAAACATAAAATTCAAGCATCAATAAGCATAAAAAT
53589665 ACGACTATTTTTTTTGTAATTTAGTCGATAACTTTCTCTTTTCCCCGATCACTTCCACTATTTCT
1 ACGACTATTTTTTTTGTAATTTAGTCGATAACTTTCTCTTTTCCCCGATCACTTCCACTATTTCT
53589730 TCTTTCTTGATCTATATTAACACAATTTAATACATTTTATCAACATTTCATTCAAATACAATTCA
66 TCTTTCTTGATCTATATTAACACAATTTAATACATTTTATCAACATTTCATTCAAATACAATTCA
53589795 TACACAACATTTTGGCAAATTTATATTTTTCCCCATAACTTTTCAAAAATTCCACTTTTGTCCCA
131 TACACAACATTTTGGCAAATTTATATTTTTCCCCATAACTTTTCAAAAATTCCACTTTTGTCCCA
53589860 AAGCTCGTAAAAATAAAATTCACTAAATTCTTAAATTTCAAACTTCACTAAATCATATTTCATGC
196 AAGCTCGTAAAAATAAAATTCACTAAATTCTTAAATTTCAAACTTCACTAAATCATATTTCATGC
53589925 TCATAACAGCCCTCAATTTCACAAAATCACAACTTTATGCACACTTTACCATTTTTCACAATTTA
261 TCATAACAGCCCTCAATTTCACAAAATCACAACTTTATGCACACTTTACCATTTTTCACAATTTA
*
53589990 GCCCTTTTTCAACATTTTCATTGAAATTGATCTAGTAAAACTTGTAATTAACACTTCAAACATTC
326 GCCATTTTTCAACATTTTCATTGAAATTGATCTAGTAAAACTTGTAATTAACACTTCAAACATTC
*
53590055 ATTATCTAACATCACTAATCAATTTACAATTATATCATGAATGGGTCAATTTTTAAACTTTAATT
391 ATTATCTAACATCACTAATCAATTTACAATTATATCATGAATGGGTCAATTTTTAAAATTTAATT
53590120 TCATTTAAATTAAATGGTAGAAACATAAAATTCAAGCATCAATAAGCATAAAAAT
456 TCATTTAAATTAAATGGTAGAAACATAAAATTCAAGCATCAATAAGCATAAAAAT
53590175 A
1 A
53590176 GGAAAATAAT
Statistics
Matches: 507, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
510 507 1.00
ACGTcount: A:0.36, C:0.20, G:0.05, T:0.39
Consensus pattern (510 bp):
ACGACTATTTTTTTTGTAATTTAGTCGATAACTTTCTCTTTTCCCCGATCACTTCCACTATTTCT
TCTTTCTTGATCTATATTAACACAATTTAATACATTTTATCAACATTTCATTCAAATACAATTCA
TACACAACATTTTGGCAAATTTATATTTTTCCCCATAACTTTTCAAAAATTCCACTTTTGTCCCA
AAGCTCGTAAAAATAAAATTCACTAAATTCTTAAATTTCAAACTTCACTAAATCATATTTCATGC
TCATAACAGCCCTCAATTTCACAAAATCACAACTTTATGCACACTTTACCATTTTTCACAATTTA
GCCATTTTTCAACATTTTCATTGAAATTGATCTAGTAAAACTTGTAATTAACACTTCAAACATTC
ATTATCTAACATCACTAATCAATTTACAATTATATCATGAATGGGTCAATTTTTAAAATTTAATT
TCATTTAAATTAAATGGTAGAAACATAAAATTCAAGCATCAATAAGCATAAAAAT
Found at i:53593623 original size:13 final size:13
Alignment explanation
Indices: 53593605--53593632 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
53593595 GATAATAAAA
53593605 CATATAGAATACC
1 CATATAGAATACC
53593618 CATATAGAATACC
1 CATATAGAATACC
53593631 CA
1 CA
53593633 GAAGAGATCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.25, G:0.07, T:0.21
Consensus pattern (13 bp):
CATATAGAATACC
Found at i:53595833 original size:21 final size:22
Alignment explanation
Indices: 53595804--53595846 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
53595794 TGAGTAAATT
*
53595804 TAACTCAATTTAATACAATTCA
1 TAACTCAATTCAATACAATTCA
*
53595826 TAAC-CAATTCAATTCAATTCA
1 TAACTCAATTCAATACAATTCA
53595847 CATTATAGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.44, C:0.21, G:0.00, T:0.35
Consensus pattern (22 bp):
TAACTCAATTCAATACAATTCA
Found at i:53603666 original size:45 final size:45
Alignment explanation
Indices: 53603602--53603695 Score: 161
Period size: 45 Copynumber: 2.1 Consensus size: 45
53603592 AACAGATACT
* *
53603602 CGGTGGATTCAGCACATAGCAACCACCTTATTAATCAATGATGTC
1 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTC
*
53603647 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTT
1 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTC
53603692 CGGT
1 CGGT
53603696 TCACATAATA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (45 bp):
CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTC
Found at i:53603815 original size:50 final size:49
Alignment explanation
Indices: 53603697--53603882 Score: 162
Period size: 50 Copynumber: 3.7 Consensus size: 49
53603687 ATGTTCGGTT
* *
53603697 CACATAATAGCCTGCACATAGTACTACACATGTGAGCATTACCATCTGATA
1 CACATAGTAGCCTGCACATAGTACTACACATGTGAGAATT--CATCTGATA
* *
53603748 CACGTAGTAGCCTGCACATAGTACTACACACTGATCGA-AATT-ATCTGGTA
1 CACATAGTAGCCTGCACATAGTACTACACA-TG-T-GAGAATTCATCTGATA
* * ** * *
53603798 CGCATAGTAGCCTGCACATAGTACTACACATGCGA-CCTATCATTCCGGTA
1 CACATAGTAGCCTGCACATAGTACTACACATGTGAGAAT-TCA-TCTGATA
** * *
53603848 CATGTAGTAGCCTGCAGATAGTATTACACATGTGA
1 CACATAGTAGCCTGCACATAGTACTACACATGTGA
53603883 CCATCATTTT
Statistics
Matches: 113, Mismatches: 16, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
47 3 0.03
48 1 0.01
49 3 0.03
50 70 0.62
51 28 0.25
52 2 0.02
53 4 0.04
54 2 0.02
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.26
Consensus pattern (49 bp):
CACATAGTAGCCTGCACATAGTACTACACATGTGAGAATTCATCTGATA
Found at i:53604958 original size:23 final size:23
Alignment explanation
Indices: 53604931--53604975 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
53604921 AAATTTGGGC
*
53604931 TATTACAAATTATGTCACTTTAT
1 TATTAAAAATTATGTCACTTTAT
* *
53604954 TATTAAAAATTGTGTCATTTTA
1 TATTAAAAATTATGTCACTTTA
53604976 ATCAAAAGGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.36, C:0.09, G:0.07, T:0.49
Consensus pattern (23 bp):
TATTAAAAATTATGTCACTTTAT
Found at i:53614206 original size:36 final size:36
Alignment explanation
Indices: 53614159--53614227 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
53614149 AAAAATAAAA
*
53614159 TTTTTATTAAATTAT-TTTTTTATAAATTTTTAATGG
1 TTTTTAATAAATT-TGTTTTTTATAAATTTTTAATGG
**
53614195 TTTTTAATAAATTTGTTTTTTATATTTTTTTAA
1 TTTTTAATAAATTTGTTTTTTATAAATTTTTAA
53614228 AAAATTATGG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
35 1 0.03
36 28 0.97
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (36 bp):
TTTTTAATAAATTTGTTTTTTATAAATTTTTAATGG
Found at i:53614214 original size:26 final size:26
Alignment explanation
Indices: 53614185--53614245 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
53614175 TTTTTATAAA
* *
53614185 TTTTTAATGGTTTTTAATAAATT-TGT
1 TTTTTAAT-GTTTTTAAAAAATTATGG
*
53614211 TTTTTATATTTTTTTAAAAAATTATGG
1 TTTTTA-ATGTTTTTAAAAAATTATGG
53614238 TTTTTAAT
1 TTTTTAAT
53614246 TAATTTCTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 20 0.67
27 10 0.33
ACGTcount: A:0.30, C:0.00, G:0.08, T:0.62
Consensus pattern (26 bp):
TTTTTAATGTTTTTAAAAAATTATGG
Found at i:53616007 original size:46 final size:46
Alignment explanation
Indices: 53615934--53616210 Score: 464
Period size: 46 Copynumber: 6.0 Consensus size: 46
53615924 ACATTGCTAT
* *
53615934 AACTCAGTATGGTTTTCTTCACGGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTTACCGAAATACCATACCTACTTTTCAC
53615980 AACTCAGTATGGTTTTCTTTACCGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTTACCGAAATACCATACCTACTTTTCAC
53616026 AACTCAGTATGGTTTTCTTTACCGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTTACCGAAATACCATACCTACTTTTCAC
* *
53616072 AACTCAGTATGGTTTTCTTTACCGAAACACCATACCTACTTTTAAC
1 AACTCAGTATGGTTTTCTTTACCGAAATACCATACCTACTTTTCAC
* *
53616118 AACTCAGTATGGTTTTCTTTACCGAAACACCACACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTTACCGAAATACCATACCTACTTTTCAC
* * * *
53616164 AACTTAGTATGGTTTTCTTCACTGAAATACCATACCTACGTTTCAC
1 AACTCAGTATGGTTTTCTTTACCGAAATACCATACCTACTTTTCAC
53616210 A
1 A
53616211 CTTTGCCATG
Statistics
Matches: 219, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 219 1.00
ACGTcount: A:0.29, C:0.26, G:0.09, T:0.35
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTTACCGAAATACCATACCTACTTTTCAC
Found at i:53618321 original size:21 final size:21
Alignment explanation
Indices: 53618297--53618338 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
53618287 CTTTTTGTTC
*
53618297 AATTAATTATCGAAACTTTAA
1 AATTAATTAACGAAACTTTAA
**
53618318 AATTTCTTAACGAAACTTTAA
1 AATTAATTAACGAAACTTTAA
53618339 TACTAACTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (21 bp):
AATTAATTAACGAAACTTTAA
Found at i:53623607 original size:71 final size:71
Alignment explanation
Indices: 53623377--53623633 Score: 284
Period size: 71 Copynumber: 3.6 Consensus size: 71
53623367 TCTCTCATTC
* * * * * ***
53623377 CTAATCCATGTACTTCACAAGGTTTGAACCTAAGATCTCTATCCTGGAAATC-AGTTTAACTCTC
1 CTAACCCATGAACTTCCCAGGGTCTGAACCTAAGATCTCTAAATTGGAAATCGA-TTTAA--CTC
*
53623441 TGTCATCCT
63 TGTCATACT
* * *
53623450 CTAACCCATGAACTTCCCAGGGTCTAAACCTAATATCTCTAAATTGGAAATGGATTTAACTCTGT
1 CTAACCCATGAACTTCCCAGGGTCTGAACCTAAGATCTCTAAATTGGAAATCGATTTAACTCTGT
53623515 CATACT
66 CATACT
* *
53623521 CTAACCCATGAACTTCCCAGGGTCTCAACCTAATATCTCTAAATTGGAAATCGATTTAACTCTGT
1 CTAACCCATGAACTTCCCAGGGTCTGAACCTAAGATCTCTAAATTGGAAATCGATTTAACTCTGT
*
53623586 CATTCT
66 CATACT
*** * * *
53623592 CTAAATTATGTACTT-CCAGGGTTTGAACCTAAGATTTCTAAA
1 CTAACCCATGAACTTCCCAGGGTCTGAACCTAAGATCTCTAAA
53623634 AGTCACATCA
Statistics
Matches: 160, Mismatches: 23, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
70 23 0.14
71 90 0.56
73 46 0.29
74 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.33
Consensus pattern (71 bp):
CTAACCCATGAACTTCCCAGGGTCTGAACCTAAGATCTCTAAATTGGAAATCGATTTAACTCTGT
CATACT
Found at i:53626949 original size:25 final size:27
Alignment explanation
Indices: 53626897--53626952 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 27
53626887 ATTTAAATTT
* *
53626897 TTTAAAAATATTTATTTTATTTTATTA
1 TTTAAAAATATTTATATAATTTTATTA
*
53626924 TTTAATAAT-TTTATATAATTTT-TTA
1 TTTAAAAATATTTATATAATTTTATTA
53626949 TTTA
1 TTTA
53626953 TTGAAAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 7 0.27
26 11 0.42
27 8 0.31
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (27 bp):
TTTAAAAATATTTATATAATTTTATTA
Found at i:53627077 original size:18 final size:18
Alignment explanation
Indices: 53627051--53627085 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
53627041 AATATGTTCT
*
53627051 AAATTACATAATATATAA
1 AAATAACATAATATATAA
53627069 AAATAACATAATATATA
1 AAATAACATAATATATA
53627086 TAAAGTATTA
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:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (18 bp):
AAATAACATAATATATAA
Found at i:53631116 original size:15 final size:15
Alignment explanation
Indices: 53631096--53631126 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
53631086 TTTAGTGTAA
53631096 AAATATTTTAATCAT
1 AAATATTTTAATCAT
53631111 AAATATTTTAATCAT
1 AAATATTTTAATCAT
53631126 A
1 A
53631127 CTCTTGGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (15 bp):
AAATATTTTAATCAT
Found at i:53631653 original size:16 final size:17
Alignment explanation
Indices: 53631621--53631656 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
53631611 ATTTTTTGAA
53631621 TTAGTGAATTCTGTGAT
1 TTAGTGAATTCTGTGAT
53631638 TTAGTGAATT-TGTGAT
1 TTAGTGAATTCTGTGAT
53631654 TTA
1 TTA
53631657 AAAAGAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.25, C:0.03, G:0.22, T:0.50
Consensus pattern (17 bp):
TTAGTGAATTCTGTGAT
Found at i:53632395 original size:46 final size:45
Alignment explanation
Indices: 53632328--53632456 Score: 195
Period size: 46 Copynumber: 2.8 Consensus size: 45
53632318 AGGGATACAC
*
53632328 AGGTATGATGTTTCAGTGAAGAAAGCCATACTGAGTTGTGAAAAGT
1 AGGTATGGTGTTTCAGTGAAGAAA-CCATACTGAGTTGTGAAAAGT
*
53632374 AGGTATGGTGTTTCAGTGAAGAAAACCATATTGAGTTGTGAAAAGT
1 AGGTATGGTGTTTCAGTGAAG-AAACCATACTGAGTTGTGAAAAGT
* *
53632420 AGGTATGGTATTTCAATGAAGGAAACCATACTGAGTT
1 AGGTATGGTGTTTCAGTGAA-GAAACCATACTGAGTT
53632457 ATAGCATTAT
Statistics
Matches: 76, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
46 72 0.95
47 4 0.05
ACGTcount: A:0.35, C:0.09, G:0.27, T:0.29
Consensus pattern (45 bp):
AGGTATGGTGTTTCAGTGAAGAAACCATACTGAGTTGTGAAAAGT
Found at i:53638943 original size:10 final size:10
Alignment explanation
Indices: 53638928--53638955 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
53638918 CCTTTAATCT
53638928 ATAAGAAACG
1 ATAAGAAACG
53638938 ATAAGAAACG
1 ATAAGAAACG
53638948 ATAAGAAA
1 ATAAGAAA
53638956 GCATACAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.64, C:0.07, G:0.18, T:0.11
Consensus pattern (10 bp):
ATAAGAAACG
Found at i:53639726 original size:22 final size:21
Alignment explanation
Indices: 53639701--53639746 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
53639691 AAATTGTTGC
* *
53639701 ATTTGTTTTGATATTGGTCTTG
1 ATTTGTTCTGAAATT-GTCTTG
*
53639723 ATTTGTTCTGAAATTGTTTTG
1 ATTTGTTCTGAAATTGTCTTG
53639744 ATT
1 ATT
53639747 GTCTGCTGGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.17, C:0.04, G:0.20, T:0.59
Consensus pattern (21 bp):
ATTTGTTCTGAAATTGTCTTG
Found at i:53639760 original size:23 final size:23
Alignment explanation
Indices: 53639732--53639815 Score: 132
Period size: 23 Copynumber: 3.7 Consensus size: 23
53639722 GATTTGTTCT
53639732 GAAATTGTTTTGATTGTCTGCTG
1 GAAATTGTTTTGATTGTCTGCTG
* * *
53639755 GAAATTGGTATGATTGGCTGCTG
1 GAAATTGTTTTGATTGTCTGCTG
53639778 GAAATTGTTTTGATTGTCTGCTG
1 GAAATTGTTTTGATTGTCTGCTG
*
53639801 GAAATTGTGTTGATT
1 GAAATTGTTTTGATT
53639816 TGTTTATGTT
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 54 1.00
ACGTcount: A:0.20, C:0.07, G:0.29, T:0.44
Consensus pattern (23 bp):
GAAATTGTTTTGATTGTCTGCTG
Found at i:53644323 original size:24 final size:25
Alignment explanation
Indices: 53644288--53644335 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
53644278 TTATGAAATT
53644288 TAATATTAATTA-TTAAATTATATG
1 TAATATTAATTATTTAAATTATATG
53644312 TAATAATT-ATTATTTTAAATTATA
1 TAAT-ATTAATTA-TTTAAATTATA
53644336 CAAATTCATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 8 0.38
25 3 0.14
26 10 0.48
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
TAATATTAATTATTTAAATTATATG
Found at i:53644394 original size:28 final size:27
Alignment explanation
Indices: 53644363--53644435 Score: 62
Period size: 28 Copynumber: 2.7 Consensus size: 27
53644353 ATTTATTAGT
53644363 TATAATTATTTTAAATTTTATGTAATCA
1 TATAATTATTTTAAATTTTATGTAAT-A
* * *
53644391 TAT-ATT-TTAATTAAAATATATTTAATA
1 TATAATTATT--TTAAATTTTATGTAATA
*
53644418 T-TAATTATTTCAAATTTT
1 TATAATTATTTTAAATTTT
53644436 CATTTGTAGT
Statistics
Matches: 35, Mismatches: 6, Indels: 10
0.69 0.12 0.20
Matches are distributed among these distances:
26 9 0.26
27 8 0.23
28 18 0.51
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (27 bp):
TATAATTATTTTAAATTTTATGTAATA
Found at i:53644516 original size:120 final size:119
Alignment explanation
Indices: 53644376--53644668 Score: 468
Period size: 120 Copynumber: 2.4 Consensus size: 119
53644366 AATTATTTTA
* * *
53644376 AATTTTATGT-AATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTT-TCA
1 AATTTTAT-TAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT--AATTTAT-A
53644438 TTTGT-AGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
62 TTT-TAAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
53644496 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
*
53644561 ACAGTATCATATATTATGATTTGAGTAAATTCATATGAGAATATTAATTATTAAG
66 A-AGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
53644616 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
53644669 TAAATATGAT
Statistics
Matches: 164, Mismatches: 4, Indels: 10
0.92 0.02 0.06
Matches are distributed among these distances:
118 1 0.01
119 10 0.06
120 151 0.92
121 2 0.01
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.50
Consensus pattern (119 bp):
AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
AAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:53644536 original size:15 final size:15
Alignment explanation
Indices: 53644501--53644552 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
53644491 TTAAGAATTT
*
53644501 TATTAAATTAT-ATA
1 TATTTAATTATAATA
53644515 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
53644529 TATTTAATAATAAT-
1 TATTTAATTATAATA
53644543 TATGTTAATT
1 TAT-TTAATT
53644553 TATATTTTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:53644651 original size:16 final size:16
Alignment explanation
Indices: 53644630--53644671 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
53644620 TTATTAAATT
*
53644630 ATATATTTTAATTATA
1 ATATATTTTAATAATA
53644646 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
53644661 AT-TATGTTTAA
1 ATATAT-TTTAA
53644672 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:53644656 original size:15 final size:15
Alignment explanation
Indices: 53644621--53644662 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
53644611 TTAAGAATTT
*
53644621 TATTAAATTAT-ATA
1 TATTTAATTATAATA
53644635 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
53644649 TATTTAATAATAAT
1 TATTTAATTATAAT
53644663 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:53644827 original size:16 final size:16
Alignment explanation
Indices: 53644806--53644845 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
53644796 ATATATTAAA
53644806 TAACAATTACAATATT
1 TAACAATTACAATATT
*
53644822 TAACAATAACAATATT
1 TAACAATTACAATATT
*
53644838 TAATAATT
1 TAACAATT
53644846 TACCAAAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.38
Consensus pattern (16 bp):
TAACAATTACAATATT
Found at i:53644905 original size:18 final size:17
Alignment explanation
Indices: 53644877--53644911 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
53644867 ATTATTAAGA
*
53644877 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
53644894 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
53644912 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:53648363 original size:21 final size:21
Alignment explanation
Indices: 53648332--53648410 Score: 77
Period size: 21 Copynumber: 3.8 Consensus size: 21
53648322 AGTCAACTCA
*
53648332 TATGAGTTTCAGTTTAACCCT
1 TATGGGTTTCAGTTTAACCCT
* * * *
53648353 TCTGGGTTTCAGTTCAGCTCT
1 TATGGGTTTCAGTTTAACCCT
* * *
53648374 TGTGAGCTTCAGTTTAACCCT
1 TATGGGTTTCAGTTTAACCCT
*
53648395 AATGGGTTTCAGTTTA
1 TATGGGTTTCAGTTTA
53648411 GCTATTTTGA
Statistics
Matches: 43, Mismatches: 15, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.19, C:0.19, G:0.20, T:0.42
Consensus pattern (21 bp):
TATGGGTTTCAGTTTAACCCT
Found at i:53648388 original size:42 final size:42
Alignment explanation
Indices: 53648334--53648427 Score: 134
Period size: 42 Copynumber: 2.2 Consensus size: 42
53648324 TCAACTCATA
* ** *
53648334 TGAGTTTCAGTTTAACCCTTCTGGGTTTCAGTTCAGCTCTTG
1 TGAGCTTCAGTTTAACCCTAATGGGTTTCAGTTCAGCTATTG
* *
53648376 TGAGCTTCAGTTTAACCCTAATGGGTTTCAGTTTAGCTATTT
1 TGAGCTTCAGTTTAACCCTAATGGGTTTCAGTTCAGCTATTG
53648418 TGAGCTTCAG
1 TGAGCTTCAG
53648428 ATTATAGGTT
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.18, C:0.19, G:0.21, T:0.41
Consensus pattern (42 bp):
TGAGCTTCAGTTTAACCCTAATGGGTTTCAGTTCAGCTATTG
Found at i:53648502 original size:77 final size:78
Alignment explanation
Indices: 53648359--53648504 Score: 179
Period size: 77 Copynumber: 1.9 Consensus size: 78
53648349 CCCTTCTGGG
* * * * * *
53648359 TTTCAGTTCAGCTCTTGTGAGCTTCAGTTTAACCCTAATGGGTTTCAGTTTAGCTATTTTGAGCT
1 TTTCAGTTCAGCTCCTATGAGCTTCAGTTTAACCCTAATAGGTTTCACTATAGCTATTATGAGCT
53648424 TCAGATTATAGGT
66 TCAGATTATAGGT
* * * *
53648437 TTTC-GTTCAGCTCCTATGAGCTTCCGTTTAACCCTTATAGGTTTCCCTATAGC-ACTTATGTGC
1 TTTCAGTTCAGCTCCTATGAGCTTCAGTTTAACCCTAATAGGTTTCACTATAGCTA-TTATGAGC
53648500 TTCAG
65 TTCAG
53648505 TGCAACCTTC
Statistics
Matches: 57, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
76 1 0.02
77 52 0.91
78 4 0.07
ACGTcount: A:0.19, C:0.21, G:0.18, T:0.41
Consensus pattern (78 bp):
TTTCAGTTCAGCTCCTATGAGCTTCAGTTTAACCCTAATAGGTTTCACTATAGCTATTATGAGCT
TCAGATTATAGGT
Found at i:53659276 original size:18 final size:16
Alignment explanation
Indices: 53659254--53659286 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
53659244 TCATGTTTCT
53659254 ATATATATACTTTTGA
1 ATATATATACTTTTGA
53659270 ATATATATACTTTTGA
1 ATATATATACTTTTGA
53659286 A
1 A
53659287 GAATTATGTA
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:0.39, C:0.06, G:0.06, T:0.48
Consensus pattern (16 bp):
ATATATATACTTTTGA
Found at i:53666160 original size:42 final size:42
Alignment explanation
Indices: 53666104--53666203 Score: 146
Period size: 42 Copynumber: 2.4 Consensus size: 42
53666094 CTATACGAAC
* * *
53666104 GGCACTAAGTGTGCGAAACTAAAATGACGATGTTGAATAACG
1 GGCACTAAGTGTGCGAAACTAAAATGACAACGTTGAATAACA
* *
53666146 GGCACTAAGTGTGCGAAATTGAAATGACAACGTTGAATAACA
1 GGCACTAAGTGTGCGAAACTAAAATGACAACGTTGAATAACA
*
53666188 AGCACTAAGTGTGCGA
1 GGCACTAAGTGTGCGA
53666204 TACCGAGAGC
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.38, C:0.15, G:0.26, T:0.21
Consensus pattern (42 bp):
GGCACTAAGTGTGCGAAACTAAAATGACAACGTTGAATAACA
Found at i:53668382 original size:32 final size:33
Alignment explanation
Indices: 53668311--53668383 Score: 105
Period size: 33 Copynumber: 2.2 Consensus size: 33
53668301 AAATGAGTAC
53668311 ATTTGTATTATTTATATATAATTAGTAAAAAGAT
1 ATTT-TATTATTTATATATAATTAGTAAAAAGAT
53668345 ATTTTATTATTTAT-TACTAATTAGT-AAAAGAT
1 ATTTTATTATTTATATA-TAATTAGTAAAAAGAT
*
53668377 TTTTTAT
1 ATTTTAT
53668384 GATAAATAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
32 15 0.41
33 18 0.49
34 4 0.11
ACGTcount: A:0.40, C:0.01, G:0.07, T:0.52
Consensus pattern (33 bp):
ATTTTATTATTTATATATAATTAGTAAAAAGAT
Found at i:53668727 original size:25 final size:25
Alignment explanation
Indices: 53668693--53668744 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
53668683 GAAGCATAAT
* *
53668693 AGAAACGAAACAGGGAGAA-AAAGAA
1 AGAAAAGAAAAAGGGA-AAGAAAGAA
53668718 AGAAAAGAAAAAGGGAAAGAAAGAA
1 AGAAAAGAAAAAGGGAAAGAAAGAA
53668743 AG
1 AG
53668745 GAGAAATAGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 2 0.08
25 22 0.92
ACGTcount: A:0.67, C:0.04, G:0.29, T:0.00
Consensus pattern (25 bp):
AGAAAAGAAAAAGGGAAAGAAAGAA
Found at i:53669717 original size:38 final size:39
Alignment explanation
Indices: 53669617--53669747 Score: 115
Period size: 38 Copynumber: 3.4 Consensus size: 39
53669607 CCTCGAGTCT
* ***
53669617 ATGAGACACTGGGTGTCACTATTTTACTTCGGATAGATTTG
1 ATGAGACACTGGGTGTCA--ACTTTACTTCGGATAGAGCCG
* * *
53669658 ATGAGATACTGGGTATC-ACTTTACTTCGGCTAG-GCCG
1 ATGAGACACTGGGTGTCAACTTTACTTCGGATAGAGCCG
* * * *
53669695 ATGAGACACTGGGTGTCAACTTTGCTTCGAAT-TATCCG
1 ATGAGACACTGGGTGTCAACTTTACTTCGGATAGAGCCG
*
53669733 ATGAGGCACTGGGTG
1 ATGAGACACTGGGTG
53669748 CCAATCTGGT
Statistics
Matches: 73, Mismatches: 15, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
37 16 0.22
38 42 0.58
41 15 0.21
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.31
Consensus pattern (39 bp):
ATGAGACACTGGGTGTCAACTTTACTTCGGATAGAGCCG
Found at i:53677349 original size:20 final size:20
Alignment explanation
Indices: 53677324--53677387 Score: 76
Period size: 20 Copynumber: 3.2 Consensus size: 20
53677314 GCATTATTTA
53677324 TTTAGGGTTTAGGATTCAAG
1 TTTAGGGTTTAGGATTCAAG
* *
53677344 TTTAGGGTTTAGGACTCTAG
1 TTTAGGGTTTAGGATTCAAG
* *
53677364 TTTGGGGTTTAAGG-TTTAAG
1 TTTAGGGTTT-AGGATTCAAG
53677384 TTTA
1 TTTA
53677388 AGATTTGAGC
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 33 0.92
21 3 0.08
ACGTcount: A:0.22, C:0.05, G:0.30, T:0.44
Consensus pattern (20 bp):
TTTAGGGTTTAGGATTCAAG
Found at i:53683801 original size:29 final size:29
Alignment explanation
Indices: 53683742--53683801 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 29
53683732 TCCGAGCCTT
53683742 GGGGCAAAAATGTAATTATGCAAAAGTTTA
1 GGGGCAAAAATGTAATTATGCAAAAG-TTA
* *
53683772 GGGGCAAAATTGTAATTGTGACAAAA-TTA
1 GGGGCAAAAATGTAATTATG-CAAAAGTTA
53683801 G
1 G
53683802 AGTCGAGGGC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 4 0.15
30 18 0.67
31 5 0.19
ACGTcount: A:0.42, C:0.07, G:0.25, T:0.27
Consensus pattern (29 bp):
GGGGCAAAAATGTAATTATGCAAAAGTTA
Found at i:53684217 original size:50 final size:50
Alignment explanation
Indices: 53684137--53684329 Score: 278
Period size: 50 Copynumber: 3.8 Consensus size: 50
53684127 ATTTGGGTAA
53684137 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
* * * *
53684187 AGAGGTCCCATGTAAGACCATGTTTGGGACATGGTGTTGGCACCGAAATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
* * * * *
53684237 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACCGAGATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
* *
53684287 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
53684330 TGTTATTATC
Statistics
Matches: 125, Mismatches: 17, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
50 91 0.73
51 34 0.27
ACGTcount: A:0.26, C:0.22, G:0.31, T:0.21
Consensus pattern (50 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
Found at i:53693943 original size:16 final size:16
Alignment explanation
Indices: 53693919--53693956 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
53693909 ACTTGTATAT
*
53693919 AACTGATTCTGCTAAC
1 AACTAATTCTGCTAAC
53693935 AACTAATTCTGCTAAC
1 AACTAATTCTGCTAAC
*
53693951 TACTAA
1 AACTAA
53693957 CTGTCTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.37, C:0.24, G:0.08, T:0.32
Consensus pattern (16 bp):
AACTAATTCTGCTAAC
Found at i:53698487 original size:16 final size:16
Alignment explanation
Indices: 53698463--53698500 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
53698453 ACTTGTATAT
*
53698463 AACTGATTCTGCTAAC
1 AACTAATTCTGCTAAC
53698479 AACTAATTCTGCTAAC
1 AACTAATTCTGCTAAC
*
53698495 TACTAA
1 AACTAA
53698501 CTGTCTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.37, C:0.24, G:0.08, T:0.32
Consensus pattern (16 bp):
AACTAATTCTGCTAAC
Found at i:53699581 original size:22 final size:22
Alignment explanation
Indices: 53699543--53699584 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
53699533 TTAAAAAATA
53699543 TATTTTAAAAATGATTTTATGT
1 TATTTTAAAAATGATTTTATGT
*
53699565 TATTTATAAATAT-ATTTTAT
1 TATTT-TAAAAATGATTTTAT
53699585 TTAAAAGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (22 bp):
TATTTTAAAAATGATTTTATGT
Found at i:53699759 original size:26 final size:28
Alignment explanation
Indices: 53699714--53699771 Score: 77
Period size: 26 Copynumber: 2.2 Consensus size: 28
53699704 AATTTTAAAA
53699714 ATTTAAATATAAAAGAAAAATT-TTATT
1 ATTTAAATATAAAAGAAAAATTATTATT
* *
53699741 ATTTAATTA-AAAAGTAAAATTATTATT
1 ATTTAAATATAAAAGAAAAATTATTATT
53699768 -TTTA
1 ATTTA
53699772 GTAATATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 15 0.54
27 13 0.46
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (28 bp):
ATTTAAATATAAAAGAAAAATTATTATT
Found at i:53701049 original size:13 final size:13
Alignment explanation
Indices: 53701031--53701061 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
53701021 ATTTAAACGT
53701031 ACACAATACCAAA
1 ACACAATACCAAA
53701044 ACACAATACCAAA
1 ACACAATACCAAA
53701057 ACACA
1 ACACA
53701062 TTCTTATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.61, C:0.32, G:0.00, T:0.06
Consensus pattern (13 bp):
ACACAATACCAAA
Found at i:53701648 original size:46 final size:46
Alignment explanation
Indices: 53701575--53701751 Score: 257
Period size: 46 Copynumber: 3.8 Consensus size: 46
53701565 ACAAGGCTAT
*
53701575 AACTCAGTATGATTTTCTTCACAGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACAGAAATACCATACCTACTTTTCAC
* *
53701621 GACTCAGTATGGTTTTCTTTATC-GAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCA-CAGAAATACCATACCTACTTTTCAC
* *
53701667 AACTCAGTATGGTTTTCTTTACCGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACAGAAATACCATACCTACTTTTCAC
* * * *
53701713 AACTTAGTATCGTTTTCTTCACTGGAATACCATACCTAC
1 AACTCAGTATGGTTTTCTTCACAGAAATACCATACCTAC
53701752 GCTTCAAACT
Statistics
Matches: 120, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
45 1 0.01
46 118 0.98
47 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.09, T:0.37
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTCACAGAAATACCATACCTACTTTTCAC
Found at i:53702533 original size:17 final size:17
Alignment explanation
Indices: 53702511--53702554 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
53702501 CTTTTTTAAA
53702511 TCACAAAATTCAATAAG
1 TCACAAAATTCAATAAG
* * *
53702528 TCACAAAATCCACTAAT
1 TCACAAAATTCAATAAG
53702545 TCA-AAAATTC
1 TCACAAAATTC
53702555 TTCTAAATCG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
16 6 0.26
17 17 0.74
ACGTcount: A:0.50, C:0.23, G:0.02, T:0.25
Consensus pattern (17 bp):
TCACAAAATTCAATAAG
Found at i:53703787 original size:31 final size:30
Alignment explanation
Indices: 53703751--53703823 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 30
53703741 GTTTGAGTTA
*
53703751 GGACTAAAATTTCAA-AATTCGAAATGTACAT
1 GGACT-AAATTT-AACAATTCGAAAAGTACAT
53703782 GGACTAAATTTAACCAATTCGAAAAGTACAT
1 GGACTAAATTTAA-CAATTCGAAAAGTACAT
* *
53703813 GAATTAAATTT
1 GGACTAAATTT
53703824 GATCAAATTA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 2 0.05
30 6 0.16
31 29 0.78
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.30
Consensus pattern (30 bp):
GGACTAAATTTAACAATTCGAAAAGTACAT
Found at i:53712873 original size:11 final size:11
Alignment explanation
Indices: 53712854--53712908 Score: 65
Period size: 11 Copynumber: 5.0 Consensus size: 11
53712844 CTCTAATATT
53712854 CTCTCAAATTC
1 CTCTCAAATTC
*
53712865 CTCTAAAATTC
1 CTCTCAAATTC
* * *
53712876 CCCTCAATTTA
1 CTCTCAAATTC
*
53712887 CTCTCAAATTT
1 CTCTCAAATTC
53712898 CTCTCAAATTC
1 CTCTCAAATTC
53712909 TTATTTACAA
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 35 1.00
ACGTcount: A:0.29, C:0.33, G:0.00, T:0.38
Consensus pattern (11 bp):
CTCTCAAATTC
Found at i:53712903 original size:22 final size:22
Alignment explanation
Indices: 53712843--53712907 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
53712833 CTAAATCCTT
* *
53712843 TCTCTAATATTCTCTCAAATTCC
1 TCTCAAAT-TTCTCTCAAATTAC
* * * *
53712866 TCTAAAATTCCCCTCAATTTAC
1 TCTCAAATTTCTCTCAAATTAC
53712888 TCTCAAATTTCTCTCAAATT
1 TCTCAAATTTCTCTCAAATT
53712908 CTTATTTACA
Statistics
Matches: 32, Mismatches: 10, Indels: 1
0.74 0.23 0.02
Matches are distributed among these distances:
22 26 0.81
23 6 0.19
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.42
Consensus pattern (22 bp):
TCTCAAATTTCTCTCAAATTAC
Found at i:53714098 original size:7 final size:7
Alignment explanation
Indices: 53714088--53714112 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
53714078 TTGGTATTTA
53714088 GTATTAT
1 GTATTAT
53714095 GTATTAT
1 GTATTAT
53714102 GTATTAT
1 GTATTAT
53714109 GTAT
1 GTAT
53714113 ATAACTAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.16, T:0.56
Consensus pattern (7 bp):
GTATTAT
Found at i:53714777 original size:18 final size:18
Alignment explanation
Indices: 53714754--53714796 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
53714744 TGCCAGGTGC
* *
53714754 GTATCCTAACTCTTTTAT
1 GTATCCTAACCCTTATAT
53714772 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
*
53714790 GTTTCCT
1 GTATCCT
53714797 TTTCCGAGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.21, C:0.26, G:0.07, T:0.47
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:53716150 original size:44 final size:44
Alignment explanation
Indices: 53716100--53716184 Score: 127
Period size: 44 Copynumber: 1.9 Consensus size: 44
53716090 CAGGCCATGC
**
53716100 GCTACTGTAGCAAAAGCGTATCCATGTGGGAGCCTT-TTTCAGAG
1 GCTACTGTAGCAAAAGCACATCCATGTGGGAG-CTTCTTTCAGAG
*
53716144 GCTACTGTAGCAAAAGCACGTCCATGTGGGAGCTTCTTTCA
1 GCTACTGTAGCAAAAGCACATCCATGTGGGAGCTTCTTTCA
53716185 ATACTTCTGC
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
43 3 0.08
44 34 0.92
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.27
Consensus pattern (44 bp):
GCTACTGTAGCAAAAGCACATCCATGTGGGAGCTTCTTTCAGAG
Found at i:53716356 original size:125 final size:126
Alignment explanation
Indices: 53716134--53716431 Score: 427
Period size: 125 Copynumber: 2.4 Consensus size: 126
53716124 TGTGGGAGCC
* *
53716134 TTTTTCAGAGGCTACTGTAGCAAAAGCACGTCCATGTGGGAGCTTCTTTCAATACTTCTGCTGAC
1 TTTTTCAGGGGCTACTGTAGCAAAAGCACGTCCACGTGGGAGCTTCTTTCAATACTTCTGCTGAC
* * *
53716199 AAAGCATCCTGCTTAAAGTGTTTTTGACACTGTTTGCTCAGAAACGTCTACTCGAAATTA-
66 AAAGCATCATGCTTAAAGCGTTTTTGACACTGTTTGCTCAGAAACGTCTACTCAAAATTAT
* * *
53716259 TTTTTCAGGGGATACTGTAGCAAAAGCACGTCCACGTGGGAGCTTCTTTTAGTACTTCTGCTGAC
1 TTTTTCAGGGGCTACTGTAGCAAAAGCACGTCCACGTGGGAGCTTCTTTCAATACTTCTGCTGAC
* * * *
53716324 AAAGCATCATTCTTAAAGCGTTTTTTACACTGTTTGCTTAGAAGCGTCTACTCAAAATTAT
66 AAAGCATCATGCTTAAAGCGTTTTTGACACTGTTTGCTCAGAAACGTCTACTCAAAATTAT
* ** * * *
53716385 TTTTTTAGGACCTACTGTAGCAAAAGCGCGACCACGTGAGAGCTTCT
1 TTTTTCAGGGGCTACTGTAGCAAAAGCACGTCCACGTGGGAGCTTCT
53716432 CTAAATTAAT
Statistics
Matches: 153, Mismatches: 19, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
125 113 0.74
126 40 0.26
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (126 bp):
TTTTTCAGGGGCTACTGTAGCAAAAGCACGTCCACGTGGGAGCTTCTTTCAATACTTCTGCTGAC
AAAGCATCATGCTTAAAGCGTTTTTGACACTGTTTGCTCAGAAACGTCTACTCAAAATTAT
Found at i:53716617 original size:96 final size:95
Alignment explanation
Indices: 53716467--53716696 Score: 273
Period size: 95 Copynumber: 2.4 Consensus size: 95
53716457 AGTAACCCTA
* * *
53716467 AACCCCAAACACTAATTTATTTGAGTTTTTACTTAAAAACCCTAAACACAAAACCCTTA-ACTAA
1 AACCCTAAACCCTAATTTATTTGA-TTTTTACTTAAAAACCCTAAACACAAAACCCTCATA-TAA
* *
53716531 TTTATTAAAAATTTATAATTAATTTACTCAAGT
64 TGT-TTAAAAATTTATAATTAAATTACTCAAGT
* * * * * * *
53716564 AACTCTAAACCCTAATTTATTTGATTTTTCCTTAAAACCCCTTAACTCTAAACCCTCATATGATG
1 AACCCTAAACCCTAATTTATTTGATTTTTACTTAAAAACCCTAAACACAAAACCCTCATATAATG
* *
53716629 TTTAAAATTTTTTAATTAAATTACTCAAGT
66 TTTAAAAATTTATAATTAAATTACTCAAGT
* * *
53716659 AACCCTAAACCTTAATTTAATTGATTTTTTCTTAAAAA
1 AACCCTAAACCCTAATTTATTTGATTTTTACTTAAAAA
53716697 ATAATAAACA
Statistics
Matches: 113, Mismatches: 19, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
95 59 0.52
96 32 0.28
97 22 0.19
ACGTcount: A:0.39, C:0.19, G:0.03, T:0.39
Consensus pattern (95 bp):
AACCCTAAACCCTAATTTATTTGATTTTTACTTAAAAACCCTAAACACAAAACCCTCATATAATG
TTTAAAAATTTATAATTAAATTACTCAAGT
Found at i:53716740 original size:95 final size:95
Alignment explanation
Indices: 53716467--53716740 Score: 221
Period size: 95 Copynumber: 2.9 Consensus size: 95
53716457 AGTAACCCTA
* * * * ** * * *
53716467 AACCCCAAACACTAATTTATTTGAGTTTTTACTTAAAAACCCTAAACACAAAACCCTTA-ACTAA
1 AACCCTAAACCCTAATTTAATTGA-TTTTTCCTTAAAAACAATAAACACGAAACACTAATAC-AA
* *
53716531 TTTATTAAAAATTTATAATTAATTTACTCAAGT
64 TGT-TTAAAAATTTATAATTAAATTACTCAAGT
* * * ** * * * * * **
53716564 AACTCTAAACCCTAATTTATTTGATTTTTCCTTAAAACCCCTTAACTCTAAACCCTCATATGATG
1 AACCCTAAACCCTAATTTAATTGATTTTTCCTTAAAAACAATAAACACGAAACACTAATACAATG
* *
53716629 TTTAAAATTTTTTAATTAAATTACTCAAGT
66 TTTAAAAATTTATAATTAAATTACTCAAGT
* * * *
53716659 AACCCTAAACCTTAATTTAATTGATTTTTTCTTAAAAAATAATAAACACGAAA-ACTAATCCAAT
1 AACCCTAAACCCTAATTTAATTGATTTTTCCTT-AAAAACAATAAACACGAAACACTAATACAAT
53716723 -TTTAAAAAATTTATAATT
65 GTTT-AAAAATTTATAATT
53716741 CATTTAATTG
Statistics
Matches: 141, Mismatches: 33, Indels: 8
0.77 0.18 0.04
Matches are distributed among these distances:
94 3 0.02
95 73 0.52
96 43 0.30
97 22 0.16
ACGTcount: A:0.42, C:0.18, G:0.03, T:0.38
Consensus pattern (95 bp):
AACCCTAAACCCTAATTTAATTGATTTTTCCTTAAAAACAATAAACACGAAACACTAATACAATG
TTTAAAAATTTATAATTAAATTACTCAAGT
Found at i:53723741 original size:18 final size:17
Alignment explanation
Indices: 53723728--53723764 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
53723718 TCATTATTAT
53723728 TATTAGTATTATTATTTA
1 TATTAGT-TTATTATTTA
53723746 TATTAGTTTATATATTTA
1 TATTAGTTTAT-TATTTA
53723764 T
1 T
53723765 CTACATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.62
Consensus pattern (17 bp):
TATTAGTTTATTATTTA
Found at i:53733334 original size:124 final size:121
Alignment explanation
Indices: 53733107--53733343 Score: 366
Period size: 124 Copynumber: 1.9 Consensus size: 121
53733097 TATGTGGGCT
* *
53733107 TTGTAACTTCATGAAAAAGGCTTCAAATAAGACTTTGATGTATGCGTTGGCTCCTTGAAGTTTTT
1 TTGTAACTTCATGAAAAAGGCTTCAAATAAGACTTTGATGTATGCGTTGGCTCCTTCAAGTTTTC
*
53733172 AATTTCTACATGCCTATGGGCTTTCTTAAATAAAGTTGATAATTTTTCAATTTCTA
66 AATTTCTACATGCCTATGGGCCTTCTTAAATAAAGTTGATAATTTTTCAATTTCTA
* * * * *
53733228 TTGTAACTTCATGACAAAGGTTTCAAATAAGACTTTGATGGTTGTGTGTTGGCTTCTTCAAGATT
1 TTGTAACTTCATGAAAAAGGCTTCAAATAAGACTTTGAT-G-TATGCGTTGGCTCCTTCAAG-TT
*
53733293 TTCAATTTCTACATGCCTATGGGCCTTCTTAAATAAAGTTGATAGTTTTTC
63 TTCAATTTCTACATGCCTATGGGCCTTCTTAAATAAAGTTGATAATTTTTC
53733344 TAGTTGGTCA
Statistics
Matches: 104, Mismatches: 9, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
121 37 0.36
122 1 0.01
123 16 0.15
124 50 0.48
ACGTcount: A:0.27, C:0.14, G:0.17, T:0.41
Consensus pattern (121 bp):
TTGTAACTTCATGAAAAAGGCTTCAAATAAGACTTTGATGTATGCGTTGGCTCCTTCAAGTTTTC
AATTTCTACATGCCTATGGGCCTTCTTAAATAAAGTTGATAATTTTTCAATTTCTA
Found at i:53734863 original size:60 final size:60
Alignment explanation
Indices: 53734770--53734892 Score: 219
Period size: 60 Copynumber: 2.0 Consensus size: 60
53734760 GGTATATAGA
*
53734770 TGGGTTGCCTCCCCCACCTATGCCATCTGGAAGTTCTTAATAGGCCTATCTATAATTCAT
1 TGGGTTGCCTCCCCCACCCATGCCATCTGGAAGTTCTTAATAGGCCTATCTATAATTCAT
* *
53734830 TGGGTTGCCTCCCCCACCCATGCCATTTGGAAGTTTTTAATAGGCCTATCTATAATTCAT
1 TGGGTTGCCTCCCCCACCCATGCCATCTGGAAGTTCTTAATAGGCCTATCTATAATTCAT
53734890 TGG
1 TGG
53734893 TCTTTTGTTA
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.21, C:0.27, G:0.18, T:0.34
Consensus pattern (60 bp):
TGGGTTGCCTCCCCCACCCATGCCATCTGGAAGTTCTTAATAGGCCTATCTATAATTCAT
Done.