Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold72
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: 5928628
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 261288 characters in sequence are not A, C, G, or T
File 27 of 39
Found at i:3920401 original size:30 final size:29
Alignment explanation
Indices: 3920367--3920472 Score: 108
Period size: 30 Copynumber: 3.5 Consensus size: 29
3920357 ACTTATAAAT
*
3920367 AATTTTAAAAAATAAATATATTTTTAATTA
1 AATTATAAAAAATAAATATATTTTTAA-TA
*
3920397 AATTTTAAAAAATAAATAAATATTTTTAA-A
1 AATTATAAAAAATAAAT--ATATTTTTAATA
*
3920427 ATATTAAAATAAAATAAATATATTTTT-ATAA
1 A-ATTATAA-AAAATAAATATATTTTTAAT-A
*
3920458 AAATATAAAAAATAA
1 AATTATAAAAAATAA
3920473 GTACCTTCAA
Statistics
Matches: 66, Mismatches: 4, Indels: 13
0.80 0.05 0.16
Matches are distributed among these distances:
29 8 0.12
30 32 0.48
31 7 0.11
32 19 0.29
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (29 bp):
AATTATAAAAAATAAATATATTTTTAATA
Found at i:3920960 original size:6 final size:6
Alignment explanation
Indices: 3920951--3920980 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
3920941 GCAGAGTCGA
*
3920951 TGATGA TGATGG TGATGG TGATGG TGATGG
1 TGATGG TGATGG TGATGG TGATGG TGATGG
3920981 GTTTGAAGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.20, C:0.00, G:0.47, T:0.33
Consensus pattern (6 bp):
TGATGG
Found at i:3922275 original size:12 final size:13
Alignment explanation
Indices: 3922248--3922282 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
3922238 TTACTTCAAG
*
3922248 ATATAAAATTTTT
1 ATATAAAATATTT
3922261 ATATAAAA-ATTT
1 ATATAAAATATTT
3922273 ATATAAAATA
1 ATATAAAATA
3922283 CGATAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
ATATAAAATATTT
Found at i:3924272 original size:22 final size:23
Alignment explanation
Indices: 3924247--3924291 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
3924237 TATATATAAA
*
3924247 TTTTAAAAATATTAT-TTTATAT
1 TTTTAAAAATATCATATTTATAT
* *
3924269 TTTTATATATATCATATTTATAT
1 TTTTAAAAATATCATATTTATAT
3924292 AATTATATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (23 bp):
TTTTAAAAATATCATATTTATAT
Found at i:3924290 original size:15 final size:15
Alignment explanation
Indices: 3924270--3924311 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
3924260 ATTTTATATT
3924270 TTTATATATATCATA
1 TTTATATATATCATA
*
3924285 TTTATATA-ATTATA
1 TTTATATATATCATA
3924299 TTTA-ATATTATCA
1 TTTATATA-TATCA
3924312 AATAATTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 3 0.13
14 9 0.39
15 11 0.48
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (15 bp):
TTTATATATATCATA
Found at i:3924332 original size:21 final size:23
Alignment explanation
Indices: 3924290--3924332 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 23
3924280 TCATATTTAT
**
3924290 ATAATTATATTTAATATTATCAA
1 ATAATTATATTTAATAACATCAA
3924313 ATAATT-T-TTTAATAACATCA
1 ATAATTATATTTAATAACATCA
3924333 TGTCACTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 11 0.61
22 1 0.06
23 6 0.33
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (23 bp):
ATAATTATATTTAATAACATCAA
Found at i:3926686 original size:28 final size:30
Alignment explanation
Indices: 3926638--3926719 Score: 87
Period size: 30 Copynumber: 2.7 Consensus size: 30
3926628 TAATTGAACT
* *
3926638 TTAAAAGAATAAATAAATATTTTTTA-AATA-
1 TTAAGAGAATAAAT--ATATTTTTTATAAAAC
3926668 TTAAGAGAATAAATATATTTTTTATAAAAC
1 TTAAGAGAATAAATATATTTTTTATAAAAC
* *
3926698 TTTAGAGAAGTAAATATCTTTT
1 TTAAGAGAA-TAAATATATTTT
3926720 ACTTTAAATT
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
28 10 0.22
29 3 0.07
30 21 0.47
31 11 0.24
ACGTcount: A:0.49, C:0.02, G:0.07, T:0.41
Consensus pattern (30 bp):
TTAAGAGAATAAATATATTTTTTATAAAAC
Found at i:3927475 original size:20 final size:19
Alignment explanation
Indices: 3927450--3927507 Score: 66
Period size: 17 Copynumber: 3.0 Consensus size: 19
3927440 CAATTTTAAA
3927450 AATATTTTATTATTTATAAT
1 AATATTTTATT-TTTATAAT
*
3927470 AATA--TTATTTTTATATT
1 AATATTTTATTTTTATAAT
3927487 AATATTATATATTTTTATAAT
1 AATATT-T-TATTTTTATAAT
3927508 TAAATTTAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
17 11 0.34
18 5 0.16
20 5 0.16
21 11 0.34
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
AATATTTTATTTTTATAAT
Found at i:3927482 original size:17 final size:18
Alignment explanation
Indices: 3927456--3927540 Score: 67
Period size: 17 Copynumber: 5.0 Consensus size: 18
3927446 TAAAAATATT
3927456 TTATTATTTATAATAATA
1 TTATTATTTATAATAATA
*
3927474 TTATT-TTTATATTAATA
1 TTATTATTTATAATAATA
*
3927491 TTATATATTT-TTAT-A-A
1 TTAT-TATTTATAATAATA
*
3927507 TTA-AATTTAATAA-AATA
1 TTATTATTT-ATAATAATA
*
3927524 TTTTTATTTA-AATAATA
1 TTATTATTTATAATAATA
3927541 ATTTAAGTTA
Statistics
Matches: 52, Mismatches: 7, Indels: 17
0.68 0.09 0.22
Matches are distributed among these distances:
14 4 0.08
16 9 0.17
17 24 0.46
18 12 0.23
19 3 0.06
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTATTATTTATAATAATA
Found at i:3927486 original size:23 final size:21
Alignment explanation
Indices: 3927454--3927544 Score: 62
Period size: 26 Copynumber: 4.1 Consensus size: 21
3927444 TTTAAAAATA
*
3927454 TTTTATTATTTATAATAATATTAT
1 TTTTA-TATTAAT-ATAATA-TAT
*
3927478 TTTTATATTAATATTATATAT
1 TTTTATATTAATATAATATAT
*
3927499 TTTTATAATTAAATTTAATAAAATAT
1 TTTTAT-ATT-AA--T-ATAATATAT
3927525 TTTTAT-TTAA-ATAATA-AT
1 TTTTATATTAATATAATATAT
3927543 TT
1 TT
3927545 AAGTTAAATT
Statistics
Matches: 57, Mismatches: 5, Indels: 16
0.73 0.06 0.21
Matches are distributed among these distances:
18 4 0.07
19 5 0.09
21 9 0.16
22 8 0.14
23 10 0.18
24 7 0.12
25 1 0.02
26 13 0.23
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
TTTTATATTAATATAATATAT
Found at i:3927502 original size:22 final size:21
Alignment explanation
Indices: 3927466--3927510 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
3927456 TTATTATTTA
3927466 TAATAATAT-TATTTTTATAT
1 TAATAATATATATTTTTATAT
*
3927486 TAATATTATATATTTTTATAAT
1 TAATAATATATATTTTTAT-AT
3927508 TAA
1 TAA
3927511 ATTTAATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 8 0.36
21 9 0.41
22 5 0.23
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
TAATAATATATATTTTTATAT
Found at i:3927839 original size:28 final size:26
Alignment explanation
Indices: 3927769--3927839 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 26
3927759 TTTTTGATCA
3927769 AAATTTTAATATTT-AAAAATTTATT
1 AAATTTTAATATTTAAAAAATTTATT
*
3927794 AAATTTTATTTATATTAAAAAATTTATT
1 AAATTTTA-ATAT-TTAAAAAATTTATT
3927822 AAATTTTAACTAATTTAA
1 AAATTTTAA-T-ATTTAA
3927840 CTGCTATCGG
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
25 8 0.21
26 3 0.08
27 2 0.05
28 24 0.62
29 2 0.05
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (26 bp):
AAATTTTAATATTTAAAAAATTTATT
Found at i:3928279 original size:11 final size:11
Alignment explanation
Indices: 3928263--3928331 Score: 51
Period size: 9 Copynumber: 6.5 Consensus size: 11
3928253 AACGTAAAAA
3928263 ATAATATAAAT
1 ATAATATAAAT
3928274 ATAATATAAAAAT
1 ATAATAT--AAAT
3928287 ATAA-A-AAAT
1 ATAATATAAAT
*
3928296 AAAATATTAAAT
1 ATAATA-TAAAT
*
3928308 -TTATAT-AAT
1 ATAATATAAAT
3928317 AT-ATATAAAT
1 ATAATATAAAT
3928327 -TAATA
1 ATAATA
3928332 ATATATAAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 17
0.70 0.04 0.25
Matches are distributed among these distances:
9 15 0.32
10 9 0.19
11 10 0.21
12 5 0.11
13 8 0.17
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
ATAATATAAAT
Found at i:3928286 original size:22 final size:22
Alignment explanation
Indices: 3928259--3928336 Score: 63
Period size: 22 Copynumber: 3.5 Consensus size: 22
3928249 AGCAAACGTA
3928259 AAAAATAATATAAATATAATAT
1 AAAAATAATATAAATATAATAT
* *
3928281 AAAAAT-ATAAAAAATAAAATAT
1 AAAAATAAT-ATAAATATAATAT
* * *
3928303 TAAATTTATAT-AATAT-ATAT
1 AAAAATAATATAAATATAATAT
3928323 AAATTAATAATATA
1 AAA--AATAATATA
3928337 TAAAAAATTT
Statistics
Matches: 42, Mismatches: 9, Indels: 9
0.70 0.15 0.15
Matches are distributed among these distances:
20 6 0.14
21 6 0.14
22 28 0.67
23 2 0.05
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (22 bp):
AAAAATAATATAAATATAATAT
Found at i:3928340 original size:42 final size:39
Alignment explanation
Indices: 3928272--3928350 Score: 90
Period size: 38 Copynumber: 1.9 Consensus size: 39
3928262 AATAATATAA
*
3928272 ATATAATATAAAAATATAAAAAATAAAATA-TTAAATTT
1 ATATAATATAAAAATATAAAAAATAAAAAATTTAAATTT
3928310 ATATAATATATATAAAT-TAATAATATATAAAAAATTTAAAT
1 ATATAATATA-A-AAATATAA-AA-A-ATAAAAAATTTAAAT
3928351 ATGTGTTTAG
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
38 10 0.29
39 4 0.12
40 6 0.18
41 1 0.03
42 7 0.21
43 6 0.18
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (39 bp):
ATATAATATAAAAATATAAAAAATAAAAAATTTAAATTT
Found at i:3928348 original size:19 final size:18
Alignment explanation
Indices: 3928304--3928348 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 18
3928294 ATAAAATATT
*
3928304 AAATTTATATAATATATAT
1 AAATTTA-ATAATATATAA
3928323 AAA-TTAATAATATATAAA
1 AAATTTAATAATATAT-AA
3928341 AAATTTAA
1 AAATTTAA
3928349 ATATGTGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 9 0.39
18 7 0.30
19 7 0.30
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AAATTTAATAATATATAA
Found at i:3929712 original size:22 final size:22
Alignment explanation
Indices: 3929686--3929758 Score: 92
Period size: 22 Copynumber: 3.3 Consensus size: 22
3929676 ATCTCGTCCG
3929686 ATATATATTTATACATACATAT
1 ATATATATTTATACATACATAT
* * *
3929708 TTATATATTTATCCATACATAC
1 ATATATATTTATACATACATAT
* * *
3929730 ATATATATATATATATATATAT
1 ATATATATTTATACATACATAT
3929752 ATATATA
1 ATATATA
3929759 GAGAGAGAGA
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (22 bp):
ATATATATTTATACATACATAT
Found at i:3929715 original size:8 final size:8
Alignment explanation
Indices: 3929686--3929758 Score: 65
Period size: 8 Copynumber: 9.1 Consensus size: 8
3929676 ATCTCGTCCG
3929686 ATATATAT
1 ATATATAT
* *
3929694 TTATACAT
1 ATATATAT
* *
3929702 ACATATTT
1 ATATATAT
*
3929710 ATATATTT
1 ATATATAT
** *
3929718 ATCCATAC
1 ATATATAT
*
3929726 ATACATAT
1 ATATATAT
3929734 ATATATAT
1 ATATATAT
3929742 ATATATAT
1 ATATATAT
3929750 ATATATAT
1 ATATATAT
3929758 A
1 A
3929759 GAGAGAGAGA
Statistics
Matches: 51, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
8 51 1.00
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (8 bp):
ATATATAT
Found at i:3929737 original size:4 final size:4
Alignment explanation
Indices: 3929730--3929758 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
3929720 CCATACATAC
3929730 ATAT ATAT ATAT ATAT ATAT ATAT ATAT A
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT A
3929759 GAGAGAGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
ATAT
Found at i:3932577 original size:24 final size:24
Alignment explanation
Indices: 3932537--3932584 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
3932527 TTTTTTATTT
*
3932537 TTTTTATATATTTAATATATCATA
1 TTTTTATATATTGAATATATCATA
*
3932561 TTTTTATACT-TTGAATATGTCATA
1 TTTTTATA-TATTGAATATATCATA
3932585 AAAATAAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 20 0.95
25 1 0.05
ACGTcount: A:0.33, C:0.06, G:0.04, T:0.56
Consensus pattern (24 bp):
TTTTTATATATTGAATATATCATA
Found at i:3933439 original size:2 final size:2
Alignment explanation
Indices: 3933426--3933456 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
3933416 TGTTAAAAGA
*
3933426 AG AG AG AA 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
3933457 ATCATGTTTA
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:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3935363 original size:27 final size:28
Alignment explanation
Indices: 3935311--3935377 Score: 82
Period size: 29 Copynumber: 2.4 Consensus size: 28
3935301 GCTACTCGTA
* *
3935311 TGTTTGTCAAAAATGGT-GGTTATTTTG
1 TGTTTGTCAAAAATAGTAGTTTATTTTG
*
3935338 TGTTTGTCAAAAATAGTAGTTTTTTTTTG
1 TGTTTGTCAAAAATAGTAG-TTTATTTTG
*
3935367 TATTTGTCAAA
1 TGTTTGTCAAA
3935378 TATGGAGGCT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 16 0.47
28 1 0.03
29 17 0.50
ACGTcount: A:0.25, C:0.04, G:0.19, T:0.51
Consensus pattern (28 bp):
TGTTTGTCAAAAATAGTAGTTTATTTTG
Found at i:3939911 original size:28 final size:27
Alignment explanation
Indices: 3939856--3939926 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
3939846 GCCACCCATA
3939856 TGTTTGTCAAAAATGGTGGTTATTTTG
1 TGTTTGTCAAAAATGGTGGTTATTTTG
3939883 TGTTTGTCAAAAATGGTGGTT-TCCTTTG
1 TGTTTGTCAAAAATGGTGGTTAT--TTTG
* *
3939911 TATTTGTCAAATATGG
1 TGTTTGTCAAAAATGG
3939927 AGGCTTGTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
26 1 0.03
27 21 0.52
28 18 0.45
ACGTcount: A:0.23, C:0.07, G:0.24, T:0.46
Consensus pattern (27 bp):
TGTTTGTCAAAAATGGTGGTTATTTTG
Found at i:3942226 original size:2 final size:2
Alignment explanation
Indices: 3942215--3942277 Score: 69
Period size: 2 Copynumber: 32.5 Consensus size: 2
3942205 AAAACAGACC
* *
3942215 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TGA AA TA TA TA TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA
*
3942257 TA -A TA TA TA TA TG TA -A TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
3942278 TGCATTAGGT
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
1 3 0.06
2 47 0.92
3 1 0.02
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (2 bp):
TA
Found at i:3942277 original size:15 final size:14
Alignment explanation
Indices: 3942215--3942277 Score: 71
Period size: 15 Copynumber: 4.6 Consensus size: 14
3942205 AAAACAGACC
*
3942215 TATATAATATATATA
1 TATAT-ATATATATG
3942230 TATATATATATATG
1 TATATATATATATG
3942244 -A-A-ATATATATG
1 TATATATATATATG
3942255 TATAATATATATATG
1 TAT-ATATATATATG
3942270 TA-ATATAT
1 TATATATAT
3942278 TGCATTAGGT
Statistics
Matches: 43, Mismatches: 1, Indels: 10
0.80 0.02 0.19
Matches are distributed among these distances:
11 9 0.21
12 2 0.05
13 7 0.16
14 9 0.21
15 16 0.37
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (14 bp):
TATATATATATATG
Found at i:3943144 original size:25 final size:24
Alignment explanation
Indices: 3943106--3943153 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
3943096 TTTTTATATT
*
3943106 AATATTTATAATTAATTTAAATAAA
1 AATATTTATAATT-ATATAAATAAA
* *
3943131 AATATTTTTTATTATATAAATAA
1 AATATTTATAATTATATAAATAA
3943154 TTTAAATCGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
AATATTTATAATTATATAAATAAA
Found at i:3943573 original size:13 final size:13
Alignment explanation
Indices: 3943557--3943581 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3943547 TTATTTTGAT
3943557 ATATTATATATTA
1 ATATTATATATTA
3943570 ATATTATATATT
1 ATATTATATATT
3943582 TTCACGTATT
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:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
ATATTATATATTA
Found at i:3945586 original size:21 final size:21
Alignment explanation
Indices: 3945547--3945587 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3945537 AAATTTAAAA
*
3945547 ATATTTTATATTAATATTTAT
1 ATATTTTATATTAAAATTTAT
3945568 ATATTTTAT-TATAAAATTTA
1 ATATTTTATAT-TAAAATTTA
3945588 AATAAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
ATATTTTATATTAAAATTTAT
Found at i:3945753 original size:31 final size:29
Alignment explanation
Indices: 3945703--3945773 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 29
3945693 ACTATTTAAT
3945703 AATAAAAAATTATTTAAATTTAATTATAAA
1 AATAAAAAATTATTTAAATTTAATTA-AAA
* *
3945733 AATAAAAATATTTTTTAAATTTTATTAAAA
1 AATAAAAA-ATTATTTAAATTTAATTAAAA
*
3945763 ATTTAAAAAAT
1 A-ATAAAAAAT
3945774 AATTCGTGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
30 14 0.39
31 22 0.61
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (29 bp):
AATAAAAAATTATTTAAATTTAATTAAAA
Found at i:3946696 original size:20 final size:20
Alignment explanation
Indices: 3946673--3946728 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 20
3946663 TATTTTTATT
*
3946673 ATATTATAAATATATTTAAA
1 ATATTATAAATATATATAAA
* * *
3946693 ATATTTTATATTTATATAAA
1 ATATTATAAATATATATAAA
*
3946713 AT-TTA-AAATATTTATA
1 ATATTATAAATATATATA
3946729 TATTTATATT
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
18 8 0.29
19 2 0.07
20 18 0.64
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATTATAAATATATATAAA
Found at i:3946701 original size:27 final size:26
Alignment explanation
Indices: 3946671--3946737 Score: 82
Period size: 27 Copynumber: 2.4 Consensus size: 26
3946661 CATATTTTTA
3946671 TTATATTATA-AATATATTTAAAATATT
1 TTATATTATATAA-A-ATTTAAAATATT
3946698 TTATATTTATATAAAATTTAAAATATT
1 TTATA-TTATATAAAATTTAAAATATT
3946725 TATATATTTATAT
1 T-TATA-TTATAT
3946738 TATATTATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
27 18 0.49
28 17 0.46
29 2 0.05
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (26 bp):
TTATATTATATAAAATTTAAAATATT
Found at i:3947026 original size:14 final size:14
Alignment explanation
Indices: 3947009--3947040 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
3946999 CTTTATTTTT
*
3947009 TTTATATTATCATA
1 TTTATATAATCATA
3947023 TTTATATAATCATA
1 TTTATATAATCATA
3947037 TTTA
1 TTTA
3947041 AAATTATGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (14 bp):
TTTATATAATCATA
Found at i:3947418 original size:24 final size:24
Alignment explanation
Indices: 3947362--3947418 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
3947352 ATTATATTTT
**
3947362 TATTTGAAT-TTAATTTTAAAATA
1 TATTTGAATATTAATAATAAAATA
*
3947385 TATTTAAATATTAATAATAAAATA
1 TATTTGAATATTAATAATAAAATA
3947409 -AGTTTGAATA
1 TA-TTTGAATA
3947419 AGTTACTATT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
23 9 0.32
24 19 0.68
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (24 bp):
TATTTGAATATTAATAATAAAATA
Found at i:3948447 original size:28 final size:30
Alignment explanation
Indices: 3948402--3948461 Score: 72
Period size: 28 Copynumber: 2.1 Consensus size: 30
3948392 ATATTTGATA
*
3948402 TTAATATTTATTAAATAT-AAAT-ATAATT
1 TTAATATTTATAAAATATCAAATAATAATT
*
3948430 TTAATATTT-TAAATATATCGAATAATAATT
1 TTAATATTTATAAA-ATATCAAATAATAATT
3948460 TT
1 TT
3948462 TTTCTCCTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 3 0.11
28 13 0.48
29 3 0.11
30 8 0.30
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (30 bp):
TTAATATTTATAAAATATCAAATAATAATT
Found at i:3949922 original size:3 final size:3
Alignment explanation
Indices: 3949914--3949940 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3949904 GTCTGAGATT
3949914 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
3949941 CAAATATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:3950120 original size:17 final size:16
Alignment explanation
Indices: 3950097--3950138 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
3950087 GGTTTGAGTA
3950097 AATATTTAATATGAAT
1 AATATTTAATATGAAT
*
3950113 ATATATTTTATATGAAT
1 A-ATATTTAATATGAAT
3950130 AAT-TTTAAT
1 AATATTTAAT
3950139 TAAAATTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 5 0.22
16 3 0.13
17 15 0.65
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (16 bp):
AATATTTAATATGAAT
Found at i:3950483 original size:2 final size:2
Alignment explanation
Indices: 3950476--3950524 Score: 71
Period size: 2 Copynumber: 24.5 Consensus size: 2
3950466 TCTATAAGTT
* *
3950476 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
3950518 TC TA TA T
1 TA TA TA T
3950525 GTGGTTGTGA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3954881 original size:15 final size:15
Alignment explanation
Indices: 3954863--3954893 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
3954853 GTATTGAATG
3954863 TGAATATATTTAATA
1 TGAATATATTTAATA
3954878 TGAATATATTTAATA
1 TGAATATATTTAATA
3954893 T
1 T
3954894 TTTTCTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (15 bp):
TGAATATATTTAATA
Found at i:3958315 original size:28 final size:29
Alignment explanation
Indices: 3958284--3958410 Score: 89
Period size: 28 Copynumber: 4.2 Consensus size: 29
3958274 ATAAATTATT
*
3958284 AATATATCAAAATTTATATAAAATATAAAATAA
1 AATATATCAAAATTAATAT-AAA-AT--AATAA
* * *
3958317 ATATATATCACAATATAATAT-AAATTAT-T
1 A-ATATATCAAAAT-TAATATAAAATAATAA
*
3958346 AATATATCAAAATTTATATAAAAT-ATAA
1 AATATATCAAAATTAATATAAAATAATAA
* * * *
3958374 AATATTTTAAAAGTAATTATAACATAATAA
1 AATATATCAAAATTAA-TATAAAATAATAA
3958404 AATATAT
1 AATATAT
3958411 GAATATGATA
Statistics
Matches: 75, Mismatches: 13, Indels: 15
0.73 0.13 0.15
Matches are distributed among these distances:
27 7 0.09
28 27 0.36
29 8 0.11
30 12 0.16
32 2 0.03
33 3 0.04
34 11 0.15
35 5 0.07
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.37
Consensus pattern (29 bp):
AATATATCAAAATTAATATAAAATAATAA
Found at i:3958323 original size:34 final size:34
Alignment explanation
Indices: 3958238--3958377 Score: 108
Period size: 28 Copynumber: 4.4 Consensus size: 34
3958228 CATAAAAAAT
*
3958238 TAAAATATAATATAAATATATATATC---TTTATA
1 TAAAATATAAAATAAATA-ATATATCAAATTTATA
* *
3958270 T--AATAT-AAATTATTAATATATCAAAATTTATA
1 TAAAATATAAAATAAATAATATATC-AAATTTATA
*
3958302 TAAAATATAAAATAAAT-ATATATCACA---ATA
1 TAAAATATAAAATAAATAATATATCAAATTTATA
* *
3958332 T--AATAT-AAATTATTAATATATCAAAATTTATA
1 TAAAATATAAAATAAATAATATATC-AAATTTATA
3958364 TAAAATATAAAATA
1 TAAAATATAAAATA
3958378 TTTTAAAAGT
Statistics
Matches: 83, Mismatches: 10, Indels: 27
0.69 0.08 0.22
Matches are distributed among these distances:
27 6 0.07
28 19 0.23
29 8 0.10
30 9 0.11
32 12 0.14
33 2 0.02
34 17 0.20
35 10 0.12
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (34 bp):
TAAAATATAAAATAAATAATATATCAAATTTATA
Found at i:3958341 original size:62 final size:63
Alignment explanation
Indices: 3958238--3958377 Score: 230
Period size: 62 Copynumber: 2.2 Consensus size: 63
3958228 CATAAAAAAT
* *
3958238 TAAAATATAATATAAATATATATATCTTTATATAATATAAATTATTAATATATCAAAATTTATA
1 TAAAATATAAAATAAATATATATATC-TAATATAATATAAATTATTAATATATCAAAATTTATA
3958302 TAAAATATAAAATAAATATATATCA-C-AATATAATATAAATTATTAATATATCAAAATTTATA
1 TAAAATATAAAATAAATATATAT-ATCTAATATAATATAAATTATTAATATATCAAAATTTATA
3958364 TAAAATATAAAATA
1 TAAAATATAAAATA
3958378 TTTTAAAAGT
Statistics
Matches: 73, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
62 49 0.67
64 23 0.32
65 1 0.01
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (63 bp):
TAAAATATAAAATAAATATATATATCTAATATAATATAAATTATTAATATATCAAAATTTATA
Found at i:3958552 original size:2 final size:2
Alignment explanation
Indices: 3958539--3958573 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
3958529 TCTTAATTTA
*
3958539 AT AT AC 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
3958574 CATTACGTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:3959448 original size:16 final size:17
Alignment explanation
Indices: 3959424--3959458 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
3959414 ATAGATATAA
3959424 AAAAATTA-TAAATATT
1 AAAAATTATTAAATATT
*
3959440 AAAATTTATTAAATATT
1 AAAAATTATTAAATATT
3959457 AA
1 AA
3959459 TATAACTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
AAAAATTATTAAATATT
Found at i:3959797 original size:31 final size:32
Alignment explanation
Indices: 3959724--3959798 Score: 86
Period size: 31 Copynumber: 2.4 Consensus size: 32
3959714 TTAAGTTTAA
*
3959724 ATTAATTTAAAATTTTATTTTATTATATATTAT
1 ATTAA-TTAAAATATTATTTTATTATATATTAT
3959757 ATTAA-TAAAATATTATTTTA-TATTAATATT-T
1 ATTAATTAAAATATTATTTTATTA-T-ATATTAT
3959788 A-TAATTAAAAT
1 ATTAATTAAAAT
3959799 TAAATATTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
30 5 0.13
31 23 0.61
32 5 0.13
33 5 0.13
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (32 bp):
ATTAATTAAAATATTATTTTATTATATATTAT
Found at i:3961305 original size:15 final size:16
Alignment explanation
Indices: 3961284--3961327 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
3961274 ATAATTTTTT
3961284 TATTTAAATTAATTTA
1 TATTTAAATTAATTTA
* *
3961300 -ATTTAATTTAAATTA
1 TATTTAAATTAATTTA
*
3961315 TTTTTAAATTAAT
1 TATTTAAATTAAT
3961328 AAAAATAATT
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TATTTAAATTAATTTA
Found at i:3961326 original size:21 final size:21
Alignment explanation
Indices: 3961285--3961341 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 21
3961275 TAATTTTTTT
* *
3961285 ATTTAAATTA-ATTTAATTTA
1 ATTTAAATTATTTTTAAATTA
3961305 ATTTAAATTATTTTTAAATTA
1 ATTTAAATTATTTTTAAATTA
** *
3961326 ATAAAAATAATTTTTA
1 ATTTAAATTATTTTTA
3961342 TTTAAATTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
20 10 0.32
21 21 0.68
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
ATTTAAATTATTTTTAAATTA
Found at i:3962904 original size:26 final size:26
Alignment explanation
Indices: 3962865--3962915 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
3962855 ATATAAATAT
** *
3962865 AATATAAATTTATAATTATATATAAA
1 AATATAAAAATATAATTATAGATAAA
*
3962891 AATATAAAAATATATTTATAGATAA
1 AATATAAAAATATAATTATAGATAA
3962916 TCGTATTCAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (26 bp):
AATATAAAAATATAATTATAGATAAA
Found at i:3963676 original size:6 final size:6
Alignment explanation
Indices: 3963667--3963691 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3963657 ATAGTAATAG
3963667 TATAAT TATAAT TATAAT TATAAT T
1 TATAAT TATAAT TATAAT TATAAT T
3963692 TTTATAATCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TATAAT
Found at i:3966637 original size:25 final size:25
Alignment explanation
Indices: 3966587--3966643 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 25
3966577 AATAAAAAAT
* *
3966587 AATTTTATTTTTATATTCAATTTTA
1 AATTTAATTTTTATATTCAATATTA
*
3966612 AATTTAATTATTTATATTTAA-ATTA
1 AATTTAATT-TTTATATTCAATATTA
*
3966637 AAATTAA
1 AATTTAA
3966644 AATTTTATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 17 0.63
26 10 0.37
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (25 bp):
AATTTAATTTTTATATTCAATATTA
Found at i:3966640 original size:26 final size:25
Alignment explanation
Indices: 3966587--3966651 Score: 67
Period size: 26 Copynumber: 2.6 Consensus size: 25
3966577 AATAAAAAAT
* * *
3966587 AATTTTATTTTTATATTCAATTTTA
1 AATTTAATTTTTATATTCAAATTAA
*
3966612 AATTTAATTATTTATATTTAAATTAA
1 AATTTAATT-TTTATATTCAAATTAA
* *
3966638 AATTAAAATTTTAT
1 AATTTAATTTTTAT
3966652 TAATAATTAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
25 13 0.39
26 20 0.61
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (25 bp):
AATTTAATTTTTATATTCAAATTAA
Found at i:3968185 original size:18 final size:20
Alignment explanation
Indices: 3968162--3968201 Score: 66
Period size: 18 Copynumber: 2.1 Consensus size: 20
3968152 AACATAAAAA
3968162 ATAATATAAA-TATT-TTAT
1 ATAATATAAATTATTATTAT
3968180 ATAATATAAATTATTATTAT
1 ATAATATAAATTATTATTAT
3968200 AT
1 AT
3968202 TAAAATTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 10 0.50
19 4 0.20
20 6 0.30
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATAATATAAATTATTATTAT
Found at i:3969250 original size:14 final size:14
Alignment explanation
Indices: 3969231--3969259 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3969221 AAATAACATC
3969231 TCCAATTGGTCAAT
1 TCCAATTGGTCAAT
3969245 TCCAATTGGTCAAT
1 TCCAATTGGTCAAT
3969259 T
1 T
3969260 TGACTTATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.38
Consensus pattern (14 bp):
TCCAATTGGTCAAT
Found at i:3969825 original size:198 final size:198
Alignment explanation
Indices: 3969480--3969874 Score: 720
Period size: 198 Copynumber: 2.0 Consensus size: 198
3969470 TTTTAAGGCC
3969480 TAGTCTTGTCCATAGAGATTCCAACACGTGTTTAATATTTTATTATTATTTTTTAAATAAAATAT
1 TAGTCTTGTCCATAGAGATTCCAACACGTGTTTAATATTTTATTATTATTTTTTAAATAAAATAT
3969545 ACTCATAAAAAAAAAAATTATCCTTGTTTGATATCGGTTAAATTATATTATCAATCCCTATAGTA
66 ACTCATAAAAAAAAAAATTATCCTTGTTTGATATCGGTTAAATTATATTATCAATCCCTATAGTA
3969610 AATTAATGAAGTTTACCTTTCTATTATTTTATCAAATTGAATCCCATACTTGTGTGTATATATAT
131 AATTAATGAAGTTTACCTTTCTATTATTTTATCAAATTGAATCCCATACTTGTGTGTATATATAT
3969675 ATA
196 ATA
3969678 TAGTCTTGTCCATAGAGATTCCAACACGTGTTTAATATTTTATTATTATTTTTTAAATAAAATAT
1 TAGTCTTGTCCATAGAGATTCCAACACGTGTTTAATATTTTATTATTATTTTTTAAATAAAATAT
** *
3969743 ACTCATAAAAAAATTTATTTATCCTTGTTTGATATC-GTTAAATTATATTATCAATCCCTATAGT
66 ACTCATAAAAAAA-AAAATTATCCTTGTTTGATATCGGTTAAATTATATTATCAATCCCTATAGT
* * *
3969807 ACATTAATGAATTTTACCTTTCTATTATTTTATCAAATTTAATCCCATACTTGTGTGTATATATA
130 AAATTAATGAAGTTTACCTTTCTATTATTTTATCAAATTGAATCCCATACTTGTGTGTATATATA
3969872 TAT
195 TAT
3969875 TTACCTTTAT
Statistics
Matches: 190, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
198 171 0.90
199 19 0.10
ACGTcount: A:0.35, C:0.12, G:0.08, T:0.45
Consensus pattern (198 bp):
TAGTCTTGTCCATAGAGATTCCAACACGTGTTTAATATTTTATTATTATTTTTTAAATAAAATAT
ACTCATAAAAAAAAAAATTATCCTTGTTTGATATCGGTTAAATTATATTATCAATCCCTATAGTA
AATTAATGAAGTTTACCTTTCTATTATTTTATCAAATTGAATCCCATACTTGTGTGTATATATAT
ATA
Found at i:3970237 original size:44 final size:44
Alignment explanation
Indices: 3970174--3970262 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
3970164 ACCTTTGAGA
3970174 TCAATAAAAGAAGGGAATCCCTTTCTTTCATACCTCTTCTAGTT
1 TCAATAAAAGAAGGGAATCCCTTTCTTTCATACCTCTTCTAGTT
3970218 TCAATAAAAGAAGGGAATCCCTTTCTTTCATACCTCTTCTAGTT
1 TCAATAAAAGAAGGGAATCCCTTTCTTTCATACCTCTTCTAGTT
3970262 T
1 T
3970263 AATTGGTGGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.29, C:0.22, G:0.11, T:0.37
Consensus pattern (44 bp):
TCAATAAAAGAAGGGAATCCCTTTCTTTCATACCTCTTCTAGTT
Found at i:3970787 original size:4 final size:4
Alignment explanation
Indices: 3970778--3970809 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
3970768 TCCTCTTTTC
3970778 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
3970810 TTATTCTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:3971489 original size:17 final size:18
Alignment explanation
Indices: 3971450--3971492 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
3971440 ACTTTTTTTT
*
3971450 ATTTTTTTAATTAACATAT
1 ATTTTTTTAA-TAACATAA
*
3971469 ATTTTTTTAA-AATATAA
1 ATTTTTTTAATAACATAA
3971486 ATTTTTT
1 ATTTTTT
3971493 ATTAATAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 12 0.55
19 10 0.45
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (18 bp):
ATTTTTTTAATAACATAA
Found at i:3973291 original size:4 final size:4
Alignment explanation
Indices: 3973282--3973309 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
3973272 GCAAGTTTAC
3973282 AATT AATT AATT AATT AATT AATT AATT
1 AATT AATT AATT AATT AATT AATT AATT
3973310 TTAAAAGATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
AATT
Found at i:3973690 original size:2 final size:2
Alignment explanation
Indices: 3973683--3973708 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3973673 ATACATATTC
3973683 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
3973709 TTGTTTTGAG
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:3974000 original size:12 final size:13
Alignment explanation
Indices: 3973978--3974010 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
3973968 AATATGTTAT
3973978 TTTATTAAAAAA-A
1 TTTA-TAAAAAATA
3973991 TTTATAAAAAATA
1 TTTATAAAAAATA
3974004 TTTATAA
1 TTTATAA
3974011 TTTTATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
TTTATAAAAAATA
Found at i:3974094 original size:18 final size:18
Alignment explanation
Indices: 3974053--3974095 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
3974043 TATTTATGGT
*
3974053 TATTATATTAAATATAAA
1 TATTAAATTAAATATAAA
* * *
3974071 TTTTAAATTATATATATA
1 TATTAAATTAAATATAAA
3974089 TATTAAA
1 TATTAAA
3974096 ATTTATCACA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TATTAAATTAAATATAAA
Found at i:3975018 original size:2 final size:2
Alignment explanation
Indices: 3975011--3975045 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3975001 TGTAGAAAAC
3975011 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 T
3975046 TCTTCAATCT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3975489 original size:24 final size:25
Alignment explanation
Indices: 3975462--3975510 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
3975452 TTATTTTTTA
3975462 AAATTTAATTAT-AAATATTAATAT
1 AAATTTAATTATAAAATATTAATAT
* * *
3975486 AAATTTATTTTTAAAATTTTAATAT
1 AAATTTAATTATAAAATATTAATAT
3975511 TATTTGTATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (25 bp):
AAATTTAATTATAAAATATTAATAT
Found at i:3977305 original size:18 final size:17
Alignment explanation
Indices: 3977271--3977323 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
3977261 TGTATAAAAT
3977271 ATTTTATATTTATATAA
1 ATTTTATATTTATATAA
3977288 ATTTTAATATATTA-AT-A
1 ATTTT-ATAT-TTATATAA
*
3977305 A-TTTATA-TAATATAA
1 ATTTTATATTTATATAA
3977320 ATTT
1 ATTT
3977324 AAAAAATTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 11
0.71 0.02 0.26
Matches are distributed among these distances:
13 2 0.07
14 2 0.07
15 5 0.17
16 5 0.17
17 7 0.23
18 6 0.20
19 3 0.10
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATTTTATATTTATATAA
Found at i:3978728 original size:19 final size:18
Alignment explanation
Indices: 3978704--3978743 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
3978694 TAGTCGAATT
3978704 TAAAATATAATATATTACA
1 TAAAATATAATATATTA-A
*
3978723 TAAAATTTAATATATTAA
1 TAAAATATAATATATTAA
3978741 TAA
1 TAA
3978744 TTCATATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (18 bp):
TAAAATATAATATATTAA
Found at i:3978729 original size:26 final size:25
Alignment explanation
Indices: 3978700--3978749 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
3978690 ATCATAGTCG
3978700 AATTTAAAATA-TAATATATTACATAA
1 AATTTAAAATATTAATA-ATT-CATAA
*
3978726 AATTTAATATATTAATAATTCATA
1 AATTTAAAATATTAATAATTCATA
3978750 TTATATATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 4 0.18
26 13 0.59
27 5 0.23
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (25 bp):
AATTTAAAATATTAATAATTCATAA
Found at i:3979337 original size:2 final size:2
Alignment explanation
Indices: 3979330--3979355 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3979320 AGTTCAAACA
3979330 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
3979356 TGCTTAAAAA
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:3979751 original size:27 final size:28
Alignment explanation
Indices: 3979705--3979757 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
3979695 TTACCCTTAT
* * *
3979705 TTAATTTTTTTATTTTATAATTTATTTA
1 TTAATTTTTATATTTAATAATATATTTA
3979733 TTAA-TTTTATATTTAATAATATATT
1 TTAATTTTTATATTTAATAATATATT
3979758 AATATTGCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 18 0.82
28 4 0.18
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (28 bp):
TTAATTTTTATATTTAATAATATATTTA
Found at i:3980123 original size:18 final size:18
Alignment explanation
Indices: 3980102--3980137 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3980092 TTTTAGGGAT
*
3980102 TTTTTTATATTTAATTAA
1 TTTTTTATATTAAATTAA
*
3980120 TTTTTTTTATTAAATTAA
1 TTTTTTATATTAAATTAA
3980138 AAAATTTATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTTTTATATTAAATTAA
Found at i:3980339 original size:18 final size:20
Alignment explanation
Indices: 3980302--3980368 Score: 64
Period size: 21 Copynumber: 3.1 Consensus size: 20
3980292 TTATCTAAAT
3980302 TTATTTATAAACTTATTTTTA
1 TTATTTATAAAC-TATTTTTA
3980323 TTATTTATAAA-TATTTTAATA
1 TTATTTATAAACTATTTT--TA
* *
3980344 ATATTTAAATAAAATATTTTTA
1 TTATTT--ATAAACTATTTTTA
3980366 TTA
1 TTA
3980369 ATTAACTAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
19 6 0.15
21 18 0.46
22 4 0.10
23 5 0.13
24 6 0.15
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (20 bp):
TTATTTATAAACTATTTTTA
Found at i:3980362 original size:34 final size:34
Alignment explanation
Indices: 3980324--3980392 Score: 79
Period size: 34 Copynumber: 2.0 Consensus size: 34
3980314 TTATTTTTAT
*
3980324 TATTTATAAATATTTTAA-TAAT-ATTTAAATAAAA
1 TATTT-TAAATA-ATTAACTAATAATTTAAATAAAA
* *
3980358 TATTTTTATTAATTAACTAATAATTTAAATAAAA
1 TATTTTAAATAATTAACTAATAATTTAAATAAAA
3980392 T
1 T
3980393 TAATTAATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
32 4 0.13
33 8 0.27
34 18 0.60
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (34 bp):
TATTTTAAATAATTAACTAATAATTTAAATAAAA
Found at i:3980704 original size:3 final size:3
Alignment explanation
Indices: 3980696--3980725 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
3980686 TTTCTTAAAT
3980696 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3980726 CAACAACAAC
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:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:3981887 original size:14 final size:14
Alignment explanation
Indices: 3981847--3981887 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
3981837 AGTTTTTTCA
*
3981847 TATATTTAGAAAAT
1 TATATTTAGAAATT
**
3981861 TATATTTCTAAATT
1 TATATTTAGAAATT
3981875 TATATTTAGAAAT
1 TATATTTAGAAAT
3981888 ATGTGGGACA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (14 bp):
TATATTTAGAAATT
Found at i:3988149 original size:16 final size:16
Alignment explanation
Indices: 3988128--3988163 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
3988118 TACTCGTTAA
*
3988128 TTAAATTTAGATCATT
1 TTAAATTTAAATCATT
3988144 TTAAATTTAAATCATT
1 TTAAATTTAAATCATT
3988160 TTAA
1 TTAA
3988164 GTTTCAGTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.50
Consensus pattern (16 bp):
TTAAATTTAAATCATT
Found at i:3988351 original size:21 final size:19
Alignment explanation
Indices: 3988326--3988371 Score: 56
Period size: 22 Copynumber: 2.3 Consensus size: 19
3988316 TTTTCTCATC
3988326 AAATTAAAATAAATTAAATTTA
1 AAATTAAAA-AAATT-AA-TTA
*
3988348 AATTTAAAAAAATTAATTA
1 AAATTAAAAAAATTAATTA
3988367 AAATT
1 AAATT
3988372 TCAAATTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 7 0.32
20 2 0.09
21 5 0.23
22 8 0.36
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
AAATTAAAAAAATTAATTA
Found at i:3988903 original size:26 final size:26
Alignment explanation
Indices: 3988867--3988918 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
3988857 TTAACAACTA
3988867 ACCTTAAACTGGTGTGTATGTTTGAG
1 ACCTTAAACTGGTGTGTATGTTTGAG
3988893 ACCTTAAACTGGTGTGTATGTTTGAG
1 ACCTTAAACTGGTGTGTATGTTTGAG
3988919 CATATATGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.23, C:0.12, G:0.27, T:0.38
Consensus pattern (26 bp):
ACCTTAAACTGGTGTGTATGTTTGAG
Found at i:3989825 original size:53 final size:53
Alignment explanation
Indices: 3989768--3989874 Score: 205
Period size: 53 Copynumber: 2.0 Consensus size: 53
3989758 CCTTAAATTT
3989768 AATCAATGTTTTATTTAATATAAAGGCCTATCAAAGTACAAATCAAAAGATAA
1 AATCAATGTTTTATTTAATATAAAGGCCTATCAAAGTACAAATCAAAAGATAA
*
3989821 AATCAATGTTTTATTTAATATAAAGGCCTATCAGAGTACAAATCAAAAGATAA
1 AATCAATGTTTTATTTAATATAAAGGCCTATCAAAGTACAAATCAAAAGATAA
3989874 A
1 A
3989875 GACTTATTTG
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.49, C:0.11, G:0.10, T:0.30
Consensus pattern (53 bp):
AATCAATGTTTTATTTAATATAAAGGCCTATCAAAGTACAAATCAAAAGATAA
Found at i:3991781 original size:2 final size:2
Alignment explanation
Indices: 3991774--3991808 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3991764 TTACCAAACA
3991774 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
3991809 ACTTTTCAAG
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:3992800 original size:2 final size:2
Alignment explanation
Indices: 3992793--3992833 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
3992783 TTAAAAGAAA
3992793 AG AG AG AG 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 AG AG AG AG A
3992834 AGGTTTTACC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3993990 original size:11 final size:11
Alignment explanation
Indices: 3993940--3993990 Score: 52
Period size: 10 Copynumber: 4.8 Consensus size: 11
3993930 TTATAAAATA
3993940 TATTTATATTT
1 TATTTATATTT
*
3993951 TA-TCATATTT
1 TATTTATATTT
*
3993961 TAATTA-ATTT
1 TATTTATATTT
* *
3993971 TATTAATATTA
1 TATTTATATTT
3993982 TATTTATAT
1 TATTTATAT
3993991 AATTATATTT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
10 17 0.53
11 15 0.47
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (11 bp):
TATTTATATTT
Found at i:3995381 original size:146 final size:144
Alignment explanation
Indices: 3995117--3995391 Score: 408
Period size: 146 Copynumber: 1.9 Consensus size: 144
3995107 TTATACACAC
* * *
3995117 TATTCTCAAAAAAACCATCAAATATGTGGCATTTAAAGTCATTTTACTCGGATCCTTTAGTTTTA
1 TATTCTCAAAAAAACCATCAAATATATGGCATTTAAAGCCATTTTACTCGGACCCTTTAGTTTTA
* * * *
3995182 CTTATATATCTATATTTGACGCTTGTAATTGATATATATTTTAATATAGGCATATAATCATATGC
66 CTTATATATCTATATTTGACACTTATAATTGATATATATTTTAATATAAGCATATAACCATATGC
3995247 CATCAAATATATAT
131 CATCAAATATATAT
* *
3995261 TATTCTCAAACAAACCATCAAATATATATGGCATTTAAAAGCCATTTTACTCGGACCCTTTGGTT
1 TATTCTCAAAAAAACCATC-AA-ATATATGGCATTT-AAAGCCATTTTACTCGGACCCTTTAGTT
* * *
3995326 TTAC-TATATATCTATATTTGATACTTATAATTGATATATATTTTGATATAAGCATATGACCATA
63 TTACTTATATATCTATATTTGACACTTATAATTGATATATATTTTAATATAAGCATATAACCATA
3995390 TG
128 TG
3995392 AGGGGTCTAA
Statistics
Matches: 116, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
144 18 0.16
145 2 0.02
146 67 0.58
147 29 0.25
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (144 bp):
TATTCTCAAAAAAACCATCAAATATATGGCATTTAAAGCCATTTTACTCGGACCCTTTAGTTTTA
CTTATATATCTATATTTGACACTTATAATTGATATATATTTTAATATAAGCATATAACCATATGC
CATCAAATATATAT
Found at i:3995818 original size:344 final size:344
Alignment explanation
Indices: 3995190--3995877 Score: 1162
Period size: 344 Copynumber: 2.0 Consensus size: 344
3995180 TACTTATATA
* *
3995190 TCTATATTTGACGCTTGTAATTGATATATATTTTAATATAGGCATATAATCATATGCCATCAAAT
1 TCTATATTTGACGCTTATAATTGATATATATTTTAATATAGGCATATAACCATATGCCATCAAAT
* *
3995255 ATATATTATTCTCAAACAAACCATCAAATATATATGGCATTTAAAAGCCATTTTACTCGGACCCT
66 ATATATTATTCTCAAACAAACCATCAAATATATATGGCATTTAAAAGCCATCTTACTCGAACCCT
* *
3995320 TTGGTTTTACTATATATCTATATTTGATACTTATAATTGATATATATTTTGATATAAGCATATGA
131 ATGGTTTTACTATATATCTATATTTGATACTTATAATAGATATATATTTTGATATAAGCATATGA
* * *
3995385 CCATATGAGGGGTCTAATCCTCTAAATAAATGAAAAAAAAAACTTCTAAAAAAATTAATATATAC
196 CCATATGAGGGGTCTAATCCTCTAAATAAATAAAAAAAAAAACTTCTAAAAAAATAAATATACAC
* * * *
3995450 ATGTCAAACACATGCATGTTCATATCTGATTTCATCTTAAATCCGAATAACATAAATTTTAAGTG
261 ATGTCAAACACATACATATTCATATCTGATTTCACCTTAAATCCGAATAACATAAATTTCAAGTG
3995515 AATTAGAATTTTTAGTTAT
326 AATTAGAATTTTTAGTTAT
* *
3995534 TCTATATTTGACGCTTATAATTGATATATATTTTGATATAGGCATATGACCATATGCCATCAAAT
1 TCTATATTTGACGCTTATAATTGATATATATTTTAATATAGGCATATAACCATATGCCATCAAAT
*
3995599 ATATGTTATTCTCAAACAAACCATCAAATATATATGGCATTT-AAAGCCATCTTACTCGAACCCT
66 ATATATTATTCTCAAACAAACCATCAAATATATATGGCATTTAAAAGCCATCTTACTCGAACCCT
* *
3995663 ATGGTTTTACTATATATCTATATTTGATATTTATAATAGATATATATTTTGATATAGGCATATGA
131 ATGGTTTTACTATATATCTATATTTGATACTTATAATAGATATATATTTTGATATAAGCATATGA
* *
3995728 CCATATGAGGGGTCTAATCTTCTAAATATATAAAAAAAAAAAACTTCTAAAAAAATAAATATACA
196 CCATATGAGGGGTCTAATCCTCTAAATAAAT-AAAAAAAAAAACTTCTAAAAAAATAAATATACA
* *
3995793 CATGTCAAACACATACATATTCATATCTGATTTCACCTTAAATCTGAATAACATAAGTTTCAAGT
260 CATGTCAAACACATACATATTCATATCTGATTTCACCTTAAATCCGAATAACATAAATTTCAAGT
3995858 GAATTAGAATTTTTAGTTAT
325 GAATTAGAATTTTTAGTTAT
3995878 CCCATTTTAA
Statistics
Matches: 321, Mismatches: 22, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
343 110 0.34
344 211 0.66
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.37
Consensus pattern (344 bp):
TCTATATTTGACGCTTATAATTGATATATATTTTAATATAGGCATATAACCATATGCCATCAAAT
ATATATTATTCTCAAACAAACCATCAAATATATATGGCATTTAAAAGCCATCTTACTCGAACCCT
ATGGTTTTACTATATATCTATATTTGATACTTATAATAGATATATATTTTGATATAAGCATATGA
CCATATGAGGGGTCTAATCCTCTAAATAAATAAAAAAAAAAACTTCTAAAAAAATAAATATACAC
ATGTCAAACACATACATATTCATATCTGATTTCACCTTAAATCCGAATAACATAAATTTCAAGTG
AATTAGAATTTTTAGTTAT
Found at i:4007921 original size:2 final size:2
Alignment explanation
Indices: 4007914--4007939 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4007904 TTCCTGTAAT
4007914 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
4007940 ATGATTCATG
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:4011224 original size:24 final size:23
Alignment explanation
Indices: 4011178--4011233 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 23
4011168 AAAAATCAAA
*
4011178 TTTAATTTA-TAAAAATTTCATT
1 TTTAATTTATTAAAAAATTCATT
4011200 TTATATATTTATTAAAAAATT-ATT
1 TT-TA-ATTTATTAAAAAATTCATT
4011224 TTTAATTTAT
1 TTTAATTTAT
4011234 AAGATTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
22 8 0.27
23 4 0.13
24 10 0.33
25 8 0.27
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (23 bp):
TTTAATTTATTAAAAAATTCATT
Found at i:4012754 original size:166 final size:166
Alignment explanation
Indices: 4012576--4012919 Score: 670
Period size: 166 Copynumber: 2.1 Consensus size: 166
4012566 ATACATTACA
*
4012576 ATATTAAAATAATTGAATCATCTAAATTTTACTTAAATTTATCCATATGTTGGACCACTTGTTTA
1 ATATTAAAATAATTGAATCATCTAAATTTTACTTAAATTTATCCATATGTTGGACCACTTGTTCA
4012641 AACCGAATCCTGACATAGTTTTAATAATTTAAATTGATCTAATTCGAATTATTATTTAATAATAA
66 AACCGAATCCTGACATAGTTTTAATAATTTAAATTGATCTAATTCGAATTATTATTTAATAATAA
*
4012706 AAAATATTTTTATTTTAATTTAATTATAAAATATAT
131 AAAATATTTTTATTTTAATTTAATTATAAAAAATAT
4012742 ATATTAAAATAATTGAATCATCTAAATTTTACTTAAATTTATCCATATGTTGGACCACTTGTTCA
1 ATATTAAAATAATTGAATCATCTAAATTTTACTTAAATTTATCCATATGTTGGACCACTTGTTCA
4012807 AACCGAATCCTGACATAGTTTTAATAATTTAAATTGATCTAATTCGAATTATTATTTAATAATAA
66 AACCGAATCCTGACATAGTTTTAATAATTTAAATTGATCTAATTCGAATTATTATTTAATAATAA
4012872 AAAATATTTTTATTTTAATTTAATTATAAAAAATAT
131 AAAATATTTTTATTTTAATTTAATTATAAAAAATAT
4012908 ATATTAAAATAA
1 ATATTAAAATAA
4012920 AAATAATTTT
Statistics
Matches: 176, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
166 176 1.00
ACGTcount: A:0.42, C:0.09, G:0.06, T:0.43
Consensus pattern (166 bp):
ATATTAAAATAATTGAATCATCTAAATTTTACTTAAATTTATCCATATGTTGGACCACTTGTTCA
AACCGAATCCTGACATAGTTTTAATAATTTAAATTGATCTAATTCGAATTATTATTTAATAATAA
AAAATATTTTTATTTTAATTTAATTATAAAAAATAT
Found at i:4012980 original size:15 final size:16
Alignment explanation
Indices: 4012949--4012996 Score: 62
Period size: 15 Copynumber: 2.9 Consensus size: 16
4012939 TATGAATAAT
4012949 AATTTAAAATTTTAAATA
1 AATTT-AAA-TTTAAATA
*
4012967 AATTTAAA-TTAAATT
1 AATTTAAATTTAAATA
4012982 AATTTAAATTTAAAT
1 AATTTAAATTTAAAT
4012997 TAAAAAAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 14 0.50
16 6 0.21
17 3 0.11
18 5 0.18
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
AATTTAAATTTAAATA
Found at i:4013006 original size:21 final size:21
Alignment explanation
Indices: 4012965--4013007 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
4012955 AAATTTTAAA
**
4012965 TAAATTTAAATTAAATTAATT
1 TAAATTTAAATTAAAAAAATT
4012986 TAAATTTAAATTAAAAAAATT
1 TAAATTTAAATTAAAAAAATT
4013007 T
1 T
4013008 CAATCATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TAAATTTAAATTAAAAAAATT
Found at i:4013301 original size:16 final size:16
Alignment explanation
Indices: 4013264--4013329 Score: 50
Period size: 16 Copynumber: 4.2 Consensus size: 16
4013254 TGGACTTCCC
*
4013264 TTAAAAATAAT-AATAA
1 TTAAAAATTATAAAT-A
*
4013280 TAAAAAATTATAAATA
1 TTAAAAATTATAAATA
*
4013296 TTAAAATTTA-AAAT-
1 TTAAAAATTATAAATA
*
4013310 TTAAATA-TATTAAATA
1 TTAAAAATTA-TAAATA
4013326 TTAA
1 TTAA
4013330 TTTTAAAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
13 2 0.05
14 5 0.12
15 8 0.20
16 22 0.55
17 3 0.08
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
TTAAAAATTATAAATA
Found at i:4013577 original size:21 final size:21
Alignment explanation
Indices: 4013537--4013578 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
4013527 ATATAATTAT
* **
4013537 ATTATATTTTTATATTTAAAA
1 ATTATATTATTATACATAAAA
4013558 ATTATATTATTATACATAAAA
1 ATTATATTATTATACATAAAA
4013579 TTTTAAAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTATATTATTATACATAAAA
Found at i:4022569 original size:19 final size:17
Alignment explanation
Indices: 4022545--4022580 Score: 54
Period size: 19 Copynumber: 2.0 Consensus size: 17
4022535 AGTAAAAAAA
4022545 AAAGGCCAATAGATAAAGG
1 AAAGGCCAA-AG-TAAAGG
4022564 AAAGGCCAAAGTAAAGG
1 AAAGGCCAAAGTAAAGG
4022581 CAGGTTCAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
18 2 0.12
19 9 0.53
ACGTcount: A:0.53, C:0.11, G:0.28, T:0.08
Consensus pattern (17 bp):
AAAGGCCAAAGTAAAGG
Found at i:4028283 original size:21 final size:21
Alignment explanation
Indices: 4028258--4028322 Score: 58
Period size: 21 Copynumber: 3.1 Consensus size: 21
4028248 AATTGGTAGA
4028258 GGTGGAGAGTAGACAGGCGGT
1 GGTGGAGAGTAGACAGGCGGT
* * ** * *
4028279 GGTGGTGAGTAAATTGGTGGA
1 GGTGGAGAGTAGACAGGCGGT
* *
4028300 GGCGGAGAGTAGACAGGGGGT
1 GGTGGAGAGTAGACAGGCGGT
4028321 GG
1 GG
4028323 AGGGGAGTGA
Statistics
Matches: 31, Mismatches: 13, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.23, C:0.06, G:0.54, T:0.17
Consensus pattern (21 bp):
GGTGGAGAGTAGACAGGCGGT
Found at i:4028293 original size:42 final size:42
Alignment explanation
Indices: 4028234--4028338 Score: 138
Period size: 42 Copynumber: 2.5 Consensus size: 42
4028224 TACGAGTGGT
* * *
4028234 GGTGGTTGTGAGAAAATTGGTAGAGGTGGAGAGTAGACAGGC
1 GGTGGTGGTGAGTAAATTGGTAGAGGCGGAGAGTAGACAGGC
* *
4028276 GGTGGTGGTGAGTAAATTGGTGGAGGCGGAGAGTAGACAGGG
1 GGTGGTGGTGAGTAAATTGGTAGAGGCGGAGAGTAGACAGGC
* * *
4028318 GGTGGAGGGGAGTGAATTGGT
1 GGTGGTGGTGAGTAAATTGGT
4028339 GGTGGCGGGG
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 55 1.00
ACGTcount: A:0.25, C:0.04, G:0.50, T:0.21
Consensus pattern (42 bp):
GGTGGTGGTGAGTAAATTGGTAGAGGCGGAGAGTAGACAGGC
Found at i:4028420 original size:21 final size:21
Alignment explanation
Indices: 4028396--4028472 Score: 73
Period size: 21 Copynumber: 3.4 Consensus size: 21
4028386 GGAATAAATG
4028396 GGTGGTGGAGGAGAGTAGACT
1 GGTGGTGGAGGAGAGTAGACT
* * *
4028417 GGTGGTGGTGGGGGTGGTGAATGAACT
1 GGTGGTGG-AGGAG-AGT--A-G-ACT
4028444 GGTGGTGGAGGAGAGTAGACT
1 GGTGGTGGAGGAGAGTAGACT
4028465 GGTGGTGG
1 GGTGGTGG
4028473 TGGGGGTGGT
Statistics
Matches: 44, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
21 19 0.43
22 4 0.09
23 3 0.07
25 3 0.07
26 4 0.09
27 11 0.25
ACGTcount: A:0.18, C:0.04, G:0.56, T:0.22
Consensus pattern (21 bp):
GGTGGTGGAGGAGAGTAGACT
Found at i:4028423 original size:24 final size:24
Alignment explanation
Indices: 4028396--4028544 Score: 92
Period size: 24 Copynumber: 6.2 Consensus size: 24
4028386 GGAATAAATG
4028396 GGTGGTGGAGGAGAGTAGACTGGT
1 GGTGGTGGAGGAGAGTAGACTGGT
* * * *
4028420 GGTGGTGGGGGTG-GT-GAATGAACT
1 GGTGGTGGAGGAGAGTAGACTG--GT
4028444 GGTGGTGGAGGAGAGTAGACTGGT
1 GGTGGTGGAGGAGAGTAGACTGGT
* * * *
4028468 GGTGGTGGGGGTG-GT-GAATAAACG-
1 GGTGGTGGAGGAGAGTAGACT---GGT
* *
4028492 GGTGGTGGAGGGGAATAGACTGGT
1 GGTGGTGGAGGAGAGTAGACTGGT
* * * *
4028516 GGTGGTGGCGGCGAGTAGACGGGA
1 GGTGGTGGAGGAGAGTAGACTGGT
4028540 GGTGG
1 GGTGG
4028545 GGGTGAGTGG
Statistics
Matches: 93, Mismatches: 22, Indels: 20
0.69 0.16 0.15
Matches are distributed among these distances:
22 7 0.08
23 5 0.05
24 70 0.75
25 4 0.04
26 7 0.08
ACGTcount: A:0.19, C:0.05, G:0.56, T:0.20
Consensus pattern (24 bp):
GGTGGTGGAGGAGAGTAGACTGGT
Found at i:4028427 original size:48 final size:48
Alignment explanation
Indices: 4028375--4028523 Score: 237
Period size: 48 Copynumber: 3.1 Consensus size: 48
4028365 TGGTGATAGG
*
4028375 GGTGGGGGTGGGGAATAAATGGGTGGTGGAGGAGAGTAGACTGGTGGT
1 GGTGGGGGTGGTGAATAAATGGGTGGTGGAGGAGAGTAGACTGGTGGT
*
4028423 GGTGGGGGTGGTGAATGAACT-GGTGGTGGAGGAGAGTAGACTGGTGGT
1 GGTGGGGGTGGTGAAT-AAATGGGTGGTGGAGGAGAGTAGACTGGTGGT
* * *
4028471 GGTGGGGGTGGTGAATAAACGGGTGGTGGAGGGGAATAGACTGGTGGT
1 GGTGGGGGTGGTGAATAAATGGGTGGTGGAGGAGAGTAGACTGGTGGT
4028519 GGTGG
1 GGTGG
4028524 CGGCGAGTAG
Statistics
Matches: 93, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
47 2 0.02
48 88 0.95
49 3 0.03
ACGTcount: A:0.19, C:0.03, G:0.56, T:0.21
Consensus pattern (48 bp):
GGTGGGGGTGGTGAATAAATGGGTGGTGGAGGAGAGTAGACTGGTGGT
Found at i:4028444 original size:27 final size:27
Alignment explanation
Indices: 4028414--4028504 Score: 86
Period size: 27 Copynumber: 3.6 Consensus size: 27
4028404 AGGAGAGTAG
4028414 ACTGGTGGTGGTGGGGGTGGTGAATGA
1 ACTGGTGGTGGTGGGGGTGGTGAATGA
* * *
4028441 ACTGGTGGTGG-AGGAG-AGT--A-G-
1 ACTGGTGGTGGTGGGGGTGGTGAATGA
*
4028462 ACTGGTGGTGGTGGGGGTGGTGAATAA
1 ACTGGTGGTGGTGGGGGTGGTGAATGA
* *
4028489 ACGGGTGGTGGAGGGG
1 ACTGGTGGTGGTGGGG
4028505 AATAGACTGG
Statistics
Matches: 49, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
21 11 0.22
22 4 0.08
23 3 0.06
25 3 0.06
26 3 0.06
27 25 0.51
ACGTcount: A:0.18, C:0.04, G:0.56, T:0.22
Consensus pattern (27 bp):
ACTGGTGGTGGTGGGGGTGGTGAATGA
Found at i:4028611 original size:21 final size:21
Alignment explanation
Indices: 4028587--4028706 Score: 107
Period size: 21 Copynumber: 5.6 Consensus size: 21
4028577 TGGGTGGTGG
*
4028587 TGGTGGTGGTGGTGAGTAGAT
1 TGGTGGTGGTGGTGAGTAGAC
* *
4028608 TGGTGGCGGTGGTGAAG-AAAC
1 TGGTGGTGGTGGTG-AGTAGAC
*
4028629 AGGTGGTGGTGGTGGTGAGTGGAC
1 ---TGGTGGTGGTGGTGAGTAGAC
* *
4028653 TGGTGGAGGTGGTGAATAGAC
1 TGGTGGTGGTGGTGAGTAGAC
* * *
4028674 GGGTGGTGGTGGTGAGTGGAT
1 TGGTGGTGGTGGTGAGTAGAC
*
4028695 TGGTGGAGGTGG
1 TGGTGGTGGTGG
4028707 CCTAGTAGGA
Statistics
Matches: 78, Mismatches: 16, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
21 59 0.76
22 2 0.03
23 2 0.03
24 15 0.19
ACGTcount: A:0.16, C:0.03, G:0.55, T:0.26
Consensus pattern (21 bp):
TGGTGGTGGTGGTGAGTAGAC
Found at i:4028657 original size:45 final size:44
Alignment explanation
Indices: 4028585--4028706 Score: 176
Period size: 45 Copynumber: 2.8 Consensus size: 44
4028575 CATGGGTGGT
* *
4028585 GGTGGTGGTGGTGGTGAGTAGATTGGTGGCGGTGGTGAAGAAAC
1 GGTGGTGGTGGTGGTGAGTGGATTGGTGGAGGTGGTGAAGAAAC
* * *
4028629 AGGTGGTGGTGGTGGTGAGTGGACTGGTGGAGGTGGTGAATAGAC
1 -GGTGGTGGTGGTGGTGAGTGGATTGGTGGAGGTGGTGAAGAAAC
4028674 -G-GGTGGTGGTGGTGAGTGGATTGGTGGAGGTGG
1 GGTGGTGGTGGTGGTGAGTGGATTGGTGGAGGTGG
4028707 CCTAGTAGGA
Statistics
Matches: 71, Mismatches: 6, Indels: 3
0.89 0.08 0.04
Matches are distributed among these distances:
42 31 0.44
43 1 0.01
45 39 0.55
ACGTcount: A:0.16, C:0.03, G:0.56, T:0.25
Consensus pattern (44 bp):
GGTGGTGGTGGTGGTGAGTGGATTGGTGGAGGTGGTGAAGAAAC
Found at i:4028832 original size:54 final size:54
Alignment explanation
Indices: 4028705--4028924 Score: 235
Period size: 54 Copynumber: 4.0 Consensus size: 54
4028695 TGGTGGAGGT
** * *
4028705 GGCCTAGTAGGAGTCACTGGAGATACTTCATGTGGATCAGATAATGGTGATGGTGCTGGT
1 GGCCTAGTAGGAGTCACTGGAGATGGTTCATATGGATC-G-----GGTGATGGTGCTGGA
* * * * * * *
4028765 CGCGTAATAGGAGTCACAGGAGGTGGTTTA-AGTGGATTGGGTGATGGTGCTGGA
1 GGCCTAGTAGGAGTCACTGGAGATGGTTCATA-TGGATCGGGTGATGGTGCTGGA
*
4028819 GGCCTAGTAGGAGTCACTGGAGATTGTTCATATGGATCGGGTGATGGTGCTGGA
1 GGCCTAGTAGGAGTCACTGGAGATGGTTCATATGGATCGGGTGATGGTGCTGGA
* * *
4028873 GGCCTAGTAGGAGCCACTGGAGATTGTTCATATGGATCGGGCGATGGTGCTG
1 GGCCTAGTAGGAGTCACTGGAGATGGTTCATATGGATCGGGTGATGGTGCTG
4028925 CTGCTGGTGA
Statistics
Matches: 137, Mismatches: 21, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
54 108 0.79
55 1 0.01
59 1 0.01
60 27 0.20
ACGTcount: A:0.21, C:0.13, G:0.39, T:0.27
Consensus pattern (54 bp):
GGCCTAGTAGGAGTCACTGGAGATGGTTCATATGGATCGGGTGATGGTGCTGGA
Found at i:4031346 original size:15 final size:15
Alignment explanation
Indices: 4031326--4031356 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
4031316 AACGATACTA
4031326 TTCTGCCAAAAAAAG
1 TTCTGCCAAAAAAAG
*
4031341 TTCTGCCAATAAAAG
1 TTCTGCCAAAAAAAG
4031356 T
1 T
4031357 AAGCTTTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.19, G:0.13, T:0.26
Consensus pattern (15 bp):
TTCTGCCAAAAAAAG
Found at i:4032643 original size:87 final size:87
Alignment explanation
Indices: 4032539--4032712 Score: 330
Period size: 87 Copynumber: 2.0 Consensus size: 87
4032529 TACTTATTTT
*
4032539 ACAGCTAAATAAAACCATACATGGCAATAAAAGAAACTTTAAATTTTAACTTAGCAGTGAGCCCA
1 ACAGCTAAATAAAACCATACATGGCAATAAAAGAAACTTTAAATTTTAACTTAGCAGTAAGCCCA
4032604 CAGACTAAAGTAATAATCTTAA
66 CAGACTAAAGTAATAATCTTAA
*
4032626 ACAGCTAAATAAAACCATACATGGCAATGAAAGAAACTTTAAATTTTAACTTAGCAGTAAGCCCA
1 ACAGCTAAATAAAACCATACATGGCAATAAAAGAAACTTTAAATTTTAACTTAGCAGTAAGCCCA
4032691 CAGACTAAAGTAATAATCTTAA
66 CAGACTAAAGTAATAATCTTAA
4032713 TTTTCTCTTA
Statistics
Matches: 85, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
87 85 1.00
ACGTcount: A:0.47, C:0.17, G:0.11, T:0.24
Consensus pattern (87 bp):
ACAGCTAAATAAAACCATACATGGCAATAAAAGAAACTTTAAATTTTAACTTAGCAGTAAGCCCA
CAGACTAAAGTAATAATCTTAA
Found at i:4032830 original size:2 final size:2
Alignment explanation
Indices: 4032823--4032855 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4032813 AAAATTTAAA
4032823 TC TC TC 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 TC TC TC T
4032856 ATATATATAT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:4032860 original size:2 final size:2
Alignment explanation
Indices: 4032855--4032881 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4032845 TCTCTCTCTC
4032855 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
4032882 GTAAAATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4034153 original size:21 final size:21
Alignment explanation
Indices: 4034129--4034168 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
4034119 TATTTAATTA
*
4034129 TATTTA-ATATTATACTTAAGT
1 TATTTAGATA-TATAATTAAGT
4034150 TATTTAGATATATAATTAA
1 TATTTAGATATATAATTAA
4034169 TATGTATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (21 bp):
TATTTAGATATATAATTAAGT
Found at i:4036156 original size:6 final size:6
Alignment explanation
Indices: 4036145--4036174 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
4036135 TATTTACTTC
4036145 ATATTA ATATTA ATATTA ATATTA ATATTA
1 ATATTA ATATTA ATATTA ATATTA ATATTA
4036175 TTTCATCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
ATATTA
Found at i:4036708 original size:15 final size:16
Alignment explanation
Indices: 4036688--4036719 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
4036678 AGATTATATT
4036688 AAATTTTA-ATTTTAA
1 AAATTTTACATTTTAA
4036703 AAATTTTACATTTTAA
1 AAATTTTACATTTTAA
4036719 A
1 A
4036720 TTTAAATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (16 bp):
AAATTTTACATTTTAA
Found at i:4036738 original size:22 final size:22
Alignment explanation
Indices: 4036682--4036756 Score: 64
Period size: 22 Copynumber: 3.4 Consensus size: 22
4036672 AATCAAAGAT
* *
4036682 TATATTAAATTTTAATTTTAAA
1 TATATTAATTTTTAAATTTAAA
* *
4036704 AATTTTACA-TTTTAAATTTAAA
1 TATATTA-ATTTTTAAATTTAAA
**
4036726 TATATTAATTTTTTTATTT-AA
1 TATATTAATTTTTAAATTTAAA
4036747 TACTATTAAT
1 TA-TATTAAT
4036757 CAAATATTGA
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
21 5 0.12
22 37 0.86
23 1 0.02
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (22 bp):
TATATTAATTTTTAAATTTAAA
Found at i:4037151 original size:16 final size:15
Alignment explanation
Indices: 4037128--4037170 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
4037118 TAGGAAGATG
4037128 AAAAAAATTAAAAAA
1 AAAAAAATTAAAAAA
*
4037143 AATAAAAATT-AAAAG
1 AA-AAAAATTAAAAAA
4037158 AAAAAAATTAAAA
1 AAAAAAATTAAAA
4037171 GATAAAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 7 0.28
15 11 0.44
16 7 0.28
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.16
Consensus pattern (15 bp):
AAAAAAATTAAAAAA
Found at i:4037163 original size:14 final size:14
Alignment explanation
Indices: 4037127--4037179 Score: 70
Period size: 14 Copynumber: 3.6 Consensus size: 14
4037117 TTAGGAAGAT
4037127 GAAAAAAATTAAAAA
1 GAAAAAAATT-AAAA
*
4037142 AAATAAAAATTAAAA
1 GAA-AAAAATTAAAA
4037157 GAAAAAAATTAAAA
1 GAAAAAAATTAAAA
*
4037171 GATAAAAAT
1 GAAAAAAAT
4037180 ATTTTTTTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
14 19 0.56
15 8 0.24
16 7 0.21
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.17
Consensus pattern (14 bp):
GAAAAAAATTAAAA
Found at i:4037337 original size:27 final size:27
Alignment explanation
Indices: 4037305--4037360 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 27
4037295 ATTATACTTA
*
4037305 TTAAAAATTA-AAATAAAATTTA-AAAT
1 TTAAAAAATATAAAT-AAATTTATAAAT
*
4037331 TTAAAAAATATAAATAATTTTATAAAT
1 TTAAAAAATATAAATAAATTTATAAAT
4037358 TTA
1 TTA
4037361 TACACACTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 15 0.58
27 11 0.42
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (27 bp):
TTAAAAAATATAAATAAATTTATAAAT
Found at i:4037828 original size:28 final size:26
Alignment explanation
Indices: 4037797--4037855 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
4037787 ATTTAATTAT
* *
4037797 ATTAAAAGTATTTTTAAGTAATATAAAA
1 ATTAAAAGTA-TTATAAAT-ATATAAAA
**
4037825 ATTAAATTTATTATAAATATATAAAA
1 ATTAAAAGTATTATAAATATATAAAA
4037851 ATTAA
1 ATTAA
4037856 TATTAAAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 13 0.48
27 6 0.22
28 8 0.30
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (26 bp):
ATTAAAAGTATTATAAATATATAAAA
Found at i:4047092 original size:11 final size:11
Alignment explanation
Indices: 4047063--4047092 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
4047053 TGTTACATCA
*
4047063 AATAAATAATT
1 AATAAATTATT
4047074 AATAAATTATT
1 AATAAATTATT
4047085 AATAAATT
1 AATAAATT
4047093 CATGTGCAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
AATAAATTATT
Found at i:4048982 original size:21 final size:23
Alignment explanation
Indices: 4048958--4049024 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 23
4048948 TATTAATTTT
4048958 ATTTATATAT-TTAATTTTATA-
1 ATTTATATATATTAATTTTATAC
* *
4048979 ATTTATA-ATGTTAATATTTTTAC
1 ATTTATATATATTAAT-TTTATAC
4049002 ATATTAT-TATCATTAATTTTATA
1 AT-TTATATAT-ATTAATTTTATA
4049025 TTACTTTGTT
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
20 2 0.05
21 12 0.32
22 5 0.14
23 2 0.05
24 11 0.30
25 5 0.14
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.58
Consensus pattern (23 bp):
ATTTATATATATTAATTTTATAC
Found at i:4051214 original size:2 final size:2
Alignment explanation
Indices: 4051207--4051255 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
4051197 TCTTAGGTTC
4051207 AT AT 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 AT AT
4051249 AT AT AT A
1 AT AT AT A
4051256 ATGAAGAAGC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4051466 original size:20 final size:22
Alignment explanation
Indices: 4051420--4051483 Score: 62
Period size: 20 Copynumber: 3.0 Consensus size: 22
4051410 ATTGTGTAAT
* * *
4051420 AAATATAAAATAAATT-ATTAA
1 AAATATAATATATATTAAATAA
* *
4051441 ATATATAA-A-ATTTTAAATAA
1 AAATATAATATATATTAAATAA
4051461 AAATATAATATATATTAAATAA
1 AAATATAATATATATTAAATAA
4051483 A
1 A
4051484 TCATATTAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
19 3 0.09
20 12 0.35
21 8 0.24
22 11 0.32
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
AAATATAATATATATTAAATAA
Found at i:4051727 original size:2 final size:2
Alignment explanation
Indices: 4051715--4051745 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
4051705 GACTCAAAAT
*
4051715 TA TA TA CA 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
4051746 TAATACCAAT
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:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:4054392 original size:21 final size:21
Alignment explanation
Indices: 4054354--4054393 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
4054344 ATTTTATAAG
*
4054354 TGAAATTAAAAAATAAACACA
1 TGAAATTAAAAAAGAAACACA
*
4054375 TGAAATTAAAAGAGAAACA
1 TGAAATTAAAAAAGAAACA
4054394 TATGTCTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.65, C:0.07, G:0.10, T:0.17
Consensus pattern (21 bp):
TGAAATTAAAAAAGAAACACA
Found at i:4058647 original size:14 final size:14
Alignment explanation
Indices: 4058607--4058662 Score: 67
Period size: 14 Copynumber: 4.0 Consensus size: 14
4058597 TTTGCAAAAG
*
4058607 GTATTTTTGTTAAA
1 GTATTTTTGTCAAA
* *
4058621 GTACTTCTGTCAAA
1 GTATTTTTGTCAAA
*
4058635 GTATTTTTATCAAA
1 GTATTTTTGTCAAA
*
4058649 ATATTTTTGTCAAA
1 GTATTTTTGTCAAA
4058663 AAGTGTTGTG
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 34 1.00
ACGTcount: A:0.32, C:0.09, G:0.11, T:0.48
Consensus pattern (14 bp):
GTATTTTTGTCAAA
Found at i:4058659 original size:28 final size:28
Alignment explanation
Indices: 4058575--4058662 Score: 70
Period size: 28 Copynumber: 3.1 Consensus size: 28
4058565 ATGTTTAATG
* * * *
4058575 AAAGTACTTCTATCGAAATATCTTTG-C
1 AAAGTATTTTTATCAAAATATTTTTGTC
* * * * *
4058602 AAAAGGTATTTTTGTTAAAGTACTTCTGTC
1 -AAA-GTATTTTTATCAAAATATTTTTGTC
4058632 AAAGTATTTTTATCAAAATATTTTTGTC
1 AAAGTATTTTTATCAAAATATTTTTGTC
4058660 AAA
1 AAA
4058663 AAGTGTTGTG
Statistics
Matches: 44, Mismatches: 14, Indels: 4
0.71 0.23 0.06
Matches are distributed among these distances:
28 26 0.59
29 17 0.39
30 1 0.02
ACGTcount: A:0.35, C:0.11, G:0.11, T:0.42
Consensus pattern (28 bp):
AAAGTATTTTTATCAAAATATTTTTGTC
Found at i:4058663 original size:14 final size:14
Alignment explanation
Indices: 4058590--4058663 Score: 60
Period size: 14 Copynumber: 5.2 Consensus size: 14
4058580 ACTTCTATCG
*
4058590 AAATATCTTTG-CA
1 AAATATTTTTGTCA
*
4058603 AAAGGTATTTTTGTTA
1 AAA--TATTTTTGTCA
* * *
4058619 AAGTACTTCTGTCA
1 AAATATTTTTGTCA
* *
4058633 AAGTATTTTTATCA
1 AAATATTTTTGTCA
4058647 AAATATTTTTGTCA
1 AAATATTTTTGTCA
4058661 AAA
1 AAA
4058664 AGTGTTGTGC
Statistics
Matches: 47, Mismatches: 11, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
13 3 0.06
14 34 0.72
15 7 0.15
16 3 0.06
ACGTcount: A:0.36, C:0.09, G:0.11, T:0.43
Consensus pattern (14 bp):
AAATATTTTTGTCA
Found at i:4062295 original size:20 final size:20
Alignment explanation
Indices: 4062257--4062313 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 20
4062247 ATAAAAAAAT
*
4062257 TATTTTTAT-ATTAATATTTA
1 TATTTTTATAAATAA-ATTTA
*
4062277 TATTTTTATAAATAAATTTC
1 TATTTTTATAAATAAATTTA
* *
4062297 T-TATTTATATATAAATT
1 TATTTTTATAAATAAATT
4062314 AAATTGAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
19 14 0.44
20 14 0.44
21 4 0.12
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.60
Consensus pattern (20 bp):
TATTTTTATAAATAAATTTA
Done.