Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D04
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: 56598092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1600000 characters in sequence are not A, C, G, or T
File 178 of 185
Found at i:54134682 original size:50 final size:50
Alignment explanation
Indices: 54134607--54134707 Score: 202
Period size: 50 Copynumber: 2.0 Consensus size: 50
54134597 AATACGAAAC
54134607 TTTGATGACTTCCTTCGGATTCATAGCTTTTCCTTGAAAGATGTACAAGT
1 TTTGATGACTTCCTTCGGATTCATAGCTTTTCCTTGAAAGATGTACAAGT
54134657 TTTGATGACTTCCTTCGGATTCATAGCTTTTCCTTGAAAGATGTACAAGT
1 TTTGATGACTTCCTTCGGATTCATAGCTTTTCCTTGAAAGATGTACAAGT
54134707 T
1 T
54134708 GCGATTTTTC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.41
Consensus pattern (50 bp):
TTTGATGACTTCCTTCGGATTCATAGCTTTTCCTTGAAAGATGTACAAGT
Found at i:54138456 original size:3 final size:3
Alignment explanation
Indices: 54138450--54138513 Score: 119
Period size: 3 Copynumber: 21.3 Consensus size: 3
54138440 ATTATTATTA
*
54138450 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTA TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
54138498 TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG T
54138514 AATACCCAAT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.02, C:0.00, G:0.31, T:0.67
Consensus pattern (3 bp):
TTG
Found at i:54141507 original size:33 final size:35
Alignment explanation
Indices: 54141450--54141520 Score: 101
Period size: 33 Copynumber: 2.1 Consensus size: 35
54141440 TACTCTTTTG
* *
54141450 TTATGTTATGCTTGAAAGTTTTGTTAAGGGATTAC
1 TTATGTTATGCTTGAAAATTTTGTTAAGGGACTAC
*
54141485 TTATGTT-TGCTT-AAAATTTTGTTAATGGACTAC
1 TTATGTTATGCTTGAAAATTTTGTTAAGGGACTAC
54141518 TTA
1 TTA
54141521 CATTTATATT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
33 21 0.64
34 5 0.15
35 7 0.21
ACGTcount: A:0.27, C:0.07, G:0.18, T:0.48
Consensus pattern (35 bp):
TTATGTTATGCTTGAAAATTTTGTTAAGGGACTAC
Found at i:54148118 original size:33 final size:33
Alignment explanation
Indices: 54148080--54148145 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
54148070 TCAAGTTTCA
54148080 AAATAAAAAGCATGGGATGGTTAAGCTTTTTTT
1 AAATAAAAAGCATGGGATGGTTAAGCTTTTTTT
54148113 AAATAAAAAGCATGGGATGGTTAAGCTTTTTTT
1 AAATAAAAAGCATGGGATGGTTAAGCTTTTTTT
54148146 TACTTTATAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.36, C:0.06, G:0.21, T:0.36
Consensus pattern (33 bp):
AAATAAAAAGCATGGGATGGTTAAGCTTTTTTT
Found at i:54148431 original size:91 final size:91
Alignment explanation
Indices: 54148276--54148457 Score: 355
Period size: 91 Copynumber: 2.0 Consensus size: 91
54148266 CGTGCCAATG
*
54148276 AAAGTGGCCACTACGGTCATCACAACGACATAAAGCTTACTTGTGTTTAAAGTTGTCAATTTTTG
1 AAAGTGGCCACTACGGTCATCACAACGACATAAAGCTTACTTGTGCTTAAAGTTGTCAATTTTTG
54148341 AAACAAAATCTTTGGGCTATGATTGA
66 AAACAAAATCTTTGGGCTATGATTGA
54148367 AAAGTGGCCACTACGGTCATCACAACGACATAAAGCTTACTTGTGCTTAAAGTTGTCAATTTTTG
1 AAAGTGGCCACTACGGTCATCACAACGACATAAAGCTTACTTGTGCTTAAAGTTGTCAATTTTTG
54148432 AAACAAAATCTTTGGGCTATGATTGA
66 AAACAAAATCTTTGGGCTATGATTGA
54148458 TGCTGATATT
Statistics
Matches: 90, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
91 90 1.00
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (91 bp):
AAAGTGGCCACTACGGTCATCACAACGACATAAAGCTTACTTGTGCTTAAAGTTGTCAATTTTTG
AAACAAAATCTTTGGGCTATGATTGA
Found at i:54153132 original size:18 final size:17
Alignment explanation
Indices: 54153104--54153141 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
54153094 TAACAATAAT
54153104 ATAAAAATATTAAAAAA
1 ATAAAAATATTAAAAAA
*
54153121 ATAAACAATATTATAAAA
1 ATAAA-AATATTAAAAAA
54153139 ATA
1 ATA
54153142 TTGAAAAGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (17 bp):
ATAAAAATATTAAAAAA
Found at i:54153176 original size:29 final size:28
Alignment explanation
Indices: 54153095--54153177 Score: 96
Period size: 29 Copynumber: 2.9 Consensus size: 28
54153085 CAGGAGCAAT
*
54153095 AACAATAATATAAAAATATTAAAAAAATA
1 AACAATAATATAAAAATA-TAGAAAAATA
* * *
54153124 AACAATATTATAAAAATATTGAAAAGTGCA
1 AACAATAATATAAAAATATAGAAAAAT--A
54153154 AACAATAATA-AAAAATATAGAAAA
1 AACAATAATATAAAAATATAGAAAA
54153178 TTTAAAAATA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
28 6 0.13
29 30 0.65
30 10 0.22
ACGTcount: A:0.67, C:0.05, G:0.05, T:0.23
Consensus pattern (28 bp):
AACAATAATATAAAAATATAGAAAAATA
Found at i:54165140 original size:20 final size:20
Alignment explanation
Indices: 54165115--54165154 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
54165105 CATGACGGAA
54165115 GCAGC-AACAGAAACAGAAAC
1 GCAGCAAACAGAAACA-AAAC
*
54165135 GCAGCAAACAGTAACAAAAC
1 GCAGCAAACAGAAACAAAAC
54165155 AACAATAGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.55, C:0.25, G:0.17, T:0.03
Consensus pattern (20 bp):
GCAGCAAACAGAAACAAAAC
Found at i:54166115 original size:3 final size:3
Alignment explanation
Indices: 54166055--54166106 Score: 54
Period size: 3 Copynumber: 17.7 Consensus size: 3
54166045 TTTGTTAACT
* *
54166055 TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA TCA TCT- TTA CTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA
*
54166099 TTA GTA TT
1 TTA TTA TT
54166107 GGTATTATTG
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
2 3 0.08
3 37 0.93
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:54168650 original size:19 final size:20
Alignment explanation
Indices: 54168610--54168653 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
54168600 GTCTCTTTAG
* *
54168610 GCATT-CATTTCATGCATCT
1 GCATTACATTGCATGCATAT
54168629 GCATTACATTGCAT-CATAT
1 GCATTACATTGCATGCATAT
54168648 GCATTA
1 GCATTA
54168654 GATTTTCACG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.27, C:0.23, G:0.11, T:0.39
Consensus pattern (20 bp):
GCATTACATTGCATGCATAT
Found at i:54173072 original size:45 final size:45
Alignment explanation
Indices: 54173021--54173160 Score: 112
Period size: 45 Copynumber: 3.2 Consensus size: 45
54173011 GGAGCTGGTT
54173021 GAAGACAAAAGATCTTGCTTTTCTACATTGACAGCGAAGTAGATC
1 GAAGACAAAAGATCTTGCTTTTCTACATTGACAGCGAAGTAGATC
* * ** * * *
54173066 GAAGACACAA-ACCTTGCCTCTTTCGGC-TGTGATA--G-AGCT-GGTT
1 GAAGACAAAAGATCTTG-CT-TTTCTACAT-TGACAGCGAAG-TAGATC
* * *
54173109 GAAGACAAAAGATCTTGCCTTCCTACATTGACAGCGAAGCAGATC
1 GAAGACAAAAGATCTTGCTTTTCTACATTGACAGCGAAGTAGATC
54173154 GAAGACA
1 GAAGACA
54173161 CAAACCTTGC
Statistics
Matches: 68, Mismatches: 17, Indels: 20
0.65 0.16 0.19
Matches are distributed among these distances:
42 8 0.12
43 15 0.22
44 13 0.19
45 23 0.34
46 9 0.13
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.24
Consensus pattern (45 bp):
GAAGACAAAAGATCTTGCTTTTCTACATTGACAGCGAAGTAGATC
Found at i:54173089 original size:88 final size:88
Alignment explanation
Indices: 54172940--54173520 Score: 997
Period size: 88 Copynumber: 6.6 Consensus size: 88
54172930 CAATGAAGTT
54172940 AAAGATCTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGT
1 AAAGATCTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGT
*
54173005 TGTGATGGAGCTGGTTGAAGACA
66 TGTGATAGAGCTGGTTGAAGACA
* * * *
54173028 AAAGATCTTGCTTTTCTACATTGACAGCGAAGTAGATCGAAGACACAAACCTTGCCTCTTTCGGC
1 AAAGATCTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGT
54173093 TGTGATAGAGCTGGTTGAAGACA
66 TGTGATAGAGCTGGTTGAAGACA
54173116 AAAGATCTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGT
1 AAAGATCTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGT
*
54173181 TGTGATGGAGCTGGTTGAAGACA
66 TGTGATAGAGCTGGTTGAAGACA
* * * *
54173204 AAAGATCTTG-CTTTCTGCATTGACAGCAAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGC
1 AAAGATCTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGT
54173268 TGTGATAGAGCTGGTTGAAGACA
66 TGTGATAGAGCTGGTTGAAGACA
54173291 AAAGATCTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGT
1 AAAGATCTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGT
*
54173356 TGTGATGGAGCTGGTTGAAGACA
66 TGTGATAGAGCTGGTTGAAGACA
* *
54173379 AAAGATCTTGCCTTTCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGT
1 AAAGATCTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGT
54173444 TGTGATAGAGCTGGTTGAAGACA
66 TGTGATAGAGCTGGTTGAAGACA
* *
54173467 AAAGATCTTGCCTTCCTACATTAACAGCGAAGCAAATCGAA-A-ACAAAGCCTTGC
1 AAAGATCTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAGACACAAA-CCTTGC
54173521 ATCCATCGAT
Statistics
Matches: 464, Mismatches: 27, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
86 5 0.01
87 89 0.19
88 370 0.80
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.25
Consensus pattern (88 bp):
AAAGATCTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGT
TGTGATAGAGCTGGTTGAAGACA
Found at i:54173425 original size:263 final size:264
Alignment explanation
Indices: 54172940--54173520 Score: 997
Period size: 263 Copynumber: 2.2 Consensus size: 264
54172930 CAATGAAGTT
*
54172940 AAAGATCTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGT
1 AAAGATCTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGC
* * * *
54173005 TGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCTTTTCTACATTGACAGCGAAGTAGATCGAAG
66 TGTGATAGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAG
54173070 ACACAAACCTTGCCTCTTTCGGCTGTGATAGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTAC
131 ACACAAACCTTGCCTCTTTCGGCTGTGATAGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTAC
*
54173135 ATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGTTGTGATGGAGCTGGTTGAA
196 ATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGTTGTGATAGAGCTGGTTGAA
54173200 GACA
261 GACA
* * *
54173204 AAAGATCTTG-CTTTCTGCATTGACAGCAAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGC
1 AAAGATCTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGC
54173268 TGTGATAGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAG
66 TGTGATAGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAG
* * * *
54173333 ACACAAACCTTGCCTCTTTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTTCTGC
131 ACACAAACCTTGCCTCTTTCGGCTGTGATAGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTAC
54173398 ATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGTTGTGATAGAGCTGGTTGAA
196 ATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGTTGTGATAGAGCTGGTTGAA
54173463 GACA
261 GACA
* *
54173467 AAAGATCTTGCCTTCCTACATTAACAGCGAAGCAAATCGAA-A-ACAAAGCCTTGC
1 AAAGATCTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAGACACAAA-CCTTGC
54173521 ATCCATCGAT
Statistics
Matches: 297, Mismatches: 18, Indels: 5
0.93 0.06 0.02
Matches are distributed among these distances:
262 5 0.02
263 257 0.87
264 35 0.12
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.25
Consensus pattern (264 bp):
AAAGATCTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGC
TGTGATAGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAG
ACACAAACCTTGCCTCTTTCGGCTGTGATAGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTAC
ATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGTTGTGATAGAGCTGGTTGAA
GACA
Found at i:54173888 original size:43 final size:44
Alignment explanation
Indices: 54173788--54173893 Score: 126
Period size: 44 Copynumber: 2.4 Consensus size: 44
54173778 GATCTTGTCC
* * *
54173788 CCCTGAAGTTACAGTGGAGCAGATTGAAGCCAGAGATCTTATCT
1 CCCTGAAGTTACAGTGGAGCAGATCGAAGACAGAGATCCTATCT
* * **
54173832 CCCCG-AGATTACAGCGGAGCAGATCGAAGACA-CTATCCTATCT
1 CCCTGAAG-TTACAGTGGAGCAGATCGAAGACAGAGATCCTATCT
54173875 CCCTGAAGTTACAGTGGAG
1 CCCTGAAGTTACAGTGGAG
54173894 TGGGTTAAAA
Statistics
Matches: 51, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
43 24 0.47
44 27 0.53
ACGTcount: A:0.29, C:0.25, G:0.25, T:0.22
Consensus pattern (44 bp):
CCCTGAAGTTACAGTGGAGCAGATCGAAGACAGAGATCCTATCT
Found at i:54174453 original size:20 final size:20
Alignment explanation
Indices: 54174428--54174467 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
54174418 CATGACGGAA
54174428 GCAGC-AACAGAAACAGAAAC
1 GCAGCAAACAGAAACA-AAAC
*
54174448 GCAGCAAACAGTAACAAAAC
1 GCAGCAAACAGAAACAAAAC
54174468 AACAATAGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.55, C:0.25, G:0.17, T:0.03
Consensus pattern (20 bp):
GCAGCAAACAGAAACAAAAC
Found at i:54175437 original size:3 final size:3
Alignment explanation
Indices: 54175373--54175428 Score: 69
Period size: 3 Copynumber: 18.7 Consensus size: 3
54175363 TTTGTTAACT
* *
54175373 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCA TCT- TTA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA
*
54175418 TTA TTA GTA TT
1 TTA TTA TTA TT
54175429 GGTATTATTG
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
2 1 0.02
3 44 0.98
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:54180215 original size:24 final size:23
Alignment explanation
Indices: 54180188--54180245 Score: 71
Period size: 24 Copynumber: 2.5 Consensus size: 23
54180178 TTATTAACAT
*
54180188 TGTTCGTGAACATGTTCAATTATA
1 TGTTCGTGAACATCTTCAATTA-A
* **
54180212 TGTTCATGAACATCTTCGTTTAA
1 TGTTCGTGAACATCTTCAATTAA
54180235 TGTTCGTGAAC
1 TGTTCGTGAAC
54180246 GAATTCGATT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 11 0.38
24 18 0.62
ACGTcount: A:0.26, C:0.16, G:0.17, T:0.41
Consensus pattern (23 bp):
TGTTCGTGAACATCTTCAATTAA
Found at i:54199727 original size:33 final size:33
Alignment explanation
Indices: 54199681--54199987 Score: 127
Period size: 43 Copynumber: 8.7 Consensus size: 33
54199671 TTAACCGTTA
* *
54199681 TCGGTGGATTCAGCACTTAGCAACCACCAGTGAT
1 TCGG-GGAATCAGCACTTAGCAACCACCAATGAT
*
54199715 TCGGGGAATCAGCACTTAGCAACCCCTTTCACATTCAAAGAT
1 TCGGGGAATCAGCACTTAGCAA---C---CAC---CAATGAT
*
54199757 AT-GGTGGAATCAGCACTTAGCAACCACCAATCAT
1 -TCGG-GGAATCAGCACTTAGCAACCACCAATGAT
*
54199791 TCGGGGAATCATCACTTAGCAACC-CC-----T
1 TCGGGGAATCAGCACTTAGCAACCACCAATGAT
* *
54199818 TGGGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAGAT
1 TCGGGGAATCAGCACTTAGCAA-CCAC--CA-A--T---GAT
*
54199860 ACGGTGGAATCAGCACTTAGCAACC-CC-----T
1 TCGG-GGAATCAGCACTTAGCAACCACCAATGAT
* *
54199888 TGGGGGAATCAGCACTTAGCAACCCCCTTTATATTTAAAGAT
1 TCGGGGAATCAGCACTTAGCAACCACC---A-A--T---GAT
* *
54199930 ACGGTGGAATCAGCACTTAGCAACCACCAATGAG
1 TCGG-GGAATCAGCACTTAGCAACCACCAATGAT
54199964 TCGGGGAATCAGCACTTAGCAACC
1 TCGGGGAATCAGCACTTAGCAACC
54199988 CCTTCATATT
Statistics
Matches: 212, Mismatches: 17, Indels: 89
0.67 0.05 0.28
Matches are distributed among these distances:
27 41 0.19
28 7 0.03
29 1 0.00
31 1 0.00
32 2 0.01
33 57 0.27
34 16 0.08
36 1 0.00
37 4 0.02
39 5 0.02
40 2 0.01
41 1 0.00
42 15 0.07
43 59 0.28
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.22
Consensus pattern (33 bp):
TCGGGGAATCAGCACTTAGCAACCACCAATGAT
Found at i:54199881 original size:70 final size:70
Alignment explanation
Indices: 54199795--54199993 Score: 301
Period size: 70 Copynumber: 2.8 Consensus size: 70
54199785 AATCATTCGG
*
54199795 GGAATCATCACTTAGCAACCCCTTGGGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAGAT
1 GGAATCAGCACTTAGCAACCCCTTGGGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAGAT
54199860 ACGGT
66 ACGGT
* *
54199865 GGAATCAGCACTTAGCAACCCCTTGGGGGAATCAGCACTTAGCAACCCCCTTTATATTTAAAGAT
1 GGAATCAGCACTTAGCAACCCCTTGGGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAGAT
54199930 ACGGT
66 ACGGT
*
54199935 GGAATCAGCACTTAGCAACCACCAATGAGTCGGGGAATCAGCACTTAGCAA-CCCCTTCA
1 GGAATCAGCACTTAGCAACC-CC--T---TGGGGGAATCAGCACTTAGCAACCCCCTTCA
54199994 TATTCAATGT
Statistics
Matches: 118, Mismatches: 5, Indels: 7
0.91 0.04 0.05
Matches are distributed among these distances:
70 87 0.74
71 2 0.02
73 1 0.01
75 7 0.06
76 21 0.18
ACGTcount: A:0.31, C:0.28, G:0.20, T:0.22
Consensus pattern (70 bp):
GGAATCAGCACTTAGCAACCCCTTGGGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAGAT
ACGGT
Found at i:54205585 original size:14 final size:15
Alignment explanation
Indices: 54205563--54205639 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
54205553 CAATCAAACA
54205563 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
54205577 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
54205592 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
54205612 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
54205626 ACGGAAAAT-ATTTT
1 CCAGAAAATCATTTT
54205640 ACTGGCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 21 0.42
15 15 0.30
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:54205604 original size:20 final size:20
Alignment explanation
Indices: 54205579--54205618 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
54205569 AATATTTTCC
*
54205579 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
54205599 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
54205619 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:54205624 original size:34 final size:35
Alignment explanation
Indices: 54205567--54205633 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
54205557 CAAACACCAG
*
54205567 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
54205602 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
54205634 TATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:54209517 original size:9 final size:9
Alignment explanation
Indices: 54209503--54209527 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
54209493 TTTTTTATTT
54209503 AAATTTTTA
1 AAATTTTTA
54209512 AAATTTTTA
1 AAATTTTTA
54209521 AAATTTT
1 AAATTTT
54209528 AAATTAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
AAATTTTTA
Found at i:54220594 original size:23 final size:22
Alignment explanation
Indices: 54220549--54220597 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
54220539 ATGTAGTTTT
*
54220549 TTTTTTTGCTTTTTTTTTCCTA
1 TTTTCTTGCTTTTTTTTTCCTA
54220571 TTTTCTTG-TTTTTTTTCTCACTA
1 TTTTCTTGCTTTTTTTT-TC-CTA
54220594 TTTT
1 TTTT
54220598 GCTACTATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 8 0.33
22 9 0.38
23 7 0.29
ACGTcount: A:0.06, C:0.14, G:0.04, T:0.76
Consensus pattern (22 bp):
TTTTCTTGCTTTTTTTTTCCTA
Found at i:54220657 original size:19 final size:17
Alignment explanation
Indices: 54220635--54220670 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 17
54220625 TATTTTTTTG
54220635 TTATTGTATAACTTTTGTT
1 TTATTGT-TAA-TTTTGTT
54220654 TTATTGTTAATTTTGTT
1 TTATTGTTAATTTTGTT
54220671 ACTATTTTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.41
18 3 0.18
19 7 0.41
ACGTcount: A:0.19, C:0.03, G:0.11, T:0.67
Consensus pattern (17 bp):
TTATTGTTAATTTTGTT
Found at i:54224920 original size:17 final size:17
Alignment explanation
Indices: 54224898--54224931 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
54224888 ATCCACTAAT
*
54224898 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
54224915 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
54224932 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:54229559 original size:17 final size:17
Alignment explanation
Indices: 54229537--54229570 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
54229527 ATCCACTAAT
*
54229537 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
54229554 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
54229571 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:54235717 original size:4 final size:4
Alignment explanation
Indices: 54235708--54235733 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
54235698 TCTCAAATAT
54235708 TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TT
54235734 GTATCTTTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:54235851 original size:11 final size:11
Alignment explanation
Indices: 54235819--54235863 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
54235809 TAAATTTTAG
*
54235819 TTTTTTATTTC
1 TTTTTTATTTT
*
54235830 ATTTTTATTTT
1 TTTTTTATTTT
54235841 TTTTTTATTTT
1 TTTTTTATTTT
*
54235852 TTCTTATATTTT
1 TT-TTTTATTTT
54235864 GGTCCTATAC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
11 21 0.72
12 8 0.28
ACGTcount: A:0.13, C:0.04, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTTTTATTTT
Found at i:54235853 original size:18 final size:19
Alignment explanation
Indices: 54235813--54235852 Score: 57
Period size: 17 Copynumber: 2.2 Consensus size: 19
54235803 CATGTATAAA
54235813 TTTTAGTTTTTTATTTCAT
1 TTTTAGTTTTTTATTTCAT
*
54235832 TTTTA-TTTTTT-TTTTAT
1 TTTTAGTTTTTTATTTCAT
54235849 TTTT
1 TTTT
54235853 TCTTATATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 9 0.45
18 6 0.30
19 5 0.25
ACGTcount: A:0.12, C:0.03, G:0.03, T:0.82
Consensus pattern (19 bp):
TTTTAGTTTTTTATTTCAT
Found at i:54237057 original size:41 final size:41
Alignment explanation
Indices: 54237000--54237159 Score: 221
Period size: 41 Copynumber: 3.9 Consensus size: 41
54236990 TTTTATTATT
*
54237000 ATTAGCGGTGCTATTTCAAAAACGCCGCTAAAGGCCCGAGC
1 ATTAGCGGCGCTATTTCAAAAACGCCGCTAAAGGCCCGAGC
* *
54237041 ATTAGTGGCGCTATTTCAAAAAAGCCGCTAAAGGCCCGAGC
1 ATTAGCGGCGCTATTTCAAAAACGCCGCTAAAGGCCCGAGC
* * *
54237082 ATTAGCGGCGCTATCTCAAAAACGCTGCTAAAGGACCGAGC
1 ATTAGCGGCGCTATTTCAAAAACGCCGCTAAAGGCCCGAGC
* * * * *
54237123 ATTAGTGGCACTACTCCAAAAACACCGCTAAAGGCCC
1 ATTAGCGGCGCTATTTCAAAAACGCCGCTAAAGGCCC
54237160 CAAAAACTCA
Statistics
Matches: 103, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 103 1.00
ACGTcount: A:0.32, C:0.28, G:0.23, T:0.18
Consensus pattern (41 bp):
ATTAGCGGCGCTATTTCAAAAACGCCGCTAAAGGCCCGAGC
Found at i:54237287 original size:40 final size:40
Alignment explanation
Indices: 54237234--54237328 Score: 118
Period size: 40 Copynumber: 2.4 Consensus size: 40
54237224 AATTCTTATT
*
54237234 TTTAGCGGCGTTTTTCGAAAAGCGCCGCTAATGCTCGATC
1 TTTAGCGGCGTTTTTAGAAAAGCGCCGCTAATGCTCGATC
* * * * *
54237274 TTTAGCTGTGTTTTTATAAAAGCGCCGCTAATGCTTGATT
1 TTTAGCGGCGTTTTTAGAAAAGCGCCGCTAATGCTCGATC
**
54237314 TTTAGTAGCGTTTTT
1 TTTAGCGGCGTTTTT
54237329 TATCCAAACG
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 46 1.00
ACGTcount: A:0.20, C:0.18, G:0.22, T:0.40
Consensus pattern (40 bp):
TTTAGCGGCGTTTTTAGAAAAGCGCCGCTAATGCTCGATC
Found at i:54238860 original size:17 final size:17
Alignment explanation
Indices: 54238838--54238871 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
54238828 ATCCACTAAT
*
54238838 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
54238855 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
54238872 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:54243499 original size:17 final size:17
Alignment explanation
Indices: 54243477--54243510 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
54243467 ATCCACTAAT
*
54243477 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
54243494 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
54243511 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:54246745 original size:19 final size:19
Alignment explanation
Indices: 54246702--54246749 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
54246692 TTAGGTTATA
*
54246702 ATCACTTCAA-TT-TTTGG
1 ATCATTTCAAGTTGTTTGG
54246719 -TC-TTTCAAGTTGTTTGG
1 ATCATTTCAAGTTGTTTGG
54246736 ATCATTTCAAGTTG
1 ATCATTTCAAGTTG
54246750 GAGCGAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
15 5 0.19
16 4 0.15
17 5 0.19
18 2 0.08
19 10 0.38
ACGTcount: A:0.21, C:0.15, G:0.17, T:0.48
Consensus pattern (19 bp):
ATCATTTCAAGTTGTTTGG
Found at i:54252081 original size:21 final size:21
Alignment explanation
Indices: 54252055--54252095 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
54252045 AGATGAGCAA
* *
54252055 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
54252076 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
54252096 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:54254354 original size:18 final size:17
Alignment explanation
Indices: 54254316--54254364 Score: 71
Period size: 18 Copynumber: 2.8 Consensus size: 17
54254306 TCCAATCCAC
*
54254316 ATAATTAATTTAATTAT
1 ATAATTAATTTAATTAA
54254333 ATAATTAATTTATATTAA
1 ATAATTAATTTA-ATTAA
*
54254351 ATAAATAATTTAAT
1 ATAATTAATTTAAT
54254365 AAAAATTGGA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 14 0.48
18 15 0.52
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
ATAATTAATTTAATTAA
Found at i:54262938 original size:17 final size:17
Alignment explanation
Indices: 54262916--54262949 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
54262906 ATCCACTAAT
*
54262916 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
54262933 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
54262950 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:54267576 original size:17 final size:17
Alignment explanation
Indices: 54267554--54267587 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
54267544 ATCCACTAAT
*
54267554 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
54267571 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
54267588 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:54271995 original size:126 final size:126
Alignment explanation
Indices: 54271768--54272007 Score: 444
Period size: 126 Copynumber: 1.9 Consensus size: 126
54271758 GAGAATTGGG
* *
54271768 TTTTTTTTTTTTCTCAGCAACCAAACGAGCTAAGAAATCTGAAAGGAAAGTGAAAAAGATATAAC
1 TTTTTTTTTTTTCTCAGCAACCAAACAAGCTAAGAAATCTGAAAAGAAAGTGAAAAAGATATAAC
*
54271833 CTTGAATTGGAACTAGTGTTTGGCTTTTGAGACAAAGCAGTCAAATGAATTGGTTCTTCTT
66 CTTGAATTGAAACTAGTGTTTGGCTTTTGAGACAAAGCAGTCAAATGAATTGGTTCTTCTT
54271894 TTTTTTTTTTTTCTCAGCAACCAAACAAGCTAAGAAATCTGAAAAGAAAGTGAAAAAGATATAAC
1 TTTTTTTTTTTTCTCAGCAACCAAACAAGCTAAGAAATCTGAAAAGAAAGTGAAAAAGATATAAC
*
54271959 CTTGAATTGAAACTAGTGTTTGGCTTTTGAGTCAAAGCAGTCAAATGAA
66 CTTGAATTGAAACTAGTGTTTGGCTTTTGAGACAAAGCAGTCAAATGAA
54272008 ATTACTCAAA
Statistics
Matches: 110, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
126 110 1.00
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.32
Consensus pattern (126 bp):
TTTTTTTTTTTTCTCAGCAACCAAACAAGCTAAGAAATCTGAAAAGAAAGTGAAAAAGATATAAC
CTTGAATTGAAACTAGTGTTTGGCTTTTGAGACAAAGCAGTCAAATGAATTGGTTCTTCTT
Found at i:54274328 original size:174 final size:175
Alignment explanation
Indices: 54274029--54274376 Score: 461
Period size: 174 Copynumber: 2.0 Consensus size: 175
54274019 GTTCCTAAGT
* *
54274029 TGTTTTTTACAATTTTGATCCTATTTCATGTTCAATGAAAACGACCAAAAGTTTGTTTTAATGTG
1 TGTTTTTTACAATTTCGATCCTATTTCATGTTCAATGAAAACGACCAAAAG-TTGTTTGAATGTG
*
54274094 GTTTTTCAGTTATAAGCAATCATCAAAGCTTTTTGGCTCAAGCTGTGTAACTTGTGGTTGTTTTA
65 GTTTTTCAGTTATAAGCAATCATCAAAGCTTTTTGGCTCAAGCTGTGTAACTTCTGGTTGTTTTA
* *
54274159 TAATATTATGTTGATTGCTAGTTGAGGTCTTTTGGTGGCAATAGTA
130 TAATATTATGTTGATTGCTAGTTGAGATCTTTTGGTGCCAATAGTA
* * * *
54274205 TGTTTTTTAGC-ATTTCGATCCTATTTTTATGTTGAATGAAAACGACCAGAAG-TG-TTGGATGT
1 TGTTTTTTA-CAATTTCGATCCTA-TTTCATGTTCAATGAAAACGACCAAAAGTTGTTTGAATGT
* ** * * *
54274267 -GTTTTTCGAGTTATATGCCCTTATCAAATCTTTTTGGCTCAAGCTGTGTAATTTCTGGTTGTTT
64 GGTTTTTC-AGTTATAAGCAATCATCAAAGCTTTTTGGCTCAAGCTGTGTAACTTCTGGTTGTTT
* * * *
54274331 TGTAATATTATGTTGGTTGTTTGTTGAGATCTTTTGGTGCCAATAG
128 TATAATATTATGTTGATTGCTAGTTGAGATCTTTTGGTGCCAATAG
54274377 CCTGGTAGCA
Statistics
Matches: 150, Mismatches: 19, Indels: 8
0.85 0.11 0.05
Matches are distributed among these distances:
173 7 0.05
174 95 0.63
175 2 0.01
176 20 0.13
177 26 0.17
ACGTcount: A:0.23, C:0.11, G:0.20, T:0.45
Consensus pattern (175 bp):
TGTTTTTTACAATTTCGATCCTATTTCATGTTCAATGAAAACGACCAAAAGTTGTTTGAATGTGG
TTTTTCAGTTATAAGCAATCATCAAAGCTTTTTGGCTCAAGCTGTGTAACTTCTGGTTGTTTTAT
AATATTATGTTGATTGCTAGTTGAGATCTTTTGGTGCCAATAGTA
Found at i:54281007 original size:174 final size:175
Alignment explanation
Indices: 54280708--54281055 Score: 461
Period size: 174 Copynumber: 2.0 Consensus size: 175
54280698 GTTCCTAAGT
* *
54280708 TGTTTTTTACAATTTTGATCCTATTTCATGTTCAATGAAAACGACCAAAAGTTTGTTTTAATGTG
1 TGTTTTTTACAATTTCGATCCTATTTCATGTTCAATGAAAACGACCAAAAG-TTGTTTGAATGTG
*
54280773 GTTTTTGAGTTATAAGCAATCACCAAAGCTTTTTGGCTCAAGCTGTGTAACTTGTGGTTGTTTTA
65 GTTTTTGAGTTATAAGCAATCACCAAAGCTTTTTGGCTCAAGCTGTGTAACTTCTGGTTGTTTTA
* *
54280838 TAATATTATGTTGATTGCTAGTTGAGGTCTTTTGGTGGCAATAGTA
130 TAATATTATGTTGATTGCTAGTTGAGATCTTTTGGTGCCAATAGTA
* * *
54280884 TGTTTTTTAGC-ATTTCGATCCTATTTTCATGTTGAATGAAAACGACCAGAAG-TG-TTGGATGT
1 TGTTTTTTA-CAATTTCGATCCTA-TTTCATGTTCAATGAAAACGACCAAAAGTTGTTTGAATGT
* ** * * * *
54280946 -GTTTTTCGAGTTATATGCCCTTATCAAATCTTTTTGGCTCAAGCTGTGTAATTTCTGGTTGTTT
64 GGTTTTT-GAGTTATAAGCAATCACCAAAGCTTTTTGGCTCAAGCTGTGTAACTTCTGGTTGTTT
* * * *
54281010 TGTAATATTATGTTGGTTGTTTGTTGAGATCTTTTGGTGCCAATAG
128 TATAATATTATGTTGATTGCTAGTTGAGATCTTTTGGTGCCAATAG
54281056 CCTGGTAGCA
Statistics
Matches: 150, Mismatches: 19, Indels: 8
0.85 0.11 0.05
Matches are distributed among these distances:
173 6 0.04
174 95 0.63
175 2 0.01
176 20 0.13
177 27 0.18
ACGTcount: A:0.23, C:0.12, G:0.21, T:0.44
Consensus pattern (175 bp):
TGTTTTTTACAATTTCGATCCTATTTCATGTTCAATGAAAACGACCAAAAGTTGTTTGAATGTGG
TTTTTGAGTTATAAGCAATCACCAAAGCTTTTTGGCTCAAGCTGTGTAACTTCTGGTTGTTTTAT
AATATTATGTTGATTGCTAGTTGAGATCTTTTGGTGCCAATAGTA
Found at i:54287701 original size:174 final size:175
Alignment explanation
Indices: 54287402--54287749 Score: 461
Period size: 174 Copynumber: 2.0 Consensus size: 175
54287392 GTTCCTAAGT
* *
54287402 TGTTTTTTACAATTTTGATCCTATTTCATGTTCAATGAAAACGACCAAAAGTTTGTTTTAATGTG
1 TGTTTTTTACAATTTCGATCCTATTTCATGTTCAATGAAAACGACCAAAAG-TTGTTTGAATGTG
*
54287467 GTTTTTGAGTTATAAGCAATCACCAAAGCTTTTTGGCTCAAGCTGTGTAACTTGTGGTTGTTTTA
65 GTTTTTGAGTTATAAGCAATCACCAAAGCTTTTTGGCTCAAGCTGTGTAACTTCTGGTTGTTTTA
* *
54287532 TAATATTATGTTGATTGCTAGTTGAGGTCTTTTGGTGGCAATAGTA
130 TAATATTATGTTGATTGCTAGTTGAGATCTTTTGGTGCCAATAGTA
* * *
54287578 TGTTTTTTAGC-ATTTCGATCCTATTTTCATGTTGAATGAAAACGACCAGAAG-TG-TTGGATGT
1 TGTTTTTTA-CAATTTCGATCCTA-TTTCATGTTCAATGAAAACGACCAAAAGTTGTTTGAATGT
* ** * * * *
54287640 -GTTTTTCGAGTTATATGCCCTTATCAAATCTTTTTGGCTCAAGCTGTGTAATTTCTGGTTGTTT
64 GGTTTTT-GAGTTATAAGCAATCACCAAAGCTTTTTGGCTCAAGCTGTGTAACTTCTGGTTGTTT
* * * *
54287704 TGTAATATTATGTTGGTTGTTTGTTGAGATCTTTTGGTGCCAATAG
128 TATAATATTATGTTGATTGCTAGTTGAGATCTTTTGGTGCCAATAG
54287750 CCTGGTAGCA
Statistics
Matches: 150, Mismatches: 19, Indels: 8
0.85 0.11 0.05
Matches are distributed among these distances:
173 6 0.04
174 95 0.63
175 2 0.01
176 20 0.13
177 27 0.18
ACGTcount: A:0.23, C:0.12, G:0.21, T:0.44
Consensus pattern (175 bp):
TGTTTTTTACAATTTCGATCCTATTTCATGTTCAATGAAAACGACCAAAAGTTGTTTGAATGTGG
TTTTTGAGTTATAAGCAATCACCAAAGCTTTTTGGCTCAAGCTGTGTAACTTCTGGTTGTTTTAT
AATATTATGTTGATTGCTAGTTGAGATCTTTTGGTGCCAATAGTA
Found at i:54294394 original size:174 final size:175
Alignment explanation
Indices: 54294095--54294442 Score: 461
Period size: 174 Copynumber: 2.0 Consensus size: 175
54294085 GTTCCTAAGT
* *
54294095 TGTTTTTTACAATTTTGATCCTATTTCATGTTCAATGAAAACGACCAAAAGTTTGTTTTAATGTG
1 TGTTTTTTACAATTTCGATCCTATTTCATGTTCAATGAAAACGACCAAAAG-TTGTTTGAATGTG
*
54294160 GTTTTTGAGTTATAAGCAATCACCAAAGCTTTTTGGCTCAAGCTGTGTAACTTGTGGTTGTTTTA
65 GTTTTTGAGTTATAAGCAATCACCAAAGCTTTTTGGCTCAAGCTGTGTAACTTCTGGTTGTTTTA
* *
54294225 TAATATTATGTTGATTGCTAGTTGAGGTCTTTTGGTGGCAATAGTA
130 TAATATTATGTTGATTGCTAGTTGAGATCTTTTGGTGCCAATAGTA
* * *
54294271 TGTTTTTTAGC-ATTTCGATCCTATTTTCATGTTGAATGAAAACGACCAGAAG-TG-TTGGATGT
1 TGTTTTTTA-CAATTTCGATCCTA-TTTCATGTTCAATGAAAACGACCAAAAGTTGTTTGAATGT
* ** * * * *
54294333 -GTTTTTCGAGTTATATGCCCTTATCAAATCTTTTTGGCTCAAGCTGTGTAATTTCTGGTTGTTT
64 GGTTTTT-GAGTTATAAGCAATCACCAAAGCTTTTTGGCTCAAGCTGTGTAACTTCTGGTTGTTT
* * * *
54294397 TGTAATATTATGTTGGTTGTTTGTTGAGATCTTTTGGTGCCAATAG
128 TATAATATTATGTTGATTGCTAGTTGAGATCTTTTGGTGCCAATAG
54294443 CCTGGTAGCA
Statistics
Matches: 150, Mismatches: 19, Indels: 8
0.85 0.11 0.05
Matches are distributed among these distances:
173 6 0.04
174 95 0.63
175 2 0.01
176 20 0.13
177 27 0.18
ACGTcount: A:0.23, C:0.12, G:0.21, T:0.44
Consensus pattern (175 bp):
TGTTTTTTACAATTTCGATCCTATTTCATGTTCAATGAAAACGACCAAAAGTTGTTTGAATGTGG
TTTTTGAGTTATAAGCAATCACCAAAGCTTTTTGGCTCAAGCTGTGTAACTTCTGGTTGTTTTAT
AATATTATGTTGATTGCTAGTTGAGATCTTTTGGTGCCAATAGTA
Found at i:54297844 original size:16 final size:16
Alignment explanation
Indices: 54297823--54297874 Score: 86
Period size: 16 Copynumber: 3.2 Consensus size: 16
54297813 TTTGGTTCGC
54297823 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
54297839 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
* *
54297855 TGTAATGGAATAGAGG
1 TGTATTGGATTAGAGG
54297871 TGTA
1 TGTA
54297875 ATAGCAAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.29, C:0.00, G:0.37, T:0.35
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:54297921 original size:45 final size:44
Alignment explanation
Indices: 54297855--54297949 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 44
54297845 GGATTAGAGG
* *
54297855 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAAC-ACTGTTTGGTTGAA
* **
54297900 TGTAATGGAATAGAGGCGTAATAGTAAAACTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
54297944 TGTAAT
1 TGTAAT
54297950 AGAGGTGTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.33
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
Found at i:54298119 original size:25 final size:25
Alignment explanation
Indices: 54298087--54298141 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
54298077 TAATTTAATC
*
54298087 ATAT-TTAAACATAATTATTATT-AA
1 ATATATTAAACAT-ATTATAATTAAA
*
54298111 ATATATTAAATATATTATAATTAAA
1 ATATATTAAACATATTATAATTAAA
54298136 ATATAT
1 ATATAT
54298142 AATTTAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 12 0.44
25 15 0.56
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (25 bp):
ATATATTAAACATATTATAATTAAA
Found at i:54298323 original size:47 final size:46
Alignment explanation
Indices: 54298272--54298432 Score: 140
Period size: 47 Copynumber: 3.6 Consensus size: 46
54298262 GATTTAATAA
54298272 AATTTAAAATAATTATAACTAATAAATTATCTTATATGAATTTGTAT
1 AATTTAAAATAATTATAA-TAATAAATTATCTTATATGAATTTGTAT
* * * * *
54298319 AATTTAAAATAATTATTATTACATATAAT-TTA-AT-AA---GATAT
1 AATTTAAAATAATTATAATAATAAATTATCTTATATGAATTTG-TAT
* * * *
54298360 AATTTCATAA-AATTATTGATAATAAATTTTCTTATATGAATTTATAT
1 AATTT-AAAATAATTA-TAATAATAAATTATCTTATATGAATTTGTAT
54298407 AATTTAAAATAATT-TATATAATAAAT
1 AATTTAAAATAATTATA-ATAATAAAT
54298433 CTATTGTATA
Statistics
Matches: 88, Mismatches: 15, Indels: 23
0.70 0.12 0.18
Matches are distributed among these distances:
40 1 0.01
41 13 0.15
42 11 0.12
43 5 0.06
44 4 0.05
45 6 0.07
46 19 0.22
47 29 0.33
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (46 bp):
AATTTAAAATAATTATAATAATAAATTATCTTATATGAATTTGTAT
Found at i:54302505 original size:32 final size:32
Alignment explanation
Indices: 54302450--54302548 Score: 128
Period size: 32 Copynumber: 3.1 Consensus size: 32
54302440 TAACTATTGG
*
54302450 TAATTAAAATCAATGCT-TAATTAAGCCTTGATT
1 TAATT-AAATCAATGCTAT-ATTAAGGCTTGATT
* *
54302483 TAATTAAATGAATGCTATATTAAGGTTTGATT
1 TAATTAAATCAATGCTATATTAAGGCTTGATT
* *
54302515 TAATTAAATCAATGCCATATGAAGGCTTGATT
1 TAATTAAATCAATGCTATATTAAGGCTTGATT
54302547 TA
1 TA
54302549 GGCCGGTCCT
Statistics
Matches: 58, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
32 52 0.90
33 6 0.10
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.39
Consensus pattern (32 bp):
TAATTAAATCAATGCTATATTAAGGCTTGATT
Found at i:54321107 original size:32 final size:32
Alignment explanation
Indices: 54321052--54321150 Score: 128
Period size: 32 Copynumber: 3.1 Consensus size: 32
54321042 TAACTATTGG
*
54321052 TAATTAAAATCAATGCT-TAATTAAGCCTTGATT
1 TAATT-AAATCAATGCTAT-ATTAAGGCTTGATT
* *
54321085 TAATTAAATGAATGCTATATTAAGGTTTGATT
1 TAATTAAATCAATGCTATATTAAGGCTTGATT
* *
54321117 TAATTAAATCAATGCCATATGAAGGCTTGATT
1 TAATTAAATCAATGCTATATTAAGGCTTGATT
54321149 TA
1 TA
54321151 GGCCGGTCCT
Statistics
Matches: 58, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
32 52 0.90
33 6 0.10
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.39
Consensus pattern (32 bp):
TAATTAAATCAATGCTATATTAAGGCTTGATT
Found at i:54326531 original size:42 final size:41
Alignment explanation
Indices: 54326377--54326532 Score: 158
Period size: 42 Copynumber: 3.7 Consensus size: 41
54326367 TATGTTATCG
*
54326377 TGTAAGACCACGTCTGGGACGTTGGCATCGAT-TTGAGATTTA
1 TGTAAGACCACGTCTGGGACGTTGGCATCGATATT--GATTCA
* * * *
54326419 TGTATAAGACCATGTCTGGGACATCGGCATC-ATATTTGATTTCG
1 TG--TAAGACCACGTCTGGGACGTTGGCATCGATA-TTGA-TTCA
54326463 TGTAAGACC-CTGTCTGGGACAG-TGGCATCGATATTGATTACA
1 TGTAAGACCAC-GTCTGGGAC-GTTGGCATCGATATTGATT-CA
54326505 TGTAAGACCACGTCTGGGACGTTGGCAT
1 TGTAAGACCACGTCTGGGACGTTGGCAT
54326533 TGTACGATTT
Statistics
Matches: 94, Mismatches: 9, Indels: 22
0.75 0.07 0.18
Matches are distributed among these distances:
41 3 0.03
42 53 0.56
43 8 0.09
44 28 0.30
45 2 0.02
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (41 bp):
TGTAAGACCACGTCTGGGACGTTGGCATCGATATTGATTCA
Found at i:54333856 original size:42 final size:41
Alignment explanation
Indices: 54333702--54333857 Score: 158
Period size: 42 Copynumber: 3.7 Consensus size: 41
54333692 TATGTTATCG
*
54333702 TGTAAGACCACGTCTGGGACGTTGGCATCGAT-TTGAGATTTA
1 TGTAAGACCACGTCTGGGACGTTGGCATCGATATT--GATTCA
* * * *
54333744 TGTATAAGACCATGTCTGGGACATCGGCATC-ATATTTGATTTCG
1 TG--TAAGACCACGTCTGGGACGTTGGCATCGATA-TTGA-TTCA
54333788 TGTAAGACC-CTGTCTGGGACAG-TGGCATCGATATTGATTACA
1 TGTAAGACCAC-GTCTGGGAC-GTTGGCATCGATATTGATT-CA
54333830 TGTAAGACCACGTCTGGGACGTTGGCAT
1 TGTAAGACCACGTCTGGGACGTTGGCAT
54333858 TGTACGATTT
Statistics
Matches: 94, Mismatches: 9, Indels: 22
0.75 0.07 0.18
Matches are distributed among these distances:
41 3 0.03
42 53 0.56
43 8 0.09
44 28 0.30
45 2 0.02
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (41 bp):
TGTAAGACCACGTCTGGGACGTTGGCATCGATATTGATTCA
Found at i:54351343 original size:19 final size:18
Alignment explanation
Indices: 54351313--54351352 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
54351303 TTGTTTTATT
*
54351313 TTTATATATATTATGTAA
1 TTTATATATATTATATAA
54351331 TTTATAGTATATTATATAA
1 TTTATA-TATATTATATAA
54351350 TTT
1 TTT
54351353 TAAATATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (18 bp):
TTTATATATATTATATAA
Found at i:54351360 original size:19 final size:19
Alignment explanation
Indices: 54351312--54351361 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
54351302 TTTGTTTTAT
* *
54351312 TTTTATATATATTATGTAA
1 TTTTAAATATATTATATAA
*
54351331 -TTTATAGTATATTATATAA
1 TTTTA-AATATATTATATAA
54351350 TTTTAAATATAT
1 TTTTAAATATAT
54351362 AATAATATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
18 4 0.16
19 17 0.68
20 4 0.16
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (19 bp):
TTTTAAATATATTATATAA
Found at i:54351453 original size:21 final size:21
Alignment explanation
Indices: 54351428--54351472 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
54351418 AAAATCATCT
*
54351428 AAAATATTAAATATTAAATTA
1 AAAATAATAAATATTAAATTA
* * *
54351449 AAAATAATATATATTTACTTA
1 AAAATAATAAATATTAAATTA
54351470 AAA
1 AAA
54351473 CGAGCTTAGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (21 bp):
AAAATAATAAATATTAAATTA
Found at i:54354853 original size:30 final size:31
Alignment explanation
Indices: 54354819--54354877 Score: 84
Period size: 32 Copynumber: 1.9 Consensus size: 31
54354809 CGCGTGTATG
*
54354819 ATTGCAC-CAAATTAAAATTCATGTATACAA
1 ATTGCACACAAATCAAAATTCATGTATACAA
*
54354849 ATTGCACATTAAATCAAAATTCATGTATA
1 ATTGCACA-CAAATCAAAATTCATGTATA
54354878 ATTTTGAGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 7 0.28
32 18 0.72
ACGTcount: A:0.46, C:0.15, G:0.07, T:0.32
Consensus pattern (31 bp):
ATTGCACACAAATCAAAATTCATGTATACAA
Found at i:54357924 original size:20 final size:22
Alignment explanation
Indices: 54357878--54357924 Score: 62
Period size: 20 Copynumber: 2.2 Consensus size: 22
54357868 AAAGTTATAA
54357878 AAAATAATTTTATATTAAATTT
1 AAAATAATTTTATATTAAATTT
*
54357900 AAAAT-ATTTT-TATTAATTTT
1 AAAATAATTTTATATTAAATTT
*
54357920 TAAAT
1 AAAAT
54357925 TGAGAAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 13 0.57
21 5 0.22
22 5 0.22
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
AAAATAATTTTATATTAAATTT
Found at i:54360076 original size:4 final size:4
Alignment explanation
Indices: 54360067--54360106 Score: 80
Period size: 4 Copynumber: 10.0 Consensus size: 4
54360057 TTTTTTTCCC
54360067 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT
54360107 ATTTAAGTCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
CTTT
Found at i:54364062 original size:16 final size:16
Alignment explanation
Indices: 54364038--54364068 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
54364028 CGAATAACCT
*
54364038 AATCTAAAACAAATTG
1 AATCCAAAACAAATTG
54364054 AATCCAAAACAAATT
1 AATCCAAAACAAATT
54364069 CAAAAAATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.16, G:0.03, T:0.23
Consensus pattern (16 bp):
AATCCAAAACAAATTG
Found at i:54365670 original size:16 final size:16
Alignment explanation
Indices: 54365651--54365688 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
54365641 TTTTATATGT
54365651 TATAAATTCTATAAT-A
1 TATAAATTCTA-AATAA
*
54365667 TATAAATTTTAAATAA
1 TATAAATTCTAAATAA
54365683 TATAAA
1 TATAAA
54365689 ACATTACAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 3 0.15
16 17 0.85
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
TATAAATTCTAAATAA
Found at i:54365677 original size:32 final size:32
Alignment explanation
Indices: 54365615--54365677 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 32
54365605 GATTATAGTA
* *
54365615 ATGTTATATATTACTATAGATTTAATTTTTAT
1 ATGTTATAAATTACTATAGATTTAAATTTTAT
54365647 ATGTTATAAATT-CTATA-ATATATAAATTTTA
1 ATGTTATAAATTACTATAGAT-T-TAAATTTTA
54365678 AATAATATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 2 0.07
31 6 0.22
32 19 0.70
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.52
Consensus pattern (32 bp):
ATGTTATAAATTACTATAGATTTAAATTTTAT
Found at i:54368291 original size:30 final size:29
Alignment explanation
Indices: 54368257--54368345 Score: 81
Period size: 29 Copynumber: 3.0 Consensus size: 29
54368247 TTAAAAATTG
*
54368257 AATTAAATC-AAATCAAAATTTCATGTATAA
1 AATTAAA-CAAAATCAAAA-TTCATATATAA
*
54368287 AATTACACAAAATCAAAATTCATATATAA
1 AATTAAACAAAATCAAAATTCATATATAA
* * * *
54368316 CATTATACATTGAATCAAATTTCATATATA
1 AATTAAACA--AAATCAAAATTCATATATA
54368346 GTTTTAATGT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 18 0.36
30 15 0.30
31 17 0.34
ACGTcount: A:0.52, C:0.12, G:0.02, T:0.34
Consensus pattern (29 bp):
AATTAAACAAAATCAAAATTCATATATAA
Found at i:54368340 original size:31 final size:29
Alignment explanation
Indices: 54368266--54368345 Score: 88
Period size: 29 Copynumber: 2.7 Consensus size: 29
54368256 GAATTAAATC
*
54368266 AAATCAAAATTTCATGTATAAAATTACACA
1 AAATC-AAATTTCATATATAAAATTACACA
* * *
54368296 AAATCAAAATTCATATATAACATTATACA
1 AAATCAAATTTCATATATAAAATTACACA
*
54368325 TTGAATCAAATTTCATATATA
1 --AAATCAAATTTCATATATA
54368346 GTTTTAATGT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
29 20 0.48
30 5 0.12
31 17 0.40
ACGTcount: A:0.51, C:0.12, G:0.03, T:0.34
Consensus pattern (29 bp):
AAATCAAATTTCATATATAAAATTACACA
Found at i:54369211 original size:32 final size:31
Alignment explanation
Indices: 54369175--54369246 Score: 85
Period size: 30 Copynumber: 2.3 Consensus size: 31
54369165 AAATTAAAGT
* *
54369175 ATGATAAAATTGTAT-TTTGTCTCCTTTCAAAA
1 ATGATAAAATT-TATGTTTAT-TCCCTTCAAAA
54369207 ATGATAAAA-TTATGTTTATTCCCTTCAAAA
1 ATGATAAAATTTATGTTTATTCCCTTCAAAA
*
54369237 ATGATGAAAT
1 ATGATAAAAT
54369247 GATAAATTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
30 21 0.60
31 5 0.14
32 9 0.26
ACGTcount: A:0.39, C:0.11, G:0.10, T:0.40
Consensus pattern (31 bp):
ATGATAAAATTTATGTTTATTCCCTTCAAAA
Found at i:54369464 original size:25 final size:24
Alignment explanation
Indices: 54369436--54369498 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 24
54369426 TTCTAAATAT
54369436 CTATCTATATATAATATGTTTTGG
1 CTATCTATATATAATATGTTTTGG
54369460 C---CTATATATAATATGTTTTGG
1 CTATCTATATATAATATGTTTTGG
*
54369481 CCTATATATATATAATAT
1 -CTATCTATATATAATAT
54369499 CTATATATGA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
21 20 0.59
22 1 0.03
24 1 0.03
25 12 0.35
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.48
Consensus pattern (24 bp):
CTATCTATATATAATATGTTTTGG
Found at i:54369492 original size:23 final size:21
Alignment explanation
Indices: 54369440--54369490 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
54369430 AAATATCTAT
54369440 CTATATATAATATGTTTTGGC
1 CTATATATAATATGTTTTGGC
54369461 CTATATATAATATGTTTTGGC
1 CTATATATAATATGTTTTGGC
54369482 CTATATATA
1 CTATATATA
54369491 TATAATATCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.31, C:0.10, G:0.12, T:0.47
Consensus pattern (21 bp):
CTATATATAATATGTTTTGGC
Found at i:54373879 original size:16 final size:16
Alignment explanation
Indices: 54373842--54373880 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
54373832 GAAGCAATAG
54373842 ATATTT-TCGTCAAAT
1 ATATTTATCGTCAAAT
*
54373857 ATAATTTATCTTCAAAT
1 AT-ATTTATCGTCAAAT
54373874 ATATTTA
1 ATATTTA
54373881 AATTTAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 2 0.10
16 9 0.43
17 10 0.48
ACGTcount: A:0.38, C:0.10, G:0.03, T:0.49
Consensus pattern (16 bp):
ATATTTATCGTCAAAT
Found at i:54393245 original size:13 final size:13
Alignment explanation
Indices: 54393227--54393274 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
54393217 TTGAAGGTGA
54393227 TTTTCTTTTTTTC
1 TTTTCTTTTTTTC
* *
54393240 TTTTCTTTGTTTA
1 TTTTCTTTTTTTC
54393253 TTTT-TGTTTTTTC
1 TTTTCT-TTTTTTC
54393266 TTCTTCTTT
1 TT-TTCTTT
54393275 GCAAAACAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
12 1 0.04
13 22 0.79
14 4 0.14
15 1 0.04
ACGTcount: A:0.02, C:0.12, G:0.04, T:0.81
Consensus pattern (13 bp):
TTTTCTTTTTTTC
Found at i:54394560 original size:26 final size:24
Alignment explanation
Indices: 54394507--54394561 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 24
54394497 CAATTTTTGG
*
54394507 TTATTTTAATTTCTTGTATATTAT
1 TTATTTTAATTTCTTGTACATTAT
54394531 TTATTTTAAATTT-TTGTACATATACT
1 TTATTTT-AATTTCTTGTACAT-TA-T
54394557 TTATT
1 TTATT
54394562 GATTTACAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
24 14 0.52
25 7 0.26
26 6 0.22
ACGTcount: A:0.27, C:0.05, G:0.04, T:0.64
Consensus pattern (24 bp):
TTATTTTAATTTCTTGTACATTAT
Found at i:54400156 original size:51 final size:52
Alignment explanation
Indices: 54400093--54400528 Score: 337
Period size: 51 Copynumber: 8.6 Consensus size: 52
54400083 CCGGTTCACA
* * * *
54400093 TAGTAGCATGCACATAGTACTACACAGGTGACCATCA-CTATCCGATACACG
1 TAGTAGCCTTCACATAGTACTACACACGTGACCATCAGTTATCCGATACACG
* * * *
54400144 TAGTAGCCTGCACATAGTCCTACACACGT-A--ATCGAAGTTATCC-AGTACGCA
1 TAGTAGCCTTCACATAGTACTACACACGTGACCATC--AGTTATCCGA-TACACG
* * * *
54400195 TAGTAGCCTGCACATAGTACTACACATGCGACCTATCA--T-TCTGATACACG
1 TAGTAGCCTTCACATAGTACTACACACGTGACC-ATCAGTTATCCGATACACG
* * * * * *
54400245 TAGTAGCCTACACATAGTACTACACACGTGATCA--AGTTTTACGGTTCACG
1 TAGTAGCCTTCACATAGTACTACACACGTGACCATCAGTTATCCGATACACG
* * * * * *
54400295 AAGTAGCCTTCACATAGTACTACACACGTGATCA-AAGCTTTTCAG-TACACA
1 TAGTAGCCTTCACATAGTACTACACACGTGACCATCAG-TTATCCGATACACG
* * * *
54400346 TAGTAGCCTTCACTTAGTACTACACATGTGACCATTATTTAT-CGATACACG
1 TAGTAGCCTTCACATAGTACTACACACGTGACCATCAGTTATCCGATACACG
* * * * * * *
54400397 TAGTAGCCTTCACACAGCACTACACAAGTGACCA-AAGCT-TCTCGGTACACA
1 TAGTAGCCTTCACATAGTACTACACACGTGACCATCAGTTATC-CGATACACG
* * * * *
54400448 TTGTAGCCTTCACTTAGTACTACACATGTGACCATTATTTAT-CGATACACG
1 TAGTAGCCTTCACATAGTACTACACACGTGACCATCAGTTATCCGATACACG
*
54400499 TAGTAGCCTTCACACAGTACTACACACGTG
1 TAGTAGCCTTCACATAGTACTACACACGTG
54400529 TTCATCGATA
Statistics
Matches: 307, Mismatches: 58, Indels: 40
0.76 0.14 0.10
Matches are distributed among these distances:
47 1 0.00
48 3 0.01
49 3 0.01
50 80 0.26
51 206 0.67
52 9 0.03
53 2 0.01
55 3 0.01
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (52 bp):
TAGTAGCCTTCACATAGTACTACACACGTGACCATCAGTTATCCGATACACG
Found at i:54400368 original size:151 final size:153
Alignment explanation
Indices: 54400138--54400524 Score: 419
Period size: 151 Copynumber: 2.5 Consensus size: 153
54400128 CACTATCCGA
* * * * * *
54400138 TACACGTAGTAGCCTGCACATAGTCCTACACACGTAATCGAAGTTATCCAGTACGCATAGTAGCC
1 TACACGAAGTAGCCTTCACATAGTACTACACACGTGATCAAAGTTATCCAGTACACATAGTAGCC
* * *
54400203 TGCACATAGTACTACACATGCGACCTATCA-TTCT-GATACACGTAGTAGCCTACACATAGTACT
66 TGCACATAGTACTACACATGCGACC-ATCATTTATCGATACACGTAGTAGCCTACACACAGCACT
* * *
54400266 ACACACGTGATC-AAG-TTTTACGG
130 ACACAAGTGACCAAAGCTTCT-CGG
* *
54400289 TTCACGAAGTAGCCTTCACATAGTACTACACACGTGATCAAAGCTT-TTCAGTACACATAGTAGC
1 TACACGAAGTAGCCTTCACATAGTACTACACACGTGATCAAAG-TTATCCAGTACACATAGTAGC
* * * * *
54400353 CTTCACTTAGTACTACACATGTGACCATTATTTATCGATACACGTAGTAGCCTTCACACAGCACT
65 CTGCACATAGTACTACACATGCGACCATCATTTATCGATACACGTAGTAGCCTACACACAGCACT
54400418 ACACAAGTGACCAAAGCTTCTCGG
130 ACACAAGTGACCAAAGCTTCTCGG
* * * * * * * *
54400442 TACAC-ATTGTAGCCTTCACTTAGTACTACACATGTGACCATTATTTATCGA-TACACGTAGTAG
1 TACACGA-AGTAGCCTTCACATAGTACTACACACGTGATCA-AAGTTATCCAGTACACATAGTAG
* *
54400505 CCTTCACACAGTACTACACA
64 CCTGCACATAGTACTACACA
54400525 CGTGTTCATC
Statistics
Matches: 197, Mismatches: 31, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
150 3 0.02
151 79 0.40
152 39 0.20
153 70 0.36
154 6 0.03
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (153 bp):
TACACGAAGTAGCCTTCACATAGTACTACACACGTGATCAAAGTTATCCAGTACACATAGTAGCC
TGCACATAGTACTACACATGCGACCATCATTTATCGATACACGTAGTAGCCTACACACAGCACTA
CACAAGTGACCAAAGCTTCTCGG
Found at i:54400433 original size:102 final size:102
Alignment explanation
Indices: 54400195--54400524 Score: 407
Period size: 102 Copynumber: 3.3 Consensus size: 102
54400185 CCAGTACGCA
* * * * * * * * *
54400195 TAGTAGCCTGCACATAGTACTACACATGCGACC-TATCATTCTGA-TACACGTAGTAGCCTACAC
1 TAGTAGCCTTCACACAGTACTACACAAGTGACCAAAGC-TTCTCAGTACACATAGTAGCCTTCAC
* * * * * *
54400258 ATAGTACTACACACGTGATCAAGT-TTTA-CGGTTCACG
65 TTAGTACTACACATGTGA-CCATTATTTATCGATACACG
* * * * *
54400295 AAGTAGCCTTCACATAGTACTACACACGTGATCAAAGCTTTTCAGTACACATAGTAGCCTTCACT
1 TAGTAGCCTTCACACAGTACTACACAAGTGACCAAAGCTTCTCAGTACACATAGTAGCCTTCACT
54400360 TAGTACTACACATGTGACCATTATTTATCGATACACG
66 TAGTACTACACATGTGACCATTATTTATCGATACACG
* * *
54400397 TAGTAGCCTTCACACAGCACTACACAAGTGACCAAAGCTTCTCGGTACACATTGTAGCCTTCACT
1 TAGTAGCCTTCACACAGTACTACACAAGTGACCAAAGCTTCTCAGTACACATAGTAGCCTTCACT
54400462 TAGTACTACACATGTGACCATTATTTATCGATACACG
66 TAGTACTACACATGTGACCATTATTTATCGATACACG
54400499 TAGTAGCCTTCACACAGTACTACACA
1 TAGTAGCCTTCACACAGTACTACACA
54400525 CGTGTTCATC
Statistics
Matches: 200, Mismatches: 26, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
100 35 0.17
101 39 0.19
102 126 0.63
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (102 bp):
TAGTAGCCTTCACACAGTACTACACAAGTGACCAAAGCTTCTCAGTACACATAGTAGCCTTCACT
TAGTACTACACATGTGACCATTATTTATCGATACACG
Found at i:54406640 original size:27 final size:27
Alignment explanation
Indices: 54406610--54406663 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
54406600 CCAGATAGGG
54406610 GCCTTATGCTTCTCTCTTTATATCTCA
1 GCCTTATGCTTCTCTCTTTATATCTCA
54406637 GCCTTATGCTTCTCTCTTTATATCTCA
1 GCCTTATGCTTCTCTCTTTATATCTCA
54406664 AACCTAGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.15, C:0.30, G:0.07, T:0.48
Consensus pattern (27 bp):
GCCTTATGCTTCTCTCTTTATATCTCA
Found at i:54408364 original size:33 final size:33
Alignment explanation
Indices: 54408286--54408374 Score: 133
Period size: 33 Copynumber: 2.7 Consensus size: 33
54408276 CACTTATTAG
54408286 TTTCCATAATAGTCCTCATCAAATACACATCAA
1 TTTCCATAATAGTCCTCATCAAATACACATCAA
* * *
54408319 TTACGATTATAGTCCTCATCAAATACACATCAA
1 TTTCCATAATAGTCCTCATCAAATACACATCAA
* *
54408352 TTTCCATAATAGTCTTTATCAAA
1 TTTCCATAATAGTCCTCATCAAA
54408375 GTAGCCTAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.38, C:0.24, G:0.04, T:0.34
Consensus pattern (33 bp):
TTTCCATAATAGTCCTCATCAAATACACATCAA
Found at i:54410215 original size:16 final size:16
Alignment explanation
Indices: 54410196--54410231 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
54410186 GATTGAAAAG
54410196 AAAATTGAAAAA-TAAA
1 AAAATT-AAAAATTAAA
54410212 AAAATTAAAAATTAAA
1 AAAATTAAAAATTAAA
54410228 AAAA
1 AAAA
54410232 ATTGTCCACA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (16 bp):
AAAATTAAAAATTAAA
Found at i:54414051 original size:20 final size:19
Alignment explanation
Indices: 54414001--54414053 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
54413991 ATAAAAAATA
54414001 TTATATT-AATTATATATG
1 TTATATTAAATTATATATG
* * *
54414019 TTAAATAATAATTATATATAT
1 TTATATTA-AATTATATAT-G
54414040 TTATATTAAATTAT
1 TTATATTAAATTAT
54414054 TAATTCAATA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
18 5 0.19
20 16 0.59
21 6 0.22
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (19 bp):
TTATATTAAATTATATATG
Found at i:54419747 original size:33 final size:33
Alignment explanation
Indices: 54419710--54419774 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
54419700 TTTAGGCTAC
* *
54419710 TTTGATAAAGACTATTATTGTAATTGATGTGTA
1 TTTGATAAAGACTATAATCGTAATTGATGTGTA
* *
54419743 TTTGATGAGGACTATAATCGTAATTGATGTGT
1 TTTGATAAAGACTATAATCGTAATTGATGTGT
54419775 CTCCAGCCCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.31, C:0.05, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTGATAAAGACTATAATCGTAATTGATGTGTA
Found at i:54419928 original size:16 final size:16
Alignment explanation
Indices: 54419907--54419942 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
54419897 TGTGGACAAT
54419907 TTTTTTTAATTTTT-AA
1 TTTTTTT-ATTTTTCAA
54419923 TTTTTTTATTTTTCAA
1 TTTTTTTATTTTTCAA
54419939 TTTT
1 TTTT
54419943 CTTTTCAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTTTTTATTTTTCAA
Found at i:54425250 original size:42 final size:40
Alignment explanation
Indices: 54425196--54425286 Score: 109
Period size: 42 Copynumber: 2.3 Consensus size: 40
54425186 GAATACAATA
54425196 ATTTTTTT--ATTTTTTTAAAATTT-AAAATACTTTTAAAAT
1 ATTTTTTTAAATTTTTTT-AAATTTAAAAATA-TTTTAAAAT
*
54425235 ACTTTTTTTAAATTTTTTTAATTTTAAAAATATTTTAAAA-
1 A-TTTTTTTAAATTTTTTTAAATTTAAAAATATTTTAAAAT
*
54425275 ATATTTTTAAAT
1 ATTTTTTTAAAT
54425287 ACTTTTATTT
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
39 11 0.24
40 8 0.17
41 13 0.28
42 14 0.30
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (40 bp):
ATTTTTTTAAATTTTTTTAAATTTAAAAATATTTTAAAAT
Found at i:54425285 original size:12 final size:11
Alignment explanation
Indices: 54425255--54425281 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
54425245 AATTTTTTTA
54425255 ATTTTAAAAAT
1 ATTTTAAAAAT
54425266 ATTTTAAAAAT
1 ATTTTAAAAAT
54425277 ATTTT
1 ATTTT
54425282 TAAATACTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
ATTTTAAAAAT
Found at i:54425345 original size:37 final size:37
Alignment explanation
Indices: 54425266--54425364 Score: 104
Period size: 33 Copynumber: 2.8 Consensus size: 37
54425256 TTTTAAAAAT
*
54425266 ATTTTAAAAATATTTTT-AAAT-ACTTTTATTTTTTTTA
1 ATTTT-AAAATATTTTTAAAATAAATTTT-TTTTTTTTA
54425303 ATTTTAAAATATTTTTAAAATAAATTTTTTTATTTTT-
1 ATTTTAAAATATTTTTAAAATAAATTTTTTT-TTTTTA
*
54425340 GTTTT---A-ATTTTTAAAATAAATTTTT
1 ATTTTAAAATATTTTTAAAATAAATTTTT
54425365 GATATTTATT
Statistics
Matches: 57, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
33 19 0.33
34 1 0.02
36 11 0.19
37 16 0.28
38 10 0.18
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (37 bp):
ATTTTAAAATATTTTTAAAATAAATTTTTTTTTTTTA
Found at i:54427133 original size:42 final size:40
Alignment explanation
Indices: 54427040--54427136 Score: 122
Period size: 43 Copynumber: 2.3 Consensus size: 40
54427030 TAGAAAAAGC
* *
54427040 AAAATATTTTTTCATTTTAGTTCTAATTTTAAAAAATTCA
1 AAAATATTTTTTCAATTTAGTTCTAATTCTAAAAAATTCA
*
54427080 ATAAATTTATTTTTTCAATTTAGTTCTAATTCTAAAAATTATTTA
1 A-AAA--TATTTTTTCAATTTAGTTCTAATTCTAAAAA--ATTCA
54427125 AAAATATTTTTT
1 AAAATATTTTTT
54427137 TTAAAAAATT
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
40 1 0.02
41 3 0.06
42 8 0.16
43 29 0.59
44 3 0.06
45 5 0.10
ACGTcount: A:0.39, C:0.06, G:0.02, T:0.53
Consensus pattern (40 bp):
AAAATATTTTTTCAATTTAGTTCTAATTCTAAAAAATTCA
Found at i:54429111 original size:26 final size:26
Alignment explanation
Indices: 54429081--54429130 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
54429071 CTTGTATTAA
54429081 GATGTTGAAAATTTCGGGAAAATGGG
1 GATGTTGAAAATTTCGGGAAAATGGG
54429107 GATGTTGAAAATTTCGGGAAAATG
1 GATGTTGAAAATTTCGGGAAAATG
54429131 AGGTATTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.36, C:0.04, G:0.32, T:0.28
Consensus pattern (26 bp):
GATGTTGAAAATTTCGGGAAAATGGG
Found at i:54430026 original size:42 final size:43
Alignment explanation
Indices: 54429962--54430050 Score: 99
Period size: 42 Copynumber: 2.1 Consensus size: 43
54429952 TATATGAATG
* * ** *
54429962 TATATACATATATAAAAAACAAATATGCATATCTATGTATATA
1 TATATAAATATATAAAAAACAAAAAAACATAACTATGTATATA
** *
54430005 TATATAAAT-TATAAAGCACAAAAAAACATAAGTATGTATATA
1 TATATAAATATATAAAAAACAAAAAAACATAACTATGTATATA
54430047 TATA
1 TATA
54430051 GATATAAATT
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
42 30 0.79
43 8 0.21
ACGTcount: A:0.54, C:0.08, G:0.06, T:0.33
Consensus pattern (43 bp):
TATATAAATATATAAAAAACAAAAAAACATAACTATGTATATA
Found at i:54430262 original size:21 final size:21
Alignment explanation
Indices: 54430233--54430284 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
54430223 CAAGACATAG
54430233 ATAATAATAATATTAATAATA
1 ATAATAATAATATTAATAATA
* * *
54430254 ATCATAATAATATTGATGATA
1 ATAATAATAATATTAATAATA
54430275 ATAATAATAA
1 ATAATAATAA
54430285 CTTATTAGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.37
Consensus pattern (21 bp):
ATAATAATAATATTAATAATA
Found at i:54430304 original size:3 final size:3
Alignment explanation
Indices: 54430233--54430284 Score: 59
Period size: 3 Copynumber: 17.3 Consensus size: 3
54430223 CAAGACATAG
* * * * *
54430233 ATA ATA ATA ATA TTA ATA ATA ATC ATA ATA ATA TTG ATG ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
54430281 ATA A
1 ATA A
54430285 CTTATTAGTT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:54435512 original size:33 final size:33
Alignment explanation
Indices: 54435466--54435530 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 33
54435456 TTTAGGCTAC
* *
54435466 TTTGATAAAGACTATTATGGAAATTGATGTGTA
1 TTTGATAAAGACTATAATCGAAATTGATGTGTA
* * *
54435499 TTTGATGAGGACTATAATCGTAATTGATGTGT
1 TTTGATAAAGACTATAATCGAAATTGATGTGT
54435531 CTCCAGCTCG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.32, C:0.05, G:0.23, T:0.40
Consensus pattern (33 bp):
TTTGATAAAGACTATAATCGAAATTGATGTGTA
Found at i:54442642 original size:20 final size:20
Alignment explanation
Indices: 54442608--54442649 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
54442598 AACTATTTAA
** *
54442608 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
54442628 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
54442648 AT
1 AT
54442650 GTGTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:54455525 original size:21 final size:21
Alignment explanation
Indices: 54455499--54455539 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
54455489 ATCTGCTCAA
* *
54455499 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
54455520 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
54455540 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:54462481 original size:6 final size:6
Alignment explanation
Indices: 54462472--54462502 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
54462462 TGGTGTTGGG
54462472 GTTGAT GTTGAT GTTGAT GTTGAT GTTGAT G
1 GTTGAT GTTGAT GTTGAT GTTGAT GTTGAT G
54462503 AAGGTGGTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.00, G:0.35, T:0.48
Consensus pattern (6 bp):
GTTGAT
Found at i:54462825 original size:16 final size:16
Alignment explanation
Indices: 54462789--54462826 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
54462779 TTTGATTCGC
*
54462789 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAAG
*
54462805 CGTAATGGAATAGAAG
1 TGTAATGGAATAGAAG
54462821 TGTAAT
1 TGTAAT
54462827 AGCTAATCTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.39, C:0.03, G:0.32, T:0.26
Consensus pattern (16 bp):
TGTAATGGAATAGAAG
Found at i:54462861 original size:46 final size:44
Alignment explanation
Indices: 54462808--54462901 Score: 134
Period size: 44 Copynumber: 2.1 Consensus size: 44
54462798 ATAGAGGCGT
* * *
54462808 AATGGAATAGAAGTGTAATAGCTAATCTTTTTGTTTGGTTGAATGG
1 AATGGAATAGAACTGTAATAG-TAATC-TTGTGTTTGGTTAAATGG
*
54462854 AATGGAATAGAACTGTAATAGTATTCTTGTGTTTGGTTAAATGG
1 AATGGAATAGAACTGTAATAGTAATCTTGTGTTTGGTTAAATGG
54462898 AATG
1 AATG
54462902 ATGTTGTAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
44 20 0.45
45 4 0.09
46 20 0.45
ACGTcount: A:0.32, C:0.04, G:0.26, T:0.38
Consensus pattern (44 bp):
AATGGAATAGAACTGTAATAGTAATCTTGTGTTTGGTTAAATGG
Found at i:54463083 original size:18 final size:17
Alignment explanation
Indices: 54463060--54463193 Score: 77
Period size: 18 Copynumber: 8.0 Consensus size: 17
54463050 TTATTATTAA
54463060 ATATAATTTAATAAAAAT
1 ATATAATTTAAT-AAAAT
54463078 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
*
54463095 ATATGAATTT-TTAAAAT
1 ATAT-AATTTAATAAAAT
* * *
54463112 -CATAATAT-ATAATACT
1 ATATAATTTAATAA-AAT
* *
54463128 ATAAAATATAATTTAAAAT
1 ATATAATTTAA--TAAAAT
* *
54463147 A-ATTA-TT-AT-TAA-
1 ATATAATTTAATAAAAT
*
54463159 ATATAATTTAACAAAAAT
1 ATATAATTTAA-TAAAAT
54463177 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
54463194 TCTTAGTATT
Statistics
Matches: 88, Mismatches: 16, Indels: 25
0.68 0.12 0.19
Matches are distributed among these distances:
12 1 0.01
13 5 0.06
14 3 0.03
15 8 0.09
16 5 0.06
17 29 0.33
18 31 0.35
19 3 0.03
20 3 0.03
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.40
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:54474538 original size:31 final size:31
Alignment explanation
Indices: 54474500--54474560 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
54474490 GGCCCATTTT
54474500 TATTTTAAAAAT-TTTAAAAAATTAAAAAAAG
1 TATTTTAAAAATATTT-AAAAATTAAAAAAAG
*
54474531 TATTTTAAAAATATTTTAAAATTAAAAAAA
1 TATTTTAAAAATATTTAAAAATTAAAAAAA
54474561 TTAAAGAAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
31 25 0.89
32 3 0.11
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (31 bp):
TATTTTAAAAATATTTAAAAATTAAAAAAAG
Found at i:54474540 original size:11 final size:11
Alignment explanation
Indices: 54474500--54474551 Score: 56
Period size: 10 Copynumber: 4.9 Consensus size: 11
54474490 GGCCCATTTT
54474500 TATTTT-AAAA
1 TATTTTAAAAA
54474510 -ATTTTAAAAA
1 TATTTTAAAAA
**
54474520 -ATTAAAAAAA
1 TATTTTAAAAA
54474530 GTATTTTAAAAA
1 -TATTTTAAAAA
54474542 TATTTTAAAA
1 TATTTTAAAA
54474552 TTAAAAAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
9 5 0.14
10 12 0.34
11 10 0.29
12 8 0.23
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:54474622 original size:11 final size:11
Alignment explanation
Indices: 54474607--54474667 Score: 56
Period size: 11 Copynumber: 5.6 Consensus size: 11
54474597 AAAATTAAAA
54474607 AAAAAGTATTTT
1 AAAAA-TATTTT
54474619 AAAAATATTTT
1 AAAAATATTTT
54474630 --AAA-ATTTT
1 AAAAATATTTT
* **
54474638 AAAAAAATTAA
1 AAAAATATTTT
54474649 AAAAAGTATTTT
1 AAAAA-TATTTT
54474661 AAAAATA
1 AAAAATA
54474668 AAAAAATAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
8 5 0.12
9 3 0.08
10 3 0.08
11 16 0.40
12 13 0.32
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:54474652 original size:19 final size:19
Alignment explanation
Indices: 54474614--54474652 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
54474604 AAAAAAAAGT
* **
54474614 ATTTTAAAAATATTTTAAA
1 ATTTTAAAAAAATTAAAAA
54474633 ATTTTAAAAAAATTAAAAA
1 ATTTTAAAAAAATTAAAAA
54474652 A
1 A
54474653 AGTATTTTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
ATTTTAAAAAAATTAAAAA
Found at i:54482141 original size:32 final size:33
Alignment explanation
Indices: 54482105--54482181 Score: 93
Period size: 39 Copynumber: 2.2 Consensus size: 33
54482095 CGCCGCATAA
54482105 GATTG-TGAAATTAATAGTTACTGTTTGATGAG
1 GATTGATGAAATTAATAGTTACTGTTTGATGAG
54482137 GATTGAAATTAATGAAATTAATAGTTACTGTTTGATGAG
1 GATTG------ATGAAATTAATAGTTACTGTTTGATGAG
54482176 GATTGA
1 GATTGA
54482182 GAGTTTAAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
32 5 0.13
33 1 0.03
39 32 0.84
ACGTcount: A:0.35, C:0.03, G:0.23, T:0.39
Consensus pattern (33 bp):
GATTGATGAAATTAATAGTTACTGTTTGATGAG
Found at i:54493406 original size:22 final size:22
Alignment explanation
Indices: 54493378--54493420 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
54493368 GAAGTTAATG
54493378 TAGGAATATTCTGTAAATATTT
1 TAGGAATATTCTGTAAATATTT
* *
54493400 TAGGAATATTTTGTAGATATT
1 TAGGAATATTCTGTAAATATT
54493421 CTTTTTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.35, C:0.02, G:0.16, T:0.47
Consensus pattern (22 bp):
TAGGAATATTCTGTAAATATTT
Found at i:54497132 original size:22 final size:22
Alignment explanation
Indices: 54497104--54497146 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
54497094 AGGGGGAGTG
54497104 TAGGAATATTCTGTAAATATTT
1 TAGGAATATTCTGTAAATATTT
* *
54497126 TAGGAATATTTTGTAGATATT
1 TAGGAATATTCTGTAAATATT
54497147 CTTTTTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.35, C:0.02, G:0.16, T:0.47
Consensus pattern (22 bp):
TAGGAATATTCTGTAAATATTT
Found at i:54500314 original size:33 final size:33
Alignment explanation
Indices: 54500259--54500324 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
54500249 CACAGAGAGT
* *
54500259 TACACATCAATTACGATTATAGTCCTCATCAAA
1 TACACATCAATTACCATAATAGTCCTCATCAAA
* * *
54500292 TACACATCAATTTCCATAATAGTCTTTATCAAA
1 TACACATCAATTACCATAATAGTCCTCATCAAA
54500325 GTAGCCTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.39, C:0.23, G:0.05, T:0.33
Consensus pattern (33 bp):
TACACATCAATTACCATAATAGTCCTCATCAAA
Found at i:54501514 original size:13 final size:13
Alignment explanation
Indices: 54501496--54501520 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54501486 TGTTATTGTA
54501496 CACTCATTTTAGT
1 CACTCATTTTAGT
54501509 CACTCATTTTAG
1 CACTCATTTTAG
54501521 GCACAAGAGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.24, G:0.08, T:0.44
Consensus pattern (13 bp):
CACTCATTTTAGT
Found at i:54506810 original size:23 final size:21
Alignment explanation
Indices: 54506783--54506825 Score: 68
Period size: 23 Copynumber: 2.0 Consensus size: 21
54506773 TTTGTTAATT
54506783 GATAAATTTTTATAAATATTGAG
1 GATAAATTTTT-TAAAT-TTGAG
54506806 GATAAATTTTTTAAATTTGA
1 GATAAATTTTTTAAATTTGA
54506826 TAGATTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 4 0.20
22 5 0.25
23 11 0.55
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.47
Consensus pattern (21 bp):
GATAAATTTTTTAAATTTGAG
Found at i:54509395 original size:24 final size:24
Alignment explanation
Indices: 54509368--54509419 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
54509358 AAATTTAGGG
*
54509368 TTTAGAAATTAGAAATAAAG-GCAA
1 TTTAGAAATTAAAAATAAAGAG-AA
**
54509392 TTTAGGTATTAAAAATAAAGAGAA
1 TTTAGAAATTAAAAATAAAGAGAA
54509416 TTTA
1 TTTA
54509420 AATAATTTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 23 0.96
25 1 0.04
ACGTcount: A:0.52, C:0.02, G:0.15, T:0.31
Consensus pattern (24 bp):
TTTAGAAATTAAAAATAAAGAGAA
Found at i:54517183 original size:16 final size:16
Alignment explanation
Indices: 54517157--54517199 Score: 70
Period size: 15 Copynumber: 2.8 Consensus size: 16
54517147 GATTGAAAAG
*
54517157 AAAATTGAAAAATT-A
1 AAAATTAAAAAATTAA
54517172 AAAATTAAAAAATTAA
1 AAAATTAAAAAATTAA
54517188 AAAATTAAAAAA
1 AAAATTAAAAAA
54517200 AATTGTCCTC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 13 0.50
16 13 0.50
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.23
Consensus pattern (16 bp):
AAAATTAAAAAATTAA
Found at i:54517199 original size:8 final size:8
Alignment explanation
Indices: 54517157--54517199 Score: 70
Period size: 8 Copynumber: 5.5 Consensus size: 8
54517147 GATTGAAAAG
*
54517157 AAAATTGA
1 AAAATTAA
54517165 AAAATT-A
1 AAAATTAA
54517172 AAAATTAA
1 AAAATTAA
54517180 AAAATTAA
1 AAAATTAA
54517188 AAAATTAA
1 AAAATTAA
54517196 AAAA
1 AAAA
54517200 AATTGTCCTC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
7 7 0.21
8 27 0.79
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.23
Consensus pattern (8 bp):
AAAATTAA
Found at i:54520616 original size:33 final size:33
Alignment explanation
Indices: 54520578--54520648 Score: 117
Period size: 33 Copynumber: 2.2 Consensus size: 33
54520568 TTTTTAAAAA
*
54520578 AAAATATTTTTAAAATACTTTTTTTTTATTTT-T
1 AAAATATTTTTAAAATA-TTTTTTTTAATTTTCT
54520611 AAAATATTTTTAAAATATTTTTTTTAATTTTCT
1 AAAATATTTTTAAAATATTTTTTTTAATTTTCT
54520644 AAAAT
1 AAAAT
54520649 TTCAACTCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
32 13 0.36
33 23 0.64
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (33 bp):
AAAATATTTTTAAAATATTTTTTTTAATTTTCT
Found at i:54520620 original size:10 final size:11
Alignment explanation
Indices: 54520578--54520632 Score: 67
Period size: 11 Copynumber: 5.0 Consensus size: 11
54520568 TTTTTAAAAA
54520578 AAAATATTTTT
1 AAAATATTTTT
54520589 AAAATACTTTTT
1 AAAATA-TTTTT
***
54520601 -TTTTATTTTT
1 AAAATATTTTT
54520611 AAAATATTTTT
1 AAAATATTTTT
54520622 AAAATATTTTT
1 AAAATATTTTT
54520633 TTTAATTTTC
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
10 5 0.14
11 26 0.72
12 5 0.14
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (11 bp):
AAAATATTTTT
Found at i:54523280 original size:31 final size:31
Alignment explanation
Indices: 54523242--54523366 Score: 119
Period size: 31 Copynumber: 4.1 Consensus size: 31
54523232 CTTTGCCAAG
*
54523242 TGTGTATTTTCAGAACAGGAAAACACCGAAA
1 TGTGTATTTTCAGAACAGGACAACACCGAAA
** ** *
54523273 TGTGTATTTAGAGAA-A-GACAACATTGAAG
1 TGTGTATTTTCAGAACAGGACAACACCGAAA
*
54523302 TGGTGTATTTTCAGAACAGGACAATACCGAAA
1 T-GTGTATTTTCAGAACAGGACAACACCGAAA
** * * *
54523334 TGCATATTTTCAAAACAAGACAATACCGAAA
1 TGTGTATTTTCAGAACAGGACAACACCGAAA
54523365 TG
1 TG
54523367 CGTAGGACAA
Statistics
Matches: 75, Mismatches: 16, Indels: 6
0.77 0.16 0.06
Matches are distributed among these distances:
29 10 0.13
30 13 0.17
31 42 0.56
32 10 0.13
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.25
Consensus pattern (31 bp):
TGTGTATTTTCAGAACAGGACAACACCGAAA
Found at i:54523430 original size:29 final size:29
Alignment explanation
Indices: 54523393--54523497 Score: 104
Period size: 29 Copynumber: 3.6 Consensus size: 29
54523383 AGTGTGTATT
* * *
54523393 TTCATAACAAGACAGCACTGAAGTGCATA
1 TTCAGAACAAGACAACACTAAAGTGCATA
* *
54523422 TTCAGAACAAGACAACA-TCAAAGTGTGTATT
1 TTCAGAACAAGACAACACT-AAA--GTGCATA
* *
54523453 TTCAGAACAGGACAACACCAAAGTGCATA
1 TTCAGAACAAGACAACACTAAAGTGCATA
*
54523482 TTCAGAACAAGGCAAC
1 TTCAGAACAAGACAAC
54523498 GCTGAAATGC
Statistics
Matches: 61, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
28 1 0.02
29 36 0.59
31 24 0.39
ACGTcount: A:0.43, C:0.21, G:0.17, T:0.19
Consensus pattern (29 bp):
TTCAGAACAAGACAACACTAAAGTGCATA
Found at i:54523477 original size:60 final size:60
Alignment explanation
Indices: 54523372--54523526 Score: 195
Period size: 60 Copynumber: 2.6 Consensus size: 60
54523362 AAATGCGTAG
* * * * * **
54523372 GACAACACCGAAGTGTGTATTTTCATAACAAGACAGCACTGAAGTGCATATTCAGAACAA
1 GACAACATCAAAGTGTGTATTTTCAGAACAGGACAACACCAAAGTGCATATTCAGAACAA
54523432 GACAACATCAAAGTGTGTATTTTCAGAACAGGACAACACCAAAGTGCATATTCAGAACAA
1 GACAACATCAAAGTGTGTATTTTCAGAACAGGACAACACCAAAGTGCATATTCAGAACAA
* * * *
54523492 GGCAACGCTGAAA-TGCGTATTTTCAGAACAGGACA
1 GACAAC-ATCAAAGTGTGTATTTTCAGAACAGGACA
54523527 GATTAAAGTG
Statistics
Matches: 83, Mismatches: 11, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
60 79 0.95
61 4 0.05
ACGTcount: A:0.40, C:0.20, G:0.19, T:0.21
Consensus pattern (60 bp):
GACAACATCAAAGTGTGTATTTTCAGAACAGGACAACACCAAAGTGCATATTCAGAACAA
Found at i:54523643 original size:29 final size:29
Alignment explanation
Indices: 54523564--54523650 Score: 77
Period size: 31 Copynumber: 2.9 Consensus size: 29
54523554 ACCGAAGCGC
* *
54523564 GTATTCAGAACAAGACAACACCGAAGTAT
1 GTATTTAGAACAAGACAACACCAAAGTAT
* * * *
54523593 TTATTTTAAGAATAAGGCAACACTAAAG-AGT
1 GTA-TTT-AGAACAAGACAACACCAAAGTA-T
*
54523624 GTATTTAGAACAAGACAACATCAAAGT
1 GTATTTAGAACAAGACAACACCAAAGT
54523651 GCATATTTTC
Statistics
Matches: 43, Mismatches: 11, Indels: 7
0.70 0.18 0.11
Matches are distributed among these distances:
29 18 0.42
30 6 0.14
31 19 0.44
ACGTcount: A:0.46, C:0.15, G:0.16, T:0.23
Consensus pattern (29 bp):
GTATTTAGAACAAGACAACACCAAAGTAT
Found at i:54523698 original size:31 final size:32
Alignment explanation
Indices: 54523638--54523703 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 32
54523628 TTAGAACAAG
* ** *
54523638 ACAACATCAAAGTGCATATTTTCAGAATAA-A
1 ACAACAACAAAGTGCATATTTAAAAAATAAGA
*
54523669 ACAACAACGAAGTGCATATTTAAAAAATAAGA
1 ACAACAACAAAGTGCATATTTAAAAAATAAGA
54523701 ACA
1 ACA
54523704 CTGAAATACA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 25 0.86
32 4 0.14
ACGTcount: A:0.53, C:0.15, G:0.11, T:0.21
Consensus pattern (32 bp):
ACAACAACAAAGTGCATATTTAAAAAATAAGA
Found at i:54525529 original size:23 final size:23
Alignment explanation
Indices: 54525503--54525571 Score: 138
Period size: 23 Copynumber: 3.0 Consensus size: 23
54525493 TCGCTCTCGT
54525503 TGTCAGTCATTGTCTCTTAACCC
1 TGTCAGTCATTGTCTCTTAACCC
54525526 TGTCAGTCATTGTCTCTTAACCC
1 TGTCAGTCATTGTCTCTTAACCC
54525549 TGTCAGTCATTGTCTCTTAACCC
1 TGTCAGTCATTGTCTCTTAACCC
54525572 ATGCTTTATT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.17, C:0.30, G:0.13, T:0.39
Consensus pattern (23 bp):
TGTCAGTCATTGTCTCTTAACCC
Found at i:54529526 original size:20 final size:20
Alignment explanation
Indices: 54529500--54529546 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
54529490 CAAAACTATG
54529500 AAAAAATATTAAAAATTATA
1 AAAAAATATTAAAAATTATA
* * *
54529520 AACAAATATTAATAATTTTA
1 AAAAAATATTAAAAATTATA
54529540 AAAAAAT
1 AAAAAAT
54529547 TCTAAAAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (20 bp):
AAAAAATATTAAAAATTATA
Found at i:54529582 original size:27 final size:27
Alignment explanation
Indices: 54529518--54529582 Score: 69
Period size: 27 Copynumber: 2.3 Consensus size: 27
54529508 TTAAAAATTA
*
54529518 TAAACAAATATTAATAATTTTAAAAAAAT
1 TAAA-AAA-ATTAATAATTGTAAAAAAAT
*
54529547 TCTAAAAAATTAA-AATTGTAAAAAAAGT
1 T-AAAAAAATTAATAATTGTAAAAAAA-T
54529575 TAAAAAAA
1 TAAAAAAA
54529583 ATTTACATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
27 18 0.58
28 7 0.23
29 4 0.13
30 2 0.06
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (27 bp):
TAAAAAAATTAATAATTGTAAAAAAAT
Found at i:54529582 original size:28 final size:28
Alignment explanation
Indices: 54529510--54529585 Score: 82
Period size: 28 Copynumber: 2.6 Consensus size: 28
54529500 AAAAAATATT
*
54529510 AAAAATTATAAACAAATATTAATAATTTTAA
1 AAAAATTA-AAA-AAA-ATTAATAATTGTAA
**
54529541 AAAAATTCTAAAAAATTAA-AATTGTAA
1 AAAAATTAAAAAAAATTAATAATTGTAA
54529568 AAAAAGTTAAAAAAAATT
1 AAAAA-TTAAAAAAAATT
54529586 TACATAAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
27 12 0.31
28 15 0.38
29 3 0.08
30 2 0.05
31 7 0.18
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.30
Consensus pattern (28 bp):
AAAAATTAAAAAAAATTAATAATTGTAA
Found at i:54529761 original size:11 final size:10
Alignment explanation
Indices: 54529740--54529775 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
54529730 TTTTTTTAAC
54529740 TTTTCTTTTT
1 TTTTCTTTTT
54529750 TTTTCTTTTT
1 TTTTCTTTTT
*
54529760 TTTTCTATTT
1 TTTTCTTTTT
*
54529770 TCTTCT
1 TTTTCT
54529776 GCTTCTCCCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (10 bp):
TTTTCTTTTT
Found at i:54532058 original size:13 final size:13
Alignment explanation
Indices: 54532040--54532064 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54532030 ATATTTTTTT
54532040 ATTTTATAATTTA
1 ATTTTATAATTTA
54532053 ATTTTATAATTT
1 ATTTTATAATTT
54532065 TTAAATAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
ATTTTATAATTTA
Found at i:54532093 original size:11 final size:11
Alignment explanation
Indices: 54532041--54532101 Score: 52
Period size: 11 Copynumber: 5.4 Consensus size: 11
54532031 TATTTTTTTA
54532041 TTTTATAATTT
1 TTTTATAATTT
54532052 AATTTTATAATTT
1 --TTTTATAATTT
**
54532065 TTAAATAA-TT
1 TTTTATAATTT
* *
54532075 ATTAATAATTT
1 TTTTATAATTT
54532086 TTTTATAATTT
1 TTTTATAATTT
54532097 CTTTT
1 -TTTT
54532102 TTTATAGTCT
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
10 8 0.20
11 17 0.43
12 4 0.10
13 11 0.28
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (11 bp):
TTTTATAATTT
Done.