Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 97880472
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: 97880472
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 192 characters in sequence are not A, C, G, or T
File 193 of 335
Found at i:58077057 original size:46 final size:46
Alignment explanation
Indices: 58077004--58077179 Score: 232
Period size: 46 Copynumber: 3.8 Consensus size: 46
58076994 TATTTGGGCA
58077004 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* * * *
58077050 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---CGA-GCG
*
58077097 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* *
58077143 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
58077180 GCGGGTTACA
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 4 0.04
45 2 0.02
46 67 0.60
47 33 0.29
48 2 0.02
50 4 0.04
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
Found at i:58077159 original size:93 final size:93
Alignment explanation
Indices: 58077000--58077171 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
58076990 GGGATATTTG
* *
58077000 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
58077065 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
*
58077093 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
58077158 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
58077172 ACTTATGGGC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:58080146 original size:15 final size:15
Alignment explanation
Indices: 58080126--58080194 Score: 84
Period size: 15 Copynumber: 4.6 Consensus size: 15
58080116 GTATCTTGGG
58080126 TTTCTTTATCCTGGA
1 TTTCTTTATCCTGGA
* *
58080141 TCTCTTTATTCTGGA
1 TTTCTTTATCCTGGA
* *
58080156 TTTCTTTATTCTGGG
1 TTTCTTTATCCTGGA
* *
58080171 TTTCTCTATCTTGGA
1 TTTCTTTATCCTGGA
58080186 TTTCTTTAT
1 TTTCTTTAT
58080195 TCGGTTTTCT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.12, C:0.17, G:0.13, T:0.58
Consensus pattern (15 bp):
TTTCTTTATCCTGGA
Found at i:58080195 original size:30 final size:30
Alignment explanation
Indices: 58080117--58080204 Score: 99
Period size: 30 Copynumber: 3.0 Consensus size: 30
58080107 CATAGTATCG
* * * *
58080117 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCTGGATTTCTC
*
58080147 TAT-TCTGGATTTCTTTATTCTGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCTGGATTTCTC
*
58080177 TATCTTGGATTTCTTTATTC-GGTTTTCT
1 TATCTTGGATTTCTTTATTCTGGATTTCT
58080205 TGTTATCTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 8 0.16
30 41 0.82
31 1 0.02
ACGTcount: A:0.10, C:0.17, G:0.16, T:0.57
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCTGGATTTCTC
Found at i:58082642 original size:46 final size:46
Alignment explanation
Indices: 58082589--58082764 Score: 232
Period size: 46 Copynumber: 3.8 Consensus size: 46
58082579 TATTTGGGCA
58082589 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* * * *
58082635 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---CGA-GCG
*
58082682 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* *
58082728 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
58082765 GCGGGTTACA
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 4 0.04
45 2 0.02
46 67 0.60
47 33 0.29
48 2 0.02
50 4 0.04
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
Found at i:58082744 original size:93 final size:93
Alignment explanation
Indices: 58082585--58082756 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
58082575 GGGATATTTG
* *
58082585 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
58082650 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
*
58082678 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
58082743 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
58082757 ACTTATGGGC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:58086360 original size:21 final size:21
Alignment explanation
Indices: 58086336--58086381 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
58086326 TAAAACTAGG
* *
58086336 ATGAATATACATGTTACTATT
1 ATGAATAGACATGTTACCATT
*
58086357 ATGAATAGATATGTTACCATT
1 ATGAATAGACATGTTACCATT
58086378 ATGA
1 ATGA
58086382 GCTTAATTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.39
Consensus pattern (21 bp):
ATGAATAGACATGTTACCATT
Found at i:58089999 original size:40 final size:40
Alignment explanation
Indices: 58089941--58090108 Score: 230
Period size: 40 Copynumber: 4.2 Consensus size: 40
58089931 TGAATGATAC
*
58089941 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
* **
58089981 CCGGGCTAAGACCTGAAGGCATTTGTGTAAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
* *
58090021 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAC
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
* * ** *
58090061 CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
58090101 CC-GGCTAA
1 CCGGGCTAA
58090109 ATTCCGAAGA
Statistics
Matches: 111, Mismatches: 17, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
39 5 0.05
40 106 0.95
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.28
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
Found at i:58092093 original size:8 final size:8
Alignment explanation
Indices: 58092080--58092111 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
58092070 CTAGATCGGC
58092080 AAAAGCCG
1 AAAAGCCG
58092088 AAAAGCCG
1 AAAAGCCG
*
58092096 AAATGCCG
1 AAAAGCCG
58092104 AAAAGCCG
1 AAAAGCCG
58092112 GTATTTTGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.47, C:0.25, G:0.25, T:0.03
Consensus pattern (8 bp):
AAAAGCCG
Found at i:58092399 original size:28 final size:28
Alignment explanation
Indices: 58092359--58092422 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
58092349 TGTACTAGAG
*
58092359 TACCCCTATGTATGCAAAATTACCAT-TA
1 TACCCCTATGTATGCAAAATGACC-TCTA
58092387 TACCCCTATGTATGCAAAATGACCTCTA
1 TACCCCTATGTATGCAAAATGACCTCTA
58092415 TACCCCTA
1 TACCCCTA
58092423 GGGTTAATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
27 1 0.03
28 33 0.97
ACGTcount: A:0.33, C:0.30, G:0.08, T:0.30
Consensus pattern (28 bp):
TACCCCTATGTATGCAAAATGACCTCTA
Found at i:58092586 original size:27 final size:28
Alignment explanation
Indices: 58092528--58092617 Score: 112
Period size: 27 Copynumber: 3.2 Consensus size: 28
58092518 AGGAAGCGTC
*
58092528 CTGGTGGCTA-TGCCACAAATTATCTGTT
1 CTGGTGGC-ACTGCCACAAAATATCTGTT
* **
58092556 CTGGTGGCCCTGCCAC-GTATATCTGTT
1 CTGGTGGCACTGCCACAAAATATCTGTT
58092583 CTGGTGGCACTGCCACAAAATATCTGTAT
1 CTGGTGGCACTGCCACAAAATATCTGT-T
58092612 CTGGTG
1 CTGGTG
58092618 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:58092628 original size:29 final size:28
Alignment explanation
Indices: 58092538--58092628 Score: 94
Period size: 27 Copynumber: 3.2 Consensus size: 28
58092528 CTGGTGGCTA
* * *
58092538 TGCCACAAATTATCTGTTCTGGTGGCCC
1 TGCCACAAAATATCTGTTCTGGTGACAC
** *
58092566 TGCCAC-GTATATCTGTTCTGGTGGCAC
1 TGCCACAAAATATCTGTTCTGGTGACAC
*
58092593 TGCCACAAAATATCTGTATCTGGTGACTC
1 TGCCACAAAATATCTGT-TCTGGTGACAC
*
58092622 TGTCACA
1 TGCCACA
58092629 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:58092636 original size:55 final size:56
Alignment explanation
Indices: 58092528--58092642 Score: 137
Period size: 55 Copynumber: 2.1 Consensus size: 56
58092518 AGGAAGCGTC
* * *
58092528 CTGGTGGCTATGCCACAAATTATCTGTTCTGGTGGCCCTGCCACGTATATCTGT-T
1 CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCACATATATCTGTAT
* * *
58092583 CTGGTGGC-ACTGCCACAAAATATCTGTATCTGGTGACTCTGTCACAT-TTTCTGTAT
1 CTGGTGGCTA-TGCCACAAAATATCTGT-TCTGGTGACCCTGCCACATATATCTGTAT
58092639 CTGG
1 CTGG
58092643 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:58093729 original size:11 final size:10
Alignment explanation
Indices: 58093701--58093734 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
58093691 AGCCTGTAAG
58093701 TATTCTGAAT
1 TATTCTGAAT
*
58093711 TTTTCTGAAT
1 TATTCTGAAT
58093721 ATATTCTGAAT
1 -TATTCTGAAT
58093732 TAT
1 TAT
58093735 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:58099887 original size:28 final size:28
Alignment explanation
Indices: 58099847--58099910 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
58099837 TGTACTAGAG
*
58099847 TACCCCTATGTATGCAAAATTACCAT-TA
1 TACCCCTATGTATGCAAAATGACC-TCTA
58099875 TACCCCTATGTATGCAAAATGACCTCTA
1 TACCCCTATGTATGCAAAATGACCTCTA
58099903 TACCCCTA
1 TACCCCTA
58099911 GGGTTAATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
27 1 0.03
28 33 0.97
ACGTcount: A:0.33, C:0.30, G:0.08, T:0.30
Consensus pattern (28 bp):
TACCCCTATGTATGCAAAATGACCTCTA
Found at i:58101533 original size:29 final size:29
Alignment explanation
Indices: 58101505--58101607 Score: 143
Period size: 29 Copynumber: 3.6 Consensus size: 29
58101495 CCTCCGAGCT
** * * *
58101505 CGCACACCCAGTGCCGTATTTTTCCAGCT
1 CGCACACTTAGTGCCATATATTTCCAGCA
* *
58101534 TGCACACTTAGTGCTATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
58101563 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
58101592 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
58101608 ATCTCGTCAC
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 65 1.00
ACGTcount: A:0.24, C:0.32, G:0.16, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATATATTTCCAGCA
Found at i:58101547 original size:58 final size:58
Alignment explanation
Indices: 58101476--58101607 Score: 131
Period size: 58 Copynumber: 2.3 Consensus size: 58
58101466 AATTTAAGCC
** * * * * *
58101476 CGCACACACAGTGCCATA-CCCTCCGAGCTCGCACACCCAGTGCCGTATTTTTCCAGCT
1 CGCACACTTAGTGCCATATACCTCC-AGCACGCACACCCAGTGCCATATATTTCCAGCA
* * ** **
58101534 TGCACACTTAGTGCTATATATTTCCAGCACGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATACCTCCAGCACGCACACCCAGTGCCATATATTTCCAGCA
58101592 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
58101608 ATCTCGTCAC
Statistics
Matches: 58, Mismatches: 15, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
58 55 0.95
59 3 0.05
ACGTcount: A:0.24, C:0.35, G:0.16, T:0.25
Consensus pattern (58 bp):
CGCACACTTAGTGCCATATACCTCCAGCACGCACACCCAGTGCCATATATTTCCAGCA
Found at i:58108928 original size:40 final size:40
Alignment explanation
Indices: 58108883--58109012 Score: 165
Period size: 40 Copynumber: 3.2 Consensus size: 40
58108873 CGGAATACAA
58108883 CCGGATATAACCACGT-GCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TAGCACGAATGCCTTCGGGTCTTAGC
* ** *
58108923 CCGGATAGAATGACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
* * *
58108963 CCGGATGTAGCCACTAGCAC-AATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCACGAA-TGCCTTCGGGTCTTAGC
58109003 CCGGATATAA
1 CCGGATATAA
58109013 TTTCCAGCAT
Statistics
Matches: 76, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
39 3 0.04
40 73 0.96
ACGTcount: A:0.24, C:0.28, G:0.25, T:0.23
Consensus pattern (40 bp):
CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
Found at i:58109027 original size:40 final size:40
Alignment explanation
Indices: 58108883--58109049 Score: 153
Period size: 40 Copynumber: 4.2 Consensus size: 40
58108873 CGGAATACAA
* **
58108883 CCGGATATAACCACGTGCACGAA-TGCCTTCGGGTCTTAGC
1 CCGGATATAATCACCAGCAC-AATTGCCTTCGGGTCTTAGC
* *
58108923 CCGGATAGAATGACTC-GCACGAA-TGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-CAGCAC-AATTGCCTTCGGGTCTTAGC
* ** * *
58108963 CCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACCAGCACAATTGCCTTCGGGTCTTAGC
** * *
58109003 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACCAGCACAATTGCCTTCGGGTCTTAGC
58109042 CCGGATAT
1 CCGGATAT
58109050 CATTCAATTT
Statistics
Matches: 104, Mismatches: 20, Indels: 7
0.79 0.15 0.05
Matches are distributed among these distances:
39 15 0.14
40 89 0.86
ACGTcount: A:0.23, C:0.28, G:0.24, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACCAGCACAATTGCCTTCGGGTCTTAGC
Found at i:58116969 original size:40 final size:40
Alignment explanation
Indices: 58116924--58117053 Score: 165
Period size: 40 Copynumber: 3.2 Consensus size: 40
58116914 CGGAATACAA
58116924 CCGGATATAACCACGT-GCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TAGCACGAATGCCTTCGGGTCTTAGC
* ** *
58116964 CCGGATAGAATGACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
* * *
58117004 CCGGATGTAGCCACTAGCAC-AATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCACGAA-TGCCTTCGGGTCTTAGC
58117044 CCGGATATAA
1 CCGGATATAA
58117054 TTTCCAGCAT
Statistics
Matches: 76, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
39 3 0.04
40 73 0.96
ACGTcount: A:0.24, C:0.28, G:0.25, T:0.23
Consensus pattern (40 bp):
CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
Found at i:58117068 original size:40 final size:40
Alignment explanation
Indices: 58116924--58117087 Score: 145
Period size: 40 Copynumber: 4.1 Consensus size: 40
58116914 CGGAATACAA
* **
58116924 CCGGATATAACCACGTGCACGAA-TGCCTTCGGGTCTTAGC
1 CCGGATATAATCACCAGCAC-AATTGCCTTCGGGTCTTAGC
* *
58116964 CCGGATAGAATGACTC-GCACGAA-TGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-CAGCAC-AATTGCCTTCGGGTCTTAGC
* ** * *
58117004 CCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACCAGCACAATTGCCTTCGGGTCTTAGC
** * * *
58117044 CCGGATATAATTTCCAGCATAATTGTCTTCGGGGCTTAGC
1 CCGGATATAATCACCAGCACAATTGCCTTCGGGTCTTAGC
58117084 CCGG
1 CCGG
58117088 GTATCATTCA
Statistics
Matches: 100, Mismatches: 21, Indels: 6
0.79 0.17 0.05
Matches are distributed among these distances:
39 2 0.02
40 98 0.98
ACGTcount: A:0.22, C:0.28, G:0.25, T:0.25
Consensus pattern (40 bp):
CCGGATATAATCACCAGCACAATTGCCTTCGGGTCTTAGC
Found at i:58121193 original size:47 final size:47
Alignment explanation
Indices: 58121132--58121261 Score: 194
Period size: 47 Copynumber: 2.8 Consensus size: 47
58121122 GTTTGAGTGA
*
58121132 TACCTTGATTTGGCTACGGGCCATGGTATAGGTATTCAAAGGG-T-AGT
1 TACCTTGATTTGGCTACGGGCCATGGTATAGGTACTC--AGGGATAAGT
*
58121179 TACCTTGATTTGGCTA-GAGGCCATGGTATAGGTACTCTGGGATAAGT
1 TACCTTGATTTGGCTACG-GGCCATGGTATAGGTACTCAGGGATAAGT
58121226 TACCTTGATTTGGCTACGGGCCATGGTATAGGTACT
1 TACCTTGATTTGGCTACGGGCCATGGTATAGGTACT
58121262 TATTGATAGA
Statistics
Matches: 77, Mismatches: 2, Indels: 8
0.89 0.02 0.09
Matches are distributed among these distances:
45 3 0.04
46 2 0.03
47 71 0.92
48 1 0.01
ACGTcount: A:0.22, C:0.16, G:0.29, T:0.32
Consensus pattern (47 bp):
TACCTTGATTTGGCTACGGGCCATGGTATAGGTACTCAGGGATAAGT
Found at i:58127374 original size:7 final size:7
Alignment explanation
Indices: 58127361--58127429 Score: 59
Period size: 7 Copynumber: 9.1 Consensus size: 7
58127351 TCTTTTTAGC
58127361 TTTATTT
1 TTTATTT
*
58127368 CTTATTT
1 TTTATTT
58127375 TTTA-TT
1 TTTATTT
58127381 TTTATTT
1 TTTATTT
58127388 TTTATTAGT
1 TTTATT--T
58127397 TTTATTTT
1 TTTA-TTT
58127405 TATTATTT
1 T-TTATTT
*
58127413 TTAATTATT
1 TTTA-T-TT
58127422 TTTATTT
1 TTTATTT
58127429 T
1 T
58127430 GTTTTAATAG
Statistics
Matches: 51, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
6 6 0.12
7 22 0.43
8 8 0.16
9 13 0.25
10 2 0.04
ACGTcount: A:0.19, C:0.01, G:0.01, T:0.78
Consensus pattern (7 bp):
TTTATTT
Found at i:58127378 original size:20 final size:20
Alignment explanation
Indices: 58127353--58127393 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
58127343 CAGTCCATTC
58127353 TTTTTAGCTTTATTTCTTAT
1 TTTTTAGCTTTATTTCTTAT
** *
58127373 TTTTTATTTTTATTTTTTAT
1 TTTTTAGCTTTATTTCTTAT
58127393 T
1 T
58127394 AGTTTTATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.05, G:0.02, T:0.78
Consensus pattern (20 bp):
TTTTTAGCTTTATTTCTTAT
Found at i:58127382 original size:6 final size:6
Alignment explanation
Indices: 58127361--58127429 Score: 54
Period size: 6 Copynumber: 11.3 Consensus size: 6
58127351 TCTTTTTAGC
* *
58127361 TTTATT TCTTATTT TTTATT TTTA-T TTT-TT ATTAGT TTTATT TTTATT
1 TTTATT T-TTA-TT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT
*
58127409 ATTT-TT AATTATT TTTATT TT
1 -TTTATT -TTTATT TTTATT TT
58127430 GTTTTAATAG
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
5 7 0.14
6 30 0.59
7 11 0.22
8 3 0.06
ACGTcount: A:0.19, C:0.01, G:0.01, T:0.78
Consensus pattern (6 bp):
TTTATT
Found at i:58127401 original size:9 final size:9
Alignment explanation
Indices: 58127372--58127427 Score: 52
Period size: 9 Copynumber: 6.8 Consensus size: 9
58127362 TTATTTCTTA
58127372 TTTT-TTAT
1 TTTTATTAT
58127380 TTTTA-T-T
1 TTTTATTAT
58127387 TTTTATTA-
1 TTTTATTAT
*
58127395 -GTT-TTAT
1 TTTTATTAT
58127402 TTTTATTAT
1 TTTTATTAT
58127411 TTTTAATTAT
1 TTTT-ATTAT
58127421 TTTTATT
1 TTTTATT
58127428 TTGTTTTAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 13
0.72 0.04 0.24
Matches are distributed among these distances:
6 3 0.08
7 8 0.21
8 8 0.21
9 11 0.28
10 9 0.23
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.79
Consensus pattern (9 bp):
TTTTATTAT
Found at i:58127404 original size:15 final size:16
Alignment explanation
Indices: 58127369--58127415 Score: 57
Period size: 15 Copynumber: 3.2 Consensus size: 16
58127359 GCTTTATTTC
58127369 TTATTTTTTA-T--TT
1 TTATTTTTTATTAGTT
58127382 TTATTTTTTATTAGTT
1 TTATTTTTTATTAGTT
*
58127398 TTA-TTTTTATTATTT
1 TTATTTTTTATTAGTT
58127413 TTA
1 TTA
58127416 ATTATTTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
13 10 0.33
14 1 0.03
15 14 0.47
16 5 0.17
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (16 bp):
TTATTTTTTATTAGTT
Found at i:58127422 original size:19 final size:20
Alignment explanation
Indices: 58127398--58127437 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
58127388 TTTATTAGTT
58127398 TTATTTTTATTAT-TTTTAA
1 TTATTTTTATTATGTTTTAA
*
58127417 TTATTTTTATTTTGTTTTAA
1 TTATTTTTATTATGTTTTAA
58127437 T
1 T
58127438 AGTGGTATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.75
Consensus pattern (20 bp):
TTATTTTTATTATGTTTTAA
Found at i:58127429 original size:15 final size:15
Alignment explanation
Indices: 58127362--58127429 Score: 70
Period size: 16 Copynumber: 4.5 Consensus size: 15
58127352 CTTTTTAGCT
58127362 TTATTTCTTA-TTTT-
1 TTATTT-TTATTTTTA
58127376 TTATTTTTATTTTTTA
1 TTATTTTTA-TTTTTA
*
58127392 TTAGTTTTATTTTTA
1 TTATTTTTATTTTTA
58127407 TTATTTTTAATTATTT-
1 TTATTTTT-ATT-TTTA
58127423 TTATTTT
1 TTATTTT
58127430 GTTTTAATAG
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
13 3 0.06
14 6 0.13
15 17 0.36
16 18 0.38
17 3 0.06
ACGTcount: A:0.19, C:0.01, G:0.01, T:0.78
Consensus pattern (15 bp):
TTATTTTTATTTTTA
Found at i:58149156 original size:28 final size:28
Alignment explanation
Indices: 58149124--58149193 Score: 99
Period size: 28 Copynumber: 2.5 Consensus size: 28
58149114 AATGAGATTG
58149124 GCACTAAGTGTGCGAGTTT-AAT-TGTATA
1 GCACTAAGTGTGCGAGTTTGAATAT-TA-A
*
58149152 GCACTAAGTGTGCGAGTTTGACTATTAA
1 GCACTAAGTGTGCGAGTTTGAATATTAA
58149180 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
58149194 GACTTACTAT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 34 0.87
29 4 0.10
30 1 0.03
ACGTcount: A:0.27, C:0.14, G:0.27, T:0.31
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGAATATTAA
Found at i:58153378 original size:80 final size:80
Alignment explanation
Indices: 58153294--58153442 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
58153284 TATGGTAACC
* * * *
58153294 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
58153358 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
58153374 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
58153439 CCGG
66 CCGG
58153443 TTATAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 56 0.98
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:58153384 original size:40 final size:38
Alignment explanation
Indices: 58153335--58153442 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
58153325 ATCACGATTT
*
58153335 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
58153375 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
58153415 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
58153443 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:58161497 original size:80 final size:80
Alignment explanation
Indices: 58161413--58161561 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
58161403 TATGGTAACC
* * * *
58161413 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
58161477 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
58161493 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
58161558 CCGG
66 CCGG
58161562 TTATAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 56 0.98
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:58161503 original size:40 final size:38
Alignment explanation
Indices: 58161454--58161561 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
58161444 ATCACGATTT
*
58161454 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
58161494 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
58161534 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
58161562 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:58164010 original size:36 final size:36
Alignment explanation
Indices: 58163961--58164061 Score: 98
Period size: 36 Copynumber: 2.8 Consensus size: 36
58163951 GAGCTAGCTA
* *
58163961 GTAAAACCAACAAATGAGTGTGCCTAGCACTGGCCG
1 GTAAAATCGACAAATGAGTGTGCCTAGCACTGGCCG
* * * *
58163997 GTATAA-CTGACAAATAAATGTGTCCT-GCACTGGTCG
1 GTAAAATC-GACAAATGAGTGTG-CCTAGCACTGGCCG
* *
58164033 GTAAAATCGAAAAATGAGTGTGCCCAGCA
1 GTAAAATCGACAAATGAGTGTGCCTAGCA
58164062 TTGGTTGATA
Statistics
Matches: 51, Mismatches: 10, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
35 3 0.06
36 44 0.86
37 4 0.08
ACGTcount: A:0.35, C:0.21, G:0.24, T:0.21
Consensus pattern (36 bp):
GTAAAATCGACAAATGAGTGTGCCTAGCACTGGCCG
Found at i:58164096 original size:72 final size:72
Alignment explanation
Indices: 58163972--58164125 Score: 166
Period size: 72 Copynumber: 2.1 Consensus size: 72
58163962 TAAAACCAAC
* * ** *** **
58163972 AAATGAGTGTGCCTAGCACTGGCCGGTATAACTGACAAATAAATGTGTCCTGCACTGGTCGGTAA
1 AAATGAGTGTGCCCAGCACTGGCCGATATAACCAACAAATAAATGCACCCTGCACTAATCGGTAA
58164037 AA-TCGAA
66 AACT-GAA
* ** *
58164044 AAATGAGTGTGCCCAGCATTGGTTGATATAACCAACAAATAAATGCACCCTGCGCTAATCGGTAA
1 AAATGAGTGTGCCCAGCACTGGCCGATATAACCAACAAATAAATGCACCCTGCACTAATCGGTAA
*
58164109 AACTGAC
66 AACTGAA
58164116 AAATGAGTGT
1 AAATGAGTGT
58164126 TCATTCATTC
Statistics
Matches: 67, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
72 66 0.99
73 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.23
Consensus pattern (72 bp):
AAATGAGTGTGCCCAGCACTGGCCGATATAACCAACAAATAAATGCACCCTGCACTAATCGGTAA
AACTGAA
Found at i:58164694 original size:107 final size:105
Alignment explanation
Indices: 58164510--58164728 Score: 339
Period size: 107 Copynumber: 2.1 Consensus size: 105
58164500 TTAGATATAA
* *
58164510 CCAGCTTTAGAAAAACACTTATTTAGCTATAATATCAGCAATAAAATCGACATAAACAATTATTT
1 CCAGCTTTAGAAAAACACTTATTCACCTATAATATCAGCAATAAAATCGACATAAACAATTATTT
*
58164575 AATCCTAACATTTAATTTAACATAAACATAATAGAAATGT
66 AATCCCAACATTTAATTTAACATAAACATAATAGAAATGT
* * ** *
58164615 CCAGCTTTGGAAAAATACACTTATTCACCTATAATATCAGCATTAAAATTTACATAAACACTTAT
1 CCAGCTTTAG-AAAA-ACACTTATTCACCTATAATATCAGCAATAAAATCGACATAAACAATTAT
58164680 TTAATCCCAACATTTAATTTAACATAAACATAATAGAAATGT
64 TTAATCCCAACATTTAATTTAACATAAACATAATAGAAATGT
*
58164722 CTAGCTT
1 CCAGCTT
58164729 GGACAACACT
Statistics
Matches: 103, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
105 9 0.09
106 4 0.04
107 90 0.87
ACGTcount: A:0.44, C:0.17, G:0.06, T:0.32
Consensus pattern (105 bp):
CCAGCTTTAGAAAAACACTTATTCACCTATAATATCAGCAATAAAATCGACATAAACAATTATTT
AATCCCAACATTTAATTTAACATAAACATAATAGAAATGT
Found at i:58164816 original size:22 final size:22
Alignment explanation
Indices: 58164757--58164818 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
58164747 GCTTTAGATG
*
58164757 ACATTTAGAACATATTTTGGACA
1 ACATTTA-AACATACTTTGGACA
* *
58164780 ACATTTATACGTACTTT-GACA
1 ACATTTAAACATACTTTGGACA
*
58164801 GCATTTGAAACATACTTT
1 ACATTT-AAACATACTTT
58164819 TGCTAGCATC
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
21 9 0.28
22 16 0.50
23 7 0.22
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.37
Consensus pattern (22 bp):
ACATTTAAACATACTTTGGACA
Found at i:58178057 original size:2 final size:2
Alignment explanation
Indices: 58178050--58178083 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
58178040 AATGGTAGAC
* *
58178050 TA TA TA TA TA TA TA TA TA TA TA TT TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
58178084 ACTGCTACAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
TA
Found at i:58178919 original size:15 final size:15
Alignment explanation
Indices: 58178901--58178932 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
58178891 AAATCGAGTA
58178901 AATTAATTTGATGCT
1 AATTAATTTGATGCT
58178916 AATTAATTTGATGCT
1 AATTAATTTGATGCT
58178931 AA
1 AA
58178933 CCTGAATCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.38, C:0.06, G:0.12, T:0.44
Consensus pattern (15 bp):
AATTAATTTGATGCT
Found at i:58180196 original size:25 final size:24
Alignment explanation
Indices: 58180149--58180206 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 24
58180139 TTATTTCATT
* *
58180149 AAATAAA-AAATTTAAAAATATAA
1 AAATAAATATATTTAAAAACATAA
58180172 TAAATCAAATATATTT-AAAACATAA
1 -AAAT-AAATATATTTAAAAACATAA
58180197 AAATAAATAT
1 AAATAAATAT
58180207 TAAAACAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
23 6 0.20
24 8 0.27
25 11 0.37
26 5 0.17
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.29
Consensus pattern (24 bp):
AAATAAATATATTTAAAAACATAA
Found at i:58180226 original size:21 final size:22
Alignment explanation
Indices: 58180178--58180235 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 22
58180168 ATAATAAATC
*
58180178 AAATATAT-TTAAAAC--ATAA
1 AAATAAATATTAAAACAAATAA
58180197 AAATAAATATTAAAACAAATAA
1 AAATAAATATTAAAACAAATAA
* *
58180219 TAAT-AATACTAAAACAA
1 AAATAAATATTAAAACAA
58180236 TTCTTAAAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 7 0.21
20 7 0.21
21 12 0.36
22 7 0.21
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.26
Consensus pattern (22 bp):
AAATAAATATTAAAACAAATAA
Found at i:58180312 original size:15 final size:16
Alignment explanation
Indices: 58180282--58180314 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
58180272 AAATAGTTAT
58180282 ATTAAAAATTTAAAATA
1 ATTAAAAA-TTAAAATA
58180299 ATTAAAAA-TAAAATA
1 ATTAAAAATTAAAATA
58180314 A
1 A
58180315 AAAATATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
17 8 0.50
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
ATTAAAAATTAAAATA
Found at i:58181438 original size:28 final size:29
Alignment explanation
Indices: 58181384--58181439 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 29
58181374 CTGAGACAAA
* *
58181384 TTAATATTTTTATTATTAAATAGATTAAT
1 TTAATATTTTTATTATTAAAAAAATTAAT
58181413 TTAAT-TTTTTATTATTAAAAAAATTAA
1 TTAATATTTTTATTATTAAAAAAATTAA
58181440 ATGATGCTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 20 0.80
29 5 0.20
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.54
Consensus pattern (29 bp):
TTAATATTTTTATTATTAAAAAAATTAAT
Found at i:58183228 original size:25 final size:24
Alignment explanation
Indices: 58183175--58183239 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 24
58183165 TTTTTCCTCA
* *
58183175 TATTATTTATTTTAAATTGTTTCAT
1 TATTATTTATTTT-AATGGTTTCAG
58183200 TATTATTTATTTTAA-GGCTTTCACG
1 TATTATTTATTTTAATGG-TTTCA-G
*
58183225 TATTATGTATTTTAA
1 TATTATTTATTTTAA
58183240 ACTATTATCC
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
23 1 0.03
24 7 0.20
25 27 0.77
ACGTcount: A:0.28, C:0.06, G:0.08, T:0.58
Consensus pattern (24 bp):
TATTATTTATTTTAATGGTTTCAG
Found at i:58183436 original size:26 final size:26
Alignment explanation
Indices: 58183403--58183463 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
58183393 CTTTTATATG
58183403 TTATTTTAAAAT-ATTATATATATTAT
1 TTATTTTAAAATGATT-TATATATTAT
** * *
58183429 TTATTTTAACTTGCTTTGTATATTAT
1 TTATTTTAAAATGATTTATATATTAT
58183455 TTATTTTAA
1 TTATTTTAA
58183464 TTTGTTTTAC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 28 0.93
27 2 0.07
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.61
Consensus pattern (26 bp):
TTATTTTAAAATGATTTATATATTAT
Found at i:58183482 original size:26 final size:26
Alignment explanation
Indices: 58183421--58183484 Score: 69
Period size: 26 Copynumber: 2.5 Consensus size: 26
58183411 AAATATTATA
*
58183421 TATATTATTTATTTTAACTTGCTTTG
1 TATATCATTTATTTTAACTTGCTTTG
* *
58183447 TATATTATTTATTTTAATTTG-TTT-
1 TATATCATTTATTTTAACTTGCTTTG
58183471 TACGTATCATTTAT
1 TA--TATCATTTAT
58183485 CTCAAATTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
24 2 0.06
25 3 0.09
26 29 0.85
ACGTcount: A:0.25, C:0.06, G:0.06, T:0.62
Consensus pattern (26 bp):
TATATCATTTATTTTAACTTGCTTTG
Found at i:58184855 original size:2 final size:2
Alignment explanation
Indices: 58184848--58184882 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
58184838 ATATGAAGTG
58184848 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 T
58184883 GAGAATATAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:58187206 original size:135 final size:135
Alignment explanation
Indices: 58186964--58187238 Score: 453
Period size: 135 Copynumber: 2.0 Consensus size: 135
58186954 AACACTTTGG
* *
58186964 TGTGGTTAGCATGGAGCAACATGACTTTTCCCAATGAAAACATCCCTAGGAACCTAATAAACCAA
1 TGTGGTTAGCATAGAGCAACATGACTTTCCCCAATGAAAACATCCCTAGGAACCTAATAAACCAA
* * *
58187029 ACATTGTCTACACATCCCCTAACTCAAGATGTTGGTCAAACTAGTAATTCCTAGCATGC-TACAA
66 ACATTGTCTACACATCCCCCAACTCAAGATGCTGGTCAAACTAGTAATTCCCAGCAT-CTTACAA
58187093 CCCATA
130 CCCATA
* * * *
58187099 TGTGGTTAGCATAGAGCAACATGACTTTCCCCAATGAAACCATCTCTAGGAACCTAGTAAACCCA
1 TGTGGTTAGCATAGAGCAACATGACTTTCCCCAATGAAAACATCCCTAGGAACCTAATAAACCAA
58187164 ACATTGTCTACACATCCCCCAACTCAAGATGCTGGTCAAACTAGTAATTCCCAGCATCTTACAAC
66 ACATTGTCTACACATCCCCCAACTCAAGATGCTGGTCAAACTAGTAATTCCCAGCATCTTACAAC
58187229 CCATA
131 CCATA
58187234 TGTGG
1 TGTGG
58187239 AAATTTATGG
Statistics
Matches: 130, Mismatches: 9, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
134 1 0.01
135 129 0.99
ACGTcount: A:0.33, C:0.27, G:0.15, T:0.25
Consensus pattern (135 bp):
TGTGGTTAGCATAGAGCAACATGACTTTCCCCAATGAAAACATCCCTAGGAACCTAATAAACCAA
ACATTGTCTACACATCCCCCAACTCAAGATGCTGGTCAAACTAGTAATTCCCAGCATCTTACAAC
CCATA
Found at i:58191045 original size:24 final size:24
Alignment explanation
Indices: 58191032--58191119 Score: 104
Period size: 24 Copynumber: 3.7 Consensus size: 24
58191022 ATTATTCTGT
*
58191032 CCAAGAGACTGCCCAGCATTCGGC
1 CCAACAGACTGCCCAGCATTCGGC
*
58191056 CCAACAGACTGCCCAGCATTCAGC
1 CCAACAGACTGCCCAGCATTCGGC
* * * * *
58191080 CTAACAGACTACCCAGCATGCAGT
1 CCAACAGACTGCCCAGCATTCGGC
*
58191104 CCAAGAGACTGCCCAG
1 CCAACAGACTGCCCAG
58191120 GAATCTGCTT
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 55 1.00
ACGTcount: A:0.30, C:0.38, G:0.20, T:0.12
Consensus pattern (24 bp):
CCAACAGACTGCCCAGCATTCGGC
Found at i:58201352 original size:19 final size:19
Alignment explanation
Indices: 58201307--58201352 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
58201297 GTGTTGCTGC
*
58201307 TATTGTTTACTTGGATTCA
1 TATTGTTTACTTGGACTCA
*
58201326 TATAGTTTACTTGGACTCA
1 TATTGTTTACTTGGACTCA
*
58201345 TGTTGTTT
1 TATTGTTT
58201353 TGCTTTTATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.20, C:0.11, G:0.17, T:0.52
Consensus pattern (19 bp):
TATTGTTTACTTGGACTCA
Found at i:58201437 original size:15 final size:16
Alignment explanation
Indices: 58201411--58201440 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
58201401 TGTTTAAAAA
58201411 TTTTAAAGAAAATTAT
1 TTTTAAAGAAAATTAT
58201427 TTTTAAA-AAAATTA
1 TTTTAAAGAAAATTA
58201441 CATAAAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (16 bp):
TTTTAAAGAAAATTAT
Found at i:58204687 original size:23 final size:21
Alignment explanation
Indices: 58204657--58204700 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 21
58204647 TTTGATAATA
58204657 TGTTTTTGATATAACAAATTAAG
1 TGTTTTTGA-ATAA-AAATTAAG
*
58204680 TGTTTTTGAATAAAAGTTAAG
1 TGTTTTTGAATAAAAATTAAG
58204701 ATGAACAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 7 0.35
22 4 0.20
23 9 0.45
ACGTcount: A:0.39, C:0.02, G:0.16, T:0.43
Consensus pattern (21 bp):
TGTTTTTGAATAAAAATTAAG
Found at i:58208676 original size:30 final size:30
Alignment explanation
Indices: 58208618--58208677 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
58208608 TTCCCGAGCC
* *
58208618 TAGGGGTAAAAGTGTAATTATGCAAAAGTT
1 TAGGGGAAAAAATGTAATTATGCAAAAGTT
* * *
58208648 TAGGGGAAAAAATGTACTTTTGCCAAAGTT
1 TAGGGGAAAAAATGTAATTATGCAAAAGTT
58208678 CGTATTAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.38, C:0.07, G:0.25, T:0.30
Consensus pattern (30 bp):
TAGGGGAAAAAATGTAATTATGCAAAAGTT
Found at i:58211154 original size:21 final size:21
Alignment explanation
Indices: 58211130--58211169 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
58211120 AAACTTGTAT
58211130 AACTATCATCACAT-ATTAATA
1 AACTATCATCA-ATCATTAATA
58211151 AACTATCATCAATCATTAA
1 AACTATCATCAATCATTAA
58211170 AATACATGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.47, C:0.20, G:0.00, T:0.33
Consensus pattern (21 bp):
AACTATCATCAATCATTAATA
Found at i:58214112 original size:29 final size:29
Alignment explanation
Indices: 58214073--58214152 Score: 108
Period size: 29 Copynumber: 2.7 Consensus size: 29
58214063 CTTAATAATC
*
58214073 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
58214103 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
58214132 AGCCCGCACACTTAGTGCCAT
1 AACCCGCACACTTAGTGCCAT
58214153 TCTCTCAACC
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 39 0.87
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.25
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:58222019 original size:29 final size:29
Alignment explanation
Indices: 58221980--58222059 Score: 108
Period size: 29 Copynumber: 2.7 Consensus size: 29
58221970 CTTAATAATC
*
58221980 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
58222010 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
58222039 AGCCCGCACACTTAGTGCCAT
1 AACCCGCACACTTAGTGCCAT
58222060 TCTCTCAACC
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 39 0.87
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.25
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:58229837 original size:2 final size:2
Alignment explanation
Indices: 58229830--58229854 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
58229820 TTGATAGAAA
58229830 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
58229855 GTGGGTTCGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:58229924 original size:29 final size:29
Alignment explanation
Indices: 58229885--58229964 Score: 108
Period size: 29 Copynumber: 2.7 Consensus size: 29
58229875 CTTAATAATC
*
58229885 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
58229915 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
58229944 AGCCCGCACACTTAGTGCCAT
1 AACCCGCACACTTAGTGCCAT
58229965 TCTCTCAACC
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 39 0.87
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.25
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:58236463 original size:27 final size:26
Alignment explanation
Indices: 58236433--58236485 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
58236423 GACCAAAATA
*
58236433 CCCCTAAAGGGTAAAATGACTGTTTTG
1 CCCCTAAAGGGT-AAATGACTGATTTG
**
58236460 CCCCTCGAGGGTAAATGACTGATTTG
1 CCCCTAAAGGGTAAATGACTGATTTG
58236486 TCTGTGACTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 13 0.57
27 10 0.43
ACGTcount: A:0.26, C:0.21, G:0.25, T:0.28
Consensus pattern (26 bp):
CCCCTAAAGGGTAAATGACTGATTTG
Found at i:58250810 original size:40 final size:40
Alignment explanation
Indices: 58250765--58250931 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
58250755 CGGAATATAA
58250765 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
58250805 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
58250845 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
58250885 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
58250924 CCGGATAT
1 CCGGATAT
58250932 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:58258026 original size:40 final size:40
Alignment explanation
Indices: 58257981--58258148 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
58257971 CGGAATATAA
58257981 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
58258021 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
58258061 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * * *
58258101 CCGGATATAATTTCCAGCATAATTGTCTTCGGGGCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
58258141 CCGGATAT
1 CCGGATAT
58258149 CATTCAATTT
Statistics
Matches: 107, Mismatches: 20, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
39 1 0.01
40 106 0.99
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:58261266 original size:27 final size:27
Alignment explanation
Indices: 58261236--58261292 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
58261226 GCCAAAAATG
*
58261236 GTAAATGTGGCAAAGCCACCAGTAACA
1 GTAAATGTGGCAAAGCCACCAATAACA
* *
58261263 GTAATTGTGGCATAGCCACCAATAACA
1 GTAAATGTGGCAAAGCCACCAATAACA
58261290 GTA
1 GTA
58261293 CTTCATCCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.19
Consensus pattern (27 bp):
GTAAATGTGGCAAAGCCACCAATAACA
Found at i:58261458 original size:27 final size:27
Alignment explanation
Indices: 58261428--58261543 Score: 135
Period size: 27 Copynumber: 4.3 Consensus size: 27
58261418 GGGCATAATC
58261428 GTCATTTTACCATACAGGGGTATTACA
1 GTCATTTTACCATACAGGGGTATTACA
* **
58261455 GTCATTTTACCCTACAGGGGTATTATG
1 GTCATTTTACCATACAGGGGTATTACA
* * *
58261482 GTCATTTTACCCTACAGAGGTATTACG
1 GTCATTTTACCATACAGGGGTATTACA
* * *
58261509 GTCATTTTA-CAAACTGGGGTATTTCA
1 GTCATTTTACCATACAGGGGTATTACA
*
58261535 GTAATTTTA
1 GTCATTTTA
58261544 AAATTTGAGG
Statistics
Matches: 77, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
26 19 0.25
27 58 0.75
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.37
Consensus pattern (27 bp):
GTCATTTTACCATACAGGGGTATTACA
Found at i:58264191 original size:40 final size:40
Alignment explanation
Indices: 58264146--58264313 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
58264136 CGGAATATAA
58264146 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
58264186 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
58264226 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * * *
58264266 CCGGATATAATTTCCAGCATAATTGTCTTCGGGGCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
58264306 CCGGATAT
1 CCGGATAT
58264314 CATTCAATTT
Statistics
Matches: 107, Mismatches: 20, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
39 1 0.01
40 106 0.99
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:58269041 original size:30 final size:30
Alignment explanation
Indices: 58269007--58269087 Score: 83
Period size: 30 Copynumber: 2.7 Consensus size: 30
58268997 TAAACTAAAA
58269007 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
58269037 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
*
58269067 TGAGCTAAGGTTTAGCTCGTG
1 TGAGCTAAGCTTTAGCTCGTG
58269088 GGTTGAAAGT
Statistics
Matches: 37, Mismatches: 12, Indels: 4
0.70 0.23 0.08
Matches are distributed among these distances:
29 2 0.05
30 32 0.86
31 3 0.08
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:58271257 original size:42 final size:42
Alignment explanation
Indices: 58271211--58271309 Score: 123
Period size: 42 Copynumber: 2.4 Consensus size: 42
58271201 GTTTCTTTTG
*
58271211 TTTCAATTTCTTTTTC-ATCTTCTTTTTCACTCTCAAATTTC-T
1 TTTCAATTTCTTTTTCAATC-TCTTTTTCAATCTC-AATTTCTT
*
58271253 TTTC-ATTCTCTTTTTCAATCTCTTTTTCAATCTCATTTTCTT
1 TTTCAATT-TCTTTTTCAATCTCTTTTTCAATCTCAATTTCTT
*
58271295 TTTCATTTTCTTTTT
1 TTTCAATTTCTTTTT
58271310 ACTTTTCAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
41 8 0.16
42 37 0.74
43 5 0.10
ACGTcount: A:0.14, C:0.22, G:0.00, T:0.64
Consensus pattern (42 bp):
TTTCAATTTCTTTTTCAATCTCTTTTTCAATCTCAATTTCTT
Found at i:58271258 original size:30 final size:31
Alignment explanation
Indices: 58271215--58271274 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
58271205 CTTTTGTTTC
*
58271215 AATTTCTTTTTCA-TCTTCTTTTTCACTCTCA
1 AATTTCTTTTTCATTC-TCTTTTTCAATCTCA
58271246 AATTTC-TTTTCATTCTCTTTTTCAATCTC
1 AATTTCTTTTTCATTCTCTTTTTCAATCTC
58271275 TTTTTCAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 19 0.70
31 8 0.30
ACGTcount: A:0.17, C:0.25, G:0.00, T:0.58
Consensus pattern (31 bp):
AATTTCTTTTTCATTCTCTTTTTCAATCTCA
Found at i:58271269 original size:12 final size:12
Alignment explanation
Indices: 58271252--58271292 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
58271242 CTCAAATTTC
*
58271252 TTTTCATTCTCT
1 TTTTCAATCTCT
58271264 TTTTCAATCTCT
1 TTTTCAATCTCT
*
58271276 TTTTCAATCTCA
1 TTTTCAATCTCT
58271288 TTTTC
1 TTTTC
58271293 TTTTTCATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.15, C:0.24, G:0.00, T:0.61
Consensus pattern (12 bp):
TTTTCAATCTCT
Found at i:58271316 original size:12 final size:12
Alignment explanation
Indices: 58271285--58271309 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
58271275 TTTTTCAATC
58271285 TCATTTTCTTTT
1 TCATTTTCTTTT
58271297 TCATTTTCTTTT
1 TCATTTTCTTTT
58271309 T
1 T
58271310 ACTTTTCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (12 bp):
TCATTTTCTTTT
Found at i:58271327 original size:12 final size:12
Alignment explanation
Indices: 58271312--58271342 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
58271302 TTCTTTTTAC
58271312 TTTTCAAAGGCT
1 TTTTCAAAGGCT
58271324 TTTTCAAAGGCT
1 TTTTCAAAGGCT
58271336 TTTTCAA
1 TTTTCAA
58271343 CACTCGCAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:58277263 original size:52 final size:52
Alignment explanation
Indices: 58277156--58277333 Score: 242
Period size: 52 Copynumber: 3.5 Consensus size: 52
58277146 ACTAGTGACT
*
58277156 CAAGTGTGGTACTATGTGAAGGTCAC-TT-T-AAGAAGAGATAGC-TTGGTCA
1 CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAA-AGATAGCTTTGGTCA
* *
58277205 AAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAATATAGCTTTGGTCA
1 CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAAGATAGCTTTGGTCA
*
58277257 CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAG-AAGATAGCTTT-GACTA
1 CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAAGATAGCTTTGGTC-A
* *
58277308 CAAGGGTGGTACTATGTGCAGGCCAC
1 CAAGTGTGGTACTATGTGAAGGCCAC
58277334 GGGGTATTCG
Statistics
Matches: 116, Mismatches: 8, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
49 24 0.21
50 4 0.03
51 42 0.36
52 46 0.40
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.28
Consensus pattern (52 bp):
CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAAGATAGCTTTGGTCA
Found at i:58277320 original size:51 final size:51
Alignment explanation
Indices: 58277151--58277333 Score: 230
Period size: 51 Copynumber: 3.6 Consensus size: 51
58277141 ATGTCACTAG
* **
58277151 TGACT-CAAGTGTGGTACTATGTGAAGGTCACTTTAAGAAG-AGATAGCTT
1 TGACTACAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAGATAGCTT
* * * *
58277200 GGTC-AAAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAATATAGCTT
1 TGACTACAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAG-AAGATAGCTT
*
58277251 TG-GTCACAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAGATAGCTT
1 TGACT-ACAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAGATAGCTT
* *
58277302 TGACTACAAGGGTGGTACTATGTGCAGGCCAC
1 TGACTACAAGTGTGGTACTATGTGAAGGCCAC
58277334 GGGGTATTCG
Statistics
Matches: 114, Mismatches: 14, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
49 33 0.29
51 45 0.39
52 36 0.32
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.28
Consensus pattern (51 bp):
TGACTACAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAGATAGCTT
Found at i:58279254 original size:22 final size:22
Alignment explanation
Indices: 58279226--58279290 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
58279216 CTATATTTAT
**
58279226 GGCCTTTAGCCACCCTGTCTAC
1 GGCCTTTAGCCGTCCTGTCTAC
58279248 GGCCTTTCA-CCGTCCTGTCTAC
1 GGCCTTT-AGCCGTCCTGTCTAC
* *
58279270 GGCGTTGAGCCGTCCTGTCTA
1 GGCCTTTAGCCGTCCTGTCTA
58279291 TGGCGTTGAG
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
21 1 0.03
22 35 0.95
23 1 0.03
ACGTcount: A:0.11, C:0.37, G:0.23, T:0.29
Consensus pattern (22 bp):
GGCCTTTAGCCGTCCTGTCTAC
Found at i:58279295 original size:22 final size:22
Alignment explanation
Indices: 58279239--58279301 Score: 83
Period size: 22 Copynumber: 2.9 Consensus size: 22
58279229 CTTTAGCCAC
* *
58279239 CCTGTCTACGGCCTTTCA-CCGT
1 CCTGTCTACGG-CGTTGAGCCGT
58279261 CCTGTCTACGGCGTTGAGCCGT
1 CCTGTCTACGGCGTTGAGCCGT
*
58279283 CCTGTCTATGGCGTTGAGC
1 CCTGTCTACGGCGTTGAGC
58279302 TGTCTTGTTG
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
21 4 0.11
22 33 0.89
ACGTcount: A:0.10, C:0.33, G:0.27, T:0.30
Consensus pattern (22 bp):
CCTGTCTACGGCGTTGAGCCGT
Found at i:58284029 original size:40 final size:40
Alignment explanation
Indices: 58283783--58284030 Score: 349
Period size: 40 Copynumber: 6.2 Consensus size: 40
58283773 CGGATGATAA
* * * *
58283783 CCGGGCTAAGTCCCAAAGGCATTTGTGCTAGTGACTAAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
58283823 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
58283863 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * * *
58283903 CCAGGCTAAGTTCTGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
58283943 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
58283982 CCGGGCTAAGTCCCGAAGGCAATTTGAGCAAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGC-ATTTGTGCGAGTTA-CTATAT
58284023 CC-GGCTAA
1 CCGGGCTAA
58284031 ATTTCGAAGG
Statistics
Matches: 188, Mismatches: 17, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
39 22 0.12
40 164 0.87
41 2 0.01
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:58288274 original size:63 final size:63
Alignment explanation
Indices: 58288194--58288319 Score: 243
Period size: 63 Copynumber: 2.0 Consensus size: 63
58288184 TCTTGATAAG
*
58288194 TATTATATTAATTTAATATTAAAGTGATTAAGTTTAATCATAGTTGAACTCTCTAAATTCTCC
1 TATTATATTAATTTAATATTAAAGTGATTAAGTTTAATCATAGTTGAACTCTCTAAACTCTCC
58288257 TATTATATTAATTTAATATTAAAGTGATTAAGTTTAATCATAGTTGAACTCTCTAAACTCTCC
1 TATTATATTAATTTAATATTAAAGTGATTAAGTTTAATCATAGTTGAACTCTCTAAACTCTCC
58288320 CTATATAAAG
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 62 1.00
ACGTcount: A:0.37, C:0.12, G:0.08, T:0.44
Consensus pattern (63 bp):
TATTATATTAATTTAATATTAAAGTGATTAAGTTTAATCATAGTTGAACTCTCTAAACTCTCC
Found at i:58292556 original size:27 final size:27
Alignment explanation
Indices: 58292525--58292708 Score: 165
Period size: 27 Copynumber: 6.9 Consensus size: 27
58292515 AAGACCCCCG
58292525 ATTTGTAAAATTACCAAAATACCCCTA
1 ATTTGTAAAATTACCAAAATACCCCTA
*
58292552 ATTTGTAAAATTACCAAAATACCCTTA
1 ATTTGTAAAATTACCAAAATACCCCTA
* * * *
58292579 ACTTGTAAAATTACTAAAATACCTCTT
1 ATTTGTAAAATTACCAAAATACCCCTA
* *
58292606 ATTTATAAAATTACCAAAATACTCCTA
1 ATTTGTAAAATTACCAAAATACCCCTA
* *** * *
58292633 ACTTGT-AAATTATTTAAATACACCTG
1 ATTTGTAAAATTACCAAAATACCCCTA
* * * *
58292659 ATTTATAAAATTATCGAAATA-CCCTCG
1 ATTTGTAAAATTACCAAAATACCCCT-A
* * *
58292686 ATTTGTGAAATTATCGAAATACC
1 ATTTGTAAAATTACCAAAATACC
58292709 TCTATGAGGT
Statistics
Matches: 128, Mismatches: 26, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
26 22 0.17
27 105 0.82
28 1 0.01
ACGTcount: A:0.42, C:0.18, G:0.05, T:0.34
Consensus pattern (27 bp):
ATTTGTAAAATTACCAAAATACCCCTA
Found at i:58292666 original size:53 final size:53
Alignment explanation
Indices: 58292527--58292683 Score: 192
Period size: 54 Copynumber: 2.9 Consensus size: 53
58292517 GACCCCCGAT
* *
58292527 TTGTAAAATTACCAAAATACCCCTAATTTGTAAAATTACCAAAATACCCTTAAC
1 TTGTAAAATTACTAAAATA-CCCTAATTTATAAAATTACCAAAATACCCTTAAC
*
58292581 TTGTAAAATTACTAAAATACCTCTTATTTATAAAATTACCAAAATACTCC-TAAC
1 TTGTAAAATTACTAAAATACC-CTAATTTATAAAATTACCAAAATAC-CCTTAAC
* * * * *
58292635 TTGT-AAATTATTTAAATACACCTGATTTATAAAATTATCGAAATACCCT
1 TTGTAAAATTACTAAAATAC-CCTAATTTATAAAATTACCAAAATACCCT
58292684 CGATTTGTGA
Statistics
Matches: 91, Mismatches: 8, Indels: 9
0.84 0.07 0.08
Matches are distributed among these distances:
52 2 0.02
53 37 0.41
54 50 0.55
55 2 0.02
ACGTcount: A:0.43, C:0.18, G:0.04, T:0.34
Consensus pattern (53 bp):
TTGTAAAATTACTAAAATACCCTAATTTATAAAATTACCAAAATACCCTTAAC
Found at i:58292771 original size:26 final size:26
Alignment explanation
Indices: 58292716--58292825 Score: 150
Period size: 26 Copynumber: 4.2 Consensus size: 26
58292706 ACCTCTATGA
* *
58292716 GGTAGGATTACCGAAATACCCCTGTGG
1 GGTAGGATTA-CAAAATACCCCTGTAG
58292743 GGTAGGATTACTAAAATA-CCCTGTAG
1 GGTAGGATTAC-AAAATACCCCTGTAG
58292769 GGTAGGATTACAAAAATACCCCTGTAG
1 GGTAGGATTAC-AAAATACCCCTGTAG
* *
58292796 GGTAGGATTACGAAATACCCTTGTAG
1 GGTAGGATTACAAAATACCCCTGTAG
58292822 GGTA
1 GGTA
58292826 AAATGCCCGT
Statistics
Matches: 76, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
26 42 0.55
27 34 0.45
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.25
Consensus pattern (26 bp):
GGTAGGATTACAAAATACCCCTGTAG
Found at i:58292787 original size:53 final size:53
Alignment explanation
Indices: 58292716--58292825 Score: 168
Period size: 53 Copynumber: 2.1 Consensus size: 53
58292706 ACCTCTATGA
** *
58292716 GGTAGGATTACCGAAATACCCCTGTGGGGTAGGATTACTAAAATACCC-TGTAG
1 GGTAGGATTACAAAAATACCCCTGTAGGGTAGGATTAC-AAAATACCCTTGTAG
*
58292769 GGTAGGATTACAAAAATACCCCTGTAGGGTAGGATTACGAAATACCCTTGTAG
1 GGTAGGATTACAAAAATACCCCTGTAGGGTAGGATTACAAAATACCCTTGTAG
58292822 GGTA
1 GGTA
58292826 AAATGCCCGT
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
52 8 0.15
53 44 0.85
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.25
Consensus pattern (53 bp):
GGTAGGATTACAAAAATACCCCTGTAGGGTAGGATTACAAAATACCCTTGTAG
Found at i:58296706 original size:17 final size:18
Alignment explanation
Indices: 58296673--58296707 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
58296663 TTGGGCCTCG
*
58296673 ATGGGCTGTGTGGGCCCA
1 ATGGGCTGTGTGAGCCCA
58296691 ATGGGCT-TGTGAGCCCA
1 ATGGGCTGTGTGAGCCCA
58296708 CACAAATAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.14, C:0.23, G:0.40, T:0.23
Consensus pattern (18 bp):
ATGGGCTGTGTGAGCCCA
Found at i:58296966 original size:27 final size:26
Alignment explanation
Indices: 58296923--58297162 Score: 130
Period size: 27 Copynumber: 8.9 Consensus size: 26
58296913 GACCCTTGAT
**
58296923 TTGTAAAATTATTGAAATA-CTCTCGA
1 TTGTAAAATTACCGAAATACCTCT-GA
* *
58296949 TATGTAAAATTACCGAAATACCCCTAA
1 T-TGTAAAATTACCGAAATACCTCTGA
* * * *
58296976 TTTGTAAAATTACTGAAATACCCCCGGG
1 -TTGTAAAATTACCGAAATA-CCTCTGA
* * *
58297004 TTATAAAATTATCGAAATACCTCTAA
1 TTGTAAAATTACCGAAATACCTCTGA
**
58297030 CTTGTAAAATTACTAAAATACC-CTTGA
1 -TTGTAAAATTACCGAAATACCTC-TGA
58297057 TTTGTAAAATTACCGAAATA-CTCCTGA
1 -TTGTAAAATTACCGAAATACCT-CTGA
*** *
58297084 CTTGTAAAATTATTAAAATACCCCTGA
1 -TTGTAAAATTACCGAAATACCTCTGA
* *
58297111 TTTGTGAAATTA-CTAGAATACCCTCT-A
1 -TTGTAAAATTACCGA-AATA-CCTCTGA
* * *
58297138 TTTGTGAAATTATCAAAATACCTCT
1 -TTGTAAAATTACCGAAATACCTCT
58297163 ATGGGGTAGG
Statistics
Matches: 168, Mismatches: 34, Indels: 24
0.74 0.15 0.11
Matches are distributed among these distances:
26 12 0.07
27 140 0.83
28 16 0.10
ACGTcount: A:0.39, C:0.18, G:0.10, T:0.34
Consensus pattern (26 bp):
TTGTAAAATTACCGAAATACCTCTGA
Found at i:58297061 original size:81 final size:79
Alignment explanation
Indices: 58296926--58297159 Score: 236
Period size: 81 Copynumber: 2.9 Consensus size: 79
58296916 CCTTGATTTG
** * *
58296926 TAAAATTATTGAAATA-CTCTCGATATGTAAAATTACCGAAATACCCCTAATTTGTAAAATTACT
1 TAAAATTATTGAAATACCTCT-GAT-TGTAAAATTACTAAAATA-CCCTTATTTGTAAAATTACC
**
58296990 GAAATACCCCCGGGTTA
63 GAAATACCCCCGACTTA
* *
58297007 TAAAATTATCGAAATACCTCTAACTTGTAAAATTACTAAAATACCCTTGATTTGTAAAATTACCG
1 TAAAATTATTGAAATACCTCTGA-TTGTAAAATTACTAAAATACCCTT-ATTTGTAAAATTACCG
* * *
58297072 AAATACTCCTGACTTG
64 AAATACCCCCGACTTA
* * * * * * *
58297088 TAAAATTATTAAAATACCCCTGATTTGTGAAATTACTAGAATACCCTCTATTTGTGAAATTATCA
1 TAAAATTATTGAAATACCTCTGA-TTGTAAAATTACTAAAATACCCT-TATTTGTAAAATTACCG
58297153 AAATACC
64 AAATACC
58297160 TCTATGGGGT
Statistics
Matches: 127, Mismatches: 22, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
80 4 0.03
81 117 0.92
82 6 0.05
ACGTcount: A:0.40, C:0.18, G:0.09, T:0.33
Consensus pattern (79 bp):
TAAAATTATTGAAATACCTCTGATTGTAAAATTACTAAAATACCCTTATTTGTAAAATTACCGAA
ATACCCCCGACTTA
Found at i:58297112 original size:54 final size:53
Alignment explanation
Indices: 58296923--58297123 Score: 224
Period size: 54 Copynumber: 3.7 Consensus size: 53
58296913 GACCCTTGAT
* * * * *
58296923 TTGTAAAATTATTGAAATA-CTCTCGATATGTAAAATTACCGAAATACCCCTAAT
1 TTGTAAAATTACTAAAATACCCCT-GATTTGTAAAATTACCGAAATA-CCCTAAC
* * ** * *
58296977 TTGTAAAATTACTGAAATACCCCCGGGTTATAAAATTATCGAAATACCTCTAAC
1 TTGTAAAATTACTAAAATACCCCTGATTTGTAAAATTACCGAAATACC-CTAAC
* *
58297031 TTGTAAAATTACTAAAATACCCTTGATTTGTAAAATTACCGAAATACTCCTGAC
1 TTGTAAAATTACTAAAATACCCCTGATTTGTAAAATTACCGAAATAC-CCTAAC
* *
58297085 TTGTAAAATTATTAAAATACCCCTGATTTGTGAAATTAC
1 TTGTAAAATTACTAAAATACCCCTGATTTGTAAAATTAC
58297124 TAGAATACCC
Statistics
Matches: 124, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
53 2 0.02
54 119 0.96
55 3 0.02
ACGTcount: A:0.39, C:0.17, G:0.10, T:0.33
Consensus pattern (53 bp):
TTGTAAAATTACTAAAATACCCCTGATTTGTAAAATTACCGAAATACCCTAAC
Found at i:58297131 original size:54 final size:54
Alignment explanation
Indices: 58296914--58297159 Score: 189
Period size: 54 Copynumber: 4.6 Consensus size: 54
58296904 GGTCATTAAG
* * * * * *
58296914 ACCCTTGATTTGTAAAATTATTGAAATA-CTCTCGATATGTAAAATTACCGAAAT
1 ACCCTCGACTTGTAAAATTATTAAAATACCCCT-GATTTGTAAAATTACAGAAAT
* * * * * ** *
58296968 ACCC-CTAATTTGTAAAATTACTGAAATACCCCCGGGTTATAAAATTATC-GAAAT
1 ACCCTC-GACTTGTAAAATTATTAAAATACCCCTGATTTGTAAAATTA-CAGAAAT
* * * *
58297022 A-CCTCTAACTTGTAAAATTACTAAAATACCCTTGATTTGTAAAATTACCGAAAT
1 ACCCTC-GACTTGTAAAATTATTAAAATACCCCTGATTTGTAAAATTACAGAAAT
*
58297076 ACTCCT-GACTTGTAAAATTATTAAAATACCCCTGATTTGTGAAATTACTAG-AAT
1 AC-CCTCGACTTGTAAAATTATTAAAATACCCCTGATTTGTAAAATTAC-AGAAAT
* * * *
58297130 ACCCTCTATTTGTGAAATTATCAAAATACC
1 ACCCTCGACTTGTAAAATTATTAAAATACC
58297160 TCTATGGGGT
Statistics
Matches: 158, Mismatches: 25, Indels: 18
0.79 0.12 0.09
Matches are distributed among these distances:
53 6 0.04
54 145 0.92
55 4 0.03
56 3 0.02
ACGTcount: A:0.39, C:0.18, G:0.10, T:0.33
Consensus pattern (54 bp):
ACCCTCGACTTGTAAAATTATTAAAATACCCCTGATTTGTAAAATTACAGAAAT
Found at i:58297176 original size:27 final size:27
Alignment explanation
Indices: 58297146--58297237 Score: 139
Period size: 27 Copynumber: 3.4 Consensus size: 27
58297136 TATTTGTGAA
* *
58297146 ATTATCAAAATACCTCTATGGGGTAGG
1 ATTATCGAAATACCTCTGTGGGGTAGG
*
58297173 ATTATCGAAATACCCCTGTGGGGTAGG
1 ATTATCGAAATACCTCTGTGGGGTAGG
* *
58297200 ATTATCGAAATACCTTTGTAGGGTAGG
1 ATTATCGAAATACCTCTGTGGGGTAGG
58297227 ATTATCGAAAT
1 ATTATCGAAAT
58297238 GTAGGGTAGG
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 59 1.00
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.30
Consensus pattern (27 bp):
ATTATCGAAATACCTCTGTGGGGTAGG
Found at i:58297204 original size:54 final size:53
Alignment explanation
Indices: 58297146--58297299 Score: 176
Period size: 54 Copynumber: 3.0 Consensus size: 53
58297136 TATTTGTGAA
* *
58297146 ATTATCAAAATACCTCTATGGGGTAGGATTATCGAAATACCCCTGTGGGGTAGG
1 ATTATCAAAATACCTCTATAGGGTAGGATTATCGAAATA-CCCTGTAGGGTAGG
* * *
58297200 ATTATCGAAATACCTTTGTAGGGTAGGATTATCG-AA-A---TGTAGGGTAGG
1 ATTATCAAAATACCTCTATAGGGTAGGATTATCGAAATACCCTGTAGGGTAGG
* *
58297248 ATTA-CAAAAATACCCCTATAGGGTAGGATTACCGAAATACCCTTGTAGGGTA
1 ATTATC-AAAATACCTCTATAGGGTAGGATTATCGAAATACCC-TGTAGGGTA
58297300 AAATGCCCAT
Statistics
Matches: 83, Mismatches: 10, Indels: 14
0.78 0.09 0.13
Matches are distributed among these distances:
47 1 0.01
48 37 0.45
49 2 0.02
50 1 0.01
52 1 0.01
53 2 0.02
54 39 0.47
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.28
Consensus pattern (53 bp):
ATTATCAAAATACCTCTATAGGGTAGGATTATCGAAATACCCTGTAGGGTAGG
Found at i:58297258 original size:21 final size:21
Alignment explanation
Indices: 58297216--58297256 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
58297206 GAAATACCTT
*
58297216 TGTAGGGTAGGATTATCGAAA
1 TGTAGGGTAGGATTATCAAAA
58297237 TGTAGGGTAGGATTA-CAAAA
1 TGTAGGGTAGGATTATCAAAA
58297257 ATACCCCTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.37, C:0.05, G:0.32, T:0.27
Consensus pattern (21 bp):
TGTAGGGTAGGATTATCAAAA
Found at i:58297270 original size:27 final size:27
Alignment explanation
Indices: 58297239--58297299 Score: 86
Period size: 27 Copynumber: 2.3 Consensus size: 27
58297229 TATCGAAATG
58297239 TAGGGTAGGATTACAAAAATACCCCTA
1 TAGGGTAGGATTACAAAAATACCCCTA
** * *
58297266 TAGGGTAGGATTACCGAAATACCCTTG
1 TAGGGTAGGATTACAAAAATACCCCTA
58297293 TAGGGTA
1 TAGGGTA
58297300 AAATGCCCAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.25
Consensus pattern (27 bp):
TAGGGTAGGATTACAAAAATACCCCTA
Found at i:58297894 original size:32 final size:32
Alignment explanation
Indices: 58297807--58297902 Score: 79
Period size: 32 Copynumber: 3.0 Consensus size: 32
58297797 CCCAAGGTTG
* * * *
58297807 TGTGCCAATTATATTACCG-TCATTGATGGCTA
1 TGTGCCAATTATAATACCGCT-ACTAATGGCTT
* ** **
58297839 TATGCCAAACATAATACAACTACTAATGGCTT
1 TGTGCCAATTATAATACCGCTACTAATGGCTT
58297871 TGTGCCAATTATAATACCGCTACTGAA-GGCTT
1 TGTGCCAATTATAATACCGCTACT-AATGGCTT
58297903 GGAGTCGCAT
Statistics
Matches: 48, Mismatches: 14, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
32 45 0.94
33 3 0.06
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (32 bp):
TGTGCCAATTATAATACCGCTACTAATGGCTT
Found at i:58298763 original size:16 final size:17
Alignment explanation
Indices: 58298731--58298763 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
58298721 AAATAAGAAG
58298731 GGTTTTCAATGAAAACAT
1 GGTTTTCAA-GAAAACAT
58298749 GGTTTTCAA-AAAACA
1 GGTTTTCAAGAAAACA
58298764 CTATAATGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.30
Consensus pattern (17 bp):
GGTTTTCAAGAAAACAT
Found at i:58299327 original size:43 final size:41
Alignment explanation
Indices: 58299275--58299381 Score: 160
Period size: 43 Copynumber: 2.6 Consensus size: 41
58299265 AAAGTGTGAT
*
58299275 TTCATGTAAGACCATGTCTGGGACATTGGCATCAGTATAAGA
1 TTCATGTAAGACCATGTCTAGGACATTGGCATC-GTATAAGA
*
58299317 TTACGTGTAAGACCATGTCTAGGACATTGGCATCGTATAAGA
1 TT-CATGTAAGACCATGTCTAGGACATTGGCATCGTATAAGA
* *
58299359 TTCATGTAAGACCCTATCTAGGA
1 TTCATGTAAGACCATGTCTAGGA
58299382 TAGTGATATC
Statistics
Matches: 59, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
41 18 0.31
42 12 0.20
43 29 0.49
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (41 bp):
TTCATGTAAGACCATGTCTAGGACATTGGCATCGTATAAGA
Found at i:58316756 original size:27 final size:27
Alignment explanation
Indices: 58316680--58316769 Score: 119
Period size: 27 Copynumber: 3.3 Consensus size: 27
58316670 TTTAGTTTAC
* *
58316680 TAAAATTACCGAAATACCCTTAG-TTTG
1 TAAAATTACTGAAATA-CCTTCGATTTG
* *
58316707 TAAAAATACTGAAATACCCTCGATTTG
1 TAAAATTACTGAAATACCTTCGATTTG
*
58316734 TAAAATTACTGAAATACCTTCGACTTG
1 TAAAATTACTGAAATACCTTCGATTTG
58316761 TAAAATTAC
1 TAAAATTAC
58316770 CAAACTACCC
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
26 4 0.07
27 51 0.93
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.32
Consensus pattern (27 bp):
TAAAATTACTGAAATACCTTCGATTTG
Found at i:58316779 original size:54 final size:54
Alignment explanation
Indices: 58316680--58316786 Score: 128
Period size: 54 Copynumber: 2.0 Consensus size: 54
58316670 TTTAGTTTAC
* * *
58316680 TAAAATTACCGAAATACCCTTAGTTTGTAAAAATACTGAAATACCCTCGATTTG
1 TAAAATTACCGAAATACCCTTAGCTTGTAAAAATACTCAAATACCCCCGATTTG
* * *
58316734 TAAAATTACTGAAATA-CCTTCGACTTGTAAAATTAC-CAAACTACCCCCGATTT
1 TAAAATTACCGAAATACCCTTAG-CTTGTAAAAATACTCAAA-TACCCCCGATTT
58316787 ACAGAATTAT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
53 8 0.18
54 37 0.82
ACGTcount: A:0.38, C:0.21, G:0.09, T:0.31
Consensus pattern (54 bp):
TAAAATTACCGAAATACCCTTAGCTTGTAAAAATACTCAAATACCCCCGATTTG
Found at i:58316794 original size:27 final size:27
Alignment explanation
Indices: 58316775--58317039 Score: 269
Period size: 27 Copynumber: 9.8 Consensus size: 27
58316765 ATTACCAAAC
*
58316775 TACCCCCGATTTACAGAATTATCGTTT
1 TACCCCCGATTTACAGAATTACCGTTT
*
58316802 TACCCCCGATTTACATAATTACCGTTT
1 TACCCCCGATTTACAGAATTACCGTTT
* *
58316829 TACCCTCGATTTACAAAATTACCGTTT
1 TACCCCCGATTTACAGAATTACCGTTT
* *
58316856 TACCCTCGATTTACAGAATTACTGTTT
1 TACCCCCGATTTACAGAATTACCGTTT
* * * *
58316883 TACCCTCGATTTATAAAATTACTGTTT
1 TACCCCCGATTTACAGAATTACCGTTT
** * *
58316910 TACCCTTGATTTATAGAATTACTGTTT
1 TACCCCCGATTTACAGAATTACCGTTT
* * *
58316937 TACCCTCGATTTACAAAATTATCGTTT
1 TACCCCCGATTTACAGAATTACCGTTT
** * **
58316964 TACCGTCGATTTATAGAATTACTATTT
1 TACCCCCGATTTACAGAATTACCGTTT
** * **
58316991 TACCCTTGATTTATAGAATTACTATTT
1 TACCCCCGATTTACAGAATTACCGTTT
* *
58317018 TACCCTCGATTTACAAAATTAC
1 TACCCCCGATTTACAGAATTAC
58317040 AGAAATACCC
Statistics
Matches: 212, Mismatches: 26, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 212 1.00
ACGTcount: A:0.29, C:0.22, G:0.09, T:0.41
Consensus pattern (27 bp):
TACCCCCGATTTACAGAATTACCGTTT
Found at i:58316992 original size:81 final size:81
Alignment explanation
Indices: 58316775--58317038 Score: 377
Period size: 81 Copynumber: 3.3 Consensus size: 81
58316765 ATTACCAAAC
* * * * * * *
58316775 TACCCCCGATTTACAGAATTATCGTTTTACCCCCGATTTACATAATTACCGTTTTACCCTCGATT
1 TACCCTCGATTTACAAAATTATCGTTTTACCCTCGATTTATAAAATTACTGTTTTACCCTTGATT
* * *
58316840 TACAAAATTACCGTTT
66 TATAGAATTACTGTTT
*
58316856 TACCCTCGATTTACAGAATTA-CTGTTTTACCCTCGATTTATAAAATTACTGTTTTACCCTTGAT
1 TACCCTCGATTTACAAAATTATC-GTTTTACCCTCGATTTATAAAATTACTGTTTTACCCTTGAT
58316920 TTATAGAATTACTGTTT
65 TTATAGAATTACTGTTT
* * *
58316937 TACCCTCGATTTACAAAATTATCGTTTTACCGTCGATTTATAGAATTACTATTTTACCCTTGATT
1 TACCCTCGATTTACAAAATTATCGTTTTACCCTCGATTTATAAAATTACTGTTTTACCCTTGATT
*
58317002 TATAGAATTACTATTT
66 TATAGAATTACTGTTT
58317018 TACCCTCGATTTACAAAATTA
1 TACCCTCGATTTACAAAATTA
58317039 CAGAAATACC
Statistics
Matches: 167, Mismatches: 14, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
80 1 0.01
81 165 0.99
82 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.09, T:0.41
Consensus pattern (81 bp):
TACCCTCGATTTACAAAATTATCGTTTTACCCTCGATTTATAAAATTACTGTTTTACCCTTGATT
TATAGAATTACTGTTT
Found at i:58317050 original size:54 final size:54
Alignment explanation
Indices: 58316775--58317041 Score: 324
Period size: 54 Copynumber: 4.9 Consensus size: 54
58316765 ATTACCAAAC
* * * * *
58316775 TACCCCCGATTTACAGAATTA-TCGTTTTACCCCCGATTTACATAATTACCGTTT
1 TACCCTCGATTTACAAAATTACT-GTTTTACCCTCGATTTACAGAATTACAGTTT
* *
58316829 TACCCTCGATTTACAAAATTACCGTTTTACCCTCGATTTACAGAATTACTGTTT
1 TACCCTCGATTTACAAAATTACTGTTTTACCCTCGATTTACAGAATTACAGTTT
* * * *
58316883 TACCCTCGATTTATAAAATTACTGTTTTACCCTTGATTTATAGAATTACTGTTT
1 TACCCTCGATTTACAAAATTACTGTTTTACCCTCGATTTACAGAATTACAGTTT
* *
58316937 TACCCTCGATTTACAAAATTA-TCGTTTTACCGTCGATTTATAGAATTACTA-TTT
1 TACCCTCGATTTACAAAATTACT-GTTTTACCCTCGATTTACAGAATTAC-AGTTT
* * * * *
58316991 TACCCTTGATTTATAGAATTACTATTTTACCCTCGATTTACAAAATTACAG
1 TACCCTCGATTTACAAAATTACTGTTTTACCCTCGATTTACAGAATTACAG
58317042 AAATACCCTC
Statistics
Matches: 187, Mismatches: 21, Indels: 10
0.86 0.10 0.05
Matches are distributed among these distances:
53 2 0.01
54 184 0.98
55 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.09, T:0.41
Consensus pattern (54 bp):
TACCCTCGATTTACAAAATTACTGTTTTACCCTCGATTTACAGAATTACAGTTT
Found at i:58317076 original size:81 final size:80
Alignment explanation
Indices: 58316708--58317174 Score: 247
Period size: 81 Copynumber: 5.8 Consensus size: 80
58316698 CTTAGTTTGT
* * * ** * *
58316708 AAAAATACTGAAATACCCTCGATTTGTAAAATTACTGAAATA-CCTTCGACTTGTAAAATTACCA
1 AAAATTAC-GAAATACCCTCAATTTATAAAATTACCAAAATACCCTT-GATTTATAAAATTACCA
*** *
58316772 AACTACCCCCGATTTAC
64 TTTTACCCTCGATTTAC
* *** * * * * **** * * *
58316789 AGAATTATCGTTTTACCCCCGATTTACATAATTACCGTTTTACCCTCGATTTACAAAATTACCGT
1 AAAATTA-CGAAATACCCTCAATTTATAAAATTACCAAAATACCCTTGATTTATAAAATTACCAT
58316854 TTTACCCTCGATTTAC
65 TTTACCCTCGATTTAC
* *** * ***** * **
58316870 AGAATTACTGTTTTACCCTCGATTTATAAAATTACTGTTTTACCCTTGATTTATAGAATTACTGT
1 AAAATTAC-GAAATACCCTCAATTTATAAAATTACCAAAATACCCTTGATTTATAAAATTACCAT
58316935 TTTACCCTCGATTTAC
65 TTTACCCTCGATTTAC
*** * * * * *** * *
58316951 AAAATTATCGTTTTACCGTCGATTTATAGAATTACTATTTTACCCTTGATTTATAGAATTACTAT
1 AAAATTA-CGAAATACCCTCAATTTATAAAATTACCAAAATACCCTTGATTTATAAAATTACCAT
58317016 TTTACCCTCGATTTAC
65 TTTACCCTCGATTTAC
* * *
58317032 AAAATTACAGAAATACCCTCAATTTGTAAAATTACCAAAATACCCCT-AGTTTGTAAAATTACCA
1 AAAATTAC-GAAATACCCTCAATTTATAAAATTACCAAAATACCCTTGA-TTTATAAAATTACCA
*** * **
58317096 AAATACCACT-GGTTTGT
64 TTTTACC-CTCGATTTAC
* * * * *
58317113 GAAATTACCGAAATACCCTCAATTTGTAAAATTACCAAAATACCCCTGATTTACAAAGTTAC
1 AAAATTA-CGAAATACCCTCAATTTATAAAATTACCAAAATACCCTTGATTTATAAAATTAC
58317175 AGAAATACCC
Statistics
Matches: 317, Mismatches: 60, Indels: 18
0.80 0.15 0.05
Matches are distributed among these distances:
80 3 0.01
81 305 0.96
82 9 0.03
ACGTcount: A:0.34, C:0.21, G:0.09, T:0.36
Consensus pattern (80 bp):
AAAATTACGAAATACCCTCAATTTATAAAATTACCAAAATACCCTTGATTTATAAAATTACCATT
TTACCCTCGATTTAC
Found at i:58317244 original size:27 final size:27
Alignment explanation
Indices: 58317018--58317248 Score: 144
Period size: 27 Copynumber: 8.5 Consensus size: 27
58317008 ATTACTATTT
* * *
58317018 TACCCTCGATTTACAAAATTACAGAAA
1 TACCCTTGATTTGCAAAATTACCGAAA
** * *
58317045 TACCCTCAATTTGTAAAATTACCAAAA
1 TACCCTTGATTTGCAAAATTACCGAAA
* * *
58317072 TACCCCT-AGTTTGTAAAATTACCAAAA
1 TACCCTTGA-TTTGCAAAATTACCGAAA
* **
58317099 TACCAC-TGGTTTGTGAAATTACCGAAA
1 TACC-CTTGATTTGCAAAATTACCGAAA
** * *
58317126 TACCCTCAATTTGTAAAATTACCAAAA
1 TACCCTTGATTTGCAAAATTACCGAAA
* * * *
58317153 TACCCCTGATTTACAAAGTTACAGAAA
1 TACCCTTGATTTGCAAAATTACCGAAA
**
58317180 TACCCTTGACTTT-CTAAAAATTATAGAAA
1 TACCCTTGA-TTTGC--AAAATTACCGAAA
* * * *
58317209 TACCATTGGTTTACAAAATTACTGAAA
1 TACCCTTGATTTGCAAAATTACCGAAA
*
58317236 TACCCTTGGTTTG
1 TACCCTTGATTTG
58317249 TAGATTTACC
Statistics
Matches: 164, Mismatches: 32, Indels: 16
0.77 0.15 0.08
Matches are distributed among these distances:
26 2 0.01
27 136 0.83
28 7 0.04
29 19 0.12
ACGTcount: A:0.39, C:0.20, G:0.10, T:0.31
Consensus pattern (27 bp):
TACCCTTGATTTGCAAAATTACCGAAA
Found at i:58317331 original size:27 final size:27
Alignment explanation
Indices: 58317300--58317392 Score: 125
Period size: 27 Copynumber: 3.4 Consensus size: 27
58317290 TACCTCTATT
*
58317300 AGGTAAAAAGACCGTAAAGCCCCTGTA
1 AGGTAAAATGACCGTAAAGCCCCTGTA
* *
58317327 GGGTAAAGTGACCGTAAAGCCCCTGTA
1 AGGTAAAATGACCGTAAAGCCCCTGTA
*
58317354 AGGTAAAGTGACCGTAATA-CCCCTGTA
1 AGGTAAAATGACCGTAA-AGCCCCTGTA
*
58317381 TGGTAAAATGAC
1 AGGTAAAATGAC
58317393 GAATATGCCC
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
27 58 0.98
28 1 0.02
ACGTcount: A:0.35, C:0.20, G:0.25, T:0.19
Consensus pattern (27 bp):
AGGTAAAATGACCGTAAAGCCCCTGTA
Found at i:58318654 original size:9 final size:9
Alignment explanation
Indices: 58318642--58318698 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
58318632 TTTGATAAAC
58318642 ATGATATGT
1 ATGATATGT
*
58318651 ATGATATGCAC
1 ATGATATG--T
*
58318662 ATGACATGT
1 ATGATATGT
*
58318671 ATGATATGCAC
1 ATGATATG--T
58318682 ATGATATGT
1 ATGATATGT
58318691 ATGATATG
1 ATGATATG
58318699 CACACGAGAT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (9 bp):
ATGATATGT
Found at i:58318665 original size:20 final size:20
Alignment explanation
Indices: 58318640--58318702 Score: 117
Period size: 20 Copynumber: 3.1 Consensus size: 20
58318630 ATTTTGATAA
58318640 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
58318660 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
58318680 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
58318700 ACA
1 ACA
58318703 CGAGATGTTC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.32
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:58318784 original size:24 final size:23
Alignment explanation
Indices: 58318757--58318959 Score: 316
Period size: 24 Copynumber: 8.6 Consensus size: 23
58318747 GAGGAAGTGA
58318757 AAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
58318780 CAAAAGGGCTTATGCCCCAGTTAT
1 -AAAAGGGCTTATGCCCCAGTTAT
58318804 AAAAAGGGCTTATGCCCCAGTTAT
1 -AAAAGGGCTTATGCCCCAGTTAT
58318828 CAAAAGGGCTTATGCCCCAGTTATT
1 -AAAAGGGCTTATGCCCCAGTTA-T
*
58318853 AAAAAGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
*
58318876 TAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
58318899 GATAAAGGGCTTATGCCCCAGTTAT
1 -A-AAAGGGCTTATGCCCCAGTTAT
*
58318924 TAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
*
58318947 TAAAGGGCTTATG
1 AAAAGGGCTTATG
58318960 GTTATTAAAA
Statistics
Matches: 169, Mismatches: 7, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
23 57 0.34
24 89 0.53
25 23 0.14
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.28
Consensus pattern (23 bp):
AAAAGGGCTTATGCCCCAGTTAT
Found at i:58318874 original size:72 final size:71
Alignment explanation
Indices: 58318757--58319011 Score: 339
Period size: 72 Copynumber: 3.7 Consensus size: 71
58318747 GAGGAAGTGA
* * *
58318757 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATAAAAAGGGCTTATGCCCC
1 AAAAGGGCTTATGCCCCAGTTATTAAAAAGGCTTATGCCCCAGTTAT-TAAAGGGCTTATGCCCC
58318822 AGTTATC
65 AGTTATC
58318829 AAAAGGGCTTATGCCCCAGTTATTAAAAAGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCA
1 AAAAGGGCTTATGCCCCAGTTATTAAAAAGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCA
*
58318894 GTTATG
66 GTTATC
*
58318900 ATAAAGGGCTTATGCCCCAGTTATT-AAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATG----
1 A-AAAGGGCTTATGCCCCAGTTATTAAAAAGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCC
*
58318960 -GTTATT
65 AGTTATC
* *
58318966 AAAA-AGCTT-TGCCCCAGTTATTAAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTATTAAAA-AGGCTTATGCC-CCAGTTAT
58319012 ATGATAAAGC
Statistics
Matches: 170, Mismatches: 9, Indels: 15
0.88 0.05 0.08
Matches are distributed among these distances:
63 13 0.08
64 12 0.07
65 14 0.08
66 6 0.04
71 57 0.34
72 68 0.40
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (71 bp):
AAAAGGGCTTATGCCCCAGTTATTAAAAAGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCA
GTTATC
Found at i:58318965 original size:18 final size:19
Alignment explanation
Indices: 58318871--58318968 Score: 63
Period size: 23 Copynumber: 4.5 Consensus size: 19
58318861 TTATGCCCCA
58318871 GTTATTAAAGGGCTTATGCCCC
1 GTTATTAAAGGGCTTATG---C
58318893 AGTTATGATAAAGGGCTTATGCCCC
1 -GTTAT--TAAAGGGCTTATG---C
58318918 AGTTATTAAAGGGCTTATGCCCC
1 -GTTATTAAAGGGCTTATG---C
58318941 AGTTATTAAAGGGCTTATG-
1 -GTTATTAAAGGGCTTATGC
58318960 GTTATTAAA
1 GTTATTAAA
58318969 AAGCTTTGCC
Statistics
Matches: 73, Mismatches: 0, Indels: 9
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.12
23 41 0.56
25 23 0.32
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.33
Consensus pattern (19 bp):
GTTATTAAAGGGCTTATGC
Found at i:58319239 original size:31 final size:31
Alignment explanation
Indices: 58319204--58319305 Score: 114
Period size: 38 Copynumber: 3.1 Consensus size: 31
58319194 CGTTTACAGT
58319204 AAAGGCTTCGGCCCAGTAATATGAAATTTGA
1 AAAGGCTTCGGCCCAGTAATATGAAATTTGA
58319235 AAAGGCTTCGGCCCTGTGTTATGTAATATGAAATTTGA
1 AAAGGCTTCGGCCC------A-GTAATATGAAATTTGA
** *
58319273 AAAGGCTTCGGCCCAGTGTTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATTTGA
58319304 AA
1 AA
58319306 TATGAAAAGG
Statistics
Matches: 61, Mismatches: 3, Indels: 14
0.78 0.04 0.18
Matches are distributed among these distances:
31 29 0.48
32 1 0.02
37 1 0.02
38 30 0.49
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.28
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATTTGA
Found at i:58319270 original size:38 final size:38
Alignment explanation
Indices: 58319219--58319328 Score: 168
Period size: 38 Copynumber: 2.9 Consensus size: 38
58319209 CTTCGGCCCA
*
58319219 GTAATATGAAATTTGAAAAGGCTTCGGCCCTGTGTTAT
1 GTAATATGAAATTTGAAAAGGCTTCGGCCCAGTGTTAT
58319257 GTAATATGAAATTTGAAAAGGCTTCGGCCCAGTGTTAT
1 GTAATATGAAATTTGAAAAGGCTTCGGCCCAGTGTTAT
* *
58319295 GAAATATGAAATATGAAAAGGGCTAT-GGCCCAGT
1 GTAATATGAAATTTGAAAA-GGCT-TCGGCCCAGT
58319329 ACATGTTTGA
Statistics
Matches: 67, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
38 54 0.81
39 12 0.18
40 1 0.01
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.29
Consensus pattern (38 bp):
GTAATATGAAATTTGAAAAGGCTTCGGCCCAGTGTTAT
Found at i:58321632 original size:49 final size:49
Alignment explanation
Indices: 58321571--58321753 Score: 217
Period size: 50 Copynumber: 3.7 Consensus size: 49
58321561 CTGGTACGTA
58321571 TAGTAGCCTGCACTTAGTACTACACATGTGACCAACAGTCTGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCAACAGTCTGGTACACG
* **
58321620 TAGTAGCCTGCACTTAGTACTACACATGTGACCTCACCA-TCTAATACACG
1 TAGTAGCCTGCACTTAGTACTACACATGTGA-C-CAACAGTCTGGTACACG
* * * * * *
58321670 TAGTAGCCTGCACTTAGTTCTACACACGTGATC-ACAGTTTTCGGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCAACAG---TCTGGTACACG
*
58321721 TAGTAGCCTGCACTTAGTACTACACATGCGACC
1 TAGTAGCCTGCACTTAGTACTACACATGTGACC
58321754 TCACAATAGA
Statistics
Matches: 112, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
47 2 0.02
48 1 0.01
49 31 0.28
50 39 0.35
51 39 0.35
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.26
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACATGTGACCAACAGTCTGGTACACG
Found at i:58321735 original size:101 final size:99
Alignment explanation
Indices: 58321571--58321757 Score: 277
Period size: 101 Copynumber: 1.9 Consensus size: 99
58321561 CTGGTACGTA
* * *
58321571 TAGTAGCCTGCACTTAGTACTACACATGTGACCAACAGTCTGGTACACGTAGTAGCCTGCACTTA
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAACAGTCGGGTACACATAGTAGCCTGCACTTA
*
58321636 GTACTACACATGTGACCTCACCATCTAATACACG
66 GTACTACACATGCGACCTCACCATCTAATACACG
* * *
58321670 TAGTAGCCTGCACTTAGTTCTACACACGTGATC-ACAGTTTTCGGGTACGCATAGTAGCCTGCAC
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAACAG---TCGGGTACACATAGTAGCCTGCAC
58321734 TTAGTACTACACATGCGACCTCAC
63 TTAGTACTACACATGCGACCTCAC
58321758 AATAGATCAT
Statistics
Matches: 78, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
98 4 0.05
99 30 0.38
101 44 0.56
ACGTcount: A:0.27, C:0.28, G:0.18, T:0.26
Consensus pattern (99 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCAACAGTCGGGTACACATAGTAGCCTGCACTTA
GTACTACACATGCGACCTCACCATCTAATACACG
Found at i:58323929 original size:15 final size:15
Alignment explanation
Indices: 58323882--58323937 Score: 71
Period size: 15 Copynumber: 3.7 Consensus size: 15
58323872 CAAGAAAATC
58323882 GAATAAAGAAATCCA
1 GAATAAAGAAATCCA
*
58323897 -AGATAGAA-AAACCCA
1 GA-ATA-AAGAAATCCA
58323912 GAATAAAGAAATCCA
1 GAATAAAGAAATCCA
58323927 GAATAAAGAAA
1 GAATAAAGAAA
58323938 CCCAAGATAC
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
14 3 0.09
15 29 0.83
16 3 0.09
ACGTcount: A:0.62, C:0.12, G:0.14, T:0.11
Consensus pattern (15 bp):
GAATAAAGAAATCCA
Found at i:58328176 original size:11 final size:11
Alignment explanation
Indices: 58328139--58328195 Score: 59
Period size: 11 Copynumber: 5.5 Consensus size: 11
58328129 ACATGGTATG
58328139 CATGATATGCA
1 CATGATATGCA
*
58328150 CATGACATG--
1 CATGATATGCA
*
58328159 TATGATATGCA
1 CATGATATGCA
58328170 CATGATATG--
1 CATGATATGCA
*
58328179 TATGATATGCA
1 CATGATATGCA
58328190 CATGAT
1 CATGAT
58328196 GTATTCATAA
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
9 15 0.42
11 21 0.58
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.32
Consensus pattern (11 bp):
CATGATATGCA
Found at i:58328195 original size:20 final size:20
Alignment explanation
Indices: 58328129--58328195 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
58328119 ATTTTGATAA
* *
58328129 ACATGGTATGCATGATATGC
1 ACATGATATGTATGATATGC
*
58328149 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
58328169 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
58328189 ACATGAT
1 ACATGAT
58328196 GTATTCATAA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.31
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:58328338 original size:47 final size:46
Alignment explanation
Indices: 58328244--58328412 Score: 225
Period size: 47 Copynumber: 3.5 Consensus size: 46
58328234 GGAGGAAATG
*
58328244 TAAAAGGGCTTATGCCCCAGTTATGATAAAGGGCTTATGCCCTAGTTAT
1 TAAAAGGGCTTATGCCCCAG-T-T-ATAAAGGGCTTATGCCCCAGTTAT
*
58328293 GATAAAGGGCTTATGCCCCAGTTATAAAGGGCTTATGCCCCAGTTAT
1 TA-AAAGGGCTTATGCCCCAGTTATAAAGGGCTTATGCCCCAGTTAT
58328340 TAAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTT-TGCCCCAGTTAT
1 TAAAAGGGCTTATGCCCCAGTTA-T-AAAGGGCTTATGCCCCAGTTAT
*
58328387 TAAAAGAGGC-TAGGCCTCCAGTTATA
1 TAAAAG-GGCTTATGCC-CCAGTTATA
58328413 TGATAAAGCA
Statistics
Matches: 111, Mismatches: 4, Indels: 13
0.87 0.03 0.10
Matches are distributed among these distances:
46 22 0.20
47 49 0.44
48 20 0.18
49 2 0.02
50 18 0.16
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.28
Consensus pattern (46 bp):
TAAAAGGGCTTATGCCCCAGTTATAAAGGGCTTATGCCCCAGTTAT
Found at i:58328350 original size:24 final size:24
Alignment explanation
Indices: 58328244--58328411 Score: 236
Period size: 25 Copynumber: 7.0 Consensus size: 24
58328234 GGAGGAAATG
58328244 TAAAAGGGCTTATGCCCCAGTTAT
1 TAAAAGGGCTTATGCCCCAGTTAT
* *
58328268 GATAAAGGGCTTATGCCCTAGTTAT
1 TA-AAAGGGCTTATGCCCCAGTTAT
*
58328293 GATAAAGGGCTTATGCCCCAGTTA-
1 TA-AAAGGGCTTATGCCCCAGTTAT
58328317 T-AAAGGGCTTATGCCCCAGTTAT
1 TAAAAGGGCTTATGCCCCAGTTAT
58328340 TAAAAGGGCTTATGCCCCAGTTAT
1 TAAAAGGGCTTATGCCCCAGTTAT
58328364 TAAAAGGGCTT-TGCCCCAGTTAT
1 TAAAAGGGCTTATGCCCCAGTTAT
*
58328387 TAAAAGAGGC-TAGGCCTCCAGTTAT
1 TAAAAG-GGCTTATGCC-CCAGTTAT
58328412 ATGATAAAGC
Statistics
Matches: 133, Mismatches: 5, Indels: 11
0.89 0.03 0.07
Matches are distributed among these distances:
22 21 0.16
23 20 0.15
24 40 0.30
25 52 0.39
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.29
Consensus pattern (24 bp):
TAAAAGGGCTTATGCCCCAGTTAT
Found at i:58328638 original size:31 final size:31
Alignment explanation
Indices: 58328603--58328663 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
58328593 CGTTTACAGT
58328603 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
**
58328634 AAAGGCTTCGGCCCAGTGTTATGAAATATG
1 AAAGGCTTCGGCCCAGTAATATGAAATATG
58328664 GCCTAGTACA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:58336165 original size:24 final size:24
Alignment explanation
Indices: 58336123--58336168 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
58336113 TTATAATATG
* * *
58336123 AAAATGACCGTTTTGCCCCTAGTA
1 AAAATGACCATTATACCCCTAGTA
58336147 AAAATGACCATTATACCCCTAG
1 AAAATGACCATTATACCCCTAG
58336169 GGTTTAAACG
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:0.35, C:0.26, G:0.13, T:0.26
Consensus pattern (24 bp):
AAAATGACCATTATACCCCTAGTA
Found at i:58336254 original size:11 final size:11
Alignment explanation
Indices: 58336218--58336273 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
58336208 CATGGTATGT
58336218 ATGATATGCAC
1 ATGATATGCAC
* *
58336229 ATGACATG--T
1 ATGATATGCAC
58336238 ATGATATGCAC
1 ATGATATGCAC
*
58336249 ATGATATG--T
1 ATGATATGCAC
58336258 ATGATATGCAC
1 ATGATATGCAC
58336269 ATGAT
1 ATGAT
58336274 GTATTCATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:58336273 original size:20 final size:20
Alignment explanation
Indices: 58336207--58336273 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
58336197 ATTTTGATAA
*
58336207 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
*
58336227 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
58336247 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
58336267 ACATGAT
1 ACATGAT
58336274 GTATTCATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:58336352 original size:25 final size:25
Alignment explanation
Indices: 58336324--58336466 Score: 229
Period size: 25 Copynumber: 5.8 Consensus size: 25
58336314 AGGAAATGTA
*
58336324 AAAGGGCTTATGCCCCAATTATGAT
1 AAAGGGCTTATGCCCCAGTTATGAT
58336349 AAAGGGCTTATGCCCCAGTTATGAT
1 AAAGGGCTTATGCCCCAGTTATGAT
*
58336374 AAAGGGCTTATGCCCCAGTTTTGAT
1 AAAGGGCTTATGCCCCAGTTATGAT
*
58336399 AAAGGGCTTATGCCCCAGTTATTA-
1 AAAGGGCTTATGCCCCAGTTATGAT
*
58336423 AAAGGGCTTATGCCCCAGTTATTA-
1 AAAGGGCTTATGCCCCAGTTATGAT
58336447 AAAGGGCTT-TGCCCCAGTTA
1 AAAGGGCTTATGCCCCAGTTA
58336467 AAAAGAGGCT
Statistics
Matches: 114, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
23 11 0.10
24 33 0.29
25 70 0.61
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (25 bp):
AAAGGGCTTATGCCCCAGTTATGAT
Done.