Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold11
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: 5230303
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 140504 characters in sequence are not A, C, G, or T
File 22 of 29
Found at i:3423399 original size:9 final size:8
Alignment explanation
Indices: 3423366--3423450 Score: 54
Period size: 7 Copynumber: 10.6 Consensus size: 8
3423356 ATATATATAT
*
3423366 ATTATTTT
1 ATTATTTA
3423374 ATT-TTTA
1 ATTATTTA
*
3423381 ATTATTTT
1 ATTATTTA
3423389 A-TA-TTA
1 ATTATTTA
3423395 ATTATTTA
1 ATTATTTA
3423403 GATTATTTCA
1 -ATTATTT-A
3423413 ATTATATT-
1 ATTAT-TTA
*
3423421 ATAATTTAA
1 ATTATTT-A
3423430 ATTATTTTA
1 ATTA-TTTA
*
3423439 AGT-TTTA
1 ATTATTTA
3423446 ATTAT
1 ATTAT
3423451 AAATTTTTTT
Statistics
Matches: 60, Mismatches: 7, Indels: 20
0.69 0.08 0.23
Matches are distributed among these distances:
6 3 0.05
7 18 0.30
8 15 0.25
9 18 0.30
10 6 0.10
ACGTcount: A:0.35, C:0.01, G:0.02, T:0.61
Consensus pattern (8 bp):
ATTATTTA
Found at i:3423421 original size:23 final size:23
Alignment explanation
Indices: 3423368--3423422 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
3423358 ATATATATAT
* *
3423368 TATTTTATT-TTTAATTATTTTA
1 TATTATATTATTTAATTATTTCA
3423390 TATTA-ATTATTTAGATTATTTCA
1 TATTATATTATTTA-ATTATTTCA
3423413 -ATTATATTAT
1 TATTATATTAT
3423423 AATTTAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
21 3 0.11
22 12 0.43
23 13 0.46
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (23 bp):
TATTATATTATTTAATTATTTCA
Found at i:3423706 original size:5 final size:5
Alignment explanation
Indices: 3423698--3423727 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
3423688 AAAAAATTAA
3423698 AATTT AATTT AATTT AATTT AATTT AATTT
1 AATTT AATTT AATTT AATTT AATTT AATTT
3423728 GTAAATTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
AATTT
Found at i:3423780 original size:23 final size:23
Alignment explanation
Indices: 3423729--3423783 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
3423719 ATTTAATTTG
*
3423729 TAAATTT-AAAATATTATTTATT
1 TAAATTTAAAAATATTATTTAAT
**
3423751 TTTATTTAAAAATATT-TTATAAT
1 TAAATTTAAAAATATTATT-TAAT
3423774 TAAATTTAAA
1 TAAATTTAAA
3423784 TAAAAATATA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
22 7 0.27
23 19 0.73
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
TAAATTTAAAAATATTATTTAAT
Found at i:3424546 original size:2 final size:2
Alignment explanation
Indices: 3424539--3424574 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3424529 AACTAAATTA
3424539 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
3424575 GCAAACTCAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3424683 original size:21 final size:22
Alignment explanation
Indices: 3424627--3424691 Score: 64
Period size: 21 Copynumber: 3.0 Consensus size: 22
3424617 ATATATATAT
*
3424627 ATAAGTAGATTTTTTAAGAAAAG
1 ATAATTAG-TTTTTTAAGAAAAG
3424650 ATAATTAG-TTTTTAAGAAAA-
1 ATAATTAGTTTTTTAAGAAAAG
*
3424670 ATGGATT-GTATTTTTAAGAAAA
1 AT-AATTAGT-TTTTTAAGAAAA
3424692 TGGGTAAGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
20 3 0.08
21 15 0.41
22 12 0.32
23 7 0.19
ACGTcount: A:0.46, C:0.00, G:0.15, T:0.38
Consensus pattern (22 bp):
ATAATTAGTTTTTTAAGAAAAG
Found at i:3424704 original size:21 final size:21
Alignment explanation
Indices: 3424637--3424711 Score: 57
Period size: 21 Copynumber: 3.5 Consensus size: 21
3424627 ATAAGTAGAT
*
3424637 TTTTTAAGAAAA--GATAATTA
1 TTTTTAAGAAAATGGAT-AGTA
*
3424657 GTTTTTAAGAAAAATGGATTGTA
1 -TTTTTAAG-AAAATGGATAGTA
*
3424680 TTTTTAAGAAAATGGGTAAGT-
1 TTTTTAAGAAAATGGAT-AGTA
*
3424701 TTTTAAAGAAA
1 TTTTTAAGAAA
3424712 TGAATAATTT
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
21 26 0.58
22 14 0.31
23 2 0.04
24 3 0.07
ACGTcount: A:0.44, C:0.00, G:0.17, T:0.39
Consensus pattern (21 bp):
TTTTTAAGAAAATGGATAGTA
Found at i:3426164 original size:27 final size:27
Alignment explanation
Indices: 3426133--3426193 Score: 113
Period size: 27 Copynumber: 2.3 Consensus size: 27
3426123 TGTTTTTACT
*
3426133 TATTTTAATTATTTTTTAAATATTATA
1 TATTTTAATTATTTTTTAAATATCATA
3426160 TATTTTAATTATTTTTTAAATATCATA
1 TATTTTAATTATTTTTTAAATATCATA
3426187 TATTTTA
1 TATTTTA
3426194 GAAAAAAACT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (27 bp):
TATTTTAATTATTTTTTAAATATCATA
Found at i:3426167 original size:16 final size:16
Alignment explanation
Indices: 3426146--3426193 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
3426136 TTTAATTATT
3426146 TTTTAAATATTATATA
1 TTTTAAATATTATATA
3426162 TTTT--A-ATTAT-T-
1 TTTTAAATATTATATA
*
3426173 TTTTAAATATCATATA
1 TTTTAAATATTATATA
3426189 TTTTA
1 TTTTA
3426194 GAAAAAAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 10
0.70 0.03 0.27
Matches are distributed among these distances:
11 4 0.15
12 1 0.04
13 6 0.23
14 5 0.19
15 1 0.04
16 9 0.35
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (16 bp):
TTTTAAATATTATATA
Found at i:3426554 original size:38 final size:40
Alignment explanation
Indices: 3426473--3426557 Score: 111
Period size: 42 Copynumber: 2.1 Consensus size: 40
3426463 TAATTTTAAA
*
3426473 TAAAAAGATAAATATATTTTTTATTAATTATTTATTTTATTTT
1 TAAAAAGATAAATATACTTTTTATTAATTATTTA---TATTTT
3426516 TAAAAA-ATAAATATACTTTTTATTAATTATTTACT-TTTT
1 TAAAAAGATAAATATACTTTTTATTAATTATTTA-TATTTT
3426555 TAA
1 TAA
3426558 TTTTTTAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
39 7 0.17
40 1 0.03
42 26 0.65
43 6 0.15
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.55
Consensus pattern (40 bp):
TAAAAAGATAAATATACTTTTTATTAATTATTTATATTTT
Found at i:3427169 original size:22 final size:21
Alignment explanation
Indices: 3427120--3427171 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
3427110 CTTACATTTG
3427120 AATTAGAATATAATTTAATAAT
1 AATTA-AATATAATTTAATAAT
*
3427142 ACTTAAATATAATTTTAA-AATT
1 AATTAAATATAA-TTTAATAA-T
3427164 AATTAAAT
1 AATTAAAT
3427172 TTCATTATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 9 0.35
22 17 0.65
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (21 bp):
AATTAAATATAATTTAATAAT
Found at i:3427347 original size:31 final size:31
Alignment explanation
Indices: 3427289--3427386 Score: 128
Period size: 30 Copynumber: 3.2 Consensus size: 31
3427279 TATCTTATGG
* *
3427289 AATAAATATATTTTTGATAAAATTTTAAAAA
1 AATAAATAAATTTTTTATAAAATTTTAAAAA
*
3427320 AATACATAAATTTTTT-TAAAATATTT-AAAA
1 AATAAATAAATTTTTTATAAAAT-TTTAAAAA
*
3427350 AATAAATATATTTTTTATAAAATTTTAAAATA
1 AATAAATAAATTTTTTATAAAATTTTAAAA-A
3427382 AATAA
1 AATAA
3427387 CTTTTACTTT
Statistics
Matches: 58, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
30 27 0.47
31 25 0.43
32 6 0.10
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (31 bp):
AATAAATAAATTTTTTATAAAATTTTAAAAA
Found at i:3428575 original size:2 final size:2
Alignment explanation
Indices: 3428568--3428609 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
3428558 TCGTGTCTCA
3428568 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
3428610 TTATTTTTCT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3429469 original size:2 final size:2
Alignment explanation
Indices: 3429454--3429490 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
3429444 TTCAGATGCA
* *
3429454 AG AG AG GG AA 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 A
3429491 AGAATCATGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3430834 original size:13 final size:14
Alignment explanation
Indices: 3430795--3430841 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
3430785 GTTATTTTTT
* *
3430795 TAATTTAATAAAAA
1 TAATTTATTAAATA
3430809 TAATTTATTAAATA
1 TAATTTATTAAATA
3430823 TAATTT-TTAAATAA
1 TAATTTATTAAAT-A
3430837 TAATT
1 TAATT
3430842 AATAATCTCC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
13 6 0.20
14 24 0.80
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TAATTTATTAAATA
Found at i:3430987 original size:2 final size:2
Alignment explanation
Indices: 3430976--3431016 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
3430966 GTTTTTGTTA
* *
3430976 AT AT -T AT AT AT AT AT AT AT AT AT AT AT GT AT AT GT 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
3431017 GAGGTTGGTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
AT
Found at i:3432056 original size:2 final size:2
Alignment explanation
Indices: 3432051--3432079 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3432041 ACAATAAAAA
3432051 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3432080 TTTGATTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3433377 original size:22 final size:21
Alignment explanation
Indices: 3433349--3433390 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
3433339 TACATAAAAA
*
3433349 AGGTTTTTTTTACTGATTTTTC
1 AGGTTTTTTTAACT-ATTTTTC
3433371 AGGTTTTTTTAACTATTTTT
1 AGGTTTTTTTAACTATTTTT
3433391 ATCTTTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.17, C:0.07, G:0.12, T:0.64
Consensus pattern (21 bp):
AGGTTTTTTTAACTATTTTTC
Found at i:3439559 original size:21 final size:20
Alignment explanation
Indices: 3439516--3439560 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
3439506 TAGAATTTTA
*
3439516 AATAAAATTTTTATAAATTT
1 AATAAAAATTTTATAAATTT
3439536 AATAATAAATTTTA-AAATATT
1 AATAA-AAATTTTATAAAT-TT
3439557 AATA
1 AATA
3439561 TTTTAATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
AATAAAAATTTTATAAATTT
Found at i:3447518 original size:18 final size:18
Alignment explanation
Indices: 3447495--3447530 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3447485 ATCGATTAAA
* *
3447495 TTTAATTTAATTAATTTT
1 TTTAATTAAATCAATTTT
3447513 TTTAATTAAATCAATTTT
1 TTTAATTAAATCAATTTT
3447531 AATCAATTTT
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:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTAATTAAATCAATTTT
Found at i:3447837 original size:19 final size:19
Alignment explanation
Indices: 3447797--3447840 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
3447787 GATAAATTTT
*
3447797 TTTAATTGAGTTAATATTA
1 TTTAATTGAGTTAATATAA
*
3447816 TTTAATTTA-TTAATATCAA
1 TTTAATTGAGTTAATAT-AA
3447835 TTTAAT
1 TTTAAT
3447841 AAAAAATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.55
Consensus pattern (19 bp):
TTTAATTGAGTTAATATAA
Found at i:3448978 original size:29 final size:30
Alignment explanation
Indices: 3448910--3449009 Score: 112
Period size: 30 Copynumber: 3.3 Consensus size: 30
3448900 TATTTTTATG
* * *
3448910 ATATTAAAATAAATTTTTAATTGTTAATTT
1 ATATTTAAATAAATTCTTAATTTTTAATTT
* * *
3448940 ATACTCAAATATA-TCTTAATTTTTAATTT
1 ATATTTAAATAAATTCTTAATTTTTAATTT
* *
3448969 ATATTTAAATAAATTTTTAATATTTAATTT
1 ATATTTAAATAAATTCTTAATTTTTAATTT
3448999 ATTATTTAAAT
1 A-TATTTAAAT
3449010 TTAAATTAAA
Statistics
Matches: 58, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
29 24 0.41
30 25 0.43
31 9 0.16
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (30 bp):
ATATTTAAATAAATTCTTAATTTTTAATTT
Found at i:3448995 original size:30 final size:29
Alignment explanation
Indices: 3448892--3449009 Score: 114
Period size: 29 Copynumber: 4.0 Consensus size: 29
3448882 ATAATTATTT
* * *
3448892 AATTTTTATATTTTTA-TGATATTAAAATA
1 AATTTTTA-ATTTTAATTTATATTTAAATA
* *
3448921 AATTTTTAATTGTTAATTTATACTCAAATA
1 AATTTTTAATT-TTAATTTATATTTAAATA
* *
3448951 TA-TCTTAATTTTTAATTTATATTTAAATA
1 AATTTTTAA-TTTTAATTTATATTTAAATA
3448980 AATTTTTAATATTTAATTTATTATTTAAAT
1 AATTTTTAAT-TTTAATTTA-TATTTAAAT
3449010 TTAAATTAAA
Statistics
Matches: 73, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
28 3 0.04
29 34 0.47
30 27 0.37
31 9 0.12
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.56
Consensus pattern (29 bp):
AATTTTTAATTTTAATTTATATTTAAATA
Found at i:3449006 original size:19 final size:19
Alignment explanation
Indices: 3448950--3449013 Score: 55
Period size: 19 Copynumber: 3.4 Consensus size: 19
3448940 ATACTCAAAT
3448950 ATATCTTAATTT-TTAATTT-
1 ATAT-TTAATTTATT-ATTTA
**
3448969 ATATTTAAATAAATT-TTTA
1 ATATTT-AATTTATTATTTA
3448988 ATATTTAATTTATTATTTA
1 ATATTTAATTTATTATTTA
3449007 A-ATTTAA
1 ATATTTAA
3449014 ATTAAAAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
18 17 0.46
19 18 0.49
20 2 0.05
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (19 bp):
ATATTTAATTTATTATTTA
Found at i:3449016 original size:19 final size:19
Alignment explanation
Indices: 3448965--3449018 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 19
3448955 TTAATTTTTA
* *
3448965 ATTTATATTTAAATAAATT
1 ATTTAAATTTAAATTAATT
*
3448984 -TTTAATATTT-AATTTATT
1 ATTTAA-ATTTAAATTAATT
3449002 ATTTAAATTTAAATTAA
1 ATTTAAATTTAAATTAA
3449019 AAATAAAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
18 14 0.50
19 14 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
ATTTAAATTTAAATTAATT
Found at i:3449610 original size:22 final size:21
Alignment explanation
Indices: 3449584--3449641 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 21
3449574 CATAAAATAT
* *
3449584 AAATATATATTTTAATGATAAA
1 AAATATAAATATTAAT-ATAAA
3449606 AAATATAAATATTAATATAAA
1 AAATATAAATATTAATATAAA
*
3449627 ATAATAATTAATATT
1 A-AAT-ATAAATATT
3449642 TTTTAATGTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 6 0.19
22 17 0.55
23 8 0.26
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.40
Consensus pattern (21 bp):
AAATATAAATATTAATATAAA
Found at i:3451180 original size:15 final size:14
Alignment explanation
Indices: 3451160--3451189 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
3451150 GGAAACTATG
3451160 AAAATTTATAAATTT
1 AAAATTTA-AAATTT
3451175 AAAATTTAAAATTT
1 AAAATTTAAAATTT
3451189 A
1 A
3451190 TATTACGTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AAAATTTAAAATTT
Found at i:3451181 original size:7 final size:7
Alignment explanation
Indices: 3451160--3451189 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
3451150 GGAAACTATG
3451160 AAAATTT
1 AAAATTT
3451167 ATAAATTT
1 A-AAATTT
3451175 AAAATTT
1 AAAATTT
3451182 AAAATTT
1 AAAATTT
3451189 A
1 A
3451190 TATTACGTGC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 15 0.68
8 7 0.32
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
AAAATTT
Found at i:3456649 original size:31 final size:29
Alignment explanation
Indices: 3456613--3456671 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 29
3456603 AAGATATATA
3456613 TATTTAT-TTTATTATTAATATATAAAATAAT
1 TATTTATATTT-TTA-TAATAT-TAAAATAAT
*
3456644 TATTTATATTTTTATGATATTAAAATAA
1 TATTTATATTTTTATAATATTAAAATAA
3456672 ATTTTTAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
29 8 0.31
30 5 0.19
31 10 0.38
32 3 0.12
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (29 bp):
TATTTATATTTTTATAATATTAAAATAAT
Found at i:3456663 original size:28 final size:28
Alignment explanation
Indices: 3456616--3456671 Score: 71
Period size: 27 Copynumber: 2.0 Consensus size: 28
3456606 ATATATATAT
3456616 TTATTTTATTATTAATATA-TAAAATAA
1 TTATTTTATTATTAATATATTAAAATAA
*
3456643 TTATTTATATT-TTTATGATATTAAAATAA
1 TTATTT-TATTATTAAT-ATATTAAAATAA
3456672 ATTTTTAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 10 0.40
28 7 0.28
29 8 0.32
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.54
Consensus pattern (28 bp):
TTATTTTATTATTAATATATTAAAATAA
Found at i:3456715 original size:29 final size:29
Alignment explanation
Indices: 3456683--3456749 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
3456673 TTTTTAACTG
*
3456683 TTAATTTATACTCAAATATA-TCTTAATTT
1 TTAATTTATACTCAAATA-AGTCTTAATAT
* * *
3456712 TTAATTTATATTTAAATAAGTTTTAATAT
1 TTAATTTATACTCAAATAAGTCTTAATAT
3456741 TTAATTTAT
1 TTAATTTAT
3456750 TATTTAAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 1 0.03
29 32 0.97
ACGTcount: A:0.39, C:0.04, G:0.01, T:0.55
Consensus pattern (29 bp):
TTAATTTATACTCAAATAAGTCTTAATAT
Found at i:3457318 original size:22 final size:21
Alignment explanation
Indices: 3457292--3457349 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 21
3457282 AATAAAATAT
* *
3457292 AAATATATATTTTAATGATAAA
1 AAATATAAATATTAAT-ATAAA
3457314 AAATATAAATATTAATATAAA
1 AAATATAAATATTAATATAAA
*
3457335 ATAATAATTAATATT
1 A-AAT-ATAAATATT
3457350 TTTAAAATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 6 0.19
22 17 0.55
23 8 0.26
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.40
Consensus pattern (21 bp):
AAATATAAATATTAATATAAA
Found at i:3463939 original size:33 final size:32
Alignment explanation
Indices: 3463865--3463939 Score: 87
Period size: 34 Copynumber: 2.3 Consensus size: 32
3463855 TAAATTTTTT
** **
3463865 TATAAATATATTTAATTTTTTTATATATTTAA
1 TATAAATATATTTAATTTAATTATATATCAAA
*
3463897 TAGATAATATATTTAAATTTAATTATATATCAAA
1 TATA-AATATATTT-AATTTAATTATATATCAAA
3463931 TATAAATAT
1 TATAAATAT
3463940 TAAATAAATA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
32 3 0.09
33 14 0.40
34 18 0.51
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (32 bp):
TATAAATATATTTAATTTAATTATATATCAAA
Found at i:3467756 original size:18 final size:19
Alignment explanation
Indices: 3467706--3467756 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 19
3467696 TAATTTTTAA
3467706 AATTTT-TTATTTAAATTT
1 AATTTTATTATTTAAATTT
** *
3467724 AATTCGATT-TATAAATTT
1 AATTTTATTATTTAAATTT
3467742 -ATTTTATTATTTAAA
1 AATTTTATTATTTAAA
3467757 AATATAAAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 4
0.71 0.17 0.11
Matches are distributed among these distances:
17 6 0.24
18 17 0.68
19 2 0.08
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (19 bp):
AATTTTATTATTTAAATTT
Found at i:3467950 original size:20 final size:21
Alignment explanation
Indices: 3467909--3467952 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
3467899 AGATCAAACA
*
3467909 AAATAAAATTAATTAATTTTT
1 AAATAAAATTAATTAATATTT
3467930 AAAT-AAATTAACTTAA-ATTT
1 AAATAAAATTAA-TTAATATTT
3467950 AAA
1 AAA
3467953 GATTAATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (21 bp):
AAATAAAATTAATTAATATTT
Found at i:3469064 original size:22 final size:23
Alignment explanation
Indices: 3469039--3469095 Score: 68
Period size: 22 Copynumber: 2.6 Consensus size: 23
3469029 ATTTATATCA
3469039 TAATTATTTTAAA-TTTTAATTT
1 TAATTATTTTAAATTTTTAATTT
3469061 TAA-TATTTATAAATTTTTTAATTT
1 TAATTATTT-TAAA-TTTTTAATTT
3469085 T-ATT-TTTTAAA
1 TAATTATTTTAAA
3469096 AAATAAATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
21 5 0.16
22 11 0.35
23 4 0.13
24 11 0.35
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (23 bp):
TAATTATTTTAAATTTTTAATTT
Found at i:3469506 original size:11 final size:12
Alignment explanation
Indices: 3469490--3469548 Score: 59
Period size: 13 Copynumber: 4.9 Consensus size: 12
3469480 TATTGTAATT
3469490 ATATAATATAAA
1 ATATAATATAAA
3469502 A-ATAAT-TAAA
1 ATATAATATAAA
3469512 ATATAATATAAA
1 ATATAATATAAA
* *
3469524 TAAATTATATAAA
1 -ATATAATATAAA
*
3469537 TTATTAATATAA
1 ATA-TAATATAA
3469549 TTAAAATATA
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
10 5 0.13
11 10 0.26
12 6 0.16
13 17 0.45
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
ATATAATATAAA
Found at i:3469544 original size:26 final size:26
Alignment explanation
Indices: 3469486--3469559 Score: 75
Period size: 26 Copynumber: 3.0 Consensus size: 26
3469476 TAAATATTGT
*
3469486 AATTATATAATAT-AA-AAATAAT-TA
1 AATTAT-TAATATAAATAAATTATATA
*
3469510 AAATA-TAATATAAATAAATTATATA
1 AATTATTAATATAAATAAATTATATA
* *
3469535 AATTATTAATATAATTAAAATATAT
1 AATTATTAATATAAATAAATTATAT
3469560 TTTTATAATA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
22 6 0.15
23 2 0.05
24 10 0.24
25 6 0.15
26 17 0.41
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (26 bp):
AATTATTAATATAAATAAATTATATA
Found at i:3469558 original size:11 final size:11
Alignment explanation
Indices: 3469490--3469558 Score: 58
Period size: 11 Copynumber: 6.5 Consensus size: 11
3469480 TATTGTAATT
3469490 ATATAATATAAA
1 ATATAAT-TAAA
3469502 A-ATAATTAAA
1 ATATAATTAAA
3469512 ATATAA-TATAA
1 ATATAATTA-AA
*
3469523 ATA-AATT-AT
1 ATATAATTAAA
*
3469532 ATA-AATTATTA
1 ATATAATTA-AA
3469543 ATATAATTAAA
1 ATATAATTAAA
3469554 ATATA
1 ATATA
3469559 TTTTTATAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 13
0.73 0.06 0.20
Matches are distributed among these distances:
9 8 0.17
10 9 0.19
11 24 0.51
12 6 0.13
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
ATATAATTAAA
Found at i:3470828 original size:11 final size:11
Alignment explanation
Indices: 3470807--3470840 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
3470797 ATATAATAAA
3470807 AATAAAGTATTT
1 AATAAA-TATTT
3470819 AATAAATATTT
1 AATAAATATTT
*
3470830 TATAAATATTT
1 AATAAATATTT
3470841 GTGTTTATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 15 0.71
12 6 0.29
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (11 bp):
AATAAATATTT
Found at i:3479398 original size:23 final size:22
Alignment explanation
Indices: 3479361--3479408 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
3479351 TTTAAATTTA
** *
3479361 TATTTATATTCATTATTTATATT
1 TATTTATATGAATTAATT-TATT
3479384 TATTTATATGAATTAATTTATT
1 TATTTATATGAATTAATTTATT
3479406 TAT
1 TAT
3479409 GAACACTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 7 0.32
23 15 0.68
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (22 bp):
TATTTATATGAATTAATTTATT
Found at i:3479494 original size:26 final size:27
Alignment explanation
Indices: 3479460--3479521 Score: 90
Period size: 26 Copynumber: 2.3 Consensus size: 27
3479450 GAATAATTAA
* *
3479460 AAATATATTTATAAATAAATTTAAA-T
1 AAATTTATTTATAAACAAATTTAAATT
*
3479486 AAATTTATTTATGAACAAATTTAAATT
1 AAATTTATTTATAAACAAATTTAAATT
3479513 AAATTTATT
1 AAATTTATT
3479522 ATATTCATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
26 22 0.69
27 10 0.31
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (27 bp):
AAATTTATTTATAAACAAATTTAAATT
Found at i:3479600 original size:10 final size:10
Alignment explanation
Indices: 3479587--3479627 Score: 64
Period size: 10 Copynumber: 4.0 Consensus size: 10
3479577 ATTTAACTTA
3479587 ATAAATAAAT
1 ATAAATAAAT
3479597 ATAAATAAAT
1 ATAAATAAAT
3479607 ATAAATAAAT
1 ATAAATAAAT
*
3479617 AAAAATTAAAT
1 ATAAA-TAAAT
3479628 TATTTATTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
10 24 0.83
11 5 0.17
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (10 bp):
ATAAATAAAT
Found at i:3479605 original size:14 final size:14
Alignment explanation
Indices: 3479586--3479619 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
3479576 AATTTAACTT
3479586 AATAAATAAATATA
1 AATAAATAAATATA
3479600 AATAAATATAA-ATA
1 AATAAATA-AATATA
3479614 AATAAA
1 AATAAA
3479620 AATTAAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 17 0.89
15 2 0.11
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
AATAAATAAATATA
Found at i:3480061 original size:23 final size:24
Alignment explanation
Indices: 3480003--3480071 Score: 61
Period size: 23 Copynumber: 2.8 Consensus size: 24
3479993 AAAAATATTT
*
3480003 ATTTTTTACTTTATTTTATTATAATA
1 ATTTTTTA-ATTA-TTTATTATAATA
**
3480029 A-TTTAAAATTATTTATTAT-ATA
1 ATTTTTTAATTATTTATTATAATA
*
3480051 ATTTTTTAATTAATATATTAT
1 ATTTTTTAATT-ATTTATTAT
3480072 TATTTAATTA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
22 4 0.11
23 15 0.43
24 11 0.31
25 4 0.11
26 1 0.03
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (24 bp):
ATTTTTTAATTATTTATTATAATA
Found at i:3480077 original size:19 final size:19
Alignment explanation
Indices: 3480045--3480094 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 19
3480035 AATTATTTAT
* *
3480045 TATATAATTTTTTAATTAA
1 TATATTATTATTTAATTAA
3480064 TATATTATTATTTAATTAA
1 TATATTATTATTTAATTAA
3480083 TAATATATATTA
1 T-ATAT-TATTA
3480095 ATATTAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 18 0.67
20 4 0.15
21 5 0.19
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TATATTATTATTTAATTAA
Found at i:3480200 original size:2 final size:2
Alignment explanation
Indices: 3480193--3480224 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3480183 CCTTTTTGTC
3480193 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
3480225 CCATTAATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3480484 original size:14 final size:14
Alignment explanation
Indices: 3480449--3480477 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3480439 AGATTATGTA
3480449 TAAAATTTAAATTT
1 TAAAATTTAAATTT
3480463 TAAAATTTAAATTT
1 TAAAATTTAAATTT
3480477 T
1 T
3480478 TTTATTTTCA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TAAAATTTAAATTT
Found at i:3481393 original size:14 final size:14
Alignment explanation
Indices: 3481374--3481410 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
3481364 ATAATTATCA
3481374 AATATATAAATATT
1 AATATATAAATATT
*
3481388 AATATAAAAATATT
1 AATATATAAATATT
3481402 -ATA-ATAAAT
1 AATATATAAAT
3481411 TAAAATTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
12 5 0.24
13 3 0.14
14 13 0.62
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
AATATATAAATATT
Found at i:3481425 original size:7 final size:7
Alignment explanation
Indices: 3481413--3481438 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
3481403 TAATAAATTA
3481413 AAATTTT
1 AAATTTT
3481420 AAATTTT
1 AAATTTT
3481427 AAATTTT
1 AAATTTT
3481434 AAATT
1 AAATT
3481439 AATTTAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (7 bp):
AAATTTT
Found at i:3486364 original size:20 final size:21
Alignment explanation
Indices: 3486339--3486383 Score: 65
Period size: 23 Copynumber: 2.1 Consensus size: 21
3486329 ATCCTTAATG
3486339 CAAACAAGG-AGAAATAACAC
1 CAAACAAGGAAGAAATAACAC
3486359 CAAACAAGGATAAGAAATAACAC
1 CAAACAAGG--AAGAAATAACAC
3486382 CA
1 CA
3486384 CAAAAGGGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 9 0.41
23 13 0.59
ACGTcount: A:0.60, C:0.20, G:0.13, T:0.07
Consensus pattern (21 bp):
CAAACAAGGAAGAAATAACAC
Found at i:3497977 original size:16 final size:13
Alignment explanation
Indices: 3497945--3497971 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3497935 ATTTTGATAA
3497945 AAAATAATAATTT
1 AAAATAATAATTT
3497958 AAAATAATAATTT
1 AAAATAATAATTT
3497971 A
1 A
3497972 TTAAAAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
AAAATAATAATTT
Found at i:3498051 original size:15 final size:15
Alignment explanation
Indices: 3498029--3498073 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
3498019 TTTATTTTTA
3498029 ATTA-TATAATATAT
1 ATTATTATAATATAT
*
3498043 ATTTTTATAATTATAT
1 ATTATTATAA-TATAT
3498059 ATTATTA-AAT-TAT
1 ATTATTATAATATAT
3498072 AT
1 AT
3498074 CATATAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
13 5 0.19
14 4 0.15
15 7 0.26
16 11 0.41
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
ATTATTATAATATAT
Found at i:3498177 original size:26 final size:26
Alignment explanation
Indices: 3498088--3498190 Score: 77
Period size: 26 Copynumber: 3.9 Consensus size: 26
3498078 TAAAAAATAT
** *
3498088 TTAAAAAATAATATTATAATATAAATA
1 TTAAAAAATAATAAAAT-ATATAATTA
* * *
3498115 TTAAAAATATATTAAATTA-ATCA-TA
1 TTAAAAA-ATAATAAAATATATAATTA
* *
3498140 CTTTAAATATAATAAAATATATAATTA
1 -TTAAAAAATAATAAAATATATAATTA
3498167 TTAAAAAATAAATAAAA-ATATAAT
1 TTAAAAAAT-AATAAAATATATAAT
3498191 ATTTTTATAA
Statistics
Matches: 59, Mismatches: 12, Indels: 11
0.72 0.15 0.13
Matches are distributed among these distances:
25 11 0.19
26 25 0.42
27 17 0.29
28 6 0.10
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (26 bp):
TTAAAAAATAATAAAATATATAATTA
Found at i:3498205 original size:26 final size:27
Alignment explanation
Indices: 3498144--3498209 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 27
3498134 ATCATACTTT
3498144 AAATATAATAAAATATATAATTATTAAA
1 AAATA-AATAAAATATATAATTATTAAA
* *
3498172 AAATAAATAAAAATATAATATTTTTATAAA
1 AAATAAAT-AAAATAT-ATAATTAT-TAAA
3498202 AAATAAAT
1 AAATAAAT
3498210 TTAAATTATC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 3 0.09
28 12 0.36
29 6 0.18
30 12 0.36
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (27 bp):
AAATAAATAAAATATATAATTATTAAA
Found at i:3499212 original size:29 final size:30
Alignment explanation
Indices: 3499154--3499214 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
3499144 TTTGAATTGA
3499154 TATTTATAAAATAATAATATATTATAAATT
1 TATTTATAAAATAATAATATATTATAAATT
* *
3499184 TATTT-TAAATTAAT-ATATATTTTATAATT
1 TATTTATAAAATAATAATATATTATA-AATT
3499213 TA
1 TA
3499215 AAATTAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 9 0.32
29 14 0.50
30 5 0.18
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (30 bp):
TATTTATAAAATAATAATATATTATAAATT
Found at i:3499219 original size:25 final size:23
Alignment explanation
Indices: 3499185--3499230 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
3499175 TTATAAATTT
*
3499185 ATTTTAAATTAATATATATTTTATA
1 ATTTAAAATTAA-ATA-ATTTTATA
3499210 ATTTAAAATTAAATAATTTTA
1 ATTTAAAATTAAATAATTTTA
3499231 ATATAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 3 0.15
25 11 0.55
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
ATTTAAAATTAAATAATTTTATA
Found at i:3499226 original size:29 final size:28
Alignment explanation
Indices: 3499162--3499226 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 28
3499152 GATATTTATA
**
3499162 AAATAATAATATATTATAAATTTATTTT
1 AAATAATAATATATTATAAATTTAAATT
*
3499190 AAATTAAT-ATATATTTTATAATTTAAAATT
1 AAA-TAATAATATATTATA-AATTT-AAATT
3499220 AAATAAT
1 AAATAAT
3499227 TTTAATATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
28 12 0.39
29 13 0.42
30 6 0.19
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (28 bp):
AAATAATAATATATTATAAATTTAAATT
Found at i:3499237 original size:21 final size:25
Alignment explanation
Indices: 3499190--3499238 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 25
3499180 AATTTATTTT
*
3499190 AAATTAATATATATTTTATAATTTA
1 AAATTAATATATATTTTATAATATA
3499215 AAATTAA-ATA-A-TTT-TAATATA
1 AAATTAATATATATTTTATAATATA
3499236 AAA
1 AAA
3499239 AATATAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 9 0.39
22 3 0.13
23 1 0.04
24 3 0.13
25 7 0.30
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (25 bp):
AAATTAATATATATTTTATAATATA
Found at i:3499291 original size:33 final size:34
Alignment explanation
Indices: 3499227--3499292 Score: 82
Period size: 32 Copynumber: 2.0 Consensus size: 34
3499217 ATTAAATAAT
* * *
3499227 TTTAATATAAAAAATATAAATTTAATCAATTTAA
1 TTTAATATAAAAAATAAAAAATTAATAAATTTAA
3499261 TTTAA-AT-AAAAATAAAAAATTAATTAAATTTA
1 TTTAATATAAAAAATAAAAAATTAA-TAAATTTA
3499293 TTAAATGGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
32 14 0.50
33 9 0.32
34 5 0.18
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (34 bp):
TTTAATATAAAAAATAAAAAATTAATAAATTTAA
Found at i:3502869 original size:136 final size:136
Alignment explanation
Indices: 3502625--3502896 Score: 526
Period size: 136 Copynumber: 2.0 Consensus size: 136
3502615 ACCAAATTGA
3502625 TAGTGATGATTTGACAATTGTTGTTAATTATTGATGGCACTCCTGTATAATGTCTATCTCGGCAG
1 TAGTGATGATTTGACAATTGTTGTTAATTATTGATGGCACTCCTGTATAATGTCTATCTCGGCAG
*
3502690 ACCACATGGATGCATATTATTTGCGTTACCTAGAAGGTAATATTGGTTCATCATCTTTTAAAATA
66 ACCACATGGATGCATATTATTTGCGTTACCTACAAGGTAATATTGGTTCATCATCTTTTAAAATA
3502755 TTTCCT
131 TTTCCT
3502761 TAGTGATGATTTGACAATTGTTGTTAATTATTGATGGCACTCCTGTATAATGTCTATCTCGGCAG
1 TAGTGATGATTTGACAATTGTTGTTAATTATTGATGGCACTCCTGTATAATGTCTATCTCGGCAG
*
3502826 ACCACATGGATGCGTATTATTTGCGTTACCTACAAGGTAATATTGGTTCATCATCTTTTAAAATA
66 ACCACATGGATGCATATTATTTGCGTTACCTACAAGGTAATATTGGTTCATCATCTTTTAAAATA
3502891 TTTCCT
131 TTTCCT
3502897 CCTTTTTATC
Statistics
Matches: 134, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
136 134 1.00
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.40
Consensus pattern (136 bp):
TAGTGATGATTTGACAATTGTTGTTAATTATTGATGGCACTCCTGTATAATGTCTATCTCGGCAG
ACCACATGGATGCATATTATTTGCGTTACCTACAAGGTAATATTGGTTCATCATCTTTTAAAATA
TTTCCT
Found at i:3507848 original size:2 final size:2
Alignment explanation
Indices: 3507830--3507873 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
3507820 CCTCTTTCTT
* *
3507830 TA TA TA GA TA TA GA 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
3507872 TA
1 TA
3507874 GTTGAATATA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (2 bp):
TA
Found at i:3508829 original size:8 final size:8
Alignment explanation
Indices: 3508818--3508868 Score: 52
Period size: 8 Copynumber: 6.2 Consensus size: 8
3508808 AAATTTAAAA
3508818 ATTTATAT
1 ATTTATAT
3508826 ATTTATATT
1 ATTTATA-T
3508835 ATATT-TAT
1 AT-TTATAT
*
3508843 ATTTA-AA
1 ATTTATAT
3508850 ATTTTATAT
1 A-TTTATAT
3508859 ATTTATAT
1 ATTTATAT
3508867 AT
1 AT
3508869 ATTTTGATAC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
7 4 0.11
8 23 0.64
9 7 0.19
10 2 0.06
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (8 bp):
ATTTATAT
Found at i:3508856 original size:33 final size:32
Alignment explanation
Indices: 3508810--3508872 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 32
3508800 TTGTAAATAA
3508810 ATTTAAAAATTTATATATTTATATTATATTTAT
1 ATTTAAAAATTTATATATTTATA-TATATTTAT
*
3508843 ATTTAAAATTTTATATATTTATATATATTT
1 ATTTAAAAATTTATATATTTATATATATTT
3508873 TGATACGTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 7 0.24
33 22 0.76
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (32 bp):
ATTTAAAAATTTATATATTTATATATATTTAT
Found at i:3508916 original size:32 final size:31
Alignment explanation
Indices: 3508854--3508943 Score: 87
Period size: 32 Copynumber: 2.9 Consensus size: 31
3508844 TTTAAAATTT
* * **
3508854 TATATAT-TTATATATATTTTGATACGTTAA
1 TATATATATTATATAAATTTTAATATATTAA
3508884 TAATATATATTATATAAATTTTAATATATTAA
1 T-ATATATATTATATAAATTTTAATATATTAA
* *
3508916 TTTATTTA-TATATAATATTTTAAT-TATT
1 TATATATATTATATAA-ATTTTAATATATT
3508944 TTTTATATTA
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
30 12 0.24
31 19 0.37
32 20 0.39
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.56
Consensus pattern (31 bp):
TATATATATTATATAAATTTTAATATATTAA
Found at i:3508928 original size:30 final size:30
Alignment explanation
Indices: 3508820--3508956 Score: 85
Period size: 30 Copynumber: 4.6 Consensus size: 30
3508810 ATTTAAAAAT
*
3508820 TTATATATTTATATTATAT-TTATA-TTTAA
1 TTAT-TATTTATATTATATATAATATTTTAA
* *
3508849 -AATT-TTATATATT-TATAT-ATATTTTGA
1 TTATTATT-TATATTATATATAATATTTTAA
* *
3508876 -TACGTTAATAATATATATTATATAA-ATTTTAA
1 TTA--TTATTTATAT-TA-TATATAATATTTTAA
3508908 TATATTAATTTAT-TTATATATAATATTTTAA
1 T-TATT-ATTTATATTATATATAATATTTTAA
*
3508939 TTATTTTTTATATTATAT
1 TTATTATTTATATTATAT
3508957 TTATATGATG
Statistics
Matches: 84, Mismatches: 9, Indels: 29
0.69 0.07 0.24
Matches are distributed among these distances:
26 8 0.10
27 13 0.15
28 2 0.02
29 11 0.13
30 19 0.23
31 10 0.12
32 14 0.17
33 5 0.06
34 2 0.02
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.58
Consensus pattern (30 bp):
TTATTATTTATATTATATATAATATTTTAA
Found at i:3508931 original size:23 final size:21
Alignment explanation
Indices: 3508905--3508957 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
3508895 ATATAAATTT
3508905 TAATATATTAATTTATTTATATA
1 TAATATATTAA-TTATTT-TATA
* *
3508928 TAATATTTTAATTATTTTTTA
1 TAATATATTAATTATTTTATA
*
3508949 TATTATATT
1 TAATATATT
3508958 TATATGATGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 10 0.38
22 6 0.23
23 10 0.38
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TAATATATTAATTATTTTATA
Found at i:3508937 original size:18 final size:18
Alignment explanation
Indices: 3508903--3508962 Score: 50
Period size: 18 Copynumber: 3.4 Consensus size: 18
3508893 TTATATAAAT
* *
3508903 TTTA-ATATATTAATTTA
1 TTTATATATAATATTTTA
3508920 TTTATATATAATATTTTA
1 TTTATATATAATATTTTA
* * * * *
3508938 ATTATTTTTTATATTATA
1 TTTATATATAATATTTTA
3508956 TTTATAT
1 TTTATAT
3508963 GATGTAATCG
Statistics
Matches: 33, Mismatches: 9, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
17 4 0.12
18 29 0.88
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTATATATAATATTTTA
Found at i:3508958 original size:23 final size:23
Alignment explanation
Indices: 3508905--3508958 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
3508895 ATATAAATTT
*
3508905 TAATATATTAATTTATTTATATA
1 TAATATTTTAATTTATTTATATA
*
3508928 TAATATTTTAA-TTATTTTTTATA
1 TAATATTTTAATTTA-TTTATATA
*
3508951 TTATATTT
1 TAATATTT
3508959 ATATGATGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 3 0.11
23 24 0.89
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (23 bp):
TAATATTTTAATTTATTTATATA
Found at i:3509114 original size:5 final size:5
Alignment explanation
Indices: 3509097--3509126 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
3509087 TTTGATAATG
*
3509097 ATTTT ATTAT ATTTT ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT
3509127 CCCATTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (5 bp):
ATTTT
Found at i:3509506 original size:3 final size:3
Alignment explanation
Indices: 3509498--3509522 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3509488 ATATTTGGCT
3509498 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
3509523 AAAAACATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3513025 original size:2 final size:2
Alignment explanation
Indices: 3513018--3513049 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3513008 GATCTTGATA
3513018 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
3513050 GTGTATGTGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3514929 original size:2 final size:2
Alignment explanation
Indices: 3514922--3514956 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3514912 ACTAATCTGA
3514922 TC 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 TC T
3514957 TAGTTTGTTT
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:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:3519369 original size:2 final size:2
Alignment explanation
Indices: 3519362--3519387 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3519352 CGAGAAAGCT
3519362 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
3519388 GCTTCTTTTT
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):
AG
Found at i:3520364 original size:14 final size:14
Alignment explanation
Indices: 3520345--3520374 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
3520335 CAAAAATGGA
3520345 TAAAGCGTGGGTCC
1 TAAAGCGTGGGTCC
3520359 TAAAGCGTGGGTCC
1 TAAAGCGTGGGTCC
3520373 TA
1 TA
3520375 GTCCTAGATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.20, G:0.33, T:0.23
Consensus pattern (14 bp):
TAAAGCGTGGGTCC
Found at i:3525515 original size:37 final size:39
Alignment explanation
Indices: 3525465--3525538 Score: 98
Period size: 37 Copynumber: 1.9 Consensus size: 39
3525455 CGATAATTTA
* * * *
3525465 AATATAATATAAAATTATTATTATATATAT-ATATATGT
1 AATATAATATAAAAATAATATAATAAATATAATATATGT
3525503 AATA-AATATAAAAATAATATAATAAATATAATATAT
1 AATATAATATAAAAATAATATAATAAATATAATATAT
3525539 TTAAATATTC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 21 0.68
38 10 0.32
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (39 bp):
AATATAATATAAAAATAATATAATAAATATAATATATGT
Found at i:3525594 original size:13 final size:12
Alignment explanation
Indices: 3525574--3525628 Score: 62
Period size: 12 Copynumber: 4.7 Consensus size: 12
3525564 AATTTATATA
3525574 TTATATTTTAAT
1 TTATATTTTAAT
3525586 TTATGATTTTAAT
1 TTAT-ATTTTAAT
*
3525599 TTAT-TTAATAAT
1 TTATATT-TTAAT
3525611 TTATA-TTT-AT
1 TTATATTTTAAT
3525621 TTATATTT
1 TTATATTT
3525629 ATAAGATTGA
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
10 7 0.19
11 5 0.14
12 13 0.35
13 12 0.32
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (12 bp):
TTATATTTTAAT
Found at i:3525652 original size:2 final size:2
Alignment explanation
Indices: 3525645--3525675 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3525635 TTGATAAACA
3525645 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 A
3525676 CACGTAAAAC
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3529350 original size:2 final size:2
Alignment explanation
Indices: 3529343--3529384 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
3529333 GTGGATATGG
3529343 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
3529385 TGGAGGATTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3530116 original size:2 final size:2
Alignment explanation
Indices: 3530109--3530133 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3530099 ATATTTAATT
3530109 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
3530134 GTCGAAAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3531138 original size:22 final size:24
Alignment explanation
Indices: 3531104--3531170 Score: 79
Period size: 24 Copynumber: 2.9 Consensus size: 24
3531094 ACAACCAATC
* *
3531104 ATATTTTTT-ATATT-TTAATAAT
1 ATATTTTTTAATATTAATAAAAAT
3531126 A-ATTTTTTAATATTAATAAAAAT
1 ATATTTTTTAATATTAATAAAAAT
3531149 ATATTTTATTAATATT-ATAAAA
1 ATATTTT-TTAATATTAATAAAA
3531171 TGTTGTAATT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
21 7 0.18
22 6 0.15
23 7 0.18
24 11 0.28
25 8 0.21
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
ATATTTTTTAATATTAATAAAAAT
Found at i:3531141 original size:20 final size:21
Alignment explanation
Indices: 3531106--3531144 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
3531096 AACCAATCAT
*
3531106 ATTTTTTATATTTTAATAATA
1 ATTTTTTATATATTAATAATA
3531127 ATTTTTTA-ATATTAATAA
1 ATTTTTTATATATTAATAA
3531145 AAATATATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
ATTTTTTATATATTAATAATA
Found at i:3532119 original size:33 final size:33
Alignment explanation
Indices: 3532081--3532146 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
3532071 GTGAAATTAT
3532081 ACAAGATGAAATGTAATGACATAACTTGCTGGC
1 ACAAGATGAAATGTAATGACATAACTTGCTGGC
3532114 ACAAGATGAAATGTAATGACATAACTTGCTGGC
1 ACAAGATGAAATGTAATGACATAACTTGCTGGC
3532147 CTAGTAACAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.24
Consensus pattern (33 bp):
ACAAGATGAAATGTAATGACATAACTTGCTGGC
Found at i:3537369 original size:2 final size:2
Alignment explanation
Indices: 3537364--3537394 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3537354 AAAAAGATGC
3537364 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
3537395 CCTTTTTCTT
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:3538268 original size:21 final size:20
Alignment explanation
Indices: 3538215--3538268 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 20
3538205 TCTTTATAAT
3538215 TATTAAA-AAAT-TATTTTA
1 TATTAAATAAATATATTTTA
**
3538233 TATTAATATTTATATATTTTA
1 TATTAA-ATAAATATATTTTA
3538254 TAATTAAATAAATAT
1 T-ATTAAATAAATAT
3538269 TAAATATTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
18 6 0.21
19 1 0.04
20 2 0.07
21 14 0.50
22 5 0.18
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TATTAAATAAATATATTTTA
Found at i:3538276 original size:40 final size:42
Alignment explanation
Indices: 3538196--3538278 Score: 100
Period size: 43 Copynumber: 2.0 Consensus size: 42
3538186 AAATTTGATT
**
3538196 TATTTATATTCTTTATAATTATTAAAAAATTATTTTATATTAA
1 TATTTATATTCTTTATAATTA-TAAAAAATTATTAAATATTAA
*
3538239 TATTTATATAT-TTTATAATTA-AATAAA-TATTAAATATTAA
1 TATTTATAT-TCTTTATAATTATAAAAAATTATTAAATATTAA
3538279 ATTAATTAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
40 11 0.31
41 5 0.14
43 19 0.53
44 1 0.03
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (42 bp):
TATTTATATTCTTTATAATTATAAAAAATTATTAAATATTAA
Found at i:3542677 original size:20 final size:20
Alignment explanation
Indices: 3542623--3542686 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 20
3542613 ACAATTTCTG
* * *
3542623 TAATTTTGATAACTTTTACA
1 TAATTTTAATAATTTTTAAA
* * *
3542643 TGATTTTCATAAATTTTTATA
1 TAATTTTAAT-AATTTTTAAA
3542664 TAATTTTAATAATTTTTAAA
1 TAATTTTAATAATTTTTAAA
3542684 TAA
1 TAA
3542687 AATAATATTT
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 20 0.56
21 16 0.44
ACGTcount: A:0.39, C:0.05, G:0.03, T:0.53
Consensus pattern (20 bp):
TAATTTTAATAATTTTTAAA
Found at i:3548102 original size:30 final size:27
Alignment explanation
Indices: 3548068--3548122 Score: 74
Period size: 30 Copynumber: 1.9 Consensus size: 27
3548058 TATTTTATAT
3548068 TTAAAATTATCAAAATTTAACATCTTATTA
1 TTAAAATTA--AAAATTT-ACATCTTATTA
*
3548098 TTAAAATTAAAAATTTATATCTTAT
1 TTAAAATTAAAAATTTACATCTTAT
3548123 CAACAGTTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 8 0.33
28 7 0.29
30 9 0.38
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.45
Consensus pattern (27 bp):
TTAAAATTAAAAATTTACATCTTATTA
Found at i:3548115 original size:20 final size:21
Alignment explanation
Indices: 3548073--3548115 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
3548063 TATATTTAAA
* *
3548073 ATTATCAAAATTTAACATCTT
1 ATTATCAAAATTAAAAATCTT
*
3548094 ATTATTAAAATTAAAAAT-TT
1 ATTATCAAAATTAAAAATCTT
3548114 AT
1 AT
3548116 ATCTTATCAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (21 bp):
ATTATCAAAATTAAAAATCTT
Found at i:3560673 original size:2 final size:2
Alignment explanation
Indices: 3560666--3560702 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3560656 AAACAGAACG
3560666 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 T
3560703 TCATGAATGT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3564296 original size:2 final size:2
Alignment explanation
Indices: 3564289--3564315 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3564279 AGAGGGATCT
3564289 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
3564316 TATTCTATAG
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:3565251 original size:29 final size:28
Alignment explanation
Indices: 3565202--3565256 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 28
3565192 TTTTTTAGTA
3565202 TTTATAAAATAGTAGTATATATATTACT
1 TTTATAAAATAGTAGTATATATATTACT
*
3565230 TTTAGTAAATATATTAG-ATATATATTA
1 TTTA-TAAA-ATAGTAGTATATATATTA
3565257 AAATTAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 4 0.17
29 14 0.58
30 6 0.25
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (28 bp):
TTTATAAAATAGTAGTATATATATTACT
Found at i:3565298 original size:16 final size:16
Alignment explanation
Indices: 3565277--3565307 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3565267 AAAAACTAAT
*
3565277 AAAATATTTTAAAAAA
1 AAAATAATTTAAAAAA
3565293 AAAATAATTTAAAAA
1 AAAATAATTTAAAAA
3565308 CAACAATGGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAATAATTTAAAAAA
Found at i:3565817 original size:2 final size:2
Alignment explanation
Indices: 3565810--3565839 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3565800 ATATTTTGGA
3565810 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
3565840 GGAATGCTTC
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:3566067 original size:2 final size:2
Alignment explanation
Indices: 3566062--3566089 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3566052 CTCTCTCTCT
3566062 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
3566090 ATTGGGAGTC
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:3571055 original size:2 final size:2
Alignment explanation
Indices: 3571044--3571081 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
3571034 ACAGAATTCT
3571044 TA TA -A 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
3571082 GCACGAAGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3575509 original size:2 final size:2
Alignment explanation
Indices: 3575502--3575527 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3575492 TGCTGTAGTG
3575502 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
3575528 TCATTTGTTT
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:3578170 original size:2 final size:2
Alignment explanation
Indices: 3578163--3578198 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3578153 GGTATGAATC
3578163 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
3578199 TCATTTATCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3590246 original size:2 final size:2
Alignment explanation
Indices: 3590239--3590265 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3590229 TTAATAGCGA
3590239 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 A
3590266 AAATAAAGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3591056 original size:18 final size:18
Alignment explanation
Indices: 3591024--3591076 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
3591014 TTATAATAAA
* *
3591024 TAAAAATAATATAAAAAT
1 TAAAAATTATTTAAAAAT
*
3591042 TAAAAATTATTTAAATAT
1 TAAAAATTATTTAAAAAT
*
3591060 AATAAAATTA-TTAAAAA
1 TA-AAAATTATTTAAAAA
3591077 AAATGATAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
18 22 0.76
19 7 0.24
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
TAAAAATTATTTAAAAAT
Found at i:3592454 original size:13 final size:13
Alignment explanation
Indices: 3592425--3592458 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
3592415 TGAGGATAAA
*
3592425 AAAATTATAATATT
1 AAAATT-TAAAATT
3592439 AAAATTTAAAATT
1 AAAATTTAAAATT
3592452 AAAATTT
1 AAAATTT
3592459 TTTAATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
AAAATTTAAAATT
Found at i:3606032 original size:2 final size:2
Alignment explanation
Indices: 3606027--3606075 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
3606017 AATCCCAACC
3606027 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
3606069 TA TA TA T
1 TA TA TA T
3606076 GAATCCCATT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3606922 original size:15 final size:14
Alignment explanation
Indices: 3606902--3606942 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
3606892 ATAATTTAAA
*
3606902 TTTTAAATCATATT
1 TTTTTAATCATATT
*
3606916 TTTTTAATTATATT
1 TTTTTAATCATATT
3606930 TTTTTCAATCATA
1 TTTTT-AATCATA
3606943 AGCTTAGAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
14 17 0.74
15 6 0.26
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (14 bp):
TTTTTAATCATATT
Found at i:3611754 original size:2 final size:2
Alignment explanation
Indices: 3611747--3611776 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3611737 GCTGATACAC
3611747 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
3611777 CAGCTTTAAC
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3629537 original size:2 final size:2
Alignment explanation
Indices: 3629530--3629558 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3629520 TCCAAGGTAC
3629530 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
3629559 GTGTGTGCGA
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:3633462 original size:21 final size:23
Alignment explanation
Indices: 3633438--3633481 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
3633428 ATAATAAATG
3633438 TTTTAATA-TA-AAATATTAATA
1 TTTTAATAGTATAAATATTAATA
*
3633459 TTTTAATAGTATTAATATTAATA
1 TTTTAATAGTATAAATATTAATA
3633482 ATAATTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 8 0.40
22 2 0.10
23 10 0.50
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (23 bp):
TTTTAATAGTATAAATATTAATA
Found at i:3637308 original size:19 final size:19
Alignment explanation
Indices: 3637280--3637316 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
3637270 TGAATTCATA
*
3637280 TAATGCAAAGAGCTTTTCT
1 TAATGAAAAGAGCTTTTCT
3637299 TAATGAAAAGAGCTTTTC
1 TAATGAAAAGAGCTTTTC
3637317 CTTATGCAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (19 bp):
TAATGAAAAGAGCTTTTCT
Found at i:3640517 original size:24 final size:23
Alignment explanation
Indices: 3640477--3640529 Score: 81
Period size: 24 Copynumber: 2.3 Consensus size: 23
3640467 ATTCATATTT
3640477 AATAT-ATATTTAAATATATAAA
1 AATATAATATTTAAATATATAAA
3640499 AATATAATATTTTAAATATATAAA
1 AATATAATA-TTTAAATATATAAA
*
3640523 AAAATAA
1 AATATAA
3640530 AAAAAATTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
22 5 0.18
23 3 0.11
24 20 0.71
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
AATATAATATTTAAATATATAAA
Found at i:3645573 original size:15 final size:15
Alignment explanation
Indices: 3645553--3645583 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3645543 ACATGAAAAA
3645553 TATGCAGGAACCGGG
1 TATGCAGGAACCGGG
*
3645568 TATGCAGGAACTGGG
1 TATGCAGGAACCGGG
3645583 T
1 T
3645584 CTAAAACAGT
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:0.26, C:0.16, G:0.39, T:0.19
Consensus pattern (15 bp):
TATGCAGGAACCGGG
Found at i:3649452 original size:2 final size:2
Alignment explanation
Indices: 3649445--3649477 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
3649435 GCGTTGAAAG
*
3649445 TC TC TC TC TG 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
3649478 TTGCGTCGCG
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:0.00, C:0.45, G:0.03, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3657410 original size:2 final size:2
Alignment explanation
Indices: 3657405--3657431 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3657395 TATATATATA
3657405 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
3657432 TTTCGTGGCG
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:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:3657788 original size:2 final size:2
Alignment explanation
Indices: 3657775--3657816 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
3657765 CTTTAGCAGG
*
3657775 AT AT AC 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
3657817 GTTGCCCGTG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3659336 original size:2 final size:2
Alignment explanation
Indices: 3659329--3659356 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3659319 AGACGACTAC
3659329 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
3659357 GTACCCAGCA
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:3659535 original size:3 final size:3
Alignment explanation
Indices: 3659527--3659555 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
3659517 TAAGCATATG
3659527 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
3659556 TAACTAAGGA
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:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:3662823 original size:155 final size:155
Alignment explanation
Indices: 3662541--3662842 Score: 559
Period size: 155 Copynumber: 1.9 Consensus size: 155
3662531 CGAGAAAGCC
* *
3662541 TTTTGCAGTCAAGAGTGCCGCTATCAGGAAATGCTCTTAGATGGAGAGGATAATTAAGAATTTCA
1 TTTTGCAGTCAAGAGTGCCGCTATCAGCAAATGCTCTTAGATGGAGAGGAGAATTAAGAATTTCA
*
3662606 TCACTGCTACTGCTTGCTTCGAGATTATTTTCAATTCCAAATGATTGATTCCGTTAAACCAAACA
66 TCACTGCTACTGCTTGCTTCGAGATTATTTTCAATTCCAAATGATTGATTCCATTAAACCAAACA
3662671 TTTCCCAGTTCTTGCTTCGAGATTA
131 TTTCCCAGTTCTTGCTTCGAGATTA
3662696 TTTTGCAGTCAAGAGTGCCGCTATCAGCAAATGCTCTTAGATGGAGAGGAGAATTAAGAATTTCA
1 TTTTGCAGTCAAGAGTGCCGCTATCAGCAAATGCTCTTAGATGGAGAGGAGAATTAAGAATTTCA
* *
3662761 TCACTGCTACTGCTTGCTTGGAGATTATTTTCTATTCCAAATGATTGATTCCATTAAACCAAACA
66 TCACTGCTACTGCTTGCTTCGAGATTATTTTCAATTCCAAATGATTGATTCCATTAAACCAAACA
3662826 TTTCCCAGTTCTTGCTT
131 TTTCCCAGTTCTTGCTT
3662843 TCTTTCTTTT
Statistics
Matches: 142, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
155 142 1.00
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (155 bp):
TTTTGCAGTCAAGAGTGCCGCTATCAGCAAATGCTCTTAGATGGAGAGGAGAATTAAGAATTTCA
TCACTGCTACTGCTTGCTTCGAGATTATTTTCAATTCCAAATGATTGATTCCATTAAACCAAACA
TTTCCCAGTTCTTGCTTCGAGATTA
Found at i:3670902 original size:117 final size:117
Alignment explanation
Indices: 3670696--3670948 Score: 425
Period size: 117 Copynumber: 2.2 Consensus size: 117
3670686 CCGCAGCTTC
*
3670696 GGTGGTCTTCCACGCTTACGAATCACACCTTCCCTTACCTTGCTATTATTTTGATCACTCCCTTC
1 GGTGGTCTCCCACGCTTACGAATCACACCTTCCCTTACCTTGCTATTATTTTGATCACTCCCTTC
* * *
3670761 CCTTTTCAACTCAACCCACTTCTTCGCTAACCCATGACTGCCCTGCACTTTG
66 CCTTTTCAACCCAACCCACTTCTTCACTAACCCATCACTGCCCTGCACTTTG
* * *
3670813 GGTGGTCTCCCACGCTTACGGATTACACTTTCCCTTACCTTGCTATTATTTTGATCACTCCCTTC
1 GGTGGTCTCCCACGCTTACGAATCACACCTTCCCTTACCTTGCTATTATTTTGATCACTCCCTTC
* *
3670878 CTTTTTCAACCCACCCCACTTCTTCACTAACCCATCACTGCCCTGCACTTTG
66 CCTTTTCAACCCAACCCACTTCTTCACTAACCCATCACTGCCCTGCACTTTG
3670930 GGTGGTCTCCCACGCTTAC
1 GGTGGTCTCCCACGCTTAC
3670949 ACTTCACCTC
Statistics
Matches: 127, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
117 127 1.00
ACGTcount: A:0.17, C:0.37, G:0.12, T:0.34
Consensus pattern (117 bp):
GGTGGTCTCCCACGCTTACGAATCACACCTTCCCTTACCTTGCTATTATTTTGATCACTCCCTTC
CCTTTTCAACCCAACCCACTTCTTCACTAACCCATCACTGCCCTGCACTTTG
Found at i:3670985 original size:117 final size:116
Alignment explanation
Indices: 3670696--3670986 Score: 293
Period size: 117 Copynumber: 2.5 Consensus size: 116
3670686 CCGCAGCTTC
* * * * * * * ***
3670696 GGTGGTCTTCCACGCTTACGAATCACACCTTCCCTTACCTTGCTATTATTTTGATCACTCCCTTC
1 GGTGGTCTCCCACGCTTACG-ATTACACTTTCCCTTACATTACAATCAAAGTGATCACTCCCTTC
* * *
3670761 CCTTTTCAACTCAACCCACTTCTTCGCTAACCCATGACTGCCCTGCACTTTG
65 CCTTTTCAACCCAACCCACTTCTTCACTAACCCATCACTGCCCTGCACTTTG
* * * * ***
3670813 GGTGGTCTCCCACGCTTACGGATTACACTTTCCCTTACCTTGCTATTATTTTGATCACTCCCTTC
1 GGTGGTCTCCCACGCTTAC-GATTACACTTTCCCTTACATTACAATCAAAGTGATCACTCCCTTC
* *
3670878 CTTTTTCAACCCACCCCACTTCTTCACTAACCCATCACTGCCCTGCACTTTG
65 CCTTTTCAACCCAACCCACTTCTTCACTAACCCATCACTGCCCTGCACTTTG
3670930 GGTGGTCTCCCACGCTTAC-ACTT-CACCTCCTT-CCTTA-ATTCACAATCAAAGTGATCA
1 GGTGGTCTCCCACGCTTACGA-TTACA-CT--TTCCCTTACATT-ACAATCAAAGTGATCA
3670987 ACCTCTCCCA
Statistics
Matches: 153, Mismatches: 15, Indels: 12
0.85 0.08 0.07
Matches are distributed among these distances:
115 3 0.02
116 6 0.04
117 141 0.92
118 3 0.02
ACGTcount: A:0.19, C:0.36, G:0.11, T:0.34
Consensus pattern (116 bp):
GGTGGTCTCCCACGCTTACGATTACACTTTCCCTTACATTACAATCAAAGTGATCACTCCCTTCC
CTTTTCAACCCAACCCACTTCTTCACTAACCCATCACTGCCCTGCACTTTG
Found at i:3677135 original size:2 final size:2
Alignment explanation
Indices: 3677128--3677170 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
3677118 AAAAGATGTT
*
3677128 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3677170 T
1 T
3677171 GGTGGGCGTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3688599 original size:18 final size:19
Alignment explanation
Indices: 3688578--3688624 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 19
3688568 TAAAATAAAG
3688578 AAAAAAAT-TAAAATTTTT
1 AAAAAAATATAAAATTTTT
*
3688596 -AAAAATTATAAAATTTTT
1 AAAAAAATATAAAATTTTT
3688614 AAAGAAAATAT
1 AAA-AAAATAT
3688625 TTAAAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 6 0.25
18 10 0.42
19 2 0.08
20 6 0.25
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (19 bp):
AAAAAAATATAAAATTTTT
Found at i:3689780 original size:23 final size:23
Alignment explanation
Indices: 3689753--3689804 Score: 70
Period size: 24 Copynumber: 2.3 Consensus size: 23
3689743 AAAAAAAAAA
* *
3689753 AAGAAAA-AATGATAAAGGAATG
1 AAGAAAATAATAATAAAGAAATG
3689775 AGAGAAAATAATAATAAAGAAATG
1 A-AGAAAATAATAATAAAGAAATG
3689799 AAGAAA
1 AAGAAA
3689805 GAAAGAATCT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 1 0.04
23 11 0.42
24 14 0.54
ACGTcount: A:0.67, C:0.00, G:0.19, T:0.13
Consensus pattern (23 bp):
AAGAAAATAATAATAAAGAAATG
Done.