Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D07
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: 58101237
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1550000 characters in sequence are not A, C, G, or T
File 184 of 199
Found at i:53461708 original size:16 final size:16
Alignment explanation
Indices: 53461674--53461708 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
53461664 TCGTTATTTT
* *
53461674 AAATAAAATAAAATGA
1 AAATAAAAGAAAATAA
53461690 AAATAAAAGAAAATAA
1 AAATAAAAGAAAATAA
53461706 AAA
1 AAA
53461709 ATATGGAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.80, C:0.00, G:0.06, T:0.14
Consensus pattern (16 bp):
AAATAAAAGAAAATAA
Found at i:53463169 original size:132 final size:132
Alignment explanation
Indices: 53462454--53463162 Score: 1071
Period size: 132 Copynumber: 5.4 Consensus size: 132
53462444 AAAATTTGCT
* * *
53462454 ATCTTT-AGTCTGCTCCACCACTGCTTAGAGAGACAAGATCTGAAATCTTCAATCTATTCCACTG
1 ATCTTTGA-TCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTG
* *
53462518 ATGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCC
65 CTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCC
*
53462583 GTC
130 GCC
* * * *
53462586 ATCTTTGATCTGCTCCACTACTTCTTAGGAAGACAATATCTGAAAACTTCAATCTATTCCGCTGC
1 ATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTGC
* * *
53462651 TGCCGATGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTG
66 TGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCG
53462716 CC
131 CC
*
53462718 ATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAATATCTGAAATCTTCAATCTATTCCGCTGC
1 ATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTGC
* * * *
53462783 TGCCGAGGGAAATAGAATTACTGGCTTCAATGTACTCCACTATAACCACTGGGAGGTAAAATCCG
66 TGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCG
53462848 CC
131 CC
* * * *
53462850 ATCTTTGATCTGCTCCACTATTGTTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCGCTGC
1 ATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTGC
*
53462915 TGCCCAGGGAAATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCG
66 TGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCG
53462980 CC
131 CC
* * * * *
53462982 ATCTTTGATCTGCTCCACTACTGCTTAAGGAGACAAGATCTAAAATCCTAAATCTATTCCACTGC
1 ATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTGC
* * *
53463047 TGCCCAGGGAAGTAGAAATT-CTGGCTTCAATTTACTCCACTGCAACCTCAGGGAGGTAAAATCC
66 TGCCCAGGGAAGTAG-AATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCC
53463111 GCC
130 GCC
* * * *
53463114 ATCTTCGATCTGCTCCACTACTGTTTAGGGAGATAAGATCTGTAATCTT
1 ATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTT
53463163 TGATCTACTT
Statistics
Matches: 526, Mismatches: 49, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
132 521 0.99
133 5 0.01
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.29
Consensus pattern (132 bp):
ATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTGC
TGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCG
CC
Found at i:53463192 original size:44 final size:43
Alignment explanation
Indices: 53463148--53463607 Score: 247
Period size: 44 Copynumber: 10.3 Consensus size: 43
53463138 TTAGGGAGAT
*
53463148 AAGATCTGTAATCTTTGATCTACTTCACGCCAGTACATGAAGAT
1 AAGATCTGT-ATCTTTGATCTACTTCACGCCAGTACATGAAGAC
* * * * * * * *** *
53463192 AAAATCTGTTTTCTTCGATTTGCTTCGCCACCAGTATGGGAAGGC
1 AAGATCTG-TATCTTTGATCTACTTC-ACGCCAGTACATGAAGAC
*
53463237 AAGATCTGCTATCTTTGATCTACTTCATGCCAGTACATGAAGAC
1 AAGATCTG-TATCTTTGATCTACTTCACGCCAGTACATGAAGAC
* * * * * *
53463281 AAGATCTGCT-TTTTCTTATTTGCTT--CGCCACG-AGTATGGAAGGC
1 AAGATCTG-TATCTT-TGATCTACTTCACGCCA-GTA-CAT-GAAGAC
* *
53463325 AAGATCTGGTATCTTTAATCTACTTCACGCCAATACATGAAGAC
1 AAGATCT-GTATCTTTGATCTACTTCACGCCAGTACATGAAGAC
* * * ***
53463369 AAGATCTGTTTTCTTCGATCTACTTCGC-CATCAGTATGGGAAGAC
1 AAGATCTG-TATCTTTGATCTACTTCACGC--CAGTACATGAAGAC
*
53463414 AAGATCTGCTATCTTTGATCTACTTCACGCCAGTACATGAAGAT
1 AAGATCTG-TATCTTTGATCTACTTCACGCCAGTACATGAAGAC
* * * * * *
53463458 AAGATC--TACTTTTTCCGATTTGCTT--CGCCACTAGTATGGGAAGGC
1 AAGATCTGTA-TCTTT--GATCTACTTCACGCCAGTA-CAT--GAAGAC
* *
53463503 AAGATCTGGTACCTTTGATCTACTTCACGCCAATACATGAAGAC
1 AAGATCT-GTATCTTTGATCTACTTCACGCCAGTACATGAAGAC
* * * ***
53463547 AAGATCTGTTTTCTTCGATCTACTTTGC-CACCAGTATGGGAAGAC
1 AAGATCTG-TATCTTTGATCTAC-TT-CACGCCAGTACATGAAGAC
53463592 AAGATCTGCTATCTTT
1 AAGATCTG-TATCTTT
53463608 TTCGCCTGCT
Statistics
Matches: 307, Mismatches: 80, Indels: 57
0.69 0.18 0.13
Matches are distributed among these distances:
41 2 0.01
42 16 0.05
43 11 0.04
44 140 0.46
45 116 0.38
46 10 0.03
47 10 0.03
48 2 0.01
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (43 bp):
AAGATCTGTATCTTTGATCTACTTCACGCCAGTACATGAAGAC
Found at i:53463256 original size:89 final size:89
Alignment explanation
Indices: 53463148--53463607 Score: 651
Period size: 89 Copynumber: 5.2 Consensus size: 89
53463138 TTAGGGAGAT
* *
53463148 AAGATCTG-TAATCTTTGATCTACTTCACGCCAGTACATGAAGATAAAATCTGTTTTCTTCGATT
1 AAGATCTGCT-ATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTTCGATT
53463212 TGCTTCGCCACCAGTATGGGAAGGC
65 TGCTTCGCCACCAGTATGGGAAGGC
*
53463237 AAGATCTGCTATCTTTGATCTACTTCATGCCAGTACATGAAGACAAGATCTGCTTTTTCTT--AT
1 AAGATCTGCTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTG--TTTTCTTCGAT
*
53463300 TTGCTTCGCCACGAGTAT-GGAAGGC
64 TTGCTTCGCCACCAGTATGGGAAGGC
* * * *
53463325 AAGATCTGGTATCTTTAATCTACTTCACGCCAATACATGAAGACAAGATCTGTTTTCTTCGATCT
1 AAGATCTGCTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTTCGATTT
* * *
53463390 ACTTCGCCATCAGTATGGGAAGAC
66 GCTTCGCCACCAGTATGGGAAGGC
* * *
53463414 AAGATCTGCTATCTTTGATCTACTTCACGCCAGTACATGAAGATAAGATCTACTTTT-TCCGATT
1 AAGATCTGCTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCT-GTTTTCTTCGATT
*
53463478 TGCTTCGCCACTAGTATGGGAAGGC
65 TGCTTCGCCACCAGTATGGGAAGGC
* * * *
53463503 AAGATCTGGTACCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGTTTTCTTCGATCT
1 AAGATCTGCTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTTCGATTT
* * *
53463568 ACTTTGCCACCAGTATGGGAAGAC
66 GCTTCGCCACCAGTATGGGAAGGC
53463592 AAGATCTGCTATCTTT
1 AAGATCTGCTATCTTT
53463608 TTCGCCTGCT
Statistics
Matches: 326, Mismatches: 37, Indels: 16
0.86 0.10 0.04
Matches are distributed among these distances:
86 7 0.02
88 75 0.23
89 232 0.71
90 5 0.02
91 7 0.02
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (89 bp):
AAGATCTGCTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTTCGATTT
GCTTCGCCACCAGTATGGGAAGGC
Found at i:53463448 original size:177 final size:178
Alignment explanation
Indices: 53463148--53463607 Score: 753
Period size: 177 Copynumber: 2.6 Consensus size: 178
53463138 TTAGGGAGAT
* * * *
53463148 AAGATCT-GTAATCTTTGATCTACTTCACGCCAGTACATGAAGATAAAATCTGTTTTCTTCGATT
1 AAGATCTGGT-ATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGTTTTCTTCGATC
* * *
53463212 TGCTTCGCCACCAGTATGGGAAGGCAAGATCTGCTATCTTTGATCTACTTCATGCCAGTACATGA
65 TACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAGTACATGA
* **
53463277 AGACAAGATCTGCTTTTTCTTATTTGCTTCGCCACGAGTAT-GGAAGGC
130 AGACAAGATCTACTTTTTCCGATTTGCTTCGCCACGAGTATGGGAAGGC
*
53463325 AAGATCTGGTATCTTTAATCTACTTCACGCCAATACATGAAGACAAGATCTGTTTTCTTCGATCT
1 AAGATCTGGTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGTTTTCTTCGATCT
*
53463390 ACTTCGCCATCAGTATGGGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAGTACATGAA
66 ACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAGTACATGAA
* *
53463455 GATAAGATCTACTTTTTCCGATTTGCTTCGCCACTAGTATGGGAAGGC
131 GACAAGATCTACTTTTTCCGATTTGCTTCGCCACGAGTATGGGAAGGC
*
53463503 AAGATCTGGTACCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGTTTTCTTCGATCT
1 AAGATCTGGTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGTTTTCTTCGATCT
*
53463568 ACTTTGCCACCAGTATGGGAAGACAAGATCTGCTATCTTT
66 ACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTT
53463608 TTCGCCTGCT
Statistics
Matches: 263, Mismatches: 18, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
177 153 0.58
178 110 0.42
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (178 bp):
AAGATCTGGTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGTTTTCTTCGATCT
ACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAGTACATGAA
GACAAGATCTACTTTTTCCGATTTGCTTCGCCACGAGTATGGGAAGGC
Found at i:53467773 original size:20 final size:20
Alignment explanation
Indices: 53467748--53467787 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
53467738 TAAAGGTCTA
53467748 TAATGCATATAATGCGATGC
1 TAATGCATATAATGCGATGC
*
53467768 TAATGCATATGATGCGATGC
1 TAATGCATATAATGCGATGC
53467788 ATGAGATGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.30
Consensus pattern (20 bp):
TAATGCATATAATGCGATGC
Found at i:53471554 original size:18 final size:18
Alignment explanation
Indices: 53471533--53471579 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 18
53471523 CTATATTTAC
53471533 AAAAA-AAAGTATATATA
1 AAAAATAAAGTATATATA
53471550 TAAAATATAAAGTATATATA
1 -AAAA-ATAAAGTATATATA
53471570 AAAAAGTAAA
1 AAAAA-TAAA
53471580 AAACAAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
18 5 0.19
19 9 0.35
20 12 0.46
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (18 bp):
AAAAATAAAGTATATATA
Found at i:53471592 original size:13 final size:14
Alignment explanation
Indices: 53471570--53471600 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
53471560 AGTATATATA
53471570 AAAAAGTAAAAAAC
1 AAAAAGTAAAAAAC
53471584 AAAAA-TAAAAAAC
1 AAAAAGTAAAAAAC
53471597 AAAA
1 AAAA
53471601 CATATGTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.84, C:0.06, G:0.03, T:0.06
Consensus pattern (14 bp):
AAAAAGTAAAAAAC
Found at i:53471751 original size:3 final size:3
Alignment explanation
Indices: 53471730--53471798 Score: 52
Period size: 3 Copynumber: 22.3 Consensus size: 3
53471720 AGAAAATATG
* * *
53471730 ATA ATA ATCA ATA ACA ATA ATAA ATA AT- ATA ATA AAA ATA ATTA ATT
1 ATA ATA AT-A ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA A-TA ATA
*
53471777 TTA ATA ATA A-A ATA ATTA ATA A
1 ATA ATA ATA ATA ATA A-TA ATA A
53471799 CAAGGGACCC
Statistics
Matches: 52, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
2 4 0.08
3 36 0.69
4 12 0.23
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:53471763 original size:21 final size:21
Alignment explanation
Indices: 53471730--53471798 Score: 77
Period size: 21 Copynumber: 3.2 Consensus size: 21
53471720 AGAAAATATG
*
53471730 ATAATAATCAATAACAATAATAA
1 ATAATAAT-AATAA-AATAATTA
53471753 ATAAT-ATAATAAAAATAATTA
1 ATAATAATAAT-AAAATAATTA
**
53471774 ATTTTAATAATAAAATAATTA
1 ATAATAATAATAAAATAATTA
53471795 ATAA
1 ATAA
53471799 CAAGGGACCC
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
21 25 0.64
22 9 0.23
23 5 0.13
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (21 bp):
ATAATAATAATAAAATAATTA
Found at i:53471770 original size:34 final size:34
Alignment explanation
Indices: 53471732--53471798 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 34
53471722 AAAATATGAT
53471732 AATAATCAATAACAATAAT-AAATAATATAATAAA
1 AATAATCAATAACAATAATAAAATAAT-TAATAAA
* ***
53471766 AATAATTAATTTTAATAATAAAATAATTAATAA
1 AATAATCAATAACAATAATAAAATAATTAATAA
53471799 CAAGGGACCC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 21 0.75
35 7 0.25
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (34 bp):
AATAATCAATAACAATAATAAAATAATTAATAAA
Found at i:53472368 original size:5 final size:5
Alignment explanation
Indices: 53472360--53472393 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
53472350 TCGTTATTTT
*
53472360 AAATA AAATA AAATGA AAATA AAAGA AAATA AAA
1 AAATA AAATA AAAT-A AAATA AAATA AAATA AAA
53472394 AAATATGGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (5 bp):
AAATA
Found at i:53472394 original size:16 final size:16
Alignment explanation
Indices: 53472360--53472394 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
53472350 TCGTTATTTT
* *
53472360 AAATAAAATAAAATGA
1 AAATAAAAGAAAATAA
53472376 AAATAAAAGAAAATAA
1 AAATAAAAGAAAATAA
53472392 AAA
1 AAA
53472395 AATATGGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.80, C:0.00, G:0.06, T:0.14
Consensus pattern (16 bp):
AAATAAAAGAAAATAA
Found at i:53472405 original size:26 final size:26
Alignment explanation
Indices: 53472360--53472409 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
53472350 TCGTTATTTT
53472360 AAATAAAATAAAATGAAAATAAAAGA
1 AAATAAAATAAAATGAAAATAAAAGA
*
53472386 AAATAAAA-AAATATGGAAATAAAA
1 AAATAAAATAAA-ATGAAAATAAAA
53472410 ACAATAGACA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 3 0.14
26 19 0.86
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (26 bp):
AAATAAAATAAAATGAAAATAAAAGA
Found at i:53473129 original size:12 final size:12
Alignment explanation
Indices: 53473114--53473149 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
53473104 TTTTTACTTA
53473114 AATTTTTTTTAT
1 AATTTTTTTTAT
53473126 AATTTTTGTTTAT
1 AATTTTT-TTTAT
*
53473139 GATTTTTTTTA
1 AATTTTTTTTA
53473150 ACCTTTCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.72
Consensus pattern (12 bp):
AATTTTTTTTAT
Found at i:53473323 original size:15 final size:15
Alignment explanation
Indices: 53473305--53473335 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
53473295 CAAACTACCT
53473305 GCTAATAGACTAACA
1 GCTAATAGACTAACA
*
53473320 GCTAATAGGCTAACA
1 GCTAATAGACTAACA
53473335 G
1 G
53473336 AATTTAGGGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (15 bp):
GCTAATAGACTAACA
Found at i:53478684 original size:16 final size:16
Alignment explanation
Indices: 53478663--53478698 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
53478653 AAACAAATTA
*
53478663 ATATAAGCAAATATTT
1 ATATAAACAAATATTT
53478679 ATATAAACAAATATTT
1 ATATAAACAAATATTT
53478695 ATAT
1 ATAT
53478699 TTATGTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.39
Consensus pattern (16 bp):
ATATAAACAAATATTT
Found at i:53481923 original size:31 final size:31
Alignment explanation
Indices: 53481888--53481946 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
53481878 AACAACTCAT
**
53481888 TGACTTAAAT-AAAAGCTTTTGAATAGTTCAG
1 TGACTTAAATGAAAA-CTTTCAAATAGTTCAG
53481919 TGACTTAAATGAAAACTTTCAAATAGTT
1 TGACTTAAATGAAAACTTTCAAATAGTT
53481947 AAATGATCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 21 0.84
32 4 0.16
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.36
Consensus pattern (31 bp):
TGACTTAAATGAAAACTTTCAAATAGTTCAG
Found at i:53482241 original size:30 final size:31
Alignment explanation
Indices: 53482205--53482276 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 31
53482195 TTAAAGTCCT
**
53482205 TTAAAAGTTGGTAAAAAATATTTT-GGG-CCC
1 TTAAAAGTTGAAAAAAAAT-TTTTGGGGCCCC
* *
53482235 TTAAAAGCTAAAAAAAAATTTTTGGGGCCCC
1 TTAAAAGTTGAAAAAAAATTTTTGGGGCCCC
53482266 TTAAAAGTTGA
1 TTAAAAGTTGA
53482277 TAATTTTTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
29 4 0.12
30 18 0.53
31 12 0.35
ACGTcount: A:0.40, C:0.11, G:0.18, T:0.31
Consensus pattern (31 bp):
TTAAAAGTTGAAAAAAAATTTTTGGGGCCCC
Found at i:53486243 original size:16 final size:17
Alignment explanation
Indices: 53486202--53486243 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
53486192 TAGTCTAATT
*
53486202 AAGAATAATTAGGAAAA
1 AAGAATAAATAGGAAAA
* *
53486219 AAGACTAAATA-GAATA
1 AAGAATAAATAGGAAAA
53486235 AAGAATAAA
1 AAGAATAAA
53486244 AGCTTAATTA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 12 0.57
17 9 0.43
ACGTcount: A:0.67, C:0.02, G:0.14, T:0.17
Consensus pattern (17 bp):
AAGAATAAATAGGAAAA
Found at i:53487569 original size:16 final size:16
Alignment explanation
Indices: 53487548--53487586 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
53487538 TTATGTGTAT
53487548 GGTAAG-CAAATAATAA
1 GGTAAGTCAAAT-ATAA
*
53487564 GGTAAGTGAAATATAA
1 GGTAAGTCAAATATAA
53487580 GGTAAGT
1 GGTAAGT
53487587 ATTATTATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.49, C:0.03, G:0.26, T:0.23
Consensus pattern (16 bp):
GGTAAGTCAAATATAA
Found at i:53487977 original size:21 final size:21
Alignment explanation
Indices: 53487931--53488010 Score: 99
Period size: 21 Copynumber: 3.8 Consensus size: 21
53487921 TTTGCCAATT
53487931 AGGCACTTTATGTGTCGTACATC
1 AGGCACTTTATGTGTCGT--ATC
53487954 AGGCACTTTATGTGTCGTATC
1 AGGCACTTTATGTGTCGTATC
* ** *
53487975 AGGCACCTCGTGTGTCGTTTC
1 AGGCACTTTATGTGTCGTATC
53487996 AGGCAC-TTATGTGTC
1 AGGCACTTTATGTGTC
53488011 ATATACTGAT
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.14
21 26 0.51
23 18 0.35
ACGTcount: A:0.17, C:0.23, G:0.25, T:0.35
Consensus pattern (21 bp):
AGGCACTTTATGTGTCGTATC
Found at i:53501400 original size:28 final size:28
Alignment explanation
Indices: 53501351--53501411 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
53501341 ATGATGATGT
*
53501351 AAGCAATGATGGAAGCTACCA-TAACAC
1 AAGCAATGATGGAAGCGACCATTAACAC
* *
53501378 AAGCAAGTGATGGAAGCGGCCATTAATAC
1 AAGCAA-TGATGGAAGCGACCATTAACAC
53501407 AAGCA
1 AAGCA
53501412 TGCAACGTGG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 6 0.21
28 13 0.45
29 10 0.34
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (28 bp):
AAGCAATGATGGAAGCGACCATTAACAC
Found at i:53502081 original size:28 final size:28
Alignment explanation
Indices: 53502033--53502093 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
53502023 CCACGTTGCA
53502033 TGCTTGTATTAATGGCTGCTTCCATCACT
1 TGCTTGTATTAATGGCTGCTTCCATCA-T
*
53502062 TGCTTGTGTT-ATGG-TAGCTTCCATCAT
1 TGCTTGTATTAATGGCT-GCTTCCATCAT
53502089 TGCTT
1 TGCTT
53502094 ACATCATCAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
27 7 0.23
28 14 0.47
29 9 0.30
ACGTcount: A:0.15, C:0.21, G:0.20, T:0.44
Consensus pattern (28 bp):
TGCTTGTATTAATGGCTGCTTCCATCAT
Found at i:53508336 original size:92 final size:92
Alignment explanation
Indices: 53508195--53508381 Score: 356
Period size: 92 Copynumber: 2.0 Consensus size: 92
53508185 ATAATAAGAT
*
53508195 ATTGTTCAAAAAAAATGTCTTGTTCTCATCTCTATATCGAGAAAATCTGAAAGAAAGACCACGAG
1 ATTGTTCAAAAAAAATGTCTTGTTCTCATCTCTATACCGAGAAAATCTGAAAGAAAGACCACGAG
*
53508260 CGAAAAATAGGTTAGAATATGTCTTAA
66 CGAAAAATAGGTTAGAATATGCCTTAA
53508287 ATTGTTCAAAAAAAATGTCTTGTTCTCATCTCTATACCGAGAAAATCTGAAAGAAAGACCACGAG
1 ATTGTTCAAAAAAAATGTCTTGTTCTCATCTCTATACCGAGAAAATCTGAAAGAAAGACCACGAG
53508352 CGAAAAATAGGTTAGAATATGCCTTAA
66 CGAAAAATAGGTTAGAATATGCCTTAA
53508379 ATT
1 ATT
53508382 CATTTAACTT
Statistics
Matches: 93, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
92 93 1.00
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.28
Consensus pattern (92 bp):
ATTGTTCAAAAAAAATGTCTTGTTCTCATCTCTATACCGAGAAAATCTGAAAGAAAGACCACGAG
CGAAAAATAGGTTAGAATATGCCTTAA
Found at i:53516344 original size:16 final size:16
Alignment explanation
Indices: 53516323--53516353 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
53516313 ATAACTAATC
*
53516323 GGTATTACTCATTCCG
1 GGTATTAATCATTCCG
53516339 GGTATTAATCATTCC
1 GGTATTAATCATTCC
53516354 AGTTTTGAAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.39
Consensus pattern (16 bp):
GGTATTAATCATTCCG
Found at i:53516552 original size:41 final size:41
Alignment explanation
Indices: 53516496--53516578 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
53516486 AAAAAAGAAT
53516496 GAATCAAACAATCCCAGTTAGAAGAAGATAGGTATAACCCA
1 GAATCAAACAATCCCAGTTAGAAGAAGATAGGTATAACCCA
*
53516537 GAATCAAACAATCCCAGTTAGAAGATGATAGGTATAACCCA
1 GAATCAAACAATCCCAGTTAGAAGAAGATAGGTATAACCCA
53516578 G
1 G
53516579 CTAAGCTTCA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.45, C:0.19, G:0.18, T:0.18
Consensus pattern (41 bp):
GAATCAAACAATCCCAGTTAGAAGAAGATAGGTATAACCCA
Found at i:53531555 original size:21 final size:21
Alignment explanation
Indices: 53531531--53531570 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
53531521 AGTTTGATAA
53531531 ATTGAAATTTT-AAAATTAATT
1 ATTG-AATTTTCAAAATTAATT
*
53531552 ATTGAATTTTCAATATTAA
1 ATTGAATTTTCAAAATTAA
53531571 ATTTGATGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (21 bp):
ATTGAATTTTCAAAATTAATT
Found at i:53532155 original size:13 final size:13
Alignment explanation
Indices: 53532139--53532166 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
53532129 TGATGATAGT
53532139 GTTAATTTATTTA
1 GTTAATTTATTTA
53532152 GTTAATTTATTTA
1 GTTAATTTATTTA
53532165 GT
1 GT
53532167 AAAATTATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.11, T:0.61
Consensus pattern (13 bp):
GTTAATTTATTTA
Found at i:53532693 original size:24 final size:24
Alignment explanation
Indices: 53532659--53532704 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
53532649 TATATGAAAT
* *
53532659 ATAAATTTTAAATATTTTTAAGTA
1 ATAAATATTAAATATTTATAAGTA
*
53532683 ATAAATATTAATTATTTATAAG
1 ATAAATATTAAATATTTATAAG
53532705 ATTTAATTAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (24 bp):
ATAAATATTAAATATTTATAAGTA
Found at i:53536949 original size:19 final size:20
Alignment explanation
Indices: 53536895--53536952 Score: 57
Period size: 19 Copynumber: 3.0 Consensus size: 20
53536885 GCCCCAGGAT
*
53536895 GCACTTCATGTGCC-AGATA
1 GCACTTCATGTACCAAGATA
* *
53536914 TGCACTACATGCACCAAGATA
1 -GCACTTCATGTACCAAGATA
*
53536935 -CACTTCATGTTCCAAGAT
1 GCACTTCATGTACCAAGAT
53536953 GTACTATGTG
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
19 15 0.48
20 11 0.35
21 5 0.16
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.26
Consensus pattern (20 bp):
GCACTTCATGTACCAAGATA
Found at i:53538776 original size:19 final size:20
Alignment explanation
Indices: 53538752--53538801 Score: 75
Period size: 21 Copynumber: 2.5 Consensus size: 20
53538742 ATGTTAGATA
*
53538752 ATTAATTAAG-AAAAGTATG
1 ATTAATTAAGAAAAAATATG
53538771 ATTAATTAAGATAAAAATATG
1 ATTAATTAAGA-AAAAATATG
53538792 ATTAATTAAG
1 ATTAATTAAG
53538802 TTTAATTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
19 10 0.36
21 18 0.64
ACGTcount: A:0.54, C:0.00, G:0.12, T:0.34
Consensus pattern (20 bp):
ATTAATTAAGAAAAAATATG
Found at i:53545217 original size:34 final size:33
Alignment explanation
Indices: 53545157--53545222 Score: 87
Period size: 34 Copynumber: 2.0 Consensus size: 33
53545147 TTTATTAGTG
* *
53545157 AGTTTTAAAGAGTTTTTATGATAATAATATTCTT
1 AGTTTTAAAGAGTTTGTATGAGAATAAT-TTCTT
* *
53545191 AGTTTTAAAGAGTTTGTGTGGGAATAATTTCT
1 AGTTTTAAAGAGTTTGTATGAGAATAATTTCT
53545223 ACTCTTTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
33 4 0.14
34 24 0.86
ACGTcount: A:0.32, C:0.03, G:0.18, T:0.47
Consensus pattern (33 bp):
AGTTTTAAAGAGTTTGTATGAGAATAATTTCTT
Found at i:53545330 original size:18 final size:18
Alignment explanation
Indices: 53545309--53545397 Score: 72
Period size: 18 Copynumber: 4.8 Consensus size: 18
53545299 ATTTTAAATT
*
53545309 TTTATAATATTTTTATAA
1 TTTATAATATTTTAATAA
*
53545327 TTTATGATATTTTAATAA
1 TTTATAATATTTTAATAA
* *
53545345 TTTCTTATCATTTTTAATAA
1 TTTATAAT-A-TTTTAATAA
* *
53545365 CTTTAATAA-AATTTAATAT
1 -TTT-ATAATATTTTAATAA
*
53545384 TTTATAAAATTTTA
1 TTTATAATATTTTA
53545398 TTTGAAAATA
Statistics
Matches: 57, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
17 4 0.07
18 30 0.53
19 8 0.14
20 10 0.18
21 3 0.05
22 2 0.04
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.56
Consensus pattern (18 bp):
TTTATAATATTTTAATAA
Found at i:53554265 original size:24 final size:24
Alignment explanation
Indices: 53554235--53554281 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
53554225 AAATTTTTTT
53554235 AAAAATGGTC-TATTTGGCCAATTA
1 AAAAATGG-CATATTTGGCCAATTA
*
53554259 AAAAATGGCATATTTGGCTAATT
1 AAAAATGGCATATTTGGCCAATT
53554282 TATTATTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.34
Consensus pattern (24 bp):
AAAAATGGCATATTTGGCCAATTA
Found at i:53554822 original size:38 final size:37
Alignment explanation
Indices: 53554742--53554821 Score: 106
Period size: 38 Copynumber: 2.1 Consensus size: 37
53554732 TATTTAATGC
*
53554742 AATAAATATTTATTATATTTATTTGTGCTTTTAATAT
1 AATAAATATTTATTATATTTATTAGTGCTTTTAATAT
*
53554779 AATAAAATATTTATTATATTTATAGTAGTGTTTTTTAATAT
1 AAT-AAATATTTATTATATTTAT--TAGTG-CTTTTAATAT
53554820 AA
1 AA
53554822 ATATTTTTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
37 3 0.08
38 19 0.51
40 4 0.11
41 11 0.30
ACGTcount: A:0.39, C:0.01, G:0.06, T:0.54
Consensus pattern (37 bp):
AATAAATATTTATTATATTTATTAGTGCTTTTAATAT
Found at i:53555270 original size:16 final size:16
Alignment explanation
Indices: 53555233--53555274 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
53555223 TTAATCATAT
*
53555233 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
53555249 TT-AAATATATTATAA
1 TTAAAATATATTATAA
53555264 TTAAAATATAT
1 TTAAAATATAT
53555275 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:53555281 original size:14 final size:15
Alignment explanation
Indices: 53555242--53555283 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
53555232 TTTAAACATA
*
53555242 ATTATTATTAAATAT
1 ATTATAATTAAATAT
53555257 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
53555271 A-TATAATTTAATA
1 ATTATAATTAAATA
53555284 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:53555333 original size:61 final size:61
Alignment explanation
Indices: 53555268--53555455 Score: 176
Period size: 61 Copynumber: 3.1 Consensus size: 61
53555258 TTATAATTAA
53555268 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTAATCAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTAATCAAATCAT
* * ** * * ** *
53555329 AATATATGATACT-ATAAAA--GATAAT--TTAACATAATTATTAT-TAAACATATTCTAAAT-A
1 AATATATAAT-TTAATAAAATTCTTAATAATT-A-AT-ATTCTTATATGAATTTAATC-AAATCA
*
53555387 A
61 T
53555388 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACA-CAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTA-ATCAAATCAT
53555449 AATATAT
1 AATATAT
53555456 GATACTATAA
Statistics
Matches: 94, Mismatches: 20, Indels: 26
0.67 0.14 0.19
Matches are distributed among these distances:
57 2 0.02
58 2 0.02
59 29 0.31
60 22 0.23
61 35 0.37
62 2 0.02
63 2 0.02
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.41
Consensus pattern (61 bp):
AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTAATCAAATCAT
Found at i:53555371 original size:120 final size:121
Alignment explanation
Indices: 53555231--53555528 Score: 503
Period size: 120 Copynumber: 2.5 Consensus size: 121
53555221 ATTTAATCAT
53555231 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
53555296 ATTAATATTCTTATATGAATTTA-ATCAAATCATAATATATGATACTATAAAAGATA
66 ATTAATATTCTTATATGAATTTACA-CAAATCATAATATATGATACTATAAAAGATA
* * *
53555352 ATTT-AACATAATTATTATTAAACATATTCTAAATAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
53555416 ATTAATATTCTTATATGAATTTACACAAATCATAATATATGATACTATAAAAGATA
66 ATTAATATTCTTATATGAATTTACACAAATCATAATATATGATACTATAAAAGATA
* * * *
53555472 ATTTGAA-ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATT
53555529 TAAAATAATT
Statistics
Matches: 167, Mismatches: 8, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
120 160 0.96
121 7 0.04
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (121 bp):
ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
ATTAATATTCTTATATGAATTTACACAAATCATAATATATGATACTATAAAAGATA
Found at i:53555638 original size:88 final size:90
Alignment explanation
Indices: 53555544--53555748 Score: 306
Period size: 88 Copynumber: 2.3 Consensus size: 90
53555534 TAATTATAAC
* * * * *
53555544 TAATAAATTTTCATATATGAATTTGTATAATTTAAAATAATTATTATTACATATAATTTAAT-A-
1 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAG
*
53555607 ATATATAATTTCATAAAATTCTTGA
66 ATATATAATTTCATAAAATTCTTAA
*
53555632 TAATAAATTTTCTTATATAAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
1 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAA-
53555697 GATATATAATTTCATAAAATTCTTAA
65 GATATATAATTTCATAAAATTCTTAA
*
53555723 TAATAAAATGTTCTTATATGAATTTA
1 TAAT-AAATTTTCTTATATGAATTTA
53555749 CTAAAATCAA
Statistics
Matches: 104, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
88 56 0.54
89 1 0.01
91 28 0.27
92 19 0.18
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (90 bp):
TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAG
ATATATAATTTCATAAAATTCTTAA
Found at i:53555708 original size:44 final size:43
Alignment explanation
Indices: 53555569--53555708 Score: 115
Period size: 44 Copynumber: 3.2 Consensus size: 43
53555559 TATGAATTTG
* *
53555569 TATAATTTAAAATAATTATTATTACATATAATTTAATAATATA
1 TATAATTTAAAATAATTAATATTAAATATAATTTAATAATATA
* ** * * * *
53555612 TA-ATTTCATAAAATTCTTGATAATAAAT-T-TTCTTATATAAATTTA
1 TATAATT--TAAAATAATTAATATTAAATATAAT-TTA-AT-AATATA
*
53555657 TACAATTTAAAATAATTAATATTAAATATAATTTAATAATGATA
1 TATAATTTAAAATAATTAATATTAAATATAATTTAATAAT-ATA
53555701 TATAATTT
1 TATAATTT
53555709 CATAAAATTC
Statistics
Matches: 71, Mismatches: 17, Indels: 17
0.68 0.16 0.16
Matches are distributed among these distances:
42 4 0.06
43 9 0.13
44 43 0.61
45 11 0.15
46 4 0.06
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (43 bp):
TATAATTTAAAATAATTAATATTAAATATAATTTAATAATATA
Found at i:53557490 original size:31 final size:31
Alignment explanation
Indices: 53557455--53557513 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
53557445 GAAAAAGAAA
*
53557455 AGAAACAGA-AGACGCAAATCGGCAGAAACTG
1 AGAAACAGAGAGA-GCAAATCAGCAGAAACTG
*
53557486 AGAAACAGAGGGAGCAAATCAGCAGAAA
1 AGAAACAGAGAGAGCAAATCAGCAGAAA
53557514 AGAAAATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 23 0.92
32 2 0.08
ACGTcount: A:0.51, C:0.17, G:0.27, T:0.05
Consensus pattern (31 bp):
AGAAACAGAGAGAGCAAATCAGCAGAAACTG
Found at i:53558862 original size:31 final size:31
Alignment explanation
Indices: 53558825--53558883 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
53558815 AATGATCACT
53558825 AACTATTCAAAAGTTTTCATTTAAGTCATTA
1 AACTATTCAAAAGTTTTCATTTAAGTCATTA
** *
53558856 AACTATTTGAAAGTTTTTATTTAAGTCA
1 AACTATTCAAAAGTTTTCATTTAAGTCA
53558884 CTAGGCTGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.37, C:0.10, G:0.08, T:0.44
Consensus pattern (31 bp):
AACTATTCAAAAGTTTTCATTTAAGTCATTA
Found at i:53570132 original size:28 final size:29
Alignment explanation
Indices: 53570073--53570134 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 29
53570063 ATAAGTTATT
*
53570073 TTTTTTTAAAATTTACCGAAATGGGCTGA
1 TTTTTTTAAAATTTACCGAAATGGGCTCA
** * *
53570102 TTTTTTTATTATTTACCGGAAT-GGTTCA
1 TTTTTTTAAAATTTACCGAAATGGGCTCA
53570130 TTTTT
1 TTTTT
53570135 CGTGAAATCG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 9 0.32
29 19 0.68
ACGTcount: A:0.24, C:0.10, G:0.15, T:0.52
Consensus pattern (29 bp):
TTTTTTTAAAATTTACCGAAATGGGCTCA
Found at i:53570595 original size:124 final size:124
Alignment explanation
Indices: 53570375--53570724 Score: 628
Period size: 124 Copynumber: 2.8 Consensus size: 124
53570365 TTATTTCGAG
*
53570375 TTGACGTTTCTGATCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
*
53570440 AAATCGCGTCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTT
66 AAATCGCGTCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAAATTTTT
53570499 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
* * *
53570564 AAATCGTGCCCTCGTGGACGCGATTTTGCTACAGTTGGTCATGTAAGAAATAAATTTTT
66 AAATCGCGTCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAAATTTTT
* *
53570623 TTGACGTTTCTAAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAAAAGAAATTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
*
53570688 AAATCGCATCCTCGTGGACGCGATTTTGCTACAGTAG
66 AAATCGCGTCCTCGTGGACGCGATTTTGCTACAGTAG
53570725 CAAGTTTGGG
Statistics
Matches: 215, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
124 215 1.00
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (124 bp):
TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
AAATCGCGTCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAAATTTTT
Found at i:53571995 original size:30 final size:29
Alignment explanation
Indices: 53571928--53572040 Score: 217
Period size: 29 Copynumber: 3.9 Consensus size: 29
53571918 TAAGGAAAAT
53571928 GGTTAGGGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
53571957 GGTTAGGGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
53571986 GGTTTAGGGTTTTTAATTAAATTAGGTTAG
1 GG-TTAGGGTTTTTAATTAAATTAGGTTAG
53572016 GGTTAGGGTTTTTAATTAAATTAGG
1 GGTTAGGGTTTTTAATTAAATTAGG
53572041 ATTTTTATTA
Statistics
Matches: 83, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
29 54 0.65
30 29 0.35
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.45
Consensus pattern (29 bp):
GGTTAGGGTTTTTAATTAAATTAGGTTAG
Found at i:53572126 original size:36 final size:36
Alignment explanation
Indices: 53572086--53572200 Score: 92
Period size: 36 Copynumber: 3.2 Consensus size: 36
53572076 ATATCAAATA
*
53572086 ATATCAAAATAACTCGAAAAAATTTCTATGCCTATT
1 ATATCAAAATAACTCGAAAAAATTTCTATGCATATT
* **** * * *
53572122 ATATC-AAATAAACTTCTATTTTA-TTATAT-CAAATA
1 ATATCAAAAT-AAC-TCGAAAAAATTTCTATGCATATT
*
53572157 ATATCAAAATAACTCGAAAAAATTTCTATGCGTATT
1 ATATCAAAATAACTCGAAAAAATTTCTATGCATATT
*
53572193 ACATCAAA
1 ATATCAAA
53572201 TAATAAATTT
Statistics
Matches: 55, Mismatches: 19, Indels: 10
0.65 0.23 0.12
Matches are distributed among these distances:
34 4 0.07
35 20 0.36
36 27 0.49
37 4 0.07
ACGTcount: A:0.46, C:0.15, G:0.04, T:0.35
Consensus pattern (36 bp):
ATATCAAAATAACTCGAAAAAATTTCTATGCATATT
Found at i:53572150 original size:71 final size:71
Alignment explanation
Indices: 53572046--53572203 Score: 289
Period size: 71 Copynumber: 2.2 Consensus size: 71
53572036 TTAGGATTTT
53572046 TATTACATCAAATAAAACTTCTATTTTATTATATCAAATAATATCAAAATAACTCGAAAAAATTT
1 TATTACATCAAAT-AAACTTCTATTTTATTATATCAAATAATATCAAAATAACTCGAAAAAATTT
53572111 CTATGCC
65 CTATGCC
*
53572118 TATTATATCAAATAAACTTCTATTTTATTATATCAAATAATATCAAAATAACTCGAAAAAATTTC
1 TATTACATCAAATAAACTTCTATTTTATTATATCAAATAATATCAAAATAACTCGAAAAAATTTC
*
53572183 TATGCG
66 TATGCC
53572189 TATTACATCAAATAA
1 TATTACATCAAATAA
53572204 TAAATTTAAA
Statistics
Matches: 83, Mismatches: 3, Indels: 1
0.95 0.03 0.01
Matches are distributed among these distances:
71 71 0.86
72 12 0.14
ACGTcount: A:0.46, C:0.14, G:0.03, T:0.37
Consensus pattern (71 bp):
TATTACATCAAATAAACTTCTATTTTATTATATCAAATAATATCAAAATAACTCGAAAAAATTTC
TATGCC
Found at i:53575631 original size:7 final size:7
Alignment explanation
Indices: 53575621--53575645 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
53575611 TTATATACAT
53575621 AATACTA
1 AATACTA
53575628 AATACTA
1 AATACTA
53575635 AATACTA
1 AATACTA
53575642 AATA
1 AATA
53575646 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:53576782 original size:30 final size:29
Alignment explanation
Indices: 53576725--53576788 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 29
53576715 GCCATTGATG
*
53576725 AAAATATAAAAAATTTAAATTTTTTTTAA
1 AAAATATAAAAAATTTAAATTTATTTTAA
53576754 AAAATATAAAAAAAATTTAAA-TTATTTTAA
1 AAAATAT--AAAAAATTTAAATTTATTTTAA
53576784 AAAAT
1 AAAAT
53576789 GAAATTGAGG
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
29 7 0.22
30 13 0.41
31 12 0.38
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (29 bp):
AAAATATAAAAAATTTAAATTTATTTTAA
Found at i:53576844 original size:29 final size:29
Alignment explanation
Indices: 53576812--53576900 Score: 75
Period size: 29 Copynumber: 3.3 Consensus size: 29
53576802 AATTTAGATT
53576812 AAATATGGATTTGAGAGAATTTTGGAAGG
1 AAATATGGATTTGAGAGAATTTTGGAAGG
* * **
53576841 AAAT-T-GA---GAG-GAA-ATTGAAATT
1 AAATATGGATTTGAGAGAATTTTGGAAGG
*
53576863 AAATATGGGTTTGAGAGAATTTTGGAAGG
1 AAATATGGATTTGAGAGAATTTTGGAAGG
*
53576892 AAATTTGGA
1 AAATATGGA
53576901 AGGAAATTGA
Statistics
Matches: 42, Mismatches: 11, Indels: 14
0.63 0.16 0.21
Matches are distributed among these distances:
22 9 0.21
23 4 0.10
24 4 0.10
27 5 0.12
28 4 0.10
29 16 0.38
ACGTcount: A:0.40, C:0.00, G:0.29, T:0.30
Consensus pattern (29 bp):
AAATATGGATTTGAGAGAATTTTGGAAGG
Found at i:53576844 original size:51 final size:51
Alignment explanation
Indices: 53576789--53576910 Score: 183
Period size: 51 Copynumber: 2.4 Consensus size: 51
53576779 TTTAAAAAAT
* * *
53576789 GAAATTGAGGGGAAATTTAGATTAAATATGGATTTGAGAGAATTTTGGAAG
1 GAAATTGAGAGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAAG
*
53576840 GAAATTGAGAGGAAATTGAAATTAAATATGGGTTTGAGAGAATTTTGGAAG
1 GAAATTGAGAGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAAG
53576891 GAAATTTG-GAAGGAAATTGA
1 GAAA-TTGAG-AGGAAATTGA
53576911 GAGGATTAGA
Statistics
Matches: 65, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
51 52 0.80
52 13 0.20
ACGTcount: A:0.41, C:0.00, G:0.30, T:0.30
Consensus pattern (51 bp):
GAAATTGAGAGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAAG
Found at i:53576900 original size:12 final size:12
Alignment explanation
Indices: 53576883--53576908 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
53576873 TTGAGAGAAT
53576883 TTTGGAAGGAAA
1 TTTGGAAGGAAA
53576895 TTTGGAAGGAAA
1 TTTGGAAGGAAA
53576907 TT
1 TT
53576909 GAGAGGATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.31, T:0.31
Consensus pattern (12 bp):
TTTGGAAGGAAA
Found at i:53578236 original size:30 final size:30
Alignment explanation
Indices: 53578195--53578257 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
53578185 TCAATAATTT
*
53578195 AATTGATTGTTTATATT-AGATT-AAAGACTC
1 AATTAATTGTTTATATTCA-ATTAAAAG-CTC
53578225 AATTAATTGTTTATATTCAATTAAAAGCTC
1 AATTAATTGTTTATATTCAATTAAAAGCTC
53578255 AAT
1 AAT
53578258 CAATGATTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
30 25 0.83
31 5 0.17
ACGTcount: A:0.40, C:0.08, G:0.10, T:0.43
Consensus pattern (30 bp):
AATTAATTGTTTATATTCAATTAAAAGCTC
Found at i:53579082 original size:11 final size:13
Alignment explanation
Indices: 53579058--53579089 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
53579048 TAGTTTATTA
53579058 ATATTTTAATATG
1 ATATTTTAATATG
53579071 AT-TTTTAA-ATG
1 ATATTTTAATATG
53579082 ATATTTTA
1 ATATTTTA
53579090 TTAATTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.28
12 11 0.61
13 2 0.11
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (13 bp):
ATATTTTAATATG
Found at i:53588985 original size:50 final size:50
Alignment explanation
Indices: 53588931--53589054 Score: 167
Period size: 50 Copynumber: 2.5 Consensus size: 50
53588921 CATTTAGGTT
* *
53588931 ATGAGAGGTCCCATGTAAGACCATGTCTAGGACATGGCGTTGGCACCAAG
1 ATGAGAGGTCCCATGTAAGACCATGTCTAGGACATGGCATGGGCACCAAG
** * *
53588981 ATGAGAGGTCCCCCGTAAGACCATGTCTAGGACATGGCATGGGCACCGAT
1 ATGAGAGGTCCCATGTAAGACCATGTCTAGGACATGGCATGGGCACCAAG
* **
53589031 ATGAAAACTCCCATGTAAGACCAT
1 ATGAGAGGTCCCATGTAAGACCAT
53589055 ATCTGAGATA
Statistics
Matches: 63, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 63 1.00
ACGTcount: A:0.30, C:0.24, G:0.27, T:0.19
Consensus pattern (50 bp):
ATGAGAGGTCCCATGTAAGACCATGTCTAGGACATGGCATGGGCACCAAG
Found at i:53602825 original size:33 final size:33
Alignment explanation
Indices: 53602764--53602831 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 33
53602754 TAATCAATTT
* *
53602764 AATATTAAATTTAATCTAATATTTATCTTGATA
1 AATATTAAATTTAATCTAATATTAATCTTAATA
* *
53602797 AATATTATA-TTAATTTAATATTAAATCTTAATA
1 AATATTAAATTTAATCTAATATT-AATCTTAATA
53602830 AA
1 AA
53602832 ATAATAGAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
32 12 0.40
33 18 0.60
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.47
Consensus pattern (33 bp):
AATATTAAATTTAATCTAATATTAATCTTAATA
Found at i:53602966 original size:19 final size:19
Alignment explanation
Indices: 53602916--53602968 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
53602906 AATAAAATAC
*
53602916 TATTAAGATAGATATTAAAT
1 TATTAAAATA-ATATTAAAT
**
53602936 T-TT-ATTTAATATTAAAT
1 TATTAAAATAATATTAAAT
53602953 TATTAAAATAATATTA
1 TATTAAAATAATATTA
53602969 TTTTTGGACT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
17 10 0.37
18 5 0.19
19 11 0.41
20 1 0.04
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (19 bp):
TATTAAAATAATATTAAAT
Found at i:53605566 original size:35 final size:35
Alignment explanation
Indices: 53605527--53605594 Score: 82
Period size: 35 Copynumber: 1.9 Consensus size: 35
53605517 TCTGAGGAGT
* *
53605527 TAGTAAACCATTTCCATGGTGTCGCTCCGTAGAGC
1 TAGTAAACCATTTCCATGATGTCGCTCCATAGAGC
* * * *
53605562 TAGTAGATCATTTTCATGATGTCTCTCCATAGA
1 TAGTAAACCATTTCCATGATGTCGCTCCATAGA
53605595 ACCAATATAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 27 1.00
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (35 bp):
TAGTAAACCATTTCCATGATGTCGCTCCATAGAGC
Found at i:53611203 original size:14 final size:14
Alignment explanation
Indices: 53611184--53611211 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
53611174 GAGCATTAAT
53611184 TTAAAGAGATTTTA
1 TTAAAGAGATTTTA
53611198 TTAAAGAGATTTTA
1 TTAAAGAGATTTTA
53611212 ATTTTCGAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (14 bp):
TTAAAGAGATTTTA
Found at i:53614229 original size:6 final size:6
Alignment explanation
Indices: 53614218--53614246 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
53614208 GTTAAACTCA
53614218 CCACCG CCACCG CCACCG CCACCG CCACC
1 CCACCG CCACCG CCACCG CCACCG CCACC
53614247 ACCCCAACCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.69, G:0.14, T:0.00
Consensus pattern (6 bp):
CCACCG
Found at i:53614248 original size:15 final size:15
Alignment explanation
Indices: 53614216--53614263 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
53614206 GAGTTAAACT
53614216 CACCACCGCCACCG-
1 CACCACCGCCACCGC
53614230 --CCACCGCCACCGC
1 CACCACCGCCACCGC
53614243 CACCACC-CCAACCGC
1 CACCACCGCC-ACCGC
53614258 CACCAC
1 CACCAC
53614264 TGCCGCCACT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
12 12 0.40
14 2 0.07
15 16 0.53
ACGTcount: A:0.23, C:0.67, G:0.10, T:0.00
Consensus pattern (15 bp):
CACCACCGCCACCGC
Found at i:53614269 original size:27 final size:27
Alignment explanation
Indices: 53614216--53614272 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
53614206 GAGTTAAACT
*
53614216 CACCACCGCCACCGCCACCGCCACCGC
1 CACCACCGCCACCGCCACCACCACCGC
**
53614243 CACCACC-CCAACCGCCACCACTGCCGC
1 CACCACCGCC-ACCGCCACCACCACCGC
53614270 CAC
1 CAC
53614273 TGATACCGCC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 2 0.08
27 24 0.92
ACGTcount: A:0.21, C:0.65, G:0.12, T:0.02
Consensus pattern (27 bp):
CACCACCGCCACCGCCACCACCACCGC
Found at i:53622285 original size:20 final size:20
Alignment explanation
Indices: 53622262--53622312 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
53622252 TGCAAGTTAT
* *
53622262 AAAAAAT-TAAATTTTATAA
1 AAAAAATATAAATGTTAGAA
53622281 AAAAAATATAAATGTTAGAA
1 AAAAAATATAAATGTTAGAA
*
53622301 AAAAATTATAAA
1 AAAAAATATAAA
53622313 AAACGTAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 7 0.25
20 21 0.75
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (20 bp):
AAAAAATATAAATGTTAGAA
Found at i:53622359 original size:12 final size:12
Alignment explanation
Indices: 53622339--53622374 Score: 56
Period size: 11 Copynumber: 3.1 Consensus size: 12
53622329 AAAAAATTGC
*
53622339 AAAATTTATAAA
1 AAAAATTATAAA
53622351 AAAAATTAT-AA
1 AAAAATTATAAA
53622362 AAAAATTATAAA
1 AAAAATTATAAA
53622374 A
1 A
53622375 TGCATCAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (12 bp):
AAAAATTATAAA
Found at i:53622591 original size:10 final size:10
Alignment explanation
Indices: 53622557--53622641 Score: 52
Period size: 10 Copynumber: 8.4 Consensus size: 10
53622547 GGTATGATAC
53622557 TTTTTATAAT
1 TTTTTATAAT
*
53622567 TTTTTTTACGA-
1 TTTTTATA--AT
53622578 TTTTTATAATT
1 TTTTTATAA-T
*
53622589 TTTTTCTAA-
1 TTTTTATAAT
53622598 TTTTTA-AAT
1 TTTTTATAAT
53622607 ATTTTTAT-AT
1 -TTTTTATAAT
*
53622617 TTTTTACTAAA
1 TTTTTA-TAAT
* *
53622628 ATTTAATAAT
1 TTTTTATAAT
53622638 TTTT
1 TTTT
53622642 AGATTGTAAC
Statistics
Matches: 57, Mismatches: 9, Indels: 18
0.68 0.11 0.21
Matches are distributed among these distances:
8 2 0.04
9 12 0.21
10 22 0.39
11 20 0.35
12 1 0.02
ACGTcount: A:0.29, C:0.04, G:0.01, T:0.66
Consensus pattern (10 bp):
TTTTTATAAT
Found at i:53622602 original size:21 final size:19
Alignment explanation
Indices: 53622557--53622622 Score: 71
Period size: 21 Copynumber: 3.3 Consensus size: 19
53622547 GGTATGATAC
53622557 TTTTTATAATTTTTTTTACGA
1 TTTTTATAATTTTTTTTA--A
53622578 TTTTTATAATTTTTTTCTAA
1 TTTTTATAATTTTTTT-TAA
* *
53622598 TTTTTA-AATATTTTTATAT
1 TTTTTATAAT-TTTTTTTAA
53622617 TTTTTA
1 TTTTTA
53622623 CTAAAATTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
19 11 0.27
20 12 0.29
21 16 0.39
22 2 0.05
ACGTcount: A:0.26, C:0.03, G:0.02, T:0.70
Consensus pattern (19 bp):
TTTTTATAATTTTTTTTAA
Found at i:53622611 original size:19 final size:20
Alignment explanation
Indices: 53622557--53622642 Score: 70
Period size: 20 Copynumber: 4.3 Consensus size: 20
53622547 GGTATGATAC
*
53622557 TTTTTATAAT-TTTTTTTACGA
1 TTTTTATAATATTTTTATA--A
* *
53622578 TTTTTATAATTTTTTTCTAA
1 TTTTTATAATATTTTTATAA
*
53622598 TTTTTA-AATATTTTTATAT
1 TTTTTATAATATTTTTATAA
* *
53622617 TTTTTACTAA-AATTTAATAA
1 TTTTTA-TAATATTTTTATAA
53622637 TTTTTA
1 TTTTTA
53622643 GATTGTAACA
Statistics
Matches: 55, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
19 16 0.29
20 20 0.36
21 12 0.22
22 7 0.13
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.65
Consensus pattern (20 bp):
TTTTTATAATATTTTTATAA
Found at i:53622632 original size:29 final size:30
Alignment explanation
Indices: 53622577--53622642 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 30
53622567 TTTTTTTACG
* **
53622577 ATTTTTATAATTTTTTTCTAATTTTTAA-A
1 ATTTTTATAATTTTTTACTAAAATTTAATA
53622606 TATTTTTAT-ATTTTTTACTAAAATTTAATA
1 -ATTTTTATAATTTTTTACTAAAATTTAATA
53622636 ATTTTTA
1 ATTTTTA
53622643 GATTGTAACA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 23 0.72
30 9 0.28
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (30 bp):
ATTTTTATAATTTTTTACTAAAATTTAATA
Found at i:53624664 original size:92 final size:93
Alignment explanation
Indices: 53624522--53624690 Score: 252
Period size: 92 Copynumber: 1.8 Consensus size: 93
53624512 TTTTGTTGCG
* * * * **
53624522 TAGTATGCTTTTCACCTAAAATCGTGATTGTGTTATAAATTGAAATACTAAATGTATTTACAAGT
1 TAGTATGCTTTTCACCCAAAATCATGATTGTGTTATAAATTGAAATACTAAATGCAATTACAAAC
53624587 AATTACACTCAATTTTTTTTTTCTTTCA
66 AATTACACTCAATTTTTTTTTTCTTTCA
*
53624615 TAGTATG-TTTTCACCCAAAATCATGATTGT-TCTATAAATTGAAATACTAAGTGCAATTACAAA
1 TAGTATGCTTTTCACCCAAAATCATGATTGTGT-TATAAATTGAAATACTAAATGCAATTACAAA
53624678 CAATTACACTCAA
65 CAATTACACTCAA
53624691 ATTTAATTAC
Statistics
Matches: 68, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
91 1 0.01
92 60 0.88
93 7 0.10
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (93 bp):
TAGTATGCTTTTCACCCAAAATCATGATTGTGTTATAAATTGAAATACTAAATGCAATTACAAAC
AATTACACTCAATTTTTTTTTTCTTTCA
Found at i:53633067 original size:26 final size:27
Alignment explanation
Indices: 53633014--53633068 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
53633004 AAATAAAATA
* * *
53633014 AAAAACTTAAAAATATGTTTGGTAATT
1 AAAAACTTAAAAATATATATGCTAATT
*
53633041 AAAAACTTAAAAATA-ATATGCTTATT
1 AAAAACTTAAAAATATATATGCTAATT
53633067 AA
1 AA
53633069 TTAAAAATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 9 0.38
27 15 0.62
ACGTcount: A:0.53, C:0.05, G:0.07, T:0.35
Consensus pattern (27 bp):
AAAAACTTAAAAATATATATGCTAATT
Found at i:53633091 original size:15 final size:13
Alignment explanation
Indices: 53633063--53633088 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
53633053 ATAATATGCT
53633063 TATTAATTAAAAA
1 TATTAATTAAAAA
53633076 TATTAATTAAAAA
1 TATTAATTAAAAA
53633089 AATTTTAAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
TATTAATTAAAAA
Found at i:53633092 original size:22 final size:22
Alignment explanation
Indices: 53633067--53633111 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
53633057 TATGCTTATT
*
53633067 AATTAAAAATATTAATTAAAAA
1 AATTAAAAACATTAATTAAAAA
** *
53633089 AATTTTAAACATTCATTAAAAA
1 AATTAAAAACATTAATTAAAAA
53633111 A
1 A
53633112 TAGTTAAATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.33
Consensus pattern (22 bp):
AATTAAAAACATTAATTAAAAA
Found at i:53662068 original size:28 final size:30
Alignment explanation
Indices: 53662014--53662069 Score: 89
Period size: 28 Copynumber: 1.9 Consensus size: 30
53662004 TTAAATTACT
*
53662014 TATTATTTAAGTAAATAGATCTTTATTATC
1 TATTATTTAAGTAAATAGATATTTATTATC
53662044 TATT-TTTAAGTAAA-AGATATTTATTA
1 TATTATTTAAGTAAATAGATATTTATTA
53662070 ATTAAATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 11 0.44
29 10 0.40
30 4 0.16
ACGTcount: A:0.39, C:0.04, G:0.07, T:0.50
Consensus pattern (30 bp):
TATTATTTAAGTAAATAGATATTTATTATC
Found at i:53663263 original size:47 final size:46
Alignment explanation
Indices: 53663174--53663264 Score: 110
Period size: 47 Copynumber: 2.0 Consensus size: 46
53663164 AATAAAATGA
* * * * * * *
53663174 ATAAAATTATGGAAATGTAAAAAGATATATATATGTGTGTATATAC
1 ATAAAATCATAGAAATGTAAAAAGAAAAATACATATATGTATATAC
53663220 ATAAAATCATAGAAATGTAAAAAAGAAAAATACATATATGTATAT
1 ATAAAATCATAGAAATGT-AAAAAGAAAAATACATATATGTATAT
53663265 CTTTTAAAAT
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
46 16 0.43
47 21 0.57
ACGTcount: A:0.54, C:0.03, G:0.12, T:0.31
Consensus pattern (46 bp):
ATAAAATCATAGAAATGTAAAAAGAAAAATACATATATGTATATAC
Found at i:53664855 original size:3 final size:3
Alignment explanation
Indices: 53664847--53664880 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
53664837 ATAAAAATTG
53664847 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
53664881 ATGATAATAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:53666693 original size:17 final size:17
Alignment explanation
Indices: 53666671--53666734 Score: 67
Period size: 17 Copynumber: 3.6 Consensus size: 17
53666661 AATCTTAGAG
53666671 TTCTAATTGTATACAGC
1 TTCTAATTGTATACAGC
* *
53666688 TTCTAATTATGTCTTAGAG-
1 TTCTAA-T-TGT-ATACAGC
53666707 TTCTAATTGTATACAGC
1 TTCTAATTGTATACAGC
*
53666724 TTTTAATTGTA
1 TTCTAATTGTA
53666735 GCCTTTGATT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
16 4 0.11
17 19 0.50
18 2 0.05
19 9 0.24
20 4 0.11
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.47
Consensus pattern (17 bp):
TTCTAATTGTATACAGC
Found at i:53666704 original size:36 final size:36
Alignment explanation
Indices: 53666663--53666731 Score: 129
Period size: 36 Copynumber: 1.9 Consensus size: 36
53666653 GATTATTTAA
53666663 TCTTAGAGTTCTAATTGTATACAGCTTCTAATTATG
1 TCTTAGAGTTCTAATTGTATACAGCTTCTAATTATG
*
53666699 TCTTAGAGTTCTAATTGTATACAGCTTTTAATT
1 TCTTAGAGTTCTAATTGTATACAGCTTCTAATT
53666732 GTAGCCTTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.46
Consensus pattern (36 bp):
TCTTAGAGTTCTAATTGTATACAGCTTCTAATTATG
Found at i:53666712 original size:19 final size:18
Alignment explanation
Indices: 53666663--53666714 Score: 54
Period size: 19 Copynumber: 2.9 Consensus size: 18
53666653 GATTATTTAA
53666663 TCTTAGAGTTCTAA-TTG
1 TCTTAGAGTTCTAATTTG
* *
53666680 T-ATACAGCTTCTAATTATG
1 TCTTAGAG-TTCTAATT-TG
53666699 TCTTAGAGTTCTAATT
1 TCTTAGAGTTCTAATT
53666715 GTATACAGCT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
16 4 0.15
17 7 0.26
18 1 0.04
19 11 0.41
20 4 0.15
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.46
Consensus pattern (18 bp):
TCTTAGAGTTCTAATTTG
Found at i:53671811 original size:17 final size:17
Alignment explanation
Indices: 53671789--53671852 Score: 67
Period size: 17 Copynumber: 3.6 Consensus size: 17
53671779 AATCTTAGAG
53671789 TTCTAATTGTATACAGC
1 TTCTAATTGTATACAGC
* *
53671806 TTCTAATTATGTCATA-GGG
1 TTCTAA-T-TGT-ATACAGC
53671825 TTCTAATTGTATACAGC
1 TTCTAATTGTATACAGC
*
53671842 TTTTAATTGTA
1 TTCTAATTGTA
53671853 GCCTTTGATT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
16 3 0.08
17 20 0.53
18 2 0.05
19 10 0.26
20 3 0.08
ACGTcount: A:0.28, C:0.12, G:0.14, T:0.45
Consensus pattern (17 bp):
TTCTAATTGTATACAGC
Found at i:53673895 original size:131 final size:131
Alignment explanation
Indices: 53673740--53674073 Score: 472
Period size: 131 Copynumber: 2.5 Consensus size: 131
53673730 CATGGTTTTA
* * *
53673740 ATCTGCTCCGCTACTGCTTAGGGAGATAAGATTTACAATCTTCAACCTACTCCACTGCTGCTCAA
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATCTTCAACCTACTCCACTGCTGCTCAA
* * * *
53673805 GGAGATAGGACTAGTGACTTAAATCTGCTTCCTACTATTTGGGGAAGATAAGATTCGCCGTATTC
66 GGAGATAGGACTAGTGACTTAAATCTACTTCCTACTATCTCGGGAAGATAAAATTCGCCGTATTC
53673870 G
131 G
* *
53673871 ATCTGCTCCACTACTACTTAGGGAGATAAGATCTGCAATCTTCAACCTACTCCACTGCTACTCAA
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATCTTCAACCTACTCCACTGCTGCTCAA
** * * * *
53673936 TAAGATAGGACTAGTGGCTTAAATCTACTTCCTACTATCTCGGGAAGATAAAATTCTCCGTCTTT
66 GGAGATAGGACTAGTGACTTAAATCTACTTCCTACTATCTCGGGAAGATAAAATTCGCCGTATTC
53674001 G
131 G
* ** * *
53674002 ATCTGCTTCACT-CATGCTTAAAGAGATAAGATCTGCAATCTTCAACCTATTCCACTGCTGCTTA
1 ATCTGCTCCACTAC-TGCTTAGGGAGATAAGATCTGCAATCTTCAACCTACTCCACTGCTGCTCA
53674066 AGGAGATA
65 AGGAGATA
53674074 AGGTTTGATA
Statistics
Matches: 178, Mismatches: 24, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
130 1 0.01
131 177 0.99
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.30
Consensus pattern (131 bp):
ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATCTTCAACCTACTCCACTGCTGCTCAA
GGAGATAGGACTAGTGACTTAAATCTACTTCCTACTATCTCGGGAAGATAAAATTCGCCGTATTC
G
Found at i:53673924 original size:44 final size:45
Alignment explanation
Indices: 53673745--53673932 Score: 109
Period size: 44 Copynumber: 4.3 Consensus size: 45
53673735 TTTTAATCTG
* * *
53673745 CTCCGCTACTGCTTAGGGAGATAAGATTTA-CAATCTTCAACCTA
1 CTCCACTACTACTTAGGGAGATAAGATCTAGCAATCTTCAACCTA
* * * * * ** * * *
53673789 CTCCACTGCTGCTCAAGGAGATAGGA-CTAGTGA-CTTAAATCTG
1 CTCCACTACTACTTAGGGAGATAAGATCTAGCAATCTTCAACCTA
* * * * ** * * * *
53673832 CTTC-CTACTATTTGGGGAAGATAAGAT-TCGCCGTATTCGATCTG
1 CTCCACTACTACTTAGGG-AGATAAGATCTAGCAATCTTCAACCTA
53673876 CTCCACTACTACTTAGGGAGATAAGATCT-GCAATCTTCAACCTA
1 CTCCACTACTACTTAGGGAGATAAGATCTAGCAATCTTCAACCTA
*
53673920 CTCCACTGCTACT
1 CTCCACTACTACT
53673933 CAATAAGATA
Statistics
Matches: 102, Mismatches: 36, Indels: 12
0.68 0.24 0.08
Matches are distributed among these distances:
42 7 0.07
43 21 0.21
44 62 0.61
45 12 0.12
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.29
Consensus pattern (45 bp):
CTCCACTACTACTTAGGGAGATAAGATCTAGCAATCTTCAACCTA
Found at i:53682912 original size:30 final size:28
Alignment explanation
Indices: 53682873--53682938 Score: 96
Period size: 28 Copynumber: 2.3 Consensus size: 28
53682863 ATGGATTTAA
53682873 ATTAATTATTATTTAAGTAAATAAATATTT
1 ATTAATTATT-TTTAAGTAAA-AAATATTT
* *
53682903 ATTATTTATTTTTAAGTAAAATATATTT
1 ATTAATTATTTTTAAGTAAAAAATATTT
53682931 ATTAATTA
1 ATTAATTA
53682939 AATAATTATA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
28 14 0.42
29 10 0.30
30 9 0.27
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (28 bp):
ATTAATTATTTTTAAGTAAAAAATATTT
Found at i:53683740 original size:14 final size:15
Alignment explanation
Indices: 53683718--53683794 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
53683708 CAATCAAACA
53683718 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
53683732 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
* *
53683747 ACAGAAAAGTAAAATATTTT
1 CCAGAAAA-T----CATTTT
53683767 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
*
53683781 ACAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
53683795 ACTGGCAATC
Statistics
Matches: 49, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
14 21 0.43
15 15 0.31
16 1 0.02
18 1 0.02
19 3 0.06
20 8 0.16
ACGTcount: A:0.44, C:0.13, G:0.08, T:0.35
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:53683780 original size:34 final size:35
Alignment explanation
Indices: 53683722--53683788 Score: 127
Period size: 34 Copynumber: 1.9 Consensus size: 35
53683712 CAAACACCAG
53683722 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
53683757 AAAATATTTTCCAG-AAATCATTTTACAGAAAA
1 AAAATATTTTCCAGTAAATCATTTTACAGAAAA
53683789 TATTTTACTG
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 18 0.56
35 14 0.44
ACGTcount: A:0.48, C:0.12, G:0.07, T:0.33
Consensus pattern (35 bp):
AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:53683795 original size:14 final size:14
Alignment explanation
Indices: 53683757--53683796 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
53683747 ACAGAAAAGT
*
53683757 AAAATATTTTCCAG
1 AAAATATTTTACAG
53683771 -AAATCATTTTACAG
1 AAAAT-ATTTTACAG
53683785 AAAATATTTTAC
1 AAAATATTTTAC
53683797 TGGCAATCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
13 4 0.17
14 15 0.65
15 4 0.17
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (14 bp):
AAAATATTTTACAG
Found at i:53684617 original size:21 final size:21
Alignment explanation
Indices: 53684592--53684666 Score: 89
Period size: 21 Copynumber: 3.6 Consensus size: 21
53684582 TCAGGCACTA
53684592 TATGTGTCGTATTAGGTACTT
1 TATGTGTCGTATTAGGTACTT
**
53684613 TATGTGTCGTATTAGGTACCA
1 TATGTGTCGTATTAGGTACTT
** *
53684634 CGTGTGTCGT-TTCAGGCACTT
1 TATGTGTCGTATT-AGGTACTT
53684655 TATGTGTCGTAT
1 TATGTGTCGTAT
53684667 ACTGCTTCTG
Statistics
Matches: 43, Mismatches: 9, Indels: 3
0.78 0.16 0.05
Matches are distributed among these distances:
20 2 0.05
21 40 0.93
22 1 0.02
ACGTcount: A:0.17, C:0.15, G:0.25, T:0.43
Consensus pattern (21 bp):
TATGTGTCGTATTAGGTACTT
Found at i:53687471 original size:44 final size:45
Alignment explanation
Indices: 53687388--53687478 Score: 116
Period size: 44 Copynumber: 2.0 Consensus size: 45
53687378 ATAACATTAT
* *
53687388 TAATTTATATGTTTTTTTGTAAATTTTAATTTTATAATTTTT-TA
1 TAATTTATATGTTTTTTTCTAAATTATAATTTTATAATTTTTCTA
*
53687432 TAATTTATATG-TTTTTTCTATATTAT-ATATTTATGAATTTTTCTA
1 TAATTTATATGTTTTTTTCTAAATTATAAT-TTTAT-AATTTTTCTA
53687477 TA
1 TA
53687479 CTTATTTCCA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
42 2 0.05
43 17 0.41
44 18 0.44
45 4 0.10
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.64
Consensus pattern (45 bp):
TAATTTATATGTTTTTTTCTAAATTATAATTTTATAATTTTTCTA
Found at i:53688197 original size:16 final size:17
Alignment explanation
Indices: 53688176--53688208 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
53688166 TATCTTTTCG
53688176 AATTTT-TATAGGTTTA
1 AATTTTATATAGGTTTA
*
53688192 AATTTTATATAGTTTTA
1 AATTTTATATAGGTTTA
53688209 TACAATTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.58
Consensus pattern (17 bp):
AATTTTATATAGGTTTA
Found at i:53689495 original size:3 final size:3
Alignment explanation
Indices: 53689487--53689518 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
53689477 AAATTAGTTA
53689487 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
53689519 AACGATAGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:53689859 original size:31 final size:32
Alignment explanation
Indices: 53689821--53689883 Score: 119
Period size: 31 Copynumber: 2.0 Consensus size: 32
53689811 AGACAAATTA
53689821 CAAGAGTAATTGAATCCTAAT-AAAACTCTTT
1 CAAGAGTAATTGAATCCTAATAAAAACTCTTT
53689852 CAAGAGTAATTGAATCCTAATAAAAACTCTTT
1 CAAGAGTAATTGAATCCTAATAAAAACTCTTT
53689884 AAAATTATCT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 21 0.68
32 10 0.32
ACGTcount: A:0.43, C:0.16, G:0.10, T:0.32
Consensus pattern (32 bp):
CAAGAGTAATTGAATCCTAATAAAAACTCTTT
Found at i:53700335 original size:58 final size:59
Alignment explanation
Indices: 53700234--53700349 Score: 180
Period size: 58 Copynumber: 2.0 Consensus size: 59
53700224 GTTAAGTTCA
* * **
53700234 GGTACCAAATTGGACCAAAAAAATATTAAGTATCAACTTAAGAAAATGTGTCAAGTTTG
1 GGTACCAAATTAGACCAAAAAAAGATTAAGTATCAACTTAAGAAAAAATGTCAAGTTTG
*
53700293 GGTACCAAATTAGACC-AAAAAGGATTAAGTATCAACTTAAGAAAAAATGTCAAGTTT
1 GGTACCAAATTAGACCAAAAAAAGATTAAGTATCAACTTAAGAAAAAATGTCAAGTTT
53700350 AGAGGCCAAG
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
58 37 0.71
59 15 0.29
ACGTcount: A:0.46, C:0.12, G:0.16, T:0.26
Consensus pattern (59 bp):
GGTACCAAATTAGACCAAAAAAAGATTAAGTATCAACTTAAGAAAAAATGTCAAGTTTG
Found at i:53700371 original size:58 final size:55
Alignment explanation
Indices: 53700250--53700371 Score: 138
Period size: 58 Copynumber: 2.1 Consensus size: 55
53700240 AAATTGGACC
* **
53700250 AAAAAAATATTAAGTATCAACTTAAGAAAATGTGTCAAGTTTGGGTACCAAATTAG
1 AAAAAAAGATTAAGTATCAACTTAAGAAAAAATGTCAAGTTTGGG-ACCAAATTAG
* *
53700306 ACCAAAAAGGATTAAGTATCAACTTAAGAAAAAATGTCAAGTTTAGAGG-CCAAGTTAGG
1 A--AAAAAAGATTAAGTATCAACTTAAGAAAAAATGTCAAGTTT-G-GGACCAAATTA-G
53700365 AAAAAAA
1 AAAAAAA
53700372 ATTTAAATTT
Statistics
Matches: 55, Mismatches: 6, Indels: 9
0.79 0.09 0.13
Matches are distributed among these distances:
56 1 0.02
57 5 0.09
58 44 0.80
59 3 0.05
60 2 0.04
ACGTcount: A:0.49, C:0.10, G:0.17, T:0.24
Consensus pattern (55 bp):
AAAAAAAGATTAAGTATCAACTTAAGAAAAAATGTCAAGTTTGGGACCAAATTAG
Found at i:53705839 original size:20 final size:19
Alignment explanation
Indices: 53705808--53705848 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
53705798 AAATGAAAAA
53705808 TTAGAATTTTTATAAA-TAT
1 TTAGAATTTTTA-AAATTAT
53705827 TTAGAATTTTTTAAAATTAT
1 TTAGAA-TTTTTAAAATTAT
53705847 TT
1 TT
53705849 TTGTATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (19 bp):
TTAGAATTTTTAAAATTAT
Found at i:53705843 original size:19 final size:20
Alignment explanation
Indices: 53705808--53705848 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
53705798 AAATGAAAAA
53705808 TTAGAATTTTTATAAA-TAT
1 TTAGAATTTTTATAAATTAT
53705827 TTAGAATTTTT-TAAAATTAT
1 TTAGAATTTTTAT-AAATTAT
53705847 TT
1 TT
53705849 TTGTATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 1 0.05
19 14 0.70
20 5 0.25
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (20 bp):
TTAGAATTTTTATAAATTAT
Found at i:53713647 original size:18 final size:19
Alignment explanation
Indices: 53713624--53713672 Score: 68
Period size: 18 Copynumber: 2.7 Consensus size: 19
53713614 TTTCAATTAA
53713624 ATAAATTATTAAAAA-ATT
1 ATAAATTATTAAAAATATT
53713642 ATAAA-TATTAAAAATATT
1 ATAAATTATTAAAAATATT
*
53713660 AAAAATTA-TAAAA
1 ATAAATTATTAAAA
53713673 TTTAATTTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 9 0.32
18 17 0.61
19 2 0.07
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
ATAAATTATTAAAAATATT
Found at i:53713656 original size:9 final size:9
Alignment explanation
Indices: 53713630--53713665 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
53713620 TTAAATAAAT
53713630 TATTAAAAA
1 TATTAAAAA
*
53713639 -ATTATAAA
1 TATTAAAAA
53713647 TATTAAAAA
1 TATTAAAAA
53713656 TATTAAAAA
1 TATTAAAAA
53713665 T
1 T
53713666 TATAAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
8 7 0.29
9 17 0.71
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (9 bp):
TATTAAAAA
Found at i:53713677 original size:16 final size:15
Alignment explanation
Indices: 53713635--53713677 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
53713625 TAAATTATTA
*
53713635 AAAAATTATAAATATT
1 AAAAATT-TAAAAATT
53713651 AAAAATATTAAAAATT
1 AAAAAT-TTAAAAATT
53713667 ATAAAATTTAA
1 A-AAAATTTAA
53713678 TTTTCTATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 18 0.75
17 6 0.25
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
AAAAATTTAAAAATT
Found at i:53721980 original size:24 final size:23
Alignment explanation
Indices: 53721936--53721980 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
53721926 GTTTTATGGC
*
53721936 TTTTAGGGTTTAGGGTGCAGGCT
1 TTTTAGGGTTTAGGGTCCAGGCT
53721959 TTTTAGGAG-TTAGGGGTCCAGG
1 TTTTAGG-GTTTA-GGGTCCAGG
53721981 AAAATTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.16, C:0.09, G:0.40, T:0.36
Consensus pattern (23 bp):
TTTTAGGGTTTAGGGTCCAGGCT
Found at i:53722142 original size:125 final size:125
Alignment explanation
Indices: 53722012--53722277 Score: 324
Period size: 125 Copynumber: 2.1 Consensus size: 125
53722002 GTTTCTAGTT
** * * * * * *
53722012 AAATAGTGGGAAATCGCTT-CTACTAGGATGCTATTTAAGAATAAATTGTGAAATAGTGGCCTCA
1 AAATAGTGTAAAATCGCTTGATACCAGGATGCTATATAAGAAGAAATTGTGAAATAGCGCCCTCA
* *
53722076 TGGACGCGATTTCGCTACAG-TGGTCATGT-GAGAAATAAATTTTTTTTGACGTTTTCTGAGG
66 TGGACGCGATTTCGCTACAGTTGGTCATGTAG-GAAAT-AATTTTTTTTAACG-TTTCTGAGC
* * * * **
53722137 AAATAGTATAAAATCG-TTGATACCAGGCTGCTATATGAGAAGAAATTGTGAAATCGCGCCCTTG
1 AAATAGTGTAAAATCGCTTGATACCAGGATGCTATATAAGAAGAAATTGTGAAATAGCGCCCTCA
53722201 TGGACGCGATTTCGCTACAGTTGGTCATGTAGGAAATAATTTTTTTTAACGTTTCTGAGC
66 TGGACGCGATTTCGCTACAGTTGGTCATGTAGGAAATAATTTTTTTTAACGTTTCTGAGC
*
53722261 AAATAGTGTCAAATCGC
1 AAATAGTGTAAAATCGC
53722278 GCCCTCGTGG
Statistics
Matches: 119, Mismatches: 18, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
124 24 0.20
125 80 0.67
126 14 0.12
127 1 0.01
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.32
Consensus pattern (125 bp):
AAATAGTGTAAAATCGCTTGATACCAGGATGCTATATAAGAAGAAATTGTGAAATAGCGCCCTCA
TGGACGCGATTTCGCTACAGTTGGTCATGTAGGAAATAATTTTTTTTAACGTTTCTGAGC
Found at i:53722329 original size:84 final size:85
Alignment explanation
Indices: 53722187--53722390 Score: 365
Period size: 85 Copynumber: 2.4 Consensus size: 85
53722177 AGAAATTGTG
*
53722187 AAATCGCGCCCTTGTGGACGCGATTTCGCTACAGTTGGTCATGTAGGAAAT-AATTTTTTTTAAC
1 AAATCGCGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAGGAAATAAATTTTTTTTAAC
*
53722251 GTTTCTGAGCAAATAGTGTC
66 GGTTCTGAGCAAATAGTGTC
* *
53722271 AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTTGGTCATGTAGGAAATAAATTTTTTTTGAC
1 AAATCGCGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAGGAAATAAATTTTTTTTAAC
53722336 GGTTCTGAGCAAATAGTGTC
66 GGTTCTGAGCAAATAGTGTC
53722356 AAATCGCGCCCTCGTGGACGCGATTTCGCTACAGT
1 AAATCGCGCCCTCGTGGACGCGATTTCGCTACAGT
53722391 AGCAAGTTTG
Statistics
Matches: 114, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
84 49 0.43
85 65 0.57
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (85 bp):
AAATCGCGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAGGAAATAAATTTTTTTTAAC
GGTTCTGAGCAAATAGTGTC
Found at i:53725593 original size:28 final size:28
Alignment explanation
Indices: 53725562--53726003 Score: 300
Period size: 23 Copynumber: 16.8 Consensus size: 28
53725552 GGTTAAGGTT
53725562 TTTAATTAAATTAGGTTAGGGTTTTTAA
1 TTTAATTAAATTAGGTTAGGGTTTTTAA
*
53725590 --T--TT-AAGTAGGTTAGGGTTTTT-A
1 TTTAATTAAATTAGGTTAGGGTTTTTAA
*
53725612 ---G-TTAAATTAGGTTAGGGTTTTTAA
1 TTTAATTAAATTAGGTTAGGGTTTTTAA
**
53725636 TTTAATTAGGTTAGGTTAGGG---TT--
1 TTTAATTAAATTAGGTTAGGGTTTTTAA
53725659 TTTAATTAAATTAGGTTAGGG-TTTTAA
1 TTTAATTAAATTAGGTTAGGGTTTTTAA
* *
53725686 TTAAATTAGGTTAGGTTAGGGTTAGGGTTTTTAA
1 TTTAATTA----A-ATTA-GGTTAGGGTTTTTAA
*
53725720 TTTAAGTAAATTAGGTTAGGGTTTTTAA
1 TTTAATTAAATTAGGTTAGGGTTTTTAA
* *
53725748 TTT-AGT--A--GGGTTAGGGTTTTTAA
1 TTTAATTAAATTAGGTTAGGGTTTTTAA
53725771 TTTAATTAAATTAGGTTAGGGTTTTTAA
1 TTTAATTAAATTAGGTTAGGGTTTTTAA
*
53725799 TTTAAGT--A--A-GTTAGGGTTTTTAA
1 TTTAATTAAATTAGGTTAGGGTTTTTAA
* *
53725822 TTAAATTAGGTTAGGTTAGGGTTAGGGTTTTTAA
1 TTTAATTA----A-ATTA-GGTTAGGGTTTTTAA
53725856 TTTAATTAAATTAGGTTAGGGTTTTTAA
1 TTTAATTAAATTAGGTTAGGGTTTTTAA
*
53725884 --T--TT-AAGTAGGTTAGGGTTTTT-A
1 TTTAATTAAATTAGGTTAGGGTTTTTAA
*
53725906 ---A-TTAAATTAGGTTAGTGTTTTTAA
1 TTTAATTAAATTAGGTTAGGGTTTTTAA
* **
53725930 TTAAATTAGGTTAGGTTAGGG---TT--
1 TTTAATTAAATTAGGTTAGGGTTTTTAA
*
53725953 TTTAATTAAATTAGGTTAAGGTTTTTAA
1 TTTAATTAAATTAGGTTAGGGTTTTTAA
* **
53725981 TTAAATTAGGTTAGGTTAGGGTT
1 TTTAATTAAATTAGGTTAGGGTT
53726004 AGGGTTTTGT
Statistics
Matches: 333, Mismatches: 35, Indels: 92
0.72 0.08 0.20
Matches are distributed among these distances:
22 6 0.02
23 140 0.42
24 9 0.03
25 7 0.02
26 6 0.02
27 11 0.03
28 100 0.30
29 6 0.02
30 2 0.01
31 1 0.00
32 4 0.01
33 8 0.02
34 33 0.10
ACGTcount: A:0.29, C:0.00, G:0.24, T:0.48
Consensus pattern (28 bp):
TTTAATTAAATTAGGTTAGGGTTTTTAA
Found at i:53725627 original size:51 final size:51
Alignment explanation
Indices: 53725531--53726003 Score: 377
Period size: 51 Copynumber: 9.2 Consensus size: 51
53725521 TACAATTTAA
* *
53725531 TTAGGGTTTTTAA-TTAAATAGGGTTAAGGTTTTTAATT-AA--A--TTAGG
1 TTAGGGTTTTTAATTTAAGTA-GGTTAGGGTTTTTAATTAAATTAGGTTAGG
*
53725577 TTAGGGTTTTTAATTTAAGTAGGTTAGGGTTTTTAGTT-AA--A--TTAGG
1 TTAGGGTTTTTAATTTAAGTAGGTTAGGGTTTTTAATTAAATTAGGTTAGG
53725623 TTAGGGTTTTTAATTTAATTAGGTTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGG
1 TTAGGGTTTTTAATTT-A--A-G-TAGGTTAGGGTTTTTAATTAAATTAGGTTA-GG
**** * ** * * * **
53725680 TTTTAATTAAATTAGGTTAGGTTAGGGTTAGGGTTTTTAATTTAAGTAAATTAGG
1 TTAGGGTT--TTTAATTTAAG-TA-GGTTAGGGTTTTTAATTAAATTAGGTTAGG
* **
53725735 TTAGGGTTTTTAATTT-AGTAGGGTTAGGGTTTTTAATTTAATTAAATTAGG
1 TTAGGGTTTTTAATTTAAGTA-GGTTAGGGTTTTTAATTAAATTAGGTTAGG
*
53725786 TTAGGGTTTTTAATTTAAGTAAGTTAGGGTTTTTAATTAAATTAGGTTAGGTTAGGG
1 TTAGGGTTTTTAATTTAAGTAGGTTAGGGTTTTTAATT-AA--A--TTAGGTTA-GG
* *
53725843 TTAGGGTTTTTAATTTAATTAAATTAGGTTAGGGTTTTTAA-T---TTAAG-TAGG
1 TTAGGGTTTTTAA--T--TT-AAGTAGGTTAGGGTTTTTAATTAAATTAGGTTAGG
* * *
53725894 TTAGGGTTTTTAATTAAATTAGGTTAGTGTTTTTAATTAAATTAGGTTAGG
1 TTAGGGTTTTTAATTTAAGTAGGTTAGGGTTTTTAATTAAATTAGGTTAGG
* * *
53725945 TTAGGGTTTTTAATTAAATTAGGTTAAGGTTTTTAATTAAATTAGGTTAGG
1 TTAGGGTTTTTAATTTAAGTAGGTTAGGGTTTTTAATTAAATTAGGTTAGG
53725996 TTAGGGTT
1 TTAGGGTT
53726004 AGGGTTTTGT
Statistics
Matches: 358, Mismatches: 37, Indels: 59
0.79 0.08 0.13
Matches are distributed among these distances:
46 71 0.20
47 9 0.03
49 2 0.01
50 5 0.01
51 158 0.44
52 10 0.03
53 9 0.03
54 2 0.01
55 10 0.03
56 33 0.09
57 21 0.06
58 1 0.00
59 6 0.02
61 3 0.01
62 18 0.05
ACGTcount: A:0.29, C:0.00, G:0.24, T:0.47
Consensus pattern (51 bp):
TTAGGGTTTTTAATTTAAGTAGGTTAGGGTTTTTAATTAAATTAGGTTAGG
Found at i:53725734 original size:34 final size:33
Alignment explanation
Indices: 53725672--53725742 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 33
53725662 AATTAAATTA
* **
53725672 GGTTAGGGTTTTAATTAAATTAGGTTAGGTTAG
1 GGTTAGGGTTTTAATTAAAGTAAATTAGGTTAG
*
53725705 GGTTAGGGTTTTTAATTTAAGTAAATTAGGTTAG
1 GGTTAGGG-TTTTAATTAAAGTAAATTAGGTTAG
53725739 GGTT
1 GGTT
53725743 TTTAATTTAG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
33 8 0.24
34 25 0.76
ACGTcount: A:0.27, C:0.00, G:0.30, T:0.44
Consensus pattern (33 bp):
GGTTAGGGTTTTAATTAAAGTAAATTAGGTTAG
Found at i:53725851 original size:34 final size:34
Alignment explanation
Indices: 53725808--53725878 Score: 115
Period size: 34 Copynumber: 2.1 Consensus size: 34
53725798 ATTTAAGTAA
**
53725808 GTTAGGGTTTTTAATTAAATTAGGTTAGGTTAGG
1 GTTAGGGTTTTTAATTAAATTAAATTAGGTTAGG
*
53725842 GTTAGGGTTTTTAATTTAATTAAATTAGGTTAGG
1 GTTAGGGTTTTTAATTAAATTAAATTAGGTTAGG
53725876 GTT
1 GTT
53725879 TTTAATTTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.46
Consensus pattern (34 bp):
GTTAGGGTTTTTAATTAAATTAAATTAGGTTAGG
Found at i:53725870 original size:108 final size:106
Alignment explanation
Indices: 53725733--53725952 Score: 282
Period size: 108 Copynumber: 2.0 Consensus size: 106
53725723 AAGTAAATTA
** * *
53725733 GGTTAGGGTTTTTAATTTAGTAGGGTTAGGGTT-TTTAATTTAATTAAATTAGGTTAGGGTTTTT
1 GGTTAGGGTTTTTAATTTAGTAGAATTA-GGTTGGTT--TTTAATTAAAGTAGGTTAGGGTTTTT
*
53725797 AATTTAAGTAAGTTAGGGTTTTTAATTAAATTAGGTTAGGTTAG
63 AATTAAAGTAAGTTAGGGTTTTTAATTAAATTAGGTTAGGTTAG
* *
53725841 GGTTAGGGTTTTTAATTTAATTA-AATTAGGTTAGGGTTTTTAATTTAAGTAGGTTAGGGTTTTT
1 GGTTAGGGTTTTTAATTT-AGTAGAATTAGGTT--GGTTTTTAATTAAAGTAGGTTAGGGTTTTT
* * *
53725905 AATTAAATTAGGTTAGTGTTTTTAATTAAATTAGGTTAGGTTAG
63 AATTAAAGTAAGTTAGGGTTTTTAATTAAATTAGGTTAGGTTAG
53725949 GGTT
1 GGTT
53725953 TTTAATTAAA
Statistics
Matches: 98, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
107 4 0.04
108 89 0.91
109 3 0.03
110 2 0.02
ACGTcount: A:0.28, C:0.00, G:0.25, T:0.48
Consensus pattern (106 bp):
GGTTAGGGTTTTTAATTTAGTAGAATTAGGTTGGTTTTTAATTAAAGTAGGTTAGGGTTTTTAAT
TAAAGTAAGTTAGGGTTTTTAATTAAATTAGGTTAGGTTAG
Found at i:53727131 original size:20 final size:20
Alignment explanation
Indices: 53727106--53727152 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
53727096 AATAAGAAAG
53727106 ATATAAATAATA-TCAATAT-A
1 ATATAAAT-ATAGT-AATATCA
53727126 ATATAAATATAGTAATATCA
1 ATATAAATATAGTAATATCA
53727146 ATATAAA
1 ATATAAA
53727153 AACAAATATC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 8 0.32
20 17 0.68
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (20 bp):
ATATAAATATAGTAATATCA
Found at i:53728928 original size:44 final size:44
Alignment explanation
Indices: 53728878--53729207 Score: 181
Period size: 44 Copynumber: 7.5 Consensus size: 44
53728868 ATCTACTCTG
* * *
53728878 CTGTAACCTCAGAGAAATAAGATCCTTTATTTTAATCTGCTCCA
1 CTGTAACCTCAGGGAGATAAGATCCTTTATTTCAATCTGCTCCA
* * ** * * * *
53728922 CTGTAACTTCAGGGAGATAGGATAGTGT-CTTCGATCTGCTCCG
1 CTGTAACCTCAGGGAGATAAGATCCTTTATTTCAATCTGCTCCA
* * ***
53728965 CTGTAATCTCAGGGAGATAAG-TTCTCTGGCTTCAATCTGCTCCA
1 CTGTAACCTCAGGGAGATAAGATCCT-TTATTTCAATCTGCTCCA
** ** *
53729009 CTGTAACCTCAGGGAGATAAGAT-CTGAAATTCTCCGGTCTACTCCA
1 CTGTAACCTCAGGGAGATAAGATCCT-TTATT-T-CAATCTGCTCCA
* * * * * * **
53729055 CTGTAACTTCAGGGAAATAAGA-CC-TGA-TGCGATCTACTCTG
1 CTGTAACCTCAGGGAGATAAGATCCTTTATTTCAATCTGCTCCA
* * * *
53729096 CTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCA
1 CTGTAACCTCAGGGAGATAAGATCCTTTATTTCAATCTGCTCCA
* * * * * *
53729140 CTGTAATCTCAGGGAGATAGGAT--TACTAGCTTCAATCTACTCCG
1 CTGTAACCTCAGGGAGATAAGATCCT-TTA-TTTCAATCTGCTCCA
* *
53729184 TTGTAATCTCAGGGAGATAAGATC
1 CTGTAACCTCAGGGAGATAAGATC
53729208 TGAAATTCTT
Statistics
Matches: 215, Mismatches: 59, Indels: 23
0.72 0.20 0.08
Matches are distributed among these distances:
41 29 0.13
42 5 0.02
43 34 0.16
44 115 0.53
45 2 0.01
46 30 0.14
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (44 bp):
CTGTAACCTCAGGGAGATAAGATCCTTTATTTCAATCTGCTCCA
Found at i:53728985 original size:87 final size:87
Alignment explanation
Indices: 53728866--53729027 Score: 209
Period size: 87 Copynumber: 1.9 Consensus size: 87
53728856 AGGCCTGATG
* * * * *
53728866 CGATCTACTCTGCTGTAACCTCAGAGAAATAAGATCCT-TTATTTTAATCTGCTCCACTGTAACT
1 CGATCTACTCCGCTGTAACCTCAGAGAAATAAG-TCCTCTGACTTCAATCTGCTCCACTGTAACC
53728930 TCAGGGAGATAGGATAGTGTCTT
65 TCAGGGAGATAGGATAGTGTCTT
* * * * * *
53728953 CGATCTGCTCCGCTGTAATCTCAGGGAGATAAGTTCTCTGGCTTCAATCTGCTCCACTGTAACCT
1 CGATCTACTCCGCTGTAACCTCAGAGAAATAAGTCCTCTGACTTCAATCTGCTCCACTGTAACCT
53729018 CAGGGAGATA
66 CAGGGAGATA
53729028 AGATCTGAAA
Statistics
Matches: 63, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
86 3 0.05
87 60 0.95
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.31
Consensus pattern (87 bp):
CGATCTACTCCGCTGTAACCTCAGAGAAATAAGTCCTCTGACTTCAATCTGCTCCACTGTAACCT
CAGGGAGATAGGATAGTGTCTT
Found at i:53729088 original size:131 final size:133
Alignment explanation
Indices: 53728917--53729158 Score: 294
Period size: 131 Copynumber: 1.8 Consensus size: 133
53728907 TTTTAATCTG
* * * * * * *
53728917 CTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTCGATCTGCTCCGCTGTAA-TCTCAGGGAG
1 CTCCACTGTAACTTCAGGGAAATAAGATACTGTATGCGATCTACTCCGCTGTAACT-TCAGAGAG
* * *
53728981 ATAAG-TTCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTCCG
65 ATAAGATCCT-TGACTTCAATCCGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTCCG
53729045 GTCTA
129 GTCTA
* *
53729050 CTCCACTGTAACTTCAGGGAAATAAGA-CCTG-ATGCGATCTACTCTGCTGTAACTTCAGAGAGA
1 CTCCACTGTAACTTCAGGGAAATAAGATACTGTATGCGATCTACTCCGCTGTAACTTCAGAGAGA
* * * *
53729113 TAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATA
66 TAAGATCCTTGACTTCAATCCGCTCCACTGTAACCTCAGGGAGATA
53729159 GGATTACTAG
Statistics
Matches: 91, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
131 60 0.66
132 6 0.07
133 25 0.27
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (133 bp):
CTCCACTGTAACTTCAGGGAAATAAGATACTGTATGCGATCTACTCCGCTGTAACTTCAGAGAGA
TAAGATCCTTGACTTCAATCCGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTCCGGT
CTA
Found at i:53742412 original size:20 final size:20
Alignment explanation
Indices: 53742387--53742433 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
53742377 AATAAGAAAG
53742387 ATATAAATAATA-TCAATAT-A
1 ATATAAAT-ATAGT-AATATCA
53742407 ATATAAATATAGTAATATCA
1 ATATAAATATAGTAATATCA
53742427 ATATAAA
1 ATATAAA
53742434 AACAAATATC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 8 0.32
20 17 0.68
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (20 bp):
ATATAAATATAGTAATATCA
Found at i:53743911 original size:28 final size:28
Alignment explanation
Indices: 53743879--53744417 Score: 369
Period size: 28 Copynumber: 18.9 Consensus size: 28
53743869 GGCTTGTACA
53743879 GGTTTTTAATTTAATTAAATTAGGTTAG
1 GGTTTTTAATTTAATTAAATTAGGTTAG
*
53743907 GGTTTTTAA--T--TT-AAGTAGGTTAG
1 GGTTTTTAATTTAATTAAATTAGGTTAG
* * *
53743930 GATTTTTAATTAAATTAGGTTAGGTTAGGGTTAG
1 GGTTTTTAATTTAATTA----A-ATTA-GGTTAG
53743964 GGTTTTTAATTTAATTAAATTAGGTTAG
1 GGTTTTTAATTTAATTAAATTAGGTTAG
*
53743992 GGTTTTTAA--T--TT-AAGTAGGTTAG
1 GGTTTTTAATTTAATTAAATTAGGTTAG
* *
53744015 GGTTTTTAATTAAATTAGGTTAGGTTAGGGTTAG
1 GGTTTTTAATTTAATTA----A-ATTA-GGTTAG
53744049 GGTTTTTAATTTAATTAAATTAGGTTAG
1 GGTTTTTAATTTAATTAAATTAGGTTAG
** * * ** *
53744077 GGTAGGGTTAGGGTTTTTAATTTAATTA-AATAA
1 GGT--TTTTA----ATTTAATTAAATTAGGTTAG
53744110 GGTTAGGGTTTTTAATTTAATTAAATTAGGTTAG
1 GGTT----TTT--AATTTAATTAAATTAGGTTAG
53744144 GG---TT--TTTAATTAAATTAGGTTAG
1 GGTTTTTAATTTAATTAAATTAGGTTAG
* **
53744167 GGTTTTTAATTAAATTAGGTTAGGTTAG
1 GGTTTTTAATTTAATTAAATTAGGTTAG
* **
53744195 GGTTTTTAATTTAAGTAGGTTAGGTTAG
1 GGTTTTTAATTTAATTAAATTAGGTTAG
**
53744223 GGTTTTTAATTTAATTAAAAAAAGGTTAG
1 GGTTTTTAATTTAATT-AAATTAGGTTAG
** *
53744252 GGTTTTTAATTTAATTAGGTTAGGTTAC
1 GGTTTTTAATTTAATTAAATTAGGTTAG
* **
53744280 GGTTTTTAATTTAAGTAGGTTAGGTTAG
1 GGTTTTTAATTTAATTAAATTAGGTTAG
* **
53744308 GGTTTTTAATTAAATTAGGTTAGGTTAG
1 GGTTTTTAATTTAATTAAATTAGGTTAG
53744336 GGTTTTTAATTTAATTAAATTAGGTTAG
1 GGTTTTTAATTTAATTAAATTAGGTTAG
* * *
53744364 GGTTAGGGTT--TTTAATT-AAGTAGGGTTTAA
1 GGTT---TTTAATTTAATTAAATTA-GG-TTAG
53744394 GGTTTTTAATTTAATTAAATTAGG
1 GGTTTTTAATTTAATTAAATTAGG
53744418 GTTTTTAATT
Statistics
Matches: 407, Mismatches: 55, Indels: 97
0.73 0.10 0.17
Matches are distributed among these distances:
23 58 0.14
24 4 0.01
26 4 0.01
27 8 0.02
28 182 0.45
29 48 0.12
30 16 0.04
31 2 0.00
32 2 0.00
33 21 0.05
34 59 0.14
35 2 0.00
37 1 0.00
ACGTcount: A:0.30, C:0.00, G:0.23, T:0.47
Consensus pattern (28 bp):
GGTTTTTAATTTAATTAAATTAGGTTAG
Found at i:53743915 original size:23 final size:23
Alignment explanation
Indices: 53743888--53744038 Score: 120
Period size: 23 Copynumber: 6.9 Consensus size: 23
53743878 AGGTTTTTAA
53743888 TTTAATTAAATTAGGTTAGGGTT
1 TTTAATTAAATTAGGTTAGGGTT
* * *
53743911 TTTAATTTAAGTAGGTTAGGATT
1 TTTAATTAAATTAGGTTAGGGTT
53743934 TTTAATTAAATTAGGTTA-GG--
1 TTTAATTAAATTAGGTTAGGGTT
*** *****
53743954 -TT-A--GGGTTAGGGTT-TTTAA
1 TTTAATTAAATTA-GGTTAGGGTT
53743973 TTTAATTAAATTAGGTTAGGGTT
1 TTTAATTAAATTAGGTTAGGGTT
* *
53743996 TTTAATTTAAGTAGGTTAGGGTT
1 TTTAATTAAATTAGGTTAGGGTT
53744019 TTTAATTAAATTAGGTTAGG
1 TTTAATTAAATTAGGTTAGG
53744039 TTAGGGTTAG
Statistics
Matches: 96, Mismatches: 23, Indels: 18
0.70 0.17 0.13
Matches are distributed among these distances:
16 3 0.03
17 4 0.04
18 1 0.01
19 2 0.02
20 2 0.02
21 1 0.01
22 5 0.05
23 78 0.81
ACGTcount: A:0.30, C:0.00, G:0.23, T:0.47
Consensus pattern (23 bp):
TTTAATTAAATTAGGTTAGGGTT
Found at i:53743972 original size:85 final size:82
Alignment explanation
Indices: 53743879--53744429 Score: 526
Period size: 85 Copynumber: 6.8 Consensus size: 82
53743869 GGCTTGTACA
*
53743879 GGTTTTTAATTTAATTAAATTAGGTTAGGGTTTTTAATTTAAGTAGGTTAGGATTTTTAATTAAA
1 GGTTTTTAATTTAATTAAATTAGGTTAGGGTTTTTAATTTAAGTAGGTTAGGGTTTTTAATT-AA
*
53743944 TTAGGTTAGGTTAGGGTTAG
65 TTA-ATTAGGTTA-GGTTAG
53743964 GGTTTTTAATTTAATTAAATTAGGTTAGGGTTTTTAATTTAAGTAGGTTAGGGTTTTTAATTAAA
1 GGTTTTTAATTTAATTAAATTAGGTTAGGGTTTTTAATTTAAGTAGGTTAGGGTTTTTAATT-AA
*
53744029 TTAGGTTAGGTTAGGGTTAG
65 TTA-ATTAGGTTA-GGTTAG
53744049 GGTTTTTAATTTAATTAAATTAGGTTAGGG---------T-AG--GGTTAGGGTTTTTAATTTAA
1 GGTTTTTAATTTAATTAAATTAGGTTAGGGTTTTTAATTTAAGTAGGTTAGGGTTTTTAA-TTAA
*
53744102 TTAA--A--TAAGGTTAG
65 TTAATTAGGTTAGGTTAG
* *
53744116 GGTTTTTAATTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATT-A-
1 GGTTTTTAATTTAATTAAATTAGGTTAGGGTTTTTAATTTAAGTAGGTTAGGGTTTTTAATTAAT
53744179 -AATTAGGTTAGGTTAG
66 TAATTAGGTTAGGTTAG
* ** *
53744195 GGTTTTTAATTTAAGTAGGTTAGGTTAGGGTTTTTAATTTAATTAAAAAAAGGTTAGGGTTTTTA
1 GGTTTTTAATTTAATTAAATTAGGTTAGGGTTTTTAATTTAAGT------AGGTTAGGGTTTTTA
*
53744260 A-T--TTAATTAGGTTAGGTTAC
60 ATTAATTAATTAGGTTAGGTTAG
* ** *
53744280 GGTTTTTAATTTAAGTAGGTTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGTTAGGGTTTTTAA
1 GGTTTTTAATTTAATTAAATTAGGTTAGGGTTTTTAA-T---TTAAG-TAGGTTAGGGTTTTTAA
53744345 TTTAATTAAATTAGGTTAGGGTTAG
61 -TTAATT-AATTAGGTTA-GGTTAG
* * * * **
53744370 GGTTTTTAA-TTAAGT--A--GGGTTTAAGGTTTTTAATTTAATTAAATTAGGGTTTTTAATTAA
1 GGTTTTTAATTTAATTAAATTAGG-TTAGGGTTTTTAATTTAAGTAGGTTAGGGTTTTTAATTAA
53744430 GTAGGGTTAG
Statistics
Matches: 408, Mismatches: 21, Indels: 79
0.80 0.04 0.16
Matches are distributed among these distances:
67 36 0.09
68 2 0.00
70 1 0.00
73 20 0.05
74 2 0.00
75 4 0.01
76 1 0.00
77 3 0.01
78 2 0.00
79 63 0.15
80 4 0.01
81 15 0.04
82 3 0.01
84 17 0.04
85 185 0.45
86 14 0.03
88 2 0.00
89 19 0.05
90 15 0.04
ACGTcount: A:0.30, C:0.00, G:0.23, T:0.47
Consensus pattern (82 bp):
GGTTTTTAATTTAATTAAATTAGGTTAGGGTTTTTAATTTAAGTAGGTTAGGGTTTTTAATTAAT
TAATTAGGTTAGGTTAG
Found at i:53743982 original size:39 final size:39
Alignment explanation
Indices: 53743934--53744116 Score: 210
Period size: 39 Copynumber: 4.5 Consensus size: 39
53743924 GGTTAGGATT
53743934 TTTAATTAAATTAGGTTAGGTTAGGGTTAGGGTTTTTAA
1 TTTAATTAAATTAGGTTAGGTTAGGGTTAGGGTTTTTAA
** *
53743973 TTTAATTAAATTAGGTTAGGGTTTTTA-ATTTAAGTAGGTTAGGGTT--
1 TTTAATTAAATTAGGTTA-GG---TTAGGGTT-AG--GGTT---TTTAA
53744019 TTTAATTAAATTAGGTTAGGTTAGGGTTAGGGTTTTTAA
1 TTTAATTAAATTAGGTTAGGTTAGGGTTAGGGTTTTTAA
*
53744058 TTTAATTAAATTAGGTTAGGGTAGGGTTAGGGTTTTTAA
1 TTTAATTAAATTAGGTTAGGTTAGGGTTAGGGTTTTTAA
*
53744097 TTTAATTAAATAAGGTTAGG
1 TTTAATTAAATTAGGTTAGG
53744117 GTTTTTAATT
Statistics
Matches: 123, Mismatches: 8, Indels: 26
0.78 0.05 0.17
Matches are distributed among these distances:
37 2 0.02
39 75 0.61
40 6 0.05
42 7 0.06
43 7 0.06
45 6 0.05
46 18 0.15
48 2 0.02
ACGTcount: A:0.30, C:0.00, G:0.25, T:0.45
Consensus pattern (39 bp):
TTTAATTAAATTAGGTTAGGTTAGGGTTAGGGTTTTTAA
Found at i:53744091 original size:124 final size:127
Alignment explanation
Indices: 53743934--53744167 Score: 402
Period size: 124 Copynumber: 1.9 Consensus size: 127
53743924 GGTTAGGATT
* *
53743934 TTTAATTAAATTAGGTTAGGTTAGGGTTAGGGTTTTTAATTTAATTAAATTAGGTTAGGGTTTTT
1 TTTAATTAAATTAGGTTAGGGTAGGGTTAGGGTTTTTAATTTAATTAAATAAGGTTAGGGTTTTT
53743999 AA-T-TT-AAGTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGTTAGGGTTAGGGTTTTTAA
66 AATTATTAAAGTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGTTAGGGTTAGGGTTTTTAA
53744058 TTTAATTAAATTAGGTTAGGGTAGGGTTAGGGTTTTTAATTTAATTAAATAAGGTTAGGGTTTTT
1 TTTAATTAAATTAGGTTAGGGTAGGGTTAGGGTTTTTAATTTAATTAAATAAGGTTAGGGTTTTT
*
53744123 AATTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGG
66 AA-TT-ATTAAAGTAGGTTAGGGTTTTTAATTAAATTAGGTTAGG
53744168 GTTTTTAATT
Statistics
Matches: 102, Mismatches: 3, Indels: 5
0.93 0.03 0.05
Matches are distributed among these distances:
124 65 0.64
126 1 0.01
128 2 0.02
129 34 0.33
ACGTcount: A:0.30, C:0.00, G:0.24, T:0.46
Consensus pattern (127 bp):
TTTAATTAAATTAGGTTAGGGTAGGGTTAGGGTTTTTAATTTAATTAAATAAGGTTAGGGTTTTT
AATTATTAAAGTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGTTAGGGTTAGGGTTTTTAA
Found at i:53744123 original size:23 final size:23
Alignment explanation
Indices: 53744097--53744456 Score: 119
Period size: 28 Copynumber: 13.6 Consensus size: 23
53744087 GGGTTTTTAA
53744097 TTTAATTAAATAAGGTTAGGGTTTTT
1 TTTAATTAAATAAGGTTAGGG---TT
*
53744123 AATTTAATTAAATTAGGTTAGGGTT
1 --TTTAATTAAATAAGGTTAGGGTT
*
53744148 TTTAATTAAATTAGGTTAGGGTT
1 TTTAATTAAATAAGGTTAGGGTT
53744171 TTTAATTAAATTAGGTTAGGTTAGGGTT
1 TTTAATTAAA-TA----AGGTTAGGGTT
*
53744199 TTTAATTTAAGTAGGTTAGGTTAGGGTTTTT
1 TTTAA-TTAA--A--TAAGGTTAGGG---TT
*
53744230 AATTTAATTAAAAAAAGGTTAGGGTT
1 --TTTAATT-AAATAAGGTTAGGGTT
* *
53744256 TTTAATTTAATTAGGTTAGGTTACGGTT
1 TTTAA-TTAA--A--TAAGGTTAGGGTT
*
53744284 TTTAATTTAAGTAGGTTAGGTTAGGGTT
1 TTTAA-TTAA--A--TAAGGTTAGGGTT
53744312 TTTAATTAAATTAGGTTAGGTTAGGGTTTTT
1 TTTAATTAAA-TA----AGGTTAGGG--T-T
*
53744343 AATTTAATTAAATTAGGTTAGGGTTAGGGTT
1 --TTTAATTAAATAAGGTTA-GG-----GTT
* * *
53744374 TTTAATTAAGTAGGGTTTAAGGTT
1 TTTAATTAAATAAGG-TTAGGGTT
* *
53744398 TTTAATTTAATTAA-ATTAGGGTT
1 TTTAA-TTAAATAAGGTTAGGGTT
* * *
53744421 TTTAATTAAGTAGGGTTAGGGAT
1 TTTAATTAAATAAGGTTAGGGTT
*
53744444 TTTAATCAAATAA
1 TTTAATTAAATAA
53744457 TGTCAAAATA
Statistics
Matches: 265, Mismatches: 29, Indels: 81
0.71 0.08 0.22
Matches are distributed among these distances:
22 6 0.02
23 62 0.23
24 17 0.06
25 11 0.04
26 3 0.01
27 4 0.02
28 101 0.38
29 28 0.11
30 4 0.02
31 6 0.02
32 5 0.02
33 17 0.06
34 1 0.00
ACGTcount: A:0.31, C:0.01, G:0.22, T:0.46
Consensus pattern (23 bp):
TTTAATTAAATAAGGTTAGGGTT
Found at i:53744161 original size:18 final size:21
Alignment explanation
Indices: 53744125--53744190 Score: 78
Period size: 23 Copynumber: 2.9 Consensus size: 21
53744115 GGGTTTTTAA
53744125 TTTAATTAAATTAGGTTAGGGTT
1 TTTAATTAAA-TA-GTTAGGGTT
53744148 TTTAATTAAATTAGGTTAGGGTT
1 TTTAATTAAA-TA-GTTAGGGTT
53744171 TTTAATTAAATTAGGTTAGG
1 TTTAATTAAA-TA-GTTAGG
53744191 TTAGGGTTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.32, C:0.00, G:0.21, T:0.47
Consensus pattern (21 bp):
TTTAATTAAATAGTTAGGGTT
Found at i:53744381 original size:24 final size:23
Alignment explanation
Indices: 53744361--53744449 Score: 108
Period size: 23 Copynumber: 3.8 Consensus size: 23
53744351 TAAATTAGGT
53744361 TAGGGTTAGGGTTTTTAATTAAG
1 TAGGGTTAGGGTTTTTAATTAAG
* *
53744384 TAGGGTTTAAGGTTTTTAATTTAAT
1 TAGGG-TTAGGGTTTTTAA-TTAAG
**
53744409 TA-AATTAGGGTTTTTAATTAAG
1 TAGGGTTAGGGTTTTTAATTAAG
*
53744431 TAGGGTTAGGGATTTTAAT
1 TAGGGTTAGGGTTTTTAAT
53744450 CAAATAATGT
Statistics
Matches: 54, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
22 6 0.11
23 30 0.56
24 12 0.22
25 6 0.11
ACGTcount: A:0.29, C:0.00, G:0.25, T:0.46
Consensus pattern (23 bp):
TAGGGTTAGGGTTTTTAATTAAG
Done.