Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008128.1 Hibiscus syriacus cultivar Beakdansim tig00110683_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: 4987688
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 20
Found at i:3246118 original size:108 final size:108
Alignment explanation
Indices: 3245976--3246263 Score: 391
Period size: 108 Copynumber: 2.7 Consensus size: 108
3245966 TTATGAATTT
* *
3245976 CCGTATAGACACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACAACCGTATAGGCA
1 CCGTATAGGCACTAAGTGTGAAACCCACAGAATTCATCATATGTTGATGAACAACCGTATAGGCA
* * * *
3246041 CTAAGTGTAAAACCCACATAATTCGTCATATGTTGATGAACAA
66 CTAAGTGTAAAACCCACAGAATTCATCATAGGTTAATGAACAA
*
3246084 CCGTATAGGCACTAAGTGTGAAACCCACAGAATTCATCTTATGTTGATGAACAACCGTATAGGCA
1 CCGTATAGGCACTAAGTGTGAAACCCACAGAATTCATCATATGTTGATGAACAACCGTATAGGCA
**
3246149 CTAAGTGTGCAACCCACAGAATTCATCATAGGTTAATGAACAA
66 CTAAGTGTAAAACCCACAGAATTCATCATAGGTTAATGAACAA
* * * * * * **
3246192 -CATATAGGCACTATGTGTGCGAA-CCACGGAATTCATAATATGTTAATGAATGACCGTATAGGC
1 CCGTATAGGCACTAAGTGTG-AAACCCACAGAATTCATCATATGTTGATGAACAACCGTATAGGC
*
3246255 ACTACGTGT
65 ACTAAGTGT
3246264 GCATCTCAAG
Statistics
Matches: 160, Mismatches: 19, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
107 59 0.37
108 101 0.63
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.25
Consensus pattern (108 bp):
CCGTATAGGCACTAAGTGTGAAACCCACAGAATTCATCATATGTTGATGAACAACCGTATAGGCA
CTAAGTGTAAAACCCACAGAATTCATCATAGGTTAATGAACAA
Found at i:3252624 original size:19 final size:19
Alignment explanation
Indices: 3252600--3252636 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
3252590 TTATATTTTA
3252600 TGATAGTCATCGATGCATT
1 TGATAGTCATCGATGCATT
3252619 TGATAGTCATCGATGCAT
1 TGATAGTCATCGATGCAT
3252637 GTTGCTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.35
Consensus pattern (19 bp):
TGATAGTCATCGATGCATT
Found at i:3252766 original size:54 final size:54
Alignment explanation
Indices: 3252717--3253115 Score: 514
Period size: 54 Copynumber: 7.4 Consensus size: 54
3252707 TATGAATTTT
* *
3252717 CGTATCGGCACTAAGTGTGCAACCCACGAAATTCATCATATGTCGATGAACAAC
1 CGTATAGGCACTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGAACAAC
*
3252771 CGTATAGGCACTAAGTGTGCAACCCACAAAATTCATCATATGTTGATGAACAAC
1 CGTATAGGCACTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGAACAAC
* * *
3252825 CGTATAGGCACTAAGTGTACAACCCACGGAATTCTTCATATGTTGATGAACAAC
1 CGTATAGGCACTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGAACAAC
* * * *
3252879 CGTATATGCACTAAGTGTGCAACCCACGGAATTCATCGTATGTTGATGAACAAT
1 CGTATAGGCACTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGAACAAC
* *
3252933 CGTATAGGCACTAAGTGTGCAACCCACGGAATTCATCATATGTTGATGAACAAT
1 CGTATAGGCACTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGAACAAC
* * * *
3252987 TGTATAGGCACTAAGTGTGGAACCCAC-AGAATTCATCATAGGTTGATGAACGAC
1 CGTATAGGCACTAAGTGTGCAACCCACGA-AATTCATCATATGTTGATGAACAAC
** * ** * * * **
3253041 CGTATATACACTATGTGTGCGAA-CCAAAAAATTCATAATATATTTATGAATGAC
1 CGTATAGGCACTAAGTGTGC-AACCCACGAAATTCATCATATGTTGATGAACAAC
* *
3253095 CATATAGGCACTATGTGTGCA
1 CGTATAGGCACTAAGTGTGCA
3253116 TCTCAACGAA
Statistics
Matches: 308, Mismatches: 34, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
53 1 0.00
54 304 0.99
55 3 0.01
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (54 bp):
CGTATAGGCACTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGAACAAC
Found at i:3255947 original size:228 final size:227
Alignment explanation
Indices: 3255607--3256018 Score: 697
Period size: 225 Copynumber: 1.8 Consensus size: 227
3255597 TACCCAAACC
*
3255607 AAAAATATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTCTATATATAA
1 AAAAATATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTATATATATAA
* *
3255672 TTTTTTTCAATTAATTCACTGTGTTTATTGAATAAAAATAATTTTTTTATTATTTCGGGTCGGAT
66 TTTTTTCCAATTAAGTCACTGTGTTTATTGAATAAAAATAA-TTTTTT-TTATTTCGGGTCGGAT
*
3255737 TTCTAATTCATATATTC-GGTCGAGTCGGGTGAAACTTTATTTTGGTCGGGTCAGGTCGGGTTCG
129 TTCTAATTCATATATTCAGGTCGAGTC-GGTGAAACTTTATTTTAGTCGGGTCAGGTCGGGTTCG
3255801 GGTTTAGGGTGAAAATACCCGACCAGACCCGACCT
193 GGTTTAGGGTGAAAATACCCGACCAGACCCGACCT
3255836 AAAAA-ATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTATATATAT-A
1 AAAAATATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTATATATATAA
*
3255899 TTTTTTCCAATTAAGTCACTGT-TTATATTGAATAAAAATAATTTTTTTTATTTCGGGTCGGGTT
66 TTTTTTCCAATTAAGTCACTGTGTT-TATTGAATAAAAATAATTTTTTTTATTTCGGGTCGGATT
* *
3255963 TTTAATTCATATATTCAGGTCGGGTCGGTGAAACTTTATTTTAGTCGGGTCAGGTC
130 TCTAATTCATATATTCAGGTCGAGTCGGTGAAACTTTATTTTAGTCGGGTCAGGTC
3256019 TCGGATGGAG
Statistics
Matches: 174, Mismatches: 7, Indels: 8
0.92 0.04 0.04
Matches are distributed among these distances:
225 60 0.34
226 16 0.09
227 37 0.21
228 56 0.32
229 5 0.03
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.41
Consensus pattern (227 bp):
AAAAATATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTATATATATAA
TTTTTTCCAATTAAGTCACTGTGTTTATTGAATAAAAATAATTTTTTTTATTTCGGGTCGGATTT
CTAATTCATATATTCAGGTCGAGTCGGTGAAACTTTATTTTAGTCGGGTCAGGTCGGGTTCGGGT
TTAGGGTGAAAATACCCGACCAGACCCGACCT
Found at i:3259229 original size:21 final size:20
Alignment explanation
Indices: 3259204--3259255 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
3259194 CTTTTCATCG
3259204 AGGGATCAATCCTATTGGTGA
1 AGGGATCAATCCT-TTGGTGA
* **
3259225 TGGGATTGATCCTTTGGTGA
1 AGGGATCAATCCTTTGGTGA
*
3259245 AGAGATCAATC
1 AGGGATCAATC
3259256 TAAACCTACT
Statistics
Matches: 24, Mismatches: 7, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
20 14 0.58
21 10 0.42
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.31
Consensus pattern (20 bp):
AGGGATCAATCCTTTGGTGA
Found at i:3259366 original size:21 final size:21
Alignment explanation
Indices: 3259341--3259391 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
3259331 CAGTGGGATC
3259341 GATCATTTGGTCAAAGGA-ATT
1 GATCATTTGG-CAAAGGAGATT
* *
3259362 GATCATTTTGCTAAGGAGATT
1 GATCATTTGGCAAAGGAGATT
*
3259383 GATCCTTTG
1 GATCATTTG
3259392 AGTCGAAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 6 0.24
21 19 0.76
ACGTcount: A:0.27, C:0.12, G:0.24, T:0.37
Consensus pattern (21 bp):
GATCATTTGGCAAAGGAGATT
Found at i:3259391 original size:20 final size:20
Alignment explanation
Indices: 3259354--3259391 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3259344 CATTTGGTCA
*
3259354 AAGGAATTGATCATTTTGCT
1 AAGGAATTGATCACTTTGCT
3259374 AAGGAGATTGATC-CTTTG
1 AAGGA-ATTGATCACTTTG
3259392 AGTCGAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.29, C:0.11, G:0.24, T:0.37
Consensus pattern (20 bp):
AAGGAATTGATCACTTTGCT
Found at i:3261143 original size:31 final size:32
Alignment explanation
Indices: 3261087--3261147 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
3261077 AACAATAAAC
*
3261087 TGAACAAAAAGTAACTCAAACCGAAAATAACA
1 TGAACAAAAAGCAACTCAAACCGAAAATAACA
* *
3261119 TGAACCAAAAGCAAC-CGAACCGAAAATAA
1 TGAACAAAAAGCAACTCAAACCGAAAATAA
3261148 TCCAAACTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 13 0.50
32 13 0.50
ACGTcount: A:0.57, C:0.21, G:0.11, T:0.10
Consensus pattern (32 bp):
TGAACAAAAAGCAACTCAAACCGAAAATAACA
Found at i:3261613 original size:19 final size:20
Alignment explanation
Indices: 3261569--3261619 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 20
3261559 AACTTTATTT
3261569 TCTATTTATAAATTTAATAA
1 TCTATTTATAAATTTAATAA
* *
3261589 T-AATTTATTAATTTAAT-A
1 TCTATTTATAAATTTAATAA
3261607 TCTATTT-TAAATT
1 TCTATTTATAAATT
3261620 CCGTTAATTA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
18 7 0.27
19 18 0.69
20 1 0.04
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (20 bp):
TCTATTTATAAATTTAATAA
Found at i:3263047 original size:20 final size:20
Alignment explanation
Indices: 3263022--3263059 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3263012 TGAAAAATTA
3263022 ATTGGTGCATCGATGCATGG
1 ATTGGTGCATCGATGCATGG
*
3263042 ATTGGTGCATCGGTGCAT
1 ATTGGTGCATCGATGCAT
3263060 CACTTTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.16, G:0.34, T:0.32
Consensus pattern (20 bp):
ATTGGTGCATCGATGCATGG
Found at i:3265254 original size:13 final size:13
Alignment explanation
Indices: 3265226--3265264 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
3265216 TGGGTAAGGT
*
3265226 TTTGAAAA-ACTA
1 TTTGAAAATAATA
3265238 TTTGAAAATAATA
1 TTTGAAAATAATA
3265251 TTTGAAAATAATA
1 TTTGAAAATAATA
3265264 T
1 T
3265265 GTATAGTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
12 8 0.32
13 17 0.68
ACGTcount: A:0.51, C:0.03, G:0.08, T:0.38
Consensus pattern (13 bp):
TTTGAAAATAATA
Found at i:3269690 original size:22 final size:21
Alignment explanation
Indices: 3269648--3269687 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3269638 GAGTTTATTT
*
3269648 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
3269669 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
3269688 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:3270938 original size:21 final size:21
Alignment explanation
Indices: 3270885--3270940 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
3270875 CACTAGTGCA
*
3270885 GGTGCATGGATCCACTGCAGG
1 GGTGCATGGATGCACTGCAGG
*
3270906 GATGCATGGATGCACTGCAGG
1 GGTGCATGGATGCACTGCAGG
3270927 GGTGCATGGATGCA
1 GGTGCATGGATGCA
3270941 TTTTTACACC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.21, C:0.20, G:0.39, T:0.20
Consensus pattern (21 bp):
GGTGCATGGATGCACTGCAGG
Found at i:3271069 original size:30 final size:30
Alignment explanation
Indices: 3271022--3271081 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
3271012 AAAATTTGAA
3271022 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
3271051 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAACCATTTTG
3271082 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:3271221 original size:21 final size:21
Alignment explanation
Indices: 3271192--3271231 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
3271182 TTGTTTAATG
3271192 AAAAAGATATCAATTGTTAAC
1 AAAAAGATATCAATTGTTAAC
*
3271213 AAAATGATATCAATTGTTA
1 AAAAAGATATCAATTGTTA
3271232 CCAATTGTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.50, C:0.07, G:0.10, T:0.33
Consensus pattern (21 bp):
AAAAAGATATCAATTGTTAAC
Found at i:3272385 original size:19 final size:20
Alignment explanation
Indices: 3272342--3272389 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
3272332 TCTAAATCCT
*
3272342 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
3272362 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
3272381 TTTTCAAAA
1 TTTTCAAAA
3272390 GAAAATCATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:3273865 original size:65 final size:64
Alignment explanation
Indices: 3273723--3273857 Score: 157
Period size: 64 Copynumber: 2.1 Consensus size: 64
3273713 TGCACTTAGA
* * * ** *
3273723 GTGCAGCGATGCATAAAATGCATTTGATGTTTTGAAAAACCTGAGTGCATCAATGCATGGTCTT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTGAAAAAACTGAGTGCATCAATGCATGGAATG
* *
3273787 GTGCATCGATGCATAAAATGCATTCGATG-TTTGAAAAATTAATTG-GTGCATCGATGCATGGAA
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTG-AAAA--AACTGAGTGCATCAATGCATGGAA
3273850 TG
63 TG
3273852 GTGCAT
1 GTGCAT
3273858 TGGTGCATCA
Statistics
Matches: 60, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
63 4 0.07
64 31 0.52
65 22 0.37
66 3 0.05
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.31
Consensus pattern (64 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTTGAAAAAACTGAGTGCATCAATGCATGGAATG
Found at i:3275060 original size:23 final size:23
Alignment explanation
Indices: 3275030--3275075 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
3275020 ATCAAAAATT
3275030 AATTTGAGGTATAATTTAAGCAC
1 AATTTGAGGTATAATTTAAGCAC
3275053 AATTTGAGGTATAATTTAAGCAC
1 AATTTGAGGTATAATTTAAGCAC
3275076 CTAAAAGTAT
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:0.39, C:0.09, G:0.17, T:0.35
Consensus pattern (23 bp):
AATTTGAGGTATAATTTAAGCAC
Found at i:3279347 original size:2 final size:2
Alignment explanation
Indices: 3279340--3279365 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3279330 CTATCATTGA
3279340 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
3279366 TTACATTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3280619 original size:7 final size:7
Alignment explanation
Indices: 3280576--3280640 Score: 69
Period size: 7 Copynumber: 9.1 Consensus size: 7
3280566 TAATCCACTT
3280576 ATTTT-A
1 ATTTTAA
3280582 ATTTTAA
1 ATTTTAA
3280589 CATTTTAAA
1 -ATTTT-AA
3280598 ATTTTAA
1 ATTTTAA
***
3280605 AACATAA
1 ATTTTAA
3280612 ATTTTAA
1 ATTTTAA
3280619 ATTTTAA
1 ATTTTAA
3280626 ATTTTAA
1 ATTTTAA
*
3280633 ATTCTAA
1 ATTTTAA
3280640 A
1 A
3280641 ATATCAAAGC
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
6 5 0.10
7 32 0.65
8 10 0.20
9 2 0.04
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (7 bp):
ATTTTAA
Found at i:3280661 original size:43 final size:43
Alignment explanation
Indices: 3280576--3280663 Score: 106
Period size: 43 Copynumber: 2.0 Consensus size: 43
3280566 TAATCCACTT
* * * *
3280576 ATTTTAATTTTAACATTTTAAAATTTTAAAACATAAATTTTAA
1 ATTTTAATTTTAACATTCTAAAATATCAAAACATAAACTTTAA
* *
3280619 ATTTTAAATTTTAA-ATTCTAAAATATCAAAGCATATACTTTAA
1 ATTTT-AATTTTAACATTCTAAAATATCAAAACATAAACTTTAA
3280662 AT
1 AT
3280664 CTCAATCCTA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
43 30 0.79
44 8 0.21
ACGTcount: A:0.47, C:0.07, G:0.01, T:0.45
Consensus pattern (43 bp):
ATTTTAATTTTAACATTCTAAAATATCAAAACATAAACTTTAA
Found at i:3281075 original size:17 final size:18
Alignment explanation
Indices: 3281053--3281086 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3281043 AATCGCTATC
*
3281053 TAATTGGAT-AATTAAAT
1 TAATTGAATAAATTAAAT
3281070 TAATTGAATAAATTAAA
1 TAATTGAATAAATTAAA
3281087 ATTATGACCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (18 bp):
TAATTGAATAAATTAAAT
Found at i:3282823 original size:15 final size:14
Alignment explanation
Indices: 3282802--3282845 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
3282792 AGGTAATATA
3282802 ATATATTTTTTATT
1 ATATATTTTTTATT
* *
3282816 ATTATATTTGTTGTT
1 A-TATATTTTTTATT
3282831 ATATATTATTTTATT
1 ATATATT-TTTTATT
3282846 TTAAAATTGA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
14 7 0.29
15 17 0.71
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (14 bp):
ATATATTTTTTATT
Found at i:3287754 original size:30 final size:30
Alignment explanation
Indices: 3287697--3287764 Score: 84
Period size: 31 Copynumber: 2.3 Consensus size: 30
3287687 TAACCATTCA
* * *
3287697 CAACTTTTCCAAAATTGTCGAATTGGTCTCC
1 CAACTTTTCAAAAATTATAGAATTGGTC-CC
3287728 CAACTTTTCAAAAATTATAGAA-TGGTCCC
1 CAACTTTTCAAAAATTATAGAATTGGTCCC
*
3287757 CAAATTTT
1 CAACTTTT
3287765 TATAAGGATT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 9 0.27
30 5 0.15
31 19 0.58
ACGTcount: A:0.32, C:0.22, G:0.10, T:0.35
Consensus pattern (30 bp):
CAACTTTTCAAAAATTATAGAATTGGTCCC
Found at i:3295173 original size:29 final size:29
Alignment explanation
Indices: 3295122--3295187 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 29
3295112 AAACCATTCA
* * * *
3295122 TAACTTTTCTAAAATTGTTGAATTGTCTC
1 TAACTTTTCAAAAATTGTAGAATAGTCCC
3295151 TAACTTTTCAAAAATT-TCAGAATAGTCCC
1 TAACTTTTCAAAAATTGT-AGAATAGTCCC
*
3295180 TAAATTTT
1 TAACTTTT
3295188 TCTAAGGCTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
28 1 0.03
29 30 0.97
ACGTcount: A:0.33, C:0.15, G:0.08, T:0.44
Consensus pattern (29 bp):
TAACTTTTCAAAAATTGTAGAATAGTCCC
Found at i:3295910 original size:30 final size:31
Alignment explanation
Indices: 3295871--3295932 Score: 99
Period size: 30 Copynumber: 2.0 Consensus size: 31
3295861 AATCACCAAT
3295871 AAACCAAGACACCTAA-CCTTATCATCGTCC
1 AAACCAAGACACCTAACCCTTATCATCGTCC
* *
3295901 AAACTAAGACACCTAACCCTTATCATCTTCC
1 AAACCAAGACACCTAACCCTTATCATCGTCC
3295932 A
1 A
3295933 TAAGTCAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 15 0.52
31 14 0.48
ACGTcount: A:0.37, C:0.35, G:0.05, T:0.23
Consensus pattern (31 bp):
AAACCAAGACACCTAACCCTTATCATCGTCC
Found at i:3297296 original size:18 final size:18
Alignment explanation
Indices: 3297273--3297308 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
3297263 CAACAAGTAT
3297273 CGAGTTCTTATCAGGGAG
1 CGAGTTCTTATCAGGGAG
3297291 CGAGTTCTTATCAGGGAG
1 CGAGTTCTTATCAGGGAG
3297309 AGTGTCAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.17, G:0.33, T:0.28
Consensus pattern (18 bp):
CGAGTTCTTATCAGGGAG
Found at i:3299760 original size:28 final size:27
Alignment explanation
Indices: 3299717--3299786 Score: 72
Period size: 28 Copynumber: 2.6 Consensus size: 27
3299707 GATGAAAAAC
* *
3299717 AAAAGTATAACT-AAACTTTCATC-AT
1 AAAAATATAACTAAAACATTCATCAAT
* *
3299742 AACAAATATCAAGTAAAACATTGATCAAT
1 AA-AAATAT-AACTAAAACATTCATCAAT
3299771 AAAAATATAACTAAAA
1 AAAAATATAACTAAAA
3299787 TTTAATAGTT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
25 2 0.06
26 5 0.14
27 10 0.28
28 15 0.42
29 4 0.11
ACGTcount: A:0.57, C:0.13, G:0.04, T:0.26
Consensus pattern (27 bp):
AAAAATATAACTAAAACATTCATCAAT
Found at i:3308814 original size:13 final size:14
Alignment explanation
Indices: 3308780--3308814 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
3308770 AAAATGAATT
3308780 ACATTTTTTGGAAA
1 ACATTTTTTGGAAA
3308794 ACATTTTTTGGAAA
1 ACATTTTTTGGAAA
*
3308808 ATATTTT
1 ACATTTT
3308815 ATGGTGTCTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.34, C:0.06, G:0.11, T:0.49
Consensus pattern (14 bp):
ACATTTTTTGGAAA
Found at i:3309113 original size:21 final size:23
Alignment explanation
Indices: 3309088--3309134 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
3309078 CCTATAAAAA
*
3309088 TAAAAATATT-AT-ATTATATTT
1 TAAAAATATTAATAAATATATTT
*
3309109 TAAAATTATTAATAAATATATTT
1 TAAAAATATTAATAAATATATTT
3309132 TAA
1 TAA
3309135 GGAATTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 9 0.41
22 2 0.09
23 11 0.50
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
TAAAAATATTAATAAATATATTT
Found at i:3309149 original size:23 final size:22
Alignment explanation
Indices: 3309088--3309150 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 22
3309078 CCTATAAAAA
* *
3309088 TAAAAATA-TTATATTATATTT
1 TAAAATTATTTATAATATATTT
*
3309109 TAAAATTATTAATAAATATATTT
1 TAAAATTATTTAT-AATATATTT
3309132 TAAGGAATT-TTTATAATAT
1 TAA--AATTATTTATAATAT
3309151 TAATATTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
21 7 0.21
22 3 0.09
23 16 0.47
24 4 0.12
25 4 0.12
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (22 bp):
TAAAATTATTTATAATATATTT
Found at i:3309377 original size:23 final size:23
Alignment explanation
Indices: 3309335--3309391 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
3309325 ATTATTATAT
3309335 TATATTATTAAAAATATTAATAAA
1 TATATT-TTAAAAATATTAATAAA
* * *
3309359 TATATTTTAAATATGTTAATAAT
1 TATATTTTAAAAATATTAATAAA
3309382 TAATATTTTA
1 T-ATATTTTA
3309392 TTAAAATGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 15 0.52
24 14 0.48
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (23 bp):
TATATTTTAAAAATATTAATAAA
Found at i:3315199 original size:15 final size:15
Alignment explanation
Indices: 3315167--3315205 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
3315157 TTTTCGCTGC
*
3315167 ATAAAATGATTAATAT
1 ATAAAAT-ATTAAAAT
*
3315183 ATTAAATATTAAAAT
1 ATAAAATATTAAAAT
3315198 ATAAAATA
1 ATAAAATA
3315206 ATTTTTACTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (15 bp):
ATAAAATATTAAAAT
Found at i:3316244 original size:15 final size:15
Alignment explanation
Indices: 3316207--3316264 Score: 64
Period size: 15 Copynumber: 3.9 Consensus size: 15
3316197 AAGTTTAGTC
*
3316207 CTTAAATTTTAAATT
1 CTTAAATTTAAAATT
* *
3316222 -TCAAATTTCAAATT
1 CTTAAATTTAAAATT
*
3316236 CTTAAATTTAAAATC
1 CTTAAATTTAAAATT
*
3316251 CTAAAATTTAAAAT
1 CTTAAATTTAAAAT
3316265 GCCTTCTTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
14 12 0.33
15 24 0.67
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.43
Consensus pattern (15 bp):
CTTAAATTTAAAATT
Found at i:3317502 original size:10 final size:10
Alignment explanation
Indices: 3317487--3317518 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
3317477 ATGTAAAATA
3317487 TAATTTATTT
1 TAATTTATTT
3317497 TAATTTATTT
1 TAATTTATTT
3317507 TAA--TATTT
1 TAATTTATTT
3317515 TAAT
1 TAAT
3317519 ATATATATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 8 0.38
10 13 0.62
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (10 bp):
TAATTTATTT
Found at i:3317524 original size:2 final size:2
Alignment explanation
Indices: 3317517--3317549 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
3317507 TAATATTTTA
3317517 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3317550 TGTGCAAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3323859 original size:3 final size:3
Alignment explanation
Indices: 3323851--3323886 Score: 56
Period size: 3 Copynumber: 12.0 Consensus size: 3
3323841 CTGAAAAGAA
3323851 AAT AAT AAT AAT AAT AAT -AT AAAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT
3323887 TTCTAATAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 27 0.87
4 2 0.06
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3324339 original size:42 final size:41
Alignment explanation
Indices: 3324244--3324343 Score: 103
Period size: 42 Copynumber: 2.4 Consensus size: 41
3324234 GGCCATATAC
*
3324244 ATGGCCCGAAAGACTTATCATCTCGCTCAAAAGACTGACAG
1 ATGGCCCGAAGGACTTATCATCTCGCTCAAAAGACTGACAG
* * * * * * *
3324285 ATGACACAAAGGATTTAATCATCAT-GCTCGAAAGACTTACTG
1 ATGGCCCGAAGGACTT-ATCATC-TCGCTCAAAAGACTGACAG
3324327 ATGGCCCGAAGGACTTA
1 ATGGCCCGAAGGACTTA
3324344 CAAATTTTGG
Statistics
Matches: 45, Mismatches: 12, Indels: 4
0.74 0.20 0.07
Matches are distributed among these distances:
41 12 0.27
42 32 0.71
43 1 0.02
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.22
Consensus pattern (41 bp):
ATGGCCCGAAGGACTTATCATCTCGCTCAAAAGACTGACAG
Found at i:3324541 original size:258 final size:258
Alignment explanation
Indices: 3324033--3324643 Score: 838
Period size: 258 Copynumber: 2.4 Consensus size: 258
3324023 GATAGATAAC
* * * * *
3324033 CCAAAGGATTCAAGCATCATGCTCGAAAGGCTTACTGATAGCCCAAAGGACTTACAAATTTTGGA
1 CCAAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACAAATTTTGGA
* **
3324098 TATAGTTTACT-GGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCATTTTCAGA
66 AATAGTTTACTGGGTAAGAAACTTTGGAAATTACTTTCTTACTTTTCAAAAATTTCATTTTCAGA
* * * *** * * *
3324162 AAACATTAAATGAGAAACTTTGGAAATTGTTTTCTCATTTTTCGAAAATGATGTGGAAGCATACT
131 AAAAACTAAATGAGAAACTTTGAAAATCACTTTCTCATTTTTCGAAAATCATGTGAAAACATACT
*
3324227 CCCCGAAGGCCATATACATGGCCCGAAAGACTTATCATCTCGCTCAAAAGACTGACAGATG-A
196 ACCCGAAGGCCATATACATGGCCCGAAAGACTTATCATCTCGCTCAAAAGACTGACAGATGAA
3324289 CACAAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACAAATTTTGG
1 C-CAAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACAAATTTTGG
3324354 AAATAGTTTACTGGGTAAGAAACTTTGGAAATTACTTTCTTACTTTTCAAAAATTTCATTTTCTA
65 AAATAGTTTACTGGGTAAGAAACTTTGGAAATTACTTTCTTACTTTTCAAAAATTTCATTTTC-A
* *
3324419 -AACAAAACTAAATGAGAAACTTTGAAAATCACTTTCTCATTTTTC-AAATTCATGTGAAAATAT
129 GAA-AAAACTAAATGAGAAACTTTGAAAATCACTTTCTCATTTTTCGAAAATCATGTGAAAACAT
* * * * * * * *
3324482 CCTACCCGAAGGTCTTATAGATGGCCTGAAGGACTTATCTTCTTGCTCGAAAA-ACTGACAGATG
193 ACTACCCGAAGGCCATATACATGGCCCGAAAGACTTATCATCTCGCTC-AAAAGACTGACAGATG
3324546 AA
257 AA
* * * * * *
3324548 CCGAAGGATTTAATCATCATGCTCAAAAGACTTATTGATGTCCCGAAGGATTTACAAATTTTGAA
1 CCAAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACAAATTTTGGA
3324613 AATAGTTTACTGGGTAAGAAAC-TTGGAAATT
66 AATAGTTTACTGGGTAAGAAACTTTGGAAATT
3324644 GTTTTCTCAT
Statistics
Matches: 315, Mismatches: 34, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
256 1 0.00
257 78 0.25
258 193 0.61
259 43 0.14
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (258 bp):
CCAAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACAAATTTTGGA
AATAGTTTACTGGGTAAGAAACTTTGGAAATTACTTTCTTACTTTTCAAAAATTTCATTTTCAGA
AAAAACTAAATGAGAAACTTTGAAAATCACTTTCTCATTTTTCGAAAATCATGTGAAAACATACT
ACCCGAAGGCCATATACATGGCCCGAAAGACTTATCATCTCGCTCAAAAGACTGACAGATGAA
Found at i:3326091 original size:73 final size:73
Alignment explanation
Indices: 3325964--3326104 Score: 196
Period size: 73 Copynumber: 1.9 Consensus size: 73
3325954 ACCCCCCTTG
* * **
3325964 GGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAGCAAAACTGTTTTA-GGGGAATCAG
1 GGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAGCAAAACTCATTTAGGGGGAATC-G
3326028 TTCCTATAT
65 TTCCTATAT
* *
3326037 GGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGGGCCAAAAC-CATTTAGGGGGAATCG
1 GGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAG-CAAAACTCATTTAGGGGGAATCG
3326101 TTCC
65 TTCC
3326105 CTCTGAGCAA
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
73 46 0.77
74 14 0.23
ACGTcount: A:0.23, C:0.23, G:0.30, T:0.25
Consensus pattern (73 bp):
GGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAGCAAAACTCATTTAGGGGGAATCGT
TCCTATAT
Found at i:3326718 original size:17 final size:17
Alignment explanation
Indices: 3326696--3326739 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
3326686 TTCATAAATC
*
3326696 CAAAATCCAACAATCCA
1 CAAAATCAAACAATCCA
3326713 CAAAATCAAACAATCCA
1 CAAAATCAAACAATCCA
3326730 -AAATATCAAA
1 CAAA-ATCAAA
3326740 AGTGTTGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 3 0.12
17 22 0.88
ACGTcount: A:0.59, C:0.27, G:0.00, T:0.14
Consensus pattern (17 bp):
CAAAATCAAACAATCCA
Found at i:3328581 original size:20 final size:20
Alignment explanation
Indices: 3328504--3328589 Score: 64
Period size: 20 Copynumber: 4.0 Consensus size: 20
3328494 AACAGAACCC
*
3328504 CAGGGGGGTATCGATTCCCCT
1 CAGGGGGGAATCGATT-CCCT
** *
3328525 GTGGGGGGAAATCGGTTCCCCTT
1 CAGGGGGG-AATCGATT-CCC-T
* *
3328548 CAAAGGGGGAATCGGTTCCCT
1 C-AGGGGGGAATCGATTCCCT
*
3328569 CAGGGGGGGATCGATTCCCT
1 CAGGGGGGAATCGATTCCCT
3328589 C
1 C
3328590 TGCACCAAAA
Statistics
Matches: 52, Mismatches: 10, Indels: 7
0.75 0.14 0.10
Matches are distributed among these distances:
20 17 0.33
21 8 0.15
22 13 0.25
23 9 0.17
24 5 0.10
ACGTcount: A:0.16, C:0.26, G:0.36, T:0.22
Consensus pattern (20 bp):
CAGGGGGGAATCGATTCCCT
Found at i:3330627 original size:150 final size:151
Alignment explanation
Indices: 3330356--3330656 Score: 579
Period size: 150 Copynumber: 2.0 Consensus size: 151
3330346 AACATAATTA
3330356 CAGATATTTCTAAGAGAAGATCGAGTAGTTACCCCTTTTGATGGATCACCTATAATTTCACATCC
1 CAGATATTTCTAAGAGAAGATCGAGTAGTTACCCCTTTTGATGGATCACCTATAATTTCACATCC
3330421 TTGACATAGTTTGTACTCTCTTGGAAAAGATACTTCCCTTTCTTCAATGGTTGGATTCTCGA-GG
66 TTGACATAGTTTGTACTCTCTTGGAAAAGATACTTCCCTTTCTTCAATGGTTGGATTCTCGAGGG
3330485 GATCATGAGTTTCTTCATCTT
131 GATCATGAGTTTCTTCATCTT
3330506 CAGATATTTCTAAGAGAAGATCGAGTAGTTACCCCTTTTGATGGATCACCTATAATTTCACCATC
1 CAGATATTTCTAAGAGAAGATCGAGTAGTTACCCCTTTTGATGGATCACCTATAATTTCA-CATC
3330571 CTTGACATAG-TTGTACTCTCTTGGAAAAGATACTTCCCTTTCTTCAATGGTTGGATTCTCGAGG
65 CTTGACATAGTTTGTACTCTCTTGGAAAAGATACTTCCCTTTCTTCAATGGTTGGATTCTCGAGG
3330635 GGATCATGAGTTTCTTCATCTT
130 GGATCATGAGTTTCTTCATCTT
3330657 TTGTTTCTTC
Statistics
Matches: 149, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
150 112 0.75
151 37 0.25
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.37
Consensus pattern (151 bp):
CAGATATTTCTAAGAGAAGATCGAGTAGTTACCCCTTTTGATGGATCACCTATAATTTCACATCC
TTGACATAGTTTGTACTCTCTTGGAAAAGATACTTCCCTTTCTTCAATGGTTGGATTCTCGAGGG
GATCATGAGTTTCTTCATCTT
Found at i:3332522 original size:22 final size:21
Alignment explanation
Indices: 3332480--3332519 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3332470 GAGTTTGTTT
*
3332480 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
3332501 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
3332520 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:3334625 original size:76 final size:76
Alignment explanation
Indices: 3334435--3334637 Score: 286
Period size: 75 Copynumber: 2.7 Consensus size: 76
3334425 CCGTTGTACA
* * * * *
3334435 AGGGGGGAATCGGTACCCCCT-TGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAG
**
3334499 CAAAACTGTTT
66 CAAAACCATTT
*
3334510 AGGGGGGAATCGGTTCCTCCTAT-GGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGGG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAG
3334574 CCAAAACCATTT
66 -CAAAACCATTT
* *
3334586 A-GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCTGAGCAATCTG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTG
3334638 TAATTTTTGG
Statistics
Matches: 115, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
75 77 0.67
76 38 0.33
ACGTcount: A:0.20, C:0.24, G:0.33, T:0.24
Consensus pattern (76 bp):
AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAG
CAAAACCATTT
Found at i:3341103 original size:30 final size:30
Alignment explanation
Indices: 3341036--3341105 Score: 131
Period size: 30 Copynumber: 2.3 Consensus size: 30
3341026 TTATAAAAGT
*
3341036 GATCAAAGTATAAACCAAATAAAATTAGAG
1 GATCAAATTATAAACCAAATAAAATTAGAG
3341066 GATCAAATTATAAACCAAATAAAATTAGAG
1 GATCAAATTATAAACCAAATAAAATTAGAG
3341096 GATCAAATTA
1 GATCAAATTA
3341106 GAAAATGAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.56, C:0.10, G:0.11, T:0.23
Consensus pattern (30 bp):
GATCAAATTATAAACCAAATAAAATTAGAG
Found at i:3342352 original size:3 final size:3
Alignment explanation
Indices: 3342339--3342384 Score: 74
Period size: 3 Copynumber: 15.3 Consensus size: 3
3342329 ATTATTATTT
* *
3342339 ATA ATA TTA ATA ATA ATA ATA ATA ATA ATA ACA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
3342385 CCCAGACAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3342353 original size:9 final size:9
Alignment explanation
Indices: 3342301--3342380 Score: 58
Period size: 9 Copynumber: 9.1 Consensus size: 9
3342291 GAAAAGAAAA
3342301 ATTAATAAT
1 ATTAATAAT
*
3342310 AAT-ATAA-
1 ATTAATAAT
3342317 ATT-ATAATT
1 ATTAATAA-T
* *
3342326 ATTATTATT
1 ATTAATAAT
*
3342335 ATTTATAAT
1 ATTAATAAT
3342344 ATTAATAAT
1 ATTAATAAT
*
3342353 AATAATAAT
1 ATTAATAAT
* *
3342362 AATAATAAC
1 ATTAATAAT
*
3342371 AATAATAAT
1 ATTAATAAT
3342380 A
1 A
3342381 ATAACCCAGA
Statistics
Matches: 57, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
7 6 0.11
8 4 0.07
9 45 0.79
10 2 0.04
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.42
Consensus pattern (9 bp):
ATTAATAAT
Found at i:3351412 original size:198 final size:199
Alignment explanation
Indices: 3351046--3351434 Score: 482
Period size: 199 Copynumber: 2.0 Consensus size: 199
3351036 AGGCACGCTC
* * *
3351046 GAGGGGTATTTTCAGGTAGTTAATCTAAAAATTTTCGAAATTTATAAGATTTGAGGCATTGTATT
1 GAGGGGTATTTTCAGGTAGTTAATCTAAAAAGTTTCGAAATTTATAAGATTAGAGGCATAGTATT
* * * ** * * *
3351111 GGAATTTTTCTTTTAGCTGAGGTCAATATTGACACATATGAGATATTGTAAGTGGGTTAAAAATC
66 GGAACTTATCTTTTAACTGAGGTCAATACCGACACATATGAAACATTGTAAGTGGGGTAAAAATC
* *
3351176 GCATTGAAAATGGTTCCAAAGCTTTTTTTGCACATGAAGAAAAAGCTAAAATAGTTTGATATGTA
131 GCATTCAAAATGGTTCCAAAGCTTTTTTTG-ACATGAAGAAAAAGCTAAAATAGCTTGATATGTA
3351241 TATTA
195 TATTA
* * * **
3351246 GAGGGGTA-TTTCGGGTAGTTAATCTAAAAAGTTTCGTAATTTATAAGATTAGCGGTGTAGTATT
1 GAGGGGTATTTTCAGGTAGTTAATCTAAAAAGTTTCGAAATTTATAAGATTAGAGGCATAGTATT
* * * *
3351310 GTAACTTATCTTTTAATTTAGTGT-AATACCGGCACATA-GAAACATTGTAA-TCGGGGTAAAAA
66 GGAACTTATCTTTTAACTGAG-GTCAATACCGACACATATGAAACATTGTAAGT-GGGGTAAAAA
* *
3351372 TCGCTTTCAAAATGGTTCCAAAGCTTGTTTTTTG-CATGAAGAAAAAGCTAAAATGGCTTGATA
129 TCGCATTCAAAATGGTTCCAAAGC-T-TTTTTTGACATGAAGAAAAAGCTAAAATAGCTTGATA
3351435 GGCATGTTCA
Statistics
Matches: 161, Mismatches: 24, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
197 1 0.01
198 68 0.42
199 75 0.47
200 17 0.11
ACGTcount: A:0.34, C:0.10, G:0.21, T:0.36
Consensus pattern (199 bp):
GAGGGGTATTTTCAGGTAGTTAATCTAAAAAGTTTCGAAATTTATAAGATTAGAGGCATAGTATT
GGAACTTATCTTTTAACTGAGGTCAATACCGACACATATGAAACATTGTAAGTGGGGTAAAAATC
GCATTCAAAATGGTTCCAAAGCTTTTTTTGACATGAAGAAAAAGCTAAAATAGCTTGATATGTAT
ATTA
Found at i:3358324 original size:25 final size:25
Alignment explanation
Indices: 3358290--3358338 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
3358280 TAATATTATG
*
3358290 TCCGTTTTGTTGTAGTTATGTAACT
1 TCCGTTTTGTTGTAGTAATGTAACT
3358315 TCCGTTTTGTTGTAGTAATGTAAC
1 TCCGTTTTGTTGTAGTAATGTAAC
3358339 GTCCTATTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.18, C:0.12, G:0.20, T:0.49
Consensus pattern (25 bp):
TCCGTTTTGTTGTAGTAATGTAACT
Found at i:3358389 original size:16 final size:16
Alignment explanation
Indices: 3358348--3358380 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
3358338 CGTCCTATTA
3358348 GTAAAGAAAAAGGAGT
1 GTAAAGAAAAAGGAGT
3358364 GTAAAGAAAAAGGAGT
1 GTAAAGAAAAAGGAGT
3358380 G
1 G
3358381 AACTGAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.33, T:0.12
Consensus pattern (16 bp):
GTAAAGAAAAAGGAGT
Found at i:3368543 original size:41 final size:41
Alignment explanation
Indices: 3368498--3368578 Score: 135
Period size: 41 Copynumber: 2.0 Consensus size: 41
3368488 AGTGAGTACA
* *
3368498 TATCAGTTCAGCTTTGGTACATTCGTGTATCAATGTTCAGT
1 TATCAGTTCAGCTTTGGTACATTCATGTATCAATGCTCAGT
*
3368539 TATCAGTTTAGCTTTGGTACATTCATGTATCAATGCTCAG
1 TATCAGTTCAGCTTTGGTACATTCATGTATCAATGCTCAG
3368579 CACCGTTGGT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.41
Consensus pattern (41 bp):
TATCAGTTCAGCTTTGGTACATTCATGTATCAATGCTCAGT
Found at i:3372348 original size:3 final size:3
Alignment explanation
Indices: 3372335--3372435 Score: 59
Period size: 3 Copynumber: 33.3 Consensus size: 3
3372325 AAAAAATACT
3372335 ATA AT- ATA ATA ATA ATA ATA AGTA AT- ATA ATA ATA A-A A-A ATA
1 ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA
* * * * *
3372377 TTAA ATAA ATA CTA CTA AT- ATA ATA ACA TAGA ATA ATA TATA ATAA
1 AT-A AT-A ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA -ATA AT-A
*
3372423 ATA ACA ATA ATA A
1 ATA ATA ATA ATA A
3372436 AAAAAAATTC
Statistics
Matches: 80, Mismatches: 9, Indels: 18
0.75 0.08 0.17
Matches are distributed among these distances:
2 10 0.12
3 53 0.66
4 17 0.21
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:3372387 original size:21 final size:22
Alignment explanation
Indices: 3372323--3372387 Score: 64
Period size: 21 Copynumber: 3.0 Consensus size: 22
3372313 TATATGTTAT
3372323 ATAAAAAATACTATAATATAATA
1 ATAAAAAATACTA-AATATAATA
* *
3372346 AT-AATAATAAGT-AATATAATA
1 ATAAAAAAT-ACTAAATATAATA
*
3372367 ATAAAAAATATTAAATA-AATA
1 ATAAAAAATACTAAATATAATA
3372388 CTACTAATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
21 17 0.49
22 14 0.40
23 4 0.11
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (22 bp):
ATAAAAAATACTAAATATAATA
Found at i:3372434 original size:38 final size:35
Alignment explanation
Indices: 3372335--3372434 Score: 89
Period size: 38 Copynumber: 2.7 Consensus size: 35
3372325 AAAAAATACT
*
3372335 ATAATATAATAAT-AATAATAAGTAATATAATAATAA
1 ATAATAT-ATAATAAATAACAA-TAATATAATAATAA
* *
3372371 AAAATAT-TAAATAAAT-ACTACTAATATAATAACATAGA
1 ATAATATAT-AATAAATAAC-AATAATATAAT-A-ATA-A
3372409 ATAATATATAATAAATAACAATAATA
1 ATAATATATAATAAATAACAATAATA
3372435 AAAAAAAATT
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
34 1 0.02
35 13 0.25
36 11 0.22
37 3 0.06
38 20 0.39
39 3 0.06
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.31
Consensus pattern (35 bp):
ATAATATATAATAAATAACAATAATATAATAATAA
Found at i:3372756 original size:86 final size:85
Alignment explanation
Indices: 3372588--3372758 Score: 195
Period size: 86 Copynumber: 2.0 Consensus size: 85
3372578 TTGATTTGAG
* * * *
3372588 TATTAATTTTATTAAATTAAATTGAAATTGAGATCAAATTGGTTCTATGTAAGCAATGAGTGTCA
1 TATTAAATTTATTAAATTAAATTAAAATTAAGATCAAATTGGTTATATGTAAGCAATGAGTG-CA
** *
3372653 CCACCTGATTTAAATATTAAA
65 CCAAATGATTAAAATATTAAA
* *
3372674 TATTAAATTTATTAAATTAAATTAAAATTAAGATCAAATTGGTTAAATGTGTAAGTAATGAG-G-
1 TATTAAATTTATTAAATTAAATTAAAATTAAGATCAAATTGGTT--ATATGTAAGCAATGAGTGC
3372737 ACCAAAT-ATATAAATATATTAA
64 ACCAAATGAT-TAAA-ATATTAA
3372759 TTTTTTTTAA
Statistics
Matches: 72, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
84 2 0.03
85 8 0.11
86 48 0.67
87 1 0.01
88 13 0.18
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.37
Consensus pattern (85 bp):
TATTAAATTTATTAAATTAAATTAAAATTAAGATCAAATTGGTTATATGTAAGCAATGAGTGCAC
CAAATGATTAAAATATTAAA
Found at i:3382855 original size:21 final size:20
Alignment explanation
Indices: 3382831--3382873 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
3382821 ATTGAGGGAC
*
3382831 AGGGTATATTTGGCATTCTAT
1 AGGGTATAGTTGGCATT-TAT
3382852 AGGGTATAGTTGGCATTTAT
1 AGGGTATAGTTGGCATTTAT
3382872 AG
1 AG
3382874 CAGTTGTAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.26, C:0.07, G:0.28, T:0.40
Consensus pattern (20 bp):
AGGGTATAGTTGGCATTTAT
Found at i:3382938 original size:39 final size:40
Alignment explanation
Indices: 3382881--3382970 Score: 128
Period size: 39 Copynumber: 2.2 Consensus size: 40
3382871 TAGCAGTTGT
*
3382881 AGGTTTATATTAGCACTAGTGGGTAAGG-ACACTAAGTGC
1 AGGTTTATATTAGAACTAGTGGGTAAGGAACACTAAGTGC
*
3382920 AGGTTTATATTAGAACTAGTGTGTAAGGACACACTAAGTGC
1 AGGTTTATATTAGAACTAGTGGGTAAGGA-ACACTAAGTGC
**
3382961 AACTTTATAT
1 AGGTTTATAT
3382971 CCAGATTAGC
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
39 26 0.58
41 19 0.42
ACGTcount: A:0.33, C:0.12, G:0.23, T:0.31
Consensus pattern (40 bp):
AGGTTTATATTAGAACTAGTGGGTAAGGAACACTAAGTGC
Found at i:3387198 original size:38 final size:38
Alignment explanation
Indices: 3387147--3387222 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
3387137 TTCATCCTAA
3387147 GTCAAATATGAATAATTAAATTTGTATCTTCCAATTTT
1 GTCAAATATGAATAATTAAATTTGTATCTTCCAATTTT
3387185 GTCAAATATGAATAATTAAATTTGTATCTTCCAATTTT
1 GTCAAATATGAATAATTAAATTTGTATCTTCCAATTTT
3387223 TCCCTTGAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.37, C:0.11, G:0.08, T:0.45
Consensus pattern (38 bp):
GTCAAATATGAATAATTAAATTTGTATCTTCCAATTTT
Found at i:3388075 original size:29 final size:29
Alignment explanation
Indices: 3388018--3388075 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
3388008 AAAAGTTAAA
*
3388018 AAATGAAAAAATAGAAAAATAAAAGAAAT
1 AAATGAAAAAATAGAAAAATAAAAAAAAT
3388047 AAATGAAAAAATA-ATAAAA-AAAATAAAAT
1 AAATGAAAAAATAGA-AAAATAAAA-AAAAT
3388076 GATGAAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
28 5 0.19
29 21 0.81
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.16
Consensus pattern (29 bp):
AAATGAAAAAATAGAAAAATAAAAAAAAT
Found at i:3388083 original size:25 final size:24
Alignment explanation
Indices: 3388030--3388085 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 24
3388020 ATGAAAAAAT
*
3388030 AGAAA-AATAAAAGAAATAAATGA
1 AGAAATAATAAAAAAAATAAATGA
*
3388053 AAAAATAATAAAAAAAATAAAATGA
1 AGAAATAATAAAAAAAAT-AAATGA
*
3388078 TGAAATAA
1 AGAAATAA
3388086 ATCCTCAGAC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 4 0.15
24 11 0.41
25 12 0.44
ACGTcount: A:0.75, C:0.00, G:0.09, T:0.16
Consensus pattern (24 bp):
AGAAATAATAAAAAAAATAAATGA
Found at i:3397326 original size:15 final size:15
Alignment explanation
Indices: 3397306--3397338 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
3397296 TATATTCTTT
3397306 ATTTCATGCA-TTTAA
1 ATTTCA-GCACTTTAA
3397321 ATTTCAGCACTTTAA
1 ATTTCAGCACTTTAA
3397336 ATT
1 ATT
3397339 ATAGTATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 3 0.18
15 14 0.82
ACGTcount: A:0.33, C:0.15, G:0.06, T:0.45
Consensus pattern (15 bp):
ATTTCAGCACTTTAA
Found at i:3417884 original size:3 final size:3
Alignment explanation
Indices: 3417876--3417902 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3417866 TTCAAATTCC
3417876 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
3417903 TTACCCATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:3420118 original size:14 final size:16
Alignment explanation
Indices: 3420091--3420123 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3420081 TGCATCAAGA
3420091 GTTATAAATATATATT
1 GTTATAAATATATATT
3420107 GTTA-AAATTATATATT
1 GTTATAAA-TATATATT
3420123 G
1 G
3420124 CAATGGTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 3 0.19
16 13 0.81
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.48
Consensus pattern (16 bp):
GTTATAAATATATATT
Found at i:3420245 original size:55 final size:55
Alignment explanation
Indices: 3420156--3420470 Score: 452
Period size: 55 Copynumber: 5.7 Consensus size: 55
3420146 GTATTACAGA
*
3420156 CACTATGTGTGTAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTACATG
1 CACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTACATG
* * *
3420211 CACTATGTGTGCAAATCCATGGAATTCATAATGAGTTGATGAATAACCGTACAAG
1 CACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTACATG
* * *
3420266 CACTATGTGTGCAAATCCATGGAATTCATCATCAGTTGATGAATAACCGTACAGG
1 CACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTACATG
* * * * *
3420321 TATTATGTGTGTAAATCCACGAAATTCATTATGAGTTGATGAATAACCGTACATG
1 CACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTACATG
* * *
3420376 CACTATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAATAATCGTATA-G
1 CACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTACATG
* * *
3420430 ACACTATGTGTACAAATCCACAGAATTCATCACGAGTTGAT
1 -CACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGAT
3420471 TAACTATCGT
Statistics
Matches: 234, Mismatches: 25, Indels: 2
0.90 0.10 0.01
Matches are distributed among these distances:
54 1 0.00
55 233 1.00
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (55 bp):
CACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTACATG
Found at i:3420437 original size:165 final size:165
Alignment explanation
Indices: 3420159--3420470 Score: 502
Period size: 165 Copynumber: 1.9 Consensus size: 165
3420149 TTACAGACAC
*
3420159 TATGTGTGTAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTACATGCACTATGTGTGCA
1 TATGTGTGTAAATCCACGAAATTCATCATGAGTTGATGAATAACCGTACATGCACTATGTGTGCA
* * * **
3420224 AATCCATGGAATTCATAATGAGTTGATGAATAACCGTACAAGCACTATGTGTGCAAATCCATGGA
66 AATCCACGAAATTCATAATGAGTTGATGAATAACCGTACAAGCACTATGTGTACAAATCCACAGA
3420289 ATTCATCATC-AGTTGATGAATAACCGTACAGGTAT
131 ATTCATCA-CGAGTTGATGAATAACCGTACAGGTAT
*
3420324 TATGTGTGTAAATCCACGAAATTCATTATGAGTTGATGAATAACCGTACATGCACTATGTGTGCA
1 TATGTGTGTAAATCCACGAAATTCATCATGAGTTGATGAATAACCGTACATGCACTATGTGTGCA
* * *
3420389 AATCCACGAAATTCATCATGAGTTGATGAATAATCGTA-TAGACACTATGTGTACAAATCCACAG
66 AATCCACGAAATTCATAATGAGTTGATGAATAACCGTACAAG-CACTATGTGTACAAATCCACAG
3420453 AATTCATCACGAGTTGAT
130 AATTCATCACGAGTTGAT
3420471 TAACTATCGT
Statistics
Matches: 135, Mismatches: 10, Indels: 4
0.91 0.07 0.03
Matches are distributed among these distances:
164 3 0.02
165 132 0.98
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (165 bp):
TATGTGTGTAAATCCACGAAATTCATCATGAGTTGATGAATAACCGTACATGCACTATGTGTGCA
AATCCACGAAATTCATAATGAGTTGATGAATAACCGTACAAGCACTATGTGTACAAATCCACAGA
ATTCATCACGAGTTGATGAATAACCGTACAGGTAT
Found at i:3426703 original size:22 final size:21
Alignment explanation
Indices: 3426654--3426724 Score: 85
Period size: 22 Copynumber: 3.5 Consensus size: 21
3426644 TGAAAAAATG
3426654 GTATCGATACCATA-T-TAGA
1 GTATCGATACCATAGTATAGA
*
3426673 GTATTGATACCATAGTATAGTA
1 GTATCGATACCATAGTATAG-A
* *
3426695 GTATCGATACCATGGTAT-GG
1 GTATCGATACCATAGTATAGA
3426715 GTATCGATAC
1 GTATCGATAC
3426725 TAATGAGCCA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
19 13 0.29
20 11 0.24
21 4 0.09
22 17 0.38
ACGTcount: A:0.32, C:0.14, G:0.21, T:0.32
Consensus pattern (21 bp):
GTATCGATACCATAGTATAGA
Found at i:3427122 original size:55 final size:55
Alignment explanation
Indices: 3427057--3427261 Score: 259
Period size: 55 Copynumber: 3.7 Consensus size: 55
3427047 GTACTACAAA
* ** * **
3427057 CACTATGTGTGAAAATTCTTGGAATTCATCACGAGTTGATGAATAACCGTACAGG
1 CACTATGTGTGAAAATCCACGGAATTCATCATGAGTTGATGAATAATAGTACAGG
* * *
3427112 CACTATGTGTGCAAATCCACGAAATTCACCATGAGTTGATGAATAATAGTACAGG
1 CACTATGTGTGAAAATCCACGGAATTCATCATGAGTTGATGAATAATAGTACAGG
* * * **
3427167 CACTATGTGTGAAAATCCACGGAATTCATCATGAGTTTATCAATAATTGTACAAA
1 CACTATGTGTGAAAATCCACGGAATTCATCATGAGTTGATGAATAATAGTACAGG
*
3427222 CACTATGTGTGCAAATCCACGGAA-TCTATCATGAGTTGAT
1 CACTATGTGTGAAAATCCACGGAATTC-ATCATGAGTTGAT
3427262 CGTACATGCA
Statistics
Matches: 130, Mismatches: 19, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
54 2 0.02
55 128 0.98
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.29
Consensus pattern (55 bp):
CACTATGTGTGAAAATCCACGGAATTCATCATGAGTTGATGAATAATAGTACAGG
Found at i:3427255 original size:110 final size:110
Alignment explanation
Indices: 3427057--3427261 Score: 286
Period size: 110 Copynumber: 1.9 Consensus size: 110
3427047 GTACTACAAA
* ** * **
3427057 CACTATGTGTGAAAATTCTTGGAATTCATCACGAGTTGATGAATAACCGTACAGGCACTATGTGT
1 CACTATGTGTGAAAATCCACGGAATTCATCACGAGTTGATCAATAACCGTACAAACACTATGTGT
3427122 GCAAATCCACGAAATTCACCATGAGTTGATGAATAATAGTACAGG
66 GCAAATCCACGAAATTCACCATGAGTTGATGAATAATAGTACAGG
* * **
3427167 CACTATGTGTGAAAATCCACGGAATTCATCATGAGTTTATCAATAATTGTACAAACACTATGTGT
1 CACTATGTGTGAAAATCCACGGAATTCATCACGAGTTGATCAATAACCGTACAAACACTATGTGT
* *
3427232 GCAAATCCACGGAA-TCTATCATGAGTTGAT
66 GCAAATCCACGAAATTC-ACCATGAGTTGAT
3427262 CGTACATGCA
Statistics
Matches: 82, Mismatches: 12, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
109 2 0.02
110 80 0.98
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.29
Consensus pattern (110 bp):
CACTATGTGTGAAAATCCACGGAATTCATCACGAGTTGATCAATAACCGTACAAACACTATGTGT
GCAAATCCACGAAATTCACCATGAGTTGATGAATAATAGTACAGG
Found at i:3444745 original size:24 final size:24
Alignment explanation
Indices: 3444700--3444749 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
3444690 GGGTGGTTGG
*
3444700 TTTAATGGATGTTTAAACTTTATT
1 TTTAATGGATATTTAAACTTTATT
*
3444724 TTTAATGGTATATTT-AAGTTTATT
1 TTTAATGG-ATATTTAAACTTTATT
3444748 TT
1 TT
3444750 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 18 0.78
25 5 0.22
ACGTcount: A:0.28, C:0.02, G:0.12, T:0.58
Consensus pattern (24 bp):
TTTAATGGATATTTAAACTTTATT
Found at i:3447933 original size:18 final size:17
Alignment explanation
Indices: 3447912--3447957 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 17
3447902 GTCGTGAGTG
*
3447912 TTTGTTTTTTTATTTTTA
1 TTTGTTTTATT-TTTTTA
3447930 TTTGTTTTATTTTTTTA
1 TTTGTTTTATTTTTTTA
3447947 ---GTTTTATTTTT
1 TTTGTTTTATTTTT
3447958 AATATTATTG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
14 11 0.41
17 6 0.22
18 10 0.37
ACGTcount: A:0.11, C:0.00, G:0.07, T:0.83
Consensus pattern (17 bp):
TTTGTTTTATTTTTTTA
Found at i:3447950 original size:14 final size:15
Alignment explanation
Indices: 3447919--3447958 Score: 64
Period size: 14 Copynumber: 2.7 Consensus size: 15
3447909 GTGTTTGTTT
*
3447919 TTTTATTTTTATTTG
1 TTTTATTTTTATTAG
3447934 TTTTATTTTT-TTAG
1 TTTTATTTTTATTAG
3447948 TTTTATTTTTA
1 TTTTATTTTTA
3447959 ATATTATTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 13 0.57
15 10 0.43
ACGTcount: A:0.15, C:0.00, G:0.05, T:0.80
Consensus pattern (15 bp):
TTTTATTTTTATTAG
Found at i:3447963 original size:23 final size:23
Alignment explanation
Indices: 3447916--3447963 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
3447906 TGAGTGTTTG
* *
3447916 TTTTTTTATTTTTATTTGTTTTA
1 TTTTTTTAGTTTTATTTGTTATA
3447939 TTTTTTTAGTTTTATTT-TTAATA
1 TTTTTTTAGTTTTATTTGTT-ATA
3447962 TT
1 TT
3447964 ATTGTTTTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 2 0.09
23 20 0.91
ACGTcount: A:0.17, C:0.00, G:0.04, T:0.79
Consensus pattern (23 bp):
TTTTTTTAGTTTTATTTGTTATA
Found at i:3450307 original size:24 final size:24
Alignment explanation
Indices: 3450262--3450311 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
3450252 TGGTGGTTGG
*
3450262 TTTAATGGATGTTTAAACTTTATT
1 TTTAATGGATATTTAAACTTTATT
*
3450286 TTTAATGGTATATTT-AAGTTTATT
1 TTTAATGG-ATATTTAAACTTTATT
3450310 TT
1 TT
3450312 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 18 0.78
25 5 0.22
ACGTcount: A:0.28, C:0.02, G:0.12, T:0.58
Consensus pattern (24 bp):
TTTAATGGATATTTAAACTTTATT
Found at i:3458473 original size:21 final size:21
Alignment explanation
Indices: 3458431--3458474 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
3458421 ACTCCAGGAG
* *
3458431 CTAGTTCCTCACGAGCTGCTC
1 CTAGCTCCTCACGAGCTCCTC
* *
3458452 CTAGCTCCTCTCGTGCTCCTC
1 CTAGCTCCTCACGAGCTCCTC
3458473 CT
1 CT
3458475 CCTCCAGCTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.43, G:0.16, T:0.32
Consensus pattern (21 bp):
CTAGCTCCTCACGAGCTCCTC
Found at i:3459160 original size:28 final size:29
Alignment explanation
Indices: 3459120--3459176 Score: 107
Period size: 28 Copynumber: 2.0 Consensus size: 29
3459110 AGGGTGAGAA
3459120 ATGTTAAAGTGTTAAAATGTTTTAAAAGG
1 ATGTTAAAGTGTTAAAATGTTTTAAAAGG
3459149 ATGTT-AAGTGTTAAAATGTTTTAAAAGG
1 ATGTTAAAGTGTTAAAATGTTTTAAAAGG
3459177 GAGAAGTGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 23 0.82
29 5 0.18
ACGTcount: A:0.40, C:0.00, G:0.21, T:0.39
Consensus pattern (29 bp):
ATGTTAAAGTGTTAAAATGTTTTAAAAGG
Found at i:3459647 original size:65 final size:63
Alignment explanation
Indices: 3459575--3459734 Score: 205
Period size: 65 Copynumber: 2.5 Consensus size: 63
3459565 AATCAAATTG
* *
3459575 AACATCGAATGCATTTAATGCATCGATGCACATACCATGCACCGATGCACTGAGGAT-TTTATGA
1 AACATCGAATGCATTTGATGCATCGATGCACA-ACCATGCACCGATGCACTCAGGATATTT-TG-
3459639 A
63 A
* * * * *
3459640 AACATCGAATGCATTTGATGTATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGA
1 AACATCGAATGCATTTGATGCATCGATGCA-CAACCATGCACCGATGCACTCAGGATATTTTGA
*
3459704 AACATCGAATGCACTTGATGCATCGATGCAC
1 AACATCGAATGCATTTGATGCATCGATGCAC
3459735 TCTTAGTGCA
Statistics
Matches: 84, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
63 1 0.01
64 29 0.35
65 49 0.58
66 5 0.06
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (63 bp):
AACATCGAATGCATTTGATGCATCGATGCACAACCATGCACCGATGCACTCAGGATATTTTGA
Found at i:3459734 original size:17 final size:19
Alignment explanation
Indices: 3459706--3459754 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
3459696 TATTTTGAAA
3459706 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
3459724 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
3459743 CACCGATGCACT
1 CATCGATGCACT
3459755 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:3462962 original size:23 final size:23
Alignment explanation
Indices: 3462936--3462985 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
3462926 CCATTTTTTT
*
3462936 AAAACAATTA-AATATTATTTTAA
1 AAAACAATTAGAAT-TTATTTGAA
*
3462959 AAAATAATTATGAATTTATTTGAA
1 AAAACAATTA-GAATTTATTTGAA
3462983 AAA
1 AAA
3462986 CAGGGAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 9 0.39
24 11 0.48
25 3 0.13
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (23 bp):
AAAACAATTAGAATTTATTTGAA
Found at i:3465639 original size:48 final size:48
Alignment explanation
Indices: 3465574--3465665 Score: 148
Period size: 48 Copynumber: 1.9 Consensus size: 48
3465564 TCAGGGGATG
* * *
3465574 ACACGGTTCCTATGTGATGAGGACGGTTGGCCATCTTTAGGGATGATA
1 ACACAGTTCCTACGTGATGAGGACGGCTGGCCATCTTTAGGGATGATA
*
3465622 ACACAGTTCCTACGTGATGAGGATGGCTGGCCATCTTTAGGGAT
1 ACACAGTTCCTACGTGATGAGGACGGCTGGCCATCTTTAGGGAT
3465666 AATGTTTCAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 40 1.00
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.28
Consensus pattern (48 bp):
ACACAGTTCCTACGTGATGAGGACGGCTGGCCATCTTTAGGGATGATA
Found at i:3465775 original size:65 final size:65
Alignment explanation
Indices: 3465667--3465809 Score: 198
Period size: 65 Copynumber: 2.2 Consensus size: 65
3465657 TTTAGGGATA
* ** * *
3465667 ATGTTTCAAGAAAAACCGTCTCAAGAGAGACAAAATTTGTTTCATGGGAAATAGA-CTCAAAGAT
1 ATGTTTCAAGAGAAACCGTCTCAAGAGAGACAAAATTCATTTCAAGGGAAAT-GATATCAAAGAT
3465731 G
65 G
* * *
3465732 ATGTTTTAAGAGAAACTGTCTCAAGAGAGACACAATTCATTTCAAGGGAAATGATATCAAAGATG
1 ATGTTTCAAGAGAAACCGTCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGATATCAAAGATG
3465797 ATGTTTCAAGAGA
1 ATGTTTCAAGAGA
3465810 GACAAAATTT
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
64 2 0.03
65 66 0.97
ACGTcount: A:0.41, C:0.13, G:0.20, T:0.26
Consensus pattern (65 bp):
ATGTTTCAAGAGAAACCGTCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGATATCAAAGATG
Found at i:3465809 original size:50 final size:50
Alignment explanation
Indices: 3465752--3465859 Score: 153
Period size: 50 Copynumber: 2.2 Consensus size: 50
3465742 AGAAACTGTC
* * * *
3465752 TCAAGAGAGACACAATTCATTTCAAGGGAAATGATATCAAAGATGATGTT
1 TCAAGAGAGACAAAATTCATTTCAAGAGAAACGATATCAAAGATGATATT
** *
3465802 TCAAGAGAGACAAAATTTGTTTCAAGAGAAACGATCTCAAAGATGATATT
1 TCAAGAGAGACAAAATTCATTTCAAGAGAAACGATATCAAAGATGATATT
3465852 TCAAGAGA
1 TCAAGAGA
3465860 AATTATCTTA
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.44, C:0.12, G:0.19, T:0.25
Consensus pattern (50 bp):
TCAAGAGAGACAAAATTCATTTCAAGAGAAACGATATCAAAGATGATATT
Found at i:3465841 original size:115 final size:115
Alignment explanation
Indices: 3465687--3465913 Score: 330
Period size: 115 Copynumber: 2.0 Consensus size: 115
3465677 AAAAACCGTC
* * * * *
3465687 TCAAGAGAGACAAAATTTGTTTCATGGGAAATAGACTCAAAGATGATGTTTTAAGAGAAACTGTC
1 TCAAGAGAGACAAAATTTGTTTCAAGAGAAATAGACTCAAAGATGATATTTCAAGAGAAACTATC
* *
3465752 TCAAGAGAGACACAATTCATTTCAAGGGAAATGATATCAAAGATGATGTT
66 TCAAGAGAGACAAAATTCATTTCAAGGGAAACGATATCAAAGATGATGTT
* *
3465802 TCAAGAGAGACAAAATTTGTTTCAAGAGAAA-CGATCTCAAAGATGATATTTCAAGAGAAATTAT
1 TCAAGAGAGACAAAATTTGTTTCAAGAGAAATAGA-CTCAAAGATGATATTTCAAGAGAAACTAT
* * *
3465866 CTTAAGAGAGACAAAATTCGTTTCAAGGGAAACGATCTCAAAGATGAT
65 CTCAAGAGAGACAAAATTCATTTCAAGGGAAACGATATCAAAGATGAT
3465914 TTTATCAATT
Statistics
Matches: 99, Mismatches: 12, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
114 2 0.02
115 97 0.98
ACGTcount: A:0.42, C:0.12, G:0.20, T:0.26
Consensus pattern (115 bp):
TCAAGAGAGACAAAATTTGTTTCAAGAGAAATAGACTCAAAGATGATATTTCAAGAGAAACTATC
TCAAGAGAGACAAAATTCATTTCAAGGGAAACGATATCAAAGATGATGTT
Found at i:3466072 original size:38 final size:37
Alignment explanation
Indices: 3465948--3466062 Score: 158
Period size: 38 Copynumber: 3.0 Consensus size: 37
3465938 ACAACTTCAG
* *
3465948 AATTTGTATTTTAAAGAAAAAAATGTCTCTAGTGAGACGA
1 AATTTGT-TTTT-AAG-AAAAATTGTCTCTAGCGAGACGA
* *
3465988 AATTTGTTTTTAAGAGAAAATTGTCTCAAGCGAGACAA
1 AATTTGTTTTTAAGA-AAAATTGTCTCTAGCGAGACGA
3466026 AATTTGTTTTTAAGAAAAATTGTCTCTAGCGAGACGA
1 AATTTGTTTTTAAGAAAAATTGTCTCTAGCGAGACGA
3466063 CGCTTTGTTT
Statistics
Matches: 68, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
37 21 0.31
38 36 0.53
39 4 0.06
40 7 0.10
ACGTcount: A:0.39, C:0.10, G:0.18, T:0.33
Consensus pattern (37 bp):
AATTTGTTTTTAAGAAAAATTGTCTCTAGCGAGACGA
Found at i:3467246 original size:10 final size:10
Alignment explanation
Indices: 3467231--3467298 Score: 55
Period size: 10 Copynumber: 6.1 Consensus size: 10
3467221 TCTTGTCCTC
3467231 TTTTTTTCTT
1 TTTTTTTCTT
3467241 TTTTTTTCTT
1 TTTTTTTCTT
3467251 TGCACTTTTTTCTT
1 T----TTTTTTCTT
*
3467265 TGTTTTTCTT
1 TTTTTTTCTT
*
3467275 TTTCTTTGCTT
1 TTT-TTTTCTT
3467286 TGCTTTTTTCTT
1 T--TTTTTTCTT
3467298 T
1 T
3467299 GCTTTAATAT
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
10 21 0.45
11 7 0.15
12 7 0.15
13 2 0.04
14 10 0.21
ACGTcount: A:0.01, C:0.15, G:0.06, T:0.78
Consensus pattern (10 bp):
TTTTTTTCTT
Found at i:3467292 original size:33 final size:33
Alignment explanation
Indices: 3467233--3467299 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 33
3467223 TTGTCCTCTT
*
3467233 TTTTTCTTTTTTTTTCTTTGCACTTTTTTCTTTG
1 TTTTTCTTTTTTTTGCTTTG-ACTTTTTTCTTTG
3467267 TTTTTCTTTTTCTTTGCTTTG-CTTTTTTCTTTG
1 TTTTTCTTTTT-TTTGCTTTGACTTTTTTCTTTG
3467300 CTTTAATATG
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
33 12 0.39
34 11 0.35
35 8 0.26
ACGTcount: A:0.01, C:0.15, G:0.07, T:0.76
Consensus pattern (33 bp):
TTTTTCTTTTTTTTGCTTTGACTTTTTTCTTTG
Found at i:3467300 original size:17 final size:17
Alignment explanation
Indices: 3467238--3467303 Score: 75
Period size: 17 Copynumber: 3.9 Consensus size: 17
3467228 CTCTTTTTTT
3467238 CTTTTTT-TTT-CTTTG
1 CTTTTTTCTTTGCTTTG
* *
3467253 CACTTTTTTCTTTGTTTTT
1 --CTTTTTTCTTTGCTTTG
3467272 C-TTTTTCTTTGCTTTG
1 CTTTTTTCTTTGCTTTG
3467288 CTTTTTTCTTTGCTTT
1 CTTTTTTCTTTGCTTT
3467304 AATATGATCT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
16 14 0.33
17 22 0.52
18 3 0.07
19 3 0.07
ACGTcount: A:0.02, C:0.17, G:0.08, T:0.74
Consensus pattern (17 bp):
CTTTTTTCTTTGCTTTG
Found at i:3469909 original size:23 final size:23
Alignment explanation
Indices: 3469877--3469934 Score: 98
Period size: 23 Copynumber: 2.5 Consensus size: 23
3469867 TCAAAACCAT
*
3469877 TTTTTTAAAAAAATAATTAAATA
1 TTTTTAAAAAAAATAATTAAATA
3469900 TTTTTAAAAAAAATAATTAAATA
1 TTTTTAAAAAAAATAATTAAATA
3469923 TTATTTAAAAAA
1 TT-TTTAAAAAA
3469935 CAATTATGAC
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 24 0.73
24 9 0.27
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
TTTTTAAAAAAAATAATTAAATA
Found at i:3472758 original size:13 final size:13
Alignment explanation
Indices: 3472723--3472760 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
3472713 CCCTGCACGT
3472723 TTGTGCGTGTAT-
1 TTGTGCGTGTATA
**
3472735 TTGTGTATGTATA
1 TTGTGCGTGTATA
3472748 TTGTGCGTGTATA
1 TTGTGCGTGTATA
3472761 CGTGTGGTAT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.16, C:0.05, G:0.29, T:0.50
Consensus pattern (13 bp):
TTGTGCGTGTATA
Found at i:3475050 original size:15 final size:14
Alignment explanation
Indices: 3475007--3475047 Score: 64
Period size: 15 Copynumber: 2.9 Consensus size: 14
3474997 TAAATCAAGG
3475007 AAAAAATAAAAATA
1 AAAAAATAAAAATA
*
3475021 AAAAACATAAGAATA
1 AAAAA-ATAAAAATA
3475036 AAAAAATAAAAA
1 AAAAAATAAAAA
3475048 ATAGATGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.83, C:0.02, G:0.02, T:0.12
Consensus pattern (14 bp):
AAAAAATAAAAATA
Found at i:3475092 original size:15 final size:14
Alignment explanation
Indices: 3475072--3475113 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
3475062 ATCGAAGAGG
*
3475072 GAAAAAATATTAAAT
1 GAAAAAATA-AAAAT
*
3475087 GAAAAATTAAAAAT
1 GAAAAAATAAAAAT
3475101 GAAAAAATAAAAA
1 GAAAAAATAAAAA
3475114 AATAGAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 16 0.67
15 8 0.33
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.19
Consensus pattern (14 bp):
GAAAAAATAAAAAT
Found at i:3476508 original size:38 final size:38
Alignment explanation
Indices: 3476461--3476632 Score: 256
Period size: 38 Copynumber: 4.5 Consensus size: 38
3476451 TTTAAAATTT
3476461 AAAACTATATAATATATATGTTTTTAAAAATAATTTTC
1 AAAACTATATAATATATATGTTTTTAAAAATAATTTTC
* *
3476499 AAAACTATATAATATATATATTTTTAAAAATAATTATC
1 AAAACTATATAATATATATGTTTTTAAAAATAATTTTC
* *
3476537 AAAATTATATAATATATAT-TTTTAAAAAATAATTTTC
1 AAAACTATATAATATATATGTTTTTAAAAATAATTTTC
* **
3476574 AAAACTATATAATATATATGTTTTCAAAAATTGTTTTC
1 AAAACTATATAATATATATGTTTTTAAAAATAATTTTC
3476612 AAAACTATAATATATATATAT
1 AAAACTAT-ATA-ATATATAT
3476633 ATATATATAT
Statistics
Matches: 122, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
37 34 0.28
38 77 0.63
39 3 0.02
40 8 0.07
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (38 bp):
AAAACTATATAATATATATGTTTTTAAAAATAATTTTC
Found at i:3476576 original size:75 final size:76
Alignment explanation
Indices: 3476461--3476632 Score: 256
Period size: 75 Copynumber: 2.2 Consensus size: 76
3476451 TTTAAAATTT
* *
3476461 AAAACTATATAATATATATGTTTTTAAAAATAATTTTCAAAACTATATAATATATATATTTTTAA
1 AAAACTATATAATATATATGTTTTAAAAAATAATTTTCAAAACTATATAATATATATATTTTCAA
3476526 AAATAATTATC
66 AAATAATTATC
* *
3476537 AAAATTATATAATATATAT-TTTTAAAAAATAATTTTCAAAACTATATAATATATATGTTTTCAA
1 AAAACTATATAATATATATGTTTTAAAAAATAATTTTCAAAACTATATAATATATATATTTTCAA
** *
3476601 AAATTGTTTTC
66 AAATAATTATC
3476612 AAAACTATAATATATATATAT
1 AAAACTAT-ATA-ATATATAT
3476633 ATATATATAT
Statistics
Matches: 86, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
75 57 0.66
76 21 0.24
77 8 0.09
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (76 bp):
AAAACTATATAATATATATGTTTTAAAAAATAATTTTCAAAACTATATAATATATATATTTTCAA
AAATAATTATC
Found at i:3476628 original size:2 final size:2
Alignment explanation
Indices: 3476617--3476662 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
3476607 TTTTCAAAAC
3476617 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3476658 TA TA T
1 TA TA T
3476663 TCAAAATATT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3476681 original size:103 final size:102
Alignment explanation
Indices: 3476537--3476799 Score: 293
Period size: 103 Copynumber: 2.6 Consensus size: 102
3476527 AATAATTATC
* * * * * *
3476537 AAAATTATATA-ATATATAT-TTTTAAAAAATAATTTTCAAAACTATATAATATATATGTTTTCA
1 AAAACTATATATATATATATATATT-CAAAATATTTTTAAAAACTATATTATATATATGTTTTC-
* *
3476600 AAAATTGTTTTCAAAACTATA-ATATATATATATATATAT-A
64 AAAA-TGTTTTAAAAACCATATAT-TATATATATATAT-TCA
* *
3476640 TATA-TATATATATATATATATATTCAAAATATTTTTAAAAACCATATATTATATATATGTTTTC
1 AAAACTATATATATATATATATATTCAAAATATTTTTAAAAA-C-TATATTATATATATGTTTTC
*
3476704 AATATGTTTTAAAAACCATATATTATATATATATATTCA
64 AAAATGTTTTAAAAACCATATATTATATATATATATTCA
* * * *
3476743 AAAACTATATATATATATATATTTTCAAAATGTTTTCAAAAACTATATTATAGATAT
1 AAAACTATATATATATATATATATTCAAAATATTTTTAAAAACTATATTATATATAT
3476800 ATATATATTT
Statistics
Matches: 137, Mismatches: 16, Indels: 15
0.82 0.10 0.09
Matches are distributed among these distances:
102 20 0.15
103 55 0.40
104 43 0.31
105 19 0.14
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.44
Consensus pattern (102 bp):
AAAACTATATATATATATATATATTCAAAATATTTTTAAAAACTATATTATATATATGTTTTCAA
AATGTTTTAAAAACCATATATTATATATATATATTCA
Found at i:3476714 original size:38 final size:38
Alignment explanation
Indices: 3476643--3476744 Score: 152
Period size: 38 Copynumber: 2.6 Consensus size: 38
3476633 ATATATATAT
3476643 ATATATATATATATATATATTCAAAATATTTTTAAAAACC
1 ATATAT-TATATATATATATTC-AAATATTTTTAAAAACC
* *
3476683 ATATATTATATATATGTTTTC-AATATGTTTTAAAAACC
1 ATATATTATATATATATATTCAAATAT-TTTTAAAAACC
3476721 ATATATTATATATATATATTCAAA
1 ATATATTATATATATATATTCAAA
3476745 AACTATATAT
Statistics
Matches: 56, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
37 5 0.09
38 30 0.54
39 15 0.27
40 6 0.11
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.45
Consensus pattern (38 bp):
ATATATTATATATATATATTCAAATATTTTTAAAAACC
Found at i:3476733 original size:25 final size:26
Alignment explanation
Indices: 3476705--3476772 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 26
3476695 TATGTTTTCA
*
3476705 ATATGTTTTAAAAACCATATATTATAT
1 ATATATTTTAAAAACCATATA-TATAT
* *
3476732 ATATATATTCAAAAACTATATATATAT
1 ATATAT-TTTAAAAACCATATATATAT
*
3476759 ATATATTTTCAAAA
1 ATATATTTTAAAAA
3476773 TGTTTTCAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
26 6 0.17
27 16 0.46
28 13 0.37
ACGTcount: A:0.49, C:0.07, G:0.01, T:0.43
Consensus pattern (26 bp):
ATATATTTTAAAAACCATATATATAT
Found at i:3476763 original size:38 final size:38
Alignment explanation
Indices: 3476632--3476807 Score: 101
Period size: 38 Copynumber: 4.6 Consensus size: 38
3476622 TATATATATA
*
3476632 TATATATATATATATATATATATATATATATTCAAAATA-
1 TATATATATACATATAT-TATATATATATATTCAAAA-AC
* * * * * * * **
3476671 TTTTTAAAAACCATATATTATATATATGTTTTCAATATG
1 TATATATATA-CATATATTATATATATATATTCAAAAAC
* * *
3476710 T-TTTAAAAACCATATATTATATATATATATTCAAAAAC
1 TATATATATA-CATATATTATATATATATATTCAAAAAC
* * * * *
3476748 TATATATATATATATATTTTCA-AAATGTTTTCAAAAAC
1 TATATATATACATATATTAT-ATATATATATTCAAAAAC
*
3476786 TATAT-TATAGATATA-TATATAT
1 TATATATATACATATATTATATAT
3476808 TTCGAAAACT
Statistics
Matches: 107, Mismatches: 25, Indels: 13
0.74 0.17 0.09
Matches are distributed among these distances:
35 1 0.01
36 3 0.03
37 9 0.08
38 59 0.55
39 29 0.27
40 6 0.06
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.45
Consensus pattern (38 bp):
TATATATATACATATATTATATATATATATTCAAAAAC
Found at i:3476805 original size:66 final size:66
Alignment explanation
Indices: 3476676--3476803 Score: 190
Period size: 65 Copynumber: 2.0 Consensus size: 66
3476666 AAATATTTTT
* *
3476676 AAAAACCATATATTATATATATGTTTTCAATATGTTTTAAAAACCATATATTATATATATATATT
1 AAAAACCATATATTATATATATATTTTCAAAATGTTTTAAAAACCATATATTATATATATATATT
3476741 C
66 C
* *
3476742 AAAAACTATATA-TATATATATATTTTCAAAATGTTTTCAAAAA-C-TATATTATAGATATATAT
1 AAAAACCATATATTATATATATATTTTCAAAATGTTTT-AAAAACCATATATTATATATATATAT
3476804 ATATTTCGAA
Statistics
Matches: 57, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
64 17 0.30
65 24 0.42
66 16 0.28
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (66 bp):
AAAAACCATATATTATATATATATTTTCAAAATGTTTTAAAAACCATATATTATATATATATATT
C
Found at i:3477720 original size:85 final size:85
Alignment explanation
Indices: 3477607--3478516 Score: 1053
Period size: 85 Copynumber: 10.7 Consensus size: 85
3477597 GTCATCGAGA
* * * ** * *
3477607 TGAATGGAATCGAACTCGACA-GTTTTTGTTGACAGATAACTTTTCTCGATTTAAGTTATACTGT
1 TGAATGTAATCGAACTCGA-AGGTCTTTGTTGACAGATAACTCTTCTCGCCTTGAGTTATGCTGT
* *
3477671 AAATTTGACATGCCCTTGAGC
65 AAATTTGATATGCCTTTGAGC
* * * * *
3477692 TGAATGGAATCGAACTCAAAGGTATTTGTTGACAGATAACTATTCTCGCCTTGAGTTATGATGTA
1 TGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACTCTTCTCGCCTTGAGTTATGCTGTA
3477757 AATTTGATATGTCC-TTGAGC
66 AATTTGATATG-CCTTTGAGC
* * * * * ** *
3477777 TGAATGTAATCGAACTCGAAGGTCTTGGTTGACAAATAGCCCTTCTCTCAATGAGCTATGCTGTA
1 TGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACTCTTCTCGCCTTGAGTTATGCTGTA
3477842 AATTTGATATGCCTTTGAGC
66 AATTTGATATGCCTTTGAGC
* * *
3477862 TGAATGTAATCGAACCCGAAGGTCTTTGCTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTA
1 TGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACTCTTCTCGCCTTGAGTTATGCTGTA
*
3477927 AATTTGATAT-TCTTCTGAGC
66 AATTTGATATGCCTT-TGAGC
** **
3477947 TGAATGTAATCGAACTCGAAGGTC-TTGATTGACAGATAGTTCTTCTCGCCTTGAGCCATGCTGT
1 TGAATGTAATCGAACTCGAAGGTCTTTG-TTGACAGATAACTCTTCTCGCCTTGAGTTATGCTGT
*
3478011 AAATTTGATATGCCTTTGAGA
65 AAATTTGATATGCCTTTGAGC
* * * * *
3478032 TGAATGTAAT-GAAACTCGCAGGTCTTGGTTGACAGATAACTCTTCTCGACTTGAGTTGTGATGT
1 TGAATGTAATCG-AACTCGAAGGTCTTTGTTGACAGATAACTCTTCTCGCCTTGAGTTATGCTGT
*
3478096 AAATTTGATATGCCTTTGAGT
65 AAATTTGATATGCCTTTGAGC
* ** * * ** *
3478117 TGAATGTAATCAAACTC-ACATATCTTAGTTGACATATAACTCTTCTCGCCTTGACCTATGCTAT
1 TGAATGTAATCGAACTCGA-AGGTCTTTGTTGACAGATAACTCTTCTCGCCTTGAGTTATGCTGT
3478181 AAATTTGATATGCCTTTGAGC
65 AAATTTGATATGCCTTTGAGC
* * * * * * * * *
3478202 TAAATGTAATCAAACTC-ACATGTCTTGGTTGACAGGTAGCCCTTCTTGCCTTGAGCTATGCTGT
1 TGAATGTAATCGAACTCGA-AGGTCTTTGTTGACAGATAACTCTTCTCGCCTTGAGTTATGCTGT
* *
3478266 AAATTTCATGTGCCTTTGAGC
65 AAATTTGATATGCCTTTGAGC
* * * * *
3478287 TTAATGTAATCGAACTCGAAGGTCTTGGTTGACAGATAACCCTTATCGCCTTGAGTTAGGCTGTA
1 TGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACTCTTCTCGCCTTGAGTTATGCTGTA
3478352 AATTTGATATGCCTTTGAGC
66 AATTTGATATGCCTTTGAGC
* * * * * * *
3478372 TGAATGTAATCGAACTCGCAGGTCTTGGTTGACAGATAGCCCTTCTCGCATTGAGCTATGTTGTA
1 TGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACTCTTCTCGCCTTGAGTTATGCTGTA
*
3478437 AATTTGATGTGCCTTTGAGC
66 AATTTGATATGCCTTTGAGC
*
3478457 TGAATGTAATCGAACTCGAAGGTCTTTTGTTGGA-AGATAACCCTTCTCGCCTTGAGTTAT
1 TGAATGTAATCGAACTCGAAGGTC-TTTGTT-GACAGATAACTCTTCTCGCCTTGAGTTAT
3478517 ACTGCGAATA
Statistics
Matches: 711, Mismatches: 101, Indels: 25
0.85 0.12 0.03
Matches are distributed among these distances:
84 10 0.01
85 663 0.93
86 36 0.05
87 2 0.00
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (85 bp):
TGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACTCTTCTCGCCTTGAGTTATGCTGTA
AATTTGATATGCCTTTGAGC
Found at i:3478695 original size:86 final size:86
Alignment explanation
Indices: 3478584--3478743 Score: 248
Period size: 86 Copynumber: 1.9 Consensus size: 86
3478574 ATAATTTTTT
* * * *
3478584 AGGTGGTTCCCCTTAGCGGGTCTGAACCAAATGATATGATTTTTGGATGACTCCCCTTCACGGGA
1 AGGTGGTTACCCTTAGCGGGTCTGAACCAAATGAGATGATCTTTGGATGACTCCCCTTCACAGGA
3478649 AAGCCATGTAGTATATTTCTC
66 AAGCCATGTAGTATATTTCTC
* **
3478670 AGGTGGTTACCCTTAGCGGGTCTGAACTAGGTGAGATGATCTTTGGATGACTCCCCTTCACAGGA
1 AGGTGGTTACCCTTAGCGGGTCTGAACCAAATGAGATGATCTTTGGATGACTCCCCTTCACAGGA
*
3478735 AAGTCATGT
66 AAGCCATGT
3478744 GTGATGTTCA
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
86 66 1.00
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (86 bp):
AGGTGGTTACCCTTAGCGGGTCTGAACCAAATGAGATGATCTTTGGATGACTCCCCTTCACAGGA
AAGCCATGTAGTATATTTCTC
Found at i:3479990 original size:95 final size:95
Alignment explanation
Indices: 3479795--3480057 Score: 339
Period size: 95 Copynumber: 2.7 Consensus size: 95
3479785 AGCTAGTTTG
* * * *
3479795 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTTTAGTGGGACAGCTCAA-CATCATTGTATAGAT
1 ATCCATAAAGTCGGGGCGTTTAACCAATTGCTTTAGAGGGACAGCTCAAGCTTTATTG--T--AT
3479859 ATTATAATCACCTATATCAGGCTAGCTGAATATT
62 ATTATAATCACCTATATCAGGCTAGCTGAATATT
* * * *
3479893 ATCCATAAAGTCGGGGCGTTTAACCAATTGCTATAGAGAGACAACTTAAGCTTTATTGTATATTA
1 ATCCATAAAGTCGGGGCGTTTAACCAATTGCTTTAGAGGGACAGCTCAAGCTTTATTGTATATTA
* * * *
3479958 TAATCACTTTTATCAGGCTAGTTGAATCTT
66 TAATCACCTATATCAGGCTAGCTGAATATT
* * *
3479988 ATCCATAAAGTCGGGGTGTTTAACTAATTACTTTAGAGGGACAGCTCAAGCTTTATTGTATATAT
1 ATCCATAAAGTCGGGGCGTTTAACCAATTGCTTTAGAGGGACAGCTCAAGCTTTATTGTATAT-T
3480053 ATAAT
65 ATAAT
3480058 ATTATAATTT
Statistics
Matches: 144, Mismatches: 19, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
95 88 0.61
96 6 0.04
97 1 0.01
98 43 0.30
99 6 0.04
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (95 bp):
ATCCATAAAGTCGGGGCGTTTAACCAATTGCTTTAGAGGGACAGCTCAAGCTTTATTGTATATTA
TAATCACCTATATCAGGCTAGCTGAATATT
Found at i:3483718 original size:39 final size:41
Alignment explanation
Indices: 3483639--3483718 Score: 110
Period size: 39 Copynumber: 2.0 Consensus size: 41
3483629 ATAAATGTTA
*
3483639 AATAAATCAAGGAAAAAATAAAAATAAAAAACATAAGAAAAC
1 AATAAATCAA-GAAAAAATAAAAATAAAAAACAGAAGAAAAC
* *
3483681 AATAAATCAA-AAAAAAT-AAAATAAAAAAGAGATGAAAA
1 AATAAATCAAGAAAAAATAAAAATAAAAAACAGAAGAAAA
3483719 TAAATCGAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
39 18 0.51
40 7 0.20
42 10 0.29
ACGTcount: A:0.75, C:0.05, G:0.07, T:0.12
Consensus pattern (41 bp):
AATAAATCAAGAAAAAATAAAAATAAAAAACAGAAGAAAAC
Found at i:3485135 original size:37 final size:38
Alignment explanation
Indices: 3485131--3485239 Score: 152
Period size: 37 Copynumber: 2.9 Consensus size: 38
3485121 TTTTGAAAAT
*
3485131 AATTTTCAAAACTATATAATATA-A-ATTTTTAAAAAT
1 AATTTTCAAAACTATATAATATATATGTTTTTAAAAAT
*
3485167 AATTTTCAAAACTATATAATATATAT-TTTTAAAAAAT
1 AATTTTCAAAACTATATAATATATATGTTTTTAAAAAT
* * *
3485204 AATTTTCAAAGCTATATAATATGTATGTTTTCAAAA
1 AATTTTCAAAACTATATAATATATATGTTTTTAAAA
3485240 CTATAATATA
Statistics
Matches: 66, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
36 23 0.35
37 35 0.53
38 8 0.12
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.42
Consensus pattern (38 bp):
AATTTTCAAAACTATATAATATATATGTTTTTAAAAAT
Found at i:3485172 original size:73 final size:73
Alignment explanation
Indices: 3485088--3485225 Score: 224
Period size: 73 Copynumber: 1.9 Consensus size: 73
3485078 AAATATAATA
**
3485088 AAAAACAATTTT-AAAACTATATAATATATATGTTTTTGAAAATAATTTTCAAAACTATATAATA
1 AAAAACAATTTTCAAAACTATATAATATATAT-TTTTAAAAAATAATTTTCAAAACTATATAATA
3485152 TAAATTTTT
65 TAAATTTTT
* *
3485161 AAAAATAATTTTCAAAACTATATAATATATATTTTTAAAAAATAATTTTCAAAGCTATATAATAT
1 AAAAACAATTTTCAAAACTATATAATATATATTTTTAAAAAATAATTTTCAAAACTATATAATAT
3485226 GTATGTTTTC
Statistics
Matches: 60, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
73 41 0.68
74 19 0.32
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.41
Consensus pattern (73 bp):
AAAAACAATTTTCAAAACTATATAATATATATTTTTAAAAAATAATTTTCAAAACTATATAATAT
AAATTTTT
Found at i:3485195 original size:36 final size:36
Alignment explanation
Indices: 3485113--3485239 Score: 182
Period size: 36 Copynumber: 3.5 Consensus size: 36
3485103 ACTATATAAT
* *
3485113 ATATATGTTTTTGAAAATAATTTTCAAAACTATATA
1 ATATATATTTTTAAAAATAATTTTCAAAACTATATA
*
3485149 ATATAAATTTTTAAAAATAATTTTCAAAACTATATA
1 ATATATATTTTTAAAAATAATTTTCAAAACTATATA
*
3485185 ATATATATTTTTAAAAAATAATTTTCAAAGCTATATA
1 ATATATATTTTT-AAAAATAATTTTCAAAACTATATA
* *
3485222 ATATGTATGTTTTCAAAA
1 ATATATAT-TTTTAAAAA
3485240 CTATAATATA
Statistics
Matches: 82, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
36 44 0.54
37 34 0.41
38 4 0.05
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (36 bp):
ATATATATTTTTAAAAATAATTTTCAAAACTATATA
Found at i:3485250 original size:25 final size:25
Alignment explanation
Indices: 3485205--3485264 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
3485195 TTAAAAAATA
* *
3485205 ATTTTCAAAGCTATATAATATGTAT
1 ATTTTCAAAACTATATAATATATAT
*
3485230 GTTTTCAAAACTATA-ATATATATAT
1 ATTTTCAAAACTATATA-ATATATAT
*
3485255 ATATTCAAAA
1 ATTTTCAAAA
3485265 ATATTTTTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
24 1 0.03
25 28 0.97
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.42
Consensus pattern (25 bp):
ATTTTCAAAACTATATAATATATAT
Found at i:3485302 original size:40 final size:38
Alignment explanation
Indices: 3485228--3485336 Score: 132
Period size: 38 Copynumber: 2.9 Consensus size: 38
3485218 TATAATATGT
* *
3485228 ATGTTTTCAAAA-C-TATAATATATATATATATTCAAAA
1 ATGTTTTAAAAACCATATATTATATATATATATTC-AAA
* * *
3485265 ATATTTTTAAAAACCATATATTATATATATGTTTTCAAA
1 AT-GTTTTAAAAACCATATATTATATATATATATTCAAA
*
3485304 ATGTTTTAAAAATCATATATTATATATATATAT
1 ATGTTTTAAAAACCATATATTATATATATATAT
3485337 ATATTCAAAC
Statistics
Matches: 60, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
37 2 0.03
38 35 0.58
39 6 0.10
40 17 0.28
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.45
Consensus pattern (38 bp):
ATGTTTTAAAAACCATATATTATATATATATATTCAAA
Found at i:3485303 original size:65 final size:62
Alignment explanation
Indices: 3485169--3485304 Score: 166
Period size: 62 Copynumber: 2.1 Consensus size: 62
3485159 TTAAAAATAA
* * * *
3485169 TTTTCAAAACTATATAATATATATTTTTAAAAAATAATTTTCAAAGCTATATAATATGTATG
1 TTTTCAAAACTATATAATATATATTATTAAAAAATAATTTTAAAACCTATATAATATATATG
* * *
3485231 TTTTCAAAACTATA-ATATATATATATATTCAAAAATATTTTTAAAAACCATATATTATATATAT
1 TTTTCAAAACTATATA-ATATATAT-TATTAAAAAATAATTTT-AAAACC-TATATAATATATAT
3485295 G
62 G
3485296 TTTTCAAAA
1 TTTTCAAAA
3485305 TGTTTTAAAA
Statistics
Matches: 63, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
61 1 0.02
62 22 0.35
63 14 0.22
64 4 0.06
65 22 0.35
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.43
Consensus pattern (62 bp):
TTTTCAAAACTATATAATATATATTATTAAAAAATAATTTTAAAACCTATATAATATATATG
Found at i:3485332 original size:42 final size:45
Alignment explanation
Indices: 3485281--3485367 Score: 110
Period size: 42 Copynumber: 2.0 Consensus size: 45
3485271 TTAAAAACCA
* * *
3485281 TATATTATATATATGTTTTCAAA-ATGTTTT-AAAAA-TCATATAT
1 TATATTATATATATATATTCAAACACGTTTTCAAAAACT-ATATAT
3485324 TATA-TATATATATATATTCAAACACGTTTTCAAAAACTATATAT
1 TATATTATATATATATATTCAAACACGTTTTCAAAAACTATATAT
3485368 ATTTTCAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
42 16 0.42
43 10 0.26
44 11 0.29
45 1 0.03
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (45 bp):
TATATTATATATATATATTCAAACACGTTTTCAAAAACTATATAT
Found at i:3485385 original size:30 final size:31
Alignment explanation
Indices: 3485330--3485402 Score: 112
Period size: 31 Copynumber: 2.4 Consensus size: 31
3485320 ATATTATATA
3485330 TATATATATATTCAAACACGTTTTCAAAAAC
1 TATATATATATTCAAACACGTTTTCAAAAAC
* *
3485361 TATATATATTTTCAAA-ATGTTTTCAAAAAC
1 TATATATATATTCAAACACGTTTTCAAAAAC
3485391 TATATTATATAT
1 TATA-TATATAT
3485403 ATATATATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
30 17 0.45
31 21 0.55
ACGTcount: A:0.44, C:0.11, G:0.03, T:0.42
Consensus pattern (31 bp):
TATATATATATTCAAACACGTTTTCAAAAAC
Found at i:3486448 original size:42 final size:43
Alignment explanation
Indices: 3486401--3486505 Score: 140
Period size: 45 Copynumber: 2.4 Consensus size: 43
3486391 TGGAAACCTT
* *
3486401 AACGGCATTTTTATACA-AAACACCACGATGGAGTAGTACTTC
1 AACGGCGTATTTATACACAAACACCACGATGGAGTAGTACTTC
***
3486443 AACGGCGTATTTATACACCGCCGCACCACGATGGAGTAGTACTTC
1 AACGGCGTATTTATACA-C-AAACACCACGATGGAGTAGTACTTC
3486488 AACGGCGTATTTATACAC
1 AACGGCGTATTTATACAC
3486506 CGCCGCAGTA
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
42 15 0.27
44 1 0.02
45 39 0.71
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (43 bp):
AACGGCGTATTTATACACAAACACCACGATGGAGTAGTACTTC
Found at i:3486479 original size:45 final size:45
Alignment explanation
Indices: 3486421--3486512 Score: 184
Period size: 45 Copynumber: 2.0 Consensus size: 45
3486411 TTATACAAAA
3486421 CACCACGATGGAGTAGTACTTCAACGGCGTATTTATACACCGCCG
1 CACCACGATGGAGTAGTACTTCAACGGCGTATTTATACACCGCCG
3486466 CACCACGATGGAGTAGTACTTCAACGGCGTATTTATACACCGCCG
1 CACCACGATGGAGTAGTACTTCAACGGCGTATTTATACACCGCCG
3486511 CA
1 CA
3486513 GTAGTTTAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.22
Consensus pattern (45 bp):
CACCACGATGGAGTAGTACTTCAACGGCGTATTTATACACCGCCG
Found at i:3486621 original size:83 final size:82
Alignment explanation
Indices: 3486471--3486677 Score: 254
Period size: 83 Copynumber: 2.5 Consensus size: 82
3486461 CGCCGCACCA
* * * * * * * *
3486471 CGATGGAGTAGTACTTCAACGGCGTATTTATAC-ACCGCCGCAGTAGTTTAATCCATAGTGGTGT
1 CGATAGAGTAGTACTTTAGCGGCGTTTTTATACAAACACCGCAGTAGGTTAATCCATAATGGTGT
*
3486535 TTTTTCAACAAACGTCG
66 TTTTTCAACAAACGCCG
* * *
3486552 TGATAGAGTAGTACTTTAGCGGCGTTTTTACACAAACACCGCAGTAGGGTTCATCCATAATGGTG
1 CGATAGAGTAGTACTTTAGCGGCGTTTTTATACAAACACCGCAGTA-GGTTAATCCATAATGGTG
3486617 TTTTTTCAACAAACGCCG
65 TTTTTTCAACAAACGCCG
* * * *
3486635 CGATAGAGTAATACTTTAGTGGCGTTTTTGTACAAACAGCGCA
1 CGATAGAGTAGTACTTTAGCGGCGTTTTTATACAAACACCGCA
3486678 ATAGTTCAAT
Statistics
Matches: 106, Mismatches: 18, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
81 27 0.25
82 10 0.09
83 69 0.65
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (82 bp):
CGATAGAGTAGTACTTTAGCGGCGTTTTTATACAAACACCGCAGTAGGTTAATCCATAATGGTGT
TTTTTCAACAAACGCCG
Found at i:3486662 original size:42 final size:42
Alignment explanation
Indices: 3486526--3486663 Score: 120
Period size: 42 Copynumber: 3.3 Consensus size: 42
3486516 GTTTAATCCA
* * * *
3486526 TAGTGGTGTTTTTTCAACAAACGTCGTGATAGAGTAGTACTT
1 TAGTGGCGTTTTTTCAACAAACGCCGCGATAGAGTAATACTT
* * * * * **
3486568 TAGCGGCGTTTTTAC-ACAAACACCGC-AGTAGGGTTCAT-CCA
1 TAGTGGCGTTTTTTCAACAAACGCCGCGA-TAGAG-TAATACTT
* *
3486609 TAATGGTGTTTTTTCAACAAACGCCGCGATAGAGTAATACTT
1 TAGTGGCGTTTTTTCAACAAACGCCGCGATAGAGTAATACTT
3486651 TAGTGGCGTTTTT
1 TAGTGGCGTTTTT
3486664 GTACAAACAG
Statistics
Matches: 69, Mismatches: 22, Indels: 10
0.68 0.22 0.10
Matches are distributed among these distances:
40 1 0.01
41 27 0.39
42 40 0.58
43 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.34
Consensus pattern (42 bp):
TAGTGGCGTTTTTTCAACAAACGCCGCGATAGAGTAATACTT
Found at i:3487310 original size:71 final size:73
Alignment explanation
Indices: 3487226--3487376 Score: 252
Period size: 72 Copynumber: 2.1 Consensus size: 73
3487216 TCTCCTAAGA
3487226 TTGCTTGATAAAATGGGAA-AATGTGTATGGCTTTGCGTTGATGGTTGTCCTT-TTTTTTCTTTT
1 TTGCTTGATAAAATGGGAAGAATGTGTATGGCTTTGCGTTGATGGTTGTCCTTCTTTTTTCTTTT
3487289 ATATAATG
66 ATATAATG
* * *
3487297 TTGCTTGATAAAATGGGAAGGATGTGTATGGTTTTGTGTTGATGGTTGTCCTTGCTTTTTTCTTT
1 TTGCTTGATAAAATGGGAAGAATGTGTATGGCTTTGCGTTGATGGTTGTCCTT-CTTTTTTCTTT
3487362 TATATAATG
65 TATATAATG
3487371 TTGCTT
1 TTGCTT
3487377 AATACACTGC
Statistics
Matches: 74, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
71 19 0.26
72 30 0.41
74 25 0.34
ACGTcount: A:0.19, C:0.08, G:0.24, T:0.49
Consensus pattern (73 bp):
TTGCTTGATAAAATGGGAAGAATGTGTATGGCTTTGCGTTGATGGTTGTCCTTCTTTTTTCTTTT
ATATAATG
Found at i:3488959 original size:43 final size:43
Alignment explanation
Indices: 3488906--3489002 Score: 124
Period size: 43 Copynumber: 2.3 Consensus size: 43
3488896 TTTGTATTAC
* **
3488906 AAACGCCACTAAAAACAATAGAATTAGTGACGTTTGT-GACAAA
1 AAACGCCACTAAAAACAAGAGAATTAGCAACGTTTGTAGAC-AA
* **
3488949 AAACACCACTAAAAACAAGATTATTAGCAACGTTTGTAGACAA
1 AAACGCCACTAAAAACAAGAGAATTAGCAACGTTTGTAGACAA
3488992 AAACGCCACTA
1 AAACGCCACTA
3489003 TAAATCACAA
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
43 43 0.93
44 3 0.07
ACGTcount: A:0.47, C:0.20, G:0.13, T:0.20
Consensus pattern (43 bp):
AAACGCCACTAAAAACAAGAGAATTAGCAACGTTTGTAGACAA
Found at i:3493093 original size:21 final size:21
Alignment explanation
Indices: 3493067--3493114 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
3493057 TGCCCCTTTT
*
3493067 TAACTT-CACAATTTCGGTGCC
1 TAACTTCCACAATGT-GGTGCC
*
3493088 TAACTTCCATAATGTGGTGCC
1 TAACTTCCACAATGTGGTGCC
3493109 TAACTT
1 TAACTT
3493115 TGATTTTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 18 0.75
22 6 0.25
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.35
Consensus pattern (21 bp):
TAACTTCCACAATGTGGTGCC
Found at i:3495862 original size:16 final size:16
Alignment explanation
Indices: 3495837--3495882 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
3495827 CCGACCAAAT
*
3495837 TTCACAATTCACATAA
1 TTCACTATTCACATAA
3495853 TTCACTATTCACGA-AA
1 TTCACTATTCAC-ATAA
3495869 TTCACTATTCACAT
1 TTCACTATTCACAT
3495883 GAATAGTAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
15 1 0.04
16 25 0.93
17 1 0.04
ACGTcount: A:0.37, C:0.26, G:0.02, T:0.35
Consensus pattern (16 bp):
TTCACTATTCACATAA
Found at i:3500520 original size:21 final size:21
Alignment explanation
Indices: 3500496--3500538 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
3500486 CCCAGAATAG
*
3500496 AGGGAATCGGTACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
3500517 AGGGAATCGATACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
3500538 A
1 A
3500539 ATATTCAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (21 bp):
AGGGAATCGATACCCCTTCAT
Done.