Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold79
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: 4189514
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 5041 characters in sequence are not A, C, G, or T
File 24 of 26
Found at i:3451028 original size:3 final size:3
Alignment explanation
Indices: 3451022--3451062 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
3451012 TTTAAAAGGA
3451022 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
3451063 ACATTTAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:3451685 original size:20 final size:20
Alignment explanation
Indices: 3451618--3451686 Score: 63
Period size: 20 Copynumber: 3.5 Consensus size: 20
3451608 AATTTAATTT
3451618 AATAAAAATAAATTTA-A-AA
1 AATAAAAAT-AATTTAGATAA
* *
3451637 AATAAAAATTTATTTTGATATA
1 AATAAAAA-TAATTTAGATA-A
*
3451659 AAT-AAAATAATTTAGATAC
1 AATAAAAATAATTTAGATAA
3451678 AATAAAAAT
1 AATAAAAAT
3451687 TTGGAAATAA
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
19 15 0.38
20 16 0.40
21 5 0.12
22 4 0.10
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.33
Consensus pattern (20 bp):
AATAAAAATAATTTAGATAA
Found at i:3452590 original size:18 final size:18
Alignment explanation
Indices: 3452569--3452685 Score: 69
Period size: 18 Copynumber: 6.4 Consensus size: 18
3452559 TAAAAATTTT
3452569 ATTTAAAT-TAAATTATAA
1 ATTTAAATATAAA-TATAA
*
3452587 ATTTTAATATAAATATAA
1 ATTTAAATATAAATATAA
* * *
3452605 TTTTTAAATAATCAATATTA
1 -ATTTAAAT-ATAAATATAA
*
3452625 TTTTAAATATAAAT-TAAA
1 ATTTAAATATAAATAT-AA
** *
3452643 ATTTTAAA-ATTGATTTAA
1 A-TTTAAATATAAATATAA
* *
3452661 ACTTAAATATAAATAAAA
1 ATTTAAATATAAATATAA
*
3452679 AATTAAA
1 ATTTAAA
3452686 AAATTACTCA
Statistics
Matches: 76, Mismatches: 16, Indels: 14
0.72 0.15 0.13
Matches are distributed among these distances:
17 6 0.08
18 37 0.49
19 25 0.33
20 8 0.11
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.43
Consensus pattern (18 bp):
ATTTAAATATAAATATAA
Found at i:3452650 original size:19 final size:19
Alignment explanation
Indices: 3452570--3452650 Score: 80
Period size: 19 Copynumber: 4.3 Consensus size: 19
3452560 AAAAATTTTA
3452570 TTTAAAT-TAAATTATAAAT
1 TTTAAATATAAA-TATAAAT
*
3452589 TTT-AATATAAATATAATT
1 TTTAAATATAAATATAAAT
* *
3452607 TTTAAATAATCAATAT-TAT
1 TTTAAAT-ATAAATATAAAT
3452626 TTTAAATATAAAT-TAAAAT
1 TTTAAATATAAATAT-AAAT
3452645 TTTAAA
1 TTTAAA
3452651 ATTGATTTAA
Statistics
Matches: 51, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
17 1 0.02
18 17 0.33
19 26 0.51
20 7 0.14
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (19 bp):
TTTAAATATAAATATAAAT
Found at i:3452873 original size:2 final size:2
Alignment explanation
Indices: 3452868--3452894 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3452858 AAAAAATAGA
3452868 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
3452895 ATGAAGGAAA
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:3453440 original size:31 final size:27
Alignment explanation
Indices: 3453397--3453474 Score: 88
Period size: 31 Copynumber: 2.8 Consensus size: 27
3453387 TTTAAAAAGT
*
3453397 AATATAAATATATTAAATTTATATAATTTA
1 AATATTAATATATTAAATTT-T-T-ATTTA
3453427 AATGATTAATATATTAAA-TTTTATTTA
1 AAT-ATTAATATATTAAATTTTTATTTA
3453454 AATATTAATAT-TTAATATTTT
1 AATATTAATATATTAA-ATTTT
3453475 AAATATAATT
Statistics
Matches: 44, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
25 4 0.09
26 9 0.20
27 11 0.25
28 1 0.02
29 1 0.02
30 5 0.11
31 13 0.30
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (27 bp):
AATATTAATATATTAAATTTTTATTTA
Found at i:3453858 original size:2 final size:2
Alignment explanation
Indices: 3453853--3453890 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
3453843 ATTCTTCCCT
*
3453853 TC TC TC TG TC TC TC TC TC -C 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 TC TC T
3453891 TGCACTCAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.00, C:0.47, G:0.03, T:0.50
Consensus pattern (2 bp):
TC
Found at i:3453874 original size:17 final size:17
Alignment explanation
Indices: 3453854--3453887 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3453844 TTCTTCCCTT
*
3453854 CTCTCTGTCTCTCTCTC
1 CTCTCTCTCTCTCTCTC
3453871 CTCTCTCTCTCTCTCTC
1 CTCTCTCTCTCTCTCTC
3453888 TCTTGCACTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.00, C:0.50, G:0.03, T:0.47
Consensus pattern (17 bp):
CTCTCTCTCTCTCTCTC
Found at i:3453875 original size:19 final size:19
Alignment explanation
Indices: 3453853--3453889 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
3453843 ATTCTTCCCT
*
3453853 TCTCTCTGTCTCTCTCTCC
1 TCTCTCTCTCTCTCTCTCC
3453872 TCTCTCTCTCTCTCTCTC
1 TCTCTCTCTCTCTCTCTC
3453890 TTGCACTCAA
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:0.00, C:0.49, G:0.03, T:0.49
Consensus pattern (19 bp):
TCTCTCTCTCTCTCTCTCC
Found at i:3453980 original size:2 final size:2
Alignment explanation
Indices: 3453973--3454002 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3453963 GTCTTCCATT
3453973 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3454003 CTTTTTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:3457522 original size:19 final size:20
Alignment explanation
Indices: 3457470--3457524 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 20
3457460 TTAATATAAT
3457470 AAAATAATATTTT-TATTTA
1 AAAATAATATTTTATATTTA
** *
3457489 AATTTAATAAATTTATA-TTA
1 AAAATAAT-ATTTTATATTTA
3457509 AAAATAATATTTTATA
1 AAAATAATATTTTATA
3457525 CCAGGAAAAC
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
19 13 0.46
20 13 0.46
21 2 0.07
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AAAATAATATTTTATATTTA
Found at i:3457948 original size:22 final size:22
Alignment explanation
Indices: 3457923--3457965 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
3457913 ATTGATATAA
3457923 AATTATTAAATTT-AATTAATTT
1 AATTATT-AATTTAAATTAATTT
*
3457945 AATTATTTATTTAAATTAATT
1 AATTATTAATTTAAATTAATT
3457966 AAAAATTGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
AATTATTAATTTAAATTAATTT
Found at i:3457952 original size:17 final size:17
Alignment explanation
Indices: 3457932--3457966 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
3457922 AAATTATTAA
*
3457932 ATTTAATTAATTTAATT
1 ATTTAATTAAATTAATT
*
3457949 ATTTATTTAAATTAATT
1 ATTTAATTAAATTAATT
3457966 A
1 A
3457967 AAAATTGTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
ATTTAATTAAATTAATT
Found at i:3459566 original size:20 final size:19
Alignment explanation
Indices: 3459543--3459588 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
3459533 CACATGTAAA
**
3459543 TTAAATAAAATATTTAAATT
1 TTAAATAAAAT-TAAAAATT
*
3459563 TTAATTAAAATTAAAAATT
1 TTAAATAAAATTAAAAATT
3459582 TTAAATA
1 TTAAATA
3459589 TATATAATAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
TTAAATAAAATTAAAAATT
Found at i:3459868 original size:3 final size:3
Alignment explanation
Indices: 3459862--3459898 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
3459852 AATATTAAGG
3459862 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
3459899 TTGTGTATAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:3460676 original size:46 final size:46
Alignment explanation
Indices: 3460612--3460701 Score: 137
Period size: 46 Copynumber: 2.0 Consensus size: 46
3460602 TTTTTTAAAC
* * *
3460612 TTTTATTGTTATCGTATCATATTTTACTGA-TCATGTAATTTTAATT
1 TTTTATTATTATCATATCATATTTTACTCACT-ATGTAATTTTAATT
3460658 TTTTATTATTATCATATCATATTTTACTCACTATGTAATTTTAA
1 TTTTATTATTATCATATCATATTTTACTCACTATGTAATTTTAA
3460702 GATATTATTA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
46 39 0.98
47 1 0.03
ACGTcount: A:0.29, C:0.10, G:0.06, T:0.56
Consensus pattern (46 bp):
TTTTATTATTATCATATCATATTTTACTCACTATGTAATTTTAATT
Found at i:3460710 original size:46 final size:46
Alignment explanation
Indices: 3460614--3460712 Score: 128
Period size: 46 Copynumber: 2.2 Consensus size: 46
3460604 TTTTAAACTT
* * * ** *
3460614 TTATTGTTATCGTATCATATTTTACTGATCATGTAATTTTAATTTT
1 TTATTATTATCATATCATATTTTACTCATCATGTAATTTTAAGATA
3460660 TTATTATTATCATATCATATTTTACTCA-CTATGTAATTTTAAGATA
1 TTATTATTATCATATCATATTTTACTCATC-ATGTAATTTTAAGATA
3460706 TTATTAT
1 TTATTAT
3460713 ATTCTTTTAA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
45 1 0.02
46 45 0.98
ACGTcount: A:0.30, C:0.09, G:0.06, T:0.55
Consensus pattern (46 bp):
TTATTATTATCATATCATATTTTACTCATCATGTAATTTTAAGATA
Found at i:3463175 original size:23 final size:24
Alignment explanation
Indices: 3463116--3463179 Score: 80
Period size: 24 Copynumber: 2.7 Consensus size: 24
3463106 TATTTTAACG
3463116 TTTTAATA-ATTTATATTAAATTAA
1 TTTTAATATA-TTATATTAAATTAA
*
3463140 TTTTAATATATTATATTATTATT-A
1 TTTTAATATATTATATTA-AATTAA
3463164 TTTT-ATATATTATATT
1 TTTTAATATATTATATT
3463180 TATATCATTG
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
23 12 0.32
24 21 0.57
25 4 0.11
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (24 bp):
TTTTAATATATTATATTAAATTAA
Found at i:3463176 original size:15 final size:13
Alignment explanation
Indices: 3463145--3463184 Score: 59
Period size: 11 Copynumber: 3.3 Consensus size: 13
3463135 ATTAATTTTA
3463145 ATATATTATA-TT
1 ATATATTATATTT
3463157 AT-TATTAT-TTT
1 ATATATTATATTT
3463168 ATATATTATATTT
1 ATATATTATATTT
3463181 ATAT
1 ATAT
3463185 CATTGTTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 10 0.40
12 8 0.32
13 7 0.28
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
ATATATTATATTT
Found at i:3464040 original size:24 final size:25
Alignment explanation
Indices: 3463993--3464062 Score: 76
Period size: 24 Copynumber: 2.9 Consensus size: 25
3463983 ATATTTTAAA
* *
3463993 ATAATTATTTA-TATAATATTTATAT
1 ATAATTATTAATTA-AATATTAATAT
*
3464018 AT-TTTA-TAATTAAAT-TTAATAT
1 ATAATTATTAATTAAATATTAATAT
3464040 ATAATTATTAATTAAATATTAAT
1 ATAATTATTAATTAAATATTAAT
3464063 TCAAACTATA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
22 8 0.22
23 8 0.22
24 14 0.38
25 7 0.19
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (25 bp):
ATAATTATTAATTAAATATTAATAT
Found at i:3464513 original size:7 final size:7
Alignment explanation
Indices: 3464501--3464526 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
3464491 TTAATTATTT
3464501 TTTAAAA
1 TTTAAAA
3464508 TTTAAAA
1 TTTAAAA
3464515 TTTAAAA
1 TTTAAAA
3464522 TTTAA
1 TTTAA
3464527 TATATAATAT
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:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (7 bp):
TTTAAAA
Found at i:3464518 original size:41 final size:41
Alignment explanation
Indices: 3464471--3464550 Score: 110
Period size: 41 Copynumber: 2.0 Consensus size: 41
3464461 TGAGATAATT
* *
3464471 AAATTTAAATTTTAATTAATTTAAT-TA-TTTTTTAAAATTTA
1 AAATTTAAAATTTAA-T-ATATAATATATTTTTTTAAAATTTA
3464512 AAATTTAAAATTTAATATATAATATATTTTTTTAAAATT
1 AAATTTAAAATTTAATATATAATATATTTTTTTAAAATT
3464551 AATAAGTCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
39 6 0.17
40 3 0.09
41 26 0.74
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (41 bp):
AAATTTAAAATTTAATATATAATATATTTTTTTAAAATTTA
Found at i:3465537 original size:27 final size:26
Alignment explanation
Indices: 3465475--3465537 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 26
3465465 ATTAGTTATT
*
3465475 ATATTT-TTTAAAATACAAAATTAAA
1 ATATTTCTTTAAAATACAAAACTAAA
* *
3465500 ATATTAACTTTAATATACAAGAACTAAA
1 ATATT-TCTTTAAAATACAA-AACTAAA
3465528 ATATTTCTTT
1 ATATTTCTTT
3465538 TATTAATGGA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
25 5 0.16
27 15 0.48
28 11 0.35
ACGTcount: A:0.49, C:0.08, G:0.02, T:0.41
Consensus pattern (26 bp):
ATATTTCTTTAAAATACAAAACTAAA
Found at i:3466900 original size:81 final size:81
Alignment explanation
Indices: 3466776--3466937 Score: 288
Period size: 81 Copynumber: 2.0 Consensus size: 81
3466766 TTGTTAAAGC
3466776 GAATAAAGGACATCCAAAAAGCTTTCTTTAGAAAACCACCATAGCTTAATTAGATAAAAACATTA
1 GAATAAAGGACATCCAAAAAGCTTTCTTTAGAAAACCACCATAGCTTAATTAGATAAAAACATTA
*
3466841 TCCCACTTGTTAGAAA
66 TCCCACTTGTCAGAAA
*
3466857 GAATAAAGGACATCCTAAAAGCTTTCTTTAGAAAACCACCATAGCTTAATTAGATAAAAACATTA
1 GAATAAAGGACATCCAAAAAGCTTTCTTTAGAAAACCACCATAGCTTAATTAGATAAAAACATTA
**
3466922 TTTCACTTGTCAGAAA
66 TCCCACTTGTCAGAAA
3466938 CGACTAATGT
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
81 77 1.00
ACGTcount: A:0.44, C:0.18, G:0.11, T:0.27
Consensus pattern (81 bp):
GAATAAAGGACATCCAAAAAGCTTTCTTTAGAAAACCACCATAGCTTAATTAGATAAAAACATTA
TCCCACTTGTCAGAAA
Found at i:3468999 original size:12 final size:12
Alignment explanation
Indices: 3468976--3469073 Score: 51
Period size: 12 Copynumber: 8.1 Consensus size: 12
3468966 TTTTTTTAAA
3468976 AATAT-TTA-TT
1 AATATATTATTT
3468986 AATATATTATTT
1 AATATATTATTT
*
3468998 AATAGTATGATATTA
1 AATA-TAT--TATTT
* *
3469013 AATATAATAATT
1 AATATATTATTT
*
3469025 AATA-ATTTTTT
1 AATATATTATTT
* *
3469036 AATGTATTTATTA
1 AATATA-TTATTT
*
3469049 AAAATATTA-TT
1 AATATATTATTT
*
3469060 AAAATATTTATTT
1 AATATA-TTATTT
3469073 A
1 A
3469074 TAAAAGATTT
Statistics
Matches: 66, Mismatches: 13, Indels: 15
0.70 0.14 0.16
Matches are distributed among these distances:
10 5 0.08
11 17 0.26
12 20 0.30
13 14 0.21
14 2 0.03
15 8 0.12
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (12 bp):
AATATATTATTT
Found at i:3469114 original size:20 final size:21
Alignment explanation
Indices: 3469089--3469127 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3469079 GATTTTAAGG
3469089 AATAAA-AA-TATATTAAAAAT
1 AATAAATAATTATA-TAAAAAT
3469109 AATAAATAATTATATAAAA
1 AATAAATAATTATATAAAA
3469128 TTAAAAACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.35
21 7 0.41
22 4 0.24
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (21 bp):
AATAAATAATTATATAAAAAT
Found at i:3481690 original size:3 final size:3
Alignment explanation
Indices: 3481682--3481708 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3481672 ATATTATCTT
3481682 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
3481709 ATTAATTAAA
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:3482318 original size:21 final size:21
Alignment explanation
Indices: 3482293--3482362 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
3482283 AAAATAAAAT
3482293 AATTAGTTTTTCTTAGAAGAA
1 AATTAGTTTTTCTTAGAAGAA
** * * * *
3482314 AATTAAATATT-TGAAAATAAA
1 AATTAGTTTTTCTTAGAA-GAA
3482335 ATAATTAGTTTTTCTTAGAAGAA
1 A--ATTAGTTTTTCTTAGAAGAA
3482358 AATTA
1 AATTA
3482363 AATATTTTAA
Statistics
Matches: 33, Mismatches: 12, Indels: 8
0.62 0.23 0.15
Matches are distributed among these distances:
20 4 0.12
21 15 0.45
23 10 0.30
24 4 0.12
ACGTcount: A:0.47, C:0.03, G:0.10, T:0.40
Consensus pattern (21 bp):
AATTAGTTTTTCTTAGAAGAA
Found at i:3482331 original size:44 final size:44
Alignment explanation
Indices: 3482281--3482369 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
3482271 AATTATGACC
3482281 TGAAAATAAAATAATTAGTTTTTCTTAGAAGAAAATTAAATATT
1 TGAAAATAAAATAATTAGTTTTTCTTAGAAGAAAATTAAATATT
3482325 TGAAAATAAAATAATTAGTTTTTCTTAGAAGAAAATTAAATATT
1 TGAAAATAAAATAATTAGTTTTTCTTAGAAGAAAATTAAATATT
3482369 T
1 T
3482370 TAAGTGTTTT
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:0.49, C:0.02, G:0.09, T:0.39
Consensus pattern (44 bp):
TGAAAATAAAATAATTAGTTTTTCTTAGAAGAAAATTAAATATT
Found at i:3488574 original size:8 final size:8
Alignment explanation
Indices: 3488561--3488586 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
3488551 TTTTTTATCA
3488561 ATATATTT
1 ATATATTT
3488569 ATATATTT
1 ATATATTT
3488577 ATATATTT
1 ATATATTT
3488585 AT
1 AT
3488587 CGCATATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
ATATATTT
Found at i:3488638 original size:18 final size:18
Alignment explanation
Indices: 3488616--3488662 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
3488606 AATTTATATA
3488616 ATTATATTATATATTATT
1 ATTATATTATATATTATT
*
3488634 TTTATATTATATATTATT
1 ATTATATTATATATTATT
3488652 ATTATAATTAT
1 ATTAT-ATTAT
3488663 TTTTCATTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 21 0.81
19 5 0.19
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
ATTATATTATATATTATT
Found at i:3488644 original size:31 final size:30
Alignment explanation
Indices: 3488609--3488666 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
3488599 TTTAATTAAT
3488609 TTATATAATTA-TATTATATATTATTTTTATA
1 TTATAT-ATTATTATTATA-ATTATTTTTATA
3488640 TTATATATTATTATTATAATTATTTTT
1 TTATATATTATTATTATAATTATTTTT
3488667 CATTTGAGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
30 13 0.50
31 13 0.50
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (30 bp):
TTATATATTATTATTATAATTATTTTTATA
Found at i:3491725 original size:12 final size:13
Alignment explanation
Indices: 3491710--3491759 Score: 52
Period size: 12 Copynumber: 3.9 Consensus size: 13
3491700 ACTGTGCAAC
3491710 CAATTTTG-AATT
1 CAATTTTGAAATT
3491722 CAA-TTTGAAATAGT
1 CAATTTTGAAAT--T
*
3491736 TAATTTTGAAATT
1 CAATTTTGAAATT
3491749 CAA-TTTGAAAT
1 CAATTTTGAAAT
3491760 AGTAAAAGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
11 4 0.12
12 14 0.44
13 3 0.09
14 3 0.09
15 8 0.25
ACGTcount: A:0.40, C:0.06, G:0.10, T:0.44
Consensus pattern (13 bp):
CAATTTTGAAATT
Found at i:3491753 original size:27 final size:26
Alignment explanation
Indices: 3491711--3491762 Score: 95
Period size: 27 Copynumber: 2.0 Consensus size: 26
3491701 CTGTGCAACC
3491711 AATTTTGAATTCAATTTGAAATAGTT
1 AATTTTGAATTCAATTTGAAATAGTT
3491737 AATTTTGAAATTCAATTTGAAATAGT
1 AATTTTG-AATTCAATTTGAAATAGT
3491763 AAAAGTTGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 7 0.28
27 18 0.72
ACGTcount: A:0.40, C:0.04, G:0.12, T:0.44
Consensus pattern (26 bp):
AATTTTGAATTCAATTTGAAATAGTT
Found at i:3496525 original size:27 final size:26
Alignment explanation
Indices: 3496483--3496534 Score: 86
Period size: 27 Copynumber: 2.0 Consensus size: 26
3496473 CTGTGCAGCC
3496483 AATTTTGAATTCAATTTAAAATAGTT
1 AATTTTGAATTCAATTTAAAATAGTT
*
3496509 AATTTTGAAATTCAATTTGAAATAGT
1 AATTTTG-AATTCAATTTAAAATAGT
3496535 AAAAGTTGCA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 7 0.29
27 17 0.71
ACGTcount: A:0.42, C:0.04, G:0.10, T:0.44
Consensus pattern (26 bp):
AATTTTGAATTCAATTTAAAATAGTT
Found at i:3496607 original size:9 final size:9
Alignment explanation
Indices: 3496593--3496625 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
3496583 AGAAGGCTCA
3496593 AGCAGAGAC
1 AGCAGAGAC
3496602 AGCAGAGAC
1 AGCAGAGAC
*
3496611 AGCAGAGAT
1 AGCAGAGAC
3496620 AGCAGA
1 AGCAGA
3496626 AAGAGAGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.45, C:0.18, G:0.33, T:0.03
Consensus pattern (9 bp):
AGCAGAGAC
Found at i:3499380 original size:21 final size:18
Alignment explanation
Indices: 3499335--3499372 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
3499325 CACTAAAAAA
3499335 TATTTTATTTATTTATAT
1 TATTTTATTTATTTATAT
3499353 T-TTTTATTTATTTA-AT
1 TATTTTATTTATTTATAT
3499369 TATT
1 TATT
3499373 AATTTTATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 3 0.16
17 15 0.79
18 1 0.05
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (18 bp):
TATTTTATTTATTTATAT
Found at i:3503696 original size:7 final size:8
Alignment explanation
Indices: 3503673--3503709 Score: 56
Period size: 8 Copynumber: 4.5 Consensus size: 8
3503663 GACCTTTCTC
3503673 ATTATAAAA
1 ATTA-AAAA
*
3503682 TTTAAAAA
1 ATTAAAAA
3503690 ATTAAAAA
1 ATTAAAAA
3503698 ATTAAAAA
1 ATTAAAAA
3503706 ATTA
1 ATTA
3503710 TTTTTTAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
8 23 0.88
9 3 0.12
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (8 bp):
ATTAAAAA
Found at i:3504902 original size:3 final size:3
Alignment explanation
Indices: 3504894--3504928 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
3504884 AGAAGCAAAT
3504894 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
3504929 TCATGGGGTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:3508550 original size:26 final size:26
Alignment explanation
Indices: 3508521--3508596 Score: 75
Period size: 26 Copynumber: 3.0 Consensus size: 26
3508511 TTAACTTATT
*
3508521 ATTTAATTATTTATATTTAAATTTAA
1 ATTTAATTATTTATATTTAAATTAAA
* * *
3508547 ATTTAATTTTTTAAATATAAATTAAA
1 ATTTAATTATTTATATTTAAATTAAA
* *
3508573 AATAAATTTATTT-TA-TTAAATTAA
1 ATTTAA-TTATTTATATTTAAATTAA
3508597 TAAAAATTAA
Statistics
Matches: 40, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
25 8 0.20
26 27 0.68
27 5 0.12
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (26 bp):
ATTTAATTATTTATATTTAAATTAAA
Found at i:3508639 original size:35 final size:35
Alignment explanation
Indices: 3508519--3508640 Score: 110
Period size: 35 Copynumber: 3.6 Consensus size: 35
3508509 ATTTAACTTA
* * *
3508519 TTATTTAATTATTTATATTTAAAT-TTAAATTTAAT
1 TTATTTAATAATATA-AATTAAATATTAAATTTAAT
* *
3508554 TT-TTT-A-AATATAAATTAAA-AATAAATTTATT
1 TTATTTAATAATATAAATTAAATATTAAATTTAAT
* *
3508585 TTATTAAATTAATAAAAATTAAATATTAAATTTAAT
1 TTATTTAA-TAATATAAATTAAATATTAAATTTAAT
* *
3508621 TTATTTGATAATTTAAATTA
1 TTATTTAATAATATAAATTA
3508641 CGTAACTATA
Statistics
Matches: 68, Mismatches: 13, Indels: 12
0.73 0.14 0.13
Matches are distributed among these distances:
31 17 0.25
32 6 0.09
33 2 0.03
34 3 0.04
35 24 0.35
36 16 0.24
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.52
Consensus pattern (35 bp):
TTATTTAATAATATAAATTAAATATTAAATTTAAT
Found at i:3514073 original size:2 final size:2
Alignment explanation
Indices: 3514066--3514092 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3514056 AGCCTTTACC
3514066 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
3514093 TTGAAGCATA
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:3521728 original size:78 final size:78
Alignment explanation
Indices: 3521599--3521757 Score: 237
Period size: 78 Copynumber: 2.0 Consensus size: 78
3521589 TGAGATTCAT
* *
3521599 TTCAGTGTTGGTTGGGTGGGGGCGCATCTGACGGAGATATTTGTTACGGGGATTCATCAAATGTA
1 TTCAGTGTTGGGTGGGTGGGGGCGCATCTGACGGAGATATTTGTTACGGGGATACATCAAATGTA
*
3521664 CCATATGAGAGAA
66 CCATATGAAAGAA
* * ** *
3521677 TTCAGTGTTGGGTGGGTTGGGGCGCATCTTACTTAGATATTTGTTATGGGGATACATCAAATGTA
1 TTCAGTGTTGGGTGGGTGGGGGCGCATCTGACGGAGATATTTGTTACGGGGATACATCAAATGTA
*
3521742 TCATATGAAAGAA
66 CCATATGAAAGAA
3521755 TTC
1 TTC
3521758 CCCCCTCAAG
Statistics
Matches: 72, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
78 72 1.00
ACGTcount: A:0.25, C:0.12, G:0.30, T:0.33
Consensus pattern (78 bp):
TTCAGTGTTGGGTGGGTGGGGGCGCATCTGACGGAGATATTTGTTACGGGGATACATCAAATGTA
CCATATGAAAGAA
Found at i:3525465 original size:2 final size:2
Alignment explanation
Indices: 3525460--3525489 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3525450 TTGTTTTTTG
*
3525460 CT CT CT CT CT CT CT CT CT TT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3525490 GTCTTCCCAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:3531151 original size:21 final size:22
Alignment explanation
Indices: 3531126--3531180 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
3531116 AAAATATTAT
**
3531126 TTTTATATTAATATTTTTATAA
1 TTTTATATTAATATTTAAATAA
3531148 -TTTATAATTAA-ATTTAAATAA
1 TTTTAT-ATTAATATTTAAATAA
*
3531169 TTTTTTATTAAT
1 TTTTATATTAAT
3531181 TAAATAATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
21 18 0.67
22 9 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
TTTTATATTAATATTTAAATAA
Found at i:3531206 original size:21 final size:21
Alignment explanation
Indices: 3531144--3531208 Score: 62
Period size: 19 Copynumber: 3.0 Consensus size: 21
3531134 TAATATTTTT
3531144 ATAATTTATAATTAAATTTAAATA
1 ATAATTTA-AA-T-AATTTAAATA
* * *
3531168 AT-TTTTTATTAA-TTAAATA
1 ATAATTTAAATAATTTAAATA
3531187 ATAATTTAAATAATTTAAATA
1 ATAATTTAAATAATTTAAATA
3531208 A
1 A
3531209 AAATAATCAT
Statistics
Matches: 33, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
19 9 0.27
20 9 0.27
21 9 0.27
22 1 0.03
23 3 0.09
24 2 0.06
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
ATAATTTAAATAATTTAAATA
Found at i:3531437 original size:2 final size:2
Alignment explanation
Indices: 3531430--3531456 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3531420 TCTATACATT
3531430 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
3531457 GGAATTAAGA
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:3541285 original size:50 final size:49
Alignment explanation
Indices: 3541226--3541385 Score: 185
Period size: 50 Copynumber: 3.2 Consensus size: 49
3541216 AGGTATTGTT
* * *
3541226 ATTGTTGACTATTTTTTACTAACCTTTGACAATCGAGAGAAGTGATCGTA
1 ATTGTTGACTATTTTTAAC-AATCTTTGACAATAGAGAGAAGTGATCGTA
* * *
3541276 ATTGTTGACTATTCTTCACCAATCTTTGACAATAGAGAGAGGTGATCGTA
1 ATTGTTGACTATT-TTTAACAATCTTTGACAATAGAGAGAAGTGATCGTA
* ** * * *
3541326 ATTGTTGATTATTCTGCAACGATCTTTGACAATAGAGAGAAGTGACCATA
1 ATTGTTGACTATT-TTTAACAATCTTTGACAATAGAGAGAAGTGATCGTA
3541376 ATTGTTGACT
1 ATTGTTGACT
3541386 CTAAACAACT
Statistics
Matches: 95, Mismatches: 14, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
50 92 0.97
51 3 0.03
ACGTcount: A:0.31, C:0.14, G:0.19, T:0.36
Consensus pattern (49 bp):
ATTGTTGACTATTTTTAACAATCTTTGACAATAGAGAGAAGTGATCGTA
Found at i:3541559 original size:14 final size:15
Alignment explanation
Indices: 3541534--3541562 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3541524 ATTATATATA
3541534 TTTAATTTTTATTTT
1 TTTAATTTTTATTTT
3541549 TTTAA-TTTTATTTT
1 TTTAATTTTTATTTT
3541563 AACTGTAACC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTAATTTTTATTTT
Found at i:3541610 original size:15 final size:13
Alignment explanation
Indices: 3541578--3541602 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3541568 TAACCTTACT
3541578 CTAACCATCAATA
1 CTAACCATCAATA
3541591 CTAACCATCAAT
1 CTAACCATCAAT
3541603 TCACTAACAT
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:0.32, G:0.00, T:0.24
Consensus pattern (13 bp):
CTAACCATCAATA
Found at i:3543285 original size:15 final size:15
Alignment explanation
Indices: 3543247--3543293 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
3543237 AATATTTTTT
*
3543247 AATTTTTTAAAA-AT
1 AATTTTTTAAAATAA
**
3543261 AATTAATTAAAATAA
1 AATTTTTTAAAATAA
3543276 AATTTTTTAAAAATAA
1 AATTTTTT-AAAATAA
3543292 AA
1 AA
3543294 ATAAAAATAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
14 10 0.38
15 7 0.27
16 9 0.35
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
AATTTTTTAAAATAA
Found at i:3543300 original size:28 final size:29
Alignment explanation
Indices: 3543247--3543302 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
3543237 AATATTTTTT
* *
3543247 AATTTTTTAAAAATAATTAATTAAAATAA
1 AATTTTTTAAAAATAATAAATAAAAATAA
3543276 AATTTTTTAAAAATAA-AAATAAAAATA
1 AATTTTTTAAAAATAATAAATAAAAATA
3543303 TTAACGAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 9 0.36
29 16 0.64
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (29 bp):
AATTTTTTAAAAATAATAAATAAAAATAA
Found at i:3543411 original size:25 final size:24
Alignment explanation
Indices: 3543360--3543411 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 24
3543350 TAACTAATTT
* *
3543360 TTTAATATATTTTTAATATAATAA
1 TTTAATATACTTTTAATAGAATAA
* *
3543384 TTTAATTATACTTTTACTAGAATCA
1 TTTAA-TATACTTTTAATAGAATAA
3543409 TTT
1 TTT
3543412 TTATATTTTC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 5 0.22
25 18 0.78
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.54
Consensus pattern (24 bp):
TTTAATATACTTTTAATAGAATAA
Found at i:3543732 original size:14 final size:15
Alignment explanation
Indices: 3543695--3543742 Score: 62
Period size: 14 Copynumber: 3.1 Consensus size: 15
3543685 AATAAATAAA
3543695 AAATTTTTAATCAGTTT
1 AAATTTTTAAT-A-TTT
3543712 AAATTTTTAAT-TTT
1 AAATTTTTAATATTT
*
3543726 AAGTTTTTAATATTT
1 AAATTTTTAATATTT
3543741 AA
1 AA
3543743 TATATTTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 13 0.45
15 5 0.17
17 11 0.38
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (15 bp):
AAATTTTTAATATTT
Found at i:3545082 original size:2 final size:2
Alignment explanation
Indices: 3545077--3545103 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3545067 GAAAAAAAAA
3545077 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
3545104 AGAAAAACTT
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:3545259 original size:14 final size:15
Alignment explanation
Indices: 3545242--3545278 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
3545232 TATTTATATG
*
3545242 TTTAATGTTAAA-AT
1 TTTAATATTAAAGAT
3545256 TTTAA-ATTAAAGAT
1 TTTAATATTAAAGAT
3545270 TTTAATATT
1 TTTAATATT
3545279 TTTTTAATCG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 5 0.25
14 12 0.60
15 3 0.15
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.51
Consensus pattern (15 bp):
TTTAATATTAAAGAT
Found at i:3545591 original size:22 final size:21
Alignment explanation
Indices: 3545562--3545612 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 21
3545552 GATTCCCGTG
3545562 CTTGTTTTCTTT-TTTTCTTTAT
1 CTTGTTTT-TTTATTTTCTTT-T
*
3545584 TTTGTTTTTTTCATTTTCTTTT
1 CTTGTTTTTTT-ATTTTCTTTT
3545606 CTTGTTT
1 CTTGTTT
3545613 ATTAAAAGGG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 3 0.12
22 14 0.56
23 8 0.32
ACGTcount: A:0.04, C:0.12, G:0.06, T:0.78
Consensus pattern (21 bp):
CTTGTTTTTTTATTTTCTTTT
Found at i:3562583 original size:27 final size:27
Alignment explanation
Indices: 3562552--3562616 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
3562542 AAGACACTTG
*
3562552 CCAGAATTGGACAACACCAGGGCCTTT
1 CCAGAATTGGACAACACCAGGGCCTTC
*** *
3562579 CCAGAATTGGATGCCACTAGGGCCTTC
1 CCAGAATTGGACAACACCAGGGCCTTC
*
3562606 CCTGAATTGGA
1 CCAGAATTGGA
3562617 TAGAATCAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.26, C:0.28, G:0.25, T:0.22
Consensus pattern (27 bp):
CCAGAATTGGACAACACCAGGGCCTTC
Found at i:3564258 original size:11 final size:12
Alignment explanation
Indices: 3564241--3564269 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
3564231 TCTGATAATT
3564241 TTAAAAAAAAAA
1 TTAAAAAAAAAA
3564253 -TAAAAAAAAAA
1 TTAAAAAAAAAA
3564264 TTAAAA
1 TTAAAA
3564270 TATGATACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (12 bp):
TTAAAAAAAAAA
Found at i:3565743 original size:2 final size:2
Alignment explanation
Indices: 3565736--3565765 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3565726 CTGCATCCAA
*
3565736 AT AT AT AT AA 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
3565766 TTCAGGATCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3566624 original size:18 final size:17
Alignment explanation
Indices: 3566570--3566674 Score: 62
Period size: 16 Copynumber: 6.4 Consensus size: 17
3566560 TATATATTTA
3566570 TATATTATAA-TTATAT
1 TATATTATAATTTATAT
* * *
3566586 T-TAATATAATTTTTAA
1 TATATTATAATTTATAT
*
3566602 AATATTAATAATTTATAT
1 TATATT-ATAATTTATAT
3566620 TATA-TA-AATTTTAATAT
1 TATATTATAA-TTT-ATAT
*
3566637 GTATA-TAT-ATTTATAC
1 -TATATTATAATTTATAT
* *
3566653 TATATT-TATTTTAAAT
1 TATATTATAATTTATAT
3566669 TATATT
1 TATATT
3566675 TAAAATTAAT
Statistics
Matches: 68, Mismatches: 12, Indels: 18
0.69 0.12 0.18
Matches are distributed among these distances:
15 14 0.21
16 24 0.35
17 11 0.16
18 19 0.28
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (17 bp):
TATATTATAATTTATAT
Found at i:3566649 original size:33 final size:32
Alignment explanation
Indices: 3566570--3566673 Score: 88
Period size: 33 Copynumber: 3.2 Consensus size: 32
3566560 TATATATTTA
* *
3566570 TATATTATAATTATATTTAATATAATTTTTAAAATAT
1 TATA-TATATTTATA-TT-ATATAAATTTT--AATAT
3566607 TA-ATA-ATTTATATTATATAAATTTTAATAT
1 TATATATATTTATATTATATAAATTTTAATAT
* **
3566637 GTATATATATTTATACTATATTTATTTTAA-AT
1 -TATATATATTTATATTATATAAATTTTAATAT
3566669 TATAT
1 TATAT
3566674 TTAAAATTAA
Statistics
Matches: 59, Mismatches: 5, Indels: 12
0.78 0.07 0.16
Matches are distributed among these distances:
30 5 0.08
31 7 0.12
32 15 0.25
33 21 0.36
34 6 0.10
35 2 0.03
36 1 0.02
37 2 0.03
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (32 bp):
TATATATATTTATATTATATAAATTTTAATAT
Found at i:3566658 original size:11 final size:10
Alignment explanation
Indices: 3566560--3566661 Score: 52
Period size: 10 Copynumber: 10.1 Consensus size: 10
3566550 TAAAATTTTT
3566560 TATATATTTA
1 TATATATTTA
*
3566570 TATAT-TATA
1 TATATATTTA
3566579 -ATTATATTTA
1 TA-TATATTTA
*
3566589 -ATATAATTTT
1 TATAT-ATTTA
* *
3566599 TAAAATATTAA
1 T-ATATATTTA
*
3566610 TAATTTATATTA
1 T-ATATAT-TTA
*
3566622 TATAAATTT-
1 TATATATTTA
*
3566631 TA-ATATGTA
1 TATATATTTA
3566640 TATATATTTA
1 TATATATTTA
3566650 TACTATATTTA
1 TA-TATATTTA
3566661 T
1 T
3566662 TTTAAATTAT
Statistics
Matches: 69, Mismatches: 14, Indels: 17
0.69 0.14 0.17
Matches are distributed among these distances:
8 5 0.07
9 13 0.19
10 23 0.33
11 22 0.32
12 6 0.09
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (10 bp):
TATATATTTA
Found at i:3567215 original size:15 final size:15
Alignment explanation
Indices: 3567183--3567226 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
3567173 TTAAATAATA
3567183 TTAAATA-TAAATTTT
1 TTAAATATTAAA-TTT
3567198 TTAAATATTAAATTT
1 TTAAATATTAAATTT
*
3567213 TTATATATTTAAAT
1 TTAAATA-TTAAAT
3567227 AATTACTTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 16 0.62
16 10 0.38
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TTAAATATTAAATTT
Found at i:3567226 original size:16 final size:16
Alignment explanation
Indices: 3567183--3567214 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
3567173 TTAAATAATA
3567183 TTAAATA-TAAATTTT
1 TTAAATATTAAATTTT
3567198 TTAAATATTAAATTTT
1 TTAAATATTAAATTTT
3567214 T
1 T
3567215 ATATATTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTAAATATTAAATTTT
Found at i:3567984 original size:6 final size:6
Alignment explanation
Indices: 3567960--3568035 Score: 52
Period size: 6 Copynumber: 12.8 Consensus size: 6
3567950 AAAAATTATA
* * *
3567960 TATATT TA-ATT T-T-TT TATATT TATATA TATATA TATATT TAAAATAT
1 TATATT TATATT TATATT TATATT TATATT TATATT TATATT T-ATAT-T
* *
3568007 TAAATT TATATT AATATT TA-ATT ATATAT
1 TATATT TATATT TATATT TATATT -TATAT
3568036 AAAATATAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
4 3 0.05
5 8 0.14
6 35 0.61
7 9 0.16
8 2 0.04
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (6 bp):
TATATT
Found at i:3568022 original size:17 final size:18
Alignment explanation
Indices: 3568002--3568035 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3567992 ATATATTTAA
3568002 AATATTAAATT-TATATT
1 AATATTAAATTATATATT
*
3568019 AATATTTAATTATATAT
1 AATATTAAATTATATAT
3568036 AAAATATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
AATATTAAATTATATATT
Found at i:3568033 original size:38 final size:35
Alignment explanation
Indices: 3567973--3568046 Score: 87
Period size: 36 Copynumber: 2.0 Consensus size: 35
3567963 ATTTAATTTT
*
3567973 TTTATATTTATATATATATATATATTTAAAATATTAAA
1 TTTATA-TTA-ATATATATATATATATAAAATA-TAAA
*
3568011 TTTATATTAATATTTA-ATTATATATAAAATATAAA
1 TTTATATTAATATATATA-TATATATAAAATATAAA
3568046 T
1 T
3568047 ATTAAAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
35 6 0.18
36 18 0.55
37 3 0.09
38 6 0.18
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (35 bp):
TTTATATTAATATATATATATATATAAAATATAAA
Found at i:3572040 original size:17 final size:18
Alignment explanation
Indices: 3572018--3572057 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
3572008 AAAATTTATT
*
3572018 TTTTTATTT-TTCTATAA
1 TTTTTATTTATCCTATAA
3572035 TTTTTATTTATCCTATAA
1 TTTTTATTTATCCTATAA
3572053 TTTTT
1 TTTTT
3572058 TCACTTAACG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTTTATTTATCCTATAA
Found at i:3582396 original size:18 final size:17
Alignment explanation
Indices: 3582375--3582424 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
3582365 TTTTATATTA
*
3582375 AAATATATAATTAAATTT
1 AAATA-ATAATTAAATAT
* *
3582393 AAATAAAAATTTTAATAT
1 AAATAATAA-TTAAATAT
3582411 AAATAATAATTAAA
1 AAATAATAATTAAA
3582425 AATGAGGAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
17 7 0.27
18 19 0.73
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
AAATAATAATTAAATAT
Found at i:3584222 original size:17 final size:20
Alignment explanation
Indices: 3584176--3584281 Score: 65
Period size: 24 Copynumber: 5.1 Consensus size: 20
3584166 AATATAGGAT
3584176 AATAATAAAAATATAATTTA
1 AATAATAAAAATATAATTTA
*
3584196 AAT-ATGAAAATA-AA-TTA
1 AATAATAAAAATATAATTTA
**
3584213 AATAATAAAATTTATATAAAATA
1 AATAATAAAA---ATATAATTTA
* **
3584236 TATAATACACATAATTATAATAAA
1 AATAATA-A-A-AA-TATAATTTA
*
3584260 AATAATAAAAATATAATATA
1 AATAATAAAAATATAATTTA
3584280 AA
1 AA
3584282 ATGAATTTGT
Statistics
Matches: 68, Mismatches: 8, Indels: 20
0.71 0.08 0.21
Matches are distributed among these distances:
17 6 0.09
18 7 0.10
19 8 0.12
20 13 0.19
21 5 0.07
22 3 0.04
23 10 0.15
24 14 0.21
25 1 0.01
26 1 0.01
ACGTcount: A:0.65, C:0.02, G:0.01, T:0.32
Consensus pattern (20 bp):
AATAATAAAAATATAATTTA
Found at i:3588740 original size:6 final size:6
Alignment explanation
Indices: 3588729--3588774 Score: 58
Period size: 6 Copynumber: 7.5 Consensus size: 6
3588719 TTAGAAAAGC
*
3588729 TATTTA TATTTA TATTTA TATTTA TA-TTA CATATTA TTATTTA TAT
1 TATTTA TATTTA TATTTA TATTTA TATTTA TAT-TTA -TATTTA TAT
3588775 ATACTGTCAC
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
5 4 0.11
6 23 0.66
7 6 0.17
8 2 0.06
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (6 bp):
TATTTA
Found at i:3589624 original size:2 final size:2
Alignment explanation
Indices: 3589617--3589649 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3589607 CCTTTTACAT
3589617 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
3589650 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:3591273 original size:2 final size:2
Alignment explanation
Indices: 3591266--3591305 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
3591256 TTTTAAGCTG
3591266 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
3591306 TTTCCTAGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3597507 original size:3 final size:3
Alignment explanation
Indices: 3597499--3597532 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
3597489 TATTAATTTA
3597499 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
3597533 CGAAGGCACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:3601062 original size:2 final size:2
Alignment explanation
Indices: 3601055--3601105 Score: 77
Period size: 2 Copynumber: 26.0 Consensus size: 2
3601045 CCTTTTAATA
*
3601055 AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT GT 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
*
3601096 AT GT AT AT AT
1 AT AT AT AT AT
3601106 CTTCTTCTCT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3615161 original size:2 final size:2
Alignment explanation
Indices: 3615154--3615188 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3615144 TAAATCAAGT
3615154 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
3615189 GTTTACATTT
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:3615213 original size:26 final size:26
Alignment explanation
Indices: 3615184--3615237 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
3615174 TATATATATA
3615184 TATATGTTTACATTTGATGCAATCAT
1 TATATGTTTACATTTGATGCAATCAT
3615210 TATATGTTTACATTTGATGCAATCAT
1 TATATGTTTACATTTGATGCAATCAT
3615236 TA
1 TA
3615238 GTAAATGCTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.31, C:0.11, G:0.11, T:0.46
Consensus pattern (26 bp):
TATATGTTTACATTTGATGCAATCAT
Found at i:3618639 original size:2 final size:2
Alignment explanation
Indices: 3618626--3618658 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
3618616 GTTTAAAAGG
*
3618626 AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3618659 GAAGAATGGA
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:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:3624756 original size:13 final size:13
Alignment explanation
Indices: 3624738--3624764 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3624728 TGTCAGATAT
3624738 ATATTTATATCCG
1 ATATTTATATCCG
3624751 ATATTTATATCCG
1 ATATTTATATCCG
3624764 A
1 A
3624765 ATATGAGTAA
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:0.33, C:0.15, G:0.07, T:0.44
Consensus pattern (13 bp):
ATATTTATATCCG
Found at i:3637457 original size:13 final size:13
Alignment explanation
Indices: 3637423--3637463 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
3637413 AATGATTTAT
3637423 TTTATTATTT-AAA
1 TTTATT-TTTAAAA
3637436 TATTA-TTTTAAAA
1 T-TTATTTTTAAAA
3637449 TTTATTTTTAAAA
1 TTTATTTTTAAAA
3637462 TT
1 TT
3637464 AAATTTAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 6 0.24
13 16 0.64
14 3 0.12
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
TTTATTTTTAAAA
Found at i:3639675 original size:2 final size:2
Alignment explanation
Indices: 3639668--3639692 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3639658 ACAGAAAATT
3639668 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
3639693 AATAAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:3640479 original size:24 final size:24
Alignment explanation
Indices: 3640432--3640479 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
3640422 TTAAAAATAT
* *
3640432 AATTTAATATAAATATATTTTTAA
1 AATTTAATATAAATAAATTATTAA
3640456 AATTT-ATATAATATAAATTATTAA
1 AATTTAATATAA-ATAAATTATTAA
3640480 TTTATTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
AATTTAATATAAATAAATTATTAA
Found at i:3640491 original size:33 final size:31
Alignment explanation
Indices: 3640375--3640492 Score: 90
Period size: 28 Copynumber: 3.8 Consensus size: 31
3640365 ATAAATGTAG
*
3640375 TAATATTAAATATATATGATTATATAAATATAATA
1 TAATA-TAAATATAT-TTATTA-A-AAATATAATA
*
3640410 -AATATAAA-ATA---ATTAAAAATATAATT
1 TAATATAAATATATTTATTAAAAATATAATA
*
3640436 TAATATAAATATATTT-TT-AAAAT-TTATA
1 TAATATAAATATATTTATTAAAAATATAATA
3640464 TAATATAAATTATTAATTTATTAAAAATA
1 TAATATAAA-TA-T-ATTTATTAAAAATA
3640493 ATATAAATTT
Statistics
Matches: 69, Mismatches: 3, Indels: 23
0.73 0.03 0.24
Matches are distributed among these distances:
26 9 0.13
27 9 0.13
28 19 0.28
29 7 0.10
30 3 0.04
31 4 0.06
32 5 0.07
33 9 0.13
34 4 0.06
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (31 bp):
TAATATAAATATATTTATTAAAAATATAATA
Found at i:3640513 original size:25 final size:25
Alignment explanation
Indices: 3640463--3640525 Score: 76
Period size: 27 Copynumber: 2.5 Consensus size: 25
3640453 TAAAATTTAT
* *
3640463 ATAATATAAATTATTAATTTATTAAAA
1 ATAATATAAA-TATTAACTTAAT-AAA
3640490 ATAATATAAAT-TTAACTTAATAAA
1 ATAATATAAATATTAACTTAATAAA
3640514 AT-ATATAAATAT
1 ATAATATAAATAT
3640526 AATAAAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
23 8 0.24
24 6 0.18
25 8 0.24
26 1 0.03
27 10 0.30
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (25 bp):
ATAATATAAATATTAACTTAATAAA
Found at i:3648446 original size:16 final size:16
Alignment explanation
Indices: 3648425--3648455 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3648415 ATTTAAATAA
*
3648425 TTTAAAATTCATAATT
1 TTTAAAATTAATAATT
3648441 TTTAAAATTAATAAT
1 TTTAAAATTAATAAT
3648456 GCTTTTCTTT
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:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (16 bp):
TTTAAAATTAATAATT
Found at i:3648908 original size:2 final size:2
Alignment explanation
Indices: 3648901--3648932 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3648891 AGATGCTCCC
3648901 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
3648933 TATGTTTGTT
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:3653060 original size:3 final size:3
Alignment explanation
Indices: 3653047--3653083 Score: 65
Period size: 3 Copynumber: 12.0 Consensus size: 3
3653037 GTTTATGAAC
3653047 CTT CTTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT C-TT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
3653084 TTAATTGTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
CTT
Found at i:3653737 original size:21 final size:21
Alignment explanation
Indices: 3653712--3653755 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
3653702 AACAATAATT
3653712 ATCTTTAAAAAATAAAAAATC
1 ATCTTTAAAAAATAAAAAATC
*
3653733 ATCTTTAAAAAATACAAAATC
1 ATCTTTAAAAAATAAAAAATC
3653754 AT
1 AT
3653756 TCCTAAGCGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.59, C:0.11, G:0.00, T:0.30
Consensus pattern (21 bp):
ATCTTTAAAAAATAAAAAATC
Found at i:3653751 original size:22 final size:22
Alignment explanation
Indices: 3653703--3653755 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
3653693 TTAAAGATGA
* *
3653703 ACAATAATTATCTTTAAAAAAT
1 ACAAAAATCATCTTTAAAAAAT
3653725 A-AAAAATCATCTTTAAAAAAT
1 ACAAAAATCATCTTTAAAAAAT
3653746 AC-AAAATCAT
1 ACAAAAATCAT
3653756 TCCTAAGCGT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 27 0.96
22 1 0.04
ACGTcount: A:0.58, C:0.11, G:0.00, T:0.30
Consensus pattern (22 bp):
ACAAAAATCATCTTTAAAAAAT
Found at i:3654905 original size:19 final size:19
Alignment explanation
Indices: 3654877--3654914 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
3654867 ATAATACGAA
3654877 TTATTAAAATA-TTAAAAT
1 TTATTAAAATATTTAAAAT
3654895 TTATATAAAATATTTAAAAT
1 TTAT-TAAAATATTTAAAAT
3654915 ATAATTATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.22
19 7 0.39
20 7 0.39
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TTATTAAAATATTTAAAAT
Found at i:3654922 original size:24 final size:23
Alignment explanation
Indices: 3654857--3654923 Score: 63
Period size: 24 Copynumber: 3.0 Consensus size: 23
3654847 AATACTATTT
*
3654857 TAAAATATTAATAATACGAATTAT-
1 TAAAATATTAA-AATA-TAATTATA
3654881 TAAAATATT-AAA-AT--TTATA
1 TAAAATATTAAAATATAATTATA
3654900 TAAAATATTTAAAATATAATTATA
1 TAAAATA-TTAAAATATAATTATA
3654924 ACGTAACAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 12
0.73 0.02 0.24
Matches are distributed among these distances:
18 4 0.11
19 7 0.19
20 2 0.06
21 4 0.11
22 4 0.11
23 1 0.03
24 14 0.39
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (23 bp):
TAAAATATTAAAATATAATTATA
Found at i:3658102 original size:3 final size:3
Alignment explanation
Indices: 3658094--3658129 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
3658084 CGAAAGGGGC
*
3658094 AAG AAG AAG AAG AAG AAG AAG AAG AGG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
3658130 GAGTGTTGGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:3661291 original size:18 final size:18
Alignment explanation
Indices: 3661268--3661367 Score: 65
Period size: 18 Copynumber: 5.3 Consensus size: 18
3661258 GATATGATAC
3661268 AAATATTATATGTTTAAT
1 AAATATTATATGTTTAAT
* *
3661286 AAATATTAGGATGATTAAAT
1 AAATATTA-TATG-TTTAAT
* * *
3661306 AGATATGATAAGTTTAAT
1 AAATATTATATGTTTAAT
* * *
3661324 ATATATTATATTTTTATT
1 AAATATTATATGTTTAAT
* * *
3661342 AAAATTTTGACATATTTAAT
1 -AAATATT-ATATGTTTAAT
3661362 AAATAT
1 AAATAT
3661368 AAATTATAAA
Statistics
Matches: 60, Mismatches: 18, Indels: 7
0.71 0.21 0.08
Matches are distributed among these distances:
18 26 0.43
19 15 0.25
20 19 0.32
ACGTcount: A:0.45, C:0.01, G:0.08, T:0.46
Consensus pattern (18 bp):
AAATATTATATGTTTAAT
Found at i:3661912 original size:2 final size:2
Alignment explanation
Indices: 3661905--3661938 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3661895 TTTAGTGCCC
3661905 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
3661939 TCTTTCTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3667164 original size:22 final size:21
Alignment explanation
Indices: 3667113--3667172 Score: 70
Period size: 22 Copynumber: 2.9 Consensus size: 21
3667103 GAACTATCGA
*
3667113 ATAA-ATTAAATTTAAATATT
1 ATAATATTTAATTTAAATATT
3667133 ATAATATTTAATTTAAATAATTT
1 ATAATATTTAATTTAAAT-A-TT
*
3667156 ATAA-GTTTAATTTAAAT
1 ATAATATTTAATTTAAAT
3667173 TTTTTATTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.11
21 12 0.34
22 13 0.37
23 6 0.17
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (21 bp):
ATAATATTTAATTTAAATATT
Found at i:3667171 original size:43 final size:43
Alignment explanation
Indices: 3667118--3667214 Score: 110
Period size: 43 Copynumber: 2.3 Consensus size: 43
3667108 ATCGAATAAA
*
3667118 TTAAATTTAAATATTATAATATTTAATTTAA-A-TAATTTATAAGT
1 TTAAATTTAAAT-TTATAATATTTAA-TTAATATTAATTTA-AAAT
* * *
3667162 TT-AATTTAAATTTTTTATTTTTAATTAATATTAATTTAAAAT
1 TTAAATTTAAATTTATAATATTTAATTAATATTAATTTAAAAT
3667204 TTAAATTTAAA
1 TTAAATTTAAA
3667215 CACAACTAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
41 4 0.09
42 16 0.35
43 24 0.52
44 2 0.04
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (43 bp):
TTAAATTTAAATTTATAATATTTAATTAATATTAATTTAAAAT
Found at i:3670253 original size:2 final size:2
Alignment explanation
Indices: 3670248--3670277 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3670238 TGTATGTGTG
*
3670248 TA TA TA TA TA TA TA TA TA TA TA TA GA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3670278 ATAGTAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:3673914 original size:27 final size:25
Alignment explanation
Indices: 3673871--3673925 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 25
3673861 GTTATTACAG
3673871 GTTTTTTCCTTTCTTTTG-CTTGTTT
1 GTTTTTTCCTTTCTTTTGTCTT-TTT
*
3673896 GTTTTTTCCTTTTTTTTTTGTCTTTTT
1 GTTTTTTCC--TTTCTTTTGTCTTTTT
3673923 GTT
1 GTT
3673926 GATTATGATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
25 9 0.35
27 14 0.54
28 3 0.12
ACGTcount: A:0.00, C:0.13, G:0.11, T:0.76
Consensus pattern (25 bp):
GTTTTTTCCTTTCTTTTGTCTTTTT
Found at i:3675531 original size:145 final size:143
Alignment explanation
Indices: 3675304--3675594 Score: 447
Period size: 145 Copynumber: 2.0 Consensus size: 143
3675294 GCGAGAGGTA
* *
3675304 ATTTGTTAAATTTTACTTCCTTTTATTTTGCATTCCCTGCATCCTTAAAGTGCCGGATATTTAAA
1 ATTTGTTAAATTTTAATTCCTTTTATTTTGCATTCCCTGCATCCTTAAAGTGCCAGATATTTAAA
* * * * * *
3675369 CGTTGATGTGATTTCCCCACCTTTAAAACGATTGCCGGCCTTTTATTTTATTTTTAAGTAAATAA
66 CGGTGATATGATTTCCCCACCTTTAAAACAATTGCCAGCCATTTATTTTACTTTTAAGTAAATAA
3675434 TGCACCAAAGTTT
131 TGCACCAAAGTTT
* *
3675447 ATTTGTTAAATTTTAATTCCTTTTATTTTGCATTCCCTGAGAGTTCTTAAAGTGCCAGATATTTA
1 ATTTGTTAAATTTTAATTCCTTTTATTTTGCATTCCCTG-CA-TCCTTAAAGTGCCAGATATTTA
3675512 AACGGTGATATGATTTCCCCACCTTTAAAACAATTGCCAGCCATTTATTTTACTTTTAAGTAAAT
64 AACGGTGATATGATTTCCCCACCTTTAAAACAATTGCCAGCCATTTATTTTACTTTTAAGTAAAT
* * *
3675577 TATGTACTAAAGTTT
129 AATGCACCAAAGTTT
3675592 ATT
1 ATT
3675595 AATTAAGTTT
Statistics
Matches: 133, Mismatches: 13, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
143 38 0.29
144 1 0.01
145 94 0.71
ACGTcount: A:0.28, C:0.17, G:0.12, T:0.43
Consensus pattern (143 bp):
ATTTGTTAAATTTTAATTCCTTTTATTTTGCATTCCCTGCATCCTTAAAGTGCCAGATATTTAAA
CGGTGATATGATTTCCCCACCTTTAAAACAATTGCCAGCCATTTATTTTACTTTTAAGTAAATAA
TGCACCAAAGTTT
Found at i:3677745 original size:2 final size:2
Alignment explanation
Indices: 3677738--3677770 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3677728 CCAGTGTCAA
3677738 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3677771 AAAGAGAGAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3678127 original size:14 final size:14
Alignment explanation
Indices: 3678108--3678155 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
3678098 AGAAATAATT
3678108 TTAAATATAATATA
1 TTAAATATAATATA
3678122 TTAAATATAA-ATA
1 TTAAATATAATATA
*
3678135 TTTAAT-TATATATA
1 TTAAATATA-ATATA
3678149 TTTAAAT
1 -TTAAAT
3678156 GAATATATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
12 2 0.07
13 9 0.31
14 13 0.45
15 5 0.17
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TTAAATATAATATA
Found at i:3681689 original size:2 final size:2
Alignment explanation
Indices: 3681682--3681716 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3681672 AGAAAATCCA
3681682 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
3681717 CAGTACAAAT
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:3682131 original size:2 final size:2
Alignment explanation
Indices: 3682109--3682149 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
3682099 CCATCGACAA
* * *
3682109 AC AC AG AC AC AC AG AC GC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
3682150 TATTGACATT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.44, G:0.07, T:0.00
Consensus pattern (2 bp):
AC
Found at i:3691787 original size:3 final size:3
Alignment explanation
Indices: 3691781--3691815 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
3691771 TAATAATTTT
3691781 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
3691816 CTCATTTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:3695089 original size:21 final size:22
Alignment explanation
Indices: 3695054--3695094 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
3695044 AAATTTTAAG
*
3695054 ATATTTATTAAAATCATCAGCC
1 ATATTTATCAAAATCATCAGCC
*
3695076 ATATTTA-CAAAATCTTCAG
1 ATATTTATCAAAATCATCAG
3695095 AAAATCACAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.37
Consensus pattern (22 bp):
ATATTTATCAAAATCATCAGCC
Found at i:3703451 original size:4 final size:4
Alignment explanation
Indices: 3703444--3703470 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
3703434 TTGAAAACTC
3703444 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
3703471 TGGGCTTTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:3709520 original size:14 final size:14
Alignment explanation
Indices: 3709501--3709527 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3709491 TGTGTTTCTT
3709501 CTCTCTCCCTCTCA
1 CTCTCTCCCTCTCA
3709515 CTCTCTCCCTCTC
1 CTCTCTCCCTCTC
3709528 TTTCTGAACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.04, C:0.59, G:0.00, T:0.37
Consensus pattern (14 bp):
CTCTCTCCCTCTCA
Found at i:3713155 original size:21 final size:21
Alignment explanation
Indices: 3713137--3713195 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
3713127 TATTAAAAGT
*
3713137 TGCATTTTTTCA-CCAAAAAA
1 TGCATTCTTTCATCCAAAAAA
**
3713157 TGCATTCTTTCATCCAACCAA
1 TGCATTCTTTCATCCAAAAAA
3713178 TGCA-TCATTTCATCCAAA
1 TGCATTC-TTTCATCCAAA
3713196 TATATCTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 13 0.39
21 20 0.61
ACGTcount: A:0.34, C:0.27, G:0.05, T:0.34
Consensus pattern (21 bp):
TGCATTCTTTCATCCAAAAAA
Found at i:3719716 original size:12 final size:13
Alignment explanation
Indices: 3719696--3719728 Score: 59
Period size: 12 Copynumber: 2.6 Consensus size: 13
3719686 CAACAATGAT
3719696 AACAAAAACAAAA
1 AACAAAAACAAAA
3719709 AA-AAAAACAAAA
1 AACAAAAACAAAA
3719721 AACAAAAA
1 AACAAAAA
3719729 AGTAGTTGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.63
13 7 0.37
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (13 bp):
AACAAAAACAAAA
Found at i:3724822 original size:8 final size:9
Alignment explanation
Indices: 3724801--3724825 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
3724791 CTCCATAGCC
3724801 AAAAATAAT
1 AAAAATAAT
3724810 AAAAATAAT
1 AAAAATAAT
3724819 AAAAATA
1 AAAAATA
3724826 TCTATTGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (9 bp):
AAAAATAAT
Found at i:3724969 original size:20 final size:20
Alignment explanation
Indices: 3724946--3724985 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
3724936 AAATGGTCTT
3724946 TTTTTTTTATAAATTATAAC
1 TTTTTTTTATAAATTATAAC
3724966 TTTTTTTTATAAATTATAAC
1 TTTTTTTTATAAATTATAAC
3724986 AAAAAAGAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTTTTTTATAAATTATAAC
Found at i:3725382 original size:8 final size:7
Alignment explanation
Indices: 3725366--3725408 Score: 52
Period size: 8 Copynumber: 6.0 Consensus size: 7
3725356 TCGATTTCAA
3725366 TTATAAT
1 TTATAAT
3725373 TTATTAAT
1 TTA-TAAT
*
3725381 TTATATT
1 TTATAAT
3725388 TTATAATT
1 TTATAA-T
3725396 TTATAA-
1 TTATAAT
3725402 TTATAAT
1 TTATAAT
3725409 AATTGTGGCA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
6 6 0.19
7 11 0.35
8 14 0.45
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (7 bp):
TTATAAT
Found at i:3725398 original size:15 final size:15
Alignment explanation
Indices: 3725366--3725403 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
3725356 TCGATTTCAA
3725366 TTATAATTTATTAAT
1 TTATAATTTATTAAT
*
3725381 TTATATTTTA-TAATT
1 TTATAATTTATTAA-T
3725396 TTATAATT
1 TTATAATT
3725404 ATAATAATTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 3 0.15
15 17 0.85
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TTATAATTTATTAAT
Found at i:3725860 original size:2 final size:2
Alignment explanation
Indices: 3725853--3725887 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
3725843 TACAAATTCT
3725853 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3725888 GTTATAGGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3740227 original size:2 final size:2
Alignment explanation
Indices: 3740222--3740263 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
3740212 TTCGAGGGGG
*
3740222 GA GA GA GA GA GA AA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
3740264 TTGACAGCTC
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3745497 original size:76 final size:76
Alignment explanation
Indices: 3745411--3745563 Score: 288
Period size: 76 Copynumber: 2.0 Consensus size: 76
3745401 TTGATTTTGT
3745411 TATATACTATTATTAATCACTTTGATTGCTAATTTTATGTTTCTCGCATTCTTCTTTTTCTCCCA
1 TATATACTATTATTAATCACTTTGATTGCTAATTTTATGTTTCTCGCATTCTTCTTTTTCTCCCA
3745476 TCTTCATGTCA
66 TCTTCATGTCA
* *
3745487 TATATACTATTATTAATCACTTTGATTGCTAATTTTATTTTTCTCGCATTCTTCTTTTTGTCCCA
1 TATATACTATTATTAATCACTTTGATTGCTAATTTTATGTTTCTCGCATTCTTCTTTTTCTCCCA
3745552 TCTTCATGTCA
66 TCTTCATGTCA
3745563 T
1 T
3745564 GCGGACGAGA
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 75 1.00
ACGTcount: A:0.21, C:0.20, G:0.07, T:0.52
Consensus pattern (76 bp):
TATATACTATTATTAATCACTTTGATTGCTAATTTTATGTTTCTCGCATTCTTCTTTTTCTCCCA
TCTTCATGTCA
Found at i:3748362 original size:22 final size:24
Alignment explanation
Indices: 3748321--3748388 Score: 58
Period size: 22 Copynumber: 3.0 Consensus size: 24
3748311 TAATTTAAAT
* *
3748321 TTATTTAATTCAATT--TAAATTA
1 TTATTTAATTTAATTAAAAAATTA
3748343 TTATTT-ATTTAA-TAAAAAA-T-
1 TTATTTAATTTAATTAAAAAATTA
*
3748363 TTATTTAAATTTAATTATAAAATTA
1 TTATTT-AATTTAATTAAAAAATTA
3748388 T
1 T
3748389 AAATATTAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 11
0.72 0.06 0.22
Matches are distributed among these distances:
20 7 0.19
21 6 0.17
22 15 0.42
23 6 0.17
24 1 0.03
25 1 0.03
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (24 bp):
TTATTTAATTTAATTAAAAAATTA
Found at i:3750763 original size:21 final size:23
Alignment explanation
Indices: 3750716--3750769 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 23
3750706 TCGATAATCA
3750716 TTAATATAA--TTTGATAATATT
1 TTAATATAATTTTTGATAATATT
3750737 TT-ATATAATTTTTG-TAAT-TT
1 TTAATATAATTTTTGATAATATT
*
3750757 TTAATATGATTTT
1 TTAATATAATTTT
3750770 ATTTAATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
20 10 0.34
21 15 0.52
22 4 0.14
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (23 bp):
TTAATATAATTTTTGATAATATT
Found at i:3751295 original size:19 final size:18
Alignment explanation
Indices: 3751271--3751306 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
3751261 ATATTTAATT
3751271 TTTTAAATATTAAATAAAA
1 TTTTAAAT-TTAAATAAAA
*
3751290 TTTTAAATTTAGATAAA
1 TTTTAAATTTAAATAAA
3751307 TAATTTGACC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (18 bp):
TTTTAAATTTAAATAAAA
Done.