Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 129 of 199
Found at i:39067558 original size:20 final size:21
Alignment explanation
Indices: 39067533--39067574 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
39067523 TGGAATGGTT
39067533 AATTTAA-TCAATTTAGCTTG
1 AATTTAATTCAATTTAGCTTG
* *
39067553 AATTTAATTCATTTTAGGTTG
1 AATTTAATTCAATTTAGCTTG
39067574 A
1 A
39067575 TTGCATTTCG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.33, C:0.07, G:0.12, T:0.48
Consensus pattern (21 bp):
AATTTAATTCAATTTAGCTTG
Found at i:39080544 original size:19 final size:18
Alignment explanation
Indices: 39080516--39080551 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
39080506 TACAATTAAA
*
39080516 TTTAATTAATGGAAAATC
1 TTTAATTAATGAAAAATC
39080534 TTTATATTAATGAAAAAT
1 TTTA-ATTAATGAAAAAT
39080552 TGTGCTACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.42
Consensus pattern (18 bp):
TTTAATTAATGAAAAATC
Found at i:39087197 original size:12 final size:13
Alignment explanation
Indices: 39087180--39087208 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
39087170 CTCATAGATG
39087180 AATAAATAAA-GC
1 AATAAATAAATGC
39087192 AATAAATAAATGC
1 AATAAATAAATGC
39087205 AATA
1 AATA
39087209 GTTATAGCCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.66, C:0.07, G:0.07, T:0.21
Consensus pattern (13 bp):
AATAAATAAATGC
Found at i:39107024 original size:25 final size:25
Alignment explanation
Indices: 39107002--39107050 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
39106992 AGTTACACTG
*
39107002 CCTGGCATACGGGCATGTGACACGA
1 CCTGGCACACGGGCATGTGACACGA
* *
39107027 CCTGGCACATGGGCGTGTGACACG
1 CCTGGCACACGGGCATGTGACACG
39107051 GCTATGTGAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.20, C:0.29, G:0.35, T:0.16
Consensus pattern (25 bp):
CCTGGCACACGGGCATGTGACACGA
Found at i:39107654 original size:21 final size:22
Alignment explanation
Indices: 39107622--39107688 Score: 68
Period size: 21 Copynumber: 3.2 Consensus size: 22
39107612 TTTTCAATCA
* *
39107622 CACACG-GGCGTGTGTTTCAGC
1 CACACGAGTCGTGTGTTTCTGC
* *
39107643 CACACGA-TCGTGTATCTCTGC
1 CACACGAGTCGTGTGTTTCTGC
*
39107664 CAAACGAGT-GTGTGTTTCTGC
1 CACACGAGTCGTGTGTTTCTGC
39107685 CACA
1 CACA
39107689 TGGATGTGCA
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
21 35 0.97
22 1 0.03
ACGTcount: A:0.19, C:0.28, G:0.25, T:0.27
Consensus pattern (22 bp):
CACACGAGTCGTGTGTTTCTGC
Found at i:39111964 original size:6 final size:6
Alignment explanation
Indices: 39111953--39112039 Score: 70
Period size: 6 Copynumber: 14.3 Consensus size: 6
39111943 GAAGTCTAAG
* * *
39111953 AAAATA AAAATA AAAATA AAAATAA AACAACTA AAAAGA AAAAGA AAAAGA
1 AAAATA AAAATA AAAATA AAAAT-A AA-AA-TA AAAATA AAAATA AAAATA
* * * *
39112004 AAACTA AAAAGA AAAA-A GAAA-A AAAATA AAACTA AA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AA
39112040 TGATCATCAT
Statistics
Matches: 69, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
5 8 0.12
6 50 0.72
7 5 0.07
8 5 0.07
9 1 0.01
ACGTcount: A:0.80, C:0.05, G:0.06, T:0.09
Consensus pattern (6 bp):
AAAATA
Found at i:39111970 original size:12 final size:12
Alignment explanation
Indices: 39111953--39112034 Score: 78
Period size: 12 Copynumber: 6.8 Consensus size: 12
39111943 GAAGTCTAAG
*
39111953 AAAATAAAAATA
1 AAAATAAAAAGA
*
39111965 AAAATAAAAATAA
1 AAAATAAAAA-GA
39111978 AACAACTAAAAAGA
1 AA-AA-TAAAAAGA
*
39111992 AAAAGAAAAAGA
1 AAAATAAAAAGA
*
39112004 AAACTAAAAAGA
1 AAAATAAAAAGA
*
39112016 AAAA-AGAAA-A
1 AAAATAAAAAGA
39112026 AAAATAAAA
1 AAAATAAAA
39112035 CTAAATGATC
Statistics
Matches: 58, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
10 5 0.09
11 7 0.12
12 30 0.52
13 5 0.09
14 5 0.09
15 6 0.10
ACGTcount: A:0.82, C:0.04, G:0.06, T:0.09
Consensus pattern (12 bp):
AAAATAAAAAGA
Found at i:39113636 original size:28 final size:30
Alignment explanation
Indices: 39113604--39113671 Score: 83
Period size: 28 Copynumber: 2.4 Consensus size: 30
39113594 AAGCACATAA
39113604 AAATAAGAATAAGAAA-ACA-AAT-AGAAAT
1 AAATAAGAATAAGAAATA-AGAATCAGAAAT
*
39113632 AAATAAGAAT-AGAAATAAGAATCATAAAT
1 AAATAAGAATAAGAAATAAGAATCAGAAAT
39113661 AAATAA-AATAA
1 AAATAAGAATAA
39113672 AATAAGGGAA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
27 6 0.17
28 17 0.49
29 12 0.34
ACGTcount: A:0.71, C:0.03, G:0.09, T:0.18
Consensus pattern (30 bp):
AAATAAGAATAAGAAATAAGAATCAGAAAT
Found at i:39113647 original size:22 final size:21
Alignment explanation
Indices: 39113611--39113676 Score: 57
Period size: 22 Copynumber: 3.0 Consensus size: 21
39113601 TAAAAATAAG
*
39113611 AATAAGAAAACAAATAGAAATA
1 AATAAGAATA-AAATAGAAATA
39113633 AATAAGAATAGAAATAAGAATCATA
1 AATAAGAATA-AAAT-AGAA--ATA
39113658 AAT-A-AATAAAATA-AAATA
1 AATAAGAATAAAATAGAAATA
39113676 A
1 A
39113677 GGGAAAAGGG
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
18 4 0.10
20 2 0.05
21 1 0.03
22 17 0.44
23 8 0.21
24 1 0.03
25 6 0.15
ACGTcount: A:0.71, C:0.03, G:0.08, T:0.18
Consensus pattern (21 bp):
AATAAGAATAAAATAGAAATA
Found at i:39114623 original size:29 final size:30
Alignment explanation
Indices: 39114573--39114629 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
39114563 TCAGACATGC
* * *
39114573 CCGTGTGTCTAGGCCGTGTGGCACACACAG
1 CCGTGTGTCCAGGCCATATGGCACACACAG
39114603 CCGTGTG-CCAGGCCATATGGCACACAC
1 CCGTGTGTCCAGGCCATATGGCACACAC
39114630 TGTCGTGTAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 17 0.71
30 7 0.29
ACGTcount: A:0.19, C:0.33, G:0.30, T:0.18
Consensus pattern (30 bp):
CCGTGTGTCCAGGCCATATGGCACACACAG
Found at i:39114647 original size:29 final size:29
Alignment explanation
Indices: 39114591--39114647 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
39114581 CTAGGCCGTG
* **
39114591 TGGCACACACAGCCGTGTGCCAGGCCATA
1 TGGCACACACAGCCGTGTACCAACCCATA
* *
39114620 TGGCACACACTGTCGTGTACCAACCCAT
1 TGGCACACACAGCCGTGTACCAACCCAT
39114648 GTGTGATTTC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.25, C:0.35, G:0.23, T:0.18
Consensus pattern (29 bp):
TGGCACACACAGCCGTGTACCAACCCATA
Found at i:39117896 original size:19 final size:18
Alignment explanation
Indices: 39117867--39117923 Score: 51
Period size: 19 Copynumber: 3.0 Consensus size: 18
39117857 AATTAGAATG
39117867 TAAAAATTAAACTAAAAATA
1 TAAAAA-TAAA-TAAAAATA
*
39117887 TAAAAATAAAATACAAATA
1 TAAAAAT-AAATAAAAATA
* * *
39117906 GATAAATTAATAAAAATA
1 TAAAAATAAATAAAAATA
39117924 AAATGTTCCG
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
18 9 0.29
19 13 0.42
20 9 0.29
ACGTcount: A:0.70, C:0.04, G:0.02, T:0.25
Consensus pattern (18 bp):
TAAAAATAAATAAAAATA
Found at i:39120428 original size:34 final size:34
Alignment explanation
Indices: 39120352--39120430 Score: 88
Period size: 34 Copynumber: 2.3 Consensus size: 34
39120342 ATCACAATGC
* **
39120352 CAGTAATCAGTAGGGCCTTTGCCCAATTTCAGTAA
1 CAGT-ATCAGTAGGGCCTTGGCCCAATAACAGTAA
* *
39120387 TAGTATCAGTGGGGCCTTGGCCC-ATAACAGTAA
1 CAGTATCAGTAGGGCCTTGGCCCAATAACAGTAA
39120420 CAGATATCAGT
1 CAG-TATCAGT
39120431 CATGTAGTGA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
33 10 0.27
34 24 0.65
35 3 0.08
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.27
Consensus pattern (34 bp):
CAGTATCAGTAGGGCCTTGGCCCAATAACAGTAA
Found at i:39120912 original size:27 final size:27
Alignment explanation
Indices: 39120890--39121084 Score: 263
Period size: 27 Copynumber: 7.2 Consensus size: 27
39120880 AGGGGTATAA
39120890 CAGTCATTTTACCCTATGAGGGTATTT
1 CAGTCATTTTACCCTATGAGGGTATTT
*
39120917 CAGTCATTTTACCCTATGATGGTATTT
1 CAGTCATTTTACCCTATGAGGGTATTT
**
39120944 TGGTCATTTTACCCTATGAGGGTATTT
1 CAGTCATTTTACCCTATGAGGGTATTT
*
39120971 C-GATCATTTTACCCTATGGGGGTATTT
1 CAG-TCATTTTACCCTATGAGGGTATTT
39120998 CAGTCATTTTACCCTAT-AGGGGTATTT
1 CAGTCATTTTACCCTATGA-GGGTATTT
*
39121025 C-GATCATTTTACCCTATGGGGGTATTT
1 CAG-TCATTTTACCCTATGAGGGTATTT
* *
39121052 -TGATCATTTTACCCTATGCGGGTATTT
1 CAG-TCATTTTACCCTATGAGGGTATTT
39121079 CAGTCA
1 CAGTCA
39121085 GAAATAATTC
Statistics
Matches: 151, Mismatches: 10, Indels: 14
0.86 0.06 0.08
Matches are distributed among these distances:
26 2 0.01
27 147 0.97
28 2 0.01
ACGTcount: A:0.21, C:0.18, G:0.19, T:0.42
Consensus pattern (27 bp):
CAGTCATTTTACCCTATGAGGGTATTT
Found at i:39120978 original size:81 final size:81
Alignment explanation
Indices: 39120893--39121084 Score: 305
Period size: 81 Copynumber: 2.4 Consensus size: 81
39120883 GGTATAACAG
* * *
39120893 TCATTTTACCCTATGAGGGTATTTCAGTCATTTTACCCTAT-GATGGTATTTTGGTCATTTTACC
1 TCATTTTACCCTATGAGGGTATTTCAGTCATTTTACCCTATAG-GGGTATTTCGATCATTTTACC
39120957 CTATGAGGGTATTTCGA
65 CTATGAGGGTATTTCGA
*
39120974 TCATTTTACCCTATGGGGGTATTTCAGTCATTTTACCCTATAGGGGTATTTCGATCATTTTACCC
1 TCATTTTACCCTATGAGGGTATTTCAGTCATTTTACCCTATAGGGGTATTTCGATCATTTTACCC
* *
39121039 TATGGGGGTATTTTGA
66 TATGAGGGTATTTCGA
*
39121055 TCATTTTACCCTATGCGGGTATTTCAGTCA
1 TCATTTTACCCTATGAGGGTATTTCAGTCA
39121085 GAAATAATTC
Statistics
Matches: 103, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
81 102 0.99
82 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.19, T:0.42
Consensus pattern (81 bp):
TCATTTTACCCTATGAGGGTATTTCAGTCATTTTACCCTATAGGGGTATTTCGATCATTTTACCC
TATGAGGGTATTTCGA
Found at i:39122179 original size:22 final size:22
Alignment explanation
Indices: 39122154--39122213 Score: 84
Period size: 22 Copynumber: 2.7 Consensus size: 22
39122144 GAGTCCACAG
*
39122154 AGAATGTTAGTACTAGGGACAA
1 AGAATGTCAGTACTAGGGACAA
* * *
39122176 AGAATGTCAGCACTAGGGATAG
1 AGAATGTCAGTACTAGGGACAA
39122198 AGAATGTCAGTACTAG
1 AGAATGTCAGTACTAG
39122214 AGGCAGTGGG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.38, C:0.12, G:0.28, T:0.22
Consensus pattern (22 bp):
AGAATGTCAGTACTAGGGACAA
Found at i:39127092 original size:29 final size:29
Alignment explanation
Indices: 39127059--39127122 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
39127049 TAATCCACCA
39127059 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
39127088 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
39127118 CCCAA
1 CCCAA
39127123 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:39127096 original size:30 final size:30
Alignment explanation
Indices: 39127066--39127122 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
39127056 CCACCCAACT
39127066 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
39127095 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
39127123 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:39128579 original size:17 final size:16
Alignment explanation
Indices: 39128552--39128583 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
39128542 TCCCAACTTC
39128552 TAAAATCCCCAAATCG
1 TAAAATCCCCAAATCG
39128568 TAAAATTCCCCAAATC
1 TAAAA-TCCCCAAATC
39128584 CATAACATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.44, C:0.31, G:0.03, T:0.22
Consensus pattern (16 bp):
TAAAATCCCCAAATCG
Found at i:39129585 original size:33 final size:33
Alignment explanation
Indices: 39129540--39129610 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 33
39129530 TACTAAGGAG
* *
39129540 GGTGATGTTGAAGGGGTGGAAGT-TGATGGGGAA
1 GGTGATGATGAAGGGGTAGAA-TCTGATGGGGAA
*
39129573 GGTGATGATGAAGGGGTAGAATCTGATGGTGAA
1 GGTGATGATGAAGGGGTAGAATCTGATGGGGAA
39129606 -GTGAT
1 GGTGAT
39129611 TTGGAAAAGG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
32 6 0.18
33 28 0.82
ACGTcount: A:0.27, C:0.01, G:0.46, T:0.25
Consensus pattern (33 bp):
GGTGATGATGAAGGGGTAGAATCTGATGGGGAA
Found at i:39129842 original size:51 final size:51
Alignment explanation
Indices: 39129780--39129884 Score: 192
Period size: 51 Copynumber: 2.1 Consensus size: 51
39129770 GAAGTTGCTA
39129780 CTGATGAATATGCTGGTGATTTTGCAACATCAGATGGAATGAATAATGTTG
1 CTGATGAATATGCTGGTGATTTTGCAACATCAGATGGAATGAATAATGTTG
* *
39129831 CTGATGAATATGCTGGTGATTTTGCAACATCAGATGGACTGGATAATGTTG
1 CTGATGAATATGCTGGTGATTTTGCAACATCAGATGGAATGAATAATGTTG
39129882 CTG
1 CTG
39129885 CTGTAAGTAG
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.29, C:0.11, G:0.27, T:0.33
Consensus pattern (51 bp):
CTGATGAATATGCTGGTGATTTTGCAACATCAGATGGAATGAATAATGTTG
Found at i:39135531 original size:71 final size:71
Alignment explanation
Indices: 39135417--39135800 Score: 387
Period size: 71 Copynumber: 5.4 Consensus size: 71
39135407 AGTCACATAG
* * * ** *
39135417 CTATTATATCAAGGCTCGCAGGTGAAAAACCGTAGCCTCCAACACAGTTAACGAGAGTTAAAAAC
1 CTATCATATTAAGGCTCGCAAGTGAAAAACCACAGCCTCCAACACAGTTAGCGAGAGTTAAAAAC
* *
39135482 TCTCAG
66 TCCCAA
* * * * * * * *
39135488 CTATCATATTAAGGCTCACAGGTGAAGAACCATAGCCTTCAACACAATTAGCTAGAGTTGAAAAC
1 CTATCATATTAAGGCTCGCAAGTGAAAAACCACAGCCTCCAACACAGTTAGCGAGAGTTAAAAAC
39135553 TCCCAA
66 TCCCAA
* * * *
39135559 C-AGTCATATTAAGGCTTGCAAGTGAAAAACCACAGCCTCTAATACAGTTAGCGAGAGTTACAAA
1 CTA-TCATATTAAGGCTCGCAAGTGAAAAACCACAGCCTCCAACACAGTTAGCGAGAGTTAAAAA
*
39135623 CTCACAA
65 CTCCCAA
* * * * * *
39135630 CTGTCATATTAAGGCTCGCAAATGAAAAACCGCAGCCTCCAACATAGCTAGAGAGAGTTAAAAAC
1 CTATCATATTAAGGCTCGCAAGTGAAAAACCACAGCCTCCAACACAGTTAGCGAGAGTTAAAAAC
39135695 -CCCTAA
66 TCCC-AA
* * * * *
39135701 CTCTCATATTAAGGCTCGCAAGTGAAAAATCGCAACCTCCAACACAGTTAGCAAGAGTTACAAAA
1 CTATCATATTAAGGCTCGCAAGTGAAAAACCACAGCCTCCAACACAGTTAGCGAGAGTTA-AAAA
*
39135766 -TCCTAA
65 CTCCCAA
* * * *
39135772 TTTTCATTTTAAGGCTCGCAGGTGAAAAA
1 CTATCATATTAAGGCTCGCAAGTGAAAAA
39135801 TCGCAGCCCC
Statistics
Matches: 259, Mismatches: 49, Indels: 10
0.81 0.15 0.03
Matches are distributed among these distances:
70 3 0.01
71 250 0.97
72 6 0.02
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.22
Consensus pattern (71 bp):
CTATCATATTAAGGCTCGCAAGTGAAAAACCACAGCCTCCAACACAGTTAGCGAGAGTTAAAAAC
TCCCAA
Found at i:39138949 original size:22 final size:22
Alignment explanation
Indices: 39138910--39138951 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
39138900 GTTGTAGTCC
* * *
39138910 ACAGAGAATGTTAGTACTAGGG
1 ACAGAGAATATCAATACTAGGG
39138932 ACAGAGAATATCAATACTAG
1 ACAGAGAATATCAATACTAG
39138952 AGGCAGTGAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.43, C:0.12, G:0.24, T:0.21
Consensus pattern (22 bp):
ACAGAGAATATCAATACTAGGG
Found at i:39139502 original size:25 final size:25
Alignment explanation
Indices: 39139458--39139505 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 25
39139448 CATGTTGGCT
39139458 TCTTATTTATTTTACAATTAATTAA
1 TCTTATTTATTTTACAATTAATTAA
39139483 TCTT-TTTATTGTTATC-ATTAATT
1 TCTTATTTATT-TTA-CAATTAATT
39139506 GTTATATTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 6 0.29
25 14 0.67
26 1 0.05
ACGTcount: A:0.29, C:0.08, G:0.02, T:0.60
Consensus pattern (25 bp):
TCTTATTTATTTTACAATTAATTAA
Found at i:39145144 original size:30 final size:29
Alignment explanation
Indices: 39145110--39145192 Score: 85
Period size: 30 Copynumber: 2.8 Consensus size: 29
39145100 ATGAAAAATT
* * **
39145110 TATAAATAAATACTAATAATTTTATTTAAA
1 TATAAATAAATATTAATAATTATAACT-AA
* * *
39145140 TATAATTAAATTTTAATTAATTATAACTAT
1 TATAAATAAATATTAA-TAATTATAACTAA
39145170 TATAAATAAATATTAATAATTAT
1 TATAAATAAATATTAATAATTAT
39145193 GAGATCTAGA
Statistics
Matches: 43, Mismatches: 9, Indels: 3
0.78 0.16 0.05
Matches are distributed among these distances:
29 7 0.16
30 28 0.65
31 8 0.19
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (29 bp):
TATAAATAAATATTAATAATTATAACTAA
Found at i:39148962 original size:174 final size:174
Alignment explanation
Indices: 39148672--39149019 Score: 696
Period size: 174 Copynumber: 2.0 Consensus size: 174
39148662 GTTCCTAGAT
39148672 GCGTGTCCTTCCCCAAGGGAAACAATCGGGGGATCAAATTGCACAAAAAATAGAATAAAAATGAT
1 GCGTGTCCTTCCCCAAGGGAAACAATCGGGGGATCAAATTGCACAAAAAATAGAATAAAAATGAT
39148737 AAATTAAAAGAAATAATAAATAGCAATAGGACGAGATTGAGAAATAGTGAAAAAGCGGAAGGACC
66 AAATTAAAAGAAATAATAAATAGCAATAGGACGAGATTGAGAAATAGTGAAAAAGCGGAAGGACC
39148802 GAAAGAGTAAATAGACCCTCAGTTCAAAAACACGCAGATCCTAG
131 GAAAGAGTAAATAGACCCTCAGTTCAAAAACACGCAGATCCTAG
39148846 GCGTGTCCTTCCCCAAGGGAAACAATCGGGGGATCAAATTGCACAAAAAATAGAATAAAAATGAT
1 GCGTGTCCTTCCCCAAGGGAAACAATCGGGGGATCAAATTGCACAAAAAATAGAATAAAAATGAT
39148911 AAATTAAAAGAAATAATAAATAGCAATAGGACGAGATTGAGAAATAGTGAAAAAGCGGAAGGACC
66 AAATTAAAAGAAATAATAAATAGCAATAGGACGAGATTGAGAAATAGTGAAAAAGCGGAAGGACC
39148976 GAAAGAGTAAATAGACCCTCAGTTCAAAAACACGCAGATCCTAG
131 GAAAGAGTAAATAGACCCTCAGTTCAAAAACACGCAGATCCTAG
39149020 AGCTTGATCA
Statistics
Matches: 174, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
174 174 1.00
ACGTcount: A:0.47, C:0.16, G:0.21, T:0.17
Consensus pattern (174 bp):
GCGTGTCCTTCCCCAAGGGAAACAATCGGGGGATCAAATTGCACAAAAAATAGAATAAAAATGAT
AAATTAAAAGAAATAATAAATAGCAATAGGACGAGATTGAGAAATAGTGAAAAAGCGGAAGGACC
GAAAGAGTAAATAGACCCTCAGTTCAAAAACACGCAGATCCTAG
Found at i:39149463 original size:15 final size:15
Alignment explanation
Indices: 39149445--39149475 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
39149435 TAACAGATTA
39149445 AAAAATAAAAAAAAG
1 AAAAATAAAAAAAAG
*
39149460 AAAAATAAATAAAAG
1 AAAAATAAAAAAAAG
39149475 A
1 A
39149476 TCACCTTTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.84, C:0.00, G:0.06, T:0.10
Consensus pattern (15 bp):
AAAAATAAAAAAAAG
Found at i:39149997 original size:57 final size:57
Alignment explanation
Indices: 39149934--39150050 Score: 225
Period size: 57 Copynumber: 2.1 Consensus size: 57
39149924 AGTCAGTTTT
*
39149934 CTCTCCATCTTCTTGATGATTTCTTTCCCCATCTCTACCATTTTCATTCCTCAATTC
1 CTCTCCATCTTCCTGATGATTTCTTTCCCCATCTCTACCATTTTCATTCCTCAATTC
39149991 CTCTCCATCTTCCTGATGATTTCTTTCCCCATCTCTACCATTTTCATTCCTCAATTC
1 CTCTCCATCTTCCTGATGATTTCTTTCCCCATCTCTACCATTTTCATTCCTCAATTC
39150048 CTC
1 CTC
39150051 ACCTTGCCGC
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 59 1.00
ACGTcount: A:0.15, C:0.37, G:0.03, T:0.44
Consensus pattern (57 bp):
CTCTCCATCTTCCTGATGATTTCTTTCCCCATCTCTACCATTTTCATTCCTCAATTC
Found at i:39152616 original size:44 final size:44
Alignment explanation
Indices: 39152543--39153060 Score: 382
Period size: 44 Copynumber: 11.7 Consensus size: 44
39152533 TCATTCTAAC
* * * * *
39152543 CCACTGCAACTTCTGAGG-TATATGATTTGTTACTTTAATCTACT
1 CCACTGCAACTTCAG-GGAGATAAGATTTGTAACTTTAATCTGCT
* * * *
39152587 CCACTACAACTTTAGGGAGATAA-AGTTTGTAGCTTCAATCTGCT
1 CCACTGCAACTTCAGGGAGATAAGA-TTTGTAACTTTAATCTGCT
* *
39152631 CCACTGCAACTTCAGGGAGATAAGATTTGTGACTTGATTTAATCCGAC-
1 CCACTGCAACTTCAGGGAGATAAGATTTGTAAC----TTTAATCTG-CT
* * * * ** *
39152679 CCACTGTAACTTCCGAGG-TATAGGATTTGTCGCTTTAATTTGCT
1 CCACTGCAACTTCAG-GGAGATAAGATTTGTAACTTTAATCTGCT
* * * *
39152723 CCACTGCAACTTCAGGGGGATGAGATTTGTAACTTCAATATGCT
1 CCACTGCAACTTCAGGGAGATAAGATTTGTAACTTTAATCTGCT
* *
39152767 CCACTGCAACTTCAAGGAGATAAGATTTGTAACTTCAATCTGCT
1 CCACTGCAACTTCAGGGAGATAAGATTTGTAACTTTAATCTGCT
* * * *
39152811 ACACTACAACTTCAGGGAGATAA-AGTTTGTAACTTCAATGTGCT
1 CCACTGCAACTTCAGGGAGATAAGA-TTTGTAACTTTAATCTGCT
* * * * *
39152855 CCACTCCAACATCATGGAGATAAGGTTTGTAGCTTTAATCTGCT
1 CCACTGCAACTTCAGGGAGATAAGATTTGTAACTTTAATCTGCT
* * ** *** *
39152899 CTAC-ACAACTTCAAAGAGATAAGATTTGTGGTTTTAATCTACT
1 CCACTGCAACTTCAGGGAGATAAGATTTGTAACTTTAATCTGCT
* ** ** * * *
39152942 CTACTGCAACTTCAAAGAGATAAGATTCACTATCTTCAATCCGCT
1 CCACTGCAACTTCAGGGAGATAAGATT-TGTAACTTTAATCTGCT
* * * ** * * *
39152987 CTATTGTAACTTCAGGGAGATAAGATTTGTTGCTTGAATTTACT
1 CCACTGCAACTTCAGGGAGATAAGATTTGTAACTTTAATCTGCT
*
39153031 CCACTGCAACTTTAGGGAGATAAGATTTGT
1 CCACTGCAACTTCAGGGAGATAAGATTTGT
39153061 CACGATAACT
Statistics
Matches: 377, Mismatches: 82, Indels: 30
0.77 0.17 0.06
Matches are distributed among these distances:
43 42 0.11
44 268 0.71
45 33 0.09
48 31 0.08
49 3 0.01
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (44 bp):
CCACTGCAACTTCAGGGAGATAAGATTTGTAACTTTAATCTGCT
Found at i:39152786 original size:136 final size:136
Alignment explanation
Indices: 39152541--39152801 Score: 371
Period size: 136 Copynumber: 1.9 Consensus size: 136
39152531 CTTCATTCTA
* * * *
39152541 ACCCACTGCAACTTCTGAGGTATATGATTTGTTACTTTAATCTACTCCACTACAACTTTAGGGAG
1 ACCCACTGCAACTTCCGAGGTATAGGATTTGTCACTTTAATCTACTCCACTACAACTTCAGGGAG
* * * *
39152606 ATAAAGTTTGTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTGACTTGATTT
66 ATAAAGTTTGTAACTTCAATATGCTCCACTGCAACTTCAAGGAGATAAGATTTGTAACTTGATTT
39152671 AATCCG
131 AATCCG
* * * * * *
39152677 ACCCACTGTAACTTCCGAGGTATAGGATTTGTCGCTTTAATTTGCTCCACTGCAACTTCAGGGGG
1 ACCCACTGCAACTTCCGAGGTATAGGATTTGTCACTTTAATCTACTCCACTACAACTTCAGGGAG
*
39152742 AT-GAGATTTGTAACTTCAATATGCTCCACTGCAACTTCAAGGAGATAAGATTTGTAACTT
66 ATAAAG-TTTGTAACTTCAATATGCTCCACTGCAACTTCAAGGAGATAAGATTTGTAACTT
39152802 CAATCTGCTA
Statistics
Matches: 109, Mismatches: 15, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
135 2 0.02
136 107 0.98
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.33
Consensus pattern (136 bp):
ACCCACTGCAACTTCCGAGGTATAGGATTTGTCACTTTAATCTACTCCACTACAACTTCAGGGAG
ATAAAGTTTGTAACTTCAATATGCTCCACTGCAACTTCAAGGAGATAAGATTTGTAACTTGATTT
AATCCG
Found at i:39152952 original size:131 final size:132
Alignment explanation
Indices: 39152719--39152964 Score: 289
Period size: 131 Copynumber: 1.9 Consensus size: 132
39152709 CGCTTTAATT
* * * * * *
39152719 TGCTCCACTGCAACTTCAGGGGGATGAGATTTGTAACTTCAATATGCTCCACTGCAACTTCAAGG
1 TGCTCCACTCCAACATCAGGGAGATAAGATTTGTAACTTCAATATGCTCCACTACAACTTCAAAG
* **
39152784 AGATAAGATTTGTAACTTCAATCTGCTACACTACAACTTCAGGGAGATAAAGTTTGTAACTTCAA
66 AGATAAGATTTGTAACTTCAATCTACTACACTACAACTTCAAAGAGATAAAGTTTGTAACTTCAA
39152849 TG
131 TG
* * * * * *
39152851 TGCTCCACTCCAACATCATGGAGATAAGGTTTGTAGCTTTAATCTGCTCTAC-ACAACTTCAAAG
1 TGCTCCACTCCAACATCAGGGAGATAAGATTTGTAACTTCAATATGCTCCACTACAACTTCAAAG
*** * *
39152915 AGATAAGATTTGTGGTTTTAATCTACT-CTACTGCAACTTCAAAGAGATAA
66 AGATAAGATTTGTAACTTCAATCTACTAC-ACTACAACTTCAAAGAGATAA
39152965 GATTCACTAT
Statistics
Matches: 93, Mismatches: 20, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
130 1 0.01
131 50 0.54
132 42 0.45
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.30
Consensus pattern (132 bp):
TGCTCCACTCCAACATCAGGGAGATAAGATTTGTAACTTCAATATGCTCCACTACAACTTCAAAG
AGATAAGATTTGTAACTTCAATCTACTACACTACAACTTCAAAGAGATAAAGTTTGTAACTTCAA
TG
Found at i:39155767 original size:41 final size:41
Alignment explanation
Indices: 39155722--39155895 Score: 276
Period size: 41 Copynumber: 4.2 Consensus size: 41
39155712 ACTGGCACTT
* * *
39155722 AGCCTGCTAGACATAAAGTATAAAATGTTTCACCGGCGTCA
1 AGCCTGCTAGACTTAAAGTCTGAAATGTTTCACCGGCGTCA
39155763 AGCCTGCTAGACTTAAAGTCTGAAATGTTTCACCGGCGTCA
1 AGCCTGCTAGACTTAAAGTCTGAAATGTTTCACCGGCGTCA
39155804 AGCCTGCTAGACTTAAAGTCTGAAATGTTTCACCGGCGTCA
1 AGCCTGCTAGACTTAAAGTCTGAAATGTTTCACCGGCGTCA
** * * *
39155845 AGCCTGCTAGACTTAAAGTCTGAAACATATCACTGGCATCA
1 AGCCTGCTAGACTTAAAGTCTGAAATGTTTCACCGGCGTCA
39155886 AGCCTGCTAG
1 AGCCTGCTAG
39155896 GCACTGAGCC
Statistics
Matches: 125, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 125 1.00
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (41 bp):
AGCCTGCTAGACTTAAAGTCTGAAATGTTTCACCGGCGTCA
Found at i:39170184 original size:18 final size:18
Alignment explanation
Indices: 39170125--39170184 Score: 52
Period size: 17 Copynumber: 3.3 Consensus size: 18
39170115 AAAATTACAA
*
39170125 AAAAATTAAAAATGATTTTT
1 AAAAATTATAAA-G-TTTTT
* *
39170145 AAAATTTATATA--TTTT
1 AAAAATTATAAAGTTTTT
39170161 AGAAAATTATAAAGTTTTT
1 A-AAAATTATAAAGTTTTT
39170180 AAAAA
1 AAAAA
39170185 AATCTAAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 8
0.71 0.11 0.18
Matches are distributed among these distances:
16 5 0.16
17 9 0.28
18 4 0.12
19 5 0.16
20 9 0.28
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (18 bp):
AAAAATTATAAAGTTTTT
Found at i:39172492 original size:17 final size:17
Alignment explanation
Indices: 39172472--39172505 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
39172462 TTTATTAATT
39172472 TATATTTT-TAAATTTTA
1 TATATTTTCT-AATTTTA
39172489 TATATTTTCTAATTTTA
1 TATATTTTCTAATTTTA
39172506 AAAAATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 15 0.94
18 1 0.06
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (17 bp):
TATATTTTCTAATTTTA
Found at i:39181944 original size:21 final size:21
Alignment explanation
Indices: 39181918--39181958 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
39181908 AACTTCTCTC
*
39181918 CTAAATTTATTATTTACATAA
1 CTAAATGTATTATTTACATAA
39181939 CTAAATGTATTATTTACATA
1 CTAAATGTATTATTTACATA
39181959 TTTAACAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.41, C:0.10, G:0.02, T:0.46
Consensus pattern (21 bp):
CTAAATGTATTATTTACATAA
Found at i:39184273 original size:15 final size:17
Alignment explanation
Indices: 39184242--39184274 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
39184232 TGAATGAAAA
39184242 ATTTATGTAATAAATAT
1 ATTTATGTAATAAATAT
39184259 ATTTAT-TAA-AAATAT
1 ATTTATGTAATAAATAT
39184274 A
1 A
39184275 AATAAAAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 3 0.19
17 6 0.38
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (17 bp):
ATTTATGTAATAAATAT
Found at i:39189447 original size:3 final size:3
Alignment explanation
Indices: 39189439--39189539 Score: 112
Period size: 3 Copynumber: 32.3 Consensus size: 3
39189429 TTACATAGTG
* * * * *
39189439 ATA ATA ATA ACTA AGA ATA ATA GTA GTAA ATAA ATAA ATA AGA GTA ATA
1 ATA ATA ATA A-TA ATA ATA ATA ATA AT-A AT-A AT-A ATA ATA ATA ATA
*
39189488 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ACA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
39189536 ATA A
1 ATA A
39189540 ATTTATTTAC
Statistics
Matches: 86, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
3 73 0.85
4 13 0.15
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:39191184 original size:129 final size:129
Alignment explanation
Indices: 39190954--39191479 Score: 718
Period size: 129 Copynumber: 4.1 Consensus size: 129
39190944 GTAACTTTAA
* * * * * * *
39190954 AGATAAGTCT-GATGCAATCTACTTTACTGCAACTTCAGAAAGATAAGATCTG-GACCTTTTAAT
1 AGATAAGACTGGATGCGATCTACTCTACTACAACGTCAGAGAGATAAGATCTGTG--GTTTTAAT
* * *
39191017 CCACTTCACTGCAACTTCAGGGAGATAGGATTTATTTCTTCTGTCTGCTCTACTGCAACTTTAGG
64 CCACTCCACTGCAACTTCAGGGAGATAGGATTTATTTCTTCTGTCTGCTCCACTGCAACTTCAGG
39191082 G
129 G
* *
39191083 AGATAAGACTGGATGCGATCTACTCTACTGCAACGTCAGATAGATAAGATCTGTGGTTTTAATCC
1 AGATAAGACTGGATGCGATCTACTCTACTACAACGTCAGAGAGATAAGATCTGTGGTTTTAATCC
* * *
39191148 GCTGCACTGTAACTTCAGGGAGATAGGATTTATTTCTTCTGTCTGCTCCACTGCAACTTCAGGG
66 ACTCCACTGCAACTTCAGGGAGATAGGATTTATTTCTTCTGTCTGCTCCACTGCAACTTCAGGG
* * *
39191212 AGATAAGATTGGATGCGATCTGCTCTACTACAATGTCAGAGAGATAAGATCTGTGGTTTTAATCC
1 AGATAAGACTGGATGCGATCTACTCTACTACAACGTCAGAGAGATAAGATCTGTGGTTTTAATCC
* *
39191277 ACTCCACTGCAACTTCAGGGAGATAGGATTGATTTCTTCTGTCTGTTCCACTGCAACTTCAGGG
66 ACTCCACTGCAACTTCAGGGAGATAGGATTTATTTCTTCTGTCTGCTCCACTGCAACTTCAGGG
* * *
39191341 AGATAAGACTGGATGCGATCTGCTCTACTACAACGTCAGAGAGATAAGATCTATGGTCTTAATCC
1 AGATAAGACTGGATGCGATCTACTCTACTACAACGTCAGAGAGATAAGATCTGTGGTTTTAATCC
* ** * * * *
39191406 ACTCCATTGCAACTTCAAAGAGATAAGA-TTATTGGCTT-TAATCTGTTCCACTGCAACTTCAGG
66 ACTCCACTGCAACTTCAGGGAGATAGGATTTATT-TCTTCT-GTCTGCTCCACTGCAACTTCAGG
39191469 G
129 G
39191470 AGATAAGACT
1 AGATAAGACT
39191480 TATAGCTGCA
Statistics
Matches: 361, Mismatches: 32, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
128 5 0.01
129 317 0.88
130 38 0.11
131 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.31
Consensus pattern (129 bp):
AGATAAGACTGGATGCGATCTACTCTACTACAACGTCAGAGAGATAAGATCTGTGGTTTTAATCC
ACTCCACTGCAACTTCAGGGAGATAGGATTTATTTCTTCTGTCTGCTCCACTGCAACTTCAGGG
Found at i:39191447 original size:44 final size:44
Alignment explanation
Indices: 39191247--39191482 Score: 123
Period size: 44 Copynumber: 5.4 Consensus size: 44
39191237 TACTACAATG
* *
39191247 TCAGAGAGATAAGATCT-GTGGTTTTAATCCACTCCACTGCAACT
1 TCAGAGAGATAAGAT-TATTGGTCTTAATCCACTCCACTGCAACT
* * ** ***
39191291 TCAGGGAGATAGGATTGATT--TCTTCTGTCTGTTCCACTGCAACT
1 TCAGAGAGATAAGATT-ATTGGTCTT-AATCCACTCCACTGCAACT
* * * ** * * *
39191335 TCAGGGAGATAAG---ACTGGATGC--GATCTGCTCTACTACAACG
1 TCAGAGAGATAAGATTATTGG-T-CTTAATCCACTCCACTGCAACT
*
39191376 TCAGAGAGATAAGATCTA-TGGTCTTAATCCACTCCATTGCAACT
1 TCAGAGAGATAAGAT-TATTGGTCTTAATCCACTCCACTGCAACT
* ***
39191420 TCAAAGAGATAAGATTATTGG-CTTTAATCTGTTCCACTGCAACT
1 TCAGAGAGATAAGATTATTGGTC-TTAATCCACTCCACTGCAACT
*
39191464 TCAGGGAGATAAGACTTAT
1 TCAGAGAGATAAGA-TTAT
39191483 AGCTGCAACT
Statistics
Matches: 144, Mismatches: 32, Indels: 31
0.70 0.15 0.15
Matches are distributed among these distances:
40 2 0.01
41 25 0.17
42 1 0.01
43 9 0.06
44 101 0.70
45 6 0.04
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.30
Consensus pattern (44 bp):
TCAGAGAGATAAGATTATTGGTCTTAATCCACTCCACTGCAACT
Found at i:39191990 original size:100 final size:101
Alignment explanation
Indices: 39191882--39192118 Score: 345
Period size: 100 Copynumber: 2.4 Consensus size: 101
39191872 TCTGCTGCAA
* * *
39191882 CGCC-AGGAAAATAAGATTCACCATTGTGGGTTCAATCTATTTAATTGCAATGTCGGGGAAACAA
1 CGCCAAGGAAAATAAGATTCACCGTTGTGGCTTCAATCTATTTAACTGCAATGTCGGGGAAACAA
*
39191946 GATCC-CTGTCGTGACTTCAATCTGTTCCACTACAC
66 GATCCGCTGTCGTGACTTCAATCTATTCCACTACAC
* ** * * *
39191981 CGCGAAGGAAGGTAAGATTCACCGTTGTGGCTTCAATCTATTTAACTGCGATGTTGGGGAAACCA
1 CGCCAAGGAAAATAAGATTCACCGTTGTGGCTTCAATCTATTTAACTGCAATGTCGGGGAAACAA
*
39192046 GATCCGCTGTCGTGGCTTCAATCTATTCCACTACAC
66 GATCCGCTGTCGTGACTTCAATCTATTCCACTACAC
*
39192082 CGCCAGGGAAAA-AAGATTCACCGTTGTGGCTTCAATC
1 CGCCAAGGAAAATAAGATTCACCGTTGTGGCTTCAATC
39192119 CATTCCACTA
Statistics
Matches: 121, Mismatches: 15, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
99 3 0.02
100 82 0.68
101 36 0.30
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (101 bp):
CGCCAAGGAAAATAAGATTCACCGTTGTGGCTTCAATCTATTTAACTGCAATGTCGGGGAAACAA
GATCCGCTGTCGTGACTTCAATCTATTCCACTACAC
Found at i:39197387 original size:3 final size:3
Alignment explanation
Indices: 39197379--39197487 Score: 69
Period size: 3 Copynumber: 35.3 Consensus size: 3
39197369 TTACATAGTG
* * *
39197379 ATA ATA ATA ACTA AGA ATA ATA ATAA ATA ATC ATA A-A TTA ATA A-A
1 ATA ATA ATA A-TA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA
** * * * * *
39197424 CGA ATA ATA GTA GTAA ATAA ATAA ATA AGA GTA GTA ATA ATA ATA ATA
1 ATA ATA ATA ATA AT-A AT-A AT-A ATA ATA ATA ATA ATA ATA ATA ATA
39197472 ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA A
39197488 ATTTATTCAC
Statistics
Matches: 86, Mismatches: 15, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
2 2 0.02
3 68 0.79
4 16 0.19
ACGTcount: A:0.62, C:0.03, G:0.06, T:0.28
Consensus pattern (3 bp):
ATA
Found at i:39197471 original size:29 final size:29
Alignment explanation
Indices: 39197379--39197472 Score: 77
Period size: 29 Copynumber: 3.2 Consensus size: 29
39197369 TTACATAGTG
* *
39197379 ATAAT-AATAACTAAGAATAATAATAAATA
1 ATAATAAATAAATAAGAGTAATAAT-AATA
* * *
39197408 ATCATAAATTAATAA-ACG-AATAATAGTA
1 ATAATAAATAAATAAGA-GTAATAATAATA
* *
39197436 GTAAATAAATAAATAAGAGTAGTAATAATA
1 AT-AATAAATAAATAAGAGTAATAATAATA
39197466 ATAATAA
1 ATAATAA
39197473 TAATAATAAT
Statistics
Matches: 49, Mismatches: 11, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
28 4 0.08
29 28 0.57
30 17 0.35
ACGTcount: A:0.62, C:0.03, G:0.07, T:0.28
Consensus pattern (29 bp):
ATAATAAATAAATAAGAGTAATAATAATA
Found at i:39201369 original size:3 final size:3
Alignment explanation
Indices: 39201361--39201394 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
39201351 TTTATATTGT
*
39201361 TTA TTA TTA TAA TTA TTA TTA -TA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
39201395 GTATTTATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:39201391 original size:14 final size:14
Alignment explanation
Indices: 39201361--39201399 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
39201351 TTTATATTGT
39201361 TTATTATTATA--A
1 TTATTATTATATTA
39201373 TTATTATTATATTA
1 TTATTATTATATTA
*
39201387 TTATTATTGTATT
1 TTATTATTATATT
39201400 TATATGTGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 11 0.46
14 13 0.54
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (14 bp):
TTATTATTATATTA
Found at i:39201433 original size:16 final size:16
Alignment explanation
Indices: 39201414--39201444 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39201404 TGTGTGCGCC
*
39201414 TATATATATATATTAA
1 TATACATATATATTAA
39201430 TATACATATATATTA
1 TATACATATATATTA
39201445 TAAATGTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (16 bp):
TATACATATATATTAA
Found at i:39205692 original size:9 final size:9
Alignment explanation
Indices: 39205675--39205755 Score: 81
Period size: 9 Copynumber: 8.7 Consensus size: 9
39205665 ATTCAGTTCA
*
39205675 AAAAAAAAA
1 AAAAAAAAG
39205684 AAGAAAAAAG
1 AA-AAAAAAG
*
39205694 GAAAAAAAG
1 AAAAAAAAG
*
39205703 AGAAAAAAG
1 AAAAAAAAG
39205712 AAAAAAAGAG
1 AAAAAAA-AG
*
39205722 AACAAAAAG
1 AAAAAAAAG
*
39205731 AACAAAAAG
1 AAAAAAAAG
*
39205740 AACAAAAAAC
1 AA-AAAAAAG
39205750 AAAAAA
1 AAAAAA
39205756 CAAAAAGAAA
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
9 39 0.64
10 22 0.36
ACGTcount: A:0.83, C:0.05, G:0.12, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:39205700 original size:18 final size:17
Alignment explanation
Indices: 39205677--39205772 Score: 81
Period size: 18 Copynumber: 5.5 Consensus size: 17
39205667 TCAGTTCAAA
39205677 AAAAAAAAAGAAAAAAGG
1 AAAAAAAAAGAAAAAA-G
*
39205695 AAAAAAAGAGAAAAAAG
1 AAAAAAAAAGAAAAAAG
*
39205712 AAAAAAAGAGAACAAAA-
1 AAAAAAAAAGAA-AAAAG
*
39205729 AGAACAAAAAGAACAAAA-
1 A-AAAAAAAAGAA-AAAAG
* *
39205747 AACAAAAAA-CAAAAAG
1 AAAAAAAAAGAAAAAAG
39205763 AAACAAAAAA
1 AAA-AAAAAA
39205773 CCTCTACTGG
Statistics
Matches: 67, Mismatches: 7, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
15 4 0.06
16 3 0.04
17 26 0.39
18 34 0.51
ACGTcount: A:0.82, C:0.06, G:0.11, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAGAAAAAAG
Found at i:39205754 original size:17 final size:15
Alignment explanation
Indices: 39205674--39205772 Score: 81
Period size: 17 Copynumber: 5.8 Consensus size: 15
39205664 GATTCAGTTC
39205674 AAAAAAAAAAAAGAA
1 AAAAAAAAAAAAGAA
39205689 AAAAGGAAAAAAAGAGAA
1 AAAA--AAAAAAA-AGAA
39205707 AAAAGAAAAAAAGAGAA
1 AAAA-AAAAAAA-AGAA
39205724 CAAAAAGAACAAAAAGAA
1 -AAAAA-AA-AAAAAGAA
*
39205742 CAAAAAACAAAAAACAA
1 -AAAAAA-AAAAAAGAA
39205759 AAAGAAACAAAAAA
1 AAA-AAA-AAAAAA
39205773 CCTCTACTGG
Statistics
Matches: 75, Mismatches: 1, Indels: 14
0.83 0.01 0.16
Matches are distributed among these distances:
15 4 0.05
16 3 0.04
17 39 0.52
18 25 0.33
19 4 0.05
ACGTcount: A:0.83, C:0.06, G:0.11, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAGAA
Found at i:39205757 original size:23 final size:25
Alignment explanation
Indices: 39205673--39205773 Score: 63
Period size: 24 Copynumber: 4.0 Consensus size: 25
39205663 AGATTCAGTT
*
39205673 CAAAA-AAAAAAAAGAAA-AAAGGAAA
1 CAAAAGAACAAAAAGAAACAAA--AAA
*
39205698 -AAAAGAGA-AAAAAGAAAAAAAGAGAA
1 CAAAAGA-ACAAAAAGAAACAAA-A-AA
*
39205724 CAAAAAGAA-CAAAA-AGAACAAAAAA
1 C-AAAAGAACAAAAAGA-AACAAAAAA
39205749 CAAAA-AACAAAAAGAAACAAAAAA
1 CAAAAGAACAAAAAGAAACAAAAAA
39205773 C
1 C
39205774 CTCTACTGGG
Statistics
Matches: 64, Mismatches: 3, Indels: 19
0.74 0.03 0.22
Matches are distributed among these distances:
23 2 0.03
24 22 0.34
25 16 0.25
26 8 0.12
27 10 0.16
28 6 0.09
ACGTcount: A:0.81, C:0.08, G:0.11, T:0.00
Consensus pattern (25 bp):
CAAAAGAACAAAAAGAAACAAAAAA
Found at i:39205770 original size:9 final size:9
Alignment explanation
Indices: 39205673--39205770 Score: 56
Period size: 9 Copynumber: 11.6 Consensus size: 9
39205663 AGATTCAGTT
39205673 CAAAA-AAA
1 CAAAAGAAA
*
39205681 AAAAAGAAA
1 CAAAAGAAA
*
39205690 -AAAGGAAA
1 CAAAAGAAA
39205698 -AAAAGAGAA
1 CAAAAGA-AA
39205707 -AAAAGAAA
1 CAAAAGAAA
39205715 -AAAAGAGAA
1 CAAAAGA-AA
39205724 CAAAA-AGAA
1 CAAAAGA-AA
39205733 CAAAA-AGAA
1 CAAAAGA-AA
39205742 C-AAA-AAA
1 CAAAAGAAA
39205749 C-AAA-AAA
1 CAAAAGAAA
39205756 CAAAAAGAAA
1 C-AAAAGAAA
39205766 CAAAA
1 CAAAA
39205771 AACCTCTACT
Statistics
Matches: 80, Mismatches: 3, Indels: 13
0.83 0.03 0.14
Matches are distributed among these distances:
7 10 0.12
8 28 0.35
9 34 0.43
10 8 0.10
ACGTcount: A:0.82, C:0.07, G:0.11, T:0.00
Consensus pattern (9 bp):
CAAAAGAAA
Found at i:39206277 original size:23 final size:23
Alignment explanation
Indices: 39206250--39206295 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
39206240 CGCAAAAAAA
*
39206250 AAAAAGATGAGAAATGAAAAAGTG
1 AAAAA-ATGAAAAATGAAAAAGTG
*
39206274 AAAAAATGAAAAATGGAAAAGT
1 AAAAAATGAAAAATGAAAAAGT
39206296 TAAATGGAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.65, C:0.00, G:0.22, T:0.13
Consensus pattern (23 bp):
AAAAAATGAAAAATGAAAAAGTG
Found at i:39207756 original size:132 final size:131
Alignment explanation
Indices: 39207519--39208311 Score: 1167
Period size: 132 Copynumber: 6.0 Consensus size: 131
39207509 TTACAGAGAA
* * *
39207519 CAGATCGAAGATGACAGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAATAATTC
1 CAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTC
* *
39207584 TACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGG
66 TA-TCCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGG
39207649 AG
130 AG
39207651 CAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTC
1 CAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTC
* *
39207716 TACTCCCCTGGGCAGCAATGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCGGTAGTGG
66 TA-TCCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGG
39207781 AG
130 AG
* *
39207783 CAGATCGAAGATGGCAGATTTTACCTCCCTATGGTTACAGTGGAGTACATTGAAGCCAATAATTC
1 CAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTC
* * * *
39207848 TATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAAATCTTATCTCCCGAGGCAGTAGTGG
66 TATC-CCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGG
39207913 AG
130 AG
* *
39207915 CAGATCAAAGATGGTAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTC
1 CAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTC
* * * * *
39207980 TACTTCCCTGGACAGCAGTGGAATAGATTGAAGATTTTAGATCTTATCTCCCTAACCAGTAATGG
66 TA-TCCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGG
39208045 AG
130 AG
* *
39208047 CAGATCGAAGATGGC-GAATTTTACCTCCCTGGGGTTACCGTGGAGTACATTGAAGCCAGTAATT
1 CAGATCGAAGATGGCAG-ATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATT
*** * *
39208111 CTATCCCCCTGGTTGGCAGTGGAATAGATTGAAGATTTCAGATCTTATTTCCCTAAGCGGTAGTG
65 CTAT-CCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTG
39208176 GAG
129 GAG
* * *
39208179 CAGATTGAAGATGGCGGATTTTACCTCCCTGGGGTTACAGTGGAGTACATTGAAGCCAGTAATTC
1 CAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTC
* * * ** *
39208244 TATCTCCCTGGTC-GACAGTGGAATCGATCGAAGAATAGCAAATCTTATCTCCCTAAGCAGTAGT
66 TATC-CCCTGGGCAG-CAGTGGAATAGATTGAAG-ATTTCAGATCTTATCTCCCTAAGCAGTAGT
39208308 GGAG
128 GGAG
39208312 TAGACTGATG
Statistics
Matches: 602, Mismatches: 51, Indels: 15
0.90 0.08 0.02
Matches are distributed among these distances:
131 6 0.01
132 565 0.94
133 31 0.05
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.28
Consensus pattern (131 bp):
CAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTC
TATCCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGA
G
Found at i:39207897 original size:44 final size:44
Alignment explanation
Indices: 39207588--39208032 Score: 173
Period size: 44 Copynumber: 10.1 Consensus size: 44
39207578 TAATTCTACT
* * *
39207588 TCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTC
1 TCCCTGGGCAGCAGTGGAGTAGATTGAAGATTACAGATCTTATC
** * * * ** * *
39207632 TCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTTTACC
1 TCCCTGGGCAGCAGTGGAGTAGATTGAAGATTACAGATCTTATC
* * * *
39207676 TCCCTGTGGTTA-CAGTGGAGTACATTGAAGCCAGTA-A-TTC-TA-C
1 TCCCTG-GG-CAGCAGTGGAGTAGATTGAAG--ATTACAGATCTTATC
* * *
39207719 TCCCCTGGGCAGCAATGGAATAGATTGAAGATTTCAGATCTTATC
1 T-CCCTGGGCAGCAGTGGAGTAGATTGAAGATTACAGATCTTATC
** * * * * ** * *
39207764 TCCCTAAGCGGTAGTGGAGCAGATCGAAGATGGCAGATTTTACC
1 TCCCTGGGCAGCAGTGGAGTAGATTGAAGATTACAGATCTTATC
** * * *
39207808 TCCCTATGGTTA-CAGTGGAGTACATTGAAGCCAATA-A-TTC-TATC
1 TCCC--TGGGCAGCAGTGGAGTAGATTGAAG--ATTACAGATCTTATC
* *
39207852 TCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAAATCTTATC
1 TCCCTGGGCAGCAGTGGAGTAGATTGAAGATTACAGATCTTATC
* * ** *** * *
39207896 TCCC-GAGGCAGTAGTGGAGCAGATCAAAGATGGTAGATTTTACC
1 TCCCTG-GGCAGCAGTGGAGTAGATTGAAGATTACAGATCTTATC
* * * *
39207940 TCCCTGTGGTTA-CAGTGGAGTACATTGAAGCCAGTA-A-TTC-TA-C
1 TCCCTG-GG-CAGCAGTGGAGTAGATTGAAG--ATTACAGATCTTATC
* * **
39207983 TTCCCTGGACAGCAGTGGAATAGATTGAAGATTTTAGATCTTATC
1 -TCCCTGGGCAGCAGTGGAGTAGATTGAAGATTACAGATCTTATC
39208028 TCCCT
1 TCCCT
39208033 AACCAGTAAT
Statistics
Matches: 279, Mismatches: 93, Indels: 58
0.65 0.22 0.13
Matches are distributed among these distances:
41 7 0.03
42 9 0.03
43 60 0.22
44 143 0.51
45 51 0.18
46 6 0.02
47 3 0.01
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (44 bp):
TCCCTGGGCAGCAGTGGAGTAGATTGAAGATTACAGATCTTATC
Found at i:39209628 original size:3 final size:3
Alignment explanation
Indices: 39209620--39209653 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
39209610 TTTATATTGT
*
39209620 TTA TTA TTA TAA TTA TTA TTA -TA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
39209654 GTATTTATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:39209650 original size:14 final size:14
Alignment explanation
Indices: 39209620--39209658 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
39209610 TTTATATTGT
39209620 TTATTATTATA--A
1 TTATTATTATATTA
39209632 TTATTATTATATTA
1 TTATTATTATATTA
*
39209646 TTATTATTGTATT
1 TTATTATTATATT
39209659 TATATGTGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 11 0.46
14 13 0.54
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (14 bp):
TTATTATTATATTA
Found at i:39209841 original size:22 final size:22
Alignment explanation
Indices: 39209813--39209965 Score: 225
Period size: 22 Copynumber: 7.0 Consensus size: 22
39209803 TGTTGATAGT
*
39209813 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTA
39209835 ACGTACTAAGCTCTCATGTTTA
1 ACGTACTAAGCTCTCATGTTTA
39209857 ACGTACTAAGCTCTCATGTTTA
1 ACGTACTAAGCTCTCATGTTTA
* * * **
39209879 ACGAACTAAACCCTCATGGCTA
1 ACGTACTAAGCTCTCATGTTTA
**
39209901 ACGTACTAAGCTCTCATGGCTA
1 ACGTACTAAGCTCTCATGTTTA
*
39209923 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTA
39209945 ACGTACTAAGCTCTCATGTTT
1 ACGTACTAAGCTCTCATGTTT
39209966 GAACAATAAA
Statistics
Matches: 119, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 119 1.00
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.33
Consensus pattern (22 bp):
ACGTACTAAGCTCTCATGTTTA
Found at i:39211846 original size:29 final size:29
Alignment explanation
Indices: 39211765--39211845 Score: 99
Period size: 31 Copynumber: 2.7 Consensus size: 29
39211755 AATTTTAAAA
*
39211765 TTATACATAAATTATGATTTAATGTGCAATT
1 TTATACATAAATTTTGATTT--TGTGCAATT
* * *
39211796 GTATATATAAATTTTAATTTTGTGCAATT
1 TTATACATAAATTTTGATTTTGTGCAATT
39211825 TTATACATGAAATTTTGATTT
1 TTATACAT-AAATTTTGATTT
39211846 GATCCAATTC
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 15 0.36
30 11 0.26
31 16 0.38
ACGTcount: A:0.36, C:0.05, G:0.10, T:0.49
Consensus pattern (29 bp):
TTATACATAAATTTTGATTTTGTGCAATT
Found at i:39221892 original size:40 final size:40
Alignment explanation
Indices: 39221847--39221950 Score: 138
Period size: 40 Copynumber: 2.6 Consensus size: 40
39221837 GAAAAAATAT
** *
39221847 CGCTATAGATCGAGCT-TTAGCGGCGCTTTTTGGAAAACGC
1 CGCTATAGATCGA-CTATTAGCGGCGCTACTTGAAAAACGC
39221887 CGCTATAGATCGACTATTAGCGGCGCTACTTGAAAAACGC
1 CGCTATAGATCGACTATTAGCGGCGCTACTTGAAAAACGC
* * *
39221927 CGCTATAGGTAGACAATTAGCGGC
1 CGCTATAGATCGACTATTAGCGGC
39221951 ACTTTCTGAA
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
39 2 0.04
40 55 0.96
ACGTcount: A:0.27, C:0.23, G:0.26, T:0.24
Consensus pattern (40 bp):
CGCTATAGATCGACTATTAGCGGCGCTACTTGAAAAACGC
Found at i:39221961 original size:40 final size:40
Alignment explanation
Indices: 39221863--39221961 Score: 119
Period size: 40 Copynumber: 2.5 Consensus size: 40
39221853 AGATCGAGCT
* * * *
39221863 TTAGCGGCGCTTTTTGGAAAACGCCGCTATAGATCGACTA
1 TTAGCGGCGCTTTCTGAAAAACGCCGCTATAGATAGACAA
* *
39221903 TTAGCGGCGC-TACTTGAAAAACGCCGCTATAGGTAGACAA
1 TTAGCGGCGCTTTC-TGAAAAACGCCGCTATAGATAGACAA
*
39221943 TTAGCGGCACTTTCTGAAA
1 TTAGCGGCGCTTTCTGAAA
39221962 TCGCCGCAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
39 1 0.02
40 46 0.94
41 2 0.04
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.25
Consensus pattern (40 bp):
TTAGCGGCGCTTTCTGAAAAACGCCGCTATAGATAGACAA
Found at i:39222078 original size:40 final size:39
Alignment explanation
Indices: 39222016--39222120 Score: 124
Period size: 40 Copynumber: 2.6 Consensus size: 39
39222006 ACTTTAGTGG
* * *
39222016 CATTAGCGACGCTTTTTAAAAAACGCCGCTA-ATGGTCGA-
1 CATTAGCGGCGC-TTTTGAAAAACGCCACTACA-GGTCGAC
39222055 CATTTAGCGGCGCTCTTTGAAAAACGCCACTACAGGTCGAC
1 CA-TTAGCGGCGCT-TTTGAAAAACGCCACTACAGGTCGAC
39222096 CATTAGCGGCGCTTTTGGAAAAACG
1 CATTAGCGGCGCTTTT-GAAAAACG
39222121 TCGCAAAAGA
Statistics
Matches: 58, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
39 6 0.10
40 49 0.84
41 3 0.05
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.24
Consensus pattern (39 bp):
CATTAGCGGCGCTTTTGAAAAACGCCACTACAGGTCGAC
Found at i:39222446 original size:7 final size:7
Alignment explanation
Indices: 39222424--39222698 Score: 121
Period size: 7 Copynumber: 38.7 Consensus size: 7
39222414 TTAATTATCA
*
39222424 TTATAGT
1 TTATGGT
*
39222431 TTAGGGT
1 TTATGGT
*
39222438 TTATAGT
1 TTATGGT
*
39222445 TTACGGT
1 TTATGGT
39222452 TTATGGT
1 TTATGGT
*
39222459 TTA-GGG
1 TTATGGT
* *
39222465 TAATAGT
1 TTATGGT
*
39222472 TTAGGGT
1 TTATGGT
*
39222479 TTAAGGT
1 TTATGGT
*
39222486 TTAAGAGT
1 TTATG-GT
39222494 TACTAT--T
1 T--TATGGT
*
39222501 TTAAGGT
1 TTATGGT
*
39222508 TTATGGA
1 TTATGGT
39222515 TTATGGGT
1 TTAT-GGT
* *
39222523 TTAGGGA
1 TTATGGT
*
39222530 TAATGGT
1 TTATGGT
39222537 TTATGGT
1 TTATGGT
39222544 TTATGGT
1 TTATGGT
*
39222551 TTAAGGT
1 TTATGGT
*
39222558 TTAAGAGT
1 TTATG-GT
39222566 TAGTAT--T
1 T--TATGGT
*
39222573 TTAAGGT
1 TTATGGT
*
39222580 TTATGGG
1 TTATGGT
39222587 TTATGGGT
1 TTAT-GGT
* *
39222595 TTAGGGA
1 TTATGGT
39222602 TTATGGT
1 TTATGGT
39222609 TTATGGT
1 TTATGGT
39222616 TTATGGT
1 TTATGGT
*
39222623 TTAAAGG-
1 TT-ATGGT
**
39222630 TTGGGGT
1 TTATGGT
*
39222637 TTAAGGT
1 TTATGGT
*
39222644 TTAAGGT
1 TTATGGT
* *
39222651 TTAGGGG
1 TTATGGT
*
39222658 TTAGGGGT
1 TTA-TGGT
*
39222666 TTAAGGT
1 TTATGGT
*
39222673 TTAAGGT
1 TTATGGT
*
39222680 TTATGTT
1 TTATGGT
*
39222687 TTATGTT
1 TTATGGT
39222694 TTATG
1 TTATG
39222699 ATTCAGAGTT
Statistics
Matches: 205, Mismatches: 47, Indels: 32
0.72 0.17 0.11
Matches are distributed among these distances:
5 4 0.02
6 6 0.03
7 166 0.81
8 25 0.12
10 4 0.02
ACGTcount: A:0.23, C:0.01, G:0.30, T:0.47
Consensus pattern (7 bp):
TTATGGT
Found at i:39222479 original size:27 final size:28
Alignment explanation
Indices: 39222424--39222523 Score: 94
Period size: 29 Copynumber: 3.5 Consensus size: 28
39222414 TTAATTATCA
* *
39222424 TTATAGTTTAGGGTTTATAGTTTACGGT
1 TTATGGTTTAGGGTTAATAGTTTACGGT
*
39222452 TTATGGTTTAGGG-TAATAGTTTAGGGT
1 TTATGGTTTAGGGTTAATAGTTTACGGT
* * * * *
39222479 TTAAGGTTTAAGAGTTACTATTTTAAGGT
1 TTATGGTTT-AGGGTTAATAGTTTACGGT
*
39222508 TTATGGATTATGGGTT
1 TTATGGTTTA-GGGTT
39222524 TAGGGATAAT
Statistics
Matches: 58, Mismatches: 11, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
27 20 0.34
28 16 0.28
29 22 0.38
ACGTcount: A:0.24, C:0.02, G:0.27, T:0.47
Consensus pattern (28 bp):
TTATGGTTTAGGGTTAATAGTTTACGGT
Found at i:39222560 original size:72 final size:72
Alignment explanation
Indices: 39222470--39222631 Score: 279
Period size: 72 Copynumber: 2.2 Consensus size: 72
39222460 TAGGGTAATA
*
39222470 GTTTAGGGTTTAAGGTTTAAGAGTTACTATTTTAAGGTTTATGGATTATGGGTTTAGGGATAATG
1 GTTTATGGTTTAAGGTTTAAGAGTTACTATTTTAAGGTTTATGGATTATGGGTTTAGGGATAATG
39222535 GTTTATG
66 GTTTATG
* * *
39222542 GTTTATGGTTTAAGGTTTAAGAGTTAGTATTTTAAGGTTTATGGGTTATGGGTTTAGGGATTATG
1 GTTTATGGTTTAAGGTTTAAGAGTTACTATTTTAAGGTTTATGGATTATGGGTTTAGGGATAATG
39222607 GTTTATG
66 GTTTATG
39222614 GTTTATGGTTTAAAGGTT
1 GTTTATGGTTT-AAGGTT
39222632 GGGGTTTAAG
Statistics
Matches: 85, Mismatches: 4, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
72 79 0.93
73 6 0.07
ACGTcount: A:0.23, C:0.01, G:0.30, T:0.46
Consensus pattern (72 bp):
GTTTATGGTTTAAGGTTTAAGAGTTACTATTTTAAGGTTTATGGATTATGGGTTTAGGGATAATG
GTTTATG
Found at i:39222710 original size:71 final size:71
Alignment explanation
Indices: 39222500--39222710 Score: 187
Period size: 72 Copynumber: 3.0 Consensus size: 71
39222490 GAGTTACTAT
* * * * * *
39222500 TTTAAGGTTTATGGATTATGGGTTTAGGGA-TAATGGTTTATGGTTTATGGTTTAAGGTTTAAGA
1 TTTAAGGTTTAGGGGTTAGGGGTTTAAGGATTAA-GGTTTATGGTTTATGGTTTAAAGATT-AGA
*
39222564 G-TT-AGTAT
64 GTTTAAG--G
* * * * * * *
39222572 TTTAAGGTTTATGGGTTATGGGTTTAGGGATTATGGTTTATGGTTTATGGTTTAAAGGTTGGGGT
1 TTTAAGGTTTAGGGGTTAGGGGTTTAAGGATTAAGGTTTATGGTTTATGGTTTAAAGATTAGAGT
39222637 TTAAGG
66 TTAAGG
* * * *
39222643 TTTAAGGTTTAGGGGTTAGGGGTTTAAGGTTTAAGGTTTATGTTTTAT-GTTTTATGATTCAGAG
1 TTTAAGGTTTAGGGGTTAGGGGTTTAAGGATTAAGGTTTATGGTTTATGGTTTAAAGATT-AGAG
39222707 TTTA
65 TTTA
39222711 GGGGATAGGG
Statistics
Matches: 117, Mismatches: 18, Indels: 9
0.81 0.12 0.06
Matches are distributed among these distances:
70 8 0.07
71 50 0.43
72 55 0.47
73 4 0.03
ACGTcount: A:0.22, C:0.00, G:0.31, T:0.46
Consensus pattern (71 bp):
TTTAAGGTTTAGGGGTTAGGGGTTTAAGGATTAAGGTTTATGGTTTATGGTTTAAAGATTAGAGT
TTAAGG
Found at i:39223688 original size:113 final size:113
Alignment explanation
Indices: 39223262--39223689 Score: 346
Period size: 113 Copynumber: 3.8 Consensus size: 113
39223252 ACAATAATTT
* * * * *
39223262 TTTTAATAAAAATGGCGCCGTTTTATTGGATTTCTTAGTGGCGGTTTTGGTTCAACGCTGTAATA
1 TTTTAATCAAAACGGCGCCGTTTTATTGGATTT-TTAGTGGCGTTTTTGGTTAAACGCTGCAATA
* * * * ** *
39223327 TGTCGGG-TTGTAGCGGCGCTATCCTAAAAACGCCATAAAAAGTTATTCTG
65 GGTAGGGCTT-TAGCGGCGCTAGCC-AAAAATGCCGCAAAAAGTTATTTTG
* * * ** * * * * *
39223377 TTTTTATCAAAACGACACTTTTTTATTTG-TTTTTAGTGGCATTTTTGGTAAAATGCCGCAATAG
1 TTTTAATCAAAACGGCGCCGTTTTATTGGATTTTTAGTGGCGTTTTTGGTTAAACGCTGCAATAG
* * ** * * *
39223441 GTCA-GGCTTTAACGGTGCTAGGTGAAAAATGCTGCAAAAGGTTAATTTG
66 GT-AGGGCTTTAGCGGCGCTA-GCCAAAAATGCCGCAAAAAGTTATTTTG
* * * * * *
39223490 TTTTAATCAAAACAGTGCCGTTTTATTTGATTTTTTAGTGGCG-TTTTCGTCGAAACGCTGCAAA
1 TTTTAATCAAAACGGCGCCGTTTTATTGGA-TTTTTAGTGGCGTTTTTGGT-TAAACGCTGCAAT
* * * **
39223554 AGGTCGGGCTTTAGTGACGCTA-CCAAAAATGCCGCAAACTGTTATTTTG
64 AGGTAGGGCTTTAGCGGCGCTAGCCAAAAATGCCGCAAAAAGTTATTTTG
*
39223603 TTTTAATCAAAACGGCGCCGTTTT-TGTAGGATTTTTAGTGGCGTTTTTAGTTAAACGCTGCAAT
1 TTTTAATCAAAACGGCGCCGTTTTAT-T-GGATTTTTAGTGGCGTTTTTGGTTAAACGCTGCAAT
* *
39223667 ATGTAGGGATTTAGCGGCGCTAG
64 AGGTAGGGCTTTAGCGGCGCTAG
39223690 TGGATAAACG
Statistics
Matches: 238, Mismatches: 64, Indels: 23
0.73 0.20 0.07
Matches are distributed among these distances:
112 1 0.00
113 161 0.68
114 19 0.08
115 57 0.24
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (113 bp):
TTTTAATCAAAACGGCGCCGTTTTATTGGATTTTTAGTGGCGTTTTTGGTTAAACGCTGCAATAG
GTAGGGCTTTAGCGGCGCTAGCCAAAAATGCCGCAAAAAGTTATTTTG
Found at i:39225885 original size:34 final size:34
Alignment explanation
Indices: 39225842--39225910 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
39225832 TAAGTTCTAG
39225842 AATTTGATAAATATTCATCAATTATAATTTGTTT
1 AATTTGATAAATATTCATCAATTATAATTTGTTT
39225876 AATTTGATAAATATTCATCAATTATAATTTGTTT
1 AATTTGATAAATATTCATCAATTATAATTTGTTT
39225910 A
1 A
39225911 TCTTCTAACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.49
Consensus pattern (34 bp):
AATTTGATAAATATTCATCAATTATAATTTGTTT
Found at i:39228939 original size:43 final size:43
Alignment explanation
Indices: 39228851--39229244 Score: 496
Period size: 43 Copynumber: 9.3 Consensus size: 43
39228841 GAACGGTACT
*
39228851 TTTAGCGGCGTTTGTGA-AAAA-CGCCGCTAAAGGTCATGTTA
1 TTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGGTCATGTTC
* * * *
39228892 TTTAGCGGCGTTTGTGCTAAAAGCGCCGTTAAAGGTCATATTT
1 TTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGGTCATGTTC
***
39228935 TTTAGCGGCGTTTGTGATAAAAGCTTTGCTAAA-G--ATGTTC
1 TTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGGTCATGTTC
* * *
39228975 TTTAGTGGCGTTTGTGATAAAA-AGTCGCTAAAGGTCATGTTC
1 TTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGGTCATGTTC
* * * * *
39229017 TTTAGCAGCGTTTATGCTAAAAGCACCACTAAAGGTCATGTTC
1 TTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGGTCATGTTC
39229060 TTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGGTCATGTTC
1 TTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGGTCATGTTC
* *
39229103 TTTAGCGGCGTTTGTAATAAAAGCGCCACTAAAGGTCATGTTC
1 TTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGGTCATGTTC
* * *
39229146 TTTAGCGCCGTTTGTCATGAAAA-TGCCGCTAAAGGTCATGTTC
1 TTTAGCGGCGTTTGTGAT-AAAAGCGCCGCTAAAGGTCATGTTC
* * * *
39229189 TTTAGCGACGATTGTGACAAAAGTGCCGCTAAAGGTCATGTTC
1 TTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGGTCATGTTC
*
39229232 TTTAACGGCGTTT
1 TTTAGCGGCGTTT
39229245 ATGTGAAAAA
Statistics
Matches: 304, Mismatches: 41, Indels: 14
0.85 0.11 0.04
Matches are distributed among these distances:
39 7 0.02
40 26 0.09
41 16 0.05
42 33 0.11
43 218 0.72
44 4 0.01
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGGTCATGTTC
Found at i:39232788 original size:14 final size:13
Alignment explanation
Indices: 39232769--39232816 Score: 66
Period size: 14 Copynumber: 3.8 Consensus size: 13
39232759 TGAAAAAGAA
39232769 AGAAAAAAATAAGG
1 AGAAAAAAAT-AGG
39232783 AGAAAAAAATAGG
1 AGAAAAAAATAGG
39232796 AG--AAAAATA-G
1 AGAAAAAAATAGG
39232806 AGAAAAAAATA
1 AGAAAAAAATA
39232817 CTTATTTCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
10 3 0.09
11 7 0.22
12 7 0.22
13 5 0.16
14 10 0.31
ACGTcount: A:0.73, C:0.00, G:0.19, T:0.08
Consensus pattern (13 bp):
AGAAAAAAATAGG
Found at i:39239887 original size:28 final size:28
Alignment explanation
Indices: 39239847--39239903 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
39239837 ACATCTGACC
*
39239847 AATTTCTTTCTTTTGGGAAATTCAACTA
1 AATTTCTTCCTTTTGGGAAATTCAACTA
39239875 AATTTCTTCCTTTTGGGAAATTCAACTA
1 AATTTCTTCCTTTTGGGAAATTCAACTA
39239903 A
1 A
39239904 CTCTCATGTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.30, C:0.16, G:0.11, T:0.44
Consensus pattern (28 bp):
AATTTCTTCCTTTTGGGAAATTCAACTA
Found at i:39240114 original size:16 final size:16
Alignment explanation
Indices: 39240093--39240131 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
39240083 GTTTGGTTCA
39240093 CTGTAATGGAAAAGAG
1 CTGTAATGGAAAAGAG
*
39240109 CTGTAATGGAATAGAG
1 CTGTAATGGAAAAGAG
39240125 CTGTAAT
1 CTGTAAT
39240132 AGTAATTCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.38, C:0.08, G:0.28, T:0.26
Consensus pattern (16 bp):
CTGTAATGGAAAAGAG
Found at i:39240163 original size:45 final size:44
Alignment explanation
Indices: 39240114--39240201 Score: 133
Period size: 45 Copynumber: 2.0 Consensus size: 44
39240104 AAGAGCTGTA
*
39240114 ATGGAATAGAGCTGTAATAGTAATTCAATG-GTTTGGTTGAATGGG
1 ATGGAATAGAGCTATAATAGT-ATT-AATGTGTTTGGTTGAATGGG
*
39240159 ATGGAATAGAGCTATAATAGTATTATTGTGTTTGGTTGAATGG
1 ATGGAATAGAGCTATAATAGTATTAATGTGTTTGGTTGAATGG
39240202 AATGATATTG
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
43 3 0.08
44 17 0.43
45 20 0.50
ACGTcount: A:0.31, C:0.03, G:0.30, T:0.36
Consensus pattern (44 bp):
ATGGAATAGAGCTATAATAGTATTAATGTGTTTGGTTGAATGGG
Found at i:39240430 original size:57 final size:56
Alignment explanation
Indices: 39240314--39240447 Score: 153
Period size: 57 Copynumber: 2.3 Consensus size: 56
39240304 AATAAGATTA
* * *
39240314 TTAATAAAAATAATAAATAATTTAATCATATTTTAACATAATTATTATTAAATATAAT
1 TTAAT-AAAATAATATATAATTTAATAAAATTTTAACATAATTATTATT-AATATAAT
* *
39240372 TTAATAAAATAATATATAATTTAATAAAATTCTTAATATAATTATTCTT-ATATGAAT
1 TTAATAAAATAATATATAATTTAATAAAATT-TTAACATAATTATTATTAATAT-AAT
* *
39240429 TTACTAAAATCATAATATA
1 TTAATAAAATAAT-ATATA
39240448 TAATACTATA
Statistics
Matches: 66, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
56 4 0.06
57 37 0.56
58 25 0.38
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.43
Consensus pattern (56 bp):
TTAATAAAATAATATATAATTTAATAAAATTTTAACATAATTATTATTAATATAAT
Found at i:39241070 original size:46 final size:46
Alignment explanation
Indices: 39241020--39241110 Score: 164
Period size: 46 Copynumber: 2.0 Consensus size: 46
39241010 TTTTGTAGTG
*
39241020 TTAATTATAATTTTTAATCAAACAATATAAGTAATATAAAATATTT
1 TTAATTATAATTTTCAATCAAACAATATAAGTAATATAAAATATTT
*
39241066 TTAATTATAATTTTCAATCATACAATATAAGTAATATAAAATATT
1 TTAATTATAATTTTCAATCAAACAATATAAGTAATATAAAATATT
39241111 GTTTGAAGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.43
Consensus pattern (46 bp):
TTAATTATAATTTTCAATCAAACAATATAAGTAATATAAAATATTT
Found at i:39242151 original size:13 final size:13
Alignment explanation
Indices: 39242133--39242163 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
39242123 AGAAATATAG
*
39242133 CAGAATGTTTTAT
1 CAGAATATTTTAT
39242146 CAGAATATTTTAT
1 CAGAATATTTTAT
39242159 CAGAA
1 CAGAA
39242164 CATCTGCTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.39
Consensus pattern (13 bp):
CAGAATATTTTAT
Found at i:39246380 original size:11 final size:10
Alignment explanation
Indices: 39246346--39246379 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
39246336 AAAGAAAAAT
39246346 AAATAAGAAGA
1 AAATAAG-AGA
39246357 AAATAAGAGA
1 AAATAAGAGA
*
39246367 AAATAAGGGA
1 AAATAAGAGA
39246377 AAA
1 AAA
39246380 AACTTATTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 15 0.68
11 7 0.32
ACGTcount: A:0.71, C:0.00, G:0.21, T:0.09
Consensus pattern (10 bp):
AAATAAGAGA
Found at i:39248645 original size:75 final size:75
Alignment explanation
Indices: 39248522--39248671 Score: 282
Period size: 75 Copynumber: 2.0 Consensus size: 75
39248512 AGAGTAATAG
*
39248522 TGGAGAATAACAATTCAGCATCATCACCTACAGAAACCAAATCTAGTGTGGAGGAGAATTCGTCT
1 TGGAGAATAACAATTCAGCATCATCACCTACAGAAACCAAATCTAGTGTGGAGGAGAATTCCTCT
39248587 GATGCTGATT
66 GATGCTGATT
*
39248597 TGGAGAATAACAATTCAGCATCATCACCTACAGAAACCAAGTCTAGTGTGGAGGAGAATTCCTCT
1 TGGAGAATAACAATTCAGCATCATCACCTACAGAAACCAAATCTAGTGTGGAGGAGAATTCCTCT
39248662 GATGCTGATT
66 GATGCTGATT
39248672 CCTCAATGAT
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
75 73 1.00
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.25
Consensus pattern (75 bp):
TGGAGAATAACAATTCAGCATCATCACCTACAGAAACCAAATCTAGTGTGGAGGAGAATTCCTCT
GATGCTGATT
Found at i:39253712 original size:26 final size:29
Alignment explanation
Indices: 39253683--39253743 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 29
39253673 TTTGTTAGGA
* *
39253683 CTTTGAAT-ATTTCCTC-TTTGAAC-TTT
1 CTTTGAATAATATCATCTTTTGAACTTTT
39253709 CTTTG-ATAATATCATCTTTTGAACTTTT
1 CTTTGAATAATATCATCTTTTGAACTTTT
39253737 CTTTGAA
1 CTTTGAA
39253744 ACATTACCTG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
25 2 0.07
26 11 0.38
27 7 0.24
28 8 0.28
29 1 0.03
ACGTcount: A:0.23, C:0.16, G:0.08, T:0.52
Consensus pattern (29 bp):
CTTTGAATAATATCATCTTTTGAACTTTT
Found at i:39257488 original size:19 final size:19
Alignment explanation
Indices: 39257451--39257486 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
39257441 TTTTGACTAA
39257451 CATCTATGATTTCTATTTT
1 CATCTATGATTTCTATTTT
39257470 CATC-ATGATTTCT-TTTT
1 CATCTATGATTTCTATTTT
39257487 TTATAATACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
18 9 0.53
19 4 0.24
ACGTcount: A:0.19, C:0.17, G:0.06, T:0.58
Consensus pattern (19 bp):
CATCTATGATTTCTATTTT
Found at i:39276065 original size:43 final size:43
Alignment explanation
Indices: 39276013--39276251 Score: 147
Period size: 43 Copynumber: 5.6 Consensus size: 43
39276003 AGATTGAAGA
*
39276013 TCTTATCTCCCTAAACAGTAGTGGAGCGGATCGAAAGTACCAG
1 TCTTATCTCCCTAAGCAGTAGTGGAGCGGATCGAAAGTACCAG
* * * *
39276056 TCTTATCTCCCTTAGTAGTAGTGGAGCAGA-C-AGAAGAAACC-G
1 TCTTATCTCCCTAAGCAGTAGTGGAGCGGATCGA-AAG-TACCAG
* * * * * * *
39276098 ATCTTATCTCTCTGAAGTTA-CAGTAGAGCAGATCG-TA-T-CCAA
1 -TCTTATCTCCCT-AAG-CAGTAGTGGAGCGGATCGAAAGTACCAG
* * * * * * *
39276140 CCTTATCTCCCTGAGCAGCAGCGGAGTAGG-TCCAAGATTGA--AG
1 TCTTATCTCCCTAAGCAGTAGTGGAG-CGGATCGAA-AGT-ACCAG
39276183 ATCTTATCTCCCTAAGCAGTAGTGGAGCGGATCGAAAGTACCAG
1 -TCTTATCTCCCTAAGCAGTAGTGGAGCGGATCGAAAGTACCAG
*
39276227 TCTTATCTCCTTAAGCAGTAGTGGA
1 TCTTATCTCCCTAAGCAGTAGTGGA
39276252 ACAGACAGAA
Statistics
Matches: 146, Mismatches: 31, Indels: 38
0.68 0.14 0.18
Matches are distributed among these distances:
39 1 0.01
40 10 0.07
41 14 0.10
42 7 0.05
43 70 0.48
44 41 0.28
45 3 0.02
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.26
Consensus pattern (43 bp):
TCTTATCTCCCTAAGCAGTAGTGGAGCGGATCGAAAGTACCAG
Found at i:39276132 original size:87 final size:84
Alignment explanation
Indices: 39276036--39276386 Score: 239
Period size: 87 Copynumber: 4.1 Consensus size: 84
39276026 AACAGTAGTG
* *
39276036 GAGCGGATCGAAAGTACCAGTCTTATCTCCCTTAGTAGTAGTGGAGCAGACAGAAGAAACCGATC
1 GAGCGGATCG-AA-T-CCAGTCTTATCTCCCTTAGCAGCAGTGGAGCAGACAGAAGAAACCGATC
39276101 TTATCTCTCTGAAGTTACAGTA
63 TTATCTCTCTGAAGTTACAGTA
* * ** * * * * *
39276123 GAGCAGATCGTATCCAACCTTATCTCCCTGAGCAGCAGCGGAGTAGGTC-CAAGATTGAA--GAT
1 GAGCGGATCGAATCCAGTCTTATCTCCCTTAGCAGCAGTGGAGCA-GACAGAAGA---AACCGAT
* * * *
39276185 CTTATCTCCCT-AAG-CAGTAGTG
62 CTTATCTCTCTGAAGTTA-CAGTA
* *
39276207 GAGCGGATCGAAAGTACCAGTCTTATCT-CCTTAAGCAGTAGTGGAACAGACAGAAGAAACCACA
1 GAGCGGATCG-AA-T-CCAGTCTTATCTCCCTT-AGCAGCAGTGGAGCAGACAGAAGAAA-C-C-
* *
39276271 GATCTTATCTCTCTAAAGTTGCAGTA
59 GATCTTATCTCTCTGAAGTTACAGTA
* * ** * * * *
39276297 GAGCGGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGAAGCAGACAAAAGAAACCAATCCT
1 GAGCGGATCGAATCCAGTCTTATCTCCCT-TAGCAGCAGTGGAGCAGACAGAAGAAACCGATCTT
* *
39276362 ATCTC-CTTGAAGTTGCAGTG
65 ATCTCTC-TGAAGTTACAGTA
39276382 GAGCG
1 GAGCG
39276387 AATTAAAACC
Statistics
Matches: 201, Mismatches: 43, Indels: 42
0.70 0.15 0.15
Matches are distributed among these distances:
83 1 0.00
84 47 0.23
85 42 0.21
86 8 0.04
87 49 0.24
88 24 0.12
89 14 0.07
90 16 0.08
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.24
Consensus pattern (84 bp):
GAGCGGATCGAATCCAGTCTTATCTCCCTTAGCAGCAGTGGAGCAGACAGAAGAAACCGATCTTA
TCTCTCTGAAGTTACAGTA
Found at i:39276173 original size:171 final size:174
Alignment explanation
Indices: 39275970--39276327 Score: 580
Period size: 171 Copynumber: 2.1 Consensus size: 174
39275960 CATATCAAAT
* *
39275970 CTTATCTCTCTGAGCAGTAGCGGAGTAGGTCCAAGATTGAAGATCTTATCTCCCTAAACAGTAGT
1 CTTATCTCCCTGAGCAGCAGCGGAGTAGGTCCAAGATTGAAGATCTTATCTCCCTAAACAGTAGT
* *
39276035 GGAGCGGATCGAAAGTACCAGTCTTATCTCCCTT-AGTAGTAGTGGAGCAGACAGAAGAAA-C-C
66 GGAGCGGATCGAAAGTACCAGTCTTATCT-CCTTAAGCAGTAGTGGAACAGACAGAAGAAACCAC
* *
39276097 -GATCTTATCTCTCTGAAGTTACAGTAGAGCAGATCGTATCCAAC
130 AGATCTTATCTCTCTAAAGTTACAGTAGAGCAGATCGCATCCAAC
*
39276141 CTTATCTCCCTGAGCAGCAGCGGAGTAGGTCCAAGATTGAAGATCTTATCTCCCTAAGCAGTAGT
1 CTTATCTCCCTGAGCAGCAGCGGAGTAGGTCCAAGATTGAAGATCTTATCTCCCTAAACAGTAGT
39276206 GGAGCGGATCGAAAGTACCAGTCTTATCTCCTTAAGCAGTAGTGGAACAGACAGAAGAAACCACA
66 GGAGCGGATCGAAAGTACCAGTCTTATCTCCTTAAGCAGTAGTGGAACAGACAGAAGAAACCACA
* * **
39276271 GATCTTATCTCTCTAAAGTTGCAGTAGAGCGGATCGCATCCAGT
131 GATCTTATCTCTCTAAAGTTACAGTAGAGCAGATCGCATCCAAC
39276315 CTTATCTCCCTGA
1 CTTATCTCCCTGA
39276328 AGTTGCAGTG
Statistics
Matches: 172, Mismatches: 11, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
170 4 0.02
171 115 0.67
172 1 0.01
173 1 0.01
174 51 0.30
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.25
Consensus pattern (174 bp):
CTTATCTCCCTGAGCAGCAGCGGAGTAGGTCCAAGATTGAAGATCTTATCTCCCTAAACAGTAGT
GGAGCGGATCGAAAGTACCAGTCTTATCTCCTTAAGCAGTAGTGGAACAGACAGAAGAAACCACA
GATCTTATCTCTCTAAAGTTACAGTAGAGCAGATCGCATCCAAC
Found at i:39280952 original size:19 final size:18
Alignment explanation
Indices: 39280919--39280965 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
39280909 ATTACTTTGT
*
39280919 ATTTCATCATTTCATATTAC
1 ATTTC-TCATCTCATATT-C
39280939 ATTTCTCATCTCATATTC
1 ATTTCTCATCTCATATTC
*
39280957 ATTTATCAT
1 ATTTCTCAT
39280966 TTTTTCCATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 9 0.36
19 11 0.44
20 5 0.20
ACGTcount: A:0.28, C:0.21, G:0.00, T:0.51
Consensus pattern (18 bp):
ATTTCTCATCTCATATTC
Found at i:39280990 original size:43 final size:43
Alignment explanation
Indices: 39280940--39281025 Score: 127
Period size: 43 Copynumber: 2.0 Consensus size: 43
39280930 TCATATTACA
*
39280940 TTTCTCATCTCATATTCATTTATCATTTTTTCCATTTCAATAT
1 TTTCTCATCTCATATTCATTTATCATCTTTTCCATTTCAATAT
* * * *
39280983 TTTCTCATCTTATATTCATTTCTCATCTTTTCTATTTTAATAT
1 TTTCTCATCTCATATTCATTTATCATCTTTTCCATTTCAATAT
39281026 CAATCACATA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.22, C:0.20, G:0.00, T:0.58
Consensus pattern (43 bp):
TTTCTCATCTCATATTCATTTATCATCTTTTCCATTTCAATAT
Found at i:39283941 original size:33 final size:33
Alignment explanation
Indices: 39283869--39283944 Score: 100
Period size: 33 Copynumber: 2.3 Consensus size: 33
39283859 TTTTAAATTT
39283869 TAATATTTTTATAAAATTTTTTTTACAATGTTAA
1 TAATATTTTTAT-AAATTTTTTTTACAATGTTAA
* * *
39283903 AAATATTCTTTAT-AATTTTTTTTACAATTTTTA
1 TAATATT-TTTATAAATTTTTTTTACAATGTTAA
39283936 TAATATTTT
1 TAATATTTT
39283945 ATTAGAAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
32 2 0.05
33 24 0.65
34 6 0.16
35 5 0.14
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.59
Consensus pattern (33 bp):
TAATATTTTTATAAATTTTTTTTACAATGTTAA
Found at i:39286520 original size:2 final size:2
Alignment explanation
Indices: 39286513--39286544 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
39286503 AGTTGTGATA
39286513 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39286545 CTGATTTGCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39289394 original size:15 final size:15
Alignment explanation
Indices: 39289364--39289404 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
39289354 TTTCATCAAC
*
39289364 ATCACTAATAAAAAA
1 ATCATTAATAAAAAA
*
39289379 ATTTATTAATAAAAAA
1 A-TCATTAATAAAAAA
39289395 ATCATTAATA
1 ATCATTAATA
39289405 CATTTGTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (15 bp):
ATCATTAATAAAAAA
Found at i:39289773 original size:6 final size:6
Alignment explanation
Indices: 39289747--39289803 Score: 62
Period size: 6 Copynumber: 9.7 Consensus size: 6
39289737 TACTCTCTAC
* * * * *
39289747 AATATT AA-ATT TATATT AATATG AATATG ACTATG AATATT AATATT
1 AATATT AATATT AATATT AATATT AATATT AATATT AATATT AATATT
39289794 AATATT AATA
1 AATATT AATA
39289804 AAAGTGTTGA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
5 4 0.09
6 40 0.91
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (6 bp):
AATATT
Found at i:39293216 original size:19 final size:18
Alignment explanation
Indices: 39293194--39293239 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 18
39293184 ACAATCTTAC
39293194 TTTCAATTAACATTATAAA
1 TTTCAATTAA-ATTATAAA
39293213 TTTCAA--AAATTATAAA
1 TTTCAATTAAATTATAAA
**
39293229 CATCAATTAAA
1 TTTCAATTAAA
39293240 ATTAATTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
16 12 0.52
17 2 0.09
18 3 0.13
19 6 0.26
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.37
Consensus pattern (18 bp):
TTTCAATTAAATTATAAA
Found at i:39293509 original size:100 final size:100
Alignment explanation
Indices: 39293336--39293536 Score: 350
Period size: 100 Copynumber: 2.0 Consensus size: 100
39293326 AAAAGGCTAA
*
39293336 ACTCGTAGATAATCATTCTATTCCTAGAAAAGTACTTAGTAAATCAAACATGATAATATAACTTT
1 ACTCGTAAATAATCATTCTATTCCTAGAAAAGTACTTAGTAAATCAAACATGATAATATAACTTT
* *
39293401 TCTAATATTTTAATCAATACTTTCCCATGTATACC
66 TCTAATATTTTAATCAATACCTTCCCATATATACC
*
39293436 ACTCGTAAATAATCATT-TCGTTCCTAGAAAAGTACTTAGTAAATCAAACATGATAATATAACTT
1 ACTCGTAAATAATCATTCT-ATTCCTAGAAAAGTACTTAGTAAATCAAACATGATAATATAACTT
39293500 TTCTAATATTTTAATCAATACCTTCCCATATATACC
65 TTCTAATATTTTAATCAATACCTTCCCATATATACC
39293536 A
1 A
39293537 AACGTTTAAA
Statistics
Matches: 96, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
99 1 0.01
100 95 0.99
ACGTcount: A:0.39, C:0.18, G:0.06, T:0.36
Consensus pattern (100 bp):
ACTCGTAAATAATCATTCTATTCCTAGAAAAGTACTTAGTAAATCAAACATGATAATATAACTTT
TCTAATATTTTAATCAATACCTTCCCATATATACC
Found at i:39296885 original size:26 final size:26
Alignment explanation
Indices: 39296853--39296905 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
39296843 AACATGGGAT
*
39296853 ATAAGAAATTAAGATCAAAATATAAA
1 ATAAGAAATTAACATCAAAATATAAA
* *
39296879 ATAAGAAATTAACATTAGAATATAAA
1 ATAAGAAATTAACATCAAAATATAAA
39296905 A
1 A
39296906 CAAATTACTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.64, C:0.04, G:0.08, T:0.25
Consensus pattern (26 bp):
ATAAGAAATTAACATCAAAATATAAA
Found at i:39297289 original size:50 final size:50
Alignment explanation
Indices: 39297214--39297316 Score: 161
Period size: 50 Copynumber: 2.1 Consensus size: 50
39297204 AAAAATACAA
* **
39297214 AAAAATATTTACAAATATAATTCATTGATAAAAGAATAAGTGTTAGTATG
1 AAAAATATATACAAATATAATTCATTGATAAAAGAATAAGCATTAGTATG
* *
39297264 AAAATTATATACAAGTATAATTCATTGATAAAAGAATAAGCATTAGTATG
1 AAAAATATATACAAATATAATTCATTGATAAAAGAATAAGCATTAGTATG
39297314 AAA
1 AAA
39297317 TAAACTTGTG
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.51, C:0.05, G:0.12, T:0.32
Consensus pattern (50 bp):
AAAAATATATACAAATATAATTCATTGATAAAAGAATAAGCATTAGTATG
Found at i:39299404 original size:43 final size:42
Alignment explanation
Indices: 39299306--39299469 Score: 177
Period size: 43 Copynumber: 3.9 Consensus size: 42
39299296 TAGGGTTACC
* * *
39299306 GAGATTACGTGTAAGACCATATCTGGGATATGACATCGATAT
1 GAGATTTCATGTAAGACCATATCTGGGATATGGCATCGATAT
* * *
39299348 GAGAATTT-GTGTAAGACCATGTCTGGGAAATTGGCATCGATAT
1 GAG-ATTTCATGTAAGACCATATCTGGGATA-TGGCATCGATAT
* ** * *
39299391 GTGATTTCATGTAAGACCATGGCTGGGCTATTGGCATCGATAC
1 GAGATTTCATGTAAGACCATATCTGGGATA-TGGCATCGATAT
* *
39299434 GAGATTACATGTAAGATCATATCTGGGATATGGCAT
1 GAGATTTCATGTAAGACCATATCTGGGATATGGCAT
39299470 TGTTACGGTA
Statistics
Matches: 103, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
42 33 0.32
43 70 0.68
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.30
Consensus pattern (42 bp):
GAGATTTCATGTAAGACCATATCTGGGATATGGCATCGATAT
Found at i:39305144 original size:25 final size:25
Alignment explanation
Indices: 39305115--39305175 Score: 104
Period size: 25 Copynumber: 2.4 Consensus size: 25
39305105 TTTTAGATCA
*
39305115 CTTGATTCATCAACTTCGTTCCTTT
1 CTTGATTCATCAACTTCGCTCCTTT
*
39305140 CTTGATTCATCTACTTCGCTCCTTT
1 CTTGATTCATCAACTTCGCTCCTTT
39305165 CTTGATTCATC
1 CTTGATTCATC
39305176 GACCATTCCG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.15, C:0.30, G:0.08, T:0.48
Consensus pattern (25 bp):
CTTGATTCATCAACTTCGCTCCTTT
Found at i:39306667 original size:21 final size:21
Alignment explanation
Indices: 39306643--39306687 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
39306633 TCAACAAGGG
* *
39306643 TGTTTTCAAAATTCAATACTT
1 TGTTTTCAAAACTCAACACTT
*
39306664 TGTTTTCGAAACTCAACACTT
1 TGTTTTCAAAACTCAACACTT
39306685 TGT
1 TGT
39306688 GCTCATAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.18, G:0.09, T:0.44
Consensus pattern (21 bp):
TGTTTTCAAAACTCAACACTT
Found at i:39308105 original size:103 final size:106
Alignment explanation
Indices: 39307934--39308219 Score: 354
Period size: 103 Copynumber: 2.7 Consensus size: 106
39307924 ATCCTTTTTT
* *
39307934 TTTCCAACAGTGAAGATGATGAAGAAAGGGGAAAAAAAATAGGAAAAT-TAAATCTCCCTAATGA
1 TTTCTAACAGTGAAGACGATGAAGAAA--GG-AAAAAAATAGGAAAATCT-AATCTCCCTAATGA
39307998 GAAATTGAATAGATGTTGAATTG-CCCAATACCCT-ATATCCCTTT-
62 GAAATTGAATAGATGTTGAATTGCCCCAA-ACCCTCA-ATCCCTTTC
* * * *
39308042 TTCTCTAACAGTG-A-A-GATGATG-AAGGAACAAAATAAGGAAAATCTAGTCTCCCTGATGAGA
1 TT-TCTAACAGTGAAGACGATGAAGAAAGGAAAAAAAT-AGGAAAATCTAATCTCCCTAATGAGA
*
39308103 AATTGAATAGATGTTGAATTGCCCCAAATCCTCAATCCCTTTC
64 AATTGAATAGATGTTGAATTGCCCCAAACCCTCAATCCCTTTC
*
39308146 TTTCTAACAGTGAAGACGATGAAGAAAGGAAAAAAGATCAGGAAAATCAAATCTCCCTAATGAGA
1 TTTCTAACAGTGAAGACGATGAAGAAAGGAAAAAA-AT-AGGAAAATCTAATCTCCCTAATGAGA
39308211 AATTGAATA
64 AATTGAATA
39308220 ACCCAAAATT
Statistics
Matches: 155, Mismatches: 12, Indels: 22
0.82 0.06 0.12
Matches are distributed among these distances:
102 7 0.05
103 67 0.43
104 10 0.06
105 3 0.02
106 12 0.08
107 10 0.06
108 37 0.24
109 9 0.06
ACGTcount: A:0.42, C:0.16, G:0.18, T:0.25
Consensus pattern (106 bp):
TTTCTAACAGTGAAGACGATGAAGAAAGGAAAAAAATAGGAAAATCTAATCTCCCTAATGAGAAA
TTGAATAGATGTTGAATTGCCCCAAACCCTCAATCCCTTTC
Found at i:39310182 original size:24 final size:24
Alignment explanation
Indices: 39310132--39310193 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 24
39310122 AAGAGTCAAA
* * *
39310132 AACTGTATTTACAGAAATGTTGGG
1 AACTGTATTTATAGAAATGTCGCG
*
39310156 AACTGTATTTATAGGAATGTCGCG
1 AACTGTATTTATAGAAATGTCGCG
*
39310180 AACTATATTGTATA
1 AACTGTATT-TATA
39310194 ATTATTGCGA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
24 28 0.88
25 4 0.12
ACGTcount: A:0.34, C:0.10, G:0.21, T:0.35
Consensus pattern (24 bp):
AACTGTATTTATAGAAATGTCGCG
Found at i:39310625 original size:39 final size:39
Alignment explanation
Indices: 39310573--39310654 Score: 101
Period size: 39 Copynumber: 2.1 Consensus size: 39
39310563 TTAGAAAACG
* * * *
39310573 GAAGGTCGAGATTGTAAGTCAGCAGACTATAAGAAAGCT
1 GAAGGTCGAGATTGTAAATCAGCAAACCATAAAAAAGCT
** *
39310612 GAAGGTCTTGATTGTAAATCAGCAAACCATAAAAAAGTT
1 GAAGGTCGAGATTGTAAATCAGCAAACCATAAAAAAGCT
39310651 GAAG
1 GAAG
39310655 CTCATGATCG
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.41, C:0.12, G:0.24, T:0.22
Consensus pattern (39 bp):
GAAGGTCGAGATTGTAAATCAGCAAACCATAAAAAAGCT
Found at i:39310670 original size:39 final size:39
Alignment explanation
Indices: 39310591--39310671 Score: 90
Period size: 39 Copynumber: 2.1 Consensus size: 39
39310581 AGATTGTAAG
* * * * * * *
39310591 TCAGCAGACTATAAGAAAGCTGAAGGTCTTGATTGTAAA
1 TCAGCAAACCATAAAAAAGCTGAAGCTCATGATCGAAAA
*
39310630 TCAGCAAACCATAAAAAAGTTGAAGCTCATGATCGAAAA
1 TCAGCAAACCATAAAAAAGCTGAAGCTCATGATCGAAAA
39310669 TCA
1 TCA
39310672 ATGGATCGTA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.43, C:0.16, G:0.19, T:0.22
Consensus pattern (39 bp):
TCAGCAAACCATAAAAAAGCTGAAGCTCATGATCGAAAA
Found at i:39321437 original size:22 final size:22
Alignment explanation
Indices: 39321411--39321457 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
39321401 ATGTGATCAA
39321411 ATGGATAATTATTCATGTACTC
1 ATGGATAATTATTCATGTACTC
*
39321433 ATGGATAATTGTTCATGTACTC
1 ATGGATAATTATTCATGTACTC
39321455 ATG
1 ATG
39321458 AAAGTTTGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.40
Consensus pattern (22 bp):
ATGGATAATTATTCATGTACTC
Found at i:39327129 original size:39 final size:39
Alignment explanation
Indices: 39327086--39327313 Score: 179
Period size: 39 Copynumber: 5.8 Consensus size: 39
39327076 CTTATGATCT
* * * *
39327086 GTTGATTTAAGATCAAGACCTTTGGCTTTCTTACGGTGC
1 GTTGATTTATGATCACGACCTTCGGCTTTCTTACGGTCC
* * *
39327125 GTTGATTTATGATCATGACCTTCAGCTTTCTTACGGTCT
1 GTTGATTTATGATCACGACCTTCGGCTTTCTTACGGTCC
** * * * * ** **
39327164 ACTGATTTACGATCATGACCTTCGACTTTCTGATAGTTT
1 GTTGATTTATGATCACGACCTTCGGCTTTCTTACGGTCC
* * * * *
39327203 GCTAATTTACGATCACGACCTTCGACTTTCTTACGATCC
1 GTTGATTTATGATCACGACCTTCGGCTTTCTTACGGTCC
* ** **
39327242 GCTT-ATTTATGACCACGACCTTTAGCTTTCTTATAGTCC
1 G-TTGATTTATGATCACGACCTTCGGCTTTCTTACGGTCC
* *
39327281 GTTGATTTATGATTACGACCTTTGGCTTTCTTA
1 GTTGATTTATGATCACGACCTTCGGCTTTCTTA
39327314 TAGTCACAGA
Statistics
Matches: 151, Mismatches: 36, Indels: 4
0.79 0.19 0.02
Matches are distributed among these distances:
38 2 0.01
39 148 0.98
40 1 0.01
ACGTcount: A:0.21, C:0.22, G:0.17, T:0.41
Consensus pattern (39 bp):
GTTGATTTATGATCACGACCTTCGGCTTTCTTACGGTCC
Found at i:39327301 original size:117 final size:117
Alignment explanation
Indices: 39327090--39327317 Score: 260
Period size: 117 Copynumber: 1.9 Consensus size: 117
39327080 TGATCTGTTG
* * * * * *
39327090 ATTTAAGATCAAGACCTTTGGCTTTCTTACGGTGCGTTGATTTATGATCATGACCTTCAGCTTTC
1 ATTTAAGATCAAGACCTTCGACTTTCTTACGATCCGTTGATTTATGACCACGACCTTCAGCTTTC
* * *
39327155 TTACGGTCTACTGATTTACGATCATGACCTTCGACTTTCTGATAGTTTGCTA
66 TTACAGTCCACTGATTTACGATCACGACCTTCGACTTTCTGATAGTTTGCTA
* * *
39327207 ATTTACGATCACGACCTTCGACTTTCTTACGATCCGCTT-ATTTATGACCACGACCTTTAGCTTT
1 ATTTAAGATCAAGACCTTCGACTTTCTTACGATCCG-TTGATTTATGACCACGACCTTCAGCTTT
* ** * * * * *
39327271 CTTATAGTCCGTTGATTTATGATTACGACCTTTGGCTTTCTTATAGT
65 CTTACAGTCCACTGATTTACGATCACGACCTTCGACTTTCTGATAGT
39327318 CACAGATTTA
Statistics
Matches: 90, Mismatches: 20, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
117 88 0.98
118 2 0.02
ACGTcount: A:0.21, C:0.22, G:0.16, T:0.41
Consensus pattern (117 bp):
ATTTAAGATCAAGACCTTCGACTTTCTTACGATCCGTTGATTTATGACCACGACCTTCAGCTTTC
TTACAGTCCACTGATTTACGATCACGACCTTCGACTTTCTGATAGTTTGCTA
Found at i:39327314 original size:39 final size:39
Alignment explanation
Indices: 39327086--39327356 Score: 174
Period size: 39 Copynumber: 7.0 Consensus size: 39
39327076 CTTATGATCT
* * * ** *
39327086 GTTGATTTAAGATCAAGACCTTTGGCTTTCTTACGGTGC
1 GTTGATTTATGATCACGACCTTCGGCTTTCTTATAGTCC
* * ** *
39327125 GTTGATTTATGATCATGACCTTCAGCTTTCTTACGGTCT
1 GTTGATTTATGATCACGACCTTCGGCTTTCTTATAGTCC
** * * * * **
39327164 ACTGATTTACGATCATGACCTTCGACTTTCTGATAGTTT
1 GTTGATTTATGATCACGACCTTCGGCTTTCTTATAGTCC
* * * * *
39327203 GCTAATTTACGATCACGACCTTCGACTTTCTTA-CGATCC
1 GTTGATTTATGATCACGACCTTCGGCTTTCTTATAG-TCC
* **
39327242 GCTT-ATTTATGACCACGACCTTTAGCTTTCTTATAGTCC
1 G-TTGATTTATGATCACGACCTTCGGCTTTCTTATAGTCC
* *
39327281 GTTGATTTATGATTACGACCTTTGGCTTTCTTATAGTCAC
1 GTTGATTTATGATCACGACCTTCGGCTTTCTTATAGTC-C
* * * *
39327321 --AGATTTATGGTCATGACCTTC-GCATTTCTTACAGTC
1 GTTGATTTATGATCACGACCTTCGGC-TTTCTTATAGTC
39327357 TACTAATTTA
Statistics
Matches: 188, Mismatches: 38, Indels: 13
0.79 0.16 0.05
Matches are distributed among these distances:
37 2 0.01
38 30 0.16
39 153 0.81
40 3 0.02
ACGTcount: A:0.21, C:0.22, G:0.17, T:0.40
Consensus pattern (39 bp):
GTTGATTTATGATCACGACCTTCGGCTTTCTTATAGTCC
Found at i:39327560 original size:98 final size:98
Alignment explanation
Indices: 39327458--39327640 Score: 287
Period size: 98 Copynumber: 1.9 Consensus size: 98
39327448 TTTAGTTCAT
* * ** *
39327458 TGATTTACGATCATGAACACTTCATAAAGAGCTCATTGATTTATGATCGT-GACTCCACTTAAAC
1 TGATTTACGATAATGAACACTTCATAAAGAGCTCACTGATTTACAATC-TCAACTCCACTTAAAC
39327522 AGTTCACTGATTTACGATCACAGCTTCAACTCAA
65 AGTTCACTGATTTACGATCACAGCTTCAACTCAA
* *
39327556 TGATTTACGATAATGAACACTTCATAAAGAGTTCGCTGATTTACAATCTCAACTCCACTTAAACA
1 TGATTTACGATAATGAACACTTCATAAAGAGCTCACTGATTTACAATCTCAACTCCACTTAAACA
39327621 GTTCACTGATTTACGATCAC
66 GTTCACTGATTTACGATCAC
39327641 GACTGTCGTT
Statistics
Matches: 77, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
97 1 0.01
98 76 0.99
ACGTcount: A:0.33, C:0.22, G:0.13, T:0.32
Consensus pattern (98 bp):
TGATTTACGATAATGAACACTTCATAAAGAGCTCACTGATTTACAATCTCAACTCCACTTAAACA
GTTCACTGATTTACGATCACAGCTTCAACTCAA
Found at i:39328378 original size:50 final size:49
Alignment explanation
Indices: 39328275--39328384 Score: 127
Period size: 50 Copynumber: 2.2 Consensus size: 49
39328265 AAAAGGGGGA
39328275 TCTCCAAACTC-TCTACTTTATTCCATCTTCTTTACCAAAAAACCCATT
1 TCTCCAAACTCTTCTACTTTATTCCATCTTCTTTACCAAAAAACCCATT
* * * * *
39328323 CCTCCAGACTCTTC-ACTTT-TTCTATCTTCTTCTCCACCAAAACACTCATT
1 TCTCCAAACTCTTCTACTTTATTCCATCTTCTT-T--ACCAAAAAACCCATT
39328373 TCTCCAAACTCT
1 TCTCCAAACTCT
39328385 AACCACCTCA
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
47 11 0.22
48 15 0.29
49 2 0.04
50 23 0.45
ACGTcount: A:0.25, C:0.36, G:0.01, T:0.37
Consensus pattern (49 bp):
TCTCCAAACTCTTCTACTTTATTCCATCTTCTTTACCAAAAAACCCATT
Found at i:39331172 original size:23 final size:23
Alignment explanation
Indices: 39331127--39331179 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
39331117 TAAACTAGTA
* * **
39331127 GAGAGAATTGAGAGAATTTGATT
1 GAGAGAACTGAAAGAATAGGATT
39331150 GAGAGAACTGAAAGAATAGGATT
1 GAGAGAACTGAAAGAATAGGATT
*
39331173 GAAAGAA
1 GAGAGAA
39331180 GACAAAAGAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.47, C:0.02, G:0.30, T:0.21
Consensus pattern (23 bp):
GAGAGAACTGAAAGAATAGGATT
Found at i:39334863 original size:12 final size:12
Alignment explanation
Indices: 39334846--39334871 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
39334836 CAAAACAGGC
39334846 TTTTAGCGGCGT
1 TTTTAGCGGCGT
39334858 TTTTAGCGGCGT
1 TTTTAGCGGCGT
39334870 TT
1 TT
39334872 GGATAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.15, G:0.31, T:0.46
Consensus pattern (12 bp):
TTTTAGCGGCGT
Found at i:39335058 original size:73 final size:72
Alignment explanation
Indices: 39334939--39335107 Score: 257
Period size: 73 Copynumber: 2.3 Consensus size: 72
39334929 AAAAAAAGCA
* * * *
39334939 TTAGCGGCGTTTTTGAGCAAAGCGCCGCAAATAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
1 TTAGCGGCGTTTTTG-GTAAAGCGCCGCAAAAAACCCAAGCCCAACGACGCCGTTTTCTGAACTT
*
39335004 TCGGGGAT
65 TCAGGGAT
* *
39335012 TTAGCGGCGTTTTTGGTAAAGCGCCGCAAAAAAACCCAAGCTCAACGATGCCGTTTTCTGAACTT
1 TTAGCGGCGTTTTTGGTAAAGCGCCGC-AAAAAACCCAAGCCCAACGACGCCGTTTTCTGAACTT
39335077 TCAGGGAT
65 TCAGGGAT
39335085 TTAGCGGCGTTTTTGGTAAAGCG
1 TTAGCGGCGTTTTTGGTAAAGCG
39335108 TTGCTAAAGG
Statistics
Matches: 88, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
72 11 0.12
73 77 0.88
ACGTcount: A:0.24, C:0.23, G:0.26, T:0.27
Consensus pattern (72 bp):
TTAGCGGCGTTTTTGGTAAAGCGCCGCAAAAAACCCAAGCCCAACGACGCCGTTTTCTGAACTTT
CAGGGAT
Found at i:39335918 original size:14 final size:15
Alignment explanation
Indices: 39335890--39335922 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
39335880 AAGTTTTATA
39335890 GATTATGGAATTAGG
1 GATTATGGAATTAGG
39335905 GATTATGG-ATTAGG
1 GATTATGGAATTAGG
39335919 GATT
1 GATT
39335923 CTGGTTTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.30, C:0.00, G:0.33, T:0.36
Consensus pattern (15 bp):
GATTATGGAATTAGG
Found at i:39336285 original size:7 final size:7
Alignment explanation
Indices: 39336275--39336329 Score: 65
Period size: 7 Copynumber: 7.7 Consensus size: 7
39336265 GATTTAAGGT
39336275 TTAGGGG
1 TTAGGGG
*
39336282 TTAGTGG
1 TTAGGGG
39336289 TTAGGGG
1 TTAGGGG
39336296 TTAGGGG
1 TTAGGGG
* *
39336303 TTAAGAG
1 TTAGGGG
*
39336310 TTAGGGAT
1 TTAGGG-G
39336318 TTAGGGG
1 TTAGGGG
39336325 TTAGG
1 TTAGG
39336330 ACTTAAGGAT
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
7 33 0.85
8 6 0.15
ACGTcount: A:0.20, C:0.00, G:0.47, T:0.33
Consensus pattern (7 bp):
TTAGGGG
Found at i:39336339 original size:22 final size:22
Alignment explanation
Indices: 39336296--39336340 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
39336286 TGGTTAGGGG
* *
39336296 TTAGGGGTTAAGAGTTAGGGAT
1 TTAGGGGTTAAGACTTAAGGAT
*
39336318 TTAGGGGTTAGGACTTAAGGAT
1 TTAGGGGTTAAGACTTAAGGAT
39336340 T
1 T
39336341 CAAGGGTCGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.27, C:0.02, G:0.38, T:0.33
Consensus pattern (22 bp):
TTAGGGGTTAAGACTTAAGGAT
Found at i:39336675 original size:19 final size:18
Alignment explanation
Indices: 39336646--39336699 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 18
39336636 GGACCAAATT
*
39336646 ATAAGAAATAAAATTAAA
1 ATAAAAAATAAAATTAAA
* *
39336664 ATACAAAAATAAAAATGAA
1 ATA-AAAAATAAAATTAAA
39336683 ATAAAAACACTAAAATT
1 ATAAAAA-A-TAAAATT
39336700 TTTAATTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 7 0.24
19 16 0.55
20 6 0.21
ACGTcount: A:0.70, C:0.06, G:0.04, T:0.20
Consensus pattern (18 bp):
ATAAAAAATAAAATTAAA
Found at i:39336753 original size:47 final size:48
Alignment explanation
Indices: 39336684--39336782 Score: 182
Period size: 47 Copynumber: 2.1 Consensus size: 48
39336674 AAAAATGAAA
*
39336684 TAAAAACACTAAAATTTTTAATTTTATCTAATTTTTATAAATATTACT
1 TAAAAACACTAAAATTTATAATTTTATCTAATTTTTATAAATATTACT
39336732 TAAAAA-ACTAAAATTTATAATTTTATCTAATTTTTATAAATATTACT
1 TAAAAACACTAAAATTTATAATTTTATCTAATTTTTATAAATATTACT
39336779 TAAA
1 TAAA
39336783 CAAAACTATG
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
47 44 0.88
48 6 0.12
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.46
Consensus pattern (48 bp):
TAAAAACACTAAAATTTATAATTTTATCTAATTTTTATAAATATTACT
Found at i:39337084 original size:16 final size:15
Alignment explanation
Indices: 39337063--39337102 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
39337053 TGGTTGAAAT
39337063 ATTTATTCCCCTCCAA
1 ATTTATTCCCCTCC-A
*
39337079 ATTTATTCCCCTTCA
1 ATTTATTCCCCTCCA
39337094 ATTT-TTCCC
1 ATTTATTCCC
39337103 ATACCCGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 5 0.22
15 5 0.22
16 13 0.57
ACGTcount: A:0.20, C:0.35, G:0.00, T:0.45
Consensus pattern (15 bp):
ATTTATTCCCCTCCA
Found at i:39341505 original size:43 final size:42
Alignment explanation
Indices: 39341477--39341685 Score: 292
Period size: 43 Copynumber: 4.9 Consensus size: 42
39341467 GCTTTTATCA
* *
39341477 AAAGCGTCGCTAAAGATTATGTTCTTTAGCGGCGTTTGTGGTT
1 AAAGCGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTGT-GTT
*
39341520 AAAGCGCCGCTAAAGATCATGTTCTTTAGCGGCATTTGTGTTT
1 AAAGCGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTGTG-TT
* * *
39341563 AAAGCGCCGCTAAAGATCATGTTCTTTAGCAGCATTTGTGGGT
1 AAAGCGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTGT-GTT
* *
39341606 AAGGCGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTGTGGGT
1 AAAGCGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTGT-GTT
* *
39341649 AAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTT
1 AAAGCGCCGCTAAAGATCATGTTCTTTAGCGGCGTTT
39341686 TGCCTCATAA
Statistics
Matches: 153, Mismatches: 11, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
42 1 0.01
43 151 0.99
44 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.32
Consensus pattern (42 bp):
AAAGCGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTGTGTT
Found at i:39342308 original size:26 final size:26
Alignment explanation
Indices: 39342250--39342308 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
39342240 GGAAAAAAAT
* *
39342250 TTTATATTATAAAAATAATTTGTGTA
1 TTTAAATTATAAAAATAATTTATGTA
* *
39342276 CTAAAATTATAAAAATATATTTAT-TA
1 TTTAAATTATAAAAATA-ATTTATGTA
39342302 TTTAAAT
1 TTTAAAT
39342309 CCTAAATTTT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
26 21 0.81
27 5 0.19
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.47
Consensus pattern (26 bp):
TTTAAATTATAAAAATAATTTATGTA
Found at i:39343110 original size:105 final size:105
Alignment explanation
Indices: 39342927--39343133 Score: 315
Period size: 105 Copynumber: 2.0 Consensus size: 105
39342917 ACTTGTTCTA
* *
39342927 AAAAAATATTTCCCATAACATAAAAAAGGTTGGGTCATACTAACATATTGAGTATTTTATAATTT
1 AAAAAATATTTCCCATAACATAAAAAAGGTTGGGTCATACTAACATATTGAATATCTTATAATTT
* *
39342992 CAATCATAGGTAGATTTGAGATGATCCATACATCAAATCT
66 CAATCATAAGTAGAATTGAGATGATCCATACATCAAATCT
** * *
39343032 AAAAAATATTTCCCATCGCATAAAAAAGGTTGGGTCGTACTGACATATTGAATATCTTATAATTT
1 AAAAAATATTTCCCATAACATAAAAAAGGTTGGGTCATACTAACATATTGAATATCTTATAATTT
* * *
39343097 CAATCATAAGTAGAATTGAGATGGTCTATACTTCAAA
66 CAATCATAAGTAGAATTGAGATGATCCATACATCAAA
39343134 GAGTACATGA
Statistics
Matches: 91, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
105 91 1.00
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.33
Consensus pattern (105 bp):
AAAAAATATTTCCCATAACATAAAAAAGGTTGGGTCATACTAACATATTGAATATCTTATAATTT
CAATCATAAGTAGAATTGAGATGATCCATACATCAAATCT
Found at i:39357737 original size:44 final size:45
Alignment explanation
Indices: 39357681--39358071 Score: 217
Period size: 44 Copynumber: 8.5 Consensus size: 45
39357671 AGTCAGATCT
*
39357681 TATCTCCCTGAGATTACAGTAGAGCAGATTGAAGCT-AGTAATCC
1 TATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCTAAGTAATCC
* * ** * *
39357725 TATCTCCTTGAGATTACAGTGGAGCGGATT-AAAATAAAG-GATCT
1 TATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCT-AAGTAATCC
* ** * * * *
39357769 TATCTCTCTGA-AGTTACAGCAGAGTAGATCGCATCAGATTGAAGTCAGATCT
1 TATCTCCCTGAGA-TTACAGTGGAGCAGATTG-A--AG-CT-AAGT-A-ATCC
* * *
39357821 TATCTCCCTAAGATTACAGTGGAGTAGATTGAAGCT-AGTAGTCC
1 TATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCTAAGTAATCC
* * ** * *
39357865 TATCTCCTTGAGATTACAGTGGAGCGGATT-AAAATAAAG-GATCT
1 TATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCT-AAGTAATCC
* *** * * * *
39357909 TATCTCTCTGA-AGTTACAACAGAGTAGATCGCATCAGATTGAAGTCAGATCT
1 TATCTCCCTGAGA-TTACAGTGGAGCAGATTG-A--AG-CT-AAGT-A-ATCC
*
39357961 TATCTCCCTGAGATTACAGTGGAGTAGATTGAAGCTAA-TAATCC
1 TATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCTAAGTAATCC
* * *
39358005 TACCTCCCTGAGATTACAGCGGAGCAGACTGAAGCT-AGTAATCC
1 TATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCTAAGTAATCC
* *
39358049 TACCTCCCTAAGATTACAGTGGA
1 TATCTCCCTGAGATTACAGTGGA
39358072 TCGAAGCTCC
Statistics
Matches: 262, Mismatches: 60, Indels: 50
0.70 0.16 0.13
Matches are distributed among these distances:
43 9 0.03
44 163 0.62
45 6 0.02
46 6 0.02
47 2 0.01
48 4 0.02
49 12 0.05
51 2 0.01
52 56 0.21
53 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (45 bp):
TATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCTAAGTAATCC
Found at i:39357846 original size:52 final size:51
Alignment explanation
Indices: 39357764--39357989 Score: 142
Period size: 52 Copynumber: 4.7 Consensus size: 51
39357754 TAAAATAAAG
* *
39357764 GATCTTATCTCTCTGAAG-TTACAGCAGAGTAGATCGCATCAGATTGAAGTCA
1 GATCTTATCTCCCT-AAGATTACAGTAGAGTAGATCGCATCAGATTGAAGT-A
* * *
39357816 GATCTTATCTCCCTAAGATTACAGTGGAGTAGATTG-A--AG-CT--AGTA
1 GATCTTATCTCCCTAAGATTACAGTAGAGTAGATCGCATCAGATTGAAGTA
* * * * * * * *
39357861 G-TCCTATCTCCTTGAGATTACAGT-G-G-AG--CGGATTAAAATAAAG--
1 GATCTTATCTCCCTAAGATTACAGTAGAGTAGATCGCATCAGATTGAAGTA
* **
39357904 GATCTTATCTCTCTGAAG-TTACAACAGAGTAGATCGCATCAGATTGAAGTCA
1 GATCTTATCTCCCT-AAGATTACAGTAGAGTAGATCGCATCAGATTGAAGT-A
* *
39357956 GATCTTATCTCCCTGAGATTACAGTGGAGTAGAT
1 GATCTTATCTCCCTAAGATTACAGTAGAGTAGAT
39357990 TGAAGCTAAT
Statistics
Matches: 129, Mismatches: 27, Indels: 36
0.67 0.14 0.19
Matches are distributed among these distances:
39 1 0.01
40 1 0.01
41 2 0.02
42 2 0.02
43 3 0.02
44 34 0.26
45 7 0.05
46 4 0.03
47 2 0.02
48 1 0.01
49 12 0.09
51 6 0.05
52 54 0.42
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.30
Consensus pattern (51 bp):
GATCTTATCTCCCTAAGATTACAGTAGAGTAGATCGCATCAGATTGAAGTA
Found at i:39357874 original size:140 final size:140
Alignment explanation
Indices: 39357622--39358029 Score: 726
Period size: 140 Copynumber: 2.9 Consensus size: 140
39357612 GTCATTATAC
*
39357622 AGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCACATCAGATTGAAGTCAGATCTTATCTC
1 AGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCATCAGATTGAAGTCAGATCTTATCTC
* *
39357687 CCTGAGATTACAGTAGAGCAGATTGAAGCTAGTAATCCTATCTCCTTGAGATTACAGTGGAGCGG
66 CCTGAGATTACAGTGGAGTAGATTGAAGCTAGTAATCCTATCTCCTTGAGATTACAGTGGAGCGG
39357752 ATTAAAATAA
131 ATTAAAATAA
39357762 AGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCATCAGATTGAAGTCAGATCTTATCTC
1 AGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCATCAGATTGAAGTCAGATCTTATCTC
* *
39357827 CCTAAGATTACAGTGGAGTAGATTGAAGCTAGTAGTCCTATCTCCTTGAGATTACAGTGGAGCGG
66 CCTGAGATTACAGTGGAGTAGATTGAAGCTAGTAATCCTATCTCCTTGAGATTACAGTGGAGCGG
39357892 ATTAAAATAA
131 ATTAAAATAA
*
39357902 AGGATCTTATCTCTCTGAAGTTACAACAGAGTAGATCGCATCAGATTGAAGTCAGATCTTATCTC
1 AGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCATCAGATTGAAGTCAGATCTTATCTC
* * * *
39357967 CCTGAGATTACAGTGGAGTAGATTGAAGCTAATAATCCTACCTCCCTGAGATTACAGCGGAGC
66 CCTGAGATTACAGTGGAGTAGATTGAAGCTAGTAATCCTATCTCCTTGAGATTACAGTGGAGC
39358030 AGACTGAAGC
Statistics
Matches: 256, Mismatches: 12, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
140 256 1.00
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (140 bp):
AGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCATCAGATTGAAGTCAGATCTTATCTC
CCTGAGATTACAGTGGAGTAGATTGAAGCTAGTAATCCTATCTCCTTGAGATTACAGTGGAGCGG
ATTAAAATAA
Found at i:39367344 original size:49 final size:49
Alignment explanation
Indices: 39367287--39367386 Score: 164
Period size: 49 Copynumber: 2.0 Consensus size: 49
39367277 GCGATTTTCT
* * *
39367287 TCCCTTCTTATAAAATGAGACTGTCGGAGTCGCGCGATATATAATTTAA
1 TCCCTTCTTATAAAATGAGACCGGCGGAGTCGCGCGATACATAATTTAA
*
39367336 TCCCTTCTTATAAAATGAGACCGGGGGAGTCGCGCGATACATAATTTAA
1 TCCCTTCTTATAAAATGAGACCGGCGGAGTCGCGCGATACATAATTTAA
39367385 TC
1 TC
39367387 GCCCTTACTT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (49 bp):
TCCCTTCTTATAAAATGAGACCGGCGGAGTCGCGCGATACATAATTTAA
Done.