Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A03
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: 108673976
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.31
Warning! 5040000 characters in sequence are not A, C, G, or T
File 125 of 333
Found at i:40379065 original size:23 final size:22
Alignment explanation
Indices: 40379023--40379065 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
40379013 AAAAAAGTTT
40379023 CGAAAAAAAAAAAGAAAAAATC
1 CGAAAAAAAAAAAGAAAAAATC
*
40379045 CGAAAAAAAAGAAGGAAAAAA
1 CGAAAAAAAA-AAAGAAAAAA
40379066 AATTGCAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.77, C:0.07, G:0.14, T:0.02
Consensus pattern (22 bp):
CGAAAAAAAAAAAGAAAAAATC
Found at i:40379077 original size:14 final size:14
Alignment explanation
Indices: 40379060--40379086 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
40379050 AAAAAGAAGG
40379060 AAAAAAAATTGCAA
1 AAAAAAAATTGCAA
40379074 AAAAAAAATTGCA
1 AAAAAAAATTGCA
40379087 TACGGTCTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.70, C:0.07, G:0.07, T:0.15
Consensus pattern (14 bp):
AAAAAAAATTGCAA
Found at i:40381362 original size:24 final size:25
Alignment explanation
Indices: 40381335--40381388 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 25
40381325 ATGAGTGATA
*
40381335 AAAAAAGAGA-GAGTGATTCAAAA-G
1 AAAAAAGAAACGAGTGA-TCAAAATG
*
40381359 -AAAAAGAAACGAGTGATGAAAATG
1 AAAAAAGAAACGAGTGATCAAAATG
40381383 AAAAAA
1 AAAAAA
40381389 AGAATTTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 13 0.52
24 7 0.28
25 5 0.20
ACGTcount: A:0.63, C:0.04, G:0.22, T:0.11
Consensus pattern (25 bp):
AAAAAAGAAACGAGTGATCAAAATG
Found at i:40385722 original size:26 final size:26
Alignment explanation
Indices: 40385675--40385727 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
40385665 AAATCGTAGC
* *
40385675 TTCGAAAAAAAAAGTTAAAAAAAAGT
1 TTCGAAAAAAAAAATCAAAAAAAAGT
40385701 TTCGAAAAAAAAAATCCGAAAAAAAAG
1 TTCGAAAAAAAAAAT-C-AAAAAAAAG
40385728 GAAAAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 14 0.61
28 9 0.39
ACGTcount: A:0.66, C:0.08, G:0.11, T:0.15
Consensus pattern (26 bp):
TTCGAAAAAAAAAATCAAAAAAAAGT
Found at i:40385746 original size:14 final size:14
Alignment explanation
Indices: 40385729--40385756 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
40385719 AAAAAAAAGG
40385729 AAAAAAAAATTGCA
1 AAAAAAAAATTGCA
40385743 AAAAAAAAATTGCA
1 AAAAAAAAATTGCA
40385757 TACGGTCTAG
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:0.71, C:0.07, G:0.07, T:0.14
Consensus pattern (14 bp):
AAAAAAAAATTGCA
Found at i:40385746 original size:24 final size:24
Alignment explanation
Indices: 40385704--40385750 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
40385694 AAAAAGTTTC
*
40385704 GAAAAAAAAAATCCGAAAAAAAAG
1 GAAAAAAAAAATCCAAAAAAAAAG
* *
40385728 GAAAAAAAAATTGCAAAAAAAAA
1 GAAAAAAAAAATCCAAAAAAAAA
40385751 ATTGCATACG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.77, C:0.06, G:0.11, T:0.06
Consensus pattern (24 bp):
GAAAAAAAAAATCCAAAAAAAAAG
Found at i:40388022 original size:24 final size:25
Alignment explanation
Indices: 40387995--40388048 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 25
40387985 GATGAGTGAT
*
40387995 AAAAAAGAGA-GAGTGATTCAAAA-G
1 AAAAAAGAAACGAGTGA-TCAAAATG
*
40388019 -AAAAAGAAACGAGTGATGAAAATG
1 AAAAAAGAAACGAGTGATCAAAATG
40388043 AAAAAA
1 AAAAAA
40388049 AGAATTTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 13 0.52
24 7 0.28
25 5 0.20
ACGTcount: A:0.63, C:0.04, G:0.22, T:0.11
Consensus pattern (25 bp):
AAAAAAGAAACGAGTGATCAAAATG
Found at i:40397653 original size:20 final size:20
Alignment explanation
Indices: 40397630--40397676 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
40397620 GGGTTAAGAT
*
40397630 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
40397650 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
40397670 TGAGCTG
1 TGAGCTG
40397677 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:40400551 original size:11 final size:11
Alignment explanation
Indices: 40400537--40400586 Score: 59
Period size: 11 Copynumber: 4.6 Consensus size: 11
40400527 TTTTGCTCGA
40400537 TTTTTTTCACT
1 TTTTTTTCACT
40400548 TTTTTTTC-CT
1 TTTTTTTCACT
40400558 TTTTTTTCGA-T
1 TTTTTTTC-ACT
* *
40400569 TTTTTTTGAAT
1 TTTTTTTCACT
40400580 TTTTTTT
1 TTTTTTT
40400587 TCTGAATTTC
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
10 11 0.31
11 24 0.69
ACGTcount: A:0.08, C:0.10, G:0.04, T:0.78
Consensus pattern (11 bp):
TTTTTTTCACT
Found at i:40400553 original size:28 final size:27
Alignment explanation
Indices: 40400476--40400554 Score: 79
Period size: 28 Copynumber: 2.8 Consensus size: 27
40400466 GCAAGACTTT
**
40400476 TCACTTTTTTTTAACTTGATTTTTTTTGC
1 TCAC-TTTTTTT-ACTTTTTTTTTTTTGC
*
40400505 TCACTTTTTTTTCTTTCTTTTTTTTTGC
1 TCACTTTTTTTACTTT-TTTTTTTTTGC
40400533 TCGA-TTTTTTTCACTTTTTTTT
1 TC-ACTTTTTTT-ACTTTTTTTT
40400555 CCTTTTTTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
27 3 0.07
28 31 0.72
29 9 0.21
ACGTcount: A:0.09, C:0.15, G:0.05, T:0.71
Consensus pattern (27 bp):
TCACTTTTTTTACTTTTTTTTTTTTGC
Found at i:40400582 original size:21 final size:21
Alignment explanation
Indices: 40400536--40400585 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
40400526 TTTTTGCTCG
*
40400536 ATTTTTTTCACTTTTTTTTCC
1 ATTTTTTTCACTTTTTTTTCA
* *
40400557 TTTTTTTTCGA-TTTTTTTTGA
1 ATTTTTTTC-ACTTTTTTTTCA
40400578 ATTTTTTT
1 ATTTTTTT
40400586 TTCTGAATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 23 0.96
22 1 0.04
ACGTcount: A:0.10, C:0.10, G:0.04, T:0.76
Consensus pattern (21 bp):
ATTTTTTTCACTTTTTTTTCA
Found at i:40402119 original size:20 final size:20
Alignment explanation
Indices: 40402096--40402142 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
40402086 GGGTTAAGAT
*
40402096 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
40402116 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
40402136 TGAGCTG
1 TGAGCTG
40402143 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:40403262 original size:30 final size:30
Alignment explanation
Indices: 40403228--40403325 Score: 81
Period size: 30 Copynumber: 3.3 Consensus size: 30
40403218 AGCTCACTCC
40403228 TAGCTCATATTCAGCTCACGAGCTAAACCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
** * * * * *
40403258 TAGCTCAGCTTCAGCTTAGGAGTTTAATCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
* * * *
40403288 CAGCTCA-ACTTTAGCTCATGAGCTAAAGCT
1 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
40403318 TAGCTCAT
1 TAGCTCAT
40403326 TTTAGTTTAA
Statistics
Matches: 50, Mismatches: 16, Indels: 3
0.72 0.23 0.04
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.31
Consensus pattern (30 bp):
TAGCTCATATTCAGCTCACGAGCTAAACCT
Found at i:40406746 original size:15 final size:15
Alignment explanation
Indices: 40406700--40406747 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
40406690 AAACCTACAA
*
40406700 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
40406715 AAA-TCCATCTACAT
1 AAACTTCATATCCAT
40406729 AAACTTCATATCCAT
1 AAACTTCATATCCAT
40406744 AAAC
1 AAAC
40406748 CCACCTTTGA
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.31
Consensus pattern (15 bp):
AAACTTCATATCCAT
Found at i:40415221 original size:24 final size:25
Alignment explanation
Indices: 40415168--40415221 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
40415158 AACAAATTCT
* *
40415168 TTTTTTCATTTTCATCACTCGTTTC
1 TTTTTTCATTTTAATCACTCGTCTC
40415193 -TTTTTC-TTTTGAATCACTC-TCTC
1 TTTTTTCATTTT-AATCACTCGTCTC
40415216 TTTTTT
1 TTTTTT
40415222 TATCACTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.11, C:0.22, G:0.04, T:0.63
Consensus pattern (25 bp):
TTTTTTCATTTTAATCACTCGTCTC
Found at i:40419454 original size:20 final size:20
Alignment explanation
Indices: 40419408--40419454 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
40419398 AGTTCGTTTC
*
40419408 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
40419428 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
40419448 CAGCTCA
1 CAGCTCA
40419455 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:40422145 original size:48 final size:47
Alignment explanation
Indices: 40422066--40422171 Score: 135
Period size: 48 Copynumber: 2.2 Consensus size: 47
40422056 GAGTGTCATG
*
40422066 GAAAAAGAAATTGAGATTGAAAAAGGATGTGA-AAAAGAGAAAGAAATC
1 GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAA-AGAAA-AAATC
* *
40422114 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAAAGAGAAAATT
1 GAAAAAGAAATTGAGATTGAA-AAAAGATGTGA-GAAAAAGAAAAAATC
40422162 GAAAAAGAAA
1 GAAAAAGAAA
40422172 GAAAAGACAA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.59, C:0.02, G:0.25, T:0.14
Consensus pattern (47 bp):
GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAAAGAAAAAATC
Found at i:40423887 original size:20 final size:20
Alignment explanation
Indices: 40423841--40423887 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
40423831 AGTTCGTTTC
*
40423841 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
40423861 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
40423881 CAGCTCA
1 CAGCTCA
40423888 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:40431993 original size:22 final size:22
Alignment explanation
Indices: 40431965--40432019 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
40431955 TATTGGATTT
***
40431965 AAAAAAAGAAGAAGAAATTCGA
1 AAAAAAAGAAGAAGAAAAAAGA
*
40431987 AAAAAAATTAA-AAGAAAAAAGA
1 AAAAAAA-GAAGAAGAAAAAAGA
40432009 AAAAAAAGAAG
1 AAAAAAAGAAG
40432020 TGACAAAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
21 2 0.08
22 22 0.85
23 2 0.08
ACGTcount: A:0.76, C:0.02, G:0.15, T:0.07
Consensus pattern (22 bp):
AAAAAAAGAAGAAGAAAAAAGA
Found at i:40432055 original size:8 final size:9
Alignment explanation
Indices: 40432038--40432069 Score: 64
Period size: 9 Copynumber: 3.6 Consensus size: 9
40432028 AAATCGAGTT
40432038 AAAAGAAAA
1 AAAAGAAAA
40432047 AAAAGAAAA
1 AAAAGAAAA
40432056 AAAAGAAAA
1 AAAAGAAAA
40432065 AAAAG
1 AAAAG
40432070 TGAAAAGTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (9 bp):
AAAAGAAAA
Found at i:40432969 original size:18 final size:18
Alignment explanation
Indices: 40432948--40432982 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
40432938 AGAAAAGAAA
40432948 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
40432966 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
40432983 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:40436792 original size:15 final size:14
Alignment explanation
Indices: 40436772--40436800 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
40436762 CGTAGCTTCG
40436772 AAAAAAAAAATTGC
1 AAAAAAAAAATTGC
40436786 AAAAAAAAAATTGC
1 AAAAAAAAAATTGC
40436800 A
1 A
40436801 TACGGTCTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.72, C:0.07, G:0.07, T:0.14
Consensus pattern (14 bp):
AAAAAAAAAATTGC
Found at i:40440486 original size:24 final size:23
Alignment explanation
Indices: 40440432--40440509 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 23
40440422 GGATAATTAA
**
40440432 GAAATGGTATTTGGTTTTGGTAC
1 GAAATGGTATTTGGAATTGGTAC
***
40440455 GCTTTGGTATTTGGGAATTGGTAC
1 GAAATGGTATTT-GGAATTGGTAC
*
40440479 GAAATGGTA--TGGAATTGGTAT
1 GAAATGGTATTTGGAATTGGTAC
*
40440500 GAAATAGTAT
1 GAAATGGTAT
40440510 GGTATTTGGT
Statistics
Matches: 43, Mismatches: 10, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
21 18 0.42
22 1 0.02
23 9 0.21
24 15 0.35
ACGTcount: A:0.27, C:0.04, G:0.31, T:0.38
Consensus pattern (23 bp):
GAAATGGTATTTGGAATTGGTAC
Found at i:40440494 original size:21 final size:21
Alignment explanation
Indices: 40440468--40440529 Score: 79
Period size: 21 Copynumber: 2.9 Consensus size: 21
40440458 TTGGTATTTG
40440468 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
40440489 GGAATTGGTATGAAATAGTAT
1 GGAATTGGTACGAAATGGTAT
* *
40440510 GGTATTTGGTACGAATTGGT
1 GG-AATTGGTACGAAATGGT
40440530 TATGATTCAA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
21 21 0.62
22 13 0.38
ACGTcount: A:0.31, C:0.03, G:0.32, T:0.34
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:40444761 original size:16 final size:16
Alignment explanation
Indices: 40444737--40444788 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
40444727 TCTCTTTTCA
*
40444737 TTCTCTTTTTTGAATT
1 TTCTTTTTTTTGAATT
* * *
40444753 TTCTTTTTTATCATTT
1 TTCTTTTTTTTGAATT
*
40444769 TTCTTTTCTTTTGTATT
1 TTCTTTT-TTTTGAATT
40444786 TTC
1 TTC
40444789 GCTCTTTTCT
Statistics
Matches: 27, Mismatches: 8, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
16 19 0.70
17 8 0.30
ACGTcount: A:0.10, C:0.13, G:0.04, T:0.73
Consensus pattern (16 bp):
TTCTTTTTTTTGAATT
Found at i:40447018 original size:13 final size:13
Alignment explanation
Indices: 40447000--40447037 Score: 51
Period size: 12 Copynumber: 2.8 Consensus size: 13
40446990 AAACCGTATG
40447000 CAATTTTTTTTTT
1 CAATTTTTTTTTT
40447013 CAA-TTTTTTTTT
1 CAATTTTTTTTTT
40447025 CGAACTTTTTTTT
1 C-AA-TTTTTTTT
40447038 ACGCACCTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 10 0.45
13 5 0.23
15 7 0.32
ACGTcount: A:0.16, C:0.11, G:0.03, T:0.71
Consensus pattern (13 bp):
CAATTTTTTTTTT
Found at i:40447021 original size:12 final size:14
Alignment explanation
Indices: 40447004--40447037 Score: 54
Period size: 12 Copynumber: 2.6 Consensus size: 14
40446994 CGTATGCAAT
40447004 TTTTTTTTTC-AA-
1 TTTTTTTTTCGAAC
40447016 TTTTTTTTTCGAAC
1 TTTTTTTTTCGAAC
40447030 TTTTTTTT
1 TTTTTTTT
40447038 ACGCACCTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 10 0.50
13 2 0.10
14 8 0.40
ACGTcount: A:0.12, C:0.09, G:0.03, T:0.76
Consensus pattern (14 bp):
TTTTTTTTTCGAAC
Found at i:40447354 original size:24 final size:23
Alignment explanation
Indices: 40447300--40447377 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 23
40447290 GGATAATTAA
**
40447300 GAAATGGTATTTGGTTTTGGTAC
1 GAAATGGTATTTGGAATTGGTAC
***
40447323 GCTTTGGTATTTGGGAATTGGTAC
1 GAAATGGTATTT-GGAATTGGTAC
*
40447347 GAAATGGTA--TGGAATTGGTAT
1 GAAATGGTATTTGGAATTGGTAC
*
40447368 GAAATAGTAT
1 GAAATGGTAT
40447378 GGTATTTGGT
Statistics
Matches: 43, Mismatches: 10, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
21 18 0.42
22 1 0.02
23 9 0.21
24 15 0.35
ACGTcount: A:0.27, C:0.04, G:0.31, T:0.38
Consensus pattern (23 bp):
GAAATGGTATTTGGAATTGGTAC
Found at i:40447362 original size:21 final size:21
Alignment explanation
Indices: 40447336--40447397 Score: 79
Period size: 21 Copynumber: 2.9 Consensus size: 21
40447326 TTGGTATTTG
40447336 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
40447357 GGAATTGGTATGAAATAGTAT
1 GGAATTGGTACGAAATGGTAT
* *
40447378 GGTATTTGGTACGAATTGGT
1 GG-AATTGGTACGAAATGGT
40447398 TATGATTCAA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
21 21 0.62
22 13 0.38
ACGTcount: A:0.31, C:0.03, G:0.32, T:0.34
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:40463420 original size:20 final size:21
Alignment explanation
Indices: 40463391--40463438 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
40463381 AAATTTGTGC
* *
40463391 AATTTACTACCATAAA-TTCT
1 AATTTTCTACAATAAATTTCT
*
40463411 CATTTTCTACAATAAATTTCT
1 AATTTTCTACAATAAATTTCT
40463432 AATTTTC
1 AATTTTC
40463439 AGCATACAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.35, C:0.19, G:0.00, T:0.46
Consensus pattern (21 bp):
AATTTTCTACAATAAATTTCT
Found at i:40464349 original size:39 final size:40
Alignment explanation
Indices: 40464306--40464389 Score: 116
Period size: 39 Copynumber: 2.1 Consensus size: 40
40464296 CGTTTGAATG
*
40464306 AAAAACGCCACTAAAGAACGAGCATTAGCGACGC-TTTTT
1 AAAAACGCCACTAAAGAACGAGAATTAGCGACGCTTTTTT
* ** *
40464345 AAAAACGCTACTAAAGATTGAGAATTAGCGGCGCTTTTTT
1 AAAAACGCCACTAAAGAACGAGAATTAGCGACGCTTTTTT
40464385 AAAAA
1 AAAAA
40464390 TACCGCTATA
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
39 29 0.74
40 10 0.26
ACGTcount: A:0.40, C:0.18, G:0.18, T:0.24
Consensus pattern (40 bp):
AAAAACGCCACTAAAGAACGAGAATTAGCGACGCTTTTTT
Found at i:40464655 original size:126 final size:126
Alignment explanation
Indices: 40464475--40464822 Score: 545
Period size: 126 Copynumber: 2.8 Consensus size: 126
40464465 CACAACACAG
** * *
40464475 TCGTTTTGTATTGAGCCTTTGGTGGCTTTAGCTGCGCTTTTTAAAAACGCCGCTAAAGATCGAGT
1 TCGTTTTGTATTGAGATTTTAGTGGCTTTAGCAGCGCTTTTTAAAAACGCCGCTAAAGATCGAGT
**
40464540 ATTAGCAGCGCTTTTTAGAAAACATTGCTAATGCTTGGCAAAATAATTTTGTAAAACGCCA
66 ATTAGCAGCGCTTTTTAGAAAACACCGCTAATGCTTGGCAAAATAATTTTGTAAAACGCCA
* **
40464601 TCGTTTTGTATTGAGATTTTAGTGGCTTTAGCGGCGCTTTTTAAAAACAACGCTAAAGATCGAGT
1 TCGTTTTGTATTGAGATTTTAGTGGCTTTAGCAGCGCTTTTTAAAAACGCCGCTAAAGATCGAGT
*
40464666 ATTAGCGGCGCTTTTTAGAAAACACCGCTAATGCTTGGCAAAATAATTTTGTAAAACGCCA
66 ATTAGCAGCGCTTTTTAGAAAACACCGCTAATGCTTGGCAAAATAATTTTGTAAAACGCCA
*
40464727 TCGTTTTGTATTGAGATTTTAGTGGCTTTAGCAGCGCTTTTTAAAAACGCCGCTAAAGATCAAGT
1 TCGTTTTGTATTGAGATTTTAGTGGCTTTAGCAGCGCTTTTTAAAAACGCCGCTAAAGATCGAGT
* * *
40464792 ATTAACGGCACTTTTTTA-AGAAACACCGCTA
66 ATTAGCAGCGC-TTTTTAGA-AAACACCGCTA
40464823 TATGTACACC
Statistics
Matches: 205, Mismatches: 15, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
126 188 0.92
127 17 0.08
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (126 bp):
TCGTTTTGTATTGAGATTTTAGTGGCTTTAGCAGCGCTTTTTAAAAACGCCGCTAAAGATCGAGT
ATTAGCAGCGCTTTTTAGAAAACACCGCTAATGCTTGGCAAAATAATTTTGTAAAACGCCA
Found at i:40464876 original size:40 final size:38
Alignment explanation
Indices: 40464752--40464898 Score: 116
Period size: 40 Copynumber: 3.7 Consensus size: 38
40464742 ATTTTAGTGG
* * *
40464752 CTTTAGCAGCGCTTTTT-AAAAACGCCGCTAAAGATCAA
1 CTTTAGCAGCACTTTTTAAAAAACGCCGCTAATG-TCAT
* * * * * *
40464790 GTATTAACGGCACTTTTTTAAGAAACACCGCTATATGTACAC
1 CT-TTAGCAGCAC-TTTTTAAAAAACGCCGCTA-ATGT-CAT
*
40464832 CTTTAGCGGCACTTTTTAAAAAACGCCGCTAATGCTCGAT
1 CTTTAGCAGCACTTTTTAAAAAACGCCGCTAATG-TC-AT
* *
40464872 CTTTAGCAGCATTTTTTGAAAAACGCC
1 CTTTAGCAGCACTTTTTAAAAAACGCC
40464899 ACAAAAAATG
Statistics
Matches: 86, Mismatches: 16, Indels: 12
0.75 0.14 0.11
Matches are distributed among these distances:
38 1 0.01
39 11 0.13
40 48 0.56
41 21 0.24
42 5 0.06
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Consensus pattern (38 bp):
CTTTAGCAGCACTTTTTAAAAAACGCCGCTAATGTCAT
Found at i:40465133 original size:15 final size:15
Alignment explanation
Indices: 40465113--40465160 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
40465103 ACTATTGTAA
40465113 GGTTTATGGATTATG
1 GGTTTATGGATTATG
*
40465128 GGTTTAAGGATTAT-
1 GGTTTATGGATTATG
*
40465142 GGTTTATGGTTTATG
1 GGTTTATGGATTATG
40465157 GGTT
1 GGTT
40465161 AAGGGTTAGG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
14 12 0.41
15 17 0.59
ACGTcount: A:0.19, C:0.00, G:0.33, T:0.48
Consensus pattern (15 bp):
GGTTTATGGATTATG
Found at i:40465135 original size:22 final size:21
Alignment explanation
Indices: 40465059--40465269 Score: 129
Period size: 22 Copynumber: 9.8 Consensus size: 21
40465049 TCATTATAGT
* *
40465059 TTAGGGTTTATGGTATAT-GG
1 TTAGGGTTTAAGGTTTATGGG
* *
40465079 TTAAGGGTTTAATGTTTATGAG
1 TT-AGGGTTTAAGGTTTATGGG
*** *
40465101 TTACTATTGTAAGGTTTATGGA
1 TTAGGGTT-TAAGGTTTATGGG
* *
40465123 TTATGGGTTTAAGGATTATGGT
1 TTA-GGGTTTAAGGTTTATGGG
* * * *
40465145 TTATGGTTTATGGGTTAAGGG
1 TTAGGGTTTAAGGTTTATGGG
*
40465166 TTAGGGTTTAAGTTTTA-GATGG
1 TTAGGGTTTAAGGTTTATG--GG
*
40465188 TTAGGGTTTAAGGTTTAGGGG
1 TTAGGGTTTAAGGTTTATGGG
* * *
40465209 TTAAGGGTTTATGTTTTATGGT
1 TT-AGGGTTTAAGGTTTATGGG
* * * *
40465231 TTAAGGTTTATGGGTTAGGGG
1 TTAGGGTTTAAGGTTTATGGG
*
40465252 TTAGGGATTTAGGGTTTA
1 TTAGGG-TTTAAGGTTTA
40465270 GATTAATTAG
Statistics
Matches: 145, Mismatches: 37, Indels: 16
0.73 0.19 0.08
Matches are distributed among these distances:
20 3 0.02
21 65 0.45
22 74 0.51
23 3 0.02
ACGTcount: A:0.22, C:0.00, G:0.33, T:0.45
Consensus pattern (21 bp):
TTAGGGTTTAAGGTTTATGGG
Found at i:40465232 original size:36 final size:36
Alignment explanation
Indices: 40465142--40465253 Score: 111
Period size: 36 Copynumber: 3.1 Consensus size: 36
40465132 TAAGGATTAT
* * * *
40465142 GGTTTATGGTTTATGGGTTAAGGGTTAGGGTTTAA-
1 GGTTTATGTTTTATGGTTTAAGGTTTAGGGGTTAAG
* * *
40465177 GTTTTA-GATGGTTAGGGTTTAAGGTTTAGGGGTTAAG
1 GGTTTATG-T-TTTATGGTTTAAGGTTTAGGGGTTAAG
* *
40465214 GGTTTATGTTTTATGGTTTAAGGTTTATGGGTTAGG
1 GGTTTATGTTTTATGGTTTAAGGTTTAGGGGTTAAG
40465250 GGTT
1 GGTT
40465254 AGGGATTTAG
Statistics
Matches: 61, Mismatches: 12, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
34 1 0.02
35 5 0.08
36 48 0.79
37 6 0.10
38 1 0.02
ACGTcount: A:0.19, C:0.00, G:0.37, T:0.45
Consensus pattern (36 bp):
GGTTTATGTTTTATGGTTTAAGGTTTAGGGGTTAAG
Found at i:40465268 original size:36 final size:36
Alignment explanation
Indices: 40465188--40465269 Score: 103
Period size: 36 Copynumber: 2.3 Consensus size: 36
40465178 TTTTAGATGG
* * *
40465188 TTAGGGTTTAAGGTTTAGGGGTTAAGGGTTTATGTT
1 TTAGGGTTTAAGGTTTAGGGGTTAAGGGGTTAGGAT
* *
40465224 TTATGGTTTAAGGTTTATGGGTT-AGGGGTTAGGGAT
1 TTAGGGTTTAAGGTTTAGGGGTTAAGGGGTTA-GGAT
40465260 TTAGGGTTTA
1 TTAGGGTTTA
40465270 GATTAATTAG
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
35 7 0.18
36 32 0.82
ACGTcount: A:0.20, C:0.00, G:0.37, T:0.44
Consensus pattern (36 bp):
TTAGGGTTTAAGGTTTAGGGGTTAAGGGGTTAGGAT
Found at i:40465269 original size:7 final size:7
Alignment explanation
Indices: 40465113--40465270 Score: 88
Period size: 7 Copynumber: 22.0 Consensus size: 7
40465103 ACTATTGTAA
*
40465113 GGTTTAT
1 GGTTTAG
*
40465120 GGATTATG
1 GGTTTA-G
*
40465128 GGTTTAA
1 GGTTTAG
* *
40465135 GGATTAT
1 GGTTTAG
*
40465142 GGTTTAT
1 GGTTTAG
40465149 GGTTTATG
1 GGTTTA-G
*
40465157 GGTTAAG
1 GGTTTAG
40465164 GG-TTAG
1 GGTTTAG
*
40465170 GGTTTAA
1 GGTTTAG
*
40465177 GTTTTAG
1 GGTTTAG
40465184 ATGG-TTAG
1 --GGTTTAG
*
40465192 GGTTTAA
1 GGTTTAG
40465199 GGTTTAGG
1 GGTTTA-G
*
40465207 GGTTAAG
1 GGTTTAG
*
40465214 GGTTTAT
1 GGTTTAG
* *
40465221 GTTTTAT
1 GGTTTAG
*
40465228 GGTTTAA
1 GGTTTAG
40465235 GGTTTATG
1 GGTTTA-G
40465243 GG-TTAG
1 GGTTTAG
*
40465249 GGGTTAG
1 GGTTTAG
40465256 GGATTTAG
1 GG-TTTAG
40465264 GGTTTAG
1 GGTTTAG
40465271 ATTAATTAGT
Statistics
Matches: 117, Mismatches: 24, Indels: 20
0.73 0.15 0.12
Matches are distributed among these distances:
6 10 0.09
7 79 0.68
8 27 0.23
9 1 0.01
ACGTcount: A:0.20, C:0.00, G:0.36, T:0.44
Consensus pattern (7 bp):
GGTTTAG
Found at i:40474042 original size:13 final size:13
Alignment explanation
Indices: 40473976--40474033 Score: 53
Period size: 13 Copynumber: 4.4 Consensus size: 13
40473966 ATATGTTTAG
40473976 ATGAAATGGTTAT
1 ATGAAATGGTTAT
** * *
40473989 ACAAAATGTTTTT
1 ATGAAATGGTTAT
* *
40474002 ATGAAAATAGATAT
1 ATG-AAATGGTTAT
40474016 ATGAAATGGTTAT
1 ATGAAATGGTTAT
40474029 ATGAA
1 ATGAA
40474034 GTGTCTATAC
Statistics
Matches: 32, Mismatches: 12, Indels: 2
0.70 0.26 0.04
Matches are distributed among these distances:
13 23 0.72
14 9 0.28
ACGTcount: A:0.45, C:0.02, G:0.17, T:0.36
Consensus pattern (13 bp):
ATGAAATGGTTAT
Found at i:40478267 original size:41 final size:41
Alignment explanation
Indices: 40478209--40478308 Score: 155
Period size: 41 Copynumber: 2.4 Consensus size: 41
40478199 GATGAATTAT
*
40478209 ACATACATGCCCCTGTTTGTACTTCAGTACCCCTAAATTGC
1 ACATACGTGCCCCTGTTTGTACTTCAGTACCCCTAAATTGC
* * *
40478250 ACATACGTGCCCTTGTTTGTACTTCGGTACCCCTGAATTGC
1 ACATACGTGCCCCTGTTTGTACTTCAGTACCCCTAAATTGC
*
40478291 ACACACGTGCCCCTGTTT
1 ACATACGTGCCCCTGTTT
40478309 AGACTTCGAA
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.20, C:0.32, G:0.16, T:0.32
Consensus pattern (41 bp):
ACATACGTGCCCCTGTTTGTACTTCAGTACCCCTAAATTGC
Found at i:40480935 original size:56 final size:56
Alignment explanation
Indices: 40480849--40481024 Score: 343
Period size: 56 Copynumber: 3.1 Consensus size: 56
40480839 ACAAGGGATG
*
40480849 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
40480905 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
40480961 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
40481017 ATGGGCAA
1 ATGGGCAA
40481025 TAAACTAATA
Statistics
Matches: 119, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
56 119 1.00
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
Found at i:40482340 original size:40 final size:40
Alignment explanation
Indices: 40482149--40482333 Score: 227
Period size: 40 Copynumber: 4.7 Consensus size: 40
40482139 TCGAATGATG
* * *
40482149 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAC-CAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAT
*
40482188 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAT
*
40482229 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
*
40482268 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
40482307 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
40482334 AACGAGTAGC
Statistics
Matches: 128, Mismatches: 11, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
39 38 0.30
40 80 0.62
41 10 0.08
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
Found at i:40482355 original size:79 final size:79
Alignment explanation
Indices: 40482202--40482366 Score: 203
Period size: 79 Copynumber: 2.1 Consensus size: 79
40482192 GGACTAAGAT
* **
40482202 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
*
40482267 TTCCGGGTTAAGTC
66 TTCCGGGTTAAATC
* *
40482281 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGTTACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-C
*
40482344 T-ATATCC-GGTTAAATT
63 TAAT-TCCGGGTTAAATC
40482360 CCGAAGG
1 CCGAAGG
40482367 TACGTGATTT
Statistics
Matches: 75, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
78 2 0.03
79 51 0.68
80 22 0.29
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
TTCCGGGTTAAATC
Found at i:40488884 original size:56 final size:56
Alignment explanation
Indices: 40488819--40488994 Score: 343
Period size: 56 Copynumber: 3.1 Consensus size: 56
40488809 ACAAGGGATG
*
40488819 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
40488875 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
40488931 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
40488987 ATGGGCAA
1 ATGGGCAA
40488995 TAAACTAATA
Statistics
Matches: 119, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
56 119 1.00
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
Found at i:40490260 original size:78 final size:75
Alignment explanation
Indices: 40490164--40490329 Score: 203
Period size: 78 Copynumber: 2.2 Consensus size: 75
40490154 ATATCCGGAC
**
40490164 TAAGATCCGAAGGCATTTGTGCGAGTTAC-TAATTCCGGGCTAAG-CCCGAAGGCATTGGTGCGA
1 TAAG-TCCGAAGGCATTTGTGCGAGTTACTTAA-T-CGGGCTAAGTCCCG-AGGCATTGGAACGA
40490227 GTTA-CTAATTCCGGGT
62 G-TAGCT-ATTCC-GGT
* *
40490243 TAAGTCCGAAGGCATTTGTGCGAGTTACTTAATCGGGCTATGTCCCGAGGCATTTGAACGAGTAG
1 TAAGTCCGAAGGCATTTGTGCGAGTTACTTAATCGGGCTAAGTCCCGAGGCATTGGAACGAGTAG
40490308 CTATTCCGGT
66 CTATTCCGGT
*
40490318 TAATTCCGAAGG
1 TAAGTCCGAAGG
40490330 TACGTGATTT
Statistics
Matches: 79, Mismatches: 5, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
75 14 0.18
76 7 0.09
77 22 0.28
78 29 0.37
79 7 0.09
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (75 bp):
TAAGTCCGAAGGCATTTGTGCGAGTTACTTAATCGGGCTAAGTCCCGAGGCATTGGAACGAGTAG
CTATTCCGGT
Found at i:40490305 original size:38 final size:40
Alignment explanation
Indices: 40490117--40490298 Score: 209
Period size: 39 Copynumber: 4.7 Consensus size: 40
40490107 TCGAATGATG
* * *
40490117 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAC-CAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAT
*
40490156 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAT
*
40490197 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
*
40490236 TCCGGGTTAAGT-CCGAAGGCATTTGTGCGAGTTACTTAA-
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTAC-TAAT
*
40490275 T-CGGGCTATGTCCCG-AGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
40490299 AACGAGTAGC
Statistics
Matches: 125, Mismatches: 10, Indels: 16
0.83 0.07 0.11
Matches are distributed among these distances:
38 17 0.14
39 62 0.50
40 36 0.29
41 10 0.08
ACGTcount: A:0.23, C:0.22, G:0.29, T:0.27
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
Found at i:40500554 original size:25 final size:26
Alignment explanation
Indices: 40500519--40500578 Score: 113
Period size: 25 Copynumber: 2.3 Consensus size: 26
40500509 NNNNNNNNNA
40500519 TAAGTGTGCGAAATCGGTATTGGCAC
1 TAAGTGTGCGAAATCGGTATTGGCAC
40500545 TAAGT-TGCGAAATCGGTATTGGCAC
1 TAAGTGTGCGAAATCGGTATTGGCAC
40500570 TAAGTGTGC
1 TAAGTGTGC
40500579 AAGTTGGTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
25 25 0.76
26 8 0.24
ACGTcount: A:0.27, C:0.15, G:0.30, T:0.28
Consensus pattern (26 bp):
TAAGTGTGCGAAATCGGTATTGGCAC
Found at i:40508056 original size:28 final size:27
Alignment explanation
Indices: 40508024--40508175 Score: 139
Period size: 28 Copynumber: 5.5 Consensus size: 27
40508014 ATTTGATACC
40508024 GAGCACTAAGTGTGCGAAATCGGTCATT
1 GAGCACTAAGTGTGCGAAATCGGT-ATT
40508052 GAGCACTAAGTGTGCGAAATCGGTCATT
1 GAGCACTAAGTGTGCGAAATCGGT-ATT
* * * *
40508080 GAGCACTGAGTGTGC-AAGTTGGTTTT
1 GAGCACTAAGTGTGCGAAATCGGTATT
* * * * *
40508106 AAGCATTAAGTGTG-TAATTTGG-ATTT
1 GAGCACTAAGTGTGCGAAATCGGTA-TT
40508132 CCGAGCACTAAGTGTGCGAAATCGGTTATT
1 --GAGCACTAAGTGTGCGAAATCGG-TATT
*
40508162 GGGCACTAAGTGTG
1 GAGCACTAAGTGTG
40508176 TGAGAAAATT
Statistics
Matches: 102, Mismatches: 15, Indels: 14
0.78 0.11 0.11
Matches are distributed among these distances:
26 21 0.21
27 6 0.06
28 67 0.66
29 5 0.05
30 2 0.02
31 1 0.01
ACGTcount: A:0.26, C:0.14, G:0.30, T:0.30
Consensus pattern (27 bp):
GAGCACTAAGTGTGCGAAATCGGTATT
Found at i:40511144 original size:48 final size:48
Alignment explanation
Indices: 40511089--40511208 Score: 188
Period size: 48 Copynumber: 2.5 Consensus size: 48
40511079 TATGAGAGCC
40511089 AGTGTAAGACCATGTCTGGGACATGGCATCAGCATTAAGAAGAAAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCAGCATTAAGAAGAAAGCT
* * * * *
40511137 AGTGTAAGACCATGTCTGGGGCATGGCATCGGCATTGAGACGAGAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCAGCATTAAGAAGAAAGCT
40511185 AGTGTAAGA-CATGTCTGGGACATG
1 AGTGTAAGACCATGTCTGGGACATG
40511209 TATCGGCCTC
Statistics
Matches: 66, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
47 14 0.21
48 52 0.79
ACGTcount: A:0.30, C:0.17, G:0.32, T:0.22
Consensus pattern (48 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCAGCATTAAGAAGAAAGCT
Found at i:40511316 original size:47 final size:47
Alignment explanation
Indices: 40511084--40511354 Score: 133
Period size: 47 Copynumber: 5.8 Consensus size: 47
40511074 CATATTATGA
* * * * * *
40511084 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATC-AGCATTAAGAAGA
1 GAGCCAATGTAAGACCATGTCTAGGACATGACATCGA-C-TTGAGATGT
* * * * * * * * *
40511132 AAGCTAGTGTAAGACCATGTCTGGGGCATGGCATCGGCATTGAGACGA
1 GAGCCAATGTAAGACCATGTCTAGGACATGACATCGAC-TTGAGATGT
* * * * * * *
40511180 GAGCTAGTGTAAGA-CATGTCTGGGACATG-TATCGGCCTCGAGAAGT
1 GAGCCAATGTAAGACCATGTCTAGGACATGACATC-GACTTGAGATGT
* * * * * *
40511226 AAGCCAGTATAAGA-AATGTCTAGGACATG-CATTG-GTTACGAGATGAT
1 GAGCCAATGTAAGACCATGTCTAGGACATGACATCGACTT--GAGATG-T
* * *
40511273 -AGTCAATGTAAGACTATGTCTGGGACATGACATCGACTTGAGATGT
1 GAGCCAATGTAAGACCATGTCTAGGACATGACATCGACTTGAGATGT
* *
40511319 GAGCCAGTGTAAGACCATGTCTAGGACATGGCATCG
1 GAGCCAATGTAAGACCATGTCTAGGACATGACATCG
40511355 GCACCTTACC
Statistics
Matches: 179, Mismatches: 35, Indels: 19
0.77 0.15 0.08
Matches are distributed among these distances:
44 1 0.01
45 1 0.01
46 51 0.28
47 66 0.37
48 58 0.32
49 2 0.01
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (47 bp):
GAGCCAATGTAAGACCATGTCTAGGACATGACATCGACTTGAGATGT
Found at i:40512317 original size:29 final size:28
Alignment explanation
Indices: 40512264--40512319 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
40512254 ACACTGGCTA
40512264 GGACACGGGCCTGTTCTGACCGTGTGAG
1 GGACACGGGCCTGTTCTGACCGTGTGAG
* *
40512292 GGACACGGGCGTGTGTCTGGCCGTGTGA
1 GGACACGGGCCTGT-TCTGACCGTGTGA
40512320 AAACCCCTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 13 0.52
29 12 0.48
ACGTcount: A:0.12, C:0.23, G:0.43, T:0.21
Consensus pattern (28 bp):
GGACACGGGCCTGTTCTGACCGTGTGAG
Found at i:40517551 original size:46 final size:46
Alignment explanation
Indices: 40517447--40517618 Score: 190
Period size: 46 Copynumber: 3.7 Consensus size: 46
40517437 GGGGCAGGAT
* * *
40517447 GCCGATGCCATGTCCTAGACATGGTTTTACACTGGC-TCATCTCGTA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTTCATCTC-AA
* *
40517493 GTCGATGCCATGTCCCAGACAT-GTCTTGCACTGGCTTACATCTCAA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTT-CATCTCAA
* * *
40517539 GGCCGATG-CATGTCCCAGATAT-GTCTTACACTAGCTCTCGTCTCAA
1 -GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCT-TCATCTCAA
*
40517585 TGTCGATGCCATGTCCCAGACATGGTCTTACACT
1 -GCCGATGCCATGTCCCAGACATGGTCTTACACT
40517619 AGCTCACAAT
Statistics
Matches: 107, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
45 11 0.10
46 60 0.56
47 26 0.24
48 10 0.09
ACGTcount: A:0.21, C:0.30, G:0.20, T:0.29
Consensus pattern (46 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTTCATCTCAA
Found at i:40521032 original size:40 final size:35
Alignment explanation
Indices: 40520952--40521043 Score: 157
Period size: 35 Copynumber: 2.6 Consensus size: 35
40520942 TCCTCATTGA
40520952 AATACCATACCTACATTTCACAACTCAGTATGGTT
1 AATACCATACCTACATTTCACAACTCAGTATGGTT
* *
40520987 AATACCATACCTACATTTCACAAGTCAGTATAGTT
1 AATACCATACCTACATTTCACAACTCAGTATGGTT
*
40521022 AATACCATACCTACGTTTCACA
1 AATACCATACCTACATTTCACA
40521044 CTTTTCCATG
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 54 1.00
ACGTcount: A:0.36, C:0.26, G:0.08, T:0.30
Consensus pattern (35 bp):
AATACCATACCTACATTTCACAACTCAGTATGGTT
Found at i:40522513 original size:6 final size:7
Alignment explanation
Indices: 40522491--40522516 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
40522481 GGTTTATAGA
40522491 TTTGCTT
1 TTTGCTT
40522498 TTTGCTT
1 TTTGCTT
40522505 TTTGCTT
1 TTTGCTT
40522512 TTTGC
1 TTTGC
40522517 GTTTATAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.15, G:0.15, T:0.69
Consensus pattern (7 bp):
TTTGCTT
Found at i:40523363 original size:64 final size:64
Alignment explanation
Indices: 40523290--40523423 Score: 241
Period size: 64 Copynumber: 2.1 Consensus size: 64
40523280 TAATATTTCT
* *
40523290 ATATTTCTATCACGATTTTTAATAAATTTATTTATTGATATAATATGTCCCATCTAATATACAA
1 ATATTTCTATCACGAGTTTTAATAAATTTATTTATTAATATAATATGTCCCATCTAATATACAA
*
40523354 ATATTTCTATCACGAGTTTTAATAAATTTATTTATTAATATAATATGTCTCATCTAATATACAA
1 ATATTTCTATCACGAGTTTTAATAAATTTATTTATTAATATAATATGTCCCATCTAATATACAA
40523418 ATATTT
1 ATATTT
40523424 AATAAAATAT
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
64 67 1.00
ACGTcount: A:0.38, C:0.11, G:0.04, T:0.46
Consensus pattern (64 bp):
ATATTTCTATCACGAGTTTTAATAAATTTATTTATTAATATAATATGTCCCATCTAATATACAA
Found at i:40523498 original size:24 final size:24
Alignment explanation
Indices: 40523471--40523541 Score: 99
Period size: 24 Copynumber: 3.0 Consensus size: 24
40523461 ATTATTATTG
*
40523471 AAATATTCTCGTCTGTTTTATCAC
1 AAATATTATCGTCTGTTTTATCAC
*
40523495 AAATATTATTG-CTCGTTTTATCAC
1 AAATATTATCGTCT-GTTTTATCAC
*
40523519 AAATATTATCGTCCGTTTTATCA
1 AAATATTATCGTCTGTTTTATCA
40523542 TTTAAGTTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
23 2 0.05
24 38 0.93
25 1 0.02
ACGTcount: A:0.28, C:0.18, G:0.08, T:0.45
Consensus pattern (24 bp):
AAATATTATCGTCTGTTTTATCAC
Found at i:40523747 original size:29 final size:29
Alignment explanation
Indices: 40523715--40523785 Score: 124
Period size: 29 Copynumber: 2.4 Consensus size: 29
40523705 AACGACATGT
* *
40523715 ATATTATTTAATTAAAATAATTTTTTTCA
1 ATATTATTTAATTAAAATAATTTTTATAA
40523744 ATATTATTTAATTAAAATAATTTTTATAA
1 ATATTATTTAATTAAAATAATTTTTATAA
40523773 ATATTATTTAATT
1 ATATTATTTAATT
40523786 CGCAACTTAC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (29 bp):
ATATTATTTAATTAAAATAATTTTTATAA
Found at i:40523769 original size:16 final size:16
Alignment explanation
Indices: 40523721--40523769 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
40523711 ATGTATATTA
40523721 TTTAATTAAAATAATT
1 TTTAATTAAAATAATT
*
40523737 TTT--TT-CAAT-ATT
1 TTTAATTAAAATAATT
40523749 ATTTAATTAAAATAATT
1 -TTTAATTAAAATAATT
40523766 TTTA
1 TTTA
40523770 TAAATATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 10
0.68 0.05 0.26
Matches are distributed among these distances:
12 3 0.12
13 6 0.23
14 2 0.08
15 2 0.08
16 10 0.38
17 3 0.12
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (16 bp):
TTTAATTAAAATAATT
Found at i:40523927 original size:9 final size:9
Alignment explanation
Indices: 40523897--40524280 Score: 433
Period size: 9 Copynumber: 43.4 Consensus size: 9
40523887 AATATTTAAC
*
40523897 ATAACTTAC
1 ATAACTTAT
* *
40523906 AAAACTTAC
1 ATAACTTAT
40523915 ATAACTTAT
1 ATAACTTAT
*
40523924 ATAACTTAG
1 ATAACTTAT
*
40523933 ATAA-ATAT
1 ATAACTTAT
*
40523941 ATAAATTAT
1 ATAACTTAT
*
40523950 ATAACTTAC
1 ATAACTTAT
40523959 ATAACTTAT
1 ATAACTTAT
*
40523968 ATAACTTAG
1 ATAACTTAT
*
40523977 ATAA-ATAT
1 ATAACTTAT
*
40523985 ATAACTTAC
1 ATAACTTAT
40523994 ATAACTTAT
1 ATAACTTAT
*
40524003 ATAACTTAG
1 ATAACTTAT
*
40524012 ATAA-ATAT
1 ATAACTTAT
40524020 ATAACTTAT
1 ATAACTTAT
*
40524029 ATAACTTAC
1 ATAACTTAT
40524038 ATAACTTAT
1 ATAACTTAT
*
40524047 ATAACTTAG
1 ATAACTTAT
*
40524056 ATAA-ATAT
1 ATAACTTAT
*
40524064 ATAACTTAC
1 ATAACTTAT
*
40524073 ATAACTTAC
1 ATAACTTAT
40524082 ATAACTTAT
1 ATAACTTAT
*
40524091 ATAACTTAG
1 ATAACTTAT
*
40524100 ATAA-ATAT
1 ATAACTTAT
40524108 ATAACTTAT
1 ATAACTTAT
40524117 ATAACTTAT
1 ATAACTTAT
*
40524126 ATAACTTAC
1 ATAACTTAT
40524135 ATAACTTAT
1 ATAACTTAT
40524144 ATAACTTAT
1 ATAACTTAT
40524153 ATAACTTAT
1 ATAACTTAT
*
40524162 ATAACTTAG
1 ATAACTTAT
*
40524171 ATAA-ATAT
1 ATAACTTAT
40524179 ATAACTTAT
1 ATAACTTAT
40524188 ATAACTTAT
1 ATAACTTAT
*
40524197 ATAACTTAC
1 ATAACTTAT
40524206 ATAACTTAT
1 ATAACTTAT
40524215 ATAACTTAT
1 ATAACTTAT
*
40524224 ATAACTTAG
1 ATAACTTAT
*
40524233 ATAA-ATAT
1 ATAACTTAT
*
40524241 ATAACTTAC
1 ATAACTTAT
*
40524250 ATAA-ATAT
1 ATAACTTAT
* *
40524258 ATATCATAT
1 ATAACTTAT
*
40524267 CATAACTTAC
1 -ATAACTTAT
40524277 ATAA
1 ATAA
40524281 TACTTAAATA
Statistics
Matches: 315, Mismatches: 51, Indels: 18
0.82 0.13 0.05
Matches are distributed among these distances:
8 47 0.15
9 262 0.83
10 6 0.02
ACGTcount: A:0.48, C:0.12, G:0.02, T:0.38
Consensus pattern (9 bp):
ATAACTTAT
Found at i:40523956 original size:44 final size:44
Alignment explanation
Indices: 40523897--40524253 Score: 491
Period size: 44 Copynumber: 8.3 Consensus size: 44
40523887 AATATTTAAC
* *
40523897 ATAACTTACAAAACTTACATAACTTATATAACTTAGATAAATAT
1 ATAACTTATATAACTTACATAACTTATATAACTTAGATAAATAT
*
40523941 ATAAATTATATAACTTACATAACTTATATAACTTAG------AT
1 ATAACTTATATAACTTACATAACTTATATAACTTAGATAAATAT
40523979 A-AA--TATATAACTTACATAACTTATATAACTTAGATAAATAT
1 ATAACTTATATAACTTACATAACTTATATAACTTAGATAAATAT
40524020 ATAACTTATATAACTTACATAACTTATATAACTTAGATAAATAT
1 ATAACTTATATAACTTACATAACTTATATAACTTAGATAAATAT
*
40524064 ATAACTTACATAACTTACATAACTTATATAACTTAGATAAATAT
1 ATAACTTATATAACTTACATAACTTATATAACTTAGATAAATAT
* * * *
40524108 ATAACTTATATAACTTATATAACTTACATAACTTATATAACTTAT
1 ATAACTTATATAACTTACATAACTTATATAACTTAGATAA-ATAT
* * * *
40524153 ATAACTTATATAACTTAGATAA-ATATATAACTTATATAACTTAT
1 ATAACTTATATAACTTACATAACTTATATAACTTAGATAA-ATAT
* *
40524197 ATAACTTACATAACTTATATAACTTATATAACTTAGATAAATAT
1 ATAACTTATATAACTTACATAACTTATATAACTTAGATAAATAT
*
40524241 ATAACTTACATAA
1 ATAACTTATATAA
40524254 ATATATATCA
Statistics
Matches: 285, Mismatches: 17, Indels: 22
0.88 0.05 0.07
Matches are distributed among these distances:
35 30 0.11
37 2 0.01
38 3 0.01
41 3 0.01
42 2 0.01
44 206 0.72
45 39 0.14
ACGTcount: A:0.48, C:0.12, G:0.02, T:0.38
Consensus pattern (44 bp):
ATAACTTATATAACTTACATAACTTATATAACTTAGATAAATAT
Found at i:40523963 original size:35 final size:36
Alignment explanation
Indices: 40523897--40524280 Score: 442
Period size: 35 Copynumber: 10.9 Consensus size: 36
40523887 AATATTTAAC
* * * * *
40523897 ATAACTTACAAAACTTACATAACTTATATAACTTAG
1 ATAACTTATATAACTTATATAACTTACATAACTTAT
* *
40523933 ATAA-ATATATAAATTATATAACTTACATAACTTAT
1 ATAACTTATATAACTTATATAACTTACATAACTTAT
* *
40523968 ATAACTTAGATAA-ATATATAACTTACATAACTTAT
1 ATAACTTATATAACTTATATAACTTACATAACTTAT
* * * *
40524003 ATAACTTAGATAA-ATATATAACTTATATAACTTAC
1 ATAACTTATATAACTTATATAACTTACATAACTTAT
* * * *
40524038 ATAACTTATATAACTTAGATAA-ATATATAACTTAC
1 ATAACTTATATAACTTATATAACTTACATAACTTAT
* * *
40524073 ATAACTTACATAACTTATATAACTTAGATAA-ATAT
1 ATAACTTATATAACTTATATAACTTACATAACTTAT
40524108 ATAACTTATATAACTTATATAACTTACATAACTTAT
1 ATAACTTATATAACTTATATAACTTACATAACTTAT
* *
40524144 ATAACTTATATAACTTATATAACTTAGATAA-ATAT
1 ATAACTTATATAACTTATATAACTTACATAACTTAT
40524179 ATAACTTATATAACTTATATAACTTACATAACTTAT
1 ATAACTTATATAACTTATATAACTTACATAACTTAT
* * * *
40524215 ATAACTTATATAACTTAGATAA-ATATATAACTTAC
1 ATAACTTATATAACTTATATAACTTACATAACTTAT
* * *
40524250 ATAA-ATATATATCATATCATAACTTACATAA
1 ATAACTTATATAACTTAT-ATAACTTACATAA
40524281 TACTTAAATA
Statistics
Matches: 302, Mismatches: 39, Indels: 14
0.85 0.11 0.04
Matches are distributed among these distances:
34 9 0.03
35 208 0.69
36 85 0.28
ACGTcount: A:0.48, C:0.12, G:0.02, T:0.38
Consensus pattern (36 bp):
ATAACTTATATAACTTATATAACTTACATAACTTAT
Found at i:40523965 original size:53 final size:54
Alignment explanation
Indices: 40523897--40524280 Score: 388
Period size: 53 Copynumber: 7.2 Consensus size: 54
40523887 AATATTTAAC
* * * *
40523897 ATAACTTACAAAACTTACATAACTTATATAACTTAGATAA-ATATATAAATTAT
1 ATAACTTACATAACTTATATAACTTATATAACTTACATAACATATATAACTTAT
* * * * *
40523950 ATAACTTACATAACTTATATAACTTAGATAA-ATATATAACTTACATAACTTAT
1 ATAACTTACATAACTTATATAACTTATATAACTTACATAACATATATAACTTAT
* * * *
40524003 ATAACTTAGATAA-ATATATAACTTATATAACTTACATAACTTATATAACTTAG
1 ATAACTTACATAACTTATATAACTTATATAACTTACATAACATATATAACTTAT
* * * * * * * *
40524056 ATAA-ATATATAACTTACATAACTTACATAACTTATATAACTTAGATAA-ATAT
1 ATAACTTACATAACTTATATAACTTATATAACTTACATAACATATATAACTTAT
* * * *
40524108 ATAACTTATATAACTTATATAACTTACATAACTTATATAACTTATATAACTTAT
1 ATAACTTACATAACTTATATAACTTATATAACTTACATAACATATATAACTTAT
* * * * *
40524162 ATAACTTAGATAA-ATATATAACTTATATAACTTATATAACTTACATAACTTAT
1 ATAACTTACATAACTTATATAACTTATATAACTTACATAACATATATAACTTAT
* * * * *
40524215 ATAACTTATATAACTTAGATAA-ATATATAACTTACATAA-ATATATATCATAT
1 ATAACTTACATAACTTATATAACTTATATAACTTACATAACATATATAACTTAT
40524267 CATAACTTACATAA
1 -ATAACTTACATAA
40524281 TACTTAAATA
Statistics
Matches: 282, Mismatches: 42, Indels: 14
0.83 0.12 0.04
Matches are distributed among these distances:
52 42 0.15
53 219 0.78
54 21 0.07
ACGTcount: A:0.48, C:0.12, G:0.02, T:0.38
Consensus pattern (54 bp):
ATAACTTACATAACTTATATAACTTATATAACTTACATAACATATATAACTTAT
Found at i:40524908 original size:58 final size:58
Alignment explanation
Indices: 40524818--40524937 Score: 240
Period size: 58 Copynumber: 2.1 Consensus size: 58
40524808 GGAAGATATG
40524818 TTGCGGGATGCATTTAATATGCATAGTCATGGTGAGCAATCGTTTCCACCTGACTTTA
1 TTGCGGGATGCATTTAATATGCATAGTCATGGTGAGCAATCGTTTCCACCTGACTTTA
40524876 TTGCGGGATGCATTTAATATGCATAGTCATGGTGAGCAATCGTTTCCACCTGACTTTA
1 TTGCGGGATGCATTTAATATGCATAGTCATGGTGAGCAATCGTTTCCACCTGACTTTA
40524934 TTGC
1 TTGC
40524938 ATCCGATGAT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 62 1.00
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (58 bp):
TTGCGGGATGCATTTAATATGCATAGTCATGGTGAGCAATCGTTTCCACCTGACTTTA
Found at i:40526225 original size:12 final size:12
Alignment explanation
Indices: 40526208--40526232 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40526198 AAGATCGAGG
40526208 GATGAATCTGAT
1 GATGAATCTGAT
40526220 GATGAATCTGAT
1 GATGAATCTGAT
40526232 G
1 G
40526233 GAGAGGATGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.08, G:0.28, T:0.32
Consensus pattern (12 bp):
GATGAATCTGAT
Found at i:40529564 original size:13 final size:14
Alignment explanation
Indices: 40529548--40529576 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
40529538 TTCTAAATAT
40529548 TTATAA-TGTTTAA
1 TTATAATTGTTTAA
40529561 TTATAATTGTTTAA
1 TTATAATTGTTTAA
40529575 TT
1 TT
40529577 CAATTCATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (14 bp):
TTATAATTGTTTAA
Found at i:40530016 original size:21 final size:21
Alignment explanation
Indices: 40529991--40530065 Score: 98
Period size: 21 Copynumber: 3.6 Consensus size: 21
40529981 CTTAGAGCGA
*
40529991 AGGCAGCAGAGAGGGAGGCAG
1 AGGCAGCAGCGAGGGAGGCAG
* *
40530012 CGGCAGCAGCGAGAGAGGCAG
1 AGGCAGCAGCGAGGGAGGCAG
40530033 AGGCA-CGAGCGAGGGAGGCAG
1 AGGCAGC-AGCGAGGGAGGCAG
*
40530054 AGGTAGCAGCGA
1 AGGCAGCAGCGA
40530066 TGGCAGCAGA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
20 1 0.02
21 44 0.96
22 1 0.02
ACGTcount: A:0.31, C:0.19, G:0.49, T:0.01
Consensus pattern (21 bp):
AGGCAGCAGCGAGGGAGGCAG
Found at i:40530359 original size:31 final size:31
Alignment explanation
Indices: 40530313--40530379 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
40530303 TGGTTGTATT
* *
40530313 TTTTATGCTAAATTTGCTGTTTTTGGCTGCA
1 TTTTATACTAAATTTGCTGTATTTGGCTGCA
* * * *
40530344 TTTTATACTATATTTGTTGTATTTGGTTGGA
1 TTTTATACTAAATTTGCTGTATTTGGCTGCA
40530375 TTTTA
1 TTTTA
40530380 ATGCAGGAAG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.18, C:0.07, G:0.18, T:0.57
Consensus pattern (31 bp):
TTTTATACTAAATTTGCTGTATTTGGCTGCA
Found at i:40531653 original size:19 final size:19
Alignment explanation
Indices: 40531626--40531690 Score: 60
Period size: 19 Copynumber: 3.2 Consensus size: 19
40531616 AAAGTTATAA
*
40531626 AAAAATCAAAATAATTTTT
1 AAAATTCAAAATAATTTTT
*
40531645 AAAATTCAAAAT-ATTTATA
1 AAAATTCAAAATAATTT-TT
40531664 AAAATTCTAAAATTTATATTTTT
1 AAAATTC-AAAA--TA-ATTTTT
40531687 AAAA
1 AAAA
40531691 AATTATAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
18 4 0.11
19 19 0.51
20 4 0.11
22 1 0.03
23 5 0.14
24 4 0.11
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (19 bp):
AAAATTCAAAATAATTTTT
Found at i:40531708 original size:18 final size:18
Alignment explanation
Indices: 40531672--40531714 Score: 63
Period size: 17 Copynumber: 2.4 Consensus size: 18
40531662 TAAAAATTCT
40531672 AAAATT-TATATTTTTAA
1 AAAATTATATATTTTTAA
40531689 AAAATTATA-ATTTTTAAA
1 AAAATTATATATTTTT-AA
40531707 AAAATTAT
1 AAAATTAT
40531715 CTAAAGAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.50
18 12 0.50
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
AAAATTATATATTTTTAA
Found at i:40532630 original size:41 final size:41
Alignment explanation
Indices: 40532573--40532657 Score: 152
Period size: 41 Copynumber: 2.1 Consensus size: 41
40532563 GACAGATTAC
*
40532573 ATTCTTAAAAAAACTCAAGTTTGAAATTTGAAAATGACATT
1 ATTCTTAAAAAAACTCAAGTTTAAAATTTGAAAATGACATT
*
40532614 ATTCTTAAAAAGACTCAAGTTTAAAATTTGAAAATGACATT
1 ATTCTTAAAAAAACTCAAGTTTAAAATTTGAAAATGACATT
40532655 ATT
1 ATT
40532658 AAAAATGTCA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.46, C:0.09, G:0.09, T:0.35
Consensus pattern (41 bp):
ATTCTTAAAAAAACTCAAGTTTAAAATTTGAAAATGACATT
Found at i:40533412 original size:2 final size:2
Alignment explanation
Indices: 40533405--40533430 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
40533395 CCTATGGCCC
40533405 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
40533431 TAATCAATGG
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:40537598 original size:20 final size:20
Alignment explanation
Indices: 40537573--40537622 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
40537563 GTAAGACCAC
*
40537573 TATTGGTAAATTATTAAAAA
1 TATTGGTAAATAATTAAAAA
* *
40537593 TATTGGTAAATAATTAGATA
1 TATTGGTAAATAATTAAAAA
*
40537613 TTTTGGTAAA
1 TATTGGTAAA
40537623 AGCATTTTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.44, C:0.00, G:0.14, T:0.42
Consensus pattern (20 bp):
TATTGGTAAATAATTAAAAA
Found at i:40544426 original size:20 final size:20
Alignment explanation
Indices: 40544403--40544466 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
40544393 TATATTTCTA
40544403 TAAATTGAATTATTAGCCAT
1 TAAATTGAATTATTAGCCAT
* * *
40544423 TAAATCGCATATT-TTA--AAA
1 TAAATTG-A-ATTATTAGCCAT
40544442 TAAATTGAATTATTAGCCAT
1 TAAATTGAATTATTAGCCAT
40544462 TAAAT
1 TAAAT
40544467 CGCATGTTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 10
0.67 0.12 0.20
Matches are distributed among these distances:
17 3 0.09
18 4 0.12
19 7 0.21
20 12 0.36
21 4 0.12
22 3 0.09
ACGTcount: A:0.44, C:0.09, G:0.08, T:0.39
Consensus pattern (20 bp):
TAAATTGAATTATTAGCCAT
Found at i:40544445 original size:39 final size:38
Alignment explanation
Indices: 40544402--40544483 Score: 146
Period size: 39 Copynumber: 2.1 Consensus size: 38
40544392 TTATATTTCT
40544402 ATAAATTGAATTATTAGCCATTAAATCGCATATTTTAAA
1 ATAAATTGAATTATTAGCCATTAAATCGCATATTTT-AA
*
40544441 ATAAATTGAATTATTAGCCATTAAATCGCATGTTTTAA
1 ATAAATTGAATTATTAGCCATTAAATCGCATATTTTAA
40544479 ATAAA
1 ATAAA
40544484 ACCTGAAAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
38 7 0.17
39 35 0.83
ACGTcount: A:0.44, C:0.10, G:0.09, T:0.38
Consensus pattern (38 bp):
ATAAATTGAATTATTAGCCATTAAATCGCATATTTTAA
Found at i:40545150 original size:8 final size:8
Alignment explanation
Indices: 40545137--40545170 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
40545127 ATATGTATAC
40545137 TTGTGAAA
1 TTGTGAAA
40545145 TTGTGAAA
1 TTGTGAAA
*
40545153 CTGTGAAA
1 TTGTGAAA
*
40545161 CTGTGAAA
1 TTGTGAAA
40545169 TT
1 TT
40545171 ATAAATATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.35, C:0.06, G:0.24, T:0.35
Consensus pattern (8 bp):
TTGTGAAA
Found at i:40551244 original size:46 final size:46
Alignment explanation
Indices: 40551083--40551256 Score: 176
Period size: 46 Copynumber: 3.8 Consensus size: 46
40551073 TAACCCACCC
* * * *
40551083 ATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCC
1 ATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCT
* * * *
40551129 ATAAGTGAACTTGGACTCAACTCAACGAGCTTAGATGCCTAGTT-ACATCT
1 ATAAGTGAACTCGGACTCAACTCAACGAG-TTCG--GAC-A-TTCGCATCT
* *
40551179 CT---CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCT
1 ATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCT
*
40551222 ATAAGTGAACTCGGACTCAACTCAATGAGTTCGGA
1 ATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
40551257 TGCTCAACCA
Statistics
Matches: 103, Mismatches: 16, Indels: 18
0.75 0.12 0.13
Matches are distributed among these distances:
42 2 0.02
43 7 0.07
44 2 0.02
46 59 0.57
47 24 0.23
49 2 0.02
50 5 0.05
51 2 0.02
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (46 bp):
ATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCT
Found at i:40555143 original size:5 final size:5
Alignment explanation
Indices: 40555133--40555220 Score: 135
Period size: 5 Copynumber: 17.8 Consensus size: 5
40555123 TTTAGAAGAA
* *
40555133 AATAC AATAC AATTC AGA-A- AATAC AATTC AATAC AATAC AATAC AATAC
1 AATAC AATAC AATAC A-ATAC AATAC AATAC AATAC AATAC AATAC AATAC
40555182 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATA
1 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATA
40555221 GAATTTAGTT
Statistics
Matches: 76, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
3 1 0.01
4 2 0.03
5 72 0.95
6 1 0.01
ACGTcount: A:0.59, C:0.18, G:0.01, T:0.22
Consensus pattern (5 bp):
AATAC
Found at i:40558374 original size:12 final size:12
Alignment explanation
Indices: 40558351--40558388 Score: 58
Period size: 13 Copynumber: 3.0 Consensus size: 12
40558341 TAAGGTTATC
40558351 AAAAGAGAAAAGG
1 AAAAG-GAAAAGG
40558364 AAAAGGAAAAGG
1 AAAAGGAAAAGG
40558376 AAAAGGGAAAAGG
1 AAAA-GGAAAAGG
40558389 GAAATAGTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 11 0.46
13 13 0.54
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (12 bp):
AAAAGGAAAAGG
Found at i:40558392 original size:7 final size:6
Alignment explanation
Indices: 40558351--40558388 Score: 58
Period size: 6 Copynumber: 6.0 Consensus size: 6
40558341 TAAGGTTATC
40558351 AAAAGAG AAAAGG AAAAGG AAAAGG AAAAGGG AAAAGG
1 AAAAG-G AAAAGG AAAAGG AAAAGG AAAA-GG AAAAGG
40558389 GAAATAGTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
6 19 0.63
7 11 0.37
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (6 bp):
AAAAGG
Found at i:40558616 original size:40 final size:40
Alignment explanation
Indices: 40558558--40558704 Score: 186
Period size: 40 Copynumber: 3.7 Consensus size: 40
40558548 CGTTTGACAA
* * **
40558558 AAAACGCCGCTATGGATTGAGCATTAGTGTTGCTTTTTGG
1 AAAACGCCGCTATAGATCGAGCATTAGTGACGCTTTTTGG
* *
40558598 AAAACGCCGCTATAGATTGAGCATTAGTGGCGCTTTTTGG
1 AAAACGCCGCTATAGATCGAGCATTAGTGACGCTTTTTGG
* * *
40558638 AAAATGCCGCTATAGATCGAGCATTAGCGACGCTTTTTAG
1 AAAACGCCGCTATAGATCGAGCATTAGTGACGCTTTTTGG
* * *
40558678 AAAACACCACTATAAATCGAGCATTAG
1 AAAACGCCGCTATAGATCGAGCATTAG
40558705 GTTTGAGAAA
Statistics
Matches: 95, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 95 1.00
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (40 bp):
AAAACGCCGCTATAGATCGAGCATTAGTGACGCTTTTTGG
Found at i:40558836 original size:40 final size:41
Alignment explanation
Indices: 40558781--40558885 Score: 131
Period size: 41 Copynumber: 2.6 Consensus size: 41
40558771 AGCTTTAGTG
* **
40558781 GCATTAGCGGCGCTTTATG-GGAAACGCCGCTATAGATCGA
1 GCATTAGCGGTGCTTTATGAAAAAACGCCGCTATAGATCGA
* *
40558821 GCATTAGCGGTGCTTTTTGAAAAAACGCCGCTATAGGTCGA
1 GCATTAGCGGTGCTTTATGAAAAAACGCCGCTATAGATCGA
* * *
40558862 GCTTTAGCGATGCTTTTTGAAAAA
1 GCATTAGCGGTGCTTTATGAAAAA
40558886 TGCCAAAAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
40 17 0.30
41 40 0.70
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.28
Consensus pattern (41 bp):
GCATTAGCGGTGCTTTATGAAAAAACGCCGCTATAGATCGA
Found at i:40558862 original size:41 final size:41
Alignment explanation
Indices: 40558802--40558885 Score: 141
Period size: 41 Copynumber: 2.0 Consensus size: 41
40558792 GCTTTATGGG
*
40558802 AAACGCCGCTATAGATCGAGCATTAGCGGTGCTTTTTGAAA
1 AAACGCCGCTATAGATCGAGCATTAGCGATGCTTTTTGAAA
* *
40558843 AAACGCCGCTATAGGTCGAGCTTTAGCGATGCTTTTTGAAA
1 AAACGCCGCTATAGATCGAGCATTAGCGATGCTTTTTGAAA
40558884 AA
1 AA
40558886 TGCCAAAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (41 bp):
AAACGCCGCTATAGATCGAGCATTAGCGATGCTTTTTGAAA
Found at i:40559219 original size:14 final size:14
Alignment explanation
Indices: 40559202--40559307 Score: 63
Period size: 14 Copynumber: 7.4 Consensus size: 14
40559192 TATAGTTTTG
40559202 GGTTTAGGGTTTAT
1 GGTTTAGGGTTTAT
* *
40559216 GGTTTAAGGTATAT
1 GGTTTAGGGTTTAT
* *
40559230 AGTTTAGGGTTTAA
1 GGTTTAGGGTTTAT
*
40559244 GGTTTAGAAGTTACTAT
1 GGTTTAG-GGTT--TAT
*
40559261 --TTTAAGGTTTAT
1 GGTTTAGGGTTTAT
* * *
40559273 GGATTATGAGTTTAG
1 GGTTTA-GGGTTTAT
* *
40559288 GGATTATGGTTTAT
1 GGTTTAGGGTTTAT
40559302 GGTTTA
1 GGTTTA
40559308 AGGATTGGGG
Statistics
Matches: 67, Mismatches: 19, Indels: 12
0.68 0.19 0.12
Matches are distributed among these distances:
12 3 0.04
14 44 0.66
15 18 0.27
17 2 0.03
ACGTcount: A:0.25, C:0.01, G:0.28, T:0.46
Consensus pattern (14 bp):
GGTTTAGGGTTTAT
Found at i:40559286 original size:22 final size:21
Alignment explanation
Indices: 40559261--40559313 Score: 70
Period size: 22 Copynumber: 2.5 Consensus size: 21
40559251 AAGTTACTAT
*
40559261 TTTAAGGTTTATGGATTATGAG
1 TTTAAGGATTATGGATTATG-G
* *
40559283 TTTAGGGATTATGGTTTATGG
1 TTTAAGGATTATGGATTATGG
40559304 TTTAAGGATT
1 TTTAAGGATT
40559314 GGGGTTTAGG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
21 10 0.37
22 17 0.63
ACGTcount: A:0.25, C:0.00, G:0.28, T:0.47
Consensus pattern (21 bp):
TTTAAGGATTATGGATTATGG
Found at i:40559291 original size:15 final size:14
Alignment explanation
Indices: 40559266--40559300 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
40559256 ACTATTTTAA
*
40559266 GGTTTATGGATTAT
1 GGTTTAGGGATTAT
40559280 GAGTTTAGGGATTAT
1 G-GTTTAGGGATTAT
40559295 GGTTTA
1 GGTTTA
40559301 TGGTTTAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.23, C:0.00, G:0.31, T:0.46
Consensus pattern (14 bp):
GGTTTAGGGATTAT
Found at i:40559319 original size:21 final size:22
Alignment explanation
Indices: 40559261--40559321 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 22
40559251 AAGTTACTAT
* * *
40559261 TTTAAGGTTTATGGATTATGAG
1 TTTAAGGATTAGGGTTTATGAG
* *
40559283 TTTAGGGATTATGGTTTATG-G
1 TTTAAGGATTAGGGTTTATGAG
*
40559304 TTTAAGGATTGGGGTTTA
1 TTTAAGGATTAGGGTTTA
40559322 GGGGCTAGGG
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 16 0.48
22 17 0.52
ACGTcount: A:0.23, C:0.00, G:0.31, T:0.46
Consensus pattern (22 bp):
TTTAAGGATTAGGGTTTATGAG
Found at i:40564858 original size:43 final size:43
Alignment explanation
Indices: 40564709--40564885 Score: 205
Period size: 42 Copynumber: 4.2 Consensus size: 43
40564699 TTTGATATGG
* *
40564709 TCTTTAGTGGCGTTTTTGGGGAAAGCGTCGCTAAAGGTCAT-A
1 TCTTTAGCGGCGTTTTTGGGGAAAGCGTCGCTAAAGGTCATGT
** * * * **
40564751 TCTTTAGCGGCGTTTAAGGAGAAAGTGTCGTTAAATATCATG-
1 TCTTTAGCGGCGTTTTTGGGGAAAGCGTCGCTAAAGGTCATGT
* * *
40564793 TCTTTAGCGGCATTTTTAGGGAAAGCGACGCTAAAGGTCATGT
1 TCTTTAGCGGCGTTTTTGGGGAAAGCGTCGCTAAAGGTCATGT
* * *
40564836 TCTTTAGCGACGTTTCTGGGGAAAGCGCCGCTAAAGGTCATGT
1 TCTTTAGCGGCGTTTTTGGGGAAAGCGTCGCTAAAGGTCATGT
40564879 TCTTTAG
1 TCTTTAG
40564886 TGCATTTTTG
Statistics
Matches: 110, Mismatches: 23, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
42 65 0.59
43 45 0.41
ACGTcount: A:0.24, C:0.16, G:0.28, T:0.32
Consensus pattern (43 bp):
TCTTTAGCGGCGTTTTTGGGGAAAGCGTCGCTAAAGGTCATGT
Found at i:40564891 original size:85 final size:83
Alignment explanation
Indices: 40564708--40564894 Score: 212
Period size: 85 Copynumber: 2.2 Consensus size: 83
40564698 ATTTGATATG
* * * *
40564708 GTCTTTAGTGGCGTTTTTGGGGAAAGCGTCGCTAAAGGTCATATCTTTAGCGGCGTTTAAGGAGA
1 GTCTTTAGT-GCATTTTTAGGGAAAGCGACGCTAAAGGTCATATCTTTAGCGACGTTTAAGGAGA
* * * *
40564773 AAGTGTCGTTAAATATCAT
65 AAGCGCCGCTAAAGATCAT
* * ** *
40564792 GTCTTTAGCGGCATTTTTAGGGAAAGCGACGCTAAAGGTCATGTTCTTTAGCGACGTTTCTGGGG
1 GTCTTTAG-TGCATTTTTAGGGAAAGCGACGCTAAAGGTCAT-ATCTTTAGCGACGTTTAAGGAG
*
40564857 AAAGCGCCGCTAAAGGTCAT
64 AAAGCGCCGCTAAAGATCAT
40564877 GTTCTTTAGTGCATTTTT
1 G-TCTTTAGTGCATTTTT
40564895 GGCAAATAAA
Statistics
Matches: 85, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
84 37 0.44
85 41 0.48
86 7 0.08
ACGTcount: A:0.23, C:0.16, G:0.28, T:0.34
Consensus pattern (83 bp):
GTCTTTAGTGCATTTTTAGGGAAAGCGACGCTAAAGGTCATATCTTTAGCGACGTTTAAGGAGAA
AGCGCCGCTAAAGATCAT
Found at i:40565839 original size:23 final size:24
Alignment explanation
Indices: 40565813--40565869 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
40565803 ATAATTTTAA
40565813 TAAATAATTATGG-ATTTTGAACC
1 TAAATAATTATGGAATTTTGAACC
* *
40565836 TAAAAGAATT-TGGAATTTTGAACG
1 T-AAATAATTATGGAATTTTGAACC
*
40565860 TAAATTATTA
1 TAAATAATTA
40565870 ATGTATATGC
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
23 10 0.37
24 17 0.63
ACGTcount: A:0.42, C:0.05, G:0.14, T:0.39
Consensus pattern (24 bp):
TAAATAATTATGGAATTTTGAACC
Found at i:40565845 original size:24 final size:24
Alignment explanation
Indices: 40565818--40565863 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
40565808 TTTAATAAAT
40565818 AATTATGG-ATTTTGAACCTAAAAG
1 AATT-TGGAATTTTGAACCTAAAAG
*
40565842 AATTTGGAATTTTGAACGTAAA
1 AATTTGGAATTTTGAACCTAAA
40565864 TTATTAATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 3 0.15
24 17 0.85
ACGTcount: A:0.41, C:0.07, G:0.17, T:0.35
Consensus pattern (24 bp):
AATTTGGAATTTTGAACCTAAAAG
Found at i:40567555 original size:21 final size:22
Alignment explanation
Indices: 40567517--40567557 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
40567507 TTTTTGCGTA
* *
40567517 TTAATTTTTTATTCAAATATTC
1 TTAAATTTTGATTCAAATATTC
40567539 TTAAATTTTGATT-AAATAT
1 TTAAATTTTGATTCAAATAT
40567558 CTGCATCTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (22 bp):
TTAAATTTTGATTCAAATATTC
Found at i:40575018 original size:17 final size:18
Alignment explanation
Indices: 40574986--40575025 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
40574976 TTGGTAAAAC
*
40574986 ATTTTATTGGAAACAACG
1 ATTTTATTGCAAACAACG
*
40575004 ATTTTA-TGCAAACAATG
1 ATTTTATTGCAAACAACG
40575021 ATTTT
1 ATTTT
40575026 CTTAAAAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (18 bp):
ATTTTATTGCAAACAACG
Found at i:40579173 original size:14 final size:14
Alignment explanation
Indices: 40579154--40579182 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
40579144 TTTGGGTTAT
40579154 CGTGGATTGATTGA
1 CGTGGATTGATTGA
40579168 CGTGGATTGATTGA
1 CGTGGATTGATTGA
40579182 C
1 C
40579183 CAAGTCTGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.10, G:0.34, T:0.34
Consensus pattern (14 bp):
CGTGGATTGATTGA
Found at i:40598203 original size:6 final size:6
Alignment explanation
Indices: 40598186--40598269 Score: 161
Period size: 6 Copynumber: 14.2 Consensus size: 6
40598176 AAAGTGCTTT
40598186 TATATG -ATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
40598233 TATATG TATATG TATATG TATATG TATATG TATATG T
1 TATATG TATATG TATATG TATATG TATATG TATATG T
40598270 TAATGGCTTC
Statistics
Matches: 77, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.06
6 72 0.94
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (6 bp):
TATATG
Found at i:40602197 original size:15 final size:15
Alignment explanation
Indices: 40602179--40602210 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
40602169 AGCTATATTT
40602179 ATATATGCCCAATCA
1 ATATATGCCCAATCA
40602194 ATATATGCCCAATCA
1 ATATATGCCCAATCA
40602209 AT
1 AT
40602211 CCCTCTACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.25, G:0.06, T:0.28
Consensus pattern (15 bp):
ATATATGCCCAATCA
Found at i:40623478 original size:18 final size:18
Alignment explanation
Indices: 40623436--40623478 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
40623426 GCCCATTCCG
*
40623436 AAGTATATATATATACAT
1 AAGTATGTATATATACAT
40623454 ATA-TATGTATATATACAT
1 A-AGTATGTATATATACAT
40623472 AAGTATG
1 AAGTATG
40623479 CCCATTCGTG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 1 0.05
18 20 0.91
19 1 0.05
ACGTcount: A:0.47, C:0.05, G:0.09, T:0.40
Consensus pattern (18 bp):
AAGTATGTATATATACAT
Found at i:40624000 original size:27 final size:28
Alignment explanation
Indices: 40623916--40624013 Score: 128
Period size: 27 Copynumber: 3.5 Consensus size: 28
40623906 CATGAGATTG
* * *
40623916 GCACTAAGTGTGCGGGTTTAAATTGT-TCA
1 GCACTAAGTGTGCGAGTTT-GATTATAT-A
40623945 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
40623973 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
40624000 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
40624014 GACTTAATAT
Statistics
Matches: 64, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
27 24 0.38
28 21 0.33
29 19 0.30
ACGTcount: A:0.26, C:0.13, G:0.29, T:0.33
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:40624027 original size:29 final size:27
Alignment explanation
Indices: 40623944--40624027 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 27
40623934 TAAATTGTTC
* *
40623944 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTAATTATAT
* *
40623972 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTAATTATAT
*
40623999 AGCACTGAGTGTGCGGACTTAATATATAT
1 AGCACTAAGTGTGC-GACTTAAT-TATAT
40624028 TTTTGAATCA
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 23 0.46
28 22 0.44
29 5 0.10
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTAATTATAT
Found at i:40631901 original size:56 final size:56
Alignment explanation
Indices: 40631810--40631929 Score: 222
Period size: 56 Copynumber: 2.1 Consensus size: 56
40631800 ACAAGGGATG
*
40631810 ATGGACAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
*
40631866 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
40631922 ATGGGCAA
1 ATGGGCAA
40631930 TAAACTAATA
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 62 1.00
ACGTcount: A:0.46, C:0.09, G:0.23, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:40633428 original size:47 final size:47
Alignment explanation
Indices: 40633374--40634068 Score: 979
Period size: 47 Copynumber: 14.6 Consensus size: 47
40633364 TATTTGAATA
*
40633374 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
*
40633421 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCAATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
40633470 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
40633519 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* * *
40633566 AATGTGAAAGTGTATATATGTGATAAGGCCTAATCGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
40633613 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCGAATGGCCAATGTGATG
40633662 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
40633709 AATGTGAAAGTGTATATATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTG----TATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
40633760 AATGTGAACA-TGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAA-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
40633807 AATGTGAACA-TGCATATATGAGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAA-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
40633854 AATGTGAACA-TG-AGTATGTGTGATAAGGCCGAATGGCCAATTTGATG
1 AATGTGAA-AGTGTA-TATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
40633901 AATGTGAACA-TGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAA-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* * *
40633948 AATGTGAACA-TGCATATATGAGATAAGGCCGAATGGCTAATGTGATG
1 AATGTGAA-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
40633995 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* * *
40634042 GATGTGGAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
40634069 TCCCGAGGGG
Statistics
Matches: 609, Mismatches: 27, Indels: 24
0.92 0.04 0.04
Matches are distributed among these distances:
46 2 0.00
47 420 0.69
49 141 0.23
51 45 0.07
52 1 0.00
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.28
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
Found at i:40633729 original size:192 final size:188
Alignment explanation
Indices: 40633374--40634068 Score: 979
Period size: 192 Copynumber: 3.6 Consensus size: 188
40633364 TATTTGAATA
*
40633374 AATGTGAA-AGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATAT
1 AATGTGAACA-TGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG--TAT
* *
40633438 ATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCT
63 ATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCG
* * *
40633503 AATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
126 AATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* * *
40633566 AATGTGAA-AGTGTATATATGTGATAAGGCCTAATCGCCGATGTGATGAATGTGAAAGTGTATAT
1 AATGTGAACA-TGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG--TAT
* *
40633630 ATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAA
63 ATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAA
40633695 TGGCCAATGTGATGAATGTGAAAGTGTATATATATATGTGATAAGGCCGAATGGCCAATGTGATG
128 TGGCCAATGTGATGAATGTGAAAGTG----TATATATGTGATAAGGCCGAATGGCCAATGTGATG
* * *
40633760 AATGTGAACATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA-TGCATAT
1 AATGTGAACATGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA-AGTGTATAT
* *
40633824 ATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA-TG-AGTATGTGTGATAAGGCCGAA
65 ATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA-AGTGTA-TATATGTGATAAGGCCGAA
* * *
40633887 TGGCCAATTTGATGAATGTGAACA-TGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATG
128 TGGCCAATGTGATGAATGTGAA-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* * *
40633948 AATGTGAACATGCATATATGAGATAAGGCCGAATGGCTAATGTGATGAATGTGAAAGTGTATATA
1 AATGTGAACATGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATA
* * *
40634013 TGTGATAAGGCCGAATGGCCAATGTGATGGATGTGGAAGTGTATAAATGTGATAAG
66 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAAG
40634069 TCCCGAGGGG
Statistics
Matches: 460, Mismatches: 31, Indels: 28
0.89 0.06 0.05
Matches are distributed among these distances:
187 2 0.00
188 137 0.30
189 1 0.00
190 45 0.10
191 1 0.00
192 187 0.41
193 2 0.00
194 83 0.18
195 2 0.00
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.28
Consensus pattern (188 bp):
AATGTGAACATGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATA
TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGG
CCAATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
Found at i:40643117 original size:18 final size:17
Alignment explanation
Indices: 40643073--40643122 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 17
40643063 ATCCGGTTCG
40643073 ATTAAATAAAATATTAAAA
1 ATTAAAT-AAA-ATTAAAA
*
40643092 ATT-TATAAAATTAAAA
1 ATTAAATAAAATTAAAA
40643108 ATATAAATAAAATTA
1 AT-TAAATAAAATTA
40643123 GATCAATTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 9 0.33
17 4 0.15
18 11 0.41
19 3 0.11
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
ATTAAATAAAATTAAAA
Found at i:40643459 original size:13 final size:13
Alignment explanation
Indices: 40643441--40643466 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40643431 CAATTAAAGG
40643441 GTTAAAATTTAAA
1 GTTAAAATTTAAA
40643454 GTTAAAATTTAAA
1 GTTAAAATTTAAA
40643467 TATGATAATC
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:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (13 bp):
GTTAAAATTTAAA
Found at i:40647594 original size:17 final size:17
Alignment explanation
Indices: 40647569--40647608 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
40647559 ATTGGGAAAG
*
40647569 TTAGCAAAATGGCCGTT
1 TTAGTAAAATGGCCGTT
40647586 TTAGTAAAATGGCCGTT
1 TTAGTAAAATGGCCGTT
40647603 TTAGTA
1 TTAGTA
40647609 TCGAGGTAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.30, C:0.12, G:0.23, T:0.35
Consensus pattern (17 bp):
TTAGTAAAATGGCCGTT
Found at i:40652574 original size:68 final size:66
Alignment explanation
Indices: 40652502--40652651 Score: 169
Period size: 67 Copynumber: 2.2 Consensus size: 66
40652492 CATCATGTGT
* * * *
40652502 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGTGATACTA-TG-TGTACACCA
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGATACCAGTGAAGGACACCA
40652565 TGTAG
62 TGTAG
** * *
40652570 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGATACCA-GTGAAGGACACCATGT
40652635 AG
65 AG
40652637 ACAAGAGAGCTACGA
1 ACAAGAGAGCTACGA
40652652 GATAAACTGG
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
64 24 0.34
65 3 0.04
66 4 0.06
67 26 0.37
68 13 0.19
ACGTcount: A:0.32, C:0.17, G:0.29, T:0.21
Consensus pattern (66 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGATACCAGTGAAGGACACCATGTA
G
Found at i:40652607 original size:64 final size:64
Alignment explanation
Indices: 40652526--40652709 Score: 194
Period size: 67 Copynumber: 2.8 Consensus size: 64
40652516 AGACATTATG
* * *
40652526 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * *
40652590 ATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTA--TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
40652655 AA
63 AA
* * * *
40652657 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCAAGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAG-ACAAGAGAGC
40652710 CGAACTATAT
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 18 0.18
64 25 0.26
66 21 0.21
67 31 0.32
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.22
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:40654398 original size:12 final size:10
Alignment explanation
Indices: 40654373--40654399 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
40654363 TGACATTATG
40654373 ATATATTTTA
1 ATATATTTTA
40654383 ATATATTTTA
1 ATATATTTTA
40654393 ATATATT
1 ATATATT
40654400 ATATTTTGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
ATATATTTTA
Found at i:40657064 original size:26 final size:27
Alignment explanation
Indices: 40657035--40657099 Score: 69
Period size: 32 Copynumber: 2.3 Consensus size: 27
40657025 CGCAAGTAAG
40657035 TTTTAA-AATTTGATAAATATTCATCT
1 TTTTAATAATTTGATAAATATTCATCT
*
40657061 TTTTAATTTGTTTATTTGATAAATATTCATCT
1 TTTTAA-----TAATTTGATAAATATTCATCT
40657093 TTTTAAT
1 TTTTAAT
40657100 TTGTTTATCT
Statistics
Matches: 32, Mismatches: 1, Indels: 11
0.73 0.02 0.25
Matches are distributed among these distances:
26 6 0.19
27 1 0.03
32 25 0.78
ACGTcount: A:0.32, C:0.06, G:0.05, T:0.57
Consensus pattern (27 bp):
TTTTAATAATTTGATAAATATTCATCT
Found at i:40657083 original size:32 final size:32
Alignment explanation
Indices: 40657042--40657107 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
40657032 AAGTTTTAAA
40657042 ATTTGATAAATATTCATCTTTTTAATTTGTTT
1 ATTTGATAAATATTCATCTTTTTAATTTGTTT
40657074 ATTTGATAAATATTCATCTTTTTAATTTGTTT
1 ATTTGATAAATATTCATCTTTTTAATTTGTTT
40657106 AT
1 AT
40657108 CTTCTAACCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.29, C:0.06, G:0.06, T:0.59
Consensus pattern (32 bp):
ATTTGATAAATATTCATCTTTTTAATTTGTTT
Found at i:40659952 original size:64 final size:66
Alignment explanation
Indices: 40659847--40660000 Score: 168
Period size: 67 Copynumber: 2.3 Consensus size: 66
40659837 CATCGTGTGT
* * * * * *
40659847 ACAAGAGAGCTACAAGACATTATGATGTAGCTTGGTCGCATGGGTGATACTA-TG-TGTACACCA
1 ACAAGAGAGCTAC--GAGA-TAT-ATGTAGCTAGGTCGCATGCGTGATACCAGTGAAGGACACCA
40659910 TGTAG
62 TGTAG
* * *
40659915 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACACCATGT
1 ACAAGAGAGCTACGAGATATATGTAGCTAGGTCGCATGCGTGATACCA-GTGAAGGACACCATGT
40659980 AG
65 AG
40659982 ACAAGAGAGCTACGAGATA
1 ACAAGAGAGCTACGAGATA
40660001 AATTGGCTAG
Statistics
Matches: 73, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
64 23 0.32
65 3 0.04
66 4 0.05
67 30 0.41
68 13 0.18
ACGTcount: A:0.32, C:0.17, G:0.29, T:0.22
Consensus pattern (66 bp):
ACAAGAGAGCTACGAGATATATGTAGCTAGGTCGCATGCGTGATACCAGTGAAGGACACCATGTA
G
Found at i:40662936 original size:40 final size:40
Alignment explanation
Indices: 40662735--40662922 Score: 306
Period size: 40 Copynumber: 4.7 Consensus size: 40
40662725 ATTCGGATTG
40662735 ATAACCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
40662774 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* * * *
40662814 ATAACCGGGCCAAGTCCCAAAGGCAATTGTGCTAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
40662854 ATAACCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
40662894 ATAACCGGGCTAAGTCCTGAAGGCATTTG
1 ATAACCGGGCTAAGTCCCGAAGGCATTTG
40662923 AGCCAGAAGC
Statistics
Matches: 137, Mismatches: 11, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
39 13 0.09
40 124 0.91
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.24
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:40662936 original size:80 final size:80
Alignment explanation
Indices: 40662735--40662955 Score: 304
Period size: 80 Copynumber: 2.8 Consensus size: 80
40662725 ATTCGGATTG
*
40662735 ATAACCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCA
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCCAGTTACTATATCCGGGCTAAGTCCCGAAGGCA
*
40662799 TTTGTGCGAGTTACT
66 ATTGTGCGAGTTACT
* * * * *
40662814 ATAACCGGGCCAAGTCCCAAAGGCAATTGTGCTAGTTACTATAACCGGGCTAAGTCCCGAAGGCA
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCCAGTTACTATATCCGGGCTAAGTCCCGAAGGCA
40662879 ATTGTGCGAGTTACT
66 ATTGTGCGAGTTACT
* * * **
40662894 ATAACCGGGCTAAGTCCTGAAGGCATTTGAGCCAG-AAGCTATATCC-GGCTAAACCCCGAAGG
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCCAGTTA-CTATATCCGGGCTAAGTCCCGAAGG
40662956 TACTTGGTTT
Statistics
Matches: 124, Mismatches: 16, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
79 28 0.23
80 96 0.77
ACGTcount: A:0.28, C:0.24, G:0.26, T:0.22
Consensus pattern (80 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCCAGTTACTATATCCGGGCTAAGTCCCGAAGGCA
ATTGTGCGAGTTACT
Found at i:40670866 original size:80 final size:79
Alignment explanation
Indices: 40670679--40670938 Score: 362
Period size: 80 Copynumber: 3.3 Consensus size: 79
40670669 ATTCGGATTG
* * * * *
40670679 ATAACCGGGCTAAG-CCCGAAGGCATTTGTGAGAGTTACTATATCCGGGCCAAGTCCCGAAAGCA
1 ATAACCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCA
*
40670743 TTTGTGCGAGTACT
66 ATTGTGCGAGTACT
*
40670757 ATAACCGGGCCAAGTCCCGAAGGCAATTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCA
1 ATAACCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCA
*
40670822 ATTGTGCTAGTTACT
66 ATTGTGCGAG-TACT
40670837 ATAACCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCA
1 ATAACCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCA
* * *
40670902 TTTGAGCGAGAAGCT
66 ATTGTGCGAGTA-CT
* **
40670917 ATATCC-GGCTAAACCCCGAAGG
1 ATAACCGGGCTAAGTCCCGAAGG
40670939 TACTTGGTTT
Statistics
Matches: 163, Mismatches: 16, Indels: 5
0.89 0.09 0.03
Matches are distributed among these distances:
78 13 0.08
79 68 0.42
80 82 0.50
ACGTcount: A:0.28, C:0.24, G:0.27, T:0.21
Consensus pattern (79 bp):
ATAACCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCA
ATTGTGCGAGTACT
Found at i:40670919 original size:40 final size:40
Alignment explanation
Indices: 40670679--40670911 Score: 362
Period size: 40 Copynumber: 5.9 Consensus size: 40
40670669 ATTCGGATTG
* *
40670679 ATAACCGGGCTAAG-CCCGAAGGCATTTGTGAGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACT
* * * *
40670718 ATATCCGGGCCAAGTCCCGAAAGCATTTGTGCGAG-TACT
1 ATAACCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACT
*
40670757 ATAACCGGGCCAAGTCCCGAAGGCAATTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACT
*
40670797 ATAACCGGGCTAAGTCCCGAAGGCAATTGTGCTAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACT
40670837 ATAACCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACT
* *
40670877 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCGAG
1 ATAACCGGGCTAAGTCCCGAAGGCAATTGTGCGAG
40670912 AAGCTATATC
Statistics
Matches: 180, Mismatches: 12, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
39 48 0.27
40 132 0.73
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.22
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACT
Found at i:40670927 original size:119 final size:118
Alignment explanation
Indices: 40670679--40670938 Score: 353
Period size: 119 Copynumber: 2.2 Consensus size: 118
40670669 ATTCGGATTG
* * *
40670679 ATAACCGGGCTAAGCCCGAAGGCATTTGTGAGAGTTACTATATCCGGGCCAAGTCCCGAAAGCAT
1 ATAACCGGGCTAAGCCCGAAGGCAATTGTGAGAGTTACTATAACCGGGCCAAGTCCCGAAAGCAA
* *
40670744 TTGTGCGAGTACTATAACCGGGCCAAGTCCCGAAGGCAATTGTGCGAGTTACT
66 TTGTGCGAGTACTATAACCGGGCCAAGTCCCGAAGGCAATTGAGCGAGTAACT
** * *
40670797 ATAACCGGGCTAAGTCCCGAAGGCAATTGTGCTAGTTACTATAACCGGGCTAAGTCCCGAAGGCA
1 ATAACCGGGCTAAG-CCCGAAGGCAATTGTGAGAGTTACTATAACCGGGCCAAGTCCCGAAAGCA
* *
40670862 ATTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-AAGCT
65 ATTGTGCGAG-TACTATAACCGGGCCAAGTCCCGAAGGCAATTGAGCGAGTAA-CT
* *
40670917 ATATCC-GGCTAAACCCCGAAGG
1 ATAACCGGGCT-AAGCCCGAAGG
40670939 TACTTGGTTT
Statistics
Matches: 125, Mismatches: 13, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
118 14 0.11
119 66 0.53
120 45 0.36
ACGTcount: A:0.28, C:0.24, G:0.27, T:0.21
Consensus pattern (118 bp):
ATAACCGGGCTAAGCCCGAAGGCAATTGTGAGAGTTACTATAACCGGGCCAAGTCCCGAAAGCAA
TTGTGCGAGTACTATAACCGGGCCAAGTCCCGAAGGCAATTGAGCGAGTAACT
Found at i:40670938 original size:39 final size:40
Alignment explanation
Indices: 40670679--40670938 Score: 213
Period size: 40 Copynumber: 6.6 Consensus size: 40
40670669 ATTCGGATTG
* * * * *
40670679 ATAACCGGGCT-AAGCCCGAAGGCATTTGTGAGAGTTACT
1 ATAACCGGGCTAAACCCCGAAGGCAATTGAGCGAGTAACT
* * ** * * *
40670718 ATATCCGGGCCAAGTCCCGAAAGCATTTGTGCGAGT-ACT
1 ATAACCGGGCTAAACCCCGAAGGCAATTGAGCGAGTAACT
* ** * *
40670757 ATAACCGGGCCAAGTCCCGAAGGCAATTGTGCGAGTTACT
1 ATAACCGGGCTAAACCCCGAAGGCAATTGAGCGAGTAACT
** * * *
40670797 ATAACCGGGCTAAGTCCCGAAGGCAATTGTGCTAGTTACT
1 ATAACCGGGCTAAACCCCGAAGGCAATTGAGCGAGTAACT
** * *
40670837 ATAACCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACT
1 ATAACCGGGCTAAACCCCGAAGGCAATTGAGCGAGTAACT
** *
40670877 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-AAGCT
1 ATAACCGGGCTAAACCCCGAAGGCAATTGAGCGAGTAA-CT
*
40670917 ATATCC-GGCTAAACCCCGAAGG
1 ATAACCGGGCTAAACCCCGAAGG
40670939 TACTTGGTTT
Statistics
Matches: 200, Mismatches: 18, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
39 60 0.30
40 140 0.70
ACGTcount: A:0.28, C:0.24, G:0.27, T:0.21
Consensus pattern (40 bp):
ATAACCGGGCTAAACCCCGAAGGCAATTGAGCGAGTAACT
Found at i:40673686 original size:40 final size:40
Alignment explanation
Indices: 40673649--40673834 Score: 227
Period size: 40 Copynumber: 4.7 Consensus size: 40
40673639 GCTACTCGTT
*
40673649 CAAATGCCTTCGGGACATAGCCCGG-TTGTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
* *
40673689 CAAATGCCTTCGGGATTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
40673729 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
40673768 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
40673809 CAAA-GCCTTCGGGACTTAGCCCGGAT
1 CAAATGCCTTCGGGACTTAGCCCGGAT
40673835 ATCATTCAAA
Statistics
Matches: 126, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
38 2 0.02
39 32 0.25
40 79 0.63
41 13 0.10
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:40673768 original size:79 final size:82
Alignment explanation
Indices: 40673649--40673833 Score: 238
Period size: 79 Copynumber: 2.3 Consensus size: 82
40673639 GCTACTCGTT
* *
40673649 CAAATGCCTTCGGGACATAGCCCGG-TTGTAGTAACTCGCACAAATGCCTTCGGGAT-TTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATGTAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
40673712 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* **
40673729 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATGTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
40673792 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
40673809 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
40673834 TATCATTCAA
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 4 0.04
79 54 0.59
80 34 0.37
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATGTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:40673835 original size:40 final size:40
Alignment explanation
Indices: 40673630--40673836 Score: 226
Period size: 40 Copynumber: 5.2 Consensus size: 40
40673620 CAGAATTTTA
** *
40673630 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* * * *
40673670 CCGGTTGTAGTAACTCGCACAAATGCCTTCGGGATTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
40673710 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
40673749 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
40673789 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
40673829 CCGGATAT
1 CCGGATAT
40673837 CATTCAAATA
Statistics
Matches: 141, Mismatches: 19, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
38 2 0.01
39 32 0.23
40 95 0.67
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:40682910 original size:28 final size:28
Alignment explanation
Indices: 40682845--40682993 Score: 210
Period size: 28 Copynumber: 5.3 Consensus size: 28
40682835 GAGATTGGCG
* * * *
40682845 CTAAGTGTGCGGGTTTAAATTGTACAGCA
1 CTAAGTGTGCGAGTTT-GATTATATAGCA
*
40682874 CTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
* *
40682902 CTAAGTGTGCGAGCTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
40682930 CTAAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
40682958 CTAAGTGTGCGAG-TTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
40682985 CTGAGTGTG
1 CTAAGTGTG
40682994 TGGACTTAAT
Statistics
Matches: 111, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
27 22 0.20
28 74 0.67
29 15 0.14
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.34
Consensus pattern (28 bp):
CTAAGTGTGCGAGTTTGATTATATAGCA
Done.