Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007979.1 Hibiscus syriacus cultivar Beakdansim tig00110418_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: 2767453
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 13
Found at i:2277554 original size:14 final size:14
Alignment explanation
Indices: 2277535--2277593 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
2277525 TTTGGTTTCG
2277535 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
2277549 CGTTGCGATTTTGGTTT
1 CGTTGCGATTTT-G--T
*
2277566 CGCGTTGCGATTCTGT
1 --CGTTGCGATTTTGT
2277582 CGTTGCGATTTT
1 CGTTGCGATTTT
2277594 CATTTTGCGT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 23 0.61
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 11 0.29
ACGTcount: A:0.07, C:0.17, G:0.29, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:2277561 original size:33 final size:33
Alignment explanation
Indices: 2277519--2277642 Score: 176
Period size: 33 Copynumber: 3.7 Consensus size: 33
2277509 AAAATCGCAA
*
2277519 TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
2277552 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
** * *
2277585 TGCGATTTTCATTTTGCGTTGCGATTCTCTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
* *
2277618 TGCGATTTTAAGTTTCGTGTTGCGA
1 TGCGATTTT-GGTTTCGCGTTGCGA
2277643 AAGAAACTAT
Statistics
Matches: 81, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
33 70 0.86
34 11 0.14
ACGTcount: A:0.09, C:0.17, G:0.27, T:0.47
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:2277573 original size:19 final size:19
Alignment explanation
Indices: 2277519--2277577 Score: 83
Period size: 19 Copynumber: 3.4 Consensus size: 19
2277509 AAAATCGCAA
2277519 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
2277538 TGCGATTTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
2277552 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
2277571 TGCGATT
1 TGCGATT
2277578 CTGTCGTTGC
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 12 0.34
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 19 0.54
ACGTcount: A:0.07, C:0.15, G:0.31, T:0.47
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:2277618 original size:14 final size:14
Alignment explanation
Indices: 2277568--2277624 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
2277558 TTTGGTTTCG
*
2277568 CGTTGCGATTCTGT
1 CGTTGCGATTCTCT
*
2277582 CGTTGCGATTTTCATTTT
1 CGTTGCGA--TTC--TCT
2277600 GCGTTGCGATTCTCT
1 -CGTTGCGATTCTCT
2277615 CGTTGCGATT
1 CGTTGCGATT
2277625 TTAAGTTTCG
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 18 0.50
15 2 0.06
16 3 0.08
17 3 0.08
18 2 0.06
19 8 0.22
ACGTcount: A:0.09, C:0.21, G:0.25, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:2279592 original size:21 final size:21
Alignment explanation
Indices: 2279538--2279602 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 21
2279528 TCTTTTGGTT
2279538 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
***
2279559 G-AATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
*
2279579 GAAATGAAAATCGCAACGATA
1 GAAATGAAAATCGCAACGAGA
2279600 GAA
1 GAA
2279603 TCGCAGAGAG
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 17 0.47
21 19 0.53
ACGTcount: A:0.48, C:0.15, G:0.25, T:0.12
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:2279612 original size:33 final size:33
Alignment explanation
Indices: 2279538--2279660 Score: 140
Period size: 33 Copynumber: 3.5 Consensus size: 33
2279528 TCTTTTGGTT
2279538 GAAATGAAAATCGCAACGAGAGAATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGAG-A--A---TCGC-A-GAGA
*
2279579 GAAATGAAAATCGCAACGATAGAATCGCAGAGA
1 GAAATGAAAATCGCAACGAGAGAATCGCAGAGA
*
2279612 GAAATGAAAATCGCAACGAGAGAATCGCA-ACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAGA-GA
2279645 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
2279661 TGCGATTTTC
Statistics
Matches: 78, Mismatches: 3, Indels: 10
0.86 0.03 0.11
Matches are distributed among these distances:
32 1 0.01
33 49 0.63
34 1 0.01
35 4 0.05
38 1 0.01
40 1 0.01
41 21 0.27
ACGTcount: A:0.47, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAGAGA
Found at i:2279711 original size:21 final size:21
Alignment explanation
Indices: 2279685--2279761 Score: 111
Period size: 21 Copynumber: 3.7 Consensus size: 21
2279675 CGCGTTGCGA
2279685 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
**
2279706 TTCTCTCGTTGCAGATAGTCAT
1 TTCTCTCGTTGC-GATTTTCAT
*
2279728 TT-TCACGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
2279748 TTCTCTCGTTGCGA
1 TTCTCTCGTTGCGA
2279762 CTCTTTCTGC
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
20 9 0.19
21 30 0.62
22 9 0.19
ACGTcount: A:0.13, C:0.23, G:0.17, T:0.47
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:2279882 original size:33 final size:33
Alignment explanation
Indices: 2279840--2279910 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
2279830 AATACTAACT
2279840 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
2279873 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
2279906 TGAAA
1 TGAAA
2279911 TCTAAGTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:2280316 original size:20 final size:20
Alignment explanation
Indices: 2280291--2280464 Score: 226
Period size: 20 Copynumber: 8.7 Consensus size: 20
2280281 CTTTAAAAAT
2280291 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
2280311 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
* *
2280331 TGTCGTTACGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
* *
2280352 TGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
2280372 CGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
2280392 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
2280412 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
2280432 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
2280452 CGCGTTGCGATTT
1 CGCGTTGCGATTT
2280465 TCATATTCGT
Statistics
Matches: 136, Mismatches: 14, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
20 118 0.87
21 18 0.13
ACGTcount: A:0.20, C:0.18, G:0.28, T:0.34
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:2280473 original size:20 final size:20
Alignment explanation
Indices: 2280432--2280483 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
2280422 TTTACGGATA
* *
2280432 CGCGTTGCGATTTATGTGTT
1 CGCGTTGCGATTTATATATT
2280452 CGCGTTGCGATTT-TCATATT
1 CGCGTTGCGATTTAT-ATATT
*
2280472 CGTGTTGCGATT
1 CGCGTTGCGATT
2280484 CTGGAAAATC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 1 0.04
20 27 0.96
ACGTcount: A:0.12, C:0.17, G:0.27, T:0.44
Consensus pattern (20 bp):
CGCGTTGCGATTTATATATT
Found at i:2280479 original size:60 final size:60
Alignment explanation
Indices: 2280290--2280483 Score: 207
Period size: 60 Copynumber: 3.2 Consensus size: 60
2280280 GCTTTAAAAA
* *
2280290 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATT-GTCGTTACGATTTACGGATA-
1 TCGCGTTGCGATTTACGGATACGCGTTGCGA-TTTACGTGTTCG-CGTTGCGATTTAC--ATAT
* * * **
2280352 T-GCGTTGCGATATACGGATACGCATTGCGATTTACG-GATACGCGTTGCGATTTACGGAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTACGTG-TTCGCGTTGCGATTTACATAT
* * * *
2280411 ACACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTACGTGTTCGCGTTGCGATTTACATAT
*
2280471 TCGTGTTGCGATT
1 TCGCGTTGCGATT
2280484 CTGGAAAATC
Statistics
Matches: 108, Mismatches: 19, Indels: 12
0.78 0.14 0.09
Matches are distributed among these distances:
58 1 0.01
60 77 0.71
61 29 0.27
62 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.27, T:0.36
Consensus pattern (60 bp):
TCGCGTTGCGATTTACGGATACGCGTTGCGATTTACGTGTTCGCGTTGCGATTTACATAT
Found at i:2281247 original size:31 final size:31
Alignment explanation
Indices: 2281212--2281281 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 31
2281202 TAAATTATGT
*
2281212 TTTTATTACCTAAACTATCAATTTTAATATA
1 TTTTAGTACCTAAACTATCAATTTTAATATA
** * * *
2281243 TTTTAGTATTTAAACTATCAGTTTTGATCTA
1 TTTTAGTACCTAAACTATCAATTTTAATATA
2281274 TTTTAGTA
1 TTTTAGTA
2281282 ATTAAATTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.33, C:0.10, G:0.06, T:0.51
Consensus pattern (31 bp):
TTTTAGTACCTAAACTATCAATTTTAATATA
Found at i:2281287 original size:31 final size:31
Alignment explanation
Indices: 2281222--2281287 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
2281212 TTTTATTACC
*
2281222 TAAACTATCAATTTTAATATATTTTAGTATT
1 TAAACTATCAATTTTAATATATTTTAGTAAT
* * *
2281253 TAAACTATCAGTTTTGATCTATTTTAGTAAT
1 TAAACTATCAATTTTAATATATTTTAGTAAT
2281284 TAAA
1 TAAA
2281288 TTTTTAATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.38, C:0.08, G:0.06, T:0.48
Consensus pattern (31 bp):
TAAACTATCAATTTTAATATATTTTAGTAAT
Found at i:2283473 original size:21 final size:21
Alignment explanation
Indices: 2283447--2283562 Score: 144
Period size: 21 Copynumber: 5.5 Consensus size: 21
2283437 TATAATAAGA
*
2283447 TTTAGGGTTTAGAAT-TTAGGG
1 TTTAGGGTTTA-TATGTTAGGG
* * *
2283468 TTTAGGGTTTATATGATACGA
1 TTTAGGGTTTATATGTTAGGG
* * *
2283489 TGTAAGGTTTATATGTTAGGA
1 TTTAGGGTTTATATGTTAGGG
2283510 TTTAGGGTTTATATGTTAGGG
1 TTTAGGGTTTATATGTTAGGG
*
2283531 TTTAGGGTTTATATGATAGGG
1 TTTAGGGTTTATATGTTAGGG
2283552 TTTAGGGTTTA
1 TTTAGGGTTTA
2283563 GGGTTTTTAT
Statistics
Matches: 82, Mismatches: 12, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
20 2 0.02
21 80 0.98
ACGTcount: A:0.24, C:0.01, G:0.30, T:0.45
Consensus pattern (21 bp):
TTTAGGGTTTATATGTTAGGG
Found at i:2283478 original size:14 final size:14
Alignment explanation
Indices: 2283446--2283472 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2283436 ATATAATAAG
2283446 ATTTAGGGTTTAGA
1 ATTTAGGGTTTAGA
2283460 ATTTAGGGTTTAG
1 ATTTAGGGTTTAG
2283473 GGTTTATATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.00, G:0.30, T:0.44
Consensus pattern (14 bp):
ATTTAGGGTTTAGA
Found at i:2283556 original size:28 final size:28
Alignment explanation
Indices: 2283524--2283590 Score: 93
Period size: 28 Copynumber: 2.4 Consensus size: 28
2283514 GGGTTTATAT
2283524 GTTAGGGTTTAGGGTTTATATGA-T-AGG
1 GTTAGGGTTTAGGGTTTATAT-ATTAAGG
*
2283551 GTTTAGGGTTTAGGGTTTTTATATTAAGG
1 G-TTAGGGTTTAGGGTTTATATATTAAGG
2283580 GTTAGGGTTTA
1 GTTAGGGTTTA
2283591 AGTTATGCAC
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
27 2 0.06
28 30 0.83
29 4 0.11
ACGTcount: A:0.21, C:0.00, G:0.34, T:0.45
Consensus pattern (28 bp):
GTTAGGGTTTAGGGTTTATATATTAAGG
Found at i:2285897 original size:15 final size:16
Alignment explanation
Indices: 2285873--2285905 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
2285863 ATTCTTATCA
*
2285873 TAAAATAACT-ATTCC
1 TAAAAAAACTCATTCC
2285888 TAAAAAAACTCATTCC
1 TAAAAAAACTCATTCC
2285904 TA
1 TA
2285906 TATAATATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.48, C:0.21, G:0.00, T:0.30
Consensus pattern (16 bp):
TAAAAAAACTCATTCC
Found at i:2291297 original size:105 final size:105
Alignment explanation
Indices: 2291098--2291300 Score: 255
Period size: 105 Copynumber: 1.9 Consensus size: 105
2291088 GACCACATAT
** * *
2291098 AAATTCCTTAAGAACCATATACATATAACAAGGATTAAGTAAGTGTCTCAAAAGACCTCATACAT
1 AAATTCCTTAAGAACCATATACATATAACAAGGACCAAATAAGTGTCGCAAAAGACCTCATACAT
2291163 GCTCCAAAGAATACATATACGTCCCGAAGGACCACGCAGA
66 GCTCCAAAGAATACATATACGTCCCGAAGGACCACGCAGA
* * * * *
2291203 AAATTCCTTAAGAATCATATACATAT-GCTAAGGACCAAATATGTGTCGCAAAGGACCTCATAGA
1 AAATTCCTTAAGAACCATATACATATAAC-AAGGACCAAATAAGTGTCGCAAAAGACCTCATACA
* * * * * *
2291267 TGTTCCATAGGATACCTATATGTCCTGAAGGACC
65 TGCTCCAAAGAATACATATACGTCCCGAAGGACC
2291301 GCGTAGACCC
Statistics
Matches: 82, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
104 1 0.01
105 81 0.99
ACGTcount: A:0.39, C:0.22, G:0.16, T:0.24
Consensus pattern (105 bp):
AAATTCCTTAAGAACCATATACATATAACAAGGACCAAATAAGTGTCGCAAAAGACCTCATACAT
GCTCCAAAGAATACATATACGTCCCGAAGGACCACGCAGA
Found at i:2296843 original size:20 final size:20
Alignment explanation
Indices: 2296816--2296859 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
2296806 CTTTGACCTA
2296816 TTGA-AGTTGATCGTTGACT
1 TTGACAGTTGATCGTTGACT
*
2296835 TTGACAGTTGATTGTTGACT
1 TTGACAGTTGATCGTTGACT
2296855 TTGAC
1 TTGAC
2296860 CCAAAAAGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 4 0.17
20 19 0.83
ACGTcount: A:0.20, C:0.11, G:0.25, T:0.43
Consensus pattern (20 bp):
TTGACAGTTGATCGTTGACT
Found at i:2298291 original size:20 final size:20
Alignment explanation
Indices: 2298227--2298291 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
2298217 GCGTTGCATT
2298227 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTG-AAA
* * * **
2298248 TCGCGTTGTGAT-TTTCCATT
1 TCGCGTTGCGATAGTT-GAAA
2298268 TCGCGTTGCGATAGTTGAAA
1 TCGCGTTGCGATAGTTGAAA
2298288 TCGC
1 TCGC
2298292 AACGCGATCT
Statistics
Matches: 32, Mismatches: 10, Indels: 5
0.68 0.21 0.11
Matches are distributed among these distances:
20 19 0.59
21 13 0.41
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.35
Consensus pattern (20 bp):
TCGCGTTGCGATAGTTGAAA
Found at i:2298357 original size:68 final size:68
Alignment explanation
Indices: 2298248--2298395 Score: 287
Period size: 68 Copynumber: 2.2 Consensus size: 68
2298238 TAGTTGAAAA
*
2298248 TCGCGTTGTGATTTTCCATTTCGCGTTGCGATAGTTGAAATCGCAACGCGATCTCCACTATCGCA
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAATCGCAACGCGATCTCCACTATCGCA
2298313 AAT
66 AAT
2298316 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAATCGCAACGCGATCTCCACTATCGCA
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAATCGCAACGCGATCTCCACTATCGCA
2298381 AAT
66 AAT
2298384 TCGCGTTGCGAT
1 TCGCGTTGCGAT
2298396 AGTCTACAGT
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 79 1.00
ACGTcount: A:0.21, C:0.26, G:0.22, T:0.32
Consensus pattern (68 bp):
TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAATCGCAACGCGATCTCCACTATCGCA
AAT
Found at i:2298415 original size:22 final size:22
Alignment explanation
Indices: 2298387--2298458 Score: 78
Period size: 22 Copynumber: 3.4 Consensus size: 22
2298377 CGCAAATTCG
2298387 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
* * **
2298409 CGTTGCGAT--TTTCCAAAT-T
1 CGTTGCGATAGTCTACAGTTGT
2298428 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
*
2298450 TGTTGCGAT
1 CGTTGCGAT
2298459 TTTCCAAATT
Statistics
Matches: 38, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
19 10 0.26
20 5 0.13
21 5 0.13
22 18 0.47
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.39
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:2298432 original size:19 final size:19
Alignment explanation
Indices: 2298408--2298473 Score: 60
Period size: 19 Copynumber: 3.3 Consensus size: 19
2298398 TCTACAGTTG
2298408 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
* * **
2298427 TCGTTGCGATAGTCTACAGTT
1 TCGTTGCGAT--TTTCCAAAT
*
2298448 GTTGTTGCGATTTTCCAAAT
1 -TCGTTGCGATTTTCCAAAT
2298468 TCGTTG
1 TCGTTG
2298474 AAAAAAAAGA
Statistics
Matches: 34, Mismatches: 10, Indels: 6
0.68 0.20 0.12
Matches are distributed among these distances:
19 15 0.44
20 5 0.15
21 5 0.15
22 9 0.26
ACGTcount: A:0.18, C:0.18, G:0.21, T:0.42
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:2298438 original size:41 final size:41
Alignment explanation
Indices: 2298387--2298473 Score: 165
Period size: 41 Copynumber: 2.1 Consensus size: 41
2298377 CGCAAATTCG
2298387 CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
*
2298428 CGTTGCGATAGTCTACAGTTGTTGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
2298469 CGTTG
1 CGTTG
2298474 AAAAAAAAGA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.18, C:0.18, G:0.23, T:0.40
Consensus pattern (41 bp):
CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
Found at i:2298473 original size:22 final size:22
Alignment explanation
Indices: 2298410--2298473 Score: 55
Period size: 22 Copynumber: 3.0 Consensus size: 22
2298400 TACAGTTGTC
2298410 GTTGCGATTTTCCAAATTC---
1 GTTGCGATTTTCCAAATTCGTT
** * *
2298429 GTTGCGATAGTCTACAGTT-GTT
1 GTTGCGATTTTCCA-AATTCGTT
2298451 GTTGCGATTTTCCAAATTCGTT
1 GTTGCGATTTTCCAAATTCGTT
2298473 G
1 G
2298474 AAAAAAAAGA
Statistics
Matches: 32, Mismatches: 8, Indels: 7
0.68 0.17 0.15
Matches are distributed among these distances:
19 11 0.34
20 3 0.09
21 3 0.09
22 15 0.47
ACGTcount: A:0.19, C:0.17, G:0.22, T:0.42
Consensus pattern (22 bp):
GTTGCGATTTTCCAAATTCGTT
Found at i:2298560 original size:6 final size:6
Alignment explanation
Indices: 2298549--2298576 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
2298539 GACACGTATT
2298549 ACCACG ACCACG ACCACG ACCACG ACCA
1 ACCACG ACCACG ACCACG ACCACG ACCA
2298577 TGAGACGAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.36, C:0.50, G:0.14, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:2299094 original size:10 final size:10
Alignment explanation
Indices: 2299066--2299119 Score: 54
Period size: 10 Copynumber: 5.4 Consensus size: 10
2299056 GTCGTCCGTC
**
2299066 TCGTCTCGTC
1 TCGTCTCGGG
2299076 TCGTCTCGGG
1 TCGTCTCGGG
2299086 TCGTCTCGGG
1 TCGTCTCGGG
**
2299096 TCGGGTCGGG
1 TCGTCTCGGG
* *
2299106 TCGTGTCGTG
1 TCGTCTCGGG
2299116 TCGT
1 TCGT
2299120 GGTCGTGGTC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
10 38 1.00
ACGTcount: A:0.00, C:0.28, G:0.39, T:0.33
Consensus pattern (10 bp):
TCGTCTCGGG
Found at i:2299099 original size:5 final size:5
Alignment explanation
Indices: 2299081--2299148 Score: 55
Period size: 5 Copynumber: 12.6 Consensus size: 5
2299071 TCGTCTCGTC
** * *
2299081 TCGGG TCGTC TCGGG TCGGG TCGGG TCGTG TCGTG TCGTGG TCGTGG TCGTGG
1 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCG-GG TCG-GG TCG-GG
2299134 TCGTGG TCGTGG TCG
1 TCG-GG TCG-GG TCG
2299149 TGGTAATACG
Statistics
Matches: 56, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
5 28 0.50
6 28 0.50
ACGTcount: A:0.00, C:0.21, G:0.49, T:0.31
Consensus pattern (5 bp):
TCGGG
Found at i:2299120 original size:10 final size:10
Alignment explanation
Indices: 2299066--2299150 Score: 53
Period size: 10 Copynumber: 8.0 Consensus size: 10
2299056 GTCGTCCGTC
* *
2299066 TCGTCTCGTC
1 TCGTGTCGTG
* *
2299076 TCGTCTCGGG
1 TCGTGTCGTG
* *
2299086 TCGTCTCGGG
1 TCGTGTCGTG
* *
2299096 TCGGGTCGGG
1 TCGTGTCGTG
2299106 TCGTGTCGTG
1 TCGTGTCGTG
2299116 TCGTGGTCGTGG
1 TCGT-GTCGT-G
2299128 TCGTGGTCGTGG
1 TCGT-GTCGT-G
2299140 TCGTGGTCGTG
1 TCGT-GTCGTG
2299151 GTAATACGTG
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
10 38 0.57
11 6 0.09
12 23 0.34
ACGTcount: A:0.00, C:0.24, G:0.44, T:0.33
Consensus pattern (10 bp):
TCGTGTCGTG
Found at i:2299126 original size:6 final size:6
Alignment explanation
Indices: 2299094--2299152 Score: 90
Period size: 6 Copynumber: 10.5 Consensus size: 6
2299084 GGTCGTCTCG
2299094 GGTCG- GGTCG- GGTCGT -GTCGT -GTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
2299138 GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGT
2299153 AATACGTGTC
Statistics
Matches: 52, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
5 20 0.38
6 32 0.62
ACGTcount: A:0.00, C:0.17, G:0.51, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:2299318 original size:21 final size:21
Alignment explanation
Indices: 2299269--2299407 Score: 122
Period size: 20 Copynumber: 6.8 Consensus size: 21
2299259 ACAACTGTAG
* **
2299269 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAATTTCA
* *
2299290 A-AATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAATTTCA
* * **
2299310 ACTATCGCAACGTGAAATGGA
1 ACTATCGCAACGCGAATTTCA
*
2299331 A-AATCGCAACGCGAATTTCA
1 ACTATCGCAACGCGAATTTCA
* **
2299351 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAATTTCA
* *
2299372 A-AATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAATTTCA
2299392 ACTATCGCAACGCGAA
1 ACTATCGCAACGCGAA
2299408 ATGCAACGCG
Statistics
Matches: 88, Mismatches: 27, Indels: 6
0.73 0.22 0.05
Matches are distributed among these distances:
20 45 0.51
21 43 0.49
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.19
Consensus pattern (21 bp):
ACTATCGCAACGCGAATTTCA
Found at i:2299364 original size:82 final size:83
Alignment explanation
Indices: 2299244--2299410 Score: 277
Period size: 82 Copynumber: 2.0 Consensus size: 83
2299234 ACAACGAATT
2299244 TGGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTC
1 TGGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTC
*
2299309 AACTATCGCAACGTGAAA
66 AACTATCGCAACGCGAAA
*
2299327 TGGAAAATCGCAACG-CGAA-TTTCA-ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTT
1 TGGAAAATCGCAACGAC-AACTGT-AGACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTT
2299389 TCAACTATCGCAACGCGAAA
64 TCAACTATCGCAACGCGAAA
2299409 TG
1 TG
2299411 CAACGCGAAT
Statistics
Matches: 80, Mismatches: 2, Indels: 5
0.92 0.02 0.06
Matches are distributed among these distances:
82 62 0.77
83 18 0.22
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.19
Consensus pattern (83 bp):
TGGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTC
AACTATCGCAACGCGAAA
Found at i:2299414 original size:21 final size:21
Alignment explanation
Indices: 2299269--2299414 Score: 136
Period size: 21 Copynumber: 7.1 Consensus size: 21
2299259 ACAACTGTAG
*
2299269 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAAATGCA
* ** *
2299290 A-AATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
* *
2299310 ACTATCGCAACGTGAAATGGA
1 ACTATCGCAACGCGAAATGCA
* * *
2299331 A-AATCGCAACGCGAATTTCA
1 ACTATCGCAACGCGAAATGCA
*
2299351 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAAATGCA
* ** *
2299372 A-AATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
2299392 ACTATCGCAACGCGAAATGCA
1 ACTATCGCAACGCGAAATGCA
2299413 AC
1 AC
2299415 GCGAATTTGC
Statistics
Matches: 93, Mismatches: 29, Indels: 6
0.73 0.23 0.05
Matches are distributed among these distances:
20 45 0.48
21 48 0.52
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.18
Consensus pattern (21 bp):
ACTATCGCAACGCGAAATGCA
Found at i:2299427 original size:41 final size:41
Alignment explanation
Indices: 2299269--2299410 Score: 266
Period size: 41 Copynumber: 3.5 Consensus size: 41
2299259 ACAACTGTAG
2299269 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
* *
2299310 ACTATCGCAACGTGAAATGGAAAATCGCAACGCGAATTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
2299351 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
2299392 ACTATCGCAACGCGAAATG
1 ACTATCGCAACGCGAAATG
2299411 CAACGCGAAT
Statistics
Matches: 97, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 97 1.00
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.19
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
Found at i:2307187 original size:13 final size:14
Alignment explanation
Indices: 2307162--2307191 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
2307152 TGAATTTTAT
2307162 TTTCTTAAAAATCA
1 TTTCTTAAAAATCA
2307176 TTTCTT-AAAATCA
1 TTTCTTAAAAATCA
2307189 TTT
1 TTT
2307192 TTACGATATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.37, C:0.13, G:0.00, T:0.50
Consensus pattern (14 bp):
TTTCTTAAAAATCA
Found at i:2307993 original size:24 final size:23
Alignment explanation
Indices: 2307951--2307999 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
2307941 AATAACATTG
2307951 AAATTATATTAAAACTATAATGTT
1 AAATTATATTAAAACTAT-ATGTT
*
2307975 AAATTATAATT-AAATTATATGTT
1 AAATTAT-ATTAAAACTATATGTT
2307998 AA
1 AA
2308000 TATGTGATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 7 0.30
24 13 0.57
25 3 0.13
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (23 bp):
AAATTATATTAAAACTATATGTT
Found at i:2308592 original size:18 final size:18
Alignment explanation
Indices: 2308569--2308604 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
2308559 TGAACGAAAC
2308569 TAACCTATAACTTCAACA
1 TAACCTATAACTTCAACA
2308587 TAACCTATAACTTCAACA
1 TAACCTATAACTTCAACA
2308605 AAAAGAGCTT
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:0.44, C:0.28, G:0.00, T:0.28
Consensus pattern (18 bp):
TAACCTATAACTTCAACA
Found at i:2322191 original size:24 final size:24
Alignment explanation
Indices: 2322155--2322220 Score: 105
Period size: 24 Copynumber: 2.8 Consensus size: 24
2322145 CAGAGGGCTC
2322155 GTTCGTTCATTTATGTTTGTTTAT
1 GTTCGTTCATTTATGTTTGTTTAT
* *
2322179 GTTCGTTCGTTTATGTTCGTTTAT
1 GTTCGTTCATTTATGTTTGTTTAT
*
2322203 GTGCGTTCATTTATGTTT
1 GTTCGTTCATTTATGTTT
2322221 AGTCCAATCT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.11, C:0.11, G:0.20, T:0.59
Consensus pattern (24 bp):
GTTCGTTCATTTATGTTTGTTTAT
Found at i:2322192 original size:14 final size:14
Alignment explanation
Indices: 2322173--2322199 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2322163 ATTTATGTTT
2322173 GTTTATGTTCGTTC
1 GTTTATGTTCGTTC
2322187 GTTTATGTTCGTT
1 GTTTATGTTCGTT
2322200 TATGTGCGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.11, G:0.22, T:0.59
Consensus pattern (14 bp):
GTTTATGTTCGTTC
Found at i:2322506 original size:14 final size:14
Alignment explanation
Indices: 2322489--2322519 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
2322479 GTTTACATAT
2322489 GTTCATTTATGTTC
1 GTTCATTTATGTTC
*
2322503 GTTCATTTGTGTTC
1 GTTCATTTATGTTC
2322517 GTT
1 GTT
2322520 TATCATTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.10, C:0.13, G:0.19, T:0.58
Consensus pattern (14 bp):
GTTCATTTATGTTC
Found at i:2322896 original size:19 final size:19
Alignment explanation
Indices: 2322853--2322901 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
2322843 CATATTGGTA
2322853 AAAATAGTTAAATTTTAACT
1 AAAATA-TTAAATTTTAACT
* *
2322873 TAAATCTTAAATTTTAGAC-
1 AAAATATTAAATTTTA-ACT
2322892 AAAATATTAA
1 AAAATATTAA
2322902 TTTAACAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 18 0.75
20 6 0.25
ACGTcount: A:0.51, C:0.06, G:0.04, T:0.39
Consensus pattern (19 bp):
AAAATATTAAATTTTAACT
Found at i:2324526 original size:24 final size:24
Alignment explanation
Indices: 2324499--2324575 Score: 61
Period size: 24 Copynumber: 3.2 Consensus size: 24
2324489 ACTATGGTAC
2324499 AATTCTACGCGACACTTCGGTGCA
1 AATTCTACGCGACACTTCGGTGCA
* *
2324523 AATTTCTACTCGGTC-CTTCGG-GACA
1 AA-TTCTACGC-GACACTTCGGTG-CA
* *
2324548 AATTCTACGTGGA-ACTTCGGTGAA
1 AATTCTACG-CGACACTTCGGTGCA
2324572 AATT
1 AATT
2324576 TATATGAGCT
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
24 21 0.51
25 18 0.44
26 2 0.05
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (24 bp):
AATTCTACGCGACACTTCGGTGCA
Found at i:2325165 original size:12 final size:12
Alignment explanation
Indices: 2325148--2325193 Score: 51
Period size: 12 Copynumber: 4.0 Consensus size: 12
2325138 ATTTTAGCGT
2325148 CGGTACTGTTCA
1 CGGTACTGTTCA
2325160 CGGTACTGTTCA
1 CGGTACTGTTCA
* *
2325172 --TTACTATTCA
1 CGGTACTGTTCA
*
2325182 CGGTATTGTTCA
1 CGGTACTGTTCA
2325194 TTAATGTTCA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
10 8 0.30
12 19 0.70
ACGTcount: A:0.20, C:0.22, G:0.20, T:0.39
Consensus pattern (12 bp):
CGGTACTGTTCA
Found at i:2325181 original size:22 final size:22
Alignment explanation
Indices: 2325151--2325196 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
2325141 TTAGCGTCGG
*
2325151 TACTGTTCACGGTACTGTTCAT
1 TACTATTCACGGTACTGTTCAT
*
2325173 TACTATTCACGGTATTGTTCAT
1 TACTATTCACGGTACTGTTCAT
2325195 TA
1 TA
2325197 ATGTTCATAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.22, C:0.20, G:0.15, T:0.43
Consensus pattern (22 bp):
TACTATTCACGGTACTGTTCAT
Found at i:2325203 original size:22 final size:22
Alignment explanation
Indices: 2325154--2325203 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
2325144 GCGTCGGTAC
*
2325154 TGTTCACGGTACTGTTCATTAC
1 TGTTCACGGTACTGTTCATTAA
* *
2325176 TATTCACGGTATTGTTCATTAA
1 TGTTCACGGTACTGTTCATTAA
2325198 TGTTCA
1 TGTTCA
2325204 TAGTACTAGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.22, C:0.18, G:0.16, T:0.44
Consensus pattern (22 bp):
TGTTCACGGTACTGTTCATTAA
Found at i:2326787 original size:2 final size:2
Alignment explanation
Indices: 2326774--2326808 Score: 52
Period size: 2 Copynumber: 17.0 Consensus size: 2
2326764 CCAAACATAA
*
2326774 AT AT AG AT AT AT AT GAT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT
2326809 TCACAAAGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.46
Consensus pattern (2 bp):
AT
Found at i:2327181 original size:23 final size:23
Alignment explanation
Indices: 2327147--2327211 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 23
2327137 CACCACAGCT
* *
2327147 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTACCA
* * *
2327170 CGTAGAATTGCACCTAAGTACCG
1 CGTAGAAATGCACCGAAGTACCA
*
2327193 CGTAGAAATGCACTGAAGT
1 CGTAGAAATGCACCGAAGT
2327212 TCCATATAAG
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTACCA
Found at i:2329244 original size:5 final size:5
Alignment explanation
Indices: 2329225--2329262 Score: 60
Period size: 5 Copynumber: 7.8 Consensus size: 5
2329215 TCACGTATGA
*
2329225 AGAA- AGAAG AAAAG AGAAG AGAAG AGAAG AGAAG AGAA
1 AGAAG AGAAG AGAAG AGAAG AGAAG AGAAG AGAAG AGAA
2329263 CTCTGGAACC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
4 4 0.13
5 27 0.87
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (5 bp):
AGAAG
Found at i:2338865 original size:21 final size:20
Alignment explanation
Indices: 2338798--2338872 Score: 78
Period size: 21 Copynumber: 3.6 Consensus size: 20
2338788 CAGTTTCCAA
* * *
2338798 AATCGCAACGCGATTCTTGAC
1 AATCGCAATGCGATT-TTCAT
2338819 AATCGCAATGCGATTTTCAT
1 AATCGCAATGCGATTTTCAT
* *
2338839 ATTCGCATTGCGATTTTCCAT
1 AATCGCAATGCGATTTT-CAT
*
2338860 AATCGCAACGCGA
1 AATCGCAATGCGA
2338873 ATATGAAAAT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 18 0.40
21 27 0.60
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.29
Consensus pattern (20 bp):
AATCGCAATGCGATTTTCAT
Found at i:2338954 original size:20 final size:20
Alignment explanation
Indices: 2338860--2339088 Score: 239
Period size: 20 Copynumber: 11.4 Consensus size: 20
2338850 GATTTTCCAT
* ** *
2338860 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
2338880 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
2338900 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2338920 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
2338940 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2338960 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2338980 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2339000 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
** * *
2339020 AATCGCAACTAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
2339040 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
2339060 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
2339080 AATCACAAC
1 AATCGCAAC
2339089 ACTGAAATTT
Statistics
Matches: 177, Mismatches: 26, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 173 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.26, G:0.17, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:2339820 original size:24 final size:24
Alignment explanation
Indices: 2339781--2339827 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2339771 AAATTTGGTC
2339781 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
2339805 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
2339828 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:2340019 original size:12 final size:12
Alignment explanation
Indices: 2340002--2340026 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2339992 ATATAATCCT
2340002 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2340014 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2340026 G
1 G
2340027 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:2342359 original size:33 final size:33
Alignment explanation
Indices: 2342308--2342558 Score: 193
Period size: 33 Copynumber: 7.2 Consensus size: 33
2342298 CGGAAATTAC
* *
2342308 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACAAGAAAATCGCAATGCGAAATGAA
*
2342341 AATCCCAACAAGAAAATCGCAATGCGGAAATGAA
1 AATCGCAACAAGAAAATCGCAATGC-GAAATGAA
* * * *
2342375 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCAC
1 AATCGCAA--C--AA-GAAAATCGCAATGCGA-AATGAA
* *
2342414 AATGCGGAA-ATGAAAATCGCAATGCGAAATGAA
1 AAT-CGCAACAAGAAAATCGCAATGCGAAATGAA
* *
2342447 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACAAGAAAATCGCAATGCGAAATGAA
* * *
2342480 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCG-C
1 AATCGCAA--C--AA-GAAAATCGCAATGCGA-AAT-GAA
* *
2342519 AATGCGGAA-ATGAAAATCGCAATGCGAAATGAA
1 AAT-CGCAACAAGAAAATCGCAATGCGAAATGAA
2342552 AATCGCA
1 AATCGCA
2342559 TTGCGATTCT
Statistics
Matches: 171, Mismatches: 29, Indels: 37
0.72 0.12 0.16
Matches are distributed among these distances:
32 8 0.05
33 64 0.37
34 43 0.25
35 3 0.02
36 1 0.01
37 1 0.01
38 17 0.10
39 25 0.15
40 9 0.05
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (33 bp):
AATCGCAACAAGAAAATCGCAATGCGAAATGAA
Found at i:2342385 original size:53 final size:53
Alignment explanation
Indices: 2342322--2342558 Score: 431
Period size: 53 Copynumber: 4.5 Consensus size: 53
2342312 GCAACGAGAG
* * *
2342322 AATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
*
2342375 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCACAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
2342428 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGC-GAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
2342480 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
2342533 AATCGCAATGCGAAATGAAAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCA
2342559 TTGCGATTCT
Statistics
Matches: 178, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
52 52 0.29
53 126 0.71
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.14
Consensus pattern (53 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
Found at i:2342391 original size:19 final size:19
Alignment explanation
Indices: 2342322--2342564 Score: 265
Period size: 19 Copynumber: 13.7 Consensus size: 19
2342312 GCAACGAGAG
2342322 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
2342341 AATCCCAA--C--AA-GAA
1 AATCGCAATGCGAAATGAA
2342355 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
2342375 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
2342394 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
2342408 AATCACAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
2342428 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
2342447 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
2342461 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
2342480 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
2342499 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
2342513 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
2342533 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
2342552 AATCGCATTGCGA
1 AATCGCAATGCGA
2342565 TTCTCTCGTT
Statistics
Matches: 190, Mismatches: 11, Indels: 46
0.77 0.04 0.19
Matches are distributed among these distances:
14 39 0.21
15 5 0.03
16 5 0.03
17 9 0.05
18 1 0.01
19 92 0.48
20 39 0.21
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:2342465 original size:86 final size:90
Alignment explanation
Indices: 2342308--2342564 Score: 270
Period size: 86 Copynumber: 2.9 Consensus size: 90
2342298 CGGAAATTAC
* *
2342308 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCCCAA--C--AA-GAAAATCGCAATGCG
1 AATCGCAACGAGAGAATCACAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCG
2342367 GAAATGAAAATCGCAATGCGAAATGAA
65 G-AATGAAAATCGCAATGCGAAATGAA
2342394 AATCGCAACGAGAGAATCACAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-C-G
1 AATCGCAACGAGAGAATCACAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGG
*
2342457 -A-GAGAATCGCAATGCGAAATGAA
66 AATGAAAATCGCAATGCGAAATGAA
* * * * * *
2342480 AATCGCAATGCGA-AATGAAAAT-CGCAACGA-GAGAATCGCAATGCGGAAATGAAAATCGCAAT
1 AATCGCAACGAGAGAATCACAATGCGGAA--ATGAAAATCGCAATGC-GAAATGAAAATCGCAA-
* *
2342542 GCGAAATGAAAATCGCATTGCGA
62 GCGGAATGAAAATCGCAATGCGA
2342565 TTCTCTCGTT
Statistics
Matches: 145, Mismatches: 12, Indels: 23
0.81 0.07 0.13
Matches are distributed among these distances:
84 4 0.03
85 20 0.14
86 73 0.50
87 16 0.11
88 1 0.01
89 2 0.01
90 2 0.01
91 16 0.11
92 11 0.08
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.14
Consensus pattern (90 bp):
AATCGCAACGAGAGAATCACAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGG
AATGAAAATCGCAATGCGAAATGAA
Found at i:2342511 original size:105 final size:106
Alignment explanation
Indices: 2342322--2342558 Score: 431
Period size: 105 Copynumber: 2.2 Consensus size: 106
2342312 GCAACGAGAG
*
2342322 AATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
1 AATCGCAATGCGAAATGAAAATCGCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
2342387 AAATGAAAATCGCAACGAGAGAATCACAATGCGGAAATGAA
66 AAATGAAAATCGCAACGAGAGAATCACAATGCGGAAATGAA
* *
2342428 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCGCAATGCG
1 AATCGCAATGCGAAATGAAAATCGCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
*
2342492 AAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
66 AAATGAAAATCGCAACGAGAGAATCACAATGCGGAAATGAA
2342533 AATCGCAATGCGAAATGAAAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCA
2342559 TTGCGATTCT
Statistics
Matches: 127, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
105 86 0.68
106 41 0.32
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.14
Consensus pattern (106 bp):
AATCGCAATGCGAAATGAAAATCGCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
AAATGAAAATCGCAACGAGAGAATCACAATGCGGAAATGAA
Found at i:2342598 original size:53 final size:52
Alignment explanation
Indices: 2342535--2342648 Score: 156
Period size: 53 Copynumber: 2.2 Consensus size: 52
2342525 GAAATGAAAA
*
2342535 TCGCAATGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
** ** **
2342587 TCCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 T-CGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
2342640 TCGCATTGC
1 TCGCATTGC
2342649 TATTTTCATT
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
52 9 0.17
53 45 0.83
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.39
Consensus pattern (52 bp):
TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:2342613 original size:19 final size:19
Alignment explanation
Indices: 2342573--2342660 Score: 114
Period size: 19 Copynumber: 4.8 Consensus size: 19
2342563 GATTCTCTCG
2342573 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
2342593 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2342612 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
2342626 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2342645 TTGCTATTTTCATTTC
1 TTGCGATTTTCATTTC
2342661 AACATAATGC
Statistics
Matches: 60, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
14 6 0.10
16 7 0.12
17 7 0.12
19 25 0.42
20 15 0.25
ACGTcount: A:0.14, C:0.23, G:0.15, T:0.49
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:2342770 original size:14 final size:14
Alignment explanation
Indices: 2342751--2342787 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
2342741 CATCAATTAC
2342751 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
2342765 ACAAATCATCTTTT
1 ACAAATCAACTTTT
2342779 ACAAATCAA
1 ACAAATCAA
2342788 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:2344755 original size:19 final size:19
Alignment explanation
Indices: 2344713--2344838 Score: 162
Period size: 19 Copynumber: 6.6 Consensus size: 19
2344703 TAGTTTACTT
* *
2344713 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
*
2344733 TCGCAACGCGAAATGAGAA
1 TCGCAACGCGAAATGAAAA
* **
2344752 TCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
2344771 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
**
2344790 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
2344809 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
2344828 TCGCAATGCGA
1 TCGCAACGCGA
2344839 TTTTGGTTTC
Statistics
Matches: 91, Mismatches: 15, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
19 79 0.87
20 12 0.13
ACGTcount: A:0.46, C:0.25, G:0.19, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:2344778 original size:38 final size:38
Alignment explanation
Indices: 2344729--2344833 Score: 192
Period size: 38 Copynumber: 2.8 Consensus size: 38
2344719 CACGAAACTT
*
2344729 AAAATCGCAACGCGAAATGAGAATCGCAACGAGAAACC
1 AAAATCGCAACGCGAAATGAAAATCGCAACGAGAAACC
*
2344767 AAAATCGCAACGCGAAATGAAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATGAAAATCGCAACGAGAAACC
2344805 AAAATCGCAACGCGAAATGAAAATCGCAA
1 AAAATCGCAACGCGAAATGAAAATCGCAA
2344834 TGCGATTTTG
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 65 1.00
ACGTcount: A:0.49, C:0.24, G:0.19, T:0.09
Consensus pattern (38 bp):
AAAATCGCAACGCGAAATGAAAATCGCAACGAGAAACC
Found at i:2344869 original size:14 final size:14
Alignment explanation
Indices: 2344850--2344908 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
2344840 TTTGGTTTCG
2344850 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
2344864 CGTTGCGATTTTGGTTT
1 CGTTGCGATTTT-G--T
*
2344881 CGCGTTGCGATTCTGT
1 --CGTTGCGATTTTGT
2344897 CGTTGCGATTTT
1 CGTTGCGATTTT
2344909 CATTTCGCGT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 23 0.61
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 11 0.29
ACGTcount: A:0.07, C:0.17, G:0.29, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:2344876 original size:33 final size:33
Alignment explanation
Indices: 2344834--2344957 Score: 185
Period size: 33 Copynumber: 3.7 Consensus size: 33
2344824 AAAATCGCAA
*
2344834 TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
2344867 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
** *
2344900 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
* *
2344933 TGCGATTTTAAGTTTCGTGTTGCGA
1 TGCGATTTT-GGTTTCGCGTTGCGA
2344958 AAGTAAACTA
Statistics
Matches: 83, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
33 71 0.86
34 12 0.14
ACGTcount: A:0.09, C:0.18, G:0.27, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:2344888 original size:19 final size:18
Alignment explanation
Indices: 2344834--2344925 Score: 83
Period size: 19 Copynumber: 5.4 Consensus size: 18
2344824 AAAATCGCAA
2344834 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
2344853 TGCGATTTTG--T--CGT
1 TGCGATTTTGTTTCGCGT
2344867 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
2344886 TGCGATTCTG--T--CGT
1 TGCGATTTTGTTTCGCGT
*
2344900 TGCGATTTTCATTTCGCGT
1 TGCGATTTT-GTTTCGCGT
2344919 TGCGATT
1 TGCGATT
2344926 CTCTCGTTGC
Statistics
Matches: 60, Mismatches: 3, Indels: 20
0.72 0.04 0.24
Matches are distributed among these distances:
14 23 0.38
15 1 0.02
16 2 0.03
17 2 0.03
18 2 0.03
19 30 0.50
ACGTcount: A:0.08, C:0.17, G:0.28, T:0.47
Consensus pattern (18 bp):
TGCGATTTTGTTTCGCGT
Found at i:2344935 original size:14 final size:14
Alignment explanation
Indices: 2344883--2344939 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
2344873 TTTGGTTTCG
*
2344883 CGTTGCGATTCTGT
1 CGTTGCGATTCTCT
*
2344897 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
2344916 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
2344930 CGTTGCGATT
1 CGTTGCGATT
2344940 TTAAGTTTCG
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 20 0.57
16 3 0.09
17 3 0.09
19 9 0.26
ACGTcount: A:0.09, C:0.23, G:0.25, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:2345214 original size:93 final size:93
Alignment explanation
Indices: 2345055--2345555 Score: 968
Period size: 93 Copynumber: 5.4 Consensus size: 93
2345045 TCAGGGTATT
2345055 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
**
2345120 TACTATTTCACAGTGTTAAAGAATACGG
66 TACTATTTCACAGTGTTAAAGAATACAC
2345148 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
2345213 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
2345241 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
2345306 TACTATTTCACAGTGTT-AAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
2345333 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
2345398 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
2345426 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
2345491 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
*
2345519 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
2345556 AAGCAATCTA
Statistics
Matches: 404, Mismatches: 3, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
92 92 0.23
93 312 0.77
ACGTcount: A:0.45, C:0.19, G:0.14, T:0.22
Consensus pattern (93 bp):
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACAC
Found at i:2345408 original size:185 final size:186
Alignment explanation
Indices: 2345055--2345555 Score: 968
Period size: 185 Copynumber: 2.7 Consensus size: 186
2345045 TCAGGGTATT
2345055 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
**
2345120 TACTATTTCACAGTGTTAAAGAATACGGAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
66 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
2345185 TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
131 TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
2345241 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
2345306 TACTATTTCACAGTGTT-AAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
66 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
2345370 TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
131 TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
2345426 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
*
2345491 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
66 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
2345556 AAGCAATCTA
Statistics
Matches: 311, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
185 183 0.59
186 128 0.41
ACGTcount: A:0.45, C:0.19, G:0.14, T:0.22
Consensus pattern (186 bp):
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
Found at i:2345497 original size:278 final size:278
Alignment explanation
Indices: 2345055--2345555 Score: 975
Period size: 278 Copynumber: 1.8 Consensus size: 278
2345045 TCAGGGTATT
2345055 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
**
2345120 TACTATTTCACAGTGTTAAAGAATACGGAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
66 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
2345185 TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCA
131 TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCA
2345250 GAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTC
196 GAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTC
2345315 ACAGTGTTAAGAATACAC
261 ACAGTGTTAAGAATACAC
2345333 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
2345398 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
66 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
2345463 TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCA
131 TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCA
*
2345528 GAATTGGCAGCAACCGAATAAATTTACT
196 GAATTGGCAGCAACCGAACAAATTTACT
2345556 AAGCAATCTA
Statistics
Matches: 220, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
278 220 1.00
ACGTcount: A:0.45, C:0.19, G:0.14, T:0.22
Consensus pattern (278 bp):
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCA
GAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTC
ACAGTGTTAAGAATACAC
Found at i:2347282 original size:20 final size:20
Alignment explanation
Indices: 2347251--2347347 Score: 100
Period size: 20 Copynumber: 5.2 Consensus size: 20
2347241 TTTTGGTTGA
2347251 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
***
2347271 AATGACTGTCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
2347291 AAATGAAAATCGCAAC--GAG
1 -AATGAAAATCGCAACGAGAG
*
2347310 -A-G--AATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
2347325 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
2347345 AAT
1 AAT
2347348 CGCAACGCGA
Statistics
Matches: 62, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
14 9 0.15
16 4 0.06
17 2 0.03
19 15 0.24
20 20 0.32
21 12 0.19
ACGTcount: A:0.46, C:0.18, G:0.25, T:0.11
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:2347303 original size:21 final size:21
Alignment explanation
Indices: 2347249--2347313 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
2347239 TCTTTTGGTT
2347249 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
***
2347270 G-AATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
2347290 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
2347311 GAA
1 GAA
2347314 TCGCAACGCG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.48, C:0.15, G:0.26, T:0.11
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:2347317 original size:14 final size:14
Alignment explanation
Indices: 2347298--2347354 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
2347288 GAGAAATGAA
2347298 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
2347312 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
2347331 AATCGCAACGAGAG
1 AATCGCAACGAGAG
2347345 AATCGCAACG
1 AATCGCAACG
2347355 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:2347330 original size:33 final size:33
Alignment explanation
Indices: 2347249--2347371 Score: 165
Period size: 33 Copynumber: 3.5 Consensus size: 33
2347239 TCTTTTGGTT
*
2347249 GAAATGAAAATCGCAACGAGAGAATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGAG-A--A---TCGCAAC--GC
2347290 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
2347323 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
2347356 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
2347372 TGCGATTTTG
Statistics
Matches: 81, Mismatches: 1, Indels: 8
0.90 0.01 0.09
Matches are distributed among these distances:
33 50 0.62
35 7 0.09
38 1 0.01
40 1 0.01
41 22 0.27
ACGTcount: A:0.46, C:0.19, G:0.24, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:2347407 original size:14 final size:14
Alignment explanation
Indices: 2347388--2347444 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
2347378 TTTGGTTTCG
2347388 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
2347402 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
2347421 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
2347435 CGTTGCGATT
1 CGTTGCGATT
2347445 TTCATTTTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:2347420 original size:33 final size:33
Alignment explanation
Indices: 2347372--2347451 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
2347362 AAAATCGCAA
**
2347372 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
2347405 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
2347438 TGCGATTTTCATTT
1 TGCGATTTTCATTT
2347452 TTCTCGTTGC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.09, C:0.21, G:0.23, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:2347457 original size:21 final size:21
Alignment explanation
Indices: 2347432--2347505 Score: 96
Period size: 21 Copynumber: 3.5 Consensus size: 21
2347422 GTTGCGATTC
2347432 TCTCGTTGCGATTTTCATTTT
1 TCTCGTTGCGATTTTCATTTT
**
2347453 TCTCGTTGCAGATAGTCA-TTT
1 TCTCGTTGC-GATTTTCATTTT
* *
2347474 TCACGTTGCGATTTTCATTTA
1 TCTCGTTGCGATTTTCATTTT
2347495 TCTCGTTGCGA
1 TCTCGTTGCGA
2347506 CTCTTCTGCA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 6 0.14
21 32 0.73
22 6 0.14
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.47
Consensus pattern (21 bp):
TCTCGTTGCGATTTTCATTTT
Found at i:2347627 original size:33 final size:33
Alignment explanation
Indices: 2347585--2347655 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
2347575 AATAATAACT
2347585 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
2347618 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
2347651 TGAAA
1 TGAAA
2347656 TATAAGTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:2348060 original size:20 final size:20
Alignment explanation
Indices: 2348035--2348166 Score: 167
Period size: 20 Copynumber: 6.6 Consensus size: 20
2348025 CTTTAAAAAT
2348035 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
2348055 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
2348075 CGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
2348095 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* * *
2348115 CACGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
2348135 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
2348155 CGCGTTGCGATT
1 CGCGTTGCGATT
2348167 ATGGAAAATC
Statistics
Matches: 98, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
20 97 0.99
21 1 0.01
ACGTcount: A:0.19, C:0.20, G:0.27, T:0.34
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:2348184 original size:21 final size:20
Alignment explanation
Indices: 2348160--2348207 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
2348150 ATATTCGCGT
2348160 TGCGATTATGGAAAATCGCAA
1 TGCGATTAT-GAAAATCGCAA
* *
2348181 TGCGAATATGAAAATCGCAT
1 TGCGATTATGAAAATCGCAA
2348201 TGCGATT
1 TGCGATT
2348208 GTCAAGAATC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (20 bp):
TGCGATTATGAAAATCGCAA
Found at i:2348576 original size:23 final size:23
Alignment explanation
Indices: 2348532--2348577 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
2348522 TTCGTATTCA
* *
2348532 GTTCGTTTAGCATTCGCTAACAT
1 GTTCGTTTAACATTCGCGAACAT
*
2348555 GTTCGTTTAACATTCTCGAACAT
1 GTTCGTTTAACATTCGCGAACAT
2348578 ATCAATGGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.22, G:0.15, T:0.39
Consensus pattern (23 bp):
GTTCGTTTAACATTCGCGAACAT
Found at i:2353557 original size:76 final size:76
Alignment explanation
Indices: 2353443--2353585 Score: 196
Period size: 76 Copynumber: 1.9 Consensus size: 76
2353433 CTGTAATCCA
* * ** * *
2353443 AATTTCTTTATATTAGTTGTTCATTTTATTAAAGGTGCTCACCCTGAAATTTTATTTGGGTCCAC
1 AATTTCTTTATATTAATCGTTCATTTTACGAAAGGTGCTCACACTGAAATTTTATTTGGGTCAAC
2353508 CTTGAAATATG
66 CTTGAAATATG
* * * *
2353519 AATTTCTTTATGTTAATCGTTCATTTTACGAAATGTGCTCACATTGAAATTTTATTTGTGTCAAC
1 AATTTCTTTATATTAATCGTTCATTTTACGAAAGGTGCTCACACTGAAATTTTATTTGGGTCAAC
2353584 CT
66 CT
2353586 CGTACGAAAA
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
76 57 1.00
ACGTcount: A:0.27, C:0.15, G:0.13, T:0.45
Consensus pattern (76 bp):
AATTTCTTTATATTAATCGTTCATTTTACGAAAGGTGCTCACACTGAAATTTTATTTGGGTCAAC
CTTGAAATATG
Found at i:2354216 original size:9 final size:9
Alignment explanation
Indices: 2354204--2354248 Score: 54
Period size: 9 Copynumber: 4.7 Consensus size: 9
2354194 TTAAATTTAG
2354204 TAAAAAAAA
1 TAAAAAAAA
2354213 TAAAAAAAA
1 TAAAAAAAA
2354222 TTAAAATAAAA
1 -TAAAA-AAAA
*
2354233 TAAATAAAA
1 TAAAAAAAA
2354242 TAGAAAA
1 TA-AAAA
2354249 TAGAGTAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
9 15 0.48
10 12 0.39
11 4 0.13
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.18
Consensus pattern (9 bp):
TAAAAAAAA
Found at i:2354229 original size:15 final size:14
Alignment explanation
Indices: 2354205--2354248 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
2354195 TAAATTTAGT
2354205 AAAA-AAAATAAAA
1 AAAATAAAATAAAA
2354218 AAAATTAAAATAAAA
1 AAAA-TAAAATAAAA
*
2354233 TAAATAAAATAGAAA
1 AAAATAAAATA-AAA
2354248 A
1 A
2354249 TAGAGTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
13 4 0.15
14 7 0.27
15 15 0.58
ACGTcount: A:0.82, C:0.00, G:0.02, T:0.16
Consensus pattern (14 bp):
AAAATAAAATAAAA
Found at i:2354231 original size:5 final size:5
Alignment explanation
Indices: 2354204--2354243 Score: 50
Period size: 5 Copynumber: 8.4 Consensus size: 5
2354194 TTAAATTTAG
2354204 TAAAA -AAAA TAAAA -AAAA TTAAAA TAAAA T-AAA TAAAA TA
1 TAAAA TAAAA TAAAA TAAAA -TAAAA TAAAA TAAAA TAAAA TA
2354244 GAAAATAGAG
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
4 12 0.39
5 15 0.48
6 4 0.13
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:2354234 original size:20 final size:19
Alignment explanation
Indices: 2354204--2354242 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
2354194 TTAAATTTAG
2354204 TAAAAAAAATAAAAAAAAT
1 TAAAAAAAATAAAAAAAAT
*
2354223 TAAAATAAAATAAATAAAAT
1 TAAAA-AAAATAAAAAAAAT
2354243 AGAAAATAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (19 bp):
TAAAAAAAATAAAAAAAAT
Found at i:2355195 original size:38 final size:38
Alignment explanation
Indices: 2355106--2355212 Score: 115
Period size: 38 Copynumber: 2.8 Consensus size: 38
2355096 GTATGTTCAA
* * * **
2355106 TTAGTTTATGTTCACAAACAAGCTCATTTATCGACTTT
1 TTAGTTTATGTTCATAAACAAGCTCGTTTATCAACTCG
* *
2355144 TTAGTTGAGGTTCATAAACAAGCTCGTTTATCAACTCG
1 TTAGTTTATGTTCATAAACAAGCTCGTTTATCAACTCG
* * **
2355182 TTCGTTTATGTTCATGAACAAATTCGTTTAT
1 TTAGTTTATGTTCATAAACAAGCTCGTTTAT
2355213 AATTTTTTAA
Statistics
Matches: 56, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
38 56 1.00
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (38 bp):
TTAGTTTATGTTCATAAACAAGCTCGTTTATCAACTCG
Found at i:2357428 original size:23 final size:23
Alignment explanation
Indices: 2357410--2357470 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
2357400 CTCGTATAAA
2357410 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
2357433 TGCACCGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
2357456 TGCACCGTAGTGCCA
1 TGCACCGAAGTGCCA
2357471 TATAAGATTG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.26, C:0.28, G:0.28, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:2357729 original size:30 final size:31
Alignment explanation
Indices: 2357695--2357753 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
2357685 TATTGTATAG
2357695 ACATATAAT-TTCCAT-ACCTTTATCACATGA
1 ACATATAATGTTCCATCA-CTTTATCACATGA
*
2357725 ACATATCATGTTCCATCACTTTATCACAT
1 ACATATAATGTTCCATCACTTTATCACAT
2357754 AGCTTATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 8 0.31
31 17 0.65
32 1 0.04
ACGTcount: A:0.34, C:0.25, G:0.03, T:0.37
Consensus pattern (31 bp):
ACATATAATGTTCCATCACTTTATCACATGA
Found at i:2357830 original size:25 final size:25
Alignment explanation
Indices: 2357797--2357858 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 25
2357787 CTTAATACAT
2357797 ATAATATGAATTCATG-TCATGTATC
1 ATAATATGAATT-ATGATCATGTATC
* *
2357822 ATAATATGAAATGTGATCATGTATC
1 ATAATATGAATTATGATCATGTATC
*
2357847 AAAATATTGAAT
1 ATAATA-TGAAT
2357859 CTAGACTTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
24 2 0.06
25 25 0.81
26 4 0.13
ACGTcount: A:0.42, C:0.08, G:0.13, T:0.37
Consensus pattern (25 bp):
ATAATATGAATTATGATCATGTATC
Found at i:2360793 original size:22 final size:22
Alignment explanation
Indices: 2360768--2360818 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
2360758 CACCACAGCT
*
2360768 CGTATAAATGCACCGAAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
*
2360790 CGTAGAATTGCACCGAAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
2360812 CGTAGAA
1 CGTAGAA
2360819 TTATGTCCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.31, C:0.25, G:0.25, T:0.18
Consensus pattern (22 bp):
CGTAGAAATGCACCGAAGTGCC
Found at i:2360819 original size:22 final size:22
Alignment explanation
Indices: 2360776--2360820 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
2360766 CTCGTATAAA
2360776 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
2360798 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
2360820 T
1 T
2360821 ATGTCCATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:2361081 original size:30 final size:31
Alignment explanation
Indices: 2361040--2361099 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
2361030 TAGACATAGT
*
2361040 ATTTCCATACCTTTAACACATAG-GCATATC
1 ATTTACATACCTTTAACACATAGTGCATATC
*
2361070 ATTTACATACCTTTATCACATAGTGCATAT
1 ATTTACATACCTTTAACACATAGTGCATAT
2361100 AACTTTTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.37
Consensus pattern (31 bp):
ATTTACATACCTTTAACACATAGTGCATATC
Found at i:2361156 original size:29 final size:29
Alignment explanation
Indices: 2361114--2361185 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
2361104 TTTTCTGCAT
**
2361114 ATTCATGTCATGTAATACATATAATATGA
1 ATTCATGTCATGTAATACATATAATACAA
*
2361143 ATTCATGTCATGTAATACATTTAATACAA
1 ATTCATGTCATGTAATACATATAATACAA
2361172 ATTCATGTCATGTA
1 ATTCATGTCATGTA
2361186 TCATAATATG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAATACAA
Found at i:2361630 original size:70 final size:70
Alignment explanation
Indices: 2361488--2361642 Score: 199
Period size: 69 Copynumber: 2.2 Consensus size: 70
2361478 TTTTTCTCAT
* * * *
2361488 GGGGGAATCGGTT-CCTCCCCTGGGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATAC
1 GGGGGTATCGGTTCCCCCCCCTGGGGGGTACCGATTCCCCTCAAGCAATCTGGAATATCATATAC
2361552 GATGA
66 GATGA
* * *
2361557 GGGGGTATCGGTTCCCCCCCCT-GGGGGTACCGATTCCCCCTCTAGCATTCTGGAA-ATCATATT
1 GGGGGTATCGGTTCCCCCCCCTGGGGGGTACCGATT-CCCCTCAAGCAATCTGGAATATCATATA
*
2361620 CGTTGA
65 CGATGA
*
2361626 AGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
2361643 TTGAATGGGT
Statistics
Matches: 75, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
69 51 0.68
70 24 0.32
ACGTcount: A:0.18, C:0.28, G:0.28, T:0.26
Consensus pattern (70 bp):
GGGGGTATCGGTTCCCCCCCCTGGGGGGTACCGATTCCCCTCAAGCAATCTGGAATATCATATAC
GATGA
Found at i:2361652 original size:21 final size:21
Alignment explanation
Indices: 2361622--2361664 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2361612 ATCATATTCG
* *
2361622 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
2361643 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
2361664 T
1 T
2361665 AGCCCTAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:2367645 original size:22 final size:22
Alignment explanation
Indices: 2367620--2367670 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
2367610 CACCACAGCT
*
2367620 CGTATAAATGCACCGAAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
*
2367642 CGTAGAATTGCACCGAAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
2367664 CGTAGAA
1 CGTAGAA
2367671 TTATGTCCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.31, C:0.25, G:0.25, T:0.18
Consensus pattern (22 bp):
CGTAGAAATGCACCGAAGTGCC
Found at i:2367671 original size:22 final size:22
Alignment explanation
Indices: 2367628--2367672 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
2367618 CTCGTATAAA
2367628 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
2367650 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
2367672 T
1 T
2367673 ATGTCCATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:2367933 original size:30 final size:31
Alignment explanation
Indices: 2367892--2367951 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
2367882 TAGACATAGT
*
2367892 ATTTCCATACCTTTAACACATAG-GCATATC
1 ATTTACATACCTTTAACACATAGTGCATATC
*
2367922 ATTTACATACCTTTATCACATAGTGCATAT
1 ATTTACATACCTTTAACACATAGTGCATAT
2367952 AACTTTTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.37
Consensus pattern (31 bp):
ATTTACATACCTTTAACACATAGTGCATATC
Found at i:2368008 original size:29 final size:29
Alignment explanation
Indices: 2367966--2368037 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
2367956 TTTTCTGCAT
**
2367966 ATTCATGTCATGTAATACATATAATATGA
1 ATTCATGTCATGTAATACATATAATACAA
*
2367995 ATTCATGTCATGTAATACATTTAATACAA
1 ATTCATGTCATGTAATACATATAATACAA
2368024 ATTCATGTCATGTA
1 ATTCATGTCATGTA
2368038 TCATAATATG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAATACAA
Found at i:2368478 original size:67 final size:68
Alignment explanation
Indices: 2368340--2368490 Score: 216
Period size: 66 Copynumber: 2.2 Consensus size: 68
2368330 TTTTTCTCAT
* * *
2368340 GGGGGAATCGGTTCCTCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACGA
1 GGGGGTATCGGTTCCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAATATCATATACGA
2368405 TGA
66 TGA
* * * *
2368408 GGGGGTATCGGTTCCCCCCCTGGGGGTA-CGATTCCCCTCTAGCATTCTGGAA-ATCATATTCGT
1 GGGGGTATCGGTTCCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAATATCATATACGA
2368471 TGA
66 TGA
*
2368474 AGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
2368491 TTGAATGGGT
Statistics
Matches: 75, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
66 27 0.36
67 22 0.29
68 26 0.35
ACGTcount: A:0.19, C:0.26, G:0.28, T:0.27
Consensus pattern (68 bp):
GGGGGTATCGGTTCCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAATATCATATACGA
TGA
Found at i:2368500 original size:21 final size:21
Alignment explanation
Indices: 2368470--2368512 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2368460 ATCATATTCG
* *
2368470 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
2368491 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
2368512 T
1 T
2368513 AGCCCGAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:2368501 original size:66 final size:67
Alignment explanation
Indices: 2368341--2368512 Score: 197
Period size: 67 Copynumber: 2.6 Consensus size: 67
2368331 TTTTCTCATG
* * *
2368341 GGGGAATCGGTTCCTCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACGAT
1 GGGGTATCGGTTCC-CCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAATATCATATACGAT
*
2368406 GAG
65 GAA
* * * *
2368409 GGGGTATCGGTTCCCCCCCTGGGGGTA-CGATTCCCCTCTAGCATTCTGGAA-ATCATATTCGTT
1 GGGGTATCGGTT-CCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAATATCATATACGAT
2368472 GAA
65 GAA
* *
2368475 GGGGTATCGGTT-CCCCTTGAATGGGTACCGATTCCCCT
1 GGGGTATCGGTTCCCCCCTG--GGGGTACCGATTCCCCT
2368513 AGCCCGAAAA
Statistics
Matches: 91, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
64 6 0.07
66 28 0.31
67 32 0.35
68 23 0.25
69 2 0.02
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.28
Consensus pattern (67 bp):
GGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAATATCATATACGATG
AA
Found at i:2370677 original size:31 final size:30
Alignment explanation
Indices: 2370633--2370692 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 30
2370623 TGTTGTATAG
2370633 ACATATAATTTCCAT-ACCTTTATCACATAA
1 ACATATAATTTCCATCA-CTTTATCACATAA
*
2370663 ACATATCATGTTCCATCACTTTATCACATA
1 ACATATAAT-TTCCATCACTTTATCACATA
2370693 GCTTATATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 8 0.30
31 18 0.67
32 1 0.04
ACGTcount: A:0.37, C:0.25, G:0.02, T:0.37
Consensus pattern (30 bp):
ACATATAATTTCCATCACTTTATCACATAA
Found at i:2376064 original size:190 final size:188
Alignment explanation
Indices: 2375697--2376065 Score: 528
Period size: 190 Copynumber: 2.0 Consensus size: 188
2375687 GATAAACCCC
* *
2375697 TTTTACCATTCAAACTTAAATAGATATTATTTTAATTTAAAATATACAAAAATATATAATTATCT
1 TTTTACCATTCAAACATAAACAGATATTATTTTAATTTAAAATATACAAAAATATATAATTATCT
* * * * *
2375762 TTAATATTTAAAGTTAAAAAGATAACAAATATTTTTTAAATTGACATATTCACAGAGTAATTATC
66 TTAATATTCAAAATTAAAAAGATAACAAATAATTTTTAAATTGACATATTAAAAGAGTAATTATC
*
2375827 CTACTAATATTCAAATTAAATAATATATTTAATTTGCAATGGTCAAAAGGTAAAATCA
131 CTACTAATATTCAAATTAAATAATATATTTAATTTGCAATAGTCAAAAGGTAAAATCA
* * * * *
2375885 TTTTACTATTCAAACATAAACATATATTATTTTAATTTGAAATATACAAAAGTATATAATTATAT
1 TTTTACCATTCAAACATAAACAGATATTATTTTAATTTAAAATATACAAAAATATATAATTAT-C
*
2375950 TTTAATATTCAAAATTAAAAAGATAACAAATACATTTTTAAATTGA-GTCATTAAAAGAGTAATT
65 TTTAATATTCAAAATTAAAAAGATAACAAATA-ATTTTTAAATTGACAT-ATTAAAAGAGTAATT
* *
2376014 ATCCTATTAATATTCAAA-TAAA-AATTATCTTTTAATTTGCAATAGTCAAAAG
128 ATCCTACTAATATTCAAATTAAATAA-TAT-ATTTAATTTGCAATAGTCAAAAG
2376066 AACTATGAAT
Statistics
Matches: 160, Mismatches: 16, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
188 59 0.37
189 38 0.24
190 63 0.39
ACGTcount: A:0.47, C:0.09, G:0.06, T:0.39
Consensus pattern (188 bp):
TTTTACCATTCAAACATAAACAGATATTATTTTAATTTAAAATATACAAAAATATATAATTATCT
TTAATATTCAAAATTAAAAAGATAACAAATAATTTTTAAATTGACATATTAAAAGAGTAATTATC
CTACTAATATTCAAATTAAATAATATATTTAATTTGCAATAGTCAAAAGGTAAAATCA
Found at i:2376509 original size:30 final size:32
Alignment explanation
Indices: 2376448--2376509 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
2376438 ATTTAACTTT
* *
2376448 TATAAAAAATAAAATTTATTTTAAATTTTAAA
1 TATAAAAAATAAAATTTATTTCAAATATTAAA
*
2376480 TATAAAATATAAAA-TTA-TTCAAATATTAAA
1 TATAAAAAATAAAATTTATTTCAAATATTAAA
2376510 AAAAATTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 11 0.41
31 3 0.11
32 13 0.48
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (32 bp):
TATAAAAAATAAAATTTATTTCAAATATTAAA
Found at i:2377258 original size:49 final size:50
Alignment explanation
Indices: 2377204--2377334 Score: 121
Period size: 51 Copynumber: 2.7 Consensus size: 50
2377194 ATTTTTTAAC
*
2377204 TTTTTAATAATTTATAAGTAATTATTTTA-TACTTATT-ATA-TATATTCAA
1 TTTTTAATAATTTATAA-TAATAATTTTAGTA-TTATTAATACTATATTCAA
* *
2377253 TTTTTAA-AATTT-TTATAATAATTTTAGTATTTTTAATACGTATATTCAA
1 TTTTTAATAATTTATAATAATAATTTTAGTATTATTAATAC-TATATTCAA
* * **
2377302 TATTTTAGTAATTTA-ATTTTTAATTTTAGTATT
1 T-TTTTAATAATTTATAATAATAATTTTAGTATT
2377335 TTTATATTTA
Statistics
Matches: 67, Mismatches: 8, Indels: 12
0.77 0.09 0.14
Matches are distributed among these distances:
46 14 0.21
47 7 0.10
48 5 0.07
49 17 0.25
50 5 0.07
51 19 0.28
ACGTcount: A:0.36, C:0.03, G:0.04, T:0.57
Consensus pattern (50 bp):
TTTTTAATAATTTATAATAATAATTTTAGTATTATTAATACTATATTCAA
Found at i:2377327 original size:21 final size:21
Alignment explanation
Indices: 2377303--2377349 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
2377293 TATATTCAAT
*
2377303 ATTTTAGTAATTTAATTTTTA
1 ATTTTAGTAATTTAATATTTA
* *
2377324 ATTTTAGTATTTTTATATTTA
1 ATTTTAGTAATTTAATATTTA
2377345 ATTTT
1 ATTTT
2377350 TTGAATATCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (21 bp):
ATTTTAGTAATTTAATATTTA
Found at i:2388343 original size:21 final size:21
Alignment explanation
Indices: 2388319--2388360 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2388309 CAATGGGATT
*
2388319 AGGATTAGGAATTGGATTTGG
1 AGGATTAGGAAGTGGATTTGG
* *
2388340 AGGATTTGGAGGTGGATTTGG
1 AGGATTAGGAAGTGGATTTGG
2388361 TTGACGGTGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.43, T:0.33
Consensus pattern (21 bp):
AGGATTAGGAAGTGGATTTGG
Found at i:2396674 original size:22 final size:22
Alignment explanation
Indices: 2396631--2396677 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
2396621 TTCTTTTTAC
2396631 TTCAAAAGGGTATTTTAGTTAT
1 TTCAAAAGGGTATTTTAGTTAT
2396653 TTCAAAAGGGTATTTTAGTTAT
1 TTCAAAAGGGTATTTTAGTTAT
2396675 TTC
1 TTC
2396678 CTATCCATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.30, C:0.06, G:0.17, T:0.47
Consensus pattern (22 bp):
TTCAAAAGGGTATTTTAGTTAT
Found at i:2399565 original size:22 final size:23
Alignment explanation
Indices: 2399540--2399583 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
2399530 AAGTGCATGA
* *
2399540 TTAAAAAGTTA-TATTTAAACAC
1 TTAAAAAATTAGTATCTAAACAC
2399562 TTAAAAAATTAGTATCTAAACA
1 TTAAAAAATTAGTATCTAAACA
2399584 ATAAAGATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.52, C:0.09, G:0.05, T:0.34
Consensus pattern (23 bp):
TTAAAAAATTAGTATCTAAACAC
Found at i:2399588 original size:22 final size:22
Alignment explanation
Indices: 2399541--2399588 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
2399531 AGTGCATGAT
* * *
2399541 TAAAAAGTTATATTTAAACACT
1 TAAAAAATTATATCTAAACACA
2399563 TAAAAAATTAGTATCTAAACA-A
1 TAAAAAATTA-TATCTAAACACA
2399585 TAAA
1 TAAA
2399589 GATTTGAGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.56, C:0.08, G:0.04, T:0.31
Consensus pattern (22 bp):
TAAAAAATTATATCTAAACACA
Found at i:2400015 original size:2 final size:2
Alignment explanation
Indices: 2400008--2400041 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2399998 GACAAAATTC
2400008 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2400042 TTTTACCTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2408969 original size:9 final size:9
Alignment explanation
Indices: 2408957--2409008 Score: 56
Period size: 9 Copynumber: 6.1 Consensus size: 9
2408947 TAATATTTTA
2408957 TATTTAATT
1 TATTTAATT
*
2408966 TATTTAA-G
1 TATTTAATT
2408974 TATTTAATT
1 TATTTAATT
2408983 TATTTAA--
1 TATTTAATT
* *
2408990 TATTTTACT
1 TATTTAATT
2408999 TATTTAATT
1 TATTTAATT
2409008 T
1 T
2409009 TTTTGCAGAT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
7 6 0.17
8 7 0.20
9 22 0.63
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (9 bp):
TATTTAATT
Found at i:2409001 original size:16 final size:16
Alignment explanation
Indices: 2408950--2409006 Score: 78
Period size: 16 Copynumber: 3.5 Consensus size: 16
2408940 ATATTTTTAA
*
2408950 TATTTTATATTTAATT
1 TATTTAATATTTAATT
2408966 TATTTAAGTATTTAATT
1 TATTTAA-TATTTAATT
* *
2408983 TATTTAATATTTTACT
1 TATTTAATATTTAATT
2408999 TATTTAAT
1 TATTTAAT
2409007 TTTTTTGCAG
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
16 21 0.57
17 16 0.43
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (16 bp):
TATTTAATATTTAATT
Found at i:2410697 original size:27 final size:27
Alignment explanation
Indices: 2410658--2410714 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
2410648 CTTCACAGCA
* * *
2410658 GCCACCGCCATTCCTTTACCCGATGCC
1 GCCACCACAATTCCCTTACCCGATGCC
2410685 GCCACCACAATTCCCTTACCCGATGCC
1 GCCACCACAATTCCCTTACCCGATGCC
2410712 GCC
1 GCC
2410715 GCCGCCACCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.18, C:0.49, G:0.14, T:0.19
Consensus pattern (27 bp):
GCCACCACAATTCCCTTACCCGATGCC
Found at i:2411061 original size:18 final size:18
Alignment explanation
Indices: 2411038--2411089 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 18
2411028 TTAGCTGCTC
2411038 AGGACGAGGACAACGACG
1 AGGACGAGGACAACGACG
* * *
2411056 AGGACGAGGACGATGATG
1 AGGACGAGGACAACGACG
* *
2411074 ATGACGATGACAACGA
1 AGGACGAGGACAACGA
2411090 GGAGTCACAA
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.38, C:0.17, G:0.37, T:0.08
Consensus pattern (18 bp):
AGGACGAGGACAACGACG
Found at i:2411244 original size:25 final size:25
Alignment explanation
Indices: 2411199--2411246 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
2411189 TGCATTTAGT
*
2411199 ACTTTTTTATTTAGTTGTTTATTGG
1 ACTTTTTTATTTAATTGTTTATTGG
2411224 ACTTTTTTATTGTAATT-TTTATT
1 ACTTTTTTATT-TAATTGTTTATT
2411247 ATTTATCATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 17 0.81
26 4 0.19
ACGTcount: A:0.19, C:0.04, G:0.10, T:0.67
Consensus pattern (25 bp):
ACTTTTTTATTTAATTGTTTATTGG
Found at i:2411344 original size:34 final size:33
Alignment explanation
Indices: 2411284--2411350 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 33
2411274 CGTTAATATA
*
2411284 GTTGGATTTATTTTAATTTATTTTGTTAAATTT
1 GTTGGATTTATTTTAAATTATTTTGTTAAATTT
*
2411317 GTTGGAGTTT-TTGTTAAATTATTTTGTTTAATTT
1 GTTGGA-TTTATT-TTAAATTATTTTGTTAAATTT
2411351 TATTTATTAC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
33 8 0.27
34 22 0.73
ACGTcount: A:0.22, C:0.00, G:0.15, T:0.63
Consensus pattern (33 bp):
GTTGGATTTATTTTAAATTATTTTGTTAAATTT
Found at i:2417143 original size:71 final size:71
Alignment explanation
Indices: 2417041--2417225 Score: 180
Period size: 71 Copynumber: 2.6 Consensus size: 71
2417031 ACAACTATAT
* * * * *
2417041 TATATTATATGTTTTCGATACGTTTTCTTTAAAAACCATATATTATACGCTTCAAAACCATT-TC
1 TATATTATATGTTTTCAAAACATTTTTTTTAAAAACC-TATATTATAAGCTTCAAAA--ATTATC
2417105 -GAAAAA-A
63 TGAAAAACA
* * ** *
2417112 TATATTATATATTTTCAAAACATTTTTTTTAAAAATTCTATATTATAAGCTTTTAAAATTATCTT
1 TATATTATATGTTTTCAAAACATTTTTTTTAAAAA-CCTATATTATAAGCTTCAAAAATTATCTG
2417177 AAAAACTA
65 AAAAAC-A
* *
2417185 TATACTATATGTTTTTAAAACTATTTTTTTTAAAAA-CTATA
1 TATATTATATGTTTTCAAAAC-ATTTTTTTTAAAAACCTATA
2417226 CATTTTACAT
Statistics
Matches: 95, Mismatches: 13, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
69 3 0.03
70 2 0.02
71 51 0.54
72 6 0.06
73 19 0.20
74 14 0.15
ACGTcount: A:0.40, C:0.11, G:0.04, T:0.45
Consensus pattern (71 bp):
TATATTATATGTTTTCAAAACATTTTTTTTAAAAACCTATATTATAAGCTTCAAAAATTATCTGA
AAAACA
Found at i:2417221 original size:39 final size:38
Alignment explanation
Indices: 2417111--2417279 Score: 132
Period size: 39 Copynumber: 4.4 Consensus size: 38
2417101 TTTCGAAAAA
* *
2417111 ATATATTATATATTTTCAAAACATTTTTTTTAAAAATT
1 ATATATTATATATTTTTAAAACATTTTTTTTAAAAACT
* * * *
2417149 CTATATTATA-AGCTTTT-AAA-A-TTATCTTAAAAACT
1 ATATATTATATA-TTTTTAAAACATTTTTTTTAAAAACT
* *
2417184 ATATACTATATGTTTTTAAAACTATTTTTTTTAAAAACT
1 ATATATTATATATTTTTAAAAC-ATTTTTTTTAAAAACT
* * * * * *
2417223 ATACATTTTACATTTTCAAAAGTATATTTTTTAAAAAAACT
1 ATATATTATATATTTTTAAAA-CAT-TTTTTT-TAAAAACT
2417264 ATATATTATAT-TTTTT
1 ATATATTATATATTTTT
2417280 CGAAAATACG
Statistics
Matches: 98, Mismatches: 24, Indels: 16
0.71 0.17 0.12
Matches are distributed among these distances:
35 23 0.23
36 4 0.04
37 4 0.04
38 13 0.13
39 29 0.30
40 10 0.10
41 15 0.15
ACGTcount: A:0.41, C:0.08, G:0.02, T:0.50
Consensus pattern (38 bp):
ATATATTATATATTTTTAAAACATTTTTTTTAAAAACT
Done.