Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold8
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: 6381039
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 22487 characters in sequence are not A, C, G, or T
File 17 of 33
Found at i:2329250 original size:9 final size:9
Alignment explanation
Indices: 2329238--2329271 Score: 61
Period size: 9 Copynumber: 3.9 Consensus size: 9
2329228 AAAAATAGAA
2329238 AGAAAAAAT
1 AGAAAAAAT
2329247 AGAAAAAAT
1 AGAAAAAAT
2329256 AG-AAAAAT
1 AGAAAAAAT
2329264 AGAAAAAA
1 AGAAAAAA
2329272 ATTATAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 8 0.33
9 16 0.67
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.09
Consensus pattern (9 bp):
AGAAAAAAT
Found at i:2329253 original size:22 final size:21
Alignment explanation
Indices: 2329209--2329260 Score: 79
Period size: 22 Copynumber: 2.5 Consensus size: 21
2329199 TTACGTGATG
*
2329209 AAAA-AGAAAGAAAGAAAGAA
1 AAAATAGAAAGAAAAAAAGAA
2329229 AAAATAGAAAGAAAAAATAGAA
1 AAAATAGAAAGAAAAAA-AGAA
2329251 AAAATAGAAA
1 AAAATAGAAA
2329261 AATAGAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 4 0.14
21 11 0.38
22 14 0.48
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (21 bp):
AAAATAGAAAGAAAAAAAGAA
Found at i:2329261 original size:8 final size:8
Alignment explanation
Indices: 2329241--2329270 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
2329231 AATAGAAAGA
2329241 AAAAATAG
1 AAAAATAG
2329249 AAAAAATAG
1 -AAAAATAG
2329258 AAAAATAG
1 AAAAATAG
2329266 AAAAA
1 AAAAA
2329271 AATTATAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.80, C:0.00, G:0.10, T:0.10
Consensus pattern (8 bp):
AAAAATAG
Found at i:2329366 original size:27 final size:27
Alignment explanation
Indices: 2329339--2329392 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
2329329 TTTTGACATA
*
2329339 TTAATA-ATTTATTTTATTTTATGTATAT
1 TTAATATATTTA--TTATTTTATATATAT
*
2329367 TTTATATATTTATTATTTTATATATA
1 TTAATATATTTATTATTTTATATATA
2329393 AGAGAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 13 0.57
28 5 0.22
29 5 0.22
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (27 bp):
TTAATATATTTATTATTTTATATATAT
Found at i:2329460 original size:19 final size:18
Alignment explanation
Indices: 2329436--2329496 Score: 68
Period size: 19 Copynumber: 3.2 Consensus size: 18
2329426 ATTTAAAATA
2329436 TTATAAATTTATGTCATAT
1 TTATAAATTT-TGTCATAT
* *
2329455 TTATAAATATTTTTTATAT
1 TTATAAAT-TTTGTCATAT
*
2329474 TTATATATTTTAGTCATAT
1 TTATAAATTTT-GTCATAT
2329493 TTAT
1 TTAT
2329497 TTTTTATATT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
18 3 0.09
19 30 0.86
20 2 0.06
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.59
Consensus pattern (18 bp):
TTATAAATTTTGTCATAT
Found at i:2331356 original size:7 final size:7
Alignment explanation
Indices: 2331344--2331375 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
2331334 TGGTAGTAAG
2331344 AATAAAT
1 AATAAAT
2331351 AATAAAT
1 AATAAAT
2331358 AATAAAT
1 AATAAAT
2331365 AAT-AAT
1 AATAAAT
2331371 AATAA
1 AATAA
2331376 TAAAAAGAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
AATAAAT
Found at i:2336805 original size:26 final size:25
Alignment explanation
Indices: 2336754--2336809 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 25
2336744 CTTAGTTAAA
* *
2336754 AAATTTAATTTTTAGATTTGATTTT
1 AAATTTAATTTTTAGATTTAAATTT
*
2336779 AAATTTAATTATTTATATTTAAATTT
1 AAATTTAATT-TTTAGATTTAAATTT
2336805 AAATT
1 AAATT
2336810 AAAAATAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 10 0.37
26 17 0.63
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (25 bp):
AAATTTAATTTTTAGATTTAAATTT
Found at i:2341113 original size:15 final size:16
Alignment explanation
Indices: 2341084--2341117 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
2341074 TCATATTATA
2341084 AAAAAATTTAAAAAAT
1 AAAAAATTTAAAAAAT
*
2341100 AAAAAA-TTATAAAAT
1 AAAAAATTTAAAAAAT
2341115 AAA
1 AAA
2341118 TTTGTAATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (16 bp):
AAAAAATTTAAAAAAT
Found at i:2341738 original size:29 final size:29
Alignment explanation
Indices: 2341701--2341764 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
2341691 AAAAATATTT
*
2341701 ATTTAAATTATAAAAATTAAAATTTAATAA
1 ATTT-AATTAGAAAAATTAAAATTTAATAA
** *
2341731 ATTTAATTAGAAAAATTATGATTTTATAA
1 ATTTAATTAGAAAAATTAAAATTTAATAA
2341760 ATTTA
1 ATTTA
2341765 TGAACTAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 26 0.87
30 4 0.13
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (29 bp):
ATTTAATTAGAAAAATTAAAATTTAATAA
Found at i:2342982 original size:30 final size:30
Alignment explanation
Indices: 2342915--2342983 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
2342905 AAATTTAATT
*
2342915 TATATAAATTTATCAAATAATTTTATTAAA
1 TATATAAATTTATCAAATAATTATATTAAA
* *
2342945 TAAATAAATTTAATACTAATAATTATA-T-AA
1 TATATAAATTT-AT-CAAATAATTATATTAAA
2342975 TATATAAAT
1 TATATAAAT
2342984 AAAATATTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
30 20 0.61
31 3 0.09
32 10 0.30
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (30 bp):
TATATAAATTTATCAAATAATTATATTAAA
Found at i:2343580 original size:29 final size:28
Alignment explanation
Indices: 2343547--2343601 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
2343537 ATAACAAAGG
*
2343547 TAATTAATTAATATATTTTAATTTTAATT
1 TAATTAATTAATATA-ATTAATTTTAATT
*
2343576 TAATTAATTTATATAATTAATTTTAA
1 TAATTAATTAATATAATTAATTTTAA
2343602 AAAATAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 10 0.42
29 14 0.58
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (28 bp):
TAATTAATTAATATAATTAATTTTAATT
Found at i:2343594 original size:13 final size:13
Alignment explanation
Indices: 2343547--2343598 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
2343537 ATAACAAAGG
*
2343547 TAATTAATTAATA
1 TAATTAATTTATA
* *
2343560 TATTTTAATTTTAATT
1 TA-ATTAA-TTT-ATA
2343576 TAATTAATTTATA
1 TAATTAATTTATA
2343589 TAATTAATTT
1 TAATTAATTT
2343599 TAAAAAATAA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
13 14 0.45
14 7 0.23
15 6 0.19
16 4 0.13
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
TAATTAATTTATA
Found at i:2343645 original size:16 final size:17
Alignment explanation
Indices: 2343605--2343645 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
2343595 ATTTTAAAAA
2343605 ATAATTTTTAATAAATTT
1 ATAATTTTTAAT-AATTT
2343623 A-AA-TTTTAAT-ATTT
1 ATAATTTTTAATAATTT
2343637 ATAATTTTT
1 ATAATTTTT
2343646 TTAAAAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
14 5 0.24
15 2 0.10
16 11 0.52
17 2 0.10
18 1 0.05
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATAATTTTTAATAATTT
Found at i:2348407 original size:19 final size:20
Alignment explanation
Indices: 2348368--2348403 Score: 58
Period size: 18 Copynumber: 1.9 Consensus size: 20
2348358 TATTTTTAAT
2348368 ATTTATTTATAATTAAAATA
1 ATTTATTTATAATTAAAATA
2348388 ATTT-TTTAT-ATTAAAA
1 ATTTATTTATAATTAAAA
2348404 ATAAAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.44
19 5 0.31
20 4 0.25
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
ATTTATTTATAATTAAAATA
Found at i:2348764 original size:30 final size:30
Alignment explanation
Indices: 2348730--2348809 Score: 88
Period size: 30 Copynumber: 2.5 Consensus size: 30
2348720 TAAAAGCATA
2348730 TTATATTTAAATAAATATTTAATATTTAAT
1 TTATATTTAAATAAATATTTAATATTTAAT
* * * *
2348760 TTATAATTAAATAAAGTTTTTTATTTTTAAT
1 TTATATTTAAATAAA-TATTTAATATTTAAT
2348791 TTCATATTTTAAAATAAAT
1 TT-ATA-TTT-AAATAAAT
2348810 TAAATTTAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
30 14 0.34
31 14 0.34
32 3 0.07
33 3 0.07
34 7 0.17
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (30 bp):
TTATATTTAAATAAATATTTAATATTTAAT
Found at i:2349479 original size:20 final size:21
Alignment explanation
Indices: 2349429--2349489 Score: 65
Period size: 20 Copynumber: 3.0 Consensus size: 21
2349419 TTATTTGATT
2349429 AAATTTAT-TTTTTA-ATTAA
1 AAATTTATATTTTTATATTAA
* * *
2349448 AAAATTAAATTTTTATATT-C
1 AAATTTATATTTTTATATTAA
2349468 AAATTTATATTTTTATCATTAA
1 AAATTTATATTTTTAT-ATTAA
2349490 TTAAAAATAA
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
19 6 0.19
20 20 0.62
21 6 0.19
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (21 bp):
AAATTTATATTTTTATATTAA
Found at i:2350519 original size:17 final size:16
Alignment explanation
Indices: 2350497--2350550 Score: 56
Period size: 19 Copynumber: 3.2 Consensus size: 16
2350487 TAAATTTTAT
2350497 AATAAATATAATATATA
1 AATAAATATAATATA-A
2350514 AATAAAATTATAATATAA
1 AAT-AAA-TATAATATAA
*
2350532 AA-AAATAAAATATACA
1 AATAAATATAATATA-A
2350548 AAT
1 AAT
2350551 TTATTAACGA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
15 8 0.25
16 6 0.19
17 3 0.09
18 6 0.19
19 9 0.28
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.30
Consensus pattern (16 bp):
AATAAATATAATATAA
Found at i:2351310 original size:19 final size:19
Alignment explanation
Indices: 2351286--2351333 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
2351276 TAATTAAATT
2351286 TTATAATTATTTTT-TAAAA
1 TTATAATT-TTTTTGTAAAA
2351305 TTATAATTTTTTTGTAAAA
1 TTATAATTTTTTTGTAAAA
*
2351324 ATATTAATTT
1 TTA-TAATTT
2351334 AATTAGTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 5 0.19
19 15 0.58
20 6 0.23
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (19 bp):
TTATAATTTTTTTGTAAAA
Found at i:2351809 original size:20 final size:17
Alignment explanation
Indices: 2351780--2351827 Score: 53
Period size: 20 Copynumber: 2.7 Consensus size: 17
2351770 ATATTTAAAA
2351780 TTTAA-TTTTTAATAAT
1 TTTAATTTTTTAATAAT
*
2351796 TAAATTAATTTTTTTATAAT
1 T---TTAATTTTTTAATAAT
2351816 TTTAATTTTTTA
1 TTTAATTTTTTA
2351828 TTTGATTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
16 1 0.04
17 10 0.38
19 4 0.15
20 11 0.42
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTAATTTTTTAATAAT
Found at i:2352443 original size:2 final size:2
Alignment explanation
Indices: 2352436--2352468 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2352426 CAGAGAACAC
2352436 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2352469 AGAAAGAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2372929 original size:21 final size:22
Alignment explanation
Indices: 2372889--2372929 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
2372879 TATCTGCAAA
* *
2372889 TTAATGTAATTTCTTGTGTTGT
1 TTAATGTAAATTCTTATGTTGT
2372911 TTAATG-AAATTCTTATGTT
1 TTAATGTAAATTCTTATGTT
2372930 TACGAGAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.24, C:0.05, G:0.15, T:0.56
Consensus pattern (22 bp):
TTAATGTAAATTCTTATGTTGT
Found at i:2380179 original size:2 final size:2
Alignment explanation
Indices: 2380172--2380201 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2380162 TTTTCCTTGT
2380172 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2380202 AATTTTTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:2388204 original size:3 final size:3
Alignment explanation
Indices: 2388196--2388227 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2388186 TGTTTTTGCT
2388196 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2388228 GAAGAGCATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2401659 original size:2 final size:2
Alignment explanation
Indices: 2401652--2401678 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2401642 GTTTGTCTAA
2401652 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
2401679 GTGAAGCCTG
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2403011 original size:2 final size:2
Alignment explanation
Indices: 2403004--2403036 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2402994 CTCACCACAA
2403004 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2403037 ATTTACTGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2410268 original size:2 final size:2
Alignment explanation
Indices: 2410261--2410297 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2410251 ACTATAATTA
2410261 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2410298 CACATACATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2413921 original size:15 final size:16
Alignment explanation
Indices: 2413901--2413941 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 16
2413891 ATAAAATTAA
2413901 TTTAATATTATA-ATT
1 TTTAATATTATATATT
2413916 TTTAATATT-TATATT
1 TTTAATATTATATATT
*
2413931 TTGAATATTAT
1 TTTAATATTAT
2413942 TAAACATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 2 0.09
15 20 0.87
16 1 0.04
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (16 bp):
TTTAATATTATATATT
Found at i:2414057 original size:17 final size:18
Alignment explanation
Indices: 2414013--2414057 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
2414003 AATAATATAA
* *
2414013 TTAATATAATTTATTATT
1 TTAATATAATATAGTATT
2414031 TTAATA-AATATAGTA-T
1 TTAATATAATATAGTATT
2414047 TTAATATAATA
1 TTAATATAATA
2414058 ATAAGTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 7 0.29
17 11 0.46
18 6 0.25
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (18 bp):
TTAATATAATATAGTATT
Found at i:2414610 original size:2 final size:2
Alignment explanation
Indices: 2414603--2414628 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2414593 CCTGAAAAGA
2414603 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
2414629 GTAATGTTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2415315 original size:2 final size:2
Alignment explanation
Indices: 2415308--2415337 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2415298 TCCGCAATTG
2415308 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2415338 GTAAACAGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2418201 original size:2 final size:2
Alignment explanation
Indices: 2418194--2418221 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2418184 CAAATATGTG
2418194 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2418222 ATTGGGTTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2419074 original size:2 final size:2
Alignment explanation
Indices: 2419069--2419096 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2419059 AGATTTTTTC
2419069 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
2419097 TCTTGCCCGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2428553 original size:26 final size:27
Alignment explanation
Indices: 2428524--2428594 Score: 83
Period size: 25 Copynumber: 2.7 Consensus size: 27
2428514 AACTTTTATG
2428524 AAATAAATTTAAAAAAATAA-TAATAA
1 AAATAAATTTAAAAAAATAATTAATAA
* * *
2428550 AAAT-AACTTCAAAAACTAATTAATAA
1 AAATAAATTTAAAAAAATAATTAATAA
*
2428576 ATAATATATTTAAAAAAAT
1 A-AATAAATTTAAAAAAAT
2428595 TTATTATAAT
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
25 12 0.34
26 11 0.31
27 3 0.09
28 9 0.26
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (27 bp):
AAATAAATTTAAAAAAATAATTAATAA
Found at i:2429777 original size:29 final size:28
Alignment explanation
Indices: 2429740--2429838 Score: 108
Period size: 29 Copynumber: 3.2 Consensus size: 28
2429730 AATATAAACC
2429740 TAATATAAATATAATTTTTAATTATTAT
1 TAATATAAATATAATTTTTAATTATTAT
* *
2429768 TCAATCTAAATATAATTATATTTATATGTTTTAT
1 T-AATATAAATATAA-T-T-TTTA-AT-TATTAT
2429802 TAATATAAATATAATTTTTAATTATTTAT
1 TAATATAAATATAATTTTTAATTA-TTAT
2429831 TATATATA
1 TA-ATATA
2429839 CATACAATAT
Statistics
Matches: 59, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
28 2 0.03
29 20 0.34
30 10 0.17
31 2 0.03
32 5 0.08
33 14 0.24
34 6 0.10
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.54
Consensus pattern (28 bp):
TAATATAAATATAATTTTTAATTATTAT
Found at i:2431205 original size:22 final size:22
Alignment explanation
Indices: 2431174--2431237 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
2431164 TTTAAATTAT
* *
2431174 AATTTTATTAAAAAATTATTTA
1 AATTTAATTATAAAATTATTTA
*
2431196 AATTTAATTATAAAA-TATATA
1 AATTTAATTATAAAATTATTTA
*
2431217 AATATCAA-TATAAAATTATTT
1 AAT-TTAATTATAAAATTATTT
2431238 TTTATCTTTG
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 15 0.43
22 20 0.57
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
AATTTAATTATAAAATTATTTA
Found at i:2431218 original size:21 final size:21
Alignment explanation
Indices: 2431167--2431232 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
2431157 AACTTGATTT
* *
2431167 AAAT-TAT-AATTTTATTAAA
1 AAATATATAAATTTAATTATA
*
2431186 AAATTATTTAAATTTAATTATA
1 AAA-TATATAAATTTAATTATA
*
2431208 AAATATATAAATATCAA-TATA
1 AAATATATAAAT-TTAATTATA
2431229 AAAT
1 AAAT
2431233 TATTTTTTAT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
19 3 0.08
20 1 0.03
21 18 0.47
22 16 0.42
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (21 bp):
AAATATATAAATTTAATTATA
Found at i:2435747 original size:2 final size:2
Alignment explanation
Indices: 2435740--2435769 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2435730 CACTGCGAGA
2435740 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
2435770 CCAGTCTCCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2435998 original size:2 final size:2
Alignment explanation
Indices: 2435991--2436021 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2435981 CCCAAAGAGA
2435991 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2436022 TAAGTGAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2440010 original size:2 final size:2
Alignment explanation
Indices: 2440003--2440053 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
2439993 AACCATTAAC
2440003 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2440045 TA TA TA TA T
1 TA TA TA TA T
2440054 CCCTAGGTTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2444305 original size:2 final size:2
Alignment explanation
Indices: 2444298--2444337 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
2444288 CAATGAGTTT
*
2444298 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2444338 AATGTAATGC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2447112 original size:16 final size:16
Alignment explanation
Indices: 2447091--2447141 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
2447081 TTCAATTTAG
2447091 ATTTAAATTATTTCAT
1 ATTTAAATTATTTCAT
* *
2447107 ATTTAAATTATTTTAAG
1 ATTTAAATTA-TTTCAT
2447124 ATTT-AA-TATTTCAT
1 ATTTAAATTATTTCAT
2447138 ATTT
1 ATTT
2447142 GATGCTCAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
14 8 0.27
15 2 0.07
16 12 0.40
17 8 0.27
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (16 bp):
ATTTAAATTATTTCAT
Found at i:2447129 original size:17 final size:16
Alignment explanation
Indices: 2447085--2447129 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
2447075 AGTTTATTCA
2447085 ATTT-AGATTTAAATT
1 ATTTAAGATTTAAATT
* *
2447100 ATTTCATATTTAAATT
1 ATTTAAGATTTAAATT
2447116 ATTTTAAGATTTAA
1 A-TTTAAGATTTAA
2447130 TATTTCATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 4 0.16
16 11 0.44
17 10 0.40
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.53
Consensus pattern (16 bp):
ATTTAAGATTTAAATT
Found at i:2448613 original size:14 final size:14
Alignment explanation
Indices: 2448594--2448621 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2448584 ATTATATATA
2448594 TTAAAAGTATTTTT
1 TTAAAAGTATTTTT
2448608 TTAAAAGTATTTTT
1 TTAAAAGTATTTTT
2448622 AATTATTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (14 bp):
TTAAAAGTATTTTT
Found at i:2451308 original size:2 final size:2
Alignment explanation
Indices: 2451301--2451339 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2451291 TTTGGAAATT
2451301 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2451340 GAAACTCGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2453544 original size:13 final size:14
Alignment explanation
Indices: 2453511--2453543 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
2453501 AATGTTTTTA
2453511 TATTTTTT--AAAT
1 TATTTTTTAAAAAT
2453523 TATTTTTTAAAAAT
1 TATTTTTTAAAAAT
2453537 TATTTTT
1 TATTTTT
2453544 ATATTTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 8 0.42
14 11 0.58
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TATTTTTTAAAAAT
Found at i:2464482 original size:3 final size:3
Alignment explanation
Indices: 2464474--2464514 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
2464464 CGAAGGATTT
*
2464474 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAT GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
2464515 CGAGTCAGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.63, C:0.00, G:0.34, T:0.02
Consensus pattern (3 bp):
GAA
Found at i:2469551 original size:19 final size:20
Alignment explanation
Indices: 2469511--2469549 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
2469501 CTTTCTTTTT
2469511 TTTTTTTAATAATTTCCAAA
1 TTTTTTTAATAATTTCCAAA
2469531 TTTTTTTAATAATTTCCAA
1 TTTTTTTAATAATTTCCAA
2469550 TTAAAGAATT
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:0.33, C:0.10, G:0.00, T:0.56
Consensus pattern (20 bp):
TTTTTTTAATAATTTCCAAA
Found at i:2470284 original size:17 final size:18
Alignment explanation
Indices: 2470262--2470295 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
2470252 AAAAAATTAA
2470262 ATATATTTATAT-TAAAT
1 ATATATTTATATCTAAAT
2470279 ATATATTTATATCTAAA
1 ATATATTTATATCTAAA
2470296 ATTTACTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (18 bp):
ATATATTTATATCTAAAT
Found at i:2474809 original size:9 final size:9
Alignment explanation
Indices: 2474791--2474825 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
2474781 TGTTTCTTGC
*
2474791 TGCTGCTGT
1 TGCTGATGT
*
2474800 TGCTGTTGT
1 TGCTGATGT
2474809 TGCTGATGT
1 TGCTGATGT
2474818 TGCTGATG
1 TGCTGATG
2474826 CTGCAGCTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.06, C:0.14, G:0.34, T:0.46
Consensus pattern (9 bp):
TGCTGATGT
Found at i:2476986 original size:2 final size:2
Alignment explanation
Indices: 2476979--2477016 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2476969 GATCCTCCAA
2476979 AT AT 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 AT AT
2477017 GAAAAACGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2480351 original size:14 final size:14
Alignment explanation
Indices: 2480334--2480366 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
2480324 CAAGTACGAC
*
2480334 TTTAAATATATATA
1 TTTAAATAAATATA
2480348 TTTAAATAAATATA
1 TTTAAATAAATATA
2480362 TTTAA
1 TTTAA
2480367 TTTTTTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TTTAAATAAATATA
Found at i:2483462 original size:43 final size:43
Alignment explanation
Indices: 2483401--2483492 Score: 175
Period size: 43 Copynumber: 2.1 Consensus size: 43
2483391 TTCAGTTGAA
2483401 TACATTAGGCTGTCTCTTACAAAATAAATCATTGTTTACATTT
1 TACATTAGGCTGTCTCTTACAAAATAAATCATTGTTTACATTT
*
2483444 TACATTAGGCTGTCTCTTACAAAATTAATCATTGTTTACATTT
1 TACATTAGGCTGTCTCTTACAAAATAAATCATTGTTTACATTT
2483487 TACATT
1 TACATT
2483493 CATTTAATAA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 48 1.00
ACGTcount: A:0.32, C:0.16, G:0.09, T:0.43
Consensus pattern (43 bp):
TACATTAGGCTGTCTCTTACAAAATAAATCATTGTTTACATTT
Found at i:2486568 original size:27 final size:27
Alignment explanation
Indices: 2486556--2486659 Score: 154
Period size: 27 Copynumber: 3.9 Consensus size: 27
2486546 CTGTTGCTGA
2486556 TGTTGCTGATGCTGCAGCTGCTGTAAC
1 TGTTGCTGATGCTGCAGCTGCTGTAAC
*
2486583 TGTTGCTGATGCTGCAGCTGCTGCAAC
1 TGTTGCTGATGCTGCAGCTGCTGTAAC
**
2486610 TGTTGCCCATGCTGCAGCTGCTGTAAC
1 TGTTGCTGATGCTGCAGCTGCTGTAAC
* * *
2486637 TGTTGCTGTTGTTGCGGCTGCTG
1 TGTTGCTGATGCTGCAGCTGCTG
2486660 CTGCTGCAAT
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 68 1.00
ACGTcount: A:0.12, C:0.24, G:0.31, T:0.34
Consensus pattern (27 bp):
TGTTGCTGATGCTGCAGCTGCTGTAAC
Found at i:2492497 original size:2 final size:2
Alignment explanation
Indices: 2492490--2492536 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
2492480 GGAGCAAACT
2492490 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2492532 AG AG A
1 AG AG A
2492537 TGGTACTAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2501419 original size:3 final size:3
Alignment explanation
Indices: 2501411--2501440 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
2501401 CTAGAGATTA
2501411 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
2501441 CTAACTGCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:2502033 original size:2 final size:2
Alignment explanation
Indices: 2502028--2502079 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
2502018 GGGGGGGGAG
2502028 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
2502070 GA GA GA GA GA
1 GA GA GA GA GA
2502080 AATTGCACAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2502131 original size:4 final size:4
Alignment explanation
Indices: 2502124--2502150 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
2502114 CGATATATAT
2502124 ATAG ATAG ATAG ATAG ATAG ATAG ATA
1 ATAG ATAG ATAG ATAG ATAG ATAG ATA
2502151 CATTTAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.22, T:0.26
Consensus pattern (4 bp):
ATAG
Found at i:2508862 original size:22 final size:24
Alignment explanation
Indices: 2508822--2508880 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 24
2508812 AAATATTATC
2508822 ATAATA-TTTTAATTAATTT-TAA
1 ATAATATTTTTAATTAATTTATAA
* *
2508844 ATAATATTTTTAA-TCATTTATTA
1 ATAATATTTTTAATTAATTTATAA
*
2508867 GTAATTATTTTTAA
1 ATAA-TATTTTTAA
2508881 ATGAAATCTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
22 11 0.35
23 11 0.35
24 9 0.29
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (24 bp):
ATAATATTTTTAATTAATTTATAA
Found at i:2510128 original size:21 final size:21
Alignment explanation
Indices: 2510066--2510128 Score: 54
Period size: 21 Copynumber: 2.9 Consensus size: 21
2510056 AAAATTATTA
* *
2510066 TAAAATATAAAATATTTATATAT
1 TAAAA-ATAATATA-TTAAATAT
* **
2510089 TAAAAATAATAAAAAAAATAT
1 TAAAAATAATATATTAAATAT
*
2510110 TATAAATAATATATTAAAT
1 TAAAAATAATATATTAAAT
2510129 CAATTTGTAC
Statistics
Matches: 31, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
21 20 0.65
22 6 0.19
23 5 0.16
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
TAAAAATAATATATTAAATAT
Found at i:2511270 original size:102 final size:101
Alignment explanation
Indices: 2511079--2511294 Score: 294
Period size: 102 Copynumber: 2.1 Consensus size: 101
2511069 TCCAGCACCT
** * * * * *
2511079 GTTGATTAAATGGTGATTTGGTAATTTATCATTATTGATTAAATGGGTGATTTGGTGGTTTGCCA
1 GTTGATTAAATGGAAATTTGGTAACTTATCATTATTAATTAAATGGGTGATTTGGTAGCTTACCA
2511144 TTGTTGACTAAATGAGAGATTTGGT-AGCTTACCATC
66 TTGTTGACTAAATGAGAGATTTGGTAAG-TTACCATC
*
2511180 GTTGATTAAATGAGAAATTTGGTAGCTTA-CTATTATTAATTAAATGGGTGATTTGGTAGCTTAC
1 GTTGATTAAATG-GAAATTTGGTAACTTATC-ATTATTAATTAAATGGGTGATTTGGTAGCTTAC
*
2511244 CATTGTTGACTAAATG-GTAGATTTGGTAAGTTACCATT
64 CATTGTTGACTAAATGAG-AGATTTGGTAAGTTACCATC
2511282 GTTGATTAAATGG
1 GTTGATTAAATGG
2511295 TGGTTTTTAC
Statistics
Matches: 102, Mismatches: 9, Indels: 8
0.86 0.08 0.07
Matches are distributed among these distances:
101 15 0.15
102 85 0.83
103 2 0.02
ACGTcount: A:0.28, C:0.07, G:0.24, T:0.41
Consensus pattern (101 bp):
GTTGATTAAATGGAAATTTGGTAACTTATCATTATTAATTAAATGGGTGATTTGGTAGCTTACCA
TTGTTGACTAAATGAGAGATTTGGTAAGTTACCATC
Found at i:2511295 original size:34 final size:33
Alignment explanation
Indices: 2511078--2511296 Score: 233
Period size: 34 Copynumber: 6.5 Consensus size: 33
2511068 CTCCAGCACC
** *
2511078 TGTTGATTAAATGGTGATTTGGTAATTTATCAT
1 TGTTGATTAAATGGTGATTTGGTAGCTTACCAT
* * * *
2511111 TATTGATTAAATGGGTGATTTGGTGGTTTGCCAT
1 TGTTGATTAAAT-GGTGATTTGGTAGCTTACCAT
* *
2511145 TGTTGACTAAATGAGAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATG-GTGATTTGGTAGCTTACCAT
* ** *
2511179 CGTTGATTAAATGAGAAATTTGGTAGCTTACTAT
1 TGTTGATTAAATG-GTGATTTGGTAGCTTACCAT
* *
2511213 TATTAATTAAATGGGTGATTTGGTAGCTTACCAT
1 TGTTGATTAAAT-GGTGATTTGGTAGCTTACCAT
*
2511247 TGTTGACTAAATGGTAGATTTGGTAAG-TTACCAT
1 TGTTGATTAAATGGT-GATTTGGT-AGCTTACCAT
2511281 TGTTGATTAAATGGTG
1 TGTTGATTAAATGGTG
2511297 GTTTTTACCA
Statistics
Matches: 156, Mismatches: 25, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
33 16 0.10
34 137 0.88
35 3 0.02
ACGTcount: A:0.28, C:0.07, G:0.24, T:0.41
Consensus pattern (33 bp):
TGTTGATTAAATGGTGATTTGGTAGCTTACCAT
Found at i:2515761 original size:34 final size:33
Alignment explanation
Indices: 2515707--2515923 Score: 263
Period size: 34 Copynumber: 6.4 Consensus size: 33
2515697 GGGAGAATTA
*
2515707 TTGATTAAATGGTGATTTGGTAGTTTACCATTG
1 TTGATTAAATGGTGATTTGGTAGCTTACCATTG
* * *
2515740 TTGATTAAATGAGTGATTTGGTGGTTTGCCATTG
1 TTGATTAAATG-GTGATTTGGTAGCTTACCATTG
* * *
2515774 TTGACTAAATGGGAGATTTGGTAACTTACCATTG
1 TTGATTAAAT-GGTGATTTGGTAGCTTACCATTG
** *
2515808 TTGATTAAATGAGAAATTTGGTAGCTTACCATTA
1 TTGATTAAATG-GTGATTTGGTAGCTTACCATTG
*
2515842 TTGATTAAATGGGTGATTTGGTGGCTTACCATTG
1 TTGATTAAAT-GGTGATTTGGTAGCTTACCATTG
* * *
2515876 TTGACTAAATGGTAGATTTGGTAGGTTGCCATTG
1 TTGATTAAATGGT-GATTTGGTAGCTTACCATTG
2515910 TTGATTAAATGGTG
1 TTGATTAAATGGTG
2515924 GTTTTTACCA
Statistics
Matches: 158, Mismatches: 21, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
33 16 0.10
34 140 0.89
35 2 0.01
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.41
Consensus pattern (33 bp):
TTGATTAAATGGTGATTTGGTAGCTTACCATTG
Found at i:2515848 original size:102 final size:101
Alignment explanation
Indices: 2515707--2515921 Score: 322
Period size: 102 Copynumber: 2.1 Consensus size: 101
2515697 GGGAGAATTA
** * * * *
2515707 TTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGATTAAATGAGTGATTTGGTGGTTTGCCAT
1 TTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGAGTGATTTGGTGGCTTACCAT
2515772 TGTTGACTAAATGGGAGATTTGGTAACTTACCATTG
66 TGTTGACTAAATGGGAGATTTGGTAACTTACCATTG
*
2515808 TTGATTAAATGAGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTACCA
1 TTGATTAAATG-GAAATTTGGTAGCTTACCATTATTGATTAAATGAGTGATTTGGTGGCTTACCA
* ** *
2515873 TTGTTGACTAAATGGTAGATTTGGTAGGTTGCCATTG
65 TTGTTGACTAAATGGGAGATTTGGTAACTTACCATTG
2515910 TTGATTAAATGG
1 TTGATTAAATGG
2515922 TGGTTTTTAC
Statistics
Matches: 102, Mismatches: 11, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
101 12 0.12
102 90 0.88
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.40
Consensus pattern (101 bp):
TTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGAGTGATTTGGTGGCTTACCAT
TGTTGACTAAATGGGAGATTTGGTAACTTACCATTG
Found at i:2522280 original size:17 final size:17
Alignment explanation
Indices: 2522260--2522292 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2522250 AATCAAAATT
2522260 TTAAATAAAAAATAAAA
1 TTAAATAAAAAATAAAA
*
2522277 TTAAATAAAAATTAAA
1 TTAAATAAAAAATAAA
2522293 TACGTAAAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
TTAAATAAAAAATAAAA
Found at i:2525700 original size:13 final size:13
Alignment explanation
Indices: 2525682--2525707 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2525672 GATATGGTTA
2525682 TTGTTGTATTTGT
1 TTGTTGTATTTGT
2525695 TTGTTGTATTTGT
1 TTGTTGTATTTGT
2525708 AATTTAGAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.00, G:0.23, T:0.69
Consensus pattern (13 bp):
TTGTTGTATTTGT
Found at i:2526920 original size:2 final size:2
Alignment explanation
Indices: 2526908--2526940 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
2526898 TACTAGTTTG
*
2526908 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2526941 GTTATTAAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2531202 original size:14 final size:14
Alignment explanation
Indices: 2531174--2531207 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
2531164 AACATTTTTA
2531174 ATTAAATATATAAT
1 ATTAAATATATAAT
2531188 ATTATAATATA-AAT
1 ATTA-AATATATAAT
2531202 ATTAAA
1 ATTAAA
2531208 AAATAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 2 0.11
14 11 0.58
15 6 0.32
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
ATTAAATATATAAT
Found at i:2536473 original size:26 final size:26
Alignment explanation
Indices: 2536442--2536499 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 26
2536432 ATTGATAGGA
*
2536442 CATTATCAGTTGCTAACAGATAAGTT
1 CATTATCAATTGCTAACAGATAAGTT
* **
2536468 CATTATCAATTGTTAATTGATAAGTT
1 CATTATCAATTGCTAACAGATAAGTT
2536494 -ATTATC
1 CATTATC
2536500 TTACAAACTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 6 0.21
26 22 0.79
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.41
Consensus pattern (26 bp):
CATTATCAATTGCTAACAGATAAGTT
Found at i:2537837 original size:8 final size:8
Alignment explanation
Indices: 2537797--2537845 Score: 52
Period size: 8 Copynumber: 6.5 Consensus size: 8
2537787 ATATTATTTT
2537797 AAATAAT-
1 AAATAATA
2537804 AAATAAT-
1 AAATAATA
2537811 AAAT--TA
1 AAATAATA
*
2537817 AATTAATTA
1 AAATAA-TA
2537826 AAATAATA
1 AAATAATA
2537834 AAATAATA
1 AAATAATA
2537842 AAAT
1 AAAT
2537846 CAAATCCGAT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
5 1 0.03
6 3 0.08
7 11 0.31
8 14 0.39
9 7 0.19
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (8 bp):
AAATAATA
Found at i:2537845 original size:26 final size:27
Alignment explanation
Indices: 2537779--2537845 Score: 66
Period size: 29 Copynumber: 2.4 Consensus size: 27
2537769 AATTAAATTT
* *
2537779 AAATAA-AAATATTATTTTAAATAATAA
1 AAATAATAAA-ATTAATTAAAATAATAA
*
2537806 ATAATAAATTAAATTAATTAAAATAAT-A
1 A-AAT-AATAAAATTAATTAAAATAATAA
2537834 AAATAATAAAAT
1 AAATAATAAAAT
2537846 CAAATCCGAT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
26 7 0.21
27 4 0.12
28 5 0.15
29 15 0.45
30 2 0.06
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (27 bp):
AAATAATAAAATTAATTAAAATAATAA
Found at i:2539627 original size:15 final size:14
Alignment explanation
Indices: 2539586--2539627 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
2539576 TAAAAATATT
2539586 TTAAATAATATT-AA
1 TTAAATAAT-TTAAA
2539600 TTAAATCAATTTAAA
1 TTAAAT-AATTTAAA
2539615 TATAAATAATTTA
1 T-TAAATAATTTA
2539628 TATAAAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 8 0.32
15 12 0.48
16 5 0.20
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (14 bp):
TTAAATAATTTAAA
Found at i:2542740 original size:2 final size:2
Alignment explanation
Indices: 2542735--2542763 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2542725 TCTCTCTCTC
2542735 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2542764 GTGTACGAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2543726 original size:14 final size:14
Alignment explanation
Indices: 2543702--2543741 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
2543692 TGAAAATATA
2543702 ATATGTATATTAAAT
1 ATAT-TATATTAAAT
* *
2543717 ATTTTATATTAATT
1 ATATTATATTAAAT
2543731 ATATTATATTA
1 ATATTATATTA
2543742 TTTTATATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
14 19 0.86
15 3 0.14
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (14 bp):
ATATTATATTAAAT
Found at i:2543738 original size:5 final size:5
Alignment explanation
Indices: 2543697--2543776 Score: 51
Period size: 5 Copynumber: 16.4 Consensus size: 5
2543687 TTAAATGAAA
* * * *
2543697 ATATA ATATGT ATATT A-AAT ATTTT ATATT A-ATT ATATT ATATT ATTTT
1 ATATT ATAT-T ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
* * *
2543746 ATATT -TATC GTATT ATTTTT ATATT A-ATT AT
1 ATATT ATATT ATATT A-TATT ATATT ATATT AT
2543777 GTAAAAATAA
Statistics
Matches: 57, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
4 14 0.25
5 35 0.61
6 8 0.14
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.59
Consensus pattern (5 bp):
ATATT
Found at i:2543747 original size:10 final size:10
Alignment explanation
Indices: 2543697--2543776 Score: 51
Period size: 9 Copynumber: 8.2 Consensus size: 10
2543687 TTAAATGAAA
*
2543697 ATATAATATGT
1 ATATTATAT-T
*
2543708 ATATTA-AAT
1 ATATTATATT
*
2543717 ATTTTATATT
1 ATATTATATT
2543727 A-ATTATATT
1 ATATTATATT
*
2543736 ATATTATTTT
1 ATATTATATT
*
2543746 ATATT-TATC
1 ATATTATATT
* *
2543755 GTATTATTTTT
1 ATATTA-TATT
2543766 ATATTA-ATT
1 ATATTATATT
2543775 AT
1 AT
2543777 GTAAAAATAA
Statistics
Matches: 52, Mismatches: 13, Indels: 10
0.69 0.17 0.13
Matches are distributed among these distances:
9 24 0.46
10 16 0.31
11 12 0.23
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.59
Consensus pattern (10 bp):
ATATTATATT
Found at i:2543759 original size:24 final size:24
Alignment explanation
Indices: 2543708--2543761 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
2543698 TATAATATGT
* *
2543708 ATATTA-AATATTTTATATTAATT
1 ATATTATATTATTTTATATTAATC
*
2543731 ATATTATATTATTTTATATTTATC
1 ATATTATATTATTTTATATTAATC
*
2543755 GTATTAT
1 ATATTAT
2543762 TTTTATATTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
23 6 0.23
24 20 0.77
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (24 bp):
ATATTATATTATTTTATATTAATC
Found at i:2544384 original size:22 final size:22
Alignment explanation
Indices: 2544359--2544413 Score: 53
Period size: 22 Copynumber: 2.6 Consensus size: 22
2544349 ATTAAACATA
2544359 AAAACATAAAATCATA-AAAATT
1 AAAACATAAAAT-ATATAAAATT
* * *
2544381 AAAATATAACATATATACAATT
1 AAAACATAAAATATATAAAATT
2544403 -AAA-ATAAAATA
1 AAAACATAAAATA
2544414 AAATAACGAC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 7 0.25
21 6 0.21
22 15 0.54
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.25
Consensus pattern (22 bp):
AAAACATAAAATATATAAAATT
Found at i:2545862 original size:2 final size:2
Alignment explanation
Indices: 2545857--2545893 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2545847 ACACACACAC
2545857 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2545894 AACACAACCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2548240 original size:7 final size:8
Alignment explanation
Indices: 2548221--2548250 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
2548211 TCTCTCCAAA
2548221 AAAAAATT
1 AAAAAATT
2548229 AAAAAATT
1 AAAAAATT
2548237 AAAAAATT
1 AAAAAATT
2548245 AAAAAA
1 AAAAAA
2548251 AAAACAGCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (8 bp):
AAAAAATT
Found at i:2548303 original size:2 final size:2
Alignment explanation
Indices: 2548263--2548290 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2548253 AACAGCTTTT
2548263 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2548291 CACGATTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:2548596 original size:3 final size:3
Alignment explanation
Indices: 2548588--2548616 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2548578 GAGATAACAA
2548588 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
2548617 AAAACATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:2552464 original size:19 final size:19
Alignment explanation
Indices: 2552440--2552477 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
2552430 TATGAAAATA
2552440 TTATTTTAT-ATTAATATTT
1 TTATTTTATAATTAA-ATTT
2552459 TTATTTTATAATTAAATTT
1 TTATTTTATAATTAAATTT
2552478 AATAAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (19 bp):
TTATTTTATAATTAAATTT
Found at i:2556249 original size:17 final size:17
Alignment explanation
Indices: 2556219--2556260 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
2556209 AATATAAATA
* *
2556219 TATTAATATTTTTAAAG
1 TATTTATATATTTAAAG
*
2556236 TTTTTATATATTTAAAG
1 TATTTATATATTTAAAG
2556253 TATTTATA
1 TATTTATA
2556261 AAAATTATAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (17 bp):
TATTTATATATTTAAAG
Found at i:2557667 original size:30 final size:29
Alignment explanation
Indices: 2557618--2557679 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 29
2557608 GTTTAAATTT
2557618 ATAATATTTTAATTTAAATTAATT-TAAA
1 ATAATATTTTAATTTAAATTAATTATAAA
*
2557646 ATAATATTTTTTATTTAAAATTAATTATAAA
1 ATAATA-TTTTAATTT-AAATTAATTATAAA
2557677 ATA
1 ATA
2557680 TATAAATATT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 6 0.20
29 8 0.27
30 9 0.30
31 7 0.23
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (29 bp):
ATAATATTTTAATTTAAATTAATTATAAA
Found at i:2558101 original size:23 final size:22
Alignment explanation
Indices: 2558039--2558103 Score: 62
Period size: 21 Copynumber: 2.9 Consensus size: 22
2558029 TATTTAAAAA
*
2558039 TATTAAAATATTAAAAATAAATTT
1 TATTTAAATATT--AAATAAATTT
*
2558063 TATTTAAATATT-AATATATTT
1 TATTTAAATATTAAATAAATTT
2558084 TATAATTAAAT-TTAAATAAA
1 TAT--TTAAATATTAAATAAA
2558104 AATATTTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
21 11 0.31
22 2 0.06
23 11 0.31
24 11 0.31
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
TATTTAAATATTAAATAAATTT
Found at i:2562525 original size:26 final size:25
Alignment explanation
Indices: 2562484--2562608 Score: 87
Period size: 26 Copynumber: 4.9 Consensus size: 25
2562474 CAATGTATTT
*
2562484 ATATATTATTAATAAATTACATAATA
1 ATAT-TTATTAATAAATTAAATAATA
2562510 ATACTTTATTAATAAA-TAAAT-ATA
1 ATA-TTTATTAATAAATTAAATAATA
* **
2562534 AAATTTTAAAAATAAATATAAATAATA
1 ATA-TTTATTAATAAAT-TAAATAATA
* *
2562561 TTATTTATTAATAATATATAAAT--TT
1 ATATTTATTAATAA-AT-TAAATAATA
* *
2562586 ATATATTAATAATATATTAAATA
1 ATAT-TTATTAATAAATTAAATA
2562609 TAAATTATTT
Statistics
Matches: 79, Mismatches: 13, Indels: 15
0.74 0.12 0.14
Matches are distributed among these distances:
24 20 0.25
25 10 0.13
26 36 0.46
27 13 0.16
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (25 bp):
ATATTTATTAATAAATTAAATAATA
Found at i:2562587 original size:23 final size:24
Alignment explanation
Indices: 2562561--2562607 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
2562551 ATAAATAATA
*
2562561 TTATTTATTAATAATATA-TAAAT
1 TTATATATTAATAATATATTAAAT
2562584 TTATATATTAATAATATATTAAAT
1 TTATATATTAATAATATATTAAAT
2562608 ATAAATTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 17 0.77
24 5 0.23
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
TTATATATTAATAATATATTAAAT
Found at i:2562610 original size:9 final size:11
Alignment explanation
Indices: 2562566--2562605 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
2562556 TAATATTATT
2562566 TATTAATAATA
1 TATTAATAATA
* *
2562577 TATAAATTTATA
1 TATTAA-TAATA
2562589 TATTAATAATA
1 TATTAATAATA
2562600 TATTAA
1 TATTAA
2562606 ATATAAATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
11 15 0.62
12 9 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
TATTAATAATA
Found at i:2566577 original size:31 final size:31
Alignment explanation
Indices: 2566478--2566577 Score: 73
Period size: 31 Copynumber: 3.1 Consensus size: 31
2566468 ACATATTTAT
*
2566478 TTTTAAATTTTTTAAAAGACATAATTATTAAAAATAA
1 TTTTATATTTTTT-AAA-A-ATAATTATT---AATAA
** *
2566515 TTTT-TA-TTTTT-AAAATTTTTAATAACT-A
1 TTTTATATTTTTTAAAAATAATTATTAA-TAA
2566543 TTTTATATTTTTTAAAAATAATTATTAATAA
1 TTTTATATTTTTTAAAAATAATTATTAATAA
2566574 TTTT
1 TTTT
2566578 TAACTTCATT
Statistics
Matches: 51, Mismatches: 7, Indels: 16
0.69 0.09 0.22
Matches are distributed among these distances:
28 7 0.14
29 3 0.06
30 6 0.12
31 22 0.43
32 1 0.02
33 2 0.04
35 5 0.10
36 1 0.02
37 4 0.08
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.54
Consensus pattern (31 bp):
TTTTATATTTTTTAAAAATAATTATTAATAA
Found at i:2567436 original size:17 final size:18
Alignment explanation
Indices: 2567414--2567450 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2567404 AATGATGTTA
2567414 TTTTATA-TTTATTAATT
1 TTTTATATTTTATTAATT
*
2567431 TTTTATATTTTTTTAATT
1 TTTTATATTTTATTAATT
2567449 TT
1 TT
2567451 ATATTTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTTATATTTTATTAATT
Found at i:2567463 original size:17 final size:15
Alignment explanation
Indices: 2567413--2567457 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 15
2567403 AAATGATGTT
2567413 ATTTTATATTTATTA
1 ATTTTATATTTATTA
*
2567428 ATTTTTTATATTTTTTTA
1 A--TTTTATA-TTTATTA
2567446 ATTTTATATTTA
1 ATTTTATATTTA
2567458 AATTAACATA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
15 4 0.16
16 7 0.28
17 7 0.28
18 7 0.28
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
ATTTTATATTTATTA
Found at i:2570069 original size:4 final size:4
Alignment explanation
Indices: 2570060--2570090 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
2570050 GCTTCCCCAC
2570060 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
2570091 TCTTTTATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:2570516 original size:24 final size:23
Alignment explanation
Indices: 2570455--2570519 Score: 78
Period size: 23 Copynumber: 2.8 Consensus size: 23
2570445 ATTATTTAAT
*
2570455 TTAAATGAACTTGTTCATGAATA
1 TTAAATGAACATGTTCATGAATA
*
2570478 TTAAATGAACATGTTTATGAA-A
1 TTAAATGAACATGTTCATGAATA
*
2570500 TTATAATCGAATATGTTCAT
1 TTA-AAT-GAACATGTTCAT
2570520 TAACAAGTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
22 4 0.11
23 22 0.61
24 10 0.28
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (23 bp):
TTAAATGAACATGTTCATGAATA
Found at i:2570662 original size:48 final size:51
Alignment explanation
Indices: 2570598--2570738 Score: 139
Period size: 54 Copynumber: 2.8 Consensus size: 51
2570588 AAAAGTCAAT
*
2570598 TTTAAGTTATAATTAAATATAAAATAATAAAATACAAATGT-AA-TA-T-AA
1 TTTAAGTTATTATTAAATATAAAATAATAAAATACAAAT-TCAATTATTAAA
* **
2570646 TTTAAGTTATTATTAAATATAAACAGTAAAACAAAATA-TTATTCAATTATTAAA
1 TTTAAGTTATTATTAAATATAAA-A-T--AATAAAATACAAATTCAATTATTAAA
* * *
2570700 TTTAAGTTATTATTAAATAGAAAATAATAGAACACAAAT
1 TTTAAGTTATTATTAAATATAAAATAATAAAATACAAAT
2570739 AATATTAATT
Statistics
Matches: 74, Mismatches: 10, Indels: 15
0.75 0.10 0.15
Matches are distributed among these distances:
48 22 0.30
49 1 0.01
50 8 0.11
51 6 0.08
52 11 0.15
53 2 0.03
54 24 0.32
ACGTcount: A:0.55, C:0.04, G:0.05, T:0.36
Consensus pattern (51 bp):
TTTAAGTTATTATTAAATATAAAATAATAAAATACAAATTCAATTATTAAA
Found at i:2570826 original size:11 final size:11
Alignment explanation
Indices: 2570803--2570869 Score: 73
Period size: 11 Copynumber: 6.0 Consensus size: 11
2570793 ATTAATATAA
*
2570803 TAAATGAATTT
1 TAAATAAATTT
*
2570814 TAAATAAACTT
1 TAAATAAATTT
* *
2570825 TAAATTATTTAT
1 TAAATAAATT-T
2570837 TAAATAAATTT
1 TAAATAAATTT
2570848 TAAAT-AATTT
1 TAAATAAATTT
2570858 ATAAATAAATTT
1 -TAAATAAATTT
2570870 ATTTGTAAAC
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
10 5 0.11
11 27 0.59
12 14 0.30
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (11 bp):
TAAATAAATTT
Found at i:2570840 original size:23 final size:22
Alignment explanation
Indices: 2570813--2570870 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 22
2570803 TAAATGAATT
*
2570813 TTAAATAAACTTTAAATTATTTA
1 TTAAATAAA-TTTAAATAATTTA
2570836 TTAAATAAATTTTAAATAATTTA
1 TTAAATAAA-TTTAAATAATTTA
2570859 -TAAATAAATTTA
1 TTAAATAAATTTA
2570871 TTTGTAAACA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
21 4 0.12
22 8 0.24
23 21 0.64
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (22 bp):
TTAAATAAATTTAAATAATTTA
Found at i:2570863 original size:34 final size:35
Alignment explanation
Indices: 2570803--2570872 Score: 90
Period size: 34 Copynumber: 2.0 Consensus size: 35
2570793 ATTAATATAA
* *
2570803 TAAATGAATTTTAAATAAACTTTAAAT-TATTTAT
1 TAAATAAATTTTAAATAAACTTTAAATAAATTTAT
*
2570837 TAAATAAATTTTAAAT-AATTTATAAATAAATTTAT
1 TAAATAAATTTTAAATAAACTT-TAAATAAATTTAT
2570872 T
1 T
2570873 TGTAAACATA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
33 4 0.13
34 20 0.65
35 7 0.23
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (35 bp):
TAAATAAATTTTAAATAAACTTTAAATAAATTTAT
Found at i:2574608 original size:23 final size:23
Alignment explanation
Indices: 2574580--2574629 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
2574570 GTATTACATT
* *
2574580 TAAAATAAAATATTTATTTAAATA
1 TAAATTAAAA-ATTTATTGAAATA
*
2574604 TAAATTAAAAATTTATTGAGATA
1 TAAATTAAAAATTTATTGAAATA
2574627 TAA
1 TAA
2574630 TTTTAGAGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 14 0.61
24 9 0.39
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (23 bp):
TAAATTAAAAATTTATTGAAATA
Found at i:2576737 original size:26 final size:27
Alignment explanation
Indices: 2576685--2576737 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
2576675 AATACTTTAT
*
2576685 AATTTAATAAAAAATATAAATATATTAA
1 AATTTAATAAAAAATAT-AATAAATTAA
*
2576713 AATTTAATAAAAAATAT-CTAAATTA
1 AATTTAATAAAAAATATAATAAATTA
2576738 GTATGGATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 6 0.26
28 17 0.74
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (27 bp):
AATTTAATAAAAAATATAATAAATTAA
Found at i:2577842 original size:25 final size:25
Alignment explanation
Indices: 2577808--2577855 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
2577798 TAGTAATATA
*
2577808 ATTAGATTATTATTAAAAATTTATT
1 ATTAGATTATTACTAAAAATTTATT
* *
2577833 ATTATATTATTACTAAAGATTTA
1 ATTAGATTATTACTAAAAATTTA
2577856 GATTTTACTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (25 bp):
ATTAGATTATTACTAAAAATTTATT
Found at i:2578070 original size:28 final size:26
Alignment explanation
Indices: 2578003--2578071 Score: 63
Period size: 26 Copynumber: 2.6 Consensus size: 26
2577993 TTAGATTATT
*
2578003 ATTAAATATATATTTA-TTATATTGATA
1 ATTAAATA-AT-TTTATTTATATTAATA
2578030 ATGTAAA-AA-TTTATTTATTATTAATAA
1 AT-TAAATAATTTTATTTA-TATTAAT-A
2578057 ATTAAATAATTTTAT
1 ATTAAATAATTTTAT
2578072 GTCATTAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 11
0.74 0.02 0.23
Matches are distributed among these distances:
24 4 0.11
25 3 0.09
26 11 0.31
27 8 0.23
28 9 0.26
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (26 bp):
ATTAAATAATTTTATTTATATTAATA
Found at i:2579743 original size:2 final size:2
Alignment explanation
Indices: 2579738--2579772 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2579728 AATTAAAACA
2579738 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2579773 GAGAGAGAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2579777 original size:2 final size:2
Alignment explanation
Indices: 2579772--2579802 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2579762 ATATATATAT
2579772 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2579803 AATTAAAAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2581902 original size:2 final size:2
Alignment explanation
Indices: 2581897--2581927 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2581887 TTTTTTTTTG
*
2581897 GT GT GT GT GT GT GT GT GT GT GT GT TT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
2581928 CGTGCGCGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
GT
Found at i:2582931 original size:2 final size:2
Alignment explanation
Indices: 2582924--2582962 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2582914 ACAGGTAAAC
2582924 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2582963 CACGCACCAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2586175 original size:1 final size:1
Alignment explanation
Indices: 2586171--2586196 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
2586161 CTTTTTTTTT
2586171 GGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGG
2586197 TTCATGAACC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:2586558 original size:5 final size:5
Alignment explanation
Indices: 2586532--2586589 Score: 50
Period size: 5 Copynumber: 11.6 Consensus size: 5
2586522 AACTGTCAAT
**
2586532 TTTAA TTTAAA TTTAA -AAAA TTTAA -TTAA -TTAA TTTAAA TTTAAA
1 TTTAA TTT-AA TTTAA TTTAA TTTAA TTTAA TTTAA TTT-AA TTT-AA
2586577 TTTAA TTTAA TTT
1 TTTAA TTTAA TTT
2586590 TGAGTTGATA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
4 10 0.22
5 19 0.42
6 16 0.36
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (5 bp):
TTTAA
Found at i:2586569 original size:22 final size:24
Alignment explanation
Indices: 2586532--2586588 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 24
2586522 AACTGTCAAT
2586532 TTTAATTTAAATTTAAA-AAATTTAA
1 TTTAA-TT-AATTTAAATAAATTTAA
2586557 -TTAATTAATTTAAATTTAAATTTAA
1 TTTAATTAATTTAAA--TAAATTTAA
2586582 TTTAATT
1 TTTAATT
2586589 TTGAGTTGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
22 8 0.29
23 2 0.07
24 4 0.14
25 8 0.29
26 6 0.21
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
TTTAATTAATTTAAATAAATTTAA
Found at i:2589425 original size:2 final size:2
Alignment explanation
Indices: 2589418--2589442 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2589408 ATAAATTTTC
2589418 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2589443 CTTTCTCCTG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2589683 original size:21 final size:22
Alignment explanation
Indices: 2589642--2589684 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
2589632 TAAAATTTTA
* *
2589642 ATTTTATTAATAAAATTAAAAT
1 ATTTTATTAAAAAAATAAAAAT
2589664 ATTTTA-TAAAAAAATAAAAAT
1 ATTTTATTAAAAAAATAAAAAT
2589685 TGATATAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
ATTTTATTAAAAAAATAAAAAT
Found at i:2591457 original size:18 final size:17
Alignment explanation
Indices: 2591434--2591482 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 17
2591424 ATTATCTTAA
2591434 TATTTTTAAATTTTTTAT
1 TATTTTTAAATTTTTT-T
2591452 TA-TTTTAAATATTTTTT
1 TATTTTTAAAT-TTTTTT
2591469 TATATTTT-AATTTT
1 TAT-TTTTAAATTTT
2591483 GTACCACACT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
17 14 0.50
18 10 0.36
19 4 0.14
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TATTTTTAAATTTTTTT
Found at i:2591467 original size:19 final size:18
Alignment explanation
Indices: 2591433--2591478 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
2591423 TATTATCTTA
*
2591433 ATATTTTTAAA-TTTTTT
1 ATATTTTAAAATTTTTTT
2591450 ATTATTTTAAATATTTTTTT
1 A-TATTTTAAA-ATTTTTTT
2591470 ATATTTTAA
1 ATATTTTAA
2591479 TTTTGTACCA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 1 0.04
18 8 0.32
19 9 0.36
20 7 0.28
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
ATATTTTAAAATTTTTTT
Found at i:2593014 original size:15 final size:14
Alignment explanation
Indices: 2592974--2593016 Score: 52
Period size: 15 Copynumber: 3.1 Consensus size: 14
2592964 TAAAATTTTA
2592974 ATTTT-ATTAAATT
1 ATTTTAATTAAATT
* *
2592987 ATATTAATAAAATAT
1 ATTTTAATTAAAT-T
2593002 ATTTTAATTAAATT
1 ATTTTAATTAAATT
2593016 A
1 A
2593017 AAAATTAGTA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
13 4 0.17
14 8 0.33
15 12 0.50
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
ATTTTAATTAAATT
Found at i:2596206 original size:2 final size:2
Alignment explanation
Indices: 2596201--2596238 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2596191 ATATTAATTT
2596201 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2596239 CCTCAATCCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2596869 original size:23 final size:23
Alignment explanation
Indices: 2596839--2596896 Score: 116
Period size: 23 Copynumber: 2.5 Consensus size: 23
2596829 AAGATTATAT
2596839 ATAAATTTTAATTTTAAACTCAA
1 ATAAATTTTAATTTTAAACTCAA
2596862 ATAAATTTTAATTTTAAACTCAA
1 ATAAATTTTAATTTTAAACTCAA
2596885 ATAAATTTTAAT
1 ATAAATTTTAAT
2596897 GTATTAAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (23 bp):
ATAAATTTTAATTTTAAACTCAA
Found at i:2600203 original size:2 final size:2
Alignment explanation
Indices: 2600196--2600236 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
2600186 ACATACATAC
* *
2600196 AT AT AT AT CT AT AT CT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2600237 GAGAGAGAGA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2604203 original size:13 final size:13
Alignment explanation
Indices: 2604185--2604209 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2604175 TTATGTTTAG
2604185 TCCAATATATTAA
1 TCCAATATATTAA
2604198 TCCAATATATTA
1 TCCAATATATTA
2604210 TGTTTAGTCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.16, G:0.00, T:0.40
Consensus pattern (13 bp):
TCCAATATATTAA
Found at i:2604656 original size:2 final size:2
Alignment explanation
Indices: 2604649--2604679 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2604639 CGAAGGTCTT
2604649 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2604680 TTGAAATTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2606812 original size:10 final size:10
Alignment explanation
Indices: 2606797--2606860 Score: 51
Period size: 10 Copynumber: 6.5 Consensus size: 10
2606787 TAATTATATC
2606797 ATATTTAAAT
1 ATATTTAAAT
*
2606807 ATATTTATAT
1 ATATTTAAAT
2606817 AT-TTTAAAT
1 ATATTTAAAT
* *
2606826 TTA-ATATAAT
1 ATATTTA-AAT
*
2606836 ATATTTATAT
1 ATATTTAAAT
* *
2606846 AAATTTTAAT
1 ATATTTAAAT
2606856 ATATT
1 ATATT
2606861 AATAATTTAT
Statistics
Matches: 40, Mismatches: 11, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
9 9 0.22
10 29 0.73
11 2 0.05
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (10 bp):
ATATTTAAAT
Found at i:2606816 original size:8 final size:8
Alignment explanation
Indices: 2606805--2606911 Score: 55
Period size: 8 Copynumber: 13.2 Consensus size: 8
2606795 TCATATTTAA
2606805 ATATATTT
1 ATATATTT
2606813 ATATATTT
1 ATATATTT
*
2606821 -TAAATTT
1 ATATATTT
*
2606828 A-ATA-TA
1 ATATATTT
2606834 ATATATTT
1 ATATATTT
2606842 ATATAAATTTT
1 ATAT--A-TTT
*
2606853 AATATATTA
1 -ATATATTT
2606862 ATA-ATTT
1 ATATATTT
*
2606869 AT-TGTTTT
1 ATAT-ATTT
*
2606877 ATAAATTTT
1 ATATA-TTT
*
2606886 AATAAATTT
1 -ATATATTT
2606895 ATATATTT
1 ATATATTT
2606903 ATAT-TTT
1 ATATATTT
2606910 AT
1 AT
2606912 TTATATTTTT
Statistics
Matches: 77, Mismatches: 10, Indels: 25
0.69 0.09 0.22
Matches are distributed among these distances:
6 2 0.03
7 21 0.27
8 32 0.42
9 8 0.10
10 7 0.09
11 3 0.04
12 4 0.05
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (8 bp):
ATATATTT
Done.