Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr6
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: 47432654
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2298022 characters in sequence are not A, C, G, or T
File 94 of 136
Found at i:31391293 original size:14 final size:13
Alignment explanation
Indices: 31391266--31391291 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
31391256 TATGATGTGG
31391266 TGTTTTTAAAAAA
1 TGTTTTTAAAAAA
31391279 TGTTTTTAAAAAA
1 TGTTTTTAAAAAA
31391292 ATTATTACAA
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:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (13 bp):
TGTTTTTAAAAAA
Found at i:31407842 original size:21 final size:21
Alignment explanation
Indices: 31407824--31407897 Score: 84
Period size: 21 Copynumber: 3.7 Consensus size: 21
31407814 ATATTTAATT
31407824 AATT-TTTT-AAAATTATTAA
1 AATTATTTTAAAAATTATTAA
*
31407843 AATTATTTTAAAAATTATGAA
1 AATTATTTTAAAAATTATTAA
* *
31407864 AATATATTTTTAATATT-TTAA
1 AAT-TATTTTAAAAATTATTAA
31407885 AATT-TTTTAAAAA
1 AATTATTTTAAAAA
31407898 GTGATCAAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
19 11 0.24
20 5 0.11
21 19 0.41
22 11 0.24
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (21 bp):
AATTATTTTAAAAATTATTAA
Found at i:31411079 original size:44 final size:44
Alignment explanation
Indices: 31411030--31411124 Score: 137
Period size: 39 Copynumber: 2.3 Consensus size: 44
31411020 AAATTATCCA
*
31411030 ACCCAACCCAATTACCCAATCCAATAAAACTAAAACTAAAGTCT
1 ACCCAACCCAATTACCCAACCCAATAAAACTAAAACTAAAGTCT
31411074 -----ACCCAATTACCCAACCCAATAAAACTAAAACTAAAGTCT
1 ACCCAACCCAATTACCCAACCCAATAAAACTAAAACTAAAGTCT
*
31411113 ACCCAACTCAAT
1 ACCCAACCCAAT
31411125 AAAACTAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
39 38 0.86
44 6 0.14
ACGTcount: A:0.47, C:0.33, G:0.02, T:0.18
Consensus pattern (44 bp):
ACCCAACCCAATTACCCAACCCAATAAAACTAAAACTAAAGTCT
Found at i:31411080 original size:31 final size:31
Alignment explanation
Indices: 31411042--31411645 Score: 1043
Period size: 31 Copynumber: 19.2 Consensus size: 31
31411032 CCAACCCAAT
31411042 TACCCAA-TCCAATAAAACTAAAACTAAAGTC
1 TACCCAACT-CAATAAAACTAAAACTAAAGTC
*
31411073 TACCCAATTACCCAACCCAATAAAACTAAAACTAAAGTC
1 TACCC-A--A--C--TC-AATAAAACTAAAACTAAAGTC
31411112 TACCCAACTCAATAAAACTAAAACTAAAGTC
1 TACCCAACTCAATAAAACTAAAACTAAAGTC
31411143 TACCCAACTCAATAAAACTAAAACTAAAGTC
1 TACCCAACTCAATAAAACTAAAACTAAAGTC
31411174 TACCCAACTCAATAAAACTAAAACTAAAGTC
1 TACCCAACTCAATAAAACTAAAACTAAAGTC
31411205 TACCCAACTCAATAAAACTAAAACTAAAGTC
1 TACCCAACTCAATAAAACTAAAACTAAAGTC
31411236 TACCCAACTCAATAAAACTAAAACTAAAGTC
1 TACCCAACTCAATAAAACTAAAACTAAAGTC
31411267 TACCCAACTCAATAAAACTAAAACTAAAGTC
1 TACCCAACTCAATAAAACTAAAACTAAAGTC
31411298 TACCCAACTCAATAAAACTAAAACTAAAGTC
1 TACCCAACTCAATAAAACTAAAACTAAAGTC
31411329 TACCCAACTCAATAAAACTAAAACTAAAGTC
1 TACCCAACTCAATAAAACTAAAACTAAAGTC
31411360 TACCCAACTCAATAAAACTAAAACTAAAGTC
1 TACCCAACTCAATAAAACTAAAACTAAAGTC
31411391 TACCCAACTCAATAAAACTAAAACTAAAGTC
1 TACCCAACTCAATAAAACTAAAACTAAAGTC
31411422 TACCCAACTCAATAAAACTAAAACTAAAGTC
1 TACCCAACTCAATAAAACTAAAACTAAAGTC
31411453 TACCCAACTCAATAAAACTAAAACTAAAGTC
1 TACCCAACTCAATAAAACTAAAACTAAAGTC
31411484 TACCCAACTCAATAAAACTAAAACTAAAGTC
1 TACCCAACTCAATAAAACTAAAACTAAAGTC
31411515 TACCCAACTCAATAAAACTAAAACTAAAGTC
1 TACCCAACTCAATAAAACTAAAACTAAAGTC
** *
31411546 TACCCAACTCAATAAAACTAAGTCTACCCA-T-
1 TACCCAACTCAATAAAACTAAAACTA--AAGTC
*
31411577 TACCCAACCCAATAAAACTAAAACTAAAGTC
1 TACCCAACTCAATAAAACTAAAACTAAAGTC
31411608 TACCCAACTCAATAAAACTAAAACTAAAGTC
1 TACCCAACTCAATAAAACTAAAACTAAAGTC
31411639 TACCCAA
1 TACCCAA
31411646 TTACCAACCC
Statistics
Matches: 550, Mismatches: 10, Indels: 26
0.94 0.02 0.04
Matches are distributed among these distances:
29 1 0.00
30 1 0.00
31 513 0.93
32 3 0.01
33 1 0.00
34 2 0.00
36 1 0.00
38 2 0.00
39 26 0.05
ACGTcount: A:0.51, C:0.27, G:0.03, T:0.19
Consensus pattern (31 bp):
TACCCAACTCAATAAAACTAAAACTAAAGTC
Found at i:31411608 original size:38 final size:38
Alignment explanation
Indices: 31411558--31411678 Score: 152
Period size: 38 Copynumber: 3.4 Consensus size: 38
31411548 CCCAACTCAA
31411558 TAAAACT-AAGTCTACCCATTACCCAACCCAATAAAAC
1 TAAAACTAAAGTCTACCCATTACCCAACCCAATAAAAC
*
31411595 TAAAACTAAAG--T---C--TACCCAACTCAATAAAAC
1 TAAAACTAAAGTCTACCCATTACCCAACCCAATAAAAC
*
31411626 TAAAACTAAAGTCTACCCAATTA-CCAACCCAATAAAAA
1 TAAAACTAAAGTCTACCC-ATTACCCAACCCAATAAAAC
31411664 TAAAACTAAAGTCTA
1 TAAAACTAAAGTCTA
31411679 ACTCTTAACT
Statistics
Matches: 72, Mismatches: 3, Indels: 17
0.78 0.03 0.18
Matches are distributed among these distances:
31 28 0.39
33 2 0.03
36 2 0.03
37 7 0.10
38 31 0.43
39 2 0.03
ACGTcount: A:0.50, C:0.26, G:0.03, T:0.20
Consensus pattern (38 bp):
TAAAACTAAAGTCTACCCATTACCCAACCCAATAAAAC
Found at i:31411834 original size:17 final size:17
Alignment explanation
Indices: 31411814--31411876 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
31411804 TAATTTCAAG
31411814 AATTATGTAATGTTTTT
1 AATTATGTAATGTTTTT
* ***
31411831 AATTATGTAGTGATTCAA
1 AATTATGTAATG-TTTTT
*
31411849 AGACTTATGTAATATTTTT
1 A-A-TTATGTAATGTTTTT
31411868 AATTATGTA
1 AATTATGTA
31411877 GTGATTCAAT
Statistics
Matches: 34, Mismatches: 9, Indels: 6
0.69 0.18 0.12
Matches are distributed among these distances:
17 18 0.53
18 4 0.12
19 4 0.12
20 8 0.24
ACGTcount: A:0.35, C:0.03, G:0.13, T:0.49
Consensus pattern (17 bp):
AATTATGTAATGTTTTT
Found at i:31411857 original size:37 final size:37
Alignment explanation
Indices: 31411811--31411885 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
31411801 TGTTAATTTC
*
31411811 AAGAATTATGTAATGTTTTTAATTATGTAGTGATTCA
1 AAGAATTATGTAATATTTTTAATTATGTAGTGATTCA
*
31411848 AAGACTTATGTAATATTTTTAATTATGTAGTGATTCA
1 AAGAATTATGTAATATTTTTAATTATGTAGTGATTCA
31411885 A
1 A
31411886 TTCGGGTAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.36, C:0.04, G:0.15, T:0.45
Consensus pattern (37 bp):
AAGAATTATGTAATATTTTTAATTATGTAGTGATTCA
Found at i:31411898 original size:9 final size:9
Alignment explanation
Indices: 31411884--31411914 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
31411874 GTAGTGATTC
*
31411884 AATTCGGGT
1 AATTCGGTT
31411893 AATTCGGTT
1 AATTCGGTT
31411902 AATTCGGTT
1 AATTCGGTT
31411911 AATT
1 AATT
31411915 TTTAACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.26, C:0.10, G:0.23, T:0.42
Consensus pattern (9 bp):
AATTCGGTT
Found at i:31412260 original size:12 final size:12
Alignment explanation
Indices: 31412243--31412267 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
31412233 AATAGTGCAA
31412243 ATGATAATAAAT
1 ATGATAATAAAT
31412255 ATGATAATAAAT
1 ATGATAATAAAT
31412267 A
1 A
31412268 CAAAAAGAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (12 bp):
ATGATAATAAAT
Found at i:31413142 original size:44 final size:44
Alignment explanation
Indices: 31413083--31413169 Score: 147
Period size: 44 Copynumber: 2.0 Consensus size: 44
31413073 CCTTCCATTT
* * *
31413083 TTTGTCTGTTTGTTTCTGGTTAATCTGGGTAACTTCATTTTCTG
1 TTTGGCTGTTTGTTTCTAGTTAATCCGGGTAACTTCATTTTCTG
31413127 TTTGGCTGTTTGTTTCTAGTTAATCCGGGTAACTTCATTTTCT
1 TTTGGCTGTTTGTTTCTAGTTAATCCGGGTAACTTCATTTTCT
31413170 TCTTCTTCTT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.13, C:0.15, G:0.20, T:0.53
Consensus pattern (44 bp):
TTTGGCTGTTTGTTTCTAGTTAATCCGGGTAACTTCATTTTCTG
Found at i:31413892 original size:3 final size:3
Alignment explanation
Indices: 31413884--31413910 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
31413874 TAACTACATT
31413884 TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC
31413911 CATTTTCTGT
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:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:31414422 original size:16 final size:15
Alignment explanation
Indices: 31414403--31414444 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 15
31414393 TTTAATCTCA
31414403 TCTTTTTTTTCTTTTT
1 TCTTTTTTTT-TTTTT
31414419 TCTTTTTTTTTTTTT
1 TCTTTTTTTTTTTTT
31414434 TGCTTTGTTTT
1 T-CTTT-TTTT
31414445 ATTGCAGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.25
16 14 0.58
17 4 0.17
ACGTcount: A:0.00, C:0.10, G:0.05, T:0.86
Consensus pattern (15 bp):
TCTTTTTTTTTTTTT
Found at i:31414426 original size:15 final size:16
Alignment explanation
Indices: 31414406--31414444 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
31414396 AATCTCATCT
31414406 TTTTTTTCTTTTTT-C
1 TTTTTTTCTTTTTTGC
*
31414421 TTTTTTTTTTTTTTGC
1 TTTTTTTCTTTTTTGC
31414437 TTTGTTTT
1 TTT-TTTT
31414445 ATTGCAGAAA
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:0.00, C:0.08, G:0.05, T:0.87
Consensus pattern (16 bp):
TTTTTTTCTTTTTTGC
Found at i:31414812 original size:16 final size:17
Alignment explanation
Indices: 31414781--31414814 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
31414771 AGCATGAGGC
31414781 ATTACCAGATTTTACCG
1 ATTACCAGATTTTACCG
31414798 ATTACCAGA-TTTACCG
1 ATTACCAGATTTTACCG
31414814 A
1 A
31414815 ATTTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.32, C:0.24, G:0.12, T:0.32
Consensus pattern (17 bp):
ATTACCAGATTTTACCG
Found at i:31419511 original size:22 final size:23
Alignment explanation
Indices: 31419485--31419530 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
31419475 TTTTAATATA
*
31419485 TATTTT-TAAATTTAAATTATTT
1 TATTTTATAAATTTAAATGATTT
*
31419507 TATTTTATAATTTTAAATGATTT
1 TATTTTATAAATTTAAATGATTT
31419530 T
1 T
31419531 TAGCATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 6 0.29
23 15 0.71
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (23 bp):
TATTTTATAAATTTAAATGATTT
Found at i:31422015 original size:62 final size:62
Alignment explanation
Indices: 31421947--31422072 Score: 225
Period size: 62 Copynumber: 2.0 Consensus size: 62
31421937 CCACCAATCC
*
31421947 TTTTTGATAAGGTGTGATCAGATCACCTTGAAAAGTGGTTGTTTTTAATAAACGATTTGATT
1 TTTTTGATAAGGTGTGATCAGATCACCTTGAAAAGTGGTTATTTTTAATAAACGATTTGATT
* *
31422009 TTTTTGATAAGGTGTGATCGGATCACCTTGAAAAGTGGTTATTTTTAATAAATGATTTGATT
1 TTTTTGATAAGGTGTGATCAGATCACCTTGAAAAGTGGTTATTTTTAATAAACGATTTGATT
31422071 TT
1 TT
31422073 ATTAAAACAA
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 61 1.00
ACGTcount: A:0.29, C:0.07, G:0.21, T:0.44
Consensus pattern (62 bp):
TTTTTGATAAGGTGTGATCAGATCACCTTGAAAAGTGGTTATTTTTAATAAACGATTTGATT
Found at i:31427964 original size:2 final size:2
Alignment explanation
Indices: 31427957--31427984 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
31427947 ATAAGCAGCA
31427957 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31427985 NNNNNNNNNN
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31429299 original size:117 final size:118
Alignment explanation
Indices: 31429153--31429389 Score: 467
Period size: 117 Copynumber: 2.0 Consensus size: 118
31429143 TTGTGTGAAA
31429153 TTCTATTTATATATATAGTTCCATACTTAATTTTAATTATTAATTAATGAATGTAAATTATTAAT
1 TTCTATTTATATATATAGTTCCATACTTAATTTTAATTATTAATTAATGAATGTAAATTATTAAT
31429218 TAAATTTAAATATCATGAACACTAAATGATTTATTGTAATATTAATAGTGTAT
66 TAAATTTAAATATCATGAACACTAAATGATTTATTGTAATATTAATAGTGTAT
31429271 TTCTATTTAT-TATATAGTTCCATACTTAATTTTAATTATTAATTAATGAATGTAAATTATTAAT
1 TTCTATTTATATATATAGTTCCATACTTAATTTTAATTATTAATTAATGAATGTAAATTATTAAT
31429335 TAAATTTAAATATCATGAACACTAAATGATTTATTGTAATATTAATAGTGTAT
66 TAAATTTAAATATCATGAACACTAAATGATTTATTGTAATATTAATAGTGTAT
31429388 TT
1 TT
31429390 AATTTGTAAA
Statistics
Matches: 119, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
117 109 0.92
118 10 0.08
ACGTcount: A:0.40, C:0.06, G:0.07, T:0.47
Consensus pattern (118 bp):
TTCTATTTATATATATAGTTCCATACTTAATTTTAATTATTAATTAATGAATGTAAATTATTAAT
TAAATTTAAATATCATGAACACTAAATGATTTATTGTAATATTAATAGTGTAT
Found at i:31439558 original size:38 final size:39
Alignment explanation
Indices: 31439481--31439569 Score: 94
Period size: 39 Copynumber: 2.3 Consensus size: 39
31439471 ATGATTAAAC
*
31439481 TATACATATATAAATTATTATATATTATAATAGTGCATG-
1 TATA-ATATATAAATTATTATATATTATAATAATGCATGT
* *
31439520 TATAATATATATATTGATT-TAATATTATATTAAT-CATGTT
1 TATAATATATAAATT-ATTAT-ATATTATAATAATGCATG-T
31439560 TATAATATAT
1 TATAATATAT
31439570 GCTAAATATA
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
38 15 0.35
39 18 0.42
40 10 0.23
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.48
Consensus pattern (39 bp):
TATAATATATAAATTATTATATATTATAATAATGCATGT
Found at i:31447630 original size:14 final size:14
Alignment explanation
Indices: 31447613--31447702 Score: 65
Period size: 16 Copynumber: 6.1 Consensus size: 14
31447603 AACTTATAAA
*
31447613 ATATTATTTATTTTAT
1 ATATTATATA-TTT-T
*
31447629 ATATTATATATTAT
1 ATATTATATATTTT
31447643 ATATTATATATTATTT
1 ATATTATATA-T-TTT
* *
31447659 ATATGAAATATTTT
1 ATATTATATATTTT
31447673 ATATGCTATATATTTT
1 ATAT--TATATATTTT
* *
31447689 TTATT-TTTATTTT
1 ATATTATATATTTT
31447702 A
1 A
31447703 AAACAATAAA
Statistics
Matches: 60, Mismatches: 10, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
13 7 0.12
14 19 0.32
15 4 0.07
16 30 0.50
ACGTcount: A:0.34, C:0.01, G:0.02, T:0.62
Consensus pattern (14 bp):
ATATTATATATTTT
Found at i:31447635 original size:7 final size:7
Alignment explanation
Indices: 31447625--31447656 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
31447615 ATTATTTATT
31447625 TTATATA
1 TTATATA
31447632 TTATATA
1 TTATATA
31447639 TTATATA
1 TTATATA
31447646 TTATATA
1 TTATATA
31447653 TTAT
1 TTAT
31447657 TTATATGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
TTATATA
Found at i:31447647 original size:23 final size:23
Alignment explanation
Indices: 31447613--31447695 Score: 78
Period size: 23 Copynumber: 3.6 Consensus size: 23
31447603 AACTTATAAA
*
31447613 ATATTATTTATTTTATATATTAT
1 ATATTATATATTTTATATATTAT
*
31447636 ATATTATATATTATATATTATT-T
1 ATATTATATATTTTATA-TATTAT
* * **
31447659 ATATGAAATATTTTATATGCTAT
1 ATATTATATATTTTATATATTAT
* *
31447682 ATATTTTTTATTTT
1 ATATTATATATTTT
31447696 TATTTTAAAA
Statistics
Matches: 47, Mismatches: 11, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
22 2 0.04
23 41 0.87
24 4 0.09
ACGTcount: A:0.35, C:0.01, G:0.02, T:0.61
Consensus pattern (23 bp):
ATATTATATATTTTATATATTAT
Found at i:31450724 original size:16 final size:16
Alignment explanation
Indices: 31450703--31450761 Score: 73
Period size: 16 Copynumber: 3.4 Consensus size: 16
31450693 TTTCCATGTA
31450703 CATGTAACATCTATAC
1 CATGTAACATCTATAC
*
31450719 CATGTAATTCATGTAAATAC
1 CATGTAA--CATCT--ATAC
31450739 CATGTAACATCTATAC
1 CATGTAACATCTATAC
31450755 CATGTAA
1 CATGTAA
31450762 TTCATGTAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
16 18 0.49
18 8 0.22
20 11 0.30
ACGTcount: A:0.39, C:0.20, G:0.08, T:0.32
Consensus pattern (16 bp):
CATGTAACATCTATAC
Found at i:31450740 original size:20 final size:20
Alignment explanation
Indices: 31450715--31450779 Score: 86
Period size: 20 Copynumber: 3.5 Consensus size: 20
31450705 TGTAACATCT
31450715 ATACCATGTAATTCATGTAA
1 ATACCATGTAATTCATGTAA
*
31450735 ATACCATGTAA--CATCT--
1 ATACCATGTAATTCATGTAA
31450751 ATACCATGTAATTCATGTAA
1 ATACCATGTAATTCATGTAA
31450771 ATA-CATGTA
1 ATACCATGTA
31450780 CTAGTTCATA
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
16 11 0.28
18 8 0.21
19 6 0.15
20 14 0.36
ACGTcount: A:0.40, C:0.17, G:0.09, T:0.34
Consensus pattern (20 bp):
ATACCATGTAATTCATGTAA
Found at i:31450744 original size:36 final size:35
Alignment explanation
Indices: 31450701--31450779 Score: 149
Period size: 36 Copynumber: 2.2 Consensus size: 35
31450691 AATTTCCATG
31450701 TACATGTAACATCTATACCATGTAATTCATGTAAA
1 TACATGTAACATCTATACCATGTAATTCATGTAAA
31450736 TACCATGTAACATCTATACCATGTAATTCATGTAAA
1 TA-CATGTAACATCTATACCATGTAATTCATGTAAA
31450772 TACATGTA
1 TACATGTA
31450780 CTAGTTCATA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
35 8 0.19
36 35 0.81
ACGTcount: A:0.39, C:0.18, G:0.09, T:0.34
Consensus pattern (35 bp):
TACATGTAACATCTATACCATGTAATTCATGTAAA
Found at i:31450996 original size:25 final size:25
Alignment explanation
Indices: 31450911--31450998 Score: 70
Period size: 25 Copynumber: 3.6 Consensus size: 25
31450901 GTACATGTAT
*
31450911 GCTCATACGAGCT-ATTAACGGTAA
1 GCTCATACGAGCTGAATAACGGTAA
* * * * ***
31450935 ACTCCTCCGAGTTGAATAATAATAA
1 GCTCATACGAGCTGAATAACGGTAA
* **
31450960 GCTCCTTTGAGCTGAATAACGGTAA
1 GCTCATACGAGCTGAATAACGGTAA
31450985 GCTCATACGAGCTG
1 GCTCATACGAGCTG
31450999 GAATCGGTAA
Statistics
Matches: 45, Mismatches: 18, Indels: 1
0.70 0.28 0.02
Matches are distributed among these distances:
24 9 0.20
25 36 0.80
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.26
Consensus pattern (25 bp):
GCTCATACGAGCTGAATAACGGTAA
Found at i:31453031 original size:19 final size:19
Alignment explanation
Indices: 31453009--31453058 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 19
31452999 TCTCAACAAA
31453009 AATTCTAAAAAATCAAAAT
1 AATTCTAAAAAATCAAAAT
* *
31453028 AATTTCCAAAAATTCAAAAT
1 AA-TTCTAAAAAATCAAAAT
* *
31453048 ATTTATAAAAA
1 AATTCTAAAAA
31453059 TTCCAAATTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
19 9 0.36
20 16 0.64
ACGTcount: A:0.60, C:0.10, G:0.00, T:0.30
Consensus pattern (19 bp):
AATTCTAAAAAATCAAAAT
Found at i:31453059 original size:19 final size:19
Alignment explanation
Indices: 31453014--31453072 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
31453004 ACAAAAATTC
* *
31453014 TAAAAAATCAAAATAATTTC
1 TAAAAATTCAAAAT-ATTTA
*
31453034 CAAAAATTCAAAATATTTA
1 TAAAAATTCAAAATATTTA
* *
31453053 TAAAAATTCCAAATTTTTA
1 TAAAAATTCAAAATATTTA
31453072 T
1 T
31453073 TTTTTTAAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 21 0.64
20 12 0.36
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.36
Consensus pattern (19 bp):
TAAAAATTCAAAATATTTA
Found at i:31458021 original size:19 final size:20
Alignment explanation
Indices: 31457999--31458039 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
31457989 TTTATATCAA
31457999 TTTATAAATTT-TAAATTTT
1 TTTATAAATTTATAAATTTT
*
31458018 TTTATTAATTTAATAAATTTT
1 TTTATAAATTT-ATAAATTTT
31458039 T
1 T
31458040 AATTGTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 10 0.53
21 9 0.47
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TTTATAAATTTATAAATTTT
Found at i:31458265 original size:26 final size:26
Alignment explanation
Indices: 31458234--31458285 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
31458224 TCTACATTTA
* *
31458234 AAAATTATAAAAA-CAATTTTTTAAAT
1 AAAATT-TAAAAATCAAATATTTAAAT
31458260 AAAATTTAAAAATCAAATATTTAAAT
1 AAAATTTAAAAATCAAATATTTAAAT
31458286 TCAAATCCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 6 0.26
26 17 0.74
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.37
Consensus pattern (26 bp):
AAAATTTAAAAATCAAATATTTAAAT
Found at i:31458567 original size:15 final size:16
Alignment explanation
Indices: 31458541--31458574 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
31458531 ATTTAAGAGT
*
31458541 TAATATAAATATTTTC
1 TAATATAAATATTTAC
31458557 TAATA-AAATATTTAC
1 TAATATAAATATTTAC
31458572 TAA
1 TAA
31458575 CTCGAATAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (16 bp):
TAATATAAATATTTAC
Found at i:31459214 original size:26 final size:27
Alignment explanation
Indices: 31459176--31459239 Score: 71
Period size: 26 Copynumber: 2.4 Consensus size: 27
31459166 TAAGTTTACC
*
31459176 TTTTAATAATTTTAATGA-TTTTT-AAT
1 TTTTAATAATTTT-ATAACTTTTTAAAT
**
31459202 TTTTAATTTTTTTATAACTTTTTAAAT
1 TTTTAATAATTTTATAACTTTTTAAAT
31459229 TTTTAA-AATTT
1 TTTTAATAATTT
31459240 AAAATATTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
25 3 0.10
26 19 0.61
27 9 0.29
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (27 bp):
TTTTAATAATTTTATAACTTTTTAAAT
Found at i:31459576 original size:198 final size:199
Alignment explanation
Indices: 31459227--31459623 Score: 787
Period size: 198 Copynumber: 2.0 Consensus size: 199
31459217 AACTTTTTAA
31459227 ATTTTTAAAATTTAAAATATTAATTAAATACTATATGTCAACAATAAAAAAACATGAAGTTATAT
1 ATTTTTAAAATTTAAAATATTAATTAAATACTATATGTCAACAATAAAAAAACATGAAGTTATAT
31459292 CTTTTTTTAAGGTGATTTGAGAGGGACAAAAAATTCTTTATGCGTTATGTAATCTAATCAACACA
66 CTTTTTTTAAGGTGATTTGAGAGGGACAAAAAATTCTTTATGCGTTATGTAATCTAATCAACACA
31459357 AGCTACCTAATATAAGATGGACAAAGAAAGAATATTTTAACTCGAATTTTTGGGATCTGTAATTT
131 AGCTACCTAATATAAGATGGACAAAGAAAGAATATTTTAACTCGAATTTTTGGGATCTGTAATTT
31459422 AGCT
196 AGCT
31459426 ATTTTTAAAA-TTAAAATATTAATTAAATACTATATGTCAACAATAAAAAAACATGAAGTTATAT
1 ATTTTTAAAATTTAAAATATTAATTAAATACTATATGTCAACAATAAAAAAACATGAAGTTATAT
31459490 CTTTTTTTAAGGTGATTTGAGAGGGACAAAAAATTCTTTATGCGTTATGTAATCTAATCAACACA
66 CTTTTTTTAAGGTGATTTGAGAGGGACAAAAAATTCTTTATGCGTTATGTAATCTAATCAACACA
31459555 AGCTACCTAATATAAGATGGACAAAGAAAGAATATTTTAACTCGAATTTTTGGGATCTGTAATTT
131 AGCTACCTAATATAAGATGGACAAAGAAAGAATATTTTAACTCGAATTTTTGGGATCTGTAATTT
31459620 AGCT
196 AGCT
31459624 GTTATAGAAT
Statistics
Matches: 198, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
198 188 0.95
199 10 0.05
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.36
Consensus pattern (199 bp):
ATTTTTAAAATTTAAAATATTAATTAAATACTATATGTCAACAATAAAAAAACATGAAGTTATAT
CTTTTTTTAAGGTGATTTGAGAGGGACAAAAAATTCTTTATGCGTTATGTAATCTAATCAACACA
AGCTACCTAATATAAGATGGACAAAGAAAGAATATTTTAACTCGAATTTTTGGGATCTGTAATTT
AGCT
Found at i:31472642 original size:26 final size:26
Alignment explanation
Indices: 31472613--31472662 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
31472603 AAACTCTAAC
31472613 GCTTCCAATGGAACTGAACTATTATA
1 GCTTCCAATGGAACTGAACTATTATA
*
31472639 GCTTCCAGTGGAACTGAACTATTA
1 GCTTCCAATGGAACTGAACTATTA
31472663 CGATAAGTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (26 bp):
GCTTCCAATGGAACTGAACTATTATA
Found at i:31480703 original size:8 final size:8
Alignment explanation
Indices: 31480690--31480718 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
31480680 TTTTAAATAA
31480690 TATTTTAT
1 TATTTTAT
31480698 TATTTTAT
1 TATTTTAT
31480706 TATTTTAT
1 TATTTTAT
31480714 TATTT
1 TATTT
31480719 AGTATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TATTTTAT
Found at i:31503328 original size:13 final size:13
Alignment explanation
Indices: 31503310--31503343 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
31503300 ACATTTGTTA
*
31503310 TTTATATTAAAAT
1 TTTATAATAAAAT
31503323 TTTATAAATAAAAT
1 TTTAT-AATAAAAT
31503337 TTTATAA
1 TTTATAA
31503344 AATTTTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TTTATAATAAAAT
Found at i:31503336 original size:14 final size:14
Alignment explanation
Indices: 31503317--31503344 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
31503307 TTATTTATAT
31503317 TAAAATTTTATAAA
1 TAAAATTTTATAAA
31503331 TAAAATTTTATAAA
1 TAAAATTTTATAAA
31503345 ATTTTATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TAAAATTTTATAAA
Found at i:31503595 original size:17 final size:17
Alignment explanation
Indices: 31503573--31503606 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
31503563 AAAATGTTTT
31503573 ACTTGTATAATT-AATTA
1 ACTTGT-TAATTGAATTA
31503590 ACTTGTTAATTGAATTA
1 ACTTGTTAATTGAATTA
31503607 GCGTCGGTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.47
Consensus pattern (17 bp):
ACTTGTTAATTGAATTA
Found at i:31504615 original size:9 final size:9
Alignment explanation
Indices: 31504588--31504624 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
31504578 TGAGTTTTTA
31504588 AATTCGAAT
1 AATTCGAAT
* *
31504597 AACTCAAAT
1 AATTCGAAT
31504606 AATTCGAAT
1 AATTCGAAT
31504615 AATTCGAAT
1 AATTCGAAT
31504624 A
1 A
31504625 TCAAACTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:31504837 original size:30 final size:31
Alignment explanation
Indices: 31504803--31504862 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
31504793 AAACCTTTTA
*
31504803 TTTTCTCCC-AAAATTTTTACTCCC-TCCCAC
1 TTTTC-CCCTAAAACTTTTACTCCCTTCCCAC
*
31504833 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCTAAAACTTTTACTCCCTTCCCA
31504863 TCCCACCTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 3 0.12
30 18 0.69
31 5 0.19
ACGTcount: A:0.20, C:0.38, G:0.00, T:0.42
Consensus pattern (31 bp):
TTTTCCCCTAAAACTTTTACTCCCTTCCCAC
Found at i:31515065 original size:23 final size:23
Alignment explanation
Indices: 31515039--31515082 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
31515029 GTAAGAAAAT
31515039 AATAAATATACATTTTTTAATTG
1 AATAAATATACATTTTTTAATTG
* * *
31515062 AATATATTTATATTTTTTAAT
1 AATAAATATACATTTTTTAAT
31515083 AAAAAAAACT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (23 bp):
AATAAATATACATTTTTTAATTG
Found at i:31516448 original size:9 final size:8
Alignment explanation
Indices: 31516422--31516521 Score: 58
Period size: 8 Copynumber: 11.6 Consensus size: 8
31516412 TATTTTTTTT
31516422 AAATTTAA
1 AAATTTAA
31516430 AAATTTAA
1 AAATTTAA
31516438 AAATTTAA
1 AAATTTAA
* *
31516446 AAAATTAT
1 AAATTTAA
31516454 AAATCATTAA
1 AAAT--TTAA
* *
31516464 TATTATTAA
1 AAAT-TTAA
31516473 ATAA-TTATA
1 A-AATTTA-A
31516482 AAATTATAAA
1 AAATT-T-AA
*
31516492 AAAATTAA
1 AAATTTAA
* *
31516500 TATTTTAA
1 AAATTTAA
31516508 AAATTTTAA
1 AAA-TTTAA
31516517 AAATT
1 AAATT
31516522 AATTGAATAT
Statistics
Matches: 70, Mismatches: 14, Indels: 16
0.70 0.14 0.16
Matches are distributed among these distances:
8 40 0.57
9 17 0.24
10 12 0.17
11 1 0.01
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (8 bp):
AAATTTAA
Found at i:31516473 original size:35 final size:35
Alignment explanation
Indices: 31516433--31516522 Score: 112
Period size: 35 Copynumber: 2.6 Consensus size: 35
31516423 AATTTAAAAA
**
31516433 TTTAAAAATTTAAAAAATTAT-AAATCATTAATAT
1 TTTAAAAATTTAAAAAATTATAAAAAAATTAATAT
*
31516467 TATTAAATAA-TTATAAAATTATAAAAAAATTAATAT
1 T-TTAAA-AATTTAAAAAATTATAAAAAAATTAATAT
*
31516503 TTTAAAAATTTTAAAAATTA
1 TTTAAAAATTTAAAAAATTA
31516523 ATTGAATATT
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
34 3 0.06
35 30 0.64
36 14 0.30
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (35 bp):
TTTAAAAATTTAAAAAATTATAAAAAAATTAATAT
Found at i:31516516 original size:17 final size:17
Alignment explanation
Indices: 31516460--31516516 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
31516450 TTATAAATCA
31516460 TTAATATTATTAAATAATT
1 TTAATATT-TTAAA-AATT
* * * **
31516479 ATAAAATTATAAAAAAA
1 TTAATATTTTAAAAATT
31516496 TTAATATTTTAAAAATT
1 TTAATATTTTAAAAATT
31516513 TTAA
1 TTAA
31516517 AAATTAATTG
Statistics
Matches: 28, Mismatches: 10, Indels: 2
0.70 0.25 0.05
Matches are distributed among these distances:
17 18 0.64
18 4 0.14
19 6 0.21
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TTAATATTTTAAAAATT
Found at i:31526217 original size:18 final size:17
Alignment explanation
Indices: 31526191--31526226 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
31526181 GTAAAGTAAT
31526191 AATACGATAATAAGAATA
1 AATACGATAATAA-AATA
*
31526209 AATATGATAATAAAATA
1 AATACGATAATAAAATA
31526226 A
1 A
31526227 CAATAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.64, C:0.03, G:0.08, T:0.25
Consensus pattern (17 bp):
AATACGATAATAAAATA
Found at i:31526704 original size:19 final size:20
Alignment explanation
Indices: 31526658--31526704 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 20
31526648 CTATTACTCT
*
31526658 AAACAGAAA-AGAAAAGAAA
1 AAACATAAAGAGAAAAGAAA
*
31526677 AAAGATAAAGAGAAAA-AAA
1 AAACATAAAGAGAAAAGAAA
*
31526696 AAACCTAAA
1 AAACATAAA
31526705 AATCTAATCT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 17 0.74
20 6 0.26
ACGTcount: A:0.77, C:0.06, G:0.13, T:0.04
Consensus pattern (20 bp):
AAACATAAAGAGAAAAGAAA
Found at i:31529950 original size:18 final size:18
Alignment explanation
Indices: 31529929--31529965 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
31529919 ATTTATATTT
31529929 TTTAAAAAATTATAAAAA
1 TTTAAAAAATTATAAAAA
*
31529947 TTTAAAAAATTCTAAAAA
1 TTTAAAAAATTATAAAAA
31529965 T
1 T
31529966 ATATATAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (18 bp):
TTTAAAAAATTATAAAAA
Found at i:31529997 original size:8 final size:9
Alignment explanation
Indices: 31529929--31529994 Score: 55
Period size: 9 Copynumber: 6.9 Consensus size: 9
31529919 ATTTATATTT
31529929 TTTAAAAAA
1 TTTAAAAAA
31529938 -TTATAAAAA
1 TTTA-AAAAA
31529947 TTTAAAAAA
1 TTTAAAAAA
31529956 TTCTAAAAATA
1 TT-TAAAAA-A
31529967 TATATAAATAAA
1 T-T-TAAA-AAA
*
31529979 GTT-AAAAA
1 TTTAAAAAA
31529987 TTTAAAAA
1 TTTAAAAA
31529995 TTTTCTAAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 14
0.73 0.05 0.22
Matches are distributed among these distances:
8 8 0.17
9 18 0.38
10 10 0.21
11 3 0.06
12 6 0.13
13 2 0.04
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (9 bp):
TTTAAAAAA
Found at i:31534529 original size:3 final size:3
Alignment explanation
Indices: 31534521--31534557 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
31534511 GAGGACATGG
*
31534521 GAA GAA GAA GAA GAA GAA GAT GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
31534558 TGAATGAAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.62, C:0.00, G:0.35, T:0.03
Consensus pattern (3 bp):
GAA
Found at i:31535632 original size:23 final size:22
Alignment explanation
Indices: 31535598--31535648 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
31535588 TCATGCAGAT
31535598 TTTTTTTATTAA-AACCATTTACA
1 TTTTTTTATTAATAACCA-TTA-A
* *
31535621 TTTTTTTGTTAATAATCATTAA
1 TTTTTTTATTAATAACCATTAA
31535643 TTTTTT
1 TTTTTT
31535649 ACATTAGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 7 0.28
23 14 0.56
24 4 0.16
ACGTcount: A:0.29, C:0.08, G:0.02, T:0.61
Consensus pattern (22 bp):
TTTTTTTATTAATAACCATTAA
Found at i:31535723 original size:6 final size:6
Alignment explanation
Indices: 31535712--31535742 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
31535702 TAAATTAATG
31535712 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA T
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA T
31535743 ATGTGTTAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTA
Found at i:31536033 original size:16 final size:16
Alignment explanation
Indices: 31536012--31536042 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
31536002 AAAATTAATA
31536012 AACAAAATTTAAAAAT
1 AACAAAATTTAAAAAT
31536028 AACAAAATTTAAAAA
1 AACAAAATTTAAAAA
31536043 AGTTGATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.23
Consensus pattern (16 bp):
AACAAAATTTAAAAAT
Found at i:31537167 original size:21 final size:21
Alignment explanation
Indices: 31537143--31537183 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
31537133 TTTTCCCTCA
*
31537143 TTTTCTCTCCTTTTTCTTTTC
1 TTTTCTCTCATTTTTCTTTTC
* *
31537164 TTTTTTCTTATTTTTCTTTT
1 TTTTCTCTCATTTTTCTTTT
31537184 TCTGGACCTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (21 bp):
TTTTCTCTCATTTTTCTTTTC
Found at i:31538252 original size:14 final size:14
Alignment explanation
Indices: 31538230--31538294 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 14
31538220 ACGAAAACGA
*
31538230 AAAAGAAAAATAAG
1 AAAATAAAAATAAG
**
31538244 AAAATAAAAA-GGG
1 AAAATAAAAATAAG
31538257 AAAATAAAAAATAA-
1 AAAAT-AAAAATAAG
31538271 AAAAT-AAAAT---
1 AAAATAAAAATAAG
31538281 AAAATAAAAATAAG
1 AAAATAAAAATAAG
31538295 GTACAAGAGG
Statistics
Matches: 40, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
10 5 0.12
11 5 0.12
12 5 0.12
13 6 0.15
14 19 0.47
ACGTcount: A:0.78, C:0.00, G:0.09, T:0.12
Consensus pattern (14 bp):
AAAATAAAAATAAG
Found at i:31549162 original size:13 final size:13
Alignment explanation
Indices: 31549141--31549172 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
31549131 AATATTAGTC
31549141 TTTTT-AACATAT
1 TTTTTAAACATAT
31549153 TTTTTAAACATAT
1 TTTTTAAACATAT
31549166 TTTTTAA
1 TTTTTAA
31549173 TTAAAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 5 0.26
13 14 0.74
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.59
Consensus pattern (13 bp):
TTTTTAAACATAT
Found at i:31549561 original size:18 final size:18
Alignment explanation
Indices: 31549511--31549562 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 18
31549501 ATATAGTTAC
31549511 TTTTAAAATAT-T-TA-A
1 TTTTAAAATATATATATA
* *
31549526 TTTTAAAATATCTTTATA
1 TTTTAAAATATATATATA
*
31549544 TTTTAATATATATATATA
1 TTTTAAAATATATATATA
31549562 T
1 T
31549563 ATAATTTCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
15 11 0.35
16 1 0.03
17 2 0.06
18 17 0.55
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTTAAAATATATATATA
Found at i:31552980 original size:13 final size:13
Alignment explanation
Indices: 31552962--31552991 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
31552952 CTGATTTATC
*
31552962 TTTTTTTTTTCCT
1 TTTTTTTTTTCAT
31552975 TTTTTTTTTTCAT
1 TTTTTTTTTTCAT
31552988 TTTT
1 TTTT
31552992 GAGAATTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.03, C:0.10, G:0.00, T:0.87
Consensus pattern (13 bp):
TTTTTTTTTTCAT
Found at i:31553707 original size:31 final size:31
Alignment explanation
Indices: 31553657--31553718 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
31553647 TTAATCGTGG
* * *
31553657 GTGACTAAAATTATAAAAGTATATAATGACA
1 GTGAATAAAATGATAAAAGTATATAACGACA
*
31553688 GTGAATAAAATGATTAAAGTATATAACGACA
1 GTGAATAAAATGATAAAAGTATATAACGACA
31553719 TTACTTATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.52, C:0.06, G:0.15, T:0.27
Consensus pattern (31 bp):
GTGAATAAAATGATAAAAGTATATAACGACA
Found at i:31554406 original size:109 final size:109
Alignment explanation
Indices: 31554234--31554516 Score: 471
Period size: 109 Copynumber: 2.6 Consensus size: 109
31554224 GTCAATCGAG
* * *
31554234 AAATCGAAACCCAGCACATTAGGGCATG-TTCCTCGAATTTCCAAACGCAAAACATTGCCTTATT
1 AAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATT
* * *
31554298 TTAAATTTTTTAAAAGGATATTTAGCCATTTGGTTGAACGAGAA
66 TTAAAATTTTTAAAACGATATTAAGCCATTTGGTTGAACGAGAA
*
31554342 AAATCGACACCCAG-ACCTTAGAGCATGTTTTCTCGAATTTCCCAAACGCAAAACATTGCCTTAT
1 AAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTT-CCAAACGCAAAACATTGCCTTAT
*
31554406 TTTAAAATTTTTAAAACGATATTAAGTCATTTGGTTGAACGAGAA
65 TTTAAAATTTTTAAAACGATATTAAGCCATTTGGTTGAACGAGAA
31554451 AAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATT
1 AAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATT
31554516 T
66 T
31554517 GAAGAAAATT
Statistics
Matches: 163, Mismatches: 9, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
107 11 0.07
108 24 0.15
109 103 0.63
110 25 0.15
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.30
Consensus pattern (109 bp):
AAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATT
TTAAAATTTTTAAAACGATATTAAGCCATTTGGTTGAACGAGAA
Found at i:31556057 original size:26 final size:25
Alignment explanation
Indices: 31556018--31556066 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
31556008 TTTATGATAC
31556018 ATATACATACGCATGGCTTTTATAAT
1 ATATACATACGCAT-GCTTTTATAAT
* * *
31556044 ATATATATAGGCATTCTTTTATA
1 ATATACATACGCATGCTTTTATA
31556067 CAGTATACAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 8 0.40
26 12 0.60
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.43
Consensus pattern (25 bp):
ATATACATACGCATGCTTTTATAAT
Found at i:31557105 original size:4 final size:4
Alignment explanation
Indices: 31557096--31557174 Score: 52
Period size: 4 Copynumber: 18.8 Consensus size: 4
31557086 ACACCATAGC
* ** *
31557096 AAAT AAAT AAAT AAAT AAAT AAACT AAAGC ATAA- AAAT GGAC AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAA-T AAA-T A-AAT AAAT AAAT AAAT AAAT
* *
31557146 AAAT ACAT AAAT GAACAT AAAA AAAT AAA
1 AAAT AAAT AAAT -AA-AT AAAT AAAT AAA
31557175 GGAAAATAGA
Statistics
Matches: 58, Mismatches: 12, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
3 2 0.03
4 43 0.74
5 9 0.16
6 4 0.07
ACGTcount: A:0.70, C:0.06, G:0.05, T:0.19
Consensus pattern (4 bp):
AAAT
Found at i:31558207 original size:19 final size:20
Alignment explanation
Indices: 31558166--31558218 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
31558156 TTTAAAAAAA
**
31558166 AAGAAAAAAAAATAAACTTT
1 AAGAAAAAAAAATAAACAGT
*
31558186 AAGAAAAAATAA-AAACAGT
1 AAGAAAAAAAAATAAACAGT
31558205 AAGCAAAAGAAAAA
1 AAG-AAAA-AAAAA
31558219 AAGAAAACTG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 8 0.30
20 15 0.56
21 4 0.15
ACGTcount: A:0.74, C:0.06, G:0.09, T:0.11
Consensus pattern (20 bp):
AAGAAAAAAAAATAAACAGT
Found at i:31559819 original size:30 final size:30
Alignment explanation
Indices: 31559774--31559838 Score: 105
Period size: 30 Copynumber: 2.2 Consensus size: 30
31559764 ACTTATTTTA
31559774 TTGTTAATTTTGTTATTATCTTAGAGGCAT
1 TTGTTAATTTTGTTATTATCTTAGAGGCAT
*
31559804 TTGTT-ATTTTCGTTATTATTTTAGAGGCAT
1 TTGTTAATTTT-GTTATTATCTTAGAGGCAT
31559834 TTGTT
1 TTGTT
31559839 TGTTAAGTTG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
29 5 0.15
30 28 0.85
ACGTcount: A:0.20, C:0.06, G:0.17, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATCTTAGAGGCAT
Found at i:31562581 original size:98 final size:98
Alignment explanation
Indices: 31562412--31562606 Score: 354
Period size: 98 Copynumber: 2.0 Consensus size: 98
31562402 ATACAATAAA
*
31562412 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATC
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
31562477 CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
66 CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
* *
31562510 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
*
31562575 CCTTTAGAATCTCAAACTCGGAATATTTCCTT
66 CCTTTAGAATCCCAAACTCGGAATATTTCCTT
31562607 CATGATTTTA
Statistics
Matches: 93, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
98 93 1.00
ACGTcount: A:0.36, C:0.25, G:0.11, T:0.28
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
Found at i:31563650 original size:19 final size:19
Alignment explanation
Indices: 31563626--31563727 Score: 123
Period size: 19 Copynumber: 5.3 Consensus size: 19
31563616 GATTACAAAA
*
31563626 ATATCATATCTAAGATTAT
1 ATATCATATCTAAGATTAC
*
31563645 ATATCATATCTAAGATTGCAT
1 ATATCATATCTAAGATT--AC
*
31563666 ATATCATATCTAAGATTGC
1 ATATCATATCTAAGATTAC
* *
31563685 ATATCATATCTAGGATTGC
1 ATATCATATCTAAGATTAC
* *
31563704 ATATCATATCTAATATTGC
1 ATATCATATCTAAGATTAC
31563723 ATATC
1 ATATC
31563728 CTCAAAAATT
Statistics
Matches: 76, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
19 57 0.75
21 19 0.25
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.39
Consensus pattern (19 bp):
ATATCATATCTAAGATTAC
Found at i:31563674 original size:40 final size:38
Alignment explanation
Indices: 31563626--31563727 Score: 141
Period size: 40 Copynumber: 2.6 Consensus size: 38
31563616 GATTACAAAA
*
31563626 ATATCATATCTAAGATTATATATCATATCTAAGATTGC
1 ATATCATATCTAAGATTACATATCATATCTAAGATTGC
* *
31563664 ATATATCATATCTAAGATTGCATATCATATCTAGGATTGC
1 --ATATCATATCTAAGATTACATATCATATCTAAGATTGC
* *
31563704 ATATCATATCTAATATTGCATATC
1 ATATCATATCTAAGATTACATATC
31563728 CTCAAAAATT
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
38 23 0.40
40 35 0.60
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.39
Consensus pattern (38 bp):
ATATCATATCTAAGATTACATATCATATCTAAGATTGC
Found at i:31572699 original size:8 final size:8
Alignment explanation
Indices: 31572686--31572718 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
31572676 AAAATTCTTT
31572686 AAAATTAA
1 AAAATTAA
31572694 AAAATTAA
1 AAAATTAA
*
31572702 AATA-TAA
1 AAAATTAA
31572709 AAAATTAA
1 AAAATTAA
31572717 AA
1 AA
31572719 TTCAATGTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
7 6 0.27
8 16 0.73
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AAAATTAA
Found at i:31572711 original size:15 final size:14
Alignment explanation
Indices: 31572684--31572720 Score: 65
Period size: 15 Copynumber: 2.6 Consensus size: 14
31572674 TAAAAATTCT
31572684 TTAAAATTAAAAAA
1 TTAAAATTAAAAAA
31572698 TTAAAATATAAAAAA
1 TTAAAAT-TAAAAAA
31572713 TTAAAATT
1 TTAAAATT
31572721 CAATGTTATC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 8 0.36
15 14 0.64
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
TTAAAATTAAAAAA
Found at i:31578226 original size:2 final size:2
Alignment explanation
Indices: 31578219--31578345 Score: 254
Period size: 2 Copynumber: 63.5 Consensus size: 2
31578209 TTTATCCTAT
31578219 TA TA TA 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
31578261 TA TA TA 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
31578303 TA TA TA 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
31578345 T
1 T
31578346 CCAGGTGGAA
Statistics
Matches: 125, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 125 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:31581119 original size:21 final size:20
Alignment explanation
Indices: 31581093--31581134 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
31581083 AAAAACTAGA
31581093 AAAAAAAATCAAAATGTTTAT
1 AAAAAAAATCAAAAT-TTTAT
* *
31581114 AAAAAAATTCCAAATTTTAT
1 AAAAAAAATCAAAATTTTAT
31581134 A
1 A
31581135 TTTTTTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.60, C:0.07, G:0.02, T:0.31
Consensus pattern (20 bp):
AAAAAAAATCAAAATTTTAT
Found at i:31584075 original size:17 final size:17
Alignment explanation
Indices: 31584055--31584088 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
31584045 ATTTTCACAC
*
31584055 TATAATGATTTTTTTAA
1 TATAATGATTATTTTAA
*
31584072 TATAATTATTATTTTAA
1 TATAATGATTATTTTAA
31584089 AAGAATAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (17 bp):
TATAATGATTATTTTAA
Found at i:31586706 original size:3 final size:3
Alignment explanation
Indices: 31586698--31586725 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
31586688 GAGAAAAACG
31586698 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
31586726 AAGTTGTGTA
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:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:31593490 original size:15 final size:15
Alignment explanation
Indices: 31593469--31593522 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
31593459 TGACTTTCCA
31593469 ATATTTGATACCCAT
1 ATATTTGATACCCAT
* ** *
31593484 ATCTTTGACTTTCTAT
1 ATATTTGA-TACCCAT
31593500 -TATTTGATACCCAT
1 ATATTTGATACCCAT
31593514 ATATTTGAT
1 ATATTTGAT
31593523 TTTCCATAAA
Statistics
Matches: 29, Mismatches: 8, Indels: 4
0.71 0.20 0.10
Matches are distributed among these distances:
14 4 0.14
15 21 0.72
16 4 0.14
ACGTcount: A:0.28, C:0.17, G:0.07, T:0.48
Consensus pattern (15 bp):
ATATTTGATACCCAT
Found at i:31593491 original size:30 final size:30
Alignment explanation
Indices: 31593455--31593528 Score: 112
Period size: 30 Copynumber: 2.5 Consensus size: 30
31593445 NNNNNNNNNN
31593455 TCTTTGACTTTCCAATATTTGATACCCATA
1 TCTTTGACTTTCCAATATTTGATACCCATA
* *
31593485 TCTTTGACTTTCTATTATTTGATACCCATA
1 TCTTTGACTTTCCAATATTTGATACCCATA
* *
31593515 TATTTGATTTTCCA
1 TCTTTGACTTTCCA
31593529 TAAATATGGA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.24, C:0.20, G:0.07, T:0.49
Consensus pattern (30 bp):
TCTTTGACTTTCCAATATTTGATACCCATA
Found at i:31596120 original size:15 final size:16
Alignment explanation
Indices: 31596102--31596142 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
31596092 TTAAGGTGTT
*
31596102 ATTTTATAA-GTTGAA
1 ATTTTATAATGTTAAA
31596117 ATTTTA-AATGTTAAA
1 ATTTTATAATGTTAAA
31596132 ATTTATATAAT
1 ATTT-TATAAT
31596143 AAATTTTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 2 0.09
15 15 0.68
16 2 0.09
17 3 0.14
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (16 bp):
ATTTTATAATGTTAAA
Found at i:31597494 original size:15 final size:13
Alignment explanation
Indices: 31597457--31597498 Score: 50
Period size: 12 Copynumber: 3.1 Consensus size: 13
31597447 TACCATGTAT
31597457 AAATGTTAGAATTA
1 AAAT-TTAGAATTA
31597471 AAA-TTAGAATTA
1 AAATTTAGAATTA
31597483 CAAATTTTAGAATTA
1 -AAA-TTTAGAATTA
31597498 A
1 A
31597499 GACTAAATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 9 0.36
13 3 0.12
14 4 0.16
15 9 0.36
ACGTcount: A:0.52, C:0.02, G:0.10, T:0.36
Consensus pattern (13 bp):
AAATTTAGAATTA
Found at i:31597867 original size:17 final size:20
Alignment explanation
Indices: 31597834--31597881 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 20
31597824 TGACATGTGG
*
31597834 TAAAAAAATTATAAAAA-TA
1 TAAAAAAATAATAAAAAGTA
31597853 -AAAAAAATAAT-AAAAGTTA
1 TAAAAAAATAATAAAAAG-TA
31597872 TAAAAAAATA
1 TAAAAAAATA
31597882 TTTTTTTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 4 0.16
18 10 0.40
19 2 0.08
20 9 0.36
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (20 bp):
TAAAAAAATAATAAAAAGTA
Found at i:31597935 original size:19 final size:19
Alignment explanation
Indices: 31597911--31597973 Score: 56
Period size: 19 Copynumber: 3.2 Consensus size: 19
31597901 TTTTTTTTAT
31597911 AAAAATCGTAAAAAATATA
1 AAAAATCGTAAAAAATATA
* **
31597930 AAAAATTGTAAAATTTCAT-
1 AAAAATCGTAAAAAAT-ATA
*
31597949 AAAAATCATAAAAAAATTATA
1 AAAAATCGT-AAAAAA-TATA
31597970 AAAA
1 AAAA
31597974 TGCATTAAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
19 20 0.61
20 8 0.24
21 5 0.15
ACGTcount: A:0.67, C:0.05, G:0.03, T:0.25
Consensus pattern (19 bp):
AAAAATCGTAAAAAATATA
Found at i:31597984 original size:30 final size:28
Alignment explanation
Indices: 31597907--31597984 Score: 77
Period size: 30 Copynumber: 2.7 Consensus size: 28
31597897 AGAATTTTTT
*
31597907 TTATAAAAAT-CGTAAAAAATATAAAAAA
1 TTATAAAAATGCAT-AAAAATATAAAAAA
* * *
31597935 TTGTAAAATTTCATAAAAATCATAAAAAAA
1 TTATAAAAATGCATAAAAAT-AT-AAAAAA
*
31597965 TTATAAAAATGCATTAAAAT
1 TTATAAAAATGCATAAAAAT
31597985 GCCCTTTAAC
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
28 14 0.35
29 4 0.10
30 22 0.55
ACGTcount: A:0.62, C:0.05, G:0.04, T:0.29
Consensus pattern (28 bp):
TTATAAAAATGCATAAAAATATAAAAAA
Found at i:31622246 original size:14 final size:14
Alignment explanation
Indices: 31622227--31622254 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
31622217 CTCAGTAACA
31622227 TTGATTGTTGATGC
1 TTGATTGTTGATGC
31622241 TTGATTGTTGATGC
1 TTGATTGTTGATGC
31622255 GTCAATCCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.07, G:0.29, T:0.50
Consensus pattern (14 bp):
TTGATTGTTGATGC
Found at i:31632075 original size:13 final size:13
Alignment explanation
Indices: 31632057--31632089 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
31632047 CGAGGAAAAA
31632057 TTTATTTTTTTAT
1 TTTATTTTTTTAT
31632070 TTTA-TTTTTTAT
1 TTTATTTTTTTAT
*
31632082 TATATTTT
1 TTTATTTT
31632090 ATGGTCTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTATTTTTTTAT
Found at i:31632986 original size:10 final size:10
Alignment explanation
Indices: 31632971--31632999 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
31632961 ATTGGTAAAA
31632971 AAAAAGTGAG
1 AAAAAGTGAG
31632981 AAAAAGTGAG
1 AAAAAGTGAG
31632991 AAAAAGTGA
1 AAAAAGTGA
31633000 AAATTCCCGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.28, T:0.10
Consensus pattern (10 bp):
AAAAAGTGAG
Found at i:31638515 original size:17 final size:17
Alignment explanation
Indices: 31638493--31638527 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
31638483 CACTTAATTT
*
31638493 ACATATATTACTGAAAC
1 ACATATATCACTGAAAC
*
31638510 ACATATATCACTGTAAC
1 ACATATATCACTGAAAC
31638527 A
1 A
31638528 TTTTCATCAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.46, C:0.20, G:0.06, T:0.29
Consensus pattern (17 bp):
ACATATATCACTGAAAC
Found at i:31641676 original size:21 final size:20
Alignment explanation
Indices: 31641654--31641729 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 20
31641644 TTTTGTTTAG
*
31641654 CTCTTTCGAGCTTCTGTTCAG
1 CTCTTT-GAGCTTCTGTTCAA
* *
31641675 CTCTTACGAGCTTATGTTCAA
1 CTCTT-TGAGCTTCTGTTCAA
31641696 CTCTTATGAGCTTCTGTTCAA
1 CTCTT-TGAGCTTCTGTTCAA
31641717 CT-TTTGAGCTTCT
1 CTCTTTGAGCTTCT
31641730 ATTGGCGTAT
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
19 9 0.18
20 2 0.04
21 38 0.78
ACGTcount: A:0.16, C:0.25, G:0.16, T:0.43
Consensus pattern (20 bp):
CTCTTTGAGCTTCTGTTCAA
Found at i:31641978 original size:10 final size:8
Alignment explanation
Indices: 31641963--31641989 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
31641953 TGATGGCACA
31641963 TGATATAT
1 TGATATAT
31641971 TGATATAT
1 TGATATAT
31641979 TGATATAT
1 TGATATAT
31641987 TGA
1 TGA
31641990 AATGGATGAT
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:0.37, C:0.00, G:0.15, T:0.48
Consensus pattern (8 bp):
TGATATAT
Found at i:31642930 original size:37 final size:38
Alignment explanation
Indices: 31642872--31642950 Score: 142
Period size: 37 Copynumber: 2.1 Consensus size: 38
31642862 AATCGATACC
31642872 TTGATATGTAAGGTATATATAACTAAATATGCTAGTAT
1 TTGATATGTAAGGTATATATAACTAAATATGCTAGTAT
*
31642910 TTGATATGT-ATGTATATATAACTAAATATGCTAGTAT
1 TTGATATGTAAGGTATATATAACTAAATATGCTAGTAT
31642947 TTGA
1 TTGA
31642951 AATACATTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
37 31 0.77
38 9 0.22
ACGTcount: A:0.38, C:0.05, G:0.15, T:0.42
Consensus pattern (38 bp):
TTGATATGTAAGGTATATATAACTAAATATGCTAGTAT
Found at i:31644422 original size:11 final size:11
Alignment explanation
Indices: 31644406--31644430 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
31644396 AGTCAAAAAA
31644406 ATTATTTTAAT
1 ATTATTTTAAT
31644417 ATTATTTTAAT
1 ATTATTTTAAT
31644428 ATT
1 ATT
31644431 TAAAGCATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
ATTATTTTAAT
Found at i:31646632 original size:15 final size:15
Alignment explanation
Indices: 31646614--31646650 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
31646604 TCAGCTGTGT
31646614 GTGACACAAGGCCAG
1 GTGACACAAGGCCAG
*
31646629 GTGACACAAGGGCAG
1 GTGACACAAGGCCAG
31646644 GTGACAC
1 GTGACAC
31646651 GGCCGTGTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.32, C:0.24, G:0.35, T:0.08
Consensus pattern (15 bp):
GTGACACAAGGCCAG
Found at i:31650984 original size:21 final size:21
Alignment explanation
Indices: 31650958--31650997 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
31650948 TTTGGGTGGA
31650958 TCAGCTCTCACGAGCTTCTGT
1 TCAGCTCTCACGAGCTTCTGT
31650979 TCAGCTCTCACGAGCTTCT
1 TCAGCTCTCACGAGCTTCT
31650998 ATTCGTGTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.15, C:0.35, G:0.17, T:0.33
Consensus pattern (21 bp):
TCAGCTCTCACGAGCTTCTGT
Found at i:31654394 original size:19 final size:22
Alignment explanation
Indices: 31654367--31654412 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
31654357 AGATAATCTC
31654367 AAAACAACAATATT-TAAATAAA
1 AAAAC-ACAATATTATAAATAAA
31654389 AAAACACAATATTATAAATAAA
1 AAAACACAATATTATAAATAAA
31654411 AA
1 AA
31654413 CTCAAAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 8 0.35
22 15 0.65
ACGTcount: A:0.70, C:0.09, G:0.00, T:0.22
Consensus pattern (22 bp):
AAAACACAATATTATAAATAAA
Found at i:31654421 original size:22 final size:21
Alignment explanation
Indices: 31654367--31654421 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
31654357 AGATAATCTC
31654367 AAAACAACAATATTTAAATAAA
1 AAAACAA-AATATTTAAATAAA
*
31654389 AAAACACAATATTATAAATAAA
1 AAAACAAAATATT-TAAATAAA
**
31654411 AACTCAAAATA
1 AAAACAAAATA
31654422 ACATATCAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 6 0.21
22 22 0.79
ACGTcount: A:0.67, C:0.11, G:0.00, T:0.22
Consensus pattern (21 bp):
AAAACAAAATATTTAAATAAA
Found at i:31661962 original size:18 final size:18
Alignment explanation
Indices: 31661916--31661962 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
31661906 AATAAAGTAT
*
31661916 TATAAGCCCAATATATTT
1 TATAAGCCCAATATATTA
* *
31661934 TATAGGTCCAATATATTA
1 TATAAGCCCAATATATTA
*
31661952 TGTAAGCCCAA
1 TATAAGCCCAA
31661963 ACTAAATAAT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.34
Consensus pattern (18 bp):
TATAAGCCCAATATATTA
Found at i:31672696 original size:6 final size:7
Alignment explanation
Indices: 31672678--31672702 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
31672668 CTATCCCTTC
31672678 GTTTTTT
1 GTTTTTT
31672685 GTTTTTT
1 GTTTTTT
31672692 GTTTTTT
1 GTTTTTT
31672699 GTTT
1 GTTT
31672703 GTAAGGGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (7 bp):
GTTTTTT
Found at i:31675431 original size:2 final size:2
Alignment explanation
Indices: 31675419--31675459 Score: 73
Period size: 2 Copynumber: 20.0 Consensus size: 2
31675409 GATAGTTAAG
31675419 AT AT CAT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31675460 GGGCAAAACA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 36 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:31680482 original size:47 final size:47
Alignment explanation
Indices: 31680413--31680625 Score: 364
Period size: 47 Copynumber: 4.6 Consensus size: 47
31680403 AAGTAAATGA
*
31680413 ATGTATATGCTGTCAAATTTTGATGTACAAATGCAGTTCAATTATAT
1 ATGTATATGCTGTCAAATTTTGATGTACAAATGCAGTCCAATTATAT
31680460 ATGTATATGCTGTCAAATTTTGATGTACAAATGCAGT-C----ATAT
1 ATGTATATGCTGTCAAATTTTGATGTACAAATGCAGTCCAATTATAT
*
31680502 ATGTATATGCTGTCAAATTTTGATGTACAAATGTAGTCCAATTATAT
1 ATGTATATGCTGTCAAATTTTGATGTACAAATGCAGTCCAATTATAT
*
31680549 ATGTATATGCTGTCAAATTTTGATGTACAAATGCAGTCCAATTATTT
1 ATGTATATGCTGTCAAATTTTGATGTACAAATGCAGTCCAATTATAT
31680596 ATGTATATGCTGTCAAATTTTGATGTACAA
1 ATGTATATGCTGTCAAATTTTGATGTACAA
31680626 TTATATATGT
Statistics
Matches: 158, Mismatches: 3, Indels: 10
0.92 0.02 0.06
Matches are distributed among these distances:
42 40 0.25
43 1 0.01
46 1 0.01
47 116 0.73
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.40
Consensus pattern (47 bp):
ATGTATATGCTGTCAAATTTTGATGTACAAATGCAGTCCAATTATAT
Found at i:31680552 original size:25 final size:24
Alignment explanation
Indices: 31680524--31680600 Score: 63
Period size: 24 Copynumber: 3.2 Consensus size: 24
31680514 TCAAATTTTG
31680524 ATGTACAAATGTAGTCCAATTATAT
1 ATGTACAAATGTAGTCCAATTAT-T
* *
31680549 ATGT--ATATGCT-GTCAAATT-TT
1 ATGTACAAATG-TAGTCCAATTATT
*
31680570 GATGTACAAATGCAGTCCAATTATTT
1 -ATGTACAAATGTAGTCCAATTA-TT
31680596 ATGTA
1 ATGTA
31680601 TATGCTGTCA
Statistics
Matches: 40, Mismatches: 5, Indels: 14
0.68 0.08 0.24
Matches are distributed among these distances:
21 1 0.03
22 5 0.12
23 11 0.28
24 12 0.30
25 9 0.22
26 2 0.05
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.39
Consensus pattern (24 bp):
ATGTACAAATGTAGTCCAATTATT
Found at i:31680561 original size:89 final size:93
Alignment explanation
Indices: 31680413--31680700 Score: 374
Period size: 89 Copynumber: 3.2 Consensus size: 93
31680403 AAGTAAATGA
*
31680413 ATGTATATGCTGTCAAATTTTGATGTACAAATGCAGTTCAATTATATATGTATATGCTGTCAAAT
1 ATGTATATGCTGTCAAATTTTGATGTACAAATGCAGTCCAATTATATATGTATATGCTGTCAAAT
31680478 TTTGATGTACAAATGCAGT-C-A-TA-T
66 TTTGATGTACAAATGCAGTCCAATTATT
*
31680502 ATGTATATGCTGTCAAATTTTGATGTACAAATGTAGTCCAATTATATATGTATATGCTGTCAAAT
1 ATGTATATGCTGTCAAATTTTGATGTACAAATGCAGTCCAATTATATATGTATATGCTGTCAAAT
31680567 TTTGATGTACAAATGCAGTCCAATTATTT
66 TTTGATGTACAAATGCAGTCCAATTA-TT
*
31680596 ATGTATATGCTGTCAAATTTTGATG------T--A---CAATTATATATGTATATGCTGTCAGAT
1 ATGTATATGCTGTCAAATTTTGATGTACAAATGCAGTCCAATTATATATGTATATGCTGTCAAAT
* *
31680650 TTTGATATATAAATGCAGTCCAAATT-TT
66 TTTGATGTACAAATGCAGTCC-AATTATT
* *
31680678 GTATATATGCTGTCCAAATTTTG
1 ATGTATATGCTGT-CAAATTTTG
31680701 GTGTGAAAAT
Statistics
Matches: 185, Mismatches: 7, Indels: 20
0.87 0.03 0.09
Matches are distributed among these distances:
82 13 0.07
83 54 0.29
84 4 0.02
86 1 0.01
88 1 0.01
89 82 0.44
90 1 0.01
91 1 0.01
92 2 0.01
94 26 0.14
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.41
Consensus pattern (93 bp):
ATGTATATGCTGTCAAATTTTGATGTACAAATGCAGTCCAATTATATATGTATATGCTGTCAAAT
TTTGATGTACAAATGCAGTCCAATTATT
Found at i:31680627 original size:36 final size:36
Alignment explanation
Indices: 31680587--31680655 Score: 120
Period size: 36 Copynumber: 1.9 Consensus size: 36
31680577 AAATGCAGTC
*
31680587 CAATTATTTATGTATATGCTGTCAAATTTTGATGTA
1 CAATTATATATGTATATGCTGTCAAATTTTGATGTA
*
31680623 CAATTATATATGTATATGCTGTCAGATTTTGAT
1 CAATTATATATGTATATGCTGTCAAATTTTGAT
31680656 ATATAAATGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.30, C:0.09, G:0.14, T:0.46
Consensus pattern (36 bp):
CAATTATATATGTATATGCTGTCAAATTTTGATGTA
Found at i:31680687 original size:22 final size:23
Alignment explanation
Indices: 31680635--31680700 Score: 82
Period size: 22 Copynumber: 2.9 Consensus size: 23
31680625 ATTATATATG
*
31680635 TATATGCTGT-CAGATTTTGATA
1 TATATGCTGTCCAAATTTTGATA
*
31680657 TATAAATGCAGTCCAAATTTTG-TA
1 TAT--ATGCTGTCCAAATTTTGATA
31680681 TATATGCTGTCCAAATTTTG
1 TATATGCTGTCCAAATTTTG
31680701 GTGTGAAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
22 19 0.50
24 11 0.29
25 8 0.21
ACGTcount: A:0.30, C:0.12, G:0.15, T:0.42
Consensus pattern (23 bp):
TATATGCTGTCCAAATTTTGATA
Found at i:31680696 original size:83 final size:83
Alignment explanation
Indices: 31680540--31680700 Score: 252
Period size: 83 Copynumber: 1.9 Consensus size: 83
31680530 AAATGTAGTC
* * *
31680540 CAATTATATATGTATATGCTGTCAAATTTTGATGTACAAATGCAGTCCAATTATTTATGTATATG
1 CAATTATATATGTATATGCTGTCAAATTTTGATATACAAATGCAGTCCAAATATTTATATATATG
31680605 CTGTCAAATTTTGATGTA
66 CTGTCAAATTTTGATGTA
* * *
31680623 CAATTATATATGTATATGCTGTCAGATTTTGATATATAAATGCAGTCCAAAT-TTTGTATATATG
1 CAATTATATATGTATATGCTGTCAAATTTTGATATACAAATGCAGTCCAAATATTTATATATATG
31680687 CTGTCCAAATTTTG
66 CTGT-CAAATTTTG
31680701 GTGTGAAAAT
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
82 14 0.20
83 57 0.80
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.42
Consensus pattern (83 bp):
CAATTATATATGTATATGCTGTCAAATTTTGATATACAAATGCAGTCCAAATATTTATATATATG
CTGTCAAATTTTGATGTA
Found at i:31681351 original size:33 final size:33
Alignment explanation
Indices: 31681314--31681381 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 33
31681304 GATTAATTTT
* *
31681314 ATATTTTATGTATCGTTATATTAAATTATTTAA
1 ATATTTCATATATCGTTATATTAAATTATTTAA
* *
31681347 ATATTTCATATCTCTTTATATTAAATTATTTAA
1 ATATTTCATATATCGTTATATTAAATTATTTAA
31681380 AT
1 AT
31681382 CTTATTTATT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.37, C:0.06, G:0.03, T:0.54
Consensus pattern (33 bp):
ATATTTCATATATCGTTATATTAAATTATTTAA
Found at i:31681383 original size:24 final size:23
Alignment explanation
Indices: 31681339--31681383 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
31681329 TTATATTAAA
*
31681339 TTATTTAAATATTTCATATCTCT
1 TTATTTAAATATTTCAAATCTCT
31681362 TTATATTAAATTATTT-AAATCT
1 TTAT-TTAAA-TATTTCAAATCT
31681384 TATTTATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 4 0.21
24 10 0.53
25 5 0.26
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.56
Consensus pattern (23 bp):
TTATTTAAATATTTCAAATCTCT
Found at i:31698844 original size:89 final size:90
Alignment explanation
Indices: 31698734--31699634 Score: 1275
Period size: 89 Copynumber: 10.1 Consensus size: 90
31698724 TATTGGTAGC
* * * ** * *
31698734 GAAGTGGATCGAATATA-CAGATCTTATCTTCCCATACTGGTGGCGAAGTAGATCAGAA-AAAGC
1 GAAGTAGATCAAAGATACCAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCAGAAGAAAAC
* *
31698797 AGATCTTGTCTTCATGCACTGGCAT
66 AGATCTTGTCTTCATGTACTGGCGT
* *
31698822 GAAGTAGATCAAAGATACCAGATCTTGTCTTCCCATACTGGTGGCGAAGCAGAT-TGAAGAAAAC
1 GAAGTAGATCAAAGATACCAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCAGAAGAAAAC
31698886 AGATCTTGTCTTCATGTACTGGCGT
66 AGATCTTGTCTTCATGTACTGGCGT
* * * * * * *
31698911 GAAGTAGATCAAAGGTAACAGATCTTGCCTCCCCATACTGGTGGTGGAGTAGAT-TGAAGAAAAG
1 GAAGTAGATCAAAGATACCAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCAGAAGAAAA-
* *
31698975 CAGATCTTCTTTTCATGTACTGGCGT
65 CAGATCTTGTCTTCATGTACTGGCGT
** * * * *
31699001 GAAGTAGATCAAAGATACCAGATCTTATCTCCCCATACTGGTGGTGGAGTAGATC-GAAGAAAAC
1 GAAGTAGATCAAAGATACCAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCAGAAGAAAAC
31699065 AGATCTTGTCTTCATGTACTGGCGT
66 AGATCTTGTCTTCATGTACTGGCGT
*
31699090 GAAGTAGATCAGAGATACCAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCA-AAGAAAAC
1 GAAGTAGATCAAAGATACCAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCAGAAGAAAAC
*
31699154 AGATCTTGTCTTCATGTACTGGTGT
66 AGATCTTGTCTTCATGTACTGGCGT
* *
31699179 GAAGTAGATCAGAGATACCAGATCTTGCCTTCCCATACTGGTGGAGAAGCAGATCA-AAGAAAAC
1 GAAGTAGATCAAAGATACCAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCAGAAGAAAAC
*
31699243 AGATCTTGTCTTCATGTACCGGCGT
66 AGATCTTGTCTTCATGTACTGGCGT
* * *
31699268 GAAGTAGATCAAAGATAACAGATCTTGCCTTCCCATGCTGGTGGCGAAGCAAATCA-AAGAAAAC
1 GAAGTAGATCAAAGATACCAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCAGAAGAAAAC
31699332 AGATCTTGTCTTCATGTACTGGCGT
66 AGATCTTGTCTTCATGTACTGGCGT
* ** * * * * *
31699357 GAAGTAGATCAAAGATAGCAGATCTTATCTTCCCATACTGGTGGTGAAGTAGATAATAA-AAAGC
1 GAAGTAGATCAAAGATACCAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCAGAAGAAAAC
31699421 AGATCTTGTCTTCATGTACTGGCGT
66 AGATCTTGTCTTCATGTACTGGCGT
**
31699446 GAAGTAGATCAAAGATACCAGATCTTATCTTCCCATACTGGTGGCGAAGCAGATC-GAAGAAAAC
1 GAAGTAGATCAAAGATACCAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCAGAAGAAAAC
*
31699510 AGATCTTGTCTTCATGTACCGGCGT
66 AGATCTTGTCTTCATGTACTGGCGT
* * *
31699535 GAAGTAGATCAAAGATAACAGATCTTGCCTTCCCATGCTGGTGGCGAAGCAAATCA-AAGAAAAC
1 GAAGTAGATCAAAGATACCAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCAGAAGAAAAC
*
31699599 AGATCTTGTCTTCATGTACCGGCGT
66 AGATCTTGTCTTCATGTACTGGCGT
31699624 GAAGTAGATCA
1 GAAGTAGATCA
31699635 CATGGAGTAG
Statistics
Matches: 743, Mismatches: 62, Indels: 15
0.91 0.08 0.02
Matches are distributed among these distances:
88 19 0.03
89 640 0.86
90 84 0.11
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.26
Consensus pattern (90 bp):
GAAGTAGATCAAAGATACCAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCAGAAGAAAAC
AGATCTTGTCTTCATGTACTGGCGT
Found at i:31704913 original size:21 final size:22
Alignment explanation
Indices: 31704887--31704930 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
31704877 CAGAAATGTT
31704887 ATAAACTAAAAGA-AAT-ATAGA
1 ATAAAC-AAAAGAGAATAATAGA
*
31704908 ATAAACAAGAGAGAATAATAGA
1 ATAAACAAAAGAGAATAATAGA
31704930 A
1 A
31704931 AAATGAAAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 5 0.25
21 9 0.45
22 6 0.30
ACGTcount: A:0.66, C:0.05, G:0.14, T:0.16
Consensus pattern (22 bp):
ATAAACAAAAGAGAATAATAGA
Found at i:31706650 original size:86 final size:86
Alignment explanation
Indices: 31706502--31706678 Score: 309
Period size: 86 Copynumber: 2.1 Consensus size: 86
31706492 AAATACATTG
*
31706502 AACTAAAGTTAGAAATGTCATTACAACCAAAGTACAGAGACTGAAAGTGTATATAAATCTAGGCT
1 AACTAAAGTTAGAAATGTCATTACAACCAAAGTACAGAGACTGAAAGTGTATATAAACCTAGGCT
*
31706567 ACAGTGATAACAAATTTAACT
66 ACAGTGATAACAAACTTAACT
* *
31706588 AACTAAAGTTAGAAATGTCATTACAACCAAAGTATAGAGATTGAAAGTGTATATAAACCTAGGCT
1 AACTAAAGTTAGAAATGTCATTACAACCAAAGTACAGAGACTGAAAGTGTATATAAACCTAGGCT
*
31706653 ACAGTGATAACTAACTTAACT
66 ACAGTGATAACAAACTTAACT
31706674 AACTA
1 AACTA
31706679 TAAGAACACC
Statistics
Matches: 86, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
86 86 1.00
ACGTcount: A:0.45, C:0.14, G:0.15, T:0.26
Consensus pattern (86 bp):
AACTAAAGTTAGAAATGTCATTACAACCAAAGTACAGAGACTGAAAGTGTATATAAACCTAGGCT
ACAGTGATAACAAACTTAACT
Found at i:31707524 original size:21 final size:22
Alignment explanation
Indices: 31707464--31707524 Score: 65
Period size: 21 Copynumber: 2.9 Consensus size: 22
31707454 ATTTGATAAC
31707464 TTTTA-AAGAATTT-TAATATGT
1 TTTTATAA-AATTTATAATATGT
*
31707485 TTTTATAAAATTTAAAATATG-
1 TTTTATAAAATTTATAATATGT
* *
31707506 TTTTATTAATTTTATAATA
1 TTTTATAAAATTTATAATA
31707525 ATTTATTAGA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
21 26 0.76
22 8 0.24
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (22 bp):
TTTTATAAAATTTATAATATGT
Found at i:31707561 original size:19 final size:19
Alignment explanation
Indices: 31707539--31707590 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
31707529 ATTAGAATTA
31707539 TATATATTTTTAT-ATTTTT
1 TATAT-TTTTTATGATTTTT
*
31707558 TATATTTTTTCTGATTTTT
1 TATATTTTTTATGATTTTT
*
31707577 TAATCTTTTTTATG
1 T-ATATTTTTTATG
31707591 GAAAAATATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 6 0.21
19 12 0.43
20 10 0.36
ACGTcount: A:0.21, C:0.04, G:0.04, T:0.71
Consensus pattern (19 bp):
TATATTTTTTATGATTTTT
Found at i:31707574 original size:10 final size:9
Alignment explanation
Indices: 31707539--31707589 Score: 57
Period size: 10 Copynumber: 5.3 Consensus size: 9
31707529 ATTAGAATTA
31707539 TATATATTTT
1 TATAT-TTTT
31707549 TATATTTTT
1 TATATTTTT
31707558 TATATTTTT
1 TATATTTTT
*
31707567 TCTGATTTTT
1 TAT-ATTTTT
*
31707577 TAATCTTTTT
1 T-ATATTTTT
31707587 TAT
1 TAT
31707590 GGAAAAATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
9 17 0.47
10 18 0.50
11 1 0.03
ACGTcount: A:0.22, C:0.04, G:0.02, T:0.73
Consensus pattern (9 bp):
TATATTTTT
Found at i:31714340 original size:41 final size:40
Alignment explanation
Indices: 31714295--31714414 Score: 107
Period size: 34 Copynumber: 3.1 Consensus size: 40
31714285 TAAAATATAA
31714295 TTATATTTAATATGTTTTAAAATTAAAACACTAATATTATT
1 TTATA-TTAATATGTTTTAAAATTAAAACACTAATATTATT
* *
31714336 TTATA--AACTA-GCTTCTTAAACA-T--AA-A-TAAT-GTA-A
1 TTATATTAA-TATG-TT-TTAAA-ATTAAAACACTAATATTATT
31714370 TTATATTAATATGTTTTAAAATTAAAACACTAATATTATT
1 TTATATTAATATGTTTTAAAATTAAAACACTAATATTATT
31714410 TTATA
1 TTATA
31714415 AACTAGCTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 29
0.65 0.04 0.31
Matches are distributed among these distances:
33 1 0.02
34 11 0.18
35 6 0.10
36 9 0.15
37 2 0.03
38 9 0.15
39 6 0.10
40 11 0.18
41 6 0.10
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (40 bp):
TTATATTAATATGTTTTAAAATTAAAACACTAATATTATT
Found at i:31714355 original size:34 final size:34
Alignment explanation
Indices: 31714317--31714429 Score: 88
Period size: 34 Copynumber: 3.1 Consensus size: 34
31714307 TGTTTTAAAA
31714317 TTAAAACACTAATATTATTTTATAAACTAGCTTC
1 TTAAAACACTAATATTATTTTATAAACTAGCTTC
* * * *
31714351 TT-AAACA-TAAATAATGTAATTATATTAA-TATGTTTTAAAA
1 TTAAAACACT-AAT-AT-T-ATTTTATAAACTA-G-CTT---C
31714391 TTAAAACACTAATATTATTTTATAAACTAGCTTC
1 TTAAAACACTAATATTATTTTATAAACTAGCTTC
31714425 TTAAA
1 TTAAA
31714430 CATAAATAAT
Statistics
Matches: 59, Mismatches: 8, Indels: 24
0.65 0.09 0.26
Matches are distributed among these distances:
32 1 0.02
33 8 0.14
34 9 0.15
35 3 0.05
36 9 0.15
37 4 0.07
38 9 0.15
39 3 0.05
40 4 0.07
41 8 0.14
42 1 0.02
ACGTcount: A:0.45, C:0.10, G:0.04, T:0.42
Consensus pattern (34 bp):
TTAAAACACTAATATTATTTTATAAACTAGCTTC
Found at i:31714388 original size:74 final size:75
Alignment explanation
Indices: 31714292--31714442 Score: 295
Period size: 74 Copynumber: 2.0 Consensus size: 75
31714282 AAATAAAATA
31714292 TAATTATATTTAATATGTTTTAAAATTAAAACACTAATATTATTTTATAAACTAGCTTCTTAAAC
1 TAATTATATTTAATATGTTTTAAAATTAAAACACTAATATTATTTTATAAACTAGCTTCTTAAAC
31714357 ATAAATAATG
66 ATAAATAATG
31714367 TAATTATA-TTAATATGTTTTAAAATTAAAACACTAATATTATTTTATAAACTAGCTTCTTAAAC
1 TAATTATATTTAATATGTTTTAAAATTAAAACACTAATATTATTTTATAAACTAGCTTCTTAAAC
31714431 ATAAATAATG
66 ATAAATAATG
31714441 TA
1 TA
31714443 TGGGTGTACT
Statistics
Matches: 76, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
74 68 0.89
75 8 0.11
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.42
Consensus pattern (75 bp):
TAATTATATTTAATATGTTTTAAAATTAAAACACTAATATTATTTTATAAACTAGCTTCTTAAAC
ATAAATAATG
Found at i:31718126 original size:14 final size:14
Alignment explanation
Indices: 31718109--31718135 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
31718099 AAAATTTAAA
31718109 AAATAAAAAAAATT
1 AAATAAAAAAAATT
31718123 AAATAAAAAAAAT
1 AAATAAAAAAAAT
31718136 AGAGGACTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (14 bp):
AAATAAAAAAAATT
Found at i:31720713 original size:16 final size:15
Alignment explanation
Indices: 31720680--31720708 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
31720670 AATTTTCACC
31720680 AAAAAAGAAAAAAAG
1 AAAAAAGAAAAAAAG
31720695 AAAAAA-AAAAAAAG
1 AAAAAAGAAAAAAAG
31720709 GGAAATTACT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (15 bp):
AAAAAAGAAAAAAAG
Found at i:31732740 original size:15 final size:15
Alignment explanation
Indices: 31732720--31732753 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
31732710 CCCTTTTTGT
* *
31732720 AAAAATTAAAAATTA
1 AAAAATAAAAAAATA
31732735 AAAAATAAAAAAATA
1 AAAAATAAAAAAATA
31732750 AAAA
1 AAAA
31732754 GGTGCAGTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (15 bp):
AAAAATAAAAAAATA
Found at i:31733352 original size:26 final size:26
Alignment explanation
Indices: 31733316--31733369 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
31733306 GACCTAAGTA
31733316 TACACATTAATCTCTGCATTACTTCT
1 TACACATTAATCTCTGCATTACTTCT
31733342 TACACATTAATCTCTGCATTACTTCT
1 TACACATTAATCTCTGCATTACTTCT
31733368 TA
1 TA
31733370 AGAAAGAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.28, C:0.26, G:0.04, T:0.43
Consensus pattern (26 bp):
TACACATTAATCTCTGCATTACTTCT
Found at i:31737830 original size:3 final size:3
Alignment explanation
Indices: 31737822--31737849 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
31737812 CTTGTTTTTC
31737822 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
31737850 CTAGGGAGGG
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:31738342 original size:16 final size:15
Alignment explanation
Indices: 31738302--31738347 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
31738292 AAAATTAAAC
31738302 CAAA-TTAAAATTT-
1 CAAATTTAAAATTTA
* *
31738315 CATATATAAAATTATA
1 CAAATTTAAAATT-TA
31738331 CAAATTTAAAATTTA
1 CAAATTTAAAATTTA
31738346 CA
1 CA
31738348 TGTTAAATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
13 3 0.12
14 7 0.27
15 5 0.19
16 11 0.42
ACGTcount: A:0.54, C:0.09, G:0.00, T:0.37
Consensus pattern (15 bp):
CAAATTTAAAATTTA
Found at i:31741134 original size:206 final size:192
Alignment explanation
Indices: 31740808--31741184 Score: 592
Period size: 194 Copynumber: 1.9 Consensus size: 192
31740798 AGTGTAAGTA
31740808 TATGAGTTAAAATAAAATGTATGAATTGTATATATATGTGTTAGTTAATGTATATTTGAGTTTTA
1 TATGAGTTAAAATAAAATGTATGAATTGTATATATATGTGTTAGTTAATGTATATTTGAGTTTTA
*
31740873 TAAGTTAAAATAAATTGCATAAATTCTATATATATATAGACGAATATATATGCTGAGTTTTGTAA
66 TAAGTTAAAATAAATTGCATAAATTCTATATATATATAGACGAATATATATGCTGAATTTTGTAA
31740938 GTTGAATGAAATTTAATGAATTACATATATGTTAGCCGAATGTATATATATGTTTTGAATTT
131 GTTGAATGAAATTTAATGAATTACATATATGTTAGCCGAATGTATATATATGTTTTGAATTT
31741000 TATGAGTTAAAATAAAATGTATGAATTGTATATATATATGTGTTAGTTAATGTATATTTGAGTTT
1 TATGAGTTAAAATAAAATGTATGAATTG--TATATATATGTGTTAGTTAATGTATATTTGAGTTT
*
31741065 TATAAGTTAAAATAAATTGCATAAATTCTCTCTCTCTATATATATATTTAGCCGAATATATATAT
64 TATAAGTTAAAATAAATTGCATAAA-------T-TCTATATATATA--TAGACG-A-ATATATAT
* *
31741130 GCTGAATTTTGTAAGTTGGATGAAATTTAATGGATTACATATATGTTAGCCGAAT
117 GCTGAATTTTGTAAGTTGAATGAAATTTAATGAATTACATATATGTTAGCCGAAT
31741185 ATATGTATTG
Statistics
Matches: 167, Mismatches: 4, Indels: 14
0.90 0.02 0.08
Matches are distributed among these distances:
192 28 0.17
194 60 0.36
201 1 0.01
202 12 0.07
204 5 0.03
205 1 0.01
206 60 0.36
ACGTcount: A:0.38, C:0.05, G:0.15, T:0.42
Consensus pattern (192 bp):
TATGAGTTAAAATAAAATGTATGAATTGTATATATATGTGTTAGTTAATGTATATTTGAGTTTTA
TAAGTTAAAATAAATTGCATAAATTCTATATATATATAGACGAATATATATGCTGAATTTTGTAA
GTTGAATGAAATTTAATGAATTACATATATGTTAGCCGAATGTATATATATGTTTTGAATTT
Found at i:31745492 original size:25 final size:26
Alignment explanation
Indices: 31745433--31745506 Score: 78
Period size: 25 Copynumber: 2.8 Consensus size: 26
31745423 GCTCATTAGA
*
31745433 CCATATAATCAGGAAGCTATCTCTCGAG
1 CCATATAA-CAGGAAGCT-TATCTCGAG
* *
31745461 CTATATAACAGGAAGCTTATGT-GAG
1 CCATATAACAGGAAGCTTATCTCGAG
**
31745486 CCATATAATGGGAAGCTTATC
1 CCATATAACAGGAAGCTTATC
31745507 CAGGCTATAT
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
25 20 0.51
26 3 0.08
27 9 0.23
28 7 0.18
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (26 bp):
CCATATAACAGGAAGCTTATCTCGAG
Found at i:31745625 original size:25 final size:24
Alignment explanation
Indices: 31745597--31745648 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 24
31745587 ATTAATCGAT
* *
31745597 AAGTTCTAGATAGTCATATATCGGG
1 AAGTTCAAGAGAGTCA-ATATCGGG
* *
31745622 AAGTTGAAGCGAGTCAATATCGGG
1 AAGTTCAAGAGAGTCAATATCGGG
31745646 AAG
1 AAG
31745649 CTCCGGAGAG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 11 0.48
25 12 0.52
ACGTcount: A:0.35, C:0.12, G:0.29, T:0.25
Consensus pattern (24 bp):
AAGTTCAAGAGAGTCAATATCGGG
Done.