Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A01
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: 104050246
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4660000 characters in sequence are not A, C, G, or T
File 4 of 316
Found at i:1061553 original size:79 final size:81
Alignment explanation
Indices: 1061417--1061601 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
1061407 TTGAATGATG
* *
1061417 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
1061481 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
1061496 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
1061558 ATTGTGCGAGTTACTATA
64 ATTGTGCGAGATACTATA
* *
1061576 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
1061602 AACGAGTAGC
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 57 0.63
80 33 0.36
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
TGTGCGAGATACTATA
Found at i:1061615 original size:40 final size:40
Alignment explanation
Indices: 1061418--1061601 Score: 207
Period size: 40 Copynumber: 4.6 Consensus size: 40
1061408 TGAATGATGT
* * * *
1061418 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
1061458 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
1061498 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* *
1061536 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
1061577 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
1061602 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
39 35 0.28
40 79 0.64
41 10 0.08
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:1061623 original size:79 final size:79
Alignment explanation
Indices: 1061470--1061634 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
1061460 GGACTAAGAT
* * **
1061470 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
1061535 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
1061549 CCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCAATTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
1061612 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
1061628 CCGAAGG
1 CCGAAGG
1061635 TACGTGATTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.03
79 47 0.64
80 25 0.34
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:1066647 original size:19 final size:19
Alignment explanation
Indices: 1066612--1066654 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
1066602 TCTTTCTTTC
*
1066612 CTTTTTCTTTATTTTATTT
1 CTTTTTCTTTATATTATTT
1066631 CTTTATTCTTT-TATTATTT
1 CTTT-TTCTTTATATTATTT
1066650 CTTTT
1 CTTTT
1066655 ATTATATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 1 0.05
19 15 0.68
20 6 0.27
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.77
Consensus pattern (19 bp):
CTTTTTCTTTATATTATTT
Found at i:1066664 original size:8 final size:8
Alignment explanation
Indices: 1066653--1066690 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
1066643 ATTATTTCTT
1066653 TTATTATA
1 TTATTATA
1066661 TTATTA-A
1 TTATTATA
*
1066668 CTATTATA
1 TTATTATA
1066676 TTATTATAA
1 TTATTAT-A
1066685 TTATTA
1 TTATTA
1066691 ATTTCTTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
7 6 0.23
8 13 0.50
9 7 0.27
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (8 bp):
TTATTATA
Found at i:1067264 original size:23 final size:23
Alignment explanation
Indices: 1067231--1067302 Score: 74
Period size: 23 Copynumber: 3.1 Consensus size: 23
1067221 TAGGGGTAAG
1067231 ATCTGAATCTGTATTTATTATGC
1 ATCTGAATCTGTATTTATTATGC
* * *
1067254 ATTTGAATCTGTGACTGA-TATGC
1 ATCTGAATCTGT-ATTTATTATGC
* * *
1067277 ATCTGAATATGTATCTGTTATGC
1 ATCTGAATCTGTATTTATTATGC
1067300 ATC
1 ATC
1067303 GATGTCTATA
Statistics
Matches: 38, Mismatches: 9, Indels: 4
0.75 0.18 0.08
Matches are distributed among these distances:
22 1 0.03
23 34 0.89
24 3 0.08
ACGTcount: A:0.26, C:0.14, G:0.17, T:0.43
Consensus pattern (23 bp):
ATCTGAATCTGTATTTATTATGC
Found at i:1069682 original size:78 final size:78
Alignment explanation
Indices: 1069553--1069709 Score: 269
Period size: 78 Copynumber: 2.0 Consensus size: 78
1069543 TCAGAGTGTG
* *
1069553 GATGGGCCAACTTCTAGCTTAGCTGATGAGATTGCAGCTGCTCCAGAATCGGATGTAGAAGTTGC
1 GATGGGCCAACTTCTAGCTTAGCTGATGAGATTGCAGCTGCTCCAGAATCGGAAGTAGAAGATGC
1069618 TACTGAATATGCC
66 TACTGAATATGCC
* *
1069631 GATGGGCCAACTTCTGGCTTAGCTGATGAGATTGCAGCTTCTCCAGAATCGGAAGTAGAAGATGC
1 GATGGGCCAACTTCTAGCTTAGCTGATGAGATTGCAGCTGCTCCAGAATCGGAAGTAGAAGATGC
*
1069696 TACTGAATCTGCC
66 TACTGAATATGCC
1069709 G
1 G
1069710 GCGGGAGGAA
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
78 74 1.00
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.26
Consensus pattern (78 bp):
GATGGGCCAACTTCTAGCTTAGCTGATGAGATTGCAGCTGCTCCAGAATCGGAAGTAGAAGATGC
TACTGAATATGCC
Found at i:1072460 original size:23 final size:23
Alignment explanation
Indices: 1072401--1072452 Score: 104
Period size: 23 Copynumber: 2.3 Consensus size: 23
1072391 TTTAAGTGGA
1072401 TGTGTTGGGAGGGTATATTTTGT
1 TGTGTTGGGAGGGTATATTTTGT
1072424 TGTGTTGGGAGGGTATATTTTGT
1 TGTGTTGGGAGGGTATATTTTGT
1072447 TGTGTT
1 TGTGTT
1072453 TGGTGGGTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.12, C:0.00, G:0.38, T:0.50
Consensus pattern (23 bp):
TGTGTTGGGAGGGTATATTTTGT
Found at i:1073496 original size:16 final size:16
Alignment explanation
Indices: 1073475--1073524 Score: 100
Period size: 16 Copynumber: 3.1 Consensus size: 16
1073465 GGTCTATGTG
1073475 AAAATAGAATGTCAAT
1 AAAATAGAATGTCAAT
1073491 AAAATAGAATGTCAAT
1 AAAATAGAATGTCAAT
1073507 AAAATAGAATGTCAAT
1 AAAATAGAATGTCAAT
1073523 AA
1 AA
1073525 TGGCAATGTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.58, C:0.06, G:0.12, T:0.24
Consensus pattern (16 bp):
AAAATAGAATGTCAAT
Found at i:1080482 original size:17 final size:15
Alignment explanation
Indices: 1080464--1080501 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
1080454 TAAAAATTTA
1080464 AAATTATAATAAATAT
1 AAATT-TAATAAATAT
*
1080480 AAATTTAATAAA-AG
1 AAATTTAATAAATAT
1080494 AAATTTAA
1 AAATTTAA
1080502 CGATTTTAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 9 0.43
15 7 0.33
16 5 0.24
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (15 bp):
AAATTTAATAAATAT
Found at i:1080778 original size:17 final size:18
Alignment explanation
Indices: 1080741--1080783 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
1080731 TTTATAATAA
* *
1080741 TTTTTAAATTTTCATTCT
1 TTTTTAAATATCCATTCT
1080759 TTTTTAAATATCCATT-T
1 TTTTTAAATATCCATTCT
1080776 TTTATTAA
1 TTT-TTAA
1080784 TTATTTGGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.28, C:0.09, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTTTAAATATCCATTCT
Found at i:1083806 original size:29 final size:29
Alignment explanation
Indices: 1083764--1083821 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
1083754 GCTCAGCTTC
1083764 AAGAATCCTCCAAAAATACGAAAAACTTA
1 AAGAATCCTCCAAAAATACGAAAAACTTA
1083793 AAGAATCCTCCAAAAATACGAAAAACTTA
1 AAGAATCCTCCAAAAATACGAAAAACTTA
1083822 GGGAAAGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.55, C:0.21, G:0.07, T:0.17
Consensus pattern (29 bp):
AAGAATCCTCCAAAAATACGAAAAACTTA
Found at i:1092906 original size:22 final size:21
Alignment explanation
Indices: 1092881--1092922 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1092871 AGTAATTTTA
1092881 TTTTACTGAAAAATGCTTTGCT
1 TTTTA-TGAAAAATGCTTTGCT
* *
1092903 TTTTATGTAAAATGTTTTGC
1 TTTTATGAAAAATGCTTTGC
1092923 AAAATTATTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.26, C:0.10, G:0.14, T:0.50
Consensus pattern (21 bp):
TTTTATGAAAAATGCTTTGCT
Found at i:1095777 original size:21 final size:20
Alignment explanation
Indices: 1095724--1095781 Score: 66
Period size: 21 Copynumber: 3.0 Consensus size: 20
1095714 AAAAAGAATA
1095724 AATTAAAAA-AA-TTAAATT
1 AATTAAAAATAATTTAAATT
*
1095742 AATTAAAAATTATTTAAATT
1 AATTAAAAATAATTTAAATT
* *
1095762 GAATTGAAACTAATTTAAAT
1 -AATTAAAAATAATTTAAAT
1095782 ATTTAATTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
18 9 0.27
19 1 0.03
20 7 0.21
21 16 0.48
ACGTcount: A:0.57, C:0.02, G:0.03, T:0.38
Consensus pattern (20 bp):
AATTAAAAATAATTTAAATT
Found at i:1099329 original size:44 final size:44
Alignment explanation
Indices: 1099266--1099355 Score: 171
Period size: 44 Copynumber: 2.0 Consensus size: 44
1099256 TTATTGTCTT
1099266 TTTTAAGGGTTAAATTACTTTTTTGGGTTTGAACTTGGCTACCA
1 TTTTAAGGGTTAAATTACTTTTTTGGGTTTGAACTTGGCTACCA
*
1099310 TTTTAAGGGTTAAATTACTTTTTTGGGTTTGAACTTGGCTGCCA
1 TTTTAAGGGTTAAATTACTTTTTTGGGTTTGAACTTGGCTACCA
1099354 TT
1 TT
1099356 CTCATGTTGG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.21, C:0.11, G:0.21, T:0.47
Consensus pattern (44 bp):
TTTTAAGGGTTAAATTACTTTTTTGGGTTTGAACTTGGCTACCA
Found at i:1100419 original size:7 final size:8
Alignment explanation
Indices: 1100392--1100418 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
1100382 ATGACTTTTA
1100392 TTTTAATT
1 TTTTAATT
1100400 TTTTAATT
1 TTTTAATT
1100408 TTTTAATT
1 TTTTAATT
1100416 TTT
1 TTT
1100419 ATTCTAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTTAATT
Found at i:1100635 original size:39 final size:39
Alignment explanation
Indices: 1100581--1100661 Score: 153
Period size: 39 Copynumber: 2.1 Consensus size: 39
1100571 AAGTTGGGTG
*
1100581 TAAATTCAGAAATATTTATAGATTATGTTAATTTAATTT
1 TAAATTCAGAAATATTTATAAATTATGTTAATTTAATTT
1100620 TAAATTCAGAAATATTTATAAATTATGTTAATTTAATTT
1 TAAATTCAGAAATATTTATAAATTATGTTAATTTAATTT
1100659 TAA
1 TAA
1100662 TTTTTTTTAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.48
Consensus pattern (39 bp):
TAAATTCAGAAATATTTATAAATTATGTTAATTTAATTT
Found at i:1102316 original size:24 final size:24
Alignment explanation
Indices: 1102288--1102336 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
1102278 TGGTTTTCAA
*
1102288 GATTATATATCCATAGTGAAGTGG
1 GATTATACATCCATAGTGAAGTGG
1102312 GATTATACATCCATAGTGAAGTGG
1 GATTATACATCCATAGTGAAGTGG
1102336 G
1 G
1102337 GTGGATTGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.10, G:0.27, T:0.31
Consensus pattern (24 bp):
GATTATACATCCATAGTGAAGTGG
Found at i:1107381 original size:185 final size:184
Alignment explanation
Indices: 1107061--1107432 Score: 534
Period size: 185 Copynumber: 2.0 Consensus size: 184
1107051 TCTTTGTATA
* * *
1107061 TTAGATTAAAGAGCAAATTAATATTTTCTGTTAAAAATTTTACCCATTTATACTGTTAAAAACTG
1 TTAGACTAAAGAGCAAACTAATATTTTCTGTCAAAAATTTTACCCATTTATACTGTTAAAAACTG
* * *
1107126 GCATAGCTAACAGAATAACTAAACAATAACACGTGGCATGCCACATGAACCTCATGCTGACGTAC
66 GCATAGCTAACAAAATAACTAAACAATAACACGTGACATGCCACATCAACCTCATGCTGACGTAC
* * *
1107191 AGGGACCAATTTTTTATAGCAAAACTGGA-TGAATTTTTTAACAAAATAATCAAT
131 AGGGACCAATTTTTAACAGCAAAA-TGGATTGAATTTTTTAACAAAAGAATCAAT
* * *
1107245 TTAGACTAAAGAGCAAAACTAATATTTTCTGTCAAAATTTTTATCCATTTTTACTGTTAAAAACT
1 TTAGACTAAAGAGC-AAACTAATATTTTCTGTCAAAAATTTTACCCATTTATACTGTTAAAAACT
* * * *
1107310 GGCAT-GTCTAATAAAATAACTAAACAATGACACGTGACGTGCCACATCTACCTCATG-TAGACG
65 GGCATAG-CTAACAAAATAACTAAACAATAACACGTGACATGCCACATCAACCTCATGCT-GACG
*
1107373 TTCAGGGACCAATTTTTAACAGCAAAATGGATTGAATTTTTTAACAAAAGAATCAAT
128 TACAGGGACCAATTTTTAACAGCAAAATGGATTGAATTTTTTAACAAAAGAATCAAT
1107430 TTA
1 TTA
1107433 CTCTTTGATC
Statistics
Matches: 167, Mismatches: 17, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
184 19 0.11
185 148 0.89
ACGTcount: A:0.40, C:0.16, G:0.13, T:0.31
Consensus pattern (184 bp):
TTAGACTAAAGAGCAAACTAATATTTTCTGTCAAAAATTTTACCCATTTATACTGTTAAAAACTG
GCATAGCTAACAAAATAACTAAACAATAACACGTGACATGCCACATCAACCTCATGCTGACGTAC
AGGGACCAATTTTTAACAGCAAAATGGATTGAATTTTTTAACAAAAGAATCAAT
Found at i:1110263 original size:51 final size:52
Alignment explanation
Indices: 1110199--1110301 Score: 133
Period size: 51 Copynumber: 2.0 Consensus size: 52
1110189 AGCAGCCGAC
*
1110199 TGACTTGATTCCAAACTTCT-TCCAG-TAATTCCAACTTCTCTTC-TAGATTCAG
1 TGACTTGACTCCAAACTTCTCT-CAGAT-ATTCCAACTTCTCTTCTTA-ATTCAG
*
1110251 TGACTTG-CTCCAAACTTCTCTCAGATATTCCAACTTCTTTTCTTAATTCAG
1 TGACTTGACTCCAAACTTCTCTCAGATATTCCAACTTCTCTTCTTAATTCAG
1110302 CAGCCTGCTC
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
51 35 0.76
52 11 0.24
ACGTcount: A:0.24, C:0.27, G:0.09, T:0.40
Consensus pattern (52 bp):
TGACTTGACTCCAAACTTCTCTCAGATATTCCAACTTCTCTTCTTAATTCAG
Found at i:1124791 original size:30 final size:29
Alignment explanation
Indices: 1124757--1124822 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 29
1124747 AATAATTATG
* *
1124757 AAAATTAAATCAAATTAAAATTTTATGTAT
1 AAAATTAAATAAAAATAAAA-TTTATGTAT
**
1124787 AAAATTGTATAAAAATAAAATTTATGTAT
1 AAAATTAAATAAAAATAAAATTTATGTAT
*
1124816 AACATTA
1 AAAATTA
1124823 TATATTGGAT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
29 14 0.47
30 16 0.53
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.38
Consensus pattern (29 bp):
AAAATTAAATAAAAATAAAATTTATGTAT
Found at i:1125054 original size:13 final size:13
Alignment explanation
Indices: 1125036--1125062 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1125026 TTATTCATAA
1125036 AAATTAAGAATTT
1 AAATTAAGAATTT
1125049 AAATTAAGAATTT
1 AAATTAAGAATTT
1125062 A
1 A
1125063 GTCCAATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (13 bp):
AAATTAAGAATTT
Found at i:1129573 original size:13 final size:13
Alignment explanation
Indices: 1129555--1129580 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1129545 CTTACTTTTC
1129555 AAAAAAAAAAGCA
1 AAAAAAAAAAGCA
1129568 AAAAAAAAAAGCA
1 AAAAAAAAAAGCA
1129581 TACTTTTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.85, C:0.08, G:0.08, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAGCA
Found at i:1134464 original size:225 final size:225
Alignment explanation
Indices: 1134073--1134524 Score: 701
Period size: 225 Copynumber: 2.0 Consensus size: 225
1134063 CAGTCCTCGG
* * * *
1134073 TTAAGCCAGTTCTATATCCTCCTAGTCTGCTGCCATCATTTGAAACATCATTTACGGCCCAGAAA
1 TTAAGCCAGTTCTATATCCTCCTAGTCCGCTGCCATCATTTAAAACATCATTCACGGCCCAAAAA
* * *
1134138 CCATCTCCATCACCTAAAGGATTGACACCACCTAAACCAACCACACCGTCTCTGAAACCCTCTTC
66 CCATCTCCATCACCAAAAGGATTGACACCACCAAAACCAACCACACCGTCTCCGAAACCCTCTTC
*
1134203 ATCGTCTTTTAAGCCAAGTCCATCCCTTAAGCCAACTCTATCAGAACTAGGGAAAGGAAAGTACA
131 ATCGTCTTCTAAGCCAAGTCCATCCCTTAAGCCAACTCTATCAGAACTAGGGAAAGGAAAGTACA
*
1134268 AAACACTCAATCCAGAGGATACATTACCGA
196 AAACACTCAATCCAAAGGATACATTACCGA
* ** *
1134298 TTAAGCC-GATTCTATATCCTCCTAGTCCGCTTCCATCATTTAAAATGTCATTCACGGCCGAAAA
1 TTAAGCCAG-TTCTATATCCTCCTAGTCCGCTGCCATCATTTAAAACATCATTCACGGCCCAAAA
* *
1134362 ACCATCTCCATCACCAAAAGGACTT-ACACCACCAAAATCAACCACACCGTCTCCGAAACGCTCT
65 ACCATCTCCATCACCAAAAGGA-TTGACACCACCAAAACCAACCACACCGTCTCCGAAACCCTCT
*
1134426 TCATCGTCTTCTAAGCCAAGTCCATCCCTTAAGCCAACTCTATCGGAACTAGGGAAAGGAAAGTA
129 TCATCGTCTTCTAAGCCAAGTCCATCCCTTAAGCCAACTCTATCAGAACTAGGGAAAGGAAAGTA
* * *
1134491 CAAAACAGTCGATCCAAAGGATACGTTACCGA
194 CAAAACACTCAATCCAAAGGATACATTACCGA
1134523 TT
1 TT
1134525 TACATGATTC
Statistics
Matches: 206, Mismatches: 19, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
224 1 0.00
225 203 0.99
226 2 0.01
ACGTcount: A:0.33, C:0.31, G:0.13, T:0.23
Consensus pattern (225 bp):
TTAAGCCAGTTCTATATCCTCCTAGTCCGCTGCCATCATTTAAAACATCATTCACGGCCCAAAAA
CCATCTCCATCACCAAAAGGATTGACACCACCAAAACCAACCACACCGTCTCCGAAACCCTCTTC
ATCGTCTTCTAAGCCAAGTCCATCCCTTAAGCCAACTCTATCAGAACTAGGGAAAGGAAAGTACA
AAACACTCAATCCAAAGGATACATTACCGA
Found at i:1137563 original size:19 final size:17
Alignment explanation
Indices: 1137539--1137583 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 17
1137529 GAGTGTTTAT
1137539 ATTATTTATTTATAATATG
1 ATTATTTATTTAT-AT-TG
1137558 ATTATTAATATTTATATTG
1 ATTATT--TATTTATATTG
1137577 ATTATTT
1 ATTATTT
1137584 TATATCTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
17 1 0.04
19 14 0.58
20 2 0.08
21 7 0.29
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (17 bp):
ATTATTTATTTATATTG
Found at i:1141120 original size:21 final size:20
Alignment explanation
Indices: 1141096--1141138 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
1141086 ACCTAAAAAA
1141096 AAAAAAC-AAATCTCAGATTTC
1 AAAAAACAAAATC-CA-ATTTC
*
1141117 AAAAATCAAAATCCAATTTC
1 AAAAAACAAAATCCAATTTC
1141137 AA
1 AA
1141139 TAAATAAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 7 0.35
21 8 0.40
22 5 0.25
ACGTcount: A:0.56, C:0.19, G:0.02, T:0.23
Consensus pattern (20 bp):
AAAAAACAAAATCCAATTTC
Found at i:1141143 original size:21 final size:21
Alignment explanation
Indices: 1141103--1141147 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 21
1141093 AAAAAAAAAC
1141103 AAATCTCAGATTTCAAAAATCA
1 AAATCTCAGATTTCAAAAAT-A
1141125 AAATC-CA-ATTTCAATAAATA
1 AAATCTCAGATTTCAA-AAATA
1141145 AAA
1 AAA
1141148 GGGAATAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 11 0.50
21 6 0.27
22 5 0.23
ACGTcount: A:0.56, C:0.16, G:0.02, T:0.27
Consensus pattern (21 bp):
AAATCTCAGATTTCAAAAATA
Found at i:1145673 original size:19 final size:19
Alignment explanation
Indices: 1145651--1145718 Score: 57
Period size: 20 Copynumber: 3.5 Consensus size: 19
1145641 TTAGAATTTT
*
1145651 TAAAATGTTGTAAAAAATA
1 TAAAATATTGTAAAAAATA
* * *
1145670 TAAATATATAT-TAGAAATTT
1 TAAA-ATAT-TGTAAAAAATA
*
1145690 TAAAATATTGAAAAAAATA
1 TAAAATATTGTAAAAAATA
1145709 TAAAAATATT
1 T-AAAATATT
1145719 AGAAATTTTA
Statistics
Matches: 37, Mismatches: 8, Indels: 7
0.71 0.15 0.13
Matches are distributed among these distances:
18 1 0.03
19 14 0.38
20 21 0.57
21 1 0.03
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (19 bp):
TAAAATATTGTAAAAAATA
Found at i:1145685 original size:39 final size:38
Alignment explanation
Indices: 1145633--1145735 Score: 154
Period size: 39 Copynumber: 2.7 Consensus size: 38
1145623 ATAAATTCTA
* * * *
1145633 AAAATATGTTAGAATTTTTAAAATGTTGTAAAAAATAT
1 AAAATATATTAGAAATTTTAAAATATTGAAAAAAATAT
1145671 AAATATATATTAGAAATTTTAAAATATTGAAAAAAATAT
1 AAA-ATATATTAGAAATTTTAAAATATTGAAAAAAATAT
1145710 AAAA-ATATTAGAAATTTTAAAATATT
1 AAAATATATTAGAAATTTTAAAATATT
1145736 ATTTTTTAAA
Statistics
Matches: 60, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
37 22 0.37
38 4 0.07
39 34 0.57
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (38 bp):
AAAATATATTAGAAATTTTAAAATATTGAAAAAAATAT
Found at i:1145731 original size:17 final size:17
Alignment explanation
Indices: 1145677--1145736 Score: 66
Period size: 17 Copynumber: 3.4 Consensus size: 17
1145667 ATATAAATAT
1145677 ATATTAGAAATTTTAAA
1 ATATTAGAAATTTTAAA
* * *
1145694 ATATTGAAAAAAATATAAAA
1 ATATT---AGAAATTTTAAA
1145714 ATATTAGAAATTTTAAA
1 ATATTAGAAATTTTAAA
1145731 ATATTA
1 ATATTA
1145737 TTTTTTAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
17 20 0.59
20 14 0.41
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (17 bp):
ATATTAGAAATTTTAAA
Found at i:1150564 original size:74 final size:75
Alignment explanation
Indices: 1150420--1150579 Score: 166
Period size: 74 Copynumber: 2.2 Consensus size: 75
1150410 GTTTGTTAAT
* * * * * *
1150420 ACTTAGATGGCTGCATATTTTCCTACGTGCCTACAAGGATGTGAAATGCAATAGTATATGGAGAA
1 ACTTAGATGGTTGCATACTTTCCTACATGCCTACAAGGATGTAAAATGCAATAATACATGGAGAA
*
1150485 GCATAATA-A
66 ACATAATATA
*** *
1150494 ACTTAGATGGTTGCATACTTTCCTACATTTGTACAAGGATG-AAAATTGCACTAATACATGTG-G
1 ACTTAGATGGTTGCATACTTTCCTACATGCCTACAAGGATGTAAAA-TGCAATAATACATG-GAG
*
1150557 AAACATAATATT
64 AAACATAATATA
1150569 ACTT-GATGGTT
1 ACTTAGATGGTT
1150580 TTCTATTCTT
Statistics
Matches: 71, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
73 3 0.04
74 63 0.89
75 5 0.07
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.32
Consensus pattern (75 bp):
ACTTAGATGGTTGCATACTTTCCTACATGCCTACAAGGATGTAAAATGCAATAATACATGGAGAA
ACATAATATA
Found at i:1152067 original size:35 final size:35
Alignment explanation
Indices: 1151993--1152069 Score: 102
Period size: 35 Copynumber: 2.2 Consensus size: 35
1151983 TCGAAGAATT
* * *
1151993 GCTCGAAATATGAAAGGATGTGGACAACTCGGATT
1 GCTCAAAATATGAAAGGATGTGGACAACTAGGATG
*
1152028 GCTCAAAATATGAAAGGATGTGGACAAGGTAGGA-G
1 GCTCAAAATATGAAAGGATGTGGACAA-CTAGGATG
1152063 GCTCAAA
1 GCTCAAA
1152070 GGGTTTAGAC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
35 33 0.89
36 4 0.11
ACGTcount: A:0.38, C:0.13, G:0.30, T:0.19
Consensus pattern (35 bp):
GCTCAAAATATGAAAGGATGTGGACAACTAGGATG
Found at i:1152093 original size:22 final size:22
Alignment explanation
Indices: 1152065--1152106 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
1152055 GGTAGGAGGC
1152065 TCAAAGGGTTTAGACAAAAAGA
1 TCAAAGGGTTTAGACAAAAAGA
1152087 TCAAAGGGTTTAGACAAAAA
1 TCAAAGGGTTTAGACAAAAA
1152107 AAAAAGTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.50, C:0.10, G:0.21, T:0.19
Consensus pattern (22 bp):
TCAAAGGGTTTAGACAAAAAGA
Found at i:1153892 original size:6 final size:6
Alignment explanation
Indices: 1153881--1153905 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1153871 TTATAAAATT
1153881 ATATAA ATATAA ATATAA ATATAA A
1 ATATAA ATATAA ATATAA ATATAA A
1153906 ATATTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
ATATAA
Found at i:1157307 original size:7 final size:7
Alignment explanation
Indices: 1157295--1157321 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
1157285 TTCGAAATAT
1157295 AAATTTC
1 AAATTTC
1157302 AAATTTC
1 AAATTTC
1157309 AAATTTC
1 AAATTTC
1157316 AAATTT
1 AAATTT
1157322 ATTTATTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (7 bp):
AAATTTC
Found at i:1168615 original size:32 final size:32
Alignment explanation
Indices: 1168576--1168646 Score: 133
Period size: 32 Copynumber: 2.2 Consensus size: 32
1168566 TACGGATTAT
*
1168576 ACAACAAACACATATTTAAAACTCAAAACCCA
1 ACAACAAAAACATATTTAAAACTCAAAACCCA
1168608 ACAACAAAAACATATTTAAAACTCAAAACCCA
1 ACAACAAAAACATATTTAAAACTCAAAACCCA
1168640 ACAACAA
1 ACAACAA
1168647 TAATTATATA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.59, C:0.27, G:0.00, T:0.14
Consensus pattern (32 bp):
ACAACAAAAACATATTTAAAACTCAAAACCCA
Found at i:1170723 original size:21 final size:20
Alignment explanation
Indices: 1170686--1170741 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
1170676 AATCGACATT
1170686 AAATTTTAGAATG-TTTAATTTA
1 AAATTTTA-AA-GATTTAA-TTA
1170708 AAATTTTAAAGATTTAATTA
1 AAATTTTAAAGATTTAATTA
*
1170728 ATATTTTAAA-ATTT
1 AAATTTTAAAGATTT
1170742 TTAAAGGGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
19 4 0.12
20 13 0.41
21 7 0.22
22 8 0.25
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (20 bp):
AAATTTTAAAGATTTAATTA
Found at i:1173272 original size:50 final size:50
Alignment explanation
Indices: 1173197--1173523 Score: 528
Period size: 50 Copynumber: 6.5 Consensus size: 50
1173187 CCATGGCAAC
* *
1173197 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAATGACAAGTGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
*
1173247 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTAATCAAGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
*
1173297 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAATGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* * *
1173347 AAGTGATAAGTGATAGCTTCGGCTACACTTATTTGATCAAGGATAAGTGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
1173397 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* * *
1173447 AAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAATGACAAATGGC
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAAT-GA
* * *
1173498 AAGTAAAAAGTGGTAGCTTCGGCTAC
1 AAGTGATAAGTGATAGCTTCGGCTAC
1173524 CTGATCAATG
Statistics
Matches: 257, Mismatches: 19, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
50 234 0.91
51 23 0.09
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (50 bp):
AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
Found at i:1173541 original size:31 final size:31
Alignment explanation
Indices: 1173503--1173561 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
1173493 ATGGCAAGTA
1173503 AAAAGTGGTAGCTTCGGCTACCTGATCAATG
1 AAAAGTGGTAGCTTCGGCTACCTGATCAATG
1173534 AAAAGTGGTAGCTTCGGCTACCTGATCA
1 AAAAGTGGTAGCTTCGGCTACCTGATCA
1173562 TCGACTACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.25
Consensus pattern (31 bp):
AAAAGTGGTAGCTTCGGCTACCTGATCAATG
Found at i:1174813 original size:6 final size:7
Alignment explanation
Indices: 1174780--1174812 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
1174770 ATAAACACAA
*
1174780 TAAAACG
1 TAAAAAG
1174787 TAAAAAG
1 TAAAAAG
1174794 TAAAAAG
1 TAAAAAG
1174801 TAAAAAG
1 TAAAAAG
1174808 TAAAA
1 TAAAA
1174813 GATGAAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.70, C:0.03, G:0.12, T:0.15
Consensus pattern (7 bp):
TAAAAAG
Found at i:1174825 original size:19 final size:18
Alignment explanation
Indices: 1174801--1174848 Score: 69
Period size: 19 Copynumber: 2.6 Consensus size: 18
1174791 AAGTAAAAAG
1174801 TAAAAAGTAAAAGATGAAA
1 TAAAAA-TAAAAGATGAAA
*
1174820 TAAAAAAAAAAAGATGAAA
1 T-AAAAATAAAAGATGAAA
1174839 TAAAAATAAA
1 TAAAAATAAA
1174849 TAACAAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 8 0.31
19 13 0.50
20 5 0.19
ACGTcount: A:0.75, C:0.00, G:0.10, T:0.15
Consensus pattern (18 bp):
TAAAAATAAAAGATGAAA
Found at i:1176881 original size:23 final size:23
Alignment explanation
Indices: 1176855--1176952 Score: 171
Period size: 23 Copynumber: 4.3 Consensus size: 23
1176845 ATAAGTGCCA
1176855 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
1176878 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
1176901 CACTG-GATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
1176923 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
1176946 CACTGAT
1 CACTGAT
1176953 CAATAACACT
Statistics
Matches: 71, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
22 21 0.30
23 50 0.70
ACGTcount: A:0.31, C:0.27, G:0.22, T:0.20
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:1176920 original size:45 final size:45
Alignment explanation
Indices: 1176862--1176950 Score: 169
Period size: 45 Copynumber: 2.0 Consensus size: 45
1176852 CCACACTGAT
*
1176862 ATGTAGCCGAAGCTACCACTGATATGTAGCCGAAGCTACCACTGG
1 ATGTAGCCGAAGCTACCACTGAAATGTAGCCGAAGCTACCACTGG
1176907 ATGTAGCCGAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
1 ATGTAGCCGAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
1176951 ATCAATAACA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.30, C:0.27, G:0.24, T:0.19
Consensus pattern (45 bp):
ATGTAGCCGAAGCTACCACTGAAATGTAGCCGAAGCTACCACTGG
Found at i:1182960 original size:23 final size:22
Alignment explanation
Indices: 1182909--1182960 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
1182899 CCTCGTCTTT
*
1182909 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
1182931 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
1182954 TTCTTTT
1 TTCTTTT
1182961 TCAAATTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:1182975 original size:18 final size:18
Alignment explanation
Indices: 1182954--1182992 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1182944 TTTCTTCAAC
* *
1182954 TTCTTTTTCAAATTTCTT
1 TTCTGTTTCAAATTCCTT
*
1182972 TTCTGTTTCACATTCCTT
1 TTCTGTTTCAAATTCCTT
1182990 TTC
1 TTC
1182993 ACTCTCAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.13, C:0.23, G:0.03, T:0.62
Consensus pattern (18 bp):
TTCTGTTTCAAATTCCTT
Found at i:1189103 original size:23 final size:23
Alignment explanation
Indices: 1189077--1189174 Score: 171
Period size: 23 Copynumber: 4.3 Consensus size: 23
1189067 ATAAGTGCCA
1189077 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
1189100 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
1189123 CACTG-GATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
1189145 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
1189168 CACTGAT
1 CACTGAT
1189175 CAATAACACT
Statistics
Matches: 71, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
22 21 0.30
23 50 0.70
ACGTcount: A:0.31, C:0.27, G:0.22, T:0.20
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:1189142 original size:45 final size:45
Alignment explanation
Indices: 1189084--1189172 Score: 169
Period size: 45 Copynumber: 2.0 Consensus size: 45
1189074 CCACACTGAT
*
1189084 ATGTAGCCGAAGCTACCACTGATATGTAGCCGAAGCTACCACTGG
1 ATGTAGCCGAAGCTACCACTGAAATGTAGCCGAAGCTACCACTGG
1189129 ATGTAGCCGAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
1 ATGTAGCCGAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
1189173 ATCAATAACA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.30, C:0.27, G:0.24, T:0.19
Consensus pattern (45 bp):
ATGTAGCCGAAGCTACCACTGAAATGTAGCCGAAGCTACCACTGG
Found at i:1190584 original size:16 final size:16
Alignment explanation
Indices: 1190554--1190601 Score: 57
Period size: 15 Copynumber: 3.1 Consensus size: 16
1190544 GAAAATTAAT
1190554 ATAAAATCT-AAAAT-A
1 ATAAAAT-TAAAAATAA
1190569 ATAATAATTAAAAATAA
1 ATAA-AATTAAAAATAA
1190586 ATAAAATT-AAAATAA
1 ATAAAATTAAAAATAA
1190601 A
1 A
1190602 CTTAAAATAG
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
15 13 0.43
16 12 0.40
17 5 0.17
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (16 bp):
ATAAAATTAAAAATAA
Found at i:1190600 original size:11 final size:11
Alignment explanation
Indices: 1190545--1190615 Score: 58
Period size: 11 Copynumber: 6.5 Consensus size: 11
1190535 ATAGCTTAAG
*
1190545 AAAATTAATAT
1 AAAATTAAAAT
1190556 AAAATCTAAAAT
1 AAAAT-TAAAAT
*
1190568 AATAA-T-AATT
1 AA-AATTAAAAT
*
1190578 AAAAAT-AAAT
1 AAAATTAAAAT
1190588 AAAATTAAAAT
1 AAAATTAAAAT
*
1190599 AAACTTAAAAT
1 AAAATTAAAAT
*
1190610 AGAATT
1 AAAATT
1190616 TCCTATTTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
9 2 0.04
10 14 0.29
11 24 0.49
12 7 0.14
13 2 0.04
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.30
Consensus pattern (11 bp):
AAAATTAAAAT
Found at i:1193069 original size:32 final size:32
Alignment explanation
Indices: 1193027--1193090 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
1193017 TTTCAGGCGT
*
1193027 TTATAGACCAAATGAACCAACTATGGCCTTAA
1 TTATAAACCAAATGAACCAACTATGGCCTTAA
1193059 TTATAAACCAAATGAACCAACTATGGCCTTAA
1 TTATAAACCAAATGAACCAACTATGGCCTTAA
1193091 ATTTATACCT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.42, C:0.22, G:0.11, T:0.25
Consensus pattern (32 bp):
TTATAAACCAAATGAACCAACTATGGCCTTAA
Found at i:1193769 original size:31 final size:29
Alignment explanation
Indices: 1193732--1193832 Score: 89
Period size: 31 Copynumber: 3.3 Consensus size: 29
1193722 ATTGGGATTT
1193732 TAATTAAAAAATTTAAAATTTTAAGAGACA
1 TAATTAAAAAATTTAAAATTTTAA-AGACA
* * **
1193762 TTAATTAAAATACTTAAAAAATTAAA-AGCA
1 -TAATTAAAAAATTTAAAATTTTAAAGA-CA
*
1193792 TAA-TAAGAAAATTTTAAAATTTTGAAAGATA
1 TAATTAA-AAAA-TTTAAAATTTT-AAAGACA
1193823 TAATTAAAAA
1 TAATTAAAAA
1193833 TTCCAAAGGA
Statistics
Matches: 55, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
28 3 0.05
29 7 0.13
30 11 0.20
31 30 0.55
32 4 0.07
ACGTcount: A:0.58, C:0.03, G:0.06, T:0.33
Consensus pattern (29 bp):
TAATTAAAAAATTTAAAATTTTAAAGACA
Found at i:1198949 original size:14 final size:15
Alignment explanation
Indices: 1198932--1198962 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
1198922 AAATATGTGG
1198932 ATGAAATA-ATAGAA
1 ATGAAATACATAGAA
1198946 ATGAAATACATAGAA
1 ATGAAATACATAGAA
1198961 AT
1 AT
1198963 TTGATATGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.61, C:0.03, G:0.13, T:0.23
Consensus pattern (15 bp):
ATGAAATACATAGAA
Found at i:1204833 original size:33 final size:33
Alignment explanation
Indices: 1204796--1204919 Score: 221
Period size: 33 Copynumber: 3.8 Consensus size: 33
1204786 CTCTGTTTCA
1204796 GGTTGCTGGACAGGAGCTGGAATGTGAGTGTTT
1 GGTTGCTGGACAGGAGCTGGAATGTGAGTGTTT
*
1204829 GGTTGCTGGACGGGAGCTGGAATGTGAGTGTTT
1 GGTTGCTGGACAGGAGCTGGAATGTGAGTGTTT
1204862 GGTTGCTGGACAGGAGCTGGAATGTGAGTGTTT
1 GGTTGCTGGACAGGAGCTGGAATGTGAGTGTTT
* *
1204895 GGTTGCTGGACAGTAGCTAGAATGT
1 GGTTGCTGGACAGGAGCTGGAATGT
1204920 CAAGAAGAAA
Statistics
Matches: 87, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 87 1.00
ACGTcount: A:0.19, C:0.10, G:0.42, T:0.30
Consensus pattern (33 bp):
GGTTGCTGGACAGGAGCTGGAATGTGAGTGTTT
Found at i:1216958 original size:21 final size:21
Alignment explanation
Indices: 1216920--1216959 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1216910 GGAATATTTA
*
1216920 CAAAACCATTTAATTTGAAAT
1 CAAAACCATTTAAATTGAAAT
1216941 CAAAACC-TATTAAATTGAA
1 CAAAACCAT-TTAAATTGAA
1216960 CAATCCAACT
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:0.50, C:0.15, G:0.05, T:0.30
Consensus pattern (21 bp):
CAAAACCATTTAAATTGAAAT
Found at i:1222966 original size:27 final size:27
Alignment explanation
Indices: 1222934--1222990 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
1222924 CGAACTCGAA
1222934 TCTATAATGCAATAATTATATTTGATG
1 TCTATAATGCAATAATTATATTTGATG
1222961 TCTATAATGCAATAATTATATTTGATG
1 TCTATAATGCAATAATTATATTTGATG
1222988 TCT
1 TCT
1222991 CTAAATTGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.35, C:0.09, G:0.11, T:0.46
Consensus pattern (27 bp):
TCTATAATGCAATAATTATATTTGATG
Found at i:1226583 original size:15 final size:15
Alignment explanation
Indices: 1226563--1226591 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1226553 TCCAAACTAA
1226563 ACAACATCATGTGAC
1 ACAACATCATGTGAC
1226578 ACAACATCATGTGA
1 ACAACATCATGTGA
1226592 TCTAATAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.24, G:0.14, T:0.21
Consensus pattern (15 bp):
ACAACATCATGTGAC
Found at i:1232887 original size:19 final size:19
Alignment explanation
Indices: 1232863--1232905 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
1232853 ATTTTTTTTT
1232863 ATAATAGGAGATAAAATTG
1 ATAATAGGAGATAAAATTG
1232882 ATAATAGGAGATAAAATTG
1 ATAATAGGAGATAAAATTG
1232901 ATAAT
1 ATAAT
1232906 TTGGTTTACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.53, C:0.00, G:0.19, T:0.28
Consensus pattern (19 bp):
ATAATAGGAGATAAAATTG
Found at i:1235832 original size:13 final size:13
Alignment explanation
Indices: 1235814--1235841 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1235804 AACATACAAG
1235814 TAAGAATACATAC
1 TAAGAATACATAC
1235827 TAAGAATACATAC
1 TAAGAATACATAC
1235840 TA
1 TA
1235842 CAATGATCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.54, C:0.14, G:0.07, T:0.25
Consensus pattern (13 bp):
TAAGAATACATAC
Found at i:1238207 original size:6 final size:7
Alignment explanation
Indices: 1238190--1238215 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1238180 AGAGCATATA
1238190 AAAAAAT
1 AAAAAAT
1238197 AAAAAAT
1 AAAAAAT
1238204 AAAAAAT
1 AAAAAAT
1238211 AAAAA
1 AAAAA
1238216 GAAAGGATGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:1241343 original size:25 final size:25
Alignment explanation
Indices: 1241315--1241369 Score: 110
Period size: 25 Copynumber: 2.2 Consensus size: 25
1241305 AATTTAAGTC
1241315 ACTTTATTTTTATTTTCAAAAATTT
1 ACTTTATTTTTATTTTCAAAAATTT
1241340 ACTTTATTTTTATTTTCAAAAATTT
1 ACTTTATTTTTATTTTCAAAAATTT
1241365 ACTTT
1 ACTTT
1241370 TATATGCTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.31, C:0.09, G:0.00, T:0.60
Consensus pattern (25 bp):
ACTTTATTTTTATTTTCAAAAATTT
Found at i:1241919 original size:14 final size:14
Alignment explanation
Indices: 1241883--1241939 Score: 50
Period size: 13 Copynumber: 4.3 Consensus size: 14
1241873 AAATGATAAT
*
1241883 TTAAATATTTAAAA
1 TTAAATATTAAAAA
1241897 -TAAA-A-TAAAAA
1 TTAAATATTAAAAA
1241908 TTAAATATT-AAAA
1 TTAAATATTAAAAA
* *
1241921 TGGAAATATTAAAAG
1 T-TAAATATTAAAAA
1241936 TTAA
1 TTAA
1241940 TTCGCCAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
11 5 0.15
12 5 0.15
13 10 0.29
14 10 0.29
15 4 0.12
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.33
Consensus pattern (14 bp):
TTAAATATTAAAAA
Found at i:1246643 original size:18 final size:18
Alignment explanation
Indices: 1246620--1246654 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1246610 AGTTAAAATA
*
1246620 TAATTTTTATTTTTATAT
1 TAATTTATATTTTTATAT
1246638 TAATTTATATTTTTATA
1 TAATTTATATTTTTATA
1246655 ATTTTCAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
TAATTTATATTTTTATAT
Found at i:1247398 original size:8 final size:9
Alignment explanation
Indices: 1247378--1247409 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
1247368 ATCTTTGAAT
1247378 AATTTTTTA
1 AATTTTTTA
1247387 AATTTTTT-
1 AATTTTTTA
1247395 AATTTTTTA
1 AATTTTTTA
1247404 AATTTT
1 AATTTT
1247410 AAAAAATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (9 bp):
AATTTTTTA
Found at i:1247399 original size:17 final size:17
Alignment explanation
Indices: 1247377--1247409 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1247367 AATCTTTGAA
1247377 TAATTTTTTAAATTTTT
1 TAATTTTTTAAATTTTT
1247394 TAATTTTTTAAATTTT
1 TAATTTTTTAAATTTT
1247410 AAAAAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
TAATTTTTTAAATTTTT
Found at i:1250158 original size:21 final size:20
Alignment explanation
Indices: 1250125--1250178 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
1250115 TAAAAAATAA
*
1250125 AAAATAAAT-TTAAAATATC
1 AAAATTAATATTAAAATATC
* *
1250144 AAAATTTTATATTAAAATTTC
1 AAAA-TTAATATTAAAATATC
*
1250165 CAAATTAATATTAA
1 AAAATTAATATTAA
1250179 CTAAAACAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 4 0.14
20 12 0.43
21 12 0.43
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.39
Consensus pattern (20 bp):
AAAATTAATATTAAAATATC
Found at i:1251449 original size:26 final size:28
Alignment explanation
Indices: 1251400--1251452 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 28
1251390 GATAATCATA
1251400 ATTAATATATCAATAAATAAAATTTTAT
1 ATTAATATATCAATAAATAAAATTTTAT
* *
1251428 ATTAA-ATAT-AATAATTACAATTTTA
1 ATTAATATATCAATAAATAAAATTTTA
1251453 AAAGTATGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 14 0.61
27 4 0.17
28 5 0.22
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (28 bp):
ATTAATATATCAATAAATAAAATTTTAT
Found at i:1255167 original size:20 final size:20
Alignment explanation
Indices: 1255129--1255167 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1255119 GTATATTTTT
*
1255129 TTTATATTATGAAATCATAG
1 TTTATATTATGAAAGCATAG
1255149 TTTATATTAT-ACAAGCATA
1 TTTATATTATGA-AAGCATA
1255168 TATAATATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 1 0.06
20 16 0.94
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.44
Consensus pattern (20 bp):
TTTATATTATGAAAGCATAG
Found at i:1255316 original size:9 final size:9
Alignment explanation
Indices: 1255304--1255333 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
1255294 ATAAATTTTT
1255304 AAAAATTTA
1 AAAAATTTA
1255313 AAAAATTTA
1 AAAAATTTA
1255322 AAAAATTTA
1 AAAAATTTA
1255331 AAA
1 AAA
1255334 TTATAGAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (9 bp):
AAAAATTTA
Found at i:1257510 original size:13 final size:13
Alignment explanation
Indices: 1257492--1257516 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1257482 TGTTACTTAC
1257492 TACAGCTCTTTAT
1 TACAGCTCTTTAT
1257505 TACAGCTCTTTA
1 TACAGCTCTTTA
1257517 CCCATTGAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.24, G:0.08, T:0.44
Consensus pattern (13 bp):
TACAGCTCTTTAT
Found at i:1257754 original size:3 final size:3
Alignment explanation
Indices: 1257746--1257770 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1257736 TGACCACCTT
1257746 TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC T
1257771 GACTCCTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:1259736 original size:17 final size:17
Alignment explanation
Indices: 1259702--1259745 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
1259692 CATAACTTTT
1259702 AAAAGTAAACACTAAAAA
1 AAAAGTAAA-ACTAAAAA
* *
1259720 TAAAGTAAAATTAAAAA
1 AAAAGTAAAACTAAAAA
1259737 AAAAG-AAAA
1 AAAAGTAAAA
1259746 AGAAAATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 4 0.17
17 11 0.48
18 8 0.35
ACGTcount: A:0.75, C:0.05, G:0.07, T:0.14
Consensus pattern (17 bp):
AAAAGTAAAACTAAAAA
Found at i:1263849 original size:27 final size:28
Alignment explanation
Indices: 1263819--1263879 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 28
1263809 AGATTCAGGG
1263819 ACTAA-AAGTTAGATTAATATTTTTTTT
1 ACTAACAAGTTAGATTAATATTTTTTTT
* *
1263846 ACTAACTATTTAGATTAATATTTTTTTT
1 ACTAACAAGTTAGATTAATATTTTTTTT
1263874 ACTAAC
1 ACTAAC
1263880 TATTCCACCC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 5 0.16
28 26 0.84
ACGTcount: A:0.36, C:0.08, G:0.05, T:0.51
Consensus pattern (28 bp):
ACTAACAAGTTAGATTAATATTTTTTTT
Found at i:1263859 original size:28 final size:28
Alignment explanation
Indices: 1263827--1263883 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
1263817 GGACTAAAAG
1263827 TTAGATTAATATTTTTTTTACTAACTAT
1 TTAGATTAATATTTTTTTTACTAACTAT
1263855 TTAGATTAATATTTTTTTTACTAACTAT
1 TTAGATTAATATTTTTTTTACTAACTAT
1263883 T
1 T
1263884 CCACCCTCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.32, C:0.07, G:0.04, T:0.58
Consensus pattern (28 bp):
TTAGATTAATATTTTTTTTACTAACTAT
Found at i:1272744 original size:18 final size:18
Alignment explanation
Indices: 1272686--1272749 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 18
1272676 GTATTGTTAT
* *
1272686 TTTTTAATAAAATTATAAA
1 TTTTTAA-ATAATTTTAAA
* *
1272705 TTTTT-TATAACTTTTATGA
1 TTTTTAAATAA-TTTTA-AA
1272724 TTTTTAAATAATTTTAAA
1 TTTTTAAATAATTTTAAA
1272742 TTTTTAAA
1 TTTTTAAA
1272750 AAGGCTTAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
17 3 0.08
18 13 0.36
19 16 0.44
20 4 0.11
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (18 bp):
TTTTTAAATAATTTTAAA
Found at i:1273524 original size:15 final size:16
Alignment explanation
Indices: 1273494--1273532 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
1273484 TAATAAAAAT
1273494 ATAATTTTATTATTTTA
1 ATAA-TTTATTATTTTA
*
1273511 ATAATTTA-TATTTTT
1 ATAATTTATTATTTTA
1273526 ATAATTT
1 ATAATTT
1273533 TAAAAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 13 0.62
16 4 0.19
17 4 0.19
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATAATTTATTATTTTA
Found at i:1273584 original size:83 final size:80
Alignment explanation
Indices: 1273460--1273621 Score: 193
Period size: 83 Copynumber: 2.0 Consensus size: 80
1273450 TTTGGGACAA
* *
1273460 AATTAAATTATATATTTTTATTGATAATAAAAATATAATTTTATTATTTTAATAATTTATATTTT
1 AATTAAATTATATATTTTTA-T-ATAATAAAAATATAATTTTATTA--TTAATAATTTAGAATTT
*
1273525 TAT-AATTTTAAAAAAATT
62 TATAAATTATAAAAAAATT
* * *
1273543 AATTAAATTATTATCATTTTTA-ATAGATTAAAATGTAATTTTATTATTATTAATTTAGAATTTT
1 AATTAAATTA-TAT-ATTTTTATATA-ATAAAAATATAATTTTATTATTAATAATTTAGAATTTT
1273607 ATAAATTATAAAAAA
63 ATAAATTATAAAAAA
1273622 TAAAATAAAA
Statistics
Matches: 69, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
81 17 0.25
82 14 0.20
83 28 0.41
84 3 0.04
85 7 0.10
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.51
Consensus pattern (80 bp):
AATTAAATTATATATTTTTATATAATAAAAATATAATTTTATTATTAATAATTTAGAATTTTATA
AATTATAAAAAAATT
Found at i:1274930 original size:19 final size:19
Alignment explanation
Indices: 1274894--1274930 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1274884 ATAATCAAAT
*
1274894 ATATATTATTGTTAAATAA
1 ATATATTATTGTCAAATAA
*
1274913 ATATATTATTGTCGAATA
1 ATATATTATTGTCAAATA
1274931 TCATATTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (19 bp):
ATATATTATTGTCAAATAA
Found at i:1274982 original size:26 final size:27
Alignment explanation
Indices: 1274938--1274990 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
1274928 ATATCATATT
* * *
1274938 TTTTTACATTTAAACTTTAGTTTTTTA
1 TTTTTACATTAAAAATTTAGTTATTTA
1274965 TTTTTA-ATTAAAAATTTAGTTATTTA
1 TTTTTACATTAAAAATTTAGTTATTTA
1274991 CAGTTTAGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 17 0.74
27 6 0.26
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.60
Consensus pattern (27 bp):
TTTTTACATTAAAAATTTAGTTATTTA
Found at i:1276766 original size:13 final size:13
Alignment explanation
Indices: 1276748--1276783 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
1276738 TTTTTACCCA
1276748 TAATAATAATTAT
1 TAATAATAATTAT
1276761 TAATAATTAA-TAT
1 TAATAA-TAATTAT
1276774 TAATAATAAT
1 TAATAATAAT
1276784 AACTCTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 3 0.14
13 15 0.71
14 3 0.14
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TAATAATAATTAT
Found at i:1276775 original size:16 final size:17
Alignment explanation
Indices: 1276747--1276783 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
1276737 ATTTTTACCC
*
1276747 ATAA-TAATAATTATTA
1 ATAATTAATAATTAATA
1276763 ATAATTAAT-ATTAATA
1 ATAATTAATAATTAATA
1276779 ATAAT
1 ATAAT
1276784 AACTCTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATAATTAATAATTAATA
Found at i:1276777 original size:10 final size:10
Alignment explanation
Indices: 1276748--1276785 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
1276738 TTTTTACCCA
1276748 TAATAATAAT
1 TAATAATAAT
*
1276758 TATTAATAAT
1 TAATAATAAT
*
1276768 TAATATTAA-
1 TAATAATAAT
1276777 TAATAATAA
1 TAATAATAA
1276786 CTCTAAAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
9 8 0.33
10 16 0.67
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (10 bp):
TAATAATAAT
Found at i:1277981 original size:14 final size:14
Alignment explanation
Indices: 1277962--1277992 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1277952 AGCACAATAT
*
1277962 TTTTATAGTTAGAG
1 TTTTATACTTAGAG
1277976 TTTTATACTTAGAG
1 TTTTATACTTAGAG
1277990 TTT
1 TTT
1277993 AAGAAAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.26, C:0.03, G:0.16, T:0.55
Consensus pattern (14 bp):
TTTTATACTTAGAG
Found at i:1278268 original size:14 final size:14
Alignment explanation
Indices: 1278246--1278278 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1278236 ATCATTTAAC
*
1278246 TATTATATTGTTAT
1 TATTTTATTGTTAT
1278260 TATTTTATTGTTAT
1 TATTTTATTGTTAT
1278274 T-TTTT
1 TATTTT
1278279 GGATATTGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.73
Consensus pattern (14 bp):
TATTTTATTGTTAT
Found at i:1280806 original size:30 final size:28
Alignment explanation
Indices: 1280763--1280818 Score: 94
Period size: 30 Copynumber: 1.9 Consensus size: 28
1280753 TGCAGCTTGG
1280763 TTATATATCCATGTGTGTTCTCCATTGA
1 TTATATATCCATGTGTGTTCTCCATTGA
1280791 TTATATAGTTCCATGTGTGTTCTCCATT
1 TTATATA--TCCATGTGTGTTCTCCATT
1280819 TCATCTGCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 7 0.27
30 19 0.73
ACGTcount: A:0.20, C:0.18, G:0.14, T:0.48
Consensus pattern (28 bp):
TTATATATCCATGTGTGTTCTCCATTGA
Found at i:1282161 original size:100 final size:100
Alignment explanation
Indices: 1281929--1282242 Score: 522
Period size: 100 Copynumber: 3.1 Consensus size: 100
1281919 CAAATTACCT
* * *
1281929 AATTAAATTATATTTAAAGTTTTATTTTAAATATTTTATTTTATTTGAATCACGGAAAATAATTT
1 AATTAAATTGTATTTAAAGTTTTATTTTAAATATTTTATTTTTTTTGAATCACGAAAAATAATTT
**
1281994 CAATA-TTTTATTTTATTTTAACATTACAAAATTA
66 CAATATTTTTATTTTATTTTAACATTACCTAATTA
**
1282028 AATTAAATTGTATTTAAAGTTTTATTTTAAATATTTTATTTTTTTTGAATCATAAAAAATAATTT
1 AATTAAATTGTATTTAAAGTTTTATTTTAAATATTTTATTTTTTTTGAATCACGAAAAATAATTT
1282093 CAATATTTTTATTTTATTTTAACATTACCTAATTA
66 CAATATTTTTATTTTATTTTAACATTACCTAATTA
*
1282128 AATTAAATTGTATTTAAAGTTTTATTGTAAATATTTTATTTTTTTTGAATCACGAAAAATAATTT
1 AATTAAATTGTATTTAAAGTTTTATTTTAAATATTTTATTTTTTTTGAATCACGAAAAATAATTT
* *
1282193 TAATATTTTTATTTTATTTTAAAATTACCTAATTA
66 CAATATTTTTATTTTATTTTAACATTACCTAATTA
*
1282228 AATTAAATTTTATTT
1 AATTAAATTGTATTT
1282243 TCAAGTTCAC
Statistics
Matches: 201, Mismatches: 13, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
99 65 0.32
100 136 0.68
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.53
Consensus pattern (100 bp):
AATTAAATTGTATTTAAAGTTTTATTTTAAATATTTTATTTTTTTTGAATCACGAAAAATAATTT
CAATATTTTTATTTTATTTTAACATTACCTAATTA
Found at i:1282276 original size:9 final size:9
Alignment explanation
Indices: 1282257--1282708 Score: 185
Period size: 9 Copynumber: 50.4 Consensus size: 9
1282247 GTTCACTAGC
*
1282257 AACTCACAT
1 AACTTACAT
*
1282266 AATTTACAT
1 AACTTACAT
* *
1282275 AATTTACAG
1 AACTTACAT
1282284 AA--TACAT
1 AACTTACAT
1282291 AACTTACAT
1 AACTTACAT
* *
1282300 AATTTAAAGTT
1 AACTTACA--T
* *
1282311 CAAATTTCAT
1 -AACTTACAT
1282321 AACTTACAT
1 AACTTACAT
1282330 AA--TACAT
1 AACTTACAT
1282337 AACTTACAT
1 AACTTACAT
*
1282346 AA--TACTT
1 AACTTACAT
*
1282353 GACTTACAT
1 AACTTACAT
*
1282362 AATTTACAT
1 AACTTACAT
1282371 AACTTACAT
1 AACTTACAT
*
1282380 AA--TACTT
1 AACTTACAT
*
1282387 TACTTACAT
1 AACTTACAT
* *
1282396 AATTTAAAGATTT
1 AACTT--ACA--T
*
1282409 AA-TTTCAT
1 AACTTACAT
1282417 AACTTACAT
1 AACTTACAT
1282426 AA--TACAT
1 AACTTACAT
1282433 AACTTACAT
1 AACTTACAT
* *
1282442 AATTTAAAGAT
1 AACTT--ACAT
*
1282453 CAAATTTA-AT
1 --AACTTACAT
1282463 AACTTACAT
1 AACTTACAT
1282472 AA--TACAT
1 AACTTACAT
1282479 AACTTACAT
1 AACTTACAT
*
1282488 AA--TACTT
1 AACTTACAT
*
1282495 GACTTACAT
1 AACTTACAT
* *
1282504 AATTTAAAGGT
1 AACTTACA--T
* *
1282515 CAAATTTCAT
1 -AACTTACAT
1282525 AACTTACAT
1 AACTTACAT
1282534 AA--TACAT
1 AACTTACAT
1282541 AACTTACAT
1 AACTTACAT
* *
1282550 AATTTAAAGAT
1 AACTT--ACAT
* *
1282561 CAAATTTCAT
1 -AACTTACAT
1282571 AACTTACAT
1 AACTTACAT
* *
1282580 AATTTAAAT
1 AACTTACAT
1282589 AACTTACAT
1 AACTTACAT
*
1282598 AACTTACGT
1 AACTTACAT
1282607 AA--TACAT
1 AACTTACAT
1282614 AACTTACAT
1 AACTTACAT
* *
1282623 AATTTAAAGAT
1 AACTT--ACAT
* *
1282634 CAAATTTCAT
1 -AACTTACAT
1282644 AACTTACAT
1 AACTTACAT
*
1282653 AATTTACAT
1 AACTTACAT
1282662 AACTTACAT
1 AACTTACAT
1282671 AA--TACAT
1 AACTTACAT
* *
1282678 AA-ATATAT
1 AACTTACAT
* *
1282686 ATCATATCAT
1 AACTTA-CAT
1282696 AACTTACAT
1 AACTTACAT
1282705 AACT
1 AACT
1282709 ACTTATAAAT
Statistics
Matches: 333, Mismatches: 67, Indels: 86
0.69 0.14 0.18
Matches are distributed among these distances:
7 62 0.19
8 13 0.04
9 201 0.60
10 15 0.05
11 14 0.04
12 20 0.06
13 8 0.02
ACGTcount: A:0.46, C:0.15, G:0.02, T:0.36
Consensus pattern (9 bp):
AACTTACAT
Found at i:1282334 original size:46 final size:46
Alignment explanation
Indices: 1282266--1282673 Score: 340
Period size: 46 Copynumber: 8.8 Consensus size: 46
1282256 CAACTCACAT
* *
1282266 AATTTACATAATTTACAGAATACATAACTTACATAATTTAAAGTTCA
1 AATTT-CATAACTTACATAATACATAACTTACATAATTTAAAGTTCA
* *
1282313 AATTTCATAACTTACATAATACATAACTTACATAATACTT-GACTTACA
1 AATTTCATAACTTACATAATACATAACTTACATAAT--TTAAAGTT-CA
* * *
1282361 TAATTTACATAACTTACATAATACTTTACTTACATAATTTAAAGATT-T
1 -AATTT-CATAACTTACATAATACATAACTTACATAATTTAAAG-TTCA
*
1282409 AATTTCATAACTTACATAATACATAACTTACATAATTTAAAGATCA
1 AATTTCATAACTTACATAATACATAACTTACATAATTTAAAGTTCA
* * *
1282455 AATTTAATAACTTACATAATACATAACTTACATAATACTT-GACTTACA
1 AATTTCATAACTTACATAATACATAACTTACATAAT--TTAAAGTT-CA
** * ** *
1282503 TAATTT-A-AAGGT-CA-AATTTCATAACTTACATAATACATAACTTACA
1 -AATTTCATAACTTACATAA-TACATAACTTACATAATTTA-AAGTT-CA
** *
1282549 TAATTT-A-AAGAT-CA-AATTTCATAACTTACATAATTTAAA--T-A
1 -AATTTCATAACTTACATAA-TACATAACTTACATAATTTAAAGTTCA
* * * *
1282590 ACTTACATAACTTACGTAATACATAACTTACATAATTTAAAGATCA
1 AATTTCATAACTTACATAATACATAACTTACATAATTTAAAGTTCA
1282636 AATTTCATAACTTACATAATTTACATAACTTACATAAT
1 AATTTCATAACTTACATAA--TACATAACTTACATAAT
1282674 ACATAAATAT
Statistics
Matches: 302, Mismatches: 35, Indels: 47
0.79 0.09 0.12
Matches are distributed among these distances:
40 3 0.01
41 2 0.01
42 3 0.01
43 23 0.08
44 2 0.01
45 6 0.02
46 175 0.58
47 18 0.06
48 28 0.09
49 11 0.04
50 31 0.10
ACGTcount: A:0.46, C:0.15, G:0.03, T:0.37
Consensus pattern (46 bp):
AATTTCATAACTTACATAATACATAACTTACATAATTTAAAGTTCA
Found at i:1282339 original size:16 final size:16
Alignment explanation
Indices: 1282270--1282706 Score: 213
Period size: 16 Copynumber: 27.0 Consensus size: 16
1282260 TCACATAATT
* *
1282270 TACATAATTTACAGAA
1 TACATAACTTACATAA
1282286 TACATAACTTACATAA
1 TACATAACTTACATAA
** *
1282302 TTTA-AAGTT-CA-AA
1 TACATAACTTACATAA
*
1282315 TTTCATAACTTACATAA
1 -TACATAACTTACATAA
1282332 TACATAACTTACATAA
1 TACATAACTTACATAA
* *
1282348 TACTTGACTTACATAA
1 TACATAACTTACATAA
1282364 TTTACATAACTTACATAA
1 --TACATAACTTACATAA
* *
1282382 TACTTTACTTACATAA
1 TACATAACTTACATAA
** * *
1282398 TTTAAAGATTTA-AT--
1 TACATA-ACTTACATAA
*
1282412 TTCATAACTTACATAA
1 TACATAACTTACATAA
1282428 TACATAACTTACATAA
1 TACATAACTTACATAA
** **
1282444 TTTA-AAGAT-CA-AA
1 TACATAACTTACATAA
1282457 TTTA-ATAACTTACATAA
1 --TACATAACTTACATAA
1282474 TACATAACTTACATAA
1 TACATAACTTACATAA
* *
1282490 TACTTGACTTACATAA
1 TACATAACTTACATAA
** **
1282506 TTTA-AAGGT-CA-AA
1 TACATAACTTACATAA
*
1282519 TTTCATAACTTACATAA
1 -TACATAACTTACATAA
1282536 TACATAACTTACATAA
1 TACATAACTTACATAA
* * *
1282552 TTTAAAGATCAAATTTCATAA
1 --T--ACAT-AACTTACATAA
* *
1282573 CTTACATAATTTAAATAA
1 --TACATAACTTACATAA
*
1282591 CTTACATAACTTACGTAA
1 --TACATAACTTACATAA
1282609 TACATAACTTACATAA
1 TACATAACTTACATAA
** **
1282625 TTTA-AAGAT-CA-AA
1 TACATAACTTACATAA
*
1282638 TTTCATAACTTACATAA
1 -TACATAACTTACATAA
1282655 TTTACATAACTTACATAA
1 --TACATAACTTACATAA
* * *
1282673 TACATAAATATATATCA
1 TACATAACT-TACATAA
1282690 TATCATAACTTACATAA
1 TA-CATAACTTACATAA
1282707 CTACTTATAA
Statistics
Matches: 320, Mismatches: 69, Indels: 63
0.71 0.15 0.14
Matches are distributed among these distances:
13 12 0.04
14 24 0.08
15 28 0.09
16 155 0.48
17 24 0.08
18 60 0.19
19 3 0.01
20 3 0.01
21 11 0.03
ACGTcount: A:0.46, C:0.15, G:0.03, T:0.36
Consensus pattern (16 bp):
TACATAACTTACATAA
Found at i:1282426 original size:96 final size:93
Alignment explanation
Indices: 1282262--1282673 Score: 349
Period size: 96 Copynumber: 4.4 Consensus size: 93
1282252 CTAGCAACTC
* *
1282262 ACATAATTTACATAATTTACAGAATACATAACTTACATAATTTAAAGTTCAAATTTCATAACTTA
1 ACATAATTTACATAACTTACATAATACATAACTTACATAATTTAAAGTTCAAATTTCATAACTTA
***
1282327 CATAATACATAACTTACATAATACTTGACTT
66 CATAATACATAACTTACATAAT--TT-AAAG
* * *
1282358 ACATAATTTACATAACTTACATAATACTTTACTTACATAATTTAAAGATT-TAATTTCATAACTT
1 ACATAATTTACATAACTTACATAATACATAACTTACATAATTTAAAG-TTCAAATTTCATAACTT
1282422 ACATAATACATAACTTACATAATTTAAAG
65 ACATAATACATAACTTACATAATTTAAAG
* *
1282451 ATCA-AATTTA-ATAACTTACATAATACATAACTTACATAATACTT-GACTTACATAATTT-A-A
1 A-CATAATTTACATAACTTACATAATACATAACTTACATAAT--TTAAAGTT-CA-AATTTCATA
** *
1282511 AGGT-CA-AATTTCATAACTTACATAA--T----
61 ACTTACATAA-TACATAACTTACATAATTTAAAG
* * * * * *
1282537 ACATAACTTACATAATTTAAAGATCAAATTTCATAACTTACATAATTTAAA--T-AACTTACATA
1 ACATAATTTACATAACTT--ACAT--AA-TACATAACTTACATAATTTAAAGTTCAAATTTCATA
*
1282599 ACTTACGTAATACATAACTTACATAATTTAAAG
61 ACTTACATAATACATAACTTACATAATTTAAAG
1282632 ATCA-AATTT-CATAACTTACATAATTTACATAACTTACATAAT
1 A-CATAATTTACATAACTTACATAA--TACATAACTTACATAAT
1282674 ACATAAATAT
Statistics
Matches: 257, Mismatches: 31, Indels: 61
0.74 0.09 0.17
Matches are distributed among these distances:
85 2 0.01
86 9 0.04
87 8 0.03
88 3 0.01
89 20 0.08
90 7 0.03
91 23 0.09
92 66 0.26
93 12 0.05
94 14 0.05
95 10 0.04
96 81 0.32
97 2 0.01
ACGTcount: A:0.46, C:0.15, G:0.03, T:0.37
Consensus pattern (93 bp):
ACATAATTTACATAACTTACATAATACATAACTTACATAATTTAAAGTTCAAATTTCATAACTTA
CATAATACATAACTTACATAATTTAAAG
Found at i:1282488 original size:108 final size:109
Alignment explanation
Indices: 1282354--1282673 Score: 462
Period size: 108 Copynumber: 2.8 Consensus size: 109
1282344 ATAATACTTG
**
1282354 ACTTACATAATTTACATAACTTACATAATACTTTACTTACATAATTTAAAGATTTAATTTCATAA
1 ACTTACATAA-TTACATAACTTACATAATACTTTACTTACATAATTTAAAGATCAAATTTCATAA
1282419 CTTACATAATACATAACTTACATAATTTAAAGATCAAATTTAATA
65 CTTACATAATACATAACTTACATAATTTAAAGATCAAATTTAATA
* *
1282464 ACTTACATAA-TACATAACTTACATAATACTTGACTTACATAATTTAAAGGTCAAATTTCATAAC
1 ACTTACATAATTACATAACTTACATAATACTTTACTTACATAATTTAAAGATCAAATTTCATAAC
*
1282528 TTACATAATACATAACTTACATAATTTAAAGATCAAATTTCATA
66 TTACATAATACATAACTTACATAATTTAAAGATCAAATTTAATA
*
1282572 ACTTACATAATTTAAATAACTTACATAACTTACGTAATACATAACTTACATAATTTAAAGATCAA
1 ACTTACATAA-TTACATAACTTACATAA--TAC-T--T---T-ACTTACATAATTTAAAGATCAA
1282637 ATTTCATAACTTACATAATTTACATAACTTACATAAT
56 ATTTCATAACTTACATAA--TACATAACTTACATAAT
1282674 ACATAAATAT
Statistics
Matches: 189, Mismatches: 8, Indels: 15
0.89 0.04 0.07
Matches are distributed among these distances:
108 103 0.54
110 25 0.13
112 3 0.02
113 1 0.01
115 1 0.01
119 39 0.21
121 17 0.09
ACGTcount: A:0.46, C:0.15, G:0.03, T:0.37
Consensus pattern (109 bp):
ACTTACATAATTACATAACTTACATAATACTTTACTTACATAATTTAAAGATCAAATTTCATAAC
TTACATAATACATAACTTACATAATTTAAAGATCAAATTTAATA
Found at i:1282697 original size:73 final size:72
Alignment explanation
Indices: 1282496--1282697 Score: 262
Period size: 73 Copynumber: 2.7 Consensus size: 72
1282486 ATAATACTTG
* * *
1282496 ACTTACATAATTTAAAGGTCAAATTTCATAACTTACATAATACATAACTTACATAATTTAAAGAT
1 ACTTACATAATTTAAA--T-AACTTACATAAC-TACATAATACATAACATACATAATTTAAAGAT
1282561 CAAATTTCATA
62 CAAATTTCATA
* *
1282572 ACTTACATAATTTAAATAACTTACATAACTTACGTAATACATAACTTACATAATTTAAAGATCAA
1 ACTTACATAATTTAAATAACTTACATAAC-TACATAATACATAACATACATAATTTAAAGATCAA
1282637 ATTTCATA
65 ATTTCATA
* * *
1282645 ACTTACATAATTTACATAACTTACATAA-TACATAAATATATATCATATCATAA
1 ACTTACATAATTTAAATAACTTACATAACTACAT-AATACATAACATA-CATAA
1282698 CTTACATAAC
Statistics
Matches: 116, Mismatches: 8, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
71 4 0.03
72 10 0.09
73 85 0.73
74 1 0.01
76 16 0.14
ACGTcount: A:0.47, C:0.15, G:0.02, T:0.36
Consensus pattern (72 bp):
ACTTACATAATTTAAATAACTTACATAACTACATAATACATAACATACATAATTTAAAGATCAAA
TTTCATA
Found at i:1283688 original size:31 final size:31
Alignment explanation
Indices: 1283650--1283709 Score: 104
Period size: 31 Copynumber: 1.9 Consensus size: 31
1283640 ATGTTATATT
1283650 TGCTACATTTGCTATATTTT-GTTGGATTTCA
1 TGCTACATTTGCTAT-TTTTGGTTGGATTTCA
1283681 TGCTACATTTGCTATTTTTGGTTGGATTT
1 TGCTACATTTGCTATTTTTGGTTGGATTT
1283710 AATGTAGGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 4 0.14
31 24 0.86
ACGTcount: A:0.17, C:0.12, G:0.18, T:0.53
Consensus pattern (31 bp):
TGCTACATTTGCTATTTTTGGTTGGATTTCA
Found at i:1285090 original size:83 final size:82
Alignment explanation
Indices: 1284955--1285132 Score: 211
Period size: 83 Copynumber: 2.2 Consensus size: 82
1284945 TATTTAGGAT
* *
1284955 AAAATTAATTAAATTATATATTTTTATTAATAATAAAAATATAATTTTATTATT-TTAACAATTT
1 AAAATAAAATAAATTATATATTTTTATTAATAATAAAAATATAATTTTATTATTATT---AATTT
* * *
1285019 ATATTTTTAT-AATTTTAAA
63 AGAATTTTATAAATTATAAA
* * *
1285038 AAAATAAAATAAATTAT-TATTATTT-TTAATGGATCAAAATGTAATTTTATTATTATTAATTTA
1 AAAATAAAATAAATTATATATT-TTTATTAAT-AATAAAAATATAATTTTATTATTATTAATTTA
1285101 GAATTTTATAAATTATAAA
64 GAATTTTATAAATTATAAA
1285120 AAAATAAAATAAA
1 AAAATAAAATAAA
1285133 ATCGAGACCG
Statistics
Matches: 83, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
81 13 0.16
82 30 0.36
83 38 0.46
84 2 0.02
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.47
Consensus pattern (82 bp):
AAAATAAAATAAATTATATATTTTTATTAATAATAAAAATATAATTTTATTATTATTAATTTAGA
ATTTTATAAATTATAAA
Found at i:1286415 original size:27 final size:28
Alignment explanation
Indices: 1286385--1286440 Score: 87
Period size: 27 Copynumber: 2.0 Consensus size: 28
1286375 TAAGCACTCG
1286385 TAAATATAGTCAAAT-ATATATTATTGT
1 TAAATATAGTCAAATAATATATTATTGT
*
1286412 TAAATATAGTTAAATAAATATATTATTGT
1 TAAATATAGTCAAAT-AATATATTATTGT
1286441 CGATTATCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 14 0.54
29 12 0.46
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.45
Consensus pattern (28 bp):
TAAATATAGTCAAATAATATATTATTGT
Found at i:1288298 original size:13 final size:13
Alignment explanation
Indices: 1288280--1288315 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
1288270 ATTTTACCCA
1288280 TAATAATAATTAT
1 TAATAATAATTAT
1288293 TAATAATTAA-TAT
1 TAATAA-TAATTAT
1288306 TAATAATAAT
1 TAATAATAAT
1288316 AACTCTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 3 0.14
13 15 0.71
14 3 0.14
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TAATAATAATTAT
Found at i:1288307 original size:16 final size:17
Alignment explanation
Indices: 1288279--1288315 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
1288269 AATTTTACCC
*
1288279 ATAA-TAATAATTATTA
1 ATAATTAATAATTAATA
1288295 ATAATTAAT-ATTAATA
1 ATAATTAATAATTAATA
1288311 ATAAT
1 ATAAT
1288316 AACTCTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATAATTAATAATTAATA
Found at i:1288309 original size:10 final size:10
Alignment explanation
Indices: 1288280--1288317 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
1288270 ATTTTACCCA
1288280 TAATAATAAT
1 TAATAATAAT
*
1288290 TATTAATAAT
1 TAATAATAAT
*
1288300 TAATATTAA-
1 TAATAATAAT
1288309 TAATAATAA
1 TAATAATAA
1288318 CTCTAAAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
9 8 0.33
10 16 0.67
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (10 bp):
TAATAATAAT
Found at i:1291582 original size:13 final size:13
Alignment explanation
Indices: 1291564--1291591 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1291554 AGCAATTAAT
1291564 AAGTTTTGCAAAC
1 AAGTTTTGCAAAC
1291577 AAGTTTTGCAAAC
1 AAGTTTTGCAAAC
1291590 AA
1 AA
1291592 TTCAATTGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (13 bp):
AAGTTTTGCAAAC
Found at i:1294028 original size:30 final size:29
Alignment explanation
Indices: 1293955--1294029 Score: 78
Period size: 30 Copynumber: 2.5 Consensus size: 29
1293945 TTGACCCTTC
* *
1293955 AACTTTTTCATATTTATACTTTAACCACT
1 AACTTTTTCATATTTACACTTAAACCACT
* * **
1293984 TACATGTTAAATATTTACACTTAAACCACAT
1 AAC-TTTTTCATATTTACACTTAAACCAC-T
1294015 AACTTTTTCATATTT
1 AACTTTTTCATATTT
1294030 TTTATGATTT
Statistics
Matches: 34, Mismatches: 10, Indels: 3
0.72 0.21 0.06
Matches are distributed among these distances:
29 2 0.06
30 29 0.85
31 3 0.09
ACGTcount: A:0.35, C:0.19, G:0.01, T:0.45
Consensus pattern (29 bp):
AACTTTTTCATATTTACACTTAAACCACT
Found at i:1297773 original size:21 final size:21
Alignment explanation
Indices: 1297747--1297787 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1297737 AGACGAGCAA
* *
1297747 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
1297768 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
1297788 TTTAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:1301507 original size:30 final size:30
Alignment explanation
Indices: 1301444--1301545 Score: 118
Period size: 30 Copynumber: 3.4 Consensus size: 30
1301434 TAAAAAATAA
* *
1301444 AAATTGCATTTTGA-CCTCTAAACTTT-TCCT
1 AAATTTCATTTTGACCCT-TAAACTTTCT-TT
1301474 AAATTTCATTTTGACCCTTAAACTTTCTTT
1 AAATTTCATTTTGACCCTTAAACTTTCTTT
* * * *
1301504 AAATTTCACTTAGACCCCTAAACTTTCATT
1 AAATTTCATTTTGACCCTTAAACTTTCTTT
1301534 AAATTTCATTTT
1 AAATTTCATTTT
1301546 AATCCTAAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
30 58 0.94
31 4 0.06
ACGTcount: A:0.29, C:0.22, G:0.04, T:0.45
Consensus pattern (30 bp):
AAATTTCATTTTGACCCTTAAACTTTCTTT
Found at i:1301920 original size:3 final size:3
Alignment explanation
Indices: 1301914--1301941 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1301904 GTGTAGGAGG
1301914 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1301942 AGAAAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:1302278 original size:7 final size:7
Alignment explanation
Indices: 1302254--1302342 Score: 90
Period size: 7 Copynumber: 12.0 Consensus size: 7
1302244 AGCAGGCCAG
1302254 GAAAAAA
1 GAAAAAA
*
1302261 GAGAGAAA
1 GA-AAAAA
1302269 GAAAAAA
1 GAAAAAA
1302276 GAAAAAA
1 GAAAAAA
*
1302283 GAAAGAA
1 GAAAAAA
1302290 GAAAAAA
1 GAAAAAA
1302297 GAAAGAGAA
1 GAAA-A-AA
*
1302306 -AAAAAG
1 GAAAAAA
1302312 GAAAAAA
1 GAAAAAA
1302319 GGAAAAAAA
1 -G-AAAAAA
1302328 GAAAAAAA
1 G-AAAAAA
1302336 GAAAAAA
1 GAAAAAA
1302343 AAAGAGTTTC
Statistics
Matches: 70, Mismatches: 6, Indels: 12
0.80 0.07 0.14
Matches are distributed among these distances:
6 1 0.01
7 41 0.59
8 20 0.29
9 8 0.11
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (7 bp):
GAAAAAA
Found at i:1302281 original size:8 final size:8
Alignment explanation
Indices: 1302255--1302343 Score: 83
Period size: 8 Copynumber: 10.8 Consensus size: 8
1302245 GCAGGCCAGG
1302255 AAAAAAGA
1 AAAAAAGA
* *
1302263 GAGAAAG-
1 AAAAAAGA
1302270 AAAAAAG-
1 AAAAAAGA
1302277 AAAAAAGA
1 AAAAAAGA
*
1302285 AAGAAGAAAA
1 AA-AA-AAGA
1302295 AAGAAAGAGA
1 AA-AAA-AGA
1302305 AAAAAAGGA
1 AAAAAA-GA
*
1302314 AAAAAGGA
1 AAAAAAGA
1302322 AAAAAAGA
1 AAAAAAGA
1302330 AAAAAAGA
1 AAAAAAGA
1302338 AAAAAA
1 AAAAAA
1302344 AAGAGTTTCA
Statistics
Matches: 68, Mismatches: 8, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
7 12 0.18
8 31 0.46
9 13 0.19
10 12 0.18
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (8 bp):
AAAAAAGA
Found at i:1302283 original size:14 final size:14
Alignment explanation
Indices: 1302254--1302342 Score: 90
Period size: 15 Copynumber: 6.0 Consensus size: 14
1302244 AGCAGGCCAG
*
1302254 GAAAAAAGAGAGAAA
1 GAAAAAAGA-AAAAA
1302269 GAAAAAAGAAAAAA
1 GAAAAAAGAAAAAA
*
1302283 GAAAGAAGAAAAAA
1 GAAAAAAGAAAAAA
*
1302297 GAAAGAGAA-AAAAAG
1 GAAA-A-AAGAAAAAA
1302312 GAAAAAAGGAAAAAAA
1 GAAAAAA-G-AAAAAA
1302328 GAAAAAAAGAAAAAA
1 G-AAAAAAGAAAAAA
1302343 AAAGAGTTTC
Statistics
Matches: 63, Mismatches: 5, Indels: 12
0.79 0.06 0.15
Matches are distributed among these distances:
13 2 0.03
14 22 0.35
15 24 0.38
16 9 0.14
17 6 0.10
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (14 bp):
GAAAAAAGAAAAAA
Found at i:1302287 original size:18 final size:17
Alignment explanation
Indices: 1302264--1302347 Score: 82
Period size: 18 Copynumber: 4.8 Consensus size: 17
1302254 GAAAAAAGAG
1302264 AGAAAGAAAAAAGAAAAA
1 AGAAA-AAAAAAGAAAAA
*
1302282 AGAAAGAAGAAAA-AAGAA
1 AGAAA-AA-AAAAGAAAAA
*
1302300 AGAGAAAAAAAGGAAAAA
1 AGA-AAAAAAAAGAAAAA
*
1302318 AG-GAAAAAAAGAAAAAA
1 AGAAAAAAAAAG-AAAAA
1302335 AGAAAAAAAAAGA
1 AGAAAAAAAAAGA
1302348 GTTTCAATTC
Statistics
Matches: 55, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
16 7 0.13
17 11 0.20
18 31 0.56
19 6 0.11
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (17 bp):
AGAAAAAAAAAGAAAAA
Found at i:1302751 original size:20 final size:19
Alignment explanation
Indices: 1302709--1302750 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
1302699 TTCTATTTTT
1302709 AAAATTTTCCGTGCCTTCA
1 AAAATTTTCCGTGCCTTCA
*
1302728 AAAATTTTCTCGTG-TTTCA
1 AAAATTTTC-CGTGCCTTCA
1302747 AAAA
1 AAAA
1302751 AATATATTCG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.33, C:0.19, G:0.10, T:0.38
Consensus pattern (19 bp):
AAAATTTTCCGTGCCTTCA
Found at i:1302966 original size:17 final size:17
Alignment explanation
Indices: 1302921--1303085 Score: 158
Period size: 17 Copynumber: 9.5 Consensus size: 17
1302911 AAAAATCCAT
*
1302921 TTTCCAAAATTTTAC-TG
1 TTTCAAAAATTTT-CGTG
*
1302938 TCTTCTAAAAATTTTTGTG
1 T-TTC-AAAAATTTTCGTG
1302957 TTTCAAAAATTTTCGT-
1 TTTCAAAAATTTTCGTG
*
1302973 TTTCAAAAATTTCCGTG
1 TTTCAAAAATTTTCGTG
1302990 TTTCAAAAATTTTCGTG
1 TTTCAAAAATTTTCGTG
*
1303007 TTTTC-AAAATTTTCGTA
1 -TTTCAAAAATTTTCGTG
** *
1303024 TTTCAAAAATCCTCTTG
1 TTTCAAAAATTTTCGTG
1303041 TTTTCAAAAA-TTTCGGTG
1 -TTTCAAAAATTTTC-GTG
**
1303059 TTTTGAAAATTTTCGTG
1 TTTCAAAAATTTTCGTG
1303076 TTTTCAAAAA
1 -TTTCAAAAA
1303086 AAAATCTCGT
Statistics
Matches: 121, Mismatches: 17, Indels: 19
0.77 0.11 0.12
Matches are distributed among these distances:
16 19 0.16
17 59 0.49
18 32 0.26
19 11 0.09
ACGTcount: A:0.30, C:0.13, G:0.10, T:0.47
Consensus pattern (17 bp):
TTTCAAAAATTTTCGTG
Found at i:1320553 original size:25 final size:26
Alignment explanation
Indices: 1320511--1320563 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 26
1320501 AATTTCTGTT
1320511 ATACCCCTAGGTGCAAATT-ACCGAA
1 ATACCCCTAGGTGCAAATTGACCGAA
* *
1320536 ATACCCCTAGG-GTTAAATTGACCTAA
1 ATACCCCTAGGTG-CAAATTGACCGAA
1320562 AT
1 AT
1320564 GCATGTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 1 0.04
25 16 0.67
26 7 0.29
ACGTcount: A:0.36, C:0.25, G:0.15, T:0.25
Consensus pattern (26 bp):
ATACCCCTAGGTGCAAATTGACCGAA
Found at i:1322681 original size:6 final size:6
Alignment explanation
Indices: 1322658--1322785 Score: 91
Period size: 6 Copynumber: 20.8 Consensus size: 6
1322648 TATCAAAACT
* * * *
1322658 AGAATC AAAATG AGAATC AGAATC AAAATC AG-GTGAC AGAATC AGAATC
1 AGAATC AGAATC AGAATC AGAATC AGAATC AGAAT--C AGAATC AGAATC
* * * *
1322707 AGAATC AGAATC AGAATT AG-GTGAC AGAATT AGAATT AGAATC AGAATC
1 AGAATC AGAATC AGAATC AGAAT--C AGAATC AGAATC AGAATC AGAATC
* *
1322756 AGTATC AGGTAA-C AGAATC AAAATC AGAAT
1 AGAATC A-G-AATC AGAATC AGAATC AGAAT
1322786 GTGAATGCAA
Statistics
Matches: 95, Mismatches: 18, Indels: 18
0.73 0.14 0.14
Matches are distributed among these distances:
5 4 0.04
6 80 0.84
7 8 0.08
8 3 0.03
ACGTcount: A:0.49, C:0.12, G:0.19, T:0.20
Consensus pattern (6 bp):
AGAATC
Found at i:1322699 original size:37 final size:37
Alignment explanation
Indices: 1322658--1322785 Score: 175
Period size: 37 Copynumber: 3.5 Consensus size: 37
1322648 TATCAAAACT
* *
1322658 AGAATCAAAATGAGAATCAGAATCAAAATCAGGTGAC
1 AGAATCAAAATCAGAATCAGAATCAGAATCAGGTGAC
* *
1322695 AGAATCAGAATCAGAATCAGAATCAGAATTAGGTGAC
1 AGAATCAAAATCAGAATCAGAATCAGAATCAGGTGAC
* * * * *
1322732 AGAATTAGAATTAGAATCAGAATCAGTATCAGGTAAC
1 AGAATCAAAATCAGAATCAGAATCAGAATCAGGTGAC
1322769 AGAATCAAAATCAGAAT
1 AGAATCAAAATCAGAAT
1322786 GTGAATGCAA
Statistics
Matches: 79, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 79 1.00
ACGTcount: A:0.49, C:0.12, G:0.19, T:0.20
Consensus pattern (37 bp):
AGAATCAAAATCAGAATCAGAATCAGAATCAGGTGAC
Found at i:1323324 original size:27 final size:27
Alignment explanation
Indices: 1323294--1323513 Score: 298
Period size: 27 Copynumber: 8.2 Consensus size: 27
1323284 AATACCCTAC
** * *
1323294 GGGTAAAATGGTAATTTTATAAATTGA
1 GGGTAAAACAGTAATTTTGTAAATCGA
* *
1323321 GGGTAAAACGGTAATTCTGTAAATCGA
1 GGGTAAAACAGTAATTTTGTAAATCGA
*
1323348 GGGTAAAATAGTAATTTTGTAAATCGA
1 GGGTAAAACAGTAATTTTGTAAATCGA
* *
1323375 GGGTAAAATAGTAATTTTGTAAATCAA
1 GGGTAAAACAGTAATTTTGTAAATCGA
1323402 GGGTAAAACAGTAATTTTGTAAATCGA
1 GGGTAAAACAGTAATTTTGTAAATCGA
* *
1323429 GGGTAAAACAGTAATTCTGTCAATCGA
1 GGGTAAAACAGTAATTTTGTAAATCGA
*
1323456 GGGTAAAACAGTAATTTTGTAAGTCGA
1 GGGTAAAACAGTAATTTTGTAAATCGA
* * *
1323483 GGGTAAAACGGTAATTCTATAAATC-A
1 GGGTAAAACAGTAATTTTGTAAATCGA
1323509 GGGTA
1 GGGTA
1323514 CTTTGGTAAT
Statistics
Matches: 174, Mismatches: 19, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
26 6 0.03
27 168 0.97
ACGTcount: A:0.40, C:0.07, G:0.23, T:0.30
Consensus pattern (27 bp):
GGGTAAAACAGTAATTTTGTAAATCGA
Found at i:1323748 original size:27 final size:27
Alignment explanation
Indices: 1323492--1323741 Score: 306
Period size: 27 Copynumber: 9.3 Consensus size: 27
1323482 AGGGTAAAAC
* * * *
1323492 GGTAATTCTATAAATCA-GGGTACTTT
1 GGTAATTTTACAAACCAGGGGTATTTT
**
1323518 GGTAATTTTACAAGTC-GAGGGTATTTT
1 GGTAATTTTACAAACCAG-GGGTATTTT
* * *
1323545 AGTAATTTCACAAATCAGGGGTATTTT
1 GGTAATTTTACAAACCAGGGGTATTTT
**
1323572 GGTAATTTTACAAATTAGGGGTATTTT
1 GGTAATTTTACAAACCAGGGGTATTTT
*
1323599 GATAATTTTACAAACCAGGGGTATTTT
1 GGTAATTTTACAAACCAGGGGTATTTT
1323626 GGTAATTTTACAAACCAGGGGTATTTT
1 GGTAATTTTACAAACCAGGGGTATTTT
* * *
1323653 GGTAATTTTATAAACAAAGGGTATTTT
1 GGTAATTTTACAAACCAGGGGTATTTT
*
1323680 AGTAATTTTACAAACCAGGGGTATTTT
1 GGTAATTTTACAAACCAGGGGTATTTT
** *
1323707 GGTAATTTTGTAAACCAAGGGTATTTT
1 GGTAATTTTACAAACCAGGGGTATTTT
1323734 GGTAATTT
1 GGTAATTT
1323742 GGTAAACTAA
Statistics
Matches: 196, Mismatches: 25, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
26 13 0.07
27 182 0.93
28 1 0.01
ACGTcount: A:0.31, C:0.08, G:0.21, T:0.40
Consensus pattern (27 bp):
GGTAATTTTACAAACCAGGGGTATTTT
Found at i:1325436 original size:25 final size:27
Alignment explanation
Indices: 1325399--1325452 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 27
1325389 TCAAACATGC
1325399 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACACCTAGGGGT
* **
1325425 ATTTCGGT-AATTTTGCACCTAGGGGT
1 ATTTAGGTCAATTTAACACCTAGGGGT
1325451 AT
1 AT
1325453 AACAGTAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 6 0.25
26 18 0.75
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.37
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACACCTAGGGGT
Found at i:1326974 original size:26 final size:26
Alignment explanation
Indices: 1326938--1327047 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
1326928 CATGAAATTC
1326938 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
1326964 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
1326990 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
* *
1327016 TTATCATGTAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
1327042 TTATCA
1 TTATCA
1327048 ATTTGTATCA
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 81 1.00
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.35
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:1330834 original size:93 final size:93
Alignment explanation
Indices: 1330722--1330891 Score: 313
Period size: 93 Copynumber: 1.8 Consensus size: 93
1330712 CCCATAAGCG
*
1330722 AACTCGGACTCAACTCAACGAGCTCAGACGTTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
1 AACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
1330787 GAGTTCGGATGCCTAGTTACATCTCACA
66 GAGTTCGGATGCCTAGTTACATCTCACA
* *
1330815 AACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
1 AACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
1330880 GAGTTCGGATGC
66 GAGTTCGGATGC
1330892 TCAATCATCC
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.21
Consensus pattern (93 bp):
AACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
GAGTTCGGATGCCTAGTTACATCTCACA
Found at i:1330886 original size:46 final size:46
Alignment explanation
Indices: 1330713--1330888 Score: 209
Period size: 46 Copynumber: 3.8 Consensus size: 46
1330703 TGTAACCCGC
* * * *
1330713 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCAGACGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
1330759 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
1330809 CTCA-CA---AACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 C-CATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1330852 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1330889 TGCTCAATCA
Statistics
Matches: 111, Mismatches: 8, Indels: 22
0.79 0.06 0.16
Matches are distributed among these distances:
42 4 0.04
43 6 0.05
44 1 0.01
46 62 0.56
47 28 0.25
49 1 0.01
50 5 0.05
51 4 0.04
ACGTcount: A:0.31, C:0.30, G:0.19, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:1334548 original size:78 final size:78
Alignment explanation
Indices: 1334419--1334569 Score: 266
Period size: 78 Copynumber: 1.9 Consensus size: 78
1334409 CCGCCAGTAG
*
1334419 ATTCAGTAGCAACTTCTACTTCAGATTCTGGAGAAACTGCAATCTCATCAGCTAAGCCAGAAGTT
1 ATTCAGTAGCAACTTCTACATCAGATTCTGGAGAAACTGCAATCTCATCAGCTAAGCCAGAAGTT
1334484 GGCCCATCGGCAT
66 GGCCCATCGGCAT
* * *
1334497 ATTCAGTAGCAACTTCTACATCCGATTCTGGAGTAGCTGCAATCTCATCAGCTAAGCCAGAAGTT
1 ATTCAGTAGCAACTTCTACATCAGATTCTGGAGAAACTGCAATCTCATCAGCTAAGCCAGAAGTT
1334562 GGCCCATC
66 GGCCCATC
1334570 CACACTTTGG
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
78 69 1.00
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.26
Consensus pattern (78 bp):
ATTCAGTAGCAACTTCTACATCAGATTCTGGAGAAACTGCAATCTCATCAGCTAAGCCAGAAGTT
GGCCCATCGGCAT
Found at i:1336778 original size:12 final size:12
Alignment explanation
Indices: 1336753--1336786 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1336743 GGAATACACC
* *
1336753 GTAACGGTAACA
1 GTAACAGTAGCA
1336765 GTAACAGTAGCA
1 GTAACAGTAGCA
1336777 GTAACAGTAG
1 GTAACAGTAG
1336787 TGGTACACAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.41, C:0.15, G:0.26, T:0.18
Consensus pattern (12 bp):
GTAACAGTAGCA
Found at i:1336881 original size:57 final size:59
Alignment explanation
Indices: 1336761--1336891 Score: 142
Period size: 57 Copynumber: 2.2 Consensus size: 59
1336751 CCGTAACGGT
* * * * *
1336761 AACAGTAACAGTAGCAGTAACAGTAGTGGTACACAGAGTACCTCATCGGAATAAATCCGG
1 AACAGTAACAGTAACAGTAACAGTAGAGGTA-ACAGAGTACCTAATCGGAACAAATCCAG
* * *
1336821 AACAGTAACAGTAACAGTAATAGTA-AGGT-ACGGAGTACC-AATTCGGAACGAATCCAG
1 AACAGTAACAGTAACAGTAACAGTAGAGGTAACAGAGTACCTAA-TCGGAACAAATCCAG
*
1336878 AACAGTAATAGTAA
1 AACAGTAACAGTAA
1336892 GGCGGCACTT
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
56 1 0.02
57 34 0.56
59 3 0.05
60 23 0.38
ACGTcount: A:0.42, C:0.18, G:0.22, T:0.18
Consensus pattern (59 bp):
AACAGTAACAGTAACAGTAACAGTAGAGGTAACAGAGTACCTAATCGGAACAAATCCAG
Done.