Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006071.1 Hibiscus syriacus cultivar Beakdansim tig00014370_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: 851632
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
File 1 of 4
Found at i:6363 original size:14 final size:15
Alignment explanation
Indices: 6346--6375 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
6336 CTTTCTTTCT
6346 TTTTTTTAT-TTTTA
1 TTTTTTTATATTTTA
6360 TTTTTTTATATTTTA
1 TTTTTTTATATTTTA
6375 T
1 T
6376 GTCAATTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTTTTATATTTTA
Found at i:11799 original size:10 final size:9
Alignment explanation
Indices: 11774--11828 Score: 56
Period size: 10 Copynumber: 5.8 Consensus size: 9
11764 GGCTGCTGGA
11774 AACCGGTTT
1 AACCGGTTT
11783 AACCGGTTCT
1 AACCGGTT-T
*
11793 GACCGGTTT
1 AACCGGTTT
* *
11802 CGACCGGTTCA
1 -AACCGGTT-T
11813 AACCGGTTT
1 AACCGGTTT
11822 AACCGGT
1 AACCGGT
11829 CTGACCCGAC
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
9 16 0.41
10 23 0.59
ACGTcount: A:0.20, C:0.27, G:0.25, T:0.27
Consensus pattern (9 bp):
AACCGGTTT
Found at i:11843 original size:9 final size:9
Alignment explanation
Indices: 11831--11858 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
11821 TAACCGGTCT
11831 GACCCGACC
1 GACCCGACC
11840 GACCCGACC
1 GACCCGACC
11849 GACCCGACC
1 GACCCGACC
11858 G
1 G
11859 TTGACCCGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.21, C:0.54, G:0.25, T:0.00
Consensus pattern (9 bp):
GACCCGACC
Found at i:11869 original size:17 final size:17
Alignment explanation
Indices: 11847--11879 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
11837 ACCGACCCGA
11847 CCGACCCGACCGTTGAC
1 CCGACCCGACCGTTGAC
11864 CCGACCCGACCGTTGA
1 CCGACCCGACCGTTGA
11880 TCGTTGATCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.45, G:0.24, T:0.12
Consensus pattern (17 bp):
CCGACCCGACCGTTGAC
Found at i:19128 original size:29 final size:30
Alignment explanation
Indices: 19065--19139 Score: 109
Period size: 29 Copynumber: 2.5 Consensus size: 30
19055 GGCTGCTGGA
*
19065 AACCGGTTTAACCGGTTTTCAACTGGTTCTG
1 AACCGGTTTGACCGG-TTTCAACTGGTTCTG
*
19096 -ACCGGTTTGACCGGTTTCGACTGGTTC-G
1 AACCGGTTTGACCGGTTTCAACTGGTTCTG
19124 AACCGGTTTGACCGGT
1 AACCGGTTTGACCGGT
19140 CTGACCCGAC
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
28 1 0.02
29 27 0.66
30 13 0.32
ACGTcount: A:0.16, C:0.24, G:0.28, T:0.32
Consensus pattern (30 bp):
AACCGGTTTGACCGGTTTCAACTGGTTCTG
Found at i:19144 original size:9 final size:9
Alignment explanation
Indices: 19066--19145 Score: 61
Period size: 9 Copynumber: 8.3 Consensus size: 9
19056 GCTGCTGGAA
*
19066 ACCGGTTTA
1 ACCGGTTTG
*
19075 ACCGGTTTTCA
1 ACCGG-TTT-G
*
19086 ACTGGTTCTG
1 ACCGGTT-TG
19096 ACCGGTTTG
1 ACCGGTTTG
19105 ACCGGTTTCG
1 ACCGGTTT-G
* *
19115 ACTGGTTCG
1 ACCGGTTTG
19124 AACCGGTTTG
1 -ACCGGTTTG
*
19134 ACCGGTCTG
1 ACCGGTTTG
19143 ACC
1 ACC
19146 CGACCGATCG
Statistics
Matches: 58, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
9 27 0.47
10 25 0.43
11 6 0.10
ACGTcount: A:0.15, C:0.26, G:0.28, T:0.31
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:19200 original size:22 final size:22
Alignment explanation
Indices: 19142--19201 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
19132 TGACCGGTCT
* *
19142 GACCCGACCGATCGACCCGACCC
1 GACCCGACCG-TTGACCCGACCA
* *
19165 GACCCGAACTTTGACCCGACCA
1 GACCCGACCGTTGACCCGACCA
19187 GACCCGACCGTTGAC
1 GACCCGACCGTTGAC
19202 AGTTGACCGT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
22 23 0.74
23 8 0.26
ACGTcount: A:0.23, C:0.45, G:0.22, T:0.10
Consensus pattern (22 bp):
GACCCGACCGTTGACCCGACCA
Found at i:27259 original size:18 final size:18
Alignment explanation
Indices: 27209--27260 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
27199 AATGATATTT
*
27209 AAATATCTTTATTTTTAAA
1 AAATATATTT-TTTTTAAA
* *
27228 AAATGGTA-TATTTTTAAA
1 AAAT-ATATTTTTTTTAAA
27246 AAATATATTTTTTTT
1 AAATATATTTTTTTT
27261 CTAAAATAGT
Statistics
Matches: 26, Mismatches: 5, Indels: 5
0.72 0.14 0.14
Matches are distributed among these distances:
17 2 0.08
18 18 0.69
19 5 0.19
20 1 0.04
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (18 bp):
AAATATATTTTTTTTAAA
Found at i:31718 original size:16 final size:16
Alignment explanation
Indices: 31686--31718 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
31676 ATTTGATCGG
31686 AAAAAAAAAAGACGAA
1 AAAAAAAAAAGACGAA
31702 AAAAATAAAAAGA-GAA
1 AAAAA-AAAAAGACGAA
31718 A
1 A
31719 TCAAGGAAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.82, C:0.03, G:0.12, T:0.03
Consensus pattern (16 bp):
AAAAAAAAAAGACGAA
Found at i:36418 original size:12 final size:12
Alignment explanation
Indices: 36384--36426 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 12
36374 TATTTTAACC
*
36384 GGTTAAAAAATC
1 GGTTAAAAAATT
36396 GGTTTGAAAAAAATT
1 GG-TT--AAAAAATT
36411 GGTTAAAAAATT
1 GGTTAAAAAATT
36423 GGTT
1 GGTT
36427 TTTATCTGGG
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
12 14 0.52
13 2 0.07
14 2 0.07
15 9 0.33
ACGTcount: A:0.44, C:0.02, G:0.21, T:0.33
Consensus pattern (12 bp):
GGTTAAAAAATT
Found at i:38717 original size:21 final size:21
Alignment explanation
Indices: 38693--38734 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
38683 AGTTTATTTT
*
38693 TAAATTTTATTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
*
38714 TAAACTTTGTTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
38735 AACTTGAAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.31, C:0.12, G:0.07, T:0.50
Consensus pattern (21 bp):
TAAACTTTATTTCAATTATCG
Found at i:38782 original size:33 final size:33
Alignment explanation
Indices: 38729--38827 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
38719 TTTGTTTCAA
38729 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
38761 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
38794 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
38827 T
1 T
38828 ATGTTGAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:42878 original size:23 final size:23
Alignment explanation
Indices: 42852--42921 Score: 58
Period size: 23 Copynumber: 3.2 Consensus size: 23
42842 CACTTTTTAA
42852 TTGAAGAACAAAAAGAATAATCC
1 TTGAAGAACAAAAAGAATAATCC
** * ***
42875 TTGAATTAC-CACTTAATAA---
1 TTGAAGAACAAAAAGAATAATCC
42894 TTGAAGAACAAAAAGAATAATCC
1 TTGAAGAACAAAAAGAATAATCC
42917 TTGAA
1 TTGAA
42922 TGACCACTTA
Statistics
Matches: 31, Mismatches: 12, Indels: 8
0.61 0.24 0.16
Matches are distributed among these distances:
19 7 0.23
20 6 0.19
22 6 0.19
23 12 0.39
ACGTcount: A:0.51, C:0.13, G:0.11, T:0.24
Consensus pattern (23 bp):
TTGAAGAACAAAAAGAATAATCC
Found at i:42901 original size:42 final size:42
Alignment explanation
Indices: 42849--42960 Score: 206
Period size: 42 Copynumber: 2.7 Consensus size: 42
42839 CATCACTTTT
*
42849 TAATTGAAGAACAAAAAGAATAATCCTTGAATTACCACTTAA
1 TAATTGAAGAACAAAAAGAATAATCCTTGAATGACCACTTAA
*
42891 TAATTGAAGAACAAAAAGAATAATCCTTGAATGACCACTTAT
1 TAATTGAAGAACAAAAAGAATAATCCTTGAATGACCACTTAA
42933 TAATTGAAGAACAAAAAGAATAATCCTT
1 TAATTGAAGAACAAAAAGAATAATCCTT
42961 TAACGACTGA
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 68 1.00
ACGTcount: A:0.50, C:0.13, G:0.11, T:0.26
Consensus pattern (42 bp):
TAATTGAAGAACAAAAAGAATAATCCTTGAATGACCACTTAA
Found at i:43322 original size:157 final size:157
Alignment explanation
Indices: 43035--43323 Score: 515
Period size: 157 Copynumber: 1.8 Consensus size: 157
43025 ATAAAGAGGG
* *
43035 TTATTCCCAGAAAATGTATTTTGGCAAATGGATGGGAACGTCAAAATGGGTTGTAAAGTTTTGGA
1 TTATTCCCAGAAAATGTATTTTGGCAAATGGATGGGAACATCAAAATGGGTTGTAAAGTTTTGAA
* * *
43100 ATTTACCACGCAGAAACTTGATGCCAGGTCTTGTCTGTTACCACTTTCATGGCTGCCCTATGAGT
66 ATTTACCACACAGAAACTTGATGCCAGGTCTTGTCTGTTACCACTTTCATGGATGCCCTAAGAGT
43165 AAATGGATGGGAATTTACCATTTTCTT
131 AAATGGATGGGAATTTACCATTTTCTT
*
43192 TTATTCCCAGAAAATGTATTTTGGCAAATGGATGGGAACATCAACATGGGTTGTAAAGTTTTGAA
1 TTATTCCCAGAAAATGTATTTTGGCAAATGGATGGGAACATCAAAATGGGTTGTAAAGTTTTGAA
*
43257 ATTTACCACACAGAAACTTGATGCCAGGTCTTGTCTGTTACCATTTTCATGGATGCCCTAAGAGT
66 ATTTACCACACAGAAACTTGATGCCAGGTCTTGTCTGTTACCACTTTCATGGATGCCCTAAGAGT
43322 AA
131 AA
43324 TCGTTTACTC
Statistics
Matches: 125, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
157 125 1.00
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (157 bp):
TTATTCCCAGAAAATGTATTTTGGCAAATGGATGGGAACATCAAAATGGGTTGTAAAGTTTTGAA
ATTTACCACACAGAAACTTGATGCCAGGTCTTGTCTGTTACCACTTTCATGGATGCCCTAAGAGT
AAATGGATGGGAATTTACCATTTTCTT
Found at i:45220 original size:2 final size:2
Alignment explanation
Indices: 45213--45239 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
45203 TTGACATTAA
45213 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 A
45240 CCAGCTGTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:50719 original size:18 final size:18
Alignment explanation
Indices: 50696--50736 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
50686 AAAAGGAGGG
50696 TGAGTTCTAAGCATGTTA
1 TGAGTTCTAAGCATGTTA
*
50714 TGAGTTCTACGCATGTTA
1 TGAGTTCTAAGCATGTTA
50732 T-AGTT
1 TGAGTT
50737 AGGTCCTGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.24, C:0.12, G:0.22, T:0.41
Consensus pattern (18 bp):
TGAGTTCTAAGCATGTTA
Found at i:54717 original size:16 final size:16
Alignment explanation
Indices: 54675--54717 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
54665 TGGATAATAG
*
54675 AAATTCATAATATTGT
1 AAATTTATAATATTGT
* *
54691 AATTTTTTAATATTGT
1 AAATTTATAATATTGT
54707 AAATTTATAAT
1 AAATTTATAAT
54718 TCTTTTAATA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (16 bp):
AAATTTATAATATTGT
Found at i:55730 original size:13 final size:13
Alignment explanation
Indices: 55712--55744 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
55702 TTTTCCCTTT
*
55712 TTTTCCTTGTTTA
1 TTTTCCTTATTTA
55725 TTTTCCTTATTTA
1 TTTTCCTTATTTA
55738 TTTTCCT
1 TTTTCCT
55745 ACAAGTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.09, C:0.18, G:0.03, T:0.70
Consensus pattern (13 bp):
TTTTCCTTATTTA
Found at i:56437 original size:20 final size:20
Alignment explanation
Indices: 56394--56437 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
56384 TTAGTTAATT
**
56394 TTATTAAAAAAATAATAGTT
1 TTATTAAAAAAATAATAGAA
56414 TTATT-AAAAAATAACTAGAA
1 TTATTAAAAAAATAA-TAGAA
56434 TTAT
1 TTAT
56438 AATGAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.39
Consensus pattern (20 bp):
TTATTAAAAAAATAATAGAA
Found at i:58583 original size:16 final size:17
Alignment explanation
Indices: 58562--58593 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
58552 AACTTAAAAC
58562 TTTAAAAATTT-AGAGG
1 TTTAAAAATTTGAGAGG
58578 TTTAAAAATTTGAGAG
1 TTTAAAAATTTGAGAG
58594 ACTTAATGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.44, C:0.00, G:0.19, T:0.38
Consensus pattern (17 bp):
TTTAAAAATTTGAGAGG
Found at i:58731 original size:30 final size:28
Alignment explanation
Indices: 58667--58743 Score: 82
Period size: 30 Copynumber: 2.7 Consensus size: 28
58657 ATTTGATATA
* *
58667 AATTTCTAAAAATTTGGGGTTAGATTAT
1 AATTTTTAAAAATTTGGGGTTAAATTAT
**
58695 TTTTTTTAAAAATTTGAGGGTCTAAATTAT
1 AATTTTTAAAAATTTG-GGGT-TAAATTAT
* *
58725 AATTTTTTAAATTTTGGGG
1 AATTTTTAAAAATTTGGGG
58744 ACTATGGCCC
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
28 13 0.33
29 7 0.18
30 19 0.49
ACGTcount: A:0.32, C:0.03, G:0.17, T:0.48
Consensus pattern (28 bp):
AATTTTTAAAAATTTGGGGTTAAATTAT
Found at i:60505 original size:27 final size:28
Alignment explanation
Indices: 60474--60528 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 28
60464 TCAAAGCTAT
**
60474 TAAATCAAATTATCAA-TAAAAAACATC
1 TAAATCAAATTAGAAATTAAAAAACATC
* *
60501 TAAATTATATTAGAAATTAAAAAACATC
1 TAAATCAAATTAGAAATTAAAAAACATC
60529 AGTAAAGAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
27 12 0.52
28 11 0.48
ACGTcount: A:0.58, C:0.11, G:0.02, T:0.29
Consensus pattern (28 bp):
TAAATCAAATTAGAAATTAAAAAACATC
Found at i:61281 original size:12 final size:12
Alignment explanation
Indices: 61264--61289 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
61254 CAACAGTTGT
61264 GCAATCTGTTAG
1 GCAATCTGTTAG
61276 GCAATCTGTTAG
1 GCAATCTGTTAG
61288 GC
1 GC
61290 TTATGTTAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.31
Consensus pattern (12 bp):
GCAATCTGTTAG
Found at i:62441 original size:36 final size:36
Alignment explanation
Indices: 62373--62441 Score: 95
Period size: 37 Copynumber: 1.9 Consensus size: 36
62363 ATTAAAATGG
*
62373 TTTTCAAGTTTGGTAAATGTTTCTTTGAAAAATAGT
1 TTTTCAAGTTTGGTAAATGTTTCGTTGAAAAATAGT
* *
62409 TTTTCAAAGTTTGGTAGATGTTT-GTTGGAAAAT
1 TTTTC-AAGTTTGGTAAATGTTTCGTTGAAAAAT
62442 GATAATTAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
36 13 0.45
37 16 0.55
ACGTcount: A:0.29, C:0.04, G:0.20, T:0.46
Consensus pattern (36 bp):
TTTTCAAGTTTGGTAAATGTTTCGTTGAAAAATAGT
Found at i:67264 original size:26 final size:28
Alignment explanation
Indices: 67197--67264 Score: 86
Period size: 30 Copynumber: 2.4 Consensus size: 28
67187 TGCTACTCAA
67197 GTAGGTCGCCATGCACTCCCAGCTACCTG
1 GTAGGTCGCCATGCACTCCCAGC-ACCTG
* *
67226 GATAGGTTGCCATGCACTCCCA-C-CGTG
1 G-TAGGTCGCCATGCACTCCCAGCACCTG
67253 GTAGGTCGCCAT
1 GTAGGTCGCCAT
67265 ACATGCCATT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
26 10 0.29
27 4 0.11
29 2 0.06
30 19 0.54
ACGTcount: A:0.18, C:0.34, G:0.26, T:0.22
Consensus pattern (28 bp):
GTAGGTCGCCATGCACTCCCAGCACCTG
Found at i:69847 original size:21 final size:21
Alignment explanation
Indices: 69823--69869 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
69813 ACTCAAGTAC
*
69823 ACTAACACTAAACTTGGTTCA
1 ACTAACACTAAACTTGGTCCA
***
69844 ACTAATTTTAAACTTGGTCCA
1 ACTAACACTAAACTTGGTCCA
69865 ACTAA
1 ACTAA
69870 TTTATAAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.38, C:0.21, G:0.09, T:0.32
Consensus pattern (21 bp):
ACTAACACTAAACTTGGTCCA
Found at i:69870 original size:21 final size:22
Alignment explanation
Indices: 69831--69877 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
69821 ACACTAACAC
*
69831 TAAACTTGGTTCAACTAATTT-
1 TAAACTTGGTCCAACTAATTTA
69852 TAAACTTGGTCCAACTAATTTA
1 TAAACTTGGTCCAACTAATTTA
69874 TAAA
1 TAAA
69878 ATCTTTTGGG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.38
Consensus pattern (22 bp):
TAAACTTGGTCCAACTAATTTA
Found at i:79998 original size:15 final size:15
Alignment explanation
Indices: 79980--80008 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
79970 ATGCAGTAGA
79980 AGCTGCTACAGTTGT
1 AGCTGCTACAGTTGT
79995 AGCTGCTACAGTTG
1 AGCTGCTACAGTTG
80009 CAGTGGCAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.31
Consensus pattern (15 bp):
AGCTGCTACAGTTGT
Found at i:91518 original size:40 final size:40
Alignment explanation
Indices: 91467--91545 Score: 158
Period size: 40 Copynumber: 2.0 Consensus size: 40
91457 TCATTGTATT
91467 AAAATTTTCCATATATATAACTATTAATTATATCAAATTA
1 AAAATTTTCCATATATATAACTATTAATTATATCAAATTA
91507 AAAATTTTCCATATATATAACTATTAATTATATCAAATT
1 AAAATTTTCCATATATATAACTATTAATTATATCAAATT
91546 TTCCAGCCAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.43
Consensus pattern (40 bp):
AAAATTTTCCATATATATAACTATTAATTATATCAAATTA
Found at i:91535 original size:23 final size:23
Alignment explanation
Indices: 91469--91535 Score: 60
Period size: 23 Copynumber: 3.2 Consensus size: 23
91459 ATTGTATTAA
91469 AATTTTCCATATATATAACTATT
1 AATTTTCCATATATATAACTATT
91492 AATTATAT-CA-A-AT-TAA--A--
1 AATT-T-TCCATATATATAACTATT
91509 AATTTTCCATATATATAACTATT
1 AATTTTCCATATATATAACTATT
91532 AATT
1 AATT
91536 ATATCAAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 20
0.63 0.00 0.37
Matches are distributed among these distances:
15 1 0.03
16 3 0.09
17 5 0.15
18 2 0.06
19 4 0.12
21 4 0.12
22 2 0.06
23 9 0.26
24 3 0.09
25 1 0.03
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (23 bp):
AATTTTCCATATATATAACTATT
Found at i:92231 original size:19 final size:22
Alignment explanation
Indices: 92177--92233 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 22
92167 TACATTTCTT
92177 ATATAA-TTTTAAAATATAGCTA
1 ATATAAGTTTTAAAATATA-CTA
*
92199 ATATAAGATTTAAAATA-A-TA
1 ATATAAGTTTTAAAATATACTA
92219 ATA-AAGTTTTAAAAT
1 ATATAAGTTTTAAAAT
92234 TAAATTCAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 11 0.34
20 5 0.16
22 7 0.22
23 9 0.28
ACGTcount: A:0.54, C:0.02, G:0.05, T:0.39
Consensus pattern (22 bp):
ATATAAGTTTTAAAATATACTA
Found at i:93970 original size:41 final size:41
Alignment explanation
Indices: 93925--94021 Score: 113
Period size: 41 Copynumber: 2.4 Consensus size: 41
93915 GATTCTGACT
* * * *
93925 ATCGCATTGCGATTTTCCTAATTCGCAATGGGAATACGTAA
1 ATCGCAATGCGATTTTCCAAAATCGCAATGCGAATACGTAA
* * **
93966 ATCGCAACGCGAATTTGGAAAATCGCAATGCGAATACGTAA
1 ATCGCAATGCGATTTTCCAAAATCGCAATGCGAATACGTAA
*
94007 ATCGCAATACGATTT
1 ATCGCAATGCGATTT
94022 ACATAGCGCC
Statistics
Matches: 45, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.27
Consensus pattern (41 bp):
ATCGCAATGCGATTTTCCAAAATCGCAATGCGAATACGTAA
Found at i:93972 original size:20 final size:20
Alignment explanation
Indices: 93947--94014 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
93937 TTTTCCTAAT
*
93947 TCGCAATGGGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* ** *
93967 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
93988 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
94008 TCGCAAT
1 TCGCAAT
94015 ACGATTTACA
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
20 22 0.58
21 16 0.42
ACGTcount: A:0.38, C:0.19, G:0.22, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:94222 original size:22 final size:22
Alignment explanation
Indices: 94197--94262 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
94187 GGCGACATCT
94197 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
*
94219 GTCCCCATCTCCGACGATATCA
1 GTCCCCATCTCCGACGAAATCA
* *
94241 GTCTCCATCTCCGGCGAAATCA
1 GTCCCCATCTCCGACGAAATCA
94263 TTCACGGTCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.24, C:0.39, G:0.15, T:0.21
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:94627 original size:33 final size:34
Alignment explanation
Indices: 94579--94651 Score: 96
Period size: 33 Copynumber: 2.2 Consensus size: 34
94569 ACTATCGCAA
** *
94579 TGCGATTCTGTCGTTGCGATTTTC-ATTTCGCGT
1 TGCGATTCTGTCGTTGCGATAGTCAAATTCGCGT
94612 TGCGATTCT-TACGTTGCGATAGTCAAATTCGCGT
1 TGCGATTCTGT-CGTTGCGATAGTCAAATTCGCGT
94646 TGCGAT
1 TGCGAT
94652 AGTCATTTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
32 1 0.03
33 20 0.57
34 14 0.40
ACGTcount: A:0.15, C:0.21, G:0.25, T:0.40
Consensus pattern (34 bp):
TGCGATTCTGTCGTTGCGATAGTCAAATTCGCGT
Found at i:94648 original size:20 final size:20
Alignment explanation
Indices: 94623--94671 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
94613 GCGATTCTTA
94623 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
94643 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
*
94663 TGTTGCGAT
1 CGTTGCGAT
94672 TTAAAGTTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.37
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:96566 original size:20 final size:20
Alignment explanation
Indices: 96541--96592 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
96531 AGAATAGTTT
* * *
96541 ACTATCGTAATGCGAAAATG
1 ACTATCGCAACGCGAAAATA
96561 ACTATCGCAACGCGAAAATA
1 ACTATCGCAACGCGAAAATA
96581 ACTATCGCAACG
1 ACTATCGCAACG
96593 AGCGAATCGC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.40, C:0.23, G:0.17, T:0.19
Consensus pattern (20 bp):
ACTATCGCAACGCGAAAATA
Found at i:96656 original size:20 final size:20
Alignment explanation
Indices: 96631--96704 Score: 112
Period size: 20 Copynumber: 3.7 Consensus size: 20
96621 TAACAACAAA
*
96631 ATCGCAACGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
96651 ATCGCAATGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
* **
96671 ATCGCAATGTGAATTTGACT
1 ATCGCAATGCGAAAATGACT
96691 ATCGCAATGCGAAA
1 ATCGCAATGCGAAA
96705 TGAAAATCGC
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (20 bp):
ATCGCAATGCGAAAATGACT
Found at i:96758 original size:20 final size:20
Alignment explanation
Indices: 96728--96796 Score: 102
Period size: 20 Copynumber: 3.5 Consensus size: 20
96718 GCGATTCTCT
* **
96728 CGTTGCTATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
*
96748 CATTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
96768 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
96788 CGTTGCGAT
1 CGTTGCGAT
96797 TTTAAGTTTC
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.19, C:0.20, G:0.23, T:0.38
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:96806 original size:20 final size:20
Alignment explanation
Indices: 96744--96806 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 20
96734 TATAGTCAAA
* * *
96744 TTCGCATTGCGATAGTCATT
1 TTCGCGTTGCGATAGTAAGT
* *
96764 TTCGCGTTGCGATAGTCATT
1 TTCGCGTTGCGATAGTAAGT
**
96784 TTCGCGTTGCGATTTTAAGT
1 TTCGCGTTGCGATAGTAAGT
96804 TTC
1 TTC
96807 AGATTCTATT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.16, C:0.19, G:0.22, T:0.43
Consensus pattern (20 bp):
TTCGCGTTGCGATAGTAAGT
Found at i:97371 original size:21 final size:20
Alignment explanation
Indices: 97280--97384 Score: 68
Period size: 21 Copynumber: 5.0 Consensus size: 20
97270 GACTCACCTT
97280 TCATCGTTCAAGAGG-CCTCC
1 TCATCGTTCAAGAGGCCCT-C
* *
97300 CCTATCGTTCAAGAGGCTCCTA
1 TC-ATCGTTCAAGAGGC-CCTC
** *
97322 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAG-GCCCTC
* * *
97343 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCC-CTC
*
97364 TCATCGTTGAAGAGGTCCCTC
1 TCATCGTTCAAGAGG-CCCTC
97385 CCAACATTCT
Statistics
Matches: 62, Mismatches: 17, Indels: 11
0.69 0.19 0.12
Matches are distributed among these distances:
20 3 0.05
21 52 0.84
22 4 0.06
23 3 0.05
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (20 bp):
TCATCGTTCAAGAGGCCCTC
Found at i:97377 original size:42 final size:42
Alignment explanation
Indices: 97305--97387 Score: 98
Period size: 42 Copynumber: 2.0 Consensus size: 42
97295 CCTCCCCTAT
97305 CGTTCAAGAGGCTCCTATCATCCCTCAAGA-GTCCCCTCCCAC
1 CGTTCAAGAGGCTCCTATCATCCCTCAAGAGGT-CCCTCCCAC
* ** *
97347 CGTTCAAGAGGC-CACTGTCATCGTTGAAGAGGTCCCTCCCA
1 CGTTCAAGAGGCTC-CTATCATCCCTCAAGAGGTCCCTCCCA
97388 ACATTCTAGA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
41 1 0.03
42 32 0.91
43 2 0.06
ACGTcount: A:0.22, C:0.37, G:0.19, T:0.22
Consensus pattern (42 bp):
CGTTCAAGAGGCTCCTATCATCCCTCAAGAGGTCCCTCCCAC
Found at i:98782 original size:14 final size:14
Alignment explanation
Indices: 98763--98798 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
98753 ATTGTTTAAT
98763 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
98777 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
98791 TGATTTGT
1 TGATTTGT
98799 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:99049 original size:34 final size:34
Alignment explanation
Indices: 99006--99101 Score: 140
Period size: 33 Copynumber: 2.9 Consensus size: 34
98996 ACTAAATTTG
99006 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
*
99040 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
** * *
99073 CGTTGCGATAGTCATTTCCGCGTTGCGAT
1 CGTTGCGATTTTCATTTTCGCATTGCGAT
99102 AGTCAATTCC
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
33 30 0.54
34 26 0.46
ACGTcount: A:0.14, C:0.24, G:0.21, T:0.42
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
Found at i:99098 original size:20 final size:20
Alignment explanation
Indices: 99073--99166 Score: 127
Period size: 20 Copynumber: 4.7 Consensus size: 20
99063 GCGATTCTCT
99073 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
99093 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCATTTCCG
* *
99113 CATTGCAATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
99133 TGTTGCGATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
*
99153 CATTGCGATAGTCA
1 CGTTGCGATAGTCA
99167 AATGAATGTC
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
20 62 0.97
21 2 0.03
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.34
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:99138 original size:40 final size:40
Alignment explanation
Indices: 99075--99166 Score: 150
Period size: 40 Copynumber: 2.3 Consensus size: 40
99065 GATTCTCTCG
99075 TTGCGATAGTCATTTCCGCGTTGCGATAGTCA-ATTCCGCA
1 TTGCGATAGTCATTTCCGCGTTGCGATAGTCATATT-CGCA
* *
99115 TTGCAATAGTCATTTCCGTGTTGCGATAGTCATATTCGCA
1 TTGCGATAGTCATTTCCGCGTTGCGATAGTCATATTCGCA
99155 TTGCGATAGTCA
1 TTGCGATAGTCA
99167 AATGAATGTC
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
40 45 0.94
41 3 0.06
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.35
Consensus pattern (40 bp):
TTGCGATAGTCATTTCCGCGTTGCGATAGTCATATTCGCA
Found at i:102494 original size:20 final size:20
Alignment explanation
Indices: 102469--102515 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
102459 AAATTCAGTA
*
102469 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCGCG
* *
102489 TTGCGATAGTCATATTCGCG
1 TTGCGATAGTCAGAATCGCG
102509 TTGCGAT
1 TTGCGAT
102516 TTACGTATTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.34
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCG
Found at i:102524 original size:20 final size:20
Alignment explanation
Indices: 102501--102612 Score: 161
Period size: 20 Copynumber: 5.5 Consensus size: 20
102491 GCGATAGTCA
*
102501 TATTCGCGTTGCGATTTACG
1 TATTCGCATTGCGATTTACG
102521 TATTCGCATTGCGATTTACG
1 TATTCGCATTGCGATTTACG
102541 TATTCGCATTGCGATTTACG
1 TATTCGCATTGCGATTTACG
* * *
102561 TAATCGCATTGCGATTTTTCA
1 TATTCGCATTGCGA-TTTACG
* *
102582 AATTCGCGTTGCGATTTACG
1 TATTCGCATTGCGATTTACG
102602 TATTCGCATTG
1 TATTCGCATTG
102613 TGAATTAGGA
Statistics
Matches: 80, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
20 65 0.81
21 15 0.19
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.40
Consensus pattern (20 bp):
TATTCGCATTGCGATTTACG
Found at i:102638 original size:21 final size:21
Alignment explanation
Indices: 102614--102657 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
102604 TTCGCATTGT
102614 GAATTAGGAAAATCGCAACGC
1 GAATTAGGAAAATCGCAACGC
* *
102635 GAATTTGGAAAATCGCAATGC
1 GAATTAGGAAAATCGCAACGC
102656 GA
1 GA
102658 TAGTCAGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.41, C:0.16, G:0.25, T:0.18
Consensus pattern (21 bp):
GAATTAGGAAAATCGCAACGC
Found at i:108494 original size:3 final size:3
Alignment explanation
Indices: 108488--108512 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
108478 TAATGTAAAT
108488 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
108513 TTGTTTCTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:110093 original size:6 final size:6
Alignment explanation
Indices: 110038--110087 Score: 55
Period size: 6 Copynumber: 8.2 Consensus size: 6
110028 TTATTATTAA
* * * *
110038 TATTAT TATTAT TATTATT TGTTTT TATTTT TGTTTT TATTTT TATTTT
1 TATTTT TATTTT TATT-TT TATTTT TATTTT TATTTT TATTTT TATTTT
110087 T
1 T
110088 TCTTTTACAT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
6 34 0.89
7 4 0.11
ACGTcount: A:0.18, C:0.00, G:0.04, T:0.78
Consensus pattern (6 bp):
TATTTT
Found at i:111079 original size:6 final size:6
Alignment explanation
Indices: 111068--111122 Score: 101
Period size: 6 Copynumber: 9.2 Consensus size: 6
111058 CAGTTATATA
111068 TGCGTG TGCGTG TGCGTG TGCGTG TGCGTG TGCGTG TGCGTG TGCGTG
1 TGCGTG TGCGTG TGCGTG TGCGTG TGCGTG TGCGTG TGCGTG TGCGTG
*
111116 TGTGTG T
1 TGCGTG T
111123 TTAACATAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 48 1.00
ACGTcount: A:0.00, C:0.15, G:0.49, T:0.36
Consensus pattern (6 bp):
TGCGTG
Found at i:117516 original size:42 final size:42
Alignment explanation
Indices: 117469--117557 Score: 178
Period size: 42 Copynumber: 2.1 Consensus size: 42
117459 TTGTTGATAT
117469 AATATTTTTTGGTTTGTATTAATTATTTAAATTATAATTTAA
1 AATATTTTTTGGTTTGTATTAATTATTTAAATTATAATTTAA
117511 AATATTTTTTGGTTTGTATTAATTATTTAAATTATAATTTAA
1 AATATTTTTTGGTTTGTATTAATTATTTAAATTATAATTTAA
117553 AATAT
1 AATAT
117558 GATTTGATGT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (42 bp):
AATATTTTTTGGTTTGTATTAATTATTTAAATTATAATTTAA
Found at i:121662 original size:59 final size:59
Alignment explanation
Indices: 121522--121662 Score: 131
Period size: 59 Copynumber: 2.4 Consensus size: 59
121512 AATGGGTAAA
* * * * * * *
121522 GTACACAATGGTCCCCGACTATAGGATATTGCTTTATTAAGTCTCTTGACTATTAAATG
1 GTACAAAATGGTCTCCGACTATAGAATATTGCTTTAGTAAGTCCCTAGACTATTAAAAG
* * ** * * *
121581 TTACAAAATGATCCTCAAACTATAGAATGTTGCTTT-GTAAGTCCCTAGATTGTTAAAAG
1 GTACAAAATGGT-CTCCGACTATAGAATATTGCTTTAGTAAGTCCCTAGACTATTAAAAG
121640 GTACAAAATGGTCATCCGACTAT
1 GTACAAAATGGTC-TCCGACTAT
121663 TCATTATGTT
Statistics
Matches: 62, Mismatches: 18, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
58 1 0.02
59 43 0.69
60 18 0.29
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (59 bp):
GTACAAAATGGTCTCCGACTATAGAATATTGCTTTAGTAAGTCCCTAGACTATTAAAAG
Found at i:122808 original size:2 final size:2
Alignment explanation
Indices: 122801--122832 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
122791 AATAAAACTC
122801 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
122833 TAGAGAATCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:130698 original size:29 final size:29
Alignment explanation
Indices: 130645--130712 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
130635 TTGGATAACT
*
130645 TCGTGTTTTGCAAAAAGCGAAGTCAAACC
1 TCGTGTTTTACAAAAAGCGAAGTCAAACC
* * * * *
130674 TTGTGTTTTACAAAATGTGAGGTCAGACC
1 TCGTGTTTTACAAAAAGCGAAGTCAAACC
*
130703 TCATGTTTTA
1 TCGTGTTTTA
130713 AATAACTTTG
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (29 bp):
TCGTGTTTTACAAAAAGCGAAGTCAAACC
Found at i:132891 original size:3 final size:3
Alignment explanation
Indices: 132883--132908 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
132873 GATTTTGAAC
132883 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
132909 AACTTTTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:132939 original size:29 final size:29
Alignment explanation
Indices: 132907--132963 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
132897 TTATTATTAT
132907 TAAACTTT-TAATTTTGA-CAATTATAACAG
1 TAAA-TTTATAATTTT-ATCAATTATAACAG
132936 TAAATTTATAATTTTATCAATTATAACA
1 TAAATTTATAATTTTATCAATTATAACA
132964 TTGGAGTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
28 4 0.15
29 22 0.85
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.44
Consensus pattern (29 bp):
TAAATTTATAATTTTATCAATTATAACAG
Found at i:135508 original size:16 final size:16
Alignment explanation
Indices: 135482--135520 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
135472 ATTCATTACT
135482 ATTTACGTGAATAGTGA
1 ATTT-CGTGAATAGTGA
135499 ATTTCGTGAATAGTGA
1 ATTTCGTGAATAGTGA
*
135515 AATTCG
1 ATTTCG
135521 GTCGGCGATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.33, C:0.08, G:0.23, T:0.36
Consensus pattern (16 bp):
ATTTCGTGAATAGTGA
Found at i:135518 original size:17 final size:17
Alignment explanation
Indices: 135482--135515 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
135472 ATTCATTACT
135482 ATTTACGTGAATAGTGA
1 ATTTACGTGAATAGTGA
135499 ATTT-CGTGAATAGTGA
1 ATTTACGTGAATAGTGA
135515 A
1 A
135516 ATTCGGTCGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.35, C:0.06, G:0.24, T:0.35
Consensus pattern (17 bp):
ATTTACGTGAATAGTGA
Found at i:137924 original size:177 final size:177
Alignment explanation
Indices: 137613--137967 Score: 694
Period size: 177 Copynumber: 2.0 Consensus size: 177
137603 CTACGAAAAT
137613 CGAAAGATCATCAGAAGCAGAGACGTCATTTTCAATGAAAATGTGATGTACAAAGATAGGTCAAC
1 CGAAAGATCATCAGAAGCAGAGACGTCATTTTCAATGAAAATGTGATGTACAAAGATAGGTCAAC
137678 CGCAGAATCAAGTAATACCGAAGCTGAAACAAAGGAATTTGCTGGTTCGAGGATATTTCTGGAAA
66 CGCAGAATCAAGTAATACCGAAGCTGAAACAAAGGAATTTGCTGGTTCGAGGATATTTCTGGAAA
137743 TGATGTTCAGATCAATCCTGAAGCAGTTCAAGAAGAACCACACACAC
131 TGATGTTCAGATCAATCCTGAAGCAGTTCAAGAAGAACCACACACAC
137790 CGAAAGATCATCAGAAGCAGAGA-GTCATTTTCAATGAAAATGTGATGTACAAAGATAGGTCAAC
1 CGAAAGATCATCAGAAGCAGAGACGTCATTTTCAATGAAAATGTGATGTACAAAGATAGGTCAAC
137854 CGCAGAATCAAGTAATACCGAAGCTGAAACAAAGGAATTTGCTGAGTTCGAGGATATTTCTGGAA
66 CGCAGAATCAAGTAATACCGAAGCTGAAACAAAGGAATTTGCTG-GTTCGAGGATATTTCTGGAA
137919 ATGATGTTCAGATCAATCCTGAAGCAGTTCAAGAAGAACCACACACAC
130 ATGATGTTCAGATCAATCCTGAAGCAGTTCAAGAAGAACCACACACAC
137967 C
1 C
137968 AGAACTGAGA
Statistics
Matches: 177, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
176 85 0.48
177 92 0.52
ACGTcount: A:0.39, C:0.18, G:0.21, T:0.21
Consensus pattern (177 bp):
CGAAAGATCATCAGAAGCAGAGACGTCATTTTCAATGAAAATGTGATGTACAAAGATAGGTCAAC
CGCAGAATCAAGTAATACCGAAGCTGAAACAAAGGAATTTGCTGGTTCGAGGATATTTCTGGAAA
TGATGTTCAGATCAATCCTGAAGCAGTTCAAGAAGAACCACACACAC
Found at i:139640 original size:71 final size:71
Alignment explanation
Indices: 139534--139677 Score: 288
Period size: 71 Copynumber: 2.0 Consensus size: 71
139524 TGAAGTTGTG
139534 TTCAGCTTCAGTTGGCATGCTAGATAACAAGACCAGACATGCTGCTGCATTGATCGAGGTGTGAA
1 TTCAGCTTCAGTTGGCATGCTAGATAACAAGACCAGACATGCTGCTGCATTGATCGAGGTGTGAA
139599 GACATA
66 GACATA
139605 TTCAGCTTCAGTTGGCATGCTAGATAACAAGACCAGACATGCTGCTGCATTGATCGAGGTGTGAA
1 TTCAGCTTCAGTTGGCATGCTAGATAACAAGACCAGACATGCTGCTGCATTGATCGAGGTGTGAA
139670 GACATA
66 GACATA
139676 TT
1 TT
139678 AAAATCAGTC
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 73 1.00
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.26
Consensus pattern (71 bp):
TTCAGCTTCAGTTGGCATGCTAGATAACAAGACCAGACATGCTGCTGCATTGATCGAGGTGTGAA
GACATA
Found at i:139672 original size:35 final size:35
Alignment explanation
Indices: 139562--139672 Score: 84
Period size: 35 Copynumber: 3.1 Consensus size: 35
139552 GCTAGATAAC
139562 AAGACCAGACATGCTGCTGCATTGATCGAGGTGTG
1 AAGACCAGACATGCTGCTGCATTGATCGAGGTGTG
* * * * * * ***
139597 AAGA-C--ATATTCAGCTTCAGTTGGCATGCTAGATAAC
1 AAGACCAGACATGCTGCTGCA-TT-G-AT-CGAGGTGTG
139633 AAGACCAGACATGCTGCTGCATTGATCGAGGTGTG
1 AAGACCAGACATGCTGCTGCATTGATCGAGGTGTG
139668 AAGAC
1 AAGAC
139673 ATATTAAAAT
Statistics
Matches: 51, Mismatches: 18, Indels: 14
0.61 0.22 0.17
Matches are distributed among these distances:
32 9 0.18
33 2 0.04
34 2 0.04
35 15 0.29
36 10 0.20
37 2 0.04
38 2 0.04
39 9 0.18
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.23
Consensus pattern (35 bp):
AAGACCAGACATGCTGCTGCATTGATCGAGGTGTG
Found at i:153448 original size:2 final size:2
Alignment explanation
Indices: 153441--153473 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
153431 ATGTTGATGA
153441 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
153474 TAAATAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:161419 original size:81 final size:78
Alignment explanation
Indices: 161256--161412 Score: 273
Period size: 81 Copynumber: 2.0 Consensus size: 78
161246 AATATGTCTC
161256 TTTTGACCAACGTTTCCATCATGATCGTTACAATACTGATGTGACGGTTCACGATGCTAATATGG
1 TTTTGACCAACGTTTCCATCATGATCGTTACAATACTGATGTGACGGTTCACGATGCTAATATGG
161321 TAGATGGGTTAAAT
66 -AGATGGGTTAAAT
161335 TTTTGACCAACGGTTTCCATCATTGATCGTTACAATACTGATGTGACGGTTCACGATGCTAATAT
1 TTTTGACCAAC-GTTTCCATCA-TGATCGTTACAATACTGATGTGACGGTTCACGATGCTAATAT
161400 -G-GATGGGTTAAAT
64 GGAGATGGGTTAAAT
161413 AGTTTTTTTA
Statistics
Matches: 76, Mismatches: 0, Indels: 5
0.94 0.00 0.06
Matches are distributed among these distances:
78 12 0.16
79 11 0.14
80 11 0.14
81 42 0.55
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (78 bp):
TTTTGACCAACGTTTCCATCATGATCGTTACAATACTGATGTGACGGTTCACGATGCTAATATGG
AGATGGGTTAAAT
Found at i:167871 original size:31 final size:32
Alignment explanation
Indices: 167834--167905 Score: 94
Period size: 32 Copynumber: 2.3 Consensus size: 32
167824 TTAAATAATT
*
167834 ATTAAATTTC-T-TAGACGGTTATAAAATGATA
1 ATTAAATTTCATCTA-ACGATTATAAAATGATA
* *
167865 ATTAAATTTCATCTAACTATTATAAAATGATC
1 ATTAAATTTCATCTAACGATTATAAAATGATA
167897 ATTAAATTT
1 ATTAAATTT
167906 ATCAAACAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
31 10 0.28
32 24 0.67
33 2 0.06
ACGTcount: A:0.43, C:0.08, G:0.07, T:0.42
Consensus pattern (32 bp):
ATTAAATTTCATCTAACGATTATAAAATGATA
Found at i:169832 original size:54 final size:53
Alignment explanation
Indices: 169698--169860 Score: 184
Period size: 60 Copynumber: 2.9 Consensus size: 53
169688 CTAATTACAC
* *
169698 ATTT-GGATGAAATTGGAATATTCAAAAGTTTGAGGACTAATTTAGAAAGAGGATCATA
1 ATTTAGGATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTT---AA-A--ATCATA
169756 ATTTAGTGATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAAAATCATA
1 ATTTAG-GATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAAAATCATA
* * * *
169810 GTTTGAGGATGAAATTAAAATATTAAAAAAATTTAAGGACTAATTTAAAAT
1 ATTT-AGGATGAAATTAGAATATT-CAAAAGTTTAAGGACTAATTTAAAAT
169861 AAAAATTATA
Statistics
Matches: 95, Mismatches: 6, Indels: 11
0.85 0.05 0.10
Matches are distributed among these distances:
54 25 0.26
55 26 0.27
56 1 0.01
57 2 0.02
58 4 0.04
59 1 0.01
60 36 0.38
ACGTcount: A:0.46, C:0.04, G:0.17, T:0.33
Consensus pattern (53 bp):
ATTTAGGATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAAAATCATA
Found at i:175938 original size:190 final size:192
Alignment explanation
Indices: 175617--176025 Score: 592
Period size: 190 Copynumber: 2.1 Consensus size: 192
175607 CATATAACAA
* * * * ** *
175617 TATCTTTTAATTTGAAATATTCAAAAGATAAAACTCTTTTTACCATTCAAACTTAATTATGTATT
1 TATCATTTAATTTGAAATAGTCAAAAGATAAAACTCCTTTTACCACTCAAACTTAAGCATATATT
*
175682 ATTTTAATTTGAAATATACAAAAATATATAATTATCTTTAATATTCAAAGTTAAAAAAAGTAACA
66 ATTTTAATTTGAAATATACAAAAATATATAATTATCTTTAATATTCAAAATTAAAAAAAGTAACA
* * *
175747 AATACATTTTTAAGTTGACATATTCAAAGAGTAATTATCCTATTAATATTCAAATTAAATAA-
131 AATACATTTTTAAATTGACATATTAAAAGAATAATTATCCTATTAATATTCAAATTAAA-AAT
* * * * *
175809 TAT-ATTTAATTTGTAATGGTCAAAAGCT-AAACTCCTTTTACTACTCAAACTTCAGCATATATT
1 TATCATTTAATTTGAAATAGTCAAAAGATAAAACTCCTTTTACCACTCAAACTTAAGCATATATT
*
175872 ATTTTAATTTGAAATATACAAAAATATATAATTATCTTTTAATATTCAAAATTAAAAAGA-TAAC
66 ATTTTAATTTGAAATATACAAAAATATATAATTATC-TTTAATATTCAAAATTAAAAAAAGTAAC
* *
175936 AAATACCTTTTTAAATTGACTTATTAAAAGAATAATTATCCTATTAATATTCAAATTAAAAAT
130 AAATACATTTTTAAATTGACATATTAAAAGAATAATTATCCTATTAATATTCAAATTAAAAAT
*
175999 TATCTTTTAATTTGAAATAGTCAAAAG
1 TATCATTTAATTTGAAATAGTCAAAAG
176026 GACTATGAAT
Statistics
Matches: 192, Mismatches: 22, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
189 2 0.01
190 126 0.66
191 61 0.32
192 3 0.02
ACGTcount: A:0.45, C:0.10, G:0.05, T:0.40
Consensus pattern (192 bp):
TATCATTTAATTTGAAATAGTCAAAAGATAAAACTCCTTTTACCACTCAAACTTAAGCATATATT
ATTTTAATTTGAAATATACAAAAATATATAATTATCTTTAATATTCAAAATTAAAAAAAGTAACA
AATACATTTTTAAATTGACATATTAAAAGAATAATTATCCTATTAATATTCAAATTAAAAAT
Found at i:187003 original size:20 final size:19
Alignment explanation
Indices: 186978--187019 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
186968 AATATACTCC
186978 TTATTTA-ACTTATAAATATA
1 TTATTTATA-TTATAAA-ATA
186998 TTATTTATATTATAAAATA
1 TTATTTATATTATAAAATA
187017 TTA
1 TTA
187020 ATCATAGTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 6 0.29
20 14 0.67
21 1 0.05
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (19 bp):
TTATTTATATTATAAAATA
Found at i:194988 original size:23 final size:22
Alignment explanation
Indices: 194932--195011 Score: 88
Period size: 23 Copynumber: 3.5 Consensus size: 22
194922 CGAGACCATC
194932 CGAGCGAGCTATGCGAGGGCAG
1 CGAGCGAGCTATGCGAGGGCAG
* * *
194954 CGAGCGAACTATGCGTGGGCATT
1 CGAGCGAGCTATGCGAGGGCA-G
* *
194977 TGAGCGAGCTATGCGAGGACAG
1 CGAGCGAGCTATGCGAGGGCAG
*
194999 CCGATCGAGCTAT
1 -CGAGCGAGCTAT
195012 ATGCACGTCC
Statistics
Matches: 46, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
22 19 0.41
23 27 0.59
ACGTcount: A:0.24, C:0.23, G:0.38, T:0.16
Consensus pattern (22 bp):
CGAGCGAGCTATGCGAGGGCAG
Found at i:195120 original size:23 final size:23
Alignment explanation
Indices: 195094--195184 Score: 119
Period size: 23 Copynumber: 4.0 Consensus size: 23
195084 CCGAGACCAT
195094 CCGAGCGAGCTATGCGAGGGCAG
1 CCGAGCGAGCTATGCGAGGGCAG
* * *
195117 CCGAGCGAACTATGCGTGGGCAT
1 CCGAGCGAGCTATGCGAGGGCAG
** *
195140 TTGAGCGAGCTATGCGAGGACAG
1 CCGAGCGAGCTATGCGAGGGCAG
*
195163 CCGATCGAGCTATGCGAGGGCA
1 CCGAGCGAGCTATGCGAGGGCA
195185 TCTGAGCAAG
Statistics
Matches: 55, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 55 1.00
ACGTcount: A:0.23, C:0.24, G:0.38, T:0.14
Consensus pattern (23 bp):
CCGAGCGAGCTATGCGAGGGCAG
Found at i:195157 original size:46 final size:46
Alignment explanation
Indices: 195091--195191 Score: 148
Period size: 46 Copynumber: 2.2 Consensus size: 46
195081 TGACCGAGAC
* * *
195091 CATCCGAGCGAGCTATGCGAGGGCAGCCGAGCGAACTATGCGTGGG
1 CATCTGAGCGAGCTATGCGAGGACAGCCGAGCGAACTATGCGAGGG
* * *
195137 CATTTGAGCGAGCTATGCGAGGACAGCCGATCGAGCTATGCGAGGG
1 CATCTGAGCGAGCTATGCGAGGACAGCCGAGCGAACTATGCGAGGG
195183 CATCTGAGC
1 CATCTGAGC
195192 AAGCGAGCAA
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.23, C:0.25, G:0.37, T:0.16
Consensus pattern (46 bp):
CATCTGAGCGAGCTATGCGAGGACAGCCGAGCGAACTATGCGAGGG
Found at i:200505 original size:9 final size:9
Alignment explanation
Indices: 200491--200523 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
200481 TATCAAAAAA
200491 TTATTATTT
1 TTATTATTT
200500 TTATTATTT
1 TTATTATTT
200509 TTATTATTT
1 TTATTATTT
200518 TT-TTAT
1 TTATTAT
200524 CGATTTTGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 4 0.17
9 20 0.83
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (9 bp):
TTATTATTT
Found at i:209063 original size:185 final size:183
Alignment explanation
Indices: 208759--209130 Score: 620
Period size: 185 Copynumber: 2.0 Consensus size: 183
208749 AAATTAAATG
* *
208759 TTTTTTAATTCAAAAAAAGTTTATAATTAATTTAAATAATATATAATTATAAAATAAAAATTTCA
1 TTTTTTAATTAAAAAAAAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATTT-A
208824 GATAAAATTTTTTATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATTATTAAT
65 GATAAAATTTTTTATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATTATTAAT
* *
208889 TGGGTTTTAAATGGTTTGGGCTTAGCCCATATGTTATATATAATATATTTAATA
130 TGGGTTTTAAATGGTTTGGGCTTAGCCCATATATTATATATAATATATTGAATA
208943 TTTTTTAATTAAAAAAAACAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATTT
1 TTTTTTAATT-AAAAAAA-AGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATTT
* * * *
209008 -TATATATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTTGATCTTAAATTATTA
64 AGATAAAATTTTTT-ATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATTATTA
*
209072 ATTGGGTTTTAAATGGTTTGGGCTTAGCCTATATATTATATATAATATATTGAATA
128 ATTGGGTTTTAAATGGTTTGGGCTTAGCCCATATATTATATATAATATATTGAATA
209128 TTT
1 TTT
209131 AAATTTTAAT
Statistics
Matches: 176, Mismatches: 9, Indels: 5
0.93 0.05 0.03
Matches are distributed among these distances:
184 20 0.11
185 111 0.63
186 45 0.26
ACGTcount: A:0.41, C:0.03, G:0.09, T:0.47
Consensus pattern (183 bp):
TTTTTTAATTAAAAAAAAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATTTAG
ATAAAATTTTTTATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATTATTAATT
GGGTTTTAAATGGTTTGGGCTTAGCCCATATATTATATATAATATATTGAATA
Found at i:211752 original size:20 final size:20
Alignment explanation
Indices: 211727--211767 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
211717 TACTAAATGC
211727 ATAACTTACCCCAGAATTAA
1 ATAACTTACCCCAGAATTAA
211747 ATAACTTACCCCAGAATTAA
1 ATAACTTACCCCAGAATTAA
211767 A
1 A
211768 AAACCCCGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.05, T:0.24
Consensus pattern (20 bp):
ATAACTTACCCCAGAATTAA
Found at i:218354 original size:19 final size:19
Alignment explanation
Indices: 218330--218403 Score: 58
Period size: 19 Copynumber: 3.8 Consensus size: 19
218320 TATTGTTCAT
218330 AGTTTGGAAACTTTGTAAG
1 AGTTTGGAAACTTTGTAAG
* * *
218349 AGTTTGAAAATTTTTATTAAG
1 AGTTTGGAAA-CTTT-GTAAG
* ** *
218370 AGTTTCGAAACTTTACAAA
1 AGTTTGGAAACTTTGTAAG
*
218389 AGTTTTGAAACTTTG
1 AGTTTGGAAACTTTG
218404 CACTCATAAA
Statistics
Matches: 42, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
19 24 0.57
20 6 0.14
21 12 0.29
ACGTcount: A:0.35, C:0.07, G:0.18, T:0.41
Consensus pattern (19 bp):
AGTTTGGAAACTTTGTAAG
Found at i:223506 original size:29 final size:29
Alignment explanation
Indices: 223474--223576 Score: 91
Period size: 29 Copynumber: 3.4 Consensus size: 29
223464 AAATTGAATC
*
223474 CTTTAGGCATTTATTTTGACCAAAAAATA
1 CTTTAGGTATTTATTTTGACCAAAAAATA
* *
223503 CTTTAGGTACTATATTTT-AGCTAAAAAGATAA
1 CTTTAGGTA-TTTATTTTGA-CCAAAAA-AT-A
* * * * *
223535 CATTATGTTTTTATTATGATCAAAAAATA
1 CTTTAGGTATTTATTTTGACCAAAAAATA
223564 CTTTAGGTATTTA
1 CTTTAGGTATTTA
223577 AATGAAAAAG
Statistics
Matches: 56, Mismatches: 13, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
29 20 0.36
30 15 0.27
31 13 0.23
32 8 0.14
ACGTcount: A:0.38, C:0.10, G:0.11, T:0.42
Consensus pattern (29 bp):
CTTTAGGTATTTATTTTGACCAAAAAATA
Found at i:228612 original size:20 final size:20
Alignment explanation
Indices: 228573--228612 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
228563 TGAAATTTTT
* *
228573 TTTCAAAAAATTTGGGTTTA
1 TTTCAAAAAATTTCGCTTTA
*
228593 TTTCAAAAAATTTCTCTTTA
1 TTTCAAAAAATTTCGCTTTA
228613 AAATTATATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.35, C:0.10, G:0.07, T:0.47
Consensus pattern (20 bp):
TTTCAAAAAATTTCGCTTTA
Found at i:236583 original size:2 final size:2
Alignment explanation
Indices: 236576--236602 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
236566 CACAAAGGGG
236576 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
236603 CTAAAACCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:237398 original size:118 final size:118
Alignment explanation
Indices: 237190--237427 Score: 397
Period size: 118 Copynumber: 2.0 Consensus size: 118
237180 TATTTTACCT
*
237190 ACTACAAATTAAATATTTTCCTTAAGTATAGCTTATCTTTTTTAATATTCTGAATCAAAAAGAAA
1 ACTACAAATTAAATATTTTCCTTAAGTATAGCTTATCTTTTTTAATAGTCTGAATCAAAAAGAAA
* *
237255 ATTATGTGATTTCCTTTTAATTTAAATATTAAATATAGTATGACTTGCAATTC
66 ATAATGCGATTTCCTTTTAATTTAAATATTAAATATAGTATGACTTGCAATTC
* * *
237308 ACTACGAATTAAATATTTTCCTTAAGTGA-AGTTTATCTTTTTTAATAGTCTGAATTAAAAAGAA
1 ACTACAAATTAAATATTTTCCTTAAGT-ATAGCTTATCTTTTTTAATAGTCTGAATCAAAAAGAA
*
237372 AATAATGCGATTTCCTTTTAATTTAAATATTAAATATAGTATGACTTGTAATTC
65 AATAATGCGATTTCCTTTTAATTTAAATATTAAATATAGTATGACTTGCAATTC
237426 AC
1 AC
237428 GAATGTATTC
Statistics
Matches: 112, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
118 111 0.99
119 1 0.01
ACGTcount: A:0.38, C:0.11, G:0.09, T:0.42
Consensus pattern (118 bp):
ACTACAAATTAAATATTTTCCTTAAGTATAGCTTATCTTTTTTAATAGTCTGAATCAAAAAGAAA
ATAATGCGATTTCCTTTTAATTTAAATATTAAATATAGTATGACTTGCAATTC
Found at i:239936 original size:31 final size:32
Alignment explanation
Indices: 239879--239944 Score: 98
Period size: 32 Copynumber: 2.1 Consensus size: 32
239869 TGACTACATT
239879 TTAAATAAATAAAAAATAAAAGTGATAATATC
1 TTAAATAAATAAAAAATAAAAGTGATAATATC
* * *
239911 TTAATTAAATAAAAATTAAGA-TGATAATATC
1 TTAAATAAATAAAAAATAAAAGTGATAATATC
239942 TTA
1 TTA
239945 TATATTTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
31 13 0.42
32 18 0.58
ACGTcount: A:0.58, C:0.03, G:0.06, T:0.33
Consensus pattern (32 bp):
TTAAATAAATAAAAAATAAAAGTGATAATATC
Found at i:240608 original size:34 final size:33
Alignment explanation
Indices: 240568--240652 Score: 134
Period size: 34 Copynumber: 2.5 Consensus size: 33
240558 CCCGAACCCG
* *
240568 AAAATATTTTATATGTAATTAATATAAAATATAT
1 AAAATATTATATATATAATTAATATAAAA-ATAT
240602 AAAATATTATATATATAATTAATATAAAAATAT
1 AAAATATTATATATATAATTAATATAAAAATAT
240635 AAAATATATATATATATA
1 AAAATAT-TATATATATA
240653 TATATATAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
33 11 0.23
34 37 0.77
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (33 bp):
AAAATATTATATATATAATTAATATAAAAATAT
Found at i:240614 original size:2 final size:2
Alignment explanation
Indices: 240596--240660 Score: 52
Period size: 2 Copynumber: 35.5 Consensus size: 2
240586 TTAATATAAA
* * *
240596 AT AT AT A- AA AT AT -T AT AT AT AT A- AT -T A- AT AT AA AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
240633 AT A- AA 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 A
240661 ATCGGGGTGG
Statistics
Matches: 53, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
1 6 0.11
2 47 0.89
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (2 bp):
AT
Found at i:240661 original size:25 final size:25
Alignment explanation
Indices: 240589--240660 Score: 57
Period size: 23 Copynumber: 3.1 Consensus size: 25
240579 TATGTAATTA
*
240589 ATATAAAATATATA-AAATAT-TAT
1 ATATAAAATATATATATATATATAT
* *
240612 ATATATAAT-TA-ATATA-A-AAAT
1 ATATAAAATATATATATATATATAT
* *
240633 ATAAAATATATATATATATATATAT
1 ATATAAAATATATATATATATATAT
240658 ATA
1 ATA
240661 ATCGGGGTGG
Statistics
Matches: 36, Mismatches: 7, Indels: 10
0.68 0.13 0.19
Matches are distributed among these distances:
21 10 0.28
22 6 0.17
23 13 0.36
24 1 0.03
25 6 0.17
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (25 bp):
ATATAAAATATATATATATATATAT
Found at i:240725 original size:13 final size:13
Alignment explanation
Indices: 240707--240733 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
240697 ACCCGACCCG
240707 AAAAAATCTCCAA
1 AAAAAATCTCCAA
240720 AAAAAATCTCCAA
1 AAAAAATCTCCAA
240733 A
1 A
240734 CCCTAACCCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.63, C:0.22, G:0.00, T:0.15
Consensus pattern (13 bp):
AAAAAATCTCCAA
Found at i:244521 original size:19 final size:19
Alignment explanation
Indices: 244499--244569 Score: 133
Period size: 19 Copynumber: 3.7 Consensus size: 19
244489 TAATTGACTG
*
244499 TTTAAATATTGATTTAAAA
1 TTTAAATATAGATTTAAAA
244518 TTTAAATATAGATTTAAAA
1 TTTAAATATAGATTTAAAA
244537 TTTAAATATAGATTTAAAA
1 TTTAAATATAGATTTAAAA
244556 TTTAAATATAGATT
1 TTTAAATATAGATT
244570 ATATTCATTT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (19 bp):
TTTAAATATAGATTTAAAA
Found at i:248883 original size:2 final size:2
Alignment explanation
Indices: 248876--248954 Score: 158
Period size: 2 Copynumber: 39.5 Consensus size: 2
248866 AATTGAAATC
248876 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
248918 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
248955 TTAAACGACT
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 77 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:251480 original size:34 final size:34
Alignment explanation
Indices: 251442--251509 Score: 111
Period size: 34 Copynumber: 2.0 Consensus size: 34
251432 TGAGTTTAAA
251442 ACATATGATTAGTTGG-GATGATCATTTTGTAACT
1 ACATATGATTAGTTGGAG-TGATCATTTTGTAACT
*
251476 ACATATGATTAGTTTGAGTGATCATTTTGTAACT
1 ACATATGATTAGTTGGAGTGATCATTTTGTAACT
251510 TTTTATAGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 31 0.97
35 1 0.03
ACGTcount: A:0.29, C:0.09, G:0.19, T:0.43
Consensus pattern (34 bp):
ACATATGATTAGTTGGAGTGATCATTTTGTAACT
Found at i:258898 original size:60 final size:60
Alignment explanation
Indices: 258834--258948 Score: 133
Period size: 60 Copynumber: 1.9 Consensus size: 60
258824 TGGTCCCTCA
* * *
258834 ACTATA-AGCTACTATTTTATTAAGTCACTTGATTATTAAAAGTTACAAAACGATCCTCTG
1 ACTATAGAG-TACTACTTTATTAAGTCACTCGACTATTAAAAGTTACAAAACGATCCTCTG
** * * * *
258894 ACTATAGAGTGTTACTTTGTTGAGTCACTCGACTATTAAAAGTTATAAAATGATC
1 ACTATAGAGTACTACTTTATTAAGTCACTCGACTATTAAAAGTTACAAAACGATC
258949 ATCCGGTTAT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
60 43 0.96
61 2 0.04
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.37
Consensus pattern (60 bp):
ACTATAGAGTACTACTTTATTAAGTCACTCGACTATTAAAAGTTACAAAACGATCCTCTG
Found at i:260009 original size:13 final size:13
Alignment explanation
Indices: 259986--260016 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
259976 AATCTACAAC
259986 TAAAA-AATAAAA
1 TAAAATAATAAAA
259998 TAAAATAATAAAA
1 TAAAATAATAAAA
260011 TAAAAT
1 TAAAAT
260017 TCTAGCTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 5 0.28
13 13 0.72
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
TAAAATAATAAAA
Found at i:261260 original size:19 final size:20
Alignment explanation
Indices: 261236--261276 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
261226 AAATTTACGT
261236 TAGTCCAAATT-CGTTGCGA
1 TAGTCCAAATTACGTTGCGA
*
261255 TAGTCCAAGTTCACGTTGCGA
1 TAGTCCAAATT-ACGTTGCGA
261276 T
1 T
261277 TTTGAAAAAT
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:0.24, C:0.22, G:0.22, T:0.32
Consensus pattern (20 bp):
TAGTCCAAATTACGTTGCGA
Found at i:261722 original size:19 final size:20
Alignment explanation
Indices: 261697--261786 Score: 103
Period size: 19 Copynumber: 4.3 Consensus size: 20
261687 CTTATTTTGG
261697 ATTTTTCACTATCGCAACAC
1 ATTTTTCACTATCGCAACAC
261717 -TTTTTCACTATCGCAACAAC
1 ATTTTTCACTATCGCAAC-AC
*
261737 ACGTTTTTCAAACTCTCGCAACAC
1 A--TTTTTC--ACTATCGCAACAC
*
261761 A-TTTTAACTATCGCAACAC
1 ATTTTTCACTATCGCAACAC
261780 ATTTTTC
1 ATTTTTC
261787 GAAATCGCGT
Statistics
Matches: 59, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
19 30 0.51
20 6 0.10
21 4 0.07
23 6 0.10
24 3 0.05
25 10 0.17
ACGTcount: A:0.30, C:0.29, G:0.06, T:0.36
Consensus pattern (20 bp):
ATTTTTCACTATCGCAACAC
Found at i:261837 original size:21 final size:21
Alignment explanation
Indices: 261789--261849 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 21
261779 CATTTTTCGA
*
261789 AATCGCGTTGCGAATCT-TAC
1 AATCGCGTTGCGAATCTGGAC
*
261809 AATCGCGTTGCGAATCTGGAT
1 AATCGCGTTGCGAATCTGGAC
* *
261830 ATTCGCGTTGCGAATTTGGA
1 AATCGCGTTGCGAATCTGGA
261850 AACGGGGTTG
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
20 17 0.47
21 19 0.53
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.31
Consensus pattern (21 bp):
AATCGCGTTGCGAATCTGGAC
Found at i:265312 original size:17 final size:17
Alignment explanation
Indices: 265290--265323 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
265280 AAGAGAAAGC
*
265290 AGTAAAACGTTTATTGA
1 AGTAAAACATTTATTGA
265307 AGTAAAACATTTATTGA
1 AGTAAAACATTTATTGA
265324 TACTCTGATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.15, T:0.35
Consensus pattern (17 bp):
AGTAAAACATTTATTGA
Found at i:265557 original size:36 final size:36
Alignment explanation
Indices: 265501--265644 Score: 146
Period size: 36 Copynumber: 3.8 Consensus size: 36
265491 AGATGAACAA
*
265501 TTGAGTCGAAAGTGCTGATGCTTCCTTCCGTTCACT
1 TTGAATCGAAAGTGCTGATGCTTCCTTCCGTTCACT
*
265537 TTGAATCGAAAGTG-TCGATGCTTTCGATGCTTCCTTTCATTCTT
1 TTGAATCGAAAGTGCT-GATGC-TTC----CTTCCGTTCA--C-T
* *
265581 CTTGAACCGAAAGTGCCGATGCTTCCTTCCGTTCACT
1 -TTGAATCGAAAGTGCTGATGCTTCCTTCCGTTCACT
*
265618 TTGAATCGAAAGTGCTTATGCTTCCTT
1 TTGAATCGAAAGTGCTGATGCTTCCTT
265645 TCGTACTTCT
Statistics
Matches: 89, Mismatches: 8, Indels: 22
0.75 0.07 0.18
Matches are distributed among these distances:
35 1 0.01
36 42 0.47
37 4 0.04
38 1 0.01
40 9 0.10
41 9 0.10
43 1 0.01
44 4 0.04
45 18 0.20
ACGTcount: A:0.19, C:0.24, G:0.19, T:0.38
Consensus pattern (36 bp):
TTGAATCGAAAGTGCTGATGCTTCCTTCCGTTCACT
Found at i:266849 original size:17 final size:17
Alignment explanation
Indices: 266827--266860 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
266817 AAGAGAAAGC
*
266827 AGTAAAACGTTTATTGA
1 AGTAAAACATTTATTGA
266844 AGTAAAACATTTATTGA
1 AGTAAAACATTTATTGA
266861 TACTCTGATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.15, T:0.35
Consensus pattern (17 bp):
AGTAAAACATTTATTGA
Found at i:269314 original size:130 final size:133
Alignment explanation
Indices: 269115--269360 Score: 399
Period size: 130 Copynumber: 1.9 Consensus size: 133
269105 TAAAAAAATG
* *
269115 ACAAAACCGGTCTATAAATGACAAAACATGTAAAGCGCTACCGGATATATTGAAAGTATCAATAC
1 ACAAAACCGGTCAATAAATGACAAAACATGTAAAGCGCTACCGGATATATTGAAAGTATCAATAA
269180 TTTATAAAAATATATCGATCCATAACAATATAACAAGTAAAAAATGACAAACAATATAACAGAAA
66 TTTATAAAAATATATCGATCCATAACAATATAACAAGTAAAAAATGACAAACAATATAACAGAAA
269245 AAA
131 AAA
* * *
269248 ACAAAACC-GTCAATAAATGACAAAACA-GTTAAGCGCTA-CGGATATATTGAAAGTGTCGATAA
1 ACAAAACCGGTCAATAAATGACAAAACATGTAAAGCGCTACCGGATATATTGAAAGTATCAATAA
* * *
269310 TTTATAAAAATGTATCGATCTATAACAATATAACATGTAAAAAATGACAAA
66 TTTATAAAAATATATCGATCCATAACAATATAACAAGTAAAAAATGACAAA
269361 ACCGGTATAT
Statistics
Matches: 105, Mismatches: 8, Indels: 3
0.91 0.07 0.03
Matches are distributed among these distances:
130 69 0.66
131 10 0.10
132 18 0.17
133 8 0.08
ACGTcount: A:0.51, C:0.14, G:0.12, T:0.23
Consensus pattern (133 bp):
ACAAAACCGGTCAATAAATGACAAAACATGTAAAGCGCTACCGGATATATTGAAAGTATCAATAA
TTTATAAAAATATATCGATCCATAACAATATAACAAGTAAAAAATGACAAACAATATAACAGAAA
AAA
Found at i:269418 original size:111 final size:108
Alignment explanation
Indices: 269229--269479 Score: 386
Period size: 111 Copynumber: 2.3 Consensus size: 108
269219 AAAAATGACA
* *
269229 AACAATATAACA-G-AAAAAA--ACAAAACC-GTCAATAAATGACAAAACAGTTAAGCGCTACGG
1 AACAATATAACATGTAAAAAATGACAAAACCGGT-AATAAATGAAAAAACAGTAAAGCGCTACGG
*
269289 ATATATTGAAAGTGTCGATAATTTATAAAAATGTATCGATCTAT
65 ATATATTGAAAGTGTCGATAATTTATAAAAATGTATCGATCCAT
269333 AACAATATAACATGTAAAAAATGACAAAACCGGTATATAAATGAAAAAACAGGTAAAGCGCTACC
1 AACAATATAACATGTAAAAAATGACAAAACCGGTA-ATAAATGAAAAAACA-GTAAAGCGCTA-C
*
269398 GGATATATTGAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
63 GGATATATTGAAAGTGTCGATAATTTATAAAAATGTATCGATCCAT
*
269444 AACAATATAACATGTAAAAAATGACAAAACAGGTAA
1 AACAATATAACATGTAAAAAATGACAAAACCGGTAA
269480 AACACTACCG
Statistics
Matches: 134, Mismatches: 5, Indels: 10
0.90 0.03 0.07
Matches are distributed among these distances:
104 12 0.09
105 1 0.01
106 6 0.04
108 9 0.07
109 16 0.12
110 11 0.08
111 79 0.59
ACGTcount: A:0.50, C:0.13, G:0.14, T:0.23
Consensus pattern (108 bp):
AACAATATAACATGTAAAAAATGACAAAACCGGTAATAAATGAAAAAACAGTAAAGCGCTACGGA
TATATTGAAAGTGTCGATAATTTATAAAAATGTATCGATCCAT
Found at i:269766 original size:181 final size:178
Alignment explanation
Indices: 269491--269834 Score: 548
Period size: 181 Copynumber: 1.9 Consensus size: 178
269481 ACACTACCGT
* * *
269491 ATATGTTGATAGTGTCGATACTTTATTATAAATATCGACACTTTTGGAATTTAAAAGAGAATAAA
1 ATATGTTGAAAGTGTCGATACTTTATTATAAATATCGACACTTTTGGAATTTAAAAGAAAAGAAA
*
269556 TTATAGCGCTAATAAAGTGTCGATACTTTATAAGAATGTATCGATCCATAACAATATAACAG-TA
66 TTATAGCGCTAATAAAGTGTCGATACTTTATAA-AATATATCGATCCATAACAATATAACAGAT-
269620 AAAATATGAAAAAATCGGTCTCGAAATGACAAAATCGGTAAAGAGCTACCAA
129 AAAA-ATGAAAAAATCGG-CTCGAAATGACAAAATCGGTAAAGAGCTACCAA
* * *
269672 ATATGTTGAAAGTGTCGATATTTTATTATAAGTATCGACACTTTTGGAATTTAAAAGAAAAGAAG
1 ATATGTTGAAAGTGTCGATACTTTATTATAAATATCGACACTTTTGGAATTTAAAAGAAAAGAAA
269737 TTATAGCG-TCAATAAAGTGTCGATACTTTATAAAATATATCGATCCATAACAATATAACAGATA
66 TTATAGCGCT-AATAAAGTGTCGATACTTTATAAAATATATCGATCCATAACAATATAACAGATA
* *
269801 AAAATGATAAAATCGGCTCGAAATGATAAAATCG
130 AAAATGAAAAAATCGGCTCGAAATGACAAAATCG
269835 TAGTAAAAAA
Statistics
Matches: 152, Mismatches: 9, Indels: 7
0.90 0.05 0.04
Matches are distributed among these distances:
178 17 0.11
179 12 0.08
180 32 0.21
181 91 0.60
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.30
Consensus pattern (178 bp):
ATATGTTGAAAGTGTCGATACTTTATTATAAATATCGACACTTTTGGAATTTAAAAGAAAAGAAA
TTATAGCGCTAATAAAGTGTCGATACTTTATAAAATATATCGATCCATAACAATATAACAGATAA
AAATGAAAAAATCGGCTCGAAATGACAAAATCGGTAAAGAGCTACCAA
Found at i:270885 original size:172 final size:171
Alignment explanation
Indices: 270540--270892 Score: 615
Period size: 172 Copynumber: 2.1 Consensus size: 171
270530 ATGGTTCCAA
*
270540 AATTATTTGAGTTGTGTTTTGCAAATAGACTTTCGATATTATGTCGTAGAACTAGTGCTTGAAAC
1 AATT-TTTAAGTTGTGTTTTGCAAATAGACTTTCGATATTATGTCGTAGAACTAGTGCTTGAAAC
270605 ATTATGTCGTTGACCCATTAAAGTAATAGTGGTATTAATAGACATCATTAAAATAATATTTTATG
65 ATTATGTCGTTGACCCATTAAAGTAATAGTGGTATTAATAGACATCATTAAAATAATATTTTATG
270670 ATATATCAGCCTGCAAATTAACGCTCGACTCAAACAATCGTC
130 ATATATCAGCCTGCAAATTAACGCTCGACTCAAACAATCGTC
270712 AATTTTTAAGTTGTGTTTTGCAAATAGACTCTTCGATTATATTATGTCGTAGAACTAGTGCTTGA
1 AATTTTTAAGTTGTGTTTTGCAAATAGACT-TTCG---ATATTATGTCGTAGAACTAGTGCTTGA
270777 AACATTATGTCGTTGACCCATTAAAAGTAATAGTGGTATT-A-AGACATCATTAAAAT-A-ATTT
62 AACATTATGTCGTTGACCCATT-AAAGTAATAGTGGTATTAATAGACATCATTAAAATAATATTT
270838 TATGATATATCAGCCTGCAAATTAACGCTCGACTCAAACAATCGTC
126 TATGATATATCAGCCTGCAAATTAACGCTCGACTCAAACAATCGTC
270884 AATTTTTAA
1 AATTTTTAA
270893 TAGAAAATAA
Statistics
Matches: 175, Mismatches: 1, Indels: 10
0.94 0.01 0.05
Matches are distributed among these distances:
171 25 0.14
172 67 0.38
173 1 0.01
174 15 0.09
175 50 0.29
176 17 0.10
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Consensus pattern (171 bp):
AATTTTTAAGTTGTGTTTTGCAAATAGACTTTCGATATTATGTCGTAGAACTAGTGCTTGAAACA
TTATGTCGTTGACCCATTAAAGTAATAGTGGTATTAATAGACATCATTAAAATAATATTTTATGA
TATATCAGCCTGCAAATTAACGCTCGACTCAAACAATCGTC
Found at i:272836 original size:24 final size:23
Alignment explanation
Indices: 272802--272846 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
272792 TAATAATACC
*
272802 AAAAATAAAAATTAAATTATTCA
1 AAAAATAAAAAATAAATTATTCA
*
272825 AAAAATTAAAAAATATATTATT
1 AAAAA-TAAAAAATAAATTATT
272847 ACTTTTTTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (23 bp):
AAAAATAAAAAATAAATTATTCA
Found at i:273178 original size:2 final size:2
Alignment explanation
Indices: 273171--273206 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
273161 AAAACAAATA
273171 AT AT AT AT AT AT A- 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 A
273207 GATTAGTAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:274335 original size:16 final size:17
Alignment explanation
Indices: 274314--274346 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
274304 AATATACTTT
274314 TTTATTAT-TTTTATGA
1 TTTATTATATTTTATGA
274330 TTTATTATATTTTATGA
1 TTTATTATATTTTATGA
274347 CATATGAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (17 bp):
TTTATTATATTTTATGA
Found at i:276775 original size:6 final size:5
Alignment explanation
Indices: 276757--276799 Score: 50
Period size: 6 Copynumber: 7.8 Consensus size: 5
276747 TTAAAAATTT
276757 GAGTC GAGATC GAGCTC GAGTC GAGTTC GAGCTC GAGTC GAGT
1 GAGTC GAG-TC GAG-TC GAGTC GAG-TC GAG-TC GAGTC GAGT
276800 TCATTCGATT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
5 14 0.41
6 20 0.59
ACGTcount: A:0.21, C:0.21, G:0.37, T:0.21
Consensus pattern (5 bp):
GAGTC
Found at i:276799 original size:17 final size:17
Alignment explanation
Indices: 276757--276801 Score: 81
Period size: 17 Copynumber: 2.6 Consensus size: 17
276747 TTAAAAATTT
*
276757 GAGTCGAGATCGAGCTC
1 GAGTCGAGTTCGAGCTC
276774 GAGTCGAGTTCGAGCTC
1 GAGTCGAGTTCGAGCTC
276791 GAGTCGAGTTC
1 GAGTCGAGTTC
276802 ATTCGATTCG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.20, C:0.22, G:0.36, T:0.22
Consensus pattern (17 bp):
GAGTCGAGTTCGAGCTC
Found at i:277621 original size:160 final size:162
Alignment explanation
Indices: 277340--277660 Score: 420
Period size: 159 Copynumber: 2.0 Consensus size: 162
277330 TGTTATATAT
* * * *
277340 ACACATATATTATCCACCAAAATCTAATTATCTTTTTGGGTAAATTAGACATTTAATATCTAAAC
1 ACACATATATTATCCACCAAAATCTAATTACCTTTTTGGGTAAACTAGACATTTAACACCTAAAC
** * *
277405 TATCAATTTTGATATATTTTAGTATTTAAATTTTTAAATTTTTAAAATTATACCTAACGTTTA-T
66 TATCAATTTTGATATATTTTAGTACCTAAATCTTCAAATTTTTAAAATTATACCTAACGTTTAGT
277469 TTTT-TTTCATTTTAGTATCACACTCTTAAAC
131 TTTTGTTTCATTTTAGTATCACACTCTTAAAC
277500 ACACATATATTATCCACCAAAATCTAATT-CCTTTTTGGGTAAACTATG-CATTTAACACCTAAA
1 ACACATATATTATCCACCAAAATCTAATTACCTTTTTGGGTAAACTA-GACATTTAACACCTAAA
* * ** * *
277563 CTATTAATTTTGAT-TCTTTTTTTTACCTAAA-CTTCAATTTTTTTAAAAATTATACCTAACTTT
65 CTATCAATTTTGATAT-ATTTTAGTACCTAAATCTTCAA-ATTTTT-AAAATTATACCTAACGTT
* *
277626 TAGTTTTTGTTTCATTTTAGTATCCCACTGTTAAA
127 TAGTTTTTGTTTCATTTTAGTATCACACTCTTAAA
277661 AACTTAACAT
Statistics
Matches: 139, Mismatches: 16, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
158 5 0.04
159 56 0.40
160 49 0.35
161 5 0.04
162 24 0.17
ACGTcount: A:0.34, C:0.15, G:0.05, T:0.46
Consensus pattern (162 bp):
ACACATATATTATCCACCAAAATCTAATTACCTTTTTGGGTAAACTAGACATTTAACACCTAAAC
TATCAATTTTGATATATTTTAGTACCTAAATCTTCAAATTTTTAAAATTATACCTAACGTTTAGT
TTTTGTTTCATTTTAGTATCACACTCTTAAAC
Found at i:278580 original size:61 final size:61
Alignment explanation
Indices: 278515--278629 Score: 149
Period size: 61 Copynumber: 1.9 Consensus size: 61
278505 TCGGGTGACT
* *
278515 ATTTTGTAACTTTTAACAGTCAAGAGACTCAACAAAGTAACAAACTATAGTCGAAGGAAAA
1 ATTTTGTAACATTTAACAGTCAAGAGACTCAACAAAATAACAAACTATAGTCGAAGGAAAA
* * * * * **
278576 ATTTTGTAACATTTAAGAGTCGAGGGACTTAATAAAATAACACCCTATAGTCGA
1 ATTTTGTAACATTTAACAGTCAAGAGACTCAACAAAATAACAAACTATAGTCGA
278630 TGAATCATTC
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
61 45 1.00
ACGTcount: A:0.43, C:0.15, G:0.16, T:0.27
Consensus pattern (61 bp):
ATTTTGTAACATTTAACAGTCAAGAGACTCAACAAAATAACAAACTATAGTCGAAGGAAAA
Found at i:286897 original size:4 final size:4
Alignment explanation
Indices: 286888--286918 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
286878 TGTCAACTTA
*
286888 TCTT TCTT TCTT TTTT TCTT TCTT TCTT TCT
1 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCT
286919 CCTTCTATGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TCTT
Found at i:287160 original size:22 final size:22
Alignment explanation
Indices: 287129--287182 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
287119 GTTTGCTTCT
287129 TTTGTGTGCTGGTAAAACCATA
1 TTTGTGTGCTGGTAAAACCATA
* *
287151 TTTGTATGCTGTTAAAACCATA
1 TTTGTGTGCTGGTAAAACCATA
287173 TTTGTGTGCT
1 TTTGTGTGCT
287183 AGTAGCATTG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.24, C:0.13, G:0.20, T:0.43
Consensus pattern (22 bp):
TTTGTGTGCTGGTAAAACCATA
Found at i:293879 original size:24 final size:23
Alignment explanation
Indices: 293852--293904 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
293842 CATCCATATC
* *
293852 CTTGTGACATAATTTTTCTTTGCT
1 CTTGTGACATAA-TTTCCTCTGCT
* *
293876 CTTGTGGCATCATTTCCTCTGCT
1 CTTGTGACATAATTTCCTCTGCT
293899 CTTGTG
1 CTTGTG
293905 GCACGATCCT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
23 15 0.60
24 10 0.40
ACGTcount: A:0.11, C:0.23, G:0.17, T:0.49
Consensus pattern (23 bp):
CTTGTGACATAATTTCCTCTGCT
Found at i:297477 original size:39 final size:39
Alignment explanation
Indices: 297337--297735 Score: 241
Period size: 39 Copynumber: 9.7 Consensus size: 39
297327 AAATAATTTC
* * *
297337 AATCCACCGATTTATTTTCTTTT-CCAAATCATGAAAATA
1 AATCCAACGATTTATTTTCTTTTACAAAAT-AGGAAAATA
* * *
297376 AATCCAACGTTTTATTTTCTTTT-CCAAATCATGAAAATA
1 AATCCAACGATTTATTTTCTTTTACAAAAT-AGGAAAATA
*
297415 AATCCAACGTTTTATTTTCTTTTACAAAATAGGAAAATA
1 AATCCAACGATTTATTTTCTTTTACAAAATAGGAAAATA
* *
297454 AATCTAACGATTTATTTTCTTTTATAAAATAGGAAAATA
1 AATCCAACGATTTATTTTCTTTTACAAAATAGGAAAATA
* *
297493 AATCAAACAATTTGTTTCGATTTATTTTCCTCTTACAAAACAGGAAAATA
1 AATC---CAA-------CGATTTATTTT-CTTTTACAAAATAGGAAAATA
* * *
297543 ACTCAAACGATTTGTTTCAATTTATTTACTTTTACAAAATAGGAAACTA
1 AATCCAACGA----TTT--A--T-TTT-CTTTTACAAAATAGGAAAATA
* * * * *
297592 AATCCAGCAATTTATTTGCTTTTTAAAAAATAAGAAAATA
1 AATCCAACGATTTATTTTC-TTTTACAAAATAGGAAAATA
* * ** * *
297632 AATCTAACGATTTATTTCCTTTTACAAACCAAGAAACTA
1 AATCCAACGATTTATTTTCTTTTACAAAATAGGAAAATA
*** *
297671 AATTTTATGATTTAATTCTT-TTTT-CAAAATA-GAAAAGTA
1 AATCCAACGATTT-ATT-TTCTTTTACAAAATAGGAAAA-TA
* *
297710 AATCCAATGATTTATTTCCTTTTACA
1 AATCCAACGATTTATTTTCTTTTACA
297736 TATAAGAATT
Statistics
Matches: 289, Mismatches: 44, Indels: 54
0.75 0.11 0.14
Matches are distributed among these distances:
37 1 0.00
38 11 0.04
39 154 0.53
40 49 0.17
41 2 0.01
42 2 0.01
43 1 0.00
44 3 0.01
45 3 0.01
46 1 0.00
47 2 0.01
48 1 0.00
49 38 0.13
50 21 0.07
ACGTcount: A:0.40, C:0.14, G:0.07, T:0.39
Consensus pattern (39 bp):
AATCCAACGATTTATTTTCTTTTACAAAATAGGAAAATA
Found at i:297477 original size:49 final size:49
Alignment explanation
Indices: 297424--297604 Score: 168
Period size: 50 Copynumber: 3.9 Consensus size: 49
297414 AAATCCAACG
*
297424 TTTTATTTTCTTTTACAAAATAGGAAAATAAATCTAAC-----G----A
1 TTTTATTTTCTTTTACAAAATAGGAAAATAAATCAAACAATTTGTTTCA
*
297464 -TTTATTTTCTTTTATAAAATAGGAAAATAAATCAAACAATTTGTTTCGA
1 TTTTATTTTCTTTTACAAAATAGGAAAATAAATCAAACAATTTGTTTC-A
* * * *
297513 -TTTATTTTCCTCTTACAAAACAGGAAAATAACTCAAACGATTTGTTTCA
1 TTTTATTTT-CTTTTACAAAATAGGAAAATAAATCAAACAATTTGTTTCA
* * * * *
297562 ATTTATTTACTTTTACAAAATAGGAAACTAAATCCAGCAATTT
1 TTTTATTTTCTTTTACAAAATAGGAAAATAAATCAAACAATTT
297605 ATTTGCTTTT
Statistics
Matches: 114, Mismatches: 15, Indels: 15
0.79 0.10 0.10
Matches are distributed among these distances:
39 35 0.31
44 1 0.01
49 37 0.32
50 41 0.36
ACGTcount: A:0.40, C:0.13, G:0.08, T:0.39
Consensus pattern (49 bp):
TTTTATTTTCTTTTACAAAATAGGAAAATAAATCAAACAATTTGTTTCA
Found at i:297549 original size:50 final size:49
Alignment explanation
Indices: 297461--297604 Score: 189
Period size: 50 Copynumber: 2.9 Consensus size: 49
297451 ATAAATCTAA
*
297461 CGATTTATTTTCTTTTATAAAATAGGAAAATAAATCAAACAATTTGTTT
1 CGATTTATTTTCTTTTACAAAATAGGAAAATAAATCAAACAATTTGTTT
* * * *
297510 CGATTTATTTTCCTCTTACAAAACAGGAAAATAACTCAAACGATTTGTTT
1 CGATTTATTTT-CTTTTACAAAATAGGAAAATAAATCAAACAATTTGTTT
* * * * *
297560 CAATTTATTTACTTTTACAAAATAGGAAACTAAATCCAGCAATTT
1 CGATTTATTTTCTTTTACAAAATAGGAAAATAAATCAAACAATTT
297605 ATTTGCTTTT
Statistics
Matches: 80, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
49 38 0.47
50 42 0.52
ACGTcount: A:0.40, C:0.14, G:0.08, T:0.38
Consensus pattern (49 bp):
CGATTTATTTTCTTTTACAAAATAGGAAAATAAATCAAACAATTTGTTT
Found at i:297622 original size:40 final size:40
Alignment explanation
Indices: 297560--297654 Score: 111
Period size: 40 Copynumber: 2.4 Consensus size: 40
297550 CGATTTGTTT
* * * *
297560 CAATTTATTTAC-TTTTACAAAATAGGAAACTAAATCCAG
1 CAATTTATTTACTTTTTAAAAAATAAGAAAATAAATCCAA
* *
297599 CAATTTATTTGCTTTTTAAAAAATAAGAAAATAAATCTAA
1 CAATTTATTTACTTTTTAAAAAATAAGAAAATAAATCCAA
* *
297639 CGATTTATTTCCTTTT
1 CAATTTATTTACTTTT
297655 ACAAACCAAG
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
39 11 0.23
40 36 0.77
ACGTcount: A:0.41, C:0.13, G:0.06, T:0.40
Consensus pattern (40 bp):
CAATTTATTTACTTTTTAAAAAATAAGAAAATAAATCCAA
Found at i:297951 original size:57 final size:59
Alignment explanation
Indices: 297844--297955 Score: 158
Period size: 57 Copynumber: 1.9 Consensus size: 59
297834 GAATCATGTG
* * *
297844 AGATTCTCAAGAAAAATAAATTTAACAATTTATTTTTATTACAATATTAGAATCATTAA
1 AGATTCTCAAGAAAAATAAATTCAACAATATATTTTCATTACAATATTAGAATCATTAA
*
297903 AGATTCTCAAG-AAAA-AAATTCAACAATATATTTTCATTTCAA-AGTTAGAATCA
1 AGATTCTCAAGAAAAATAAATTCAACAATATATTTTCATTACAATA-TTAGAATCA
297956 ACACAATATT
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
56 1 0.02
57 32 0.67
58 4 0.08
59 11 0.23
ACGTcount: A:0.47, C:0.11, G:0.06, T:0.36
Consensus pattern (59 bp):
AGATTCTCAAGAAAAATAAATTCAACAATATATTTTCATTACAATATTAGAATCATTAA
Found at i:298168 original size:45 final size:44
Alignment explanation
Indices: 298119--298267 Score: 167
Period size: 45 Copynumber: 3.3 Consensus size: 44
298109 TTTTACCAAC
* *
298119 CCAATAATCAAAATGAACTAATCATTTGATTTTAATTTT-CTAA
1 CCAATAATCAAAAGGAACTAATCATTTGATTTTACTTTTGCTAA
** * * *
298162 GTCCAATAATTGAAGGGAACTAGTCCTTTGATTTTACTTTTGGC-AA
1 --CCAATAATCAAAAGGAACTAATCATTTGATTTTACTTTT-GCTAA
*
298208 CACAATAATCAAAAGGAACTAATCATTTGATTTTACTTTTGATAA
1 C-CAATAATCAAAAGGAACTAATCATTTGATTTTACTTTTGCTAA
298253 CCCAATAATCAAAAG
1 -CCAATAATCAAAAG
298268 CATTAGATTA
Statistics
Matches: 86, Mismatches: 13, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
44 2 0.02
45 80 0.93
46 3 0.03
47 1 0.01
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.35
Consensus pattern (44 bp):
CCAATAATCAAAAGGAACTAATCATTTGATTTTACTTTTGCTAA
Found at i:298877 original size:30 final size:30
Alignment explanation
Indices: 298843--298904 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
298833 AATGTTACTT
298843 TAACGATAATTTATATTACATATATTTGTC
1 TAACGATAATTTATATTACATATATTTGTC
*
298873 TAACGATAATTTCTATTACATATATTTGTC
1 TAACGATAATTTATATTACATATATTTGTC
298903 TA
1 TA
298905 CTTTAAAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.35, C:0.11, G:0.06, T:0.47
Consensus pattern (30 bp):
TAACGATAATTTATATTACATATATTTGTC
Found at i:309891 original size:16 final size:16
Alignment explanation
Indices: 309867--309900 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
309857 AGCAAAATCC
* *
309867 ATCATCTACATAGCTT
1 ATCACCTACATAGATT
309883 ATCACCTACATAGATT
1 ATCACCTACATAGATT
309899 AT
1 AT
309901 ATGCTCTTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.35, C:0.24, G:0.06, T:0.35
Consensus pattern (16 bp):
ATCACCTACATAGATT
Found at i:315024 original size:2 final size:2
Alignment explanation
Indices: 315019--315057 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
315009 ATCAAAGTTT
*
315019 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GG GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
315058 TACACTGAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (2 bp):
GA
Done.