Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002637.1 Hibiscus syriacus cultivar Beakdansim tig00005377_pilon, whole genome shotgun sequence
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: 3156206
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 14
Found at i:1487557 original size:83 final size:82
Alignment explanation
Indices: 1487418--1487606 Score: 243
Period size: 83 Copynumber: 2.3 Consensus size: 82
1487408 CGGTCAGCCA
** * *
1487418 TCCTCATCACGTAGGAATCGTGTCATCCACCGACCAGATCTCCTCATCACGTAGGAGCTGCGTGA
1 TCCTCATCACGTAGGAAT-GTGTCATCCACAAACCAGATCTCCTCATCACGTAGGAGCCGCGTCA
*
1487483 ACCTTAGATAACCAGTCG
65 ACCTTAGATAACCAATCG
* *
1487501 TCCTCATCACGTAGGAACTGTGTCATCCACAAACCAGATCTCTTTATCACGTAGGAGCCGCGTCA
1 TCCTCATCACGTAGGAA-TGTGTCATCCACAAACCAGATCTCCTCATCACGTAGGAGCCGCGTCA
* * *
1487566 CCCTTAGATAATCAATTG
65 ACCTTAGATAACCAATCG
**
1487584 TCCTCATTGCGTAGGAATTGTGT
1 TCCTCATCACGTAGGAA-TGTGT
1487607 TATCACTATT
Statistics
Matches: 92, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
83 91 0.99
84 1 0.01
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.26
Consensus pattern (82 bp):
TCCTCATCACGTAGGAATGTGTCATCCACAAACCAGATCTCCTCATCACGTAGGAGCCGCGTCAA
CCTTAGATAACCAATCG
Found at i:1487975 original size:122 final size:122
Alignment explanation
Indices: 1487776--1488059 Score: 381
Period size: 122 Copynumber: 2.3 Consensus size: 122
1487766 ACTTCCAGAA
* * * * * *
1487776 CTCTTCATCACGGATGAGTAGTGTCGTCTTCAACAACAAATTATCTCTAAATTGACCAGACTTCC
1 CTCTTCAACATGGATGAGCAGTGTCGTCTTCAACAACAAATCATCTCCAAATTGACCAGACTTAC
1487841 TCAACCAAAAGGAACAGTGTCATCTTCAGAAAATAATTTACC-ACAAAGCAACCATAT
66 TCAACCAAAAGGAACAGTGTCATCTTCAGAAAATAATTTACCTA-AAAGCAACCATAT
* *
1487898 CTCTTCAACATGGATGAGCAGTGTCGTCTTCAACACCAAATCATCTCCAAATTGACCATACTTAC
1 CTCTTCAACATGGATGAGCAGTGTCGTCTTCAACAACAAATCATCTCCAAATTGACCAGACTTAC
* * * **
1487963 TCAACGAGAAGGAACAGTGTCATCTTCAGCAAATAATTTACCTAAAAGCGGCCATAT
66 TCAACCAAAAGGAACAGTGTCATCTTCAGAAAATAATTTACCTAAAAGCAACCATAT
* * * * * *
1488020 CTCTTCAGCGTGAATGAGCAGTGTCATTTTCAACATCAAA
1 CTCTTCAACATGGATGAGCAGTGTCGTCTTCAACAACAAA
1488060 ATTACCTAAA
Statistics
Matches: 142, Mismatches: 19, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
122 141 0.99
123 1 0.01
ACGTcount: A:0.35, C:0.25, G:0.14, T:0.26
Consensus pattern (122 bp):
CTCTTCAACATGGATGAGCAGTGTCGTCTTCAACAACAAATCATCTCCAAATTGACCAGACTTAC
TCAACCAAAAGGAACAGTGTCATCTTCAGAAAATAATTTACCTAAAAGCAACCATAT
Found at i:1495069 original size:29 final size:29
Alignment explanation
Indices: 1495031--1495100 Score: 140
Period size: 29 Copynumber: 2.4 Consensus size: 29
1495021 ATTGTTTTGG
1495031 TCACTCAACTTTAAAAAATTTAAACTCGA
1 TCACTCAACTTTAAAAAATTTAAACTCGA
1495060 TCACTCAACTTTAAAAAATTTAAACTCGA
1 TCACTCAACTTTAAAAAATTTAAACTCGA
1495089 TCACTCAACTTT
1 TCACTCAACTTT
1495101 TGAATTAATC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.41, C:0.23, G:0.03, T:0.33
Consensus pattern (29 bp):
TCACTCAACTTTAAAAAATTTAAACTCGA
Found at i:1496042 original size:26 final size:25
Alignment explanation
Indices: 1496013--1496215 Score: 69
Period size: 20 Copynumber: 9.0 Consensus size: 25
1496003 CATTTATACA
1496013 TTAAAATCATGGCATCCTTTCATGCC
1 TTAAAAT-ATGGCATCCTTTCATGCC
*
1496039 TT---A-AT-GCATCCTTTCATGCAT
1 TTAAAATATGGCATCCTTTCATGC-C
* * *
1496060 TTTAATTATGGCATCCTTTCATGTC
1 TTAAAATATGGCATCCTTTCATGCC
* *
1496085 TT---A-AT-GAATCCTTTCATGTC
1 TTAAAATATGGCATCCTTTCATGCC
1496105 TT---A-AT-GCATCCTTTCATG-C
1 TTAAAATATGGCATCCTTTCATGCC
* *
1496124 TT--TA-AT-GCATCCTTTCATGCAT
1 TTAAAATATGGCATCCTTTCATGC-C
* * *
1496146 TTTAATTATGGCATCCTTTCATGCA
1 TTAAAATATGGCATCCTTTCATGCC
*
1496171 TT---A-AT-GCATCCTTTCATGCAT
1 TTAAAATATGGCATCCTTTCATGC-C
* *
1496192 TTTAATTATGGCATCCTTTCATGC
1 TTAAAATATGGCATCCTTTCATGC
1496216 ATTTTGCATA
Statistics
Matches: 144, Mismatches: 14, Indels: 38
0.73 0.07 0.19
Matches are distributed among these distances:
19 3 0.02
20 75 0.52
21 10 0.07
22 2 0.01
23 1 0.01
25 10 0.07
26 43 0.30
ACGTcount: A:0.23, C:0.23, G:0.11, T:0.43
Consensus pattern (25 bp):
TTAAAATATGGCATCCTTTCATGCC
Found at i:1496049 original size:46 final size:46
Alignment explanation
Indices: 1496021--1496215 Score: 303
Period size: 46 Copynumber: 4.4 Consensus size: 46
1496011 CATTAAAATC
1496021 ATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAATT
1 ATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAATT
* * *
1496067 ATGGCATCCTTTCATGTCTTAATGAATCCTTTCATG--TCTT-A--
1 ATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAATT
*
1496108 AT-GCATCCTTTCATGCTTTAATGCATCCTTTCATGCATTTTAATT
1 ATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAATT
*
1496153 ATGGCATCCTTTCATGCATTAATGCATCCTTTCATGCATTTTAATT
1 ATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAATT
1496199 ATGGCATCCTTTCATGC
1 ATGGCATCCTTTCATGC
1496216 ATTTTGCATA
Statistics
Matches: 135, Mismatches: 8, Indels: 12
0.87 0.05 0.08
Matches are distributed among these distances:
40 30 0.22
41 2 0.01
42 3 0.02
43 2 0.01
44 3 0.02
45 2 0.01
46 93 0.69
ACGTcount: A:0.22, C:0.23, G:0.11, T:0.44
Consensus pattern (46 bp):
ATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAATT
Found at i:1496132 original size:86 final size:86
Alignment explanation
Indices: 1496024--1496188 Score: 296
Period size: 86 Copynumber: 1.9 Consensus size: 86
1496014 TAAAATCATG
1496024 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGTC-TTA
1 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAATTATGGCATCCTTTCATG-CATTA
1496088 ATGAATCCTTTCATGTCTTAAT
65 ATGAATCCTTTCATGTCTTAAT
*
1496110 GCATCCTTTCATGCTTTAATGCATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCATTAA
1 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCATTAA
*
1496175 TGCATCCTTTCATG
66 TGAATCCTTTCATG
1496189 CATTTTAATT
Statistics
Matches: 76, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
85 1 0.01
86 75 0.99
ACGTcount: A:0.22, C:0.24, G:0.11, T:0.44
Consensus pattern (86 bp):
GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCATTAA
TGAATCCTTTCATGTCTTAAT
Found at i:1496190 original size:20 final size:20
Alignment explanation
Indices: 1496024--1496192 Score: 171
Period size: 20 Copynumber: 7.8 Consensus size: 20
1496014 TAAAATCATG
*
1496024 GCATCCTTTCATGCCTTAAT
1 GCATCCTTTCATGCATTAAT
1496044 GCATCCTTTCATGCATTTTAATTAT
1 GCATCCTTTCATGCA--TT-A--AT
1496069 GGCATCCTTTCATGTC-TTAAT
1 -GCATCCTTTCATG-CATTAAT
*
1496090 GAATCCTTTCATGTC-TTAAT
1 GCATCCTTTCATG-CATTAAT
*
1496110 GCATCCTTTCATGCTTTAAT
1 GCATCCTTTCATGCATTAAT
1496130 GCATCCTTTCATGCATTTTAATTAT
1 GCATCCTTTCATGCA--TT-A--AT
1496155 GGCATCCTTTCATGCATTAAT
1 -GCATCCTTTCATGCATTAAT
1496176 GCATCCTTTCATGCATT
1 GCATCCTTTCATGCATT
1496193 TTAATTATGG
Statistics
Matches: 131, Mismatches: 4, Indels: 28
0.80 0.02 0.17
Matches are distributed among these distances:
19 1 0.01
20 81 0.62
21 4 0.03
22 4 0.03
23 4 0.03
24 4 0.03
25 4 0.03
26 28 0.21
27 1 0.01
ACGTcount: A:0.22, C:0.24, G:0.11, T:0.44
Consensus pattern (20 bp):
GCATCCTTTCATGCATTAAT
Found at i:1496711 original size:22 final size:23
Alignment explanation
Indices: 1496669--1496721 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 23
1496659 CTGGTATCGA
*
1496669 TACCCTTACCATGGTATCGATAC
1 TACCCTTACCATGGTACCGATAC
*
1496692 TACCC-TACTATGGTACCGATA-
1 TACCCTTACCATGGTACCGATAC
*
1496713 TCCCCTTAC
1 TACCCTTAC
1496722 GATATCGATA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 4 0.15
22 17 0.65
23 5 0.19
ACGTcount: A:0.25, C:0.34, G:0.11, T:0.30
Consensus pattern (23 bp):
TACCCTTACCATGGTACCGATAC
Found at i:1504062 original size:29 final size:29
Alignment explanation
Indices: 1504029--1504115 Score: 79
Period size: 29 Copynumber: 2.9 Consensus size: 29
1504019 GCCAAAATAT
1504029 AACTTTTTAAATTACTATTTTGGTC-CCTA
1 AACTTTTTAAATTACTATTTTGGTCACC-A
*
1504058 AACTTTTCTAAAGTTTA-TACTTTGGTCACCA
1 AACTTTT-TAAA--TTACTATTTTGGTCACCA
** * *
1504089 AACTTTCAAAATTTCCATTTTGGTCAC
1 AACTTTTTAAATTACTATTTTGGTCAC
1504116 TATTTAAATT
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
28 2 0.04
29 17 0.36
30 7 0.15
31 16 0.34
32 5 0.11
ACGTcount: A:0.29, C:0.20, G:0.08, T:0.44
Consensus pattern (29 bp):
AACTTTTTAAATTACTATTTTGGTCACCA
Found at i:1504570 original size:58 final size:58
Alignment explanation
Indices: 1504490--1504600 Score: 150
Period size: 58 Copynumber: 1.9 Consensus size: 58
1504480 AATCATGATA
* *
1504490 GGGATATAATCCCATACAAAATCACGACGGGGATATAATATCACGTAAAATCAAGAAG
1 GGGATATAATCCCATACAAAATCACGACAGGGATATAATATCACGCAAAATCAAGAAG
* * * * * *
1504548 GGGATTTAATCTCATACAAAATCAGGACAGGTATATAATCTCATGCAAAATCA
1 GGGATATAATCCCATACAAAATCACGACAGGGATATAATATCACGCAAAATCA
1504601 GGATGAGATT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
58 45 1.00
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.23
Consensus pattern (58 bp):
GGGATATAATCCCATACAAAATCACGACAGGGATATAATATCACGCAAAATCAAGAAG
Found at i:1504601 original size:29 final size:29
Alignment explanation
Indices: 1504469--1504603 Score: 119
Period size: 29 Copynumber: 4.7 Consensus size: 29
1504459 TTAGCAAATG
* * * *
1504469 ATCTCATGGAGAATCATGATAGGGATATA
1 ATCTCATGCAAAATCAGGACAGGGATATA
* * * *
1504498 ATCCCATACAAAATCACGACGGGGATATA
1 ATCTCATGCAAAATCAGGACAGGGATATA
* * * * *
1504527 ATATCACGTAAAATCAAGA-AGGGGATTTA
1 ATCTCATGCAAAATCAGGACA-GGGATATA
* *
1504556 ATCTCATACAAAATCAGGACAGGTATATA
1 ATCTCATGCAAAATCAGGACAGGGATATA
1504585 ATCTCATGCAAAATCAGGA
1 ATCTCATGCAAAATCAGGA
1504604 TGAGATTATG
Statistics
Matches: 81, Mismatches: 23, Indels: 4
0.75 0.21 0.04
Matches are distributed among these distances:
29 80 0.99
30 1 0.01
ACGTcount: A:0.42, C:0.16, G:0.19, T:0.23
Consensus pattern (29 bp):
ATCTCATGCAAAATCAGGACAGGGATATA
Found at i:1505196 original size:46 final size:45
Alignment explanation
Indices: 1505123--1505274 Score: 209
Period size: 46 Copynumber: 3.4 Consensus size: 45
1505113 ATAAAATCTT
* *
1505123 TTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAATATAC
1 TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACAAATATAC
*
1505168 TTACCATTTATTACCATAAGCTCTTAAGCTTATTTTACAAATATAC
1 TTACCATTTATT-CCATAAGCTCGTAAGCTTATTTTACAAATATAC
* * *
1505214 TTACCATTTGTT-CATAAGCTCGTAAGCTTATTTTACTAATACAC
1 TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACAAATATAC
* *
1505258 TTGCCA-TTATTGCATAA
1 TTACCATTTATTCCATAA
1505275 CCATATACCA
Statistics
Matches: 96, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
43 4 0.04
44 39 0.41
45 11 0.11
46 42 0.44
ACGTcount: A:0.32, C:0.21, G:0.07, T:0.40
Consensus pattern (45 bp):
TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACAAATATAC
Found at i:1505474 original size:59 final size:59
Alignment explanation
Indices: 1505382--1505510 Score: 159
Period size: 59 Copynumber: 2.2 Consensus size: 59
1505372 CGTAGTGGAA
** * ** *
1505382 TCCCGAATATGACACATAAGGTCATGTCCACCATCTGTACTAGGTATCCTTAAGTACAG
1 TCCCGAATATGACACATAAGGTCATACCCACCATATAAACTAGGCATCCTTAAGTACAG
* * ** *
1505441 TCCCGAATATGACACATAAGGTCGTACCCACCATATAAACTAGGCATCCTTTAGTGTAT
1 TCCCGAATATGACACATAAGGTCATACCCACCATATAAACTAGGCATCCTTAAGTACAG
1505500 TCCCGAATATG
1 TCCCGAATATG
1505511 CAGCCTATTG
Statistics
Matches: 59, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.27
Consensus pattern (59 bp):
TCCCGAATATGACACATAAGGTCATACCCACCATATAAACTAGGCATCCTTAAGTACAG
Found at i:1511627 original size:46 final size:45
Alignment explanation
Indices: 1511554--1511705 Score: 236
Period size: 46 Copynumber: 3.4 Consensus size: 45
1511544 ATGAAATCTT
*
1511554 TTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAATATAC
1 TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATAC
*
1511599 TTACCATTTATTACCATAAGCTCTTAAGCTTATTTTACCAATATAC
1 TTACCATTTATT-CCATAAGCTCGTAAGCTTATTTTACCAATATAC
* * *
1511645 TTACCATTTGTT-TATAAGCTCGTAAGCTTATTTTACCAATACAC
1 TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATAC
1511689 TTACCA-TTATTCCATAA
1 TTACCATTTATTCCATAA
1511706 CCATATACCA
Statistics
Matches: 97, Mismatches: 8, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
43 4 0.04
44 39 0.40
45 11 0.11
46 43 0.44
ACGTcount: A:0.32, C:0.22, G:0.06, T:0.40
Consensus pattern (45 bp):
TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATAC
Found at i:1511731 original size:90 final size:90
Alignment explanation
Indices: 1511568--1511731 Score: 201
Period size: 90 Copynumber: 1.8 Consensus size: 90
1511558 CATTTATCCC
* * * **
1511568 ATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTATTACCATAAGCTCTTAAGCTTATT
1 ATAAGCTCGTAAGCTTATTTTACCAATACACTTACCATTTATTACCATAAGCTCATAACCTTACC
* *
1511633 TTACCAATATACTTACCATTTGTTT
66 ATAACAATATACTTACCATTTGTTT
1511658 ATAAGCTCGTAAGCTTATTTTACCAATACACTTACCA-TTATT-CCATAA-C-CATATACCATAT
1 ATAAGCTCGTAAGCTTATTTTACCAATACACTTACCATTTATTACCATAAGCTCATA-ACC-T-T
1511719 ACCATAGACAATA
63 ACCATA-ACAATA
1511732 GCCATAAACA
Statistics
Matches: 63, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
86 3 0.05
87 3 0.05
88 7 0.11
89 9 0.14
90 41 0.65
ACGTcount: A:0.35, C:0.22, G:0.06, T:0.37
Consensus pattern (90 bp):
ATAAGCTCGTAAGCTTATTTTACCAATACACTTACCATTTATTACCATAAGCTCATAACCTTACC
ATAACAATATACTTACCATTTGTTT
Found at i:1511732 original size:7 final size:7
Alignment explanation
Indices: 1511722--1511772 Score: 52
Period size: 7 Copynumber: 7.6 Consensus size: 7
1511712 ACCATATACC
1511722 ATAGACA
1 ATAGACA
*
1511729 ATAG-CC
1 ATAGACA
*
1511735 ATAAACA
1 ATAGACA
1511742 ATAGACA
1 ATAGACA
*
1511749 ATAG-CC
1 ATAGACA
*
1511755 ATAAACA
1 ATAGACA
1511762 ATAGACA
1 ATAGACA
1511769 ATAG
1 ATAG
1511773 TCCAATATAC
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
6 8 0.24
7 26 0.76
ACGTcount: A:0.55, C:0.18, G:0.12, T:0.16
Consensus pattern (7 bp):
ATAGACA
Found at i:1511736 original size:20 final size:20
Alignment explanation
Indices: 1511722--1511772 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
1511712 ACCATATACC
1511722 ATAGACAATAGCCATAAACA
1 ATAGACAATAGCCATAAACA
1511742 ATAGACAATAGCCATAAACA
1 ATAGACAATAGCCATAAACA
1511762 ATAGACAATAG
1 ATAGACAATAG
1511773 TCCAATATAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.55, C:0.18, G:0.12, T:0.16
Consensus pattern (20 bp):
ATAGACAATAGCCATAAACA
Found at i:1511925 original size:59 final size:59
Alignment explanation
Indices: 1511833--1511960 Score: 184
Period size: 59 Copynumber: 2.2 Consensus size: 59
1511823 CAAAGTGCAA
* * **
1511833 TCCCGAATATGACACATAAGGTCGTGTCCACCATCTGTACTAGGTATCCTTAAGTACAG
1 TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAG
* ** *
1511892 TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTTAGTGTAT
1 TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAG
1511951 TCCCGAATAT
1 TCCCGAATAT
1511961 ACAGCCTACT
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
59 61 1.00
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.28
Consensus pattern (59 bp):
TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAG
Found at i:1514360 original size:26 final size:26
Alignment explanation
Indices: 1514299--1514361 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 26
1514289 TAAAAAAAGC
1514299 CAACGGATCAAAGTCAAAGTCACCAGT
1 CAACGG-TCAAAGTCAAAGTCACCAGT
* ** *
1514326 TAAAAGTCAAAGTGATAAGTCA-CAGT
1 CAACGGTCAAAGTCA-AAGTCACCAGT
1514352 CAACGGTCAA
1 CAACGGTCAA
1514362 TGGGTCAACG
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
26 19 0.68
27 9 0.32
ACGTcount: A:0.43, C:0.21, G:0.19, T:0.17
Consensus pattern (26 bp):
CAACGGTCAAAGTCAAAGTCACCAGT
Found at i:1521104 original size:29 final size:29
Alignment explanation
Indices: 1521072--1521147 Score: 84
Period size: 31 Copynumber: 2.6 Consensus size: 29
1521062 GACCAAAATT
1521072 TAAATTTTAAAAGTTAAGTG-ACTAAAGTA
1 TAAATTTTAAAAGTTAAG-GAACTAAAGTA
* *
1521101 TAAACTTTAGAAAAGTTTAGGAACTAAAGTA
1 TAAA-TTT-TAAAAGTTAAGGAACTAAAGTA
1521132 T-AATTTTAAAAAGTTA
1 TAAATTTT-AAAAGTTA
1521148 TGTAACCTGA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
29 14 0.36
30 6 0.15
31 19 0.49
ACGTcount: A:0.49, C:0.04, G:0.13, T:0.34
Consensus pattern (29 bp):
TAAATTTTAAAAGTTAAGGAACTAAAGTA
Found at i:1523543 original size:19 final size:19
Alignment explanation
Indices: 1523515--1523554 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1523505 ATTTGATTCT
1523515 CCCTTAAAAACCGAGAGCC
1 CCCTTAAAAACCGAGAGCC
* *
1523534 CCCTTCAAAATCGAGAGCC
1 CCCTTAAAAACCGAGAGCC
1523553 CC
1 CC
1523555 ATACATTATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.33, C:0.40, G:0.15, T:0.12
Consensus pattern (19 bp):
CCCTTAAAAACCGAGAGCC
Found at i:1524054 original size:3 final size:3
Alignment explanation
Indices: 1524034--1524096 Score: 67
Period size: 3 Copynumber: 21.0 Consensus size: 3
1524024 CATTCAAATA
* *
1524034 AAT AAT ATT AAT TA- AAT AAT AAT AAT AAT AAT AAT AAT AAT ATAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT
*
1524079 ATAT AAT -AT AAT ATT AAT
1 A-AT AAT AAT AAT AAT AAT
1524097 GGGACAAAAC
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
2 3 0.06
3 41 0.80
4 7 0.14
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
AAT
Found at i:1524475 original size:55 final size:55
Alignment explanation
Indices: 1524407--1524555 Score: 208
Period size: 55 Copynumber: 2.7 Consensus size: 55
1524397 ATATTAGAAG
* * * * *
1524407 ACGAGTCTACTCCACTATTCTTTCAGGGAGATTAGACTCGAGAAATCTTTGGAAG
1 ACGAGTATGCTCCACTCTTCTTTCAGGGAGATAAGACTCGAGAAATCTTTGGAAA
* * *
1524462 ACGGGTATGCTCCACTCTTTTTTCAGGGAGATAAGACTCGAGAAATTTTTGGAAA
1 ACGAGTATGCTCCACTCTTCTTTCAGGGAGATAAGACTCGAGAAATCTTTGGAAA
* *
1524517 ACGAGTATGCTCCACTCTTGTTTTAGGGAGATAAGACTC
1 ACGAGTATGCTCCACTCTTCTTTCAGGGAGATAAGACTC
1524556 AAGATTGATT
Statistics
Matches: 83, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
55 83 1.00
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (55 bp):
ACGAGTATGCTCCACTCTTCTTTCAGGGAGATAAGACTCGAGAAATCTTTGGAAA
Found at i:1524851 original size:29 final size:28
Alignment explanation
Indices: 1524809--1524907 Score: 85
Period size: 29 Copynumber: 3.5 Consensus size: 28
1524799 GGATAATAAA
*
1524809 GATTGACTTCTCTTTATGAGAAAGTCAAG
1 GATTGACTCCTCTTTA-GAGAAAGTCAAG
* *
1524838 GATTGACTCCTCTTCAG-GAATAG-CAAA
1 GATTGACTCCTCTTTAGAGAA-AGTCAAG
* * *
1524865 GATTGACTTCTCTTTACGAGGAAGTTAAG
1 GATTGACTCCTCTTTA-GAGAAAGTCAAG
**
1524894 GATTGGTTCCTCTT
1 GATTGACTCCTCTT
1524908 CACAATGGAG
Statistics
Matches: 55, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
27 20 0.36
28 6 0.11
29 29 0.53
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.34
Consensus pattern (28 bp):
GATTGACTCCTCTTTAGAGAAAGTCAAG
Found at i:1524877 original size:27 final size:29
Alignment explanation
Indices: 1524806--1524878 Score: 89
Period size: 27 Copynumber: 2.6 Consensus size: 29
1524796 CAGGGATAAT
*
1524806 AAAGATTGACTTCTCTTTATGAGAAAGTC
1 AAAGATTGACTTCTCTTCATGAGAAAGTC
* *
1524835 AAGGATTGACTCCTCTTCA-G-GAATAG-C
1 AAAGATTGACTTCTCTTCATGAGAA-AGTC
1524862 AAAGATTGACTTCTCTT
1 AAAGATTGACTTCTCTT
1524879 TACGAGGAAG
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
27 19 0.50
28 3 0.08
29 16 0.42
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Consensus pattern (29 bp):
AAAGATTGACTTCTCTTCATGAGAAAGTC
Found at i:1524895 original size:56 final size:56
Alignment explanation
Indices: 1524806--1525143 Score: 226
Period size: 56 Copynumber: 5.6 Consensus size: 56
1524796 CAGGGATAAT
* * *
1524806 AAAGATTGACTTCTCTTTATGAGAAAGTCAAGGATTGACTCCTCTTCAGGAATAGC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCAGGAATAGC
* * ** * *
1524862 AAAGATTGACTTCTCTTTACGAGGAAGTTAAGGATTGGTTCCTCTTCACAATGGAGTCAGGAATA
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTT--C-A-GGAAT-A-G---C
* * * * * *
1524927 AAAAATTTTGACTTATCTTCATGAGGATGTCAAGGATTTACTCCTCTTCAGGAATATC
1 AAAGA--TTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCAGGAATAGC
* * *
1524985 AAAGATTGACTTCTATTCACGAGGAATTCAAGGATTGATTCCTCTTCACAAGGGAGTCATGAATA
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTT--C-----AG----GAATA
*
1525050 AC
55 GC
* * * * * * *
1525052 AAAGATTGATTTATCTTCACAAGGAAGTCAAGGAATGACTCCTTTTTAGGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCAGGAATAGC
* *
1525108 AAAGATTTACTTCTCTTCACGAGGAAGTCAATGATT
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATT
1525144 TGTTCCTCTT
Statistics
Matches: 217, Mismatches: 43, Indels: 44
0.71 0.14 0.14
Matches are distributed among these distances:
56 112 0.52
58 6 0.03
59 1 0.00
60 6 0.03
61 1 0.00
62 2 0.01
63 6 0.03
64 1 0.00
65 5 0.02
67 77 0.35
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (56 bp):
AAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCAGGAATAGC
Found at i:1524951 original size:123 final size:123
Alignment explanation
Indices: 1524790--1525206 Score: 530
Period size: 123 Copynumber: 3.4 Consensus size: 123
1524780 GAGTCTGTTG
* * * * *
1524790 GGGAGTCAGGGATAATAAAGATTGACTTCTCTTTATGAGAAAGTCAAGGATTGACTCCTCTTCAG
1 GGGAGTCAGGAATAAAAAAGATTGACTTATCTTCATGAGGAAGTCAAGGATTGACTCCTCTTCAG
* *
1524855 GAATAGCAAAGATTGACTTCTCTTTACGAGGAAGTTAAGGATTGGTTCCTCTTCACAA
66 GAATAACAAAGATTGACTTCTCTTCACGAGGAAGTTAAGGATTGGTTCCTCTTCACAA
* ** * *
1524913 TGGAGTCAGGAATAAAAAATTTTGACTTATCTTCATGAGGATGTCAAGGATTTACTCCTCTTCAG
1 GGGAGTCAGGAATAAAAAAGATTGACTTATCTTCATGAGGAAGTCAAGGATTGACTCCTCTTCAG
* * *
1524978 GAATATCAAAGATTGACTTCTATTCACGAGGAA-TTCAAGGATTGATTCCTCTTCACAA
66 GAATAACAAAGATTGACTTCTCTTCACGAGGAAGTT-AAGGATTGGTTCCTCTTCACAA
* * * ** * * *
1525036 GGGAGTCATGAATAACAAAGATTGATTTATCTTCACAAGGAAGTCAAGGAATGACTCCTTTTTAG
1 GGGAGTCAGGAATAAAAAAGATTGACTTATCTTCATGAGGAAGTCAAGGATTGACTCCTCTTCAG
* * * * *
1525101 GAATAACAAAGATTTACTTCTCTTCACGAGGAAGTCAATGATTTGTTCCTCTTCACGA
66 GAATAACAAAGATTGACTTCTCTTCACGAGGAAGTTAAGGATTGGTTCCTCTTCACAA
* * * *
1525159 GGGAGTCAGGAATGAAAAAGATTGACTTCTCTTCACGAGGGAGTCAAG
1 GGGAGTCAGGAATAAAAAAGATTGACTTATCTTCATGAGGAAGTCAAG
1525207 TTGAAGCTTC
Statistics
Matches: 250, Mismatches: 42, Indels: 4
0.84 0.14 0.01
Matches are distributed among these distances:
122 2 0.01
123 247 0.99
124 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (123 bp):
GGGAGTCAGGAATAAAAAAGATTGACTTATCTTCATGAGGAAGTCAAGGATTGACTCCTCTTCAG
GAATAACAAAGATTGACTTCTCTTCACGAGGAAGTTAAGGATTGGTTCCTCTTCACAA
Found at i:1525032 original size:29 final size:30
Alignment explanation
Indices: 1524942--1525033 Score: 79
Period size: 29 Copynumber: 3.2 Consensus size: 30
1524932 TTTTGACTTA
* * * *
1524942 TCTTCATGAGG-ATGTCAAGGATTTACTCC
1 TCTTCACGAGGAATATCAAGGATTGATTCC
*
1524971 TCTT--C-AGGAATATCAAAGATTGACTT-C
1 TCTTCACGAGGAATATCAAGGATTGA-TTCC
*
1524998 TATTCACGAGGAAT-TCAAGGATTGATTCC
1 TCTTCACGAGGAATATCAAGGATTGATTCC
1525027 TCTTCAC
1 TCTTCAC
1525034 AAGGGAGTCA
Statistics
Matches: 49, Mismatches: 8, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
26 3 0.06
27 15 0.31
28 3 0.06
29 22 0.45
30 6 0.12
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (30 bp):
TCTTCACGAGGAATATCAAGGATTGATTCC
Found at i:1525144 original size:29 final size:29
Alignment explanation
Indices: 1525111--1525166 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
1525101 GAATAACAAA
1525111 GATTTACTT-CTCTTCACGAGGAAGTCAAT
1 GATTT-CTTCCTCTTCACGAGGAAGTCAAT
* *
1525140 GATTTGTTCCTCTTCACGAGGGAGTCA
1 GATTTCTTCCTCTTCACGAGGAAGTCA
1525167 GGAATGAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 2 0.08
29 22 0.92
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.34
Consensus pattern (29 bp):
GATTTCTTCCTCTTCACGAGGAAGTCAAT
Found at i:1531545 original size:14 final size:14
Alignment explanation
Indices: 1531526--1531552 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1531516 AATTACTTTT
1531526 AAAATAATTTTAAG
1 AAAATAATTTTAAG
1531540 AAAATAATTTTAA
1 AAAATAATTTTAA
1531553 AAGATAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (14 bp):
AAAATAATTTTAAG
Found at i:1532044 original size:20 final size:21
Alignment explanation
Indices: 1532019--1532057 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1532009 AGAAAATTAA
*
1532019 CAAAT-ATATAAATGATGAAC
1 CAAATAATAAAAATGATGAAC
1532039 CAAATAATAAAAATGATGA
1 CAAATAATAAAAATGATGA
1532058 CTTTGGGGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.59, C:0.08, G:0.10, T:0.23
Consensus pattern (21 bp):
CAAATAATAAAAATGATGAAC
Found at i:1535281 original size:40 final size:39
Alignment explanation
Indices: 1535222--1535319 Score: 142
Period size: 40 Copynumber: 2.5 Consensus size: 39
1535212 GCATATCGAT
*
1535222 TAAGCACTTCAGTGCATATGGTGGGCACAACATTATGTG
1 TAAGCACTTCGGTGCATATGGTGGGCACAACATTATGTG
* * *
1535261 TAATTCACTTCGGTGCATATGGTGGGCACCACCTTATGTG
1 TAA-GCACTTCGGTGCATATGGTGGGCACAACATTATGTG
*
1535301 TAAGCACTACGGTGCATAT
1 TAAGCACTTCGGTGCATAT
1535320 ATTTGACTCG
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
39 17 0.33
40 35 0.67
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (39 bp):
TAAGCACTTCGGTGCATATGGTGGGCACAACATTATGTG
Found at i:1554428 original size:14 final size:14
Alignment explanation
Indices: 1554409--1554441 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
1554399 TGAAATGTCG
1554409 ATGTTACAAGTTAT
1 ATGTTACAAGTTAT
1554423 ATGTTACAAGTTAT
1 ATGTTACAAGTTAT
1554437 ATGTT
1 ATGTT
1554442 GATCGAAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.33, C:0.06, G:0.15, T:0.45
Consensus pattern (14 bp):
ATGTTACAAGTTAT
Found at i:1570930 original size:21 final size:21
Alignment explanation
Indices: 1570900--1570939 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1570890 CAACAAGGCC
* *
1570900 TTTGTTGAAGCCATGAAATTT
1 TTTGTCGAAGCCATAAAATTT
1570921 TTTGTCGAAGCCATAAAAT
1 TTTGTCGAAGCCATAAAAT
1570940 ATTACAGAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (21 bp):
TTTGTCGAAGCCATAAAATTT
Found at i:1575400 original size:18 final size:18
Alignment explanation
Indices: 1575374--1575408 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1575364 GAAGGGATAC
*
1575374 CCTCTAAATCTGCAATAA
1 CCTCCAAATCTGCAATAA
*
1575392 CCTCCAAATGTGCAATA
1 CCTCCAAATCTGCAATA
1575409 CCTAAAAGTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.29, G:0.09, T:0.26
Consensus pattern (18 bp):
CCTCCAAATCTGCAATAA
Found at i:1599527 original size:20 final size:20
Alignment explanation
Indices: 1599502--1599601 Score: 119
Period size: 20 Copynumber: 4.7 Consensus size: 20
1599492 TTTATTTATG
1599502 GCATCATTTCATGCCTTAAT
1 GCATCATTTCATGCCTTAAT
*
1599522 GCATCATTTTATGCCTTAAT
1 GCATCATTTCATGCCTTAAT
*
1599542 GCATCATTTCATGCATTTCATTTAT
1 GCATCATTTCATGC----C-TTAAT
*
1599567 GGCATCCTTTCATGCCTTAAT
1 -GCATCATTTCATGCCTTAAT
1599588 GCATCATTTCATGC
1 GCATCATTTCATGC
1599602 ATTTCTTTTA
Statistics
Matches: 68, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
20 45 0.66
21 4 0.06
22 1 0.01
24 1 0.01
25 4 0.06
26 13 0.19
ACGTcount: A:0.23, C:0.24, G:0.11, T:0.42
Consensus pattern (20 bp):
GCATCATTTCATGCCTTAAT
Found at i:1599582 original size:46 final size:46
Alignment explanation
Indices: 1599522--1599614 Score: 159
Period size: 46 Copynumber: 2.0 Consensus size: 46
1599512 ATGCCTTAAT
*
1599522 GCATCATTTTATGCCTTAATGCATCATTTCATGCATTTCATTTATG
1 GCATCATTTCATGCCTTAATGCATCATTTCATGCATTTCATTTATG
* *
1599568 GCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTCTTTTATG
1 GCATCATTTCATGCCTTAATGCATCATTTCATGCATTTCATTTATG
1599614 G
1 G
1599615 ATTCGTTTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.22, C:0.22, G:0.12, T:0.45
Consensus pattern (46 bp):
GCATCATTTCATGCCTTAATGCATCATTTCATGCATTTCATTTATG
Found at i:1600877 original size:93 final size:93
Alignment explanation
Indices: 1600709--1600897 Score: 281
Period size: 93 Copynumber: 2.0 Consensus size: 93
1600699 GATAACTCAA
* * *
1600709 TATTATAATCACCTTTATCAGGCTAGTTGAATCTTATCCATAAAGTCGGGGCGTTTAACCAATTT
1 TATTATAATCACCTTTATCAGGCTAATTGAATCTTATCCATAAAGCCGGGGCGTTTAACCAATTG
*
1600774 CTCTAAAGGGA-GATCTCAAGCTTTATTG
66 CTCTAAAGGGACG-GCTCAAGCTTTATTG
** *
1600802 TATTATAATCACCTTTATCAGGCTAATTGAATCTTATCCATAAAGCCGTTGTGTTTAACCAATTG
1 TATTATAATCACCTTTATCAGGCTAATTGAATCTTATCCATAAAGCCGGGGCGTTTAACCAATTG
* *
1600867 CTTTAGAGGGACGGCTCAAGCTTTATTG
66 CTCTAAAGGGACGGCTCAAGCTTTATTG
1600895 TAT
1 TAT
1600898 ACATATAATA
Statistics
Matches: 86, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
93 85 0.99
94 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.37
Consensus pattern (93 bp):
TATTATAATCACCTTTATCAGGCTAATTGAATCTTATCCATAAAGCCGGGGCGTTTAACCAATTG
CTCTAAAGGGACGGCTCAAGCTTTATTG
Found at i:1606254 original size:29 final size:29
Alignment explanation
Indices: 1606176--1606280 Score: 68
Period size: 30 Copynumber: 3.4 Consensus size: 29
1606166 TAGGTTCTAA
* *
1606176 TTTATTTGTTTTAACTATTTTAGTCCCTTAAAT
1 TTTATTT-TTTTAA-T-TTTGA-TCCTTTAAAT
** * *
1606209 TTCTATTTTTTCCA-TTTGAGTTCTTTAACT
1 TT-TATTTTTTTAATTTTGA-TCCTTTAAAT
*
1606239 TTTATTTTTTTAATTTTGATCCTTTACATT
1 TTTATTTTTTTAATTTTGATCCTTTA-AAT
*
1606269 TTTATTTGTTTA
1 TTTATTTTTTTA
1606281 TTTATTTTAT
Statistics
Matches: 58, Mismatches: 11, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
29 15 0.26
30 32 0.55
33 6 0.10
34 5 0.09
ACGTcount: A:0.20, C:0.11, G:0.06, T:0.63
Consensus pattern (29 bp):
TTTATTTTTTTAATTTTGATCCTTTAAAT
Found at i:1610626 original size:165 final size:164
Alignment explanation
Indices: 1610327--1610733 Score: 489
Period size: 165 Copynumber: 2.5 Consensus size: 164
1610317 GCGATATACT
** * * * * *
1610327 AATATATAGTGGCATTTTTGGGAAAATGTCGCTACAAACGCGTACTTTAGTGGAGTTTATGTAAA
1 AATATATAGTGGTGTTTTTGTGAAAACGCCGCTAAAAATGCGTACTTTAGTGGAGTTTATGTAAA
** * * * ***
1610392 AAATGCTGCTATAGCCAGATATATAGAGGCGTTTTTGTGACAACGCCACTAAAAATGTGTACTTT
66 AAACACTGCTATAGCCAGATATATAGAGGCATTTTCGTGAAAACGCCACTAAAAATACATACTTT
*
1610457 AGTGGCGTTTATGTAAAAAAT-TCCACTATAGCCA
131 AGTGGCGTTTATGTAAAAAATGT-CACGATAGCCA
*
1610491 AATATATAGTGGTGTTTTTGTGCAAACGCCGCTAAAAATGCGTACTTTAGTGGTA-TTTATGTAA
1 AATATATAGTGGTGTTTTTGTGAAAACGCCGCTAAAAATGCGTACTTTAGTGG-AGTTTATGT-A
* * * *
1610555 AAAAACACTGCTATAGCCATATATATAGTGGCATTTTCGTGAAAATGCCGCTAAAAATACATACT
64 AAAAACACTGCTATAGCCAGATATATAGAGGCATTTTCGTGAAAACGCCACTAAAAATACATACT
* *
1610620 TTAGTGGCGTTTATGTAAAAAATGTCGCGATAGCCC
129 TTAGTGGCGTTTATGTAAAAAATGTCACGATAGCCA
* * * * *
1610656 AATATATAGTGGTGTTTGTGTAAAAACGCCGCTATAAATGCATACTTTAGTGGCGTTT-TAG-AA
1 AATATATAGTGGTGTTTTTGTGAAAACGCCGCTAAAAATGCGTACTTTAGTGGAGTTTAT-GTAA
*
1610719 AAAACACTTCTATAG
65 AAAACACTGCTATAG
1610734 AAGGATAATA
Statistics
Matches: 208, Mismatches: 30, Indels: 11
0.84 0.12 0.04
Matches are distributed among these distances:
163 16 0.08
164 53 0.25
165 138 0.66
166 1 0.00
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.32
Consensus pattern (164 bp):
AATATATAGTGGTGTTTTTGTGAAAACGCCGCTAAAAATGCGTACTTTAGTGGAGTTTATGTAAA
AAACACTGCTATAGCCAGATATATAGAGGCATTTTCGTGAAAACGCCACTAAAAATACATACTTT
AGTGGCGTTTATGTAAAAAATGTCACGATAGCCA
Found at i:1610722 original size:82 final size:83
Alignment explanation
Indices: 1610328--1610713 Score: 429
Period size: 82 Copynumber: 4.7 Consensus size: 83
1610318 CGATATACTA
* * * * * * * *
1610328 ATATATAGTGGCATTTTTGGGAAAATGTCGCTACAAACGCGTACTTTAGTGGAGTTTATGTAAAA
1 ATATATAGTGGCGTTTTTGTGAAAACGCCGCTAAAAATGCATACTTTAGTGGCGTTTATGTAAAA
1610393 AATG-CTGCTATAGCCAG
66 AATGTCTGCTATAGCCAG
* * * **
1610410 ATATATAGAGGCGTTTTTGTGACAACGCCACTAAAAATGTGTACTTTAGTGGCGTTTATGTAAAA
1 ATATATAGTGGCGTTTTTGTGAAAACGCCGCTAAAAATGCATACTTTAGTGGCGTTTATGTAAAA
** *
1610475 AAT-TCCACTATAGCCAA
66 AATGTCTGCTATAGCCAG
* * * **
1610492 ATATATAGTGGTGTTTTTGTGCAAACGCCGCTAAAAATGCGTACTTTAGTGGTATTTATGTAAAA
1 ATATATAGTGGCGTTTTTGTGAAAACGCCGCTAAAAATGCATACTTTAGTGGCGTTTATGTAAAA
*** *
1610557 AAACACTGCTATAGCCAT
66 AATGTCTGCTATAGCCAG
* * * *
1610575 ATATATAGTGGCATTTTCGTGAAAATGCCGCTAAAAATACATACTTTAGTGGCGTTTATGTAAAA
1 ATATATAGTGGCGTTTTTGTGAAAACGCCGCTAAAAATGCATACTTTAGTGGCGTTTATGTAAAA
*
1610640 AATGTC-GCGATAGCCCA-
66 AATGTCTGCTATAG-CCAG
* * * *
1610657 ATATATAGTGGTGTTTGTGTAAAAACGCCGCTATAAATGCATACTTTAGTGGCGTTT
1 ATATATAGTGGCGTTTTTGTGAAAACGCCGCTAAAAATGCATACTTTAGTGGCGTTT
1610714 TAGAAAAAAC
Statistics
Matches: 253, Mismatches: 48, Indels: 6
0.82 0.16 0.02
Matches are distributed among these distances:
82 181 0.72
83 72 0.28
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.33
Consensus pattern (83 bp):
ATATATAGTGGCGTTTTTGTGAAAACGCCGCTAAAAATGCATACTTTAGTGGCGTTTATGTAAAA
AATGTCTGCTATAGCCAG
Found at i:1616630 original size:26 final size:26
Alignment explanation
Indices: 1616601--1616651 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
1616591 TTAGGGAATT
*
1616601 TAATGATTTTA-ATCATTTTTTTAAAG
1 TAATGATTTTATA-CATTTTCTTAAAG
1616627 TAATGATTTTATACATTTTCTTAAA
1 TAATGATTTTATACATTTTCTTAAA
1616652 ATAAATTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 22 0.96
27 1 0.04
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.53
Consensus pattern (26 bp):
TAATGATTTTATACATTTTCTTAAAG
Found at i:1617401 original size:60 final size:60
Alignment explanation
Indices: 1617267--1617391 Score: 182
Period size: 60 Copynumber: 2.1 Consensus size: 60
1617257 GAAGAACACC
* *
1617267 AATGATC-CT-GATTATAAAATATTATTTTATTGAGTCATCCGACTATTAAAAGTTATAA
1 AATGATCTCTCGACTATAAAATATTATTTTATTGAGTCATCCGACTATTAAAAGTTACAA
* * * *
1617325 TATGATCTCTCGACTATAAGATATTATTTTGTTGAGTCATTCGACTATTAAAAGTTACAA
1 AATGATCTCTCGACTATAAAATATTATTTTATTGAGTCATCCGACTATTAAAAGTTACAA
1617385 AATGATC
1 AATGATC
1617392 ATTTGACTAT
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
58 6 0.10
59 2 0.03
60 50 0.86
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.39
Consensus pattern (60 bp):
AATGATCTCTCGACTATAAAATATTATTTTATTGAGTCATCCGACTATTAAAAGTTACAA
Found at i:1618211 original size:103 final size:101
Alignment explanation
Indices: 1617997--1618213 Score: 258
Period size: 103 Copynumber: 2.1 Consensus size: 101
1617987 AAATTAGCAC
* * * *
1617997 TTAACACATATTTACAGC-GGTGTAAGTGAATAAAATAAACAAGTGTAGTACGTAACACATACTT
1 TTAACACATA-CTACA-CTGGTGTAAGTAAATAAAATAAAAAAGTGTAGCACGTAACACATACTT
* * *
1618061 ACACCGTTGTAACTAAATAAAACAAAAAAGTGTAGCAT
64 ACAACGGTGTAACTAAATAAAACAAAAAAGTGTACCAT
* * * *
1618099 TTAATACATACTACACTGGTGTAAGTAAATAAAATAAAAAAAAGTGTAGCACTTAATATATACTT
1 TTAACACATACTACACTGGTGTAAGTAAATAAAAT--AAAAAAGTGTAGCACGTAACACATACTT
* *
1618164 ACAACGGTGTAAGTAAATAAAATAAAAAAGTGTACCACT
64 ACAACGGTGTAACTAAATAAAACAAAAAAGTGTACCA-T
1618203 TT-ACACATACT
1 TTAACACATACT
1618214 TACTATGATG
Statistics
Matches: 97, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
100 1 0.01
101 21 0.22
102 9 0.09
103 63 0.65
104 3 0.03
ACGTcount: A:0.47, C:0.14, G:0.13, T:0.27
Consensus pattern (101 bp):
TTAACACATACTACACTGGTGTAAGTAAATAAAATAAAAAAGTGTAGCACGTAACACATACTTAC
AACGGTGTAACTAAATAAAACAAAAAAGTGTACCAT
Found at i:1618229 original size:51 final size:51
Alignment explanation
Indices: 1617991--1618216 Score: 274
Period size: 51 Copynumber: 4.4 Consensus size: 51
1617981 TAAAGAAAAT
* * * *
1617991 TAGCACTTAACACATATTTACAGCGGTGTAAGTGAATAAAATAAACAAGTG
1 TAGCACTTAACACATACTTACACCGGTGTAAGTAAATAAAATAAAAAAGTG
* * * * *
1618042 TAGTACGTAACACATACTTACACCGTTGTAACTAAATAAAACAAAAAAGTG
1 TAGCACTTAACACATACTTACACCGGTGTAAGTAAATAAAATAAAAAAGTG
* * *
1618093 TAGCATTTAATACATAC-TACACTGGTGTAAGTAAATAAAATAAAAAAAAGTG
1 TAGCACTTAACACATACTTACACCGGTGTAAGTAAATAAAAT--AAAAAAGTG
* * *
1618145 TAGCACTTAATATATACTTACAACGGTGTAAGTAAATAAAATAAAAAAGTG
1 TAGCACTTAACACATACTTACACCGGTGTAAGTAAATAAAATAAAAAAGTG
* *
1618196 TACCACTTTACACATACTTAC
1 TAGCACTTAACACATACTTAC
1618217 TATGATGTAA
Statistics
Matches: 147, Mismatches: 25, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
50 20 0.14
51 81 0.55
52 24 0.16
53 22 0.15
ACGTcount: A:0.46, C:0.15, G:0.13, T:0.27
Consensus pattern (51 bp):
TAGCACTTAACACATACTTACACCGGTGTAAGTAAATAAAATAAAAAAGTG
Found at i:1619007 original size:6 final size:6
Alignment explanation
Indices: 1618996--1619040 Score: 72
Period size: 6 Copynumber: 7.5 Consensus size: 6
1618986 TTTTACACCT
* *
1618996 TGGTCA TGGTCA TGGTCA TGATCA TGGTCA TGGTCA TGGACA TGG
1 TGGTCA TGGTCA TGGTCA TGGTCA TGGTCA TGGTCA TGGTCA TGG
1619041 ACATAGACAT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.20, C:0.16, G:0.33, T:0.31
Consensus pattern (6 bp):
TGGTCA
Found at i:1619261 original size:35 final size:35
Alignment explanation
Indices: 1619221--1619458 Score: 147
Period size: 35 Copynumber: 6.9 Consensus size: 35
1619211 TGATCATATT
*
1619221 TTTGAAAATGTATAATATATGGTTTTTAAAACATG
1 TTTGAAAATGTATAATATATGGTTTTGAAAACATG
* * *
1619256 TTTGAAAACGTATGATATATGGTTTTGAAAGCAT-
1 TTTGAAAATGTATAATATATGGTTTTGAAAACATG
* * *
1619290 TTT-----TG-AAAACATATGGTTTTGAAAACATTT
1 TTTGAAAATGTATAATATATGGTTTTGAAAACA-TG
* * **
1619320 TTTGAAAACGTATATAATATATAGTTTT-AAAA-AAA
1 TTTGAAAA--TGTATAATATATGGTTTTGAAAACATG
** * * *
1619355 AATGAAAACGTATAATATAT-GATTTGAAAACATT
1 TTTGAAAATGTATAATATATGGTTTTGAAAACATG
* * *
1619389 TTTGAAAACGTATAATATATGATTTTGATAACGTATGG
1 TTTGAAAATGTATAATATATGGTTTTGAAAAC--AT-G
*
1619427 TTTTGAAAATGTAT-ATAATATAGTTTTGAAAA
1 -TTTGAAAATGTATAAT-ATATGGTTTTGAAAA
1619459 TATATATATA
Statistics
Matches: 153, Mismatches: 32, Indels: 32
0.71 0.15 0.15
Matches are distributed among these distances:
28 18 0.12
29 2 0.01
30 3 0.02
32 4 0.03
33 14 0.09
34 22 0.14
35 44 0.29
36 1 0.01
37 7 0.05
38 14 0.09
39 24 0.16
ACGTcount: A:0.42, C:0.04, G:0.14, T:0.39
Consensus pattern (35 bp):
TTTGAAAATGTATAATATATGGTTTTGAAAACATG
Found at i:1619311 original size:16 final size:13
Alignment explanation
Indices: 1619278--1619328 Score: 59
Period size: 16 Copynumber: 3.8 Consensus size: 13
1619268 TGATATATGG
*
1619278 TTTTGAAAGCA-T
1 TTTTGAAAACATT
1619290 TTTTGAAAACATAT
1 TTTTGAAAACAT-T
1619304 GGTTTTGAAAACATT
1 --TTTTGAAAACATT
1619319 TTTTGAAAAC
1 TTTTGAAAAC
1619329 GTATATAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
12 10 0.29
13 10 0.29
14 1 0.03
15 1 0.03
16 12 0.35
ACGTcount: A:0.37, C:0.08, G:0.14, T:0.41
Consensus pattern (13 bp):
TTTTGAAAACATT
Found at i:1619312 original size:28 final size:29
Alignment explanation
Indices: 1619272--1619328 Score: 98
Period size: 28 Copynumber: 2.0 Consensus size: 29
1619262 AACGTATGAT
*
1619272 ATATGGTTTTGAAAGCA-TTTTTGAAAAC
1 ATATGGTTTTGAAAACATTTTTTGAAAAC
1619300 ATATGGTTTTGAAAACATTTTTTGAAAAC
1 ATATGGTTTTGAAAACATTTTTTGAAAAC
1619329 GTATATAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
28 16 0.59
29 11 0.41
ACGTcount: A:0.37, C:0.07, G:0.16, T:0.40
Consensus pattern (29 bp):
ATATGGTTTTGAAAACATTTTTTGAAAAC
Found at i:1619400 original size:34 final size:34
Alignment explanation
Indices: 1619307--1619413 Score: 119
Period size: 34 Copynumber: 3.1 Consensus size: 34
1619297 AACATATGGT
1619307 TTTGAAAACATTTTTTGAAAACGTATATAATATAT-A
1 TTTGAAAACA-TTTTTGAAAACG--TATAATATATGA
* ****
1619343 GTTTTAAAA-AAAAATGAAAACGTATAATATATGA
1 -TTTGAAAACATTTTTGAAAACGTATAATATATGA
1619377 TTTGAAAACATTTTTGAAAACGTATAATATATGA
1 TTTGAAAACATTTTTGAAAACGTATAATATATGA
1619411 TTT
1 TTT
1619414 TGATAACGTA
Statistics
Matches: 58, Mismatches: 10, Indels: 7
0.77 0.13 0.09
Matches are distributed among these distances:
33 17 0.29
34 25 0.43
35 8 0.14
36 1 0.02
37 7 0.12
ACGTcount: A:0.47, C:0.05, G:0.10, T:0.38
Consensus pattern (34 bp):
TTTGAAAACATTTTTGAAAACGTATAATATATGA
Found at i:1619452 original size:23 final size:24
Alignment explanation
Indices: 1619426--1619472 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
1619416 ATAACGTATG
*
1619426 GTTTTGAAAATGTATATA-ATATA
1 GTTTTGAAAATATATATATATATA
1619449 GTTTTGAAAATATATATATATATA
1 GTTTTGAAAATATATATATATATA
1619473 TATATAGTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 17 0.77
24 5 0.23
ACGTcount: A:0.45, C:0.00, G:0.11, T:0.45
Consensus pattern (24 bp):
GTTTTGAAAATATATATATATATA
Found at i:1619528 original size:15 final size:14
Alignment explanation
Indices: 1619505--1619574 Score: 72
Period size: 15 Copynumber: 4.9 Consensus size: 14
1619495 TTTTGAAAAC
1619505 ATATTATATATTAT
1 ATATTATATATTAT
*
1619519 ATAGTTATATATTTT
1 ATA-TTATATATTAT
1619534 CATATTATATATTATT
1 -ATATTATATATTA-T
1619550 ATATT-TATATT-T
1 ATATTATATATTAT
*
1619562 ATTATTATTTATT
1 A-TATTATATATT
1619575 TATTAATTTC
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
12 2 0.04
13 4 0.08
14 14 0.29
15 24 0.50
16 4 0.08
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.61
Consensus pattern (14 bp):
ATATTATATATTAT
Found at i:1619539 original size:23 final size:23
Alignment explanation
Indices: 1619512--1619575 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 23
1619502 AACATATTAT
1619512 ATATTATATAGTTA-TATATTTTC
1 ATATTATATA-TTATTATATTTTC
1619535 ATATTATATATTATTATA-TTT-
1 ATATTATATATTATTATATTTTC
1619556 ATATT-TATTATTATT-TATTT
1 ATATTATA-TATTATTATATTT
1619576 ATTAATTTCA
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
20 4 0.11
21 14 0.37
22 6 0.16
23 14 0.37
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (23 bp):
ATATTATATATTATTATATTTTC
Found at i:1619566 original size:25 final size:24
Alignment explanation
Indices: 1619512--1619555 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
1619502 AACATATTAT
1619512 ATATTATATAGTTA-TATATTTTC
1 ATATTATATAGTTATTATATTTTC
1619535 ATATTATATA-TTATTATATTT
1 ATATTATATAGTTATTATATTT
1619556 ATATTTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 3 0.15
23 17 0.85
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.59
Consensus pattern (24 bp):
ATATTATATAGTTATTATATTTTC
Found at i:1619590 original size:28 final size:28
Alignment explanation
Indices: 1619506--1619583 Score: 81
Period size: 30 Copynumber: 2.7 Consensus size: 28
1619496 TTTGAAAACA
1619506 TATTATATATTA-TATAGTTATATATTT-T
1 TATTATATATTATTATA-TT-TATATTTAT
1619534 CATATTATATATTATTATATTTATATTTAT
1 --TATTATATATTATTATATTTATATTTAT
*
1619564 TATTATTTATTTATTA-ATTT
1 TATTATATA-TTATTATATTT
1619584 CATTTTAACA
Statistics
Matches: 44, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
28 12 0.27
29 13 0.30
30 15 0.34
31 4 0.09
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.63
Consensus pattern (28 bp):
TATTATATATTATTATATTTATATTTAT
Found at i:1620395 original size:18 final size:18
Alignment explanation
Indices: 1620372--1620412 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
1620362 CGGTCCAGGC
1620372 GATGGGCTACGGTGGTGA
1 GATGGGCTACGGTGGTGA
*
1620390 GATGGGCTATGGTGGTGA
1 GATGGGCTACGGTGGTGA
1620408 GATGG
1 GATGG
1620413 CCGACGTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.17, C:0.07, G:0.51, T:0.24
Consensus pattern (18 bp):
GATGGGCTACGGTGGTGA
Found at i:1620804 original size:13 final size:13
Alignment explanation
Indices: 1620788--1620836 Score: 64
Period size: 14 Copynumber: 3.6 Consensus size: 13
1620778 CTTTTAATTC
1620788 TTTTATTTATTTA
1 TTTTATTTATTTA
1620801 TTTTATTTATTTTA
1 TTTTATTTA-TTTA
1620815 TTTTA-TTATTTAA
1 TTTTATTTATTT-A
1620828 CTTTTATTT
1 -TTTTATTT
1620837 TTGACTTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
12 3 0.09
13 13 0.41
14 14 0.44
15 2 0.06
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTATTTATTTA
Found at i:1620816 original size:14 final size:14
Alignment explanation
Indices: 1620788--1620836 Score: 66
Period size: 13 Copynumber: 3.6 Consensus size: 14
1620778 CTTTTAATTC
1620788 TTTTATTTA-TTTA
1 TTTTATTTATTTTA
1620801 TTTTATTTATTTTA
1 TTTTATTTATTTTA
*
1620815 TTTTA-TTATTTAA
1 TTTTATTTATTTTA
1620828 CTTTTATTT
1 -TTTTATTT
1620837 TTGACTTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
13 16 0.50
14 14 0.44
15 2 0.06
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTTATTTATTTTA
Found at i:1620846 original size:14 final size:14
Alignment explanation
Indices: 1620787--1620850 Score: 55
Period size: 13 Copynumber: 4.7 Consensus size: 14
1620777 CCTTTTAATT
1620787 CTTTTATTTATTT-A
1 CTTTTA-TTATTTAA
*
1620801 -TTTTATTTATTTTA
1 CTTTTA-TTATTTAA
1620815 -TTTTATTATTTAA
1 CTTTTATTATTTAA
*
1620828 CTTTTATT-TTTGA
1 CTTTTATTATTTAA
*
1620841 CTTTTTTTAT
1 CTTTTATTAT
1620851 AGGACAATTT
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
13 30 0.68
14 14 0.32
ACGTcount: A:0.20, C:0.05, G:0.02, T:0.73
Consensus pattern (14 bp):
CTTTTATTATTTAA
Found at i:1622177 original size:2 final size:2
Alignment explanation
Indices: 1622145--1622311 Score: 145
Period size: 2 Copynumber: 90.5 Consensus size: 2
1622135 TAGTAGAATA
*
1622145 AT AT AT A- AT AA AT AT A- AT -T AT A- AT A- AT AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1622181 -T A- AT AT AT AT AT AT AT AT AT ACT AC AT AT AT AT ACT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT A-T AT AT AT
*
1622223 AT AT AT AT -T AT AT A- AT -T AT A- AT AT AC A- AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1622259 A- ACT AT AT A- AT AT AT AT AT AT AT AT AT AT AT ACT AT A- AT AT
1 AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
1622300 AT AT AT -T AT AT A
1 AT AT AT AT AT AT A
1622312 CTAAAAAATA
Statistics
Matches: 138, Mismatches: 5, Indels: 44
0.74 0.03 0.24
Matches are distributed among these distances:
1 18 0.13
2 113 0.82
3 7 0.05
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:1634088 original size:17 final size:16
Alignment explanation
Indices: 1634050--1634094 Score: 58
Period size: 17 Copynumber: 2.9 Consensus size: 16
1634040 AAAATAAAGC
1634050 AAAAAAA-A-TAAATG
1 AAAAAAATATTAAATG
*
1634064 AAAAAAATATTAAATT
1 AAAAAAATATTAAATG
1634080 AAAAGAAATATTAAA
1 AAAA-AAATATTAAA
1634095 GAAGGATTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 7 0.26
15 1 0.04
16 9 0.33
17 10 0.37
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.22
Consensus pattern (16 bp):
AAAAAAATATTAAATG
Found at i:1635493 original size:5 final size:5
Alignment explanation
Indices: 1635485--1635810 Score: 595
Period size: 5 Copynumber: 65.0 Consensus size: 5
1635475 ATTAACAAAT
1635485 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1635535 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1635585 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1635635 ATATA ATATA ATATA ATATA ATAT- ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1635684 TATATA ATATA ATATA ATATA TATATA ATATA ATATA ATATA TATATA
1 -ATATA ATATA ATATA ATATA -ATATA ATATA ATATA ATATA -ATATA
1635732 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1635782 ATATA ATATA ATATA A-A-A ATATA TATATA
1 ATATA ATATA ATATA ATATA ATATA -ATATA
1635811 CTAAAAAAAT
Statistics
Matches: 314, Mismatches: 0, Indels: 13
0.96 0.00 0.04
Matches are distributed among these distances:
3 2 0.01
4 6 0.02
5 286 0.91
6 20 0.06
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:1637159 original size:29 final size:29
Alignment explanation
Indices: 1637127--1637182 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
1637117 TACTAAAAGG
1637127 AAAAAGGAAAAAATCG-ATAAAATAAAATA
1 AAAAAGGAAAAAA-CGAATAAAATAAAATA
***
1637156 AAAACTTAAAAAACGAATAAAATAAAA
1 AAAAAGGAAAAAACGAATAAAATAAAA
1637183 CAAATACTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 2 0.09
29 21 0.91
ACGTcount: A:0.73, C:0.05, G:0.07, T:0.14
Consensus pattern (29 bp):
AAAAAGGAAAAAACGAATAAAATAAAATA
Found at i:1638548 original size:16 final size:17
Alignment explanation
Indices: 1638519--1638556 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
1638509 AAAATAGAAT
*
1638519 AAAAAGAATAAAATAAC
1 AAAATGAATAAAATAAC
*
1638536 AAAATGAAT-AAATAAT
1 AAAATGAATAAAATAAC
1638552 AAAAT
1 AAAAT
1638557 AAAATTATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.74, C:0.03, G:0.05, T:0.18
Consensus pattern (17 bp):
AAAATGAATAAAATAAC
Found at i:1638579 original size:24 final size:26
Alignment explanation
Indices: 1638552--1638606 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
1638542 AATAAATAAT
1638552 AAAATAA-A-ATTATATATATTTTTA
1 AAAATAAGATATTATATATATTTTTA
*
1638576 AAAA-AATGATATTATATATATTTTTG
1 AAAATAA-GATATTATATATATTTTTA
1638602 AAAAT
1 AAAAT
1638607 GTTTTCAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
23 2 0.08
24 4 0.15
25 1 0.04
26 19 0.73
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.44
Consensus pattern (26 bp):
AAAATAAGATATTATATATATTTTTA
Found at i:1638634 original size:37 final size:37
Alignment explanation
Indices: 1638584--1638820 Score: 343
Period size: 37 Copynumber: 6.4 Consensus size: 37
1638574 TAAAAAAATG
*
1638584 ATATTATATATATTTTTGAAAATGTTTTCAAAACTAT
1 ATATTATATATATTTTCGAAAATGTTTTCAAAACTAT
1638621 ATATTATATATATTTTCGAAAATGTTTTCAAAACTAT
1 ATATTATATATATTTTCGAAAATGTTTTCAAAACTAT
* * *
1638658 ATATTATATATATTTTCAAAAAAGGTATTCAAAACTAT
1 ATATTATATATATTTTC-GAAAATGTTTTCAAAACTAT
*
1638696 ATATTATATATATTTTCAAAAATGTTTTCAAAACTAT
1 ATATTATATATATTTTCGAAAATGTTTTCAAAACTAT
* *
1638733 ATATTATATATATTTTTGAAAATGTTTTCACAACTAT
1 ATATTATATATATTTTCGAAAATGTTTTCAAAACTAT
* ***
1638770 ATATTATAAATATTTTCGAAAAAAAATTTCAAAAC--T
1 ATATTATATATATTTTCG-AAAATGTTTTCAAAACTAT
1638806 ATATTATATATATTT
1 ATATTATATATATTT
1638821 ATTAAACCTG
Statistics
Matches: 182, Mismatches: 16, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
36 15 0.08
37 121 0.66
38 46 0.25
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.45
Consensus pattern (37 bp):
ATATTATATATATTTTCGAAAATGTTTTCAAAACTAT
Found at i:1638706 original size:75 final size:74
Alignment explanation
Indices: 1638584--1638820 Score: 352
Period size: 75 Copynumber: 3.2 Consensus size: 74
1638574 TAAAAAAATG
1638584 ATATTATATATATTTTTGAAAATGTTTTCAAAACTATATATTATATATATTTTCGAAAATGTTTT
1 ATATTATATATATTTTTGAAAATGTTTTCAAAACTATATATTATATATATTTTCGAAAATGTTTT
1638649 CAAAACTAT
66 CAAAACTAT
** * * *
1638658 ATATTATATATATTTTCAAAAAAGGTATTCAAAACTATATATTATATATATTTTCAAAAATGTTT
1 ATATTATATATATTTT-TGAAAATGTTTTCAAAACTATATATTATATATATTTTCGAAAATGTTT
1638723 TCAAAACTAT
65 TCAAAACTAT
* * ***
1638733 ATATTATATATATTTTTGAAAATGTTTTCACAACTATATATTATAAATATTTTCGAAAAAAAATT
1 ATATTATATATATTTTTGAAAATGTTTTCAAAACTATATATTATATATATTTTCG-AAAATGTTT
1638798 TCAAAAC--T
65 TCAAAACTAT
1638806 ATATTATATATATTT
1 ATATTATATATATTT
1638821 ATTAAACCTG
Statistics
Matches: 146, Mismatches: 15, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
73 16 0.11
74 48 0.33
75 82 0.56
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.45
Consensus pattern (74 bp):
ATATTATATATATTTTTGAAAATGTTTTCAAAACTATATATTATATATATTTTCGAAAATGTTTT
CAAAACTAT
Found at i:1638706 original size:112 final size:110
Alignment explanation
Indices: 1638584--1638820 Score: 377
Period size: 112 Copynumber: 2.1 Consensus size: 110
1638574 TAAAAAAATG
**
1638584 ATATTATATATATTTTTGAAAATGTTTTCAAAACTATATATTATATATATTTTCGAAAATGTTTT
1 ATATTATATATATTTTCAAAAATGTTTTCAAAACTATATATTATATATATTTTCGAAAATGTTTT
* **
1638649 CAAAACTATATATTATATATATTTTC-AAAAAAGGTATTCAAAACTAT
66 CAAAACTATATATTATAAATATTTTCGAAAAAAAAT-TTCAAAAC--T
*
1638696 ATATTATATATATTTTCAAAAATGTTTTCAAAACTATATATTATATATATTTTTGAAAATGTTTT
1 ATATTATATATATTTTCAAAAATGTTTTCAAAACTATATATTATATATATTTTCGAAAATGTTTT
*
1638761 CACAACTATATATTATAAATATTTTCGAAAAAAAATTTCAAAACT
66 CAAAACTATATATTATAAATATTTTCGAAAAAAAATTTCAAAACT
1638806 ATATTATATATATTT
1 ATATTATATATATTT
1638821 ATTAAACCTG
Statistics
Matches: 117, Mismatches: 7, Indels: 4
0.91 0.05 0.03
Matches are distributed among these distances:
110 16 0.14
112 94 0.80
113 7 0.06
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.45
Consensus pattern (110 bp):
ATATTATATATATTTTCAAAAATGTTTTCAAAACTATATATTATATATATTTTCGAAAATGTTTT
CAAAACTATATATTATAAATATTTTCGAAAAAAAATTTCAAAACT
Found at i:1639578 original size:201 final size:201
Alignment explanation
Indices: 1639308--1640143 Score: 1028
Period size: 201 Copynumber: 4.2 Consensus size: 201
1639298 GTTATCGAAC
* *
1639308 TGAATGGAATCGAACTCGAAAGTTTTCGA-TGACAGATAACCCTTATCGCCTTTAGCTATGCAGT
1 TGAATGGAATCGAACTCGAAAGTTTTC-ATTGACAGATAACCCTTCTCGCCTTGAGCTATGCAGT
*
1639372 AAATTCGGCTAGGAGATAGTTCTTTGTTGCTAAATCACATCCAACCTAGGTCTTCTTCTTGACTT
65 AAATTCGGCTAGGAGATAGTTCCTTGTTGCTAAATCACATCCAACCTAGGTCTTCTTCTTGACTT
* * * **
1639437 AAAGAACTCAGTTTAAATTTCAATCGGAAAGTAGTTCCTCACTGCTACCATACGGATGATATATC
130 AAAGAACTCAGTTTAAACTTCAATCGGAAAGTAGTTCCTCACTGCTACCATGCGGCTGATATGCC
1639502 ATCGAGA
195 ATCGAGA
* * * * * * * *
1639509 TGAATGGGATCAAACTCGAAAGTTTTCATTAATAGATAGCCCTTCTCACCTTGAGCTATACAATA
1 TGAATGGAATCGAACTCGAAAGTTTTCATTGACAGATAACCCTTCTCGCCTTGAGCTATGCAGTA
* * * * * * * * *
1639574 AATTCAGTTGGGAGATAGTTCATTATTGCTAGATCACAACCAACTTAGGCCTTCTTCTTGACTTA
66 AATTCGGCTAGGAGATAGTTCCTTGTTGCTAAATCACATCCAACCTAGGTCTTCTTCTTGACTTA
* * * * * *
1639639 AAGACCTCAGTTTAAACTTCAATCGGAAAGTAGTTTCTTATTGCTACCATGCGGCTTATATTCCA
131 AAGAACTCAGTTTAAACTTCAATCGGAAAGTAGTTCCTCACTGCTACCATGCGGCTGATATGCCA
* *
1639704 TTGAGC
196 TCGAGA
* * * * * *
1639710 TGAATGGAATTGAACTTGAAAGATTTCATTGACATATAAACCTTCTCGCCTTGAGCTATGTAGTA
1 TGAATGGAATCGAACTCGAAAGTTTTCATTGACAGATAACCCTTCTCGCCTTGAGCTATGCAGTA
* * *
1639775 AATTCGGCTGGGAGATAGTTCCTTGTTACTAAATCACATCCAACCTAGATCTTCTTCTTGACTTA
66 AATTCGGCTAGGAGATAGTTCCTTGTTGCTAAATCACATCCAACCTAGGTCTTCTTCTTGACTTA
* * * * *
1639840 AAGACCTCAGTTTAAACTTCAACCGAAAAGTAGTTCCTCACTGCTACCATGTGGTTGATATGCCA
131 AAGAACTCAGTTTAAACTTCAATCGGAAAGTAGTTCCTCACTGCTACCATGCGGCTGATATGCCA
*
1639905 TCGAGC
196 TCGAGA
* * ** * * ** * *
1639911 TTAATGGAATCGAACTGGAAAGTTTTTGTTCACATATTGCCCTTCTCGTCTTGAGTTATGCAGTA
1 TGAATGGAATCGAACTCGAAAGTTTTCATTGACAGATAACCCTTCTCGCCTTGAGCTATGCAGTA
* * *
1639976 AATTCGGCTAGGAGATAGTTCCTTGTTGCTAAATCATAGCCAACCTAGGTCTTCTTCTTGACTTC
66 AATTCGGCTAGGAGATAGTTCCTTGTTGCTAAATCACATCCAACCTAGGTCTTCTTCTTGACTTA
* *
1640041 AAG-ACATCAGTTTAAACTTCAATCGGAAAGTAGTTCCTCGCTGCTACCATTCGGCTGATATGCC
131 AAGAAC-TCAGTTTAAACTTCAATCGGAAAGTAGTTCCTCACTGCTACCATGCGGCTGATATGCC
*
1640105 ATCGATA
195 ATCGAGA
* * * *
1640112 TGAATAGAATCAAACTCAAAAGTTTTCGTTGA
1 TGAATGGAATCGAACTCGAAAGTTTTCATTGA
1640144 TAGACAACTT
Statistics
Matches: 533, Mismatches: 100, Indels: 4
0.84 0.16 0.01
Matches are distributed among these distances:
200 2 0.00
201 531 1.00
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.33
Consensus pattern (201 bp):
TGAATGGAATCGAACTCGAAAGTTTTCATTGACAGATAACCCTTCTCGCCTTGAGCTATGCAGTA
AATTCGGCTAGGAGATAGTTCCTTGTTGCTAAATCACATCCAACCTAGGTCTTCTTCTTGACTTA
AAGAACTCAGTTTAAACTTCAATCGGAAAGTAGTTCCTCACTGCTACCATGCGGCTGATATGCCA
TCGAGA
Found at i:1646925 original size:15 final size:15
Alignment explanation
Indices: 1646888--1646917 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1646878 TGAAATATAT
1646888 ATAAAAAAAGTTAAA
1 ATAAAAAAAGTTAAA
1646903 ATAAAAAAAGTTAAA
1 ATAAAAAAAGTTAAA
1646918 TAGAAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (15 bp):
ATAAAAAAAGTTAAA
Found at i:1646961 original size:29 final size:28
Alignment explanation
Indices: 1646929--1647000 Score: 81
Period size: 29 Copynumber: 2.5 Consensus size: 28
1646919 AGAAAAATAC
* *
1646929 TAAAAGAAAAATGAATAAAATGGATAAAA
1 TAAAACAAAAATGAA-AAAATGAATAAAA
* *
1646958 TAAAATAAAAACTTAAAAAATGAATAAAA
1 TAAAACAAAAA-TGAAAAAATGAATAAAA
1646987 TAAAACAAATAATG
1 TAAAACAAA-AATG
1647001 TTAGATTTTG
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
29 31 0.86
30 5 0.14
ACGTcount: A:0.69, C:0.03, G:0.08, T:0.19
Consensus pattern (28 bp):
TAAAACAAAAATGAAAAAATGAATAAAA
Found at i:1647048 original size:17 final size:15
Alignment explanation
Indices: 1647021--1647066 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 15
1647011 AAAGAAATAT
1647021 AAAAAATGTTAAAAGA
1 AAAAAATGTTAAAA-A
*
1647037 AAAAAATAGTTAACAA
1 AAAAAAT-GTTAAAAA
*
1647053 AAAAAATGCTAAAA
1 AAAAAATGTTAAAA
1647067 CAGAAAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
15 5 0.19
16 15 0.58
17 6 0.23
ACGTcount: A:0.70, C:0.04, G:0.09, T:0.17
Consensus pattern (15 bp):
AAAAAATGTTAAAAA
Found at i:1648354 original size:16 final size:16
Alignment explanation
Indices: 1648322--1648370 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
1648312 AAAAAAGAAT
1648322 AAAATGAATAAAAATAAC
1 AAAATGAAT--AAATAAC
* *
1648340 GAAATGAATAAATAAT
1 AAAATGAATAAATAAC
*
1648356 AAAATAAATAAATAA
1 AAAATGAATAAATAA
1648371 AATAAAATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
16 19 0.70
18 8 0.30
ACGTcount: A:0.71, C:0.02, G:0.06, T:0.20
Consensus pattern (16 bp):
AAAATGAATAAATAAC
Found at i:1648371 original size:13 final size:12
Alignment explanation
Indices: 1648346--1648376 Score: 53
Period size: 13 Copynumber: 2.5 Consensus size: 12
1648336 TAACGAAATG
1648346 AATAAATAATAA
1 AATAAATAATAA
1648358 AATAAATAAATAA
1 AATAAAT-AATAA
1648371 AATAAA
1 AATAAA
1648377 ATTATATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 7 0.39
13 11 0.61
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (12 bp):
AATAAATAATAA
Found at i:1648394 original size:17 final size:17
Alignment explanation
Indices: 1648368--1648401 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1648358 AATAAATAAA
* *
1648368 TAAAATAAAATTATATT
1 TAAAAAAAAATAATATT
1648385 TAAAAAAAAATAATATT
1 TAAAAAAAAATAATATT
1648402 ATATATATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
TAAAAAAAAATAATATT
Found at i:1648438 original size:37 final size:37
Alignment explanation
Indices: 1648397--1648599 Score: 307
Period size: 37 Copynumber: 5.4 Consensus size: 37
1648387 AAAAAAAATA
*
1648397 ATATTATATATATTTTCAAAAATGTTTTCAAAACTAT
1 ATATTATATATATTTTCAAAAATATTTTCAAAACTAT
1648434 ATATTATATATATTTTCAAAAAATATTTTCAAAAAACTAT
1 ATATTATATATATTTTC-AAAAATATTTTC--AAAACTAT
1648474 ATATTATATATATTTTCAAAAATATTTTCAAAACTAT
1 ATATTATATATATTTTCAAAAATATTTTCAAAACTAT
* * * * *
1648511 ATATTATATATATTTTCGAAAATGTTATCACAACTAC
1 ATATTATATATATTTTCAAAAATATTTTCAAAACTAT
*
1648548 ATATTATATATATTTTCGAAAAATATTTTCAAAGCTAT
1 ATATTATATATATTTTC-AAAAATATTTTCAAAACTAT
1648586 ATATTATATATATT
1 ATATTATATATATT
1648600 AAATAAACTC
Statistics
Matches: 150, Mismatches: 12, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
37 74 0.49
38 39 0.26
39 12 0.08
40 25 0.17
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.45
Consensus pattern (37 bp):
ATATTATATATATTTTCAAAAATATTTTCAAAACTAT
Found at i:1648469 original size:77 final size:76
Alignment explanation
Indices: 1648388--1648599 Score: 313
Period size: 77 Copynumber: 2.8 Consensus size: 76
1648378 TTATATTTAA
* *
1648388 AAAAAAATA-ATATTATATATATTTTCAAAAATGTTTTCAAAACTATATATTATATATATTTTCA
1 AAAAAACTACATATTATATATATTTTCAAAAATATTTTCAAAACTATATATTATATATATTTTC-
*
1648452 AAAAATATTTTC
65 AAAAATATTATC
* *
1648464 AAAAAACTATATATTATATATATTTTCAAAAATATTTTCAAAACTATATATTATATATATTTTCG
1 AAAAAACTACATATTATATATATTTTCAAAAATATTTTCAAAACTATATATTATATATATTTTCA
*
1648529 AAAATGTTATC
66 AAAATATTATC
* *
1648540 --ACAACTACATATTATATATATTTTCGAAAAATATTTTCAAAGCTATATATTATATATATT
1 AAAAAACTACATATTATATATATTTTC-AAAAATATTTTCAAAACTATATATTATATATATT
1648600 AAATAAACTC
Statistics
Matches: 126, Mismatches: 8, Indels: 5
0.91 0.06 0.04
Matches are distributed among these distances:
74 23 0.18
75 33 0.26
76 17 0.13
77 53 0.42
ACGTcount: A:0.46, C:0.08, G:0.02, T:0.43
Consensus pattern (76 bp):
AAAAAACTACATATTATATATATTTTCAAAAATATTTTCAAAACTATATATTATATATATTTTCA
AAAATATTATC
Found at i:1654311 original size:10 final size:9
Alignment explanation
Indices: 1654295--1654327 Score: 57
Period size: 9 Copynumber: 3.6 Consensus size: 9
1654285 GGATCACATC
1654295 ATTTTTTTT
1 ATTTTTTTT
1654304 ATTTTTTTT
1 ATTTTTTTT
1654313 ATTTTTTTT
1 ATTTTTTTT
1654322 ACTTTT
1 A-TTTT
1654328 ATTCTTCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 19 0.83
10 4 0.17
ACGTcount: A:0.12, C:0.03, G:0.00, T:0.85
Consensus pattern (9 bp):
ATTTTTTTT
Found at i:1654327 original size:15 final size:16
Alignment explanation
Indices: 1654309--1654343 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1654299 TTTTTATTTT
*
1654309 TTTTATT-TTTTTTAC
1 TTTTATTCTTCTTTAC
1654324 TTTTATTCTTCTTTAC
1 TTTTATTCTTCTTTAC
1654340 TTTT
1 TTTT
1654344 TTATTTAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTATTCTTCTTTAC
Found at i:1654345 original size:18 final size:17
Alignment explanation
Indices: 1654307--1654349 Score: 54
Period size: 15 Copynumber: 2.6 Consensus size: 17
1654297 TTTTTTTATT
*
1654307 TTTTTTATTTTTTTTAC
1 TTTTTTATTTTCTTTAC
1654324 --TTTTATTCTTCTTTAC
1 TTTTTTATT-TTCTTTAC
1654340 TTTTTTATTT
1 TTTTTTATTT
1654350 AACATAGGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 6
0.76 0.03 0.21
Matches are distributed among these distances:
15 7 0.32
16 7 0.32
17 1 0.05
18 7 0.32
ACGTcount: A:0.12, C:0.09, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTTTATTTTCTTTAC
Found at i:1654557 original size:16 final size:16
Alignment explanation
Indices: 1654536--1654576 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
1654526 TTTCCGATCC
1654536 AAAATTACGGATCACT
1 AAAATTACGGATCACT
*
1654552 AAAATTACAGATCACT
1 AAAATTACGGATCACT
1654568 AAAATTACG
1 AAAATTACG
1654577 CTCCAAATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.49, C:0.17, G:0.10, T:0.24
Consensus pattern (16 bp):
AAAATTACGGATCACT
Found at i:1655728 original size:21 final size:21
Alignment explanation
Indices: 1655680--1655728 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 21
1655670 CAATTTTTAA
1655680 TGAA-TAA-TATTCAAATATT
1 TGAATTAATTATTCAAATATT
*
1655699 TG-ATAAATTATTCAAA-ATTT
1 TGAATTAATTATTCAAATA-TT
1655719 TGAATTAATT
1 TGAATTAATT
1655729 TTTTTTAGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
18 1 0.04
19 5 0.21
20 12 0.50
21 6 0.25
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (21 bp):
TGAATTAATTATTCAAATATT
Found at i:1658929 original size:14 final size:15
Alignment explanation
Indices: 1658910--1658944 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
1658900 ATTTATTGTA
1658910 AGATTTAG-ATTTAG
1 AGATTTAGAATTTAG
1658924 AGATTTAGAATTTAG
1 AGATTTAGAATTTAG
1658939 AG-TTTA
1 AGATTTA
1658945 ATCATTAGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.37, C:0.00, G:0.20, T:0.43
Consensus pattern (15 bp):
AGATTTAGAATTTAG
Found at i:1660228 original size:27 final size:27
Alignment explanation
Indices: 1660182--1660236 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
1660172 ATACTCTTAA
* * *
1660182 CCATTTGATAATGAATGCTCAATCACC
1 CCATTTGACAATAAAAGCTCAATCACC
*
1660209 CCATTTGACAATAAAAGCTCAATTACC
1 CCATTTGACAATAAAAGCTCAATCACC
1660236 C
1 C
1660237 TGATGCAACT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.36, C:0.27, G:0.09, T:0.27
Consensus pattern (27 bp):
CCATTTGACAATAAAAGCTCAATCACC
Found at i:1662668 original size:2 final size:2
Alignment explanation
Indices: 1662663--1662801 Score: 63
Period size: 2 Copynumber: 74.0 Consensus size: 2
1662653 TATTACGTAG
* *
1662663 TA TA TA T- TA TA TA T- TA TA AA T- TA TA T- TA TA GTA TA TA TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
* * *
1662702 T- TA TA TT TA T- TT TA TA TA T- TA TA TT TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
1662740 TA GTA CA TA GA -A TT TA TA TA T- TA TA T- TA TA TA GTA TA GTA
1 TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA -TA
1662780 TA GTA TA -A TA T- TA TA TA T- TA TA
1 TA -TA TA TA TA TA TA TA TA TA TA TA
1662802 CTTATTCTTT
Statistics
Matches: 105, Mismatches: 13, Indels: 38
0.67 0.08 0.24
Matches are distributed among these distances:
1 14 0.13
2 81 0.77
3 10 0.10
ACGTcount: A:0.42, C:0.01, G:0.05, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1662673 original size:7 final size:7
Alignment explanation
Indices: 1662663--1662801 Score: 87
Period size: 7 Copynumber: 19.6 Consensus size: 7
1662653 TATTACGTAG
1662663 TATATAT
1 TATATAT
1662670 TATATAT
1 TATATAT
*
1662677 TATAAAT
1 TATATAT
1662684 TATATTAT
1 TATA-TAT
1662692 AGTATATAT
1 --TATATAT
1662701 GT-TATAT
1 -TATATAT
*
1662708 T-TATTT
1 TATATAT
1662714 TATATAT
1 TATATAT
1662721 TATAT-T
1 TATATAT
1662727 TATATAT
1 TATATAT
1662734 TATATA-
1 TATATAT
*
1662740 TAGTACA-
1 TA-TATAT
*
1662747 TAGA-AT
1 TATATAT
1662753 T-TATA-
1 TATATAT
1662758 TATTATAT
1 TA-TATAT
1662766 TATATAGT
1 TATATA-T
*
1662774 ATAGTATAG
1 -TA-TATAT
1662783 TATAATAT
1 TAT-ATAT
1662791 TATATAT
1 TATATAT
1662798 TATA
1 TATA
1662802 CTTATTCTTT
Statistics
Matches: 108, Mismatches: 9, Indels: 30
0.73 0.06 0.20
Matches are distributed among these distances:
5 3 0.03
6 17 0.16
7 60 0.56
8 15 0.14
9 5 0.05
10 8 0.07
ACGTcount: A:0.42, C:0.01, G:0.05, T:0.53
Consensus pattern (7 bp):
TATATAT
Found at i:1662680 original size:5 final size:5
Alignment explanation
Indices: 1662665--1662806 Score: 56
Period size: 5 Copynumber: 29.6 Consensus size: 5
1662655 TTACGTAGTA
* * *
1662665 TATAT TATA- TAT-T ATAAAT TATAT TATAG TATA- TATGT TATAT T-TAT
1 TATAT TATAT TATAT -TATAT TATAT TATAT TATAT TATAT TATAT TATAT
* * * *
1662712 TTTA- TATAT TATAT T-TA- TATAT TATA- TATAG TACA- TAGAAT T-TA-
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TA-TAT TATAT
* * *
1662756 TATAT TATAT TATAT AGTATAG TATAG TATAA TAT-T ATATAT TATACT
1 TATAT TATAT TATAT --TATAT TATAT TATAT TATAT -TATAT TATA-T
1662804 TAT
1 TAT
1662807 TCTTTTTTAT
Statistics
Matches: 107, Mismatches: 12, Indels: 35
0.69 0.08 0.23
Matches are distributed among these distances:
3 2 0.02
4 26 0.24
5 68 0.64
6 7 0.07
7 4 0.04
ACGTcount: A:0.41, C:0.01, G:0.05, T:0.53
Consensus pattern (5 bp):
TATAT
Found at i:1662717 original size:20 final size:21
Alignment explanation
Indices: 1662663--1662740 Score: 81
Period size: 24 Copynumber: 3.7 Consensus size: 21
1662653 TATTACGTAG
*
1662663 TATATATTATATATTATAAATT
1 TATATATTATATATT-TATATT
*
1662685 ATATTATAGTATATATGTTATATT
1 -TA-TATATTATATAT-TTATATT
1662709 TAT-T-TTATATA-TTATATT
1 TATATATTATATATTTATATT
1662727 TATATATTATATAT
1 TATATATTATATAT
1662741 AGTACATAGA
Statistics
Matches: 47, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
18 10 0.21
19 1 0.02
20 13 0.28
21 1 0.02
22 1 0.02
23 4 0.09
24 16 0.34
25 1 0.02
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.58
Consensus pattern (21 bp):
TATATATTATATATTTATATT
Found at i:1662718 original size:11 final size:13
Alignment explanation
Indices: 1662663--1662806 Score: 106
Period size: 13 Copynumber: 11.2 Consensus size: 13
1662653 TATTACGTAG
1662663 TATATATTATATAT
1 TATATATTATAT-T
*
1662677 TATAAATTATA-T
1 TATATATTATATT
1662689 TATAGTA-TATATGT
1 TATA-TATTATAT-T
1662703 TATAT-TTAT-TT
1 TATATATTATATT
1662714 TATATATTATATT
1 TATATATTATATT
*
1662727 TATATATTATATA
1 TATATATTATATT
* *
1662740 TAGTACA-TAGAATT
1 TA-TATATTA-TATT
1662754 TATATATTATA-T
1 TATATATTATATT
* *
1662766 TATATAGTATA-G
1 TATATATTATATT
*
1662778 TATAGTATAATA-T
1 TATA-TATTATATT
*
1662791 TATATATTATACT
1 TATATATTATATT
1662804 TAT
1 TAT
1662807 TCTTTTTTAT
Statistics
Matches: 105, Mismatches: 14, Indels: 23
0.74 0.10 0.16
Matches are distributed among these distances:
11 6 0.06
12 35 0.33
13 40 0.38
14 24 0.23
ACGTcount: A:0.41, C:0.01, G:0.05, T:0.53
Consensus pattern (13 bp):
TATATATTATATT
Found at i:1677731 original size:138 final size:138
Alignment explanation
Indices: 1677482--1677735 Score: 418
Period size: 138 Copynumber: 1.8 Consensus size: 138
1677472 TAAGTATATT
* *
1677482 AAACTAAGTTAAAGATCCTTAGTGTTCGAGAGAAACTAGTGGAAGATCAACGTGAAAAATGGGTT
1 AAACTAAGTTAAAGATCCTTAGCGTTCGAGAGAAACTAGGGGAAGATCAACGTGAAAAATGGGTT
* * *
1677547 TTAGCTAATAACTAGAGCCTAATCCAATATTAGTGTTAGAGAGAAACTAAGTACATTAATTGGTG
66 TTAGCTAATAACCAGAACCTAATCCAACATTAGTGTTAGAGAGAAACTAAGTACATTAATTGGTG
1677612 TTGGAGAG
131 TTGGAGAG
* * *
1677620 AAACTAAGTTAAAGATCTTTAGCGTTCGAGAGAAACTAGGGGAAGATCAACGTGAATAATGGTTT
1 AAACTAAGTTAAAGATCCTTAGCGTTCGAGAGAAACTAGGGGAAGATCAACGTGAAAAATGGGTT
* *
1677685 TTAGCTAATAACCAGAACCTAATCCAACATTAGTGTTCGAGTGAAACTAAG
66 TTAGCTAATAACCAGAACCTAATCCAACATTAGTGTTAGAGAGAAACTAAG
1677736 ATAGGATTTC
Statistics
Matches: 106, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
138 106 1.00
ACGTcount: A:0.39, C:0.13, G:0.22, T:0.27
Consensus pattern (138 bp):
AAACTAAGTTAAAGATCCTTAGCGTTCGAGAGAAACTAGGGGAAGATCAACGTGAAAAATGGGTT
TTAGCTAATAACCAGAACCTAATCCAACATTAGTGTTAGAGAGAAACTAAGTACATTAATTGGTG
TTGGAGAG
Found at i:1688976 original size:16 final size:17
Alignment explanation
Indices: 1688955--1688986 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1688945 TCAACTACCT
1688955 AGAACAA-CATTTTTAA
1 AGAACAATCATTTTTAA
1688971 AGAACAATCATTTTTA
1 AGAACAATCATTTTTA
1688987 GTCAAAACGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.47, C:0.12, G:0.06, T:0.34
Consensus pattern (17 bp):
AGAACAATCATTTTTAA
Found at i:1692873 original size:29 final size:28
Alignment explanation
Indices: 1692841--1692918 Score: 64
Period size: 25 Copynumber: 3.0 Consensus size: 28
1692831 CTTAAAATAG
1692841 ATGAACAATAGCCAAATCAGAAATAAACA
1 ATGAACAATAGCCAAATCAGAAATAAA-A
*
1692870 ATGATTAAAAT-G-C--AT-A-AAAT-AAA
1 ATGA--ACAATAGCCAAATCAGAAATAAAA
1692893 A-GAACAATAGCCAAATCAGAAATAAA
1 ATGAACAATAGCCAAATCAGAAATAAA
1692919 TAGGGACTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 20
0.63 0.03 0.33
Matches are distributed among these distances:
20 4 0.11
21 1 0.03
22 3 0.08
23 2 0.05
24 4 0.11
25 5 0.13
26 5 0.13
27 4 0.11
29 5 0.13
30 1 0.03
31 4 0.11
ACGTcount: A:0.60, C:0.13, G:0.10, T:0.17
Consensus pattern (28 bp):
ATGAACAATAGCCAAATCAGAAATAAAA
Found at i:1692888 original size:51 final size:51
Alignment explanation
Indices: 1692828--1692944 Score: 162
Period size: 51 Copynumber: 2.3 Consensus size: 51
1692818 AGTGACTCAT
* * * * *
1692828 ATGCTTAAAATAGATGAACAATAGCCAAATCAGAAATAAACAATGATTAAA
1 ATGCATAAAATAAAAGAACAATAGCCAAATCAGAAATAAACAAGGACTAAA
* *
1692879 ATGCATAAAATAAAAGAACAATAGCCAAATCAGAAATAAATAGGGACTAAA
1 ATGCATAAAATAAAAGAACAATAGCCAAATCAGAAATAAACAAGGACTAAA
*
1692930 ATGCATAAATTAAAA
1 ATGCATAAAATAAAA
1692945 ATACAACACA
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 58 1.00
ACGTcount: A:0.57, C:0.11, G:0.12, T:0.20
Consensus pattern (51 bp):
ATGCATAAAATAAAAGAACAATAGCCAAATCAGAAATAAACAAGGACTAAA
Found at i:1692968 original size:51 final size:51
Alignment explanation
Indices: 1692808--1692971 Score: 136
Period size: 51 Copynumber: 3.2 Consensus size: 51
1692798 TAACCAACTT
* * * * * * * * *
1692808 AGAAATGAATAGTGACTCATATGCTTAAAATAGATGAACAATAGCCAAATC
1 AGAAATAAATAGGGACTAAAATGCATAAAATAAAAGAACAACAGCAAAATC
* ** * * *
1692859 AGAAATAAACAATGATTAAAATGCATAAAATAAAAGAACAATAGCCAAATC
1 AGAAATAAATAGGGACTAAAATGCATAAAATAAAAGAACAACAGCAAAATC
*
1692910 AGAAATAAATAGGGACTAAAATGCATAAATTAAAA-ATACAACA-CAAAATTC
1 AGAAATAAATAGGGACTAAAATGCATAAAATAAAAGA-ACAACAGCAAAA-TC
1692961 ATG-AATAAATA
1 A-GAAATAAATA
1692972 ATAAAACAAT
Statistics
Matches: 94, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
50 5 0.05
51 88 0.94
52 1 0.01
ACGTcount: A:0.56, C:0.12, G:0.12, T:0.21
Consensus pattern (51 bp):
AGAAATAAATAGGGACTAAAATGCATAAAATAAAAGAACAACAGCAAAATC
Found at i:1693902 original size:42 final size:42
Alignment explanation
Indices: 1693798--1693909 Score: 129
Period size: 42 Copynumber: 2.7 Consensus size: 42
1693788 TGACCCAAGT
1693798 TGATGTTGATCCAACTA-CTTATGTGATGGACGAACAACATGA
1 TGATGTTGATCCAAC-ACCTTATGTGATGGACGAACAACATGA
* * * **
1693840 TGATGCTGATCCAACTCCTTATGTGATGGACGAGCAAGGT-A
1 TGATGTTGATCCAACACCTTATGTGATGGACGAACAACATGA
* *
1693881 TTGGTGTTGATTCAACACCTTATGTGATG
1 -TGATGTTGATCCAACACCTTATGTGATG
1693910 CAAACGAGAT
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
41 1 0.02
42 58 0.98
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (42 bp):
TGATGTTGATCCAACACCTTATGTGATGGACGAACAACATGA
Found at i:1694965 original size:48 final size:49
Alignment explanation
Indices: 1694884--1694976 Score: 118
Period size: 48 Copynumber: 1.9 Consensus size: 49
1694874 TTTGAAAACA
* *
1694884 TCAAGAAACCCCTGAAAATCAGGCTTAGATTCTTTCAAA-TTCATCATG
1 TCAAGAAACCCCTAAAAATCAGACTTAGATTCTTTCAAAGTTCATCATG
* * *
1694932 TCAAGAAACCTCTAAAAATCATACTTA-ATTTCTTTGAAAGTTCAT
1 TCAAGAAACCCCTAAAAATCAGACTTAGA-TTCTTTCAAAGTTCAT
1694977 TTAAAAATCA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
47 1 0.03
48 32 0.84
49 5 0.13
ACGTcount: A:0.38, C:0.20, G:0.10, T:0.32
Consensus pattern (49 bp):
TCAAGAAACCCCTAAAAATCAGACTTAGATTCTTTCAAAGTTCATCATG
Found at i:1695019 original size:55 final size:55
Alignment explanation
Indices: 1694932--1695262 Score: 362
Period size: 55 Copynumber: 6.0 Consensus size: 55
1694922 ATTCATCATG
* * * * * **
1694932 TCAAGAAACCTCTAAAAATCATACTTAATTTCTTTGAAAGTTCATTTAAAAATCA
1 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAACTCATTTAAAAATCA
* * * *
1694987 TCAAGAAACTTCTGAAAATCAGAATTTGTTTCTTTAAAAACTCATTTGAAAATCG
1 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAACTCATTTAAAAATCA
* * * * * * *
1695042 TCAAGGAATTTCTAAAAATTAGACTTAGTTTCTTTGAAAGCTCATTTAAAAATAA
1 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAACTCATTTAAAAATCA
* * * *
1695097 TCAAGAAACTTCTGAAAAT-AGGATTTAGTTTCTTTAAAAGCTTATTTAAAAATAA
1 TCAAGAAACTTCTGAAAATCA-GACTTAGTTTCTTTAAAAACTCATTTAAAAATCA
* * * *
1695152 TCAAGAAACTTCAGAAAATCGGACTTAATTTCTTTAAACAAATTCATTT-AAAATCA
1 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTT-AA-AAACTCATTTAAAAATCA
* *
1695208 GCATGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAACTCATTT-AAAATCA
1 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAACTCATTTAAAAATCA
1695262 T
1 T
1695263 TTTAAAAACT
Statistics
Matches: 229, Mismatches: 43, Indels: 9
0.81 0.15 0.03
Matches are distributed among these distances:
54 17 0.07
55 167 0.73
56 38 0.17
57 7 0.03
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (55 bp):
TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAACTCATTTAAAAATCA
Found at i:1695257 original size:12 final size:12
Alignment explanation
Indices: 1695240--1695281 Score: 61
Period size: 12 Copynumber: 3.6 Consensus size: 12
1695230 ACTTAGTTTC
1695240 TTTAAAAACTCA
1 TTTAAAAACTCA
1695252 TTT-AAAA-TCA
1 TTTAAAAACTCA
1695262 TTTTAAAAACTCA
1 -TTTAAAAACTCA
1695275 TTTAAAA
1 TTTAAAA
1695282 TCATCAGGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 3 0.11
11 7 0.26
12 14 0.52
13 3 0.11
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (12 bp):
TTTAAAAACTCA
Found at i:1695264 original size:10 final size:11
Alignment explanation
Indices: 1695244--1695285 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
1695234 AGTTTCTTTA
1695244 AAAACTCATTT
1 AAAACTCATTT
1695255 AAAA-TCATTTT
1 AAAACTCA-TTT
1695266 AAAAACTCATTT
1 -AAAACTCATTT
1695278 AAAA-TCAT
1 AAAACTCAT
1695286 CAGGAAACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
10 7 0.25
11 11 0.39
12 7 0.25
13 3 0.11
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (11 bp):
AAAACTCATTT
Found at i:1695266 original size:23 final size:23
Alignment explanation
Indices: 1695240--1695285 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
1695230 ACTTAGTTTC
1695240 TTTAAAAACTCATTTAAAATCAT
1 TTTAAAAACTCATTTAAAATCAT
1695263 TTTAAAAACTCATTTAAAATCAT
1 TTTAAAAACTCATTTAAAATCAT
1695286 CAGGAAACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.13, G:0.00, T:0.39
Consensus pattern (23 bp):
TTTAAAAACTCATTTAAAATCAT
Found at i:1695357 original size:55 final size:55
Alignment explanation
Indices: 1695263--1695971 Score: 707
Period size: 54 Copynumber: 13.0 Consensus size: 55
1695253 TTAAAATCAT
* * *
1695263 TTTAAAAACTCATTT-AAAATCATCAGGAAACTTTTGAAAATCAGACTTAGTTTC
1 TTTAAAAACTCATTTAAAAATAATCAAGAAACTTCTGAAAATCAGACTTAGTTTC
* ** * *
1695317 TTTGAAAGTTTATTTAAAAATAATCAAGAAACTTCTGAAAATCGGACTTAGTTTC
1 TTTAAAAACTCATTTAAAAATAATCAAGAAACTTCTGAAAATCAGACTTAGTTTC
* *
1695372 TTTAAAAACTCATTTAAAACCATAA-C--GAAACTTCTAAAAAGCAGACTTAGTTTC
1 TTTAAAAACTCATTTAAAA--ATAATCAAGAAACTTCTGAAAATCAGACTTAGTTTC
* * * * *
1695426 TTTGAAAGCTCATTTAAAAATAATCAAGAAACATTC--AAAATTCGGACTCAATTT-
1 TTTAAAAACTCATTTAAAAATAATCAAGAAAC-TTCTGAAAA-TCAGACTTAGTTTC
* ** *
1695480 TTTAAAAACTCATTTGAAAATTGTCAAGAAACTTCTGAAAATCAGACTTAATTTC
1 TTTAAAAACTCATTTAAAAATAATCAAGAAACTTCTGAAAATCAGACTTAGTTTC
* * ** * *
1695535 CTCAAAAACTCATTT-AAAATTGTAAAGAAACTTCTAAAAATCAGACTTAGTTTC
1 TTTAAAAACTCATTTAAAAATAATCAAGAAACTTCTGAAAATCAGACTTAGTTTC
* *
1695589 TTTAAAAACTCATTTAAAAATCATCAAGAAACTTTTGAAAATCAGACTTAGTTTC
1 TTTAAAAACTCATTTAAAAATAATCAAGAAACTTCTGAAAATCAGACTTAGTTTC
* *
1695644 TTT-AAAACTCATTTAAGAATCATCAAGAAACTTCTGAAAATCAGACTTAGTTTC
1 TTTAAAAACTCATTTAAAAATAATCAAGAAACTTCTGAAAATCAGACTTAGTTTC
* * * * *
1695698 TTTGAAAGA-TCATTTAAAAATAATCAAGAAACTTCCGAAAATCAAACTTAGCTGC
1 TTT-AAAAACTCATTTAAAAATAATCAAGAAACTTCTGAAAATCAGACTTAGTTTC
* * * ** ** *
1695753 TTTCAAAATTCATTTAAAAATCATCAAGAAACTTCCAAAAATGGGACTTAGCTTC
1 TTTAAAAACTCATTTAAAAATAATCAAGAAACTTCTGAAAATCAGACTTAGTTTC
* * * * * *
1695808 TTTTAAAATTCATTTACAAAT-ATCAAGAAACCTCCGAAAAT-TGAACTTA-TCTTC
1 TTTAAAAACTCATTTAAAAATAATCAAGAAACTTCTGAAAATCAG-ACTTAGT-TTC
* **
1695862 TTTCAAAAA-TCATTTAAAAATAATCAAGAAACTTCTAAAAATCAGACTTAACCTT-
1 TTT-AAAAACTCATTTAAAAATAATCAAGAAACTTCTGAAAATCAGACTT-AGTTTC
* **
1695917 TTTCAAAA-T-ATATTAAAAATAATCAAGAAACTT-TCGAAAATTGGACTTAGTTTC
1 TTTAAAAACTCAT-TTAAAAATAATCAAGAAACTTCT-GAAAATCAGACTTAGTTTC
1695971 T
1 T
1695972 AAAAAAATCG
Statistics
Matches: 554, Mismatches: 76, Indels: 50
0.81 0.11 0.07
Matches are distributed among these distances:
52 4 0.01
53 11 0.02
54 276 0.50
55 248 0.45
56 11 0.02
57 4 0.01
ACGTcount: A:0.43, C:0.16, G:0.08, T:0.33
Consensus pattern (55 bp):
TTTAAAAACTCATTTAAAAATAATCAAGAAACTTCTGAAAATCAGACTTAGTTTC
Found at i:1695366 original size:132 final size:134
Alignment explanation
Indices: 1695129--1695390 Score: 359
Period size: 132 Copynumber: 2.0 Consensus size: 134
1695119 ATTTAGTTTC
* * *
1695129 TTTAAAAGCTTATTTAAAAATAATCAAGAAACTTCAGAAAATCGGACTTAATTTCTTTAAACAAA
1 TTTAAAAACTCATTTAAAAATAATCAAGAAACTTCAGAAAATCAGACTTAATTTCTTTAAACAAA
* *
1695194 TTCATTTAAAATCAGCATGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAACTCATTTAAAA
66 TTCATTTAAAATAAGCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAACTCATTTAAAA
1695259 TCAT
131 TCAT
* * ** * * *
1695263 TTTAAAAACTCATTT-AAAATCATCAGGAAACTTTTGAAAATCAGACTTAGTTTCTTT-GA-AAG
1 TTTAAAAACTCATTTAAAAATAATCAAGAAACTTCAGAAAATCAGACTTAATTTCTTTAAACAAA
* * *
1695325 TTTATTTAAAAATAATCAAGAAACTTCTGAAAATCGGACTTAGTTTCTTTAAAAACTCATTTAAA
66 TTCATTT-AAAATAAGCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAACTCATTTAAA
1695390 A
130 A
1695391 CCATAACGAA
Statistics
Matches: 112, Mismatches: 15, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
131 8 0.07
132 55 0.49
133 36 0.32
134 13 0.12
ACGTcount: A:0.43, C:0.13, G:0.08, T:0.35
Consensus pattern (134 bp):
TTTAAAAACTCATTTAAAAATAATCAAGAAACTTCAGAAAATCAGACTTAATTTCTTTAAACAAA
TTCATTTAAAATAAGCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAACTCATTTAAAA
TCAT
Found at i:1695454 original size:109 final size:109
Alignment explanation
Indices: 1695263--1695971 Score: 726
Period size: 109 Copynumber: 6.5 Consensus size: 109
1695253 TTAAAATCAT
* * * ** *
1695263 TTTAAAAACTCATTTAAAATCATCAGGAAACTTTTGAAAATCAGACTTAGTTTCTTTGAAAGTTT
1 TTTAAAAACTCATTTAAAATCATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTCAAAACTC
* *
1695328 ATTTAAAAATAATCAAGAAACTTCTGAAAATCGGACTTAGTTTC
66 ATTTAAAAATAATCAAGAAACTTCTAAAAATCAGACTTAGTTTC
* * * * *
1695372 TTTAAAAACTCATTTAAAACCAT-AACGAAACTTCTAAAAAGCAGACTTAGTTTCTTTGAAAGCT
1 TTTAAAAACTCATTTAAAATCATCAA-GAAACTTCTGAAAATCAGACTTAGTTTCTTTCAAAACT
* * * *
1695436 CATTTAAAAATAATCAAGAAACATTC-AAAATTCGGACTCAATTT-
65 CATTTAAAAATAATCAAGAAAC-TTCTAAAAATCAGACTTAGTTTC
** * *
1695480 TTTAAAAACTCATTTGAAAATTGTCAAGAAACTTCTGAAAATCAGACTTAATTTC-CTCAAAAAC
1 TTTAAAAACTCATTT-AAAATCATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTC-AAAAC
** *
1695544 TCATTT-AAAATTGTAAAGAAACTTCTAAAAATCAGACTTAGTTTC
64 TCATTTAAAAATAATCAAGAAACTTCTAAAAATCAGACTTAGTTTC
*
1695589 TTTAAAAACTCATTTAAAAATCATCAAGAAACTTTTGAAAATCAGACTTAGTTTCTTT-AAAACT
1 TTTAAAAACTCATTT-AAAATCATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTCAAAACT
* * *
1695653 CATTTAAGAATCATCAAGAAACTTCTGAAAATCAGACTTAGTTTC
65 CATTTAAAAATAATCAAGAAACTTCTAAAAATCAGACTTAGTTTC
* * * * * * *
1695698 TTTGAAAGA-TCATTTAAAAATAATCAAGAAACTTCCGAAAATCAAACTTAGCTGCTTTCAAAAT
1 TTT-AAAAACTCATTT-AAAATCATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTCAAAAC
* * ** *
1695762 TCATTTAAAAATCATCAAGAAACTTCCAAAAATGGGACTTAGCTTC
64 TCATTTAAAAATAATCAAGAAACTTCTAAAAATCAGACTTAGTTTC
* * * * *
1695808 TTTTAAAATTCATTTACAAAT-ATCAAGAAACCTCCGAAAAT-TGAACTTA-TCTTCTTTCAAAA
1 TTTAAAAACTCATTTA-AAATCATCAAGAAACTTCTGAAAATCAG-ACTTAGT-TTCTTTCAAAA
* *
1695870 ATCATTTAAAAATAATCAAGAAACTTCTAAAAATCAGACTTAACCTTT-
63 CTCATTTAAAAATAATCAAGAAACTTCTAAAAATCAGACTT-A-GTTTC
* * * **
1695918 TTCAAAATA-T-ATTAAAAATAATCAAGAAACTT-TCGAAAATTGGACTTAGTTTCT
1 TTTAAAA-ACTCATTTAAAATCATCAAGAAACTTCT-GAAAATCAGACTTAGTTTCT
1695972 AAAAAAATCG
Statistics
Matches: 506, Mismatches: 72, Indels: 44
0.81 0.12 0.07
Matches are distributed among these distances:
107 3 0.01
108 59 0.12
109 365 0.72
110 76 0.15
111 3 0.01
ACGTcount: A:0.43, C:0.16, G:0.08, T:0.33
Consensus pattern (109 bp):
TTTAAAAACTCATTTAAAATCATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTCAAAACTC
ATTTAAAAATAATCAAGAAACTTCTAAAAATCAGACTTAGTTTC
Found at i:1698075 original size:17 final size:16
Alignment explanation
Indices: 1698030--1698093 Score: 58
Period size: 17 Copynumber: 3.8 Consensus size: 16
1698020 GTTTTATTTC
1698030 TTCTTTTTCTTTTTTCT
1 TTCTTTTTCTTTTTT-T
* * *
1698047 CTCTCTTACTTTTTTT
1 TTCTTTTTCTTTTTTT
1698063 ATTCTTTTTCTTTTATTT
1 -TTCTTTTTCTTTT-TTT
1698081 TCTCTTTTT-TTTT
1 T-TCTTTTTCTTTT
1698094 CTCTATTTTC
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
16 1 0.03
17 27 0.71
18 10 0.26
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.78
Consensus pattern (16 bp):
TTCTTTTTCTTTTTTT
Found at i:1698091 original size:21 final size:20
Alignment explanation
Indices: 1698067--1698122 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 20
1698057 TTTTTTATTC
*
1698067 TTTTTCTTTTATTTTCTCT-
1 TTTTTTTTTTATTTTCTCTG
*
1698086 TTTTTTTTCTCTATTTTCTGTG
1 TTTTTTTT-T-TATTTTCTCTG
*
1698108 TTTTTTTTTCATTTT
1 TTTTTTTTTTATTTT
1698123 TCTATATCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
19 7 0.23
20 6 0.19
21 10 0.32
22 8 0.26
ACGTcount: A:0.05, C:0.12, G:0.04, T:0.79
Consensus pattern (20 bp):
TTTTTTTTTTATTTTCTCTG
Found at i:1699504 original size:20 final size:20
Alignment explanation
Indices: 1699457--1699532 Score: 89
Period size: 20 Copynumber: 3.6 Consensus size: 20
1699447 ACATACGAAT
*
1699457 GCAAAAACGCAAACATGGAC
1 GCAAAAATGCAAACATGGAC
1699477 GCAAAAATGCAAACATGGAC
1 GCAAAAATGCAAACATGGAC
* * *
1699497 GCAAAAATACAAAAAATGGGAAT
1 GCAAAAATGC-AAACAT-GG-AC
1699520 GCAAAAATGCAAA
1 GCAAAAATGCAAA
1699533 ATGCAAATGC
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
20 28 0.58
21 5 0.10
22 5 0.10
23 10 0.21
ACGTcount: A:0.55, C:0.17, G:0.18, T:0.09
Consensus pattern (20 bp):
GCAAAAATGCAAACATGGAC
Found at i:1700088 original size:29 final size:30
Alignment explanation
Indices: 1700036--1700093 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
1700026 AGCACAAGAT
*
1700036 AAGACAAAAGGAAACCAAGTTAGTAGAAAC
1 AAGACAAAAAGAAACCAAGTTAGTAGAAAC
* *
1700066 AAGACAAAAAG-AATCAAGTTAGTTGAAA
1 AAGACAAAAAGAAACCAAGTTAGTAGAAA
1700094 TGATTAGTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 15 0.60
30 10 0.40
ACGTcount: A:0.57, C:0.10, G:0.19, T:0.14
Consensus pattern (30 bp):
AAGACAAAAAGAAACCAAGTTAGTAGAAAC
Found at i:1702649 original size:20 final size:20
Alignment explanation
Indices: 1702624--1702687 Score: 53
Period size: 20 Copynumber: 3.1 Consensus size: 20
1702614 AAATACACCA
1702624 AAAAATTAAAACTTAAAAAT
1 AAAAATTAAAACTTAAAAAT
* *
1702644 AAAAATGGAAAA-TAACAAAAT
1 AAAAAT-TAAAACTTA-AAAAT
1702665 AAAGACATT-AAACTT-AAAAT
1 AAA-A-ATTAAAACTTAAAAAT
1702685 AAA
1 AAA
1702688 CTGAAATAGG
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
20 16 0.46
21 15 0.43
22 2 0.06
23 2 0.06
ACGTcount: A:0.69, C:0.06, G:0.05, T:0.20
Consensus pattern (20 bp):
AAAAATTAAAACTTAAAAAT
Found at i:1703468 original size:16 final size:16
Alignment explanation
Indices: 1703444--1703483 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
1703434 GGTTGGTGAT
*
1703444 TGGTAGTGACAGGGCA
1 TGGTGGTGACAGGGCA
* *
1703460 TGGTGGTGATAGGGCT
1 TGGTGGTGACAGGGCA
1703476 TGGTGGTG
1 TGGTGGTG
1703484 TTCTAGTTGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.15, C:0.07, G:0.50, T:0.28
Consensus pattern (16 bp):
TGGTGGTGACAGGGCA
Found at i:1708499 original size:61 final size:61
Alignment explanation
Indices: 1708417--1708548 Score: 158
Period size: 61 Copynumber: 2.2 Consensus size: 61
1708407 AAGGACACTA
* * * * *
1708417 AGTGAAGGTGGTGGGTATGACCTTATGTGTCATATCC-AGATTAGAACTAGAGTGTAAACCT
1 AGTGAAGGTTGTGGGCATGACCCTACGTGTCATATCCGA-ATTAGAACTAGAGCGTAAACCT
* * * *
1708478 AGTGTAGGTTGTGGGCATGACCCTACGTGTCATATCCGAATTAGCACTAGAGCGTAATCTT
1 AGTGAAGGTTGTGGGCATGACCCTACGTGTCATATCCGAATTAGAACTAGAGCGTAAACCT
*
1708539 AGTGCAGGTT
1 AGTGAAGGTT
1708549 TAGCACTACG
Statistics
Matches: 60, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
61 59 0.98
62 1 0.02
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.30
Consensus pattern (61 bp):
AGTGAAGGTTGTGGGCATGACCCTACGTGTCATATCCGAATTAGAACTAGAGCGTAAACCT
Found at i:1712548 original size:20 final size:20
Alignment explanation
Indices: 1712523--1712598 Score: 152
Period size: 20 Copynumber: 3.8 Consensus size: 20
1712513 CTACGGAGGT
1712523 GATTCATCTACTTCGAAGGC
1 GATTCATCTACTTCGAAGGC
1712543 GATTCATCTACTTCGAAGGC
1 GATTCATCTACTTCGAAGGC
1712563 GATTCATCTACTTCGAAGGC
1 GATTCATCTACTTCGAAGGC
1712583 GATTCATCTACTTCGA
1 GATTCATCTACTTCGA
1712599 CGGCTTATGG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 56 1.00
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (20 bp):
GATTCATCTACTTCGAAGGC
Found at i:1716463 original size:61 final size:61
Alignment explanation
Indices: 1716382--1716499 Score: 148
Period size: 61 Copynumber: 1.9 Consensus size: 61
1716372 AAGGACACTA
* * * * *
1716382 AGTGAAGGCGGTGGGTATGACCTTATGTGTCATATCC-AGATTAGAACTAGAGTGTAAACCT
1 AGTGAAGGCGGTGGGCATGACCCTACGTATCATATCCGA-ATTAGAACTAGAGCGTAAACCT
* * *
1716443 AGTGTAGGTGGTGGGCATGACCCTACGTATCATATCCGAATTAGCACTAGAGCGTAA
1 AGTGAAGGCGGTGGGCATGACCCTACGTATCATATCCGAATTAGAACTAGAGCGTAA
1716500 TCTTCGTGCA
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
61 47 0.98
62 1 0.02
ACGTcount: A:0.29, C:0.17, G:0.28, T:0.26
Consensus pattern (61 bp):
AGTGAAGGCGGTGGGCATGACCCTACGTATCATATCCGAATTAGAACTAGAGCGTAAACCT
Found at i:1722342 original size:2 final size:2
Alignment explanation
Indices: 1722335--1722388 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
1722325 ATCATAAATA
1722335 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1722377 AT AT AT AT AT AT
1 AT AT AT AT AT AT
1722389 TGTGAAGGGC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1726701 original size:14 final size:13
Alignment explanation
Indices: 1726676--1726700 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1726666 AGAGGAAGCT
1726676 ACAAAAAATTTTC
1 ACAAAAAATTTTC
1726689 ACAAAAAATTTT
1 ACAAAAAATTTT
1726701 TATGCACTAA
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:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (13 bp):
ACAAAAAATTTTC
Found at i:1732266 original size:44 final size:44
Alignment explanation
Indices: 1732209--1732959 Score: 1061
Period size: 44 Copynumber: 17.0 Consensus size: 44
1732199 ATACCATGAG
1732209 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* * **
1732253 TGGAACTTTTCTGCCAATAATGCATTGTTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* *
1732297 TGGCACCTTTCTGCCAATAATACATCGTTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* ** *
1732341 TGGCACCTTTCTACCAATAATGCACCGTTATATATTTTCATTTTTT
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCA--TTTA
* * **
1732387 TGGCACATTTCTACCAATAATGCACTTTTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* *
1732431 TGGCATCTTTCTGCCAATAATGCACTGTTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
** * * *
1732475 TGAAACCTTTCTTCCAATAATGCACCGTTATGCGTTTTCGTTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
*
1732519 TGACACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* * *
1732563 TGGCACCTTTCTACCAATAATGCACCGTTATACATTTTCGTTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* * *
1732607 TGACACCTATCTGCCAGTAATGCACCGTTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* * *
1732651 TGGCACCTTTCTACCAATAATGCACTGTTATGCATTTTTATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
*
1732695 TGGCACCTTTCTGCCAATAATGCATCGTTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* * *
1732739 TGACACATTTCTGCCAATAATGCATCGTTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
** *
1732783 TGGCACCTTTCTGTAAATAATGCACTGTTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* * **
1732827 GGGCACCTTTCTGCCAATAATACATTGTTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* * *
1732871 GGGAACCATTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* *
1732915 TGTCACCTTTCTGCCAATAATGCACTGTTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
1732959 T
1 T
1732960 TTCAGTAGCA
Statistics
Matches: 627, Mismatches: 78, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
44 589 0.94
46 38 0.06
ACGTcount: A:0.25, C:0.22, G:0.12, T:0.41
Consensus pattern (44 bp):
TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
Found at i:1738660 original size:44 final size:44
Alignment explanation
Indices: 1738610--1738874 Score: 422
Period size: 44 Copynumber: 6.0 Consensus size: 44
1738600 ATAGCATGAG
*
1738610 TGGCACCTTTCTGCCAATAATGCACCGTTATGTATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* *
1738654 TGGCACCTTTCTGCCAATAATGCACCATTTTGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* **
1738698 TGGCACCTTTCTACCAATAATGCATTGTTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* * *
1738742 TGGTACCTTTCTACCAATAATGCACTGTTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
*
1738786 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTAA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* *
1738830 TGGTACCTTTCTGCCAATAATGCACTGTTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
1738874 T
1 T
1738875 TTTAGTAACA
Statistics
Matches: 204, Mismatches: 17, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 204 1.00
ACGTcount: A:0.24, C:0.22, G:0.12, T:0.42
Consensus pattern (44 bp):
TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
Found at i:1742156 original size:41 final size:41
Alignment explanation
Indices: 1742111--1742274 Score: 229
Period size: 41 Copynumber: 4.0 Consensus size: 41
1742101 TGGAAGCAAG
* *
1742111 CAATACTTCACCATTCAACTTGATTCGATCATGGTATCATA
1 CAATAATTCACCATTCAACTTGATTCGATCATGGTAACATA
** * * *
1742152 CAATAATTCATGATTCAACTTGATTAGATCATGGGAGCATA
1 CAATAATTCACCATTCAACTTGATTCGATCATGGTAACATA
* *
1742193 CAATAATTCATCATTCAACTTGATTCGAACATGGTAACATA
1 CAATAATTCACCATTCAACTTGATTCGATCATGGTAACATA
*
1742234 CAATAATTCACCATTCAACTTGATTCGATCATTGATAACAT
1 CAATAATTCACCATTCAACTTGATTCGATCA-TGGTAACAT
1742275 GTATTTATTC
Statistics
Matches: 108, Mismatches: 14, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
41 100 0.93
42 8 0.07
ACGTcount: A:0.36, C:0.20, G:0.11, T:0.33
Consensus pattern (41 bp):
CAATAATTCACCATTCAACTTGATTCGATCATGGTAACATA
Found at i:1742317 original size:41 final size:42
Alignment explanation
Indices: 1742261--1742340 Score: 144
Period size: 41 Copynumber: 1.9 Consensus size: 42
1742251 ACTTGATTCG
*
1742261 ATCATTGATAACATGTATTTATTCACAAACCAATTCAATTAT
1 ATCATTGATAACATGTATTAATTCACAAACCAATTCAATTAT
1742303 ATCA-TGATAACATGTATTAATTCACAAACCAATTCAAT
1 ATCATTGATAACATGTATTAATTCACAAACCAATTCAAT
1742341 CTAAATCGAG
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
41 33 0.89
42 4 0.11
ACGTcount: A:0.42, C:0.17, G:0.05, T:0.35
Consensus pattern (42 bp):
ATCATTGATAACATGTATTAATTCACAAACCAATTCAATTAT
Found at i:1752474 original size:36 final size:36
Alignment explanation
Indices: 1752405--1752475 Score: 97
Period size: 36 Copynumber: 2.0 Consensus size: 36
1752395 GAAGGCTAGG
* * *
1752405 ATTCTTACATTTAAAATGTCAATATATGCCTATAGA
1 ATTCTTACATTTAAAATGCCAATATAGGACTATAGA
* *
1752441 ATTCTTATATTTAAAATGCCAATCTAGGACTATAG
1 ATTCTTACATTTAAAATGCCAATATAGGACTATAG
1752476 GGCCACAAAG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (36 bp):
ATTCTTACATTTAAAATGCCAATATAGGACTATAGA
Found at i:1756127 original size:22 final size:23
Alignment explanation
Indices: 1756097--1756140 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
1756087 ACTTGGCTTG
*
1756097 ATTCTAATATAAT-TGAATTTAAA
1 ATTCTAATA-AATGTGAAATTAAA
1756120 ATTC-AATAAATGTGAAATTAA
1 ATTCTAATAAATGTGAAATTAA
1756141 TATTTTGCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 3 0.16
22 12 0.63
23 4 0.21
ACGTcount: A:0.50, C:0.05, G:0.07, T:0.39
Consensus pattern (23 bp):
ATTCTAATAAATGTGAAATTAAA
Done.