Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397265.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_146.0, 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: 8065533
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 116430 characters in sequence are not A, C, G, or T
File 6 of 18
Found at i:2396868 original size:17 final size:17
Alignment explanation
Indices: 2396846--2396879 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
2396836 GTTATTTGAG
2396846 CATATGATCT-TTATTGT
1 CATATGAT-TGTTATTGT
2396863 CATATGATTGTTATTGT
1 CATATGATTGTTATTGT
2396880 TGATTAGATG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 1 0.06
17 15 0.94
ACGTcount: A:0.24, C:0.09, G:0.15, T:0.53
Consensus pattern (17 bp):
CATATGATTGTTATTGT
Found at i:2398989 original size:19 final size:20
Alignment explanation
Indices: 2398948--2398989 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
2398938 TCCATGAAAG
*
2398948 ATATGTGAGAAGTAAGTTAT
1 ATATGTGAGAAGTAAGATAT
* *
2398968 ATAT-TGAGAATTAAGATCT
1 ATATGTGAGAAGTAAGATAT
2398987 ATA
1 ATA
2398990 GAAATAGATC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.43, C:0.02, G:0.19, T:0.36
Consensus pattern (20 bp):
ATATGTGAGAAGTAAGATAT
Found at i:2400885 original size:29 final size:30
Alignment explanation
Indices: 2400853--2400937 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 30
2400843 ATTGGAGGGA
2400853 TAAATTGAAAAAGAGAAATGTTGA-AGGAC
1 TAAATTGAAAAAGAGAAATGTTGACAGGAC
*
2400882 TAAATTAAAAAAGAGAAAAATGTT-ACAGGAC
1 TAAATTGAAAAAGAG--AAATGTTGACAGGAC
*
2400913 TAAATTGGAAATAA-AGAAAAGTTGA
1 TAAATT-GAAA-AAGAGAAATGTTGA
2400938 GAACCCTATT
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
29 14 0.30
30 7 0.15
31 19 0.40
32 5 0.11
33 2 0.04
ACGTcount: A:0.55, C:0.04, G:0.20, T:0.21
Consensus pattern (30 bp):
TAAATTGAAAAAGAGAAATGTTGACAGGAC
Found at i:2401850 original size:23 final size:22
Alignment explanation
Indices: 2401732--2401872 Score: 79
Period size: 22 Copynumber: 6.4 Consensus size: 22
2401722 AATAAATAAG
* *
2401732 TTGATTTTTTATTGAGCATGAA
1 TTGATTTGTTAATGAGCATGAA
* * *
2401754 CTGGA-TTGCTAAAGAGCAT-AA
1 -TTGATTTGTTAATGAGCATGAA
* * * *
2401775 GTTAATTTGCTGATAAGCATGAA
1 -TTGATTTGTTAATGAGCATGAA
* * * *
2401798 TTGAGTTGTTAATGAGAACGAG
1 TTGATTTGTTAATGAGCATGAA
* *
2401820 CTGGTTTGTTAAATGAGCATGAA
1 TTGATTTGTT-AATGAGCATGAA
* *
2401843 TTGATTTGTTAATAAGCATGAC
1 TTGATTTGTTAATGAGCATGAA
*
2401865 TAGATTTG
1 TTGATTTG
2401873 CAAGATGTTG
Statistics
Matches: 85, Mismatches: 30, Indels: 7
0.70 0.25 0.06
Matches are distributed among these distances:
21 4 0.05
22 59 0.69
23 22 0.26
ACGTcount: A:0.32, C:0.08, G:0.23, T:0.37
Consensus pattern (22 bp):
TTGATTTGTTAATGAGCATGAA
Found at i:2402783 original size:25 final size:25
Alignment explanation
Indices: 2402753--2402811 Score: 109
Period size: 25 Copynumber: 2.4 Consensus size: 25
2402743 TGCATATTTG
*
2402753 GCAAAAGTGCGTCAAAGTATTTGTT
1 GCAAAAGTGCATCAAAGTATTTGTT
2402778 GCAAAAGTGCATCAAAGTATTTGTT
1 GCAAAAGTGCATCAAAGTATTTGTT
2402803 GCAAAAGTG
1 GCAAAAGTG
2402812 ACTCTCCTCA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.29
Consensus pattern (25 bp):
GCAAAAGTGCATCAAAGTATTTGTT
Found at i:2420133 original size:19 final size:19
Alignment explanation
Indices: 2420109--2420147 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
2420099 TGTAGTAAGG
2420109 ATAGATAATGGGCCAATGA
1 ATAGATAATGGGCCAATGA
2420128 ATAGATAATGGGCCAATGA
1 ATAGATAATGGGCCAATGA
2420147 A
1 A
2420148 CAAAGTGGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.44, C:0.10, G:0.26, T:0.21
Consensus pattern (19 bp):
ATAGATAATGGGCCAATGA
Found at i:2428691 original size:36 final size:35
Alignment explanation
Indices: 2428651--2428777 Score: 110
Period size: 36 Copynumber: 3.6 Consensus size: 35
2428641 TGTGTGTGCG
* **
2428651 GTGTGGGAGTGCACATGACGATAATGGTGGTGTACA
1 GTGTGGGAGTGCACATGAC-ACAATGACGGTGTACA
* * *
2428687 GTGTGGGAGTGCTCATGACACGATGACGGTGTGCA
1 GTGTGGGAGTGCACATGACACAATGACGGTGTACA
* * * ** *
2428722 ATGTGGGAGTGCACATGATGACAATAACTATGTACG
1 GTGTGGGAGTGCACATGA-CACAATGACGGTGTACA
* *
2428758 GAGTGGGAGTGAACATGACA
1 GTGTGGGAGTGCACATGACA
2428778 ATAATAGCTA
Statistics
Matches: 71, Mismatches: 19, Indels: 3
0.76 0.20 0.03
Matches are distributed among these distances:
35 28 0.39
36 43 0.61
ACGTcount: A:0.28, C:0.13, G:0.36, T:0.23
Consensus pattern (35 bp):
GTGTGGGAGTGCACATGACACAATGACGGTGTACA
Found at i:2428727 original size:35 final size:36
Alignment explanation
Indices: 2428652--2428746 Score: 111
Period size: 35 Copynumber: 2.7 Consensus size: 36
2428642 GTGTGTGCGG
* ** *
2428652 TGTGGGAGTGCACATGACGATAATGGTGGTGTACAG
1 TGTGGGAGTGCACATGACGACAATGACGGTGTACAA
* * *
2428688 TGTGGGAGTGCTCATGAC-ACGATGACGGTGTGCAA
1 TGTGGGAGTGCACATGACGACAATGACGGTGTACAA
*
2428723 TGTGGGAGTGCACATGATGACAAT
1 TGTGGGAGTGCACATGACGACAAT
2428747 AACTATGTAC
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
35 27 0.56
36 21 0.44
ACGTcount: A:0.25, C:0.14, G:0.37, T:0.24
Consensus pattern (36 bp):
TGTGGGAGTGCACATGACGACAATGACGGTGTACAA
Found at i:2433184 original size:2 final size:2
Alignment explanation
Indices: 2433177--2433230 Score: 74
Period size: 2 Copynumber: 26.5 Consensus size: 2
2433167 TATTCTTCTT
*
2433177 TA TA TA TA TA TA TA TA TA TA TA TA TA TGA AA T- TA TGA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA T-A TA TA TA
2433220 TA TA TA TA TA T
1 TA TA TA TA TA T
2433231 GAAATTATGA
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
1 1 0.02
2 43 0.91
3 3 0.06
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2433224 original size:27 final size:27
Alignment explanation
Indices: 2433186--2433240 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
2433176 TTATATATAT
2433186 ATATATATATATATATATGAAATTATG
1 ATATATATATATATATATGAAATTATG
2433213 ATATATATATATATATATGAAATTATG
1 ATATATATATATATATATGAAATTATG
2433240 A
1 A
2433241 ATGGCCATTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (27 bp):
ATATATATATATATATATGAAATTATG
Found at i:2436291 original size:21 final size:19
Alignment explanation
Indices: 2436266--2436306 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
2436256 ATTTTAAAAC
2436266 AAAATAACATAAAATTTAACT
1 AAAATAAC-TAAAA-TTAACT
*
2436287 AAAATAACTTAAATTAACT
1 AAAATAACTAAAATTAACT
2436306 A
1 A
2436307 CTCAACATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 4 0.21
21 8 0.42
ACGTcount: A:0.61, C:0.10, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAATAACTAAAATTAACT
Found at i:2445469 original size:2 final size:2
Alignment explanation
Indices: 2445429--2445461 Score: 57
Period size: 2 Copynumber: 16.0 Consensus size: 2
2445419 ATTTCTCCTT
2445429 TA TA TA TA TA TA TA TA TA TA TA TA TA TA CTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
2445462 AAATATATCA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2445658 original size:21 final size:22
Alignment explanation
Indices: 2445623--2445666 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
2445613 TATGAAAATT
2445623 TTAAATAATAAATTAATTTGTC
1 TTAAATAATAAATTAATTTGTC
*
2445645 TTAAA-AATGAATTAATTTGTC
1 TTAAATAATAAATTAATTTGTC
2445666 T
1 T
2445667 CTCACTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (22 bp):
TTAAATAATAAATTAATTTGTC
Found at i:2453092 original size:16 final size:16
Alignment explanation
Indices: 2453071--2453101 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2453061 TTTATGAATG
2453071 TAGTATTCGTAGCATA
1 TAGTATTCGTAGCATA
2453087 TAGTATTCGTAGCAT
1 TAGTATTCGTAGCAT
2453102 TTTATTTCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.29, C:0.13, G:0.19, T:0.39
Consensus pattern (16 bp):
TAGTATTCGTAGCATA
Found at i:2454412 original size:62 final size:62
Alignment explanation
Indices: 2454315--2454440 Score: 252
Period size: 62 Copynumber: 2.0 Consensus size: 62
2454305 TACAATTTAC
2454315 CAGCTTTATTGTGATTAATTCCAATATCTTTCAATAAGGATATTAGCCATAGTATTTCATAG
1 CAGCTTTATTGTGATTAATTCCAATATCTTTCAATAAGGATATTAGCCATAGTATTTCATAG
2454377 CAGCTTTATTGTGATTAATTCCAATATCTTTCAATAAGGATATTAGCCATAGTATTTCATAG
1 CAGCTTTATTGTGATTAATTCCAATATCTTTCAATAAGGATATTAGCCATAGTATTTCATAG
2454439 CA
1 CA
2454441 AGTGGCTGCC
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 64 1.00
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.40
Consensus pattern (62 bp):
CAGCTTTATTGTGATTAATTCCAATATCTTTCAATAAGGATATTAGCCATAGTATTTCATAG
Found at i:2469772 original size:20 final size:20
Alignment explanation
Indices: 2469734--2469773 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2469724 ATTGCTTAAA
*
2469734 ATTAAAAAGTTAAATTTTAT
1 ATTAAAAAGTTAAAATTTAT
2469754 ATTAAAAA-TTATAAATTTAT
1 ATTAAAAAGTTA-AAATTTAT
2469774 TCAACTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 3 0.17
20 15 0.83
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (20 bp):
ATTAAAAAGTTAAAATTTAT
Found at i:2469951 original size:15 final size:15
Alignment explanation
Indices: 2469931--2469969 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
2469921 CTGTAAAATT
2469931 ATATTCCCAACAATC
1 ATATTCCCAACAATC
*
2469946 ATATTCTCAACAATC
1 ATATTCCCAACAATC
*
2469961 ACATTCCCA
1 ATATTCCCA
2469970 GTAATATATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.38, C:0.33, G:0.00, T:0.28
Consensus pattern (15 bp):
ATATTCCCAACAATC
Found at i:2473203 original size:31 final size:31
Alignment explanation
Indices: 2473158--2473220 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
2473148 ATACCCTTTG
* *
2473158 ACTGAAATTTATGAAGAATGAGAAGAAGCTA
1 ACTGAAATTGATGAAGAATGACAAGAAGCTA
* *
2473189 ACTGATATTGATGAAGAATGACAATAAGCTA
1 ACTGAAATTGATGAAGAATGACAAGAAGCTA
2473220 A
1 A
2473221 TTGAGGGATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.48, C:0.08, G:0.21, T:0.24
Consensus pattern (31 bp):
ACTGAAATTGATGAAGAATGACAAGAAGCTA
Found at i:2475694 original size:21 final size:21
Alignment explanation
Indices: 2475668--2475712 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
2475658 AGAAATTTTT
2475668 TTTTAAAAAATAAATAATAAA
1 TTTTAAAAAATAAATAATAAA
2475689 TTTTAAAAAATAAATAATAAA
1 TTTTAAAAAATAAATAATAAA
2475710 TTT
1 TTT
2475713 ACCATATTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
TTTTAAAAAATAAATAATAAA
Found at i:2479250 original size:68 final size:68
Alignment explanation
Indices: 2479134--2479344 Score: 201
Period size: 72 Copynumber: 3.0 Consensus size: 68
2479124 CTTTAAGGTG
* * *
2479134 GGCAAGAACTT-TTGTTTTACGTTATTACTGGATGGTAGAA-AGTTATTAGCAGTTGGTTTGTTT
1 GGCAAGAACTTGTTGTTTTACGATATTATTGGATGG-AGAAGA-TAATTAGCAGTTGGTTTGTTT
2479197 ACGAA
64 ACGAA
* * *
2479202 GGCAAGAACTTGTTGCTTTATGATGTTATTGGATGGAGAAGATAATTAGCAGTTGGTTTGATCAG
1 GGCAAGAACTTGTTGTTTTACGATATTATTGGATGGAGAAGATAATTAGCAGTTGGTTTG-T---
** *
2479267 GAATGAA
62 TTACGAA
* * * * * *
2479274 GGCGAGAACTTGTTATTTTACAATATTATTGGATGGGAGAAGATATTTAGCGGTTGATTTGTTTA
1 GGCAAGAACTTGTTGTTTTACGATATTATTGGAT-GGAGAAGATAATTAGCAGTTGGTTTGTTTA
*
2479339 GGAA
65 CGAA
2479343 GG
1 GG
2479345 AACCTCAGTT
Statistics
Matches: 115, Mismatches: 21, Indels: 13
0.77 0.14 0.09
Matches are distributed among these distances:
68 32 0.28
69 27 0.23
72 33 0.29
73 23 0.20
ACGTcount: A:0.28, C:0.07, G:0.28, T:0.36
Consensus pattern (68 bp):
GGCAAGAACTTGTTGTTTTACGATATTATTGGATGGAGAAGATAATTAGCAGTTGGTTTGTTTAC
GAA
Found at i:2488550 original size:2 final size:2
Alignment explanation
Indices: 2488543--2488580 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
2488533 AGTTGCTGCA
2488543 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2488581 AACTGTACCA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2497080 original size:63 final size:63
Alignment explanation
Indices: 2496975--2497112 Score: 204
Period size: 63 Copynumber: 2.2 Consensus size: 63
2496965 CCAAGTTAAG
* * * * * *
2496975 GAAGAATCGACATTTTAGGAAAGAAGAATCGATTCTCCAAAAATAGAAAGTTCTTGACTTTAT
1 GAAGAATTGACATCTTAGAAAAGAAGAATCAATTCTCCAAAAACAGAAAGTTCTAGACTTTAT
**
2497038 GAAGAATTGACATCTTAGAAAAGAAGAATCAATTCTTTAAAAACAGAAAGTTCTAGACTTTAT
1 GAAGAATTGACATCTTAGAAAAGAAGAATCAATTCTCCAAAAACAGAAAGTTCTAGACTTTAT
2497101 GAAGAATTGACA
1 GAAGAATTGACA
2497113 ACTCAATCAA
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
63 67 1.00
ACGTcount: A:0.44, C:0.12, G:0.17, T:0.28
Consensus pattern (63 bp):
GAAGAATTGACATCTTAGAAAAGAAGAATCAATTCTCCAAAAACAGAAAGTTCTAGACTTTAT
Found at i:2500209 original size:51 final size:51
Alignment explanation
Indices: 2500133--2500236 Score: 208
Period size: 51 Copynumber: 2.0 Consensus size: 51
2500123 TCGATAAGAG
2500133 TAAATTTTCAATCGATAGATATTGTTAGCTTTATTAGCTTTAAAATGACTA
1 TAAATTTTCAATCGATAGATATTGTTAGCTTTATTAGCTTTAAAATGACTA
2500184 TAAATTTTCAATCGATAGATATTGTTAGCTTTATTAGCTTTAAAATGACTA
1 TAAATTTTCAATCGATAGATATTGTTAGCTTTATTAGCTTTAAAATGACTA
2500235 TA
1 TA
2500237 CTTTTGAAAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.36, C:0.10, G:0.12, T:0.43
Consensus pattern (51 bp):
TAAATTTTCAATCGATAGATATTGTTAGCTTTATTAGCTTTAAAATGACTA
Found at i:2500326 original size:21 final size:21
Alignment explanation
Indices: 2500261--2500320 Score: 84
Period size: 21 Copynumber: 2.9 Consensus size: 21
2500251 AAAAATTATC
* *
2500261 TTTGAACTTGTTTGAGTGATC
1 TTTGAACTTGTTTGAATGATT
*
2500282 CTTGAACTTGTTTGAATGATT
1 TTTGAACTTGTTTGAATGATT
*
2500303 TTTGAAGTTGTTTGAATG
1 TTTGAACTTGTTTGAATG
2500321 TGTTTTTCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.22, C:0.07, G:0.23, T:0.48
Consensus pattern (21 bp):
TTTGAACTTGTTTGAATGATT
Found at i:2500449 original size:21 final size:22
Alignment explanation
Indices: 2500423--2500510 Score: 99
Period size: 21 Copynumber: 4.1 Consensus size: 22
2500413 TTTAATGATC
*
2500423 TTTAAACTTATTTGAATTA-TT
1 TTTAAACTTGTTTGAATTAGTT
* *
2500444 TTTAAAGTTGTTTGAATGAGTT
1 TTTAAACTTGTTTGAATTAGTT
* *
2500466 TTTGAACTTGTTTGAA-TAGAT
1 TTTAAACTTGTTTGAATTAGTT
* *
2500487 TTTAAACTTGTTTAAATAAGTT
1 TTTAAACTTGTTTGAATTAGTT
2500509 TT
1 TT
2500511 GAAGATCTTA
Statistics
Matches: 54, Mismatches: 11, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
21 33 0.61
22 21 0.39
ACGTcount: A:0.31, C:0.03, G:0.14, T:0.52
Consensus pattern (22 bp):
TTTAAACTTGTTTGAATTAGTT
Found at i:2500480 original size:43 final size:43
Alignment explanation
Indices: 2500427--2500510 Score: 107
Period size: 43 Copynumber: 2.0 Consensus size: 43
2500417 ATGATCTTTA
* * * *
2500427 AACTTATTTGAATTA-TTTTTAAAGTTGTTTGAATGAGTTTTTG
1 AACTTATTTGAA-TAGATTTTAAACTTGTTTAAATAAGTTTTTG
*
2500470 AACTTGTTTGAATAGATTTTAAACTTGTTTAAATAAGTTTT
1 AACTTATTTGAATAGATTTTAAACTTGTTTAAATAAGTTTT
2500511 GAAGATCTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 2 0.06
43 33 0.94
ACGTcount: A:0.31, C:0.04, G:0.14, T:0.51
Consensus pattern (43 bp):
AACTTATTTGAATAGATTTTAAACTTGTTTAAATAAGTTTTTG
Found at i:2501317 original size:36 final size:36
Alignment explanation
Indices: 2501270--2501338 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 36
2501260 AAAGGTAATG
2501270 TTGAAAGGTTGTACTTGATCCATAAAAGGTATTATA
1 TTGAAAGGTTGTACTTGATCCATAAAAGGTATTATA
* * * *
2501306 TTGAGAGGTTGTGCTTGATCCTTGAAAGGTATT
1 TTGAAAGGTTGTACTTGATCCATAAAAGGTATT
2501339 GCAAAGGTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.29, C:0.09, G:0.25, T:0.38
Consensus pattern (36 bp):
TTGAAAGGTTGTACTTGATCCATAAAAGGTATTATA
Found at i:2506445 original size:2 final size:2
Alignment explanation
Indices: 2506440--2506466 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2506430 CTCTCTCTCT
2506440 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
2506467 TTGATCTCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2508481 original size:27 final size:26
Alignment explanation
Indices: 2508458--2508520 Score: 94
Period size: 26 Copynumber: 2.5 Consensus size: 26
2508448 ACGTTATATT
2508458 ATTT-TTT-AAAGATTAATAATTTATA
1 ATTTATTTAAAAGATTAAT-ATTTATA
*
2508483 ATTTATTTAAAATATTAATATTTATA
1 ATTTATTTAAAAGATTAATATTTATA
2508509 ATTTATTTAAAA
1 ATTTATTTAAAA
2508521 TGTTCATAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
25 4 0.11
26 22 0.63
27 9 0.26
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (26 bp):
ATTTATTTAAAAGATTAATATTTATA
Found at i:2508520 original size:26 final size:27
Alignment explanation
Indices: 2508469--2508566 Score: 112
Period size: 26 Copynumber: 3.7 Consensus size: 27
2508459 TTTTTTAAAG
2508469 ATTAATAATTTATAATTTATTTAAAAT
1 ATTAATAATTTATAATTTATTTAAAAT
2508496 ATTAAT-ATTTATAATTTATTTAAAAT
1 ATTAATAATTTATAATTTATTTAAAAT
* * * **
2508522 GTTCATAATTTATGATTTAAATAATAAT
1 ATTAATAATTTATAATTTATTTAA-AAT
*
2508550 ATT--TTATTTATAATTTA
1 ATTAATAATTTATAATTTA
2508567 ATAATTAATA
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
26 36 0.59
27 20 0.33
28 5 0.08
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (27 bp):
ATTAATAATTTATAATTTATTTAAAAT
Found at i:2508556 original size:42 final size:41
Alignment explanation
Indices: 2508510--2508609 Score: 112
Period size: 42 Copynumber: 2.4 Consensus size: 41
2508500 ATATTTATAA
* *
2508510 TTTATTTAAAATGTTCATAATTTATGATTT-AAATAATAATAT
1 TTTATTTAAAAT-TTAATAATTAAT-ATTTAAAATAATAATAT
* *
2508552 TTTATTTATAATTTAATAATTAATATTTCAAAATATTAATAT
1 TTTATTTAAAATTTAATAATTAATATTT-AAAATAATAATAT
* *
2508594 TTAATTTATAATTTAA
1 TTTATTTAAAATTTAA
2508610 ATGTTATTAT
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
40 4 0.08
41 10 0.20
42 37 0.73
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (41 bp):
TTTATTTAAAATTTAATAATTAATATTTAAAATAATAATAT
Found at i:2508575 original size:26 final size:26
Alignment explanation
Indices: 2508476--2508579 Score: 79
Period size: 26 Copynumber: 4.0 Consensus size: 26
2508466 AAGATTAATA
** *
2508476 ATTTATAATTTATTTAA-AATATTAAT
1 ATTTATAATTTAAATAATAATATT-TT
** * *
2508502 ATTTATAATTTATTTAA-AATGTTCATA
1 ATTTATAATTTAAATAATAATATT--TT
*
2508529 ATTTATGATTTAAATAATAATATTTT
1 ATTTATAATTTAAATAATAATATTTT
2508555 ATTTATAATTT-AATAATTAATATTT
1 ATTTATAATTTAAATAA-TAATATTT
2508580 CAAAATATTA
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
25 5 0.08
26 41 0.62
27 15 0.23
28 5 0.08
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (26 bp):
ATTTATAATTTAAATAATAATATTTT
Found at i:2510190 original size:19 final size:20
Alignment explanation
Indices: 2510146--2510182 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
2510136 CTCCACAATT
*
2510146 GGTGCCTTTCACAACGTCCA
1 GGTGTCTTTCACAACGTCCA
2510166 GGTGTCTTT-ACAACGTC
1 GGTGTCTTTCACAACGTC
2510183 TCGGTGTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.19, C:0.30, G:0.22, T:0.30
Consensus pattern (20 bp):
GGTGTCTTTCACAACGTCCA
Found at i:2515720 original size:16 final size:16
Alignment explanation
Indices: 2515699--2515744 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
2515689 AAACCAAAAC
2515699 TTAGATTTTTATTATT
1 TTAGATTTTTATTATT
* *
2515715 TTAGATTTTGATTTTT
1 TTAGATTTTTATTATT
*
2515731 TTGATATTTTTATT
1 TT-AGATTTTTATT
2515745 GAATCCAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
16 16 0.64
17 9 0.36
ACGTcount: A:0.22, C:0.00, G:0.09, T:0.70
Consensus pattern (16 bp):
TTAGATTTTTATTATT
Found at i:2517284 original size:64 final size:63
Alignment explanation
Indices: 2517203--2517356 Score: 231
Period size: 64 Copynumber: 2.4 Consensus size: 63
2517193 TCCCAGAGCT
* *
2517203 TTCACATAGTGTGAGGTAACATTCCACATGTGGTGAATTGCA-TCTAGTATGATGATGATAGTAC
1 TTCACACAGTGTGAGGTAACATTCCACATGTGGTGAATTG-AGCCTAGTATGATGATGATA--AC
2517267 -
63 A
*
2517267 TTCACACAATGTGAGGTAACATTCCACATGTGGTGAATTGAGCCTAGTATGATGATGATAACA
1 TTCACACAGTGTGAGGTAACATTCCACATGTGGTGAATTGAGCCTAGTATGATGATGATAACA
2517330 TTCCACACAGTGTGAGGTAACATTCCA
1 TT-CACACAGTGTGAGGTAACATTCCA
2517357 TATGCGATGC
Statistics
Matches: 83, Mismatches: 4, Indels: 6
0.89 0.04 0.06
Matches are distributed among these distances:
62 2 0.02
63 3 0.04
64 78 0.94
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (63 bp):
TTCACACAGTGTGAGGTAACATTCCACATGTGGTGAATTGAGCCTAGTATGATGATGATAACA
Found at i:2519419 original size:25 final size:25
Alignment explanation
Indices: 2519390--2519445 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
2519380 TCACAACCAT
*
2519390 GTATATCAACCTGTGGCCTAGCCAC
1 GTATATCAACCTATGGCCTAGCCAC
* *
2519415 GTATATCAACCTATGGCCTTGCCAT
1 GTATATCAACCTATGGCCTAGCCAC
2519440 GTATAT
1 GTATAT
2519446 ATATCATAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.30
Consensus pattern (25 bp):
GTATATCAACCTATGGCCTAGCCAC
Found at i:2520882 original size:15 final size:14
Alignment explanation
Indices: 2520836--2520889 Score: 55
Period size: 15 Copynumber: 4.1 Consensus size: 14
2520826 TCTTCAAACT
2520836 TTTCTC-TTCCTTC
1 TTTCTCTTTCCTTC
2520849 TTT-TCTTT-C--C
1 TTTCTCTTTCCTTC
2520859 TTTCTCTTTCCTTC
1 TTTCTCTTTCCTTC
*
2520873 TTTCTCCTTTCTTTC
1 TTTCT-CTTTCCTTC
2520888 TT
1 TT
2520890 CTTTTTGCTT
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
10 4 0.12
11 5 0.15
12 4 0.12
13 5 0.15
14 6 0.18
15 10 0.29
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTCTCTTTCCTTC
Found at i:2531564 original size:73 final size:73
Alignment explanation
Indices: 2531481--2531617 Score: 184
Period size: 73 Copynumber: 1.9 Consensus size: 73
2531471 GAGACAGTGC
* * * *
2531481 TAGTCGACTAAGAGCTTATTGCCAAAAATTAAGTTCAGAGATAGACACAACTTAATAGACTAAGA
1 TAGTCGACTAAGAGCCTACTGCCAAAAACTAAGTTCAGAGACAGACACAACTTAATAGACTAAGA
2531546 AGTTTTGT
66 AGTTTTGT
* ** * * *
2531554 TAGTCGACTAAGAGCCTACTGCCAGAAACTGGGTTCAGAGACAGAGACGACTTAATTGACTAAG
1 TAGTCGACTAAGAGCCTACTGCCAAAAACTAAGTTCAGAGACAGACACAACTTAATAGACTAAG
2531618 TAGCAATGTT
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
73 54 1.00
ACGTcount: A:0.37, C:0.17, G:0.21, T:0.25
Consensus pattern (73 bp):
TAGTCGACTAAGAGCCTACTGCCAAAAACTAAGTTCAGAGACAGACACAACTTAATAGACTAAGA
AGTTTTGT
Found at i:2540200 original size:35 final size:33
Alignment explanation
Indices: 2540124--2540246 Score: 131
Period size: 35 Copynumber: 3.6 Consensus size: 33
2540114 NNNNNNNNNN
* *
2540124 TAATTAAACAATTTGATCAATTAAGACCAATAACT
1 TAATTAAACAATTTAATCAATT-AGGCCAA-AACT
* *
2540159 TGATTAAACAAATTTAATCAATTAGGCCCAAAACA
1 TAATTAAAC-AATTTAATCAATTAGG-CCAAAACT
* *
2540194 TAATTAAACAATTTAATAAATTAGG-CACAACT
1 TAATTAAACAATTTAATCAATTAGGCCAAAACT
*
2540226 TAATTAAATAATTTTAATCAA
1 TAATTAAACAA-TTTAATCAA
2540247 GNNNNNNNNN
Statistics
Matches: 75, Mismatches: 10, Indels: 8
0.81 0.11 0.09
Matches are distributed among these distances:
32 15 0.20
33 8 0.11
34 15 0.20
35 21 0.28
36 16 0.21
ACGTcount: A:0.50, C:0.13, G:0.06, T:0.32
Consensus pattern (33 bp):
TAATTAAACAATTTAATCAATTAGGCCAAAACT
Found at i:2542266 original size:62 final size:62
Alignment explanation
Indices: 2542169--2542293 Score: 223
Period size: 62 Copynumber: 2.0 Consensus size: 62
2542159 TTGTGTAAGA
* *
2542169 GAGCTAATGTGGAGTGGGGATTTAGGGAAGAATTACTTTATCCTATGGGTCTGATTGATGAT
1 GAGCTAATGTGGAGTGGGGATTTAAGGAAGAATTACGTTATCCTATGGGTCTGATTGATGAT
*
2542231 GAGCTGATGTGGAGTGGGGATTTAAGGAAGAATTACGTTATCCTATGGGTCTGATTGATGAT
1 GAGCTAATGTGGAGTGGGGATTTAAGGAAGAATTACGTTATCCTATGGGTCTGATTGATGAT
2542293 G
1 G
2542294 GAATAATGGA
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 60 1.00
ACGTcount: A:0.26, C:0.08, G:0.34, T:0.33
Consensus pattern (62 bp):
GAGCTAATGTGGAGTGGGGATTTAAGGAAGAATTACGTTATCCTATGGGTCTGATTGATGAT
Found at i:2548779 original size:40 final size:40
Alignment explanation
Indices: 2548729--2548810 Score: 146
Period size: 40 Copynumber: 2.0 Consensus size: 40
2548719 AAGATTTAGG
*
2548729 ATTGGAAATAGAAAAATTAAGCTTAATCATATTTAAAGTT
1 ATTGGAAATAGAAAAATTAAGCTCAATCATATTTAAAGTT
*
2548769 ATTGGCAATAGAAAAATTAAGCTCAATCATATTTAAAGTT
1 ATTGGAAATAGAAAAATTAAGCTCAATCATATTTAAAGTT
2548809 AT
1 AT
2548811 CTCTTTACTT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.46, C:0.07, G:0.12, T:0.34
Consensus pattern (40 bp):
ATTGGAAATAGAAAAATTAAGCTCAATCATATTTAAAGTT
Found at i:2553427 original size:253 final size:254
Alignment explanation
Indices: 2552973--2553481 Score: 957
Period size: 253 Copynumber: 2.0 Consensus size: 254
2552963 CATGAGTAGC
2552973 ATCTAGCAATACAACATGACCACCCAAATGTTAGGAGAGTCAATATGATTTGACTAACCTTTCAG
1 ATCTAGCAATACAACATGACCACCCAAATGTTAGGAGAGTCAATATGATTTGACTAACCTTTCAG
2553038 TGTACAGTATCTTAGTGTAATTCGATCCTTTCATCATATATCTCAGATAGATAGAAGGCCTGGCT
66 TGTACAGTATCTTAGTGTAATTCGATCCTTTCATCATATATCTCAGATAGATAGAAGGCCTGGCT
*
2553103 CAGTGTCTACTTTCTAACATATCCATATTAGTCCCGCAGCTTTTATATTAACCTATCAATATTGC
131 CAGTGTCTACTTTCTAACATATCCATATTAGTCCCGCAGCTTTTATATTAACCTATCAAGATTGC
* *
2553168 CTTGGCCAAAGACTTTTAATTAATATAAGTTAAGAACAAATGAGATATGTACCCTTCAT
196 CTTGGCCAAAGACTTTTAATCAATATAAGTCAAGAACAAATGAGATATGTACCCTTCAT
*
2553227 ATCTA-CAATACATCATGACCACCCAAATGTTAGGAGAGTCAATATGATTTGACTAACCTTTCAG
1 ATCTAGCAATACAACATGACCACCCAAATGTTAGGAGAGTCAATATGATTTGACTAACCTTTCAG
2553291 TGTACAGTATCTTAGTGTAATTCGATCCTTTCATCATATATCTCAGATAGATAGAAGGCCTGGCT
66 TGTACAGTATCTTAGTGTAATTCGATCCTTTCATCATATATCTCAGATAGATAGAAGGCCTGGCT
*
2553356 CGGTGTCTACTTTCTAACATATCCATATTAGTCCCGCAGCTTTTATATTAACCTATCAAGATTGC
131 CAGTGTCTACTTTCTAACATATCCATATTAGTCCCGCAGCTTTTATATTAACCTATCAAGATTGC
*
2553421 CTTGGCCAAAGACTTTTAATCAATATAAGTCAGGAACAAATGAGATATGTACCCTTCAT
196 CTTGGCCAAAGACTTTTAATCAATATAAGTCAAGAACAAATGAGATATGTACCCTTCAT
2553480 AT
1 AT
2553482 GACTTAAGGT
Statistics
Matches: 249, Mismatches: 6, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
253 244 0.98
254 5 0.02
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.33
Consensus pattern (254 bp):
ATCTAGCAATACAACATGACCACCCAAATGTTAGGAGAGTCAATATGATTTGACTAACCTTTCAG
TGTACAGTATCTTAGTGTAATTCGATCCTTTCATCATATATCTCAGATAGATAGAAGGCCTGGCT
CAGTGTCTACTTTCTAACATATCCATATTAGTCCCGCAGCTTTTATATTAACCTATCAAGATTGC
CTTGGCCAAAGACTTTTAATCAATATAAGTCAAGAACAAATGAGATATGTACCCTTCAT
Found at i:2557048 original size:2 final size:2
Alignment explanation
Indices: 2557041--2557065 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2557031 CAGGAGCATG
2557041 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2557066 TCAATATTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2557743 original size:17 final size:18
Alignment explanation
Indices: 2557723--2557762 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
2557713 CAACTTCGGG
*
2557723 TTCTTT-TTTTTTTCATT
1 TTCTTTCTTTTTCTCATT
2557740 TTCTTTCTTTTTCTCATT
1 TTCTTTCTTTTTCTCATT
*
2557758 CTCTT
1 TTCTT
2557763 CTGTAGTGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.05, C:0.20, G:0.00, T:0.75
Consensus pattern (18 bp):
TTCTTTCTTTTTCTCATT
Found at i:2567813 original size:33 final size:33
Alignment explanation
Indices: 2567775--2567838 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
2567765 CTTATAAATT
*
2567775 AAATATTAATAT-TTTAATAATATTTTATTCAAA
1 AAATATTAATATATTTAAAAATATTTT-TTCAAA
* *
2567808 AAATATTATTTTATTTAAAAATATTTTTTCA
1 AAATATTAATATATTTAAAAATATTTTTTCA
2567839 CCAATCACCG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 14 0.52
34 13 0.48
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (33 bp):
AAATATTAATATATTTAAAAATATTTTTTCAAA
Found at i:2567829 original size:18 final size:19
Alignment explanation
Indices: 2567790--2567836 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
2567780 TTAATATTTT
*
2567790 AATAATATTTTATTCAAAA
1 AATATTATTTTATTCAAAA
*
2567809 AATATTATTTTATT-TAAA
1 AATATTATTTTATTCAAAA
2567827 AATATT-TTTT
1 AATATTATTTT
2567837 CACCAATCAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 4 0.15
18 9 0.35
19 13 0.50
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (19 bp):
AATATTATTTTATTCAAAA
Found at i:2572943 original size:29 final size:28
Alignment explanation
Indices: 2572902--2573046 Score: 164
Period size: 28 Copynumber: 5.0 Consensus size: 28
2572892 GGCAACTTTG
*
2572902 ACATGGTTGTCTTAATTTAGACAAGAAA
1 ACATGTTTGTCTTAATTTAGACAAGAAA
2572930 ACATGTTTGGTCTTAATTTAGACAAGAAA
1 ACATGTTT-GTCTTAATTTAGACAAGAAA
* *
2572959 ATATGTTTGTCTTAATTTAAGACAAAAAAA
1 ACATGTTTGTCTTAATTT-AGAC-AAGAAA
* * * *
2572989 ATATTTTTTCTCTTAATCTAGACAAGAAA
1 ACA-TGTTTGTCTTAATTTAGACAAGAAA
* * *
2573018 ACATATTTGTCTCAATTTAGATAAGAAA
1 ACATGTTTGTCTTAATTTAGACAAGAAA
2573046 A
1 A
2573047 AAATTTTTTG
Statistics
Matches: 100, Mismatches: 13, Indels: 8
0.83 0.11 0.07
Matches are distributed among these distances:
28 38 0.38
29 38 0.38
30 12 0.12
31 12 0.12
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.36
Consensus pattern (28 bp):
ACATGTTTGTCTTAATTTAGACAAGAAA
Found at i:2573012 original size:59 final size:57
Alignment explanation
Indices: 2572908--2573062 Score: 193
Period size: 59 Copynumber: 2.7 Consensus size: 57
2572898 TTTGACATGG
* * * * * * *
2572908 TTGTCTTAATTTAGACAAGAAAACATGTTTGGTCTTAATTTAGACAAGAAAATATGT
1 TTGTCTTAATTTAGACAAAAAAAAATTTTTTGTCTTAATCTAGACAAGAAAACATAT
*
2572965 TTGTCTTAATTTAAGACAAAAAAAATATTTTTTCTCTTAATCTAGACAAGAAAACATAT
1 TTGTCTTAATTT-AGACAAAAAAAA-ATTTTTTGTCTTAATCTAGACAAGAAAACATAT
* *
2573024 TTGTCTCAATTTAGATAAGAAAAAAATTTTTTGTCTTAA
1 TTGTCTTAATTTAGACAA-AAAAAAATTTTTTGTCTTAA
2573063 ATTAAGATCA
Statistics
Matches: 84, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
57 12 0.14
58 28 0.33
59 44 0.52
ACGTcount: A:0.41, C:0.10, G:0.11, T:0.39
Consensus pattern (57 bp):
TTGTCTTAATTTAGACAAAAAAAAATTTTTTGTCTTAATCTAGACAAGAAAACATAT
Found at i:2578813 original size:35 final size:35
Alignment explanation
Indices: 2578788--2578854 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 35
2578778 TTAATTGTCT
*
2578788 AATTTAATCAATTTGACCCAATAACTTAATTAAAC
1 AATTTAATCAATTAGACCCAATAACTTAATTAAAC
* *
2578823 AATTTAATCAATTAGGCCCAATAACTTGATTA
1 AATTTAATCAATTAGACCCAATAACTTAATTA
2578855 NNNNNNNNNN
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.43, C:0.16, G:0.06, T:0.34
Consensus pattern (35 bp):
AATTTAATCAATTAGACCCAATAACTTAATTAAAC
Found at i:2583470 original size:41 final size:41
Alignment explanation
Indices: 2583425--2583510 Score: 100
Period size: 41 Copynumber: 2.1 Consensus size: 41
2583415 AATTTTATTG
* *
2583425 ATACACTCTAGAATATATTGATACATGCAAGGAGTATATCA
1 ATACACTATAGAATATATTGATACATGCAAGAAGTATATCA
* * * * * *
2583466 ATACATTATGGAATGTATTGATACATTCAAGAAGTCTATCG
1 ATACACTATAGAATATATTGATACATGCAAGAAGTATATCA
2583507 ATAC
1 ATAC
2583511 CTTTAGGAAA
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.31
Consensus pattern (41 bp):
ATACACTATAGAATATATTGATACATGCAAGAAGTATATCA
Found at i:2584317 original size:80 final size:80
Alignment explanation
Indices: 2584164--2584317 Score: 204
Period size: 80 Copynumber: 1.9 Consensus size: 80
2584154 ATACTTAGCC
* **
2584164 CATAGTGTATATGACTATCTCAACACATACATCTCATGGCATACATTTAATAACCTCATAAATTA
1 CATAGTGTATATGACTATCTCAACACATACATCTCATGGCATACATTTAATAACCTCAAAAAGAA
**
2584229 TTTACATGCTTTGCT
66 ACTACATGCTTTGCT
* * *
2584244 CATAGTGTATATGACTATCTCAACACGTGCATCTCATGGCATACATGTTAA-AATCTCAAAAAAG
1 CATAGTGTATATGACTATCTCAACACATACATCTCATGGCATACAT-TTAATAACCTC-AAAAAG
2584308 AAACT-CATGC
64 AAACTACATGC
2584318 ATCCAACATT
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
80 54 0.84
81 10 0.16
ACGTcount: A:0.36, C:0.21, G:0.11, T:0.32
Consensus pattern (80 bp):
CATAGTGTATATGACTATCTCAACACATACATCTCATGGCATACATTTAATAACCTCAAAAAGAA
ACTACATGCTTTGCT
Found at i:2586573 original size:71 final size:71
Alignment explanation
Indices: 2586446--2586697 Score: 212
Period size: 71 Copynumber: 3.5 Consensus size: 71
2586436 GGGAGTCATG
* * * * *
2586446 CATTCTAGTCCAGGATGGACTATATG-CCCTCTATAGTTGATCTTAT-AAAGAGAAAATGGAAGA
1 CATTCTAGTCCAAGATTGACTATA-GACCCTCTATAGTCGATCTTGTGAAGGA-AAAATGGAAGA
*
2586509 ATTGCAAA
64 AATGCAAA
*
2586517 CATTCTAGTCCAAGATTGACTAT-GAACCCTCTATAGTCGATCTTGTGACGGAAAAATGAGTGAA
1 CATTCTAGTCCAAGATTGACTATAG-ACCCTCTATAGTCGATCTTGTGAAGGAAAAAT--G-GAA
*
2586581 -AAATG--GA
62 GAAATGCAAA
* * * * ** * *
2586588 CATTCTAGTCCAAGATCGACTATAAACCCTGTACAGTTAATCTTGTGAAGGGAAAATGGATGAAA
1 CATTCTAGTCCAAGATTGACTATAGACCCTCTATAGTCGATCTTGTGAAGGAAAAATGGAAGAAA
**
2586653 CACAAA
66 TGCAAA
*
2586659 -ATCTTCTAGTCCAAGATTGACTATAGACCCTCCATAGTC
1 CA--TTCTAGTCCAAGATTGACTATAGACCCTCTATAGTC
2586698 TATTATGGAC
Statistics
Matches: 143, Mismatches: 26, Indels: 23
0.74 0.14 0.12
Matches are distributed among these distances:
68 2 0.01
69 5 0.03
70 1 0.01
71 94 0.66
72 33 0.23
73 5 0.03
74 3 0.02
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.27
Consensus pattern (71 bp):
CATTCTAGTCCAAGATTGACTATAGACCCTCTATAGTCGATCTTGTGAAGGAAAAATGGAAGAAA
TGCAAA
Found at i:2589125 original size:21 final size:21
Alignment explanation
Indices: 2589072--2589127 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
2589062 GCTTACAAGT
*
2589072 ATTGATACTTTCCTCAAAAGC
1 ATTGATACTTTTCTCAAAAGC
2589093 ATTGATACTTTTCTCAAAAGC
1 ATTGATACTTTTCTCAAAAGC
2589114 ATTGATACTTTTCT
1 ATTGATACTTTTCT
2589128 AGTAGAATGA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.30, C:0.20, G:0.09, T:0.41
Consensus pattern (21 bp):
ATTGATACTTTTCTCAAAAGC
Found at i:2599055 original size:68 final size:67
Alignment explanation
Indices: 2598904--2599161 Score: 171
Period size: 68 Copynumber: 3.8 Consensus size: 67
2598894 AACTTACTCT
* * * ***
2598904 CTCATAAGGTATATGGAAAATACATCATATATATAATCTCATGGCATTCATCATGCTTTTTGAAT
1 CTCATATGGTATATGGATAA-ACATCATATAAATAATCTCATGGCATTCATCATGCAACTTGAAT
*
2598969 CAT
65 CAC
* * * *
2598972 CTCATGTAGTGTATGGTATAAACATCATATAAACT-ATCTCATGGCATTTATCATGCAAACTT-A
1 CTCATATGGTATATGG-ATAAACATCATATAAA-TAATCTCATGGCATTCATCATGC-AACTTGA
*
2599035 ATTAC
63 ATCAC
** *** * * * *
2599040 CTCATATGGTATATGGAATTTACATCATATATGCAATCTTATAGTATACATCATGCATACTT-AA
1 CTCATATGGTATATGG-ATAAACATCATATAAATAATCTCATGGCATTCATCATGCA-ACTTGAA
*
2599104 TCAT
64 TCAC
* * * ** * *
2599108 CTTATGTGGTATATGAAATTTACATCATATACATAATCTTATGGCATTCATCAT
1 CTCATATGGTATATG-GATAAACATCATATAAATAATCTCATGGCATTCATCAT
2599162 ACTAAACATG
Statistics
Matches: 147, Mismatches: 37, Indels: 12
0.75 0.19 0.06
Matches are distributed among these distances:
67 1 0.01
68 140 0.95
69 6 0.04
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.38
Consensus pattern (67 bp):
CTCATATGGTATATGGATAAACATCATATAAATAATCTCATGGCATTCATCATGCAACTTGAATC
AC
Found at i:2599152 original size:136 final size:136
Alignment explanation
Indices: 2598904--2599161 Score: 295
Period size: 136 Copynumber: 1.9 Consensus size: 136
2598894 AACTTACTCT
* * * **
2598904 CTCATAAGGTATATGGAAAATACATCATATATATAATCTCATGGCATTCATCATGCTTTTTGAAT
1 CTCATAAGGTATATGGAAAATACATCATATATACAATCTCATAGCATACATCATGCTACTTGAAT
* ** *
2598969 CATCTCATGTAGTGTATGGTATAAACATCATATAAACTATCTCATGGCATTTATCATGCAAACTT
66 CATCTCATGTAGTATATGAAATAAACATCATATAAACTATCTCATGGCATTCATCATGCAAACTT
2599034 AATTAC
131 AATTAC
* ** * * *
2599040 CTCATATGGTATATGGAATTTACATCATATATGCAATCTTATAGTATACATCATGCATACTT-AA
1 CTCATAAGGTATATGGAAAATACATCATATATACAATCTCATAGCATACATCATGC-TACTTGAA
* * ** * *
2599104 TCATCTTATGTGGTATATGAAATTTACATCATATACA-TAATCTTATGGCATTCATCAT
65 TCATCTCATGTAGTATATGAAATAAACATCATATAAACT-ATCTCATGGCATTCATCAT
2599162 ACTAAACATG
Statistics
Matches: 99, Mismatches: 21, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
135 1 0.01
136 95 0.96
137 3 0.03
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.38
Consensus pattern (136 bp):
CTCATAAGGTATATGGAAAATACATCATATATACAATCTCATAGCATACATCATGCTACTTGAAT
CATCTCATGTAGTATATGAAATAAACATCATATAAACTATCTCATGGCATTCATCATGCAAACTT
AATTAC
Found at i:2600172 original size:16 final size:16
Alignment explanation
Indices: 2600148--2600178 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2600138 ATAAACATAT
2600148 AAAAAAATCAAAATCC
1 AAAAAAATCAAAATCC
*
2600164 AAAAGAATCAAAATC
1 AAAAAAATCAAAATC
2600179 TAATTTTTGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.68, C:0.16, G:0.03, T:0.13
Consensus pattern (16 bp):
AAAAAAATCAAAATCC
Found at i:2606702 original size:68 final size:68
Alignment explanation
Indices: 2606614--2606916 Score: 313
Period size: 68 Copynumber: 4.5 Consensus size: 68
2606604 GGAAAAATAT
* * * * * *
2606614 ATCATATACATAAT-TCCATGGCATTCATCATGCTTCCTTAATCATCTTATGTAGTATATGGAAT
1 ATCATATACATAATCT-CATGGCATTCATCATGCATACTTAATCATCTCATATAGCATATAGAAT
2606678 ATAC
65 ATAC
* * * * * *
2606682 ATCACATACCTAATCTCATGGCATTCA-CAATGCTTTCTTAATCATCTCATGTAGCATCTAGAAT
1 ATCATATACATAATCTCATGGCATTCATC-ATGCATACTTAATCATCTCATATAGCATATAGAAT
2606746 ATAC
65 ATAC
* * * * *
2606750 ATCATATACATGATCTCATGGCATTTATCATGCATACTTAATCACCTCATATGGCATATAGAATT
1 ATCATATACATAATCTCATGGCATTCATCATGCATACTTAATCATCTCATATAGCATATAGAATA
2606815 TAC
66 TAC
* * * * ** * * * *
2606818 ATCATATACACAATCTTATAGTACACATCATGCATACTTAATCATCTCATATGGTATATGGAATT
1 ATCATATACATAATCTCATGGCATTCATCATGCATACTTAATCATCTCATATAGCATATAGAATA
2606883 TAC
66 TAC
* *
2606886 ATCATATACATAATCTTATGGCTTTCATCAT
1 ATCATATACATAATCTCATGGCATTCATCAT
2606917 ACCAAACATG
Statistics
Matches: 197, Mismatches: 35, Indels: 6
0.83 0.15 0.03
Matches are distributed among these distances:
67 1 0.01
68 194 0.98
69 2 0.01
ACGTcount: A:0.34, C:0.21, G:0.09, T:0.36
Consensus pattern (68 bp):
ATCATATACATAATCTCATGGCATTCATCATGCATACTTAATCATCTCATATAGCATATAGAATA
TAC
Found at i:2608128 original size:16 final size:16
Alignment explanation
Indices: 2608104--2608134 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2608094 AAGAAATATA
2608104 AAAAAAATCAAAATCC
1 AAAAAAATCAAAATCC
*
2608120 AAAAGAATCAAAATC
1 AAAAAAATCAAAATC
2608135 GAATTTTTAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.68, C:0.16, G:0.03, T:0.13
Consensus pattern (16 bp):
AAAAAAATCAAAATCC
Found at i:2621302 original size:20 final size:20
Alignment explanation
Indices: 2621277--2621322 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
2621267 CATTGTTTTC
2621277 CTAATTACCCTCATTTT-CCA
1 CTAATTACCC-CATTTTACCA
*
2621297 CTAATT-TCCCATTTTACCA
1 CTAATTACCCCATTTTACCA
2621316 CTAATTA
1 CTAATTA
2621323 AGGGGATTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 6 0.26
19 11 0.48
20 6 0.26
ACGTcount: A:0.28, C:0.30, G:0.00, T:0.41
Consensus pattern (20 bp):
CTAATTACCCCATTTTACCA
Found at i:2621886 original size:68 final size:67
Alignment explanation
Indices: 2621777--2622011 Score: 222
Period size: 68 Copynumber: 3.5 Consensus size: 67
2621767 GAGGAGCCTT
* * * * * *
2621777 TTTAAAATTATACAACCTCATTATATATGAAGAGTTTAAAGTTAGGCAACCTCATTCCAGATGAA
1 TTTAAAGTTACACAACCTCATTCTAGATGAGGAGTTTAAAGTTA-GCAACCTCATTCAAGATGAA
2621842 GAG
65 GAG
* *
2621845 TTTAAAGTTACACAACCTCATTCTAGATGAGGAGTTTAAAGTTATGCAGCCTCATTCTAGATG-A
1 TTTAAAGTTACACAACCTCATTCTAGATGAGGAGTTTAAAGTTA-GCAACCTCATTCAAGATGAA
2621909 GAAG
65 G-AG
* *** * * * *
2621913 CTTAAAGTTATGTAGCCTCATTCAAGATAAGGAGTTTAAATTTA-CATAGCCTCATTCAAGATGA
1 TTTAAAGTTACACAACCTCATTCTAGATGAGGAGTTTAAAGTTAGCA-A-CCTCATTCAAGATGA
*
2621977 GGAG
64 AGAG
* * * *
2621981 TTTAAAGTTACATAGCCTTATTCTAAATGAG
1 TTTAAAGTTACACAACCTCATTCTAGATGAG
2622012 TTTAAAGTTA
Statistics
Matches: 137, Mismatches: 26, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
66 2 0.01
67 2 0.01
68 132 0.96
69 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (67 bp):
TTTAAAGTTACACAACCTCATTCTAGATGAGGAGTTTAAAGTTAGCAACCTCATTCAAGATGAAG
AG
Found at i:2621932 original size:102 final size:102
Alignment explanation
Indices: 2621777--2622029 Score: 291
Period size: 102 Copynumber: 2.5 Consensus size: 102
2621767 GAGGAGCCTT
* * * * * * * *
2621777 TTTAAAATTATACAACCTCATTATATATGA-AGAGTTTAAAGTTAGGCAACCTCATTCCAGATGA
1 TTTAAAGTTATACAGCCTCATTCTAAATGAGA-AGTTTAAAGTTATGTAGCCTCATTCAAGAT-A
*
2621841 A-GAGTTTAAAGTTACACAACCTCATTCTAGATGAGGAG
64 AGGAGTTTAAAGTTACACAACCTCATTCAAGATGAGGAG
* * *
2621879 TTTAAAGTTATGCAGCCTCATTCTAGATGAGAAGCTTAAAGTTATGTAGCCTCATTCAAGATAAG
1 TTTAAAGTTATACAGCCTCATTCTAAATGAGAAGTTTAAAGTTATGTAGCCTCATTCAAGATAAG
* * *
2621944 GAGTTTAAATTTACATAGCCTCATTCAAGATGAGGAG
66 GAGTTTAAAGTTACACAACCTCATTCAAGATGAGGAG
* * *
2621981 TTTAAAGTTACATAGCCTTATTCTAAAT--G-AGTTTAAAGTTATGTAGCCT
1 TTTAAAGTTATACAGCCTCATTCTAAATGAGAAGTTTAAAGTTATGTAGCCT
2622030 TGTTTAATAT
Statistics
Matches: 129, Mismatches: 20, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
99 19 0.15
100 1 0.01
101 2 0.02
102 106 0.82
103 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.33
Consensus pattern (102 bp):
TTTAAAGTTATACAGCCTCATTCTAAATGAGAAGTTTAAAGTTATGTAGCCTCATTCAAGATAAG
GAGTTTAAAGTTACACAACCTCATTCAAGATGAGGAG
Found at i:2621992 original size:34 final size:34
Alignment explanation
Indices: 2621803--2622011 Score: 217
Period size: 34 Copynumber: 6.1 Consensus size: 34
2621793 CTCATTATAT
* *
2621803 ATGAAGAGTTTAAAGTTAGGCA-A-CCTCATTCCAG
1 ATGAGGAGTTTAAAGTTA--CATAGCCTCATTCAAG
* * * *
2621837 ATGAAGAGTTTAAAGTTACACAACCTCATTCTAG
1 ATGAGGAGTTTAAAGTTACATAGCCTCATTCAAG
*** *
2621871 ATGAGGAGTTTAAAGTTATGCAGCCTCATTCTAG
1 ATGAGGAGTTTAAAGTTACATAGCCTCATTCAAG
* * **
2621905 ATGAGAAGCTTAAAGTTATGTAGCCTCATTCAAG
1 ATGAGGAGTTTAAAGTTACATAGCCTCATTCAAG
* *
2621939 ATAAGGAGTTTAAATTTACATAGCCTCATTCAAG
1 ATGAGGAGTTTAAAGTTACATAGCCTCATTCAAG
*
2621973 ATGAGGAGTTTAAAGTTACATAGCCTTATTCTAA-
1 ATGAGGAGTTTAAAGTTACATAGCCTCATTC-AAG
2622007 ATGAG
1 ATGAG
2622012 TTTAAAGTTA
Statistics
Matches: 154, Mismatches: 18, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
32 2 0.01
33 1 0.01
34 149 0.97
35 2 0.01
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (34 bp):
ATGAGGAGTTTAAAGTTACATAGCCTCATTCAAG
Found at i:2622042 original size:31 final size:31
Alignment explanation
Indices: 2621944--2622030 Score: 95
Period size: 34 Copynumber: 2.7 Consensus size: 31
2621934 TCAAGATAAG
* *
2621944 GAGTTTAAATTTACATAGCCTCATTC-AAGAT
1 GAGTTTAAAGTTACATAGCCTTATTCTAA-AT
2621975 GAGGAGTTTAAAGTTACATAGCCTTATTCTAAAT
1 ---GAGTTTAAAGTTACATAGCCTTATTCTAAAT
**
2622009 GAGTTTAAAGTTATGTAGCCTT
1 GAGTTTAAAGTTACATAGCCTT
2622031 GTTTAATATG
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
31 20 0.42
34 26 0.54
35 2 0.04
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (31 bp):
GAGTTTAAAGTTACATAGCCTTATTCTAAAT
Found at i:2622177 original size:43 final size:43
Alignment explanation
Indices: 2622087--2622178 Score: 112
Period size: 43 Copynumber: 2.1 Consensus size: 43
2622077 CAAGGTAGGG
* * * * **
2622087 AGTTTAGTCCTTTTAAAGTTACACAACGTCATTCTAGATGAGG
1 AGTTTAGTCCTTTTAAAGTTACACAACCTCATTCCAAATAAAA
* *
2622130 AGTTTAGTCCTTTTAAAGTTACATAGCCTCATTCCAAATAAAA
1 AGTTTAGTCCTTTTAAAGTTACACAACCTCATTCCAAATAAAA
2622173 AGTTTA
1 AGTTTA
2622179 ACATAGCTCC
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (43 bp):
AGTTTAGTCCTTTTAAAGTTACACAACCTCATTCCAAATAAAA
Found at i:2622286 original size:43 final size:43
Alignment explanation
Indices: 2622188--2622289 Score: 125
Period size: 43 Copynumber: 2.4 Consensus size: 43
2622178 AACATAGCTC
* * *
2622188 CATTTCAAATGAGGAGTTTAGTCCTTTTAAAGTTGCGTAGACT
1 CATTTCAAATGAGGAGTTTAGTCATTTTAAAATTACGTAGACT
* * *
2622231 CA-TTCTAGATGAGGAGTTTGGTCATTTTAAAATTACGTAGCCT
1 CATTTC-AAATGAGGAGTTTAGTCATTTTAAAATTACGTAGACT
*
2622274 TATTTCAAATGAGGAG
1 CATTTCAAATGAGGAG
2622290 CTTATTTCTT
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
42 3 0.06
43 43 0.88
44 3 0.06
ACGTcount: A:0.29, C:0.13, G:0.22, T:0.36
Consensus pattern (43 bp):
CATTTCAAATGAGGAGTTTAGTCATTTTAAAATTACGTAGACT
Found at i:2622779 original size:24 final size:24
Alignment explanation
Indices: 2622727--2622781 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
2622717 ACACACACAC
*
2622727 AAAG-AAAAAATTAGGAAGAGCAA
1 AAAGAAAAAAATTAGGAAGAGAAA
* *
2622750 ACAGAAAAAAATTAAGG-AGTGAAA
1 AAAGAAAAAAATT-AGGAAGAGAAA
2622774 AAAGAAAA
1 AAAGAAAA
2622782 GAAAAACAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 3 0.12
24 20 0.77
25 3 0.12
ACGTcount: A:0.67, C:0.04, G:0.20, T:0.09
Consensus pattern (24 bp):
AAAGAAAAAAATTAGGAAGAGAAA
Found at i:2629965 original size:28 final size:28
Alignment explanation
Indices: 2629932--2630312 Score: 363
Period size: 28 Copynumber: 13.3 Consensus size: 28
2629922 ACATGTTTTA
*
2629932 TCTTAATTTAGACAAGAAAATATGTTCG
1 TCTTAATTTAGACAAGAAAATATGTTTG
* * *
2629960 TCTTAATTTAGATAAGAACCATA-CTTTG
1 TCTTAATTTAGACAAGAA-AATATGTTTG
* ** * *
2629988 TCTTATTTTTTATAAGAAAACATGTTATG
1 TCTTAATTTAGACAAGAAAATATGTT-TG
* * *
2630017 TCTTAATTTAGATAAGAAAACATGTCTG
1 TCTTAATTTAGACAAGAAAATATGTTTG
* * *
2630045 TCTTAATTTAGATAAGAAAACATCTTTG
1 TCTTAATTTAGACAAGAAAATATGTTTG
*
2630073 TCTTAATTTAGACAAGAAAATGTGTTTTG
1 TCTTAATTTAGACAAGAAAATATG-TTTG
* * *
2630102 TCTTAATTTGGATAAGAAAAATATGTTTA
1 TCTTAATTTAGACAAG-AAAATATGTTTG
*
2630131 TCTTAATTTAGACAAGAAAACATGTTTG
1 TCTTAATTTAGACAAGAAAATATGTTTG
2630159 TCTTAATTTAAGACAAGAAAAATATG-TTG
1 TCTTAATTT-AGACAAG-AAAATATGTTTG
*
2630188 TCTTAATCTAGACAAGAAAATATGTTTG
1 TCTTAATTTAGACAAGAAAATATGTTTG
* * *
2630216 TTTTCATTTAAGACAAGAAAAAAATGTTTTG
1 TCTTAATTT-AGACAAG-AAAATATG-TTTG
* * *
2630247 TCTTAATCTAGACAAGAAAACATATTTG
1 TCTTAATTTAGACAAGAAAATATGTTTG
* * *
2630275 T-TTCAATTTAGAAAAAATAACATATTTTTG
1 TCTT-AATTTAGACAAGA-AA-ATATGTTTG
2630305 TCTTAATT
1 TCTTAATT
2630313 AAAGATAAAA
Statistics
Matches: 294, Mismatches: 44, Indels: 28
0.80 0.12 0.08
Matches are distributed among these distances:
27 12 0.04
28 135 0.46
29 95 0.32
30 40 0.14
31 12 0.04
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.39
Consensus pattern (28 bp):
TCTTAATTTAGACAAGAAAATATGTTTG
Found at i:2630032 original size:57 final size:55
Alignment explanation
Indices: 2629932--2630265 Score: 240
Period size: 57 Copynumber: 5.9 Consensus size: 55
2629922 ACATGTTTTA
* * * * *
2629932 TCTTAATTTAGACAAGAAAATATGTTCGTCTTAATTTAGATAAGAACCATACTTTG
1 TCTTAATTTAGATAAGAAAACATGTTTGTCTTAATTTAGATAAGAAACAT-CTCTG
* ** *
2629988 TCTTATTTTTTATAAGAAAACATGTTATGTCTTAATTTAGATAAGAAAACATGTCTG
1 TCTTAATTTAGATAAGAAAACATGTT-TGTCTTAATTTAGATAAG-AAACATCTCTG
* * * *
2630045 TCTTAATTTAGATAAGAAAACATCTTTGTCTTAATTTAGACAAGAAA-ATGTGTTTTG
1 TCTTAATTTAGATAAGAAAACATGTTTGTCTTAATTTAGATAAGAAACA--T-CTCTG
* * * * * *
2630102 TCTTAATTTGGATAAGAAAAATATGTTTATCTTAATTTAGACAAGAAAACATGTTTG
1 TCTTAATTTAGATAAG-AAAACATGTTTGTCTTAATTTAGATAAG-AAACATCTCTG
* * * * * * *
2630159 TCTTAATTTAAGACAAGAAAA-ATATGTTGTCTTAATCTAGACAAGAAAATATGTTTG
1 TCTTAATTT-AGATAAGAAAACATGT-TTGTCTTAATTTAGATAAG-AAACATCTCTG
* * * * * *
2630216 TTTTCATTTAAGACAAGAAAAAAATGTTTTGTCTTAATCTAGACAAGAAA
1 TCTTAATTT-AGATAAG-AAAACATG-TTTGTCTTAATTTAGATAAGAAA
2630266 ACATATTTGT
Statistics
Matches: 235, Mismatches: 30, Indels: 24
0.81 0.10 0.08
Matches are distributed among these distances:
54 1 0.00
55 3 0.01
56 42 0.18
57 120 0.51
58 43 0.18
59 24 0.10
60 2 0.01
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38
Consensus pattern (55 bp):
TCTTAATTTAGATAAGAAAACATGTTTGTCTTAATTTAGATAAGAAACATCTCTG
Found at i:2630072 original size:85 final size:84
Alignment explanation
Indices: 2629921--2630286 Score: 371
Period size: 85 Copynumber: 4.3 Consensus size: 84
2629911 TGACAGCTTT
* * *
2629921 AACATGTTTTATCTTAATTTAGACAAGAAAATATGTTCGTCTTAATTTAGATAAG-AACCATACT
1 AACATGTTTTGTCTTAATTTAGATAAGAAAATATGTT-GTCTTAATTTAGATAAGAAAACAT-CT
* ** *
2629985 TTGTCTTATTTTTTATAAGAA
64 TTGTCTTAATTTAGACAAGAA
* *
2630006 AACATGTTATGTCTTAATTTAGATAAGAAAACATGTCTGTCTTAATTTAGATAAGAAAACATCTT
1 AACATGTTTTGTCTTAATTTAGATAAGAAAATATGT-TGTCTTAATTTAGATAAGAAAACATCTT
2630071 TGTCTTAATTTAGACAAGAA
65 TGTCTTAATTTAGACAAGAA
** * * * *
2630091 AATGTGTTTTGTCTTAATTTGGATAAGAAAAATATGTTTATCTTAATTTAGACAAGAAAACATGT
1 AACATGTTTTGTCTTAATTTAGATAAG-AAAATATG-TTGTCTTAATTTAGATAAGAAAACATCT
2630156 TTGTCTTAATTTAAGACAAGAA
64 TTGTCTTAATTT-AGACAAGAA
* * * * * * * *
2630178 AA-ATATGTTGTCTTAATCTAGACAAGAAAATATGTTTGTTTTCATTTAAGACAAGAAAAAAATG
1 AACATGTTTTGTCTTAATTTAGATAAGAAAATATG-TTGTCTTAATTT-AGATAAG-AAAACAT-
* *
2630242 TTTTGTCTTAATCTAGACAAGAA
62 CTTTGTCTTAATTTAGACAAGAA
*
2630265 AACAT-ATTTGT-TTCAATTTAGA
1 AACATGTTTTGTCTT-AATTTAGA
2630287 AAAAATAACA
Statistics
Matches: 239, Mismatches: 32, Indels: 18
0.83 0.11 0.06
Matches are distributed among these distances:
85 109 0.46
86 76 0.32
87 40 0.17
88 14 0.06
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.39
Consensus pattern (84 bp):
AACATGTTTTGTCTTAATTTAGATAAGAAAATATGTTGTCTTAATTTAGATAAGAAAACATCTTT
GTCTTAATTTAGACAAGAA
Found at i:2639952 original size:15 final size:16
Alignment explanation
Indices: 2639914--2639955 Score: 59
Period size: 15 Copynumber: 2.6 Consensus size: 16
2639904 AAACTTATGT
2639914 CTTTATTTTTATTGTCA
1 CTTTA-TTTTATTGTCA
2639931 CTTTATTTTATTG-CA
1 CTTTATTTTATTGTCA
*
2639946 TTTTATTTTA
1 CTTTATTTTA
2639956 AGATAATCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 11 0.46
16 8 0.33
17 5 0.21
ACGTcount: A:0.19, C:0.10, G:0.05, T:0.67
Consensus pattern (16 bp):
CTTTATTTTATTGTCA
Found at i:2643251 original size:20 final size:20
Alignment explanation
Indices: 2643222--2643281 Score: 97
Period size: 20 Copynumber: 3.1 Consensus size: 20
2643212 AGCCAAGTTC
2643222 AAAA-GTATCGATACATCTT
1 AAAATGTATCGATACATCTT
*
2643241 AAAATGTATCGATACATCCT
1 AAAATGTATCGATACATCTT
2643261 AAAATGTATCGATACAT-TT
1 AAAATGTATCGATACATCTT
2643280 AA
1 AA
2643282 GCAGGAATTC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.18
20 31 0.82
ACGTcount: A:0.43, C:0.15, G:0.10, T:0.32
Consensus pattern (20 bp):
AAAATGTATCGATACATCTT
Found at i:2644531 original size:35 final size:35
Alignment explanation
Indices: 2644505--2644609 Score: 149
Period size: 35 Copynumber: 3.0 Consensus size: 35
2644495 CTTAATTGTT
*
2644505 TAATTTAATCAATTAGGCCCAATAACTTAATTAAA
1 TAATTTAATTAATTAGGCCCAATAACTTAATTAAA
* *
2644540 TAATTTAATTAATTAGGCCTAATGACTTAATTAAA
1 TAATTTAATTAATTAGGCCCAATAACTTAATTAAA
* *
2644575 CAGA-TTAATTAATTAAGCCCAATAACTTAATTAAA
1 TA-ATTTAATTAATTAGGCCCAATAACTTAATTAAA
2644610 CGATTTTAAT
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
35 61 0.98
36 1 0.02
ACGTcount: A:0.46, C:0.12, G:0.07, T:0.35
Consensus pattern (35 bp):
TAATTTAATTAATTAGGCCCAATAACTTAATTAAA
Found at i:2654311 original size:14 final size:16
Alignment explanation
Indices: 2654287--2654318 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
2654277 TTAAAAAACT
2654287 TGATAAAACCT-TCAA
1 TGATAAAACCTCTCAA
2654302 TGAT-AAACCTCTCAA
1 TGATAAAACCTCTCAA
2654317 TG
1 TG
2654319 CAATACAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.41, C:0.22, G:0.09, T:0.28
Consensus pattern (16 bp):
TGATAAAACCTCTCAA
Found at i:2657893 original size:2 final size:2
Alignment explanation
Indices: 2657881--2657911 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
2657871 CACATATCAA
2657881 AT AT AT CAT 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
2657912 TGCAAAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2662174 original size:21 final size:22
Alignment explanation
Indices: 2662149--2662192 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
2662139 AAGTGATTAA
2662149 TTTAAGTTATTTTA-GTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
*
2662170 TTTAAGTTATTTTATTTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
2662192 T
1 T
2662193 ACTTTAAGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (22 bp):
TTTAAGTTATTTTATGTTAAAT
Found at i:2672021 original size:64 final size:63
Alignment explanation
Indices: 2671827--2672019 Score: 350
Period size: 64 Copynumber: 3.0 Consensus size: 63
2671817 TAGTTAGACA
*
2671827 TTCTTTGAGCTGTAAACTTATGAGATTGAATGTGGAAAACAATCTTTGGGATTGTAATTTGGTT
1 TTCTTTGAG-TGTAAACTTATGAGATTGAATGTGGAAAACAGTCTTTGGGATTGTAATTTGGTT
2671891 TTCTTTGAGTGTAAACTTATGAGATTGAATGTGGAAAACAGTCTTTGGGATTGTAAATTTGGTT
1 TTCTTTGAGTGTAAACTTATGAGATTGAATGTGGAAAACAGTCTTTGGGATTGT-AATTTGGTT
*
2671955 TTCTTTGAGTGTAAACTTATGAGATTGAATGTGGAAAACAGTCTTTGGGATTGTAGTTTGGTT
1 TTCTTTGAGTGTAAACTTATGAGATTGAATGTGGAAAACAGTCTTTGGGATTGTAATTTGGTT
2672018 TT
1 TT
2672020 TCAAACTTCG
Statistics
Matches: 126, Mismatches: 2, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
63 54 0.43
64 72 0.57
ACGTcount: A:0.27, C:0.07, G:0.25, T:0.41
Consensus pattern (63 bp):
TTCTTTGAGTGTAAACTTATGAGATTGAATGTGGAAAACAGTCTTTGGGATTGTAATTTGGTT
Found at i:2675805 original size:19 final size:19
Alignment explanation
Indices: 2675768--2675803 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2675758 AAATTTAAGG
2675768 CCACATAAATAATATAAAC
1 CCACATAAATAATATAAAC
*
2675787 CCACCTAAATAA-ATAAA
1 CCACATAAATAATATAAA
2675804 ACAAATCCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.58, C:0.22, G:0.00, T:0.19
Consensus pattern (19 bp):
CCACATAAATAATATAAAC
Found at i:2678544 original size:15 final size:15
Alignment explanation
Indices: 2678515--2678562 Score: 69
Period size: 15 Copynumber: 3.1 Consensus size: 15
2678505 GTTTAGTACT
2678515 TTACAATGCAATGTGA
1 TTACAA-GCAATGTGA
*
2678531 TTACAAGTAATGTGA
1 TTACAAGCAATGTGA
*
2678546 TTGCAAGCAATGTGA
1 TTACAAGCAATGTGA
2678561 TT
1 TT
2678563 GTAGAAAAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
15 23 0.79
16 6 0.21
ACGTcount: A:0.35, C:0.10, G:0.21, T:0.33
Consensus pattern (15 bp):
TTACAAGCAATGTGA
Found at i:2678814 original size:33 final size:33
Alignment explanation
Indices: 2678777--2678860 Score: 116
Period size: 33 Copynumber: 2.6 Consensus size: 33
2678767 TTTTAATATC
* * *
2678777 ATATATTTTATTTTTATTTTTTATTATAATTTT
1 ATATATTTTATTTTCATTTCTTAATATAATTTT
2678810 ATATATTTTATTTTCATTTCTTAATATAATTTT
1 ATATATTTTATTTTCATTTCTTAATATAATTTT
* *
2678843 CTATATTATA-TTTCATTT
1 ATATATTTTATTTTCATTT
2678861 AAATTTCTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
32 8 0.17
33 38 0.83
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.67
Consensus pattern (33 bp):
ATATATTTTATTTTCATTTCTTAATATAATTTT
Found at i:2678853 original size:38 final size:37
Alignment explanation
Indices: 2678750--2678869 Score: 104
Period size: 33 Copynumber: 3.2 Consensus size: 37
2678740 TTATATAATA
* *
2678750 TCATCTCTTAAATATAATTTTAATATCATATATTTTATTT
1 TCATTTCTT-AATATAATTTTTATAT--TATATTTTATTT
* * *
2678790 TTATTTTTTATTATAA--TTT-TA-TATATTTTATTT
1 TCATTTCTTAATATAATTTTTATATTATATTTTATTT
*
2678823 TCATTTCTTAATATAATTTTCTATATTATATTTCATTT
1 TCATTTCTTAATATAATTTT-TATATTATATTTTATTT
**
2678861 AAATTTCTT
1 TCATTTCTT
2678870 TTTCCTTTAA
Statistics
Matches: 64, Mismatches: 11, Indels: 12
0.74 0.13 0.14
Matches are distributed among these distances:
33 25 0.39
35 2 0.03
36 3 0.05
37 4 0.06
38 18 0.28
39 6 0.09
40 6 0.09
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (37 bp):
TCATTTCTTAATATAATTTTTATATTATATTTTATTT
Found at i:2682599 original size:4 final size:4
Alignment explanation
Indices: 2682590--2682623 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
2682580 CACAAATATG
* *
2682590 TACA TACA TACC TACA TACA TACA CACA TACA TA
1 TACA TACA TACA TACA TACA TACA TACA TACA TA
2682624 TATATCTATA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.47, C:0.29, G:0.00, T:0.24
Consensus pattern (4 bp):
TACA
Found at i:2707316 original size:25 final size:25
Alignment explanation
Indices: 2707264--2707322 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 25
2707254 GTGGTCTCAA
**
2707264 CCACATATATCAACTTGTGACCTAG
1 CCACATATATCAACCCGTGACCTAG
* *
2707289 CCACATATATCAACCCGTGGCCTTG
1 CCACATATATCAACCCGTGACCTAG
*
2707314 CCACGTATA
1 CCACATATA
2707323 ATCACAGACT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.29, C:0.32, G:0.14, T:0.25
Consensus pattern (25 bp):
CCACATATATCAACCCGTGACCTAG
Found at i:2717449 original size:28 final size:28
Alignment explanation
Indices: 2717418--2717583 Score: 176
Period size: 29 Copynumber: 5.7 Consensus size: 28
2717408 ATATTTTATT
* * *
2717418 TTGTTTAAATTGAGACAAATATGATTTC
1 TTGTCTAAATTAAGACAAACATGATTTC
* *
2717446 TTGTCTAGATTAAGACAAAAAAAAT-ATTTTTC
1 TTGTCTAAATTAAGAC---AAACATGA--TTTC
2717478 TTGTCTTAAATTAAGACAAACAT-ATGTTC
1 TTGTC-TAAATTAAGACAAACATGAT-TTC
2717507 TTGTCTAAATTAAGACCAAACATGATTTC
1 TTGTCTAAATTAAGA-CAAACATGATTTC
2717536 TTGTCTAAATTAAGACATAACATG-TTTC
1 TTGTCTAAATTAAGACA-AACATGATTTC
2717564 TTTGTCTAAATTAAGACAAA
1 -TTGTCTAAATTAAGACAAA
2717584 TATGTTAAAA
Statistics
Matches: 121, Mismatches: 6, Indels: 22
0.81 0.04 0.15
Matches are distributed among these distances:
28 32 0.26
29 56 0.46
30 9 0.07
31 5 0.04
32 9 0.07
33 10 0.08
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.38
Consensus pattern (28 bp):
TTGTCTAAATTAAGACAAACATGATTTC
Found at i:2717487 original size:61 final size:61
Alignment explanation
Indices: 2717404--2717583 Score: 205
Period size: 61 Copynumber: 3.0 Consensus size: 61
2717394 TAATTAAGAG
* * * *
2717404 AAAAATATTTTATTTTGT-TTAAATTGAGACAAATATGATTTCTTGTCTAGATTAAGACAAA
1 AAAAATATTTT-TCTTGTCTTAAATTAAGACAAACATGATTTCTTGTCTAAATTAAGACAAA
*
2717465 AAAAATATTTTTCTTGTCTTAAATTAAGACAAACAT-ATGTTCTTGTCTAAATTAAGAC--C
1 AAAAATATTTTTCTTGTCTTAAATTAAGACAAACATGAT-TTCTTGTCTAAATTAAGACAAA
*
2717524 AAACATGA--TTTCTTGTC-TAAATTAAGACATAACATG-TTTCTTTGTCTAAATTAAGACAAA
1 AAAAAT-ATTTTTCTTGTCTTAAATTAAGACA-AACATGATTTC-TTGTCTAAATTAAGACAAA
2717584 TATGTTAAAA
Statistics
Matches: 104, Mismatches: 7, Indels: 17
0.81 0.05 0.13
Matches are distributed among these distances:
57 15 0.14
58 31 0.30
59 5 0.05
60 8 0.08
61 45 0.43
ACGTcount: A:0.40, C:0.11, G:0.10, T:0.39
Consensus pattern (61 bp):
AAAAATATTTTTCTTGTCTTAAATTAAGACAAACATGATTTCTTGTCTAAATTAAGACAAA
Found at i:2720569 original size:20 final size:20
Alignment explanation
Indices: 2720546--2720583 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
2720536 TGAAATTGTA
2720546 CAAATGTATCGATACATTCC
1 CAAATGTATCGATACATTCC
2720566 CAAATGTATCGATACATT
1 CAAATGTATCGATACATT
2720584 ACTGGGGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.21, G:0.11, T:0.32
Consensus pattern (20 bp):
CAAATGTATCGATACATTCC
Found at i:2721547 original size:9 final size:9
Alignment explanation
Indices: 2721533--2721580 Score: 53
Period size: 9 Copynumber: 5.2 Consensus size: 9
2721523 GAGTGGTGTT
2721533 ATAATTAAA
1 ATAATTAAA
*
2721542 ATAATTATA
1 ATAATTAAA
2721551 ATAATTAAA
1 ATAATTAAA
*
2721560 A-AAATATAA
1 ATAATTA-AA
2721569 ATATATTAAA
1 ATA-ATTAAA
2721579 AT
1 AT
2721581 TCATAGACTA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
8 4 0.12
9 20 0.62
10 5 0.16
11 3 0.09
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (9 bp):
ATAATTAAA
Found at i:2721556 original size:18 final size:19
Alignment explanation
Indices: 2721533--2721580 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
2721523 GAGTGGTGTT
*
2721533 ATAATTAAAATAATTAT-A
1 ATAATTAAAATAAATATAA
2721551 ATAATTAAAA-AAATATAA
1 ATAATTAAAATAAATATAA
2721569 ATATATTAAAAT
1 ATA-ATTAAAAT
2721581 TCATAGACTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 5 0.19
18 14 0.54
19 7 0.27
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
ATAATTAAAATAAATATAA
Found at i:2729159 original size:501 final size:504
Alignment explanation
Indices: 2728199--2729206 Score: 1799
Period size: 501 Copynumber: 2.0 Consensus size: 504
2728189 TATCATGTTT
*
2728199 TATGGCATACCCAAAAACACCGTGTTAGCCATCTGGTCATCTCTAGACCCATAGGGTGAAACTAA
1 TATGGCATACCCAAAAACACCCTGTTAGCCATCTGGTCATCTCTAGACCCATAGGGTGAAACTAA
*
2728264 AGTATGTCATTCTCCATATAAGATGACTTGGTGTTTCAAGTCCAAGGACTAGTTGCACGACTATC
66 AGTATGTCATTCTCCATATAAGATGACTTGGTGTTTCAAGTCCAAGGACTAGTTACACGACTATC
* *
2728329 ATATGTGAATATATTCCATAGACACTTGAGCGAAATACTAAATAGAATTCTCATAGCGGGTCATG
131 ATATGTGAATATATTCCATAAACACTTGAGCGAAACACTAAATAGAATTCTCATAGCGGGTCATG
* *
2728394 TTTAGTGAGCCTGTTCTTTAAAAGCATTTACATGTTATTCATAAATATCCCATATACTTCAATCT
196 TTTAGTGAGCCTATTCTTTAAAAGCACTTACATGTTATTCATAAATATCCCATATACTTCAATCT
2728459 ATGAGATTGATTGTTCACTTCCCAAGTAAAGATACTTAACATGTACCAGTCTTTGAGCATTGTCA
261 ATGAGATTGATTGTTCACTTCCCAAGTAAAGATACTTAACATGTACCAGTCTTTGAGCATTGTCA
*
2728524 ATGCTTTATCTTGACAATACAATGATCAAGAATAATTTTAGAAACTTGGCTTTGATGCATAGTGA
326 ATGCCTTATCTTGACAATACAATGATCAAGAATAATTTTAGAAACTTGGCTTTGATGCATAGTGA
*
2728589 TCTCATAATTGTAACAACATTACAATGCTCTTACAAGACTTTTATGTTCCATGAGCTTCATCTAA
391 TCTCATAATTGTAACAACATTACAATGCTCTTACAAGACTTTTATGTTCCATGAGCTTCATCCAA
2728654 TTAGTATTTAATAATCC-TTGATTATTGCATTAACATAAAGGGAAACCTC
456 TTAGTATTTAATAA-CCTTTGATTATTGCATTAACATAAAGGGAAACCTC
*
2728703 TATGGCATACCCAAAAACACCCTGTTAGGCATCTGGTCATCTCTAGACCCATAGGGTGAAACTAA
1 TATGGCATACCCAAAAACACCCTGTTAGCCATCTGGTCATCTCTAGACCCATAGGGTGAAACTAA
*
2728768 AGTATGTTATTCTCCATAT-A-A-GACTTGGTGTTTCAAGTCCAAGGACTAGTTACACGACTATC
66 AGTATGTCATTCTCCATATAAGATGACTTGGTGTTTCAAGTCCAAGGACTAGTTACACGACTATC
* * * *
2728830 ATATGTGAATTTATTTCATAAACGCTTGAGTGAAACACTAAATAGAATTCTCATAGCGGGTCATG
131 ATATGTGAATATATTCCATAAACACTTGAGCGAAACACTAAATAGAATTCTCATAGCGGGTCATG
*
2728895 TTTAGTGAGCTTATTCTTTAAAAGCACTTACATGTTATTCATAAATATCCCATATACTTCAATCT
196 TTTAGTGAGCCTATTCTTTAAAAGCACTTACATGTTATTCATAAATATCCCATATACTTCAATCT
*
2728960 ATGAGATTGATTGTTCACTTCCCAAGTAAGGATACTTAACATGTACCAGTCTTTGAGCATTGTCA
261 ATGAGATTGATTGTTCACTTCCCAAGTAAAGATACTTAACATGTACCAGTCTTTGAGCATTGTCA
*
2729025 ATGCCTTATCTTGACAATACAATGATCAAGAATAATTTTAGGAACTTGGCTTTGATGCATAGTGA
326 ATGCCTTATCTTGACAATACAATGATCAAGAATAATTTTAGAAACTTGGCTTTGATGCATAGTGA
* *
2729090 TCTCATAATTGTAACAACATTACAATGCTCTTACAAGACTTTTATGTTCCATGGGTTTCATCCAA
391 TCTCATAATTGTAACAACATTACAATGCTCTTACAAGACTTTTATGTTCCATGAGCTTCATCCAA
*
2729155 TTAGTATTTAATAACCTTTTATTATTGCATTAACATAAAGGGAAACCTC
456 TTAGTATTTAATAACCTTTGATTATTGCATTAACATAAAGGGAAACCTC
2729204 TAT
1 TAT
2729207 CATATATAGT
Statistics
Matches: 483, Mismatches: 20, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
500 2 0.00
501 398 0.82
502 1 0.00
503 1 0.00
504 81 0.17
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (504 bp):
TATGGCATACCCAAAAACACCCTGTTAGCCATCTGGTCATCTCTAGACCCATAGGGTGAAACTAA
AGTATGTCATTCTCCATATAAGATGACTTGGTGTTTCAAGTCCAAGGACTAGTTACACGACTATC
ATATGTGAATATATTCCATAAACACTTGAGCGAAACACTAAATAGAATTCTCATAGCGGGTCATG
TTTAGTGAGCCTATTCTTTAAAAGCACTTACATGTTATTCATAAATATCCCATATACTTCAATCT
ATGAGATTGATTGTTCACTTCCCAAGTAAAGATACTTAACATGTACCAGTCTTTGAGCATTGTCA
ATGCCTTATCTTGACAATACAATGATCAAGAATAATTTTAGAAACTTGGCTTTGATGCATAGTGA
TCTCATAATTGTAACAACATTACAATGCTCTTACAAGACTTTTATGTTCCATGAGCTTCATCCAA
TTAGTATTTAATAACCTTTGATTATTGCATTAACATAAAGGGAAACCTC
Found at i:2747222 original size:20 final size:20
Alignment explanation
Indices: 2747197--2747250 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
2747187 CATTATGAAC
2747197 ATGTATCGATACATGACCAT
1 ATGTATCGATACATGACCAT
2747217 ATGTATCGATACATGACCAT
1 ATGTATCGATACATGACCAT
*
2747237 ATGTATTGATACAT
1 ATGTATCGATACAT
2747251 CATAAACATG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACATGACCAT
Found at i:2771955 original size:19 final size:18
Alignment explanation
Indices: 2771921--2771960 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
2771911 CAAGGGGAAA
*
2771921 ATTTTATAATAAAATAAT
1 ATTTTATAAAAAAATAAT
2771939 ATTTTATTAAAAAAATAAT
1 ATTTTA-TAAAAAAATAAT
2771958 ATT
1 ATT
2771961 AAAATAATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
ATTTTATAAAAAAATAAT
Found at i:2773124 original size:13 final size:12
Alignment explanation
Indices: 2773102--2773157 Score: 53
Period size: 12 Copynumber: 4.7 Consensus size: 12
2773092 GAATCGGCTT
*
2773102 GGAAGCAAAGAGA
1 GGAAG-AAAGAAA
2773115 GGAAAGAAAGAAA
1 GG-AAGAAAGAAA
2773128 GGAAGAAAGAAA
1 GGAAGAAAGAAA
* *
2773140 GAAAG-GAGAAA
1 GGAAGAAAGAAA
2773151 -GAAGAAA
1 GGAAGAAA
2773158 AAGACAAGGA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
10 3 0.08
11 6 0.17
12 14 0.39
13 10 0.28
14 3 0.08
ACGTcount: A:0.64, C:0.02, G:0.34, T:0.00
Consensus pattern (12 bp):
GGAAGAAAGAAA
Found at i:2773125 original size:4 final size:4
Alignment explanation
Indices: 2773116--2773157 Score: 52
Period size: 4 Copynumber: 11.0 Consensus size: 4
2773106 GCAAAGAGAG
* *
2773116 GAAA GAAA GAAA GGAA GAAA GAAA GAAA G-GA GAAA G-AA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
2773158 AAGACAAGGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
3 5 0.16
4 27 0.84
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:2773133 original size:8 final size:8
Alignment explanation
Indices: 2773102--2773169 Score: 54
Period size: 8 Copynumber: 8.6 Consensus size: 8
2773092 GAATCGGCTT
2773102 GGAAGCAAA
1 GGAAG-AAA
*
2773111 GAGAGGAAA
1 G-GAAGAAA
*
2773120 GAAAGAAA
1 GGAAGAAA
2773128 GGAAGAAA
1 GGAAGAAA
*
2773136 GAAAGAAA
1 GGAAGAAA
2773144 GG-AGAAA
1 GGAAGAAA
2773151 -GAAGAAA
1 GGAAGAAA
2773158 --AAGACAA
1 GGAAGA-AA
2773165 GGAAG
1 GGAAG
2773170 GTTCGGCCTA
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
6 5 0.10
7 12 0.25
8 20 0.42
9 8 0.17
10 3 0.06
ACGTcount: A:0.63, C:0.03, G:0.34, T:0.00
Consensus pattern (8 bp):
GGAAGAAA
Found at i:2773160 original size:16 final size:16
Alignment explanation
Indices: 2773116--2773157 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
2773106 GCAAAGAGAG
2773116 GAAAGAAAGAAAGGAA
1 GAAAGAAAGAAAGGAA
2773132 GAAAGAAAGAAAGG-A
1 GAAAGAAAGAAAGGAA
2773147 GAAAG-AAGAAA
1 GAAAGAAAGAAA
2773158 AAGACAAGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.23
15 6 0.23
16 14 0.54
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (16 bp):
GAAAGAAAGAAAGGAA
Found at i:2777450 original size:20 final size:20
Alignment explanation
Indices: 2777425--2777463 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
2777415 TTGCAACGTG
2777425 AAAAAGGTTGAATTTTGCTA
1 AAAAAGGTTGAATTTTGCTA
2777445 AAAAAGGTTGAATTTTGCT
1 AAAAAGGTTGAATTTTGCT
2777464 CATCGAGGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.05, G:0.21, T:0.36
Consensus pattern (20 bp):
AAAAAGGTTGAATTTTGCTA
Found at i:2781246 original size:27 final size:27
Alignment explanation
Indices: 2781177--2781247 Score: 88
Period size: 27 Copynumber: 2.6 Consensus size: 27
2781167 CCTAGTAGAA
**
2781177 CATGCCTCGATGTGTAATAAAGTGATT
1 CATGCCTTAATGTGTAATAAAGTGATT
* **
2781204 TATGCCTTAACATGTAATAAAGTGATT
1 CATGCCTTAATGTGTAATAAAGTGATT
*
2781231 CATGCCTTTATGTGTAA
1 CATGCCTTAATGTGTAA
2781248 CATTAGTAAG
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.37
Consensus pattern (27 bp):
CATGCCTTAATGTGTAATAAAGTGATT
Found at i:2781401 original size:34 final size:34
Alignment explanation
Indices: 2781352--2781440 Score: 99
Period size: 34 Copynumber: 2.6 Consensus size: 34
2781342 ACATCTTTTA
* *
2781352 CTTTGGCTTTGGCGTGTAACA-TCGGATGGTGAAG
1 CTTTGGCTTTAGCGTGTAACATTCGG-TGCTGAAG
* * * *
2781386 CTTTGGCCTTAGCGTGTAATATTTGGTGCTGAAT
1 CTTTGGCTTTAGCGTGTAACATTCGGTGCTGAAG
*
2781420 CTTTGACTTTAGCGTGTAACA
1 CTTTGGCTTTAGCGTGTAACA
2781441 GTTGTTGTTG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
34 42 0.93
35 3 0.07
ACGTcount: A:0.19, C:0.16, G:0.28, T:0.37
Consensus pattern (34 bp):
CTTTGGCTTTAGCGTGTAACATTCGGTGCTGAAG
Found at i:2789270 original size:18 final size:18
Alignment explanation
Indices: 2789247--2789285 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
2789237 CAAGTTGAAA
2789247 ATTTTA-AAATAAAATAAT
1 ATTTTATAAATAAAA-AAT
*
2789265 ATTTTATTAATAAAAAAT
1 ATTTTATAAATAAAAAAT
2789283 ATT
1 ATT
2789286 AAAATATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATTTTATAAATAAAAAAT
Found at i:2792193 original size:4 final size:4
Alignment explanation
Indices: 2792184--2792214 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
2792174 AAGAGAAGGG
*
2792184 AAGA AAGA AAGA AAGA AAGA AAGG AAGA AAG
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAG
2792215 GGGGACGAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:2792215 original size:8 final size:8
Alignment explanation
Indices: 2792177--2792215 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
2792167 AAGTGAGAAG
*
2792177 AGAAGGGA
1 AGAAAGGA
*
2792185 AGAAAGAA
1 AGAAAGGA
*
2792193 AGAAAGAA
1 AGAAAGGA
2792201 AGAAAGGA
1 AGAAAGGA
2792209 AGAAAGG
1 AGAAAGG
2792216 GGGACGAAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (8 bp):
AGAAAGGA
Found at i:2814135 original size:14 final size:14
Alignment explanation
Indices: 2814116--2814153 Score: 76
Period size: 14 Copynumber: 2.7 Consensus size: 14
2814106 GGATATTGCT
2814116 TGTTGATGATGATA
1 TGTTGATGATGATA
2814130 TGTTGATGATGATA
1 TGTTGATGATGATA
2814144 TGTTGATGAT
1 TGTTGATGAT
2814154 AGTTGGTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.26, C:0.00, G:0.29, T:0.45
Consensus pattern (14 bp):
TGTTGATGATGATA
Found at i:2814933 original size:74 final size:74
Alignment explanation
Indices: 2814720--2814914 Score: 284
Period size: 74 Copynumber: 2.6 Consensus size: 74
2814710 GTAGATTGTG
* * * * *
2814720 AGACAAAGAGAACTTAATCAACTAAGAAGCATGGTTAGTCAATTAAGAGCTCACTGCTAGAGACT
1 AGACAGAGAGAACTTAATCAACTAAGAAGTATGGTTAGTCAACTAAGAGCTCACTGCTAGAAAAT
2814785 TCAATTACA
66 TCAATTACA
* *
2814794 AGACAGAGAGAACTTAATCAACTAAGAAGTATGATTAGTCAACTAAGAGCTCACTGCCAGAAAAT
1 AGACAGAGAGAACTTAATCAACTAAGAAGTATGGTTAGTCAACTAAGAGCTCACTGCTAGAAAAT
2814859 TCAATTACA
66 TCAATTACA
* * *
2814868 AGATAGTGA-AGACTTAATCGACTAAGAAGTATGGTTAGTCAACTAAG
1 AGACAGAGAGA-ACTTAATCAACTAAGAAGTATGGTTAGTCAACTAAG
2814915 GGCACTCTAT
Statistics
Matches: 109, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
73 1 0.01
74 108 0.99
ACGTcount: A:0.43, C:0.16, G:0.18, T:0.23
Consensus pattern (74 bp):
AGACAGAGAGAACTTAATCAACTAAGAAGTATGGTTAGTCAACTAAGAGCTCACTGCTAGAAAAT
TCAATTACA
Found at i:2816384 original size:15 final size:15
Alignment explanation
Indices: 2816364--2816397 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
2816354 CATGGAGTAG
2816364 AAATTATAATTAAAT
1 AAATTATAATTAAAT
2816379 AAATTATAATTAAAT
1 AAATTATAATTAAAT
2816394 AAAT
1 AAAT
2816398 AATCCTAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AAATTATAATTAAAT
Found at i:2816785 original size:190 final size:193
Alignment explanation
Indices: 2816406--2816790 Score: 695
Period size: 190 Copynumber: 2.0 Consensus size: 193
2816396 ATAATCCTAA
2816406 TTTATTGATTGTAATTGTGAATGGTAAATATTAATTTAATTTTCATTAATTAAATTAATAAAATG
1 TTTATTGATTGTAATTGTGAATGGTAAATATTAATTTAATTTTCATTAATTAAATTAATAAAATG
*
2816471 GAGTTTTAAAAGAGAAATAACTCTCTCTCTCTCATAAAAATTAAATGAAGGCCAAAAATTAAATT
66 GAGTTTTAAAAGAGAAATAAC-CTCTCTCTCTCATAAAAATTAAATAAAGGCCAAAAATTAAATT
* **
2816536 TATAAATATGTAATTCAACAAGCCCTAATGACTAAGGAAGAGAGGCCCTAGTTGAACCTCTTAC
130 TATAAATATGTAATTCAACAAGCCCTAATGACCAAGGAAGAGAGGCCCTAGCCGAACCTCTTAC
2816600 TTTATTGATTGTAATTGTGAATGGTAAATATTAATTTAA-TTTCATTAATTAAATTAATAAAATG
1 TTTATTGATTGTAATTGTGAATGGTAAATATTAATTTAATTTTCATTAATTAAATTAATAAAATG
*
2816664 GAGTTTTAAGAGAGAAATAA-CTCTCTCTCTCATAAAAATTAAATAAAGGCCAAAAATTAAATTT
66 GAGTTTTAAAAGAGAAATAACCTCTCTCTCTCATAAAAATTAAATAAAGGCCAAAAATTAAATTT
2816728 -TAAATATGTAATTCAACAAGCCCTAATGACCAAGGAAGAGAGGCCCTAGCCGAACCTCTTAC
131 ATAAATATGTAATTCAACAAGCCCTAATGACCAAGGAAGAGAGGCCCTAGCCGAACCTCTTAC
2816790 T
1 T
2816791 CCTCTATCTC
Statistics
Matches: 186, Mismatches: 5, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
190 60 0.32
191 43 0.23
193 44 0.24
194 39 0.21
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.33
Consensus pattern (193 bp):
TTTATTGATTGTAATTGTGAATGGTAAATATTAATTTAATTTTCATTAATTAAATTAATAAAATG
GAGTTTTAAAAGAGAAATAACCTCTCTCTCTCATAAAAATTAAATAAAGGCCAAAAATTAAATTT
ATAAATATGTAATTCAACAAGCCCTAATGACCAAGGAAGAGAGGCCCTAGCCGAACCTCTTAC
Found at i:2817820 original size:14 final size:14
Alignment explanation
Indices: 2817790--2817841 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
2817780 TTTTATGCCT
* *
2817790 AAAACCCTAACCAC
1 AAAACCCAAAACAC
*
2817804 AAAACCCAAAACTC
1 AAAACCCAAAACAC
* *
2817818 AAAAGCTAAAACAC
1 AAAACCCAAAACAC
*
2817832 AAAGCCCAAA
1 AAAACCCAAA
2817842 CCCCAAAAGT
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.58, C:0.33, G:0.04, T:0.06
Consensus pattern (14 bp):
AAAACCCAAAACAC
Found at i:2817956 original size:16 final size:16
Alignment explanation
Indices: 2817934--2817973 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 16
2817924 AATAATTATT
2817934 ATTATTTTT-TAAAAA
1 ATTATTTTTCTAAAAA
2817949 ATTTATTTTTTCTAAAAA
1 A-TTA-TTTTTCTAAAAA
2817967 ATTATTT
1 ATTATTT
2817974 ATATTTTTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 1 0.05
16 6 0.27
17 8 0.36
18 7 0.32
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (16 bp):
ATTATTTTTCTAAAAA
Found at i:2817964 original size:18 final size:17
Alignment explanation
Indices: 2817931--2817973 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 17
2817921 ATTAATAATT
*
2817931 ATTATTATTTTTTAAAAA
1 ATTATT-TTTTCTAAAAA
2817949 ATTTATTTTTTCTAAAAA
1 A-TTATTTTTTCTAAAAA
2817967 ATTATTT
1 ATTATTT
2817974 ATATTTTTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 6 0.26
18 12 0.52
19 5 0.22
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (17 bp):
ATTATTTTTTCTAAAAA
Found at i:2820266 original size:54 final size:54
Alignment explanation
Indices: 2820179--2820288 Score: 202
Period size: 54 Copynumber: 2.0 Consensus size: 54
2820169 CTGATCAAGA
*
2820179 AAGGAATCATCACTCTAAGTGATTCAAACGGAAATATCTCATTAGTTTTTGGTT
1 AAGGAATCATCACTCTAAGTGATTCAAAAGGAAATATCTCATTAGTTTTTGGTT
*
2820233 AAGGAATCATCATTCTAAGTGATTCAAAAGGAAATATCTCATTAGTTTTTGGTT
1 AAGGAATCATCACTCTAAGTGATTCAAAAGGAAATATCTCATTAGTTTTTGGTT
2820287 AA
1 AA
2820289 TATTAGCTTA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (54 bp):
AAGGAATCATCACTCTAAGTGATTCAAAAGGAAATATCTCATTAGTTTTTGGTT
Found at i:2821713 original size:28 final size:28
Alignment explanation
Indices: 2821643--2821719 Score: 93
Period size: 28 Copynumber: 2.8 Consensus size: 28
2821633 TTTCACCAAG
* * *
2821643 CTTTTACTAGATAAGCTTCTAACCTAAG
1 CTTTTACAAGATGAGCTTCTAACCTAAA
* *
2821671 CTTTTATAA-AGTGAGTTTCTAACCTAAA
1 CTTTTACAAGA-TGAGCTTCTAACCTAAA
2821699 CTTTTACAAGATGAGCTTCTA
1 CTTTTACAAGATGAGCTTCTA
2821720 GCCCAAGCTC
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
27 1 0.03
28 38 0.95
29 1 0.03
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.38
Consensus pattern (28 bp):
CTTTTACAAGATGAGCTTCTAACCTAAA
Found at i:2824512 original size:19 final size:19
Alignment explanation
Indices: 2824484--2824527 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
2824474 ATTCGAAGAT
*
2824484 GAAGACTTAAAGGTGCCAC
1 GAAGATTTAAAGGTGCCAC
2824503 GAAGATTTAAAGGTGCCAC
1 GAAGATTTAAAGGTGCCAC
2824522 GAAGAT
1 GAAGAT
2824528 ACTAGGAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.39, C:0.16, G:0.27, T:0.18
Consensus pattern (19 bp):
GAAGATTTAAAGGTGCCAC
Found at i:2826441 original size:23 final size:23
Alignment explanation
Indices: 2826369--2826449 Score: 72
Period size: 23 Copynumber: 3.5 Consensus size: 23
2826359 TCTATGGAGG
* * *
2826369 GAATATGTGAGATGCCAAGGTGA
1 GAATATGTGACATGACATGGTGA
** * * *
2826392 GAATATGTGACATGAGTTAGAGG
1 GAATATGTGACATGACATGGTGA
*
2826415 GAATATGTGATATGACATGGTGA
1 GAATATGTGACATGACATGGTGA
*
2826438 GAATGTGTGACA
1 GAATATGTGACA
2826450 CACTAGTGTC
Statistics
Matches: 42, Mismatches: 16, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.35, C:0.06, G:0.33, T:0.26
Consensus pattern (23 bp):
GAATATGTGACATGACATGGTGA
Found at i:2826781 original size:47 final size:47
Alignment explanation
Indices: 2826671--2826784 Score: 140
Period size: 47 Copynumber: 2.4 Consensus size: 47
2826661 TGTGAGACGG
* *
2826671 CTGTGACACGCCAAGGTTTAGAGTTTGTGACACGCCATAGAGGGAAT
1 CTGTGACACGCCAGGGTTTAGAGTTTGTGACACACCATAGAGGGAAT
* * * * *
2826718 CTATGACATGCTAGGGTTTAGAGTTTGTGACATATCAT-GAAGGGAAT
1 CTGTGACACGCCAGGGTTTAGAGTTTGTGACACACCATAG-AGGGAAT
*
2826765 CTGTGACACACCAGGGTTTA
1 CTGTGACACGCCAGGGTTTA
2826785 AAGTGTGTCA
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
46 1 0.02
47 54 0.98
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.27
Consensus pattern (47 bp):
CTGTGACACGCCAGGGTTTAGAGTTTGTGACACACCATAGAGGGAAT
Found at i:2827466 original size:31 final size:31
Alignment explanation
Indices: 2827431--2827602 Score: 220
Period size: 31 Copynumber: 5.6 Consensus size: 31
2827421 GTGTCAGCGT
2827431 TGGCGTGTAACAACATTTTACTTGATATGCA
1 TGGCGTGTAACAACATTTTACTTGATATGCA
* *
2827462 TGGCGTGTAACAACATTTTTCTCGATATGCA
1 TGGCGTGTAACAACATTTTACTTGATATGCA
* * * *
2827493 TAGCATGTAACAACAATTT-CTTGATATACA
1 TGGCGTGTAACAACATTTTACTTGATATGCA
** *
2827523 TGGCACGTAACAACATTTTACTTGATATGAA
1 TGGCGTGTAACAACATTTTACTTGATATGCA
* *
2827554 TGGTGTGTAACAACATTTTAATTGATATGCA
1 TGGCGTGTAACAACATTTTACTTGATATGCA
* *
2827585 TGGTGTGTAATAACATTT
1 TGGCGTGTAACAACATTT
2827603 ATTTCTTTCT
Statistics
Matches: 122, Mismatches: 18, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
30 25 0.20
31 97 0.80
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (31 bp):
TGGCGTGTAACAACATTTTACTTGATATGCA
Found at i:2827525 original size:61 final size:62
Alignment explanation
Indices: 2827436--2827602 Score: 210
Period size: 61 Copynumber: 2.7 Consensus size: 62
2827426 AGCGTTGGCG
* *
2827436 TGTAACAACATTTTACTTGATATGCATGGCGTGTAACAACATTTTTCTCGATATGCATAGCA
1 TGTAACAACATTTTACTTGATATGCATGGCGTGTAACAACATTTTACTCGATATGAATAGCA
* * ** * * **
2827498 TGTAACAACAATTT-CTTGATATACATGGCACGTAACAACATTTTACTTGATATGAATGGTG
1 TGTAACAACATTTTACTTGATATGCATGGCGTGTAACAACATTTTACTCGATATGAATAGCA
* * *
2827559 TGTAACAACATTTTAATTGATATGCATGGTGTGTAATAACATTT
1 TGTAACAACATTTTACTTGATATGCATGGCGTGTAACAACATTT
2827603 ATTTCTTTCT
Statistics
Matches: 87, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
61 51 0.59
62 36 0.41
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (62 bp):
TGTAACAACATTTTACTTGATATGCATGGCGTGTAACAACATTTTACTCGATATGAATAGCA
Found at i:2831296 original size:31 final size:31
Alignment explanation
Indices: 2831132--2831576 Score: 121
Period size: 31 Copynumber: 14.3 Consensus size: 31
2831122 ACATAACAAG
* *
2831132 TCAGCGTGTCACCCCATAAATATGCTTTCAC
1 TCAGCGTGTCACCCCATAAATCTGCTTCCAC
** * * *
2831163 TCAATGTGCCACGCCC-TAAATCTAG-TACCAG
1 TCAGCGTGTCAC-CCCATAAATCT-GCTTCCAC
* * * * *
2831194 TCAGCATGTCACGCCATATATCTGCTACTAC
1 TCAGCGTGTCACCCCATAAATCTGCTTCCAC
* * * * * * **
2831225 TTAACGTGTGATGCCAATAAATTTGCCACCAC
1 TCAGCGTGTCA-CCCCATAAATCTGCTTCCAC
* * *
2831257 TAAACGTGTCACCCCATAAATCTGCTTTCAC
1 TCAGCGTGTCACCCCATAAATCTGCTTCCAC
** * * * *
2831288 TCAGCGTGTCA-TGCACTAAATCTGGTACTAG
1 TCAGCGTGTCACCCCA-TAAATCTGCTTCCAC
* * * * * *
2831319 TTAGCGTGTCACACCATATATCTACTACTAC
1 TCAGCGTGTCACCCCATAAATCTGCTTCCAC
* * * **
2831350 TCAGCATGTCATCCCATAAATCTACCACCAC
1 TCAGCGTGTCACCCCATAAATCTGCTTCCAC
* * * * ** *
2831381 TCAACGTGTCACCCTATAAATATACTTTTAA
1 TCAGCGTGTCACCCCATAAATCTGCTTCCAC
** * * *
2831412 TCAATGTGTCACGCCTTAAATCTAG-TACCAC
1 TCAGCGTGTCACCCCATAAATCT-GCTTCCAC
* ** * * ***
2831443 TCAACGTGTCATGCCATATATCTCCTAGTAC
1 TCAGCGTGTCACCCCATAAATCTGCTTCCAC
* * * *
2831474 TCAGCATGTCACGCCATAAATCT-ATCACCAC
1 TCAGCGTGTCACCCCATAAATCTGCT-TCCAC
* * *** * *
2831505 TCAACATGTCATGGCACAAATCTG-TCACCAC
1 TCAGCGTGTCACCCCATAAATCTGCT-TCCAC
*
2831536 TCAGCGTGTCACCCCATAAATCTGCTTTCAC
1 TCAGCGTGTCACCCCATAAATCTGCTTCCAC
2831567 -CTAGCGTGTC
1 TC-AGCGTGTC
2831577 GTGCCCTAAA
Statistics
Matches: 298, Mismatches: 103, Indels: 26
0.70 0.24 0.06
Matches are distributed among these distances:
30 7 0.02
31 262 0.88
32 29 0.10
ACGTcount: A:0.29, C:0.31, G:0.13, T:0.28
Consensus pattern (31 bp):
TCAGCGTGTCACCCCATAAATCTGCTTCCAC
Found at i:2831389 original size:62 final size:61
Alignment explanation
Indices: 2831172--2831515 Score: 199
Period size: 62 Copynumber: 5.5 Consensus size: 61
2831162 CTCAATGTGC
* ** * * * * * * *
2831172 CACGCCCTAAATCTAGTACCAGTCAGCATGTCACGCCATATATCTGCTACTACTTAACGTGT
1 CACGCCATAAATCTACCACCACTCAACGTGTCAC-CCATATATCTACTACTACTCAGCATGT
* * * * * * * * *
2831234 GATGCCAATAAATTTGCCACCACTAAACGTGTCACCCCATAAATCTGCT-TTCACTCAGCGTGT
1 CACGCC-ATAAATCTACCACCACTCAACGTGTCA-CCCATATATCTACTACT-ACTCAGCATGT
* *** * * * *
2831297 CATG-CACTAAATCTGGTACTAGTTAGCGTGTCACACCATATATCTACTACTACTCAGCATGT
1 CACGCCA-TAAATCTACCACCACTCAACGTGTCAC-CCATATATCTACTACTACTCAGCATGT
* * ** * ***
2831359 CATC-CCATAAATCTACCACCACTCAACGTGTCACCCTATAAATATACTTTTAATCAATGTGT
1 CA-CGCCATAAATCTACCACCACTCAACGTGTCACCC-ATATATCTACTACTACTCAGCATGT
* ** * * *
2831421 CACGCCTTAAATCTAGTACCACTCAACGTGTCATGCCATATATCTCCTAGTACTCAGCATGT
1 CACGCCATAAATCTACCACCACTCAACGTGTCA-CCCATATATCTACTACTACTCAGCATGT
* *
2831483 CACGCCATAAATCTATCACCACTCAACATGTCA
1 CACGCCATAAATCTACCACCACTCAACGTGTCA
2831516 TGGCACAAAT
Statistics
Matches: 211, Mismatches: 60, Indels: 22
0.72 0.20 0.08
Matches are distributed among these distances:
61 5 0.02
62 158 0.75
63 47 0.22
64 1 0.00
ACGTcount: A:0.30, C:0.30, G:0.12, T:0.28
Consensus pattern (61 bp):
CACGCCATAAATCTACCACCACTCAACGTGTCACCCATATATCTACTACTACTCAGCATGT
Found at i:2831421 original size:124 final size:123
Alignment explanation
Indices: 2831136--2831515 Score: 438
Period size: 124 Copynumber: 3.1 Consensus size: 123
2831126 AACAAGTCAG
* *
2831136 CGTGTCACCCCATAAATATGCTTTCACTCAATGTGCCACGCCCTAAATCTAGTACCAGTCAGCAT
1 CGTGTCACCCCATAAATATGCTTTCACTCAATGTGTCACG-CCTAAATCTAGTACCAGTCAGCGT
* * * * * * * * *
2831201 GTCACGCCATATATCTGCTACTACTTAACGTGTGATGCCAATAAATTTGCCACCACTAAA
65 GTCACGCCATATATCTACTACTACTCAGCATGTCAT-CCCATAAATCTACCACCACTCAA
* ** * * * *
2831261 CGTGTCACCCCATAAATCTGCTTTCACTCAGCGTGTCATGCACTAAATCTGGTACTAGTTAGCGT
1 CGTGTCACCCCATAAATATGCTTTCACTCAATGTGTCACGC-CTAAATCTAGTACCAGTCAGCGT
*
2831326 GTCACACCATATATCTACTACTACTCAGCATGTCATCCCATAAATCTACCACCACTCAA
65 GTCACGCCATATATCTACTACTACTCAGCATGTCATCCCATAAATCTACCACCACTCAA
* * * * * *
2831385 CGTGTCACCCTATAAATATACTTTTAATCAATGTGTCACGCCTTAAATCTAGTACCACTCAACGT
1 CGTGTCACCCCATAAATATGCTTTCACTCAATGTGTCACGCC-TAAATCTAGTACCAGTCAGCGT
* * * *
2831450 GTCATGCCATATATCTCCTAGTACTCAGCATGTCA-CGCCATAAATCTATCACCACTCAA
65 GTCACGCCATATATCTACTACTACTCAGCATGTCATC-CCATAAATCTACCACCACTCAA
*
2831509 CATGTCA
1 CGTGTCA
2831516 TGGCACAAAT
Statistics
Matches: 214, Mismatches: 38, Indels: 7
0.83 0.15 0.03
Matches are distributed among these distances:
123 2 0.01
124 128 0.60
125 84 0.39
ACGTcount: A:0.29, C:0.30, G:0.12, T:0.28
Consensus pattern (123 bp):
CGTGTCACCCCATAAATATGCTTTCACTCAATGTGTCACGCCTAAATCTAGTACCAGTCAGCGTG
TCACGCCATATATCTACTACTACTCAGCATGTCATCCCATAAATCTACCACCACTCAA
Found at i:2831516 original size:62 final size:62
Alignment explanation
Indices: 2831323--2831558 Score: 201
Period size: 62 Copynumber: 3.8 Consensus size: 62
2831313 TACTAGTTAG
** *
2831323 CGTGTCACACCATATATCTACTACTACTCAGCATGTCATC-CCATAAATCTACCACCACTCAA
1 CGTGTCATGCCATATATCTACTACTACTCAGCATGTCA-CGCCATAAATCTATCACCACTCAA
* * * ** * *** *
2831385 CGTGTCA-CCCTATAAATATACTTTTAATCAATGTGTCACGCCTTAAATCTAGT-ACCACTCAA
1 CGTGTCATGCC-ATATATCTACTACTACTCAGCATGTCACGCCATAAATCTA-TCACCACTCAA
* *
2831447 CGTGTCATGCCATATATCTCCTAGTACTCAGCATGTCACGCCATAAATCTATCACCACTCAA
1 CGTGTCATGCCATATATCTACTACTACTCAGCATGTCACGCCATAAATCTATCACCACTCAA
* * * * * * * *
2831509 CATGTCATGGCACAAATCT-GTCACCACTCAGCGTGTCACCCCATAAATCT
1 CGTGTCATGCCATATATCTACT-ACTACTCAGCATGTCACGCCATAAATCT
2831559 GCTTTCACCT
Statistics
Matches: 137, Mismatches: 31, Indels: 12
0.76 0.17 0.07
Matches are distributed among these distances:
61 5 0.04
62 130 0.95
63 2 0.01
ACGTcount: A:0.31, C:0.32, G:0.10, T:0.28
Consensus pattern (62 bp):
CGTGTCATGCCATATATCTACTACTACTCAGCATGTCACGCCATAAATCTATCACCACTCAA
Found at i:2833989 original size:21 final size:21
Alignment explanation
Indices: 2833963--2834007 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
2833953 TATCAAAATA
*
2833963 ATCTTCTTTTAAACCTTTTTC
1 ATCTTCATTTAAACCTTTTTC
*
2833984 ATCTTCATTTAAACGTTTTTC
1 ATCTTCATTTAAACCTTTTTC
2834005 ATC
1 ATC
2834008 CCCAACATCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.22, C:0.22, G:0.02, T:0.53
Consensus pattern (21 bp):
ATCTTCATTTAAACCTTTTTC
Found at i:2839525 original size:23 final size:23
Alignment explanation
Indices: 2839495--2839616 Score: 85
Period size: 23 Copynumber: 5.4 Consensus size: 23
2839485 TCAGTCATGT
2839495 TGTTACATGCCATTTTTCAAAAA
1 TGTTACATGCCATTTTTCAAAAA
*
2839518 TGTTACATGCCATGTTT-AAAAA
1 TGTTACATGCCATTTTTCAAAAA
* * * *
2839540 GTGATACACGCCA-TGTGCAAAAA
1 -TGTTACATGCCATTTTTCAAAAA
**
2839563 TGTTACA--CACAAGTTT-AAAAA
1 TGTTACATGC-CATTTTTCAAAAA
** *
2839584 TTGTTACACACC-TTATTCAAAAA
1 -TGTTACATGCCATTTTTCAAAAA
2839607 TGTTACATGC
1 TGTTACATGC
2839617 AAGTTCAAAA
Statistics
Matches: 76, Mismatches: 15, Indels: 17
0.70 0.14 0.16
Matches are distributed among these distances:
20 1 0.01
21 7 0.09
22 30 0.39
23 37 0.49
24 1 0.01
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (23 bp):
TGTTACATGCCATTTTTCAAAAA
Done.