Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 103066607
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: 103066607
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 238 characters in sequence are not A, C, G, or T
File 154 of 345
Found at i:42287385 original size:42 final size:43
Alignment explanation
Indices: 42287302--42287439 Score: 138
Period size: 42 Copynumber: 3.2 Consensus size: 43
42287292 TCCCGGATGT
* * ** *
42287302 GGTCTTACATGTAATTCAG-TACTGATGCCTCTGTCTTAGACAG
1 GGTCTTACATGTAAATCAGATAC-GATGCCTATGTCCCAGACAC
*
42287345 GGTCTTACATG-AAATCAGATACGATGCCTATGTCCCAGACAT
1 GGTCTTACATGTAAATCAGATACGATGCCTATGTCCCAGACAC
* * * *
42287387 GGTCTTACACGTAAATCTCAAAT-CGAGGCCTGTGTCCCAGACAC
1 GGTCTTACATGTAAA--TCAGATACGATGCCTATGTCCCAGACAC
42287431 GGTCTTACA
1 GGTCTTACA
42287440 CGATATCTCA
Statistics
Matches: 81, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
42 32 0.40
43 17 0.21
44 27 0.33
45 5 0.06
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (43 bp):
GGTCTTACATGTAAATCAGATACGATGCCTATGTCCCAGACAC
Found at i:42290216 original size:33 final size:34
Alignment explanation
Indices: 42290154--42290218 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
42290144 TGCATTTTGT
* *
42290154 ACTGATACTGTTACTGAATTGGGCTAAGGCCCGC
1 ACTGATACTGTTACTGAAATGGGCGAAGGCCCGC
42290188 ACTGATACTGTTACT-AAATGGGCGAAGGCCC
1 ACTGATACTGTTACTGAAATGGGCGAAGGCCC
42290219 TAACTGAGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 14 0.48
34 15 0.52
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (34 bp):
ACTGATACTGTTACTGAAATGGGCGAAGGCCCGC
Found at i:42290225 original size:33 final size:34
Alignment explanation
Indices: 42290154--42290225 Score: 101
Period size: 33 Copynumber: 2.1 Consensus size: 34
42290144 TGCATTTTGT
* * *
42290154 ACTGATACTGTTACTGAATTGGGCTAAGGCCCGC
1 ACTGATACTGTTACTGAAATGGGCGAAGGCCCGA
*
42290188 ACTGATACTGTTACT-AAATGGGCGAAGGCCCTA
1 ACTGATACTGTTACTGAAATGGGCGAAGGCCCGA
42290221 ACTGA
1 ACTGA
42290226 GATTGGACTG
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
33 19 0.56
34 15 0.44
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.25
Consensus pattern (34 bp):
ACTGATACTGTTACTGAAATGGGCGAAGGCCCGA
Found at i:42298041 original size:33 final size:34
Alignment explanation
Indices: 42297980--42298044 Score: 105
Period size: 33 Copynumber: 1.9 Consensus size: 34
42297970 TGCATTTTGT
* *
42297980 ACTGATACTGTTACTGAATTGGGCTAAGGCCCGC
1 ACTGATACTGTCACTGAAATGGGCTAAGGCCCGC
42298014 ACTGATACTGTCACT-AAATGGGCTAAGGCCC
1 ACTGATACTGTCACTGAAATGGGCTAAGGCCC
42298045 TAACTGAGAC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 15 0.52
34 14 0.48
ACGTcount: A:0.26, C:0.25, G:0.25, T:0.25
Consensus pattern (34 bp):
ACTGATACTGTCACTGAAATGGGCTAAGGCCCGC
Found at i:42299376 original size:7 final size:7
Alignment explanation
Indices: 42299364--42299389 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
42299354 AATACCCCTA
42299364 CTCATCC
1 CTCATCC
42299371 CTCATCC
1 CTCATCC
42299378 CTCATCC
1 CTCATCC
42299385 CTCAT
1 CTCAT
42299390 TCATTCATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.54, G:0.00, T:0.31
Consensus pattern (7 bp):
CTCATCC
Found at i:42311034 original size:40 final size:39
Alignment explanation
Indices: 42310989--42311118 Score: 136
Period size: 40 Copynumber: 3.3 Consensus size: 39
42310979 TCGGAAATAA
42310989 CCGGATATAACCATGTGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAT-TGCACAAATGCCTTCGGGTCTTAGC
* * * *
42311029 CCGGATAGAATGTC-TCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAA--CCATTGCACAAATGCCTTCGGGTCTTAGC
* * * * *
42311069 CCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCA-TTGCACAAATGCCTTCGGGTCTTAGC
42311109 CCGGATATAA
1 CCGGATATAA
42311119 TTTCCAGCAT
Statistics
Matches: 72, Mismatches: 14, Indels: 8
0.77 0.15 0.09
Matches are distributed among these distances:
38 1 0.01
40 69 0.96
41 1 0.01
42 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.25
Consensus pattern (39 bp):
CCGGATATAACCATTGCACAAATGCCTTCGGGTCTTAGC
Found at i:42311133 original size:40 final size:40
Alignment explanation
Indices: 42311005--42311156 Score: 148
Period size: 40 Copynumber: 3.8 Consensus size: 40
42310995 ATAACCATGT
* * *
42311005 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGTCTC-
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCTC-CA
* ** * *
42311045 GCACGAA-TGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATTGCCTTCGGGTCTTAGCCCGGATATAATCTCCA
* *
42311085 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTCCA
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCTCCA
* *
42311125 GCATAATTGTCTTCGGGAT-TTAGCCCGGATAT
1 GCACAATTGCCTTCGGG-TCTTAGCCCGGATAT
42311157 CATTCAATTT
Statistics
Matches: 91, Mismatches: 17, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
39 2 0.02
40 86 0.95
41 3 0.03
ACGTcount: A:0.22, C:0.26, G:0.24, T:0.28
Consensus pattern (40 bp):
GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCTCCA
Found at i:42311139 original size:80 final size:80
Alignment explanation
Indices: 42311005--42311154 Score: 198
Period size: 80 Copynumber: 1.9 Consensus size: 80
42310995 ATAACCATGT
*
42311005 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGTCTCGCACGAATGCCTTCGGG-TCTTAGC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTCGCACGAATGCCTTCGGGAT-TTAGC
42311069 CCGGATGTAGCCACTA
65 CCGGATGTAGCCACTA
* * * * *
42311085 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAATTGTCTTCGGGATTTAG
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTC-GCACGAA-TGCCTTCGGGATTTAG
42311148 CCCGGAT
64 CCCGGAT
42311155 ATCATTCAAT
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
79 3 0.05
80 57 0.93
81 1 0.02
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.27
Consensus pattern (80 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTCGCACGAATGCCTTCGGGATTTAGCC
CGGATGTAGCCACTA
Found at i:42319030 original size:40 final size:39
Alignment explanation
Indices: 42318985--42319111 Score: 130
Period size: 40 Copynumber: 3.2 Consensus size: 39
42318975 CGGAACATAA
42318985 CCGGATATAACCATGTGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAT-TGCACAAATGCCTTCGGGTCTTAGC
* * * *
42319025 CCGGATAGAATGTC-TCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAA--CCATTGCACAAATGCCTTCGGGTCTTAGC
* * * * *
42319065 CCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCA-TTGCACAAATGCCTTCGGGTCTTAGC
42319105 CCGGATA
1 CCGGATA
42319112 AATTTCCAGC
Statistics
Matches: 70, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
38 1 0.01
40 67 0.96
41 1 0.01
42 1 0.01
ACGTcount: A:0.23, C:0.28, G:0.24, T:0.24
Consensus pattern (39 bp):
CCGGATATAACCATTGCACAAATGCCTTCGGGTCTTAGC
Found at i:42327236 original size:28 final size:28
Alignment explanation
Indices: 42327196--42327287 Score: 168
Period size: 28 Copynumber: 3.3 Consensus size: 28
42327186 ATGTACTAGA
42327196 ATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATTACCATT
42327224 ATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATTACCATT
*
42327252 ATACCCCTATGTATGCAAAATGACC-TT
1 ATACCCCTATGTATGCAAAATTACCATT
42327279 ATACCCCTA
1 ATACCCCTA
42327288 GGGTTAATTT
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
27 11 0.17
28 52 0.83
ACGTcount: A:0.35, C:0.27, G:0.08, T:0.30
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATTACCATT
Found at i:42327451 original size:27 final size:28
Alignment explanation
Indices: 42327393--42327482 Score: 112
Period size: 27 Copynumber: 3.2 Consensus size: 28
42327383 AGGAAGCGTC
*
42327393 CTGGTGGCTA-TGCCACAAATTATCTGTT
1 CTGGTGGC-ACTGCCACAAAATATCTGTT
* **
42327421 CTGGTGGCCCTGCCAC-GTATATCTGTT
1 CTGGTGGCACTGCCACAAAATATCTGTT
42327448 CTGGTGGCACTGCCACAAAATATCTGTAT
1 CTGGTGGCACTGCCACAAAATATCTGT-T
42327477 CTGGTG
1 CTGGTG
42327483 ACTCTGTCAC
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
27 23 0.44
28 22 0.42
29 7 0.13
ACGTcount: A:0.19, C:0.24, G:0.24, T:0.32
Consensus pattern (28 bp):
CTGGTGGCACTGCCACAAAATATCTGTT
Found at i:42327493 original size:29 final size:28
Alignment explanation
Indices: 42327403--42327493 Score: 94
Period size: 27 Copynumber: 3.2 Consensus size: 28
42327393 CTGGTGGCTA
* * *
42327403 TGCCACAAATTATCTGTTCTGGTGGCCC
1 TGCCACAAAATATCTGTTCTGGTGACAC
** *
42327431 TGCCAC-GTATATCTGTTCTGGTGGCAC
1 TGCCACAAAATATCTGTTCTGGTGACAC
*
42327458 TGCCACAAAATATCTGTATCTGGTGACTC
1 TGCCACAAAATATCTGT-TCTGGTGACAC
*
42327487 TGTCACA
1 TGCCACA
42327494 TTTTCTGTAT
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
27 23 0.44
28 14 0.27
29 15 0.29
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.32
Consensus pattern (28 bp):
TGCCACAAAATATCTGTTCTGGTGACAC
Found at i:42327501 original size:55 final size:56
Alignment explanation
Indices: 42327393--42327507 Score: 137
Period size: 55 Copynumber: 2.1 Consensus size: 56
42327383 AGGAAGCGTC
* * *
42327393 CTGGTGGCTATGCCACAAATTATCTGTTCTGGTGGCCCTGCCACGTATATCTGT-T
1 CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCACATATATCTGTAT
* * *
42327448 CTGGTGGC-ACTGCCACAAAATATCTGTATCTGGTGACTCTGTCACAT-TTTCTGTAT
1 CTGGTGGCTA-TGCCACAAAATATCTGT-TCTGGTGACCCTGCCACATATATCTGTAT
42327504 CTGG
1 CTGG
42327508 CAGCCATGCT
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
54 1 0.02
55 30 0.59
56 20 0.39
ACGTcount: A:0.18, C:0.24, G:0.23, T:0.35
Consensus pattern (56 bp):
CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCACATATATCTGTAT
Found at i:42328588 original size:11 final size:10
Alignment explanation
Indices: 42328560--42328593 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
42328550 AGCCTGTAAG
42328560 TATTCTGAAT
1 TATTCTGAAT
*
42328570 TTTTCTGAAT
1 TATTCTGAAT
42328580 ATATTCTGAAT
1 -TATTCTGAAT
42328591 TAT
1 TAT
42328594 CTGTCTGTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.29, C:0.09, G:0.09, T:0.53
Consensus pattern (10 bp):
TATTCTGAAT
Found at i:42335118 original size:28 final size:28
Alignment explanation
Indices: 42335078--42335170 Score: 152
Period size: 28 Copynumber: 3.3 Consensus size: 28
42335068 ATGTACTAGA
42335078 ATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATTACCATT
*
42335106 ATACCCCTATGTATGCAAAATTACAATT
1 ATACCCCTATGTATGCAAAATTACCATT
*
42335134 ATACCCCTATGTATGCAAAATGACC-TCT
1 ATACCCCTATGTATGCAAAATTACCAT-T
42335162 ATACCCCTA
1 ATACCCCTA
42335171 GGGTTAATTT
Statistics
Matches: 61, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
27 1 0.02
28 60 0.98
ACGTcount: A:0.35, C:0.27, G:0.08, T:0.30
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATTACCATT
Found at i:42335328 original size:27 final size:28
Alignment explanation
Indices: 42335286--42335364 Score: 97
Period size: 27 Copynumber: 2.8 Consensus size: 28
42335276 CTAGTGGCTA
* *
42335286 TGCCACAAATTATCTGTTCTGGTAGCCC
1 TGCCACAAAATATCTGTTCTGGTAGCAC
** *
42335314 TGCCAC-GTATATCTGTTCTGGTGGCAC
1 TGCCACAAAATATCTGTTCTGGTAGCAC
42335341 TGCCACAAAATATCTGTATCTGGT
1 TGCCACAAAATATCTGT-TCTGGT
42335365 GACTCTGTCA
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
27 22 0.52
28 14 0.33
29 6 0.14
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.33
Consensus pattern (28 bp):
TGCCACAAAATATCTGTTCTGGTAGCAC
Found at i:42335376 original size:29 final size:28
Alignment explanation
Indices: 42335286--42335376 Score: 87
Period size: 27 Copynumber: 3.2 Consensus size: 28
42335276 CTAGTGGCTA
* *
42335286 TGCCACAAATTATCTGTTCTGGT-AGCCC
1 TGCCACAAAATATCTGTTCTGGTGA-CAC
** *
42335314 TGCCAC-GTATATCTGTTCTGGTGGCAC
1 TGCCACAAAATATCTGTTCTGGTGACAC
*
42335341 TGCCACAAAATATCTGTATCTGGTGACTC
1 TGCCACAAAATATCTGT-TCTGGTGACAC
*
42335370 TGTCACA
1 TGCCACA
42335377 TTTTCTGTAT
Statistics
Matches: 50, Mismatches: 10, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
27 21 0.42
28 14 0.28
29 15 0.30
ACGTcount: A:0.22, C:0.26, G:0.20, T:0.32
Consensus pattern (28 bp):
TGCCACAAAATATCTGTTCTGGTGACAC
Found at i:42335384 original size:55 final size:56
Alignment explanation
Indices: 42335286--42335390 Score: 126
Period size: 55 Copynumber: 1.9 Consensus size: 56
42335276 CTAGTGGCTA
* *
42335286 TGCCACAAATTATCTGTTCTGGTAGCCCTGCCACGTATATCTGT-TCTGGTGGCAC
1 TGCCACAAAATATCTGTTCTGGTAGCCCTGCCACATATATCTGTATCTGGTGGCAC
* * *
42335341 TGCCACAAAATATCTGTATCTGGT-GACTCTGTCACAT-TTTCTGTATCTGG
1 TGCCACAAAATATCTGT-TCTGGTAG-CCCTGCCACATATATCTGTATCTGG
42335391 CAGCCATGCT
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
55 23 0.55
56 19 0.45
ACGTcount: A:0.20, C:0.25, G:0.20, T:0.35
Consensus pattern (56 bp):
TGCCACAAAATATCTGTTCTGGTAGCCCTGCCACATATATCTGTATCTGGTGGCAC
Found at i:42341316 original size:28 final size:28
Alignment explanation
Indices: 42341251--42341351 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
42341241 ATAGTGAATC
*
42341251 CGCACACTTAGTGCTATATGTATTC-AACT
1 CGCACACTTAGTGCTATA--TAATCAAACT
42341280 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
42341308 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAA--TCAAACT
42341338 CGCACACTTAGTGC
1 CGCACACTTAGTGC
42341352 CAATCTTGTC
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.06
28 23 0.36
29 18 0.28
30 19 0.30
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.30
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:42343496 original size:40 final size:40
Alignment explanation
Indices: 42343441--42343604 Score: 176
Period size: 40 Copynumber: 4.1 Consensus size: 40
42343431 TGAATGATAC
* *
42343441 CCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACTT-TAT
1 CCGGGCTAAGACCCGAAGGCAATTGTGCAAGTG-CTTATAT
42343481 CCGGGCTAAGACCCGAAGGC-ATTCGTGCAAGTTG-TTATAT
1 CCGGGCTAAGACCCGAAGGCAATT-GTGCAAG-TGCTTATAT
* * *
42343521 CCGGGCTAATACCCGAAGGCATTTGTGCGAGT-CGTTATAT
1 CCGGGCTAAGACCCGAAGGCAATTGTGCAAGTGC-TTATAT
** *
42343561 CCGGGCTAAGACCCGAAGGC-ATTCGTGCGTGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCAATT-GTGCAAGTGCTTATAT
42343601 CCGG
1 CCGG
42343605 TTGTATTCCG
Statistics
Matches: 107, Mismatches: 9, Indels: 16
0.81 0.07 0.12
Matches are distributed among these distances:
39 8 0.07
40 95 0.89
41 4 0.04
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCAATTGTGCAAGTGCTTATAT
Found at i:42343574 original size:80 final size:79
Alignment explanation
Indices: 42343441--42343604 Score: 231
Period size: 80 Copynumber: 2.1 Consensus size: 79
42343431 TGAATGATAC
* *
42343441 CCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACTTTATCCGGGCTAAGACCCGAAGGCATTCG
1 CCGGGCTAAGACCCGAAGGCAATTGTGCGAGTGA-TTTATCCGGGCTAAGACCCGAAGGCATTCG
*
42343506 TGCAAGTTGTTATAT
65 TGCAAGTGGTTATAT
* *
42343521 CCGGGCTAATACCCGAAGGCATTTGTGCGAGTCG-TTATATCCGGGCTAAGACCCGAAGGCATTC
1 CCGGGCTAAGACCCGAAGGCAATTGTGCGAGT-GATT-TATCCGGGCTAAGACCCGAAGGCATTC
**
42343585 GTGCGTGTGGTTATAT
64 GTGCAAGTGGTTATAT
42343601 CCGG
1 CCGG
42343605 TTGTATTCCG
Statistics
Matches: 75, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
79 2 0.03
80 72 0.96
81 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.26
Consensus pattern (79 bp):
CCGGGCTAAGACCCGAAGGCAATTGTGCGAGTGATTTATCCGGGCTAAGACCCGAAGGCATTCGT
GCAAGTGGTTATAT
Found at i:42346200 original size:12 final size:12
Alignment explanation
Indices: 42346183--42346208 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
42346173 GAGATATCAG
42346183 ATTTTTCTGAAA
1 ATTTTTCTGAAA
42346195 ATTTTTCTGAAA
1 ATTTTTCTGAAA
42346207 AT
1 AT
42346209 GTGATGTCAT
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:0.35, C:0.08, G:0.08, T:0.50
Consensus pattern (12 bp):
ATTTTTCTGAAA
Found at i:42350597 original size:40 final size:40
Alignment explanation
Indices: 42350540--42350714 Score: 246
Period size: 40 Copynumber: 4.4 Consensus size: 40
42350530 TTGTGCTAGT
*
42350540 GGCTAAG-CCCGAAGGCATATGTGCGAGTTACCATATCCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCATATCCG
*
42350579 GGCTAAGTCCCAAAGGCATTTGTGCGAGTTACCATATCCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCATATCCG
* * *
42350619 GGGTAAGTCCCGAAGGCATTTGTGCGAGTTACTAGT-TTCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCA-TATCCG
* * *
42350659 GGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATACCCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCATATCCG
*
42350699 GGCTATGTCCCGAAGG
1 GGCTAAGTCCCGAAGG
42350715 TATTCGAGTG
Statistics
Matches: 122, Mismatches: 11, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
39 8 0.07
40 113 0.93
41 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.25
Consensus pattern (40 bp):
GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCATATCCG
Found at i:42356907 original size:40 final size:40
Alignment explanation
Indices: 42356769--42356909 Score: 196
Period size: 40 Copynumber: 3.5 Consensus size: 40
42356759 ACCCAAGTTT
* * * *
42356769 CTTCGGGAT-TTAG-CCGGATATAACCACACGCCCAATTGC
1 CTTCGGG-TCTTAGCCCGGATATAACAACTCGCACAAATGC
* * *
42356808 CTTCGGGTCTTAACCCGGACATAGCAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAACAACTCGCACAAATGC
42356848 CTTCGGGTCTTAGCCCGGATATAACAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAACAACTCGCACAAATGC
42356888 CTTCGGGTCTTAGCCCGGATAT
1 CTTCGGGTCTTAGCCCGGATAT
42356910 CATTCAAATG
Statistics
Matches: 90, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
38 1 0.01
39 10 0.11
40 79 0.88
ACGTcount: A:0.25, C:0.30, G:0.21, T:0.23
Consensus pattern (40 bp):
CTTCGGGTCTTAGCCCGGATATAACAACTCGCACAAATGC
Found at i:42361860 original size:40 final size:40
Alignment explanation
Indices: 42361760--42362016 Score: 326
Period size: 40 Copynumber: 6.5 Consensus size: 40
42361750 AGATTGATAA
* **
42361760 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGGCTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
* * *
42361800 CCGGGCTAAG-CCCGAAGGCATATGTGTGAGTTACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
42361839 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
42361879 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TAT
42361919 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * * * *
42361959 CCGGGCTATGTCCCGAAGGTATTCGAGTGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
42361999 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
42362017 TACTTGGCTT
Statistics
Matches: 195, Mismatches: 17, Indels: 11
0.87 0.08 0.05
Matches are distributed among these distances:
39 47 0.24
40 147 0.75
41 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:42364813 original size:58 final size:59
Alignment explanation
Indices: 42364685--42364928 Score: 364
Period size: 59 Copynumber: 4.2 Consensus size: 59
42364675 AGCTAAATTG
* * *
42364685 ATATGTAATACATGCTAGGGTCCGGATGCCTTTGAGTAGCCCCGTTGAGAGGCATGTGA
1 ATATGTGATACATGCTAGGGTCCGGGTGCTTTTGAGTAGCCCCGTTGAGAGGCATGTGA
* * *
42364744 TTATGTCATACATGCTAGGGTCCGGGTGCTTTTGATTAG-CCCGTTGAGAGGCATGTGA
1 ATATGTGATACATGCTAGGGTCCGGGTGCTTTTGAGTAGCCCCGTTGAGAGGCATGTGA
* *
42364802 ATATGTGATACATGCTAGGGTCTGAGTGCTTTTGAGTAGCCCCGTTGAGAGGCATGTGA
1 ATATGTGATACATGCTAGGGTCCGGGTGCTTTTGAGTAGCCCCGTTGAGAGGCATGTGA
* * *
42364861 ATATGTGATACATCCTAGGGCCCAGGTGCTTTTGAGTAGCCCCGTTGAGAGGCATGTGA
1 ATATGTGATACATGCTAGGGTCCGGGTGCTTTTGAGTAGCCCCGTTGAGAGGCATGTGA
* *
42364920 TTCTGTGAT
1 ATATGTGAT
42364929 CTATGGCACT
Statistics
Matches: 167, Mismatches: 17, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
58 53 0.32
59 114 0.68
ACGTcount: A:0.21, C:0.18, G:0.31, T:0.30
Consensus pattern (59 bp):
ATATGTGATACATGCTAGGGTCCGGGTGCTTTTGAGTAGCCCCGTTGAGAGGCATGTGA
Found at i:42364891 original size:117 final size:118
Alignment explanation
Indices: 42364685--42364928 Score: 366
Period size: 117 Copynumber: 2.1 Consensus size: 118
42364675 AGCTAAATTG
* *
42364685 ATATGTAATACATGCTAGGGTCCGGATGCCTTTGAGTAGCCCCGTTGAGAGGCATGTGATTATGT
1 ATATGTGATACATGCTAGGGTCCGGATGCCTTTGAGTAGCCCCGTTGAGAGGCATGTGAATATGT
* * * *
42364750 CATACATGCTAGGGTCCGGGTGCTTTTGATTAG-CCCGTTGAGAGGCATGTGA
66 CATACATCCTAGGGCCCAGGTGCTTTTGAGTAGCCCCGTTGAGAGGCATGTGA
* *
42364802 ATATGTGATACATGCTAGGGT-CTGAGTGCTTTTGAGTAGCCCCGTTGAGAGGCATGTGAATATG
1 ATATGTGATACATGCTAGGGTCCGGA-TGCCTTTGAGTAGCCCCGTTGAGAGGCATGTGAATATG
*
42364866 TGATACATCCTAGGGCCCAGGTGCTTTTGAGTAGCCCCGTTGAGAGGCATGTGA
65 TCATACATCCTAGGGCCCAGGTGCTTTTGAGTAGCCCCGTTGAGAGGCATGTGA
* *
42364920 TTCTGTGAT
1 ATATGTGAT
42364929 CTATGGCACT
Statistics
Matches: 114, Mismatches: 11, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
116 3 0.03
117 85 0.75
118 26 0.23
ACGTcount: A:0.21, C:0.18, G:0.31, T:0.30
Consensus pattern (118 bp):
ATATGTGATACATGCTAGGGTCCGGATGCCTTTGAGTAGCCCCGTTGAGAGGCATGTGAATATGT
CATACATCCTAGGGCCCAGGTGCTTTTGAGTAGCCCCGTTGAGAGGCATGTGA
Found at i:42376429 original size:25 final size:25
Alignment explanation
Indices: 42376401--42376492 Score: 112
Period size: 25 Copynumber: 3.7 Consensus size: 25
42376391 GATACTCCAC
*
42376401 AGCTTGTGAGAGCATACCAATTTAT
1 AGCTCGTGAGAGCATACCAATTTAT
*
42376426 AGCTCGTGAGAGCATACCAATTTAC
1 AGCTCGTGAGAGCATACCAATTTAT
* * * *
42376451 AACTCGTGAAAGCATACCGATTCAT
1 AGCTCGTGAGAGCATACCAATTTAT
* *
42376476 AGTTCGTGTGAGCATAC
1 AGCTCGTGAGAGCATAC
42376493 ATGTATAGGA
Statistics
Matches: 56, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 56 1.00
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.27
Consensus pattern (25 bp):
AGCTCGTGAGAGCATACCAATTTAT
Found at i:42376874 original size:31 final size:31
Alignment explanation
Indices: 42376836--42376898 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
42376826 TACCTATTAC
42376836 TTGATCAAATGGTAAGTTAAATTCTAAGTTA
1 TTGATCAAATGGTAAGTTAAATTCTAAGTTA
42376867 TTGATCAAATGGTAAGTTAAATTCTAAGTTA
1 TTGATCAAATGGTAAGTTAAATTCTAAGTTA
42376898 T
1 T
42376899 ATGAACTTAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.38, C:0.06, G:0.16, T:0.40
Consensus pattern (31 bp):
TTGATCAAATGGTAAGTTAAATTCTAAGTTA
Found at i:42377691 original size:42 final size:41
Alignment explanation
Indices: 42377628--42377709 Score: 119
Period size: 42 Copynumber: 2.0 Consensus size: 41
42377618 TTTCGTCCAC
* *
42377628 ACGGTAGAGACACAGGCGTGTGTCTTAGTCGTGTGTGACAT
1 ACGGTAGAGACACAGGCGTGTGTCTCAGCCGTGTGTGACAT
**
42377669 ACGGCTAGAGACATGGGCGTGTGTCTCAGCCGTGTGTGACA
1 ACGG-TAGAGACACAGGCGTGTGTCTCAGCCGTGTGTGACA
42377710 CATGGCCAGG
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 4 0.11
42 32 0.89
ACGTcount: A:0.21, C:0.20, G:0.35, T:0.24
Consensus pattern (41 bp):
ACGGTAGAGACACAGGCGTGTGTCTCAGCCGTGTGTGACAT
Found at i:42386761 original size:29 final size:27
Alignment explanation
Indices: 42386727--42386829 Score: 98
Period size: 29 Copynumber: 3.6 Consensus size: 27
42386717 TACTCAATCA
*
42386727 CGCACACTTAGTGCCATGTGATTCAAGCC
1 CGCACACTTAGTGCCAT-T-ATTCAAGCT
* * *
42386756 CGCACACATAGTGCCATATAGTCCAAACT
1 CGCACACTTAGTGCCAT-TA-TTCAAGCT
*
42386785 CGCACACTTAGTGCCATACATTACAAGCT
1 CGCACACTTAGTGCCAT-TATT-CAAGCT
*
42386814 CGCACACTCAGTGCCA
1 CGCACACTTAGTGCCA
42386830 ATCTCGTCAC
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
28 2 0.03
29 60 0.97
ACGTcount: A:0.29, C:0.33, G:0.17, T:0.21
Consensus pattern (27 bp):
CGCACACTTAGTGCCATTATTCAAGCT
Found at i:42390983 original size:29 final size:29
Alignment explanation
Indices: 42390948--42391005 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
42390938 CAACTCATAC
*
42390948 TTATATCATATGTTCAGCAAAGTACAGGT
1 TTATATCATATGTTCACCAAAGTACAGGT
*
42390977 TTATATCATATGTTCACCAAGGTACAGGT
1 TTATATCATATGTTCACCAAAGTACAGGT
42391006 ACTTACCTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (29 bp):
TTATATCATATGTTCACCAAAGTACAGGT
Found at i:42391199 original size:43 final size:43
Alignment explanation
Indices: 42391151--42391307 Score: 122
Period size: 43 Copynumber: 3.7 Consensus size: 43
42391141 AGGTCATACA
* *
42391151 ATGCCAATATCCCAGATGTGGTCTTACATGTAATCAAATATCG
1 ATGCCAATATCCCAGACGTGGTCTTACACGTAATCAAATATCG
* * * * * *
42391194 ATGCCACTGTCTCAGATAG-GGTCTTACACGAAATCAAATA-CA
1 ATGCCAATATCCCAGA-CGTGGTCTTACACGTAATCAAATATCG
* * * * * *
42391236 ATGCCGATGTCCCGGACATGGTCTTACACATAAATCATAA-GTCG
1 ATGCCAATATCCCAGACGTGGTCTTACACGT-AATCA-AATATCG
* *
42391280 ATGCCAACATCCTAGACGTGGTCTTACA
1 ATGCCAATATCCCAGACGTGGTCTTACA
42391308 TGGATATGGA
Statistics
Matches: 86, Mismatches: 23, Indels: 9
0.73 0.19 0.08
Matches are distributed among these distances:
42 23 0.27
43 37 0.43
44 26 0.30
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (43 bp):
ATGCCAATATCCCAGACGTGGTCTTACACGTAATCAAATATCG
Found at i:42399534 original size:29 final size:29
Alignment explanation
Indices: 42399501--42399660 Score: 180
Period size: 29 Copynumber: 5.5 Consensus size: 29
42399491 GTGACGAGAT
42399501 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
42399530 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
42399559 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
* ** * ***
42399588 CGGCACTGGGTGTGCGA-GCTCGAAGGGTA
1 TGGCACTAAGTGTGC-ATGCTGGAAATATA
* ** * *
42399617 TGGCACTATGTGTGCGGGCT-TAAATCACA
1 TGGCACTAAGTGTGCATGCTGGAAAT-ATA
42399646 TGGCACTAAGTGTGC
1 TGGCACTAAGTGTGC
42399661 GAAATCGAGT
Statistics
Matches: 111, Mismatches: 17, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
28 2 0.02
29 108 0.97
30 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.31, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAATATA
Found at i:42407486 original size:29 final size:29
Alignment explanation
Indices: 42407453--42407612 Score: 180
Period size: 29 Copynumber: 5.5 Consensus size: 29
42407443 GTGACGAGAT
42407453 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
42407482 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
42407511 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
* ** * ***
42407540 CGGCACTGGGTGTGCGA-GCTCGAAGGGTA
1 TGGCACTAAGTGTGC-ATGCTGGAAATATA
* ** * *
42407569 TGGCACTATGTGTGCGGGCT-TAAATCACA
1 TGGCACTAAGTGTGCATGCTGGAAAT-ATA
42407598 TGGCACTAAGTGTGC
1 TGGCACTAAGTGTGC
42407613 GAAATCGAGT
Statistics
Matches: 111, Mismatches: 17, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
28 2 0.02
29 108 0.97
30 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.31, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAATATA
Found at i:42409755 original size:43 final size:44
Alignment explanation
Indices: 42409635--42409769 Score: 122
Period size: 43 Copynumber: 3.1 Consensus size: 44
42409625 ATCTCATACA
* *
42409635 ATGCCAAC-GTCCCAAACGTGGTCTTACATGT-AATCAAATATCG
1 ATGCC-ACTGTCCCAAACATGGTCTTACACGTAAATCAAATATCG
* * *
42409678 GTGCCACTGTCCCAGACA-GTGTCTTACAC-AAAATCAAATA-CG
1 ATGCCACTGTCCCAAACATG-GTCTTACACGTAAATCAAATATCG
* *
42409720 ATGCTGA-TGTCCCAAACATGGTCTTACACGTAAATCATAA-GTCG
1 ATGC-CACTGTCCCAAACATGGTCTTACACGTAAATCA-AATATCG
42409764 ATGCCA
1 ATGCCA
42409770 ACGTCCTAAT
Statistics
Matches: 73, Mismatches: 11, Indels: 16
0.73 0.11 0.16
Matches are distributed among these distances:
42 27 0.37
43 38 0.52
44 8 0.11
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (44 bp):
ATGCCACTGTCCCAAACATGGTCTTACACGTAAATCAAATATCG
Found at i:42412880 original size:27 final size:28
Alignment explanation
Indices: 42412840--42412907 Score: 113
Period size: 28 Copynumber: 2.5 Consensus size: 28
42412830 TTTAAAACCC
*
42412840 TAGGGGT-ATATCGGTAA-TTTGCTCTT
1 TAGGGGTAATTTCGGTAATTTTGCTCTT
42412866 TAGGGGTAATTTCGGTAATTTTGCTCTT
1 TAGGGGTAATTTCGGTAATTTTGCTCTT
42412894 TAGGGGTAATTTCG
1 TAGGGGTAATTTCG
42412908 TGATCTACGC
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
26 7 0.18
27 9 0.23
28 23 0.59
ACGTcount: A:0.19, C:0.10, G:0.28, T:0.43
Consensus pattern (28 bp):
TAGGGGTAATTTCGGTAATTTTGCTCTT
Found at i:42414735 original size:19 final size:18
Alignment explanation
Indices: 42414698--42414741 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
42414688 ATACATACAG
42414698 TAAT-ATTTTTCTAATAA
1 TAATAATTTTTCTAATAA
*
42414715 TAATAATTTTATCTCATAA
1 TAATAATTTT-TCTAATAA
*
42414734 TACTAATT
1 TAATAATT
42414742 AAAATTTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 4 0.17
18 5 0.22
19 14 0.61
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATAATTTTTCTAATAA
Found at i:42417124 original size:27 final size:28
Alignment explanation
Indices: 42417084--42417151 Score: 113
Period size: 28 Copynumber: 2.5 Consensus size: 28
42417074 TTTAAAACCC
*
42417084 TAGGGGT-ATATCGGTAA-TTTGCTCTT
1 TAGGGGTAATTTCGGTAATTTTGCTCTT
42417110 TAGGGGTAATTTCGGTAATTTTGCTCTT
1 TAGGGGTAATTTCGGTAATTTTGCTCTT
42417138 TAGGGGTAATTTCG
1 TAGGGGTAATTTCG
42417152 TGATCTACGC
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
26 7 0.18
27 9 0.23
28 23 0.59
ACGTcount: A:0.19, C:0.10, G:0.28, T:0.43
Consensus pattern (28 bp):
TAGGGGTAATTTCGGTAATTTTGCTCTT
Found at i:42418978 original size:19 final size:18
Alignment explanation
Indices: 42418941--42418984 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
42418931 ATACATACAG
42418941 TAAT-ATTTTTCTAATAA
1 TAATAATTTTTCTAATAA
*
42418958 TAATAATTTTATCTCATAA
1 TAATAATTTT-TCTAATAA
*
42418977 TACTAATT
1 TAATAATT
42418985 AAAATTTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 4 0.17
18 5 0.22
19 14 0.61
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATAATTTTTCTAATAA
Found at i:42429394 original size:16 final size:17
Alignment explanation
Indices: 42429358--42429396 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
42429348 TTTTAAAAGG
42429358 AAAACAAATGAATCTTA
1 AAAACAAATGAATCTTA
*
42429375 AAAACAATTGAATCTTA
1 AAAACAAATGAATCTTA
42429392 AAAAC
1 AAAAC
42429397 TTAATGAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.59, C:0.13, G:0.05, T:0.23
Consensus pattern (17 bp):
AAAACAAATGAATCTTA
Found at i:42439857 original size:49 final size:49
Alignment explanation
Indices: 42439712--42440072 Score: 582
Period size: 49 Copynumber: 7.4 Consensus size: 49
42439702 TACATATATG
* * * * *
42439712 TGTGATAAGG-CTGAATGGCCAATGCGATGAATGTGAAAGTGGATGTATA
1 TGTGATGAGGCCT-AATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA
* *
42439761 TGTGATGAGGCCTAATGTCCGATG-GATGAATGTGAAAGTGTATGTATA
1 TGTGATGAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA
*
42439809 TGTGATGAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATGTATA
1 TGTGATGAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA
42439858 TGTGATGAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA
1 TGTGATGAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA
*
42439907 TGTGATGAGGCCTAATGGCCAATGTGGTGAATGTGAAAGTGTATGTATA
1 TGTGATGAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA
*
42439956 TGTGATGAGGCCTAATGGCCGATGTGGTGAATGTGAAAGCGTATGTATA
1 TGTGATGAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA
* *
42440005 TGTGATAAGGCCTAATGGCCGATGTGGTGAATGTGAAAGCGTATGTATA
1 TGTGATGAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA
*
42440054 TGTGATAAGGCCTAATGGC
1 TGTGATGAGGCCTAATGGC
42440073 TAATGTAAAA
Statistics
Matches: 300, Mismatches: 10, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
48 46 0.15
49 252 0.84
50 2 0.01
ACGTcount: A:0.29, C:0.09, G:0.33, T:0.29
Consensus pattern (49 bp):
TGTGATGAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA
Found at i:42440224 original size:37 final size:37
Alignment explanation
Indices: 42440174--42440258 Score: 143
Period size: 37 Copynumber: 2.3 Consensus size: 37
42440164 GGAATATGTT
*
42440174 CCGGGTGAGACCCGATGACTACGTGTGGAGATTATGA
1 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGA
*
42440211 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGT
1 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGA
*
42440248 CTGGGTAAGAC
1 CCGGGTAAGAC
42440259 TTCTTTTATA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 45 1.00
ACGTcount: A:0.25, C:0.19, G:0.34, T:0.22
Consensus pattern (37 bp):
CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGA
Found at i:42442694 original size:25 final size:25
Alignment explanation
Indices: 42442666--42442777 Score: 125
Period size: 25 Copynumber: 4.5 Consensus size: 25
42442656 TCCACAGTTT
*
42442666 GTGAGAGCATACCGATTTATAGCTC
1 GTGAGAGCATACCGATTCATAGCTC
* *
42442691 GTGAGAGCATACCGATTTAAAGCTC
1 GTGAGAGCATACCGATTCATAGCTC
* *
42442716 GTGAAAGCATACCGATTCATAGTTC
1 GTGAGAGCATACCGATTCATAGCTC
* * * * *
42442741 ATGAAAACATACTGATTCACAGCTC
1 GTGAGAGCATACCGATTCATAGCTC
*
42442766 GTGTGAGCATAC
1 GTGAGAGCATAC
42442778 ATGTATAGGA
Statistics
Matches: 73, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 73 1.00
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (25 bp):
GTGAGAGCATACCGATTCATAGCTC
Found at i:42446866 original size:28 final size:28
Alignment explanation
Indices: 42446713--42446866 Score: 191
Period size: 28 Copynumber: 5.5 Consensus size: 28
42446703 TTCTTATTTT
** * * *
42446713 AGATAGTCCTTGATGAACTTTCCATATA
1 AGATAGTCCTTGGCGGACTTTTCACATA
* *
42446741 AGATAGTCCTTGGTGGACTTTCCACATA
1 AGATAGTCCTTGGCGGACTTTTCACATA
* * *
42446769 AGATAGTCATTGGCAGACTTTTCATATA
1 AGATAGTCCTTGGCGGACTTTTCACATA
42446797 AGATAGTCCTTGGCGGACTTTTCACATA
1 AGATAGTCCTTGGCGGACTTTTCACATA
*
42446825 AGACAGTCCTTGGCGGACTTTTCACATA
1 AGATAGTCCTTGGCGGACTTTTCACATA
* *
42446853 AGAGAATCCTTGGC
1 AGATAGTCCTTGGC
42446867 AAATTTTCCC
Statistics
Matches: 112, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 112 1.00
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (28 bp):
AGATAGTCCTTGGCGGACTTTTCACATA
Found at i:42446866 original size:84 final size:84
Alignment explanation
Indices: 42446713--42446867 Score: 211
Period size: 84 Copynumber: 1.8 Consensus size: 84
42446703 TTCTTATTTT
* * * * * *
42446713 AGATAGTCCTTGATGAACTTTCCATATAAGATAGTCCTTGGTGGACTTTCCACATAAGATAGTCA
1 AGATAGTCCTTGACGAACTTTCCACATAAGACAGTCCTTGGCGGACTTTCCACATAAGAGAATCA
42446778 TTGGCAGACTTTTCATATA
66 TTGGCAGACTTTTCATATA
* * * * *
42446797 AGATAGTCCTTGGCGGACTTTTCACATAAGACAGTCCTTGGCGGACTTTTCACATAAGAGAATCC
1 AGATAGTCCTTGACGAACTTTCCACATAAGACAGTCCTTGGCGGACTTTCCACATAAGAGAATCA
42446862 TTGGCA
66 TTGGCA
42446868 AATTTTCCCT
Statistics
Matches: 60, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
84 60 1.00
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (84 bp):
AGATAGTCCTTGACGAACTTTCCACATAAGACAGTCCTTGGCGGACTTTCCACATAAGAGAATCA
TTGGCAGACTTTTCATATA
Found at i:42457579 original size:42 final size:41
Alignment explanation
Indices: 42457532--42457732 Score: 170
Period size: 42 Copynumber: 4.6 Consensus size: 41
42457522 TGTGGATTCG
*
42457532 TGTAAGACCATATCTAGGATATGGCCTCGATATGTGATCCCA
1 TGTAAGACCATATCT-GGATATGGCATCGATATGTGATCCCA
* * ** *
42457574 TGTAAGTCCATATCTAGGATATGGCATTGGCATCAATATGTGATTTCG
1 TGTAAGACCATATCT-GG--AT---A-TGGCATCGATATGTGATCCCA
* * * *
42457622 TGTAAGACCATGTCTGGAACATGGCATCGATATGAGA-CATCA
1 TGTAAGACCATATCTGG-ATATGGCATCGATATGTGATC-CCA
* * *
42457664 TGTAATACCATAGCTGGGTATTGGCATCGATATGTGATCCCA
1 TGTAAGACCATATCTGGATA-TGGCATCGATATGTGATCCCA
42457706 TGTAAGACCATATCTGGTATATGGCAT
1 TGTAAGACCATATCTGG-ATATGGCAT
42457733 TCGCATCTTA
Statistics
Matches: 125, Mismatches: 24, Indels: 20
0.74 0.14 0.12
Matches are distributed among these distances:
41 1 0.01
42 85 0.68
43 4 0.03
44 2 0.02
46 1 0.01
47 3 0.02
48 29 0.23
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (41 bp):
TGTAAGACCATATCTGGATATGGCATCGATATGTGATCCCA
Found at i:42460734 original size:43 final size:42
Alignment explanation
Indices: 42460570--42460735 Score: 147
Period size: 43 Copynumber: 3.9 Consensus size: 42
42460560 ATAAGCTTGT
* * ** *
42460570 ACAATGCC-ATATCCCAGATATGGTCTTACATATTAT-TATA
1 ACAATGCCAATGTCCCAGACATGGTCTTACACGTAATCTATA
* * * *
42460610 TATCAATGCCACTGTCCCAGACAGGGTCTTACACGAAATCGATTA
1 -A-CAATGCCAATGTCCCAGACATGGTCTTACACGTAATCTA-TA
* ** * *
42460655 ACGATGCCAATGTCCTGGACATGGTATTACACGTAATCTAAA
1 ACAATGCCAATGTCCCAGACATGGTCTTACACGTAATCTATA
*
42460697 CACAATGCCAATGTCCCAGACATGGTCTTACATGTAATC
1 -ACAATGCCAATGTCCCAGACATGGTCTTACACGTAATC
42460736 ACATCTCCAT
Statistics
Matches: 97, Mismatches: 23, Indels: 8
0.76 0.18 0.06
Matches are distributed among these distances:
41 1 0.01
42 8 0.08
43 84 0.87
44 2 0.02
45 2 0.02
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.28
Consensus pattern (42 bp):
ACAATGCCAATGTCCCAGACATGGTCTTACACGTAATCTATA
Found at i:42461249 original size:29 final size:29
Alignment explanation
Indices: 42461217--42461276 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
42461207 TTTATTTCAT
*
42461217 AATTTAACCCCTCAATTTACATTTTT-CTC
1 AATTTAACCCCT-AATATACATTTTTACTC
* *
42461246 AATTTAATCCCTAATATGCATTTTTACTC
1 AATTTAACCCCTAATATACATTTTTACTC
42461275 AA
1 AA
42461277 AATCACTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 11 0.41
29 16 0.59
ACGTcount: A:0.32, C:0.23, G:0.02, T:0.43
Consensus pattern (29 bp):
AATTTAACCCCTAATATACATTTTTACTC
Found at i:42461313 original size:19 final size:19
Alignment explanation
Indices: 42461289--42461326 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
42461279 TCACTTTACA
42461289 AAACATGTATATTAAACAC
1 AAACATGTATATTAAACAC
42461308 AAACATGTATATTAAACAC
1 AAACATGTATATTAAACAC
42461327 CAAGCTTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.53, C:0.16, G:0.05, T:0.26
Consensus pattern (19 bp):
AAACATGTATATTAAACAC
Found at i:42471075 original size:25 final size:25
Alignment explanation
Indices: 42471041--42471092 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
42471031 AGAATTTTGC
42471041 TTGATAAACCGTAATTTATACATAT
1 TTGATAAACCGTAATTTATACATAT
42471066 TTGATAAACCGTAATTTATACATAT
1 TTGATAAACCGTAATTTATACATAT
42471091 TT
1 TT
42471093 TTACCCCATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (25 bp):
TTGATAAACCGTAATTTATACATAT
Found at i:42473999 original size:13 final size:14
Alignment explanation
Indices: 42473966--42474015 Score: 50
Period size: 13 Copynumber: 3.7 Consensus size: 14
42473956 ACATAGAACA
*
42473966 ATATATATATTATT
1 ATATATATATTACT
42473980 ATATATA-ATTACT
1 ATATATATATTACT
* **
42473993 ATTTATATA-TAAA
1 ATATATATATTACT
42474006 ATATATATAT
1 ATATATATAT
42474016 AATTCTTAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
13 21 0.72
14 8 0.28
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (14 bp):
ATATATATATTACT
Found at i:42479989 original size:30 final size:30
Alignment explanation
Indices: 42479934--42480093 Score: 213
Period size: 29 Copynumber: 5.5 Consensus size: 30
42479924 ATAGTGAATC
42479934 CGCACACTTAGTGCTATAT-ATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAGCT
42479963 CGCACACTTAGTGCTATATAATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAGCT
42479993 CGCACACTTAGTGCTATAT-ATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAGCT
* *
42480022 CGCACACTTAGTGCTGTATAA---TCAAACT
1 CGCACACTTAGTGCTATATAATTTTC-AGCT
* * * * *
42480050 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAATTTTCAGCT
42480080 CGCACACTTAGTGC
1 CGCACACTTAGTGC
42480094 CAATCTTGTC
Statistics
Matches: 120, Mismatches: 5, Indels: 11
0.88 0.04 0.08
Matches are distributed among these distances:
27 2 0.02
28 23 0.19
29 47 0.39
30 47 0.39
31 1 0.01
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.33
Consensus pattern (30 bp):
CGCACACTTAGTGCTATATAATTTTCAGCT
Found at i:42480026 original size:59 final size:57
Alignment explanation
Indices: 42479934--42480093 Score: 214
Period size: 59 Copynumber: 2.8 Consensus size: 57
42479924 ATAGTGAATC
*
42479934 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATTTTC-AGCT
1 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAA---TCAAACT
*
42479993 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTGTATAATCAAACT
1 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATCAAACT
* * * * *
42480050 CGCACACTTAGTGCTGTACAATTTTAAACCCGCACACTTAGTGC
1 CGCACACTTAGTGCTATA-TATTTTCAGCTCGCACACTTAGTGC
42480094 CAATCTTGTC
Statistics
Matches: 92, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
56 2 0.02
57 20 0.22
58 21 0.23
59 49 0.53
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.33
Consensus pattern (57 bp):
CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATCAAACT
Found at i:42488034 original size:30 final size:30
Alignment explanation
Indices: 42487979--42488138 Score: 213
Period size: 29 Copynumber: 5.5 Consensus size: 30
42487969 ATAGTGAATC
42487979 CGCACACTTAGTGCTATAT-ATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAGCT
42488008 CGCACACTTAGTGCTATATAATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAGCT
42488038 CGCACACTTAGTGCTATAT-ATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAGCT
* *
42488067 CGCACACTTAGTGCTGTATAA---TCAAACT
1 CGCACACTTAGTGCTATATAATTTTC-AGCT
* * * * *
42488095 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAATTTTCAGCT
42488125 CGCACACTTAGTGC
1 CGCACACTTAGTGC
42488139 CAATCTTGTC
Statistics
Matches: 120, Mismatches: 5, Indels: 11
0.88 0.04 0.08
Matches are distributed among these distances:
27 2 0.02
28 23 0.19
29 47 0.39
30 47 0.39
31 1 0.01
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.33
Consensus pattern (30 bp):
CGCACACTTAGTGCTATATAATTTTCAGCT
Found at i:42488071 original size:59 final size:57
Alignment explanation
Indices: 42487979--42488138 Score: 214
Period size: 59 Copynumber: 2.8 Consensus size: 57
42487969 ATAGTGAATC
*
42487979 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATTTTC-AGCT
1 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAA---TCAAACT
*
42488038 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTGTATAATCAAACT
1 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATCAAACT
* * * * *
42488095 CGCACACTTAGTGCTGTACAATTTTAAACCCGCACACTTAGTGC
1 CGCACACTTAGTGCTATA-TATTTTCAGCTCGCACACTTAGTGC
42488139 CAATCTTGTC
Statistics
Matches: 92, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
56 2 0.02
57 20 0.22
58 21 0.23
59 49 0.53
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.33
Consensus pattern (57 bp):
CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATCAAACT
Found at i:42495849 original size:17 final size:15
Alignment explanation
Indices: 42495827--42495861 Score: 52
Period size: 17 Copynumber: 2.2 Consensus size: 15
42495817 ATATTTGAGG
42495827 CATTTTCACACACAACT
1 CATTTTCAC-CACAA-T
42495844 CATTTTCACCACAAT
1 CATTTTCACCACAAT
42495859 CAT
1 CAT
42495862 ACAAATGCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.22
16 5 0.28
17 9 0.50
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.31
Consensus pattern (15 bp):
CATTTTCACCACAAT
Found at i:42496086 original size:30 final size:30
Alignment explanation
Indices: 42496031--42496190 Score: 213
Period size: 29 Copynumber: 5.5 Consensus size: 30
42496021 ATAGTGAATC
42496031 CGCACACTTAGTGCTATAT-ATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAGCT
42496060 CGCACACTTAGTGCTATATAATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAGCT
42496090 CGCACACTTAGTGCTATAT-ATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAGCT
* *
42496119 CGCACACTTAGTGCTGTATAA---TCAAACT
1 CGCACACTTAGTGCTATATAATTTTC-AGCT
* * * * *
42496147 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAATTTTCAGCT
42496177 CGCACACTTAGTGC
1 CGCACACTTAGTGC
42496191 CAATCTTGTC
Statistics
Matches: 120, Mismatches: 5, Indels: 11
0.88 0.04 0.08
Matches are distributed among these distances:
27 2 0.02
28 23 0.19
29 47 0.39
30 47 0.39
31 1 0.01
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.33
Consensus pattern (30 bp):
CGCACACTTAGTGCTATATAATTTTCAGCT
Found at i:42496123 original size:59 final size:57
Alignment explanation
Indices: 42496031--42496190 Score: 214
Period size: 59 Copynumber: 2.8 Consensus size: 57
42496021 ATAGTGAATC
*
42496031 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATTTTC-AGCT
1 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAA---TCAAACT
*
42496090 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTGTATAATCAAACT
1 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATCAAACT
* * * * *
42496147 CGCACACTTAGTGCTGTACAATTTTAAACCCGCACACTTAGTGC
1 CGCACACTTAGTGCTATA-TATTTTCAGCTCGCACACTTAGTGC
42496191 CAATCTTGTC
Statistics
Matches: 92, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
56 2 0.02
57 20 0.22
58 21 0.23
59 49 0.53
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.33
Consensus pattern (57 bp):
CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATCAAACT
Found at i:42504142 original size:30 final size:30
Alignment explanation
Indices: 42504087--42504246 Score: 213
Period size: 29 Copynumber: 5.5 Consensus size: 30
42504077 ATAGTGAATC
42504087 CGCACACTTAGTGCTATAT-ATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAGCT
42504116 CGCACACTTAGTGCTATATAATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAGCT
42504146 CGCACACTTAGTGCTATAT-ATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAGCT
* *
42504175 CGCACACTTAGTGCTGTATAA---TCAAACT
1 CGCACACTTAGTGCTATATAATTTTC-AGCT
* * * * *
42504203 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAATTTTCAGCT
42504233 CGCACACTTAGTGC
1 CGCACACTTAGTGC
42504247 CAATCTTGTC
Statistics
Matches: 120, Mismatches: 5, Indels: 11
0.88 0.04 0.08
Matches are distributed among these distances:
27 2 0.02
28 23 0.19
29 47 0.39
30 47 0.39
31 1 0.01
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.33
Consensus pattern (30 bp):
CGCACACTTAGTGCTATATAATTTTCAGCT
Found at i:42504179 original size:59 final size:57
Alignment explanation
Indices: 42504087--42504246 Score: 214
Period size: 59 Copynumber: 2.8 Consensus size: 57
42504077 ATAGTGAATC
*
42504087 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATTTTC-AGCT
1 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAA---TCAAACT
*
42504146 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTGTATAATCAAACT
1 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATCAAACT
* * * * *
42504203 CGCACACTTAGTGCTGTACAATTTTAAACCCGCACACTTAGTGC
1 CGCACACTTAGTGCTATA-TATTTTCAGCTCGCACACTTAGTGC
42504247 CAATCTTGTC
Statistics
Matches: 92, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
56 2 0.02
57 20 0.22
58 21 0.23
59 49 0.53
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.33
Consensus pattern (57 bp):
CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATCAAACT
Found at i:42517903 original size:46 final size:46
Alignment explanation
Indices: 42517762--42517893 Score: 210
Period size: 46 Copynumber: 2.9 Consensus size: 46
42517752 ATATATATTT
* * *
42517762 ATATACATCTCATACATATCTCACATTAGCCATTCGGCTTTACCTC
1 ATATACATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCTC
* *
42517808 ATATCCATCTCATACACGTTTCGCATTAGCCATTCGGCTTTACCTC
1 ATATACATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCTC
*
42517854 ATATTCATCTCATACACATTTCGCATTAGCCATTCGGCTT
1 ATATACATCTCATACACATTTCGCATTAGCCATTCGGCTT
42517894 CGCCACATAT
Statistics
Matches: 79, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 79 1.00
ACGTcount: A:0.25, C:0.30, G:0.09, T:0.36
Consensus pattern (46 bp):
ATATACATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCTC
Found at i:42517948 original size:47 final size:47
Alignment explanation
Indices: 42517917--42518157 Score: 385
Period size: 47 Copynumber: 5.1 Consensus size: 47
42517907 CACTTCCACG
* **
42517917 TTCATCACATCGGCCATTCTACCTTATCACATATATGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
*
42517964 TTCATCATATTGGCCATTCGGCCTTATCACATATA-GCCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATATG-CATGTTCACA
* *
42518011 TTCATCACATTGGCCATTCGGCCTTATCACACATATGCAAGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
* *
42518058 TTCATCACATTGGCCATTCAGCCTTATCACGTATATGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
*
42518105 TTCATTACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
42518152 TTCATC
1 TTCATC
42518158 TCATAAAATC
Statistics
Matches: 177, Mismatches: 15, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
46 1 0.01
47 175 0.99
48 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.12, T:0.34
Consensus pattern (47 bp):
TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
Found at i:42518086 original size:22 final size:22
Alignment explanation
Indices: 42517967--42518087 Score: 77
Period size: 22 Copynumber: 5.2 Consensus size: 22
42517957 GTTCACATTC
* *
42517967 ATCATATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCAGCCTT
* *
42517989 ATCACATATAGCCATGTTCA-CATT
1 ATCACAT-TGGCCA--TTCAGCCTT
*
42518013 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCAGCCTT
* *
42518036 ATCACACATAT-GCAAGTTCA-CATT
1 AT--CACAT-TGGCCA-TTCAGCCTT
42518060 CATCACATTGGCCATTCAGCCTT
1 -ATCACATTGGCCATTCAGCCTT
42518083 ATCAC
1 ATCAC
42518088 GTATATGCAT
Statistics
Matches: 75, Mismatches: 12, Indels: 24
0.68 0.11 0.22
Matches are distributed among these distances:
22 21 0.28
23 19 0.25
24 19 0.25
25 16 0.21
ACGTcount: A:0.26, C:0.30, G:0.12, T:0.31
Consensus pattern (22 bp):
ATCACATTGGCCATTCAGCCTT
Found at i:42521045 original size:40 final size:40
Alignment explanation
Indices: 42520992--42521390 Score: 629
Period size: 40 Copynumber: 10.0 Consensus size: 40
42520982 GAATACACAT
* * *
42520992 CACCAGCATGAATGCTCTTTGGGACCTAGCCCGGATATAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
* *
42521032 CTCCAGCACGAATGCTCTTCGAGACTTAGCCCGGATATAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
*
42521072 CACCAGCACGAATGCTCTTCGGGACTTATCCCGGATATAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
* * * *
42521112 CACCAGCACGAATGCTCTTCGAGACTTAGCTCGGATACAT
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
** * *
42521152 CACTTGCACGAATGCTCTTCAGGACTTAGCCTGGATATAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
42521192 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
*
42521232 CACCAGCACGAATGCTCTTTGGGACTTAGCCCGGATATAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
* *
42521272 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATACAT
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
42521312 C-CCTAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
1 CACC-AGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
42521352 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATA
42521391 TATAACTCTC
Statistics
Matches: 326, Mismatches: 31, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
39 2 0.01
40 322 0.99
41 2 0.01
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.22
Consensus pattern (40 bp):
CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
Found at i:42523012 original size:46 final size:46
Alignment explanation
Indices: 42522871--42523002 Score: 201
Period size: 46 Copynumber: 2.9 Consensus size: 46
42522861 ATATATATAT
* * * *
42522871 ATATACATCTCATACATATCTCACATTAGCCATTCGACTTTACCTC
1 ATATACATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCTC
* *
42522917 ATATCCATCTCATACACGTTTCGCATTAGCCATTCGGCTTTACCTC
1 ATATACATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCTC
*
42522963 ATATTCATCTCATACACATTTCGCATTAGCCATTCGGCTT
1 ATATACATCTCATACACATTTCGCATTAGCCATTCGGCTT
42523003 CGCCACATAT
Statistics
Matches: 78, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 78 1.00
ACGTcount: A:0.26, C:0.30, G:0.08, T:0.36
Consensus pattern (46 bp):
ATATACATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCTC
Found at i:42523057 original size:47 final size:47
Alignment explanation
Indices: 42523026--42523266 Score: 419
Period size: 47 Copynumber: 5.1 Consensus size: 47
42523016 CACTTCCACG
* **
42523026 TTCATCACATCGGCCATTCTACCTTATCACATATATGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
*
42523073 TTCATCACATTGGCCATTCGGTCTTATCACATATATGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
* *
42523120 TTCATCACATTGGCCATTCGGCCTTATCACACATATGCAAGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
*
42523167 TTCATCACATTGGCCATTCGGCCTTATCACGTATATGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
42523214 TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
42523261 TTCATC
1 TTCATC
42523267 TCATAAAATC
Statistics
Matches: 183, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 183 1.00
ACGTcount: A:0.26, C:0.28, G:0.12, T:0.34
Consensus pattern (47 bp):
TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
Found at i:42523243 original size:22 final size:22
Alignment explanation
Indices: 42523123--42523245 Score: 67
Period size: 22 Copynumber: 5.3 Consensus size: 22
42523113 GTTCACATTC
42523123 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
* * *
42523145 ATCACACATAT-GCAAGTTC-ACATT
1 AT--CACAT-TGGCCA-TTCGGCCTT
42523169 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
* *
42523192 ATCACGTATAT-G-CATGTTC-ACATT
1 ATCAC--AT-TGGCCA--TTCGGCCTT
42523216 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
42523239 ATCACAT
1 ATCACAT
42523246 ATATGCATGT
Statistics
Matches: 75, Mismatches: 10, Indels: 32
0.64 0.09 0.27
Matches are distributed among these distances:
22 22 0.29
23 19 0.25
24 19 0.25
25 15 0.20
ACGTcount: A:0.25, C:0.29, G:0.14, T:0.32
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:42529573 original size:43 final size:43
Alignment explanation
Indices: 42529493--42529595 Score: 122
Period size: 43 Copynumber: 2.4 Consensus size: 43
42529483 TTTACGTGCA
* ***
42529493 TGTCTGGGAC-ATCAGCATCATATTTGATTTTGTGTAAGACC-C
1 TGTCTGGGACAAT-GGCATCATATTTGATTACATGTAAGACCAC
42529535 TGTCTGGGACAATGGCATCGATATTTGATTACATGTAAGACCAC
1 TGTCTGGGACAATGGCATC-ATATTTGATTACATGTAAGACCAC
*
42529579 -GTCTGGGACATTGGCAT
1 TGTCTGGGACAATGGCAT
42529596 TGTACGAGTT
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
42 15 0.28
43 37 0.70
44 1 0.02
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.32
Consensus pattern (43 bp):
TGTCTGGGACAATGGCATCATATTTGATTACATGTAAGACCAC
Found at i:42530842 original size:17 final size:17
Alignment explanation
Indices: 42530820--42530856 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
42530810 GGTGTGTTTG
42530820 ATAACCCTGTGAGTCAC
1 ATAACCCTGTGAGTCAC
*
42530837 ATAACCGTGTGAGTCAC
1 ATAACCCTGTGAGTCAC
42530854 ATA
1 ATA
42530857 GCCTGTTCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.24
Consensus pattern (17 bp):
ATAACCCTGTGAGTCAC
Found at i:42534016 original size:40 final size:40
Alignment explanation
Indices: 42533959--42534083 Score: 182
Period size: 40 Copynumber: 3.1 Consensus size: 40
42533949 TCGAATGATG
* * *
42533959 TCCGGGCTAAG-TCCCGAAGGC-TTTGTGCTAAGTGACTAAA
1 TCCGGACTAAGAT-CCGAAGGCATTTGTGC-GAGTTACTAAA
*
42533999 TCCGGACTAAGATCCGAAAGCATTTGTGCGAGTTACTAAA
1 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
42534039 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
42534079 TCCGG
1 TCCGG
42534084 GTTGTGCAAC
Statistics
Matches: 78, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
40 70 0.90
41 8 0.10
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.25
Consensus pattern (40 bp):
TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:42538824 original size:47 final size:47
Alignment explanation
Indices: 42538767--42538932 Score: 314
Period size: 47 Copynumber: 3.5 Consensus size: 47
42538757 GTATGAGATA
42538767 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
*
42538814 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGCGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
*
42538861 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTA
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
42538908 TATATATGTGATAAGGCCTAATGGC
1 TATATATGTGATAAGGCCTAATGGC
42538933 TAATGTGAAA
Statistics
Matches: 116, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
47 116 1.00
ACGTcount: A:0.33, C:0.10, G:0.28, T:0.30
Consensus pattern (47 bp):
TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
Found at i:42538847 original size:22 final size:22
Alignment explanation
Indices: 42538819--42538894 Score: 62
Period size: 22 Copynumber: 3.3 Consensus size: 22
42538809 AAGTGTATAT
42538819 ATGTGATAAGGCCTAATGGCCG
1 ATGTGATAAGGCCTAATGGCCG
* ** ****
42538841 ATGTGATGAATGCGAAAGTGTATAT
1 ATGTGAT-AAGGCCTAA-TG-GCCG
42538866 ATGTGATAAGGCCTAATGGCCG
1 ATGTGATAAGGCCTAATGGCCG
42538888 ATGTGAT
1 ATGTGAT
42538895 GAATGTGAAA
Statistics
Matches: 37, Mismatches: 14, Indels: 6
0.65 0.25 0.11
Matches are distributed among these distances:
22 14 0.38
23 8 0.22
24 8 0.22
25 7 0.19
ACGTcount: A:0.30, C:0.12, G:0.30, T:0.28
Consensus pattern (22 bp):
ATGTGATAAGGCCTAATGGCCG
Found at i:42538983 original size:48 final size:48
Alignment explanation
Indices: 42538910--42539181 Score: 427
Period size: 48 Copynumber: 5.7 Consensus size: 48
42538900 TGAAAGTATA
* * *
42538910 TATATGTGATAAGGCCTAATGGCTAATGTGAAATATATGTGTGATATG
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATGTGTGATATG
* * *
42538958 TATATGTGGTAAAGCTGAATAGCTAATATGAAATATATGTGTGATATG
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATGTGTGATATG
*
42539006 TATATGTGGTAAAGCCAAATGGCTAATGTGAAATATATGTGTGATATG
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATGTGTGATATG
*
42539054 TATATGTGGTAAACCCGAATGGCTAATGTGAAATATATGTGTGATATG
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATGTGTGATATG
* * * *
42539102 TATATGTGGTAAAGCCGAATGGCGAATGTGAAATATGTATGAGATATG
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATGTGTGATATG
*
42539150 AATATGTGGTAAAGCCGAATGGCTAATGTGAA
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAA
42539182 TGTTGTAACA
Statistics
Matches: 205, Mismatches: 19, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 205 1.00
ACGTcount: A:0.35, C:0.07, G:0.26, T:0.32
Consensus pattern (48 bp):
TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATGTGTGATATG
Found at i:42539332 original size:37 final size:37
Alignment explanation
Indices: 42539226--42539334 Score: 173
Period size: 37 Copynumber: 2.9 Consensus size: 37
42539216 GGAAATATAT
* *
42539226 TCCGGGTAAGACCCGATGACTACGTGTGGAGACTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
42539263 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
* * *
42539300 TCCGGGTGAGACCCGATAACTTCGTGTGGAGATTT
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTT
42539335 CGTCTGAGCT
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 67 1.00
ACGTcount: A:0.22, C:0.20, G:0.32, T:0.26
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
Found at i:42541667 original size:42 final size:42
Alignment explanation
Indices: 42541573--42541717 Score: 148
Period size: 43 Copynumber: 3.4 Consensus size: 42
42541563 TAAGACTACG
** * *
42541573 TCTGGGACATTGGCATCGGCTTATGATTTATGTGTAAGACCATA
1 TCTGGGACATTGGCATCGTATT-TGATTTCT-TGTAAGACCCTA
*
42541617 TCTAGGACATTGGCATCGTATTTGATTTCTTGTAAGACCCTA
1 TCTGGGACATTGGCATCGTATTTGATTTCTTGTAAGACCCTA
* * * * *
42541659 TTTGGGACAGTGGCATCAATATTTGATTACATGTAAGACCAC-A
1 TCTGGGACATTGGCATC-GTATTTGATTTCTTGTAAGACC-CTA
*
42541702 TCTGGGACCTTGGCAT
1 TCTGGGACATTGGCAT
42541718 TGTACGAGCT
Statistics
Matches: 85, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
42 25 0.29
43 40 0.47
44 20 0.24
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.34
Consensus pattern (42 bp):
TCTGGGACATTGGCATCGTATTTGATTTCTTGTAAGACCCTA
Found at i:42547229 original size:29 final size:28
Alignment explanation
Indices: 42547195--42547297 Score: 116
Period size: 29 Copynumber: 3.6 Consensus size: 28
42547185 TACTCAATCA
*
42547195 CGCACACTTAGTGCCATATGATTCAAGCC
1 CGCACACTTAGTGCCATAT-ATTCAAGCT
* * *
42547224 CGCACACATAGTGCCATATAGTCCAAACT
1 CGCACACTTAGTGCCATATA-TTCAAGCT
* *
42547253 CGCACACTTAGTGCCGTACATTACAAGCT
1 CGCACACTTAGTGCCATATATT-CAAGCT
*
42547282 CGCACACTCAGTGCCA
1 CGCACACTTAGTGCCA
42547298 ATCTCGTCAC
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
28 2 0.03
29 59 0.97
ACGTcount: A:0.29, C:0.33, G:0.17, T:0.21
Consensus pattern (28 bp):
CGCACACTTAGTGCCATATATTCAAGCT
Found at i:42554200 original size:29 final size:28
Alignment explanation
Indices: 42554166--42554268 Score: 116
Period size: 29 Copynumber: 3.6 Consensus size: 28
42554156 TACTCAATCA
*
42554166 CGCACACTTAGTGCCATATGATTCAAGCC
1 CGCACACTTAGTGCCATAT-ATTCAAGCT
* * *
42554195 CGCACACATAGTGCCATATAGTCCAAACT
1 CGCACACTTAGTGCCATATA-TTCAAGCT
* *
42554224 CGCACACTTAGTGCCGTACATTACAAGCT
1 CGCACACTTAGTGCCATATATT-CAAGCT
*
42554253 CGCACACTCAGTGCCA
1 CGCACACTTAGTGCCA
42554269 ATCTCGTCAC
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
28 2 0.03
29 59 0.97
ACGTcount: A:0.29, C:0.33, G:0.17, T:0.21
Consensus pattern (28 bp):
CGCACACTTAGTGCCATATATTCAAGCT
Found at i:42561436 original size:42 final size:43
Alignment explanation
Indices: 42561319--42561458 Score: 158
Period size: 44 Copynumber: 3.3 Consensus size: 43
42561309 CATAAGATCT
* * * *
42561319 GATATGTGTTTTCGTGTAAGACCATGTCTGGAACGTTGGCATC
1 GATATTTGATTTCGTGTAAGACCATGTCTGGGACATTGGCATC
* *
42561362 GACT-TATGATTTACATGTAAGACCATGTCTGGGACATTGGCATC
1 GA-TATTTGATTT-CGTGTAAGACCATGTCTGGGACATTGGCATC
* * *
42561406 -ATATTTGATTTCGTGTAAGACCCTGTCTGGGATAGTGGCATC
1 GATATTTGATTTCGTGTAAGACCATGTCTGGGACATTGGCATC
*
42561448 GATACTTGATT
1 GATATTTGATT
42561459 ACATGTATAA
Statistics
Matches: 82, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
42 28 0.34
43 25 0.30
44 29 0.35
ACGTcount: A:0.24, C:0.16, G:0.25, T:0.35
Consensus pattern (43 bp):
GATATTTGATTTCGTGTAAGACCATGTCTGGGACATTGGCATC
Found at i:42561629 original size:26 final size:26
Alignment explanation
Indices: 42561600--42561653 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
42561590 GGTATGTTTG
*
42561600 AAATTGTACATCATATTTGATGTTAA
1 AAATTGTACATCATATTTAATGTTAA
*
42561626 AAATTGTATATCATATTTAATGTTAA
1 AAATTGTACATCATATTTAATGTTAA
42561652 AA
1 AA
42561654 GGTAAGTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.43
Consensus pattern (26 bp):
AAATTGTACATCATATTTAATGTTAA
Found at i:42571581 original size:40 final size:40
Alignment explanation
Indices: 42571536--42571702 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
42571526 CGGAATATAA
42571536 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
42571576 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
42571616 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
42571656 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
42571695 CCGGATAT
1 CCGGATAT
42571703 CATTCAATTT
Statistics
Matches: 107, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
39 14 0.13
40 93 0.87
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:42579588 original size:40 final size:40
Alignment explanation
Indices: 42579543--42579709 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
42579533 CGGAATATAA
42579543 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
42579583 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
42579623 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
42579663 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
42579702 CCGGATAT
1 CCGGATAT
42579710 CATTCAATTT
Statistics
Matches: 107, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
39 14 0.13
40 93 0.87
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:42587073 original size:22 final size:22
Alignment explanation
Indices: 42587045--42587094 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
42587035 AAACATATAT
42587045 CACATATCTCATGAGCTCAGAC
1 CACATATCTCATGAGCTCAGAC
*
42587067 CACATATCTCATGAGCTCAGAT
1 CACATATCTCATGAGCTCAGAC
42587089 CACATA
1 CACATA
42587095 GTTCCTAGTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.34, C:0.30, G:0.12, T:0.24
Consensus pattern (22 bp):
CACATATCTCATGAGCTCAGAC
Found at i:42592484 original size:40 final size:40
Alignment explanation
Indices: 42592429--42592592 Score: 195
Period size: 40 Copynumber: 4.1 Consensus size: 40
42592419 TGAATGATAC
* * *
42592429 CCGGGCTAAGCCCCGAAGGCATTTATGCTAG-TGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-TTATAT
*
42592469 CCGGGTTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
* * *
42592509 CCGGGCTAAGACCCAAAGGCATTTGTGCGAGTTGCTATAC
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
* * * ** *
42592549 CCAGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
42592589 CCGG
1 CCGG
42592593 CCAAATTTCG
Statistics
Matches: 105, Mismatches: 18, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
40 103 0.98
41 2 0.02
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
Found at i:42595806 original size:38 final size:38
Alignment explanation
Indices: 42595755--42595828 Score: 148
Period size: 38 Copynumber: 1.9 Consensus size: 38
42595745 GCCACAAGTG
42595755 AAAATAAATCCTTCGCTCGTGTAGAGACTCGAACTCTA
1 AAAATAAATCCTTCGCTCGTGTAGAGACTCGAACTCTA
42595793 AAAATAAATCCTTCGCTCGTGTAGAGACTCGAACTC
1 AAAATAAATCCTTCGCTCGTGTAGAGACTCGAACTC
42595829 CTGACCCCTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (38 bp):
AAAATAAATCCTTCGCTCGTGTAGAGACTCGAACTCTA
Found at i:42604840 original size:24 final size:24
Alignment explanation
Indices: 42604812--42604857 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
42604802 AATAGTTGAT
42604812 AATTAGTA-CTTCTAACTTGGTTAG
1 AATTAGTACCTTCT-ACTTGGTTAG
* *
42604836 AATTATTACCTTCTCCTTGGTT
1 AATTAGTACCTTCTACTTGGTT
42604858 TCCACCCCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 14 0.74
25 5 0.26
ACGTcount: A:0.24, C:0.17, G:0.13, T:0.46
Consensus pattern (24 bp):
AATTAGTACCTTCTACTTGGTTAG
Found at i:42605907 original size:46 final size:46
Alignment explanation
Indices: 42605710--42605924 Score: 172
Period size: 46 Copynumber: 4.6 Consensus size: 46
42605700 GGTTATTGTG
* * *
42605710 AGCTAGTGTAAGACATGTTTGGGACATGCATCAGCTAC-ATTATGAG
1 AGCTAGTGTAAGACATGTCTGGGACATGCATCAGCTACGA-GATGAT
* * *
42605756 AGCCAGTGTAAGAACATGTCTGGGACATGGCATCAGC-ATCAAGACGAGT
1 AGCTAGTGTAAG-ACATGTCTGGGACAT-GCATCAGCTA-CGAGATGA-T
** **
42605805 -GCTAGTGTAAGACATGTCTAAGACATGCATTGGCCT-CGAGATG-T
1 AGCTAGTGTAAGACATGTCTGGGACATGCATCAG-CTACGAGATGAT
* * *
42605849 AAGCCAAG-GTAAGACATGTCGGGGACATGCATCGGCTACGAGATGAT
1 -AG-CTAGTGTAAGACATGTCTGGGACATGCATCAGCTACGAGATGAT
* *
42605896 AGTTAGTGTAAGACCATGTCTGAGACATG
1 AGCTAGTGTAAGA-CATGTCTGGGACATG
42605925 GTATTGACTT
Statistics
Matches: 134, Mismatches: 21, Indels: 27
0.74 0.12 0.15
Matches are distributed among these distances:
44 1 0.01
45 4 0.03
46 60 0.45
47 46 0.34
48 22 0.16
49 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.28, T:0.23
Consensus pattern (46 bp):
AGCTAGTGTAAGACATGTCTGGGACATGCATCAGCTACGAGATGAT
Found at i:42605939 original size:93 final size:94
Alignment explanation
Indices: 42605756--42605977 Score: 224
Period size: 93 Copynumber: 2.4 Consensus size: 94
42605746 ACATTATGAG
* * * * *
42605756 AGCCAGTGTAAGAACATGTCTG-GGACATGGCATCAGC-ATCAAGACGAGT-GCTAGTGTAAGAC
1 AGCCAGTGTAAGACCATGTC-GAGGACATGGCATCGGCTA-CGAGATGA-TAGTTAGTGTAAGAC
* *
42605818 ATGTCTAAGACATGCATTGGCCTCGAGATGTA
63 ATGTCTAAGACATGCATTGGACTCGAGATATA
*
42605850 AGCCAAG-GTAAGA-CATGTCGGGGACAT-GCATCGGCTACGAGATGATAGTTAGTGTAAGACCA
1 AGCC-AGTGTAAGACCATGTCGAGGACATGGCATCGGCTACGAGATGATAGTTAGTGTAAGA-CA
* * * *
42605912 TGTCTGAGACATGGTATT-GACTTGAGATATG
64 TGTCTAAGACAT-GCATTGGACTCGAGATATA
*
42605943 AGCCAGTGTAAGACCATGTCTAGGACATGGCATCG
1 AGCCAGTGTAAGACCATGTCGAGGACATGGCATCG
42605978 ACACCTTACC
Statistics
Matches: 107, Mismatches: 12, Indels: 17
0.79 0.09 0.12
Matches are distributed among these distances:
91 1 0.01
92 27 0.25
93 45 0.42
94 26 0.24
95 8 0.07
ACGTcount: A:0.30, C:0.18, G:0.29, T:0.23
Consensus pattern (94 bp):
AGCCAGTGTAAGACCATGTCGAGGACATGGCATCGGCTACGAGATGATAGTTAGTGTAAGACATG
TCTAAGACATGCATTGGACTCGAGATATA
Found at i:42612614 original size:47 final size:46
Alignment explanation
Indices: 42612499--42612627 Score: 161
Period size: 46 Copynumber: 2.8 Consensus size: 46
42612489 AATTTCACCT
* * *
42612499 ATAATGAACTCGGAACGCAACTCAAGGAGCTCGGGTGTTCACATCC
1 ATAATGAACTCGGAACGCAACTCAACGAGTTCGGATGTTCACATCC
* * * * *
42612545 ATAATGAACTCGGGACACAACTCAACGAGTTTGGATGCTT-GCTTCC
1 ATAATGAACTCGGAACGCAACTCAACGAGTTCGGATG-TTCACATCC
42612591 ATAAGTGAACTCGGAACGCAACTCAACGAGTTCGGAT
1 ATAA-TGAACTCGGAACGCAACTCAACGAGTTCGGAT
42612628 CTCAATTTCC
Statistics
Matches: 70, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
46 39 0.56
47 31 0.44
ACGTcount: A:0.31, C:0.24, G:0.23, T:0.22
Consensus pattern (46 bp):
ATAATGAACTCGGAACGCAACTCAACGAGTTCGGATGTTCACATCC
Found at i:42628993 original size:2 final size:2
Alignment explanation
Indices: 42628942--42628978 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
42628932 TAATGGTGTG
42628942 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 T
42628979 GTTCACTTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:42629037 original size:3 final size:3
Alignment explanation
Indices: 42629029--42629094 Score: 123
Period size: 3 Copynumber: 22.0 Consensus size: 3
42629019 AACTTAATGT
42629029 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
42629077 ATA ATA ATA ATA GTA ATA
1 ATA ATA ATA ATA ATA ATA
42629095 GGTGCAAATA
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:42632340 original size:2 final size:2
Alignment explanation
Indices: 42632333--42632368 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
42632323 AACTTCCTCT
42632333 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
42632369 AAAGGGCAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:42633289 original size:26 final size:26
Alignment explanation
Indices: 42633253--42633304 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
42633243 GAAGATTTTT
42633253 GTAAACTTTTTTTAAGTATTTTTGTA
1 GTAAACTTTTTTTAAGTATTTTTGTA
42633279 GTAAACTTTTTTTAAGTATTTTTGTA
1 GTAAACTTTTTTTAAGTATTTTTGTA
42633305 AAATTTGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.27, C:0.04, G:0.12, T:0.58
Consensus pattern (26 bp):
GTAAACTTTTTTTAAGTATTTTTGTA
Found at i:42633296 original size:15 final size:15
Alignment explanation
Indices: 42633253--42633296 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 15
42633243 GAAGATTTTT
42633253 GTAAACTTTTTTTAA
1 GTAAACTTTTTTTAA
*
42633268 GT--A-TTTTTGT-A
1 GTAAACTTTTTTTAA
42633279 GTAAACTTTTTTTAA
1 GTAAACTTTTTTTAA
42633294 GTA
1 GTA
42633297 TTTTTGTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 8
0.70 0.06 0.24
Matches are distributed among these distances:
11 3 0.13
12 6 0.26
13 2 0.09
14 6 0.26
15 6 0.26
ACGTcount: A:0.30, C:0.05, G:0.11, T:0.55
Consensus pattern (15 bp):
GTAAACTTTTTTTAA
Found at i:42633722 original size:11 final size:11
Alignment explanation
Indices: 42633636--42633778 Score: 60
Period size: 11 Copynumber: 12.7 Consensus size: 11
42633626 CAAATGCTTT
42633636 TAAAATAATAA
1 TAAAATAATAA
* *
42633647 CAAAATTAACAA
1 TAAAA-TAATAA
*
42633659 TAAAATAA-ATT
1 TAAAATAATA-A
* * *
42633670 TTATATAATAT
1 TAAAATAATAA
*
42633681 TCAAATAATAA
1 TAAAATAATAA
*
42633692 CAACAA-AATAA
1 TAA-AATAATAA
42633703 TAGCTAAATAATAA
1 TA---AAATAATAA
* *
42633717 TAAAATGATAG
1 TAAAATAATAA
*
42633728 TAAAATAGA-GA
1 TAAAATA-ATAA
*
42633739 GAAAATAATAA
1 TAAAATAATAA
* *
42633750 TAAATTAATAT
1 TAAAATAATAA
42633761 TAAAA-AATAA
1 TAAAATAATAA
*
42633771 AAAAATAA
1 TAAAATAA
42633779 AAATTTTTTA
Statistics
Matches: 96, Mismatches: 25, Indels: 22
0.67 0.17 0.15
Matches are distributed among these distances:
10 10 0.10
11 63 0.66
12 13 0.14
13 2 0.02
14 8 0.08
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.27
Consensus pattern (11 bp):
TAAAATAATAA
Found at i:42633919 original size:21 final size:21
Alignment explanation
Indices: 42633895--42633938 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
42633885 TATCCAAACG
42633895 TATTTTTCAAATTTATATTTT
1 TATTTTTCAAATTTATATTTT
*
42633916 TATTTTTCAGATTTATATTTT
1 TATTTTTCAAATTTATATTTT
42633937 TA
1 TA
42633939 GCCAAATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.66
Consensus pattern (21 bp):
TATTTTTCAAATTTATATTTT
Found at i:42643421 original size:46 final size:45
Alignment explanation
Indices: 42643354--42643528 Score: 208
Period size: 46 Copynumber: 3.8 Consensus size: 45
42643344 TGTAACCCGC
42643354 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGTAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGC-TTCGTAT
* *
42643400 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGT-T
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--GCTTCGTAT
* *** * * *
42643446 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGGC-TTCGTAT
*
42643493 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG
42643529 ATGCCCAAAC
Statistics
Matches: 109, Mismatches: 15, Indels: 10
0.81 0.11 0.07
Matches are distributed among these distances:
45 1 0.01
46 71 0.65
47 35 0.32
48 2 0.02
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (45 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCTTCGTAT
Found at i:42643474 original size:93 final size:93
Alignment explanation
Indices: 42643362--42643533 Score: 299
Period size: 93 Copynumber: 1.8 Consensus size: 93
42643352 GCCCATAAGT
* * *
42643362 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGTATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
42643427 CGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
*
42643455 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
42643520 CGAGTTCGGATGCC
66 CGAGCTCGGATGCC
42643534 CAAACATCCT
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:42643548 original size:46 final size:46
Alignment explanation
Indices: 42643359--42643548 Score: 149
Period size: 46 Copynumber: 4.1 Consensus size: 46
42643349 CCCGCCCATA
* ** ** *
42643359 AGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGT--ATCCAT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCATACATCC-T
* *
42643404 AAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCT
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCA--TACATC-CT
* * * * *
42643454 --CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCAT--A
1 AGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGCCCATACATCCT
*
42643498 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAAACATCCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCATACATCCT
42643544 AGTGA
1 AGTGA
42643549 CATGTCACTT
Statistics
Matches: 114, Mismatches: 19, Indels: 22
0.74 0.12 0.14
Matches are distributed among these distances:
44 8 0.07
46 65 0.57
47 31 0.27
48 1 0.01
49 4 0.04
50 4 0.04
51 1 0.01
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (46 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCATACATCCT
Found at i:42649177 original size:31 final size:31
Alignment explanation
Indices: 42649142--42649210 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
42649132 TACAAAATGA
42649142 TCATTGAATTATTCAGAAGTTTTCATTTAAG
1 TCATTGAATTATTCAGAAGTTTTCATTTAAG
* ** *
42649173 TCATTAAATTATTTGGAAGTTTTTATTTAAG
1 TCATTGAATTATTCAGAAGTTTTCATTTAAG
42649204 TCATTGA
1 TCATTGA
42649211 GTTAAGTTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.32, C:0.07, G:0.13, T:0.48
Consensus pattern (31 bp):
TCATTGAATTATTCAGAAGTTTTCATTTAAG
Found at i:42656571 original size:29 final size:29
Alignment explanation
Indices: 42656527--42656599 Score: 137
Period size: 29 Copynumber: 2.5 Consensus size: 29
42656517 GTGACAAGAT
*
42656527 TGGCACTAAGTATGCAAGCTTGAAAAGTA
1 TGGCACTAAGTGTGCAAGCTTGAAAAGTA
42656556 TGGCACTAAGTGTGCAAGCTTGAAAAGTA
1 TGGCACTAAGTGTGCAAGCTTGAAAAGTA
42656585 TGGCACTAAGTGTGC
1 TGGCACTAAGTGTGC
42656600 GAATTTAAAT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.33, C:0.15, G:0.27, T:0.25
Consensus pattern (29 bp):
TGGCACTAAGTGTGCAAGCTTGAAAAGTA
Found at i:42656618 original size:29 final size:29
Alignment explanation
Indices: 42656586--42656658 Score: 92
Period size: 29 Copynumber: 2.5 Consensus size: 29
42656576 TGAAAAGTAT
* * *
42656586 GGCACTAAGTGTGCGAATTTAAATTATAC
1 GGCACTAAGTGTGCGAACTTAAATCACAC
* * *
42656615 GGCACTATGTGTGCGAGCTTAAATCACAT
1 GGCACTAAGTGTGCGAACTTAAATCACAC
42656644 GGCACTAAGTGTGCG
1 GGCACTAAGTGTGCG
42656659 TGATCGATTA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.27
Consensus pattern (29 bp):
GGCACTAAGTGTGCGAACTTAAATCACAC
Found at i:42664518 original size:29 final size:29
Alignment explanation
Indices: 42664476--42664544 Score: 138
Period size: 29 Copynumber: 2.4 Consensus size: 29
42664466 GTGACAAGAT
42664476 TGGCACTAAGTGTGCAAGCTTGAAAAGTA
1 TGGCACTAAGTGTGCAAGCTTGAAAAGTA
42664505 TGGCACTAAGTGTGCAAGCTTGAAAAGTA
1 TGGCACTAAGTGTGCAAGCTTGAAAAGTA
42664534 TGGCACTAAGT
1 TGGCACTAAGT
42664545 TTAAATTATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.33, C:0.14, G:0.28, T:0.25
Consensus pattern (29 bp):
TGGCACTAAGTGTGCAAGCTTGAAAAGTA
Found at i:42673607 original size:28 final size:29
Alignment explanation
Indices: 42673575--42673673 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 29
42673565 ATAATAAGCC
*
42673575 CGCACACTTAGTGCTTA-ATAGTCAAACT
1 CGCACACTTAGTGCTTATATAATCAAACT
42673603 CGCACACTTAGTGC-TATATAATCAAACT
1 CGCACACTTAGTGCTTATATAATCAAACT
* * ** *
42673631 TGCACACTTAGTGC-TATACAATTTGAACC
1 CGCACACTTAGTGCTTATATAA-TCAAACT
42673660 CGCACACTTAGTGC
1 CGCACACTTAGTGC
42673674 CAATTTATGA
Statistics
Matches: 62, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
27 2 0.03
28 43 0.69
29 17 0.27
ACGTcount: A:0.31, C:0.26, G:0.14, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCTTATATAATCAAACT
Found at i:42675524 original size:17 final size:18
Alignment explanation
Indices: 42675497--42675542 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
42675487 GTATTAATTT
42675497 TATAT-TATTATAAT-TG
1 TATATATATTATAATGTG
* *
42675513 TGTATATATTAT-GTGTG
1 TATATATATTATAATGTG
42675530 TATATATATTATA
1 TATATATATTATA
42675543 TGCATATTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
16 5 0.21
17 19 0.79
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.54
Consensus pattern (18 bp):
TATATATATTATAATGTG
Found at i:42676156 original size:11 final size:11
Alignment explanation
Indices: 42676140--42676164 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
42676130 GTTTTGGAAC
42676140 AAAAAAAAAAG
1 AAAAAAAAAAG
42676151 AAAAAAAAAAG
1 AAAAAAAAAAG
42676162 AAA
1 AAA
42676165 GTCAAAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:42681883 original size:40 final size:40
Alignment explanation
Indices: 42681837--42681955 Score: 159
Period size: 40 Copynumber: 3.0 Consensus size: 40
42681827 CGGGATTTAA
42681837 CCGGATATAACAACTCGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAACAACTCGCACAAATGCCTTCGGGTCTTAGC
* * * *
42681877 CCGGATATAATC-GCTAGCATAAATGCCTTCGGGTCATAGC
1 CCGGATATAA-CAACTCGCACAAATGCCTTCGGGTCTTAGC
* * *
42681917 CCGGATATAGCAACTCGCACGAATGCCTTCGGATCTTAG
1 CCGGATATAACAACTCGCACAAATGCCTTCGGGTCTTAG
42681956 TCCAGTTATC
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
39 1 0.02
40 64 0.97
41 1 0.02
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CCGGATATAACAACTCGCACAAATGCCTTCGGGTCTTAGC
Found at i:42689345 original size:28 final size:28
Alignment explanation
Indices: 42689313--42689371 Score: 109
Period size: 28 Copynumber: 2.1 Consensus size: 28
42689303 GCAGATATGA
42689313 TGACTAAGTCACTTCCTATAACCAAGTT
1 TGACTAAGTCACTTCCTATAACCAAGTT
*
42689341 TGACTAAGTCATTTCCTATAACCAAGTT
1 TGACTAAGTCACTTCCTATAACCAAGTT
42689369 TGA
1 TGA
42689372 GCATTGCTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.34
Consensus pattern (28 bp):
TGACTAAGTCACTTCCTATAACCAAGTT
Found at i:42694297 original size:26 final size:26
Alignment explanation
Indices: 42694244--42694299 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
42694234 TGGGCAAAGG
* *
42694244 GACCCCCACAGGGGGCTCCATCCCTT
1 GACCCCCACAAGGGGCTCCAGCCCTT
42694270 GACCCCCACAAGGGGCTCC-GCCCATT
1 GACCCCCACAAGGGGCTCCAGCCC-TT
42694296 GACC
1 GACC
42694300 TCATGTGTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
25 3 0.11
26 24 0.89
ACGTcount: A:0.18, C:0.46, G:0.23, T:0.12
Consensus pattern (26 bp):
GACCCCCACAAGGGGCTCCAGCCCTT
Found at i:42697016 original size:14 final size:15
Alignment explanation
Indices: 42696997--42697034 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
42696987 AATAACTTAA
*
42696997 AATCTAA-CCATTTT
1 AATCTAATCCATGTT
42697011 AATCTAAATCCATGTT
1 AATCT-AATCCATGTT
42697027 AATCTAAT
1 AATCTAAT
42697035 ATGCAAGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 5 0.24
15 5 0.24
16 11 0.52
ACGTcount: A:0.39, C:0.18, G:0.03, T:0.39
Consensus pattern (15 bp):
AATCTAATCCATGTT
Found at i:42698381 original size:24 final size:24
Alignment explanation
Indices: 42698349--42698395 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
42698339 TTCTTCGGTT
*
42698349 TCTTGAATCAAATTAACCCAAATC
1 TCTTGAATCAAATCAACCCAAATC
42698373 TCTTGAATCAAATCAACCCAAAT
1 TCTTGAATCAAATCAACCCAAAT
42698396 AGCTTTTTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.43, C:0.26, G:0.04, T:0.28
Consensus pattern (24 bp):
TCTTGAATCAAATCAACCCAAATC
Found at i:42703726 original size:39 final size:39
Alignment explanation
Indices: 42703672--42703824 Score: 252
Period size: 39 Copynumber: 3.9 Consensus size: 39
42703662 GAATGTTCGA
*
42703672 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAATT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT
*
42703711 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGCT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT
*
42703750 ATGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT
* *
42703789 GTGATATCCGGGTTAAGTCCCGAAGGCATTTGTGCG
1 GTGATATCCGGGCTAAG-CCCGAAGGCAATTGTGCG
42703825 GGTTACCATA
Statistics
Matches: 106, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
39 89 0.84
40 17 0.16
ACGTcount: A:0.24, C:0.21, G:0.32, T:0.24
Consensus pattern (39 bp):
GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT
Found at i:42703840 original size:40 final size:39
Alignment explanation
Indices: 42703673--42703854 Score: 247
Period size: 39 Copynumber: 4.6 Consensus size: 39
42703663 AATGTTCGAG
* *
42703673 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAATTG
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
*
42703712 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGCTA
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
*
42703751 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTG
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
* * *
42703790 TGATATCCGGGTTAAGTCCCGAAGGCATTTGTGCGGGTTA
1 TGATATCCGGGCTAAG-CCCGAAGGCAATTGTGCGAGTTA
** * *
42703830 CCATAACCGGGCTATGTCCCGAAGG
1 TGATATCCGGGCTAAG-CCCGAAGG
42703855 TGTTTTGAAC
Statistics
Matches: 128, Mismatches: 14, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
39 88 0.69
40 40 0.31
ACGTcount: A:0.24, C:0.22, G:0.31, T:0.23
Consensus pattern (39 bp):
TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
Found at i:42711809 original size:39 final size:39
Alignment explanation
Indices: 42711755--42711907 Score: 252
Period size: 39 Copynumber: 3.9 Consensus size: 39
42711745 GAATGTTCGA
*
42711755 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAATT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT
*
42711794 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGCT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT
*
42711833 ATGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT
* *
42711872 GTGATATCCGGGTTAAGTCCCGAAGGCATTTGTGCG
1 GTGATATCCGGGCTAAG-CCCGAAGGCAATTGTGCG
42711908 GGTTACCATA
Statistics
Matches: 106, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
39 89 0.84
40 17 0.16
ACGTcount: A:0.24, C:0.21, G:0.32, T:0.24
Consensus pattern (39 bp):
GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT
Found at i:42711923 original size:40 final size:39
Alignment explanation
Indices: 42711756--42711937 Score: 247
Period size: 39 Copynumber: 4.6 Consensus size: 39
42711746 AATGTTCGAG
* *
42711756 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAATTG
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
*
42711795 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGCTA
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
*
42711834 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTG
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
* * *
42711873 TGATATCCGGGTTAAGTCCCGAAGGCATTTGTGCGGGTTA
1 TGATATCCGGGCTAAG-CCCGAAGGCAATTGTGCGAGTTA
** * *
42711913 CCATAACCGGGCTATGTCCCGAAGG
1 TGATATCCGGGCTAAG-CCCGAAGG
42711938 TGTTTTGAAC
Statistics
Matches: 128, Mismatches: 14, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
39 88 0.69
40 40 0.31
ACGTcount: A:0.24, C:0.22, G:0.31, T:0.23
Consensus pattern (39 bp):
TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
Found at i:42713660 original size:24 final size:24
Alignment explanation
Indices: 42713633--42713695 Score: 126
Period size: 24 Copynumber: 2.6 Consensus size: 24
42713623 CTTATTATGT
42713633 TCGCACACATAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
42713657 TCGCACACATAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
42713681 TCGCACACATAGTGC
1 TCGCACACATAGTGC
42713696 ATTTGAGATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.35, C:0.27, G:0.17, T:0.21
Consensus pattern (24 bp):
TCGCACACATAGTGCCATAGTAAA
Found at i:42721488 original size:24 final size:23
Alignment explanation
Indices: 42721456--42721636 Score: 227
Period size: 24 Copynumber: 7.6 Consensus size: 23
42721446 ACCAAACGTT
* **
42721456 GCACACATAGTGCTTATTATGTTC
1 GCACACATAGTGCTTAGTA-AATC
*
42721480 GCACACATAGTGCCATAGTAAATC
1 GCACACATAGTG-CTTAGTAAATC
42721504 GCACACATAGTGCTATAGTAAATC
1 GCACACATAGTGCT-TAGTAAATC
* *
42721528 GCACACATAGTGCCATACTAAATC
1 GCACACATAGTG-CTTAGTAAATC
42721552 GCACACATAGTGCTATAGTAAATC
1 GCACACATAGTGCT-TAGTAAATC
*
42721576 GCACACATAGTGCCATAGTAAATC
1 GCACACATAGTG-CTTAGTAAATC
*
42721600 GCACACATAGTGCCATAGTAAATC
1 GCACACATAGTG-CTTAGTAAATC
42721624 GCACACATAGTGC
1 GCACACATAGTGC
42721637 ATTTGAGATT
Statistics
Matches: 142, Mismatches: 10, Indels: 11
0.87 0.06 0.07
Matches are distributed among these distances:
23 3 0.02
24 132 0.93
25 7 0.05
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (23 bp):
GCACACATAGTGCTTAGTAAATC
Found at i:42721530 original size:48 final size:48
Alignment explanation
Indices: 42721456--42721636 Score: 301
Period size: 48 Copynumber: 3.8 Consensus size: 48
42721446 ACCAAACGTT
* **
42721456 GCACACATAGTGCT-TATTATGTTCGCACACATAGTGCCATAGTAAATC
1 GCACACATAGTGCTATAGTA-AATCGCACACATAGTGCCATAGTAAATC
*
42721504 GCACACATAGTGCTATAGTAAATCGCACACATAGTGCCATACTAAATC
1 GCACACATAGTGCTATAGTAAATCGCACACATAGTGCCATAGTAAATC
42721552 GCACACATAGTGCTATAGTAAATCGCACACATAGTGCCATAGTAAATC
1 GCACACATAGTGCTATAGTAAATCGCACACATAGTGCCATAGTAAATC
*
42721600 GCACACATAGTGCCATAGTAAATCGCACACATAGTGC
1 GCACACATAGTGCTATAGTAAATCGCACACATAGTGC
42721637 ATTTGAGATT
Statistics
Matches: 126, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
48 122 0.97
49 4 0.03
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (48 bp):
GCACACATAGTGCTATAGTAAATCGCACACATAGTGCCATAGTAAATC
Found at i:42721573 original size:72 final size:72
Alignment explanation
Indices: 42721478--42721636 Score: 291
Period size: 72 Copynumber: 2.2 Consensus size: 72
42721468 CTTATTATGT
*
42721478 TCGCACACATAGTGCCATAGTAAATCGCACACATAGTGCTATAGTAAATCGCACACATAGTGCCA
1 TCGCACACATAGTGCCATAGTAAATCGCACACATAGTGCCATAGTAAATCGCACACATAGTGCCA
42721543 TACTAAA
66 TACTAAA
*
42721550 TCGCACACATAGTGCTATAGTAAATCGCACACATAGTGCCATAGTAAATCGCACACATAGTGCCA
1 TCGCACACATAGTGCCATAGTAAATCGCACACATAGTGCCATAGTAAATCGCACACATAGTGCCA
*
42721615 TAGTAAA
66 TACTAAA
42721622 TCGCACACATAGTGC
1 TCGCACACATAGTGC
42721637 ATTTGAGATT
Statistics
Matches: 84, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 84 1.00
ACGTcount: A:0.36, C:0.25, G:0.16, T:0.22
Consensus pattern (72 bp):
TCGCACACATAGTGCCATAGTAAATCGCACACATAGTGCCATAGTAAATCGCACACATAGTGCCA
TACTAAA
Found at i:42723787 original size:29 final size:28
Alignment explanation
Indices: 42723755--42723857 Score: 116
Period size: 29 Copynumber: 3.6 Consensus size: 28
42723745 GTGACGAGAT
* *
42723755 TGGCACTGAGTGTGCGAGCTTGTAATGTA
1 TGGCACTAAGTGTGCGAGCTTG-AATATA
* *
42723784 TGGCACTAAGTGTGCGAGTTTGGACTATA
1 TGGCACTAAGTGTGCGAGCTT-GAATATA
* * *
42723813 TGGCACTATGTGTGCGGGCTTGAATCACA
1 TGGCACTAAGTGTGCGAGCTTGAAT-ATA
42723842 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
42723858 TGATTGAGTA
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
28 3 0.05
29 58 0.94
30 1 0.02
ACGTcount: A:0.21, C:0.17, G:0.33, T:0.29
Consensus pattern (28 bp):
TGGCACTAAGTGTGCGAGCTTGAATATA
Done.