Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168481.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_8, 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: 25818110
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 67000 characters in sequence are not A, C, G, or T
File 113 of 127
Found at i:21146186 original size:14 final size:14
Alignment explanation
Indices: 21146139--21146196 Score: 57
Period size: 14 Copynumber: 4.2 Consensus size: 14
21146129 TTTATCTTAA
21146139 TTTTA-TTTT-TAT
1 TTTTATTTTTCTAT
* * *
21146151 TTTTGTTTTACTTT
1 TTTTATTTTTCTAT
21146165 TCTTTATTTTTCTAT
1 T-TTTATTTTTCTAT
*
21146180 TTTTATTATTCTAT
1 TTTTATTTTTCTAT
21146194 TTT
1 TTT
21146197 CTTTAAATAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
12 4 0.11
13 3 0.08
14 18 0.50
15 11 0.31
ACGTcount: A:0.14, C:0.07, G:0.02, T:0.78
Consensus pattern (14 bp):
TTTTATTTTTCTAT
Found at i:21146201 original size:17 final size:17
Alignment explanation
Indices: 21146162--21146201 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 17
21146152 TTTGTTTTAC
*
21146162 TTTTCTTTATTTTTCTA
1 TTTTCTTTATTATTCTA
21146179 --TT-TTTATTATTCTA
1 TTTTCTTTATTATTCTA
21146193 TTTTCTTTA
1 TTTTCTTTA
21146202 AATAAAAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 6
0.73 0.04 0.23
Matches are distributed among these distances:
14 11 0.58
15 2 0.11
16 2 0.11
17 4 0.21
ACGTcount: A:0.15, C:0.10, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTTCTTTATTATTCTA
Found at i:21156058 original size:8 final size:8
Alignment explanation
Indices: 21156045--21156131 Score: 88
Period size: 8 Copynumber: 10.6 Consensus size: 8
21156035 ACTATGCCTG
21156045 AAAAATGA
1 AAAAATGA
21156053 AAAAATGA
1 AAAAATGA
21156061 AGAAAA-GA
1 A-AAAATGA
*
21156069 AAAAATAAA
1 AAAAAT-GA
21156078 AAAAATGA
1 AAAAATGA
*
21156086 AAAAATTAA
1 AAAAA-TGA
*
21156095 AAAAATAA
1 AAAAATGA
21156103 AAAAAT-A
1 AAAAATGA
*
21156110 AAAAATAAA
1 AAAAAT-GA
21156119 AAAAATGA
1 AAAAATGA
21156127 AAAAA
1 AAAAA
21156132 AAGTGAAAAA
Statistics
Matches: 69, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
7 11 0.16
8 33 0.48
9 25 0.36
ACGTcount: A:0.82, C:0.00, G:0.07, T:0.11
Consensus pattern (8 bp):
AAAAATGA
Found at i:21156082 original size:33 final size:34
Alignment explanation
Indices: 21156045--21156132 Score: 119
Period size: 33 Copynumber: 2.6 Consensus size: 34
21156035 ACTATGCCTG
* *
21156045 AAAAATGAAAAAATGAAGAAAA-GAAAAAATAAA
1 AAAAATGAAAAAATGAAAAAAATAAAAAAATAAA
*
21156078 AAAAATGAAAAAATTAAAAAAATAAAAAAATAAA
1 AAAAATGAAAAAATGAAAAAAATAAAAAAATAAA
21156112 AAATAA--AAAAAATGAAAAAAA
1 AAA-AATGAAAAAATGAAAAAAA
21156133 AGTGAAAAAG
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
33 34 0.69
34 13 0.27
35 2 0.04
ACGTcount: A:0.82, C:0.00, G:0.07, T:0.11
Consensus pattern (34 bp):
AAAAATGAAAAAATGAAAAAAATAAAAAAATAAA
Found at i:21156090 original size:41 final size:41
Alignment explanation
Indices: 21156052--21156131 Score: 133
Period size: 41 Copynumber: 1.9 Consensus size: 41
21156042 CTGAAAAATG
*
21156052 AAAAAATGAAGAAAAGAAAAAATAAAAAAAATGAAAAAATTA
1 AAAAAAT-AAAAAAAGAAAAAATAAAAAAAATGAAAAAATTA
*
21156094 AAAAAATAAAAAAATAAAAAATAAAAAAAATGAAAAAA
1 AAAAAATAAAAAAAGAAAAAATAAAAAAAATGAAAAAA
21156132 AAGTGAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
41 29 0.81
42 7 0.19
ACGTcount: A:0.82, C:0.00, G:0.06, T:0.11
Consensus pattern (41 bp):
AAAAAATAAAAAAAGAAAAAATAAAAAAAATGAAAAAATTA
Found at i:21156138 original size:11 final size:10
Alignment explanation
Indices: 21156068--21156141 Score: 60
Period size: 9 Copynumber: 8.3 Consensus size: 10
21156058 TGAAGAAAAG
21156068 AAAAAAT-AA
1 AAAAAATGAA
21156077 AAAAAATG--
1 AAAAAATGAA
*
21156085 AAAAAAT-TA
1 AAAAAATGAA
21156094 AAAAAAT--A
1 AAAAAATGAA
21156102 AAAAAAT---
1 AAAAAATGAA
21156109 AAAAAAT-AA
1 AAAAAATGAA
21156118 AAAAAATGAA
1 AAAAAATGAA
21156128 AAAAAAGTGAA
1 AAAAAA-TGAA
21156139 AAA
1 AAA
21156142 GAAGGACTCA
Statistics
Matches: 58, Mismatches: 0, Indels: 12
0.83 0.00 0.17
Matches are distributed among these distances:
7 7 0.12
8 15 0.26
9 21 0.36
10 8 0.14
11 7 0.12
ACGTcount: A:0.82, C:0.00, G:0.05, T:0.12
Consensus pattern (10 bp):
AAAAAATGAA
Found at i:21157232 original size:42 final size:42
Alignment explanation
Indices: 21157156--21157365 Score: 284
Period size: 42 Copynumber: 5.0 Consensus size: 42
21157146 GATTGTGAAT
*
21157156 GAGCAATTTA-TTTTTCAAAGTTTCGT--TGCCTCTGTTTAGAG
1 GAGCAATTTACTTTTCCAAAG--TCGTGGTGCCTCTGTTTAGAG
*
21157197 GAGCAATTTACTTTTCCAAAGTCGTGGTGCTTCTGTTTAGAG
1 GAGCAATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAG
* *
21157239 GAGCAATTTACTTTTCCAAAGTCGTGGTGTCTCTGTTTAGAT
1 GAGCAATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAG
* * *
21157281 GAACAATTTACTTTTCAAAAGTCGTTGTGCCTCTGTTTAGAG
1 GAGCAATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAG
* * *
21157323 GAGTAATTTA-TTTTCCAAAGTCGTTGAGCCTCTGTTTAGAG
1 GAGCAATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAG
21157364 GA
1 GA
21157366 ACTTTGGTCA
Statistics
Matches: 152, Mismatches: 14, Indels: 6
0.88 0.08 0.03
Matches are distributed among these distances:
40 4 0.03
41 41 0.27
42 107 0.70
ACGTcount: A:0.23, C:0.16, G:0.21, T:0.40
Consensus pattern (42 bp):
GAGCAATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAG
Found at i:21157396 original size:12 final size:12
Alignment explanation
Indices: 21157375--21157416 Score: 50
Period size: 11 Copynumber: 3.4 Consensus size: 12
21157365 AACTTTGGTC
21157375 AAAAACAAAAAA
1 AAAAACAAAAAA
*
21157387 AAAAA-GAAAAA
1 AAAAACAAAAAA
21157398 AAAAACAACAACAA
1 AAAAACAA-AA-AA
21157412 AAAAA
1 AAAAA
21157417 TGACAATGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
11 10 0.40
12 6 0.24
13 2 0.08
14 7 0.28
ACGTcount: A:0.88, C:0.10, G:0.02, T:0.00
Consensus pattern (12 bp):
AAAAACAAAAAA
Found at i:21157400 original size:14 final size:15
Alignment explanation
Indices: 21157378--21157416 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
21157368 TTTGGTCAAA
*
21157378 AACAAAAAAAAAAAG
1 AACAAAAAAAAAAAC
*
21157393 AA-AAAAAAAACAAC
1 AACAAAAAAAAAAAC
21157407 AACAAAAAAA
1 AACAAAAAAA
21157417 TGACAATGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.87, C:0.10, G:0.03, T:0.00
Consensus pattern (15 bp):
AACAAAAAAAAAAAC
Found at i:21157632 original size:3 final size:3
Alignment explanation
Indices: 21157614--21157659 Score: 78
Period size: 3 Copynumber: 16.0 Consensus size: 3
21157604 CCTTCTTTTG
21157614 TAT T-T TAT TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
21157660 GTATATCTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 4 0.10
3 37 0.90
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:21157819 original size:26 final size:25
Alignment explanation
Indices: 21157765--21157824 Score: 61
Period size: 24 Copynumber: 2.4 Consensus size: 25
21157755 GATTTATTTT
21157765 ATTTTATTTTTTAATTATCTG-TTA
1 ATTTTATTTTTTAATTATCTGTTTA
*
21157789 ATTTTATTTTATTCATTTATCTGATTT-
1 ATTTTATTTT-TT-AATTATCTG-TTTA
*
21157816 TTTTTATTT
1 ATTTTATTT
21157825 ATCCGATTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
24 10 0.33
25 2 0.07
26 8 0.27
27 8 0.27
28 2 0.07
ACGTcount: A:0.22, C:0.05, G:0.03, T:0.70
Consensus pattern (25 bp):
ATTTTATTTTTTAATTATCTGTTTA
Found at i:21157840 original size:18 final size:18
Alignment explanation
Indices: 21157797--21157841 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
21157787 TAATTTTATT
* *
21157797 TTATTCATTTATCTGATTT
1 TTATT-ATTTATCCGATTA
*
21157816 TTTTTATTTATCCGATTA
1 TTATTATTTATCCGATTA
21157834 TTATTATT
1 TTATTATT
21157842 ATTATTATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 18 0.82
19 4 0.18
ACGTcount: A:0.22, C:0.09, G:0.04, T:0.64
Consensus pattern (18 bp):
TTATTATTTATCCGATTA
Found at i:21158301 original size:11 final size:11
Alignment explanation
Indices: 21158279--21158314 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
21158269 ATCCCAGAAA
*
21158279 CCGGTGACCTT
1 CCGGTGAACTT
*
21158290 CTGGTGAACTT
1 CCGGTGAACTT
21158301 CCGGTGAACTT
1 CCGGTGAACTT
21158312 CCG
1 CCG
21158315 ACGAAAAAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.14, C:0.31, G:0.28, T:0.28
Consensus pattern (11 bp):
CCGGTGAACTT
Found at i:21158335 original size:20 final size:20
Alignment explanation
Indices: 21158310--21158347 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
21158300 TCCGGTGAAC
21158310 TTCCGACGAAAAAACCCAGA
1 TTCCGACGAAAAAACCCAGA
* *
21158330 TTCCGATGACAAAACCCA
1 TTCCGACGAAAAAACCCA
21158348 AAATCTGGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.32, G:0.13, T:0.13
Consensus pattern (20 bp):
TTCCGACGAAAAAACCCAGA
Found at i:21158748 original size:4 final size:4
Alignment explanation
Indices: 21158699--21158732 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
21158689 TTTTTTGAAT
* *
21158699 TTTA TTTA TTTA TTTA TTTG TTTT TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
21158733 AGATTAGGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (4 bp):
TTTA
Found at i:21158775 original size:17 final size:16
Alignment explanation
Indices: 21158741--21158780 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
21158731 TTAGATTAGG
*
21158741 TTTATTTAATATTCTT
1 TTTATTTAATATTATT
*
21158757 TTTATCTTAATTTTATT
1 TTTAT-TTAATATTATT
21158774 TTTATTT
1 TTTATTT
21158781 TTGTTTTACT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTATTTAATATTATT
Found at i:21158787 original size:17 final size:17
Alignment explanation
Indices: 21158767--21158814 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
21158757 TTTATCTTAA
21158767 TTTTATTTTTATTT-TT
1 TTTTATTTTTATTTATT
* *
21158783 GTTTTACTTTTCTTTATT
1 -TTTTATTTTTATTTATT
21158801 TTTCTATTTTTATT
1 TTT-TATTTTTATT
21158815 ATTCTATTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
17 15 0.60
18 10 0.40
ACGTcount: A:0.12, C:0.06, G:0.02, T:0.79
Consensus pattern (17 bp):
TTTTATTTTTATTTATT
Found at i:21158814 original size:14 final size:14
Alignment explanation
Indices: 21158767--21158825 Score: 59
Period size: 14 Copynumber: 4.3 Consensus size: 14
21158757 TTTATCTTAA
21158767 TTTTA-TTTT-TAT
1 TTTTATTTTTCTAT
* * *
21158779 TTTTGTTTTACTTT
1 TTTTATTTTTCTAT
21158793 TCTTTATTTTTCTAT
1 T-TTTATTTTTCTAT
*
21158808 TTTTATTATTCTAT
1 TTTTATTTTTCTAT
21158822 TTTT
1 TTTT
21158826 TTTAAATAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
12 4 0.11
13 3 0.08
14 19 0.51
15 11 0.30
ACGTcount: A:0.14, C:0.07, G:0.02, T:0.78
Consensus pattern (14 bp):
TTTTATTTTTCTAT
Found at i:21158919 original size:58 final size:57
Alignment explanation
Indices: 21158853--21159006 Score: 265
Period size: 56 Copynumber: 2.7 Consensus size: 57
21158843 ATTTCCAAAA
21158853 AAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
1 AAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAA-TTTC
*
21158911 AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAA-TTTCCTTAAAAATAAATTTC
1 AAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTC
* *
21158967 AAAAAAATGTTTTTTGGGAAAAGTTGAAAGTATCAATTTT
1 AAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTT
21159007 TCCTACACAA
Statistics
Matches: 92, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
56 38 0.41
57 19 0.21
58 35 0.38
ACGTcount: A:0.45, C:0.06, G:0.13, T:0.36
Consensus pattern (57 bp):
AAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTC
Found at i:21159734 original size:32 final size:33
Alignment explanation
Indices: 21159687--21159758 Score: 87
Period size: 32 Copynumber: 2.2 Consensus size: 33
21159677 TGTTATATAA
* *
21159687 AATTTAAAAATGATTTGAA-TTAACTAA-AATTTG
1 AATTTGAAAATGATTTGAACTCAA--AATAATTTG
21159720 AATTTGAAAA-GATTTGAACTCAAAATAATTTG
1 AATTTGAAAATGATTTGAACTCAAAATAATTTG
21159752 AATTTGA
1 AATTTGA
21159759 CAAAACATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
31 2 0.06
32 21 0.60
33 12 0.34
ACGTcount: A:0.47, C:0.04, G:0.11, T:0.38
Consensus pattern (33 bp):
AATTTGAAAATGATTTGAACTCAAAATAATTTG
Found at i:21160494 original size:31 final size:30
Alignment explanation
Indices: 21160457--21160514 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
21160447 AAAAATTACA
21160457 AGTAGATTTTGTAT-AATATTTTGTATTAATC
1 AGTAGATTTT-TATCAATATTTT-TATTAATC
*
21160488 AGTAGATTTTTATCATTATTTTTATTA
1 AGTAGATTTTTATCAATATTTTTATTA
21160515 GCAACATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 8 0.32
31 17 0.68
ACGTcount: A:0.31, C:0.03, G:0.10, T:0.55
Consensus pattern (30 bp):
AGTAGATTTTTATCAATATTTTTATTAATC
Found at i:21168087 original size:14 final size:14
Alignment explanation
Indices: 21168068--21168125 Score: 57
Period size: 14 Copynumber: 4.2 Consensus size: 14
21168058 TTATTTAAAG
*
21168068 AAAATAGAATAATA
1 AAAATAGAAAAATA
21168082 AAAATAGAAAAATA
1 AAAATAGAAAAATA
* * *
21168096 AAGAAAAGTAAAACA
1 AA-AATAGAAAAATA
21168111 AAAAT--AAAAATA
1 AAAATAGAAAAATA
21168123 AAA
1 AAA
21168126 TTAAGATAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
12 8 0.22
14 17 0.47
15 11 0.31
ACGTcount: A:0.78, C:0.02, G:0.07, T:0.14
Consensus pattern (14 bp):
AAAATAGAAAAATA
Found at i:21168095 original size:17 final size:17
Alignment explanation
Indices: 21168075--21168125 Score: 52
Period size: 17 Copynumber: 2.9 Consensus size: 17
21168065 AAGAAAATAG
21168075 AATAATAAAAATAGAAA-
1 AATAATAAAAATA-AAAC
21168092 AATAA-AGAAAAGTAAAAC
1 AATAATA-AAAA-TAAAAC
*
21168110 AAAAATAAAAATAAAA
1 AATAATAAAAATAAAA
21168126 TTAAGATAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
16 1 0.03
17 17 0.59
18 10 0.34
19 1 0.03
ACGTcount: A:0.78, C:0.02, G:0.06, T:0.14
Consensus pattern (17 bp):
AATAATAAAAATAAAAC
Found at i:21168134 original size:17 final size:16
Alignment explanation
Indices: 21168112--21168151 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
21168102 AGTAAAACAA
*
21168112 AAATAAAAATAAAATT
1 AAATAAAAAGAAAATT
*
21168128 AAGATAAAAAGAATATT
1 AA-ATAAAAAGAAAATT
21168145 AAATAAA
1 AAATAAA
21168152 CCTAATCTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (16 bp):
AAATAAAAAGAAAATT
Found at i:21169155 original size:14 final size:16
Alignment explanation
Indices: 21169136--21169186 Score: 56
Period size: 15 Copynumber: 3.4 Consensus size: 16
21169126 ATAAATTATA
21169136 ATATAA-TA-ATAAAT
1 ATATAACTATATAAAT
21169150 ATATAACTATATAAAT
1 ATATAACTATATAAAT
* *
21169166 AAATTAC-ATATAAAT
1 ATATAACTATATAAAT
21169181 AT-TAAC
1 ATATAAC
21169187 AGAAAAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
14 9 0.29
15 11 0.35
16 11 0.35
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (16 bp):
ATATAACTATATAAAT
Found at i:21169260 original size:13 final size:12
Alignment explanation
Indices: 21169238--21169280 Score: 59
Period size: 14 Copynumber: 3.3 Consensus size: 12
21169228 AATAAAATAC
21169238 AAAAAAAGATAA
1 AAAAAAAGATAA
21169250 AAAAAAGAGATAA
1 AAAAAA-AGATAA
21169263 AAAATACAAGATAA
1 AAAA-A-AAGATAA
21169277 AAAA
1 AAAA
21169281 TTGAATTGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
12 6 0.21
13 10 0.36
14 11 0.39
15 1 0.04
ACGTcount: A:0.79, C:0.02, G:0.09, T:0.09
Consensus pattern (12 bp):
AAAAAAAGATAA
Found at i:21169265 original size:14 final size:13
Alignment explanation
Indices: 21169238--21169280 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
21169228 AATAAAATAC
21169238 AAAAAAAGATAAA
1 AAAAAAAGATAAA
*
21169251 AAAAAGAGATAAA
1 AAAAAAAGATAAA
*
21169264 AAATACAAGATAAA
1 AAA-AAAAGATAAA
21169278 AAA
1 AAA
21169281 TTGAATTGAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
13 15 0.58
14 11 0.42
ACGTcount: A:0.79, C:0.02, G:0.09, T:0.09
Consensus pattern (13 bp):
AAAAAAAGATAAA
Found at i:21169281 original size:14 final size:13
Alignment explanation
Indices: 21169222--21169281 Score: 63
Period size: 12 Copynumber: 4.7 Consensus size: 13
21169212 AATAATAATA
*
21169222 ATAAATAATAAA-
1 ATAAAAAATAAAG
*
21169234 ATACAAAA-AAAG
1 ATAAAAAATAAAG
21169246 ATAAAAAA-AAGAG
1 ATAAAAAATAA-AG
21169259 ATAAAAAATACAAG
1 ATAAAAAATA-AAG
21169273 ATAAAAAAT
1 ATAAAAAAT
21169282 TGAATTGAGT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
11 3 0.07
12 15 0.37
13 10 0.24
14 12 0.29
15 1 0.02
ACGTcount: A:0.75, C:0.03, G:0.07, T:0.15
Consensus pattern (13 bp):
ATAAAAAATAAAG
Found at i:21169890 original size:3 final size:3
Alignment explanation
Indices: 21169884--21169914 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
21169874 TTTAAAAGAG
21169884 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
21169915 CAAAGCGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:21170355 original size:7 final size:7
Alignment explanation
Indices: 21170345--21170410 Score: 60
Period size: 7 Copynumber: 8.9 Consensus size: 7
21170335 AAAAATAAAA
21170345 TTTTATT
1 TTTTATT
21170352 TTTTATAT
1 TTTTAT-T
21170360 TTTTATT
1 TTTTATT
21170367 TTTTATT
1 TTTTATT
* *
21170374 TTATCTT
1 TTTTATT
*
21170381 TTATATAT
1 TTTTAT-T
*
21170389 TTATATT
1 TTTTATT
21170396 TTGTTAATT
1 TT-TT-ATT
21170405 TTTTAT
1 TTTTAT
21170411 AAATATATAT
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
7 29 0.57
8 17 0.33
9 5 0.10
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.76
Consensus pattern (7 bp):
TTTTATT
Found at i:21170365 original size:15 final size:15
Alignment explanation
Indices: 21170345--21170407 Score: 67
Period size: 15 Copynumber: 4.3 Consensus size: 15
21170335 AAAAATAAAA
21170345 TTTTATTTTTTATAT
1 TTTTATTTTTTATAT
21170360 TTTTATTTTTTAT-T
1 TTTTATTTTTTATAT
* * *
21170374 TTATCTTTTATATAT
1 TTTTATTTTTTATAT
*
21170389 TTATATTTTGTTA-AT
1 TTTTATTTT-TTATAT
21170404 TTTT
1 TTTT
21170408 TATAAATATA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
14 11 0.28
15 27 0.68
16 2 0.05
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.76
Consensus pattern (15 bp):
TTTTATTTTTTATAT
Found at i:21170374 original size:27 final size:27
Alignment explanation
Indices: 21170344--21170421 Score: 86
Period size: 27 Copynumber: 2.9 Consensus size: 27
21170334 AAAAAATAAA
* *
21170344 ATTTTATTTTTTATATTTTTATTTTTT
1 ATTTTATTTTTTATATATTTATATTTT
*
21170371 ATTTTATCTTTTATATATTTATATTTT
1 ATTTTATTTTTTATATATTTATATTTT
* * * *
21170398 -GTTAATTTTTTATAAATATATATT
1 ATTTTATTTTTTATATATTTATATT
21170422 AATATTTTTT
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
26 19 0.44
27 24 0.56
ACGTcount: A:0.27, C:0.01, G:0.01, T:0.71
Consensus pattern (27 bp):
ATTTTATTTTTTATATATTTATATTTT
Found at i:21175708 original size:2 final size:2
Alignment explanation
Indices: 21175701--21175735 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
21175691 TGCGGTAAAA
21175701 AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
21175736 CATTGACTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:21175723 original size:13 final size:12
Alignment explanation
Indices: 21175701--21175735 Score: 56
Period size: 11 Copynumber: 3.1 Consensus size: 12
21175691 TGCGGTAAAA
21175701 ATATATATATAT
1 ATATATATATAT
21175713 ATATA-ATATAT
1 ATATATATATAT
21175724 ATATAT-TATAT
1 ATATATATATAT
21175735 A
1 A
21175736 CATTGACTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 17 0.77
12 5 0.23
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (12 bp):
ATATATATATAT
Found at i:21177560 original size:31 final size:31
Alignment explanation
Indices: 21177507--21177565 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
21177497 TTTATGTTGC
21177507 TAATAAAAATAATGATAAAAAATCTACTGAT
1 TAATAAAAATAATGATAAAAAATCTACTGAT
* *
21177538 TAATACAAAAT-ATTATACAAAATCTACT
1 TAATA-AAAATAATGATAAAAAATCTACT
21177566 TGTAATTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 20 0.80
32 5 0.20
ACGTcount: A:0.56, C:0.10, G:0.03, T:0.31
Consensus pattern (31 bp):
TAATAAAAATAATGATAAAAAATCTACTGAT
Found at i:21178321 original size:32 final size:33
Alignment explanation
Indices: 21178264--21178335 Score: 87
Period size: 32 Copynumber: 2.2 Consensus size: 33
21178254 ATATGTTTTG
*
21178264 TCAAATTCAAATTATTTTGAGTTCAAATC-TTT
1 TCAAATTCAAATTATTTTGAATTCAAATCATTT
21178296 TCAAATTCAAATT-TTAGTT-AATTCAAATCATTT
1 TCAAATTCAAATTATT--TTGAATTCAAATCATTT
*
21178329 TTAAATT
1 TCAAATT
21178336 TTATATAACA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
31 2 0.06
32 22 0.63
33 11 0.31
ACGTcount: A:0.38, C:0.11, G:0.04, T:0.47
Consensus pattern (33 bp):
TCAAATTCAAATTATTTTGAATTCAAATCATTT
Found at i:21179134 original size:57 final size:57
Alignment explanation
Indices: 21179015--21179228 Score: 333
Period size: 58 Copynumber: 3.7 Consensus size: 57
21179005 TTTGTGTAGG
* *
21179015 GAAAATTGATACTTTCAACTTTTCCCAAAAAACATTTTTTTTG-AAATTTATTTTTAAG
1 GAAAATTGATACTTTCAACTTTTCCC-AAAAATA-TTTTTTTGAAAATTTATTTTTAAA
21179073 GAAAATTGATACTTTCAACTTTTCCCAAAAATATTTTTTTGAAAATTTATTTTTAAA
1 GAAAATTGATACTTTCAACTTTTCCCAAAAATATTTTTTTGAAAATTTATTTTTAAA
*
21179130 GAAAATTGATACTTTCAACTTTTCCCCAAAAATGTTTTTTTGAAAATTTATTTTT-AA
1 GAAAATTGATACTTTCAACTTTT-CCCAAAAATATTTTTTTGAAAATTTATTTTTAAA
*
21179187 GAAAAATTGATACTTTCAACTTTTTCCTAAAAATATTTTTTT
1 G-AAAATTGATACTTTCAAC-TTTTCCCAAAAATATTTTTTT
21179229 TTTGGAAATT
Statistics
Matches: 147, Mismatches: 5, Indels: 8
0.92 0.03 0.05
Matches are distributed among these distances:
56 8 0.05
57 46 0.31
58 89 0.61
59 4 0.03
ACGTcount: A:0.36, C:0.12, G:0.06, T:0.46
Consensus pattern (57 bp):
GAAAATTGATACTTTCAACTTTTCCCAAAAATATTTTTTTGAAAATTTATTTTTAAA
Found at i:21179210 original size:115 final size:116
Alignment explanation
Indices: 21179015--21179228 Score: 362
Period size: 115 Copynumber: 1.9 Consensus size: 116
21179005 TTTGTGTAGG
*
21179015 GAAAATTGATACTTTCAACTTTTCCCAAAAAACATTTTTTTTGAAATTTATTTTTAAGGAAAATT
1 GAAAATTGATACTTTCAACTTTTCCCAAAAAACATTTTTTTTGAAATTTATTTTTAAGAAAAATT
21179080 GATACTTTCAAC-TTTTCCCAAAAATATTTTTTTGAAAATTTATTTTTAAA
66 GATACTTTCAACTTTTTCCCAAAAATATTTTTTTGAAAATTTATTTTTAAA
*
21179130 GAAAATTGATACTTTCAACTTTTCCC-CAAAA-ATGTTTTTTTGAAAATTTATTTTTAAGAAAAA
1 GAAAATTGATACTTTCAACTTTTCCCAAAAAACAT-TTTTTTTG-AAATTTATTTTTAAGAAAAA
*
21179193 TTGATACTTTCAACTTTTTCCTAAAAATATTTTTTT
64 TTGATACTTTCAACTTTTTCCCAAAAATATTTTTTT
21179229 TTTGGAAATT
Statistics
Matches: 93, Mismatches: 3, Indels: 5
0.92 0.03 0.05
Matches are distributed among these distances:
113 2 0.02
114 12 0.13
115 59 0.63
116 20 0.22
ACGTcount: A:0.36, C:0.12, G:0.06, T:0.46
Consensus pattern (116 bp):
GAAAATTGATACTTTCAACTTTTCCCAAAAAACATTTTTTTTGAAATTTATTTTTAAGAAAAATT
GATACTTTCAACTTTTTCCCAAAAATATTTTTTTGAAAATTTATTTTTAAA
Found at i:21179283 original size:17 final size:18
Alignment explanation
Indices: 21179263--21179313 Score: 63
Period size: 17 Copynumber: 2.9 Consensus size: 18
21179253 AAGAAAATAG
21179263 AATAATAAAAATAAAA-A
1 AATAATAAAAATAAAACA
21179280 AATAA-AGAAAAGTAAAACA
1 AATAATA-AAAA-TAAAACA
21179299 AA-AATAAAAATAAAA
1 AATAATAAAAATAAAA
21179314 TTAAGATAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
16 1 0.03
17 14 0.47
18 11 0.37
19 4 0.13
ACGTcount: A:0.80, C:0.02, G:0.04, T:0.14
Consensus pattern (18 bp):
AATAATAAAAATAAAACA
Found at i:21179322 original size:17 final size:16
Alignment explanation
Indices: 21179300--21179339 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
21179290 AGTAAAACAA
*
21179300 AAATAAAAATAAAATT
1 AAATAAAAAGAAAATT
*
21179316 AAGATAAAAAGAATATT
1 AA-ATAAAAAGAAAATT
21179333 AAATAAA
1 AAATAAA
21179340 CCTAATCTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (16 bp):
AAATAAAAAGAAAATT
Found at i:21179746 original size:20 final size:20
Alignment explanation
Indices: 21179721--21179758 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
21179711 CACCAGATTT
21179721 TGGGTTTTGTCATCGGAATC
1 TGGGTTTTGTCATCGGAATC
* *
21179741 TGGGTTTTTTCGTCGGAA
1 TGGGTTTTGTCATCGGAA
21179759 GTTCACCGGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.13, G:0.32, T:0.42
Consensus pattern (20 bp):
TGGGTTTTGTCATCGGAATC
Found at i:21179770 original size:11 final size:11
Alignment explanation
Indices: 21179754--21179789 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
21179744 GTTTTTTCGT
21179754 CGGAAGTTCAC
1 CGGAAGTTCAC
21179765 CGGAAGTTCAC
1 CGGAAGTTCAC
* *
21179776 CAGAAGGTCAC
1 CGGAAGTTCAC
21179787 CGG
1 CGG
21179790 TTTCTGGGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.28, C:0.28, G:0.31, T:0.14
Consensus pattern (11 bp):
CGGAAGTTCAC
Found at i:21180425 original size:16 final size:16
Alignment explanation
Indices: 21180404--21180440 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
21180394 AAATAAAGAT
21180404 ATAAATAATAATAATA-
1 ATAAATAATAA-AATAC
21180420 ATAAATAATAAAATAC
1 ATAAATAATAAAATAC
21180436 ATAAA
1 ATAAA
21180441 ATACAAAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (16 bp):
ATAAATAATAAAATAC
Found at i:21180445 original size:9 final size:8
Alignment explanation
Indices: 21180406--21180443 Score: 51
Period size: 9 Copynumber: 4.6 Consensus size: 8
21180396 ATAAAGATAT
21180406 AAATAATA
1 AAATAATA
21180414 ATAATAAT-
1 A-AATAATA
21180422 AAATAATA
1 AAATAATA
21180430 AAATACATA
1 AAATA-ATA
21180439 AAATA
1 AAATA
21180444 CAAAAGAAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
7 6 0.22
8 7 0.26
9 14 0.52
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (8 bp):
AAATAATA
Found at i:21180663 original size:10 final size:10
Alignment explanation
Indices: 21180644--21180693 Score: 66
Period size: 10 Copynumber: 5.0 Consensus size: 10
21180634 ACATTTTCAT
21180644 TTTTTGTTTTG
1 TTTTT-TTTTG
21180655 TTTTTTTTTG
1 TTTTTTTTTG
*
21180665 TGTTTTTTTG
1 TTTTTTTTTG
*
21180675 TTGTTTTTT-
1 TTTTTTTTTG
21180684 TTTTTTTTTG
1 TTTTTTTTTG
21180694 ACCAAAGCTC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
9 8 0.24
10 21 0.62
11 5 0.15
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (10 bp):
TTTTTTTTTG
Found at i:21180757 original size:41 final size:41
Alignment explanation
Indices: 21180700--21180984 Score: 338
Period size: 40 Copynumber: 7.1 Consensus size: 41
21180690 TTTGACCAAA
* * * *
21180700 GCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAATG
1 GCTCCTCTAAACAGAGGCACAACGACTTTGGAAAGTAAATT
* *
21180741 GCTCCTCTAAACAGAGGCACAATGACTTTTGAAAGTAAA-T
1 GCTCCTCTAAACAGAGGCACAACGACTTTGGAAAGTAAATT
* * * *
21180781 ACTCATCT-AACAGA-GTAC-ACGAC-TTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACAACGACTTTGGAAAGTAAATT
*
21180818 GCTCCTCTAAACAGAGGCACCACGACTTT-GAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACAACGACTTTGGAAAGTAAATT
* * *
21180858 GCTCCTCTAAATAGAAGCACCACGAC-TTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACAACGACTTTGGAAAGTAAATT
*
21180898 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAA-T
1 GCTCCTCTAAACAGAGGCACAACGACTTTGGAAAGTAAATT
*
21180938 GCTCCTCTAAACAGAGG--CAACGAAACTTTGGAAAATAAATT
1 GCTCCTCTAAACAGAGGCACAACG--ACTTTGGAAAGTAAATT
21180979 GCTCCT
1 GCTCCT
21180985 TCACAATCAT
Statistics
Matches: 212, Mismatches: 22, Indels: 20
0.83 0.09 0.08
Matches are distributed among these distances:
36 10 0.05
37 11 0.05
38 13 0.06
39 11 0.05
40 112 0.53
41 55 0.26
ACGTcount: A:0.38, C:0.22, G:0.17, T:0.23
Consensus pattern (41 bp):
GCTCCTCTAAACAGAGGCACAACGACTTTGGAAAGTAAATT
Found at i:21182005 original size:12 final size:11
Alignment explanation
Indices: 21181988--21182057 Score: 58
Period size: 11 Copynumber: 6.3 Consensus size: 11
21181978 TGAGTCCTCC
21181988 TTTTTTCACTTT
1 TTTTTTCA-TTT
21182000 TTTTTTCA-TT
1 TTTTTTCATTT
*
21182010 TTTTCT-ATTT
1 TTTTTTCATTT
21182020 TTCATTTT--TTT
1 TT--TTTTCATTT
21182031 CATTTTTTCATTT
1 --TTTTTTCATTT
21182044 TTTTTTCATTT
1 TTTTTTCATTT
21182055 TTT
1 TTT
21182058 CTTTTCTTCA
Statistics
Matches: 49, Mismatches: 2, Indels: 15
0.74 0.03 0.23
Matches are distributed among these distances:
9 1 0.02
10 11 0.22
11 21 0.43
12 11 0.22
13 5 0.10
ACGTcount: A:0.10, C:0.11, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTTTTCATTT
Found at i:21182011 original size:8 final size:8
Alignment explanation
Indices: 21182000--21182073 Score: 80
Period size: 8 Copynumber: 8.8 Consensus size: 8
21181990 TTTTCACTTT
21182000 TTTTTTCA
1 TTTTTTCA
21182008 TTTTTTC-
1 TTTTTTCA
21182015 TATTTTTCA
1 T-TTTTTCA
21182024 TTTTTTTCA
1 -TTTTTTCA
21182033 TTTTTTCA
1 TTTTTTCA
21182041 TTTTTTTTTCA
1 ---TTTTTTCA
21182052 TTTTTTC-
1 TTTTTTCA
21182059 TTTTCTTCA
1 TTTT-TTCA
21182068 TTTTTT
1 TTTTTT
21182074 TTATTTTTCA
Statistics
Matches: 58, Mismatches: 0, Indels: 16
0.78 0.00 0.22
Matches are distributed among these distances:
7 5 0.09
8 33 0.57
9 11 0.19
10 1 0.02
11 8 0.14
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTTTTCA
Found at i:21182022 original size:16 final size:15
Alignment explanation
Indices: 21181997--21182083 Score: 78
Period size: 16 Copynumber: 5.8 Consensus size: 15
21181987 CTTTTTTCAC
21181997 TTTT-TTTTTCATTT
1 TTTTATTTTTCATTT
21182011 TTTCTATTTTTCATTT
1 TTT-TATTTTTCATTT
21182027 TTTTCATTTTTTCA---
1 TTTT-A-TTTTTCATTT
21182041 TTTT-TTTTTCATTT
1 TTTTATTTTTCATTT
21182055 TTTCT-TTTCTTCATTTT
1 TTT-TATTT-TTCA-TTT
21182072 TTTTATTTTTCA
1 TTTTATTTTTCA
21182084 GGCATAGTAC
Statistics
Matches: 62, Mismatches: 0, Indels: 20
0.76 0.00 0.24
Matches are distributed among these distances:
11 7 0.11
14 10 0.16
15 6 0.10
16 23 0.37
17 16 0.26
ACGTcount: A:0.10, C:0.11, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTTATTTTTCATTT
Found at i:21182028 original size:17 final size:17
Alignment explanation
Indices: 21182000--21182073 Score: 91
Period size: 16 Copynumber: 4.4 Consensus size: 17
21181990 TTTTCACTTT
21182000 TTTTTTCA-TTTTTTC-
1 TTTTTTCATTTTTTTCA
21182015 TATTTTTCATTTTTTTCA
1 T-TTTTTCATTTTTTTCA
21182033 TTTTTTCATTTTTTTTTCA
1 TTTTTTCA--TTTTTTTCA
*
21182052 TTTTTTC-TTTTCTTCA
1 TTTTTTCATTTTTTTCA
21182068 TTTTTT
1 TTTTTT
21182074 TTATTTTTCA
Statistics
Matches: 53, Mismatches: 1, Indels: 9
0.84 0.02 0.14
Matches are distributed among these distances:
15 1 0.02
16 21 0.40
17 14 0.26
18 1 0.02
19 16 0.30
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTTTCATTTTTTTCA
Found at i:21182033 original size:25 final size:24
Alignment explanation
Indices: 21181999--21182081 Score: 95
Period size: 25 Copynumber: 3.6 Consensus size: 24
21181989 TTTTTCACTT
21181999 TTTTTTTCATTTTTTCTATTTTTCA
1 TTTTTTTCATTTTTTC-ATTTTTCA
21182024 TTTTTTTCATTTTTTCA---TT--
1 TTTTTTTCATTTTTTCATTTTTCA
*
21182043 TTTTTTTCATTTTTTCTTTTCTTCA
1 TTTTTTTCATTTTTTCATTT-TTCA
*
21182068 TTTTTTTTATTTTT
1 TTTTTTTCATTTTT
21182082 CAGGCATAGT
Statistics
Matches: 50, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
19 16 0.32
21 2 0.04
23 2 0.04
24 1 0.02
25 29 0.58
ACGTcount: A:0.10, C:0.11, G:0.00, T:0.80
Consensus pattern (24 bp):
TTTTTTTCATTTTTTCATTTTTCA
Found at i:21182045 original size:44 final size:45
Alignment explanation
Indices: 21181988--21182081 Score: 156
Period size: 44 Copynumber: 2.1 Consensus size: 45
21181978 TGAGTCCTCC
21181988 TTTTTTCACTTTTTTTTTCATTTTTTCTATTT-TTCATTTTTTTCA
1 TTTTTTCACTTTTTTTTTCATTTTTTCT-TTTCTTCATTTTTTTCA
*
21182033 TTTTTTCA-TTTTTTTTTCATTTTTTCTTTTCTTCATTTTTTTTA
1 TTTTTTCACTTTTTTTTTCATTTTTTCTTTTCTTCATTTTTTTCA
21182077 TTTTT
1 TTTTT
21182082 CAGGCATAGT
Statistics
Matches: 47, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
43 3 0.06
44 36 0.77
45 8 0.17
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.79
Consensus pattern (45 bp):
TTTTTTCACTTTTTTTTTCATTTTTTCTTTTCTTCATTTTTTTCA
Found at i:21182073 original size:11 final size:10
Alignment explanation
Indices: 21181988--21182081 Score: 59
Period size: 8 Copynumber: 10.3 Consensus size: 10
21181978 TGAGTCCTCC
21181988 TTTTTTCACTTT
1 TTTTTTCA--TT
21182000 TTTTTTCA--
1 TTTTTTCATT
21182008 TTTTTTC--T
1 TTTTTTCATT
*
21182016 ATTTTTCA-T
1 TTTTTTCATT
21182025 TTTTTTCA--
1 TTTTTTCATT
21182033 TTTTTTCATTT
1 TTTTTTCA-TT
21182044 TTTTTTCA--
1 TTTTTTCATT
21182052 TTTTTTC--T
1 TTTTTTCATT
*
21182060 TTTCTTCATT
1 TTTTTTCATT
21182070 TTTTTT-ATT
1 TTTTTTCATT
21182079 TTT
1 TTT
21182082 CAGGCATAGT
Statistics
Matches: 70, Mismatches: 4, Indels: 19
0.75 0.04 0.20
Matches are distributed among these distances:
8 34 0.49
9 14 0.20
10 6 0.09
11 8 0.11
12 8 0.11
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTTTTCATT
Found at i:21182079 original size:9 final size:9
Alignment explanation
Indices: 21181998--21182081 Score: 50
Period size: 9 Copynumber: 9.6 Consensus size: 9
21181988 TTTTTTCACT
21181998 TTTTTTTTCA
1 TTTTTTTT-A
*
21182008 TTTTTTCTA
1 TTTTTTTTA
*
21182017 --TTTTTCA
1 TTTTTTTTA
*
21182024 TTTTTTTCA
1 TTTTTTTTA
*
21182033 -TTTTTTCA
1 TTTTTTTTA
21182041 TTTTTTTT-
1 TTTTTTTTA
* *
21182049 TCATTTTTTC
1 T-TTTTTTTA
* *
21182059 TTTTCTTCA
1 TTTTTTTTA
21182068 TTTTTTTTA
1 TTTTTTTTA
21182077 TTTTT
1 TTTTT
21182082 CAGGCATAGT
Statistics
Matches: 58, Mismatches: 11, Indels: 11
0.73 0.14 0.14
Matches are distributed among these distances:
7 5 0.09
8 9 0.16
9 36 0.62
10 8 0.14
ACGTcount: A:0.10, C:0.11, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:21192624 original size:14 final size:14
Alignment explanation
Indices: 21192605--21192662 Score: 57
Period size: 14 Copynumber: 4.2 Consensus size: 14
21192595 TTATTTAAAG
*
21192605 AAAATAGAATAATA
1 AAAATAGAAAAATA
21192619 AAAATAGAAAAATA
1 AAAATAGAAAAATA
* * *
21192633 AAGAAAAGTAAAACA
1 AA-AATAGAAAAATA
21192648 AAAAT--AAAAATA
1 AAAATAGAAAAATA
21192660 AAA
1 AAA
21192663 TTAAGATAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
12 8 0.22
14 17 0.47
15 11 0.31
ACGTcount: A:0.78, C:0.02, G:0.07, T:0.14
Consensus pattern (14 bp):
AAAATAGAAAAATA
Found at i:21192632 original size:17 final size:17
Alignment explanation
Indices: 21192612--21192662 Score: 52
Period size: 17 Copynumber: 2.9 Consensus size: 17
21192602 AAGAAAATAG
21192612 AATAATAAAAATAGAAA-
1 AATAATAAAAATA-AAAC
21192629 AATAA-AGAAAAGTAAAAC
1 AATAATA-AAAA-TAAAAC
*
21192647 AAAAATAAAAATAAAA
1 AATAATAAAAATAAAA
21192663 TTAAGATAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
16 1 0.03
17 17 0.59
18 10 0.34
19 1 0.03
ACGTcount: A:0.78, C:0.02, G:0.06, T:0.14
Consensus pattern (17 bp):
AATAATAAAAATAAAAC
Found at i:21192671 original size:17 final size:16
Alignment explanation
Indices: 21192649--21192688 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 16
21192639 AGTAAAACAA
21192649 AAATAAAAATAAA-ATT
1 AAATAAAAA-AAATATT
21192665 AAGATAAAAAAAATATT
1 AA-ATAAAAAAAATATT
21192682 AAATAAA
1 AAATAAA
21192689 CCTAATCTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 10 0.45
17 12 0.55
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.23
Consensus pattern (16 bp):
AAATAAAAAAAATATT
Found at i:21193692 original size:14 final size:16
Alignment explanation
Indices: 21193673--21193723 Score: 56
Period size: 15 Copynumber: 3.4 Consensus size: 16
21193663 ATAAATTATA
21193673 ATATAA-TA-ATAAAT
1 ATATAACTATATAAAT
21193687 ATATAACTATATAAAT
1 ATATAACTATATAAAT
* *
21193703 AAATTAC-ATATAAAT
1 ATATAACTATATAAAT
21193718 AT-TAAC
1 ATATAAC
21193724 AGAAAAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
14 9 0.29
15 11 0.35
16 11 0.35
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (16 bp):
ATATAACTATATAAAT
Found at i:21193721 original size:69 final size:64
Alignment explanation
Indices: 21193644--21193782 Score: 172
Period size: 69 Copynumber: 2.1 Consensus size: 64
21193634 AATAAATCCA
* * * * *
21193644 AAAATATTACCAGAAAAAAATAAA-TTATAATATAATAATAAATATATAACTATATAAATAAATT
1 AAAATATTAACAGAAAAAAATAAAGATAT-ACATAATAAT-AATA-ATAA-TAAAT-AATAAAAT
21193708 ACAT
61 ACAT
21193712 ATAAATATTAACAGAAAAAAATAAAGATATACATAATAATAATAATAATAAATAATAAAATACAT
1 A-AAATATTAACAGAAAAAAATAAAGATATACATAATAATAATAATAATAAATAATAAAATACAT
21193777 AAAATA
1 AAAATA
21193783 CAAAGAAGGA
Statistics
Matches: 64, Mismatches: 5, Indels: 8
0.83 0.06 0.10
Matches are distributed among these distances:
64 5 0.08
65 12 0.19
66 4 0.06
67 4 0.06
68 5 0.08
69 31 0.48
70 3 0.05
ACGTcount: A:0.65, C:0.05, G:0.02, T:0.28
Consensus pattern (64 bp):
AAAATATTAACAGAAAAAAATAAAGATATACATAATAATAATAATAATAAATAATAAAATACAT
Found at i:21193767 original size:16 final size:16
Alignment explanation
Indices: 21193740--21193779 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
21193730 AAATAAAGAT
21193740 ATACAT-AATAATAATA
1 ATACATAAATAATAA-A
21193756 ATA-ATAAATAATAAA
1 ATACATAAATAATAAA
21193771 ATACATAAA
1 ATACATAAA
21193780 ATACAAAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 6 0.27
16 16 0.73
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.28
Consensus pattern (16 bp):
ATACATAAATAATAAA
Found at i:21194436 original size:3 final size:3
Alignment explanation
Indices: 21194430--21194454 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
21194420 TTTAAAAGAG
21194430 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
21194455 CAAAGCGTTT
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:21194891 original size:7 final size:7
Alignment explanation
Indices: 21194880--21194920 Score: 64
Period size: 7 Copynumber: 5.7 Consensus size: 7
21194870 AAAAAATAAA
21194880 ATTTTAT
1 ATTTTAT
*
21194887 TTTTTAT
1 ATTTTAT
21194894 ATTTTAT
1 ATTTTAT
21194901 ATTTTAT
1 ATTTTAT
21194908 ATATTTAT
1 AT-TTTAT
21194916 ATTTT
1 ATTTT
21194921 GATAATTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
7 24 0.77
8 7 0.23
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (7 bp):
ATTTTAT
Found at i:21194899 original size:14 final size:15
Alignment explanation
Indices: 21194880--21194929 Score: 59
Period size: 16 Copynumber: 3.3 Consensus size: 15
21194870 AAAAAATAAA
21194880 ATTTTATTTTT-TAT
1 ATTTTATTTTTATAT
21194894 ATTTTATATTTTATAT
1 ATTTTAT-TTTTATAT
*
21194910 ATTTATATTTTGATA-
1 ATTT-TATTTTTATAT
21194925 ATTTT
1 ATTTT
21194930 TTTATAAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
14 8 0.25
15 8 0.25
16 13 0.41
17 3 0.09
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (15 bp):
ATTTTATTTTTATAT
Found at i:21204162 original size:28 final size:29
Alignment explanation
Indices: 21204130--21204187 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 29
21204120 GATATATGAG
* *
21204130 ATTGTATTAATCAGTAG-ATTTTTTATCT
1 ATTGTATTAAGCAGAAGAATTTTTTATCT
*
21204158 ATTGTATTAAGGAGAAGAATTTTTTATCT
1 ATTGTATTAAGCAGAAGAATTTTTTATCT
21204187 A
1 A
21204188 AAAGATAAGG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 14 0.54
29 12 0.46
ACGTcount: A:0.33, C:0.05, G:0.14, T:0.48
Consensus pattern (29 bp):
ATTGTATTAAGCAGAAGAATTTTTTATCT
Found at i:21208270 original size:32 final size:31
Alignment explanation
Indices: 21208234--21208294 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 31
21208224 ATATGTCTTG
21208234 TCAAATTCAAATTATT-TTGAATTCAAATCTGT
1 TCAAATTCAAATT-TTATT-AATTCAAATCTGT
21208266 TCAAATTCAAATTTTAGTTAATTCAAATC
1 TCAAATTCAAATTTTA-TTAATTCAAATC
21208295 ATTTTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
31 2 0.07
32 23 0.85
33 2 0.07
ACGTcount: A:0.39, C:0.13, G:0.05, T:0.43
Consensus pattern (31 bp):
TCAAATTCAAATTTTATTAATTCAAATCTGT
Found at i:21209036 original size:3 final size:3
Alignment explanation
Indices: 21209030--21209063 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
21209020 TTTTTAAGAG
21209030 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
21209064 CAAAGCGTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:21209516 original size:21 final size:22
Alignment explanation
Indices: 21209492--21209538 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
21209482 AAAAATAAAT
* *
21209492 TTTTATTTTTTATAT-TTTTTA
1 TTTTATCTTTTATATATTTATA
21209513 TTTTATCTTTTATATATTTATA
1 TTTTATCTTTTATATATTTATA
21209535 TTTT
1 TTTT
21209539 GATAGTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 14 0.61
22 9 0.39
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (22 bp):
TTTTATCTTTTATATATTTATA
Found at i:21209534 original size:8 final size:7
Alignment explanation
Indices: 21209492--21209538 Score: 58
Period size: 7 Copynumber: 6.6 Consensus size: 7
21209482 AAAAATAAAT
*
21209492 TTTTATT
1 TTTTATA
21209499 TTTTATA
1 TTTTATA
*
21209506 TTTTTTA
1 TTTTATA
*
21209513 TTTTATC
1 TTTTATA
21209520 TTTTATA
1 TTTTATA
21209527 TATTTATA
1 T-TTTATA
21209535 TTTT
1 TTTT
21209539 GATAGTTTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
7 27 0.79
8 7 0.21
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTTATA
Found at i:21214824 original size:2 final size:2
Alignment explanation
Indices: 21214817--21214845 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
21214807 GTTGCGGTAA
21214817 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 A
21214846 CATTGTCTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:21216009 original size:15 final size:15
Alignment explanation
Indices: 21215989--21216019 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
21215979 ATTATGAGTT
21215989 TGAAAATTTTTTATA
1 TGAAAATTTTTTATA
21216004 TGAAAATTTTTTATA
1 TGAAAATTTTTTATA
21216019 T
1 T
21216020 TTTCTTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (15 bp):
TGAAAATTTTTTATA
Found at i:21216949 original size:40 final size:40
Alignment explanation
Indices: 21216902--21216984 Score: 166
Period size: 40 Copynumber: 2.1 Consensus size: 40
21216892 ATTAGCCTCG
21216902 TACAATTTTATATTTTTGAATTGTGATTGTTTAATTATAA
1 TACAATTTTATATTTTTGAATTGTGATTGTTTAATTATAA
21216942 TACAATTTTATATTTTTGAATTGTGATTGTTTAATTATAA
1 TACAATTTTATATTTTTGAATTGTGATTGTTTAATTATAA
21216982 TAC
1 TAC
21216985 GATAATTATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.33, C:0.04, G:0.10, T:0.54
Consensus pattern (40 bp):
TACAATTTTATATTTTTGAATTGTGATTGTTTAATTATAA
Found at i:21223266 original size:2 final size:2
Alignment explanation
Indices: 21223261--21223285 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
21223251 TTCAGACTCT
21223261 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 T
21223286 TTGAAACAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:21237015 original size:35 final size:35
Alignment explanation
Indices: 21236964--21237031 Score: 120
Period size: 35 Copynumber: 1.9 Consensus size: 35
21236954 AAAGGAAAAG
21236964 TAAAAGCAAAAGCAGTATTAATTCACATTTTCACT
1 TAAAAGCAAAAGCAGTATTAATTCACATTTTCACT
21236999 TAAAAGC-AAAGCCAGTATTAATTCACATTTTCA
1 TAAAAGCAAAAG-CAGTATTAATTCACATTTTCA
21237032 TTTCTCTTAC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
34 4 0.12
35 28 0.88
ACGTcount: A:0.43, C:0.18, G:0.09, T:0.31
Consensus pattern (35 bp):
TAAAAGCAAAAGCAGTATTAATTCACATTTTCACT
Found at i:21241981 original size:10 final size:10
Alignment explanation
Indices: 21241964--21241995 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
21241954 TGTATCAAAA
21241964 TTTT-TAAAT
1 TTTTATAAAT
21241973 TTTTATAAAT
1 TTTTATAAAT
21241983 TTTTATAAAT
1 TTTTATAAAT
21241993 TTT
1 TTT
21241996 ATACATTTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 4 0.18
10 18 0.82
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (10 bp):
TTTTATAAAT
Found at i:21241985 original size:9 final size:9
Alignment explanation
Indices: 21241961--21242003 Score: 52
Period size: 9 Copynumber: 4.7 Consensus size: 9
21241951 AAATGTATCA
21241961 AAATTTT-T
1 AAATTTTAT
21241969 AAATTTTTAT
1 AAA-TTTTAT
21241979 AAATTTTTAT
1 AAA-TTTTAT
21241989 AAATTTTAT
1 AAATTTTAT
*
21241998 ACATTT
1 AAATTT
21242004 GACATATATA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
8 3 0.09
9 15 0.47
10 14 0.44
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (9 bp):
AAATTTTAT
Found at i:21241995 original size:19 final size:18
Alignment explanation
Indices: 21241961--21242003 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
21241951 AAATGTATCA
*
21241961 AAATTTTTAAATTTTTAT
1 AAATTTTTAAAATTTTAT
21241979 AAATTTTTATAAATTTTAT
1 AAATTTTTA-AAATTTTAT
*
21241998 ACATTT
1 AAATTT
21242004 GACATATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 9 0.41
19 13 0.59
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (18 bp):
AAATTTTTAAAATTTTAT
Found at i:21242049 original size:13 final size:13
Alignment explanation
Indices: 21242033--21242057 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21242023 TTAATGTATC
21242033 AATTTAATTTTTT
1 AATTTAATTTTTT
21242046 AATTTAATTTTT
1 AATTTAATTTTT
21242058 ATGTGATCAA
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
AATTTAATTTTTT
Found at i:21244742 original size:21 final size:18
Alignment explanation
Indices: 21244718--21244777 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 18
21244708 AAACATTAAT
21244718 AATAAAATTTAAAATAACAAA
1 AATAAAA-TTAAAA-AA-AAA
* *
21244739 AATAATATTAAAAAAATA
1 AATAAAATTAAAAAAAAA
21244757 AATCAAAATTAAAAAAAAA
1 AAT-AAAATTAAAAAAAAA
21244776 AA
1 AA
21244778 AATTTTATCT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
18 5 0.15
19 17 0.50
20 6 0.18
21 6 0.18
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (18 bp):
AATAAAATTAAAAAAAAA
Found at i:21249775 original size:2 final size:2
Alignment explanation
Indices: 21249768--21249794 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
21249758 TTAATTTATC
21249768 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 T
21249795 GAGGAATAAA
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:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:21249889 original size:8 final size:8
Alignment explanation
Indices: 21249876--21249909 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
21249866 TAAGATTAAA
21249876 TTATTTTT
1 TTATTTTT
21249884 TTATTTTT
1 TTATTTTT
*
21249892 TTATCTTTC
1 TTAT-TTTT
21249901 TTATTTTT
1 TTATTTTT
21249909 T
1 T
21249910 AAATTTATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.82
Consensus pattern (8 bp):
TTATTTTT
Found at i:21250311 original size:11 final size:11
Alignment explanation
Indices: 21250297--21250335 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
21250287 AAATTTAAAA
*
21250297 TTATATGAAAT
1 TTATATCAAAT
21250308 TTAT-TCAAAT
1 TTATATCAAAT
21250318 ATTATATCAAAT
1 -TTATATCAAAT
21250330 TTATAT
1 TTATAT
21250336 TTATATAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
10 5 0.20
11 14 0.56
12 6 0.24
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.49
Consensus pattern (11 bp):
TTATATCAAAT
Found at i:21251470 original size:23 final size:23
Alignment explanation
Indices: 21251433--21251487 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
21251423 TTAATTTATG
* *
21251433 TTTATTT-GTATTTATAAATATA
1 TTTATTTAATATTTATAAATAAA
*
21251455 TTTATTTAATATTTATGAATAAA
1 TTTATTTAATATTTATAAATAAA
*
21251478 TTCATTTAAT
1 TTTATTTAAT
21251488 TTAAATAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 7 0.25
23 21 0.75
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (23 bp):
TTTATTTAATATTTATAAATAAA
Found at i:21252339 original size:153 final size:152
Alignment explanation
Indices: 21252029--21252303 Score: 345
Period size: 153 Copynumber: 1.8 Consensus size: 152
21252019 ATAAATATTT
* * * * *
21252029 TTATAAATTTTAAAAAATAAAAAATTTACCTTTAAATTTTTAACATTTTTTATTTATTTATTAAA
1 TTATAAATTTAAAAAAATAAAAAATTTACATTTAAATTTCTAACATTATTTATTTATTTAATAAA
* * * * **
21252094 GATTATTTGTTATTAAATATATAACTTTTATTAGTTAATTATTTAAATTTATATCTAAAAGCGTT
66 GATTATTTATCATAAAATATATAACTTTTATTAGTTAATTATTTAAATTTAAATCTAAAAAAGTT
**
21252159 AAAAATGAATAGCATAAATACCC
131 AAAAATGAATA-CATAAATACAA
* * * *
21252182 TTATAAATTTAAAAAAATAACAAATTTATATTTCAATTTCTAGCATTATTTATTTATTTAATAAA
1 TTATAAATTTAAAAAAATAAAAAATTTACATTTAAATTTCTAACATTATTTATTTATTTAATAAA
* * *
21252247 GATTATTTATCATAAAATATATAATTTTTTATTCG-TAGTTATTTAAATTTAAATCTA
66 GATTATTTATCATAAAATATATAA-CTTTTATTAGTTAATTATTTAAATTTAAATCTA
21252304 TTAAAAATTT
Statistics
Matches: 105, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
153 97 0.92
154 8 0.08
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (152 bp):
TTATAAATTTAAAAAAATAAAAAATTTACATTTAAATTTCTAACATTATTTATTTATTTAATAAA
GATTATTTATCATAAAATATATAACTTTTATTAGTTAATTATTTAAATTTAAATCTAAAAAAGTT
AAAAATGAATACATAAATACAA
Found at i:21252791 original size:23 final size:24
Alignment explanation
Indices: 21252744--21252795 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 24
21252734 AATTTAGATT
*
21252744 AATTA-AAATTAAAGTTCATACAA
1 AATTATAAATTAAAGTTCATAAAA
21252767 AATTATAAATTAAA-TT-ATCAAAA
1 AATTATAAATTAAAGTTCAT-AAAA
21252790 AATTAT
1 AATTAT
21252796 TCAAAAAGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
22 2 0.08
23 16 0.62
24 8 0.31
ACGTcount: A:0.58, C:0.06, G:0.02, T:0.35
Consensus pattern (24 bp):
AATTATAAATTAAAGTTCATAAAA
Found at i:21269311 original size:2 final size:2
Alignment explanation
Indices: 21269304--21269364 Score: 113
Period size: 2 Copynumber: 30.5 Consensus size: 2
21269294 AGAAAGCAAA
*
21269304 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21269346 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
21269365 GGTTTTGATG
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:21279587 original size:2 final size:2
Alignment explanation
Indices: 21279580--21279616 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
21279570 TCGGTAGTAC
21279580 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
21279617 TAGGTAGTAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:21280111 original size:12 final size:13
Alignment explanation
Indices: 21280082--21280133 Score: 56
Period size: 12 Copynumber: 4.2 Consensus size: 13
21280072 ATTAATATTT
*
21280082 TTTATTAAAAATA
1 TTTATTTAAAATA
21280095 TTTATTTAAAA-A
1 TTTATTTAAAATA
* *
21280107 TTTATATCAAA-A
1 TTTATTTAAAATA
21280119 TTTA-TTAAAATA
1 TTTATTTAAAATA
21280131 TTT
1 TTT
21280134 TTAAATTTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
11 4 0.12
12 19 0.58
13 10 0.30
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (13 bp):
TTTATTTAAAATA
Found at i:21280200 original size:13 final size:13
Alignment explanation
Indices: 21280169--21280205 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
21280159 TAACAAAATT
*
21280169 TTTTAATTTATTGA
1 TTTTAATTT-TTAA
21280183 TTTTAATTTTTAA
1 TTTTAATTTTTAA
21280196 TTTTAATTTT
1 TTTTAATTTT
21280206 ATTTAATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 13 0.59
14 9 0.41
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (13 bp):
TTTTAATTTTTAA
Found at i:21282734 original size:27 final size:25
Alignment explanation
Indices: 21282702--21282780 Score: 90
Period size: 27 Copynumber: 3.1 Consensus size: 25
21282692 TTCCATTTGT
21282702 TAATAATAATAATAATATATTATTTAA
1 TAATAATAATAATAATAT-TTA-TTAA
21282729 TAATAA-ATATAATAATATTTATTAA
1 TAATAATA-ATAATAATATTTATTAA
* *
21282754 T-ATAATAAAAATATTATTTTATTAA
1 TAATAATAATAATAATA-TTTATTAA
21282779 TA
1 TA
21282781 TATTATTTGT
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
24 11 0.24
25 15 0.33
26 4 0.09
27 16 0.35
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (25 bp):
TAATAATAATAATAATATTTATTAA
Found at i:21282783 original size:27 final size:25
Alignment explanation
Indices: 21282701--21282780 Score: 87
Period size: 24 Copynumber: 3.2 Consensus size: 25
21282691 ATTCCATTTG
*
21282701 TTAATAATAATAATAATATATTAT-
1 TTAATAATAATAATAATATATTTTA
21282725 TTAATAATAA-ATATAATA-ATATTTA
1 TTAATAATAATA-ATAATATAT-TTTA
*
21282750 TTAAT-ATAATAAAAATATTATTTTA
1 TTAATAATAATAATAATA-TATTTTA
21282775 TTAATA
1 TTAATA
21282781 TATTATTTGT
Statistics
Matches: 47, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
23 3 0.06
24 27 0.57
25 15 0.32
26 2 0.04
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (25 bp):
TTAATAATAATAATAATATATTTTA
Found at i:21286267 original size:34 final size:34
Alignment explanation
Indices: 21286227--21286292 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
21286217 TACACTATTA
* *
21286227 TAGCTATGAGCAATATACCATTATAAACAAATTG
1 TAGCTATGAACAATACACCATTATAAACAAATTG
**
21286261 TAGCTATGAATGATACACCATTATAAACAAAT
1 TAGCTATGAACAATACACCATTATAAACAAAT
21286293 AATTCAAGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.45, C:0.15, G:0.11, T:0.29
Consensus pattern (34 bp):
TAGCTATGAACAATACACCATTATAAACAAATTG
Found at i:21288423 original size:24 final size:24
Alignment explanation
Indices: 21288396--21288445 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
21288386 ATCATGTGGT
21288396 AGATAAAAGCAGAAATACAAAAGC
1 AGATAAAAGCAGAAATACAAAAGC
* *
21288420 AGATAGAAGCAGAAATACAGAAGC
1 AGATAAAAGCAGAAATACAAAAGC
21288444 AG
1 AG
21288446 TCTGGTAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.58, C:0.12, G:0.22, T:0.08
Consensus pattern (24 bp):
AGATAAAAGCAGAAATACAAAAGC
Found at i:21288441 original size:14 final size:14
Alignment explanation
Indices: 21288402--21288445 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
21288392 TGGTAGATAA
*
21288402 AAGCAGAAATACAA
1 AAGCAGAAATACAG
21288416 AAGCAG--AT--AG
1 AAGCAGAAATACAG
21288426 AAGCAGAAATACAG
1 AAGCAGAAATACAG
21288440 AAGCAG
1 AAGCAG
21288446 TCTGGTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 8
0.74 0.03 0.24
Matches are distributed among these distances:
10 7 0.28
12 4 0.16
14 14 0.56
ACGTcount: A:0.57, C:0.14, G:0.23, T:0.07
Consensus pattern (14 bp):
AAGCAGAAATACAG
Found at i:21292202 original size:14 final size:14
Alignment explanation
Indices: 21292173--21292213 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
21292163 GTTTTAAGAG
*
21292173 TTTAGGGTTTTAGGT
1 TTTAGGATTTT-GGT
21292188 TTTAGGATTTTGGT
1 TTTAGGATTTTGGT
*
21292202 TTTGGGATTTTG
1 TTTAGGATTTTG
21292214 AAATTTCAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 14 0.58
15 10 0.42
ACGTcount: A:0.12, C:0.00, G:0.32, T:0.56
Consensus pattern (14 bp):
TTTAGGATTTTGGT
Found at i:21292296 original size:15 final size:15
Alignment explanation
Indices: 21292273--21292322 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
21292263 TTAAATGGCA
*
21292273 TAGGATTTTGGATTT
1 TAGGATTTTGAATTT
* *
21292288 TAGGGTTTTGAAATT
1 TAGGATTTTGAATTT
*
21292303 TAGTATTTTGAAATTT
1 TAGGATTTTG-AATTT
21292319 TAGG
1 TAGG
21292323 GTTTCAAGGG
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
15 20 0.74
16 7 0.26
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (15 bp):
TAGGATTTTGAATTT
Found at i:21292404 original size:23 final size:23
Alignment explanation
Indices: 21292378--21292426 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 23
21292368 GTTTTGTATA
21292378 TTTAAGGTTT-A-AGATTTTAAGGG
1 TTTAAGGTTTCACA-ATTTT-AGGG
*
21292401 TTTAGGGTTTCACAATTTTAGGG
1 TTTAAGGTTTCACAATTTTAGGG
21292424 TTT
1 TTT
21292427 TAAAATTTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 16 0.70
24 6 0.26
25 1 0.04
ACGTcount: A:0.24, C:0.04, G:0.24, T:0.47
Consensus pattern (23 bp):
TTTAAGGTTTCACAATTTTAGGG
Found at i:21292433 original size:16 final size:16
Alignment explanation
Indices: 21292401--21292434 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
21292391 ATTTTAAGGG
*
21292401 TTTAGGGTTTCACAAT
1 TTTAGGGTTTCAAAAT
*
21292417 TTTAGGGTTTTAAAAT
1 TTTAGGGTTTCAAAAT
21292433 TT
1 TT
21292435 GGATTTTTAG
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:0.26, C:0.06, G:0.18, T:0.50
Consensus pattern (16 bp):
TTTAGGGTTTCAAAAT
Found at i:21292955 original size:3 final size:3
Alignment explanation
Indices: 21292947--21292973 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
21292937 AAAATGATAG
21292947 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
21292974 ATCTAATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:21295844 original size:19 final size:18
Alignment explanation
Indices: 21295820--21295876 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
21295810 ACATGTCAAG
* *
21295820 TATTTACTTATTATTTATT
1 TATTTAATTATTATTTA-A
* *
21295839 TATTTATTTATTTTTTAA
1 TATTTAATTATTATTTAA
*
21295857 TATTTAATTAATATTTAA
1 TATTTAATTATTATTTAA
21295875 TA
1 TA
21295877 ATATAAACTT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
18 17 0.53
19 15 0.47
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (18 bp):
TATTTAATTATTATTTAA
Found at i:21296038 original size:26 final size:28
Alignment explanation
Indices: 21295982--21296038 Score: 82
Period size: 26 Copynumber: 2.1 Consensus size: 28
21295972 ATAAGGTTAT
*
21295982 TATTTTATAGTTTAATTTAAGATATTAA
1 TATTTTATAATTTAATTTAAGATATTAA
*
21296010 TATTTTA-AATTTAATTT-AGATATTCA
1 TATTTTATAATTTAATTTAAGATATTAA
21296036 TAT
1 TAT
21296039 GATATTATGG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
26 11 0.41
27 9 0.33
28 7 0.26
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (28 bp):
TATTTTATAATTTAATTTAAGATATTAA
Found at i:21297324 original size:19 final size:18
Alignment explanation
Indices: 21297300--21297335 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
21297290 TTATTAATTA
21297300 TATGAAAATAATATTTAAT
1 TATGAAAATAAT-TTTAAT
*
21297319 TATGAATATAATTTTAA
1 TATGAAAATAATTTTAA
21297336 AAAAATTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (18 bp):
TATGAAAATAATTTTAAT
Found at i:21305434 original size:91 final size:91
Alignment explanation
Indices: 21305278--21305461 Score: 305
Period size: 91 Copynumber: 2.0 Consensus size: 91
21305268 CAATCACTTA
* *
21305278 TTCTTTATCAAAATTTGGTTGTTCCAAATATTAGCAAATGCTTATTTGATATAACAATTTTGCTG
1 TTCTTTATCAAAATTTGGTTGTTCCAAATATTAGCAAATACTTATTTGATATAACAATTTCGCTG
21305343 GTATTTTACTTTTAGTGGTGTCCTAT
66 GTATTTTACTTTTAGTGGTGTCCTAT
* ** *
21305369 TTCTTTATCAAAATTTGGTTGTTCCAAATATTAGCATATACTTATTTGATATCGCAGTTTCGCTG
1 TTCTTTATCAAAATTTGGTTGTTCCAAATATTAGCAAATACTTATTTGATATAACAATTTCGCTG
*
21305434 GTATTTTACTTTTAGTTGTGTCCTAT
66 GTATTTTACTTTTAGTGGTGTCCTAT
21305460 TT
1 TT
21305462 TGCGATAAAG
Statistics
Matches: 86, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
91 86 1.00
ACGTcount: A:0.24, C:0.13, G:0.14, T:0.48
Consensus pattern (91 bp):
TTCTTTATCAAAATTTGGTTGTTCCAAATATTAGCAAATACTTATTTGATATAACAATTTCGCTG
GTATTTTACTTTTAGTGGTGTCCTAT
Found at i:21307113 original size:30 final size:30
Alignment explanation
Indices: 21307074--21307148 Score: 100
Period size: 30 Copynumber: 2.5 Consensus size: 30
21307064 TTGATTTATG
21307074 TTAATAATTTATTTAGG-TA-CAAATTAAAAA
1 TTAATAATTTATTT-GGATATC-AATTAAAAA
*
21307104 TTAAAAATTTATTTGGATATCAATTAAAAA
1 TTAATAATTTATTTGGATATCAATTAAAAA
*
21307134 TTAATGATTTATTTG
1 TTAATAATTTATTTG
21307149 AGTGTAACTT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
29 2 0.05
30 37 0.93
31 1 0.03
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (30 bp):
TTAATAATTTATTTGGATATCAATTAAAAA
Found at i:21308292 original size:31 final size:32
Alignment explanation
Indices: 21308234--21308294 Score: 81
Period size: 31 Copynumber: 1.9 Consensus size: 32
21308224 ATTCAAAAAA
* *
21308234 TAAAATAAAATAAAATAGAATTTTGGGACATC
1 TAAAATAAAATAAAAAAGAATTATGGGACATC
21308266 TAAAA-AAAATAAACAAAGAA-TATGGGACA
1 TAAAATAAAATAAA-AAAGAATTATGGGACA
21308295 GAGAGAGTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
31 16 0.62
32 10 0.38
ACGTcount: A:0.59, C:0.07, G:0.13, T:0.21
Consensus pattern (32 bp):
TAAAATAAAATAAAAAAGAATTATGGGACATC
Found at i:21309174 original size:23 final size:20
Alignment explanation
Indices: 21309147--21309195 Score: 53
Period size: 23 Copynumber: 2.3 Consensus size: 20
21309137 TTTCTTAATT
*
21309147 TTTTTGATTATTTTATTTTGAAC
1 TTTTTGATTATATT-TTTT--AC
*
21309170 TTTTTAATTATATTTTTTAC
1 TTTTTGATTATATTTTTTAC
21309190 TTTTTG
1 TTTTTG
21309196 GGCTTGAACC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 7 0.30
22 4 0.17
23 12 0.52
ACGTcount: A:0.20, C:0.04, G:0.06, T:0.69
Consensus pattern (20 bp):
TTTTTGATTATATTTTTTAC
Found at i:21309314 original size:7 final size:7
Alignment explanation
Indices: 21309270--21309311 Score: 52
Period size: 7 Copynumber: 6.1 Consensus size: 7
21309260 ATTTCCCTTC
21309270 TCTTCTTT
1 TCTT-TTT
21309278 TCTTTTT
1 TCTTTTT
21309285 TCTTTTT
1 TCTTTTT
*
21309292 CCTTTTT
1 TCTTTTT
21309299 T-TTTTT
1 TCTTTTT
21309305 T-TTTTT
1 TCTTTTT
21309311 T
1 T
21309312 TTTCATCTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
6 12 0.38
7 16 0.50
8 4 0.12
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (7 bp):
TCTTTTT
Found at i:21315150 original size:33 final size:34
Alignment explanation
Indices: 21315102--21315186 Score: 111
Period size: 33 Copynumber: 2.6 Consensus size: 34
21315092 GTATAAAAAT
* * *
21315102 AATATATTTTTGAAAAATATTACAATTATCC-AG
1 AATATATTTTCGAAAAATATTAAAATTATCCGAA
* *
21315135 AATATAATTTCGAAAAGTATTAAAATTATCCGAA
1 AATATATTTTCGAAAAATATTAAAATTATCCGAA
21315169 AATATATTTTC-AAAAATA
1 AATATATTTTCGAAAAATA
21315187 AATTTTTACT
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
33 33 0.75
34 11 0.25
ACGTcount: A:0.49, C:0.08, G:0.06, T:0.36
Consensus pattern (34 bp):
AATATATTTTCGAAAAATATTAAAATTATCCGAA
Found at i:21326743 original size:17 final size:17
Alignment explanation
Indices: 21326721--21326753 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
21326711 GGCTTAAACT
21326721 TTTCTCTATC-CTCTTGC
1 TTTCTCT-TCTCTCTTGC
21326738 TTTCTCTTCTCTCTTG
1 TTTCTCTTCTCTCTTG
21326754 TAGCTTCGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.13
17 13 0.87
ACGTcount: A:0.03, C:0.33, G:0.06, T:0.58
Consensus pattern (17 bp):
TTTCTCTTCTCTCTTGC
Found at i:21339284 original size:13 final size:13
Alignment explanation
Indices: 21339266--21339299 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
21339256 ATTGGTTCTC
*
21339266 TCAAAATCAAATA
1 TCAAAATCAAACA
21339279 TCAAAATCAAACA
1 TCAAAATCAAACA
21339292 TCAAAATC
1 TCAAAATC
21339300 TACCATTGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.59, C:0.21, G:0.00, T:0.21
Consensus pattern (13 bp):
TCAAAATCAAACA
Found at i:21339287 original size:6 final size:6
Alignment explanation
Indices: 21339266--21339299 Score: 50
Period size: 6 Copynumber: 5.3 Consensus size: 6
21339256 ATTGGTTCTC
21339266 TCAAAA TCAAATA TCAAAA TCAAACA TCAAAA TC
1 TCAAAA TCAAA-A TCAAAA TCAAA-A TCAAAA TC
21339300 TACCATTGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 14 0.54
7 12 0.46
ACGTcount: A:0.59, C:0.21, G:0.00, T:0.21
Consensus pattern (6 bp):
TCAAAA
Found at i:21344312 original size:29 final size:29
Alignment explanation
Indices: 21344266--21344322 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
21344256 CATTCAACTA
* * *
21344266 ATTACTTCTTTTCCATTTCATAGTTTTCT
1 ATTACTTCATTTACATTTCAGAGTTTTCT
*
21344295 ATTACTTCATTTATATTTCAGAGTTTTC
1 ATTACTTCATTTACATTTCAGAGTTTTC
21344323 AACTAGACTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.21, C:0.18, G:0.05, T:0.56
Consensus pattern (29 bp):
ATTACTTCATTTACATTTCAGAGTTTTCT
Found at i:21351932 original size:2 final size:2
Alignment explanation
Indices: 21351925--21351952 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
21351915 TCGATTGTAA
21351925 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
21351953 GATAATAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21352016 original size:2 final size:2
Alignment explanation
Indices: 21352009--21352045 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
21351999 TTGGATTAAT
21352009 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
21352046 TTCAACAAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:21358163 original size:13 final size:13
Alignment explanation
Indices: 21358145--21358171 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
21358135 GAACAAGAAG
21358145 AGCATATTTAGTT
1 AGCATATTTAGTT
21358158 AGCATATTTAGTT
1 AGCATATTTAGTT
21358171 A
1 A
21358172 AGTATAATGC
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:0.33, C:0.07, G:0.15, T:0.44
Consensus pattern (13 bp):
AGCATATTTAGTT
Found at i:21367707 original size:3 final size:3
Alignment explanation
Indices: 21367699--21367731 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
21367689 TCCTTGAATC
21367699 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
21367732 CTTTTTTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:21388314 original size:30 final size:30
Alignment explanation
Indices: 21388273--21388358 Score: 102
Period size: 30 Copynumber: 2.8 Consensus size: 30
21388263 TTCCGACTAA
*
21388273 TAAAGGCTCAATTAGGTGAAACTAAATGTT
1 TAAAGGCTCAATTAGGTGAAAATAAATGTT
* * *
21388303 TAAAGGTTCAATTGGGTGAAAATAGATGGTT
1 TAAAGGCTCAATTAGGTGAAAATAAAT-GTT
*
21388334 TAAGGGCTCAATT-GGATGAAAATAA
1 TAAAGGCTCAATTAGG-TGAAAATAA
21388359 TATTTGAGGG
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
30 25 0.53
31 22 0.47
ACGTcount: A:0.40, C:0.07, G:0.24, T:0.29
Consensus pattern (30 bp):
TAAAGGCTCAATTAGGTGAAAATAAATGTT
Found at i:21388345 original size:31 final size:30
Alignment explanation
Indices: 21388273--21388358 Score: 109
Period size: 31 Copynumber: 2.8 Consensus size: 30
21388263 TTCCGACTAA
* *
21388273 TAAAGGCTCAATTAGGTGAAACTAAATGTT
1 TAAAGGCTCAATTGGGTGAAAATAAATGTT
* *
21388303 TAAAGGTTCAATTGGGTGAAAATAGATGGTT
1 TAAAGGCTCAATTGGGTGAAAATAAAT-GTT
* *
21388334 TAAGGGCTCAATTGGATGAAAATAA
1 TAAAGGCTCAATTGGGTGAAAATAA
21388359 TATTTGAGGG
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
30 23 0.49
31 24 0.51
ACGTcount: A:0.40, C:0.07, G:0.24, T:0.29
Consensus pattern (30 bp):
TAAAGGCTCAATTGGGTGAAAATAAATGTT
Found at i:21404254 original size:22 final size:22
Alignment explanation
Indices: 21404228--21404271 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
21404218 TGTATATTTA
* *
21404228 TATTTGTATCTCTAGAATTAAG
1 TATTTGTATCCCTAAAATTAAG
21404250 TATTTGTATCCCTAAAATTAAG
1 TATTTGTATCCCTAAAATTAAG
21404272 GACAAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.43
Consensus pattern (22 bp):
TATTTGTATCCCTAAAATTAAG
Found at i:21407457 original size:25 final size:25
Alignment explanation
Indices: 21407429--21407483 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 25
21407419 AGTAGTAACT
*
21407429 TTTTGTACTGGTAGCCAAAAGTACA
1 TTTTGTACTGGTAGCAAAAAGTACA
*
21407454 TTTTGTACTTGTAGCAAAAAGTACA
1 TTTTGTACTGGTAGCAAAAAGTACA
21407479 TTTTG
1 TTTTG
21407484 ATATAGATGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.31, C:0.13, G:0.18, T:0.38
Consensus pattern (25 bp):
TTTTGTACTGGTAGCAAAAAGTACA
Found at i:21409163 original size:14 final size:15
Alignment explanation
Indices: 21409144--21409172 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
21409134 CATGACTTGC
21409144 ACTAAAAAAC-AAGA
1 ACTAAAAAACGAAGA
21409158 ACTAAAAAACGAAGA
1 ACTAAAAAACGAAGA
21409173 GAATTTGCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.69, C:0.14, G:0.10, T:0.07
Consensus pattern (15 bp):
ACTAAAAAACGAAGA
Done.