Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009611.1 Hibiscus syriacus cultivar Beakdansim tig00116997_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 6671611
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 22 of 27
Found at i:5596042 original size:20 final size:21
Alignment explanation
Indices: 5596017--5596057 Score: 75
Period size: 20 Copynumber: 2.0 Consensus size: 21
5596007 GCAACCGTTT
5596017 TTATTTTAAAAAATCT-GAAA
1 TTATTTTAAAAAATCTAGAAA
5596037 TTATTTTAAAAAATCTAGAAA
1 TTATTTTAAAAAATCTAGAAA
5596058 AATTCATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.39
Consensus pattern (21 bp):
TTATTTTAAAAAATCTAGAAA
Found at i:5597522 original size:18 final size:19
Alignment explanation
Indices: 5597501--5597538 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
5597491 TAATAGTGAG
5597501 TTATTATAA-AATATATTT
1 TTATTATAATAATATATTT
*
5597519 TTATTATAATTATATATTT
1 TTATTATAATAATATATTT
5597538 T
1 T
5597539 ATTTATATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TTATTATAATAATATATTT
Found at i:5597665 original size:39 final size:40
Alignment explanation
Indices: 5597622--5597697 Score: 127
Period size: 40 Copynumber: 1.9 Consensus size: 40
5597612 CTTTTACAAA
* *
5597622 TCATTTTT-TCAAAAGTCTTACCAAACTCGCCCTTAAAAG
1 TCATTTTTCTCAAAAATCTTACCAAACTAGCCCTTAAAAG
5597661 TCATTTTTCTCAAAAATCTTACCAAACTAGCCCTTAA
1 TCATTTTTCTCAAAAATCTTACCAAACTAGCCCTTAA
5597698 TACAAGAGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
39 8 0.24
40 26 0.76
ACGTcount: A:0.34, C:0.26, G:0.05, T:0.34
Consensus pattern (40 bp):
TCATTTTTCTCAAAAATCTTACCAAACTAGCCCTTAAAAG
Found at i:5599033 original size:21 final size:21
Alignment explanation
Indices: 5599003--5599067 Score: 112
Period size: 21 Copynumber: 3.1 Consensus size: 21
5598993 AATATAAATT
*
5599003 GTGTACCGATGCACTGCTACA
1 GTGTATCGATGCACTGCTACA
*
5599024 GTGTATCGATGCATTGCTACA
1 GTGTATCGATGCACTGCTACA
5599045 GTGTATCGATGCACTGCTACA
1 GTGTATCGATGCACTGCTACA
5599066 GT
1 GT
5599068 ACTTCAGCTC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.29
Consensus pattern (21 bp):
GTGTATCGATGCACTGCTACA
Found at i:5599781 original size:21 final size:21
Alignment explanation
Indices: 5599755--5599811 Score: 78
Period size: 22 Copynumber: 2.7 Consensus size: 21
5599745 GGCATGTGAA
*
5599755 ATTTGTCCCGAAGGCCTTTGT
1 ATTTGTCCCGAAGGCCTCTGT
*
5599776 ATTTGTCCCGAAGAACCTCTGT
1 ATTTGTCCCGAAG-GCCTCTGT
*
5599798 ATATGTCCCGAAGG
1 ATTTGTCCCGAAGG
5599812 ACCGCGTAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 13 0.42
22 18 0.58
ACGTcount: A:0.21, C:0.25, G:0.23, T:0.32
Consensus pattern (21 bp):
ATTTGTCCCGAAGGCCTCTGT
Found at i:5601185 original size:22 final size:22
Alignment explanation
Indices: 5601159--5601230 Score: 74
Period size: 22 Copynumber: 3.2 Consensus size: 22
5601149 ACATACGAAG
5601159 TGTTAGAATTAGATTTAGAACA
1 TGTTAGAATTAGATTTAGAACA
** *
5601181 TGTTAGAAATTGAGAGATACGAA-G
1 TGTTAG-AATT-AGATTTA-GAACA
*
5601205 TATTAGAATTAGATTTAGAACA
1 TGTTAGAATTAGATTTAGAACA
5601227 TGTT
1 TGTT
5601231 GGAAATTGAG
Statistics
Matches: 38, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
21 3 0.08
22 14 0.37
23 8 0.21
24 10 0.26
25 3 0.08
ACGTcount: A:0.40, C:0.04, G:0.21, T:0.35
Consensus pattern (22 bp):
TGTTAGAATTAGATTTAGAACA
Found at i:5601204 original size:46 final size:46
Alignment explanation
Indices: 5601142--5601240 Score: 162
Period size: 46 Copynumber: 2.2 Consensus size: 46
5601132 TCATCGACTT
* *
5601142 AATTAAGACATACGAAGTGTTAGAATTAGATTTAGAACATGTTAGA
1 AATTGAGACATACGAAGTATTAGAATTAGATTTAGAACATGTTAGA
* *
5601188 AATTGAGAGATACGAAGTATTAGAATTAGATTTAGAACATGTTGGA
1 AATTGAGACATACGAAGTATTAGAATTAGATTTAGAACATGTTAGA
5601234 AATTGAG
1 AATTGAG
5601241 GGAGATTCTT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.42, C:0.05, G:0.22, T:0.30
Consensus pattern (46 bp):
AATTGAGACATACGAAGTATTAGAATTAGATTTAGAACATGTTAGA
Found at i:5601546 original size:64 final size:64
Alignment explanation
Indices: 5601478--5601599 Score: 174
Period size: 64 Copynumber: 1.9 Consensus size: 64
5601468 ATTGTTCAAG
* * *
5601478 GTGTATCGATGCAC-ATGAAGTATATCGATGCACTCCTTTAAAATAAAAACATCGAATGTCATCA
1 GTGTATCGATGCACGA-GAAGTACATCGATGCACCCCCTTAAAATAAAAACATCGAATGTCATCA
* * *
5601542 GTGTATCGATGCACGAGTAGTGCATCGATGCACCCCCTTAAAATACAAACATCGAATG
1 GTGTATCGATGCACGAGAAGTACATCGATGCACCCCCTTAAAATAAAAACATCGAATG
5601600 AGATTTATGT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
64 50 0.98
65 1 0.02
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.25
Consensus pattern (64 bp):
GTGTATCGATGCACGAGAAGTACATCGATGCACCCCCTTAAAATAAAAACATCGAATGTCATCA
Found at i:5601616 original size:64 final size:64
Alignment explanation
Indices: 5601501--5601640 Score: 176
Period size: 64 Copynumber: 2.2 Consensus size: 64
5601491 CATGAAGTAT
* * * *
5601501 ATCGATGCACTCCTTTAAAATAAAAACATCGAATGTCATCAGTGTATCGATGCACGAG-TAGTGC
1 ATCGATGCACCCCCTTAAAATAAAAACATCGAATGACATCAGTGTACCGATGCA-GAGATAGTGC
* * * *
5601565 ATCGATGCACCCCCTTAAAATACAAACATCGAATGAGATTTA-TGTACCGATGCATAGATAGTGC
1 ATCGATGCACCCCCTTAAAATAAAAACATCGAATGACA-TCAGTGTACCGATGCAGAGATAGTGC
5601629 ATCGATGCACCC
1 ATCGATGCACCC
5601641 GTCAAGGGAT
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
63 2 0.03
64 62 0.94
65 2 0.03
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (64 bp):
ATCGATGCACCCCCTTAAAATAAAAACATCGAATGACATCAGTGTACCGATGCAGAGATAGTGC
Found at i:5603426 original size:17 final size:17
Alignment explanation
Indices: 5603404--5603436 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5603394 CTCACGTAGG
*
5603404 AAGAAGAAGAATAAAGC
1 AAGAAGAAGAAGAAAGC
5603421 AAGAAGAAGAAGAAAG
1 AAGAAGAAGAAGAAAG
5603437 TTTTCAGATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.67, C:0.03, G:0.27, T:0.03
Consensus pattern (17 bp):
AAGAAGAAGAAGAAAGC
Found at i:5626732 original size:31 final size:28
Alignment explanation
Indices: 5626686--5626745 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 28
5626676 GGAAAAATGG
*
5626686 CCAAATAATGTGGTTGGGAATATTTAATTC
1 CCAAATAATGCGGTTGGGAA-A-TTAATTC
*
5626716 CCAACATAATGCGGTTGGTAAATTAATTC
1 CCAA-ATAATGCGGTTGGGAAATTAATTC
5626745 C
1 C
5626746 TCATATAGGG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 8 0.30
30 5 0.19
31 14 0.52
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.33
Consensus pattern (28 bp):
CCAAATAATGCGGTTGGGAAATTAATTC
Found at i:5629607 original size:20 final size:21
Alignment explanation
Indices: 5629584--5629655 Score: 94
Period size: 21 Copynumber: 3.5 Consensus size: 21
5629574 CTCAGTTTCC
*
5629584 AAAATCGCAGCGTGAATAGTA
1 AAAATCGCAACGTGAATAGTA
5629605 AAAATCGCAACGTGAATAGT-
1 AAAATCGCAACGTGAATAGTA
* *
5629625 AAAATCGCAACGCGAAT-TTA
1 AAAATCGCAACGTGAATAGTA
5629645 GAAAATCGCAA
1 -AAAATCGCAA
5629656 AATCGCGTTA
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
19 1 0.02
20 16 0.35
21 29 0.63
ACGTcount: A:0.46, C:0.17, G:0.19, T:0.18
Consensus pattern (21 bp):
AAAATCGCAACGTGAATAGTA
Found at i:5630045 original size:20 final size:20
Alignment explanation
Indices: 5630031--5630097 Score: 89
Period size: 20 Copynumber: 3.4 Consensus size: 20
5630021 ACGTTACGAT
*
5630031 TTTGACTATCGCGTTGTGAA
1 TTTGACTATCGCGTTGCGAA
* * **
5630051 TTTGACTTTTGTATTGCGAA
1 TTTGACTATCGCGTTGCGAA
5630071 TTTGACTATCGCGTTGCGAA
1 TTTGACTATCGCGTTGCGAA
5630091 TTTGACT
1 TTTGACT
5630098 TCTGTGTTGC
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.19, C:0.15, G:0.22, T:0.43
Consensus pattern (20 bp):
TTTGACTATCGCGTTGCGAA
Found at i:5630078 original size:40 final size:40
Alignment explanation
Indices: 5630031--5630130 Score: 132
Period size: 40 Copynumber: 2.5 Consensus size: 40
5630021 ACGTTACGAT
* *
5630031 TTTGACTATCGCGTTGTGAATTTGACTTTTGTATTGCGAA
1 TTTGACTATCGCGTTGCGAATTTGACTTCTGTATTGCGAA
*
5630071 TTTGACTATCGCGTTGCGAATTTGACTTCTGTGTTGCG-A
1 TTTGACTATCGCGTTGCGAATTTGACTTCTGTATTGCGAA
*
5630110 TTT-ACAAATTCGCGTTGCGAA
1 TTTGAC-TA-TCGCGTTGCGAA
5630131 ATTGGAAAAT
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
38 2 0.04
39 5 0.09
40 47 0.87
ACGTcount: A:0.20, C:0.16, G:0.23, T:0.41
Consensus pattern (40 bp):
TTTGACTATCGCGTTGCGAATTTGACTTCTGTATTGCGAA
Found at i:5630106 original size:20 final size:20
Alignment explanation
Indices: 5630043--5630109 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
5630033 TGACTATCGC
* *
5630043 GTTGTGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTCTGT
* *
5630063 ATTGCGAATTTGACTATC-GC
1 GTTGCGAATTTGACT-TCTGT
5630083 GTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTGACTTCTGT
5630103 GTTGCGA
1 GTTGCGA
5630110 TTTACAAATT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
19 2 0.05
20 36 0.92
21 1 0.03
ACGTcount: A:0.18, C:0.13, G:0.25, T:0.43
Consensus pattern (20 bp):
GTTGCGAATTTGACTTCTGT
Found at i:5643448 original size:5 final size:5
Alignment explanation
Indices: 5643433--5643519 Score: 59
Period size: 6 Copynumber: 15.6 Consensus size: 5
5643423 ATTATTTACT
* *
5643433 TATTT TATTA TGTTA TATTA TA-TA TATATA TATATA TATATA TATATA
1 TATTA TATTA TATTA TATTA TATTA TAT-TA TAT-TA TAT-TA TAT-TA
5643481 TATATA TATATA TATATA TATATA TATATA TATATA TAT
1 TAT-TA TAT-TA TAT-TA TAT-TA TAT-TA TAT-TA TAT
5643520 ACGTTATTTC
Statistics
Matches: 77, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
4 4 0.05
5 14 0.18
6 59 0.77
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (5 bp):
TATTA
Found at i:5643458 original size:2 final size:2
Alignment explanation
Indices: 5643446--5643520 Score: 143
Period size: 2 Copynumber: 38.0 Consensus size: 2
5643436 TTTATTATGT
5643446 TA TA T- 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
5643487 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
5643521 CGTTATTTCT
Statistics
Matches: 72, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 71 0.99
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5643695 original size:39 final size:39
Alignment explanation
Indices: 5643618--5643696 Score: 90
Period size: 39 Copynumber: 1.9 Consensus size: 39
5643608 TTTGTTTATT
5643618 TATTTTATTTTTATTTTCTTTATTCATTGATTCATTTTTCC
1 TATTTTA-TTTTATTTTCTTTATTCATTGATT-ATTTTTCC
*
5643659 TATTTTA-TTTATTTATC-TTATTCCATTGTATTTTTTTT
1 TATTTTATTTTATTT-TCTTTATT-CATTG-ATTATTTTT
5643697 ATATATTCCT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
39 12 0.35
40 12 0.35
41 10 0.29
ACGTcount: A:0.18, C:0.10, G:0.03, T:0.70
Consensus pattern (39 bp):
TATTTTATTTTATTTTCTTTATTCATTGATTATTTTTCC
Found at i:5644761 original size:13 final size:13
Alignment explanation
Indices: 5644745--5644773 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
5644735 TCTCTTATGT
5644745 TTTTTTCTTGCCA
1 TTTTTTCTTGCCA
5644758 TTTTTTCTTGCCA
1 TTTTTTCTTGCCA
5644771 TTT
1 TTT
5644774 ATTTTTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.21, G:0.07, T:0.66
Consensus pattern (13 bp):
TTTTTTCTTGCCA
Found at i:5644761 original size:14 final size:14
Alignment explanation
Indices: 5644744--5644778 Score: 54
Period size: 13 Copynumber: 2.5 Consensus size: 14
5644734 TTCTCTTATG
5644744 TTTTTTTCTTGCCA
1 TTTTTTTCTTGCCA
5644758 -TTTTTTCTTGCCA
1 TTTTTTTCTTGCCA
5644771 TTTATTTT
1 TTT-TTTT
5644779 TATTTTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 13 0.68
14 2 0.11
15 4 0.21
ACGTcount: A:0.09, C:0.17, G:0.06, T:0.69
Consensus pattern (14 bp):
TTTTTTTCTTGCCA
Found at i:5648270 original size:16 final size:15
Alignment explanation
Indices: 5648244--5648295 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 15
5648234 AGATTCAATC
5648244 AAGAACAAAAAAGAA
1 AAGAACAAAAAAGAA
5648259 AAGAAGCAAAAAAGAA
1 AAGAA-CAAAAAAGAA
*
5648275 AAAAACAAGAACAA-AA
1 AAGAACAA-AA-AAGAA
5648291 AAGAA
1 AAGAA
5648296 AATAAGCAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
15 8 0.25
16 22 0.69
17 2 0.06
ACGTcount: A:0.79, C:0.08, G:0.13, T:0.00
Consensus pattern (15 bp):
AAGAACAAAAAAGAA
Found at i:5648273 original size:11 final size:10
Alignment explanation
Indices: 5648257--5648295 Score: 51
Period size: 11 Copynumber: 3.7 Consensus size: 10
5648247 AACAAAAAAG
5648257 AAAAGAAGCAA
1 AAAAGAA-CAA
*
5648268 AAAAGAAAAA
1 AAAAGAACAA
5648278 AACAAGAACAA
1 AA-AAGAACAA
5648289 AAAAGAA
1 AAAAGAA
5648296 AATAAGCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 9 0.36
11 16 0.64
ACGTcount: A:0.79, C:0.08, G:0.13, T:0.00
Consensus pattern (10 bp):
AAAAGAACAA
Found at i:5648284 original size:22 final size:22
Alignment explanation
Indices: 5648250--5648306 Score: 71
Period size: 21 Copynumber: 2.5 Consensus size: 22
5648240 AATCAAGAAC
5648250 AAAAAAGAAAAGAAGCAAAAAAG
1 AAAAAAGAAAAGAA-CAAAAAAG
*
5648273 AAAAAA-ACAAGAACAAAAAAG
1 AAAAAAGAAAAGAACAAAAAAG
5648294 AAAATAAGCAAAA
1 AAAA-AAG-AAAA
5648307 ATCAAAAGGA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
21 12 0.41
22 8 0.28
23 6 0.21
24 3 0.10
ACGTcount: A:0.79, C:0.07, G:0.12, T:0.02
Consensus pattern (22 bp):
AAAAAAGAAAAGAACAAAAAAG
Found at i:5648305 original size:16 final size:16
Alignment explanation
Indices: 5648249--5648307 Score: 55
Period size: 16 Copynumber: 3.4 Consensus size: 16
5648239 CAATCAAGAA
*
5648249 CAAAAAAGAAAAGAAG
1 CAAAAAAGAAAACAAG
5648265 CAAAAAAGAAAAAAACAAG
1 CAAAAAAG---AAAACAAG
*
5648284 AACAAAAAAGAAAATAAG
1 --CAAAAAAGAAAACAAG
5648302 CAAAAA
1 CAAAAA
5648308 TCAAAAGGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
16 14 0.39
18 7 0.19
19 7 0.19
21 8 0.22
ACGTcount: A:0.78, C:0.08, G:0.12, T:0.02
Consensus pattern (16 bp):
CAAAAAAGAAAACAAG
Found at i:5648313 original size:22 final size:21
Alignment explanation
Indices: 5648265--5648313 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 21
5648255 AGAAAAGAAG
*
5648265 CAAAAAAGAAAAAAACAAGAA
1 CAAAAAAGAAAAAAACAAAAA
*
5648286 CAAAAAAGAAAATAAGCAAAAA
1 CAAAAAAGAAAA-AAACAAAAA
5648308 TCAAAA
1 -CAAAA
5648314 GGAAAAGGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 12 0.50
22 7 0.29
23 5 0.21
ACGTcount: A:0.78, C:0.10, G:0.08, T:0.04
Consensus pattern (21 bp):
CAAAAAAGAAAAAAACAAAAA
Found at i:5649411 original size:18 final size:18
Alignment explanation
Indices: 5649377--5649412 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
5649367 TTAACATCAA
* *
5649377 ATATTGGGGTATTTTTGG
1 ATATTGGGGCATCTTTGG
5649395 ATATTGGGGCATCTTTGG
1 ATATTGGGGCATCTTTGG
5649413 GGATTCAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.06, G:0.33, T:0.44
Consensus pattern (18 bp):
ATATTGGGGCATCTTTGG
Found at i:5650965 original size:106 final size:106
Alignment explanation
Indices: 5650780--5651099 Score: 523
Period size: 106 Copynumber: 3.0 Consensus size: 106
5650770 TCGCGCCACC
* *
5650780 CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTAGTTGTCAACAAATAATTTCCCAAT
1 CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAAT
* *
5650845 TTCAGAGCCAATTTCAACTTCACAGCGAAGGACATTGGACT
66 TTCAGAACCAATTTCAACTTCACAGCGAAGGATATTGGACT
*
5650886 CGAGACAGCACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAAT
1 CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAAT
* *
5650951 TTCAGAACCAATTTCAACTTCACAGTGAAGGATATTAGACT
66 TTCAGAACCAATTTCAACTTCACAGCGAAGGATATTGGACT
** *
5650992 CGAGACAACACAAGTTCAACTTCACAACGAAGGGACAACTGGTTGTCAACAAACAATTTCCCAGT
1 CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAAT
* * *
5651057 TTCAAAACCAATTTCAACTTCACGGCGGAGGATATTGGACT
66 TTCAGAACCAATTTCAACTTCACAGCGAAGGATATTGGACT
5651098 CG
1 CG
5651100 GAACAATACA
Statistics
Matches: 198, Mismatches: 16, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
106 198 1.00
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22
Consensus pattern (106 bp):
CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAAT
TTCAGAACCAATTTCAACTTCACAGCGAAGGATATTGGACT
Found at i:5652606 original size:16 final size:16
Alignment explanation
Indices: 5652581--5652611 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5652571 TTCGATGAGG
*
5652581 TTAACGAGCAACGAGC
1 TTAACCAGCAACGAGC
5652597 TTAACCAGCAACGAG
1 TTAACCAGCAACGAG
5652612 TCGAATCAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.26, G:0.23, T:0.13
Consensus pattern (16 bp):
TTAACCAGCAACGAGC
Found at i:5655809 original size:50 final size:50
Alignment explanation
Indices: 5655750--5655849 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
5655740 GAGGGGTTTA
5655750 TTTTCAACTGATGGGGTTTATTTTTACTTAATAACGCCCTCTCTGCTTTC
1 TTTTCAACTGATGGGGTTTATTTTTACTTAATAACGCCCTCTCTGCTTTC
5655800 TTTTCAACTGATGGGGTTTATTTTTACTTAATAACGCCCTCTCTGCTTTC
1 TTTTCAACTGATGGGGTTTATTTTTACTTAATAACGCCCTCTCTGCTTTC
5655850 CTGGATTACT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.18, C:0.22, G:0.14, T:0.46
Consensus pattern (50 bp):
TTTTCAACTGATGGGGTTTATTTTTACTTAATAACGCCCTCTCTGCTTTC
Found at i:5656891 original size:45 final size:45
Alignment explanation
Indices: 5656840--5656930 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
5656830 TGGATGATTA
5656840 TGAAGTAGTCAAAGAATGACAATATTTTGAGGGGAAAAAACCCTC
1 TGAAGTAGTCAAAGAATGACAATATTTTGAGGGGAAAAAACCCTC
5656885 TGAAGTAGTCAAAGAATGACAATATTTTGAGGGGAAAAAACCCTC
1 TGAAGTAGTCAAAGAATGACAATATTTTGAGGGGAAAAAACCCTC
5656930 T
1 T
5656931 AAGCTCTACC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.42, C:0.13, G:0.22, T:0.23
Consensus pattern (45 bp):
TGAAGTAGTCAAAGAATGACAATATTTTGAGGGGAAAAAACCCTC
Found at i:5657092 original size:13 final size:13
Alignment explanation
Indices: 5657074--5657098 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5657064 ATTAAAAATA
5657074 AAAAATTAATTTT
1 AAAAATTAATTTT
5657087 AAAAATTAATTT
1 AAAAATTAATTT
5657099 GATTATATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAAAATTAATTTT
Found at i:5657792 original size:18 final size:19
Alignment explanation
Indices: 5657771--5657806 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
5657761 ATTCTAATTG
*
5657771 AATAAATATA-TTTTATAT
1 AATAAAAATAGTTTTATAT
5657789 AATAAAAATAGTTTTATA
1 AATAAAAATAGTTTTATA
5657807 CCATATATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (19 bp):
AATAAAAATAGTTTTATAT
Found at i:5665616 original size:20 final size:20
Alignment explanation
Indices: 5665576--5665616 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
5665566 TTTGATCATG
*
5665576 ATATTTCAATATGCATGTAT
1 ATATTTCAATATGCATATAT
5665596 ATATTTC-ATATGACATATAT
1 ATATTTCAATATG-CATATAT
5665616 A
1 A
5665617 ACCAAGTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.44
Consensus pattern (20 bp):
ATATTTCAATATGCATATAT
Found at i:5667269 original size:7 final size:7
Alignment explanation
Indices: 5667257--5667284 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
5667247 TTTTTATAGG
5667257 TGACTAA
1 TGACTAA
5667264 TGACTAA
1 TGACTAA
5667271 TGACTAA
1 TGACTAA
5667278 TGACTAA
1 TGACTAA
5667285 AATAATAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (7 bp):
TGACTAA
Found at i:5669157 original size:125 final size:125
Alignment explanation
Indices: 5668935--5669185 Score: 475
Period size: 125 Copynumber: 2.0 Consensus size: 125
5668925 GGTGTCACTT
*
5668935 TAACTTTTCAAAACTCTTTTCTTTACAAATCCACCAAAATCTTAAATTCATCATTTGAAAAAGTG
1 TAACTTTTCAAAACTCTTTTATTTACAAATCCACCAAAATCTTAAATTCATCATTTGAAAAAGTG
5669000 AGTACTTTTTAGAAATAAATATAATCAAATTGTTTTACAAACCAATCAGAGCATATTCAA
66 AGTACTTTTTAGAAATAAATATAATCAAATTGTTTTACAAACCAATCAGAGCATATTCAA
*
5669060 TAACTTTTTAAAACTCTTTTATTTACAAATCCACCAAAATCTTAAATTCATCATTTGAAAAAGTG
1 TAACTTTTCAAAACTCTTTTATTTACAAATCCACCAAAATCTTAAATTCATCATTTGAAAAAGTG
*
5669125 AGTACTTTTTAGAACTAAATATAATCAAATTGTTTTACAAACCAATCAGAGCATATTCAA
66 AGTACTTTTTAGAAATAAATATAATCAAATTGTTTTACAAACCAATCAGAGCATATTCAA
5669185 T
1 T
5669186 CCAAATCTTG
Statistics
Matches: 123, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
125 123 1.00
ACGTcount: A:0.41, C:0.16, G:0.06, T:0.36
Consensus pattern (125 bp):
TAACTTTTCAAAACTCTTTTATTTACAAATCCACCAAAATCTTAAATTCATCATTTGAAAAAGTG
AGTACTTTTTAGAAATAAATATAATCAAATTGTTTTACAAACCAATCAGAGCATATTCAA
Found at i:5669873 original size:31 final size:31
Alignment explanation
Indices: 5669832--5669959 Score: 114
Period size: 31 Copynumber: 4.1 Consensus size: 31
5669822 GAACCTCGAC
* *
5669832 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATATGTCCCGAAGAACATAGGTA
* * **
5669863 AATTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTCCCGAAGAACATAGGTA
* *
5669894 TACTGTCCATATGTCCC-AAAAGACATAGGTA
1 AACTGTCCATATGTCCCGAAGA-ACATAGGTA
* * * * *
5669925 ATTCTGTTCATATGTTCCGTAGAACATAGATA
1 A-ACTGTCCATATGTCCCGAAGAACATAGGTA
5669957 AAC
1 AAC
5669960 CCTCGACTCT
Statistics
Matches: 75, Mismatches: 19, Indels: 6
0.75 0.19 0.06
Matches are distributed among these distances:
30 2 0.03
31 49 0.65
32 22 0.29
33 2 0.03
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (31 bp):
AACTGTCCATATGTCCCGAAGAACATAGGTA
Found at i:5670816 original size:45 final size:45
Alignment explanation
Indices: 5670752--5670858 Score: 196
Period size: 45 Copynumber: 2.4 Consensus size: 45
5670742 ACACTCTGTA
5670752 GTGTATCGATGCACTAATTACATTCGATATTTCAATTTCAAGGGG
1 GTGTATCGATGCACTAATTACATTCGATATTTCAATTTCAAGGGG
*
5670797 GTGTATCGATGCATTAATTACATTCGATATTTCAATTTCAAGGGG
1 GTGTATCGATGCACTAATTACATTCGATATTTCAATTTCAAGGGG
*
5670842 GTGCATCGATGCACTAA
1 GTGTATCGATGCACTAA
5670859 CTGTGCATCG
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 59 1.00
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.35
Consensus pattern (45 bp):
GTGTATCGATGCACTAATTACATTCGATATTTCAATTTCAAGGGG
Found at i:5673295 original size:30 final size:30
Alignment explanation
Indices: 5673239--5673422 Score: 280
Period size: 30 Copynumber: 6.1 Consensus size: 30
5673229 GAAGGACCTA
* *
5673239 TCCAGAGGTCACAAAGA-CCCCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
5673268 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
*
5673298 TCCAGAGTTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
5673328 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
5673358 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
* ** * *
5673388 TCCATAGGTCCCAAAGAACCTAGGTAAACTG
1 TCCAGAGGTCATAAAGATCCTCGGT-AACTG
5673419 TCCA
1 TCCA
5673423 TATGTTCCTT
Statistics
Matches: 144, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
29 16 0.11
30 119 0.83
31 9 0.06
ACGTcount: A:0.31, C:0.26, G:0.22, T:0.22
Consensus pattern (30 bp):
TCCAGAGGTCATAAAGATCCTCGGTAACTG
Found at i:5673488 original size:63 final size:61
Alignment explanation
Indices: 5673380--5673508 Score: 188
Period size: 63 Copynumber: 2.1 Consensus size: 61
5673370 AAAGATCCTC
* *
5673380 GGTAACTGTCCATAGGTCCCAAAGAACCTAGGTAAACTGTCCATATGTTCCTTAGAACATA
1 GGTAACTGTCCATAGGTCCCAAAGAACATAGGTAAACTGTCCATATGTTCCGTAGAACATA
* *
5673441 GGTATACTGTCCATATGTCTCGAAAG-ACATAGGTAAAACTGTCCATATGTTCCGTAGAACATA
1 GGTA-ACTGTCCATAGGTC-CCAAAGAACATAGGT-AAACTGTCCATATGTTCCGTAGAACATA
5673504 GGTAA
1 GGTAA
5673509 ACCCTCGACT
Statistics
Matches: 61, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
61 4 0.07
62 21 0.34
63 36 0.59
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.27
Consensus pattern (61 bp):
GGTAACTGTCCATAGGTCCCAAAGAACATAGGTAAACTGTCCATATGTTCCGTAGAACATA
Found at i:5673503 original size:32 final size:31
Alignment explanation
Indices: 5673383--5673510 Score: 143
Period size: 31 Copynumber: 4.1 Consensus size: 31
5673373 GATCCTCGGT
* * ** *
5673383 AACTGTCCATAGGTCCCAAAGAACCTAGGTA
1 AACTGTCCATATGTTCCGTAGAACATAGGTA
*
5673414 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTTCCGTAGAACATAGGTA
* *
5673445 TACTGTCCATATG-TCTCG-AAAGACATAGGTAA
1 AACTGTCCATATGTTC-CGTAGA-ACATAGGT-A
5673477 AACTGTCCATATGTTCCGTAGAACATAGGTA
1 AACTGTCCATATGTTCCGTAGAACATAGGTA
5673508 AAC
1 AAC
5673511 CCTCGACTCT
Statistics
Matches: 82, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
30 4 0.05
31 51 0.62
32 23 0.28
33 4 0.05
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (31 bp):
AACTGTCCATATGTTCCGTAGAACATAGGTA
Found at i:5674408 original size:21 final size:21
Alignment explanation
Indices: 5674378--5674422 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
5674368 ATTCTGTCAT
* *
5674378 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
5674399 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
5674420 TTG
1 TTG
5674423 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:5676897 original size:31 final size:31
Alignment explanation
Indices: 5676862--5676963 Score: 116
Period size: 31 Copynumber: 3.3 Consensus size: 31
5676852 TCGAATAACC
*
5676862 TAGGTAAATTGTCCATATGTTCCTTAGAACA
1 TAGGTAAATTGTCCATATGTTCCATAGAACA
* * * * *
5676893 TAGGTATACTGTTCATATGTCCCA-AAAGACA
1 TAGGTAAATTGTCCATATGTTCCATAGA-ACA
*
5676924 TAGGTAATTCTGTCCATATGTTCCATAGAACA
1 TAGGTAAAT-TGTCCATATGTTCCATAGAACA
5676956 TAGGTAAA
1 TAGGTAAA
5676964 CCCTCGACTC
Statistics
Matches: 55, Mismatches: 13, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
30 2 0.04
31 28 0.51
32 23 0.42
33 2 0.04
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (31 bp):
TAGGTAAATTGTCCATATGTTCCATAGAACA
Found at i:5676957 original size:32 final size:32
Alignment explanation
Indices: 5676862--5676962 Score: 118
Period size: 32 Copynumber: 3.2 Consensus size: 32
5676852 TCGAATAACC
* *
5676862 TAGGTAAAT-TGTCCATATGTTCCTTAGAACA
1 TAGGTAATTCTGTCCATATGTTCCATAGAACA
* * * *
5676893 TAGGT-ATACTGTTCATATGTCCCA-AAAGACA
1 TAGGTAATTCTGTCCATATGTTCCATAGA-ACA
5676924 TAGGTAATTCTGTCCATATGTTCCATAGAACA
1 TAGGTAATTCTGTCCATATGTTCCATAGAACA
5676956 TAGGTAA
1 TAGGTAA
5676963 ACCCTCGACT
Statistics
Matches: 56, Mismatches: 10, Indels: 7
0.77 0.14 0.10
Matches are distributed among these distances:
30 3 0.05
31 25 0.45
32 26 0.46
33 2 0.04
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Consensus pattern (32 bp):
TAGGTAATTCTGTCCATATGTTCCATAGAACA
Found at i:5680045 original size:14 final size:16
Alignment explanation
Indices: 5680010--5680046 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
5680000 GAAATCATTG
5680010 AAAATTATATAGAAAT
1 AAAATTATATAGAAAT
*
5680026 AAAATTATGTA-AAA-
1 AAAATTATATAGAAAT
5680040 AAAATTA
1 AAAATTA
5680047 GAGATGGAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 3 0.15
16 10 0.50
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (16 bp):
AAAATTATATAGAAAT
Found at i:5680228 original size:20 final size:19
Alignment explanation
Indices: 5680184--5680259 Score: 75
Period size: 20 Copynumber: 3.9 Consensus size: 19
5680174 CAAAACATTT
* *
5680184 GTGTTGCGAAAATAAAAGC
1 GTGTTGCGAAATTAAAATC
5680203 -TGTTGCGAAATTAAAATTC
1 GTGTTGCGAAATTAAAA-TC
5680222 GTGTTGCG-AATTCGAAAATC
1 GTGTTGCGAAATT--AAAATC
* *
5680242 GAGTTGCGAAATCAAAAT
1 GTGTTGCGAAATTAAAAT
5680260 TCCTATTGCG
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
18 15 0.31
19 10 0.21
20 16 0.33
21 7 0.15
ACGTcount: A:0.38, C:0.12, G:0.22, T:0.28
Consensus pattern (19 bp):
GTGTTGCGAAATTAAAATC
Found at i:5680253 original size:40 final size:40
Alignment explanation
Indices: 5680204--5680281 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
5680194 AATAAAAGCT
* * * *
5680204 GTTGCGAAATTAAAATTCGTGTTGCGAATTCGAAAATCGA
1 GTTGCGAAATCAAAATTCCTATTGCGAATTAGAAAATCGA
*
5680244 GTTGCGAAATCAAAATTCCTATTGCGATTTAGAAAATC
1 GTTGCGAAATCAAAATTCCTATTGCGAATTAGAAAATC
5680282 TTGTTGTGAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31
Consensus pattern (40 bp):
GTTGCGAAATCAAAATTCCTATTGCGAATTAGAAAATCGA
Found at i:5680268 original size:20 final size:20
Alignment explanation
Indices: 5680205--5680270 Score: 55
Period size: 20 Copynumber: 3.3 Consensus size: 20
5680195 ATAAAAGCTG
* * *
5680205 TTGCGAAATTAAAATTCGTG
1 TTGCGAAATCAAAATTCCTA
* *
5680225 TTGCGAATTCGAAAA-T-CGA
1 TTGCGAAATC-AAAATTCCTA
5680244 GTTGCGAAATCAAAATTCCTA
1 -TTGCGAAATCAAAATTCCTA
5680265 TTGCGA
1 TTGCGA
5680271 TTTAGAAAAT
Statistics
Matches: 35, Mismatches: 7, Indels: 8
0.70 0.14 0.16
Matches are distributed among these distances:
19 4 0.11
20 25 0.71
21 6 0.17
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (20 bp):
TTGCGAAATCAAAATTCCTA
Found at i:5680366 original size:20 final size:19
Alignment explanation
Indices: 5680318--5680394 Score: 82
Period size: 20 Copynumber: 3.8 Consensus size: 19
5680308 TGAAAAATAA
*
5680318 ATTCGCGTTGCGATTTATAT
1 ATTCGCGTTGCGATTTA-CT
**
5680338 ATTATCGTTGCGATTTACCT
1 ATTCGCGTTGCGATTTA-CT
*
5680358 ATTCGCGTTACGAATTTGACT
1 ATTCGCGTTGCG-ATTT-ACT
5680379 ATTCGCGTTGCGATTT
1 ATTCGCGTTGCGATTT
5680395 TGGAACCTGT
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
20 29 0.62
21 17 0.36
22 1 0.02
ACGTcount: A:0.19, C:0.18, G:0.19, T:0.43
Consensus pattern (19 bp):
ATTCGCGTTGCGATTTACT
Found at i:5680380 original size:21 final size:21
Alignment explanation
Indices: 5680356--5680396 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
5680346 TGCGATTTAC
5680356 CTATTCGCGTTACGAATTTGA
1 CTATTCGCGTTACGAATTTGA
* *
5680377 CTATTCGCGTTGCGATTTTG
1 CTATTCGCGTTACGAATTTG
5680397 GAACCTGTGT
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:0.17, C:0.20, G:0.22, T:0.41
Consensus pattern (21 bp):
CTATTCGCGTTACGAATTTGA
Found at i:5686964 original size:37 final size:37
Alignment explanation
Indices: 5686922--5687007 Score: 145
Period size: 37 Copynumber: 2.3 Consensus size: 37
5686912 CATGAAAAAT
5686922 AAGTTGGCCACCTAACAAAGAATTTTCCAATGTGTAC
1 AAGTTGGCCACCTAACAAAGAATTTTCCAATGTGTAC
* *
5686959 AAGTTGACCACCTACCAAAGAATTTTCCAATGTGTAC
1 AAGTTGGCCACCTAACAAAGAATTTTCCAATGTGTAC
*
5686996 AAGTTAGCCACC
1 AAGTTGGCCACC
5687008 AAATATAAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 45 1.00
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.26
Consensus pattern (37 bp):
AAGTTGGCCACCTAACAAAGAATTTTCCAATGTGTAC
Found at i:5691412 original size:2 final size:2
Alignment explanation
Indices: 5691405--5691430 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5691395 CATCAAATAT
5691405 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
5691431 AGAATGATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:5694574 original size:12 final size:12
Alignment explanation
Indices: 5694557--5694581 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5694547 TTTGTGTTTC
5694557 TGTTATAGTTGG
1 TGTTATAGTTGG
5694569 TGTTATAGTTGG
1 TGTTATAGTTGG
5694581 T
1 T
5694582 AGGCTATGTC
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:0.16, C:0.00, G:0.32, T:0.52
Consensus pattern (12 bp):
TGTTATAGTTGG
Found at i:5695641 original size:23 final size:23
Alignment explanation
Indices: 5695590--5695657 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 23
5695580 CAATTAAAGA
*
5695590 AATTATCTTTTG-GAACTTTAGGG
1 AATTATCTTTTGTGAATTTTA-GG
* *
5695613 ATTTATCTTTTGTGAGTTTTAGG
1 AATTATCTTTTGTGAATTTTAGG
* *
5695636 AATTATCTTGTGT-ATTTTTAGG
1 AATTATCTTTTGTGAATTTTAGG
5695658 GTTTTAGGAA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
22 8 0.21
23 24 0.63
24 6 0.16
ACGTcount: A:0.22, C:0.06, G:0.21, T:0.51
Consensus pattern (23 bp):
AATTATCTTTTGTGAATTTTAGG
Found at i:5697168 original size:146 final size:147
Alignment explanation
Indices: 5696904--5697196 Score: 579
Period size: 146 Copynumber: 2.0 Consensus size: 147
5696894 ATCGAAGACT
5696904 TCTTCATTCTCATAAGAAATGTGAATTGAACATGAAATACTATTAGATAAAAATTAAAAGTATAT
1 TCTTCATTCTCATAAGAAATGTGAATTGAACATGAAATACTATTAGATAAAAATTAAAAGTATAT
5696969 GTGATAATCTTGCTAGTTGTGAAATTATCTCTGAGTATGAACATGTCACTGTAATTTG-AATGGT
66 GTGATAATCTTGCTAGTTGTGAAATTATCTCTGAGTATGAACATGTCACTGTAATTTGAAATGGT
5697033 CTCTCTTCTAAGTATGA
131 CTCTCTTCTAAGTATGA
5697050 TCTTCATTCTCATAAGAAATGTGAATTGAACATGAAATACTATTAGATAAAAATTAAAAGTATAT
1 TCTTCATTCTCATAAGAAATGTGAATTGAACATGAAATACTATTAGATAAAAATTAAAAGTATAT
5697115 GTGATAATCTTGCTAGTTGTGAAATTATCTCTGAGTATGAACATGTCACTGTAATTTGAAATGGT
66 GTGATAATCTTGCTAGTTGTGAAATTATCTCTGAGTATGAACATGTCACTGTAATTTGAAATGGT
5697180 CTCTCTTCTAAGTATGA
131 CTCTCTTCTAAGTATGA
5697197 GTTTATCATT
Statistics
Matches: 146, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
146 123 0.84
147 23 0.16
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.37
Consensus pattern (147 bp):
TCTTCATTCTCATAAGAAATGTGAATTGAACATGAAATACTATTAGATAAAAATTAAAAGTATAT
GTGATAATCTTGCTAGTTGTGAAATTATCTCTGAGTATGAACATGTCACTGTAATTTGAAATGGT
CTCTCTTCTAAGTATGA
Found at i:5698654 original size:23 final size:26
Alignment explanation
Indices: 5698617--5698693 Score: 92
Period size: 24 Copynumber: 3.2 Consensus size: 26
5698607 TTCTCTTGTG
5698617 ATCATGTATCTCATATCAC-T-TCAT
1 ATCATGTATCTCATATCACATGTCAT
5698641 ATCATGT-TCTCATATCACATGTCAT
1 ATCATGTATCTCATATCACATGTCAT
* * *
5698666 ATCA--CATGTCATATCACATATCAT
1 ATCATGTATCTCATATCACATGTCAT
5698690 ATCA
1 ATCA
5698694 CATGAACATA
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
23 11 0.23
24 28 0.60
25 8 0.17
ACGTcount: A:0.32, C:0.25, G:0.05, T:0.38
Consensus pattern (26 bp):
ATCATGTATCTCATATCACATGTCAT
Found at i:5698667 original size:12 final size:12
Alignment explanation
Indices: 5698650--5698697 Score: 87
Period size: 12 Copynumber: 4.0 Consensus size: 12
5698640 TATCATGTTC
5698650 TCATATCACATG
1 TCATATCACATG
5698662 TCATATCACATG
1 TCATATCACATG
*
5698674 TCATATCACATA
1 TCATATCACATG
5698686 TCATATCACATG
1 TCATATCACATG
5698698 AACATATATA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 34 1.00
ACGTcount: A:0.35, C:0.25, G:0.06, T:0.33
Consensus pattern (12 bp):
TCATATCACATG
Found at i:5699028 original size:11 final size:11
Alignment explanation
Indices: 5699012--5699047 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
5699002 GGTATACATC
5699012 GATGCACTACT
1 GATGCACTACT
5699023 GATGCA-T-C-
1 GATGCACTACT
5699031 GATGCACTACT
1 GATGCACTACT
5699042 GATGCA
1 GATGCA
5699048 TCGGTGCATA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
8 6 0.27
9 2 0.09
10 2 0.09
11 12 0.55
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.25
Consensus pattern (11 bp):
GATGCACTACT
Found at i:5699032 original size:19 final size:19
Alignment explanation
Indices: 5699008--5699055 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
5698998 TGAAGGTATA
5699008 CATCGATGCACTACTGATG
1 CATCGATGCACTACTGATG
5699027 CATCGATGCACTACTGATG
1 CATCGATGCACTACTGATG
*
5699046 CATCGGTGCA
1 CATCGATGCA
5699056 TAAAAGGTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (19 bp):
CATCGATGCACTACTGATG
Found at i:5699132 original size:64 final size:62
Alignment explanation
Indices: 5699023--5699143 Score: 152
Period size: 64 Copynumber: 1.9 Consensus size: 62
5699013 ATGCACTACT
* * *
5699023 GATGCATCGATGCACTACTGATGCATCGGTGCATAAAAGGTATTCGATGTAGTTTTATTGCTGG
1 GATGCATCGATGCACTACTGATGCATCGATGCACAAAAGGCATTCGATGT--TTTTATTGCTGG
* * * **
5699087 GATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTTTATT
1 GATGCATCGATGCACTACTGATGCATCGATGCACAAAAGGCATTCGATGTTTTTATT
5699144 TTAAAAGAGT
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
62 7 0.14
64 42 0.86
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (62 bp):
GATGCATCGATGCACTACTGATGCATCGATGCACAAAAGGCATTCGATGTTTTTATTGCTGG
Found at i:5705351 original size:23 final size:26
Alignment explanation
Indices: 5705314--5705382 Score: 85
Period size: 24 Copynumber: 2.8 Consensus size: 26
5705304 TTCTCTTGTG
5705314 ATCATGTATCTCATATCAC-T-TCAT
1 ATCATGTATCTCATATCACATGTCAT
5705338 ATCATGT-TCTCATATCACATGTCAT
1 ATCATGTATCTCATATCACATGTCAT
* *
5705363 ATCA--CATATCATATCACATG
1 ATCATGTATCTCATATCACATG
5705383 AACATTTATA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
23 11 0.28
24 21 0.52
25 8 0.20
ACGTcount: A:0.32, C:0.25, G:0.06, T:0.38
Consensus pattern (26 bp):
ATCATGTATCTCATATCACATGTCAT
Found at i:5705364 original size:12 final size:12
Alignment explanation
Indices: 5705347--5705382 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
5705337 TATCATGTTC
5705347 TCATATCACATG
1 TCATATCACATG
*
5705359 TCATATCACATA
1 TCATATCACATG
5705371 TCATATCACATG
1 TCATATCACATG
5705383 AACATTTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.33
Consensus pattern (12 bp):
TCATATCACATG
Found at i:5705713 original size:11 final size:11
Alignment explanation
Indices: 5705697--5705732 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
5705687 GGTATGCATC
5705697 GATGCACTACT
1 GATGCACTACT
5705708 GATGCA-T-C-
1 GATGCACTACT
5705716 GATGCACTACT
1 GATGCACTACT
5705727 GATGCA
1 GATGCA
5705733 TCGATGCATA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
8 6 0.27
9 2 0.09
10 2 0.09
11 12 0.55
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.25
Consensus pattern (11 bp):
GATGCACTACT
Found at i:5705714 original size:19 final size:19
Alignment explanation
Indices: 5705690--5705740 Score: 102
Period size: 19 Copynumber: 2.7 Consensus size: 19
5705680 TAATGAAGGT
5705690 ATGCATCGATGCACTACTG
1 ATGCATCGATGCACTACTG
5705709 ATGCATCGATGCACTACTG
1 ATGCATCGATGCACTACTG
5705728 ATGCATCGATGCA
1 ATGCATCGATGCA
5705741 TAAAATGTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.27, C:0.25, G:0.22, T:0.25
Consensus pattern (19 bp):
ATGCATCGATGCACTACTG
Found at i:5705719 original size:8 final size:8
Alignment explanation
Indices: 5705690--5705741 Score: 50
Period size: 8 Copynumber: 5.8 Consensus size: 8
5705680 TAATGAAGGT
5705690 ATGCATCG
1 ATGCATCG
5705698 ATGCACTACTG
1 ATGCA-T-C-G
5705709 ATGCATCG
1 ATGCATCG
5705717 ATGCACTACTG
1 ATGCA-T-C-G
5705728 ATGCATCG
1 ATGCATCG
5705736 ATGCAT
1 ATGCAT
5705742 AAAATGTATT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
8 18 0.47
9 4 0.11
10 4 0.11
11 12 0.32
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (8 bp):
ATGCATCG
Found at i:5712072 original size:18 final size:18
Alignment explanation
Indices: 5712049--5712109 Score: 70
Period size: 18 Copynumber: 3.4 Consensus size: 18
5712039 TGTTAATGAA
5712049 TATAAAAAATTAAATTAT
1 TATAAAAAATTAAATTAT
** *
5712067 TATAAAATGTT-AATGAT
1 TATAAAAAATTAAATTAT
*
5712084 TATAAAAAAATTAAAATAT
1 TAT-AAAAAATTAAATTAT
5712103 TATAAAA
1 TATAAAA
5712110 TAATCATTAA
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
17 8 0.24
18 19 0.56
19 7 0.21
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (18 bp):
TATAAAAAATTAAATTAT
Found at i:5712073 original size:17 final size:17
Alignment explanation
Indices: 5712053--5712109 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 17
5712043 AATGAATATA
5712053 AAAAATTAAATTATTAT
1 AAAAATTAAATTATTAT
* *
5712070 AAAATGTTAATGATTA-TAA
1 AAAA-ATTAA--ATTATTAT
*
5712089 AAAAATTAAAATATTAT
1 AAAAATTAAATTATTAT
5712106 AAAA
1 AAAA
5712110 TAATCATTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 8
0.70 0.11 0.18
Matches are distributed among these distances:
16 3 0.10
17 10 0.32
18 8 0.26
19 6 0.19
20 4 0.13
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (17 bp):
AAAAATTAAATTATTAT
Found at i:5712078 original size:35 final size:36
Alignment explanation
Indices: 5712039--5712110 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
5712029 ATGCACATAT
*
5712039 TGTTAATGAATAT-AAAAAATTAAATTATTATAAAA
1 TGTTAATGAATATAAAAAAATTAAAATATTATAAAA
*
5712074 TGTTAATGATTATAAAAAAATTAAAATATTATAAAA
1 TGTTAATGAATATAAAAAAATTAAAATATTATAAAA
5712110 T
1 T
5712111 AATCATTAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
35 12 0.35
36 22 0.65
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.38
Consensus pattern (36 bp):
TGTTAATGAATATAAAAAAATTAAAATATTATAAAA
Found at i:5713047 original size:14 final size:14
Alignment explanation
Indices: 5713028--5713056 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
5713018 AACAAGAGAC
5713028 TTTGATCAAATTTA
1 TTTGATCAAATTTA
5713042 TTTGATCAAATTTA
1 TTTGATCAAATTTA
5713056 T
1 T
5713057 GGCTTAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.07, G:0.07, T:0.52
Consensus pattern (14 bp):
TTTGATCAAATTTA
Found at i:5720664 original size:74 final size:76
Alignment explanation
Indices: 5720542--5720682 Score: 214
Period size: 74 Copynumber: 1.9 Consensus size: 76
5720532 AAAATAAAAA
* * *
5720542 TTTTAAAATTTCGAAGTTAAAAATAATATGAAACTTTTAGAAATTTTTAATAAATTT-TAAAAAA
1 TTTTAAAATTTCGAAGTTAAAAATAATATGAAACTTGTAGAAATTTTTAACAAATTTGGAAAAAA
5720606 AATATTAAATT
66 AATATTAAATT
* * *
5720617 TTTTAAAGTTTCGAATTTAAAAA-AATATGAAACTTGTATAAATTTTTAACAAATTTGGAAAAAA
1 TTTTAAAATTTCGAAGTTAAAAATAATATGAAACTTGTAGAAATTTTTAACAAATTTGGAAAAAA
5720681 AA
66 AA
5720683 AAACGTTTGG
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
74 30 0.51
75 29 0.49
ACGTcount: A:0.50, C:0.04, G:0.07, T:0.39
Consensus pattern (76 bp):
TTTTAAAATTTCGAAGTTAAAAATAATATGAAACTTGTAGAAATTTTTAACAAATTTGGAAAAAA
AATATTAAATT
Found at i:5720921 original size:25 final size:25
Alignment explanation
Indices: 5720870--5720923 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
5720860 AATTATTTGC
***
5720870 TTAAGTTATAATATATTTTTGTGCA
1 TTAAGTTATAATATATTTAAATGCA
* *
5720895 TTAATTTATAATATATTTAAATTCA
1 TTAAGTTATAATATATTTAAATGCA
5720920 TTAA
1 TTAA
5720924 AAATATATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.04, G:0.06, T:0.52
Consensus pattern (25 bp):
TTAAGTTATAATATATTTAAATGCA
Found at i:5723146 original size:2 final size:2
Alignment explanation
Indices: 5723139--5723179 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
5723129 GTTATCTTTG
5723139 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5723180 ATTTAAAGGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5729767 original size:19 final size:19
Alignment explanation
Indices: 5729743--5729780 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
5729733 TAAGAATGTC
5729743 ATGAAAATGAAGAAAAGTT
1 ATGAAAATGAAGAAAAGTT
5729762 ATGAAAATGAAGAAAAGTT
1 ATGAAAATGAAGAAAAGTT
5729781 CAATATCATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.21, T:0.21
Consensus pattern (19 bp):
ATGAAAATGAAGAAAAGTT
Found at i:5732341 original size:12 final size:12
Alignment explanation
Indices: 5732314--5732351 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
5732304 TGGATTAGGA
5732314 CAAAAGT-AAAG
1 CAAAAGTAAAAG
*
5732325 TAAAAGTAAAAG
1 CAAAAGTAAAAG
*
5732337 CAAAAGCAAAAG
1 CAAAAGTAAAAG
5732349 CAA
1 CAA
5732352 CTTTTGCTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
11 6 0.26
12 17 0.74
ACGTcount: A:0.66, C:0.11, G:0.16, T:0.08
Consensus pattern (12 bp):
CAAAAGTAAAAG
Found at i:5732999 original size:13 final size:13
Alignment explanation
Indices: 5732981--5733024 Score: 79
Period size: 13 Copynumber: 3.4 Consensus size: 13
5732971 TAAATTTTAT
*
5732981 AGAGTATTGTTAA
1 AGAGTACTGTTAA
5732994 AGAGTACTGTTAA
1 AGAGTACTGTTAA
5733007 AGAGTACTGTTAA
1 AGAGTACTGTTAA
5733020 AGAGT
1 AGAGT
5733025 CCAAACTTGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.39, C:0.05, G:0.25, T:0.32
Consensus pattern (13 bp):
AGAGTACTGTTAA
Found at i:5734266 original size:28 final size:28
Alignment explanation
Indices: 5734234--5734288 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
5734224 TATTCAAATA
*
5734234 TACATTGAATTTTCATATAATTTTTAGG
1 TACATTAAATTTTCATATAATTTTTAGG
5734262 TACATTAAATTTTCATATAATTTTTAG
1 TACATTAAATTTTCATATAATTTTTAG
5734289 ATTTAGAGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.35, C:0.07, G:0.07, T:0.51
Consensus pattern (28 bp):
TACATTAAATTTTCATATAATTTTTAGG
Found at i:5742778 original size:38 final size:39
Alignment explanation
Indices: 5742727--5742814 Score: 110
Period size: 38 Copynumber: 2.3 Consensus size: 39
5742717 TTCCCTTGGC
*
5742727 TTTTTA-GT-TTTCAATAATTATGCATTTATAACAC-AT
1 TTTTTATGTCTTTCAATAACTATGCATTTATAACACGAT
* * * *
5742763 TTTTTATGTCTTTCAATAACTCTGCCTTTGTGACACGAT
1 TTTTTATGTCTTTCAATAACTATGCATTTATAACACGAT
5742802 TTTTTATGTCTTT
1 TTTTTATGTCTTT
5742815 ATGACATGTT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
36 6 0.14
37 2 0.05
38 21 0.48
39 15 0.34
ACGTcount: A:0.24, C:0.15, G:0.09, T:0.52
Consensus pattern (39 bp):
TTTTTATGTCTTTCAATAACTATGCATTTATAACACGAT
Found at i:5745667 original size:23 final size:23
Alignment explanation
Indices: 5745633--5745717 Score: 79
Period size: 23 Copynumber: 3.7 Consensus size: 23
5745623 GCATATTATA
*
5745633 TGGCACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
5745656 TGGCACTTCGGTGC-ATCTCTACG
1 TGGCACTTCGGTGCAAT-TCTACG
* *
5745679 CGGTC-CTTTGG-GACAAATTCTACG
1 TGG-CACTTCGGTG-C-AATTCTACG
5745703 T-GCACTTCGGTGCAA
1 TGGCACTTCGGTGCAA
5745718 ATTTATATGA
Statistics
Matches: 50, Mismatches: 5, Indels: 15
0.71 0.07 0.21
Matches are distributed among these distances:
22 6 0.12
23 34 0.68
24 8 0.16
25 2 0.04
ACGTcount: A:0.19, C:0.27, G:0.26, T:0.28
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:5746310 original size:21 final size:22
Alignment explanation
Indices: 5746270--5746313 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
5746260 ACGGAAGTAA
*
5746270 TGTAGCAGGGGAATCGATTCCC
1 TGTAGCAGGGGAACCGATTCCC
*
5746292 TGTAGCA-GGGTACCGATTCCC
1 TGTAGCAGGGGAACCGATTCCC
5746313 T
1 T
5746314 ATTTGTGTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.20, C:0.25, G:0.30, T:0.25
Consensus pattern (22 bp):
TGTAGCAGGGGAACCGATTCCC
Found at i:5747882 original size:13 final size:13
Alignment explanation
Indices: 5747855--5747890 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
5747845 CCTTATTATA
*
5747855 ATATTGTTCTTTCT
1 ATATT-TTCTCTCT
5747869 ATATTTTCTCTCT
1 ATATTTTCTCTCT
5747882 ATATTTTCT
1 ATATTTTCT
5747891 GTTTTTAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 16 0.76
14 5 0.24
ACGTcount: A:0.17, C:0.17, G:0.03, T:0.64
Consensus pattern (13 bp):
ATATTTTCTCTCT
Found at i:5748362 original size:14 final size:14
Alignment explanation
Indices: 5748340--5748373 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
5748330 TCGATTATAT
*
5748340 GTTCGTTTATGTTA
1 GTTCATTTATGTTA
*
5748354 GTTCATTTATGTTC
1 GTTCATTTATGTTA
5748368 GTTCAT
1 GTTCAT
5748374 CTGTGTTCGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.15, C:0.12, G:0.18, T:0.56
Consensus pattern (14 bp):
GTTCATTTATGTTA
Found at i:5748381 original size:24 final size:26
Alignment explanation
Indices: 5748328--5748383 Score: 64
Period size: 24 Copynumber: 2.2 Consensus size: 26
5748318 GTTCGTAAAC
* *
5748328 GTTCGATTATATGTTCGTTTATGTTA
1 GTTCGATTATATGTTCGTTCATCTTA
5748354 GTTC-ATT-TATGTTCGTTCATCTGT-
1 GTTCGATTATATGTTCGTTCATCT-TA
5748378 GTTCGA
1 GTTCGA
5748384 ACAAATGGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 17 0.65
25 5 0.19
26 4 0.15
ACGTcount: A:0.16, C:0.12, G:0.20, T:0.52
Consensus pattern (26 bp):
GTTCGATTATATGTTCGTTCATCTTA
Found at i:5755760 original size:3 final size:3
Alignment explanation
Indices: 5755752--5755788 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
5755742 ATAATTTGTA
5755752 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
5755789 TCAGACGAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:5755926 original size:23 final size:23
Alignment explanation
Indices: 5755895--5755974 Score: 99
Period size: 23 Copynumber: 3.4 Consensus size: 23
5755885 TTCACCAACA
*
5755895 GTTCGTTTATTGTGTTCGTTTAT
1 GTTCGTTTATTGTGTTCGTTTAC
* *
5755918 GTTCATTTATTATGTTCGTTTAC
1 GTTCGTTTATTGTGTTCGTTTAC
*
5755941 ATTCGTTCGT-TTGTGTTCGTTTAC
1 GTTCGTT--TATTGTGTTCGTTTAC
5755965 GTTCGTTTAT
1 GTTCGTTTAT
5755975 CATTTAAATG
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
22 1 0.02
23 26 0.55
24 19 0.40
25 1 0.02
ACGTcount: A:0.11, C:0.12, G:0.19, T:0.57
Consensus pattern (23 bp):
GTTCGTTTATTGTGTTCGTTTAC
Found at i:5759464 original size:23 final size:22
Alignment explanation
Indices: 5759436--5759527 Score: 87
Period size: 23 Copynumber: 4.1 Consensus size: 22
5759426 GGCTGTAATT
*
5759436 TTTATTTATTTATTTTAATTTTT
1 TTTATTTATTTATTTTAA-TTTA
* *
5759459 TTTATTTTTTTATTTCAAATTTA
1 TTTATTTATTTATTT-TAATTTA
* *
5759482 TGTATTCATTTATTTCTAATTTA
1 TTTATTTATTTATTT-TAATTTA
* *
5759505 TTTGTTTATTT-TTTTTATTTA
1 TTTATTTATTTATTTTAATTTA
5759526 TT
1 TT
5759528 CCACTCGAAT
Statistics
Matches: 57, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
21 8 0.14
22 3 0.05
23 44 0.77
24 2 0.04
ACGTcount: A:0.22, C:0.03, G:0.02, T:0.73
Consensus pattern (22 bp):
TTTATTTATTTATTTTAATTTA
Found at i:5760089 original size:43 final size:42
Alignment explanation
Indices: 5760035--5760117 Score: 107
Period size: 43 Copynumber: 2.0 Consensus size: 42
5760025 AAATTAAACA
*
5760035 TATAATTATTTAAATCTATG-TTTATTTATTGTAATTTATTTATT
1 TATAATTATTTAAAT-TATGTTTTAGTTATTGT-ATTT-TTTATT
*
5760079 TATAA-TATTTAAATTTTGTTTTAGTTATTGTATTTTTTA
1 TATAATTATTTAAATTATGTTTTAGTTATTGTATTTTTTA
5760118 AGATAATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
41 4 0.11
42 7 0.19
43 20 0.56
44 5 0.14
ACGTcount: A:0.30, C:0.01, G:0.06, T:0.63
Consensus pattern (42 bp):
TATAATTATTTAAATTATGTTTTAGTTATTGTATTTTTTATT
Found at i:5765824 original size:2 final size:2
Alignment explanation
Indices: 5765817--5765865 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
5765807 AATGATGTAA
* *
5765817 AT AT AT AT AT AT GT AA AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5765859 AT AT AT A
1 AT AT AT A
5765866 CAATTGCATT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5765832 original size:16 final size:16
Alignment explanation
Indices: 5765811--5765860 Score: 82
Period size: 16 Copynumber: 3.1 Consensus size: 16
5765801 ACCTTAAATG
5765811 ATGTAAATATATATAT
1 ATGTAAATATATATAT
5765827 ATGTAAATATATATAT
1 ATGTAAATATATATAT
* *
5765843 ATATATATATATATAT
1 ATGTAAATATATATAT
5765859 AT
1 AT
5765861 ATATACAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (16 bp):
ATGTAAATATATATAT
Found at i:5768413 original size:13 final size:13
Alignment explanation
Indices: 5768392--5768439 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 13
5768382 TATAATTATG
*
5768392 TTATATTTTTACA
1 TTATTTTTTTACA
5768405 TTA-TTTTTTACCA
1 TTATTTTTTTA-CA
5768418 TTATTTTTTTA-A
1 TTATTTTTTTACA
5768430 -TATTTTTTTA
1 TTATTTTTTTA
5768440 TTTGTAATAC
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
11 10 0.31
12 7 0.22
13 8 0.25
14 7 0.22
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.69
Consensus pattern (13 bp):
TTATTTTTTTACA
Found at i:5768414 original size:12 final size:13
Alignment explanation
Indices: 5768392--5768426 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
5768382 TATAATTATG
5768392 TTATATTTTTA-CA
1 TTAT-TTTTTACCA
5768405 TTATTTTTTACCA
1 TTATTTTTTACCA
5768418 TTATTTTTT
1 TTATTTTTT
5768427 TAATATTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.23, C:0.09, G:0.00, T:0.69
Consensus pattern (13 bp):
TTATTTTTTACCA
Found at i:5769104 original size:29 final size:29
Alignment explanation
Indices: 5769062--5769118 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
5769052 AGTGTTGGCC
5769062 GTAGGTCGCCATGCACTCCAGGCGACCTT
1 GTAGGTCGCCATGCACTCCAGGCGACCTT
*
5769091 GTAGGTCGCCATGCACTCCGGGCGACCT
1 GTAGGTCGCCATGCACTCCAGGCGACCT
5769119 ACCCTTGCTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.16, C:0.35, G:0.30, T:0.19
Consensus pattern (29 bp):
GTAGGTCGCCATGCACTCCAGGCGACCTT
Found at i:5769228 original size:29 final size:29
Alignment explanation
Indices: 5769181--5769261 Score: 117
Period size: 29 Copynumber: 2.8 Consensus size: 29
5769171 AACACATAGG
5769181 TCGCCATGCCCTCCGGGCGACCTTGTAGA
1 TCGCCATGCCCTCCGGGCGACCTTGTAGA
* * *
5769210 TCGTCATGCCCTCCAGGCGACCTTGTAGG
1 TCGCCATGCCCTCCGGGCGACCTTGTAGA
* *
5769239 TCGCCATGCACTCCGGGCAACCT
1 TCGCCATGCCCTCCGGGCGACCT
5769262 ACCCTCGCTC
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.15, C:0.38, G:0.26, T:0.21
Consensus pattern (29 bp):
TCGCCATGCCCTCCGGGCGACCTTGTAGA
Found at i:5769306 original size:33 final size:33
Alignment explanation
Indices: 5769269--5769351 Score: 96
Period size: 33 Copynumber: 2.5 Consensus size: 33
5769259 CCTACCCTCG
* *
5769269 CTCGGCTT-CCCTCGGATTCCCTCGCATAGCTCA
1 CTCGG-TTGCCCTCAGATGCCCTCGCATAGCTCA
*
5769302 CTCGGTTGCCCTCAGATGCCCTCGCATAGCTCG
1 CTCGGTTGCCCTCAGATGCCCTCGCATAGCTCA
* * *
5769335 TTCGGATGGCCTCAGAT
1 CTCGGTTGCCCTCAGAT
5769352 ACCCAACGTG
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
32 2 0.05
33 41 0.95
ACGTcount: A:0.13, C:0.37, G:0.23, T:0.27
Consensus pattern (33 bp):
CTCGGTTGCCCTCAGATGCCCTCGCATAGCTCA
Found at i:5771525 original size:123 final size:121
Alignment explanation
Indices: 5771239--5771509 Score: 273
Period size: 122 Copynumber: 2.2 Consensus size: 121
5771229 TTAGAAATCT
* * * * * *
5771239 AAAATCTAAATAGGGGAAAGTGTGAGG-GTTTTCATTAAATTTTA-CTATTTAATTAAAACAAAA
1 AAAATCTAAATAGGAGAAACTATG-GGAGATTTCATGAAATTTCATC-ATTTAATTAAAACAAAA
* * * *
5771302 GTATGAGGGTGGGTAGTGTAATTTAGCGATGTATTTTGAAACATAAACATAGATTGTCT
64 GTATGAGGGTGGGTAGTGTAATTTAGCCATGTATTAT-AAACACAAACATAGATTGTCC
* *
5771361 AAAATCTAAATAGGAGAAACTATGGGAGATTTCATGAAATTTCATCATTTAAATTAAAATACAAG
1 AAAATCTAAATAGGAGAAACTATGGGAGATTTCATGAAATTTCATCATTT-AATTAAAACAAAAG
** * *
5771426 TATG-GGGTGGGTAGTGTAATTTAGCCATGCCTATTAT-AACACGCACATGCGTTTGTCC
65 TATGAGGGTGGGTAGTGTAATTTAGCCATG--TATTATAAACACAAACAT-AGATTGTCC
* *
5771484 AAAATTTAAAT-GTGAGAAATTATGGG
1 AAAATCTAAATAG-GAGAAACTATGGG
5771510 GGTTTCTATG
Statistics
Matches: 124, Mismatches: 18, Indels: 13
0.80 0.12 0.08
Matches are distributed among these distances:
121 2 0.02
122 72 0.58
123 45 0.36
124 5 0.04
ACGTcount: A:0.38, C:0.09, G:0.21, T:0.32
Consensus pattern (121 bp):
AAAATCTAAATAGGAGAAACTATGGGAGATTTCATGAAATTTCATCATTTAATTAAAACAAAAGT
ATGAGGGTGGGTAGTGTAATTTAGCCATGTATTATAAACACAAACATAGATTGTCC
Found at i:5774199 original size:5 final size:5
Alignment explanation
Indices: 5774185--5774382 Score: 109
Period size: 5 Copynumber: 39.6 Consensus size: 5
5774175 AACATTATTA
*
5774185 ATAA- ATAAT ATAAT ATAAT ATAAT A-ACT ATAAT AT-AT ATAAT ACTAA-
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT A-TAAT
* * *
5774232 ATAAT ATACT ATAAT AT-A- GTAAT ATAA- ATACT ATAATAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT AT-A-AT ATAAT ATAAT
*
5774281 ACTGTAAT AT-AT ATACT AT-A- ATAAT ATAAT AT-AT AT-AT ATATAT
1 A---TAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATA-AT
* *
5774325 ATATAT ATACACT ATATT GT-AT ACT-AT ATTAAT ATAAT ATATACT ATAAT
1 ATA-AT ATA-A-T ATAAT ATAAT A-TAAT A-TAAT ATAAT ATA-A-T ATAAT
5774375 ATAAT ATA
1 ATAAT ATA
5774383 TACTATACAA
Statistics
Matches: 155, Mismatches: 16, Indels: 45
0.72 0.07 0.21
Matches are distributed among these distances:
3 3 0.02
4 33 0.21
5 81 0.52
6 22 0.14
7 11 0.07
8 5 0.03
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (5 bp):
ATAAT
Found at i:5774223 original size:2 final size:2
Alignment explanation
Indices: 5774192--5774389 Score: 98
Period size: 2 Copynumber: 104.5 Consensus size: 2
5774182 TTAATAAATA
5774192 AT AT A- AT AT A- AT AT A- AT A- ACT AT A- AT AT AT AT A- AT ACT
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT A-T
* *
5774230 AA AT A- AT AT ACT AT A- AT AT AGT A- AT AT AA AT ACT AT A- AT
1 AT AT AT AT AT A-T AT AT AT AT A-T AT AT AT AT AT A-T AT AT AT
*
5774269 AT AT A- AT AT A- AT ACT GT A- AT AT AT AT ACT AT A- AT A- AT AT
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT A-T AT AT AT AT AT AT
* *
5774308 A- AT AT AT AT AT AT AT AT AT AT AT AT AC ACT AT AT -T GT AT ACT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT A-T
5774350 AT AT -T A- AT AT A- AT AT AT ACT AT A- AT AT A- AT AT AT ACT AT
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT A-T AT
5774389 A
1 A
5774390 CAATAAAATA
Statistics
Matches: 154, Mismatches: 9, Indels: 66
0.67 0.04 0.29
Matches are distributed among these distances:
1 22 0.14
2 113 0.73
3 19 0.12
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.41
Consensus pattern (2 bp):
AT
Found at i:5774389 original size:22 final size:21
Alignment explanation
Indices: 5774189--5774395 Score: 152
Period size: 22 Copynumber: 10.0 Consensus size: 21
5774179 TTATTAATAA
*
5774189 ATAATATA-ATATAATATAAT
1 ATAATATATATATACTATAAT
*
5774209 A-ACTATA-ATATA-TATAAT
1 ATAATATATATATACTATAAT
5774227 ACTAA-ATA-ATATACTATAAT
1 A-TAATATATATATACTATAAT
* *
5774247 ATAGTAATATAAATACTATAAT
1 ATAAT-ATATATATACTATAAT
*
5774269 AT-ATA-ATATAATACTGTAAT
1 ATAATATATAT-ATACTATAAT
*
5774289 AT-ATATACTATAATAATATAAT
1 ATAATATA-TAT-ATACTATAAT
5774311 AT-ATATATATATA-TATATAT
1 ATAATATATATATACTATA-AT
*
5774331 ATACACTATATTGTATACTAT-AT
1 ATA-A-TATA-TATATACTATAAT
5774354 -TAATATAATATATACTATAAT
1 ATAATAT-ATATATACTATAAT
*
5774375 ATAATATATACTATACAATAA
1 ATAATATATA-TATACTATAA
5774396 AATATACAAC
Statistics
Matches: 156, Mismatches: 12, Indels: 36
0.76 0.06 0.18
Matches are distributed among these distances:
18 7 0.04
19 27 0.17
20 43 0.28
21 15 0.10
22 50 0.32
23 6 0.04
24 5 0.03
25 3 0.02
ACGTcount: A:0.53, C:0.06, G:0.01, T:0.40
Consensus pattern (21 bp):
ATAATATATATATACTATAAT
Found at i:5779549 original size:18 final size:19
Alignment explanation
Indices: 5779515--5779551 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
5779505 AAATATTAGT
5779515 TTTTAAAATTATTAATTAA
1 TTTTAAAATTATTAATTAA
5779534 TTTTAAAATT-TTAATTAA
1 TTTTAAAATTATTAATTAA
5779552 ATAATTATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TTTTAAAATTATTAATTAA
Found at i:5800221 original size:39 final size:40
Alignment explanation
Indices: 5800178--5800258 Score: 137
Period size: 40 Copynumber: 2.0 Consensus size: 40
5800168 AAATACTAAT
*
5800178 TAATAATTTAGTA-TTTTTTGTTGTTTATTAAAAAATTAA
1 TAATAATTTAGTATTTTTTTATTGTTTATTAAAAAATTAA
*
5800217 TAATAATTTAGTATTTTTTTATTGTTTATTAGAAAATTAA
1 TAATAATTTAGTATTTTTTTATTGTTTATTAAAAAATTAA
5800257 TA
1 TA
5800259 GATTAACAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 13 0.33
40 26 0.67
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.54
Consensus pattern (40 bp):
TAATAATTTAGTATTTTTTTATTGTTTATTAAAAAATTAA
Found at i:5801638 original size:2 final size:2
Alignment explanation
Indices: 5801631--5801655 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5801621 TACGACCATC
5801631 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
5801656 GTAATCCAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5803482 original size:21 final size:20
Alignment explanation
Indices: 5803434--5803512 Score: 113
Period size: 21 Copynumber: 3.9 Consensus size: 20
5803424 AACCTAGGTT
5803434 TCAAATTCGCAACGCGAAAG
1 TCAAATTCGCAACGCGAAAG
* *
5803454 TCAAATTCACAACGTGAAAG
1 TCAAATTCGCAACGCGAAAG
*
5803474 TCGAAATTCGCAACGCGATAG
1 TC-AAATTCGCAACGCGAAAG
5803495 TCAAAATTCGCAACGCGA
1 TC-AAATTCGCAACGCGA
5803513 TACTCCAAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
20 20 0.38
21 32 0.62
ACGTcount: A:0.39, C:0.24, G:0.19, T:0.18
Consensus pattern (20 bp):
TCAAATTCGCAACGCGAAAG
Found at i:5803526 original size:21 final size:21
Alignment explanation
Indices: 5803436--5803528 Score: 91
Period size: 21 Copynumber: 4.5 Consensus size: 21
5803426 CCTAGGTTTC
* *
5803436 AAATTCGCAACGCGAAAGTC-
1 AAATTCGCAACGCGATACTCA
* * * * *
5803456 AAATTCACAACGTGAAAGTCG
1 AAATTCGCAACGCGATACTCA
*
5803477 AAATTCGCAACGCGATAGTCA
1 AAATTCGCAACGCGATACTCA
5803498 AAATTCGCAACGCGATACTCCA
1 AAATTCGCAACGCGATACT-CA
5803520 AAA-TCGCAA
1 AAATTCGCAA
5803529 TGCAATTGTT
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
20 18 0.28
21 41 0.64
22 5 0.08
ACGTcount: A:0.41, C:0.25, G:0.17, T:0.17
Consensus pattern (21 bp):
AAATTCGCAACGCGATACTCA
Found at i:5803527 original size:42 final size:41
Alignment explanation
Indices: 5803435--5803528 Score: 116
Period size: 42 Copynumber: 2.3 Consensus size: 41
5803425 ACCTAGGTTT
* *
5803435 CAAATTCGCAACGCGAAAGTCAAATTCACAACGTGAAAGTC
1 CAAATTCGCAACGCGAAAGTCAAATTCACAACGCGAAACTC
* * * *
5803476 GAAATTCGCAACGCGATAGTCAAAATTCGCAACGCGATACTC
1 CAAATTCGCAACGCGAAAGTC-AAATTCACAACGCGAAACTC
*
5803518 CAAAATCGCAA
1 CAAATTCGCAA
5803529 TGCAATTGTT
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
41 19 0.43
42 25 0.57
ACGTcount: A:0.40, C:0.26, G:0.17, T:0.17
Consensus pattern (41 bp):
CAAATTCGCAACGCGAAAGTCAAATTCACAACGCGAAACTC
Found at i:5804476 original size:41 final size:41
Alignment explanation
Indices: 5804431--5804534 Score: 140
Period size: 40 Copynumber: 2.6 Consensus size: 41
5804421 ATGCATTGTG
*
5804431 ATTTTGGAGTATCGAGTTGCGAATCTT-AAATCGCGTTGCGA
1 ATTTT-GAGTATCGCGTTGCGAATCTTAAAATCGCGTTGCGA
* *
5804472 ATTTTGACTGTCGCGTTGCGAATCTTAAAATCGCGTTGCGA
1 ATTTTGAGTATCGCGTTGCGAATCTTAAAATCGCGTTGCGA
* *
5804513 AATTTGAG-ATCGCGTTACGAAT
1 ATTTTGAGTATCGCGTTGCGAAT
5804535 TTGTTGGTCA
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
40 30 0.55
41 25 0.45
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (41 bp):
ATTTTGAGTATCGCGTTGCGAATCTTAAAATCGCGTTGCGA
Found at i:5804524 original size:20 final size:19
Alignment explanation
Indices: 5804441--5804537 Score: 81
Period size: 20 Copynumber: 4.9 Consensus size: 19
5804431 ATTTTGGAGT
* *
5804441 ATCGAGTTGCGAATCTT-AA
1 ATCGCGTTGCGAAT-TTGAG
5804460 ATCGCGTTGCGAATTTTGACTG
1 ATCGCGTTGCGAA-TTTGA--G
* *
5804482 -TCGCGTTGCGAATCTTAAA
1 ATCGCGTTGCGAAT-TTGAG
5804501 ATCGCGTTGCGAAATTTGAG
1 ATCGCGTTGCG-AATTTGAG
*
5804521 ATCGCGTTACGAATTTG
1 ATCGCGTTGCGAATTTG
5804538 TTGGTCATTT
Statistics
Matches: 64, Mismatches: 7, Indels: 14
0.75 0.08 0.16
Matches are distributed among these distances:
19 20 0.31
20 26 0.41
21 18 0.28
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.33
Consensus pattern (19 bp):
ATCGCGTTGCGAATTTGAG
Found at i:5805568 original size:21 final size:21
Alignment explanation
Indices: 5805542--5805584 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
5805532 GACCGCGTAG
*
5805542 AAATGTCCCGAAGGACCACAT
1 AAATGTCCAGAAGGACCACAT
*
5805563 AAATGTCCAGAAGGACCGCAT
1 AAATGTCCAGAAGGACCACAT
5805584 A
1 A
5805585 TAACACATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.40, C:0.26, G:0.21, T:0.14
Consensus pattern (21 bp):
AAATGTCCAGAAGGACCACAT
Found at i:5805692 original size:23 final size:21
Alignment explanation
Indices: 5805623--5805697 Score: 89
Period size: 21 Copynumber: 3.6 Consensus size: 21
5805613 TTAAATATCA
* *
5805623 CATATATATTCC-AAAAGACCA
1 CATATATGTTCCGAAAA-ACCC
*
5805644 AATATATGTTCCGAAAAACCC
1 CATATATGTTCCGAAAAACCC
*
5805665 CATATATGTTCCGAAGAACCC
1 CATATATGTTCCGAAAAACCC
*
5805686 CATATATATTCC
1 CATATATGTTCC
5805698 AAAGGATTAC
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
21 43 0.91
22 4 0.09
ACGTcount: A:0.40, C:0.25, G:0.08, T:0.27
Consensus pattern (21 bp):
CATATATGTTCCGAAAAACCC
Found at i:5807599 original size:33 final size:33
Alignment explanation
Indices: 5807562--5807666 Score: 99
Period size: 33 Copynumber: 3.2 Consensus size: 33
5807552 GGTAAGAAAT
* * * *
5807562 TTATTTTTATGTTAGTAT-TTTTTTAAATAGTTA
1 TTATTTTTATATTAATATATTATGTAAATA-TTA
5807595 TTATTTTTATATTAATATATTATGTAAATATTA
1 TTATTTTTATATTAATATATTATGTAAATATTA
* * *
5807628 TT-TTTTTAT-TAAAATAATATTATATAATTATTA
1 TTATTTTTATAT-TAAT-ATATTATGTAAATATTA
5807661 TTATTT
1 TTATTT
5807667 AGAATTATTA
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
31 1 0.02
32 10 0.16
33 38 0.62
34 12 0.20
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (33 bp):
TTATTTTTATATTAATATATTATGTAAATATTA
Found at i:5809430 original size:21 final size:21
Alignment explanation
Indices: 5809387--5809431 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
5809377 GCAAGGGTAC
* *
5809387 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
5809408 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
5809429 ATG
1 ATG
5809432 TCATCTCCGC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.38, G:0.13, T:0.24
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:5809464 original size:21 final size:21
Alignment explanation
Indices: 5809438--5809531 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
5809428 TATGTCATCT
* *
5809438 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATGCCTAGC
*
5809459 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATGCCTAGC
5809480 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
5809501 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
5809522 CCGCAGGGTT
1 CCGCAGGGTT
5809532 TTGTACCATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 2 0.03
21 65 0.94
22 2 0.03
ACGTcount: A:0.18, C:0.35, G:0.27, T:0.20
Consensus pattern (21 bp):
CCGCAGGGTTACATGCCTAGC
Found at i:5810103 original size:33 final size:34
Alignment explanation
Indices: 5810053--5810149 Score: 135
Period size: 33 Copynumber: 2.9 Consensus size: 34
5810043 TAAATGTTTT
*
5810053 TAAAATACAAATTATATTATTCGAAATTTAAA-A
1 TAAAATAAAAATTATATTATTCGAAATTTAAATA
* *
5810086 TAAAATAAAAATAATATTATTC-AAATTTAAATT
1 TAAAATAAAAATTATATTATTCGAAATTTAAATA
* *
5810119 TAAAATATAAATTATAGTATTCGAAATTTAA
1 TAAAATAAAAATTATATTATTCGAAATTTAA
5810150 CATTAAATTT
Statistics
Matches: 56, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
32 9 0.16
33 39 0.70
34 8 0.14
ACGTcount: A:0.55, C:0.04, G:0.03, T:0.38
Consensus pattern (34 bp):
TAAAATAAAAATTATATTATTCGAAATTTAAATA
Found at i:5810788 original size:128 final size:128
Alignment explanation
Indices: 5810550--5811181 Score: 1210
Period size: 128 Copynumber: 4.9 Consensus size: 128
5810540 TTACCTGATT
5810550 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *
5810615 TGATGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTTATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
5810678 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *
5810743 TGACGAAATAATGAAAGGCGCGCCCCCGGGAACGCACCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
*
5810806 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATTATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
5810871 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
5810934 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
5810999 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
5811062 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
5811127 TGACGAAATAATGGAAGGTGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAA
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAA
5811182 CCGATTATAG
Statistics
Matches: 495, Mismatches: 9, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
128 495 1.00
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.23
Consensus pattern (128 bp):
TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
Found at i:5811262 original size:8 final size:8
Alignment explanation
Indices: 5811249--5811289 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
5811239 TCACAATCTT
5811249 TCAAATTC
1 TCAAATTC
5811257 TCAAATTC
1 TCAAATTC
* *
5811265 CCAAACTC
1 TCAAATTC
5811273 T-AAATTC
1 TCAAATTC
5811280 TCAAATTC
1 TCAAATTC
5811288 TC
1 TC
5811290 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:5827340 original size:19 final size:19
Alignment explanation
Indices: 5827316--5827362 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
5827306 ATATAATATA
*
5827316 TATTAT-TAATGATATATGT
1 TATTATCTAATGA-AAATGT
*
5827335 TATTATCTAATTAAAATGT
1 TATTATCTAATGAAAATGT
5827354 TATTATCTA
1 TATTATCTA
5827363 TATTTTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 20 0.80
20 5 0.20
ACGTcount: A:0.38, C:0.04, G:0.06, T:0.51
Consensus pattern (19 bp):
TATTATCTAATGAAAATGT
Found at i:5828298 original size:23 final size:23
Alignment explanation
Indices: 5828260--5828310 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
5828250 GATTACTTTA
* * * *
5828260 TCTTTGTGACATGTTTATTTTTG
1 TCTTTGTAACACGTTTATCTCTG
5828283 TCTTTGTAACACGTTTATCTCTG
1 TCTTTGTAACACGTTTATCTCTG
5828306 TCTTT
1 TCTTT
5828311 TAGTAATTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.14, C:0.16, G:0.14, T:0.57
Consensus pattern (23 bp):
TCTTTGTAACACGTTTATCTCTG
Found at i:5829822 original size:20 final size:20
Alignment explanation
Indices: 5829728--5830096 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
5829718 GATTTTCCAT
* ** *
5829728 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
5829748 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
5829768 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
5829788 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
5829808 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
5829828 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
5829848 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
5829868 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
5829888 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
5829908 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
5829928 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
5829948 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
5829968 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
5829988 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
5830008 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
5830028 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
5830048 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
5830068 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
5830088 AATCACAAC
1 AATCGCAAC
5830097 ACTGAAATTT
Statistics
Matches: 305, Mismatches: 36, Indels: 16
0.85 0.10 0.04
Matches are distributed among these distances:
19 3 0.01
20 299 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:5830809 original size:24 final size:24
Alignment explanation
Indices: 5830770--5830816 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
5830760 AAATTTGGTC
5830770 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
5830794 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
5830817 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:5831007 original size:12 final size:12
Alignment explanation
Indices: 5830990--5831014 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5830980 ATATAATCCT
5830990 GAAGAAGAAAAA
1 GAAGAAGAAAAA
5831002 GAAGAAGAAAAA
1 GAAGAAGAAAAA
5831014 G
1 G
5831015 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:5833343 original size:19 final size:19
Alignment explanation
Indices: 5833321--5833627 Score: 351
Period size: 19 Copynumber: 17.4 Consensus size: 19
5833311 CGGAAAATAC
*
5833321 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
5833340 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
5833354 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
5833374 AATCGCAA--CG---TGAG
1 AATCGCAATGCGAAATGAA
5833388 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
5833407 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
5833426 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
5833440 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
5833459 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
5833478 AATCG-AA--CAGACAT---
1 AATCGCAATGC-GAAATGAA
*
5833492 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
5833511 AATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAA
5833530 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
5833549 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
5833568 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
5833582 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
5833601 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
5833620 AATCGCAA
1 AATCGCAA
5833628 CGAGATAATC
Statistics
Matches: 249, Mismatches: 11, Indels: 56
0.79 0.03 0.18
Matches are distributed among these distances:
14 46 0.18
15 3 0.01
16 16 0.06
17 15 0.06
18 4 0.02
19 152 0.61
20 13 0.05
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:5833441 original size:52 final size:52
Alignment explanation
Indices: 5833349--5833627 Score: 347
Period size: 52 Copynumber: 5.2 Consensus size: 52
5833339 AAATCCCAAC
* *
5833349 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGTGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAAAATCGCAATGCGAA
*
5833402 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAA
5833454 ATGAAAATCGCAATGCGAAATGAAAATCG-AAC-AGACATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGA-A-AATCGCAATGCGAA
* *
5833506 ATTAAAATCGCAATACGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAAAATCGCAATGCGAA
5833563 ATGAAAATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAAAATCGCAATGCGAA
5833615 ATGAAAATCGCAA
1 ATGAAAATCGCAA
5833628 CGAGATAATC
Statistics
Matches: 212, Mismatches: 5, Indels: 19
0.90 0.02 0.08
Matches are distributed among these distances:
50 3 0.01
51 3 0.01
52 151 0.71
53 18 0.08
54 1 0.00
55 6 0.03
57 26 0.12
58 2 0.01
59 2 0.01
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAA
Found at i:5833472 original size:71 final size:71
Alignment explanation
Indices: 5833388--5833627 Score: 348
Period size: 71 Copynumber: 3.4 Consensus size: 71
5833378 GCAACGTGAG
*
5833388 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
5833453 AATGAA
66 AATGAA
* *
5833459 AATCGCAATGCGAAATGAAAATCG-AA--CAGACAT---AATCGCAATGCGAAATTAAAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAA--CG-AA--AGAATCGCA
*
5833518 ATACGAAATGAA
60 ATGCGAAATGAA
5833530 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
5833595 AATGAA
66 AATGAA
5833601 AATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAA
5833628 CGAGATAATC
Statistics
Matches: 150, Mismatches: 7, Indels: 24
0.83 0.04 0.13
Matches are distributed among these distances:
66 8 0.05
68 3 0.02
69 5 0.03
70 2 0.01
71 113 0.75
72 2 0.01
73 6 0.04
74 3 0.02
76 8 0.05
ACGTcount: A:0.48, C:0.17, G:0.20, T:0.15
Consensus pattern (71 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
AATGAA
Done.