Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006607.1 Hibiscus syriacus cultivar Beakdansim tig00016212_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: 1995858
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 8
Found at i:9062 original size:2 final size:2
Alignment explanation
Indices: 9055--9097 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
9045 CCATAAATAA
9055 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
9097 A
1 A
9098 GAAGTGAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:12556 original size:18 final size:18
Alignment explanation
Indices: 12533--12574 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
12523 TGTTTCCAAA
* *
12533 ACTTATCCTACAACAATC
1 ACTTATCCAAAAACAATC
12551 ACTTATCCAAAAACAATC
1 ACTTATCCAAAAACAATC
12569 ACTTAT
1 ACTTAT
12575 TTCTAGGTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.43, C:0.29, G:0.00, T:0.29
Consensus pattern (18 bp):
ACTTATCCAAAAACAATC
Found at i:13711 original size:20 final size:21
Alignment explanation
Indices: 13686--13724 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
13676 ACTTTTTGGG
13686 TCAAAGTCAAC-GGTTAACAA
1 TCAAAGTCAACGGGTTAACAA
13706 TCAAAGTCAACGGGTTAAC
1 TCAAAGTCAACGGGTTAAC
13725 TCGGACGAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.41, C:0.21, G:0.18, T:0.21
Consensus pattern (21 bp):
TCAAAGTCAACGGGTTAACAA
Found at i:21121 original size:27 final size:27
Alignment explanation
Indices: 21061--21114 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
21051 AATTAAATCC
* * *
21061 ATATAAAAATATTGAATTTAGTTTAAA
1 ATATAAAAATAATAAAGTTAGTTTAAA
*
21088 ATATAAAAATAATAAAGTTATTTTAAA
1 ATATAAAAATAATAAAGTTAGTTTAAA
21115 TTTTAAATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.39
Consensus pattern (27 bp):
ATATAAAAATAATAAAGTTAGTTTAAA
Found at i:21481 original size:24 final size:24
Alignment explanation
Indices: 21449--21505 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
21439 ATTATACCAA
* *
21449 TTTCGTTAATTGCCACGTAAGTAG
1 TTTCGTTAATTACCACGTAAGCAG
*
21473 TTTCGTTAATTACCATGTAAGCAG
1 TTTCGTTAATTACCACGTAAGCAG
21497 TTTCGTTAA
1 TTTCGTTAA
21506 ATGTTAACGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.26, C:0.16, G:0.18, T:0.40
Consensus pattern (24 bp):
TTTCGTTAATTACCACGTAAGCAG
Found at i:22207 original size:3 final size:3
Alignment explanation
Indices: 22199--22322 Score: 248
Period size: 3 Copynumber: 41.3 Consensus size: 3
22189 CCCCATGTGT
22199 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
22247 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
22295 CTC CTC CTC CTC CTC CTC CTC CTC CTC C
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC C
22323 AATTGTTTAT
Statistics
Matches: 121, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 121 1.00
ACGTcount: A:0.00, C:0.67, G:0.00, T:0.33
Consensus pattern (3 bp):
CTC
Found at i:38655 original size:54 final size:54
Alignment explanation
Indices: 38571--39095 Score: 513
Period size: 54 Copynumber: 9.7 Consensus size: 54
38561 GAATTGACAT
* *
38571 TGTGTGTGCAACCTAAGAAATTCATTATAAGTTTATGAGTTTCCGTATTGGCAC
1 TGTGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCAC
* **
38625 TGTGTGTGCAACCTAAGAAATTCATAATAAGTTAATGAATTTTTGTATTGGCAC
1 TGTGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCAC
* * *
38679 TGTGTGTGCAACCTAAGAAATTCATAATAAATTTATGAATTTTCGTATAGGCAC
1 TGTGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCAC
* * * ** * *
38733 TGAGTGCGCAACCTAATAAATTCATAATAAGTTTATGAATTTATGTATTAGAAC
1 TGTGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCAC
* * * * * * * *
38787 TCTGCGTGC-ACCATAAGAAATTCATAATAACTTTATGACTTTCCTTTTTTGAAC
1 TGTGTGTGCAACC-TAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCAC
* * **
38841 TATGTGTGCAACCTAAGAAATTCATAATAAGTTTATAAATTTCATTATTGGCAC
1 TGTGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCAC
*** * *
38895 TGTGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTTTTATTGCCAT
1 TGTGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCAC
* *** **
38949 TGTGTGTGCAATCC-ACGAAATTCATAATAAGTTTATGAACGACCGTATCAGCAC
1 TGTGTGTGCAA-CCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCAC
** * *** **
39003 TAAGTGTGCAACCCACA-AAATTCATAATATA-TTTATGAACGACCGTATCAGCAC
1 TGTGTGTGCAACCTA-AGAAATTCATAATA-AGTTTATGAATTTCCGTATTGGCAC
** *
39057 TAAGTGTGCAACCCACA-AAATTCATAATATA-TTTATGAA
1 TGTGTGTGCAACCTA-AGAAATTCATAATA-AGTTTATGAA
39096 CGACTGTATC
Statistics
Matches: 406, Mismatches: 59, Indels: 12
0.85 0.12 0.03
Matches are distributed among these distances:
53 5 0.01
54 395 0.97
55 6 0.01
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (54 bp):
TGTGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCAC
Found at i:39096 original size:54 final size:54
Alignment explanation
Indices: 38952--39138 Score: 272
Period size: 54 Copynumber: 3.5 Consensus size: 54
38942 TTGCCATTGT
* *
38952 GTGTGCAATCCACGAAATTCATAATA-AGTTTATGAACGACCGTATCAGCACTAA
1 GTGTGCAACCCACAAAATTCATAATATA-TTTATGAACGACCGTATCAGCACTAA
39006 GTGTGCAACCCACAAAATTCATAATATATTTATGAACGACCGTATCAGCACTAA
1 GTGTGCAACCCACAAAATTCATAATATATTTATGAACGACCGTATCAGCACTAA
* *
39060 GTGTGCAACCCACAAAATTCATAATATATTTATGAACGACTGTATC-GACACTAT
1 GTGTGCAACCCACAAAATTCATAATATATTTATGAACGACCGTATCAG-CACTAA
* *
39114 GTGTGCACCCCAAAGAAATT-ATAAT
1 GTGTGCAACCCACA-AAATTCATAAT
39139 GTTATGAAAA
Statistics
Matches: 124, Mismatches: 6, Indels: 6
0.91 0.04 0.04
Matches are distributed among these distances:
53 1 0.01
54 117 0.94
55 6 0.05
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.27
Consensus pattern (54 bp):
GTGTGCAACCCACAAAATTCATAATATATTTATGAACGACCGTATCAGCACTAA
Found at i:52377 original size:138 final size:138
Alignment explanation
Indices: 52038--52378 Score: 368
Period size: 138 Copynumber: 2.5 Consensus size: 138
52028 AGGGGGATTC
* * * *
52038 TTAATTTGGTCTTCACTTTTGCTCGAGGTTGCATTTTAATTATTCAATCCAA-AATTTGGTTAAA
1 TTAATTTGGTCATCGCTTTTGCTCGAGGTTCCATTTTAATTATTCGATCCAATAA-TTGGTTAAA
* * * *
52102 ATTTACTAGGTTAATAATTCAGGCCTCCATTTTAGATTTAATTTCAAACCTAGTCCTTTAGTTTA
65 ATTAACTAGGTTAATAATTCAGGCATCCAGTTTAGATTTAATTTCAAACCTAGTCCTTTAGTTCA
* *
52167 GGAGAATTT
130 AGAGAATTA
* * * * * *
52176 TTAATTTAGTCATCGCTTGTGCTCAAGGTTCCATTTTAATTATAT-GATTCAATAATCGATTAAA
1 TTAATTTGGTCATCGCTTTTGCTCGAGGTTCCATTTTAATTAT-TCGATCCAATAATTGGTTAAA
** * * * **
52240 ATTAACTAGGTTAATTGTT-AGAGCATTCAGTTTA-TTCTTAATTTCATATTTAGTCCTTTTA-T
65 ATTAACTAGGTTAATAATTCAG-GCATCCAGTTTAGAT-TTAATTTCAAACCTAGTCC-TTTAGT
*
52302 TCAATAGAATTA
127 TCAAGAGAATTA
* *
52314 TTAATTTGGTCCTCGCTTTTGCTCGAGGTTCCATTTTAATTATTCGATCCAATCATTGGTTAAAA
1 TTAATTTGGTCATCGCTTTTGCTCGAGGTTCCATTTTAATTATTCGATCCAATAATTGGTTAAAA
52379 ATTGATCATA
Statistics
Matches: 165, Mismatches: 32, Indels: 12
0.79 0.15 0.06
Matches are distributed among these distances:
137 4 0.02
138 154 0.93
139 7 0.04
ACGTcount: A:0.28, C:0.14, G:0.13, T:0.44
Consensus pattern (138 bp):
TTAATTTGGTCATCGCTTTTGCTCGAGGTTCCATTTTAATTATTCGATCCAATAATTGGTTAAAA
TTAACTAGGTTAATAATTCAGGCATCCAGTTTAGATTTAATTTCAAACCTAGTCCTTTAGTTCAA
GAGAATTA
Found at i:62334 original size:30 final size:30
Alignment explanation
Indices: 62276--62344 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
62266 AATAATCCAC
* * *
62276 AACTTTTCAAAAATTACCTATTTGGTCCCCT
1 AACTTTTCAAAAAGTA-CTATATGGTCCCCA
62307 AACTTTTCAAAAAGTA-TATAATGGTCCCCA
1 AACTTTTCAAAAAGTACTAT-ATGGTCCCCA
*
62337 AAATTTTC
1 AACTTTTC
62345 TAAGGCTTGT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 3 0.09
30 15 0.45
31 15 0.45
ACGTcount: A:0.35, C:0.22, G:0.07, T:0.36
Consensus pattern (30 bp):
AACTTTTCAAAAAGTACTATATGGTCCCCA
Found at i:66966 original size:21 final size:20
Alignment explanation
Indices: 66938--66978 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
66928 CATTATAGGA
* *
66938 ATTTATGGTCTCGACAAAAG
1 ATTTATGGCCTCAACAAAAG
66958 ATTTCATGGCCTCAACAAAAG
1 ATTT-ATGGCCTCAACAAAAG
66979 CCTTGATGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.27
Consensus pattern (20 bp):
ATTTATGGCCTCAACAAAAG
Found at i:67575 original size:16 final size:17
Alignment explanation
Indices: 67544--67579 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
67534 ATACCTAGGA
67544 AGTAATGAAACTTTACC
1 AGTAATGAAACTTTACC
*
67561 AGTAAT-AATCTTTACC
1 AGTAATGAAACTTTACC
67577 AGT
1 AGT
67580 GAAACCTTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (17 bp):
AGTAATGAAACTTTACC
Found at i:67591 original size:14 final size:14
Alignment explanation
Indices: 67549--67591 Score: 50
Period size: 16 Copynumber: 2.9 Consensus size: 14
67539 TAGGAAGTAA
67549 TGAAACTTTACCAG
1 TGAAACTTTACCAG
*
67563 TAATAATCTTTACCAG
1 TGA-AA-CTTTACCAG
*
67579 TGAAACCTTACCA
1 TGAAACTTTACCA
67592 TATGCATGCA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
14 9 0.38
15 4 0.17
16 11 0.46
ACGTcount: A:0.37, C:0.23, G:0.09, T:0.30
Consensus pattern (14 bp):
TGAAACTTTACCAG
Found at i:77040 original size:16 final size:16
Alignment explanation
Indices: 77019--77120 Score: 55
Period size: 16 Copynumber: 6.1 Consensus size: 16
77009 ATAGTTGAAT
77019 AAAAGGAAAAAAGAAA
1 AAAAGGAAAAAAGAAA
77035 AAAAGGAAAATAA-AAA
1 AAAAGGAAAA-AAGAAA
* * *
77051 TAAAATAGAAAAAATAGA
1 -AAAA-GGAAAAAAGAAA
**
77069 AAAAGTG-AAAAAGTGA
1 AAAAG-GAAAAAAGAAA
*
77085 AAAAGTGAAAAGAGAAA
1 AAAAG-GAAAAAAGAAA
* * *
77102 GAAAAAGAGAGAAGAAA
1 -AAAAGGAAAAAAGAAA
77119 AA
1 AA
77121 TAAAAATAGG
Statistics
Matches: 67, Mismatches: 12, Indels: 14
0.72 0.13 0.15
Matches are distributed among these distances:
16 29 0.43
17 27 0.40
18 11 0.16
ACGTcount: A:0.74, C:0.00, G:0.20, T:0.07
Consensus pattern (16 bp):
AAAAGGAAAAAAGAAA
Found at i:77096 original size:7 final size:8
Alignment explanation
Indices: 77067--77095 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
77057 AGAAAAAATA
77067 GAAAAAGT
1 GAAAAAGT
77075 GAAAAAGT
1 GAAAAAGT
77083 GAAAAAGT
1 GAAAAAGT
77091 GAAAA
1 GAAAA
77096 GAGAAAGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.66, C:0.00, G:0.24, T:0.10
Consensus pattern (8 bp):
GAAAAAGT
Found at i:77114 original size:14 final size:13
Alignment explanation
Indices: 77092--77120 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
77082 TGAAAAAGTG
77092 AAAAGAGA-AAGA
1 AAAAGAGAGAAGA
77104 AAAAGAGAGAAGA
1 AAAAGAGAGAAGA
77117 AAAA
1 AAAA
77121 TAAAAATAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (13 bp):
AAAAGAGAGAAGA
Found at i:77116 original size:19 final size:19
Alignment explanation
Indices: 77083--77126 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
77073 GTGAAAAAGT
* *
77083 GAAAAAGTGAAAAGAGAAA
1 GAAAAAGAGAAAAGAAAAA
*
77102 GAAAAAGAGAGAAGAAAAA
1 GAAAAAGAGAAAAGAAAAA
*
77121 TAAAAA
1 GAAAAA
77127 TAGGGTTCAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.73, C:0.00, G:0.23, T:0.05
Consensus pattern (19 bp):
GAAAAAGAGAAAAGAAAAA
Found at i:79334 original size:37 final size:37
Alignment explanation
Indices: 79265--79361 Score: 106
Period size: 37 Copynumber: 2.6 Consensus size: 37
79255 AAATATAATT
* * * * *
79265 TTGAAATTGTTTCTCTCGAAACAAATTTTTATCTCAC
1 TTGAGATTATTTCTCTTGAAACAAAATGTTATCTCAC
* *
79302 TTGAGATTATTTCTCTTGAAATAAAATGTTATCTCGC
1 TTGAGATTATTTCTCTTGAAACAAAATGTTATCTCAC
*
79339 ATGAGA-TAGTTTCTCTTGAAACA
1 TTGAGATTA-TTTCTCTTGAAACA
79362 CAAACTTTAA
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
36 2 0.04
37 48 0.96
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.41
Consensus pattern (37 bp):
TTGAGATTATTTCTCTTGAAACAAAATGTTATCTCAC
Found at i:82484 original size:12 final size:12
Alignment explanation
Indices: 82467--82494 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
82457 TAGATTATTC
82467 TTCCAATACTAA
1 TTCCAATACTAA
82479 TTCCAATACTAA
1 TTCCAATACTAA
82491 TTCC
1 TTCC
82495 TTGGAGCTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.36, C:0.29, G:0.00, T:0.36
Consensus pattern (12 bp):
TTCCAATACTAA
Found at i:88605 original size:119 final size:118
Alignment explanation
Indices: 88393--88681 Score: 284
Period size: 116 Copynumber: 2.5 Consensus size: 118
88383 TTTACAAACT
* * * * *
88393 CAAATCCATCATAGAAGGAGGTGGATTAACATTTCCAATGAAGAATTCATAATGAGAATGACTCA
1 CAAATCCATCAGAGAAGGAGGTGGATCAACATTTCCAATGAAGAACTCATAATGAGAATAAATCA
* * *
88458 TCTGAAGAGGGAGAAGAAGTTCAAAATGAGAAGAACTTGTTTGAACTTTTATA
66 TCGGAAGAAGGAGAAAAAGTTCAAAATGAGAAGAACTTGTTTGAACTTTTATA
* * * **
88511 CAAATCCCTCAGAGAAGGAGGTGGGTCAACATTTCCAATTGAGGGGCTCATAATGAG-ATAAAAT
1 CAAATCCATCAGAGAAGGAGGTGGATCAACATTTCCAA-TGAAGAACTCATAATGAGAAT-AAAT
* * * *
88575 CGTCGGAAGAATGAGAAAAAGTTCATAAT--G-AGAACTTGTTT-AACCTTTTGCT-
64 CATCGGAAGAAGGAGAAAAAGTTCAAAATGAGAAGAACTTGTTTGAA-CTTTT-ATA
* * * * * **
88627 TAAATCCATCACAGAAGGAGGTGAATCAACATTTTCAACGAAGAGTTCATAATGA
1 CAAATCCATCAGAGAAGGAGGTGGATCAACATTTCCAATGAAGAACTCATAATGA
88682 CAAGAACTTA
Statistics
Matches: 140, Mismatches: 27, Indels: 11
0.79 0.15 0.06
Matches are distributed among these distances:
115 15 0.11
116 48 0.34
117 2 0.01
118 36 0.26
119 39 0.28
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.26
Consensus pattern (118 bp):
CAAATCCATCAGAGAAGGAGGTGGATCAACATTTCCAATGAAGAACTCATAATGAGAATAAATCA
TCGGAAGAAGGAGAAAAAGTTCAAAATGAGAAGAACTTGTTTGAACTTTTATA
Found at i:88831 original size:3 final size:3
Alignment explanation
Indices: 88823--88860 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
88813 ATATGTATAT
88823 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
88861 TACATAAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:90036 original size:17 final size:16
Alignment explanation
Indices: 90014--90069 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 16
90004 TTACCTTCAT
90014 TTTTAATTTTCCATTTA
1 TTTTAATTTTCC-TTTA
*
90031 TTTTAATTTTTACCTTCA
1 TTTTAA-TTTT-CCTTTA
90049 TTTTAATTTTCCTTTTA
1 TTTTAATTTTCC-TTTA
90066 TTTT
1 TTTT
90070 GCATGTAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
16 2 0.06
17 17 0.50
18 13 0.38
19 2 0.06
ACGTcount: A:0.20, C:0.12, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTTAATTTTCCTTTA
Found at i:90037 original size:36 final size:35
Alignment explanation
Indices: 89997--90069 Score: 119
Period size: 35 Copynumber: 2.1 Consensus size: 35
89987 TGTCACTTAC
89997 TTAATCTTTACCTTCATTTTTAATTTTCCATTTATT
1 TTAATCTTTACCTTCA-TTTTAATTTTCCATTTATT
* *
90033 TTAATTTTTACCTTCATTTTAATTTTCCTTTTATT
1 TTAATCTTTACCTTCATTTTAATTTTCCATTTATT
90068 TT
1 TT
90070 GCATGTAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
35 20 0.57
36 15 0.43
ACGTcount: A:0.21, C:0.15, G:0.00, T:0.64
Consensus pattern (35 bp):
TTAATCTTTACCTTCATTTTAATTTTCCATTTATT
Found at i:94232 original size:20 final size:20
Alignment explanation
Indices: 94165--94234 Score: 58
Period size: 20 Copynumber: 3.6 Consensus size: 20
94155 GAATGTTTGA
94165 GATCGATCTTTTAAGCAAGG
1 GATCGATCTTTTAAGCAAGG
* * * *
94185 AATTG-TTTTTTTAG---GG
1 GATCGATCTTTTAAGCAAGG
*
94201 GGTCGATCCTTTTAAGCAAGG
1 GATCGAT-CTTTTAAGCAAGG
94222 GATCGATCTTTTA
1 GATCGATCTTTTA
94235 TTTTTTGGAA
Statistics
Matches: 35, Mismatches: 10, Indels: 10
0.64 0.18 0.18
Matches are distributed among these distances:
16 4 0.11
17 1 0.03
18 6 0.17
19 7 0.20
20 9 0.26
21 8 0.23
ACGTcount: A:0.24, C:0.13, G:0.24, T:0.39
Consensus pattern (20 bp):
GATCGATCTTTTAAGCAAGG
Found at i:97967 original size:40 final size:42
Alignment explanation
Indices: 97921--98026 Score: 128
Period size: 40 Copynumber: 2.6 Consensus size: 42
97911 AGATCCATAC
*
97921 CTTAGTGGCGTTTGTT-ATAAAAACGTAGAAATAGAGGC-AA-
1 CTTAGTGGCGTTTGTTAAT-AAAACGCAGAAATAGAGGCGAAT
* * *
97961 CTTAGTGGCGTTTGTTAATAAAATGCCGCAATAGAGGCGAAT
1 CTTAGTGGCGTTTGTTAATAAAACGCAGAAATAGAGGCGAAT
* *
98003 CTTAGTGGCGTTTGTCACTAAAAC
1 CTTAGTGGCGTTTGTTAATAAAAC
98027 ACCGCTATAT
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
40 31 0.55
41 4 0.07
42 21 0.38
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.29
Consensus pattern (42 bp):
CTTAGTGGCGTTTGTTAATAAAACGCAGAAATAGAGGCGAAT
Found at i:98017 original size:42 final size:42
Alignment explanation
Indices: 97919--98163 Score: 210
Period size: 42 Copynumber: 5.9 Consensus size: 42
97909 AAAGATCCAT
** *
97919 ACCTTAGTGGCGTTTGTT-ATAAAAACGTAGAAATAGAGGC-A
1 ACCTTAGTGGCGTTTGTTAAT-AAAACGCCGCAATAGAGGCGA
*
97960 A-CTTAGTGGCGTTTGTTAATAAAATGCCGCAATAGAGGCGA
1 ACCTTAGTGGCGTTTGTTAATAAAACGCCGCAATAGAGGCGA
* * * * * * * *
98001 ATCTTAGTGGCGTTTGTCACTAAAACACCGCTATATAGTCGT
1 ACCTTAGTGGCGTTTGTTAATAAAACGCCGCAATAGAGGCGA
* *
98043 ACCTTTGTGGCGTTTGTT-ATAAAAACGCCGCAATAGAGACGA
1 ACCTTAGTGGCGTTTGTTAAT-AAAACGCCGCAATAGAGGCGA
* *** * * * *
98085 ACCATAGTTATGTTTGGTATTAAAATGCCGCAATAGAGGCAA
1 ACCTTAGTGGCGTTTGTTAATAAAACGCCGCAATAGAGGCGA
* * * *
98127 ACCTTAGTGGCATTCGGTATTAAAACGCCGCAATAGA
1 ACCTTAGTGGCGTTTGTTAATAAAACGCCGCAATAGA
98164 TCCATAACTT
Statistics
Matches: 161, Mismatches: 38, Indels: 9
0.77 0.18 0.04
Matches are distributed among these distances:
40 31 0.19
41 6 0.04
42 123 0.76
43 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (42 bp):
ACCTTAGTGGCGTTTGTTAATAAAACGCCGCAATAGAGGCGA
Found at i:98182 original size:126 final size:126
Alignment explanation
Indices: 97911--98186 Score: 303
Period size: 126 Copynumber: 2.2 Consensus size: 126
97901 AAGGTGTTAA
* * * * *
97911 AGATCCATACCTTAGTGGCGTTTGTTATAAAAACGTAGAAATAGAGGCAACTTAGTGGCGTTTGT
1 AGATCCATACCTTAGTGGCGTTTGTTATAAAAACGCAGAAATAGAGACAACATAGTGACGTTTGG
* * * *
97976 TAATAAAATGCCGCAATAGAGGCGAATCTTAGTGGCGTTTGTCACTAAAACACCGCTATAT
66 TAATAAAATGCCGCAATAGAGGCAAACCTTAGTGGCATTGGTCACTAAAACACCGCTATAT
* * * * * *
98037 AG-T-CGTACCTTTGTGGCGTTTGTTATAAAAACGCCGCAATAGAGACGAACCATAGTTATGTTT
1 AGATCCATACCTTAGTGGCGTTTGTTATAAAAACGCAGAAATAGAGAC-AA-CATAGTGACGTTT
* * *
98100 GGTATTAAAATGCCGCAATAGAGGCAAACCTTAGTGGCATTCGGT-ATTAAAACGCCGC-A-AT
64 GGTAATAAAATGCCGCAATAGAGGCAAACCTTAGTGGCATT-GGTCACTAAAACACCGCTATAT
*
98161 AGATCCATAACTTAGCT-GCGTTTGTT
1 AGATCCATACCTTAG-TGGCGTTTGTT
98187 GTTGAAACGC
Statistics
Matches: 123, Mismatches: 21, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
124 41 0.33
125 5 0.04
126 74 0.60
127 3 0.02
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (126 bp):
AGATCCATACCTTAGTGGCGTTTGTTATAAAAACGCAGAAATAGAGACAACATAGTGACGTTTGG
TAATAAAATGCCGCAATAGAGGCAAACCTTAGTGGCATTGGTCACTAAAACACCGCTATAT
Found at i:98385 original size:21 final size:21
Alignment explanation
Indices: 98343--98385 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
98333 TCGGCACGCT
* * *
98343 AGTCACTACCGTCGCGTCGCC
1 AGTCACCACCGTCACATCGCC
*
98364 AGTCACCACCGTCACATTGCC
1 AGTCACCACCGTCACATCGCC
98385 A
1 A
98386 TGATCTCCTC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.21, C:0.42, G:0.19, T:0.19
Consensus pattern (21 bp):
AGTCACCACCGTCACATCGCC
Found at i:104228 original size:12 final size:12
Alignment explanation
Indices: 104211--104235 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
104201 AGCCAAAGAA
104211 AATCTCCATGTG
1 AATCTCCATGTG
104223 AATCTCCATGTG
1 AATCTCCATGTG
104235 A
1 A
104236 CTTTGCAGGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (12 bp):
AATCTCCATGTG
Found at i:114801 original size:21 final size:21
Alignment explanation
Indices: 114775--114837 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
114765 AGCCGAAGCT
* *
114775 GAAGTGAAAGAAGCAGAGAGA
1 GAAGTGAGAGAACCAGAGAGA
*
114796 GAAGTGAGATAACCAGAGAGA
1 GAAGTGAGAGAACCAGAGAGA
* *
114817 AAAGCGAGAGAACCAGAGAGA
1 GAAGTGAGAGAACCAGAGAGA
114838 AAAACAACAT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.51, C:0.10, G:0.35, T:0.05
Consensus pattern (21 bp):
GAAGTGAGAGAACCAGAGAGA
Found at i:115312 original size:43 final size:44
Alignment explanation
Indices: 115264--115348 Score: 127
Period size: 44 Copynumber: 2.0 Consensus size: 44
115254 CTCCACTACA
*
115264 TATCAAATCTATTGCGGCA-TTTGTGACTACAAACACCGCTATT
1 TATCAAATATATTGCGGCATTTTGTGACTACAAACACCGCTATT
* * *
115307 TATCAAATATATTGCGGCATTTTTTTACTACAAACGCCGCTA
1 TATCAAATATATTGCGGCATTTTGTGACTACAAACACCGCTA
115349 AATATTTATT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
43 18 0.49
44 19 0.51
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.34
Consensus pattern (44 bp):
TATCAAATATATTGCGGCATTTTGTGACTACAAACACCGCTATT
Found at i:115364 original size:44 final size:44
Alignment explanation
Indices: 115263--115372 Score: 123
Period size: 44 Copynumber: 2.5 Consensus size: 44
115253 ACTCCACTAC
*
115263 ATATCAAATCTATTGCGGCA-TTTGTGACTACAAACACCGCTAT
1 ATATCAAATCTATTGCGGCATTTTGTGACTACAAACACCGCTAA
* * * * *
115306 TTATCAAATATATTGCGGCATTTTTTTACTACAAACGCCGCTAA
1 ATATCAAATCTATTGCGGCATTTTGTGACTACAAACACCGCTAA
** * *
115350 ATATTTATTCTATTGCGGAATTT
1 ATATCAAATCTATTGCGGCATTT
115373 GTAGTAACAA
Statistics
Matches: 54, Mismatches: 12, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
43 18 0.33
44 36 0.67
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (44 bp):
ATATCAAATCTATTGCGGCATTTTGTGACTACAAACACCGCTAA
Found at i:115995 original size:52 final size:53
Alignment explanation
Indices: 115930--116037 Score: 166
Period size: 52 Copynumber: 2.0 Consensus size: 53
115920 CAGAAGATGG
*
115930 GGCACATAGAAATAAGAA-ACTAGCCTAGAGTTAGGGGATTACAACAAATTACAA
1 GGCACATA-AAAT-AGAAGACTAGACTAGAGTTAGGGGATTACAACAAATTACAA
*
115984 GGCACAT-AAATAGAAGACTAGACTAGAGTTAGGGGATTACAACTAATTACAA
1 GGCACATAAAATAGAAGACTAGACTAGAGTTAGGGGATTACAACAAATTACAA
116036 GG
1 GG
116038 ATATCATAAT
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
51 4 0.08
52 40 0.78
54 7 0.14
ACGTcount: A:0.44, C:0.14, G:0.22, T:0.19
Consensus pattern (53 bp):
GGCACATAAAATAGAAGACTAGACTAGAGTTAGGGGATTACAACAAATTACAA
Found at i:120540 original size:52 final size:53
Alignment explanation
Indices: 120452--120559 Score: 146
Period size: 52 Copynumber: 2.0 Consensus size: 53
120442 CACAAGATGG
* * *
120452 GGCACATAGAAATATGAAACTAGCCTAAAGTCAGGGGATTACAACTAATTGCAA
1 GGCACATA-AAATAGGAAACTAGCCTAAAGTCAGGGGATTAAAACTAATTACAA
* * *
120506 GGCACAT-AAATAGGAGACTAGCCTAGAGTTAGGGGATTAAAACTAATTACAA
1 GGCACATAAAATAGGAAACTAGCCTAAAGTCAGGGGATTAAAACTAATTACAA
120558 GG
1 GG
120560 ATATTATTAT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
52 41 0.85
54 7 0.15
ACGTcount: A:0.42, C:0.15, G:0.23, T:0.20
Consensus pattern (53 bp):
GGCACATAAAATAGGAAACTAGCCTAAAGTCAGGGGATTAAAACTAATTACAA
Found at i:124589 original size:21 final size:21
Alignment explanation
Indices: 124543--124581 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
124533 ATAGAACTTA
*
124543 AATTCAAATATATAAAATAAT
1 AATTAAAATATATAAAATAAT
124564 AATTAAAATATA-AAAATA
1 AATTAAAATATATAAAATA
124582 TCATATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (21 bp):
AATTAAAATATATAAAATAAT
Found at i:126429 original size:92 final size:93
Alignment explanation
Indices: 126281--126486 Score: 283
Period size: 92 Copynumber: 2.2 Consensus size: 93
126271 CTTGCTTCTG
* *
126281 CTTCACTATTC-TTCTGTGAAGGCTGAATCATGAATGACTTGGACAGAATCTGTTTCACTATTCT
1 CTTCACTACTCTTTC-GTGAAGGCTGAAT-ATGAATGACTTGGACAGAATCTGTTTCACTACTCT
* *
126345 TTCGTGAAGATCAGACTTGAAATTGGATTA
64 TCCGTGAAGATCAGACTCGAAATTGGATTA
* *
126375 CTTCACTACTCTTTCGTGAAGGTTGAAT-TGATTGACTTGAGA-AGAATCTGTTTCACTACTCTT
1 CTTCACTACTCTTTCGTGAAGGCTGAATATGAATGACTTG-GACAGAATCTGTTTCACTACTCTT
*
126438 CCGTGAAGATCATACTCGAAATTGGATTA
65 CCGTGAAGATCAGACTCGAAATTGGATTA
* *
126467 CTTTACTACTATTTCGTGAA
1 CTTCACTACTCTTTCGTGAA
126487 TGTTCATACT
Statistics
Matches: 101, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
92 74 0.73
93 2 0.02
94 22 0.22
95 3 0.03
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (93 bp):
CTTCACTACTCTTTCGTGAAGGCTGAATATGAATGACTTGGACAGAATCTGTTTCACTACTCTTC
CGTGAAGATCAGACTCGAAATTGGATTA
Found at i:126660 original size:20 final size:20
Alignment explanation
Indices: 126635--126740 Score: 133
Period size: 20 Copynumber: 5.3 Consensus size: 20
126625 CAAAATATTT
*
126635 ACAAATGACCAGGAGGCTTA
1 ACAAATGACCCGGAGGCTTA
*
126655 ACAAATGACCCTGAGGCTTTA
1 ACAAATGACCCGGAGGC-TTA
*
126676 A-AAATGACCCGGAGGCTTT
1 ACAAATGACCCGGAGGCTTA
*
126695 ACAAATGACCCGGAGGCTTT
1 ACAAATGACCCGGAGGCTTA
* * *
126715 ACAAATGACCCGAAGGATTT
1 ACAAATGACCCGGAGGCTTA
126735 ACAAAT
1 ACAAAT
126741 TCGTGGGAAA
Statistics
Matches: 78, Mismatches: 6, Indels: 4
0.89 0.07 0.05
Matches are distributed among these distances:
19 3 0.04
20 71 0.91
21 4 0.05
ACGTcount: A:0.37, C:0.22, G:0.22, T:0.20
Consensus pattern (20 bp):
ACAAATGACCCGGAGGCTTA
Found at i:126692 original size:40 final size:40
Alignment explanation
Indices: 126632--126740 Score: 164
Period size: 40 Copynumber: 2.7 Consensus size: 40
126622 ACCCAAAATA
* * *
126632 TTTACAAATGACCAGGAGGCTTAACAAATGACCCTGAGGC
1 TTTACAAATGACCCGGAGGCTTTACAAATGACCCGGAGGC
*
126672 TTTAAAAATGACCCGGAGGCTTTACAAATGACCCGGAGGC
1 TTTACAAATGACCCGGAGGCTTTACAAATGACCCGGAGGC
* *
126712 TTTACAAATGACCCGAAGGATTTACAAAT
1 TTTACAAATGACCCGGAGGCTTTACAAAT
126741 TCGTGGGAAA
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 62 1.00
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.22
Consensus pattern (40 bp):
TTTACAAATGACCCGGAGGCTTTACAAATGACCCGGAGGC
Found at i:131389 original size:18 final size:18
Alignment explanation
Indices: 131344--131379 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
131334 CATGCTATGC
131344 AAAATATGAATGTAAATA
1 AAAATATGAATGTAAATA
*
131362 AAAATGTGAATGTAAATA
1 AAAATATGAATGTAAATA
131380 CATGTATGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.14, T:0.28
Consensus pattern (18 bp):
AAAATATGAATGTAAATA
Found at i:135020 original size:11 final size:11
Alignment explanation
Indices: 135004--135028 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
134994 AAATAATAAT
135004 TATTATTATTA
1 TATTATTATTA
135015 TATTATTATTA
1 TATTATTATTA
135026 TAT
1 TAT
135029 AATATATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
TATTATTATTA
Found at i:135035 original size:2 final size:2
Alignment explanation
Indices: 135013--135057 Score: 55
Period size: 2 Copynumber: 25.0 Consensus size: 2
135003 TTATTATTAT
135013 TA TA T- TA T- TA T- TA TA TA -A TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
135051 TA -A TA TA
1 TA TA TA TA
135058 AACGTCACTC
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
1 5 0.13
2 33 0.87
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:135039 original size:6 final size:6
Alignment explanation
Indices: 135013--135057 Score: 55
Period size: 5 Copynumber: 8.3 Consensus size: 6
135003 TTATTATTAT
135013 TATAT- TAT-TA T-TATA TA-ATA TATATA TATATA TATATA TA-ATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
135056 TA
1 TA
135058 AACGTCACTC
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
4 2 0.06
5 17 0.47
6 17 0.47
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (6 bp):
TATATA
Found at i:145453 original size:17 final size:17
Alignment explanation
Indices: 145433--145466 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
145423 TGAGAGTATG
145433 GTTTTATTGAAATCATA
1 GTTTTATTGAAATCATA
145450 GTTTTATTGAAATCATA
1 GTTTTATTGAAATCATA
145467 TTCTTGATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.06, G:0.12, T:0.47
Consensus pattern (17 bp):
GTTTTATTGAAATCATA
Found at i:147026 original size:26 final size:26
Alignment explanation
Indices: 146987--147037 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
146977 AAGTGCATAT
146987 GGTGGGCACAACCTTATGTGTATTAC
1 GGTGGGCACAACCTTATGTGTATTAC
*
147013 GGTGGGCACGACCTTATGTGTATTA
1 GGTGGGCACAACCTTATGTGTATTA
147038 TCACTTTGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.22, C:0.18, G:0.29, T:0.31
Consensus pattern (26 bp):
GGTGGGCACAACCTTATGTGTATTAC
Found at i:150734 original size:18 final size:18
Alignment explanation
Indices: 150713--150769 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
150703 CTAATCTAAA
150713 AAAAAAGAACATGATATG
1 AAAAAAGAACATGATATG
*
150731 AAAAAAGCTA-ATCGA-A--
1 AAAAAAG-AACAT-GATATG
150747 AAAAAAGAACATGATATG
1 AAAAAAGAACATGATATG
150765 AAAAA
1 AAAAA
150770 GCAATATCCT
Statistics
Matches: 31, Mismatches: 2, Indels: 12
0.69 0.04 0.27
Matches are distributed among these distances:
15 3 0.10
16 10 0.32
18 15 0.48
19 3 0.10
ACGTcount: A:0.65, C:0.07, G:0.14, T:0.14
Consensus pattern (18 bp):
AAAAAAGAACATGATATG
Found at i:150736 original size:19 final size:19
Alignment explanation
Indices: 150712--150769 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 19
150702 GCTAATCTAA
150712 AAAAAAAGAACATGATATG
1 AAAAAAAGAACATGATATG
150731 -AAAAAAG--C-T-A-ATCG
1 AAAAAAAGAACATGATAT-G
150745 AAAAAAAAGAACATGATATG
1 -AAAAAAAGAACATGATATG
150765 AAAAA
1 AAAAA
150770 GCAATATCCT
Statistics
Matches: 31, Mismatches: 0, Indels: 16
0.66 0.00 0.34
Matches are distributed among these distances:
13 2 0.06
14 2 0.06
15 1 0.03
16 8 0.26
18 8 0.26
19 6 0.19
20 2 0.06
21 2 0.06
ACGTcount: A:0.66, C:0.07, G:0.14, T:0.14
Consensus pattern (19 bp):
AAAAAAAGAACATGATATG
Found at i:150738 original size:35 final size:34
Alignment explanation
Indices: 150697--150769 Score: 128
Period size: 34 Copynumber: 2.1 Consensus size: 34
150687 TCAAAGGTTG
150697 AAAAAGCTAATCTAAAAAAAAAGAACATGATATGA
1 AAAAAGCTAATC-AAAAAAAAAGAACATGATATGA
*
150732 AAAAAGCTAATCGAAAAAAAAGAACATGATATGA
1 AAAAAGCTAATCAAAAAAAAAGAACATGATATGA
150766 AAAA
1 AAAA
150770 GCAATATCCT
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
34 25 0.68
35 12 0.32
ACGTcount: A:0.64, C:0.08, G:0.12, T:0.15
Consensus pattern (34 bp):
AAAAAGCTAATCAAAAAAAAAGAACATGATATGA
Found at i:153834 original size:24 final size:24
Alignment explanation
Indices: 153807--153861 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
153797 CCATTGATTA
153807 TGGTATCAGTACTACTATGTATAG
1 TGGTATCAGTACTACTATGTATAG
* *
153831 TGGTATCGGTATTACTATGTATAG
1 TGGTATCAGTACTACTATGTATAG
*
153855 GGGTATC
1 TGGTATC
153862 GATACCATGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.25, C:0.11, G:0.25, T:0.38
Consensus pattern (24 bp):
TGGTATCAGTACTACTATGTATAG
Found at i:153862 original size:24 final size:23
Alignment explanation
Indices: 153808--153884 Score: 81
Period size: 24 Copynumber: 3.4 Consensus size: 23
153798 CATTGATTAT
* *
153808 GGTATCAGTACTACTATGTATAGT
1 GGTATCGGTA-TACTATGTATAGG
153832 GGTATCGGTATTACTATGTATAGG
1 GGTATCGGTA-TACTATGTATAGG
*
153856 GGTATC-G-ATACCATGTA-A-G
1 GGTATCGGTATACTATGTATAGG
153875 GGTATCGGTA
1 GGTATCGGTA
153885 CCACTTTAGC
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
19 7 0.15
20 2 0.04
21 9 0.19
22 1 0.02
23 1 0.02
24 27 0.57
ACGTcount: A:0.27, C:0.12, G:0.27, T:0.34
Consensus pattern (23 bp):
GGTATCGGTATACTATGTATAGG
Found at i:156537 original size:21 final size:21
Alignment explanation
Indices: 156511--156583 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
156501 CAATACAAGG
*
156511 GTATCGATACCCATTAAAGTA
1 GTATCGATACCCATTAAAGCA
** *
156532 GTATCGATA-CTGTTAAGAACA
1 GTATCGATACCCATTAA-AGCA
* *
156553 ATATCGATACCCATTGAAGCA
1 GTATCGATACCCATTAAAGCA
156574 GTATCGATAC
1 GTATCGATAC
156584 TATGCTATAG
Statistics
Matches: 40, Mismatches: 10, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
20 5 0.12
21 31 0.77
22 4 0.10
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.27
Consensus pattern (21 bp):
GTATCGATACCCATTAAAGCA
Found at i:162967 original size:59 final size:59
Alignment explanation
Indices: 162888--163120 Score: 331
Period size: 59 Copynumber: 3.9 Consensus size: 59
162878 AAATTACCAA
162888 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAATGTATGAATTTCCAGAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAATGTATGAATTTCCAGAT
* * * *
162947 AGGGCACTTTGTTTGTTAAAATGGTAAGGAAATCATATTAAATGTATGAATTTCCAGGT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAATGTATGAATTTCCAGAT
* * * * * *
163006 GGGGCACTTTGTGTGCTAAAATGGTAAGCAAATCATACTAAGTATATGAATTTTCAAAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAATGTATGAATTTCCAGAT
* * * * *
163065 AGGGCACTTTGTGTGCTAAAATGGTAAGAAAATCATATTTATTGTATGAAATTCCA
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAATGTATGAATTTCCA
163121 ATTGAATTTA
Statistics
Matches: 152, Mismatches: 22, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
59 152 1.00
ACGTcount: A:0.35, C:0.11, G:0.21, T:0.33
Consensus pattern (59 bp):
AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAATGTATGAATTTCCAGAT
Found at i:163098 original size:118 final size:118
Alignment explanation
Indices: 162889--163120 Score: 365
Period size: 118 Copynumber: 2.0 Consensus size: 118
162879 AATTACCAAA
* * *
162889 GGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAATGTATGAATTTCCAGATAGGGCAC
1 GGGCACTTTGTGTGCTAAAATGGTAAGCAAATCATACTAAATATATGAATTTCCAAATAGGGCAC
* * * *
162954 TTTGTTTGTTAAAATGGTAAGGAAATCATATTAAATGTATGAATTTCCAGGTG
66 TTTGTGTGCTAAAATGGTAAGAAAATCATATTAAATGTATGAAATTCCAGGTG
* *
163007 GGGCACTTTGTGTGCTAAAATGGTAAGCAAATCATACTAAGTATATGAATTTTCAAATAGGGCAC
1 GGGCACTTTGTGTGCTAAAATGGTAAGCAAATCATACTAAATATATGAATTTCCAAATAGGGCAC
* *
163072 TTTGTGTGCTAAAATGGTAAGAAAATCATATTTATTGTATGAAATTCCA
66 TTTGTGTGCTAAAATGGTAAGAAAATCATATTAAATGTATGAAATTCCA
163121 ATTGAATTTA
Statistics
Matches: 103, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
118 103 1.00
ACGTcount: A:0.35, C:0.11, G:0.21, T:0.33
Consensus pattern (118 bp):
GGGCACTTTGTGTGCTAAAATGGTAAGCAAATCATACTAAATATATGAATTTCCAAATAGGGCAC
TTTGTGTGCTAAAATGGTAAGAAAATCATATTAAATGTATGAAATTCCAGGTG
Found at i:169272 original size:53 final size:53
Alignment explanation
Indices: 169210--169320 Score: 213
Period size: 53 Copynumber: 2.1 Consensus size: 53
169200 CCATCAGGCA
*
169210 TGTATCGATACCTGTAAACATCGAATTTAATTTGGGTACCGATACCCCAGTAG
1 TGTATCGATACCTGTAAACATCGAAGTTAATTTGGGTACCGATACCCCAGTAG
169263 TGTATCGATACCTGTAAACATCGAAGTTAATTTGGGTACCGATACCCCAGTAG
1 TGTATCGATACCTGTAAACATCGAAGTTAATTTGGGTACCGATACCCCAGTAG
169316 TGTAT
1 TGTAT
169321 TGATGCCCTT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 57 1.00
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.31
Consensus pattern (53 bp):
TGTATCGATACCTGTAAACATCGAAGTTAATTTGGGTACCGATACCCCAGTAG
Found at i:169813 original size:59 final size:59
Alignment explanation
Indices: 169737--170082 Score: 524
Period size: 59 Copynumber: 6.0 Consensus size: 59
169727 AAATTACCAA
*
169737 AGGGCACTTTGTCTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAAAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAAAT
* *
169796 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGATTTTCCAGAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAAAT
* *
169855 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTATATGAATTTTCAAAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAAAT
*
169914 AGGGCACTTTGTGTGCTAAAATGGTAAGG-----A-ACTAAGTGTATGAATTTCCAGAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAAAT
*
169967 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCTAAAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAAAT
* * * * * * *
170026 AGAGCACTTTGTGTTCTAAAATGGTAAGAAAATCATATTGATTGTATGAAATTCCAA
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAA
170083 TTGAATTAAT
Statistics
Matches: 261, Mismatches: 20, Indels: 12
0.89 0.07 0.04
Matches are distributed among these distances:
53 49 0.19
54 1 0.00
58 1 0.00
59 210 0.80
ACGTcount: A:0.35, C:0.11, G:0.22, T:0.32
Consensus pattern (59 bp):
AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAAAT
Found at i:170015 original size:112 final size:114
Alignment explanation
Indices: 169737--170053 Score: 514
Period size: 112 Copynumber: 2.8 Consensus size: 114
169727 AAATTACCAA
* *
169737 AGGGCACTTTGTCTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAAATAGGGCA
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTTCAAATAGGGCA
*
169802 CTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGATTTTCCAGAT
66 CTTTGTGTGCTAAAATGGTAAGG--A--ATACTAAGTGTATGAATTTCCAGAT
*
169855 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTATATGAATTTTCAAATAGGGCA
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTTCAAATAGGGCA
169920 CTTTGTGTGCTAAAATGGTAAGG-A-ACTAAGTGTATGAATTTCCAGAT
66 CTTTGTGTGCTAAAATGGTAAGGAATACTAAGTGTATGAATTTCCAGAT
*
169967 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAA-TTTCTAAATAGAGC
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTTC-AAATAGGGC
*
170031 ACTTTGTGTTCTAAAATGGTAAG
65 ACTTTGTGTGCTAAAATGGTAAG
170054 AAAATCATAT
Statistics
Matches: 191, Mismatches: 7, Indels: 8
0.93 0.03 0.04
Matches are distributed among these distances:
111 4 0.02
112 101 0.53
113 1 0.01
118 85 0.45
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.32
Consensus pattern (114 bp):
AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTTCAAATAGGGCA
CTTTGTGTGCTAAAATGGTAAGGAATACTAAGTGTATGAATTTCCAGAT
Found at i:170035 original size:171 final size:173
Alignment explanation
Indices: 169737--170062 Score: 530
Period size: 171 Copynumber: 1.9 Consensus size: 173
169727 AAATTACCAA
169737 AGGGCACTTTGTCTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAAATAGGGCA
1 AGGGCACTTTGTCTGCTAAAATGGTAAGG--A--ATACTAAGTGTATGAATTTCCAAATAGGGCA
* * *
169802 CTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGATTTTCCAGATAGGGCACTTTGT
62 CTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAAATAGAGCACTTTGT
*
169867 GTGCTAAAATGGTAAGGAAATCATACTAAGTATATGAATTTTCAAAT
127 GTGCTAAAATGGTAAGAAAATCATACTAAGTATATGAATTTTCAAAT
* *
169914 AGGGCACTTTGTGTGCTAAAATGGTAAGG-A-ACTAAGTGTATGAATTTCCAGATAGGGCACTTT
1 AGGGCACTTTGTCTGCTAAAATGGTAAGGAATACTAAGTGTATGAATTTCCAAATAGGGCACTTT
* *
169977 GTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCTAAATAGAGCACTTTGTGTTC
66 GTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAAATAGAGCACTTTGTGTGC
170042 TAAAATGGTAAGAAAATCATA
131 TAAAATGGTAAGAAAATCATA
170063 TTGATTGTAT
Statistics
Matches: 141, Mismatches: 8, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
171 112 0.79
172 1 0.01
177 28 0.20
ACGTcount: A:0.35, C:0.11, G:0.22, T:0.31
Consensus pattern (173 bp):
AGGGCACTTTGTCTGCTAAAATGGTAAGGAATACTAAGTGTATGAATTTCCAAATAGGGCACTTT
GTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAAATAGAGCACTTTGTGTGC
TAAAATGGTAAGAAAATCATACTAAGTATATGAATTTTCAAAT
Found at i:171280 original size:11 final size:11
Alignment explanation
Indices: 171266--171299 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
171256 TTAAAGCGTC
*
171266 AAAAAAGAAG-
1 AAAAAACAAGA
171276 AAAAAACAAGA
1 AAAAAACAAGA
171287 AAAAAACAAGA
1 AAAAAACAAGA
171298 AA
1 AA
171300 CCTCATAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 9 0.41
11 13 0.59
ACGTcount: A:0.82, C:0.06, G:0.12, T:0.00
Consensus pattern (11 bp):
AAAAAACAAGA
Found at i:171289 original size:9 final size:10
Alignment explanation
Indices: 171266--171299 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
171256 TTAAAGCGTC
*
171266 AAAAAAGAAG
1 AAAAAACAAG
171276 AAAAAACAAG
1 AAAAAACAAG
171286 AAAAAAACAAG
1 -AAAAAACAAG
171297 AAA
1 AAA
171300 CCTCATAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 12 0.55
11 10 0.45
ACGTcount: A:0.82, C:0.06, G:0.12, T:0.00
Consensus pattern (10 bp):
AAAAAACAAG
Found at i:185154 original size:14 final size:14
Alignment explanation
Indices: 185132--185170 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
185122 CTTTTTGAAT
*
185132 GGTGATCTTCAAGA
1 GGTGGTCTTCAAGA
185146 GGTGGTCTTCAAGA
1 GGTGGTCTTCAAGA
185160 GGTGGTCTTCA
1 GGTGGTCTTCA
185171 TGCAACAGCC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.21, C:0.15, G:0.33, T:0.31
Consensus pattern (14 bp):
GGTGGTCTTCAAGA
Found at i:185366 original size:27 final size:27
Alignment explanation
Indices: 185332--185389 Score: 116
Period size: 27 Copynumber: 2.1 Consensus size: 27
185322 CACGAGCTGA
185332 TGTGTCCTTGTTTATCAAGAAGGAGGG
1 TGTGTCCTTGTTTATCAAGAAGGAGGG
185359 TGTGTCCTTGTTTATCAAGAAGGAGGG
1 TGTGTCCTTGTTTATCAAGAAGGAGGG
185386 TGTG
1 TGTG
185390 CACTACATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.21, C:0.10, G:0.34, T:0.34
Consensus pattern (27 bp):
TGTGTCCTTGTTTATCAAGAAGGAGGG
Found at i:188149 original size:14 final size:13
Alignment explanation
Indices: 188130--188179 Score: 55
Period size: 14 Copynumber: 3.7 Consensus size: 13
188120 AGAGCTAGGC
188130 AGAGAAGAAAAATG
1 AGAGAAGAAAAA-G
188144 AGAGAAGAAAGAAG
1 AGAGAAGAAA-AAG
* *
188158 AGAAAAGAGAAAG
1 AGAGAAGAAAAAG
*
188171 AAAGAAGAA
1 AGAGAAGAA
188180 GAGAAGAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
13 9 0.30
14 19 0.63
15 2 0.07
ACGTcount: A:0.68, C:0.00, G:0.30, T:0.02
Consensus pattern (13 bp):
AGAGAAGAAAAAG
Found at i:188170 original size:16 final size:16
Alignment explanation
Indices: 188149--188188 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
188139 AAATGAGAGA
188149 AGAAAGAAGAGAA-AAG
1 AGAAAGAA-AGAAGAAG
188165 AGAAAGAAAGAAGAAG
1 AGAAAGAAAGAAGAAG
188181 AG-AAGAAA
1 AGAAAGAAA
188189 TACTCTCGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (16 bp):
AGAAAGAAAGAAGAAG
Found at i:189690 original size:12 final size:12
Alignment explanation
Indices: 189673--189730 Score: 66
Period size: 12 Copynumber: 4.8 Consensus size: 12
189663 TTAAATTAAA
189673 ATTATATTATAT
1 ATTATATTATAT
189685 ATTATA-TATAT
1 ATTATATTATAT
189696 ATATATATATATAT
1 AT-TATAT-TATAT
*
189710 ATT-TATTTATTT
1 ATTATA-TTATAT
189722 ATTATATTA
1 ATTATATTA
189731 CAAGGCAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
11 7 0.17
12 22 0.55
13 4 0.10
14 7 0.17
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
ATTATATTATAT
Found at i:189692 original size:2 final size:2
Alignment explanation
Indices: 189675--189711 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
189665 AAATTAAAAT
189675 TA TA T- TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
189712 TTATTTATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:200976 original size:31 final size:30
Alignment explanation
Indices: 200941--201041 Score: 91
Period size: 31 Copynumber: 3.3 Consensus size: 30
200931 GACTTATTAA
200941 ATATATTTTACTTTTATTTTAATGTAAAAAT
1 ATATATTTTACTTTTATTTTAAT-TAAAAAT
* * *
200972 ATATATTTTTC-TTTATATTCACTT-AAAA-
1 ATATATTTTACTTTTAT-TTTAATTAAAAAT
* *
201000 ATATATTTTATTTTTATCTTAATTTTTAAAAAT
1 ATATATTTTACTTTTATTTTAA---TTAAAAAT
201033 ATATATTTT
1 ATATATTTT
201042 TAAAATATCT
Statistics
Matches: 55, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
28 11 0.20
29 9 0.16
30 6 0.11
31 16 0.29
32 4 0.07
33 9 0.16
ACGTcount: A:0.37, C:0.05, G:0.01, T:0.57
Consensus pattern (30 bp):
ATATATTTTACTTTTATTTTAATTAAAAAT
Found at i:201062 original size:61 final size:59
Alignment explanation
Indices: 200939--201068 Score: 154
Period size: 61 Copynumber: 2.2 Consensus size: 59
200929 AAGACTTATT
* *** *
200939 AAATATATTTTACTTTTATTTTAATGTAAAAATATATATTTTTCTTTATATTCACTTAA
1 AAATATATTTTACTTTTATCTTAATGTAAAAATATATATTTTTAAATATATTAACTTAA
* * *
200998 AAATATATTTTATTTTTATCTTAATTTTTAAAAATATATATTTTTAAAATATCTTAACTT-A
1 AAATATATTTTACTTTTATCTTAA--TGTAAAAATATATATTTTT-AAATATATTAACTTAA
201059 AAATATATTT
1 AAATATATTT
201069 AGATATTTTG
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
59 22 0.37
61 29 0.48
62 9 0.15
ACGTcount: A:0.40, C:0.05, G:0.01, T:0.54
Consensus pattern (59 bp):
AAATATATTTTACTTTTATCTTAATGTAAAAATATATATTTTTAAATATATTAACTTAA
Found at i:201176 original size:29 final size:27
Alignment explanation
Indices: 201102--201176 Score: 66
Period size: 24 Copynumber: 2.7 Consensus size: 27
201092 ATAAATATAT
**
201102 ATATATATTATTAGTATCTTCTATTAAAA
1 ATATAT-TTATTA-TATCTTAAATTAAAA
*
201131 ATATA-TTCTTAT-T-TTAAATTAAAA
1 ATATATTTATTATATCTTAAATTAAAA
201155 ATATATTTTATTATTATCTTAA
1 ATATA-TTTATTA-TATCTTAA
201177 CTTTTAATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
24 14 0.38
25 1 0.03
26 6 0.16
27 6 0.16
28 1 0.03
29 9 0.24
ACGTcount: A:0.41, C:0.05, G:0.01, T:0.52
Consensus pattern (27 bp):
ATATATTTATTATATCTTAAATTAAAA
Found at i:201229 original size:17 final size:17
Alignment explanation
Indices: 201189--201229 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
201179 TTTAATTTTT
*
201189 TTAAAAAATATATTAAT
1 TTAAAAAATATATTAAC
* *
201206 TTCAAAAATATTTTAAC
1 TTAAAAAATATATTAAC
201223 TTAAAAA
1 TTAAAAA
201230 CAATTTTTTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (17 bp):
TTAAAAAATATATTAAC
Found at i:205960 original size:19 final size:20
Alignment explanation
Indices: 205932--205975 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
205922 TTTTCCTTGG
*
205932 CTTTGCTTTTTGCTTTTTGT
1 CTTTGCTTTTTGATTTTTGT
* *
205952 -TTTGGTTTTTTATTTTTGT
1 CTTTGCTTTTTGATTTTTGT
205971 CTTTG
1 CTTTG
205976 AACTCTTTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.02, C:0.09, G:0.16, T:0.73
Consensus pattern (20 bp):
CTTTGCTTTTTGATTTTTGT
Found at i:209984 original size:20 final size:20
Alignment explanation
Indices: 209944--209982 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
209934 CATTGCAGTA
209944 ATTTATGGCTTCAACAAAAG
1 ATTTATGGCTTCAACAAAAG
209964 ATTTCATGGCTTCAACAAA
1 ATTT-ATGGCTTCAACAAA
209983 GACCTTGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31
Consensus pattern (20 bp):
ATTTATGGCTTCAACAAAAG
Found at i:218399 original size:18 final size:18
Alignment explanation
Indices: 218360--218403 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
218350 ATTGGATAAT
* *
218360 GAAGAAAGAAAGGAAGGA
1 GAAGAAAGAAAGAAAGAA
218378 GAAGAAAGAAA-AAAGAA
1 GAAGAAAGAAAGAAAGAA
218395 GGAAGAAAG
1 -GAAGAAAG
218404 GAATAAGGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 4 0.17
18 19 0.83
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (18 bp):
GAAGAAAGAAAGAAAGAA
Found at i:218673 original size:18 final size:19
Alignment explanation
Indices: 218650--218694 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
218640 ACGATGGTGT
218650 TATTATTATTTAAT-AAAA
1 TATTATTATTTAATAAAAA
* *
218668 TATTATGATTTGATAAAAA
1 TATTATTATTTAATAAAAA
218687 TATTATTA
1 TATTATTA
218695 GTAAATGGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 12 0.52
19 11 0.48
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (19 bp):
TATTATTATTTAATAAAAA
Found at i:219691 original size:16 final size:16
Alignment explanation
Indices: 219656--219702 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
219646 AAAAGAAGGT
* *
219656 ATATTATATAATACATA
1 ATATAATATAAT-TATA
219673 ATATAATATAATTATA
1 ATATAATATAATTATA
219689 ATACTAA-ATAATTA
1 ATA-TAATATAATTA
219703 AATTAAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 13 0.48
17 14 0.52
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.40
Consensus pattern (16 bp):
ATATAATATAATTATA
Found at i:219730 original size:14 final size:15
Alignment explanation
Indices: 219700--219744 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 15
219690 TACTAAATAA
219700 TTAAATTAAATTTAT
1 TTAAATTAAATTTAT
219715 TTAAATTAAA-TTAT
1 TTAAATTAAATTTAT
* *
219729 TTATATT-TATTTAT
1 TTAAATTAAATTTAT
219743 TT
1 TT
219745 CGTTTTTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
13 1 0.04
14 16 0.59
15 10 0.37
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TTAAATTAAATTTAT
Found at i:222995 original size:17 final size:17
Alignment explanation
Indices: 222964--223001 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
222954 AAACATATTG
*
222964 AAATTTAAATAATAAATT
1 AAATTAAAATAATAAA-T
222982 AAATTAAAAT-ATAAAT
1 AAATTAAAATAATAAAT
222998 AAAT
1 AAAT
223002 AGTGACTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 5 0.26
17 5 0.26
18 9 0.47
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AAATTAAAATAATAAAT
Found at i:224374 original size:3 final size:3
Alignment explanation
Indices: 224349--224458 Score: 107
Period size: 3 Copynumber: 36.3 Consensus size: 3
224339 ATTTGGGCCT
* * * *
224349 ATA ATA GTA TTA ATA ATA TTA ATA ATA ATA ATA ATA ATA ATA ATA AAA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
224397 ATA AGTA AT- ATA ATA AAA ATA ATA ATA GTA ATAA ATA A-A TATA ATA
1 ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA -ATA ATA
* *
224443 ATG ATA ATA AAA ATA A
1 ATA ATA ATA ATA ATA A
224459 AAAACCCAAT
Statistics
Matches: 87, Mismatches: 15, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
2 3 0.03
3 77 0.89
4 7 0.08
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:228537 original size:21 final size:22
Alignment explanation
Indices: 228511--228591 Score: 78
Period size: 21 Copynumber: 3.8 Consensus size: 22
228501 CAGAACCCCA
*
228511 GGGGGGTATCGATTCCCCT-AT
1 GGGGGGAATCGATTCCCCTCAT
* *
228532 GGGGGGAATCGGTTCCCCTTCAA
1 GGGGGGAATCGATTCCCC-TCAT
* *
228555 AGGGGGAATCGGTT-CCCTCAT
1 GGGGGGAATCGATTCCCCTCAT
*
228576 -GGGGGTATCGATTCCC
1 GGGGGGAATCGATTCCC
228592 TCTGCACCAA
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
20 11 0.22
21 21 0.42
22 4 0.08
23 14 0.28
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.25
Consensus pattern (22 bp):
GGGGGGAATCGATTCCCCTCAT
Found at i:228585 original size:20 final size:21
Alignment explanation
Indices: 228512--228593 Score: 69
Period size: 20 Copynumber: 3.9 Consensus size: 21
228502 AGAACCCCAG
* *
228512 GGGGGTATCGATTCCC-CTAT
1 GGGGGAATCGATTCCCTCAAT
* *
228532 GGGGGGAATCGGTTCCCCTTCAAA
1 -GGGGGAATCGATT-CCC-TCAAT
*
228556 GGGGGAATCGGTTCCCTC-AT
1 GGGGGAATCGATTCCCTCAAT
*
228576 GGGGGTATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
228594 TGCACCAAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
20 17 0.33
21 13 0.25
22 6 0.12
23 13 0.25
24 2 0.04
ACGTcount: A:0.16, C:0.26, G:0.33, T:0.26
Consensus pattern (21 bp):
GGGGGAATCGATTCCCTCAAT
Found at i:232443 original size:22 final size:21
Alignment explanation
Indices: 232401--232440 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
232391 GAGTTTATTT
*
232401 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
232422 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
232441 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:235534 original size:18 final size:19
Alignment explanation
Indices: 235511--235557 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 19
235501 TATTATATCA
*
235511 TTCTTCCTTCTT-CTTTCT
1 TTCTTCCTTCTTCCTTTAT
*
235529 TTCTT-CTTATTCCTTTAT
1 TTCTTCCTTCTTCCTTTAT
*
235547 TTCTTCATTCT
1 TTCTTCCTTCT
235558 CCTATTTTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 5 0.22
18 15 0.65
19 3 0.13
ACGTcount: A:0.06, C:0.28, G:0.00, T:0.66
Consensus pattern (19 bp):
TTCTTCCTTCTTCCTTTAT
Found at i:235814 original size:39 final size:39
Alignment explanation
Indices: 235754--235843 Score: 99
Period size: 39 Copynumber: 2.3 Consensus size: 39
235744 GTGTAATGCG
*
235754 TCTTTGGGGGTAAGAGGAGAGACACATGGACTATAATGAA
1 TCTTT-GGGGTAAGAGGAGAGACACATGGACTACAATGAA
* * * * * **
235794 TCTTTGGGGTTAGGGGAGAGACTCATTGACTGCAATGCG
1 TCTTTGGGGTAAGAGGAGAGACACATGGACTACAATGAA
235833 TCTTTGGGGTA
1 TCTTTGGGGTA
235844 TACTATAGCA
Statistics
Matches: 41, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
39 36 0.88
40 5 0.12
ACGTcount: A:0.26, C:0.12, G:0.34, T:0.28
Consensus pattern (39 bp):
TCTTTGGGGTAAGAGGAGAGACACATGGACTACAATGAA
Found at i:237130 original size:15 final size:15
Alignment explanation
Indices: 237092--237144 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
237082 ATTCGATTGA
*
237092 TTAATTTTTTGCTAT
1 TTAATTTTCTGCTAT
*
237107 TTACA-TTTCAGCTAT
1 TTA-ATTTTCTGCTAT
*
237122 TTAATTTTCTGTTAT
1 TTAATTTTCTGCTAT
237137 TATAATTT
1 T-TAATTT
237145 CTACTTTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
14 1 0.03
15 23 0.74
16 7 0.23
ACGTcount: A:0.25, C:0.09, G:0.06, T:0.60
Consensus pattern (15 bp):
TTAATTTTCTGCTAT
Found at i:237739 original size:140 final size:141
Alignment explanation
Indices: 237365--237756 Score: 395
Period size: 140 Copynumber: 2.8 Consensus size: 141
237355 AAAATTAATG
* *
237365 GAATTTTTAATTTGGTCATCACTTTTGCTTGAGGTTCTATTTTAATTATTCGAATCAAATAATTG
1 GAATTTTTAATTTGGTCATCACTTTTGCTCGAGGTTCCATTTTAATTATTCGAATCAAATAATTG
* * * **
237430 GTT--GTGATTGACTA-GGTTAGCA-ATTAAAGCCTCC--TTTTAGCTTTAATTTCACACTTCGT
66 GTTAAAT-ATTGACTAGGGTTA--ATATTAAAGCCTCCATTTTTAGATTTAATTTCACAATTAAT
**
237489 CCTTAAATTTTGGA
128 AATTAAATTTTGGA
* * * * * *
237503 GAATTTTTAATTTGGTCCTCGCTATTGCTCAAGGTTCCATTGTAATTATTTGAATCAAATAATTG
1 GAATTTTTAATTTGGTCATCACTTTTGCTCGAGGTTCCATTTTAATTATTCGAATCAAATAATTG
* * ** * * ** * * *
237568 GTTAAA-ATTAATTAGGAATATTTTTGGAGCCTCCATTTTTAGGTTTAGTTTCATAATTAATAAT
66 GTTAAATATTGACTAGGGTTAATATTAAAGCCTCCATTTTTAGATTTAATTTCACAATTAATAAT
*
237632 TTAATTTTGGA
131 TAAATTTTGGA
* * * *
237643 GAATTCTTAATTTGGTCATCTCTTTTGCTCGAGGTTCCATTTTAATTACTCGATTC-AATAATTG
1 GAATTTTTAATTTGGTCATCACTTTTGCTCGAGGTTCCATTTTAATTATTCGAATCAAATAATTG
* * *
237707 GTTAAATATTGACCAGGGTTAATACTAAAGCCTACATTTTTAGATTTAAT
66 GTTAAATATTGACTAGGGTTAATATTAAAGCCTCCATTTTTAGATTTAAT
237757 CCCCTAAGTT
Statistics
Matches: 199, Mismatches: 48, Indels: 12
0.77 0.19 0.05
Matches are distributed among these distances:
138 75 0.38
139 17 0.09
140 107 0.54
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.44
Consensus pattern (141 bp):
GAATTTTTAATTTGGTCATCACTTTTGCTCGAGGTTCCATTTTAATTATTCGAATCAAATAATTG
GTTAAATATTGACTAGGGTTAATATTAAAGCCTCCATTTTTAGATTTAATTTCACAATTAATAAT
TAAATTTTGGA
Found at i:243335 original size:27 final size:27
Alignment explanation
Indices: 243303--243366 Score: 92
Period size: 27 Copynumber: 2.4 Consensus size: 27
243293 CAAAAACGTT
243303 AGACCCCCACCAATAGAAGAACTAATC
1 AGACCCCCACCAATAGAAGAACTAATC
* * *
243330 ATACCCCCACCAGTAGAAGAAGTAATC
1 AGACCCCCACCAATAGAAGAACTAATC
*
243357 AGGCCCCCAC
1 AGACCCCCAC
243367 ACATTTTCTT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.39, C:0.36, G:0.14, T:0.11
Consensus pattern (27 bp):
AGACCCCCACCAATAGAAGAACTAATC
Found at i:248646 original size:32 final size:32
Alignment explanation
Indices: 248605--248669 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
248595 CACGACGAGC
*
248605 AACCAAAACTAGATAAGTAGCTATCACTGAGA
1 AACCAAAACTAGACAAGTAGCTATCACTGAGA
*
248637 AACCAAAACTAGACAAGTAGGTATCACTGAGA
1 AACCAAAACTAGACAAGTAGCTATCACTGAGA
248669 A
1 A
248670 GCCACTCCTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.48, C:0.18, G:0.17, T:0.17
Consensus pattern (32 bp):
AACCAAAACTAGACAAGTAGCTATCACTGAGA
Found at i:250188 original size:2 final size:2
Alignment explanation
Indices: 250181--250209 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
250171 TGTTGCAACC
250181 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
250210 TTCGAGGACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:251072 original size:20 final size:21
Alignment explanation
Indices: 251043--251082 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
251033 TAGTTTAAGA
*
251043 TTTATCTTTAGGATTTATCTC
1 TTTATCTTTAGGAATTATCTC
251064 TTTAT-TTTAGGAATTATCT
1 TTTATCTTTAGGAATTATCT
251083 TATACTTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.23, C:0.10, G:0.10, T:0.57
Consensus pattern (21 bp):
TTTATCTTTAGGAATTATCTC
Found at i:254805 original size:22 final size:22
Alignment explanation
Indices: 254780--254821 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
254770 ATTTTTCAGA
* *
254780 TATTTTCTTTCATTAAATTTCT
1 TATTTTATTCCATTAAATTTCT
254802 TATTTTATTCCATTAAATTT
1 TATTTTATTCCATTAAATTT
254822 TTAATATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.26, C:0.12, G:0.00, T:0.62
Consensus pattern (22 bp):
TATTTTATTCCATTAAATTTCT
Found at i:258826 original size:19 final size:19
Alignment explanation
Indices: 258779--258826 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
258769 AAGTTGCTGA
*
258779 CATCATGCCACATTAGATG
1 CATCATGCCCCATTAGATG
258798 CATCATGCCCCATTAGATG
1 CATCATGCCCCATTAGATG
258817 CATCATGCCC
1 CATCATGCCC
258827 ACTAATCCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.27, C:0.33, G:0.15, T:0.25
Consensus pattern (19 bp):
CATCATGCCCCATTAGATG
Found at i:271877 original size:21 final size:21
Alignment explanation
Indices: 271847--271898 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
271837 ATAAGGATGA
* *
271847 GGTGTATCCAATGCTTGGGGT
1 GGTGTGTCCAACGCTTGGGGT
271868 GGTGTGTCCAACGCTTGGGGT
1 GGTGTGTCCAACGCTTGGGGT
*
271889 GGTATGTCCA
1 GGTGTGTCCA
271899 GTGTTTGTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.13, C:0.17, G:0.38, T:0.31
Consensus pattern (21 bp):
GGTGTGTCCAACGCTTGGGGT
Found at i:276547 original size:7 final size:7
Alignment explanation
Indices: 276529--276609 Score: 57
Period size: 7 Copynumber: 12.0 Consensus size: 7
276519 AAATTAAATG
276529 AATAACTA
1 AATAA-TA
276537 AATAATA
1 AATAATA
276544 AAT-AT-
1 AATAATA
276549 AAT-ATA
1 AATAATA
276555 ATATAATA
1 A-ATAATA
*
276563 AATTAT-
1 AATAATA
276569 AAT-ATA
1 AATAATA
276575 AATAATA
1 AATAATA
*
276582 TATAATA
1 AATAATA
*
276589 TATAATA
1 AATAATA
*
276596 TAT-ATA
1 AATAATA
276602 ATATAATA
1 A-ATAATA
276610 CGTAAACTAT
Statistics
Matches: 63, Mismatches: 3, Indels: 14
0.79 0.04 0.17
Matches are distributed among these distances:
5 7 0.11
6 12 0.19
7 32 0.51
8 12 0.19
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (7 bp):
AATAATA
Found at i:276578 original size:16 final size:15
Alignment explanation
Indices: 276541--276607 Score: 82
Period size: 16 Copynumber: 4.3 Consensus size: 15
276531 TAACTAAATA
276541 ATAAATATAATATAAT
1 ATAAATA-AATATAAT
276557 AT-AATAAATTATAAT
1 ATAAATAAA-TATAAT
276572 ATAAATAATATATAAT
1 ATAAATAA-ATATAAT
*
276588 ATATAATATATATAAT
1 ATA-AATAAATATAAT
276604 ATAA
1 ATAA
276608 TACGTAAACT
Statistics
Matches: 46, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
14 2 0.04
15 13 0.28
16 26 0.57
17 5 0.11
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
ATAAATAAATATAAT
Found at i:276626 original size:5 final size:5
Alignment explanation
Indices: 276538--276609 Score: 84
Period size: 5 Copynumber: 15.2 Consensus size: 5
276528 GAATAACTAA
276538 ATAAT A-AAT ATAAT ATAAT ATAAT A-AATT ATAAT ATAA- ATAAT AT-AT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAA-T ATAAT ATAAT ATAAT ATAAT
276585 A-ATAT ATAAT AT-AT ATAAT ATAAT A
1 ATA-AT ATAAT ATAAT ATAAT ATAAT A
276610 CGTAAACTAT
Statistics
Matches: 59, Mismatches: 0, Indels: 16
0.79 0.00 0.21
Matches are distributed among these distances:
4 17 0.29
5 39 0.66
6 3 0.05
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATAAT
Found at i:276658 original size:23 final size:21
Alignment explanation
Indices: 276613--276660 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 21
276603 TATAATACGT
* *
276613 AAACTATATAATATGTTTTCA
1 AAACTATATAATACGTTTCCA
276634 AAACTATATTATATACGTTTCCA
1 AAACTATA-TA-ATACGTTTCCA
276657 AAAC
1 AAAC
276661 GTGCTCAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 8 0.35
22 2 0.09
23 13 0.57
ACGTcount: A:0.44, C:0.15, G:0.04, T:0.38
Consensus pattern (21 bp):
AAACTATATAATACGTTTCCA
Found at i:276685 original size:27 final size:28
Alignment explanation
Indices: 276646--276702 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 28
276636 ACTATATTAT
*
276646 ATACGTTTCC-AAAACGTGCTCAAAACC
1 ATACATTTCCAAAAACGTGCTCAAAACC
* * *
276673 ATACATTTTCAAAAACGTGTTCAAAGCC
1 ATACATTTCCAAAAACGTGCTCAAAACC
276701 AT
1 AT
276703 TATATTATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
27 8 0.32
28 17 0.68
ACGTcount: A:0.39, C:0.25, G:0.11, T:0.26
Consensus pattern (28 bp):
ATACATTTCCAAAAACGTGCTCAAAACC
Found at i:276794 original size:73 final size:72
Alignment explanation
Indices: 276703--276901 Score: 258
Period size: 73 Copynumber: 2.7 Consensus size: 72
276693 TCAAAGCCAT
* *
276703 TATATTATATATG-TTTTCAAAACTATTTTAAAAACTATATATTATACATTTTCAAAACTATTTT
1 TATATAATATATGTTTTTCAAAACTATTTTAAAAACTATATATTATATATTTTCAAAACTATTTT
276767 AAAAAAAC
66 -AAAAAAC
* ** * **
276775 TATATACTATATGTTTTTCAAAACCGTGTTAAAAACTATATATTATATGCTTTCAAAACTATTTT
1 TATATAATATATGTTTTTCAAAACTATTTTAAAAACTATATATTATATATTTTCAAAACTATTTT
276840 AAAAAAC
66 AAAAAAC
* *
276847 TATATAATATATGTTTTTTAAAA-TAAGTTTTCAAAAACGATATATTATATATTTT
1 TATATAATATATGTTTTTCAAAACT-A-TTTT-AAAAACTATATATTATATATTTT
276902 GAAATTATTA
Statistics
Matches: 107, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
72 39 0.36
73 48 0.45
74 20 0.19
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.44
Consensus pattern (72 bp):
TATATAATATATGTTTTTCAAAACTATTTTAAAAACTATATATTATATATTTTCAAAACTATTTT
AAAAAAC
Found at i:276816 original size:36 final size:36
Alignment explanation
Indices: 276710--276901 Score: 210
Period size: 36 Copynumber: 5.3 Consensus size: 36
276700 CATTATATTA
276710 TATATGTTTTCAAAACTATTTT-AAAAACTATATAT
1 TATATGTTTTCAAAACTATTTTAAAAAACTATATAT
** *
276745 TATACATTTTCAAAACTATTTTAAAAAAACTATATAC
1 TATATGTTTTCAAAACTATTTT-AAAAAACTATATAT
** *
276782 TATATGTTTTTCAAAACCGTGTT-AAAAACTATATAT
1 TATATG-TTTTCAAAACTATTTTAAAAAACTATATAT
* *
276818 TATATGCTTTCAAAACTATTTTAAAAAACTATATAA
1 TATATGTTTTCAAAACTATTTTAAAAAACTATATAT
* * *
276854 TATATGTTTTTTAAAA-TAAGTTTTCAAAAACGATATAT
1 TATATG-TTTTCAAAACT-A-TTTTAAAAAACTATATAT
*
276892 TATATATTTT
1 TATATGTTTT
276902 GAAATTATTA
Statistics
Matches: 130, Mismatches: 20, Indels: 12
0.80 0.12 0.07
Matches are distributed among these distances:
35 32 0.25
36 37 0.28
37 28 0.22
38 33 0.25
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.43
Consensus pattern (36 bp):
TATATGTTTTCAAAACTATTTTAAAAAACTATATAT
Found at i:278702 original size:27 final size:25
Alignment explanation
Indices: 278672--278755 Score: 71
Period size: 25 Copynumber: 3.2 Consensus size: 25
278662 ATTTCCTCTC
278672 TTTTTATCTCTCTTTTCTTTTTCTTCA
1 TTTTT-TCTCTCTTTTCTTTTT-TTCA
* * *
278699 TTTTTCTTTCTATTTTTCCTTTTTTC-
1 TTTTT-TCTCT-CTTTTCTTTTTTTCA
* *
278725 TCTTTTCTTTTCTTTTCTTTTTTTCA
1 TTTTTTC-TCTCTTTTCTTTTTTTCA
278751 TTTTT
1 TTTTT
278756 CATTTTTTAT
Statistics
Matches: 44, Mismatches: 10, Indels: 7
0.72 0.16 0.11
Matches are distributed among these distances:
25 13 0.30
26 10 0.23
27 12 0.27
28 9 0.20
ACGTcount: A:0.05, C:0.19, G:0.00, T:0.76
Consensus pattern (25 bp):
TTTTTTCTCTCTTTTCTTTTTTTCA
Found at i:278743 original size:15 final size:14
Alignment explanation
Indices: 278684--278803 Score: 66
Period size: 15 Copynumber: 7.9 Consensus size: 14
278674 TTTATCTCTC
*
278684 TTTTCTTTTTCTTCAT
1 TTTTC-TTTTCTT-TT
278700 TTTTC-TTTCTATTT
1 TTTTCTTTTCT-TTT
*
278714 TTCCTTTTTTCTCTTTT
1 TT--TTCTTT-TCTTTT
278731 CTTTTCTTTTC-TTT
1 -TTTTCTTTTCTTTT
278745 TTTTCATTTTTCATTTT
1 TTTTC--TTTTC-TTTT
*
278762 TTAT-TTTTCTTTT
1 TTTTCTTTTCTTTT
* *
278775 GCTTTCTTTTCTCTAT
1 -TTTTCTTTTCT-TTT
278791 TTTTCTTTTCTTT
1 TTTTCTTTTCTTT
278804 AGGTGTAATT
Statistics
Matches: 82, Mismatches: 9, Indels: 28
0.69 0.08 0.24
Matches are distributed among these distances:
13 9 0.11
14 19 0.23
15 24 0.29
16 14 0.17
17 11 0.13
18 5 0.06
ACGTcount: A:0.05, C:0.17, G:0.01, T:0.77
Consensus pattern (14 bp):
TTTTCTTTTCTTTT
Found at i:278773 original size:39 final size:42
Alignment explanation
Indices: 278682--278799 Score: 126
Period size: 39 Copynumber: 2.9 Consensus size: 42
278672 TTTTTATCTC
* * *
278682 TCTTTTCTTTTTC-TTCATTTTTCTTTCTATTTTTCCTTTTTTC
1 TCTTTTCTTTTGCTTTC--TTTTCTTTCTATTTTTCATTTTTTA
278725 TCTTTTCTTTT-CTTTTCTTTT-TTTC-ATTTTTCATTTTTTA
1 TCTTTTCTTTTGC-TTTCTTTTCTTTCTATTTTTCATTTTTTA
278765 T-TTTTCTTTTGCTTTCTTTTC--TCTATTTTTC-TTTT
1 TCTTTTCTTTTGCTTTCTTTTCTTTCTATTTTTCATTTT
278800 CTTTAGGTGT
Statistics
Matches: 68, Mismatches: 2, Indels: 15
0.80 0.02 0.18
Matches are distributed among these distances:
38 6 0.09
39 24 0.35
40 15 0.22
41 4 0.06
42 5 0.07
43 11 0.16
44 3 0.04
ACGTcount: A:0.05, C:0.18, G:0.01, T:0.76
Consensus pattern (42 bp):
TCTTTTCTTTTGCTTTCTTTTCTTTCTATTTTTCATTTTTTA
Found at i:293950 original size:22 final size:22
Alignment explanation
Indices: 293932--293973 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
293922 TTTATTTATT
*
293932 TATTTATTTATTTGCATTTTTA
1 TATTCATTTATTTGCATTTTTA
* *
293954 TATTCGTTTATTTTCATTTT
1 TATTCATTTATTTGCATTTT
293974 AGCTATTATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.19, C:0.07, G:0.05, T:0.69
Consensus pattern (22 bp):
TATTCATTTATTTGCATTTTTA
Found at i:298494 original size:39 final size:39
Alignment explanation
Indices: 298440--298517 Score: 138
Period size: 39 Copynumber: 2.0 Consensus size: 39
298430 CCCCTCAGCC
298440 CATATCCCTATGTTATGTCGGAAGATGACAGGATATGTG
1 CATATCCCTATGTTATGTCGGAAGATGACAGGATATGTG
* *
298479 CATATCCCTATGTTATGTCGGAAGATGAGATGATATGTG
1 CATATCCCTATGTTATGTCGGAAGATGACAGGATATGTG
298518 GGAAATGACC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.28, C:0.14, G:0.26, T:0.32
Consensus pattern (39 bp):
CATATCCCTATGTTATGTCGGAAGATGACAGGATATGTG
Found at i:305856 original size:120 final size:120
Alignment explanation
Indices: 305691--306220 Score: 702
Period size: 120 Copynumber: 4.4 Consensus size: 120
305681 AAAATAATTT
* *
305691 TTGGATTTCAACTTCACGATGAAGGATATCC-ATATCGAGGCTCAACTTCACGATGAAAGGGCCA
1 TTGGATTTCAACTTCACGACGAAGGATATCCAAT-TCGAGGCTCAACTTCACGACGAAAGGGCCA
* * * *
305755 TCCATGATTTTAACTTCACGACAAAGGATATCGTGTCTATCAGCAATATCTTTAGA
65 TCCACGATTTCAACTTCACGACAAAGGATATCGTGTCCATCAGCAACATCTTTAGA
** * * ***
305811 TTGGATTTCAACTTCACGAAAAAGGATATCCAATTCGAAGTTCAACTTCACGACGAAAGGGTTGT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCGAGGCTCAACTTCACGACGAAAGGGCCAT
*
305876 CCACGATTTCAACTTCACGACAAAGAATATCGTGTCCATCAGCAACATCTTTAGA
66 CCACGATTTCAACTTCACGACAAAGGATATCGTGTCCATCAGCAACATCTTTAGA
* * * * *
305931 TTGGATTTCAACTTCACGACGAAGGATATCCAATTTGAGGCTCAATTTCATGACGAAGGGGCCGT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCGAGGCTCAACTTCACGACGAAAGGGCCAT
* ** *
305996 CCACGATTTCAACTTCACGACGAAGGATATCGTGTCCATCAAAAACATCCTTAGA
66 CCACGATTTCAACTTCACGACAAAGGATATCGTGTCCATCAGCAACATCTTTAGA
* * * *
306051 TTGGATTTTAACTTCACGATGAAGGATATCCAATTCGAGGCTCCACTTCACGACGAAGGGGCCAT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCGAGGCTCAACTTCACGACGAAAGGGCCAT
* * * *
306116 CCATGATTTCAACTTCACAACGAAGGATATCGTGCCCATCAGCAACATCCTTCCTTAGA
66 CCACGATTTCAACTTCACGACAAAGGATATCGTGTCCATCAGCAACAT-C-T--TTAGA
* * *
306175 TTGGATTTCAACTTAACGACGAAGGATATCCAATTCAAAGCTCAAC
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCGAGGCTCAAC
306221 CTCATAGCGA
Statistics
Matches: 358, Mismatches: 47, Indels: 6
0.87 0.11 0.01
Matches are distributed among these distances:
120 310 0.87
121 3 0.01
124 45 0.13
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (120 bp):
TTGGATTTCAACTTCACGACGAAGGATATCCAATTCGAGGCTCAACTTCACGACGAAAGGGCCAT
CCACGATTTCAACTTCACGACAAAGGATATCGTGTCCATCAGCAACATCTTTAGA
Found at i:315114 original size:20 final size:21
Alignment explanation
Indices: 315066--315118 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
315056 TTCAAAGGGT
* *
315066 AGTATCGATACTAATTGAGTA
1 AGTATCGATACTAAATAAGTA
*
315087 AGGTATCGATACTAAATAAG-G
1 A-GTATCGATACTAAATAAGTA
315108 AGTATCGATAC
1 AGTATCGATAC
315119 CAAGGGTATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 10 0.36
21 2 0.07
22 16 0.57
ACGTcount: A:0.40, C:0.11, G:0.21, T:0.28
Consensus pattern (21 bp):
AGTATCGATACTAAATAAGTA
Found at i:319838 original size:14 final size:15
Alignment explanation
Indices: 319821--319875 Score: 55
Period size: 14 Copynumber: 3.8 Consensus size: 15
319811 TTTAAAATTA
319821 TATTATAAAA-AAAT
1 TATTATAAAATAAAT
319835 TATTA-AAAATAAAT
1 TATTATAAAATAAAT
*
319849 TATTGATAATTATAAAT
1 TATT-ATAA-AATAAAT
319866 T-TTA-AAAATA
1 TATTATAAAATA
319876 TTAAAAATTC
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
13 7 0.20
14 15 0.43
15 2 0.06
16 4 0.11
17 7 0.20
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (15 bp):
TATTATAAAATAAAT
Found at i:320032 original size:7 final size:7
Alignment explanation
Indices: 320006--320090 Score: 57
Period size: 7 Copynumber: 12.4 Consensus size: 7
319996 GTTAGATTAC
320006 ACCCTAA
1 ACCCTAA
*
320013 ACTCTAA
1 ACCCTAA
*
320020 A-TCTAA
1 ACCCTAA
320026 ACCCTAA
1 ACCCTAA
*
320033 ACTCTAA
1 ACCCTAA
**
320040 ACTATAA
1 ACCCTAA
* *
320047 ATCTTAA
1 ACCCTAA
*
320054 ACCCTAT
1 ACCCTAA
*
320061 TCCC-AA
1 ACCCTAA
320067 ACCCTAA
1 ACCCTAA
* *
320074 ATCATAA
1 ACCCTAA
320081 ACCCTAA
1 ACCCTAA
320088 ACC
1 ACC
320091 ATAAGCCATA
Statistics
Matches: 59, Mismatches: 17, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
6 10 0.17
7 49 0.83
ACGTcount: A:0.44, C:0.33, G:0.00, T:0.24
Consensus pattern (7 bp):
ACCCTAA
Found at i:320040 original size:14 final size:13
Alignment explanation
Indices: 320009--320088 Score: 72
Period size: 14 Copynumber: 5.9 Consensus size: 13
319999 AGATTACACC
*
320009 CTAAACTCTAAAT
1 CTAAACCCTAAAT
320022 CTAAACCCTAAACT
1 CTAAACCCTAAA-T
**
320036 CTAAACTATAAAT
1 CTAAACCCTAAAT
*
320049 CTTAAACCCT-ATT
1 C-TAAACCCTAAAT
*
320062 CCCAAACCCTAAAT
1 -CTAAACCCTAAAT
320076 CATAAACCCTAAA
1 C-TAAACCCTAAA
320089 CCATAAGCCA
Statistics
Matches: 53, Mismatches: 9, Indels: 9
0.75 0.13 0.13
Matches are distributed among these distances:
13 23 0.43
14 30 0.57
ACGTcount: A:0.45, C:0.30, G:0.00, T:0.25
Consensus pattern (13 bp):
CTAAACCCTAAAT
Found at i:320068 original size:27 final size:27
Alignment explanation
Indices: 320011--320089 Score: 88
Period size: 27 Copynumber: 2.9 Consensus size: 27
320001 ATTACACCCT
*
320011 AAACTCTAAATCTAAACCCTAAACTCT
1 AAACTCTAAATCTAAACCCTAAACTCC
* **
320038 AAACTATAAATCTTAAACCCTATTC-CC
1 AAACTCTAAATC-TAAACCCTAAACTCC
*
320065 AAACCCTAAATCATAAACCCTAAAC
1 AAACTCTAAATC-TAAACCCTAAAC
320090 CATAAGCCAT
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
27 32 0.76
28 10 0.24
ACGTcount: A:0.46, C:0.30, G:0.00, T:0.24
Consensus pattern (27 bp):
AAACTCTAAATCTAAACCCTAAACTCC
Found at i:320093 original size:14 final size:14
Alignment explanation
Indices: 320065--320094 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
320055 CCCTATTCCC
*
320065 AAACCCTAAATCAT
1 AAACCCTAAACCAT
320079 AAACCCTAAACCAT
1 AAACCCTAAACCAT
320093 AA
1 AA
320095 GCCATAAGTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.53, C:0.30, G:0.00, T:0.17
Consensus pattern (14 bp):
AAACCCTAAACCAT
Found at i:320239 original size:21 final size:21
Alignment explanation
Indices: 320215--320262 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
320205 ACCCTAAATT
320215 TTAAACTATAAATCCCAAACC
1 TTAAACTATAAATCCCAAACC
* * * *
320236 TTAAAATCTAAGTCCTAAACC
1 TTAAACTATAAATCCCAAACC
320257 TTAAAC
1 TTAAAC
320263 CCTTAATCCG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.46, C:0.25, G:0.02, T:0.27
Consensus pattern (21 bp):
TTAAACTATAAATCCCAAACC
Found at i:321518 original size:12 final size:11
Alignment explanation
Indices: 321501--321602 Score: 78
Period size: 12 Copynumber: 8.8 Consensus size: 11
321491 GTCGAGCTTG
321501 AATCGAGCTCAA
1 AATCGAGCTC-A
321513 AATCGAGCTTCA
1 AATCGAGC-TCA
**
321525 AATCGAGCTTG
1 AATCGAGCTCA
321536 AATCGAGCTTCA
1 AATCGAGC-TCA
*
321548 ATTCGAGCTTCA
1 AATCGAGC-TCA
* **
321560 ATTCGAGCTTG
1 AATCGAGCTCA
**
321571 AATCGAGCTTG
1 AATCGAGCTCA
321582 AATCGAGCTTCA
1 AATCGAGC-TCA
*
321594 ATTCGAGCT
1 AATCGAGCT
321603 TAAAATCAAG
Statistics
Matches: 76, Mismatches: 11, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
11 29 0.38
12 45 0.59
13 2 0.03
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (11 bp):
AATCGAGCTCA
Found at i:321518 original size:23 final size:22
Alignment explanation
Indices: 321492--321638 Score: 123
Period size: 23 Copynumber: 6.4 Consensus size: 22
321482 ATAAAACCCG
321492 TCGAGCTTGAATCGAGCTCAAAA
1 TCGAGCTTGAATCGAGCT-AAAA
* **
321515 TCGAGCTTCAAATCGAGCTTGAA
1 TCGAGCTT-GAATCGAGCTAAAA
* * *
321538 TCGAGCTTCAATTCGAGCTTCAAT
1 TCGAGCTTGAA-TCGAGC-TAAAA
**
321562 TCGAGCTTGAATCGAGCTTGAA
1 TCGAGCTTGAATCGAGCTAAAA
*
321584 TCGAGCTTCAATTCGAGCTTAAAA
1 TCGAGCTTGAA-TCGAGC-TAAAA
* **
321608 TCAAGCTTGAATCGAAATTAAAA
1 TCGAGCTTGAATCG-AGCTAAAA
321631 TCGAGCTT
1 TCGAGCTT
321639 CAGTCGAGTT
Statistics
Matches: 99, Mismatches: 19, Indels: 12
0.76 0.15 0.09
Matches are distributed among these distances:
22 14 0.14
23 51 0.52
24 34 0.34
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (22 bp):
TCGAGCTTGAATCGAGCTAAAA
Found at i:321622 original size:35 final size:34
Alignment explanation
Indices: 321492--321673 Score: 186
Period size: 35 Copynumber: 5.2 Consensus size: 34
321482 ATAAAACCCG
** *
321492 TCGAGCTTGAATCGAGCTCAAAATCGAGCTTCAAA
1 TCGAGCTTGAATCGAGCT-TGAATCGAGCTTCAAT
*
321527 TCGAGCTTGAATCGAGCTTCAATTCGAGCTTCAAT
1 TCGAGCTTGAATCGAGCTTGAA-TCGAGCTTCAAT
321562 TCGAGCTTGAATCGAGCTTGAATCGAGCTTCAAT
1 TCGAGCTTGAATCGAGCTTGAATCGAGCTTCAAT
* * ** * *
321596 TCGAGCTTAAAATCAAGCTTGAATCGAAATTAAAA
1 TCGAGCTT-GAATCGAGCTTGAATCGAGCTTCAAT
* * * *
321631 TCGAGCTTCAGTCGAGTTTGAGTCTCGAGCTTCAAT
1 TCGAGCTTGAATCGAGCTTGA--ATCGAGCTTCAAT
321667 T-GAGCTT
1 TCGAGCTT
321674 TTGAATTTTT
Statistics
Matches: 124, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
34 31 0.25
35 84 0.68
36 9 0.07
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (34 bp):
TCGAGCTTGAATCGAGCTTGAATCGAGCTTCAAT
Found at i:321646 original size:46 final size:46
Alignment explanation
Indices: 321492--321640 Score: 192
Period size: 46 Copynumber: 3.2 Consensus size: 46
321482 ATAAAACCCG
* * *
321492 TCGAGCTTGAA-TCGAGCTCAAAATCGAGCTTCAAATCGAGCTTGAA
1 TCGAGCTTCAATTCGAGCTTAAAATCGAGCTT-GAATCGAGCTTGAA
* *
321538 TCGAGCTTCAATTCGAGCTTCAATTCGAGCTTGAATCGAGCTTGAA
1 TCGAGCTTCAATTCGAGCTTAAAATCGAGCTTGAATCGAGCTTGAA
* ** *
321584 TCGAGCTTCAATTCGAGCTTAAAATCAAGCTTGAATCGAAATTAAAA
1 TCGAGCTTCAATTCGAGCTTAAAATCGAGCTTGAATCGAGCTT-GAA
321631 TCGAGCTTCA
1 TCGAGCTTCA
321641 GTCGAGTTTG
Statistics
Matches: 90, Mismatches: 11, Indels: 3
0.87 0.11 0.03
Matches are distributed among these distances:
46 61 0.68
47 29 0.32
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (46 bp):
TCGAGCTTCAATTCGAGCTTAAAATCGAGCTTGAATCGAGCTTGAA
Found at i:322047 original size:49 final size:49
Alignment explanation
Indices: 321952--322057 Score: 122
Period size: 49 Copynumber: 2.2 Consensus size: 49
321942 AAAATTGATT
* * * *
321952 GAAATCAATTTGAGTTAAAATTGTTTGTAATCTAAGGTAGTAGTGATCC
1 GAAATCAACTTGAGATAAAATTGTTTGTAATCCAAGATAGTAGTGATCC
* * * * * *
322001 GAAATCGACTTGAGATAAAATTGTTTGTGATCCGAGATGGTGGTGATCT
1 GAAATCAACTTGAGATAAAATTGTTTGTAATCCAAGATAGTAGTGATCC
322050 GAAATCAA
1 GAAATCAA
322058 TTCAAGTTTA
Statistics
Matches: 46, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.34, C:0.09, G:0.24, T:0.33
Consensus pattern (49 bp):
GAAATCAACTTGAGATAAAATTGTTTGTAATCCAAGATAGTAGTGATCC
Found at i:323728 original size:48 final size:48
Alignment explanation
Indices: 323671--323867 Score: 295
Period size: 48 Copynumber: 4.1 Consensus size: 48
323661 ACATACTTTG
* *
323671 TGTATGATGGTTATTGATCGATTTCGTTTAATGCATAAGTTGCATTTT
1 TGTATGATGGTTATCGATCGATTTTGTTTAATGCATAAGTTGCATTTT
* * * * *
323719 TGTATGATGGTTATCAAACGATTGTGTTTAATACATAAGTTACATTTT
1 TGTATGATGGTTATCGATCGATTTTGTTTAATGCATAAGTTGCATTTT
*
323767 TGTATGATGGTTATCGATCGTTTTTGTTTAATGCATAAGTTGCATTTT
1 TGTATGATGGTTATCGATCGATTTTGTTTAATGCATAAGTTGCATTTT
* * *
323815 CGTATGATGGTTATTGATCGATTTTGTTTAATGCATATGTTGCATTTT
1 TGTATGATGGTTATCGATCGATTTTGTTTAATGCATAAGTTGCATTTT
323863 TGTAT
1 TGTAT
323868 CAGTACTATA
Statistics
Matches: 131, Mismatches: 18, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 131 1.00
ACGTcount: A:0.24, C:0.08, G:0.20, T:0.48
Consensus pattern (48 bp):
TGTATGATGGTTATCGATCGATTTTGTTTAATGCATAAGTTGCATTTT
Found at i:323814 original size:24 final size:24
Alignment explanation
Indices: 323787--323865 Score: 56
Period size: 24 Copynumber: 3.3 Consensus size: 24
323777 TTATCGATCG
323787 TTTTTGTTTAATGCATAAGTTGCA
1 TTTTTGTTTAATGCATAAGTTGCA
* * * * *
323811 TTTTCGTATGATG-GTTA-TTG-A
1 TTTTTGTTTAATGCATAAGTTGCA
*
323832 TCGATTTTGTTTAATGCATATGTTGCA
1 T---TTTTGTTTAATGCATAAGTTGCA
323859 TTTTTGT
1 TTTTTGT
323866 ATCAGTACTA
Statistics
Matches: 38, Mismatches: 11, Indels: 12
0.62 0.18 0.20
Matches are distributed among these distances:
21 2 0.05
22 3 0.08
23 2 0.05
24 25 0.66
25 1 0.03
26 3 0.08
27 2 0.05
ACGTcount: A:0.20, C:0.08, G:0.19, T:0.53
Consensus pattern (24 bp):
TTTTTGTTTAATGCATAAGTTGCA
Found at i:323967 original size:53 final size:53
Alignment explanation
Indices: 323890--323992 Score: 152
Period size: 53 Copynumber: 1.9 Consensus size: 53
323880 TACTTTCGAT
*
323890 ACTATGTGTGCAACCATGGTATTCATAATGAGTTTATGAATGACCATTTCGGA
1 ACTATGTGTGCAACCATGGAATTCATAATGAGTTTATGAATGACCATTTCGGA
* * * * *
323943 ACTATGTGTGCATCCATGGAATTCATAATGATTTTGTGGATTACCATTTC
1 ACTATGTGTGCAACCATGGAATTCATAATGAGTTTATGAATGACCATTTC
323993 AGCACTTAGG
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 44 1.00
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.37
Consensus pattern (53 bp):
ACTATGTGTGCAACCATGGAATTCATAATGAGTTTATGAATGACCATTTCGGA
Found at i:324996 original size:22 final size:23
Alignment explanation
Indices: 324962--325013 Score: 97
Period size: 22 Copynumber: 2.3 Consensus size: 23
324952 CTCGTGCCAA
324962 ATAGAATGCATAAATAGTGTCGC
1 ATAGAATGCATAAATAGTGTCGC
324985 ATAGAA-GCATAAATAGTGTCGC
1 ATAGAATGCATAAATAGTGTCGC
325007 ATAGAAT
1 ATAGAAT
325014 TGCACATACA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 22 0.79
23 6 0.21
ACGTcount: A:0.42, C:0.12, G:0.21, T:0.25
Consensus pattern (23 bp):
ATAGAATGCATAAATAGTGTCGC
Found at i:325031 original size:24 final size:24
Alignment explanation
Indices: 325008--325166 Score: 165
Period size: 24 Copynumber: 6.6 Consensus size: 24
324998 TAGTGTCGCA
* * *
325008 TAGAATTGCACATACAGTGCCGCA
1 TAGAATTGCACATAAAGTGCCACG
* * * *
325032 TAAAATTGCTCATACAGTTCCACG
1 TAGAATTGCACATAAAGTGCCACG
* *
325056 TAGAATTGCACATATAGTGCCATG
1 TAGAATTGCACATAAAGTGCCACG
*
325080 TAGATTTGCACATAAAGTGCCACG
1 TAGAATTGCACATAAAGTGCCACG
* * *
325104 TAGAATTTACATATAAAGTGCCACA
1 TAGAA-TTGCACATAAAGTGCCACG
* *
325129 TAGAGTTGCACATAAAGTTCCACG
1 TAGAATTGCACATAAAGTGCCACG
*
325153 TGGAATTGCACATA
1 TAGAATTGCACATA
325167 TAATGATTTA
Statistics
Matches: 110, Mismatches: 24, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
24 90 0.82
25 20 0.18
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.26
Consensus pattern (24 bp):
TAGAATTGCACATAAAGTGCCACG
Done.