Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 167 of 226
Found at i:53244875 original size:17 final size:17
Alignment explanation
Indices: 53244853--53244888 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
53244843 AAATCTCAGA
*
53244853 TTTTGATACCCATATCT
1 TTTTGATACACATATCT
53244870 TTTTGATACACATATCT
1 TTTTGATACACATATCT
53244887 TT
1 TT
53244889 GACTTTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.25, C:0.19, G:0.06, T:0.50
Consensus pattern (17 bp):
TTTTGATACACATATCT
Found at i:53252664 original size:41 final size:41
Alignment explanation
Indices: 53252607--53252768 Score: 270
Period size: 41 Copynumber: 4.0 Consensus size: 41
53252597 TATCTTATGC
53252607 GATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGT
1 GATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGT
53252648 GATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGT
1 GATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGT
* * * *
53252689 GATCTGAATCAGGTTATAAACCTAGCACGCTAAATGCCGGT
1 GATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGT
* *
53252730 GATCTAAACCAGGCTATAAGCCTAGCAGGCTAAGTGCCG
1 GATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCG
53252769 ATGAATCTAT
Statistics
Matches: 111, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 111 1.00
ACGTcount: A:0.29, C:0.23, G:0.27, T:0.22
Consensus pattern (41 bp):
GATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGT
Found at i:53288339 original size:51 final size:50
Alignment explanation
Indices: 53288268--53288390 Score: 140
Period size: 51 Copynumber: 2.4 Consensus size: 50
53288258 CAAAACACCA
* * * * *
53288268 TTTGTGCACAAGCCATCACTGACTTGCAGATAAATTGCCACTAATA-ACACT
1 TTTGTGAACAAGCCACCACTGAATTGAAGATAAACTGCCACTAATATA-A-T
* * *
53288319 TTTGTGGACAAGCCACCACTGAATTTAAGATATACTGCCACTAATATAAT
1 TTTGTGAACAAGCCACCACTGAATTGAAGATAAACTGCCACTAATATAAT
*
53288369 TTTGTGAACATGCCACCACTGA
1 TTTGTGAACAAGCCACCACTGA
53288391 TTTGTAGACA
Statistics
Matches: 62, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
50 21 0.34
51 40 0.65
52 1 0.02
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.28
Consensus pattern (50 bp):
TTTGTGAACAAGCCACCACTGAATTGAAGATAAACTGCCACTAATATAAT
Found at i:53288404 original size:50 final size:51
Alignment explanation
Indices: 53288303--53288404 Score: 129
Period size: 50 Copynumber: 2.0 Consensus size: 51
53288293 GCAGATAAAT
* *
53288303 TGCCACTAATAACACTTTTGTGGACAAGCCACCACTGAATTTAAGATATAC
1 TGCCACTAATAACACTTTTGTGAACAAGCCACCACTGAATTTAAGACATAC
* *
53288354 TGCCACTAATATA-A-TTTTGTGAACATGCCACCACTG-ATTTGTAGACATAC
1 TGCCACTAATA-ACACTTTTGTGAACAAGCCACCACTGAATTT-AAGACATAC
53288404 T
1 T
53288405 TTTGTGAACA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
49 4 0.09
50 28 0.62
51 12 0.27
52 1 0.02
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.30
Consensus pattern (51 bp):
TGCCACTAATAACACTTTTGTGAACAAGCCACCACTGAATTTAAGACATAC
Found at i:53308984 original size:43 final size:44
Alignment explanation
Indices: 53308875--53308995 Score: 147
Period size: 43 Copynumber: 2.7 Consensus size: 44
53308865 CTAAGGTAAA
* * *
53308875 TCCAACAACCCATGTTTATCTTCTCCTCTTTTTTAAATTATTTTT
1 TCCAACAACCCAAGATTATCTTCTCCTCTTTTCTAAATTA-TTTT
** *
53308920 TTGAACAACCCAAAATTATCTTCTCCTC-TTTCTAAATTCA-TTT
1 TCCAACAACCCAAGATTATCTTCTCCTCTTTTCTAAATT-ATTTT
53308963 TCCAACAACCCAAGATTATCTTCTCCTCCTTTT
1 TCCAACAACCCAAGATTATCTTCTCCT-CTTTT
53308996 TAGCTAGATT
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
43 27 0.42
44 10 0.16
45 27 0.42
ACGTcount: A:0.26, C:0.28, G:0.02, T:0.44
Consensus pattern (44 bp):
TCCAACAACCCAAGATTATCTTCTCCTCTTTTCTAAATTATTTT
Found at i:53309108 original size:42 final size:42
Alignment explanation
Indices: 53309047--53309194 Score: 208
Period size: 42 Copynumber: 3.5 Consensus size: 42
53309037 GGATACTGAG
* *
53309047 ATGTGATTATGTGTAAGACCATGTCTGAGACATTGGCATCGTT
1 ATGTGATT-CGTGTAAGACCATGTCTGAGACATTGGCATCGAT
* *
53309090 TTGTGATTCGTGTAAGACCATGTCTGGGACATTGGCATCGAT
1 ATGTGATTCGTGTAAGACCATGTCTGAGACATTGGCATCGAT
*
53309132 ATGAT-ATTCGTGTAAGACCATGTCTAAGACATTGGCATCGAT
1 ATG-TGATTCGTGTAAGACCATGTCTGAGACATTGGCATCGAT
**
53309174 ATAAGATTCGTGTAAGACCAT
1 ATGTGATTCGTGTAAGACCAT
53309195 AGCTGGCTAT
Statistics
Matches: 94, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
42 86 0.91
43 8 0.09
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (42 bp):
ATGTGATTCGTGTAAGACCATGTCTGAGACATTGGCATCGAT
Found at i:53309230 original size:84 final size:84
Alignment explanation
Indices: 53309058--53309236 Score: 213
Period size: 84 Copynumber: 2.1 Consensus size: 84
53309048 TGTGATTATG
* * * **
53309058 TGTAAGACCATGTCTGAGACATTGGCATCGTTTTGTGATTCGTGTAAGACCATGTCTGGGACATT
1 TGTAAGACCATGTCTAAGACATTGGCATCGATATAAGATTCGTGTAAGACCATGTCTGGGACATT
* * * *
53309123 GGCATCGATATGATATTCG
66 AGAATCGATATGATATGCA
53309142 TGTAAGACCATGTCTAAGACATTGGCATCGATATAAGATTCGTGTAAGACCATAG-CT-GG-CTA
1 TGTAAGACCATGTCTAAGACATTGGCATCGATATAAGATTCGTGTAAGACCAT-GTCTGGGAC-A
53309204 TTAGAATCGATAT-ATGATAGCA
64 TTAGAATCGATATGAT-AT-GCA
53309226 TGTAAGACCAT
1 TGTAAGACCAT
53309237 ATCTGGGATA
Statistics
Matches: 82, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
82 3 0.04
83 16 0.20
84 62 0.76
85 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (84 bp):
TGTAAGACCATGTCTAAGACATTGGCATCGATATAAGATTCGTGTAAGACCATGTCTGGGACATT
AGAATCGATATGATATGCA
Found at i:53313018 original size:35 final size:35
Alignment explanation
Indices: 53312979--53313045 Score: 134
Period size: 35 Copynumber: 1.9 Consensus size: 35
53312969 TTCCGCTTCT
53312979 AAGAGTGATGGCCTTACATTGTTCCTTCCTTTATG
1 AAGAGTGATGGCCTTACATTGTTCCTTCCTTTATG
53313014 AAGAGTGATGGCCTTACATTGTTCCTTCCTTT
1 AAGAGTGATGGCCTTACATTGTTCCTTCCTTT
53313046 GTGATCTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.40
Consensus pattern (35 bp):
AAGAGTGATGGCCTTACATTGTTCCTTCCTTTATG
Found at i:53317619 original size:28 final size:31
Alignment explanation
Indices: 53317561--53317624 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
53317551 GGGTAAATCC
*
53317561 AACAACCCATGTTTATCTTCTTCTCTTTTTT
1 AACAACCCATGATTATCTTCTTCTCTTTTTT
*
53317592 AACAACCCATGATTATCTTCTTCTTTTTTTT
1 AACAACCCATGATTATCTTCTTCTCTTTTTT
53317623 AA
1 AA
53317625 ATTCTTTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.23, C:0.23, G:0.03, T:0.50
Consensus pattern (31 bp):
AACAACCCATGATTATCTTCTTCTCTTTTTT
Found at i:53317650 original size:44 final size:43
Alignment explanation
Indices: 53317584--53317667 Score: 132
Period size: 44 Copynumber: 1.9 Consensus size: 43
53317574 TATCTTCTTC
* * *
53317584 TCTTTTTTAACAACCCATGATTATCTTCTTCTTTTTTTTAAAT
1 TCTTTTTTAACAACCCAAGATTATCTTCTCCTGTTTTTTAAAT
53317627 TCTTTTTTCAACAACCCAAGATTATCTTCTCCTGTTTTTTA
1 TCTTTTTT-AACAACCCAAGATTATCTTCTCCTGTTTTTTA
53317668 GGCAGATTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
43 8 0.22
44 29 0.78
ACGTcount: A:0.23, C:0.21, G:0.04, T:0.52
Consensus pattern (43 bp):
TCTTTTTTAACAACCCAAGATTATCTTCTCCTGTTTTTTAAAT
Found at i:53324399 original size:20 final size:20
Alignment explanation
Indices: 53324370--53324424 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
53324360 GAAGACACCA
* *
53324370 AAGTGTAAACATAGGCATTG
1 AAGTGCAAACATAGGCACTG
*
53324390 AAGTGCAAACAAAGG-ACTG
1 AAGTGCAAACATAGGCACTG
*
53324409 AAGTGCAATCATAGGC
1 AAGTGCAAACATAGGC
53324425 TGTGCAATCT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.42, C:0.15, G:0.25, T:0.18
Consensus pattern (20 bp):
AAGTGCAAACATAGGCACTG
Found at i:53335643 original size:20 final size:20
Alignment explanation
Indices: 53335618--53335723 Score: 81
Period size: 20 Copynumber: 5.3 Consensus size: 20
53335608 CACTTATGTG
*
53335618 CCCCTGTTTGTTCTTCGGTA
1 CCCCTGTTTGTACTTCGGTA
* * *
53335638 CCCCTGATTGTACTTAC-ATG
1 CCCCTGTTTGTACTT-CGGTA
*
53335658 CCCCTATTTGTACTTCGGTA
1 CCCCTGTTTGTACTTCGGTA
** * * *
53335678 CCCCTAATTGCATTTAC-GTT
1 CCCCTGTTTGTACTT-CGGTA
*
53335698 CCCCTATTTGTACTTCGGTA
1 CCCCTGTTTGTACTTCGGTA
53335718 CCCCTG
1 CCCCTG
53335724 ATTCCACTTA
Statistics
Matches: 65, Mismatches: 17, Indels: 8
0.72 0.19 0.09
Matches are distributed among these distances:
19 2 0.03
20 61 0.94
21 2 0.03
ACGTcount: A:0.14, C:0.32, G:0.15, T:0.39
Consensus pattern (20 bp):
CCCCTGTTTGTACTTCGGTA
Found at i:53335660 original size:40 final size:40
Alignment explanation
Indices: 53335602--53335760 Score: 219
Period size: 40 Copynumber: 4.0 Consensus size: 40
53335592 AATTATTCAA
* * *
53335602 TGATTGCACTTATGTGCCCCTGTTTGTTCTTCGGTACCCC
1 TGATTGCACTTACGTGCCCCTATTTGTACTTCGGTACCCC
* *
53335642 TGATTGTACTTACATGCCCCTATTTGTACTTCGGTACCCC
1 TGATTGCACTTACGTGCCCCTATTTGTACTTCGGTACCCC
* * *
53335682 TAATTGCATTTACGTTCCCCTATTTGTACTTCGGTACCCC
1 TGATTGCACTTACGTGCCCCTATTTGTACTTCGGTACCCC
* * *
53335722 TGATTCCACTTACGTGCCCCTACTTGTACTCCGGTACCC
1 TGATTGCACTTACGTGCCCCTATTTGTACTTCGGTACCC
53335761 TTTGTTGCAC
Statistics
Matches: 103, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 103 1.00
ACGTcount: A:0.15, C:0.32, G:0.16, T:0.37
Consensus pattern (40 bp):
TGATTGCACTTACGTGCCCCTATTTGTACTTCGGTACCCC
Found at i:53339400 original size:38 final size:37
Alignment explanation
Indices: 53339348--53339438 Score: 137
Period size: 38 Copynumber: 2.4 Consensus size: 37
53339338 GATTTGACTA
* *
53339348 CATGTTAAACATGCCCTACAGGATATTATTCGATTTG
1 CATGTTAAACATGCCCCACAGGATATTATTCGATTCG
*
53339385 CATGTTAAAACATGCCCCACATGATATTATTCGATTCG
1 CATGTT-AAACATGCCCCACAGGATATTATTCGATTCG
*
53339423 CATGTTCAACATGCCC
1 CATGTTAAACATGCCC
53339439 AATGTGACAA
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
37 15 0.31
38 34 0.69
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.32
Consensus pattern (37 bp):
CATGTTAAACATGCCCCACAGGATATTATTCGATTCG
Found at i:53340357 original size:22 final size:22
Alignment explanation
Indices: 53340293--53340358 Score: 63
Period size: 22 Copynumber: 3.2 Consensus size: 22
53340283 TATGTGCTTG
53340293 AATGTTATGTGATTATATGAGT
1 AATGTTATGTGATTATATGAGT
**
53340315 -A---T-TGTGA-TATATGCTT
1 AATGTTATGTGATTATATGAGT
53340331 AAATGTTATGTGATTATATGAGT
1 -AATGTTATGTGATTATATGAGT
53340354 AATGT
1 AATGT
53340359 GATATATGCT
Statistics
Matches: 33, Mismatches: 4, Indels: 14
0.65 0.08 0.27
Matches are distributed among these distances:
16 7 0.21
17 5 0.15
18 2 0.06
21 2 0.06
22 10 0.30
23 7 0.21
ACGTcount: A:0.32, C:0.02, G:0.21, T:0.45
Consensus pattern (22 bp):
AATGTTATGTGATTATATGAGT
Found at i:53340372 original size:39 final size:39
Alignment explanation
Indices: 53340154--53340369 Score: 353
Period size: 39 Copynumber: 5.5 Consensus size: 39
53340144 AATTTGTCTT
* * *
53340154 TGAGTATTGTGATATATACTTGAATGTTCTATGATTATA
1 TGAGTATTGTGATATATGCTTGAATGTTATGTGATTATA
*
53340193 TGAGTATTGTGATATACGCTTGAATGTTATGTGATTATA
1 TGAGTATTGTGATATATGCTTGAATGTTATGTGATTATA
53340232 TGAGTATTGTGATATATGCTTGAATGTTATGTGATTATA
1 TGAGTATTGTGATATATGCTTGAATGTTATGTGATTATA
*
53340271 TGAGTA-TGTTGATATGTGCTTGAATGTTATGTGATTATA
1 TGAGTATTG-TGATATATGCTTGAATGTTATGTGATTATA
*
53340310 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
1 TGAGTATTGTGATATATGCTTGAATGTTATGTGATTATA
*
53340349 TGAGTAATGTGATATATGCTT
1 TGAGTATTGTGATATATGCTT
53340370 AAAAGTGAAT
Statistics
Matches: 166, Mismatches: 9, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
38 2 0.01
39 162 0.98
40 2 0.01
ACGTcount: A:0.29, C:0.04, G:0.22, T:0.45
Consensus pattern (39 bp):
TGAGTATTGTGATATATGCTTGAATGTTATGTGATTATA
Found at i:53358019 original size:21 final size:22
Alignment explanation
Indices: 53357995--53358038 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
53357985 AATTAGGGAT
53357995 TTCAT-TGTAAAATGTGAAATA
1 TTCATGTGTAAAATGTGAAATA
**
53358016 TTCATGGTGTAATTTGTGAAATA
1 TTCAT-GTGTAAAATGTGAAATA
53358039 ATGAAATATG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 5 0.26
23 14 0.74
ACGTcount: A:0.36, C:0.05, G:0.18, T:0.41
Consensus pattern (22 bp):
TTCATGTGTAAAATGTGAAATA
Found at i:53358604 original size:90 final size:90
Alignment explanation
Indices: 53358505--53358788 Score: 319
Period size: 90 Copynumber: 3.2 Consensus size: 90
53358495 GACCATCGAA
* *
53358505 CTATAAAAAGGGATGGTGACGACGATCGAACTATGAAAAAGGATGGCTTCGGCTATCAATCTATG
1 CTATGAAAAGGGATGGTGACGACCATCGAACTATGAAAAAGGATGGCTTCGGCTATCAATCTATG
*
53358570 AAAAGGGATGGCTTCAGCTATCAAT
66 AAAAGGGATAGCTTCAGCTATCAAT
* * *
53358595 CTATGAAAAGGGATGGCT-TCGACTATC-AATCTAT-AAAAAGGGATGGCTTCGACTATCAATCT
1 CTATGAAAAGGGATGG-TGACGACCATCGAA-CTATGAAAAA-GGATGGCTTCGGCTATCAATCT
* * *
53358657 ATAAAAAGGGATAGCTTCTGTTATCAAAT
63 ATGAAAAGGGATAGCTTCAGCTATC-AAT
* * * * *
53358686 -TATGAAAAGGGATGGTGACAACCATTGAACTATGAAAAGGGATGG-TGGCGGCCATCAAAT-TA
1 CTATGAAAAGGGATGGTGACGACCATCGAACTATGAAAAAGGATGGCT-TCGGCTATC-AATCTA
* * *
53358748 TGAAAAGGGATAACTTCGGCTATCAAA
64 TGAAAAGGGATAGCTTCAGCTATCAAT
53358775 CTATGAAAAGGGAT
1 CTATGAAAAGGGAT
53358789 AACTTCAATT
Statistics
Matches: 163, Mismatches: 21, Indels: 20
0.80 0.10 0.10
Matches are distributed among these distances:
89 11 0.07
90 139 0.85
91 13 0.08
ACGTcount: A:0.37, C:0.14, G:0.24, T:0.24
Consensus pattern (90 bp):
CTATGAAAAGGGATGGTGACGACCATCGAACTATGAAAAAGGATGGCTTCGGCTATCAATCTATG
AAAAGGGATAGCTTCAGCTATCAAT
Found at i:53358794 original size:30 final size:30
Alignment explanation
Indices: 53358476--53358788 Score: 256
Period size: 30 Copynumber: 10.4 Consensus size: 30
53358466 GGCTATCGAT
* * * *
53358476 TATGAAAAGGGATGG-TGACGACCATCGAAC
1 TATGAAAAGGGATGGCT-TCGGCTATCAAAC
* * * * *
53358506 TATAAAAAGGGATGG-TGACGACGATCGAAC
1 TATGAAAAGGGATGGCT-TCGGCTATCAAAC
* *
53358536 TATGAAAAAGGATGGCTTCGGCTATCAATC
1 TATGAAAAGGGATGGCTTCGGCTATCAAAC
* *
53358566 TATGAAAAGGGATGGCTTCAGCTATCAATC
1 TATGAAAAGGGATGGCTTCGGCTATCAAAC
* *
53358596 TATGAAAAGGGATGGCTTCGACTATCAATC
1 TATGAAAAGGGATGGCTTCGGCTATCAAAC
* * *
53358626 TATAAAAAGGGATGGCTTCGACTATCAATC
1 TATGAAAAGGGATGGCTTCGGCTATCAAAC
* * * * *
53358656 TATAAAAAGGGATAGCTTCTGTTATCAAAT
1 TATGAAAAGGGATGGCTTCGGCTATCAAAC
* ** * **
53358686 TATGAAAAGGGATGG-TGACAACCATTGAAC
1 TATGAAAAGGGATGGCT-TCGGCTATCAAAC
* * *
53358716 TATGAAAAGGGATGG-TGGCGGCCATCAAAT
1 TATGAAAAGGGATGGCT-TCGGCTATCAAAC
**
53358746 TATGAAAAGGGATAACTTCGGCTATCAAAC
1 TATGAAAAGGGATGGCTTCGGCTATCAAAC
53358776 TATGAAAAGGGAT
1 TATGAAAAGGGAT
53358789 AACTTCAATT
Statistics
Matches: 239, Mismatches: 41, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
29 1 0.00
30 236 0.99
31 2 0.01
ACGTcount: A:0.37, C:0.14, G:0.25, T:0.24
Consensus pattern (30 bp):
TATGAAAAGGGATGGCTTCGGCTATCAAAC
Found at i:53358807 original size:60 final size:59
Alignment explanation
Indices: 53358533--53358819 Score: 238
Period size: 60 Copynumber: 4.8 Consensus size: 59
53358523 ACGACGATCG
* * * *
53358533 AACTATGAAAAAGGATGGCTTCGGCTATCAATCTATGAAAAGGGATGGCTTCAGCTATCA
1 AACTATGAAAAGGGATAGCTTCGACTATCAAT-TATGAAAAGGGATGGCTTCAACTATCA
* * * *
53358593 ATCTATGAAAAGGGATGGCTTCGACTATCAATCTATAAAAAGGGATGGCTTCGACTATCA
1 AACTATGAAAAGGGATAGCTTCGACTATCAAT-TATGAAAAGGGATGGCTTCAACTATCA
* * * * * **
53358653 ATCTATAAAAAGGGATAGCTTCTG-TTATCAAATTATGAAAAGGGATGG-TGACAACCATTG
1 AACTATGAAAAGGGATAGCTTC-GACTATC-AATTATGAAAAGGGATGGCT-TCAACTATCA
* * * * ** **
53358713 AACTATGAAAAGGGAT-GGTGGCGGCCATCAAATTATGAAAAGGGATAACTTCGGCTATCA
1 AACTATGAAAAGGGATAGCT-TCGACTATC-AATTATGAAAAGGGATGGCTTCAACTATCA
* * * *
53358773 AACTATGAAAAGGGATAACTTCAATTATCGAATTACGAAAAGGGATG
1 AACTATGAAAAGGGATAGCTTCGACTATC-AATTATGAAAAGGGATG
53358820 TGTCAACCAT
Statistics
Matches: 181, Mismatches: 39, Indels: 14
0.77 0.17 0.06
Matches are distributed among these distances:
59 4 0.02
60 171 0.94
61 6 0.03
ACGTcount: A:0.38, C:0.14, G:0.23, T:0.25
Consensus pattern (59 bp):
AACTATGAAAAGGGATAGCTTCGACTATCAATTATGAAAAGGGATGGCTTCAACTATCA
Found at i:53358813 original size:30 final size:30
Alignment explanation
Indices: 53358557--53358818 Score: 122
Period size: 30 Copynumber: 8.7 Consensus size: 30
53358547 ATGGCTTCGG
** *
53358557 CTATC-AATCTATGAAAAGGGATGGCTTCAG
1 CTATCAAAT-TATGAAAAGGGATAACTTCAA
** *
53358587 CTATC-AATCTATGAAAAGGGATGGCTTCGA
1 CTATCAAAT-TATGAAAAGGGATAACTTCAA
* ** *
53358617 CTATC-AATCTATAAAAAGGGATGGCTTCGA
1 CTATCAAAT-TATGAAAAGGGATAACTTCAA
* * **
53358647 CTATC-AATCTATAAAAAGGGATAGCTTCTG
1 CTATCAAAT-TATGAAAAGGGATAACTTCAA
* ** *
53358677 TTATCAAATTATGAAAAGGGAT-GGTGACAA
1 CTATCAAATTATGAAAAGGGATAACT-TCAA
* ** * ** * **
53358707 CCATTGAACTATGAAAAGGGAT-GGTGGCGG
1 CTATCAAATTATGAAAAGGGATAACT-TCAA
* **
53358737 CCATCAAATTATGAAAAGGGATAACTTCGG
1 CTATCAAATTATGAAAAGGGATAACTTCAA
*
53358767 CTATCAAACTATGAAAAGGGATAACTTCAA
1 CTATCAAATTATGAAAAGGGATAACTTCAA
* * *
53358797 TTATCGAATTACGAAAAGGGAT
1 CTATCAAATTATGAAAAGGGAT
53358819 GTGTCAACCA
Statistics
Matches: 195, Mismatches: 34, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
29 2 0.01
30 189 0.97
31 4 0.02
ACGTcount: A:0.38, C:0.15, G:0.22, T:0.26
Consensus pattern (30 bp):
CTATCAAATTATGAAAAGGGATAACTTCAA
Found at i:53358813 original size:90 final size:89
Alignment explanation
Indices: 53358529--53358819 Score: 273
Period size: 90 Copynumber: 3.2 Consensus size: 89
53358519 GGTGACGACG
* * * * * *
53358529 ATCGAACTATGAAAAAGGATGGCTTCGGCTATCAATCTATGAAAAGGGATGGCTTCAGCTATCAA
1 ATCGAATTATGAAAAGGGATGGCTGCGACCATCAATCTATGAAAAGGGATAGCTTCAGCTATCAA
* *
53358594 TCTATGAAAAGGGATGGCTTCGACT
66 ACTATGAAAAGGGAT-GCTTCAACT
* * * * * *
53358619 ATC-AATCTATAAAAAGGGATGGCTTCGACTATCAATCTATAAAAAGGGATAGCTTCTGTTATCA
1 ATCGAAT-TATGAAAAGGGATGGCTGCGACCATCAATCTATGAAAAGGGATAGCTTCAGCTATCA
* * * *
53358683 AATTATGAAAAGGGATGGTGACAACC
65 AACTATGAAAAGGGATGCT-TCAACT
* * * * *
53358709 ATTGAACTATGAAAAGGGATGG-TGGCGGCCATCAAAT-TATGAAAAGGGATAACTTCGGCTATC
1 ATCGAATTATGAAAAGGGATGGCT-GCGACCATC-AATCTATGAAAAGGGATAGCTTCAGCTATC
* *
53358772 AAACTATGAAAAGGGATAACTTCAATT
64 AAACTATGAAAAGGGAT-GCTTCAACT
*
53358799 ATCGAATTACGAAAAGGGATG
1 ATCGAATTATGAAAAGGGATG
53358820 TGTCAACCAT
Statistics
Matches: 162, Mismatches: 33, Indels: 12
0.78 0.16 0.06
Matches are distributed among these distances:
89 5 0.03
90 151 0.93
91 6 0.04
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.25
Consensus pattern (89 bp):
ATCGAATTATGAAAAGGGATGGCTGCGACCATCAATCTATGAAAAGGGATAGCTTCAGCTATCAA
ACTATGAAAAGGGATGCTTCAACT
Found at i:53359168 original size:30 final size:30
Alignment explanation
Indices: 53359104--53359172 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
53359094 ACAGACGACT
* * **
53359104 AGGTGACATGGTCATGTGTGACACATGGTT
1 AGGTGACACGGTCATGTGTGACACACGGCC
53359134 AGGTGACACGGTTC-TGTGTGACACACGGCC
1 AGGTGACACGG-TCATGTGTGACACACGGCC
53359164 AGGTGACAC
1 AGGTGACAC
53359173 AGCTGCATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 32 0.94
31 2 0.06
ACGTcount: A:0.23, C:0.20, G:0.33, T:0.23
Consensus pattern (30 bp):
AGGTGACACGGTCATGTGTGACACACGGCC
Found at i:53376128 original size:20 final size:20
Alignment explanation
Indices: 53376103--53376158 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
53376093 CGAAGACACC
*
53376103 GAAGTGCAAACAGAGGCATT
1 GAAGTGCAAACAGAGGCACT
*
53376123 GAAGTGCAAACA-ATAGCACT
1 GAAGTGCAAACAGA-GGCACT
*
53376143 GAAGTGCAATCAGAGG
1 GAAGTGCAAACAGAGG
53376159 TAGTGCAATC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
19 1 0.03
20 28 0.93
21 1 0.03
ACGTcount: A:0.41, C:0.16, G:0.29, T:0.14
Consensus pattern (20 bp):
GAAGTGCAAACAGAGGCACT
Found at i:53382070 original size:30 final size:30
Alignment explanation
Indices: 53382036--53382092 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
53382026 TTTACGAGCC
* *
53382036 TAGGGGCAAAATCATAATTTTGTGAAACTT
1 TAGGGGCAAAAACATAATTTTGGGAAACTT
53382066 TAGGGGCAAAAACATAATTTTGGGAAA
1 TAGGGGCAAAAACATAATTTTGGGAAA
53382093 GTATTATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.40, C:0.09, G:0.23, T:0.28
Consensus pattern (30 bp):
TAGGGGCAAAAACATAATTTTGGGAAACTT
Found at i:53382467 original size:45 final size:45
Alignment explanation
Indices: 53382416--53382501 Score: 145
Period size: 45 Copynumber: 1.9 Consensus size: 45
53382406 TGTGAACCGA
* * *
53382416 ACATCATTGATTAGTAAGGTGGTTGCTATTTGCTGATTCCACCAG
1 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACCAG
53382461 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCA
1 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCA
53382502 TCTAGTATCT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.35
Consensus pattern (45 bp):
ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACCAG
Found at i:53387595 original size:30 final size:30
Alignment explanation
Indices: 53387561--53387617 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
53387551 TTTTACGAGC
53387561 TAGGGGC-AAAATCGTAATTTTGTGAAATTT
1 TAGGGGCAAAAAT-GTAATTTTGTGAAATTT
53387591 TAGGGGCAAAAATGTAATTTTGTGAAA
1 TAGGGGCAAAAATGTAATTTTGTGAAA
53387618 GTATGATTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.37, C:0.05, G:0.25, T:0.33
Consensus pattern (30 bp):
TAGGGGCAAAAATGTAATTTTGTGAAATTT
Found at i:53387918 original size:51 final size:50
Alignment explanation
Indices: 53387848--53387957 Score: 132
Period size: 51 Copynumber: 2.2 Consensus size: 50
53387838 TGAAAGTGAT
* * *
53387848 GGCTACTATGCGTACCGGATAGT-TTCGATCACCTGTGTAGTACTATGTGTA
1 GGCTACTACGCGTACCGGATAGTATT-G-TCACATGTGTAGTACTATATGTA
* * *
53387899 GGCTACTACGTGTATCGGATGGTAATTGTCACATGTGTAGTACTATATGTA
1 GGCTACTACGCGTACCGGATAGT-ATTGTCACATGTGTAGTACTATATGTA
53387950 GGCTACTA
1 GGCTACTA
53387958 TGTGAACAGA
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
51 48 0.94
52 1 0.02
53 2 0.04
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (50 bp):
GGCTACTACGCGTACCGGATAGTATTGTCACATGTGTAGTACTATATGTA
Found at i:53388019 original size:45 final size:45
Alignment explanation
Indices: 53387968--53388056 Score: 151
Period size: 45 Copynumber: 2.0 Consensus size: 45
53387958 TGTGAACAGA
* * *
53387968 ACATCATTGATTAGTAAGGTTGTTGCTATGTGCTGATTCCACCGG
1 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACCGG
53388013 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACCG
1 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACCG
53388057 AGTATCTGTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.34
Consensus pattern (45 bp):
ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACCGG
Found at i:53400364 original size:37 final size:37
Alignment explanation
Indices: 53400299--53400390 Score: 114
Period size: 37 Copynumber: 2.5 Consensus size: 37
53400289 TGATGTTTGA
* *
53400299 TTGCATGTTAAACATGCCCTGCAGGATA-TATCCAAT
1 TTGCATGTTAAACATGCCCTACACGATATTATCCAAT
**
53400335 TTGCATGTTAAAACATGCCCTACACGATATTATCTGAT
1 TTGCATGTT-AAACATGCCCTACACGATATTATCCAAT
* *
53400373 TCGCATGTTCAACATGCC
1 TTGCATGTTAAACATGCC
53400391 AAATGTGACA
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
36 9 0.19
37 25 0.52
38 14 0.29
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (37 bp):
TTGCATGTTAAACATGCCCTACACGATATTATCCAAT
Found at i:53401162 original size:39 final size:39
Alignment explanation
Indices: 53401108--53401323 Score: 405
Period size: 39 Copynumber: 5.5 Consensus size: 39
53401098 AATTTGTATT
53401108 TGAGTATTGTGATATATGCTTGAATGTTATGTGATTATA
1 TGAGTATTGTGATATATGCTTGAATGTTATGTGATTATA
* *
53401147 TGAGTATTGTGATATACGATTGAATGTTATGTGATTATA
1 TGAGTATTGTGATATATGCTTGAATGTTATGTGATTATA
53401186 TGAGTATTGTGATATATGCTTGAATGTTATGTGATTATA
1 TGAGTATTGTGATATATGCTTGAATGTTATGTGATTATA
53401225 TGAGTATTGTGATATATGCTTGAATGTTATGTGATTATA
1 TGAGTATTGTGATATATGCTTGAATGTTATGTGATTATA
53401264 TGAGTATTGTGATATATGCTTGAATGTTATGTGATTATA
1 TGAGTATTGTGATATATGCTTGAATGTTATGTGATTATA
*
53401303 TGAGTAATGTGATATATGCTT
1 TGAGTATTGTGATATATGCTT
53401324 AAAAGTGAAT
Statistics
Matches: 172, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 172 1.00
ACGTcount: A:0.29, C:0.03, G:0.23, T:0.45
Consensus pattern (39 bp):
TGAGTATTGTGATATATGCTTGAATGTTATGTGATTATA
Found at i:53405605 original size:56 final size:55
Alignment explanation
Indices: 53405515--53405763 Score: 220
Period size: 56 Copynumber: 4.7 Consensus size: 55
53405505 GGGAATGAGA
53405515 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATGAAAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCA-TGAGATTATGAAAGG
* *
53405571 TCCCATGTAAGACCATGTTTGGGACATGGAATTGGCATCGACATCGAG---ATGAAAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT---CAT-GAGATTATGAAAGG
* * *
53405627 TCCCATGTAAGACCATTTCTAGGACATGGCATTCGCATC--GAGATTA-G--AGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATGAGATTATGAAAGG
** * * * *
53405677 TCCCCCGTAGGACCATGTCTGGGACATGGCATGGGCA-C---CGA-TATGAGAA-C
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATGAGATTATGA-AAGG
* * *
53405727 TCCCATGTAAAACCATATCTGGGATATGGCATTGGCA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
53405764 GTACAATAAA
Statistics
Matches: 159, Mismatches: 23, Indels: 28
0.76 0.11 0.13
Matches are distributed among these distances:
47 2 0.01
48 3 0.02
49 1 0.01
50 66 0.42
51 1 0.01
52 1 0.01
53 2 0.01
56 77 0.48
58 1 0.01
59 5 0.03
ACGTcount: A:0.28, C:0.21, G:0.27, T:0.24
Consensus pattern (55 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATGAGATTATGAAAGG
Found at i:53405666 original size:50 final size:50
Alignment explanation
Indices: 53405515--53405812 Score: 237
Period size: 50 Copynumber: 5.8 Consensus size: 50
53405505 GGGAATGAGA
53405515 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATGAAAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATC---GAG---ATGAAAGG
* *
53405571 TCCCATGTAAGACCATGTTTGGGACATGGAATTGGCATCGACATCGAGATGAAAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATT-G----G-CATCGAGATGAAAGG
* * * * *
53405627 TCCCATGTAAGACCATTTCTAGGACATGGCATTCGCATCGAGATTAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGAGATGAAAGG
** * * * * *
53405677 TCCCCCGTAGGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAA-C
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGAGATGA-AAGG
* * * **
53405727 TCCCATGTAAAACCATATCTGGGATATGGCATTGGCAGTAC-A-AT-AAACA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-T-CGAGATGAAAGG
* *
53405776 T-CCATGTAAGACCATGTCTAGGACATGGCTTTGGCAT
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
53405813 GTTATTATGA
Statistics
Matches: 197, Mismatches: 35, Indels: 29
0.75 0.13 0.11
Matches are distributed among these distances:
47 1 0.01
48 32 0.16
49 2 0.01
50 81 0.41
51 3 0.02
52 1 0.01
56 68 0.35
57 1 0.01
59 3 0.02
61 1 0.01
62 4 0.02
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.24
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGAGATGAAAGG
Found at i:53415157 original size:51 final size:50
Alignment explanation
Indices: 53415097--53415271 Score: 163
Period size: 51 Copynumber: 3.5 Consensus size: 50
53415087 CGTGCGTAGT
* * *
53415097 CACATAGTACTAAACACGTGACCATTAATATCCGGTACACGTAGTAGCTTG
1 CACATAGTACTACACACGTGACC-TTAATATCCGGTACACGTAGTAGCCTC
* * ** * * *
53415148 TACATAGTACTACACACGTGATCGGAGCTATCCGGTACGCATAGTAGCCTC
1 CACATAGTACTACACACGTGACCTTA-ATATCCGGTACACGTAGTAGCCTC
* * * * *
53415199 CACATAGTACTACACATGCGACCTTTCAT-TCCGGTACACGTAGTAGTCTA
1 CACATAGTACTACACACGTGACC-TTAATATCCGGTACACGTAGTAGCCTC
* *
53415249 CACATAGTATTACACATGTGACC
1 CACATAGTACTACACACGTGACC
53415272 ATCACTTTCA
Statistics
Matches: 98, Mismatches: 24, Indels: 5
0.77 0.19 0.04
Matches are distributed among these distances:
50 39 0.40
51 59 0.60
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (50 bp):
CACATAGTACTACACACGTGACCTTAATATCCGGTACACGTAGTAGCCTC
Found at i:53420663 original size:51 final size:51
Alignment explanation
Indices: 53420601--53420777 Score: 184
Period size: 51 Copynumber: 3.5 Consensus size: 51
53420591 CGTTTGTAGT
* *
53420601 CACATAATACTACACACGTGACCATTAATATCCGATACACGTAGTGGCCTG
1 CACATAGTACTACACACGTGACCATTAATATCCGATACACGTAGTAGCCTG
* * *
53420652 CACATAGTACTACACACGTG-CTCGA--AGCTATCC-AGTACGCATAGTAGCCTG
1 CACATAGTACTACACACGTGAC-C-ATTA-ATATCCGA-TACACGTAGTAGCCTG
* * * * * *
53420703 CACATAGTACTACACATGCGACCTTTCAT-TCCGGTACACGTAGTAGCCTA
1 CACATAGTACTACACACGTGACCATTAATATCCGATACACGTAGTAGCCTG
53420753 CACATAGTACTACACACGTGACCAT
1 CACATAGTACTACACACGTGACCAT
53420778 CACTTTCACT
Statistics
Matches: 101, Mismatches: 17, Indels: 17
0.75 0.13 0.13
Matches are distributed among these distances:
50 41 0.41
51 58 0.57
52 2 0.02
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.23
Consensus pattern (51 bp):
CACATAGTACTACACACGTGACCATTAATATCCGATACACGTAGTAGCCTG
Found at i:53423217 original size:50 final size:50
Alignment explanation
Indices: 53423114--53423355 Score: 245
Period size: 50 Copynumber: 4.7 Consensus size: 50
53423104 GGGAATGAGA
* *
53423114 TCCCATGTAAGACCATGTTTGGGACATGGCATTGGCATCATTGAGATTATGAGAGC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--TGAG---ATGAGAAC
* * **
53423170 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATGAGAAC
** * *
53423220 TTTCATGTAAGACCATGTCTGGGACATGGCGTTGGCACTGATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATGAGAAC
* * * * * *
53423270 TGCCATGTAAGACCATATCTGGGATATGGCATTGGCAGT-ACAAGA-AAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATGAGAAC
* *
53423318 ATCCCACGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 -TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
53423356 TGTTATTATC
Statistics
Matches: 162, Mismatches: 23, Indels: 9
0.84 0.12 0.05
Matches are distributed among these distances:
48 3 0.02
49 36 0.22
50 84 0.52
53 3 0.02
55 1 0.01
56 35 0.22
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.25
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATGAGAAC
Found at i:53423299 original size:100 final size:104
Alignment explanation
Indices: 53423117--53423306 Score: 271
Period size: 100 Copynumber: 1.8 Consensus size: 104
53423107 AATGAGATCC
* *
53423117 CATGTAAGACCATGTTTGGGACATGGCATTGGCATCATTGAGATTATGAGAGCTCCCATGTAAGA
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCATCA-T-AGATTATGAGAACTCCCATGTAAGA
* *
53423182 CCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTTT
64 CCATATCTGGGACATGGCATTGGCACCGAGATGAGAGGTTT
* *
53423223 CATGTAAGACCATGTCTGGGACATGGCGTTGGCA-C-T-GA-TATGAGAACTGCCATGTAAGACC
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCATCATAGATTATGAGAACTCCCATGTAAGACC
*
53423284 ATATCTGGGATATGGCATTGGCA
66 ATATCTGGGACATGGCATTGGCA
53423307 GTACAAGAAA
Statistics
Matches: 77, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
100 41 0.53
101 2 0.03
103 1 0.01
105 1 0.01
106 32 0.42
ACGTcount: A:0.26, C:0.18, G:0.29, T:0.26
Consensus pattern (104 bp):
CATGTAAGACCATGTCTGGGACATGGCATTGGCATCATAGATTATGAGAACTCCCATGTAAGACC
ATATCTGGGACATGGCATTGGCACCGAGATGAGAGGTTT
Found at i:53425488 original size:39 final size:39
Alignment explanation
Indices: 53425271--53425485 Score: 331
Period size: 39 Copynumber: 5.5 Consensus size: 39
53425261 ACATGTATTC
*
53425271 GAGTATTGTGATATATGCTTGAATGTTATTTGATTATAT
1 GAGTATTGTGATATATGCTTGAATGTTATGTGATTATAT
* *
53425310 GAGTATTGTGATGTATGCTTGAATGTTATGTGATTACAT
1 GAGTATTGTGATATATGCTTGAATGTTATGTGATTATAT
* * *
53425349 GAGTATTATGATATATGTTTGAATGTTATGTGACTATAT
1 GAGTATTGTGATATATGCTTGAATGTTATGTGATTATAT
* *
53425388 GAGTATTGTGATGTATGCTTGAATGTTATGTAATTATAT
1 GAGTATTGTGATATATGCTTGAATGTTATGTGATTATAT
* *
53425427 GAATATTGTGATATATGCTTAAATGTTATGTGATTATAT
1 GAGTATTGTGATATATGCTTGAATGTTATGTGATTATAT
*
53425466 GTGTATTGTGATATATGCTT
1 GAGTATTGTGATATATGCTT
53425486 AAAAGTGAAT
Statistics
Matches: 157, Mismatches: 19, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 157 1.00
ACGTcount: A:0.28, C:0.03, G:0.22, T:0.47
Consensus pattern (39 bp):
GAGTATTGTGATATATGCTTGAATGTTATGTGATTATAT
Found at i:53430708 original size:40 final size:40
Alignment explanation
Indices: 53430658--53430853 Score: 164
Period size: 40 Copynumber: 4.8 Consensus size: 40
53430648 ATTTCTTTCG
** *
53430658 TCTGCTCCACTACAACTTAGGGAGATAAGACTGGATGCGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTGGATGTGA
* * *
53430698 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTTAA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGA-C--TGGATGTGA
* ** * * * *
53430741 T-TCGCTCCACTGCAACTTTAGGGAAATAGGA-TTGATTTTTTTG-
1 TCT-GCTCCACTACTGC-TTAGGGAGATAAGACTGGA----TGTGA
53430784 TCTGCTCCACTACTGCTTAGGGAGATAAGACTGGATGTGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTGGATGTGA
*
53430824 TCTGCTCCACTACTGCTTACGGAGATAAGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGA
53430854 TCTGTGGTTT
Statistics
Matches: 122, Mismatches: 22, Indels: 24
0.73 0.13 0.14
Matches are distributed among these distances:
39 3 0.02
40 59 0.48
41 1 0.01
42 13 0.11
43 30 0.25
44 16 0.13
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (40 bp):
TCTGCTCCACTACTGCTTAGGGAGATAAGACTGGATGTGA
Found at i:53430848 original size:126 final size:126
Alignment explanation
Indices: 53430617--53430953 Score: 548
Period size: 126 Copynumber: 2.7 Consensus size: 126
53430607 GATGCGATCT
* * *
53430617 GCTCTACTGCAACTTCAGAGAGATAGGATTGATTTCTTTCGTCTGCTCCACTACAACTTAGGGAG
1 GCTCCACTGCAACTTCAGGGAGATAGGATTGATTT-TTTTGTCTGCTCCACTACAACTTAGGGAG
*
53430682 ATAAGACTGGATGCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTTAATTC
65 ATAAGACTGGATGCGATCTGCTCCACTACTGCTTACGGAGATAAGATCTGTGGTTTTAATTC
* * **
53430744 GCTCCACTGCAACTTTAGGGAAATAGGATTGATTTTTTTGTCTGCTCCACTACTGCTTAGGGAGA
1 GCTCCACTGCAACTTCAGGGAGATAGGATTGATTTTTTTGTCTGCTCCACTACAACTTAGGGAGA
*
53430809 TAAGACTGGATGTGATCTGCTCCACTACTGCTTACGGAGATAAGATCTGTGGTTTTAATTC
66 TAAGACTGGATGCGATCTGCTCCACTACTGCTTACGGAGATAAGATCTGTGGTTTTAATTC
*
53430870 GCTCCACTGCAACTTCAGGGAGATAGGATTGATTTTTTTCGTCTGCTCCACTGCAACTTCAGGGA
1 GCTCCACTGCAACTTCAGGGAGATAGGATTGATTTTTTT-GTCTGCTCCACTACAACTT-AGGGA
*
53430935 GATAAAACTGGATGCGATC
64 GATAAGACTGGATGCGATC
53430954 CACTCTACTG
Statistics
Matches: 192, Mismatches: 16, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
126 123 0.64
127 47 0.24
128 22 0.11
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (126 bp):
GCTCCACTGCAACTTCAGGGAGATAGGATTGATTTTTTTGTCTGCTCCACTACAACTTAGGGAGA
TAAGACTGGATGCGATCTGCTCCACTACTGCTTACGGAGATAAGATCTGTGGTTTTAATTC
Found at i:53430918 original size:44 final size:43
Alignment explanation
Indices: 53430614--53430939 Score: 169
Period size: 44 Copynumber: 7.7 Consensus size: 43
53430604 CTTGATGCGA
* * * * *
53430614 TCTGCTCTACTGCAACTTCAGAGAGATAGGATTGATTTCTTTCG
1 TCTGCTCCACTACAACTT-AGGGAGATAAGATTGATTTTTTTCG
* *
53430658 TCTGCTCCACTACAACTTAGGGAGATAAGACTGGA-----TGCG
1 TCTGCTCCACTACAACTTAGGGAGATAAGA-TTGATTTTTTTCG
** ** **
53430697 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTG-TGGTTTTAA
1 -TCTGCTCCACTACAACTTAGGGAGATAAGAT-TGATTTTTTTCG
* * *
53430741 T-TCGCTCCACTGCAACTTTAGGGAAATAGGATTGATTTTTTT-G
1 TCT-GCTCCACTACAAC-TTAGGGAGATAAGATTGATTTTTTTCG
** * *
53430784 TCTGCTCCACTACTGCTTAGGGAGATAAGACTGGA----TGT-G
1 TCTGCTCCACTACAACTTAGGGAGATAAGA-TTGATTTTTTTCG
** * ** **
53430823 ATCTGCTCCACTACTGCTTACGGAGATAAGATCTG-TGGTTTTAA
1 -TCTGCTCCACTACAACTTAGGGAGATAAGAT-TGATTTTTTTCG
* *
53430867 T-TCGCTCCACTGCAACTTCAGGGAGATAGGATTGATTTTTTTCG
1 TCT-GCTCCACTACAACTT-AGGGAGATAAGATTGATTTTTTTCG
*
53430911 TCTGCTCCACTGCAACTTCAGGGAGATAA
1 TCTGCTCCACTACAACTT-AGGGAGATAA
53430940 AACTGGATGC
Statistics
Matches: 217, Mismatches: 41, Indels: 48
0.71 0.13 0.16
Matches are distributed among these distances:
39 8 0.04
40 59 0.27
42 14 0.06
43 54 0.25
44 81 0.37
45 1 0.00
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.33
Consensus pattern (43 bp):
TCTGCTCCACTACAACTTAGGGAGATAAGATTGATTTTTTTCG
Found at i:53431214 original size:131 final size:131
Alignment explanation
Indices: 53431057--53431671 Score: 842
Period size: 131 Copynumber: 4.7 Consensus size: 131
53431047 TCTTACACTT
*** * * * **
53431057 GAAGATAAGATTCACCGTCTTCGATCTACTCCACTACTGCTTAGGGAGACAAGATCTGTAAT-TT
1 GAAGATAAGATTTGTCGTCTTTGATCTACTCCACTACTACTTAGGGAGATAAGATCTACAATCTT
** * * * **
53431121 CCAACCTATTCCACTGCTGGTCAGGGACATAAGAATTGTGGCTTAAATCTGTTTCCCTACTCCT-
66 -CAACCTGCTCCACTGCTGCTCAGGGAGACAAGGCTTGTGGCTTAAATCTGTTTCCCTACTCCTA
53431185 GAG
130 G-G
*
53431188 GAAGATAAGATTTGTCGTCTTTGATCTACTCCACTACTGCTTAGGGAGATAAGATCTACAATCTT
1 GAAGATAAGATTTGTCGTCTTTGATCTACTCCACTACTACTTAGGGAGATAAGATCTACAATCTT
*
53431253 CAACCTGCTCCACTGCTGCTCAGGGAGACAAGGCTTGTGGCTTAAATTTGTTTCCCTACTCCTAG
66 CAACCTGCTCCACTGCTGCTCAGGGAGACAAGGCTTGTGGCTTAAATCTGTTTCCCTACTCCTAG
53431318 G
131 G
* **
53431319 GAAGATAAGATTT-TCCGTTTTTGATCTGTTCCACTACTACTTAGGGAGATAAGATCTACAATCT
1 GAAGATAAGATTTGT-CGTCTTTGATCTACTCCACTACTACTTAGGGAGATAAGATCTACAATCT
*
53431383 TCAACCTGCTCCGCTGCTGCTCAGGGAGACAAGGCTTGTGGCTTAAATCTGTTTCCCTACTCCTA
65 TCAACCTGCTCCACTGCTGCTCAGGGAGACAAGGCTTGTGGCTTAAATCTGTTTCCCTACTCCTA
53431448 GG
130 GG
* *
53431450 GAAGATAAGATTTGCCGTCTTTGATCTGCTCCACTACTACTTAGGGAGATAAGATCTACAATCTT
1 GAAGATAAGATTTGTCGTCTTTGATCTACTCCACTACTACTTAGGGAGATAAGATCTACAATCTT
* *
53431515 CAACCTGCTCCGCTGCTGCTCAGGGAGACAAGGCTTGTGGCTTAAATCTGTTTCCCTACTCCTGG
66 CAACCTGCTCCACTGCTGCTCAGGGAGACAAGGCTTGTGGCTTAAATCTGTTTCCCTACTCCTAG
53431580 G
131 G
* * * * * * *
53431581 GAAGATAAGATTTGTCATCTTCGATCCA-TCCACTATTTCTTAGGGAGATAAGATCTGCAATCTC
1 GAAGATAAGATTTGTCGTCTTTGATCTACTCCACTACTACTTAGGGAGATAAGATCTACAATCTT
* ** *
53431645 CAAACTTATTCCACTGCTGGTCAGGGA
66 C-AACCTGCTCCACTGCTGCTCAGGGA
53431672 CATAGGACTT
Statistics
Matches: 440, Mismatches: 39, Indels: 10
0.90 0.08 0.02
Matches are distributed among these distances:
130 34 0.08
131 403 0.92
132 3 0.01
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.31
Consensus pattern (131 bp):
GAAGATAAGATTTGTCGTCTTTGATCTACTCCACTACTACTTAGGGAGATAAGATCTACAATCTT
CAACCTGCTCCACTGCTGCTCAGGGAGACAAGGCTTGTGGCTTAAATCTGTTTCCCTACTCCTAG
G
Found at i:53431264 original size:44 final size:44
Alignment explanation
Indices: 53431211--53431542 Score: 154
Period size: 44 Copynumber: 7.6 Consensus size: 44
53431201 GTCGTCTTTG
* *
53431211 ATCTACTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCA
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAGTCTTCA
* * * * * *** * *
53431255 ACCTGCTCCACTGCTGCTCAGGGAGACAAG-GCTTGTGGCTTAA
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAGTCTTCA
* * * * * * * **
53431298 ATTTGTTTCC-CTACT-CCTAGGGAAGATAAGATTTTCCGTTTTTG
1 ATCTG-CTCCACTACTGCTTAGGG-AGATAAGATCTACAGTCTTCA
* * *
53431342 ATCTGTTCCACTACTACTTAGGGAGATAAGATCTACAATCTTCA
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAGTCTTCA
* * * * * * *** * *
53431386 ACCTGCTCCGCTGCTGCTCAGGGAGACAAG-GCTTGTGGCTTAA
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAGTCTTCA
* * * * * **
53431429 ATCTGTTTCC-CTACT-CCTAGGGAAGATAAGATTTGCCGTCTTTG
1 ATCTG-CTCCACTACTGCTTAGGG-AGATAAGATCTACAGTCTTCA
* *
53431473 ATCTGCTCCACTACTACTTAGGGAGATAAGATCTACAATCTTCA
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAGTCTTCA
* * * *
53431517 ACCTGCTCCGCTGCTGCTCAGGGAGA
1 ATCTGCTCCACTACTGCTTAGGGAGA
53431543 CAAGGCTTGT
Statistics
Matches: 201, Mismatches: 77, Indels: 20
0.67 0.26 0.07
Matches are distributed among these distances:
42 10 0.05
43 46 0.23
44 133 0.66
45 12 0.06
ACGTcount: A:0.24, C:0.25, G:0.20, T:0.30
Consensus pattern (44 bp):
ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAGTCTTCA
Found at i:53432821 original size:15 final size:16
Alignment explanation
Indices: 53432802--53432837 Score: 58
Period size: 14 Copynumber: 2.4 Consensus size: 16
53432792 CATTTTTGTA
53432802 CTTTTTCA-TTTTCA-
1 CTTTTTCATTTTTCAC
53432816 CTTTTTCATTTTTCAC
1 CTTTTTCATTTTTCAC
53432832 CTTTTT
1 CTTTTT
53432838 TTTTTGAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 8 0.40
15 6 0.30
16 6 0.30
ACGTcount: A:0.11, C:0.22, G:0.00, T:0.67
Consensus pattern (16 bp):
CTTTTTCATTTTTCAC
Found at i:53433723 original size:28 final size:27
Alignment explanation
Indices: 53433656--53433720 Score: 87
Period size: 29 Copynumber: 2.4 Consensus size: 27
53433646 CTTTTTCATA
* *
53433656 TTTTTATTTTGACTTTAATTGATTTCTCT
1 TTTTTCTTTTGACTTTGATT--TTTCTCT
53433685 TTTTTCTTTTGACTTTGATTTTT-TCT
1 TTTTTCTTTTGACTTTGATTTTTCTCT
53433711 TTTTTCTTTT
1 TTTTTCTTTT
53433721 TTGTTTTTGA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
26 13 0.38
27 3 0.09
29 18 0.53
ACGTcount: A:0.11, C:0.11, G:0.06, T:0.72
Consensus pattern (27 bp):
TTTTTCTTTTGACTTTGATTTTTCTCT
Found at i:53433749 original size:34 final size:33
Alignment explanation
Indices: 53433677--53433749 Score: 76
Period size: 34 Copynumber: 2.2 Consensus size: 33
53433667 ACTTTAATTG
* *
53433677 ATTTCTCTTTTTTCTTTTGACTTTGATTTTTTC
1 ATTTTTCTTTTTTCTTTTGACTTTGATTTTATC
* * *
53433710 TTTTTTCTTTTTTGTTTTTGATTTTGATTTTGAT-
1 ATTTTTCTTTTTT-CTTTTGACTTTGATTTT-ATC
53433744 ATTTTT
1 ATTTTT
53433750 TTTATTGAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
33 11 0.34
34 20 0.62
35 1 0.03
ACGTcount: A:0.10, C:0.08, G:0.08, T:0.74
Consensus pattern (33 bp):
ATTTTTCTTTTTTCTTTTGACTTTGATTTTATC
Found at i:53435444 original size:50 final size:49
Alignment explanation
Indices: 53435382--53435552 Score: 200
Period size: 50 Copynumber: 3.4 Consensus size: 49
53435372 CAATGACATA
* * *
53435382 TCCCAGATATGGTCTTACATGGGAGTTCTCAAATTGGTGTCC-ATGCCATG
1 TCCCAGACATGGTCTTACATGGGAG-TCTCATATTGGTG-CCAACGCCATG
** * *
53435432 TCCCAGACATGGTCTTACGGGGGACCTCTCATTTTGGTGCCAACGCCATG
1 TCCCAGACATGGTCTTACATGGGA-GTCTCATATTGGTGCCAACGCCATG
* * * *
53435482 TCCCAGACATGGTCTTACATGGGACGTCTTATCTCGGTGCCAACGCCATT
1 TCCCAGACATGGTCTTACATGGGA-GTCTCATATTGGTGCCAACGCCATG
53435532 TCCCAGACATGGTCTTACATG
1 TCCCAGACATGGTCTTACATG
53435553 TGACCTCATT
Statistics
Matches: 105, Mismatches: 14, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
49 2 0.02
50 103 0.98
ACGTcount: A:0.20, C:0.27, G:0.23, T:0.29
Consensus pattern (49 bp):
TCCCAGACATGGTCTTACATGGGAGTCTCATATTGGTGCCAACGCCATG
Found at i:53442900 original size:50 final size:50
Alignment explanation
Indices: 53442841--53443022 Score: 186
Period size: 50 Copynumber: 3.6 Consensus size: 50
53442831 GTCCCAATGT
* * ** * *
53442841 CATGTCCCAGATATGATCTTACATGCGAGTTCTCATATTGGTGTCC-ATGC
1 CATGTCCCAGACATGGTCTTACATGCGACCTCTCATATCGGTG-CCAACGC
** * *
53442891 CATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGGTGCCAACGC
1 CATGTCCCAGACATGGTCTTACATGCGACCTCTCATATCGGTGCCAACGC
* * * * *
53442941 CATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCAGTGCCAATGC
1 CATGTCCCAGACATGGTCTTACATGCGACCTCTCATATCGGTGCCAACGC
* * *
53442991 CATGTCCTAGACATAGTCTTACATGAGACCTC
1 CATGTCCCAGACATGGTCTTACATGCGACCTC
53443023 ATTCCCTTAA
Statistics
Matches: 113, Mismatches: 18, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
49 2 0.02
50 111 0.98
ACGTcount: A:0.22, C:0.29, G:0.21, T:0.28
Consensus pattern (50 bp):
CATGTCCCAGACATGGTCTTACATGCGACCTCTCATATCGGTGCCAACGC
Found at i:53448617 original size:101 final size:101
Alignment explanation
Indices: 53448457--53448638 Score: 247
Period size: 101 Copynumber: 1.8 Consensus size: 101
53448447 AAAGTGATGG
* * * * * * *
53448457 TCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTACCGGAATGAAAGGTCGCATGTGTAGTAC
1 TCACGTGTGTAGTACTATGCGCAGGCTACTACGTGAACCGAAAAGAAAGATCACATGTGTAGTAC
*
53448522 TATGTGCAGGCTACTATGCGAACCAGATAGCTTCGA
66 TATGTGAAGGCTACTATGCGAACCAGATAGCTTCGA
* *** *
53448558 TCACGTGTGTAGTACTATGCGCAGGCTACTACGTGAACTGAAAAGTTTGATCACGTGTGTAGTAC
1 TCACGTGTGTAGTACTATGCGCAGGCTACTACGTGAACCGAAAAGAAAGATCACATGTGTAGTAC
53448623 TATGTGAAGGCTACTA
66 TATGTGAAGGCTACTA
53448639 CATATATTGA
Statistics
Matches: 68, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
101 68 1.00
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.29
Consensus pattern (101 bp):
TCACGTGTGTAGTACTATGCGCAGGCTACTACGTGAACCGAAAAGAAAGATCACATGTGTAGTAC
TATGTGAAGGCTACTATGCGAACCAGATAGCTTCGA
Found at i:53448634 original size:50 final size:49
Alignment explanation
Indices: 53448457--53448639 Score: 177
Period size: 50 Copynumber: 3.7 Consensus size: 49
53448447 AAAGTGATGG
* * * * ** *
53448457 TCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTACCGGAATGAAAGG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTG-AACGAAAAGTTAGA
* * * * * * *
53448507 TCGCATGTGTAGTACTATGTGCAGGCTACTATGCGAACCAGATAGCTTCGA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGAACGA-AAAG-TTAGA
* *
53448558 TCACGTGTGTAGTACTATGCGCAGGCTACTACGTGAACTGAAAAGTTTGA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGAAC-GAAAAGTTAGA
*
53448608 TCACGTGTGTAGTACTATGTGAAGGCTACTAC
1 TCACGTGTGTAGTACTATGTGCAGGCTACTAC
53448640 ATATATTGAA
Statistics
Matches: 106, Mismatches: 24, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
49 2 0.02
50 66 0.62
51 37 0.35
52 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.28
Consensus pattern (49 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGAACGAAAAGTTAGA
Found at i:53456707 original size:24 final size:24
Alignment explanation
Indices: 53456675--53456720 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
53456665 GTCTTTTACC
* *
53456675 ACCCTTAAAGGGCTTTCATATACT
1 ACCCCTAAAGGGATTTCATATACT
53456699 ACCCCTAAAGGGATTTCATATA
1 ACCCCTAAAGGGATTTCATATA
53456721 TTGGTGCGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.33, C:0.24, G:0.13, T:0.30
Consensus pattern (24 bp):
ACCCCTAAAGGGATTTCATATACT
Found at i:53458431 original size:45 final size:45
Alignment explanation
Indices: 53458367--53458543 Score: 207
Period size: 45 Copynumber: 4.0 Consensus size: 45
53458357 ACCGAGTACC
* *
53458367 ATTGATTATAAAGGTGGTTGTTGTGTGCTAATTCCACCGGGTATT
1 ATTGATTATAAAGGTGGTTGTTATGTGCTGATTCCACCGGGTATT
* * *
53458412 ATTGATTATAAAGGTGGTTGTTGTGTGCTGATTCCACCAGGTACT
1 ATTGATTATAAAGGTGGTTGTTATGTGCTGATTCCACCGGGTATT
* * * *
53458457 ATTGATTCTGAAGGTGGTT-TCTATGTGCTGATTCCACCGAGTATC
1 ATTGATTATAAAGGTGGTTGT-TATGTGCTGATTCCACCGGGTATT
* * * *
53458502 ATTGACTATAAGGGTGG-TGTTATGTGATGA-TCCACCGTGTAT
1 ATTGATTATAAAGGTGGTTGTTATGTGCTGATTCCACCGGGTAT
53458544 CTGTTATTAT
Statistics
Matches: 114, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
43 11 0.10
44 11 0.10
45 92 0.81
ACGTcount: A:0.22, C:0.14, G:0.27, T:0.38
Consensus pattern (45 bp):
ATTGATTATAAAGGTGGTTGTTATGTGCTGATTCCACCGGGTATT
Found at i:53469653 original size:42 final size:42
Alignment explanation
Indices: 53469606--53469713 Score: 162
Period size: 42 Copynumber: 2.6 Consensus size: 42
53469596 ACGACCTAGC
*
53469606 ACACGGCCTGGCACACGGGCGTGTGGAATTACTTCGAAGGGT
1 ACACGGCCTGGCACACGAGCGTGTGGAATTACTTCGAAGGGT
* * *
53469648 ACACGGCCTGGCGCATGAGCGTGTGGGATTACTTCGAAGGGT
1 ACACGGCCTGGCACACGAGCGTGTGGAATTACTTCGAAGGGT
**
53469690 ACGTGGCCTGGCACACGAGCGTGT
1 ACACGGCCTGGCACACGAGCGTGT
53469714 AACTTGGTCG
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 58 1.00
ACGTcount: A:0.19, C:0.24, G:0.37, T:0.19
Consensus pattern (42 bp):
ACACGGCCTGGCACACGAGCGTGTGGAATTACTTCGAAGGGT
Found at i:53476588 original size:21 final size:21
Alignment explanation
Indices: 53476563--53476602 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
53476553 AGCTCGGTAT
* *
53476563 TTATTTTTTGAAATTATAAAA
1 TTATTTTGTAAAATTATAAAA
53476584 TTATTTTGTAAAATTATAA
1 TTATTTTGTAAAATTATAA
53476603 TTATGTAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (21 bp):
TTATTTTGTAAAATTATAAAA
Found at i:53477802 original size:17 final size:17
Alignment explanation
Indices: 53477776--53477809 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
53477766 TTGTATTAAC
*
53477776 TTTGAATTTTTTAATTT
1 TTTGAATTTTTAAATTT
*
53477793 TTTGATTTTTTAAATTT
1 TTTGAATTTTTAAATTT
53477810 AATTTTTTTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (17 bp):
TTTGAATTTTTAAATTT
Found at i:53478137 original size:15 final size:17
Alignment explanation
Indices: 53478117--53478163 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 17
53478107 TAAAAGCATC
*
53478117 TAAATTTAATAT-AA-T
1 TAAATTCAATATGAACT
53478132 TAAATTCAATATGAACT
1 TAAATTCAATATGAACT
53478149 TAAATATCAA-ATGAA
1 TAAAT-TCAATATGAA
53478164 ATATGTTGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 11 0.39
16 2 0.07
17 11 0.39
18 4 0.14
ACGTcount: A:0.53, C:0.06, G:0.04, T:0.36
Consensus pattern (17 bp):
TAAATTCAATATGAACT
Found at i:53480709 original size:28 final size:28
Alignment explanation
Indices: 53480669--53480837 Score: 148
Period size: 28 Copynumber: 6.0 Consensus size: 28
53480659 AGCAGGAGAA
*
53480669 AAAAACTGTAAAATCTGAAAAATAGGGG
1 AAAAACTATAAAATCTGAAAAATAGGGG
* * *
53480697 AAAAACTGTAAAATCAT-AAAAACATGGG
1 AAAAACTATAAAATC-TGAAAAATAGGGG
* *
53480725 AAAAATTGTAAAAT-TAGAAAAAATAGGGG
1 AAAAACTATAAAATCT-G-AAAAATAGGGG
* * *
53480754 CAAAACTATAAAATATGAGAAATA-GGG
1 AAAAACTATAAAATCTGAAAAATAGGGG
* *
53480781 AAAAACTAT-AAATCTGAGAAATATGGG
1 AAAAACTATAAAATCTGAAAAATAGGGG
* * *
53480808 AAAAACTATAAACTTTAAAAAAATAGGGG
1 AAAAACTATAAAATCT-GAAAAATAGGGG
53480837 A
1 A
53480838 CACACGATCG
Statistics
Matches: 117, Mismatches: 16, Indels: 15
0.79 0.11 0.10
Matches are distributed among these distances:
26 14 0.12
27 23 0.20
28 47 0.40
29 32 0.27
30 1 0.01
ACGTcount: A:0.56, C:0.07, G:0.18, T:0.20
Consensus pattern (28 bp):
AAAAACTATAAAATCTGAAAAATAGGGG
Found at i:53480782 original size:56 final size:56
Alignment explanation
Indices: 53480669--53480819 Score: 175
Period size: 56 Copynumber: 2.7 Consensus size: 56
53480659 AGCAGGAGAA
*
53480669 AAAAACTGTAAAATCTGAAAAATAGGGGAAAAACTGTAAAATCATAAAAACATGGG
1 AAAAACTGTAAAATCTGAAAAATAGGGGAAAAACTATAAAATCATAAAAACATGGG
* * * *
53480725 AAAAATTGTAAAAT-TAGAAAAAATAGGGGCAAAACTATAAAAT-ATGAGAA-ATAGGG
1 AAAAACTGTAAAATCT-G-AAAAATAGGGGAAAAACTATAAAATCATAAAAACAT-GGG
* * *
53480781 AAAAACTAT-AAATCTGAGAAATATGGGAAAAACTATAAA
1 AAAAACTGTAAAATCTGAAAAATAGGGGAAAAACTATAAA
53480820 CTTTAAAAAA
Statistics
Matches: 81, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
54 20 0.25
55 8 0.10
56 30 0.37
57 23 0.28
ACGTcount: A:0.57, C:0.07, G:0.17, T:0.19
Consensus pattern (56 bp):
AAAAACTGTAAAATCTGAAAAATAGGGGAAAAACTATAAAATCATAAAAACATGGG
Found at i:53480793 original size:26 final size:27
Alignment explanation
Indices: 53480745--53480819 Score: 107
Period size: 27 Copynumber: 2.8 Consensus size: 27
53480735 AAATTAGAAA
*
53480745 AAATAGGGGCAAAACTATAAAATATGAG
1 AAATAGGGGAAAAACTAT-AAATATGAG
*
53480773 AAATA-GGGAAAAACTATAAATCTGAG
1 AAATAGGGGAAAAACTATAAATATGAG
*
53480799 AAATATGGGAAAAACTATAAA
1 AAATAGGGGAAAAACTATAAA
53480820 CTTTAAAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
26 13 0.30
27 26 0.59
28 5 0.11
ACGTcount: A:0.56, C:0.07, G:0.19, T:0.19
Consensus pattern (27 bp):
AAATAGGGGAAAAACTATAAATATGAG
Found at i:53494199 original size:2 final size:2
Alignment explanation
Indices: 53494192--53494224 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
53494182 TTAAAATTTG
53494192 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
53494225 NNNNNNNNNN
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:53500988 original size:2 final size:2
Alignment explanation
Indices: 53500952--53500980 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
53500942 ACTTACCTTT
53500952 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
53500981 CGATATATGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:53510914 original size:126 final size:126
Alignment explanation
Indices: 53510682--53511035 Score: 573
Period size: 126 Copynumber: 2.8 Consensus size: 126
53510672 TAATTTCGAG
* * * *
53510682 TTGACTTTTCTGATCAAATAGTATAAAATCGCTTCTAGTAGGATGCTATTTGGGAAGAATTTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
* * *
53510747 AAATCGCGCCCTCGTGGACGCGCTTTTGCTATAGTATGTCACGGAAGAAACATTTATTTTT
66 AAATCACGCCCTCGTGGACGCGCTTTTGCTATAGTAGGTCACGGAAGAAACAATTATTTTT
53510808 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
* * * *
53510873 AAATCACGCACTCGTGGACGCGTTTTTGCTACAGTAGGTCACGGAAGAAATAATTATTTTT
66 AAATCACGCCCTCGTGGACGCGCTTTTGCTATAGTAGGTCACGGAAGAAACAATTATTTTT
* * *
53510934 TTGACGTTTTTGAGAAAATAGTATAAAATTGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
*
53510999 AAATCACGCCCTCGTGGACGCGCTGTTGCTATAGTAG
66 AAATCACGCCCTCGTGGACGCGCTTTTGCTATAGTAG
53511036 CATGTTTGGG
Statistics
Matches: 210, Mismatches: 18, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
126 210 1.00
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.34
Consensus pattern (126 bp):
TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
AAATCACGCCCTCGTGGACGCGCTTTTGCTATAGTAGGTCACGGAAGAAACAATTATTTTT
Found at i:53514132 original size:37 final size:38
Alignment explanation
Indices: 53514083--53514251 Score: 91
Period size: 37 Copynumber: 4.4 Consensus size: 38
53514073 CAAAAAATTG
*
53514083 TATTAATGGTTAGTAAAATTATCAAATTATATAAAAT-
1 TATTAATTGTTAGTAAAATTATCAAATTATATAAAATC
* * * * * *
53514120 TATTAATTGTTAGTACCAGTGA-AAACATT-TTTCCAAATC
1 TATTAATTGTTAGTA-AAATTATCAA-ATTATAT-AAAATC
** * * * * *
53514159 TAACATTATGTGAATGTAAAATTATCAACTCTA-A-AAATTG
1 TATTAAT-TGT-TA-GTAAAATTATCAAAT-TATATAAAATC
53514199 TATTAA-TGATTAGTAAAATTATCAAATTATATAAAAT-
1 TATTAATTG-TTAGTAAAATTATCAAATTATATAAAATC
53514236 TATTAATTGTTAGTAA
1 TATTAATTGTTAGTAA
53514252 CAGTCAAAAC
Statistics
Matches: 92, Mismatches: 26, Indels: 28
0.63 0.18 0.19
Matches are distributed among these distances:
36 2 0.02
37 46 0.50
38 19 0.21
39 5 0.05
40 9 0.10
41 5 0.05
42 6 0.07
ACGTcount: A:0.44, C:0.07, G:0.09, T:0.40
Consensus pattern (38 bp):
TATTAATTGTTAGTAAAATTATCAAATTATATAAAATC
Found at i:53514273 original size:116 final size:116
Alignment explanation
Indices: 53514069--53514304 Score: 418
Period size: 116 Copynumber: 2.0 Consensus size: 116
53514059 AAATTGTATT
*
53514069 AACTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATTATATAAAATTATTAATTGTTAGT
1 AACTCAAAAAATTGTATTAATGATTAGTAAAATTATCAAATTATATAAAATTATTAATTGTTAGT
* * *
53514134 ACCAGTGAAAACATTTTTCCAAATCTAACATTATGTGAATGTAAAATTATC
66 AACAGTCAAAACATTTTTCCAAATCTAACATTACGTGAATGTAAAATTATC
*
53514185 AACTCTAAAAATTGTATTAATGATTAGTAAAATTATCAAATTATATAAAATTATTAATTGTTAGT
1 AACTCAAAAAATTGTATTAATGATTAGTAAAATTATCAAATTATATAAAATTATTAATTGTTAGT
*
53514250 AACAGTCAAAACATTTTTCCAAATCTAACATTACGTGAATGTAAAATTATT
66 AACAGTCAAAACATTTTTCCAAATCTAACATTACGTGAATGTAAAATTATC
53514301 AACT
1 AACT
53514305 TTGTTTAGGG
Statistics
Matches: 114, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
116 114 1.00
ACGTcount: A:0.44, C:0.10, G:0.08, T:0.37
Consensus pattern (116 bp):
AACTCAAAAAATTGTATTAATGATTAGTAAAATTATCAAATTATATAAAATTATTAATTGTTAGT
AACAGTCAAAACATTTTTCCAAATCTAACATTACGTGAATGTAAAATTATC
Found at i:53514359 original size:21 final size:22
Alignment explanation
Indices: 53514333--53514523 Score: 99
Period size: 21 Copynumber: 8.4 Consensus size: 22
53514323 TAAATTAGGC
53514333 TAGGGTTTTAAAGTTAA-GGGT
1 TAGGGTTTTAAAGTTAAGGGGT
*
53514354 TAGGGTTTTTAAGTTAAGGGGT
1 TAGGGTTTTAAAGTTAAGGGGT
*
53514376 TAGGGTTTTTAA-TTAAATTAGGTTAGGGT
1 TAGGGTTTTAAAGTT--A--AGG---G-GT
* **
53514405 TAGGGTTTTTAA-TTAAATTAGGT
1 TAGGGTTTTAAAGTT-AA-GGGGT
*
53514428 TAGGGTTTTTAAAGTTAA-GGTT
1 TAGGG-TTTTAAAGTTAAGGGGT
* * *
53514450 TAAGGTTTTTAAGTTAA-GGTT
1 TAGGGTTTTAAAGTTAAGGGGT
* **
53514471 TAGGGTTTTTAA-TTAAATTAGGT
1 TAGGGTTTTAAAGTT-AA-GGGGT
*
53514494 TAGGGTTTTAAAGTTAA-GGTT
1 TAGGGTTTTAAAGTTAAGGGGT
53514515 TAGGGTTTT
1 TAGGGTTTT
53514524 TAATTAAATT
Statistics
Matches: 140, Mismatches: 14, Indels: 32
0.75 0.08 0.17
Matches are distributed among these distances:
20 2 0.01
21 57 0.41
22 22 0.16
23 23 0.16
24 11 0.08
25 5 0.04
26 1 0.01
28 3 0.02
29 16 0.11
ACGTcount: A:0.27, C:0.00, G:0.28, T:0.45
Consensus pattern (22 bp):
TAGGGTTTTAAAGTTAAGGGGT
Found at i:53514404 original size:29 final size:29
Alignment explanation
Indices: 53514372--53514434 Score: 126
Period size: 29 Copynumber: 2.2 Consensus size: 29
53514362 TTAAGTTAAG
53514372 GGGTTAGGGTTTTTAATTAAATTAGGTTA
1 GGGTTAGGGTTTTTAATTAAATTAGGTTA
53514401 GGGTTAGGGTTTTTAATTAAATTAGGTTA
1 GGGTTAGGGTTTTTAATTAAATTAGGTTA
53514430 GGGTT
1 GGGTT
53514435 TTTAAAGTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.25, C:0.00, G:0.30, T:0.44
Consensus pattern (29 bp):
GGGTTAGGGTTTTTAATTAAATTAGGTTA
Found at i:53514416 original size:95 final size:95
Alignment explanation
Indices: 53514309--53514500 Score: 332
Period size: 95 Copynumber: 2.0 Consensus size: 95
53514299 TTAACTTTGT
*
53514309 TTAGGGTTTTTAATTAAATTAGGCTAGGG-TTTTAAAGTTAAGGGTTAGGGTTTTTAAGTTAAGG
1 TTAGGGTTTTTAATTAAATTAGGCTAGGGTTTTTAAAGTTAAGGGTTAAGGTTTTTAAGTTAA-G
53514373 GGTTAGGGTTTTTAATTAAATTAGGTTAGGG
65 GGTTAGGGTTTTTAATTAAATTAGGTTAGGG
* *
53514404 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAAGTTAAGGTTTAAGGTTTTTAAGTTAAGG
1 TTAGGGTTTTTAATTAAATTAGGCTAGGGTTTTTAAAGTTAAGGGTTAAGGTTTTTAAGTTAAGG
*
53514469 TTTAGGGTTTTTAATTAAATTAGGTTAGGG
66 GTTAGGGTTTTTAATTAAATTAGGTTAGGG
53514499 TT
1 TT
53514501 TTAAAGTTAA
Statistics
Matches: 92, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
95 61 0.66
96 31 0.34
ACGTcount: A:0.28, C:0.01, G:0.27, T:0.45
Consensus pattern (95 bp):
TTAGGGTTTTTAATTAAATTAGGCTAGGGTTTTTAAAGTTAAGGGTTAAGGTTTTTAAGTTAAGG
GTTAGGGTTTTTAATTAAATTAGGTTAGGG
Found at i:53514476 original size:66 final size:64
Alignment explanation
Indices: 53514404--53514530 Score: 227
Period size: 66 Copynumber: 2.0 Consensus size: 64
53514394 TAGGTTAGGG
53514404 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAAGTTAAGGTTTAAGGTTTTTAAGTTAAGG
1 TTAGGGTTTTTAATTAAATTAGGTTAGGG-TTTTAAAGTTAAGGTTTAAGGTTTTTAA-TTAAGG
53514469 T
64 T
*
53514470 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTAAAGTTAAGGTTTAGGGTTTTTAATTAA
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTAAAGTTAAGGTTTAAGGTTTTTAATTAA
53514531 ATTAGGTTAG
Statistics
Matches: 60, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
64 4 0.07
65 27 0.45
66 29 0.48
ACGTcount: A:0.29, C:0.00, G:0.24, T:0.47
Consensus pattern (64 bp):
TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTAAAGTTAAGGTTTAAGGTTTTTAATTAAGGT
Found at i:53514527 original size:44 final size:43
Alignment explanation
Indices: 53514351--53514607 Score: 207
Period size: 44 Copynumber: 5.8 Consensus size: 43
53514341 TAAAGTTAAG
53514351 GGTTAGGGTTTTTAAGTTAAGGGGTTAGGGTTTTTAATTAAATTAGGTTA
1 GGTTAGGGTTTTTAAGTTAA--GGTTAGGGTTTTTAATT-AA--A--TTA
*
53514401 GGGTTAGGGTTTTTAA-TTAAATTAGGTTAGGGTTTTT-A--AAGTTAA
1 -GGTTAGGGTTTTTAAGTT--A--AGGTTAGGGTTTTTAATTAAATT-A
*
53514446 GGTTTAAGGTTTTTAAGTTAAGGTTTAGGGTTTTTAATTAAATTA
1 GG-TTAGGGTTTTTAAGTTAAGG-TTAGGGTTTTTAATTAAATTA
*
53514491 GGTTAGGGTTTTAAAGTTAAGGTTTAGGGTTTTTAATTAAATTA
1 GGTTAGGGTTTTTAAGTTAAGG-TTAGGGTTTTTAATTAAATTA
53514535 GGTTAGGG---TT-AG----GGTTAGGGTTTTTAATTAAATTA
1 GGTTAGGGTTTTTAAGTTAAGGTTAGGGTTTTTAATTAAATTA
*
53514570 GGTTAGGGTTTTGTATTAAATT-AGGTTAGGGTTTTTAA
1 GGTTAGGG--TT-T-TTAAGTTAAGGTTAGGGTTTTTAA
53514608 AGTTAAGGTT
Statistics
Matches: 177, Mismatches: 7, Indels: 49
0.76 0.03 0.21
Matches are distributed among these distances:
35 29 0.16
36 2 0.01
40 2 0.01
41 1 0.01
42 5 0.03
43 12 0.07
44 54 0.31
45 16 0.09
46 21 0.12
48 2 0.01
50 2 0.01
51 16 0.09
52 14 0.08
54 1 0.01
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.46
Consensus pattern (43 bp):
GGTTAGGGTTTTTAAGTTAAGGTTAGGGTTTTTAATTAAATTA
Found at i:53514577 original size:23 final size:23
Alignment explanation
Indices: 53514547--53514884 Score: 198
Period size: 23 Copynumber: 13.6 Consensus size: 23
53514537 TTAGGGTTAG
53514547 GGTTAGGGTTTTTAATTAAATTA
1 GGTTAGGGTTTTTAATTAAATTA
53514570 GGTTAGGGTTTTGT-ATTAAATTA
1 GGTTAGGGTTTT-TAATTAAATTA
*
53514593 GGTTAGGGTTTTT-A--AAGTTAA
1 GGTTAGGGTTTTTAATTAAATT-A
53514614 GGTTTAGGGTTTTTAATTAAATTA
1 GG-TTAGGGTTTTTAATTAAATTA
53514638 GGTTAGGGTTAGGGCTTTTAATTAAATCAAGTTA
1 GGTTAGGG-T-----TTTTAATT--A--AA-TTA
*
53514672 GGGTTAGGATTTTTAATTAAATTA
1 -GGTTAGGGTTTTTAATTAAATTA
53514696 GGTTAGGGTTTTGT-ATTAAATTA
1 GGTTAGGGTTTT-TAATTAAATTA
*
53514719 GGTTAGGGTTAGGGTTTTGTATTAAATTA
1 GGTTAGGG-T----TTTT-AATTAAATTA
*
53514748 GGTTAGGGTTTTT-A--AAGTTAA
1 GGTTAGGGTTTTTAATTAAATT-A
53514769 GGTTTAGGGTTTTTAAGTT--A--A
1 GG-TTAGGGTTTTTAA-TTAAATTA
53514790 GGTTTAGGGTTTTTAATTAAATTAAATCA
1 GG-TTAGGGTTTTTAATTAAA-T---T-A
53514819 GGTTAGGGTTAGGGTTTTTAATTAAATTA
1 GGTTA-GG-----GTTTTTAATTAAATTA
*
53514848 GGTTAGGG-TTTAAAGTTAAATTA
1 GGTTAGGGTTTTTAA-TTAAATTA
53514871 GGTTAGGGTTTTTA
1 GGTTAGGGTTTTTA
53514885 TTACATCAAA
Statistics
Matches: 258, Mismatches: 8, Indels: 97
0.71 0.02 0.27
Matches are distributed among these distances:
20 10 0.04
21 23 0.09
22 31 0.12
23 86 0.33
24 18 0.07
25 6 0.02
27 2 0.01
28 9 0.03
29 44 0.17
30 1 0.00
31 1 0.00
33 3 0.01
34 17 0.07
35 7 0.03
ACGTcount: A:0.28, C:0.01, G:0.26, T:0.45
Consensus pattern (23 bp):
GGTTAGGGTTTTTAATTAAATTA
Found at i:53514650 original size:29 final size:29
Alignment explanation
Indices: 53514617--53514757 Score: 179
Period size: 29 Copynumber: 5.1 Consensus size: 29
53514607 AAGTTAAGGT
53514617 TTAGGGTTTTTAATTAAATTAGGTTAGGG
1 TTAGGGTTTTTAATTAAATTAGGTTAGGG
* * *
53514646 TTAGGGCTTTTAATTAAATCAAGTTAGGG
1 TTAGGGTTTTTAATTAAATTAGGTTAGGG
*
53514675 TTAGGATTTTTAATTAAATTAGGTTAGGG
1 TTAGGGTTTTTAATTAAATTAGGTTAGGG
*
53514704 -T----TTTGT-ATTAAATTAGGTTAGGG
1 TTAGGGTTTTTAATTAAATTAGGTTAGGG
53514727 TTAGGGTTTTGT-ATTAAATTAGGTTAGGG
1 TTAGGGTTTT-TAATTAAATTAGGTTAGGG
53514756 TT
1 TT
53514758 TTTAAAGTTA
Statistics
Matches: 97, Mismatches: 9, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
23 17 0.18
24 5 0.05
28 4 0.04
29 71 0.73
ACGTcount: A:0.28, C:0.01, G:0.26, T:0.45
Consensus pattern (29 bp):
TTAGGGTTTTTAATTAAATTAGGTTAGGG
Found at i:53514677 original size:103 final size:101
Alignment explanation
Indices: 53514460--53514757 Score: 354
Period size: 103 Copynumber: 2.8 Consensus size: 101
53514450 TAAGGTTTTT
*
53514460 AAGTTAAGGTTTAGGGTTTTTAATTAAATTAGGTTAGGG-TTTTAAAGTTAAGGTTTAGGGTTTT
1 AAGTT-AGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAAGTTAAGGTTTAGGGTTTT
* *
53514524 TAATTAAATTAGGTTAGGGTTAGGGTTAGGGTTTTTAATT
65 TAATTAAATTAGGTTAGGGTTAGGGTT---GTTTTAAATC
*
53514564 AAATTA-GGTTAGGGTTTTGT-ATTAAATTAGGTTAGGGTTTTTAAAGTTAAGGTTTAGGGTTTT
1 AAGTTAGGGTTAGGGTTTT-TAATTAAATTAGGTTAGGGTTTTTAAAGTTAAGGTTTAGGGTTTT
53514627 TAATTAAATTAGGTTAGGGTTAGGGCTT-TTAATTAAATC
65 TAATTAAATTAGGTTAGGGTTAGGG-TTGTT--TTAAATC
* * *
53514666 AAGTTAGGGTTAGGATTTTTAATTAAATTAGGTTAGGGTTTTGTATTAAATTAGGTTAGGGTTAG
1 AAGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTT-TA--AAGTTA----AGGTTTAG
53514731 GGTTTTGT-ATTAAATTAGGTTAGGGTT
59 GGTTTT-TAATTAAATTAGGTTAGGGTT
53514758 TTTAAAGTTA
Statistics
Matches: 171, Mismatches: 8, Indels: 24
0.84 0.04 0.12
Matches are distributed among these distances:
100 2 0.01
102 39 0.23
103 84 0.49
104 8 0.05
106 5 0.03
110 32 0.19
111 1 0.01
ACGTcount: A:0.28, C:0.01, G:0.27, T:0.45
Consensus pattern (101 bp):
AAGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAAGTTAAGGTTTAGGGTTTTT
AATTAAATTAGGTTAGGGTTAGGGTTGTTTTAAATC
Found at i:53514714 original size:52 final size:53
Alignment explanation
Indices: 53514607--53514858 Score: 201
Period size: 52 Copynumber: 4.8 Consensus size: 53
53514597 AGGGTTTTTA
* *
53514607 AAGTTAAGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGCTTTTAATTAAATC
1 AAGTT-AGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTT-----TTGTAATTAAATC
* *
53514666 AAGTTAGGGTTAGGATTTTTAATTAAATTAGGTTAGGGTTTTGT-ATTAAATT
1 AAGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTGTAATTAAATC
*
53514718 AGGTTAGGGTTAGGGTTTTGT-ATTAAATTAGGTTAGGG--TT-T--TT--A--
1 AAGTTAGGGTTAGGGTTTT-TAATTAAATTAGGTTAGGGTTTTGTAATTAAATC
* *
53514762 AAGTTAAGGTTTAGGGTTTTTAAGTT--A--AGGTTTAGGGTTTTTAATTAAATTAAATC
1 AAGTT-AGGGTTAGGGTTTTTAA-TTAAATTAGG-TTAGGG-TTTT--GT-AATTAAATC
*
53514818 AGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTT
1 AAGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTT
53514859 AAAGTTAAAT
Statistics
Matches: 161, Mismatches: 10, Indels: 47
0.74 0.05 0.22
Matches are distributed among these distances:
42 3 0.02
43 6 0.04
44 6 0.04
45 14 0.09
46 5 0.03
48 2 0.01
49 2 0.01
50 2 0.01
52 43 0.27
53 4 0.02
54 3 0.02
55 16 0.10
56 8 0.05
57 6 0.04
58 36 0.22
59 5 0.03
ACGTcount: A:0.29, C:0.01, G:0.26, T:0.44
Consensus pattern (53 bp):
AAGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTGTAATTAAATC
Found at i:53514778 original size:22 final size:22
Alignment explanation
Indices: 53514750--53514805 Score: 105
Period size: 21 Copynumber: 2.6 Consensus size: 22
53514740 TTAAATTAGG
53514750 TTAGGGTTTTTAAAGTTAAGGT
1 TTAGGGTTTTTAAAGTTAAGGT
53514772 TTAGGGTTTTT-AAGTTAAGGT
1 TTAGGGTTTTTAAAGTTAAGGT
53514793 TTAGGGTTTTTAA
1 TTAGGGTTTTTAA
53514806 TTAAATTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 21 0.64
22 12 0.36
ACGTcount: A:0.25, C:0.00, G:0.27, T:0.48
Consensus pattern (22 bp):
TTAGGGTTTTTAAAGTTAAGGT
Found at i:53514908 original size:25 final size:25
Alignment explanation
Indices: 53514880--53514992 Score: 96
Period size: 25 Copynumber: 4.7 Consensus size: 25
53514870 AGGTTAGGGT
*
53514880 TTTTATTACATCAAATAAACTTATG
1 TTTTATTACATCAAATAAACTTATA
53514905 TTTTATTACATCAAAT-AA--TATGA
1 TTTTATTACATCAAATAAACTTAT-A
** * * *
53514928 --AAATAAC-TCGAAA-AAATTTCTA
1 TTTTATTACATC-AAATAAACTTATA
*
53514950 TTTTATTACATCAAATAAACTTCTA
1 TTTTATTACATCAAATAAACTTATA
53514975 TTTTATTACATCAAATAA
1 TTTTATTACATCAAATAA
53514993 TATCAAAATA
Statistics
Matches: 70, Mismatches: 9, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
20 2 0.03
21 9 0.13
22 4 0.06
23 2 0.03
24 9 0.13
25 44 0.63
ACGTcount: A:0.44, C:0.12, G:0.03, T:0.41
Consensus pattern (25 bp):
TTTTATTACATCAAATAAACTTATA
Found at i:53514958 original size:70 final size:69
Alignment explanation
Indices: 53514880--53515036 Score: 253
Period size: 70 Copynumber: 2.3 Consensus size: 69
53514870 AGGTTAGGGT
* *
53514880 TTTTATTACATCAAATAAACTTATGTTTTATTACATCAAATAATATGAAAATAACTCGAAAAAAT
1 TTTTATTACATCAAATAAACTTATATTTTATTACATCAAATAATATCAAAATAACTC-AAAAAAT
53514945 TTCTA
65 TTCTA
*
53514950 TTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCAAAAAATT
1 TTTTATTACATCAAATAAACTTATATTTTATTACATCAAATAATATCAAAATAACTCAAAAAATT
53515015 TCTA
66 TCTA
* *
53515019 TTGT-TTACATAAAATAAA
1 TTTTATTACATCAAATAAA
53515037 ATCAAAATAT
Statistics
Matches: 82, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
68 13 0.16
69 15 0.18
70 54 0.66
ACGTcount: A:0.46, C:0.12, G:0.03, T:0.39
Consensus pattern (69 bp):
TTTTATTACATCAAATAAACTTATATTTTATTACATCAAATAATATCAAAATAACTCAAAAAATT
TCTA
Found at i:53515034 original size:43 final size:45
Alignment explanation
Indices: 53514960--53515045 Score: 122
Period size: 43 Copynumber: 2.0 Consensus size: 45
53514950 TTTTATTACA
* * *
53514960 TCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAAC
1 TCAAATAAACTTCTATTGTATTACATAAAATAAAATCAAAATAAC
*
53515005 TCAAA-AAATTTCTATTGT-TTACATAAAATAAAATCAAAATA
1 TCAAATAAACTTCTATTGTATTACATAAAATAAAATCAAAATA
53515046 TTCAAAATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
43 21 0.57
44 11 0.30
45 5 0.14
ACGTcount: A:0.51, C:0.13, G:0.01, T:0.35
Consensus pattern (45 bp):
TCAAATAAACTTCTATTGTATTACATAAAATAAAATCAAAATAAC
Found at i:53515491 original size:18 final size:18
Alignment explanation
Indices: 53515468--53515502 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
53515458 CGGAAAAGGA
*
53515468 TACATATAAGGGTTAGGG
1 TACATATAAGGGCTAGGG
53515486 TACATATAAGGGCTAGG
1 TACATATAAGGGCTAGG
53515503 AAACGCACCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.09, G:0.31, T:0.26
Consensus pattern (18 bp):
TACATATAAGGGCTAGGG
Found at i:53516164 original size:7 final size:7
Alignment explanation
Indices: 53516154--53516178 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
53516144 TTATATACAT
53516154 AATACTA
1 AATACTA
53516161 AATACTA
1 AATACTA
53516168 AATACTA
1 AATACTA
53516175 AATA
1 AATA
53516179 TCAATCGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:53517375 original size:51 final size:51
Alignment explanation
Indices: 53517320--53517435 Score: 196
Period size: 51 Copynumber: 2.3 Consensus size: 51
53517310 TATTTTAAAA
*
53517320 AAGGAAATTAAGAGCAAAGTGAAATTAAATATGGATTTCAGAGAATTTTGG
1 AAGGAAATTGAGAGCAAAGTGAAATTAAATATGGATTTCAGAGAATTTTGG
* * *
53517371 AAGGAAATTGAGAGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGG
1 AAGGAAATTGAGAGCAAAGTGAAATTAAATATGGATTTCAGAGAATTTTGG
53517422 AAGGAAATTGAGAG
1 AAGGAAATTGAGAG
53517436 AATTTTGGAT
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 61 1.00
ACGTcount: A:0.45, C:0.02, G:0.27, T:0.27
Consensus pattern (51 bp):
AAGGAAATTGAGAGCAAAGTGAAATTAAATATGGATTTCAGAGAATTTTGG
Found at i:53517432 original size:22 final size:22
Alignment explanation
Indices: 53517407--53517457 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
53517397 AAATATGGAT
53517407 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
*
53517429 TTGAGAGAATTTTGGATGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
53517451 TTGAGAG
1 TTGAGAG
53517458 GAAATTGAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.37, C:0.00, G:0.33, T:0.29
Consensus pattern (22 bp):
TTGAGAGAATTTTGGAAGGAAA
Found at i:53517471 original size:22 final size:22
Alignment explanation
Indices: 53517407--53517480 Score: 73
Period size: 22 Copynumber: 3.3 Consensus size: 22
53517397 AAATATGGAT
*
53517407 TTGAGA-GAATTTTGGAAGGAAA
1 TTGAGAGGAATATTGG-AGGAAA
*
53517429 TTGAGA-GAATTTTGGATGGAAA
1 TTGAGAGGAATATTGGA-GGAAA
53517451 TTGAGAGGAA-ATTGAGAGGAAA
1 TTGAGAGGAATATTG-GAGGAAA
53517473 TATGAGAG
1 T-TGAGAG
53517481 AGGATTTGTT
Statistics
Matches: 47, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
21 1 0.02
22 35 0.74
23 11 0.23
ACGTcount: A:0.41, C:0.00, G:0.34, T:0.26
Consensus pattern (22 bp):
TTGAGAGGAATATTGGAGGAAA
Found at i:53517480 original size:12 final size:11
Alignment explanation
Indices: 53517423--53517480 Score: 66
Period size: 11 Copynumber: 5.2 Consensus size: 11
53517413 GAATTTTGGA
53517423 AGGAAATTGAG
1 AGGAAATTGAG
*
53517434 A-GAATTTTG-G
1 AGGAA-ATTGAG
53517444 ATGGAAATTGAG
1 A-GGAAATTGAG
53517456 AGGAAATTGAG
1 AGGAAATTGAG
53517467 AGGAAATATGAG
1 AGGAAAT-TGAG
53517479 AG
1 AG
53517481 AGGATTTGTT
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
10 5 0.12
11 24 0.60
12 11 0.28
ACGTcount: A:0.43, C:0.00, G:0.34, T:0.22
Consensus pattern (11 bp):
AGGAAATTGAG
Found at i:53522517 original size:42 final size:42
Alignment explanation
Indices: 53522458--53522539 Score: 110
Period size: 42 Copynumber: 2.0 Consensus size: 42
53522448 ATTTACCGTG
* *
53522458 AGGATTTCGTTCCTGTGTTCTTCCACGATCATCATCAGCACA
1 AGGATTTCGTTCCTGTGTCCTTCCACAATCATCATCAGCACA
* * * *
53522500 AGGATTTTGTTCTTGTGTCCTTCTATAATCATCATCAGCA
1 AGGATTTCGTTCCTGTGTCCTTCCACAATCATCATCAGCA
53522540 TTGCGATCTT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.22, C:0.24, G:0.16, T:0.38
Consensus pattern (42 bp):
AGGATTTCGTTCCTGTGTCCTTCCACAATCATCATCAGCACA
Found at i:53530975 original size:25 final size:25
Alignment explanation
Indices: 53530872--53530966 Score: 156
Period size: 25 Copynumber: 3.8 Consensus size: 25
53530862 ATGCTCATAC
* *
53530872 GAGCTGTA-AACGATAAGCTCCTCT
1 GAGCTGAATAACGGTAAGCTCCTCT
53530896 GAGCTGAATAACGGTAAGCTCCTCT
1 GAGCTGAATAACGGTAAGCTCCTCT
53530921 GAGCTGAATAACGGTAAGCTCCTCT
1 GAGCTGAATAACGGTAAGCTCCTCT
*
53530946 GAGCTGAATAATGGTAAGCTC
1 GAGCTGAATAACGGTAAGCTC
53530967 ATAAGAGCTA
Statistics
Matches: 67, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
24 7 0.10
25 60 0.90
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.24
Consensus pattern (25 bp):
GAGCTGAATAACGGTAAGCTCCTCT
Found at i:53530975 original size:50 final size:49
Alignment explanation
Indices: 53530864--53530979 Score: 153
Period size: 50 Copynumber: 2.4 Consensus size: 49
53530854 GTACATGTAT
* *
53530864 GCTCATACGAGCTGTAAACGATAAGCTCCTCTGAGCTGAATAACGGTAA
1 GCTCATAAGAGCTGAAAACGATAAGCTCCTCTGAGCTGAATAACGGTAA
* ** * *
53530913 GCTCCTCTGAGCTGAATAACGGTAAGCTCCTCTGAGCTGAATAATGGTAA
1 GCTCATAAGAGCTGAA-AACGATAAGCTCCTCTGAGCTGAATAACGGTAA
53530963 GCTCATAAGAGCT-AAAA
1 GCTCATAAGAGCTGAAAA
53530980 TCGGTAACCC
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
48 2 0.04
49 14 0.25
50 41 0.72
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.23
Consensus pattern (49 bp):
GCTCATAAGAGCTGAAAACGATAAGCTCCTCTGAGCTGAATAACGGTAA
Found at i:53536163 original size:14 final size:14
Alignment explanation
Indices: 53536144--53536172 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
53536134 CATTTCTTGG
53536144 TCGGTTCAGTTCAA
1 TCGGTTCAGTTCAA
53536158 TCGGTTCAGTTCAA
1 TCGGTTCAGTTCAA
53536172 T
1 T
53536173 TGGACCACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (14 bp):
TCGGTTCAGTTCAA
Found at i:53537647 original size:139 final size:140
Alignment explanation
Indices: 53537368--53537808 Score: 494
Period size: 140 Copynumber: 3.2 Consensus size: 140
53537358 TTATAGTCGG
* * * * *
53537368 GAGCTTTTAACTCTCGCTAACTGTGTGGGGGCTGCGGTATTAAACCTGTGAGCCTTAAAATGATA
1 GAGCTTTTAACTCTTGCTAACTAT-TTGGGGCTGCGGTATTAAACCTGCGAGCCTTAAAATGACA
* * * *
53537433 GCT-GAGAGCTTTTTAACTCTCGTTAACTATTTGGAGGCTGTGGTATTAAATCTGCAAGCCTTAA
65 ACTGGAGAGC-TTTTAACTCTCGTTAACTATTTGGGGGCTGTGATATTAAACCTGCAAGCCTTAA
53537497 AATGACAGCTGA
129 AATGACAGCTGA
* * *
53537509 GAGTTTTTAACTCTTGCTGACTATTTGGGGCTGCGGTGTTAAACCTGCGAGCCTTAAAATGACAA
1 GAGCTTTTAACTCTTGCTAACTATTTGGGGCTGCGGTATTAAACCTGCGAGCCTTAAAATGACAA
* * * * * * * * * *
53537574 TTGGA-AGCTTTTAAATTTTGTTAACTGTTTGGGGGCTGCGTTATTATACCTGCGAGTCTTAAAA
66 CTGGAGAGCTTTTAACTCTCGTTAACTATTTGGGGGCTGTGATATTAAACCTGCAAGCCTTAAAA
* *
53537638 AGATAGCTGA
131 TGACAGCTGA
* * ** * * * *
53537648 GAGCTTTTAACTCTTACTAACTATTTAGAGATTGTGGTACTAAACCTGCGAGCTTTAAAATAAC-
1 GAGCTTTTAACTCTTGCTAACTATTT-GGGGCTGCGGTATTAAACCTGCGAGCCTTAAAATGACA
* * * *
53537712 AGTGAAGAGCTTTTAACTCTCGCTAACTATTTGGGGGCTGTGATATTAAACCTACAAGCCTT-AA
65 ACTGGAGAGCTTTTAACTCTCGTTAACTATTTGGGGGCTGTGATATTAAACCTGCAAGCCTTAAA
*
53537776 ATGACAGCTGG
130 ATGACAGCTGA
53537787 GAGCTTTTAACTCTTGCTAACT
1 GAGCTTTTAACTCTTGCTAACT
53537809 GCCTAGAGTT
Statistics
Matches: 246, Mismatches: 51, Indels: 8
0.81 0.17 0.03
Matches are distributed among these distances:
139 111 0.45
140 113 0.46
141 22 0.09
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.33
Consensus pattern (140 bp):
GAGCTTTTAACTCTTGCTAACTATTTGGGGCTGCGGTATTAAACCTGCGAGCCTTAAAATGACAA
CTGGAGAGCTTTTAACTCTCGTTAACTATTTGGGGGCTGTGATATTAAACCTGCAAGCCTTAAAA
TGACAGCTGA
Found at i:53537653 original size:70 final size:70
Alignment explanation
Indices: 53537368--53537808 Score: 440
Period size: 70 Copynumber: 6.3 Consensus size: 70
53537358 TTATAGTCGG
* * * * * *
53537368 GAGCTTTTAACTCTCGCTAACTGTGTGGGGGCTGCGGTATTAAACCTGTGAGCCTTAAAATGATA
1 GAGCTTTTAACTCTTGTTAACTATTTGGGGGCTGCGGTATTAAACCTGCGAGCCTTAAAATGACA
53537433 GCTGA
66 GCTGA
* * * * *
53537438 GAGCTTTTTAACTCTCGTTAACTATTTGGAGGCTGTGGTATTAAATCTGCAAGCCTTAAAATGAC
1 GAGC-TTTTAACTCTTGTTAACTATTTGGGGGCTGCGGTATTAAACCTGCGAGCCTTAAAATGAC
53537503 AGCTGA
65 AGCTGA
* * * *
53537509 GAGTTTTTAACTCTTGCTGACTATTT-GGGGCTGCGGTGTTAAACCTGCGAGCCTTAAAATGACA
1 GAGCTTTTAACTCTTGTTAACTATTTGGGGGCTGCGGTATTAAACCTGCGAGCCTTAAAATGACA
**
53537573 ATTG-
66 GCTGA
* * * * * * * *
53537577 GAAGCTTTTAAATTTTGTTAACTGTTTGGGGGCTGCGTTATTATACCTGCGAGTCTTAAAAAGAT
1 G-AGCTTTTAACTCTTGTTAACTATTTGGGGGCTGCGGTATTAAACCTGCGAGCCTTAAAATGAC
53537642 AGCTGA
65 AGCTGA
** * * ** * * * *
53537648 GAGCTTTTAACTCTTACTAACTATTTAGAGATTGTGGTACTAAACCTGCGAGCTTTAAAATAACA
1 GAGCTTTTAACTCTTGTTAACTATTTGGGGGCTGCGGTATTAAACCTGCGAGCCTTAAAATGACA
53537713 G-TGAA
66 GCTG-A
* * * * * *
53537718 GAGCTTTTAACTCTCGCTAACTATTTGGGGGCTGTGATATTAAACCTACAAGCCTT-AAATGACA
1 GAGCTTTTAACTCTTGTTAACTATTTGGGGGCTGCGGTATTAAACCTGCGAGCCTTAAAATGACA
*
53537782 GCTGG
66 GCTGA
*
53537787 GAGCTTTTAACTCTTGCTAACT
1 GAGCTTTTAACTCTTGTTAACT
53537809 GCCTAGAGTT
Statistics
Matches: 299, Mismatches: 66, Indels: 13
0.79 0.17 0.03
Matches are distributed among these distances:
68 1 0.00
69 85 0.28
70 152 0.51
71 61 0.20
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.33
Consensus pattern (70 bp):
GAGCTTTTAACTCTTGTTAACTATTTGGGGGCTGCGGTATTAAACCTGCGAGCCTTAAAATGACA
GCTGA
Found at i:53544364 original size:2 final size:2
Alignment explanation
Indices: 53544357--53544395 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
53544347 AGCTTCACCA
53544357 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
53544396 AGCTTTAGCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:53546529 original size:2 final size:2
Alignment explanation
Indices: 53546522--53546568 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
53546512 TTGTATCAAT
53546522 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
53546564 TA TA T
1 TA TA T
53546569 TCGACTAGCT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:53546848 original size:22 final size:22
Alignment explanation
Indices: 53546818--53546860 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
53546808 ACAGCAGAAC
* *
53546818 AGGTTTTTAGCGGCGTTTTTTT
1 AGGTCTTTAGCGGCGCTTTTTT
53546840 AGGTCTTTAGCGGCGCTTTTT
1 AGGTCTTTAGCGGCGCTTTTT
53546861 AACGCCACTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.09, C:0.14, G:0.28, T:0.49
Consensus pattern (22 bp):
AGGTCTTTAGCGGCGCTTTTTT
Found at i:53546986 original size:30 final size:31
Alignment explanation
Indices: 53546939--53546998 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 31
53546929 TAACTTTTGT
53546939 GGCGCTTACATAAAAAAACGCCGCTAAAGAA
1 GGCGCTTACATAAAAAAACGCCGCTAAAGAA
*
53546970 GGCGCTTAGA-AAAAAAACGCCGCTAAAGA
1 GGCGCTTACATAAAAAAACGCCGCTAAAGA
53546999 TCATGTTCTT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 19 0.68
31 9 0.32
ACGTcount: A:0.45, C:0.22, G:0.22, T:0.12
Consensus pattern (31 bp):
GGCGCTTACATAAAAAAACGCCGCTAAAGAA
Found at i:53547039 original size:42 final size:42
Alignment explanation
Indices: 53546970--53547145 Score: 228
Period size: 42 Copynumber: 4.2 Consensus size: 42
53546960 CGCTAAAGAA
* * *
53546970 GGCGCTTAGAAAAAAAACGCCGCTAAAGATCATGTTCTTTAGT
1 GGCGCTTA-CAAATAAACGCCGCTAAAGATCATGTTCTTTAGC
* * *
53547013 GGCGGTTATAAA-AATACGCCGCTAAAGATCATGTTCTTTAGT
1 GGCGCTTACAAATAA-ACGCCGCTAAAGATCATGTTCTTTAGC
* **
53547055 GGCGCTTACAAATAAACGCCGCTAAAGAACATAATCTTTAGC
1 GGCGCTTACAAATAAACGCCGCTAAAGATCATGTTCTTTAGC
* *
53547097 GGCGCTTAGAAATAAACGCCGCTAAATATCATGTTCTTTAGC
1 GGCGCTTACAAATAAACGCCGCTAAAGATCATGTTCTTTAGC
53547139 GGCGCTT
1 GGCGCTT
53547146 TTGAGGAAAA
Statistics
Matches: 118, Mismatches: 13, Indels: 5
0.87 0.10 0.04
Matches are distributed among these distances:
41 2 0.02
42 107 0.91
43 9 0.08
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.27
Consensus pattern (42 bp):
GGCGCTTACAAATAAACGCCGCTAAAGATCATGTTCTTTAGC
Found at i:53547174 original size:43 final size:41
Alignment explanation
Indices: 53546982--53547230 Score: 184
Period size: 42 Copynumber: 5.9 Consensus size: 41
53546972 CGCTTAGAAA
* * * * *
53546982 AAAAACGCCGCT-AAAGATCATGTTCTTTAGTGGCGGTTATA
1 AAAAACGCCGCTAAAAG-TAATGTTCTTTAGCGGCGCTTTTG
* * ***
53547023 AAAATACGCCGCT-AAAGATCATGTTCTTTAGTGGCGCTTACA
1 AAAA-ACGCCGCTAAAAG-TAATGTTCTTTAGCGGCGCTTTTG
* ** *
53547065 AATAAACGCCGCT-AAAGAACATAATCTTTAGCGGCGC-TTAG
1 AA-AAACGCCGCTAAAAGTA-ATGTTCTTTAGCGGCGCTTTTG
*
53547106 AAATAAACGCCGCTAAATA-TCATGTTCTTTAGCGGCGCTTTTG
1 -AA-AAACGCCGCTAAA-AGTAATGTTCTTTAGCGGCGCTTTTG
* * * *
53547149 AGGAAAACGCCTCTAAAAGTAATGTTCTATAGCGGTGCTTGTTC
1 A--AAAACGCCGCTAAAAGTAATGTTCTTTAGCGGCGCTT-TTG
*
53547193 AAAAACGCCGCTAAAAGTAGTGTTCTTTAGCGGCGCTT
1 AAAAACGCCGCTAAAAGTAATGTTCTTTAGCGGCGCTT
53547231 ATTTCACAAA
Statistics
Matches: 173, Mismatches: 24, Indels: 21
0.79 0.11 0.10
Matches are distributed among these distances:
41 5 0.03
42 126 0.73
43 37 0.21
44 5 0.03
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (41 bp):
AAAAACGCCGCTAAAAGTAATGTTCTTTAGCGGCGCTTTTG
Found at i:53547668 original size:12 final size:12
Alignment explanation
Indices: 53547651--53547690 Score: 71
Period size: 12 Copynumber: 3.3 Consensus size: 12
53547641 TTTTGAGCCT
*
53547651 CTGCTTCTATCG
1 CTGCTTCTCTCG
53547663 CTGCTTCTCTCG
1 CTGCTTCTCTCG
53547675 CTGCTTCTCTCG
1 CTGCTTCTCTCG
53547687 CTGC
1 CTGC
53547691 GGCCTCTGCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.03, C:0.40, G:0.17, T:0.40
Consensus pattern (12 bp):
CTGCTTCTCTCG
Found at i:53547701 original size:21 final size:22
Alignment explanation
Indices: 53547646--53547730 Score: 77
Period size: 21 Copynumber: 3.9 Consensus size: 22
53547636 ATTTCTTTTG
*
53547646 AGCCT-CTGCTTCTATCGCTGC
1 AGCCTGCTGCTTCTCTCGCTGC
**
53547667 TTCTCTCGCTGCTTCTCTCGCTGC
1 AGC-CT-GCTGCTTCTCTCGCTGC
* * *
53547691 GGCCT-CTGCTTCTCTCACTGT
1 AGCCTGCTGCTTCTCTCGCTGC
53547712 AG-CTGCTGCTTCTCTCGCT
1 AGCCTGCTGCTTCTCTCGCT
53547731 ACCGCATCTG
Statistics
Matches: 51, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
20 2 0.04
21 29 0.57
22 2 0.04
23 2 0.04
24 16 0.31
ACGTcount: A:0.05, C:0.39, G:0.19, T:0.38
Consensus pattern (22 bp):
AGCCTGCTGCTTCTCTCGCTGC
Found at i:53551346 original size:25 final size:25
Alignment explanation
Indices: 53551312--53551468 Score: 190
Period size: 25 Copynumber: 6.3 Consensus size: 25
53551302 TTCCGTCAAC
*
53551312 TTATGTAAGTTGTGTATTATG-ATGG
1 TTATGTAAGTTGTGTATTATGTA-AG
53551337 TTATGTAAGTTGTGTATTATGTAAG
1 TTATGTAAGTTGTGTATTATGTAAG
* * *
53551362 TTATGTTAGTTGTGTATTATGAAAC
1 TTATGTAAGTTGTGTATTATGTAAG
* *
53551387 TTATGTAAGTTATGTCTTATGTAAG
1 TTATGTAAGTTGTGTATTATGTAAG
* ** *
53551412 TGATGTAAAATATGTATTATGTAAG
1 TTATGTAAGTTGTGTATTATGTAAG
* *
53551437 TTATGTCAGTTGTGTATTATGTAAA
1 TTATGTAAGTTGTGTATTATGTAAG
53551462 TTATGTA
1 TTATGTA
53551469 TTATGTAAGT
Statistics
Matches: 111, Mismatches: 20, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
25 110 0.99
26 1 0.01
ACGTcount: A:0.29, C:0.02, G:0.22, T:0.47
Consensus pattern (25 bp):
TTATGTAAGTTGTGTATTATGTAAG
Found at i:53551352 original size:9 final size:9
Alignment explanation
Indices: 53551336--53551521 Score: 121
Period size: 9 Copynumber: 22.2 Consensus size: 9
53551326 TATTATGATG
53551336 GTTATGTAA
1 GTTATGTAA
*
53551345 GTTGTGT-A
1 GTTATGTAA
53551353 -TTATGTAA
1 GTTATGTAA
*
53551361 GTTATGTTA
1 GTTATGTAA
*
53551370 GTTGTGT-A
1 GTTATGTAA
*
53551378 -TTATGAAA
1 GTTATGTAA
*
53551386 CTTATGTAA
1 GTTATGTAA
53551395 GTTATGT--
1 GTTATGTAA
*
53551402 CTTATGTAA
1 GTTATGTAA
*
53551411 GTGATGTAA
1 GTTATGTAA
**
53551420 AATATGT-A
1 GTTATGTAA
53551428 -TTATGTAA
1 GTTATGTAA
*
53551436 GTTATGTCA
1 GTTATGTAA
*
53551445 GTTGTGT-A
1 GTTATGTAA
53551453 -TTATGTAA
1 GTTATGTAA
*
53551461 ATTATGT-A
1 GTTATGTAA
53551469 -TTATGTAA
1 GTTATGTAA
53551477 GTTATGTAA
1 GTTATGTAA
* *
53551486 TTTGTGT-A
1 GTTATGTAA
53551494 -TTATGTAA
1 GTTATGTAA
* *
53551502 CTTATTTAA
1 GTTATGTAA
*
53551511 TTTATGTAA
1 GTTATGTAA
53551520 GT
1 GT
53551522 GTGTATTATT
Statistics
Matches: 138, Mismatches: 25, Indels: 28
0.72 0.13 0.15
Matches are distributed among these distances:
7 36 0.26
8 12 0.09
9 90 0.65
ACGTcount: A:0.30, C:0.02, G:0.19, T:0.48
Consensus pattern (9 bp):
GTTATGTAA
Found at i:53551356 original size:16 final size:16
Alignment explanation
Indices: 53551337--53551484 Score: 115
Period size: 16 Copynumber: 9.0 Consensus size: 16
53551327 ATTATGATGG
*
53551337 TTATGTAAGTTGTGTA
1 TTATGTAAGTTATGTA
53551353 TTATGTAAGTTATGTTA
1 TTATGTAAGTTATG-TA
* *
53551370 GTTGTGT-A-TTATGAAA
1 -TTATGTAAGTTATG-TA
*
53551386 CTTATGTAAGTTATGTC
1 -TTATGTAAGTTATGTA
*
53551403 TTATGTAAGTGATGTAAA
1 TTATGTAAGTTATGT--A
*
53551421 ATATGT-A-TTATGTAA
1 TTATGTAAGTTATGT-A
* *
53551436 GTTATGTCAGTTGTGTA
1 -TTATGTAAGTTATGTA
*
53551453 TTATGTAAATTATGTA
1 TTATGTAAGTTATGTA
53551469 TTATGTAAGTTATGTA
1 TTATGTAAGTTATGTA
53551485 ATTTGTGTAT
Statistics
Matches: 105, Mismatches: 18, Indels: 18
0.74 0.13 0.13
Matches are distributed among these distances:
15 2 0.02
16 76 0.72
17 7 0.07
18 20 0.19
ACGTcount: A:0.30, C:0.02, G:0.20, T:0.47
Consensus pattern (16 bp):
TTATGTAAGTTATGTA
Found at i:53551432 original size:41 final size:40
Alignment explanation
Indices: 53551387--53551501 Score: 133
Period size: 41 Copynumber: 2.8 Consensus size: 40
53551377 ATTATGAAAC
53551387 TTATGTAAGTTATGTC-TTATGTAAGTGATGTAAAATATGTA
1 TTATGTAAGTTATGTCATTATGT-A-TGATGTAAAATATGTA
* * *
53551428 TTATGTAAGTTATGTCAGTTGTGTATTATGTAAATTATGTA
1 TTATGTAAGTTATGTCA-TTATGTATGATGTAAAATATGTA
* * *
53551469 TTATGTAAGTTATGTAATTTGTGTATTATGTAA
1 TTATGTAAGTTATGTCA-TTATGTATGATGTAA
53551502 CTTATTTAAT
Statistics
Matches: 67, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
41 61 0.91
42 1 0.01
43 5 0.07
ACGTcount: A:0.31, C:0.02, G:0.19, T:0.48
Consensus pattern (40 bp):
TTATGTAAGTTATGTCATTATGTATGATGTAAAATATGTA
Found at i:53551432 original size:75 final size:76
Alignment explanation
Indices: 53551309--53551475 Score: 218
Period size: 75 Copynumber: 2.2 Consensus size: 76
53551299 ATTTTCCGTC
* * * ** * *
53551309 AACTTATGTAAGTTGTGTATTATGATGGTTATGTAAGTTGTGTATTATGTAAGTTATGTTAGTTG
1 AACTTATGTAAGTTATGTATTATGATAGTGATGTAAAATATGTATTATGTAAGTTATGTCAGTTG
53551374 TGTATTATG-A
66 TGTATTATGTA
*
53551384 AACTTATGTAAGTTATGTCTTATG-TAAGTGATGTAAAATATGTATTATGTAAGTTATGTCAGTT
1 AACTTATGTAAGTTATGTATTATGAT-AGTGATGTAAAATATGTATTATGTAAGTTATGTCAGTT
53551448 GTGTATTATGTA
65 GTGTATTATGTA
53551460 AA-TTATGT-A-TTATGTA
1 AACTTATGTAAGTTATGTA
53551476 AGTTATGTAA
Statistics
Matches: 81, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
73 6 0.07
74 2 0.02
75 70 0.86
76 3 0.04
ACGTcount: A:0.30, C:0.02, G:0.21, T:0.47
Consensus pattern (76 bp):
AACTTATGTAAGTTATGTATTATGATAGTGATGTAAAATATGTATTATGTAAGTTATGTCAGTTG
TGTATTATGTA
Found at i:53551481 original size:25 final size:24
Alignment explanation
Indices: 53551352--53551542 Score: 102
Period size: 25 Copynumber: 7.6 Consensus size: 24
53551342 TAAGTTGTGT
* *
53551352 ATTATGTAAGTTATGTTAGTTGTGT-
1 ATTATGTAATTTATG-TA-TTATGTA
* *
53551377 ATTATGAAACTTATGTAAGTTATGT-
1 ATTATGTAATTTATGT-A-TTATGTA
* * * *
53551402 CTTATGTAAGTGATGTAAAATATGT-
1 ATTATGTAATTTATGT--ATTATGTA
* *
53551427 ATTATGTAAGTTATGTCAGTTGTGT-
1 ATTATGTAATTTATGT-A-TTATGTA
*
53551452 ATTATGTAAATTATGTATTATGTA
1 ATTATGTAATTTATGTATTATGTA
*
53551476 AGTTATGTAATTTGTGTATTATGTA
1 A-TTATGTAATTTATGTATTATGTA
* * *
53551501 ACTTATTTAATTTATGTAAGTGTGTA
1 A-TTATGTAATTTATGT-ATTATGTA
53551527 TTATTATGTAATTTAT
1 --ATTATGTAATTTAT
53551543 AATGTAGGAT
Statistics
Matches: 135, Mismatches: 23, Indels: 14
0.78 0.13 0.08
Matches are distributed among these distances:
23 5 0.04
24 4 0.03
25 105 0.78
26 8 0.06
27 12 0.09
28 1 0.01
ACGTcount: A:0.31, C:0.02, G:0.18, T:0.49
Consensus pattern (24 bp):
ATTATGTAATTTATGTATTATGTA
Found at i:53551482 original size:50 final size:48
Alignment explanation
Indices: 53551336--53551506 Score: 167
Period size: 50 Copynumber: 3.6 Consensus size: 48
53551326 TATTATGATG
* *
53551336 GTTATGTAAGTTGTGTATTATGTAAGTTATGTTAGTTGTGTATTATGAAA
1 GTTATGTAAGTTGTGTATTATGTAAGTTATG-TA-TTATGTATTATGTAA
* * * * *
53551386 CTTATGTAAGTTATGTCTTATGTAAGTGATGTAAAATATGTATTATGTAA
1 GTTATGTAAGTTGTGTATTATGTAAGTTATGT--ATTATGTATTATGTAA
*
53551436 GTTATGTCAGTTGTGTATTATGT-A---A---ATTATGTATTATGTAA
1 GTTATGTAAGTTGTGTATTATGTAAGTTATGTATTATGTATTATGTAA
* *
53551477 GTTATGTAATTTGTGTATTATGTAACTTAT
1 GTTATGTAAGTTGTGTATTATGTAAGTTAT
53551507 TTAATTTATG
Statistics
Matches: 100, Mismatches: 14, Indels: 18
0.76 0.11 0.14
Matches are distributed among these distances:
41 36 0.36
42 1 0.01
45 1 0.01
46 1 0.01
49 2 0.02
50 58 0.58
51 1 0.01
ACGTcount: A:0.30, C:0.02, G:0.20, T:0.48
Consensus pattern (48 bp):
GTTATGTAAGTTGTGTATTATGTAAGTTATGTATTATGTATTATGTAA
Found at i:53551930 original size:18 final size:18
Alignment explanation
Indices: 53551870--53551930 Score: 58
Period size: 17 Copynumber: 3.5 Consensus size: 18
53551860 ATTTTATAGG
53551870 TTAT-ATTAAAACAATAT
1 TTATAATTAAAACAATAT
* *
53551887 TTATAA-TACTAATAA-AT
1 TTATAATTA-AAACAATAT
53551904 TTA-ATATTAAAACAATAT
1 TTATA-ATTAAAACAATAT
53551922 TTATAATTA
1 TTATAATTA
53551931 TTTAGAAAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 11
0.69 0.08 0.22
Matches are distributed among these distances:
16 1 0.03
17 16 0.47
18 16 0.47
19 1 0.03
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (18 bp):
TTATAATTAAAACAATAT
Found at i:53551945 original size:87 final size:85
Alignment explanation
Indices: 53551799--53552195 Score: 457
Period size: 87 Copynumber: 4.6 Consensus size: 85
53551789 NNNNNNNNNN
* *
53551799 TTTATAATACTAATAAATTTA-ATATTTAAACAATATTTATAATTATCTAGAAAACTTTTAAATT
1 TTTATAATACTAAT--A-TTAGATATTAAAACAATATTTATAATTATTTAGAAAACTTTTAAATT
53551863 TTATAGGTTATATTAAAACAATA
63 TTATAGGTTATATTAAAACAATA
53551886 TTTATAATACTAATAAATTTA-ATATTAAAACAATATTTATAATTATTTAGAAAACTTTTAAATT
1 TTTATAATACTAAT--A-TTAGATATTAAAACAATATTTATAATTATTTAGAAAACTTTTAAATT
53551950 TTATAGGTTATATTAAAACAATA
63 TTATAGGTTATATTAAAACAATA
* * * *
53551973 TTTATAATACTAATA-TAGATATTAAAACAATATTTAGAATTATTTATAAATTTAATAGTAATAA
1 TTTATAATACTAATATTAGATATTAAAACAATATTTATAATTATTTAGAAA---ACT--T-TTAA
* * * *
53552037 ATTTAATA-CTAATA-TAGAAACCTTATAAA
60 ATTTTATAGGTTATATTA-AAA-C--A-ATA
* * *
53552066 TTTAGAAAACTTATA-TAGATATTAAAACAATATTTATAATTATTTAGAAAACTTTTAAATTTTA
1 TTTATAATACTAATATTAGATATTAAAACAATATTTATAATTATTTAGAAAACTTTTAAATTTTA
53552130 TAGGTTATATTAAAACAATA
66 TAGGTTATATTAAAACAATA
* *
53552150 TTTATAATACTAATA-TAGATATTAAAACAATATTTAGAATTTTTTA
1 TTTATAATACTAATATTAGATATTAAAACAATATTTATAATTATTTA
53552196 TAAATTTAAT
Statistics
Matches: 270, Mismatches: 26, Indels: 31
0.83 0.08 0.09
Matches are distributed among these distances:
83 2 0.01
84 73 0.27
85 2 0.01
87 112 0.41
88 10 0.04
89 10 0.04
90 13 0.05
92 1 0.00
93 47 0.17
ACGTcount: A:0.48, C:0.05, G:0.04, T:0.43
Consensus pattern (85 bp):
TTTATAATACTAATATTAGATATTAAAACAATATTTATAATTATTTAGAAAACTTTTAAATTTTA
TAGGTTATATTAAAACAATA
Found at i:53552038 original size:15 final size:15
Alignment explanation
Indices: 53552018--53552050 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
53552008 AGAATTATTT
*
53552018 ATAAATTTAATAGTA
1 ATAAATTTAATACTA
53552033 ATAAATTTAATACTA
1 ATAAATTTAATACTA
53552048 ATA
1 ATA
53552051 TAGAAACCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (15 bp):
ATAAATTTAATACTA
Found at i:53552093 original size:177 final size:177
Alignment explanation
Indices: 53551907--53552292 Score: 736
Period size: 177 Copynumber: 2.2 Consensus size: 177
53551897 AATAAATTTA
53551907 ATATTAAAACAATATTTATAATTATTTAGAAAACTTTTAAATTTTATAGGTTATATTAAAACAAT
1 ATATTAAAACAATATTTATAATTATTTAGAAAACTTTTAAATTTTATAGGTTATATTAAAACAAT
53551972 ATTTATAATACTAATATAGATATTAAAACAATATTTAGAATTATTTATAAATTTAATAGTAATAA
66 ATTTATAATACTAATATAGATATTAAAACAATATTTAGAATTATTTATAAATTTAATAGTAATAA
53552037 ATTTAATACTAATATAGAAACCTTATAAATTTAGAAAACTTATATAG
131 ATTTAATACTAATATAGAAACCTTATAAATTTAGAAAACTTATATAG
53552084 ATATTAAAACAATATTTATAATTATTTAGAAAACTTTTAAATTTTATAGGTTATATTAAAACAAT
1 ATATTAAAACAATATTTATAATTATTTAGAAAACTTTTAAATTTTATAGGTTATATTAAAACAAT
*
53552149 ATTTATAATACTAATATAGATATTAAAACAATATTTAGAATTTTTTATAAATTTAATAGTAATAA
66 ATTTATAATACTAATATAGATATTAAAACAATATTTAGAATTATTTATAAATTTAATAGTAATAA
*
53552214 ATTTAATACTAATATAGAAACCTTATAAGTTTAGAAAACTTATATAG
131 ATTTAATACTAATATAGAAACCTTATAAATTTAGAAAACTTATATAG
* *
53552261 ATATTAAAACAACATTCATAATTATTTAGAAA
1 ATATTAAAACAATATTTATAATTATTTAGAAA
53552293 TGTTATCATT
Statistics
Matches: 205, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
177 205 1.00
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.40
Consensus pattern (177 bp):
ATATTAAAACAATATTTATAATTATTTAGAAAACTTTTAAATTTTATAGGTTATATTAAAACAAT
ATTTATAATACTAATATAGATATTAAAACAATATTTAGAATTATTTATAAATTTAATAGTAATAA
ATTTAATACTAATATAGAAACCTTATAAATTTAGAAAACTTATATAG
Found at i:53552122 original size:21 final size:21
Alignment explanation
Indices: 53552065--53552126 Score: 51
Period size: 21 Copynumber: 3.0 Consensus size: 21
53552055 AACCTTATAA
*
53552065 ATTTAGAAAACTTATATAGA-T
1 ATTTAGAAAACTTTTATA-ATT
*
53552086 A-TTA-AAACAATATTTATAATT
1 ATTTAGAAA-ACT-TTTATAATT
53552107 ATTTAGAAAACTTTTA-AATT
1 ATTTAGAAAACTTTTATAATT
53552127 TTATAGGTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 11
0.70 0.06 0.23
Matches are distributed among these distances:
19 3 0.09
20 10 0.30
21 12 0.36
22 5 0.15
23 3 0.09
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.42
Consensus pattern (21 bp):
ATTTAGAAAACTTTTATAATT
Found at i:53552215 original size:15 final size:15
Alignment explanation
Indices: 53552195--53552227 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
53552185 AGAATTTTTT
*
53552195 ATAAATTTAATAGTA
1 ATAAATTTAATACTA
53552210 ATAAATTTAATACTA
1 ATAAATTTAATACTA
53552225 ATA
1 ATA
53552228 TAGAAACCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (15 bp):
ATAAATTTAATACTA
Found at i:53554035 original size:22 final size:22
Alignment explanation
Indices: 53554009--53554057 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
53553999 CCCTAAGTTT
*
53554009 AACCCGTAACCTTTATACTTTA
1 AACCCGTAACCTTTAAACTTTA
53554031 AACCCGTAACCTTTAAACTTTA
1 AACCCGTAACCTTTAAACTTTA
53554053 AACCC
1 AACCC
53554058 TAAACTACAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.35, C:0.31, G:0.04, T:0.31
Consensus pattern (22 bp):
AACCCGTAACCTTTAAACTTTA
Found at i:53558208 original size:46 final size:46
Alignment explanation
Indices: 53558141--53558405 Score: 422
Period size: 46 Copynumber: 5.8 Consensus size: 46
53558131 CCTGTTTTGA
*
53558141 ACAGCATTAATATGCTCAAAATGGACAGCATTATACATCAAATTGG
1 ACAGCATCAATATGCTCAAAATGGACAGCATTATACATCAAATTGG
53558187 ACAGCATCAATATGCTCAAAATGGACAGCATTATACATCAAATTGG
1 ACAGCATCAATATGCTCAAAATGGACAGCATTATACATCAAATTGG
* * * *
53558233 ACAGCTTTAATATGCTCAAATTGGACAGCTTTATACATCAAATTGG
1 ACAGCATCAATATGCTCAAAATGGACAGCATTATACATCAAATTGG
* *
53558279 ACAGCATCAATATTCTCAAAATGGACAGCATTATACATTAAATTGG
1 ACAGCATCAATATGCTCAAAATGGACAGCATTATACATCAAATTGG
* * * *
53558325 ACAGCACCAATATACTCAAAATGGACAACATTATACAACAAATTGG
1 ACAGCATCAATATGCTCAAAATGGACAGCATTATACATCAAATTGG
*
53558371 ACAGCATCAATCTGCTCAAAATGGACAGCATTATA
1 ACAGCATCAATATGCTCAAAATGGACAGCATTATA
53558406 ACATATAAAA
Statistics
Matches: 199, Mismatches: 20, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 199 1.00
ACGTcount: A:0.41, C:0.19, G:0.14, T:0.26
Consensus pattern (46 bp):
ACAGCATCAATATGCTCAAAATGGACAGCATTATACATCAAATTGG
Found at i:53558415 original size:24 final size:23
Alignment explanation
Indices: 53558158--53558415 Score: 90
Period size: 24 Copynumber: 11.2 Consensus size: 23
53558148 TAATATGCTC
*
53558158 AAAATGGACAGCATTAT-ACATC
1 AAAATGGACAGCATTATAACATT
* * * *
53558180 AAATTGGACAGCATCAATATGC-TC
1 AAAATGGACAGCAT-TATA-ACATT
*
53558204 AAAATGGACAGCATTAT-ACATC
1 AAAATGGACAGCATTATAACATT
* *
53558226 AAATTGGACAGC-TT-TAATATGCT
1 AAAATGGACAGCATTATAACAT--T
* * *
53558249 CAAATTGGACAGCTTTAT-ACATC
1 -AAAATGGACAGCATTATAACATT
* * * *
53558272 AAATTGGACAGCATCAATATTC-TC
1 AAAATGGACAGCAT-TATA-ACATT
53558296 AAAATGGACAGCATTAT-ACATT
1 AAAATGGACAGCATTATAACATT
* ** *
53558318 AAATTGGACAGCACCAATATAC-TC
1 AAAATGGACAGCA-TTATA-ACATT
* **
53558342 AAAATGGACAACATTAT-ACAAC
1 AAAATGGACAGCATTATAACATT
* * *
53558364 AAATTGGACAGCATCA-ATC-TGCT
1 AAAATGGACAGCATTATAACAT--T
53558387 CAAAATGGACAGCATTATAACATAT
1 -AAAATGGACAGCATTATAACAT-T
53558412 AAAA
1 AAAA
53558416 ATAGCAACAT
Statistics
Matches: 175, Mismatches: 37, Indels: 46
0.68 0.14 0.18
Matches are distributed among these distances:
20 1 0.01
21 9 0.05
22 67 0.38
23 12 0.07
24 72 0.41
25 12 0.07
26 2 0.01
ACGTcount: A:0.43, C:0.19, G:0.14, T:0.25
Consensus pattern (23 bp):
AAAATGGACAGCATTATAACATT
Found at i:53559209 original size:40 final size:40
Alignment explanation
Indices: 53559075--53559227 Score: 157
Period size: 41 Copynumber: 3.8 Consensus size: 40
53559065 AATGTTTCGT
* *
53559075 ACACTAATTGCCATCGTACAGCCGAAGCTATT-ATAATCTCGC
1 ACACTAAGTGCCAT-ATACAGCCGAAGCTATTCATAA--TCGC
* * * * *
53559117 ACACTAAGTGCCTTACATAACCGAAGCTATCTCAGT-CTCGC
1 ACACTAAGTGCCATATACAGCCGAAGCTAT-TCA-TAATCGC
*
53559158 ACACTAAGTGCCATATACAGCCGAAGCTATTCCTAATCGC
1 ACACTAAGTGCCATATACAGCCGAAGCTATTCATAATCGC
* *
53559198 ACACTAAGTGCCATAAATAGCCGAAGCTAT
1 ACACTAAGTGCCATATACAGCCGAAGCTAT
53559228 CTCGAATTTC
Statistics
Matches: 92, Mismatches: 15, Indels: 10
0.79 0.13 0.09
Matches are distributed among these distances:
39 1 0.01
40 34 0.37
41 42 0.46
42 13 0.14
43 1 0.01
44 1 0.01
ACGTcount: A:0.33, C:0.29, G:0.15, T:0.24
Consensus pattern (40 bp):
ACACTAAGTGCCATATACAGCCGAAGCTATTCATAATCGC
Found at i:53559222 original size:81 final size:82
Alignment explanation
Indices: 53559075--53559230 Score: 226
Period size: 81 Copynumber: 1.9 Consensus size: 82
53559065 AATGTTTCGT
* * * *
53559075 ACACTAATTGCCATCGTACAGCCGAAGCTATTATAATCTCGCACACTAAGTGCCTTACATAACCG
1 ACACTAAGTGCCATCATACAGCCGAAGCTATTATAA-CTCGCACACTAAGTGCCATAAATAACCG
53559140 AAGCTATCTCAGTCTCGC
65 AAGCTATCTCAGTCTCGC
* *
53559158 ACACTAAGTGCCAT-ATACAGCCGAAGCTATTCCTAA-TCGCACACTAAGTGCCATAAATAGCCG
1 ACACTAAGTGCCATCATACAGCCGAAGCTATT-ATAACTCGCACACTAAGTGCCATAAATAACCG
53559221 AAGCTATCTC
65 AAGCTATCTC
53559231 GAATTTCATA
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
81 34 0.52
82 16 0.24
83 16 0.24
ACGTcount: A:0.32, C:0.29, G:0.15, T:0.24
Consensus pattern (82 bp):
ACACTAAGTGCCATCATACAGCCGAAGCTATTATAACTCGCACACTAAGTGCCATAAATAACCGA
AGCTATCTCAGTCTCGC
Found at i:53559244 original size:40 final size:39
Alignment explanation
Indices: 53559115--53559248 Score: 135
Period size: 40 Copynumber: 3.3 Consensus size: 39
53559105 TTATAATCTC
* * * *
53559115 GCACACTAAGTGCCTTACATAACCGAAGCTATCTCAGTCT
1 GCACACTAAGTGCCATAAATAGCCGAAGCTATCTCAAT-T
* * *
53559155 CGCACACTAAGTGCCATATACAGCCGAAGCTAT-TCCTAATC
1 -GCACACTAAGTGCCATAAATAGCCGAAGCTATCT-C-AATT
53559196 GCACACTAAGTGCCATAAATAGCCGAAGCTATCTCGAATT
1 GCACACTAAGTGCCATAAATAGCCGAAGCTATCTC-AATT
* *
53559236 TCATACTAAGTGC
1 GCACACTAAGTGC
53559249 TAAACATAGC
Statistics
Matches: 78, Mismatches: 12, Indels: 7
0.80 0.12 0.07
Matches are distributed among these distances:
40 46 0.59
41 30 0.38
42 2 0.03
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (39 bp):
GCACACTAAGTGCCATAAATAGCCGAAGCTATCTCAATT
Found at i:53570726 original size:5 final size:5
Alignment explanation
Indices: 53570710--53570739 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
53570700 TGTTGCATTT
53570710 TTAAA TTAAAA TTAAA TTAAA TTAAA TTAA
1 TTAAA TT-AAA TTAAA TTAAA TTAAA TTAA
53570740 TTTTTTTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TTAAA
Found at i:53571529 original size:2 final size:2
Alignment explanation
Indices: 53571522--53571560 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
53571512 TGATCACAAT
53571522 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
53571561 TGCAATTACA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:53586528 original size:173 final size:172
Alignment explanation
Indices: 53586349--53586821 Score: 546
Period size: 173 Copynumber: 2.7 Consensus size: 172
53586339 TAAGTAAACA
* * *
53586349 AGTCTTATCCTCCTGAAGTTATAGT-GAGGCAGACTAAAG-ATGGCAAATCTTAA-CTCCCTGAG
1 AGTCTTAT-CTCCTGAAGTTACAGTGGA-GCAGACT-AAGTA-AGCAAATCTTAACCT-CCTGAA
* * *
53586411 GTTGCAGTG-GAGTAGA-TTAA-A-GCCGATAATCCTATCTCTCTGAAGTTGCAGTGGAGCGGAT
61 GTTGCAGTGAG-GCAGACTGAAGATGCC-A-AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGAT
*
53586472 TAAAACCTTGGATCTTATCTCTCTGAAGTTACAGAGAGCAGATCGCATTT
123 TAAAACCTTGGATCTTATCTCTCTGAAGTTACAGAGAGCAGATCGCATCT
* * * * *
53586522 AGTCTTATCTCCCGGATGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTG
1 AGTCTTATCT-CCTGAAGTTACAGTGGAGCAGACTAAGTAAGCAAATCTTAACCTCCTGAAGTTG
* * * *
53586587 CAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTGTAGTGGAGTGGATTAAAACC
65 CAGTGAGGCAGACTGAAGATGCCAAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACC
*
53586652 TTGGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCT
130 TTGGATCTTATCTCTCTGAAGTTACAGAGAGCAGATCGCATCT
* * ** * * *
53586695 AGTCTTATCTCGCTGAAGTTGCAGTGGAGCAAACTAAGTAAATAAGTCTTATCCTCCTAAAGTTG
1 AGTCTTATCTC-CTGAAGTTACAGTGGAGCAGACTAAGTAAGCAAATCTTAACCTCCTGAAGTTG
* * * **
53586760 CAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAGGTTGCAGTGGAGTAGATTAAA
65 CAGTGAGGCAGACTGAAGATGCCAAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAA
53586822 GCCGATAATC
Statistics
Matches: 265, Mismatches: 26, Indels: 18
0.86 0.08 0.06
Matches are distributed among these distances:
172 33 0.12
173 226 0.85
174 4 0.02
175 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (172 bp):
AGTCTTATCTCCTGAAGTTACAGTGGAGCAGACTAAGTAAGCAAATCTTAACCTCCTGAAGTTGC
AGTGAGGCAGACTGAAGATGCCAAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCT
TGGATCTTATCTCTCTGAAGTTACAGAGAGCAGATCGCATCT
Found at i:53586584 original size:84 final size:84
Alignment explanation
Indices: 53586484--53586771 Score: 253
Period size: 84 Copynumber: 3.4 Consensus size: 84
53586474 AAACCTTGGA
* * * *
53586484 TCTTATCTCTCTGAAGTTACAGAGAGCAGATCGCATTTAGTCTTATCTCCCGGATGTTGCAGTGG
1 TCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGG
*
53586549 AGCAGACTAAGTAAGCAAG
66 AGCAGACTAAGTAAACAAG
* * * *
53586568 TCTTATC-CTCCTGAAGTTGCAGTGAGGCAGA-CTGAAGATGGCAAATCTTATCTCCCTGAAGTT
1 TCTTATCTCT-CTGAAGTTGCAGAGA-GCAGATC-G--CAT--CTAGTCTTATCTCCCTGAAGTT
* ** * * **
53586631 GTAGTGGAGTGGATTAA--AACCTTGG
59 GCAGTGGAGCAGACTAAGTAAAC-AAG
*
53586656 ATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCGCTGAAGTTGCAGTG
1 -TCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTG
* *
53586721 GAGCAAACTAAGTAAATAAG
65 GAGCAGACTAAGTAAACAAG
* *
53586741 TCTTATC-CTCCTAAAGTTGCAGTGAGGCAGA
1 TCTTATCTCT-CTGAAGTTGCAGAGA-GCAGA
53586772 CTGAAGATGG
Statistics
Matches: 158, Mismatches: 31, Indels: 29
0.72 0.14 0.13
Matches are distributed among these distances:
83 4 0.03
84 72 0.46
85 12 0.08
86 4 0.03
87 5 0.03
88 7 0.04
89 52 0.33
90 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (84 bp):
TCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGG
AGCAGACTAAGTAAACAAG
Done.