Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008736.1 Hibiscus syriacus cultivar Beakdansim tig00111810_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: 2478687
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 13
Found at i:2181273 original size:47 final size:47
Alignment explanation
Indices: 2181180--2181276 Score: 110
Period size: 47 Copynumber: 2.1 Consensus size: 47
2181170 AATTAATTTC
* * * *
2181180 TTTCTTCTTTTTTCTTTGTTCGAAACAGTGAACATTTTTTTTCTTTT
1 TTTCTTCTTTTTTCTCTGTTAGAAACAATGAACATTTTTTTACTTTT
2181227 TTTCTT-TTTTTTCTGCTGTTAGAAACAATG-A-ATTTTTCTCTACTTTT
1 TTTCTTCTTTTTTCT-CTGTTAGAAACAATGAACATTTTT-T-TACTTTT
2181274 TTT
1 TTT
2181277 GTGTGGAACA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
45 6 0.14
46 10 0.23
47 27 0.63
ACGTcount: A:0.16, C:0.14, G:0.08, T:0.61
Consensus pattern (47 bp):
TTTCTTCTTTTTTCTCTGTTAGAAACAATGAACATTTTTTTACTTTT
Found at i:2183546 original size:24 final size:24
Alignment explanation
Indices: 2183514--2183577 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 24
2183504 AGAGTCCATG
* *
2183514 TCAAGTATCATATAAAAATTCAGA
1 TCAAATATCATATAAAAATCCAGA
* * *
2183538 TCAAATATCATATCAGAATCCAGG
1 TCAAATATCATATAAAAATCCAGA
* *
2183562 TCAAAAATCAGATAAA
1 TCAAATATCATATAAA
2183578 CTATGTATAT
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.50, C:0.16, G:0.09, T:0.25
Consensus pattern (24 bp):
TCAAATATCATATAAAAATCCAGA
Found at i:2184330 original size:28 final size:30
Alignment explanation
Indices: 2184273--2184340 Score: 88
Period size: 29 Copynumber: 2.3 Consensus size: 30
2184263 CATTTTACAC
2184273 AAATAGCACCCTTTTTAAAATAATTACC-A
1 AAATAGCACCCTTTTTAAAATAATTACCAA
* *
2184302 ATATAGCACCC-TTTTAGAATTAATT-CCAA
1 AAATAGCACCCTTTTTA-AAATAATTACCAA
2184331 AAATAGCACC
1 AAATAGCACC
2184341 AAAATCAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 7 0.21
29 27 0.79
ACGTcount: A:0.43, C:0.22, G:0.06, T:0.29
Consensus pattern (30 bp):
AAATAGCACCCTTTTTAAAATAATTACCAA
Found at i:2184388 original size:13 final size:13
Alignment explanation
Indices: 2184370--2184434 Score: 61
Period size: 13 Copynumber: 5.3 Consensus size: 13
2184360 GAATAGCACC
2184370 GGTCAACGGGTCG
1 GGTCAACGGGTCG
2184383 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
2184396 GGT---CGGGTCAAC
1 GGTCAACGGGTC--G
2184408 GGT---CGGGTCG
1 GGTCAACGGGTCG
2184418 GGTCAACGGGTCG
1 GGTCAACGGGTCG
2184431 GGTC
1 GGTC
2184435 GTGACCGGTC
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
10 9 0.20
12 9 0.20
13 27 0.60
ACGTcount: A:0.12, C:0.23, G:0.48, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:2184399 original size:18 final size:18
Alignment explanation
Indices: 2184376--2184435 Score: 113
Period size: 18 Copynumber: 3.4 Consensus size: 18
2184366 CACCGGTCAA
2184376 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
2184394 CGGGTCGGGTCAAC-GGT
1 CGGGTCGGGTCAACGGGT
2184411 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
2184429 CGGGTCG
1 CGGGTCG
2184436 TGACCGGTCA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
17 17 0.41
18 24 0.59
ACGTcount: A:0.10, C:0.23, G:0.50, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:2184452 original size:9 final size:9
Alignment explanation
Indices: 2184438--2184492 Score: 65
Period size: 9 Copynumber: 5.7 Consensus size: 9
2184428 TCGGGTCGTG
2184438 ACCGGTCAA
1 ACCGGTCAA
2184447 ACCGGTCAA
1 ACCGGTCAA
2184456 CACCGGTTCAAA
1 -ACCGG-TC-AA
*
2184468 ACCGGTTAA
1 ACCGGTCAA
2184477 ACCGGTCAAA
1 ACCGGTC-AA
2184487 ACCGGT
1 ACCGGT
2184493 TTCCAGCGTT
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
9 17 0.43
10 14 0.35
11 7 0.17
12 2 0.05
ACGTcount: A:0.33, C:0.31, G:0.22, T:0.15
Consensus pattern (9 bp):
ACCGGTCAA
Found at i:2184493 original size:19 final size:20
Alignment explanation
Indices: 2184438--2184493 Score: 80
Period size: 19 Copynumber: 2.9 Consensus size: 20
2184428 TCGGGTCGTG
*
2184438 ACCGGTC-AAACCGGTCAAC
1 ACCGGTCAAAACCGGTTAAC
2184457 ACCGGTTCAAAACCGGTTAA-
1 ACCGG-TCAAAACCGGTTAAC
2184477 ACCGGTCAAAACCGGTT
1 ACCGGTCAAAACCGGTT
2184494 TCCAGCGTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
19 17 0.50
20 7 0.21
21 10 0.29
ACGTcount: A:0.32, C:0.30, G:0.21, T:0.16
Consensus pattern (20 bp):
ACCGGTCAAAACCGGTTAAC
Found at i:2190767 original size:24 final size:24
Alignment explanation
Indices: 2190735--2190798 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 24
2190725 AGAGTCCATG
* *
2190735 TCAAGTATCATATAAAAATTCAGA
1 TCAAATATCATATAAAAATCCAGA
* * *
2190759 TCAAATATCATATCAGAATCCAGG
1 TCAAATATCATATAAAAATCCAGA
* *
2190783 TCAAAAATCAGATAAA
1 TCAAATATCATATAAA
2190799 CTATTTATAT
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.50, C:0.16, G:0.09, T:0.25
Consensus pattern (24 bp):
TCAAATATCATATAAAAATCCAGA
Found at i:2191523 original size:29 final size:28
Alignment explanation
Indices: 2191481--2191554 Score: 87
Period size: 29 Copynumber: 2.5 Consensus size: 28
2191471 GTTGAACATT
2191481 TTACACAAATAGCACCCTTTTTA-AAATAA
1 TTAC-CAAATAGCACCC-TTTTAGAAATAA
*
2191510 TTACCAATATAGCACCCTTTTAGAATTAA
1 TTACCAA-ATAGCACCCTTTTAGAAATAA
*
2191539 TTCCCAAAATAGCACC
1 TTACC-AAATAGCACC
2191555 AAAATCGAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
28 8 0.20
29 30 0.75
30 2 0.05
ACGTcount: A:0.41, C:0.24, G:0.05, T:0.30
Consensus pattern (28 bp):
TTACCAAATAGCACCCTTTTAGAAATAA
Found at i:2191602 original size:13 final size:13
Alignment explanation
Indices: 2191584--2191648 Score: 61
Period size: 13 Copynumber: 5.3 Consensus size: 13
2191574 TAATAGCACC
2191584 GGTCAACGGGTCG
1 GGTCAACGGGTCG
2191597 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
2191610 GGT---CGGGTCAAC
1 GGTCAACGGGTC--G
2191622 GGT---CGGGTCG
1 GGTCAACGGGTCG
2191632 GGTCAACGGGTCG
1 GGTCAACGGGTCG
2191645 GGTC
1 GGTC
2191649 GTGACCGGTC
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
10 9 0.20
12 9 0.20
13 27 0.60
ACGTcount: A:0.12, C:0.23, G:0.48, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:2191613 original size:18 final size:18
Alignment explanation
Indices: 2191590--2191649 Score: 113
Period size: 18 Copynumber: 3.4 Consensus size: 18
2191580 CACCGGTCAA
2191590 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
2191608 CGGGTCGGGTCAAC-GGT
1 CGGGTCGGGTCAACGGGT
2191625 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
2191643 CGGGTCG
1 CGGGTCG
2191650 TGACCGGTCA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
17 17 0.41
18 24 0.59
ACGTcount: A:0.10, C:0.23, G:0.50, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:2191674 original size:10 final size:9
Alignment explanation
Indices: 2191652--2191695 Score: 52
Period size: 10 Copynumber: 4.7 Consensus size: 9
2191642 TCGGGTCGTG
2191652 ACCGGTCAA
1 ACCGGTCAA
2191661 ACCGGTCAA
1 ACCGGTCAA
*
2191670 CACCGGTTAA
1 -ACCGGTCAA
*
2191680 ACCAGTCAAA
1 ACCGGTC-AA
2191690 ACCGGT
1 ACCGGT
2191696 TTCCAGCGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
9 14 0.48
10 15 0.52
ACGTcount: A:0.34, C:0.32, G:0.20, T:0.14
Consensus pattern (9 bp):
ACCGGTCAA
Found at i:2191696 original size:19 final size:19
Alignment explanation
Indices: 2191652--2191696 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
2191642 TCGGGTCGTG
* * *
2191652 ACCGGTCAAACCGGTCAAC
1 ACCGGTTAAACCAGTCAAA
2191671 ACCGGTTAAACCAGTCAAA
1 ACCGGTTAAACCAGTCAAA
2191690 ACCGGTT
1 ACCGGTT
2191697 TCCAGCGTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.33, C:0.31, G:0.20, T:0.16
Consensus pattern (19 bp):
ACCGGTTAAACCAGTCAAA
Found at i:2197802 original size:21 final size:21
Alignment explanation
Indices: 2197772--2197839 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
2197762 GCTTTGGAAT
*
2197772 TTTTCATGGGATTTAACCAGC
1 TTTTCATGGGATGTAACCAGC
* * * *
2197793 TTTTCTTGGGATGCAACAAGT
1 TTTTCATGGGATGTAACCAGC
* *
2197814 TTTTCATGGTATGTAACCAAC
1 TTTTCATGGGATGTAACCAGC
2197835 TTTTC
1 TTTTC
2197840 TTGTGAAATT
Statistics
Matches: 36, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.41
Consensus pattern (21 bp):
TTTTCATGGGATGTAACCAGC
Found at i:2198862 original size:20 final size:20
Alignment explanation
Indices: 2198837--2198876 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2198827 ATGTAGCAAT
* *
2198837 GTATCGGTACCCCTATAGCA
1 GTATCGATACACCTATAGCA
*
2198857 GTATCGATACACCTGTAGCA
1 GTATCGATACACCTATAGCA
2198877 TTCGATGTTT
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:0.28, C:0.28, G:0.20, T:0.25
Consensus pattern (20 bp):
GTATCGATACACCTATAGCA
Found at i:2198975 original size:19 final size:20
Alignment explanation
Indices: 2198926--2198977 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
2198916 ACACAATATT
*
2198926 GATACTATTCATACATTACA
1 GATACTATTCATACAGTACA
*
2198946 GGTACTATTCATACAGTACA
1 GATACTATTCATACAGTACA
*
2198966 -ATATTATTCATA
1 GATACTATTCATA
2198978 AAAACATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 10 0.36
20 18 0.64
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.37
Consensus pattern (20 bp):
GATACTATTCATACAGTACA
Found at i:2199219 original size:21 final size:21
Alignment explanation
Indices: 2199194--2199235 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
2199184 TATTGAAAAA
*
2199194 GATATCAATTGTTAACAAGAT
1 GATATCAATTGTTAAAAAGAT
2199215 GATATCAATTGTTAAAAAGAT
1 GATATCAATTGTTAAAAAGAT
2199236 ACAAATTGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.45, C:0.07, G:0.14, T:0.33
Consensus pattern (21 bp):
GATATCAATTGTTAAAAAGAT
Found at i:2199242 original size:18 final size:18
Alignment explanation
Indices: 2199189--2199245 Score: 71
Period size: 21 Copynumber: 3.0 Consensus size: 18
2199179 ATGTTTATTG
2199189 AAAAAGATATCAATTGTT
1 AAAAAGATATCAATTGTT
2199207 AACAAGATGATATCAATTGTT
1 AA-AA-A-GATATCAATTGTT
2199228 AAAAAGATA-CAAATTGTT
1 AAAAAGATATC-AATTGTT
2199246 GGAAAATATA
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
17 1 0.03
18 13 0.37
19 3 0.09
20 3 0.09
21 15 0.43
ACGTcount: A:0.49, C:0.07, G:0.12, T:0.32
Consensus pattern (18 bp):
AAAAAGATATCAATTGTT
Found at i:2199788 original size:20 final size:19
Alignment explanation
Indices: 2199737--2199790 Score: 85
Period size: 18 Copynumber: 2.9 Consensus size: 19
2199727 TTGAAAATTT
2199737 GATATCAATTG-TTAGAGA
1 GATATCAATTGATTAGAGA
2199755 GATATCAATT-ATTAGAGA
1 GATATCAATTGATTAGAGA
2199773 GATATCAATTGCATTAGA
1 GATATCAATTG-ATTAGA
2199791 ACCAATTTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
18 27 0.82
20 6 0.18
ACGTcount: A:0.41, C:0.07, G:0.19, T:0.33
Consensus pattern (19 bp):
GATATCAATTGATTAGAGA
Found at i:2202940 original size:18 final size:18
Alignment explanation
Indices: 2202917--2202952 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
2202907 GCTTAATTAG
2202917 GTTGAACTTGAGCCCAAT
1 GTTGAACTTGAGCCCAAT
2202935 GTTGAACTTGAGCCCAAT
1 GTTGAACTTGAGCCCAAT
2202953 TAGCCAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (18 bp):
GTTGAACTTGAGCCCAAT
Found at i:2209082 original size:6 final size:6
Alignment explanation
Indices: 2209071--2209112 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
2209061 ATTTCGTTAC
* *
2209071 ATTTTT ATTTTT ATTTTT -GTTTT ATTTTT TTATTTT ATTTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT AT-TTTT ATTTTT
2209113 TCGATCGAGC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
5 4 0.13
6 21 0.70
7 5 0.17
ACGTcount: A:0.14, C:0.00, G:0.02, T:0.83
Consensus pattern (6 bp):
ATTTTT
Found at i:2209097 original size:23 final size:23
Alignment explanation
Indices: 2209052--2209112 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
2209042 AGGCAACCCA
* *
2209052 TTATTTTTAATTTCGTTACATTT
1 TTATTTTTATTTTTGTTACATTT
**
2209075 TTATTTTTATTTTTGTTTTATTT
1 TTATTTTTATTTTTGTTACATTT
*
2209098 TTTTATTTTATTTTT
1 TTAT-TTTTATTTTT
2209113 TCGATCGAGC
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
23 22 0.69
24 10 0.31
ACGTcount: A:0.16, C:0.03, G:0.03, T:0.77
Consensus pattern (23 bp):
TTATTTTTATTTTTGTTACATTT
Found at i:2209100 original size:13 final size:13
Alignment explanation
Indices: 2209072--2209113 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
2209062 TTTCGTTACA
*
2209072 TTTTTATTTT-TA
1 TTTTTATTTTATT
*
2209084 TTTTTGTTTTATT
1 TTTTTATTTTATT
2209097 TTTTTATTTTATT
1 TTTTTATTTTATT
2209110 TTTT
1 TTTT
2209114 CGATCGAGCA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
12 9 0.35
13 17 0.65
ACGTcount: A:0.12, C:0.00, G:0.02, T:0.86
Consensus pattern (13 bp):
TTTTTATTTTATT
Found at i:2214460 original size:33 final size:33
Alignment explanation
Indices: 2214423--2214485 Score: 126
Period size: 33 Copynumber: 1.9 Consensus size: 33
2214413 GAGTATGTAT
2214423 CAAAGAAGTTTATACCAACTTCTAAGTAAACCC
1 CAAAGAAGTTTATACCAACTTCTAAGTAAACCC
2214456 CAAAGAAGTTTATACCAACTTCTAAGTAAA
1 CAAAGAAGTTTATACCAACTTCTAAGTAAA
2214486 GCCTTTAACT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.44, C:0.21, G:0.10, T:0.25
Consensus pattern (33 bp):
CAAAGAAGTTTATACCAACTTCTAAGTAAACCC
Found at i:2219426 original size:22 final size:23
Alignment explanation
Indices: 2219387--2219437 Score: 77
Period size: 22 Copynumber: 2.3 Consensus size: 23
2219377 AGAGTTACAA
* *
2219387 GAGTTACATTGATTTAATTTCAG
1 GAGTTACATTGATATAATATCAG
2219410 GAGTTACA-TGATATAATATCAG
1 GAGTTACATTGATATAATATCAG
2219432 GAGTTA
1 GAGTTA
2219438 TAACAGCTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 18 0.69
23 8 0.31
ACGTcount: A:0.35, C:0.08, G:0.20, T:0.37
Consensus pattern (23 bp):
GAGTTACATTGATATAATATCAG
Found at i:2225181 original size:22 final size:23
Alignment explanation
Indices: 2225142--2225192 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 23
2225132 GGAGTTACAA
* * *
2225142 GAGTAACATTGATTTAATTTAAG
1 GAGTTACATTGATATAATATAAG
*
2225165 GAGTTACA-TGATATAATATCAG
1 GAGTTACATTGATATAATATAAG
2225187 GAGTTA
1 GAGTTA
2225193 TAACAGCTGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 17 0.71
23 7 0.29
ACGTcount: A:0.39, C:0.06, G:0.20, T:0.35
Consensus pattern (23 bp):
GAGTTACATTGATATAATATAAG
Found at i:2228515 original size:17 final size:18
Alignment explanation
Indices: 2228493--2228571 Score: 76
Period size: 17 Copynumber: 4.4 Consensus size: 18
2228483 CAAAGAGGTT
2228493 TTATATTTAATTTT-ATA
1 TTATATTTAATTTTAATA
2228510 TTATATTTAATTTTAATA
1 TTATATTTAATTTTAATA
*
2228528 TTA-ATTT--TTTAAATAAA
1 TTATATTTAATTTTAAT--A
*
2228545 TTAAATATTAATTTTTAATA
1 TTATAT-TTAA-TTTTAATA
2228565 TTATATT
1 TTATATT
2228572 ATAGATATTA
Statistics
Matches: 51, Mismatches: 3, Indels: 14
0.75 0.04 0.21
Matches are distributed among these distances:
15 6 0.12
17 22 0.43
18 8 0.16
19 3 0.06
20 6 0.12
22 6 0.12
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TTATATTTAATTTTAATA
Found at i:2228551 original size:24 final size:27
Alignment explanation
Indices: 2228512--2228594 Score: 88
Period size: 26 Copynumber: 3.3 Consensus size: 27
2228502 ATTTTATATT
* *
2228512 ATATTTAATTTTAATATTAATTTTTTA
1 ATATTAAATTATAATATTAATTTTTTA
2228539 A-A-TAAATTA-AATATTAA-TTTTTA
1 ATATTAAATTATAATATTAATTTTTTA
*
2228562 ATATTATATTATAGATATTAA--TTTTA
1 ATATTAAATTATA-ATATTAATTTTTTA
2228588 ATATTAA
1 ATATTAA
2228595 GTTTTTAAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
23 7 0.15
24 9 0.19
25 11 0.23
26 13 0.27
27 8 0.17
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (27 bp):
ATATTAAATTATAATATTAATTTTTTA
Found at i:2228594 original size:63 final size:64
Alignment explanation
Indices: 2228498--2228652 Score: 246
Period size: 63 Copynumber: 2.5 Consensus size: 64
2228488 AGGTTTTATA
* *
2228498 TTTAATTTTATATTAT--AT-TTAATTTTAATATTAATTTTTTAAATAAATTAAATATTA-ATT
1 TTTAATATTATATTATAGATATTAATTTTAATATTAAGTTTTTAAATAAATTAAATATTACATT
*
2228558 TTTAATATTATATTATAGATATTAATTTTAATATTAAGTTTTTAAATAAATTAAATATTACTTT
1 TTTAATATTATATTATAGATATTAATTTTAATATTAAGTTTTTAAATAAATTAAATATTACATT
2228622 TTTAATATTATATTATAGATATTTAATTTTA
1 TTTAATATTATATTATAGATA-TTAATTTTA
2228653 TATCATATAA
Statistics
Matches: 87, Mismatches: 3, Indels: 5
0.92 0.03 0.05
Matches are distributed among these distances:
60 15 0.17
62 2 0.02
63 38 0.44
64 23 0.26
65 9 0.10
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.56
Consensus pattern (64 bp):
TTTAATATTATATTATAGATATTAATTTTAATATTAAGTTTTTAAATAAATTAAATATTACATT
Found at i:2228646 original size:21 final size:21
Alignment explanation
Indices: 2228558--2228655 Score: 60
Period size: 21 Copynumber: 4.6 Consensus size: 21
2228548 AATATTAATT
2228558 TTTAATATTATATTATAGATA
1 TTTAATATTATATTATAGATA
* *
2228579 -TTAATTTTAATATTA-AG-TT
1 TTTAATATT-ATATTATAGATA
* ** *
2228598 TTTAAATAAATTA-AATATTACTTT
1 TTT-AAT--ATTATATTA-TAGATA
2228622 TTTAATATTATATTATAGATA
1 TTTAATATTATATTATAGATA
*
2228643 TTTAATTTTATAT
1 TTTAATATTATAT
2228656 CATATAAATT
Statistics
Matches: 58, Mismatches: 10, Indels: 18
0.67 0.12 0.21
Matches are distributed among these distances:
19 1 0.02
20 11 0.19
21 31 0.53
22 4 0.07
23 6 0.10
24 5 0.09
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (21 bp):
TTTAATATTATATTATAGATA
Found at i:2229220 original size:31 final size:31
Alignment explanation
Indices: 2229162--2229221 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
2229152 TAGTTGTATG
* * *
2229162 AATTATTTAAATTTTAGTTTTGTAAAACTAA
1 AATTATTTAAATCTCAGTTTTGAAAAACTAA
2229193 AATTATTTAAATCTCA-TTATTGAAAAACT
1 AATTATTTAAATCTCAGTT-TTGAAAAACT
2229222 CTTTTAAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 2 0.08
31 23 0.92
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.45
Consensus pattern (31 bp):
AATTATTTAAATCTCAGTTTTGAAAAACTAA
Found at i:2230389 original size:160 final size:163
Alignment explanation
Indices: 2230203--2230531 Score: 583
Period size: 165 Copynumber: 2.0 Consensus size: 163
2230193 GTGGCGTTTG
2230203 TTCCCAAAATGCCAGTAAAGGTAAATGACATATAGTGGCATTTGTGAATGT-ACCACTATTGTCT
1 TTCCCAAAATGCCAGTAAAGGTAAATGACATATAGTGGCATTTGTGAATGTAACCACTATTGTCT
2230267 ATGGCTATAGTCTCGTTTTTTGTATAAACACTGTAAAAGATCTAGAACTTTAGTGGCA-TTTTTC
66 ATGGCTATAGTCTCGTTTTTTGTATAAACACTGTAAAAGATCTAGAACTTTAGTGGCATTTTTTC
2230331 TAAAAAGTCGGGATTTG-TTAATGGTGTTTTTT
131 TAAAAAGTCGGGATTTGTTTAATGGTGTTTTTT
2230363 TTCCCAAAATGCCAGTAAAGGTAAATGACATATAGTGGCATTTGTGAATGTAAAACACCACTATT
1 TTCCCAAAATGCCAGTAAAGGTAAATGACATATAGTGGCATTTGTGAATGT---A-ACCACTATT
2230428 GTCTATGGCTATAGTCTCGTTTTTTGTATAAACACTGTAAAAGATCTAGAACTTTAGTGGCATTT
62 GTCTATGGCTATAGTCTCGTTTTTTGTATAAACACTGTAAAAGATCTAGAACTTTAGTGGCA-TT
*
2230493 TTTTCTAAAAAGTCGGTATTTGTTTAATGGTGTTTTTT
126 TTTTCTAAAAAGTCGGGATTTGTTTAATGGTGTTTTTT
2230531 T
1 T
2230532 ATACAAACGC
Statistics
Matches: 160, Mismatches: 1, Indels: 8
0.95 0.01 0.05
Matches are distributed among these distances:
160 51 0.32
165 71 0.44
167 22 0.14
168 16 0.10
ACGTcount: A:0.30, C:0.13, G:0.19, T:0.39
Consensus pattern (163 bp):
TTCCCAAAATGCCAGTAAAGGTAAATGACATATAGTGGCATTTGTGAATGTAACCACTATTGTCT
ATGGCTATAGTCTCGTTTTTTGTATAAACACTGTAAAAGATCTAGAACTTTAGTGGCATTTTTTC
TAAAAAGTCGGGATTTGTTTAATGGTGTTTTTT
Found at i:2230651 original size:21 final size:21
Alignment explanation
Indices: 2230622--2230685 Score: 101
Period size: 21 Copynumber: 3.0 Consensus size: 21
2230612 GTAGCATTAT
* *
2230622 ACAATAAACTTGACATCCATA
1 ACAACAAACTTGAAATCCATA
2230643 ACAACAAACTTGAAATCCATA
1 ACAACAAACTTGAAATCCATA
*
2230664 ACAACCAACTTGAAATCCATA
1 ACAACAAACTTGAAATCCATA
2230685 A
1 A
2230686 TAATAAATCA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.50, C:0.25, G:0.05, T:0.20
Consensus pattern (21 bp):
ACAACAAACTTGAAATCCATA
Found at i:2234104 original size:41 final size:41
Alignment explanation
Indices: 2234010--2234265 Score: 230
Period size: 41 Copynumber: 6.3 Consensus size: 41
2234000 GATTTGTTTC
* * * * *
2234010 CTAAAGTACAAATCTTTAGTGGTGTTTGTAT-AAAACAACA
1 CTAAAGTACGAGTCTATAGCGGTGTTTGTATAAAAACACCA
*
2234050 CTAAAGTACGAGTCTATAGTGGTGTTTGTATAAAAACACCA
1 CTAAAGTACGAGTCTATAGCGGTGTTTGTATAAAAACACCA
** * **
2234091 CTAAAGTGTGAGTCTATAGCGACT-TTTGTATAAAAATGCCA
1 CTAAAGTACGAGTCTATAGCG-GTGTTTGTATAAAAACACCA
* * ** ** *
2234132 CTAAATTACGAGTATATAATGACGTTTGTATAAAAACGCCA
1 CTAAAGTACGAGTCTATAGCGGTGTTTGTATAAAAACACCA
* * * **
2234173 CAAAAGTACGAGTCTTTAGCAGTGTTTGTATAAAAATGCCA
1 CTAAAGTACGAGTCTATAGCGGTGTTTGTATAAAAACACCA
* * * *
2234214 CTAAAGTATGAGTTTATAGCGGCGTTTGAATAAAAACACCA
1 CTAAAGTACGAGTCTATAGCGGTGTTTGTATAAAAACACCA
2234255 CTACAA-TACGA
1 CTA-AAGTACGA
2234266 TTCTTTTACG
Statistics
Matches: 173, Mismatches: 39, Indels: 7
0.79 0.18 0.03
Matches are distributed among these distances:
40 28 0.16
41 142 0.82
42 3 0.02
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (41 bp):
CTAAAGTACGAGTCTATAGCGGTGTTTGTATAAAAACACCA
Found at i:2234256 original size:123 final size:122
Alignment explanation
Indices: 2234033--2234265 Score: 306
Period size: 123 Copynumber: 1.9 Consensus size: 122
2234023 CTTTAGTGGT
* **
2234033 GTTTGTATAAAACAACACTAAAGTACGAGTCTATAGTGGTGTTTGTATAAAAACACCACTAAAGT
1 GTTTGTATAAAACAACACAAAAGTACGAGTCTATAGCAGTGTTTGTATAAAAACACCACTAAAGT
* * * **
2234098 GTGAGTCTATAGCGACTTTTGTATAAAAATGCCACTA-AATTACGAGTATATAATGAC
66 ATGAGTCTATAGCGACGTTTGAATAAAAACACCACTACAA-TACGAGTATATAATGAC
** * **
2234155 GTTTGTATAAAAACGCCACAAAAGTACGAGTCTTTAGCAGTGTTTGTATAAAAATGCCACTAAAG
1 GTTTGTAT-AAAACAACACAAAAGTACGAGTCTATAGCAGTGTTTGTATAAAAACACCACTAAAG
* *
2234220 TATGAGTTTATAGCGGCGTTTGAATAAAAACACCACTACAATACGA
65 TATGAGTCTATAGCGACGTTTGAATAAAAACACCACTACAATACGA
2234266 TTCTTTTACG
Statistics
Matches: 94, Mismatches: 15, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
122 8 0.09
123 84 0.89
124 2 0.02
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.29
Consensus pattern (122 bp):
GTTTGTATAAAACAACACAAAAGTACGAGTCTATAGCAGTGTTTGTATAAAAACACCACTAAAGT
ATGAGTCTATAGCGACGTTTGAATAAAAACACCACTACAATACGAGTATATAATGAC
Found at i:2234271 original size:82 final size:82
Alignment explanation
Indices: 2234010--2234271 Score: 280
Period size: 82 Copynumber: 3.2 Consensus size: 82
2234000 GATTTGTTTC
* * ** * * *
2234010 CTAAAGTACAAATCTTTAGTGGTGTTTGTATAAAACA--ACACTAAAGTACGAGTCTATAGTGGT
1 CTAAAGTACGAGTCTTTAGCAGTGTTTGTATAAAA-ATGCCACTAAAGTACGAGTATATAGTGGC
2234073 GTTTGTATAAAAACACCA
65 GTTTGTATAAAAACACCA
** * * * * *
2234091 CTAAAGTGTGAGTCTATAGCGACT-TTTGTATAAAAATGCCACTAAATTACGAGTATATAATGAC
1 CTAAAGTACGAGTCTTTAGC-AGTGTTTGTATAAAAATGCCACTAAAGTACGAGTATATAGTGGC
*
2234155 GTTTGTATAAAAACGCCA
65 GTTTGTATAAAAACACCA
* * * *
2234173 CAAAAGTACGAGTCTTTAGCAGTGTTTGTATAAAAATGCCACTAAAGTATGAGTTTATAGCGGCG
1 CTAAAGTACGAGTCTTTAGCAGTGTTTGTATAAAAATGCCACTAAAGTACGAGTATATAGTGGCG
*
2234238 TTTGAATAAAAACACCA
66 TTTGTATAAAAACACCA
*
2234255 CTACAA-TACGATTCTTT
1 CTA-AAGTACGAGTCTTT
2234272 TACGGCGTTT
Statistics
Matches: 146, Mismatches: 30, Indels: 9
0.79 0.16 0.05
Matches are distributed among these distances:
80 1 0.01
81 27 0.18
82 116 0.79
83 2 0.01
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (82 bp):
CTAAAGTACGAGTCTTTAGCAGTGTTTGTATAAAAATGCCACTAAAGTACGAGTATATAGTGGCG
TTTGTATAAAAACACCA
Found at i:2247871 original size:111 final size:112
Alignment explanation
Indices: 2247707--2248413 Score: 1032
Period size: 111 Copynumber: 6.4 Consensus size: 112
2247697 CCCGCTACTA
* * * * * * * * *
2247707 ATACAAAAATTTATACACTTACTATAAATTTCCT-AGTTTTGCCCATATAGTGCCCATACATAAA
1 ATACAGAAATTCATCCACTTAATATGAATTTCTTAAGTTTTACACATATAGTGCCCATACAGAAA
* *
2247771 TCCATCCACTTAGTATGAATCTCTT-AGTTTTACACATATAGCGCCC
66 TTCATCCACTTAGTATGAATCTCTTAAGTTTTACACATATAGTGCCC
*
2247817 ATACAGAAATTCATCCACTTAATATGAATTTCTTAAGTTTTACACATATAGTGCCCATACAAAAA
1 ATACAGAAATTCATCCACTTAATATGAATTTCTTAAGTTTTACACATATAGTGCCCATACAGAAA
*
2247882 TTCATACACTTAGTATGAATCTCTT-AGTTTTACACATATAGTGCCC
66 TTCATCCACTTAGTATGAATCTCTTAAGTTTTACACATATAGTGCCC
* *
2247928 ATACATAAATTCATCCACTTAATATGAATTTCTTAAGTTTTACACATATAGTGCCCATACAAAAA
1 ATACAGAAATTCATCCACTTAATATGAATTTCTTAAGTTTTACACATATAGTGCCCATACAGAAA
* *
2247993 TTCATACACTTAGTATAAATCTCTT-AGTTTTACACATATAGTGCCC
66 TTCATCCACTTAGTATGAATCTCTTAAGTTTTACACATATAGTGCCC
* * * *
2248039 ATACATAAATTCATCCACTTAGTATGAATTTCTTAAGTTTTACA-ATATAGTACCCATATAGAAA
1 ATACAGAAATTCATCCACTTAATATGAATTTCTTAAGTTTTACACATATAGTGCCCATACAGAAA
* *
2248103 TTCATCCACTTAGTATGAATTTCTTAAGTTTTACACATATAGTTCCC
66 TTCATCCACTTAGTATGAATCTCTTAAGTTTTACACATATAGTGCCC
* * *
2248150 ATACAGAAATTCATCCACTTAGTATGAATCTCTTAAGTTTTACACATATAGTGCCCATAAAGAAA
1 ATACAGAAATTCATCCACTTAATATGAATTTCTTAAGTTTTACACATATAGTGCCCATACAGAAA
* *
2248215 TTCATCCACTTAGTATGAATTTCTTAATTTTTACACATATAGTGCCC
66 TTCATCCACTTAGTATGAATCTCTTAAGTTTTACACATATAGTGCCC
* * * * **
2248262 ATACAGAAATTCATCCACTTAGTATGAATCTGTT-CGTTTTACACATATAGTGCCCATATGGAAA
1 ATACAGAAATTCATCCACTTAATATGAATTTCTTAAGTTTTACACATATAGTGCCCATACAGAAA
* *
2248326 TTCATCCACTTAGTATGAATTTCTTAAGTTTTACACATATAGTGCTC
66 TTCATCCACTTAGTATGAATCTCTTAAGTTTTACACATATAGTGCCC
2248373 ATACAGAAATTCATCCACTTAGA-ATGAATTTCTTAAGTTTT
1 ATACAGAAATTCATCCACTTA-ATATGAATTTCTTAAGTTTT
2248414 TGCACAGTTA
Statistics
Matches: 554, Mismatches: 38, Indels: 8
0.92 0.06 0.01
Matches are distributed among these distances:
110 67 0.12
111 386 0.70
112 101 0.18
ACGTcount: A:0.35, C:0.20, G:0.09, T:0.36
Consensus pattern (112 bp):
ATACAGAAATTCATCCACTTAATATGAATTTCTTAAGTTTTACACATATAGTGCCCATACAGAAA
TTCATCCACTTAGTATGAATCTCTTAAGTTTTACACATATAGTGCCC
Found at i:2247876 original size:56 final size:56
Alignment explanation
Indices: 2247707--2248413 Score: 1048
Period size: 56 Copynumber: 12.7 Consensus size: 56
2247697 CCCGCTACTA
* * * * * * * *
2247707 ATACAAAAATTTATACACTTACTATAAATTTCCT-AGTTTTGCCCATATAGTGCCC
1 ATACAGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTTACACATATAGTGCCC
* * * *
2247762 ATACATAAATCCATCCACTTAGTATGAATCTCTT-AGTTTTACACATATAGCGCCC
1 ATACAGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTTACACATATAGTGCCC
*
2247817 ATACAGAAATTCATCCACTTAATATGAATTTCTTAAGTTTTACACATATAGTGCCC
1 ATACAGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTTACACATATAGTGCCC
* * *
2247873 ATACAAAAATTCATACACTTAGTATGAATCTCTT-AGTTTTACACATATAGTGCCC
1 ATACAGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTTACACATATAGTGCCC
* *
2247928 ATACATAAATTCATCCACTTAATATGAATTTCTTAAGTTTTACACATATAGTGCCC
1 ATACAGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTTACACATATAGTGCCC
* * * *
2247984 ATACAAAAATTCATACACTTAGTATAAATCTCTT-AGTTTTACACATATAGTGCCC
1 ATACAGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTTACACATATAGTGCCC
* *
2248039 ATACATAAATTCATCCACTTAGTATGAATTTCTTAAGTTTTACA-ATATAGTACCC
1 ATACAGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTTACACATATAGTGCCC
* *
2248094 ATATAGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTTACACATATAGTTCCC
1 ATACAGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTTACACATATAGTGCCC
*
2248150 ATACAGAAATTCATCCACTTAGTATGAATCTCTTAAGTTTTACACATATAGTGCCC
1 ATACAGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTTACACATATAGTGCCC
* *
2248206 ATAAAGAAATTCATCCACTTAGTATGAATTTCTTAATTTTTACACATATAGTGCCC
1 ATACAGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTTACACATATAGTGCCC
* * *
2248262 ATACAGAAATTCATCCACTTAGTATGAATCTGTT-CGTTTTACACATATAGTGCCC
1 ATACAGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTTACACATATAGTGCCC
** *
2248317 ATATGGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTTACACATATAGTGCTC
1 ATACAGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTTACACATATAGTGCCC
*
2248373 ATACAGAAATTCATCCACTTAGAATGAATTTCTTAAGTTTT
1 ATACAGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTT
2248414 TGCACAGTTA
Statistics
Matches: 590, Mismatches: 57, Indels: 9
0.90 0.09 0.01
Matches are distributed among these distances:
55 277 0.47
56 313 0.53
ACGTcount: A:0.35, C:0.20, G:0.09, T:0.36
Consensus pattern (56 bp):
ATACAGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTTACACATATAGTGCCC
Found at i:2248793 original size:22 final size:21
Alignment explanation
Indices: 2248760--2248821 Score: 67
Period size: 19 Copynumber: 3.0 Consensus size: 21
2248750 TATCAATACC
*
2248760 CCTACCATGGTATCGATACTA
1 CCTACTATGGTATCGATACTA
2248781 CCTTACTATGGTA-CTGATAC--
1 CC-TACTATGGTATC-GATACTA
*
2248801 CCTACTATAGTATCGATACTA
1 CCTACTATGGTATCGATACTA
2248822 TTTTTGCATT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
19 14 0.41
20 3 0.09
21 3 0.09
22 14 0.41
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (21 bp):
CCTACTATGGTATCGATACTA
Found at i:2248818 original size:19 final size:19
Alignment explanation
Indices: 2248748--2248819 Score: 56
Period size: 19 Copynumber: 3.6 Consensus size: 19
2248738 TTGGCTCCTC
* *
2248748 AGTATCAATACCCCTACCAT
1 AGTATCGATA-CCCTACTAT
*
2248768 GGTATCGATACTACCTTACTAT
1 AGTATCGATAC--CC-TACTAT
*
2248790 GGTA-CTGATACCCTACTAT
1 AGTATC-GATACCCTACTAT
2248809 AGTATCGATAC
1 AGTATCGATAC
2248820 TATTTTTGCA
Statistics
Matches: 43, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
19 15 0.35
20 11 0.26
21 3 0.07
22 14 0.33
ACGTcount: A:0.31, C:0.26, G:0.12, T:0.31
Consensus pattern (19 bp):
AGTATCGATACCCTACTAT
Found at i:2249495 original size:8 final size:8
Alignment explanation
Indices: 2249479--2249512 Score: 59
Period size: 8 Copynumber: 4.2 Consensus size: 8
2249469 CCTAGTAAAA
*
2249479 TCCCATTT
1 TCCCCTTT
2249487 TCCCCTTT
1 TCCCCTTT
2249495 TCCCCTTT
1 TCCCCTTT
2249503 TCCCCTTT
1 TCCCCTTT
2249511 TC
1 TC
2249513 ATCCTCTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.03, C:0.47, G:0.00, T:0.50
Consensus pattern (8 bp):
TCCCCTTT
Found at i:2263501 original size:6 final size:6
Alignment explanation
Indices: 2263490--2263535 Score: 58
Period size: 6 Copynumber: 7.7 Consensus size: 6
2263480 GCTACACTTG
* *
2263490 AAGAAA AAGAAA AATGAAA AAGAAA TA-AAA ATGAAA AAGAAA AAGA
1 AAGAAA AAGAAA AA-GAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGA
2263536 GATGAAAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
5 3 0.09
6 25 0.74
7 6 0.18
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (6 bp):
AAGAAA
Found at i:2263526 original size:23 final size:23
Alignment explanation
Indices: 2263493--2263566 Score: 78
Period size: 23 Copynumber: 3.0 Consensus size: 23
2263483 ACACTTGAAG
2263493 AAAAA-GAAAAATGAAAAAGAAAT
1 AAAAATGAAAAA-GAAAAAGAAAT
*
2263516 AAAAATGAAAAAGAAAAAGAGAT
1 AAAAATGAAAAAGAAAAAGAAAT
*
2263539 GAAAATTAGAAAAAGGAAAAAGGAAAT
1 -AAAAAT-GAAAAA-GAAAAA-GAAAT
2263566 A
1 A
2263567 GAGAAAAAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
23 15 0.35
24 11 0.26
25 6 0.14
26 7 0.16
27 4 0.09
ACGTcount: A:0.73, C:0.00, G:0.18, T:0.09
Consensus pattern (23 bp):
AAAAATGAAAAAGAAAAAGAAAT
Found at i:2263540 original size:17 final size:17
Alignment explanation
Indices: 2263490--2263553 Score: 67
Period size: 17 Copynumber: 3.5 Consensus size: 17
2263480 GCTACACTTG
2263490 AAGAAAAAGAAAAATGAAA
1 AAGAAAAAG--AAATGAAA
2263509 AAGAAATAA-AAATGAAA
1 AAGAAA-AAGAAATGAAA
*
2263526 AAGAAAAAGAGATGAAA
1 AAGAAAAAGAAATGAAA
2263543 ATTAGAAAAAG
1 A--AGAAAAAG
2263554 GAAAAAGGAA
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
16 2 0.05
17 22 0.55
19 14 0.35
20 2 0.05
ACGTcount: A:0.73, C:0.00, G:0.17, T:0.09
Consensus pattern (17 bp):
AAGAAAAAGAAATGAAA
Found at i:2263580 original size:22 final size:22
Alignment explanation
Indices: 2263546--2263587 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
2263536 GATGAAAATT
*
2263546 AGAAAAAGGAAAAAGGAAATAG
1 AGAAAAAAGAAAAAGGAAATAG
* *
2263568 AGAAAAAATAAAAATGAAAT
1 AGAAAAAAGAAAAAGGAAAT
2263588 GAAATGAAAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.71, C:0.00, G:0.19, T:0.10
Consensus pattern (22 bp):
AGAAAAAAGAAAAAGGAAATAG
Found at i:2263669 original size:39 final size:39
Alignment explanation
Indices: 2263615--2263689 Score: 141
Period size: 39 Copynumber: 1.9 Consensus size: 39
2263605 GAAAAGAGAG
*
2263615 ATATTTTGTAACATCACTTTCTAAAATCATTTTTCAGAA
1 ATATTTTGTAACATCACTTTCTAAAATCATATTTCAGAA
2263654 ATATTTTGTAACATCACTTTCTAAAATCATATTTCA
1 ATATTTTGTAACATCACTTTCTAAAATCATATTTCA
2263690 AAAAACGATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.36, C:0.16, G:0.04, T:0.44
Consensus pattern (39 bp):
ATATTTTGTAACATCACTTTCTAAAATCATATTTCAGAA
Found at i:2265925 original size:6 final size:6
Alignment explanation
Indices: 2265916--2266003 Score: 158
Period size: 6 Copynumber: 14.7 Consensus size: 6
2265906 TAAGTTTAAG
* *
2265916 TATATA TATATA TATAGA TATAGA TATAGA TATAGA TATAGA TATAGA
1 TATAGA TATAGA TATAGA TATAGA TATAGA TATAGA TATAGA TATAGA
2265964 TATAGA TATAGA TATAGA TATAGA TATAGA TATAGA TATA
1 TATAGA TATAGA TATAGA TATAGA TATAGA TATAGA TATA
2266004 CTTAAACTTA
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
6 81 1.00
ACGTcount: A:0.50, C:0.00, G:0.14, T:0.36
Consensus pattern (6 bp):
TATAGA
Found at i:2268652 original size:21 final size:21
Alignment explanation
Indices: 2268614--2268653 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2268604 CGTGATTGTG
*
2268614 GCCGTCGCGAGCGTTATTACA
1 GCCGTCGCGAGCGCTATTACA
2268635 GCCGTCGCG-GACGCTATTA
1 GCCGTCGCGAG-CGCTATTA
2268654 AGCGCTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.17, C:0.30, G:0.30, T:0.23
Consensus pattern (21 bp):
GCCGTCGCGAGCGCTATTACA
Found at i:2271988 original size:22 final size:22
Alignment explanation
Indices: 2271931--2271989 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 22
2271921 ACGCGATTCT
2271931 GACTATCGCATTGCGATTTTCC
1 GACTATCGCATTGCGATTTTCC
* * *
2271953 AAAT-TCGCGTTGCGATTTTCC
1 GACTATCGCATTGCGATTTTCC
*
2271974 GACTATCGCAATGCGA
1 GACTATCGCATTGCGA
2271990 ATATGTAAAT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
21 18 0.62
22 11 0.38
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.32
Consensus pattern (22 bp):
GACTATCGCATTGCGATTTTCC
Found at i:2272024 original size:20 final size:20
Alignment explanation
Indices: 2272001--2272071 Score: 115
Period size: 20 Copynumber: 3.5 Consensus size: 20
2271991 TATGTAAATA
*
2272001 GCAACGCGATTCTGACTGTC
1 GCAACGCGATTCTGACTATC
*
2272021 GCAACGCGATTCTTACTATC
1 GCAACGCGATTCTGACTATC
2272041 GCAACGCGATTCTGACTATC
1 GCAACGCGATTCTGACTATC
*
2272061 GCAATGCGATT
1 GCAACGCGATT
2272072 TTCAAAGCGC
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.27
Consensus pattern (20 bp):
GCAACGCGATTCTGACTATC
Found at i:2272743 original size:20 final size:20
Alignment explanation
Indices: 2272672--2272743 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
2272662 ATCGCAATGT
*
2272672 GATTTT-AGTTTCGCGTTGC
1 GATTTTCAGTTTCGTGTTGC
** *
2272691 GATAGTCATTTTCGTGTTGC
1 GATTTTCAGTTTCGTGTTGC
* *
2272711 GAGTTTCATTTTCGTGTTGC
1 GATTTTCAGTTTCGTGTTGC
*
2272731 GATTTTAAGTTTC
1 GATTTTCAGTTTC
2272744 AGAAACTATT
Statistics
Matches: 42, Mismatches: 10, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
19 4 0.10
20 38 0.90
ACGTcount: A:0.14, C:0.14, G:0.24, T:0.49
Consensus pattern (20 bp):
GATTTTCAGTTTCGTGTTGC
Found at i:2274494 original size:18 final size:18
Alignment explanation
Indices: 2274471--2274520 Score: 91
Period size: 18 Copynumber: 2.8 Consensus size: 18
2274461 TTTACTCGTA
*
2274471 ATTTCACTTAGATTAACT
1 ATTTCACTTAGATTAACC
2274489 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
2274507 ATTTCACTTAGATT
1 ATTTCACTTAGATT
2274521 GCTTAGTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.32, C:0.18, G:0.06, T:0.44
Consensus pattern (18 bp):
ATTTCACTTAGATTAACC
Found at i:2274698 original size:20 final size:20
Alignment explanation
Indices: 2274673--2274734 Score: 97
Period size: 20 Copynumber: 3.1 Consensus size: 20
2274663 TACTTTTGCA
2274673 AACGCGAAAATGACTATCGC
1 AACGCGAAAATGACTATCGC
2274693 AACGCGAAAATGACTATCGC
1 AACGCGAAAATGACTATCGC
* **
2274713 AACGTGAATTTGACTATCGC
1 AACGCGAAAATGACTATCGC
2274733 AA
1 AA
2274735 TGTGAAATGA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.39, C:0.23, G:0.19, T:0.19
Consensus pattern (20 bp):
AACGCGAAAATGACTATCGC
Found at i:2274739 original size:20 final size:20
Alignment explanation
Indices: 2274673--2274741 Score: 93
Period size: 20 Copynumber: 3.5 Consensus size: 20
2274663 TACTTTTGCA
*
2274673 AACGCGAAAATGACTATCGC
1 AACGTGAAAATGACTATCGC
*
2274693 AACGCGAAAATGACTATCGC
1 AACGTGAAAATGACTATCGC
**
2274713 AACGTGAATTTGACTATCGC
1 AACGTGAAAATGACTATCGC
*
2274733 AATGTGAAA
1 AACGTGAAA
2274742 TGAAAATCGC
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:0.39, C:0.20, G:0.20, T:0.20
Consensus pattern (20 bp):
AACGTGAAAATGACTATCGC
Found at i:2274807 original size:18 final size:19
Alignment explanation
Indices: 2274765--2274811 Score: 69
Period size: 18 Copynumber: 2.5 Consensus size: 19
2274755 GCGATTCTCT
2274765 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTC-AATTCG
2274785 CGTTGCGATAGTC-ATTCG
1 CGTTGCGATAGTCAATTCG
*
2274803 TGTTGCGAT
1 CGTTGCGAT
2274812 TTTAAGTTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 13 0.50
20 13 0.50
ACGTcount: A:0.19, C:0.19, G:0.28, T:0.34
Consensus pattern (19 bp):
CGTTGCGATAGTCAATTCG
Found at i:2275321 original size:21 final size:21
Alignment explanation
Indices: 2275295--2275381 Score: 75
Period size: 21 Copynumber: 4.1 Consensus size: 21
2275285 ACCCGACTCA
2275295 CCTATCATCGTTCAAGAGGCC
1 CCTATCATCGTTCAAGAGGCC
** *
2275316 CCTATCATCCCTCAAGAGTCC
1 CCTATCATCGTTCAAGAGGCC
** *
2275337 CCTCCCACCGTTCAAGAGGCC
1 CCTATCATCGTTCAAGAGGCC
* * * * *
2275358 ACTGTCATCATTGAAGAGGTC
1 CCTATCATCGTTCAAGAGGCC
2275379 CCT
1 CCT
2275382 CCCAACATTC
Statistics
Matches: 49, Mismatches: 17, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.23, C:0.37, G:0.17, T:0.23
Consensus pattern (21 bp):
CCTATCATCGTTCAAGAGGCC
Found at i:2275375 original size:42 final size:42
Alignment explanation
Indices: 2275303--2275385 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
2275293 CACCTATCAT
* *
2275303 CGTTCAAGAGGCCCCTATCATCCCTCAAGA-GTCCCCTCCCAC
1 CGTTCAAGAGGCCACTATCATCACTCAAGAGGT-CCCTCCCAC
* * *
2275345 CGTTCAAGAGGCCACTGTCATCATTGAAGAGGTCCCTCCCA
1 CGTTCAAGAGGCCACTATCATCACTCAAGAGGTCCCTCCCA
2275386 ACATTCTAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 33 0.94
43 2 0.06
ACGTcount: A:0.23, C:0.39, G:0.18, T:0.20
Consensus pattern (42 bp):
CGTTCAAGAGGCCACTATCATCACTCAAGAGGTCCCTCCCAC
Found at i:2275738 original size:12 final size:12
Alignment explanation
Indices: 2275721--2275753 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
2275711 GGGGTAAGTA
2275721 TTATATTTCTTC
1 TTATATTTCTTC
2275733 TTATATTTCTTC
1 TTATATTTCTTC
2275745 TTATATTTC
1 TTATATTTC
2275754 ATTTTGATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.18, C:0.15, G:0.00, T:0.67
Consensus pattern (12 bp):
TTATATTTCTTC
Found at i:2276821 original size:14 final size:14
Alignment explanation
Indices: 2276784--2276845 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
2276774 TTTCTTGTTT
*
2276784 AATTGATTTATAAA
1 AATTGATTTGTAAA
2276798 AATTGATTTGTAAA
1 AATTGATTTGTAAA
* *
2276812 AGTTGATTTGTTTAA
1 AATTGATTTG-TAAA
* *
2276827 TATTGATGTGTAAA
1 AATTGATTTGTAAA
2276841 TAATT
1 -AATT
2276846 CTTATTTGTG
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
14 25 0.66
15 13 0.34
ACGTcount: A:0.39, C:0.00, G:0.15, T:0.47
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:2276997 original size:20 final size:20
Alignment explanation
Indices: 2276944--2276997 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
2276934 AGGTACACTT
* **
2276944 TCGCAACGCTAAACTCAAAA
1 TCGCAACGCAAAAGACAAAA
* *
2276964 TCGCAATGCGAAAGACAAAA
1 TCGCAACGCAAAAGACAAAA
2276984 TCGCAACGCAAAAG
1 TCGCAACGCAAAAG
2276998 TCAATTCACG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.46, C:0.26, G:0.17, T:0.11
Consensus pattern (20 bp):
TCGCAACGCAAAAGACAAAA
Found at i:2277067 original size:20 final size:20
Alignment explanation
Indices: 2277042--2277270 Score: 229
Period size: 20 Copynumber: 11.8 Consensus size: 20
2277032 GATTTTCTCA
* *
2277042 TTGCGATAGTCAAATACCCG
1 TTGCGATAGTCAAATTCGCG
* * *
2277062 TTGCGATAATTAAATTCACG
1 TTGCGATAGTCAAATTCGCG
* *
2277082 TTGCGATACTCAAATTTGCG
1 TTGCGATAGTCAAATTCGCG
*
2277102 TTGCGATATTCAAATTCGCG
1 TTGCGATAGTCAAATTCGCG
* *
2277122 TTGC-A-A-T---TTTCTCG
1 TTGCGATAGTCAAATTCGCG
*
2277136 TTGCGATAGTCAAA-TAGCCG
1 TTGCGATAGTCAAATTCG-CG
*
2277156 TTGCGATAATCAAATTCGCG
1 TTGCGATAGTCAAATTCGCG
2277176 TTGCGATAGTCAAATTCGCG
1 TTGCGATAGTCAAATTCGCG
*
2277196 TTGCGATAGACAAATTCGCG
1 TTGCGATAGTCAAATTCGCG
** * *
2277216 TTGTTATAGTCATATTCGTG
1 TTGCGATAGTCAAATTCGCG
*
2277236 TTGCGATAGTCAAACTCGCG
1 TTGCGATAGTCAAATTCGCG
*
2277256 TTGCGATATTCAAAT
1 TTGCGATAGTCAAAT
2277271 GAATGTGTAA
Statistics
Matches: 170, Mismatches: 31, Indels: 16
0.78 0.14 0.07
Matches are distributed among these distances:
14 9 0.05
15 1 0.01
16 1 0.01
17 2 0.01
18 1 0.01
19 2 0.01
20 152 0.89
21 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCG
Found at i:2277140 original size:94 final size:94
Alignment explanation
Indices: 2277000--2277218 Score: 312
Period size: 94 Copynumber: 2.3 Consensus size: 94
2276990 CGCAAAAGTC
* * * * * *
2277000 AATTCACGTTGCGATAGTCTAATACGCTTTACGATTTTCTCATTGCGATAGTCAAATACCCGTTG
1 AATTCGCGTTGCGATAGTCAAATTCGCGTTGCAATTTTCTCATTGCGATAGTCAAATACCCGTTG
*
2277065 CGATAATTAAATTCACGTTGCGATACTCA
66 CGATAATCAAATTCACGTTGCGATACTCA
* * * *
2277094 AATTTGCGTTGCGATATTCAAATTCGCGTTGCAATTTTCTCGTTGCGATAGTCAAATAGCCGTTG
1 AATTCGCGTTGCGATAGTCAAATTCGCGTTGCAATTTTCTCATTGCGATAGTCAAATACCCGTTG
* *
2277159 CGATAATCAAATTCGCGTTGCGATAGTCA
66 CGATAATCAAATTCACGTTGCGATACTCA
*
2277188 AATTCGCGTTGCGATAGACAAATTCGCGTTG
1 AATTCGCGTTGCGATAGTCAAATTCGCGTTG
2277219 TTATAGTCAT
Statistics
Matches: 109, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
94 109 1.00
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (94 bp):
AATTCGCGTTGCGATAGTCAAATTCGCGTTGCAATTTTCTCATTGCGATAGTCAAATACCCGTTG
CGATAATCAAATTCACGTTGCGATACTCA
Found at i:2277143 original size:74 final size:74
Alignment explanation
Indices: 2277060--2277199 Score: 210
Period size: 74 Copynumber: 1.9 Consensus size: 74
2277050 GTCAAATACC
* * * * *
2277060 CGTTGCGATAATTAAAT-TCACGTTGCGATACTCAAATTTGCGTTGCGATATTCAAATTCGCGTT
1 CGTTGCGATAATCAAATAGC-CGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTT
2277124 GCAATTTTCT
65 GCAATTTTCT
*
2277134 CGTTGCGATAGTCAAATAGCCGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTG
1 CGTTGCGATAATCAAATAGCCGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTG
2277199 C
66 C
2277200 GATAGACAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
74 58 0.98
75 1 0.02
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.34
Consensus pattern (74 bp):
CGTTGCGATAATCAAATAGCCGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTG
CAATTTTCT
Found at i:2277493 original size:140 final size:140
Alignment explanation
Indices: 2277241--2277510 Score: 513
Period size: 140 Copynumber: 1.9 Consensus size: 140
2277231 TCGTGTTGCG
*
2277241 ATAGTCAAACTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
1 ATAGTCAAACTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
2277306 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
2277371 AATACACATA
131 AATACACATA
* *
2277381 ATAGTCAAATTTGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
1 ATAGTCAAACTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
2277446 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
2277511 TACAACGTTT
Statistics
Matches: 127, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
140 127 1.00
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.29
Consensus pattern (140 bp):
ATAGTCAAACTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
AATACACATA
Found at i:2280094 original size:42 final size:42
Alignment explanation
Indices: 2280042--2280140 Score: 117
Period size: 42 Copynumber: 2.3 Consensus size: 42
2280032 AATCTAGGTC
* *
2280042 CCTAACTTTTTCAATATCACTTTCTACCTTAATAATTGAAGGA
1 CCTAA-TTTTTCAATATCACTTTCTACCATAATAATTGAAGCA
* * * * *
2280085 CCTAATTTTTTAATCTCACTTTTTACCATCATAATTGAAGCC
1 CCTAATTTTTCAATATCACTTTCTACCATAATAATTGAAGCA
*
2280127 CCTATTTTTTCAAT
1 CCTAATTTTTCAAT
2280141 CCAACTCTTT
Statistics
Matches: 47, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
42 42 0.89
43 5 0.11
ACGTcount: A:0.29, C:0.22, G:0.05, T:0.43
Consensus pattern (42 bp):
CCTAATTTTTCAATATCACTTTCTACCATAATAATTGAAGCA
Found at i:2280152 original size:42 final size:40
Alignment explanation
Indices: 2280073--2280175 Score: 100
Period size: 42 Copynumber: 2.5 Consensus size: 40
2280063 TTCTACCTTA
* *
2280073 ATAATTGAAGGACCTAATTTTTTAATCTCACTTTTTACCATC
1 ATAATTGAA-GCCCT-ATTTTTTAATCTCACTCTTTACCATC
** *
2280115 ATAATTGAAGCCCCTATTTTTTCAATC-CAACTCTTTACTTTT
1 ATAATTGAAG-CCCTATTTTTT-AATCTC-ACTCTTTACCATC
*
2280157 ATAATTTAAGCCCTATTTT
1 ATAATTGAAGCCCTATTTT
2280176 AATTATTTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
41 18 0.35
42 34 0.65
ACGTcount: A:0.29, C:0.20, G:0.06, T:0.45
Consensus pattern (40 bp):
ATAATTGAAGCCCTATTTTTTAATCTCACTCTTTACCATC
Found at i:2280353 original size:119 final size:119
Alignment explanation
Indices: 2280208--2280454 Score: 449
Period size: 119 Copynumber: 2.1 Consensus size: 119
2280198 TTAAATTAAT
* * *
2280208 TCTTCAAAGTAATATAATATATTTTCGTTGTACAATGACCTATTTTTTAGTTTTGCTTAGGGTTT
1 TCTTCAAATTAATATAATATACTTTCGTTGTACAATGACCTATTTTTTAGTTTTGCTTAGGGATT
*
2280273 TGAAACGGTTTTACCTTCAACCACGAAGATCGTTTGATTCGTGTTCTACGATAA
66 TGAAACGGTTTTACCTTCAACCAAGAAGATCGTTTGATTCGTGTTCTACGATAA
2280327 TCTTCAAATTAATATAATATACTTTCGTTGTACAATGACCTATTTTTTAGTTTTGCTTAGGGATT
1 TCTTCAAATTAATATAATATACTTTCGTTGTACAATGACCTATTTTTTAGTTTTGCTTAGGGATT
2280392 TGAAACGGTTTTACCTTCAACCAAGAAGATCGTTTGATTCGTGTTCTACGATAA
66 TGAAACGGTTTTACCTTCAACCAAGAAGATCGTTTGATTCGTGTTCTACGATAA
*
2280446 TCTTTAAAT
1 TCTTCAAAT
2280455 ATAAATGATG
Statistics
Matches: 123, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
119 123 1.00
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.42
Consensus pattern (119 bp):
TCTTCAAATTAATATAATATACTTTCGTTGTACAATGACCTATTTTTTAGTTTTGCTTAGGGATT
TGAAACGGTTTTACCTTCAACCAAGAAGATCGTTTGATTCGTGTTCTACGATAA
Found at i:2282190 original size:2 final size:2
Alignment explanation
Indices: 2282183--2282211 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2282173 TTAACAAATC
2282183 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 T
2282212 GCATATTTTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2283475 original size:6 final size:6
Alignment explanation
Indices: 2283469--2283539 Score: 124
Period size: 6 Copynumber: 11.8 Consensus size: 6
2283459 GTTTAAGTAT
* *
2283469 ATATAT ATATAT ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG
1 ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG
2283517 ATATAG ATATAG ATATAG ATATA
1 ATATAG ATATAG ATATAG ATATA
2283540 CTTAAACTTA
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 64 1.00
ACGTcount: A:0.51, C:0.00, G:0.13, T:0.37
Consensus pattern (6 bp):
ATATAG
Found at i:2289447 original size:20 final size:20
Alignment explanation
Indices: 2289417--2289592 Score: 131
Period size: 20 Copynumber: 8.7 Consensus size: 20
2289407 GTTTCCAGAT
*
2289417 TCGCAACGCGATTCTGACTA
1 TCGCAATGCGATTCTGACTA
* ** *
2289437 TCGCATTGCGATT-TTCCAAA
1 TCGCAATGCGATTCTGAC-TA
** *
2289457 TTCGCGTTGCGATTTTCCGACTA
1 -TCGCAATGCGA--TTCTGACTA
* * *
2289480 TCGCAATGCGAATATGTA-AA
1 TCGCAATGCGATTCTG-ACTA
* *
2289500 TAGCAATGCGATTTTGACTA
1 TCGCAATGCGATTCTGACTA
* *
2289520 TCGCAACGCGATTCTGACTG
1 TCGCAATGCGATTCTGACTA
* *
2289540 TCGCAACGCGATTCTGACTG
1 TCGCAATGCGATTCTGACTA
*
2289560 TCGCAACGCGATTCTGACTA
1 TCGCAATGCGATTCTGACTA
2289580 TCGCAATGCGATT
1 TCGCAATGCGATT
2289593 TTCAAAGCGC
Statistics
Matches: 123, Mismatches: 26, Indels: 14
0.75 0.16 0.09
Matches are distributed among these distances:
19 3 0.02
20 96 0.78
21 11 0.09
22 9 0.07
23 3 0.02
24 1 0.01
ACGTcount: A:0.24, C:0.25, G:0.21, T:0.30
Consensus pattern (20 bp):
TCGCAATGCGATTCTGACTA
Found at i:2289551 original size:40 final size:40
Alignment explanation
Indices: 2289502--2289594 Score: 150
Period size: 40 Copynumber: 2.3 Consensus size: 40
2289492 TATGTAAATA
*
2289502 GCAATGCGATTTTGACTATCGCAACGCGATTCTGACTGTC
1 GCAATGCGATTTTGACTATCGCAACGCGATTCTGACTATC
* * *
2289542 GCAACGCGATTCTGACTGTCGCAACGCGATTCTGACTATC
1 GCAATGCGATTTTGACTATCGCAACGCGATTCTGACTATC
2289582 GCAATGCGATTTT
1 GCAATGCGATTTT
2289595 CAAAGCGCCA
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 47 1.00
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.29
Consensus pattern (40 bp):
GCAATGCGATTTTGACTATCGCAACGCGATTCTGACTATC
Found at i:2289793 original size:22 final size:21
Alignment explanation
Indices: 2289767--2289807 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
2289757 GGCGACATCT
*
2289767 GTCCCCATCTCTGACGAAATAA
1 GTCCCCATCTCGGA-GAAATAA
2289789 GTCCCCATCTCGGAGAAAT
1 GTCCCCATCTCGGAGAAAT
2289808 CCGTCTATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.29, C:0.32, G:0.17, T:0.22
Consensus pattern (21 bp):
GTCCCCATCTCGGAGAAATAA
Found at i:2290225 original size:20 final size:20
Alignment explanation
Indices: 2290196--2290245 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
2290186 GCGATTTTAG
*
2290196 TTTCGCGTTGCGA-TAGTCAT
1 TTTCGTGTTGCGAGT-GTCAT
*
2290216 TTTCGTGTTGCGAGTTTCAT
1 TTTCGTGTTGCGAGTGTCAT
2290236 TTTCGTGTTG
1 TTTCGTGTTG
2290246 TGATTTTAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 26 0.96
21 1 0.04
ACGTcount: A:0.10, C:0.16, G:0.26, T:0.48
Consensus pattern (20 bp):
TTTCGTGTTGCGAGTGTCAT
Found at i:2290259 original size:20 final size:20
Alignment explanation
Indices: 2290216--2290259 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
2290206 CGATAGTCAT
* *
2290216 TTTCGTGTTGCGAGTTTCAT
1 TTTCGTGTTGCGAGTTTAAG
* *
2290236 TTTCGTGTTGTGATTTTAAG
1 TTTCGTGTTGCGAGTTTAAG
2290256 TTTC
1 TTTC
2290260 AGAAACTATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.11, C:0.11, G:0.23, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGCGAGTTTAAG
Found at i:2292011 original size:18 final size:18
Alignment explanation
Indices: 2291988--2292037 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
2291978 TTTACTCGTA
2291988 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
2292006 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
2292024 ATTTCACTTAGATT
1 ATTTCACTTAGATT
2292038 GCTTAGTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.32, C:0.20, G:0.06, T:0.42
Consensus pattern (18 bp):
ATTTCACTTAGATTAACC
Found at i:2292215 original size:20 final size:20
Alignment explanation
Indices: 2292190--2292258 Score: 102
Period size: 20 Copynumber: 3.5 Consensus size: 20
2292180 TACTTTTGCA
2292190 AACGCGAAAATGACTATCGC
1 AACGCGAAAATGACTATCGC
2292210 AACGCGAAAATGACTATCGC
1 AACGCGAAAATGACTATCGC
* **
2292230 AACGTGAATTTGACTATCGC
1 AACGCGAAAATGACTATCGC
*
2292250 AATGCGAAA
1 AACGCGAAA
2292259 TGAAAATCGC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.19
Consensus pattern (20 bp):
AACGCGAAAATGACTATCGC
Found at i:2292324 original size:18 final size:19
Alignment explanation
Indices: 2292282--2292328 Score: 69
Period size: 18 Copynumber: 2.5 Consensus size: 19
2292272 GCGATTCTCT
2292282 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTC-AATTCG
2292302 CGTTGCGATAGTC-ATTCG
1 CGTTGCGATAGTCAATTCG
*
2292320 TGTTGCGAT
1 CGTTGCGAT
2292329 TTTAAGTTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 13 0.50
20 13 0.50
ACGTcount: A:0.19, C:0.19, G:0.28, T:0.34
Consensus pattern (19 bp):
CGTTGCGATAGTCAATTCG
Found at i:2292892 original size:42 final size:42
Alignment explanation
Indices: 2292821--2292902 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 42
2292811 ACCTGTCATC
*
2292821 GTTCAAGAGGCCCCTATCATCCCTCAAGA-GTCCCCTCCCACT
1 GTTCAAGAGGCCACTATCATCCCTCAAGAGGT-CCCTCCCACT
* ** *
2292863 GTTCAAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCA
1 GTTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCA
2292903 ACATTCTAGA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 32 0.94
43 2 0.06
ACGTcount: A:0.22, C:0.37, G:0.20, T:0.22
Consensus pattern (42 bp):
GTTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCACT
Found at i:2293255 original size:12 final size:12
Alignment explanation
Indices: 2293238--2293270 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
2293228 GGGGTAAGTA
2293238 TTATATTTCTTC
1 TTATATTTCTTC
2293250 TTATATTTCTTC
1 TTATATTTCTTC
2293262 TTATATTTC
1 TTATATTTC
2293271 ATTTTGATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.18, C:0.15, G:0.00, T:0.67
Consensus pattern (12 bp):
TTATATTTCTTC
Found at i:2294343 original size:14 final size:14
Alignment explanation
Indices: 2294306--2294367 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
2294296 TTTCTTGTTT
*
2294306 AATTGATTTATAAA
1 AATTGATTTGTAAA
2294320 AATTGATTTGTAAA
1 AATTGATTTGTAAA
* *
2294334 AGTTGATTTGTTTAA
1 AATTGATTTG-TAAA
* *
2294349 TATTGATGTGTAAA
1 AATTGATTTGTAAA
2294363 TAATT
1 -AATT
2294368 CTTATTTGTG
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
14 25 0.66
15 13 0.34
ACGTcount: A:0.39, C:0.00, G:0.15, T:0.47
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:2294502 original size:20 final size:20
Alignment explanation
Indices: 2294479--2294517 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2294469 ACGATAAACT
*
2294479 CAAAATCGCAATGCGAAAGA
1 CAAAATCGCAACGCGAAAGA
2294499 CAAAATCGCAACGCGAAAG
1 CAAAATCGCAACGCGAAAG
2294518 TCAATTCGCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.23, G:0.21, T:0.08
Consensus pattern (20 bp):
CAAAATCGCAACGCGAAAGA
Found at i:2294585 original size:20 final size:20
Alignment explanation
Indices: 2294560--2294790 Score: 197
Period size: 20 Copynumber: 11.8 Consensus size: 20
2294550 ACGATTTTCT
* *
2294560 CGTTGCGATAGTCAAATACC
1 CGTTGCGATAGTCAAATTCG
* * *
2294580 CGTTGCGATAATTAAATTCA
1 CGTTGCGATAGTCAAATTCG
* *
2294600 CGTTGCGATACTCAAATTTG
1 CGTTGCGATAGTCAAATTCG
2294620 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
** *
2294640 CGTT--G-TA---ATTTTCT
1 CGTTGCGATAGTCAAATTCG
* *
2294654 CGTTGCGATTGTCAAA-TAG
1 CGTTGCGATAGTCAAATTCG
* *
2294673 CCGTTGCGTTAATCAAATTCG
1 -CGTTGCGATAGTCAAATTCG
2294694 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* * *
2294714 CGTTACGATAGACAAATTTG
1 CGTTGCGATAGTCAAATTCG
* *
2294734 CGTTGTGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCG
* * *
2294754 TGTTACGATAGTCAAACTCG
1 CGTTGCGATAGTCAAATTCG
*
2294774 CGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
2294791 GAATGTGTAA
Statistics
Matches: 162, Mismatches: 41, Indels: 16
0.74 0.19 0.07
Matches are distributed among these distances:
14 8 0.05
16 1 0.01
17 3 0.02
18 1 0.01
19 1 0.01
20 146 0.90
21 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.34
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:2294651 original size:94 final size:95
Alignment explanation
Indices: 2294520--2294739 Score: 302
Period size: 94 Copynumber: 2.3 Consensus size: 95
2294510 CGCGAAAGTC
* *
2294520 AATTCGCGTTGCGATAGTCTAATACGC-TT-TACGATTTTCTCGTTGCGATAGTCAAATACCCGT
1 AATTCGCGTTGCGATAGTCAAATTCGCGTTGTAC-ATTTTCTCGTTGCGATAGTCAAATACCCGT
*
2294583 TGCGATAATTAAATTCACGTTGCGATACTCA
65 TGCGATAATCAAATTCACGTTGCGATACTCA
* * *
2294614 AATTTGCGTTGCGATAGTCAAATTCGCGTTGTA-ATTTTCTCGTTGCGATTGTCAAATAGCCGTT
1 AATTCGCGTTGCGATAGTCAAATTCGCGTTGTACATTTTCTCGTTGCGATAGTCAAATACCCGTT
* * *
2294678 GCGTTAATCAAATTCGCGTTGCGATAGTCA
66 GCGATAATCAAATTCACGTTGCGATACTCA
* * *
2294708 AATTCGCGTTACGATAGACAAATTTGCGTTGT
1 AATTCGCGTTGCGATAGTCAAATTCGCGTTGT
2294740 GATAGTCATA
Statistics
Matches: 111, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
94 107 0.96
95 2 0.02
96 2 0.02
ACGTcount: A:0.25, C:0.19, G:0.20, T:0.35
Consensus pattern (95 bp):
AATTCGCGTTGCGATAGTCAAATTCGCGTTGTACATTTTCTCGTTGCGATAGTCAAATACCCGTT
GCGATAATCAAATTCACGTTGCGATACTCA
Found at i:2294659 original size:74 final size:74
Alignment explanation
Indices: 2294580--2294717 Score: 197
Period size: 74 Copynumber: 1.9 Consensus size: 74
2294570 GTCAAATACC
* * * *
2294580 CGTTGCGATAATTAAAT-TCACGTTGCGATACTCAAATTTGCGTTGCGATAGTCAAATTCGCGTT
1 CGTTGCGATAATCAAATAGC-CGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTT
2294644 GTAATTTTCT
65 GTAATTTTCT
** *
2294654 CGTTGCGATTGTCAAATAGCCGTTGCGTTAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTT
1 CGTTGCGATAATCAAATAGCCGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTT
2294718 ACGATAGACA
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
74 55 0.98
75 1 0.02
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.36
Consensus pattern (74 bp):
CGTTGCGATAATCAAATAGCCGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTG
TAATTTTCT
Found at i:2295013 original size:140 final size:140
Alignment explanation
Indices: 2294761--2295030 Score: 495
Period size: 140 Copynumber: 1.9 Consensus size: 140
2294751 TCGTGTTACG
*
2294761 ATAGTCAAACTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
1 ATAGTCAAACTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
*
2294826 TAGTAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
2294891 AATACACATA
131 AATACACATA
* * *
2294901 ATAGTCAAATTTGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAATAGATCA
1 ATAGTCAAACTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
2294966 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
2295031 TACAACGTTT
Statistics
Matches: 125, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
140 125 1.00
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.29
Consensus pattern (140 bp):
ATAGTCAAACTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
AATACACATA
Found at i:2295113 original size:18 final size:18
Alignment explanation
Indices: 2295090--2295125 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2295080 AAGCCGGTTG
*
2295090 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
2295108 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
2295126 CCTTTTTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:2298199 original size:20 final size:20
Alignment explanation
Indices: 2298174--2298238 Score: 94
Period size: 20 Copynumber: 3.2 Consensus size: 20
2298164 GAAATTCAGT
2298174 GTTGCGACAGTCAGAATCGC
1 GTTGCGACAGTCAGAATCGC
*
2298194 GTTGCGACAGTCAGAATCGT
1 GTTGCGACAGTCAGAATCGC
* *
2298214 GTTGCGATAGTCATAATCGC
1 GTTGCGACAGTCAGAATCGC
*
2298234 ATTGC
1 GTTGC
2298239 TATTTACATA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (20 bp):
GTTGCGACAGTCAGAATCGC
Found at i:2298248 original size:20 final size:20
Alignment explanation
Indices: 2298225--2298298 Score: 105
Period size: 20 Copynumber: 3.7 Consensus size: 20
2298215 TTGCGATAGT
*
2298225 CATAATCGCATTGCTATTTA
1 CATATTCGCATTGCTATTTA
* *
2298245 CATATTCACATTGCGATTTA
1 CATATTCGCATTGCTATTTA
2298265 CATATTCGCATTG-TGATTTA
1 CATATTCGCATTGCT-ATTTA
2298285 CATATTCGCATTGC
1 CATATTCGCATTGC
2298299 GATAGTCGAA
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.27, C:0.20, G:0.12, T:0.41
Consensus pattern (20 bp):
CATATTCGCATTGCTATTTA
Found at i:2298259 original size:40 final size:40
Alignment explanation
Indices: 2298215--2298305 Score: 123
Period size: 40 Copynumber: 2.3 Consensus size: 40
2298205 CAGAATCGTG
2298215 TTGCGATAGTCATAATCGCATTGCT-ATTTACATATTCACA
1 TTGCGATAGTCATAATCGCATTG-TGATTTACATATTCACA
* * *
2298255 TTGCGAT-TTACATATTCGCATTGTGATTTACATATTCGCA
1 TTGCGATAGT-CATAATCGCATTGTGATTTACATATTCACA
2298295 TTGCGATAGTC
1 TTGCGATAGTC
2298306 GAAAAATCAC
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
39 2 0.05
40 41 0.93
41 1 0.02
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (40 bp):
TTGCGATAGTCATAATCGCATTGTGATTTACATATTCACA
Found at i:2298401 original size:20 final size:20
Alignment explanation
Indices: 2298339--2298403 Score: 55
Period size: 20 Copynumber: 3.2 Consensus size: 20
2298329 AAAATCGCAA
*
2298339 TGCGATAGTCAGA-ATCGCGT
1 TGCGATA-TCGGAGATCGCGT
**
2298359 TGCGA-ATCTGGAGA-CTGATT
1 TGCGATATC-GGAGATC-GCGT
2298379 TGCGATATCGGAGATCGCGT
1 TGCGATATCGGAGATCGCGT
2298399 TGCGA
1 TGCGA
2298404 ATTATCGATC
Statistics
Matches: 35, Mismatches: 5, Indels: 10
0.70 0.10 0.20
Matches are distributed among these distances:
18 2 0.06
19 4 0.11
20 25 0.71
21 4 0.11
ACGTcount: A:0.23, C:0.18, G:0.32, T:0.26
Consensus pattern (20 bp):
TGCGATATCGGAGATCGCGT
Found at i:2300028 original size:8 final size:8
Alignment explanation
Indices: 2300015--2300039 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
2300005 TCCCACTCTT
2300015 GAAAAGAA
1 GAAAAGAA
2300023 GAAAAGAA
1 GAAAAGAA
2300031 GAAAAGAA
1 GAAAAGAA
2300039 G
1 G
2300040 CTAATTTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (8 bp):
GAAAAGAA
Found at i:2304937 original size:13 final size:14
Alignment explanation
Indices: 2304918--2304955 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
2304908 AAAGTTCTGA
2304918 AAAATAAAGGATAG
1 AAAATAAAGGATAG
**
2304932 -AAATAAAAAATAG
1 AAAATAAAGGATAG
2304945 AAAATAAAGGA
1 AAAATAAAGGA
2304956 ATGGAATTAG
Statistics
Matches: 19, Mismatches: 4, Indels: 2
0.76 0.16 0.08
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.71, C:0.00, G:0.16, T:0.13
Consensus pattern (14 bp):
AAAATAAAGGATAG
Found at i:2305037 original size:16 final size:16
Alignment explanation
Indices: 2305025--2305064 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
2305015 CATAAAATTT
*
2305025 AAATAACAAAAAATAA
1 AAATAAAAAAAAATAA
2305041 AAATAAAAAAAAATAA
1 AAATAAAAAAAAATAA
2305057 AAATAAAA
1 AAATAAAA
2305065 TGTTAGTGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.85, C:0.03, G:0.00, T:0.12
Consensus pattern (16 bp):
AAATAAAAAAAAATAA
Found at i:2305042 original size:6 final size:6
Alignment explanation
Indices: 2305033--2305064 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
2305023 TTAAATAACA
2305033 AAAAAT AAAAAT -AAAA- AAAAAT AAAAAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAA
2305065 TGTTAGTGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 8 0.33
6 16 0.67
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (6 bp):
AAAAAT
Found at i:2306252 original size:16 final size:17
Alignment explanation
Indices: 2306226--2306273 Score: 64
Period size: 16 Copynumber: 2.9 Consensus size: 17
2306216 TAATGACTTT
*
2306226 TATTTTTTATATTTATA
1 TATTATTTATATTTATA
2306243 -ATTATTTATATTTATA
1 TATTATTTATATTTATA
2306259 TTATTATTTAT-TTTA
1 -TATTATTTATATTTA
2306274 GGATAAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 15 0.54
17 4 0.14
18 9 0.32
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TATTATTTATATTTATA
Found at i:2309345 original size:16 final size:18
Alignment explanation
Indices: 2309324--2309364 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
2309314 AACATTCCCA
2309324 GTAATCCT-ATTCCA-TG
1 GTAATCCTAATTCCACTG
*
2309340 GTAATCTTACATTCCACTG
1 GTAATCCTA-ATTCCACTG
2309359 GTAATC
1 GTAATC
2309365 TTACATTCGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 7 0.33
18 6 0.29
19 8 0.38
ACGTcount: A:0.27, C:0.24, G:0.12, T:0.37
Consensus pattern (18 bp):
GTAATCCTAATTCCACTG
Found at i:2309355 original size:18 final size:19
Alignment explanation
Indices: 2309332--2309372 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
2309322 CAGTAATCCT
2309332 ATTCCA-TGGTAATCTTAC
1 ATTCCACTGGTAATCTTAC
2309350 ATTCCACTGGTAATCTTAC
1 ATTCCACTGGTAATCTTAC
2309369 ATTC
1 ATTC
2309373 GTGAACCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.27, C:0.24, G:0.10, T:0.39
Consensus pattern (19 bp):
ATTCCACTGGTAATCTTAC
Found at i:2311886 original size:22 final size:20
Alignment explanation
Indices: 2311836--2311898 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
2311826 CCGAAATTTG
*
2311836 GTATCGATACTCAAGC-A-A
1 GTATCGATACTCAACCTAGA
*
2311854 -TATAGATACTCCAACACTAGA
1 GTATCGATACT-CAAC-CTAGA
*
2311875 GTATCGATACTCAGCCTAGA
1 GTATCGATACTCAACCTAGA
2311895 GTAT
1 GTAT
2311899 AAATACTACT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
17 9 0.25
18 3 0.08
19 1 0.03
20 10 0.28
21 4 0.11
22 9 0.25
ACGTcount: A:0.37, C:0.22, G:0.16, T:0.25
Consensus pattern (20 bp):
GTATCGATACTCAACCTAGA
Found at i:2311981 original size:20 final size:20
Alignment explanation
Indices: 2311958--2312007 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
2311948 CAACAGGTGG
*
2311958 GTATCGATACCAAAGGTTTT
1 GTATCGATACCAAAGGTTTA
2311978 GTATCGATACCAAAGGTTTA
1 GTATCGATACCAAAGGTTTA
2311998 GTATCGATAC
1 GTATCGATAC
2312008 TAAAAGGTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (20 bp):
GTATCGATACCAAAGGTTTA
Found at i:2312020 original size:20 final size:20
Alignment explanation
Indices: 2311958--2312023 Score: 71
Period size: 20 Copynumber: 3.3 Consensus size: 20
2311948 CAACAGGTGG
* **
2311958 GTATCGATACCAAAGGTTTT
1 GTATCGATACAAAAGGTTCA
* *
2311978 GTATCGATACCAAAGGTTTA
1 GTATCGATACAAAAGGTTCA
2311998 GTATCGATACTAAAAGG-TCA
1 GTATCGATAC-AAAAGGTTCA
2312018 GTATCG
1 GTATCG
2312024 GTACCTACAA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
20 37 0.88
21 5 0.12
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.30
Consensus pattern (20 bp):
GTATCGATACAAAAGGTTCA
Found at i:2313402 original size:17 final size:17
Alignment explanation
Indices: 2313370--2313403 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2313360 TTTTGGGCTT
*
2313370 ATTTTCAAATCAAAAAA
1 ATTTTCAAAACAAAAAA
*
2313387 ATTTTCAAAACCAAAAA
1 ATTTTCAAAACAAAAAA
2313404 GTCAACGTTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.59, C:0.15, G:0.00, T:0.26
Consensus pattern (17 bp):
ATTTTCAAAACAAAAAA
Found at i:2313403 original size:18 final size:17
Alignment explanation
Indices: 2313370--2313403 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2313360 TTTTGGGCTT
*
2313370 ATTTTCAAATCAAAAAA
1 ATTTTCAAACCAAAAAA
2313387 ATTTTCAAAACCAAAAA
1 ATTTTC-AAACCAAAAA
2313404 GTCAACGTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.59, C:0.15, G:0.00, T:0.26
Consensus pattern (17 bp):
ATTTTCAAACCAAAAAA
Found at i:2318207 original size:15 final size:13
Alignment explanation
Indices: 2318176--2318202 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2318166 GTTTAAGTAG
2318176 TTTAGGATTTATC
1 TTTAGGATTTATC
2318189 TTTAGGATTTATC
1 TTTAGGATTTATC
2318202 T
1 T
2318203 CTTTATTTTA
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:0.22, C:0.07, G:0.15, T:0.56
Consensus pattern (13 bp):
TTTAGGATTTATC
Found at i:2319303 original size:23 final size:23
Alignment explanation
Indices: 2319267--2319356 Score: 83
Period size: 23 Copynumber: 3.9 Consensus size: 23
2319257 CGAACTAACG
* *
2319267 TAAATGAGCATAAACAAACACAA
1 TAAATGAACGTAAACAAACACAA
* *
2319290 TAAATGAATGTAAATGAATACA-AA
1 TAAATGAACGTAAA-CAA-ACACAA
* * **
2319314 TGAACGAACGTAAAGGAACACAA
1 TAAATGAACGTAAACAAACACAA
2319337 TAAATGAACGTAAACAAACA
1 TAAATGAACGTAAACAAACA
2319357 TAAATAAAAA
Statistics
Matches: 52, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
22 3 0.06
23 31 0.60
24 15 0.29
25 3 0.06
ACGTcount: A:0.58, C:0.13, G:0.13, T:0.16
Consensus pattern (23 bp):
TAAATGAACGTAAACAAACACAA
Found at i:2319551 original size:14 final size:13
Alignment explanation
Indices: 2319532--2319625 Score: 62
Period size: 14 Copynumber: 7.6 Consensus size: 13
2319522 GATTGGGTTA
2319532 AACATAAATGAACG
1 AACATAAAT-AACG
2319546 AACATAAAT---G
1 AACATAAATAACG
*
2319556 AACATAAACAAACG
1 AACATAAA-TAACG
2319570 AACAT--A-AACG
1 AACATAAATAACG
* *
2319580 AATATAAATGAACA
1 AACATAAAT-AACG
2319594 AACAT--A-AACG
1 AACATAAATAACG
2319604 AACATAAATGAACG
1 AACATAAAT-AACG
2319618 AACATAAA
1 AACATAAA
2319626 CCAACATATT
Statistics
Matches: 63, Mismatches: 5, Indels: 24
0.68 0.05 0.26
Matches are distributed among these distances:
10 25 0.40
12 4 0.06
14 34 0.54
ACGTcount: A:0.62, C:0.15, G:0.10, T:0.14
Consensus pattern (13 bp):
AACATAAATAACG
Found at i:2319587 original size:34 final size:34
Alignment explanation
Indices: 2319542--2319616 Score: 107
Period size: 34 Copynumber: 2.2 Consensus size: 34
2319532 AACATAAATG
2319542 AACGAACATAAATGAACATAA-ACAAACGAACATA
1 AACGAACATAAATGAACA-AACACAAACGAACATA
* *
2319576 AACGAATATAAATGAACAAACATAAACGAACATA
1 AACGAACATAAATGAACAAACACAAACGAACATA
*
2319610 AATGAAC
1 AACGAAC
2319617 GAACATAAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
33 2 0.06
34 34 0.94
ACGTcount: A:0.61, C:0.16, G:0.09, T:0.13
Consensus pattern (34 bp):
AACGAACATAAATGAACAAACACAAACGAACATA
Found at i:2319667 original size:24 final size:24
Alignment explanation
Indices: 2319532--2319666 Score: 157
Period size: 24 Copynumber: 5.7 Consensus size: 24
2319522 GATTGGGTTA
*
2319532 AACATAAATGAACGAACATAAATG
1 AACATAAATGAACGAACATAAACG
**
2319556 AACATAAACAAACGAACATAAACG
1 AACATAAATGAACGAACATAAACG
* *
2319580 AATATAAATGAACAAACATAAACG
1 AACATAAATGAACGAACATAAACG
*
2319604 AACATAAATGAACGAACATAAACC
1 AACATAAATGAACGAACATAAACG
* * * **
2319628 AACAT--ATTACCGAACGTTCACG
1 AACATAAATGAACGAACATAAACG
2319650 AACATAAATGAACGAAC
1 AACATAAATGAACGAAC
2319667 GAGCCCTCTG
Statistics
Matches: 91, Mismatches: 18, Indels: 4
0.81 0.16 0.04
Matches are distributed among these distances:
22 16 0.18
24 75 0.82
ACGTcount: A:0.56, C:0.19, G:0.10, T:0.15
Consensus pattern (24 bp):
AACATAAATGAACGAACATAAACG
Found at i:2328647 original size:14 final size:15
Alignment explanation
Indices: 2328614--2328657 Score: 72
Period size: 14 Copynumber: 3.0 Consensus size: 15
2328604 GAGGACCAAC
*
2328614 TTTATTTTAATTTAT
1 TTTATTTTAATATAT
2328629 TTTATTTTAATAT-T
1 TTTATTTTAATATAT
2328643 TTTATTTTAATATAT
1 TTTATTTTAATATAT
2328658 GGTTAACTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
14 14 0.52
15 13 0.48
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTATTTTAATATAT
Found at i:2331155 original size:18 final size:18
Alignment explanation
Indices: 2331132--2331168 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
2331122 AATATAACAT
2331132 TATTATGGGAATGTAATA
1 TATTATGGGAATGTAATA
*
2331150 TATTATGGGAATGTTATA
1 TATTATGGGAATGTAATA
2331168 T
1 T
2331169 TACTTTGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.22, T:0.43
Consensus pattern (18 bp):
TATTATGGGAATGTAATA
Found at i:2339563 original size:84 final size:84
Alignment explanation
Indices: 2339422--2339590 Score: 320
Period size: 84 Copynumber: 2.0 Consensus size: 84
2339412 AAATTGATCA
*
2339422 TTGGTTCAATACCCTGAGACACTTGTTTGAGCCTATTTATCATTTTCTTTCATAACCATGAACCA
1 TTGGTTCAATACCCTGAGACACTTGTTTGAGCCTATTTATCATTTTATTTCATAACCATGAACCA
2339487 TGGCCTACATTACGTACCT
66 TGGCCTACATTACGTACCT
*
2339506 TTGGTTCAATACCCTGAGACACTTGTTTGGGCCTATTTATCATTTTATTTCATAACCATGAACCA
1 TTGGTTCAATACCCTGAGACACTTGTTTGAGCCTATTTATCATTTTATTTCATAACCATGAACCA
2339571 TGGCCTACATTACGTACCT
66 TGGCCTACATTACGTACCT
2339590 T
1 T
2339591 AAAAAGTCCA
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 83 1.00
ACGTcount: A:0.25, C:0.24, G:0.14, T:0.37
Consensus pattern (84 bp):
TTGGTTCAATACCCTGAGACACTTGTTTGAGCCTATTTATCATTTTATTTCATAACCATGAACCA
TGGCCTACATTACGTACCT
Found at i:2340771 original size:64 final size:64
Alignment explanation
Indices: 2340691--2340815 Score: 214
Period size: 64 Copynumber: 2.0 Consensus size: 64
2340681 TGAGAGTCTA
*
2340691 TCAACAAACAACTTTCCAATTTCATTCAGAGTCAATTTTAACTTCACAACGAAGGATATTGTAC
1 TCAACAAACAACTTTCCAATTTCATTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGTAC
* * *
2340755 TCAACAAACAATTTTCCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTG
1 TCAACAAACAACTTTCCAATTTCATTCAGAGTCAATTTCAACTTCACAACGAAGGATATTG
2340816 AACTAGAACC
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
64 57 1.00
ACGTcount: A:0.36, C:0.22, G:0.11, T:0.31
Consensus pattern (64 bp):
TCAACAAACAACTTTCCAATTTCATTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGTAC
Found at i:2341080 original size:43 final size:43
Alignment explanation
Indices: 2341026--2341149 Score: 135
Period size: 43 Copynumber: 2.9 Consensus size: 43
2341016 ACTAAGGGGT
* *
2341026 CATCCGCGATTTCAACTCCACGACGAAGGATATCGTACCAACG
1 CATCCACGATTTCAACTCCACGACGAAGGATATCGTACCAACA
* * * *
2341069 GATCCACGATTTCAACTCTACGACGGAA-GATATCGTGCCCACA
1 CATCCACGATTTCAACTCCACGAC-GAAGGATATCGTACCAACA
* * *
2341112 CATCCACGGTTTCAACTTCACAACGAAGGGA-ATCGTAC
1 CATCCACGATTTCAACTCCACGACGAA-GGATATCGTAC
2341150 ACACAAGTAA
Statistics
Matches: 66, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
42 3 0.05
43 58 0.88
44 5 0.08
ACGTcount: A:0.31, C:0.31, G:0.19, T:0.20
Consensus pattern (43 bp):
CATCCACGATTTCAACTCCACGACGAAGGATATCGTACCAACA
Found at i:2341427 original size:42 final size:43
Alignment explanation
Indices: 2341368--2341483 Score: 126
Period size: 43 Copynumber: 2.7 Consensus size: 43
2341358 GGGTCATATG
* **
2341368 CGATTTTAACTCCACGACGGAGGAT-TCGTACCCACGGATCCA
1 CGATTTCAACTCCACGACGGAGGATATCGTACCCACACATCCA
* * *
2341410 CGATTTCAACTCCACGACGGGGGATATCGTGCTCACACATCCA
1 CGATTTCAACTCCACGACGGAGGATATCGTACCCACACATCCA
* * * * *
2341453 CGGTTTCAACTTCACGATGAAGGAAATCGTA
1 CGATTTCAACTCCACGACGGAGGATATCGTA
2341484 TACACAAGCA
Statistics
Matches: 60, Mismatches: 13, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
42 23 0.38
43 37 0.62
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (43 bp):
CGATTTCAACTCCACGACGGAGGATATCGTACCCACACATCCA
Found at i:2341988 original size:165 final size:159
Alignment explanation
Indices: 2341557--2342076 Score: 504
Period size: 165 Copynumber: 3.2 Consensus size: 159
2341547 AAGAAGGAGA
* *
2341557 ATCTGCCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACTC
1 ATCTGCCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTC
* * *
2341622 AAGGCTAGAAGGGTTATCTGTCAATAAATACCTTCGAGTTTGATTACACTCAGCTCAAAGGTGCA
66 AAGGCAAGAAGGGTTATCTG-CAATAAAGACCTTCGAGTTCGATTACACT---CTCAAAGGTGCA
* *
2341687 TCATTTGCAGCAGAGCTCAAGGCAAGAAGGGCT
127 TCATTTGCAACAGAACTCAAGGCAAGAAGGGCT
* * * *
2341720 ATCTGCCAAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGTCACATCATTTGTAGCATAGCTT
1 ATCTGCCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTC
* * * * *
2341785 AAGGCGAGAAGGGTTATCTGCCAACCAAAGAACTTCGAGTTCGATTACAACT-TCGAGGGTGCAT
66 AAGGCAAGAAGGGTTATCTG-CAA-TAAAGACCTTCGAGTTCGATTAC-ACTCTCAAAGGTGCAT
* * * *
2341849 TATTTGCAATATAACTCAAGGCAAGAAGGGTT
128 CATTTGCAACAGAACTCAAGGCAAGAAGGGCT
* * **
2341881 ATCTGCCAACAAAAGACCTTCAAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAATATA
1 ATCTG-C--C-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATA
* * * * *
2341946 GCTCAAGGAAAGACA-GGCTATTTGCAAATAAAAGACCTTCGAGTTCGATTATACTCAGCTTAAA
62 GCTCAAGGCAAGA-AGGGTTATCTGC-AAT-AAAGACCTTCGAGTTCGATTACACT---CTCAAA
** * * * * *
2342010 GGCACATCATTTGTAACATAACTCAAGACGAGAAGGGTT
121 GGTGCATCATTTGCAACAGAACTCAAGGCAAGAAGGGCT
* *
2342049 ATTTGTCATAAAAGACCTTCGAGTTCGA
1 ATCTG-C--CAAAGACCTTCGAGTTCGA
2342077 TTTCATTCAG
Statistics
Matches: 294, Mismatches: 50, Indels: 22
0.80 0.14 0.06
Matches are distributed among these distances:
161 41 0.14
162 1 0.00
163 81 0.28
164 24 0.08
165 89 0.30
166 1 0.00
167 17 0.06
168 40 0.14
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.25
Consensus pattern (159 bp):
ATCTGCCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTC
AAGGCAAGAAGGGTTATCTGCAATAAAGACCTTCGAGTTCGATTACACTCTCAAAGGTGCATCAT
TTGCAACAGAACTCAAGGCAAGAAGGGCT
Found at i:2341991 original size:84 final size:83
Alignment explanation
Indices: 2341564--2342101 Score: 466
Period size: 84 Copynumber: 6.5 Consensus size: 83
2341554 AGAATCTGCC
* * * * *
2341564 AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACTCAAGGCTA
1 AAAGACCTTCGAGTTCGACTACACTCAGCTCAAAGGCACATCATTTGCAACATAACTCAAGGCAA
2341629 GAAGGGTTATCTGTCAAT-
66 GAAGGGTTATCTG-CAATA
* * * ** * * *
2341647 AAATACCTTCGAGTTTGATTACACTCAGCTCAAAGGTGCATCATTTGCAGCAGAGCTCAAGGCAA
1 AAAGACCTTCGAGTTCGACTACACTCAGCTCAAAGGCACATCATTTGCAACATAACTCAAGGCAA
* *
2341712 GAAGGGCTATCTGC---C
66 GAAGGGTTATCTGCAATA
* * * * * * * *
2341727 AAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGTCACATCATTTGTAGCATAGCTTAAGGCGA
1 AAAGACCTTCGAGTTCGACTACACTCAGCTCAAAGGCACATCATTTGCAACATAACTCAAGGCAA
**
2341792 GAAGGGTTATCTGCCAACC
66 GAAGGGTTATCTG-CAATA
* * * * ** * *
2341811 AAAGAACTTCGAGTTCGATTACA---A-CTTCGAGGGTGCATTATTTGCAATATAACTCAAGGCA
1 AAAGACCTTCGAGTTCGACTACACTCAGC-TCAAAGGCACATCATTTGCAACATAACTCAAGGCA
*
2341872 AGAAGGGTTATCTGCCAACA
65 AGAAGGGTTATCTG-CAATA
* * * * *
2341892 AAAGACCTTCAAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAATATAGCTCAAGGAAA
1 AAAGACCTTCGAGTTCGACTACACTCAGCTCAAAGGCACATCATTTGCAACATAACTCAAGGCAA
* *
2341957 GACA-GGCTATTTGCAAATA
66 GA-AGGGTTATCTGC-AATA
* * * * * *
2341976 AAAGACCTTCGAGTTCGATTATACTCAGCTTAAAGGCACATCATTTGTAACATAACTCAAGACGA
1 AAAGACCTTCGAGTTCGACTACACTCAGCTCAAAGGCACATCATTTGCAACATAACTCAAGGCAA
*
2342041 GAAGGGTTATTTGTC-ATA
66 GAAGGGTTATCTG-CAATA
* * * * *
2342059 AAAGACCTTCGAGTTCGATTTCATTCAGCTCAGAGGCATATCA
1 AAAGACCTTCGAGTTCGACTACACTCAGCTCAAAGGCACATCA
2342102 ACCACATTGT
Statistics
Matches: 369, Mismatches: 72, Indels: 28
0.79 0.15 0.06
Matches are distributed among these distances:
80 66 0.18
81 64 0.17
82 1 0.00
83 108 0.29
84 127 0.34
85 3 0.01
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (83 bp):
AAAGACCTTCGAGTTCGACTACACTCAGCTCAAAGGCACATCATTTGCAACATAACTCAAGGCAA
GAAGGGTTATCTGCAATA
Found at i:2342799 original size:2 final size:2
Alignment explanation
Indices: 2342792--2342821 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2342782 TACGGTTTTA
2342792 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
2342822 GAGTTAGGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2345840 original size:28 final size:28
Alignment explanation
Indices: 2345797--2345856 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 28
2345787 ACATAACACC
* *
2345797 TAAAATCAATGACTAAATA-GAAATTAA
1 TAAAATCAATGACTAAAAATGAAATAAA
2345824 TAAAATCACAGTG-CTAAAAATGAAATAAA
1 TAAAATCA-A-TGACTAAAAATGAAATAAA
2345853 TAAA
1 TAAA
2345857 CATAGAGATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 8 0.29
28 7 0.25
29 13 0.46
ACGTcount: A:0.60, C:0.08, G:0.08, T:0.23
Consensus pattern (28 bp):
TAAAATCAATGACTAAAAATGAAATAAA
Found at i:2347973 original size:117 final size:117
Alignment explanation
Indices: 2347764--2348034 Score: 352
Period size: 117 Copynumber: 2.3 Consensus size: 117
2347754 AATGTTAATG
* *
2347764 CAAGGTTGAA-AGAGTTCTTCTCATTATGAACTTTTTCTTCCTCGTTAGATAAGTCCTTCTCATT
1 CAAGGTTGAACA-AGTTCTTCTCATTATGAACTTCTTCTTCCTCATTAGATAAGTCCTTCTCATT
* * *
2347828 ATGAACTCTTCATTGGAAATGTTGATCCATCTCCTTCCGTGATGGAATCGAAC
65 ATGAACTCTTCACTGGAAATGTTGATCCACCTCCTTCCGTGATGGAATCAAAC
* * * **
2347881 CAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCATTGGATGAGTTGTTCTCATTA
1 CAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCATTAGATAAGTCCTTCTCATTA
* * ** *
2347946 TGAACT-TTCCACT-GAAACTGTTTATCCACCTCTTTCTTTGATGGAATCAAAT
66 TGAACTCTT-CACTGGAAA-TGTTGATCCACCTCCTTCCGTGATGGAATCAAAC
2347998 CAAGGTTGAACAAGTTCTTCTCATTATGAAC-TCTTCT
1 CAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCT
2348035 GGAAATGTTG
Statistics
Matches: 136, Mismatches: 15, Indels: 7
0.86 0.09 0.04
Matches are distributed among these distances:
116 12 0.09
117 123 0.90
118 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.39
Consensus pattern (117 bp):
CAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCATTAGATAAGTCCTTCTCATTA
TGAACTCTTCACTGGAAATGTTGATCCACCTCCTTCCGTGATGGAATCAAAC
Found at i:2348138 original size:16 final size:16
Alignment explanation
Indices: 2348082--2348139 Score: 55
Period size: 16 Copynumber: 3.4 Consensus size: 16
2348072 AATGAACAAG
2348082 TTCTTCTCATTATGAA
1 TTCTTCTCATTATGAA
* *
2348098 TT-TTCTCCTTTAGGACAA
1 TTCTTCT-CATTATG--AA
2348116 GTTCTTCTCATTATGAA
1 -TTCTTCTCATTATGAA
2348133 TTCTTCT
1 TTCTTCT
2348140 GGAAATGTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 10
0.70 0.09 0.21
Matches are distributed among these distances:
15 4 0.12
16 14 0.42
17 2 0.06
18 2 0.06
19 7 0.21
20 4 0.12
ACGTcount: A:0.21, C:0.21, G:0.09, T:0.50
Consensus pattern (16 bp):
TTCTTCTCATTATGAA
Found at i:2349570 original size:52 final size:51
Alignment explanation
Indices: 2349502--2349752 Score: 306
Period size: 52 Copynumber: 4.9 Consensus size: 51
2349492 TATCCCAACC
* * * * *
2349502 TTTTCATGTTGGTGTGAGCCTTCAAGATACCCCACATGGATAATATCTATCT
1 TTTTCATGCTGATGTGAACCTTCAAGATGCCTCACATGGATAAT-TCTATCT
* * * *
2349554 TTTTCATACTGATGTGAACCTTCAAGATGCCTCACATGGATTACTTTTGTCT
1 TTTTCATGCTGATGTGAACCTTCAAGATGCCTCACATGGA-TAATTCTATCT
* *
2349606 TTTT-ATGCTGATGTGAACCTTCAAGATGCCTCATATGGATTATTTCTATCT
1 TTTTCATGCTGATGTGAACCTTCAAGATGCCTCACATGGA-TAATTCTATCT
* * *
2349657 TTTTCATGCTGATGTAAACCTTCAAGATGCCTCACATGGATTACTTCTGTCT
1 TTTTCATGCTGATGTGAACCTTCAAGATGCCTCACATGGA-TAATTCTATCT
* * *
2349709 TTTTCATGCTGATGTGAGCCTTCAAGATGCCCCACATAGATAAT
1 TTTTCATGCTGATGTGAACCTTCAAGATGCCTCACATGGATAAT
2349753 ATAGACCTCC
Statistics
Matches: 174, Mismatches: 23, Indels: 5
0.86 0.11 0.02
Matches are distributed among these distances:
51 49 0.28
52 122 0.70
53 3 0.02
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.38
Consensus pattern (51 bp):
TTTTCATGCTGATGTGAACCTTCAAGATGCCTCACATGGATAATTCTATCT
Done.