Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold500
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: 2046043
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 10
Found at i:3411 original size:25 final size:23
Alignment explanation
Indices: 3374--3431 Score: 64
Period size: 23 Copynumber: 2.4 Consensus size: 23
3364 ATTACTTATC
3374 TAAATTAAT-ATATTCGAAATGATTT
1 TAAA-TAATAATATTCGAAAT--TTT
**
3399 TAAATAATAATATTTTAAATTTT
1 TAAATAATAATATTCGAAATTTT
3422 TAAATAATAA
1 TAAATAATAA
3432 AATAAAATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 13 0.43
24 4 0.13
25 13 0.43
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (23 bp):
TAAATAATAATATTCGAAATTTT
Found at i:3894 original size:25 final size:25
Alignment explanation
Indices: 3862--3945 Score: 82
Period size: 25 Copynumber: 3.4 Consensus size: 25
3852 ATATAAATAA
3862 ATAAAATATAATATTTAAATTAATT
1 ATAAAATATAATATTTAAATTAATT
* * *
3887 ATAAAATATAATAATCAAATTAA-A
1 ATAAAATATAATATTTAAATTAATT
* *
3911 AT-AAATATAAATCATTTAAAATATTT
1 ATAAAATAT-AAT-ATTTAAATTAATT
*
3937 TTAAAATAT
1 ATAAAATAT
3946 TTTTAAAATA
Statistics
Matches: 46, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
23 6 0.13
24 5 0.11
25 28 0.61
26 1 0.02
27 6 0.13
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.39
Consensus pattern (25 bp):
ATAAAATATAATATTTAAATTAATT
Found at i:3939 original size:11 final size:11
Alignment explanation
Indices: 3925--3956 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
3915 ATATAAATCA
3925 TTTAAAATATT
1 TTTAAAATATT
3936 TTTAAAATATT
1 TTTAAAATATT
3947 TTTAAAATAT
1 TTTAAAATAT
3957 GTAAAATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
TTTAAAATATT
Found at i:5061 original size:24 final size:24
Alignment explanation
Indices: 5034--5086 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
5024 TCTGATTGCT
*
5034 GTTGCGGTTACCAATCTGCTTCTG
1 GTTGCGGTTACCAATCTGCCTCTG
* **
5058 GTTGCTGTTGTCAATCTGCCTCTG
1 GTTGCGGTTACCAATCTGCCTCTG
5082 GTTGC
1 GTTGC
5087 TGATTTGCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.09, C:0.25, G:0.26, T:0.40
Consensus pattern (24 bp):
GTTGCGGTTACCAATCTGCCTCTG
Found at i:11080 original size:2 final size:2
Alignment explanation
Indices: 11073--11098 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
11063 AAAGTTCTAA
11073 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
11099 TTACACACAT
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:12226 original size:15 final size:15
Alignment explanation
Indices: 12200--12236 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
12190 TATATTTTTA
12200 AAAATATTTAAAAATT
1 AAAATATTTAAAAA-T
12216 AAAAT-TTTAAAAAT
1 AAAATATTTAAAAAT
12230 AAAATAT
1 AAAATAT
12237 ATAATTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 6 0.30
15 9 0.45
16 5 0.25
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
AAAATATTTAAAAAT
Found at i:12530 original size:2 final size:2
Alignment explanation
Indices: 12523--12556 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
12513 GTGACTCTGC
*
12523 CT CT CT CT CT CT CT CT CT CT CT CT CT GT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
12557 TTCTTCTTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.47, G:0.03, T:0.50
Consensus pattern (2 bp):
CT
Found at i:12776 original size:19 final size:20
Alignment explanation
Indices: 12739--12778 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
12729 TTTTTGTTTA
12739 TTTGTTGTTGGGATTTTGGATC
1 TTTGTTGTTGGG--TTTGGATC
12761 TTTGTTGTTGGG-TTGGAT
1 TTTGTTGTTGGGTTTGGAT
12779 TTCATAAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
22 12 0.67
ACGTcount: A:0.07, C:0.03, G:0.35, T:0.55
Consensus pattern (20 bp):
TTTGTTGTTGGGTTTGGATC
Found at i:18674 original size:3 final size:3
Alignment explanation
Indices: 18656--18697 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
18646 GTAGTTGTTT
* *
18656 TTA TTA TTT TTT TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
18698 GAGTAATGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:21552 original size:22 final size:22
Alignment explanation
Indices: 21499--21552 Score: 74
Period size: 24 Copynumber: 2.4 Consensus size: 22
21489 GGTTAAAAGA
*
21499 TTATT-AAATATATTTTTTATT
1 TTATTAAAATATATATTTTATT
21520 TATATTTAAAATATATATTTTATT
1 T-TA-TTAAAATATATATTTTATT
21544 TTATTAAAA
1 TTATTAAAA
21553 CATTTGTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
21 1 0.03
22 8 0.28
23 4 0.14
24 16 0.55
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
TTATTAAAATATATATTTTATT
Found at i:22468 original size:17 final size:16
Alignment explanation
Indices: 22442--22497 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
22432 TCAAGAAAGT
*
22442 TTAAATTTGAAAAAAAC
1 TTAAACTTG-AAAAAAC
*
22459 TTAAACTTGAAATAAC
1 TTAAACTTGAAAAAAC
**
22475 TTAAACCCGAAAAAAC
1 TTAAACTTGAAAAAAC
*
22491 TTGAACT
1 TTAAACT
22498 AAAGATTGAT
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
16 24 0.75
17 8 0.25
ACGTcount: A:0.52, C:0.14, G:0.07, T:0.27
Consensus pattern (16 bp):
TTAAACTTGAAAAAAC
Found at i:23760 original size:15 final size:17
Alignment explanation
Indices: 23740--23776 Score: 67
Period size: 16 Copynumber: 2.2 Consensus size: 17
23730 ATAAATTATT
23740 TAAAAATTAATT-TATA
1 TAAAAATTAATTATATA
23756 TAAAAATTAATTATATA
1 TAAAAATTAATTATATA
23773 TAAA
1 TAAA
23777 TATAGATTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 12 0.60
17 8 0.40
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAAAATTAATTATATA
Found at i:23772 original size:17 final size:16
Alignment explanation
Indices: 23735--23776 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
23725 TAATAATAAA
*
23735 TTATTTAAAAATTAAT
1 TTATATAAAAATTAAT
23751 TTATATAAAAATTAAT
1 TTATATAAAAATTAAT
23767 TATATATAAA
1 T-TATATAAA
23777 TATAGATTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 16 0.67
17 8 0.33
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TTATATAAAAATTAAT
Found at i:23897 original size:19 final size:20
Alignment explanation
Indices: 23869--23911 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
23859 TATTTTTTTA
23869 AAAAATATTA-AATT-ATAT
1 AAAAATATTATAATTAATAT
*
23887 AAAAATGATTATATTTAATAT
1 AAAAAT-ATTATAATTAATAT
23908 AAAA
1 AAAA
23912 TAAAAAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 6 0.29
19 4 0.19
20 3 0.14
21 8 0.38
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.37
Consensus pattern (20 bp):
AAAAATATTATAATTAATAT
Found at i:24098 original size:18 final size:18
Alignment explanation
Indices: 24071--24121 Score: 50
Period size: 18 Copynumber: 2.7 Consensus size: 18
24061 ATAAAGCTTC
*
24071 AAAAATATAAAA-AAGTAA
1 AAAAAAATAAAATAA-TAA
24089 AAAAAAATAATAATAATAA
1 AAAAAAATAA-AATAATAA
24108 ATAAATAAATAAAA
1 A-AAA-AAATAAAA
24122 GTGATTTAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
18 9 0.32
19 6 0.21
20 7 0.25
21 6 0.21
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (18 bp):
AAAAAAATAAAATAATAA
Found at i:32499 original size:12 final size:13
Alignment explanation
Indices: 32477--32505 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
32467 AGTTATAAAA
32477 AACATAATACGCT
1 AACATAATACGCT
32490 AACA-AATACGCT
1 AACATAATACGCT
32502 AACA
1 AACA
32506 GTTTTTCAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.52, C:0.24, G:0.07, T:0.17
Consensus pattern (13 bp):
AACATAATACGCT
Found at i:35732 original size:13 final size:15
Alignment explanation
Indices: 35691--35737 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
35681 CATTTTTATA
*
35691 AATATAATCAATATT
1 AATATAATAAATATT
*
35706 ATTATAATAAATATT
1 AATATAATAAATATT
35721 AAT-TAA-AAATATT
1 AATATAATAAATATT
35734 AATA
1 AATA
35738 ATAAAAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
13 10 0.36
14 3 0.11
15 15 0.54
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (15 bp):
AATATAATAAATATT
Found at i:35744 original size:15 final size:14
Alignment explanation
Indices: 35700--35744 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 14
35690 AAATATAATC
*
35700 AATATTATTATAATA
1 AATATTAATATAA-A
35715 AATATTAAT-TAAA
1 AATATTAATATAAA
35728 AATATTAATAATAAA
1 AATATTAAT-ATAAA
35743 AA
1 AA
35745 ATTTTATAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
13 10 0.37
14 3 0.11
15 14 0.52
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
AATATTAATATAAA
Found at i:36926 original size:19 final size:18
Alignment explanation
Indices: 36902--36941 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
36892 ATAAAATAAA
*
36902 ATTTTTATTTTTATTATAT
1 ATTTTTATTTTAATTA-AT
36921 ATTTTTATTTTAATTAAT
1 ATTTTTATTTTAATTAAT
36939 ATT
1 ATT
36942 AAAAAATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (18 bp):
ATTTTTATTTTAATTAAT
Found at i:37060 original size:48 final size:47
Alignment explanation
Indices: 36980--37073 Score: 113
Period size: 48 Copynumber: 2.0 Consensus size: 47
36970 AATTTGAATA
*
36980 TAAATAATTAAATTTAAAAATAAACATATAAATTAAATTT-ATTTTTAC
1 TAAATAAATAAATTTAAAAATAAACATATAAA-T-AATTTAATTTTTAC
*
37028 TAAATAAATAATTTTAATTAAATAAAC-T-TAAATAATTTAATTTTTA
1 TAAATAAATAAATTTAA--AAATAAACATATAAATAATTTAATTTTTA
37074 TTTTAAACTA
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
46 5 0.12
47 8 0.20
48 19 0.46
49 1 0.02
50 8 0.20
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (47 bp):
TAAATAAATAAATTTAAAAATAAACATATAAATAATTTAATTTTTAC
Found at i:37452 original size:55 final size:56
Alignment explanation
Indices: 37381--37487 Score: 162
Period size: 55 Copynumber: 1.9 Consensus size: 56
37371 TCAAGATAGC
* * *
37381 TAACGATTCAATTATCTAATTATTTATGAAAAAAATAAATAT-TTACATAAATATA
1 TAACAATTCAACTATCTAATTATTTATAAAAAAAATAAATATGTTACATAAATATA
* *
37436 TAACAATTCAACTATCTGATTATTTATAAAAAAAATAAATATGTTGCATAAA
1 TAACAATTCAACTATCTAATTATTTATAAAAAAAATAAATATGTTACATAAA
37488 ACTTTATTAT
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
55 38 0.83
56 8 0.17
ACGTcount: A:0.50, C:0.08, G:0.05, T:0.36
Consensus pattern (56 bp):
TAACAATTCAACTATCTAATTATTTATAAAAAAAATAAATATGTTACATAAATATA
Found at i:38692 original size:18 final size:19
Alignment explanation
Indices: 38665--38700 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
38655 ATATCAATGT
*
38665 ATAAATTTATATATTATTA
1 ATAAATTTATATAATATTA
38684 ATAAA-TTATATAATATT
1 ATAAATTTATATAATATT
38701 GCATATTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
ATAAATTTATATAATATTA
Found at i:39161 original size:13 final size:13
Alignment explanation
Indices: 39143--39167 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39133 AAAGCCATGC
39143 AGAAAAAAAAAAA
1 AGAAAAAAAAAAA
39156 AGAAAAAAAAAA
1 AGAAAAAAAAAA
39168 TGTTGCAAAT
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:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (13 bp):
AGAAAAAAAAAAA
Found at i:40132 original size:16 final size:16
Alignment explanation
Indices: 40086--40137 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
40076 TATCCAAGTA
40086 ATTTCGAGTTCGAATC
1 ATTTCGAGTTCGAATC
* * *
40102 ATTTCAATTTTGAATC
1 ATTTCGAGTTCGAATC
* *
40118 ATTTTGAGTTCGAATT
1 ATTTCGAGTTCGAATC
40134 ATTT
1 ATTT
40138 TAAATTTCGA
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.27, C:0.12, G:0.13, T:0.48
Consensus pattern (16 bp):
ATTTCGAGTTCGAATC
Found at i:42680 original size:16 final size:16
Alignment explanation
Indices: 42659--42704 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
42649 TAAAGTTAAA
42659 TTTTAAAATAAATAAT
1 TTTTAAAATAAATAAT
* *
42675 TTTTAAATTATAAT-TT
1 TTTTAAAATA-AATAAT
42691 TTTTAAAA-AAATAA
1 TTTTAAAATAAATAA
42705 AAATAAAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 5
0.73 0.12 0.15
Matches are distributed among these distances:
14 3 0.12
15 1 0.04
16 17 0.71
17 3 0.12
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TTTTAAAATAAATAAT
Found at i:42689 original size:14 final size:14
Alignment explanation
Indices: 42641--42692 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
42631 ATAATATTTA
*
42641 ATAAATTTTAAAGTT
1 ATAATTTTTAAA-TT
* *
42656 A-AATTTTAAAATAA
1 ATAATTTTTAAAT-T
42670 ATAATTTTTAAATT
1 ATAATTTTTAAATT
42684 ATAATTTTT
1 ATAATTTTT
42693 TTAAAAAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
13 1 0.03
14 18 0.60
15 11 0.37
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (14 bp):
ATAATTTTTAAATT
Found at i:46592 original size:34 final size:34
Alignment explanation
Indices: 46526--46594 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 34
46516 CTTATATTAA
* * *
46526 ATATAACACTTAATTTCATAAGTTTTCAAAAAAT
1 ATATAACACTTAATATAATAACTTTTCAAAAAAT
* *
46560 ATATATCACTTAATATAATAACTTTTTTAAAAAAT
1 ATATAACACTTAATATAATAAC-TTTTCAAAAAAT
46595 TACTCTTAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
34 18 0.62
35 11 0.38
ACGTcount: A:0.48, C:0.10, G:0.01, T:0.41
Consensus pattern (34 bp):
ATATAACACTTAATATAATAACTTTTCAAAAAAT
Found at i:53239 original size:3 final size:3
Alignment explanation
Indices: 53231--53261 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
53221 AAAATAGAGT
53231 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
53262 AACATATCTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:54785 original size:2 final size:2
Alignment explanation
Indices: 54778--54812 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
54768 GCTTGATCCA
54778 AT AT AT AT AT AT AT AT AT A- 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
54813 GTGTGTGTGT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:54802 original size:17 final size:17
Alignment explanation
Indices: 54780--54812 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
54770 TTGATCCAAT
54780 ATATATATATATATATA
1 ATATATATATATATATA
54797 ATATATATATATATAT
1 ATATATATATATATAT
54813 GTGTGTGTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
ATATATATATATATATA
Found at i:55332 original size:22 final size:23
Alignment explanation
Indices: 55306--55356 Score: 58
Period size: 22 Copynumber: 2.4 Consensus size: 23
55296 ATAATTTAAA
55306 TTAATTTAA-T-AAAAATTATTAT
1 TTAATTTAATTAAAAAATTATT-T
55328 TTAA--TAATTAAAAAATTATTT
1 TTAATTTAATTAAAAAATTATTT
55349 TT-ATTTAA
1 TTAATTTAA
55357 ATTTAATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
20 4 0.16
21 4 0.16
22 17 0.68
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TTAATTTAATTAAAAAATTATTT
Found at i:55340 original size:20 final size:19
Alignment explanation
Indices: 55296--55395 Score: 50
Period size: 19 Copynumber: 5.4 Consensus size: 19
55286 AACAATTTTT
* *
55296 ATAATTTAAAT-TAATTTA
1 ATAATTAAAATATTATTTA
*
55314 ATAA--AAATTATTATTTA
1 ATAATTAAAATATTATTTA
*
55331 ATAATTAAAAAATTATTT-
1 ATAATTAAAATATTATTTA
* * *
55349 TTATTTAAATTTAATTA-TTA
1 ATAATTAAA-AT-ATTATTTA
*
55369 TTAATATAAAATATT-TTTA
1 ATAAT-TAAAATATTATTTA
55388 ATTAATTA
1 A-TAATTA
55396 TTATTTTAAA
Statistics
Matches: 61, Mismatches: 12, Indels: 17
0.68 0.13 0.19
Matches are distributed among these distances:
16 3 0.05
17 10 0.16
18 11 0.18
19 20 0.33
20 13 0.21
21 4 0.07
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
ATAATTAAAATATTATTTA
Found at i:55402 original size:16 final size:16
Alignment explanation
Indices: 55383--55413 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
55373 TATAAAATAT
*
55383 TTTTAATTAATTATTA
1 TTTTAAATAATTATTA
55399 TTTTAAATAATTATT
1 TTTTAAATAATTATT
55414 TAAACTTTCA
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:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTTAAATAATTATTA
Found at i:55414 original size:30 final size:34
Alignment explanation
Indices: 55334--55414 Score: 89
Period size: 36 Copynumber: 2.4 Consensus size: 34
55324 TTATTTAATA
* *
55334 ATTAAAAAATTATTTTTATTTAAATTTAATTATT
1 ATTAAATAATTATTTTTAATTAAATTTAATTATT
*
55368 ATTAATATAAAATATTTTTAATT-AA-TT-ATTATT
1 ATTAA-AT-AATTATTTTTAATTAAATTTAATTATT
55401 -TTAAATAATTATTT
1 ATTAAATAATTATTT
55415 AAACTTTCAA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
30 7 0.17
31 2 0.05
32 4 0.10
33 6 0.15
34 7 0.17
35 3 0.07
36 12 0.29
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (34 bp):
ATTAAATAATTATTTTTAATTAAATTTAATTATT
Found at i:56434 original size:2 final size:2
Alignment explanation
Indices: 56427--56454 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
56417 GAATATAAGT
56427 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
56455 AAGAGTGGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:57887 original size:2 final size:2
Alignment explanation
Indices: 57880--57905 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
57870 TTATGTAATA
57880 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
57906 TAACTAAATG
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:58008 original size:50 final size:50
Alignment explanation
Indices: 57933--58091 Score: 239
Period size: 50 Copynumber: 3.2 Consensus size: 50
57923 AATTGTTATT
* * * *
57933 ATTGTTGACTA-TCATTCACCAACCTTTGATAATAGAAAGAGGTGGCTATA
1 ATTGTTGACAATTC-TTCACCAACCTTTGACAATAGAAGGAGGTGGCCATA
* *
57983 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAAGGAGGTGACCATA
1 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAAGGAGGTGGCCATA
*
58033 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGGGAGGTGGCCATA
1 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAAGGAGGTGGCCATA
58083 ATTGTTGAC
1 ATTGTTGAC
58092 TCTAAGTATA
Statistics
Matches: 100, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
50 98 0.98
51 2 0.02
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.30
Consensus pattern (50 bp):
ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAAGGAGGTGGCCATA
Found at i:62564 original size:50 final size:50
Alignment explanation
Indices: 62486--62694 Score: 314
Period size: 50 Copynumber: 4.2 Consensus size: 50
62476 AGTTGTTGTC
* *
62486 ATTGTTGACTA-TCATTCACCAACCTTTGACAATAG-AGAGAGGTGGGCATA
1 ATTGTTGACGATTC-TTCACCAACCTTTGACAATAGAAG-GAGGTGGTCATA
*
62536 ATTGTTGACGATTCTTCACCAACATTTGACAATAGAAGGAGGTGGTCATA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAAGGAGGTGGTCATA
* * **
62586 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGGGAGGTGACCATA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAAGGAGGTGGTCATA
*
62636 ATTGTTGACGATTCTTCACTAACCTTTGACAATAGAAGGAGGTGGTCATA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAAGGAGGTGGTCATA
62686 ATTGTTGAC
1 ATTGTTGAC
62695 TCTAAGTATA
Statistics
Matches: 144, Mismatches: 13, Indels: 4
0.89 0.08 0.02
Matches are distributed among these distances:
50 140 0.97
51 4 0.03
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (50 bp):
ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAAGGAGGTGGTCATA
Found at i:62664 original size:100 final size:100
Alignment explanation
Indices: 62486--62694 Score: 348
Period size: 100 Copynumber: 2.1 Consensus size: 100
62476 AGTTGTTGTC
* **
62486 ATTGTTGACTATCATTCACCAACCTTTGACAATAGAGAGAGGTGGGCATAATTGTTGACGATTCT
1 ATTGTTGACAATCATTCACCAACCTTTGACAATAGAGAGAGGTGACCATAATTGTTGACGATTCT
62551 TCACCAACATTTGACAATAGAAGGAGGTGGTCATA
66 TCACCAACATTTGACAATAGAAGGAGGTGGTCATA
*
62586 ATTGTTGACAATTC-TTCACCAACCTTTGACAATAGAGGGAGGTGACCATAATTGTTGACGATTC
1 ATTGTTGACAA-TCATTCACCAACCTTTGACAATAGAGAGAGGTGACCATAATTGTTGACGATTC
* *
62650 TTCACTAACCTTTGACAATAGAAGGAGGTGGTCATA
65 TTCACCAACATTTGACAATAGAAGGAGGTGGTCATA
62686 ATTGTTGAC
1 ATTGTTGAC
62695 TCTAAGTATA
Statistics
Matches: 102, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
100 100 0.98
101 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (100 bp):
ATTGTTGACAATCATTCACCAACCTTTGACAATAGAGAGAGGTGACCATAATTGTTGACGATTCT
TCACCAACATTTGACAATAGAAGGAGGTGGTCATA
Found at i:65395 original size:3 final size:3
Alignment explanation
Indices: 65387--65411 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
65377 TGCTAATCTA
65387 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
65412 TGAAATATAA
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):
TAT
Found at i:65795 original size:2 final size:2
Alignment explanation
Indices: 65788--65812 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
65778 TAATTAACCA
65788 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
65813 ATTAACAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:66957 original size:14 final size:14
Alignment explanation
Indices: 66940--66981 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
66930 ATATTAAAAA
66940 ATATTAATTAATAT
1 ATATTAATTAATAT
* * *
66954 ATATTACTTAAAAA
1 ATATTAATTAATAT
66968 ATATTAATTAATAT
1 ATATTAATTAATAT
66982 TTATAGATAT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (14 bp):
ATATTAATTAATAT
Found at i:67346 original size:16 final size:16
Alignment explanation
Indices: 67325--67358 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
67315 ATGATTAAAA
* *
67325 AATCATGGTGATATAT
1 AATCATAGTGAAATAT
67341 AATCATAGTGAAATAT
1 AATCATAGTGAAATAT
67357 AA
1 AA
67359 AATGGTGAGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.47, C:0.06, G:0.15, T:0.32
Consensus pattern (16 bp):
AATCATAGTGAAATAT
Found at i:70566 original size:16 final size:19
Alignment explanation
Indices: 70545--70585 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
70535 TAATTGAAAG
70545 ATTAA-TAAT-AATT-TTA
1 ATTAATTAATCAATTGTTA
70561 ATTAATTAATCAATTGGTTA
1 ATTAATTAATCAATT-GTTA
70581 ATTAA
1 ATTAA
70586 AACTGTAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 5 0.24
17 4 0.19
18 4 0.19
20 8 0.38
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.46
Consensus pattern (19 bp):
ATTAATTAATCAATTGTTA
Found at i:71231 original size:3 final size:3
Alignment explanation
Indices: 71223--71258 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
71213 AATCAAAGGT
71223 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
71259 GATTGTAACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.67
Consensus pattern (3 bp):
TTG
Found at i:71626 original size:2 final size:2
Alignment explanation
Indices: 71619--71653 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
71609 ATAAACATCT
71619 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
71654 GCATGTAAAA
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:74780 original size:4 final size:4
Alignment explanation
Indices: 74765--74794 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
74755 TGTTATGTGC
*
74765 TTAT TCAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
74795 GGTTGTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.73
Consensus pattern (4 bp):
TTAT
Found at i:79200 original size:12 final size:11
Alignment explanation
Indices: 79156--79200 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
79146 CATATCCTTT
79156 AAATATAATAA
1 AAATATAATAA
*
79167 AAATA-ATTAA
1 AAATATAATAA
*
79177 AAATAAAATAA
1 AAATATAATAA
79188 AATATATAATAA
1 AA-ATATAATAA
79200 A
1 A
79201 CTTTTAACCC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
10 9 0.31
11 11 0.38
12 9 0.31
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
AAATATAATAA
Found at i:80871 original size:15 final size:15
Alignment explanation
Indices: 80809--80879 Score: 61
Period size: 17 Copynumber: 4.3 Consensus size: 15
80799 TTATATATTT
80809 TTAAATTAAATTTAAA
1 TTAAATT-AATTTAAA
* *
80825 TAAAAATTATTTTAACTA
1 T-TAAATTAATTTAA--A
*
80843 TTAAATGATAATTTGAA
1 TTAAAT--TAATTTAAA
80860 TTAAATTAATTTAAA
1 TTAAATTAATTTAAA
80875 TTAAA
1 TTAAA
80880 AAAATTATAT
Statistics
Matches: 44, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
15 13 0.30
16 7 0.16
17 16 0.36
18 2 0.05
19 6 0.14
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.44
Consensus pattern (15 bp):
TTAAATTAATTTAAA
Found at i:84516 original size:3 final size:3
Alignment explanation
Indices: 84510--84560 Score: 93
Period size: 3 Copynumber: 17.0 Consensus size: 3
84500 AATCATCATC
*
84510 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AGT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
84558 ATT
1 ATT
84561 TGCTTTTCTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:85735 original size:2 final size:2
Alignment explanation
Indices: 85728--85765 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
85718 AATCCCACAT
85728 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
85766 ACAATAATGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:86282 original size:2 final size:2
Alignment explanation
Indices: 86277--86308 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
86267 AGCGTGTGTG
*
86277 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
86309 AACACTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:89233 original size:31 final size:32
Alignment explanation
Indices: 89181--89249 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 32
89171 AGATCTGATG
*
89181 TTAATTTAATTAAAAATTAAA-TAAAAAAT-T
1 TTAAATTAATTAAAAATTAAATTAAAAAATAT
89211 TTAAATTATATTAACAAA-TAAATTAAAAAATAT
1 TTAAATTA-ATTAA-AAATTAAATTAAAAAATAT
89244 TTAAAT
1 TTAAAT
89250 ATTTTTATTA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
30 7 0.21
31 9 0.26
32 11 0.32
33 7 0.21
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.39
Consensus pattern (32 bp):
TTAAATTAATTAAAAATTAAATTAAAAAATAT
Found at i:89279 original size:15 final size:16
Alignment explanation
Indices: 89259--89297 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
89249 TATTTTTATT
89259 AATTATTTA-TTAAAA
1 AATTATTTACTTAAAA
*
89274 AATTATTCACTTAAAA
1 AATTATTTACTTAAAA
*
89290 AATAATTT
1 AATTATTT
89298 TTTTATTTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (16 bp):
AATTATTTACTTAAAA
Found at i:92341 original size:18 final size:20
Alignment explanation
Indices: 92304--92341 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
92294 ATCTAATATC
*
92304 ATATTAATATATAAACTTAT
1 ATATAAATATATAAACTTAT
92324 ATATAAATA-ATAAA-TTAT
1 ATATAAATATATAAACTTAT
92342 TTATTATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 5 0.29
20 8 0.47
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (20 bp):
ATATAAATATATAAACTTAT
Found at i:92348 original size:25 final size:25
Alignment explanation
Indices: 92320--92382 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 25
92310 ATATATAAAC
*
92320 TTATATATAAATAAT-AAATTATTTA
1 TTATATATAAA-AATAAAATTATATA
* *
92345 TTATTTATTAAAATAAAATTATATA
1 TTATATATAAAAATAAAATTATATA
* *
92370 TTATTTTTAAAAA
1 TTATATATAAAAA
92383 ATAATTAATT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
24 3 0.09
25 29 0.91
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
TTATATATAAAAATAAAATTATATA
Found at i:92383 original size:21 final size:24
Alignment explanation
Indices: 92335--92389 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 24
92325 TATAAATAAT
*
92335 AAATTATTTATTATTTATTAAAATA
1 AAATTATATATTATTTATT-AAATA
*
92360 AAATTATATATTATTT-TTAAAAA
1 AAATTATATATTATTTATTAAATA
92383 ATAATTA
1 A-AATTA
92390 ATTTTAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 5 0.19
24 7 0.26
25 15 0.56
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
AAATTATATATTATTTATTAAATA
Found at i:93600 original size:20 final size:19
Alignment explanation
Indices: 93575--93628 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
93565 TATTAATAAT
*
93575 AATATTATAATTTAATTATA
1 AATATTATAATTTAA-AATA
*
93595 AATATTATTATTTAAAATA
1 AATATTATAATTTAAAATA
*
93614 AATTATTAAAATTTA
1 AA-TATTATAATTTA
93629 GTTCACTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 5 0.17
20 24 0.83
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
AATATTATAATTTAAAATA
Found at i:93705 original size:18 final size:17
Alignment explanation
Indices: 93682--93718 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
93672 CATATTATAT
*
93682 ATAAATACAAATAAATAA
1 ATAAATAAAAATAAA-AA
93700 ATAAATAAAAATAAAAA
1 ATAAATAAAAATAAAAA
93717 AT
1 AT
93719 CCTTGGATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.22
Consensus pattern (17 bp):
ATAAATAAAAATAAAAA
Found at i:94173 original size:32 final size:32
Alignment explanation
Indices: 94137--94212 Score: 82
Period size: 32 Copynumber: 2.3 Consensus size: 32
94127 ATTCTTAATC
94137 AATTAT-AATTATAATAAAAATAATTAAATTAA
1 AATTATAAATTA-AATAAAAATAATTAAATTAA
* * * *
94169 AATTATAAATTAAATGATATTAATTTAATTAAA
1 AATTATAAATTAAATAAAAATAATTAAATT-AA
*
94202 AATTAAAAATT
1 AATTATAAATT
94213 TATTATTAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
32 20 0.54
33 17 0.46
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.39
Consensus pattern (32 bp):
AATTATAAATTAAATAAAAATAATTAAATTAA
Found at i:94183 original size:26 final size:25
Alignment explanation
Indices: 94132--94218 Score: 72
Period size: 26 Copynumber: 3.4 Consensus size: 25
94122 CTTAGATTCT
* *
94132 TAATCAATTATAATTAT-AATAAAAA
1 TAATTAATTATAATTATAAAT-TAAA
*
94157 TAATTAAATTAAAATTATAAATTAAA
1 TAATT-AATTATAATTATAAATTAAA
*
94183 TGATATTAATT-TAATTAAAAATTAAA
1 T-A-ATTAATTATAATTATAAATTAAA
*
94209 -AATTTATTAT
1 TAATTAATTAT
94219 TAAAATATAT
Statistics
Matches: 51, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
23 6 0.12
24 2 0.04
25 4 0.08
26 28 0.55
27 8 0.16
28 3 0.06
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (25 bp):
TAATTAATTATAATTATAAATTAAA
Found at i:94259 original size:14 final size:14
Alignment explanation
Indices: 94219--94265 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
94209 AATTTATTAT
94219 TAAAATATATTTAAA
1 TAAAAT-TATTTAAA
*
94234 -ATAATTATTTTAAA
1 TAAAATTA-TTTAAA
94248 TAAAATTATTT-AA
1 TAAAATTATTTAAA
94261 TAAAA
1 TAAAA
94266 AATTAACTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
13 9 0.32
14 13 0.46
15 6 0.21
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TAAAATTATTTAAA
Found at i:94262 original size:13 final size:13
Alignment explanation
Indices: 94219--94265 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 13
94209 AATTTATTAT
94219 TAAAATATATTTAA
1 TAAAAT-TATTTAA
94233 -AATAATTATTTTAAA
1 TAA-AATTA-TTT-AA
94248 TAAAATTATTTAA
1 TAAAATTATTTAA
94261 TAAAA
1 TAAAA
94266 AATTAACTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.38
14 9 0.31
15 7 0.24
16 2 0.07
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
TAAAATTATTTAA
Found at i:94267 original size:15 final size:16
Alignment explanation
Indices: 94230--94293 Score: 51
Period size: 15 Copynumber: 3.8 Consensus size: 16
94220 AAAATATATT
94230 TAAAATAATTATTTTAA
1 TAAAA-AATTATTTTAA
*
94247 -ATAAAATTA-TTTAA
1 TAAAAAATTATTTTAA
*
94261 TAAAAAATTAACTATTTAT
1 TAAAAAATT-A-T-TTTAA
94280 TAAAAAAATTATTT
1 T-AAAAAATTATTT
94294 ATCATCTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 12
0.72 0.06 0.23
Matches are distributed among these distances:
14 5 0.13
15 12 0.32
16 4 0.11
17 2 0.05
18 1 0.03
19 6 0.16
20 8 0.21
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (16 bp):
TAAAAAATTATTTTAA
Found at i:94378 original size:14 final size:14
Alignment explanation
Indices: 94361--94391 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
94351 TTTTACATTA
*
94361 TTTTAATTTAATAT
1 TTTTAATATAATAT
94375 TTTTAATATAATAT
1 TTTTAATATAATAT
94389 TTT
1 TTT
94392 AAAAAATACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TTTTAATATAATAT
Found at i:94958 original size:32 final size:34
Alignment explanation
Indices: 94922--95003 Score: 79
Period size: 33 Copynumber: 2.5 Consensus size: 34
94912 AAAATTATAA
*
94922 AATTTTTAAA-ATTTAAAATTTATATTT-AA-TTT
1 AATTTTTAAATAATTAAAATTT-TATTTAAATTTT
94954 AA--TTTAAATTAATTAAAATTTTATTTAAATTTT
1 AATTTTTAAA-TAATTAAAATTTTATTTAAATTTT
94987 AA--TTTAAATAAATTAAA
1 AATTTTTAAAT-AATTAAA
95004 TCAAACTAAT
Statistics
Matches: 44, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
30 6 0.14
31 5 0.11
32 15 0.34
33 18 0.41
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (34 bp):
AATTTTTAAATAATTAAAATTTTATTTAAATTTT
Found at i:94963 original size:6 final size:6
Alignment explanation
Indices: 94930--94995 Score: 52
Period size: 6 Copynumber: 11.7 Consensus size: 6
94920 AAAATTTTTA
* *
94930 AAATTT AAAATTT ATATTT -AATTT -AATTT AAA-TT -AATTA AAATTT
1 AAATTT -AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
* *
94975 -TATTT AAATTT TAATTT AAAT
1 AAATTT AAATTT AAATTT AAAT
94996 AAATTAAATC
Statistics
Matches: 47, Mismatches: 8, Indels: 9
0.73 0.12 0.14
Matches are distributed among these distances:
4 2 0.04
5 16 0.34
6 23 0.49
7 6 0.13
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (6 bp):
AAATTT
Found at i:94977 original size:33 final size:32
Alignment explanation
Indices: 94934--95003 Score: 97
Period size: 33 Copynumber: 2.2 Consensus size: 32
94924 TTTTTAAAAT
* *
94934 TTAAAATTTATATTTAA-TTTAATTTAAATTAA
1 TTAAAATTTAT-TTAAATTTTAATTTAAATAAA
94966 TTAAAATTTTATTTAAATTTTAATTTAAATAAA
1 TTAAAA-TTTATTTAAATTTTAATTTAAATAAA
94999 TTAAA
1 TTAAA
95004 TCAAACTAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
32 10 0.29
33 24 0.71
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (32 bp):
TTAAAATTTATTTAAATTTTAATTTAAATAAA
Found at i:94985 original size:11 final size:11
Alignment explanation
Indices: 94932--94995 Score: 60
Period size: 11 Copynumber: 5.7 Consensus size: 11
94922 AATTTTTAAA
94932 ATTTAAAATTTAT
1 ATTT-AAATTT-T
*
94945 ATTT-AATTTA
1 ATTTAAATTTT
*
94955 ATTTAAA-TTA
1 ATTTAAATTTT
*
94965 ATTAAAATTTT
1 ATTTAAATTTT
94976 ATTTAAATTTT
1 ATTTAAATTTT
94987 AATTTAAAT
1 -ATTTAAAT
94996 AAATTAAATC
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
10 13 0.30
11 19 0.43
12 8 0.18
13 4 0.09
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
ATTTAAATTTT
Found at i:97144 original size:23 final size:23
Alignment explanation
Indices: 97114--97159 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
97104 TCCCTATTTA
97114 TATATATAACTTTCTTA-TTGGTT
1 TATATATAACTTT-TTAGTTGGTT
97137 TATATATAACTTTTTAGTTGGTT
1 TATATATAACTTTTTAGTTGGTT
97160 CAATTGTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 3 0.14
23 19 0.86
ACGTcount: A:0.26, C:0.07, G:0.11, T:0.57
Consensus pattern (23 bp):
TATATATAACTTTTTAGTTGGTT
Found at i:98315 original size:17 final size:17
Alignment explanation
Indices: 98281--98331 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
98271 TAAATTTAAA
*
98281 TTAATTTTTTTTATATT
1 TTAATTTTATTTATATT
98298 TTAATTTTAATTTA-ATT
1 TTAATTTT-ATTTATATT
* *
98315 TAAAATATTATTTATAT
1 T-TAATTTTATTTATAT
98332 AATAAATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
17 17 0.61
18 11 0.39
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTAATTTTATTTATATT
Found at i:99556 original size:13 final size:13
Alignment explanation
Indices: 99526--99558 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
99516 TTACATTAGA
99526 TAAAATTTAAATT
1 TAAAATTTAAATT
*
99539 T-AAATTTAGATT
1 TAAAATTTAAATT
99551 TAAAATTT
1 TAAAATTT
99559 TTTTGTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (13 bp):
TAAAATTTAAATT
Found at i:99768 original size:2 final size:2
Alignment explanation
Indices: 99761--99795 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
99751 ATAATTTCAA
99761 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
99796 ATTCGTTCTA
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:100510 original size:19 final size:19
Alignment explanation
Indices: 100486--100554 Score: 70
Period size: 19 Copynumber: 3.6 Consensus size: 19
100476 AATAAAAAAT
100486 TTTTATT-TATATTAATATA
1 TTTTATTATATATTAAT-TA
*
100505 TTTTATTATATTTTAATTA
1 TTTTATTATATATTAATTA
** *
100524 TTTTAAAAT-TATTAATAA
1 TTTTATTATATATTAATTA
100542 TTTATATTATATA
1 TTT-TATTATATA
100555 AAATTTAAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
18 10 0.25
19 20 0.50
20 10 0.25
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TTTTATTATATATTAATTA
Found at i:100515 original size:18 final size:18
Alignment explanation
Indices: 100486--100553 Score: 59
Period size: 18 Copynumber: 3.6 Consensus size: 18
100476 AATAAAAAAT
100486 TTTTATTTATATTAATATA
1 TTTTA-TTATATTAATATA
100505 TTTTATTATATTTTAAT-TA
1 TTTTATTATA--TTAATATA
**
100524 TTTTAAAATTATTAATA-A
1 TTTTATTA-TATTAATATA
100542 TTTATATTATAT
1 TTT-TATTATAT
100554 AAAATTTAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
18 17 0.43
19 16 0.40
20 7 0.17
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTTATTATATTAATATA
Found at i:100547 original size:33 final size:33
Alignment explanation
Indices: 100494--100585 Score: 98
Period size: 33 Copynumber: 2.7 Consensus size: 33
100484 ATTTTTATTT
*
100494 ATATTAATATATTT-TATTATATTTTAATTATTTTAAA
1 ATATTAATATATTTATATTATA---TAA--AATTTAAA
100531 ATTATTAATA-ATTTATATTATATAAAATTTAAA
1 A-TATTAATATATTTATATTATATAAAATTTAAA
*
100564 ATATTTATATATTTATATTATA
1 ATATTAATATATTTATATTATA
100586 GATTTTTTTA
Statistics
Matches: 50, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
32 7 0.14
33 20 0.40
35 3 0.06
37 5 0.10
38 15 0.30
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (33 bp):
ATATTAATATATTTATATTATATAAAATTTAAA
Found at i:100595 original size:17 final size:18
Alignment explanation
Indices: 100575--100616 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
100565 TATTTATATA
100575 TTTATATTATAGATTT-T
1 TTTATATTATAGATTTAT
* **
100592 TTTAGATTATATTTTTAT
1 TTTATATTATAGATTTAT
100610 TTTATAT
1 TTTATAT
100617 ATTACTTTAG
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.67
Consensus pattern (18 bp):
TTTATATTATAGATTTAT
Found at i:100626 original size:30 final size:30
Alignment explanation
Indices: 100568--100626 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
100558 TTTAAAATAT
**
100568 TTATATATTTATATTATAGATTTTTTTAGA
1 TTATATATTTATATTATAGATTACTTTAGA
* * *
100598 TTATATTTTTATTTTATATATTACTTTAG
1 TTATATATTTATATTATAGATTACTTTAG
100627 TCTCATATAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.63
Consensus pattern (30 bp):
TTATATATTTATATTATAGATTACTTTAGA
Found at i:102908 original size:19 final size:19
Alignment explanation
Indices: 102871--102926 Score: 53
Period size: 19 Copynumber: 3.0 Consensus size: 19
102861 ATTTTTTTCG
* *
102871 TATAAAATATATAAGTATAA
1 TATAAATTAT-TAAATATAA
*
102891 TATAAATTATTAAATATAT
1 TATAAATTATTAAATATAA
*
102910 TA-AAATT-TTAAAAATAA
1 TATAAATTATTAAATATAA
102927 ATTAATATAC
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
17 8 0.26
18 5 0.16
19 9 0.29
20 9 0.29
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (19 bp):
TATAAATTATTAAATATAA
Found at i:103301 original size:32 final size:34
Alignment explanation
Indices: 103229--103308 Score: 83
Period size: 32 Copynumber: 2.4 Consensus size: 34
103219 TTACATAAAA
*
103229 TAAAATAATATGAATATAAAATAAATATATATATC
1 TAAATTAATAT-AATATAAAATAAATATATATATC
* * * *
103264 GAAATTAATATAATAT-AAATTATTA-ATATATT
1 TAAATTAATATAATATAAAATAAATATATATATC
*
103296 TAAATTTATATAA
1 TAAATTAATATAA
103309 ATTATATTGT
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
32 17 0.45
33 7 0.18
34 5 0.13
35 9 0.24
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.40
Consensus pattern (34 bp):
TAAATTAATATAATATAAAATAAATATATATATC
Found at i:105142 original size:33 final size:32
Alignment explanation
Indices: 105040--105144 Score: 87
Period size: 32 Copynumber: 3.3 Consensus size: 32
105030 TATCTTTAAC
*
105040 ATATTATAATTATATTT-AAAATATATAT-TATT
1 ATATTAT-ATTA-ATTTAAAAATATTTATATATT
* * *
105072 -T-TTATATAAATTTTAATAA-ATTAATA-ATTT
1 ATATTATATTAA-TTTAAAAATATTTATATA-TT
105102 ATATTATATTAATTTAAAAATATTTATATATCT
1 ATATTATATTAATTTAAAAATATTTATATAT-T
105135 ATATTATATT
1 ATATTATATT
105145 TTTTATATTT
Statistics
Matches: 57, Mismatches: 7, Indels: 17
0.70 0.09 0.21
Matches are distributed among these distances:
28 1 0.02
29 11 0.19
30 9 0.16
31 9 0.16
32 15 0.26
33 12 0.21
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (32 bp):
ATATTATATTAATTTAAAAATATTTATATATT
Found at i:105143 original size:19 final size:19
Alignment explanation
Indices: 105121--105171 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
105111 TAATTTAAAA
*
105121 ATATTTATATATCTATATT
1 ATATTTTTATATCTATATT
*
105140 ATATTTTTTATAT-TTTATT
1 ATA-TTTTTATATCTATATT
105159 ATATTTTTATATC
1 ATATTTTTATATC
105172 GCATTTCTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 9 0.32
19 11 0.39
20 8 0.29
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (19 bp):
ATATTTTTATATCTATATT
Found at i:105162 original size:10 final size:10
Alignment explanation
Indices: 105136--105165 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
105126 TATATATCTA
105136 TATTATATTT
1 TATTATATTT
105146 T-TTATATTT
1 TATTATATTT
105155 TATTATATTT
1 TATTATATTT
105165 T
1 T
105166 TATATCGCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.47
10 10 0.53
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (10 bp):
TATTATATTT
Found at i:116806 original size:13 final size:13
Alignment explanation
Indices: 116788--116813 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
116778 GTCTTCTTAG
116788 AACTATTAGCTTC
1 AACTATTAGCTTC
116801 AACTATTAGCTTC
1 AACTATTAGCTTC
116814 TGGCTGGTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (13 bp):
AACTATTAGCTTC
Found at i:120912 original size:12 final size:12
Alignment explanation
Indices: 120897--120937 Score: 66
Period size: 12 Copynumber: 3.5 Consensus size: 12
120887 AATTAAAACA
120897 AAATATAAAAAT
1 AAATATAAAAAT
120909 AAATAT-AAAAT
1 AAATATAAAAAT
120920 AAATATAAAAAT
1 AAATATAAAAAT
*
120932 ATATAT
1 AAATAT
120938 TATATAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
11 11 0.41
12 16 0.59
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (12 bp):
AAATATAAAAAT
Found at i:120920 original size:11 final size:11
Alignment explanation
Indices: 120897--120929 Score: 57
Period size: 11 Copynumber: 2.9 Consensus size: 11
120887 AATTAAAACA
120897 AAATATAAAAAT
1 AAATAT-AAAAT
120909 AAATATAAAAT
1 AAATATAAAAT
120920 AAATATAAAA
1 AAATATAAAA
120930 ATATATATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 15 0.71
12 6 0.29
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (11 bp):
AAATATAAAAT
Found at i:120924 original size:23 final size:23
Alignment explanation
Indices: 120897--120946 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
120887 AATTAAAACA
120897 AAATATAAAAATAAATATAAAAT
1 AAATATAAAAATAAATATAAAAT
* * *
120920 AAATATAAAAATATATATTATAT
1 AAATATAAAAATAAATATAAAAT
120943 AAAT
1 AAAT
120947 TTATAATATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (23 bp):
AAATATAAAAATAAATATAAAAT
Found at i:124275 original size:2 final size:2
Alignment explanation
Indices: 124258--124300 Score: 54
Period size: 2 Copynumber: 22.5 Consensus size: 2
124248 CGTATTTATG
* *
124258 TA TA TA -A TA TA CA TA TA TA TA TA TA TA TA AA TA TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
124298 TA T
1 TA T
124301 GATAACAACT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
1 2 0.06
2 33 0.94
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:124697 original size:54 final size:54
Alignment explanation
Indices: 124615--124719 Score: 210
Period size: 54 Copynumber: 1.9 Consensus size: 54
124605 GCACCATGAA
124615 CATGACAAGGAGAGACGTGAAGTTCAATGCGGTCAAAAAACATCACCCCCAGGC
1 CATGACAAGGAGAGACGTGAAGTTCAATGCGGTCAAAAAACATCACCCCCAGGC
124669 CATGACAAGGAGAGACGTGAAGTTCAATGCGGTCAAAAAACATCACCCCCA
1 CATGACAAGGAGAGACGTGAAGTTCAATGCGGTCAAAAAACATCACCCCCA
124720 TGCCTCACGC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.38, C:0.26, G:0.23, T:0.13
Consensus pattern (54 bp):
CATGACAAGGAGAGACGTGAAGTTCAATGCGGTCAAAAAACATCACCCCCAGGC
Found at i:132686 original size:119 final size:119
Alignment explanation
Indices: 132510--132727 Score: 373
Period size: 119 Copynumber: 1.8 Consensus size: 119
132500 AGGAACAAGG
* * *
132510 AGTTCTGCTCGTCGGGATACTGGCTAAGGAGAGAGTAGTTGGATCTTCGACCGGGCATTTCCATC
1 AGTTCTGCTCGTCGGGATACTGGCTAAGGAGAGAGTAGTTGGATCTTCCACCAGGCATTTACATC
* *
132575 GAAAATCTCTACACAAATCGCCGATCACAAAACCCTAGAAACATACGGACACGA
66 GAAAATCTCTACACAAATCACCAATCACAAAACCCTAGAAACATACGGACACGA
*
132629 AGTTCTGCTCGTCGGGATACTGGGTAAGGAGAGAGTAGTTGGATCTTCCACCAGGCATTTACATC
1 AGTTCTGCTCGTCGGGATACTGGCTAAGGAGAGAGTAGTTGGATCTTCCACCAGGCATTTACATC
*
132694 GATAATCTCTACACAAATCACCAATCACAAAACC
66 GAAAATCTCTACACAAATCACCAATCACAAAACC
132728 TAAAAAACCC
Statistics
Matches: 92, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
119 92 1.00
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.22
Consensus pattern (119 bp):
AGTTCTGCTCGTCGGGATACTGGCTAAGGAGAGAGTAGTTGGATCTTCCACCAGGCATTTACATC
GAAAATCTCTACACAAATCACCAATCACAAAACCCTAGAAACATACGGACACGA
Found at i:134373 original size:2 final size:2
Alignment explanation
Indices: 134361--134403 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
134351 CCAATGAAAG
*
134361 AT AT AT GT 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
134403 A
1 A
134404 CACATAGAAC
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:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:137874 original size:2 final size:2
Alignment explanation
Indices: 137867--137902 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
137857 GATTACAAAG
137867 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
137903 GAAACGTGCT
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:139782 original size:43 final size:43
Alignment explanation
Indices: 139722--139828 Score: 178
Period size: 43 Copynumber: 2.5 Consensus size: 43
139712 ATTGTTAAGC
* *
139722 TAAGTTAGGAGTTGGTAGATTAGAGAATGTCATTGTTAATTGT
1 TAAGTTATGAGTTGGTAGATCAGAGAATGTCATTGTTAATTGT
*
139765 TAAGTTATGAGTCGGTAGATCAGAGAATGTCATTGTTAATTGT
1 TAAGTTATGAGTTGGTAGATCAGAGAATGTCATTGTTAATTGT
*
139808 TAAGCTATGAGTTGGTAGATC
1 TAAGTTATGAGTTGGTAGATC
139829 GTGGGAAATA
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 59 1.00
ACGTcount: A:0.30, C:0.06, G:0.27, T:0.37
Consensus pattern (43 bp):
TAAGTTATGAGTTGGTAGATCAGAGAATGTCATTGTTAATTGT
Found at i:145984 original size:2 final size:2
Alignment explanation
Indices: 145979--146018 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
145969 GAGAGCACTT
145979 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
146019 ATGCCTTCTA
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:153359 original size:24 final size:24
Alignment explanation
Indices: 153332--153379 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
153322 TAGAGGTAAA
*
153332 CAGTTCATTGAAAAAATATATTTT
1 CAGTTCATTGAAAAAAAATATTTT
** *
153356 CAGTTTTTTTAAAAAAAATATTTT
1 CAGTTCATTGAAAAAAAATATTTT
153380 TTATCAAAAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.46
Consensus pattern (24 bp):
CAGTTCATTGAAAAAAAATATTTT
Found at i:153647 original size:20 final size:19
Alignment explanation
Indices: 153622--153659 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
153612 TATACGATAA
153622 AATATTAAAATTTTAATTTT
1 AATATTAAAA-TTTAATTTT
153642 AATATTAAAATTTAATTT
1 AATATTAAAATTTAATTT
153660 ATGATGCCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
AATATTAAAATTTAATTTT
Found at i:165805 original size:24 final size:24
Alignment explanation
Indices: 165773--165822 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
165763 GGTTAGTTGA
165773 AAATTAGTTGAAAATTCTTTTCTT
1 AAATTAGTTGAAAATTCTTTTCTT
*
165797 AAATTAGTTGAAAATTCTTTTTTT
1 AAATTAGTTGAAAATTCTTTTCTT
165821 AA
1 AA
165823 TATTCTCTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.06, G:0.08, T:0.50
Consensus pattern (24 bp):
AAATTAGTTGAAAATTCTTTTCTT
Found at i:165912 original size:25 final size:25
Alignment explanation
Indices: 165857--165913 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 25
165847 AACATTTTAA
* *
165857 ATAAAATTATTATGTACAAAAATAT
1 ATAAAATTATTATATAAAAAAATAT
*
165882 ATTAAAA-TATTATATATAAAAAATTT
1 A-TAAAATTATTATATA-AAAAAATAT
165908 ATAAAA
1 ATAAAA
165914 ATAAAAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
25 14 0.52
26 13 0.48
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (25 bp):
ATAAAATTATTATATAAAAAAATAT
Found at i:165990 original size:20 final size:18
Alignment explanation
Indices: 165958--166012 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 18
165948 AAATATTATT
*
165958 TTTTA-TAAAATTTAAAA
1 TTTTATTAATATTTAAAA
165975 TTTTTCATTAATATTTTAAAA
1 -TTTT-ATTAATA-TTTAAAA
*
165996 TTTTATTTATATTTAAA
1 TTTTATTAATATTTAAA
166013 TAATTTTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
18 10 0.31
19 7 0.22
20 8 0.25
21 7 0.22
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTTATTAATATTTAAAA
Found at i:165994 original size:21 final size:20
Alignment explanation
Indices: 165968--166021 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
165958 TTTTATAAAA
165968 TTTAAAATTTTTCATTAATAT
1 TTTAAAATTTTT-ATTAATAT
*
165989 TTTAAAA-TTTTATTTATAT
1 TTTAAAATTTTTATTAATAT
*
166008 TTAAATAATTTTTA
1 TTTAA-AATTTTTA
166022 ACATCGTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 11 0.38
20 6 0.21
21 12 0.41
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTAAAATTTTTATTAATAT
Found at i:166009 original size:19 final size:20
Alignment explanation
Indices: 165968--166019 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 20
165958 TTTTATAAAA
165968 TTTAAAATTTTTCATTAATAT
1 TTTAAAA-TTTTCATTAATAT
*
165989 TTTAAAATTTT-ATTTATAT
1 TTTAAAATTTTCATTAATAT
*
166008 TTAAATAATTTT
1 TTTAA-AATTTT
166020 TAACATCGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 11 0.39
20 10 0.36
21 7 0.25
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTAAAATTTTCATTAATAT
Found at i:166017 original size:20 final size:20
Alignment explanation
Indices: 165967--166019 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
165957 TTTTTATAAA
*
165967 ATTTAAAATTTTTCATTAAT
1 ATTTAAAAATTTTCATTAAT
* *
165987 ATTTTAAAATTTT-ATTTAT
1 ATTTAAAAATTTTCATTAAT
166006 ATTTAAATAATTTT
1 ATTTAAA-AATTTT
166020 TAACATCGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 11 0.39
20 17 0.61
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (20 bp):
ATTTAAAAATTTTCATTAAT
Found at i:166091 original size:96 final size:97
Alignment explanation
Indices: 165987--166169 Score: 232
Period size: 96 Copynumber: 1.9 Consensus size: 97
165977 TTTCATTAAT
165987 ATTTTAAAATTTTATT-T-ATATTTAAATAATTTTTAACATCGTT-ATTA-TTT-TTATTATAAT
1 ATTTTAAAATTTT-TTATAATATTTAAAT--TTTTTAACATCGTTAATTATTTTATTATTATAAT
166047 TTTAAAAAATATAAATATTAAATTTAATAATTAAAA
63 TTTAAAAAA-ATAAATATTAAATTTAATAATTAAAA
* *
166083 ATTTTAAAATTTTTTATCAATATTTAAATTTTTTAATATTGTTAATTATTTTTTAATTATTATAA
1 ATTTTAAAATTTTTTAT-AATATTTAAATTTTTTAACATCGTTAATTA--TTTT-ATTATTATAA
*
166148 TTTTTAAAAAATAAATATTAAA
62 TTTTAAAAAAATAAATATTAAA
166170 ATATTAAGTT
Statistics
Matches: 75, Mismatches: 3, Indels: 13
0.82 0.03 0.14
Matches are distributed among these distances:
95 2 0.03
96 26 0.35
97 4 0.05
98 10 0.13
100 3 0.04
101 12 0.16
102 18 0.24
ACGTcount: A:0.44, C:0.02, G:0.01, T:0.53
Consensus pattern (97 bp):
ATTTTAAAATTTTTTATAATATTTAAATTTTTTAACATCGTTAATTATTTTATTATTATAATTTT
AAAAAAATAAATATTAAATTTAATAATTAAAA
Found at i:166148 original size:20 final size:20
Alignment explanation
Indices: 166110--166149 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
166100 CAATATTTAA
*
166110 ATTTTTTAATATTGTTAATT
1 ATTTTTTAATATTGATAATT
166130 ATTTTTTAATTATT-ATAATT
1 ATTTTTTAA-TATTGATAATT
166150 TTTAAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (20 bp):
ATTTTTTAATATTGATAATT
Found at i:169602 original size:29 final size:29
Alignment explanation
Indices: 169570--169664 Score: 68
Period size: 29 Copynumber: 3.2 Consensus size: 29
169560 TTTACGCATA
169570 AAAATTATAATAATAATAATTAATATTTT
1 AAAATTATAATAATAATAATTAATATTTT
** * * *
169599 AAAAAGATATTGATAAAAATTTAAT-TTTGT
1 AAAATTATAATAATAATAA-TTAATATTT-T
* * *
169629 AAAA-TAAAAAAATAATAATTATCATAATTT
1 AAAATTATAATAATAATAATTA--ATATTTT
169659 AAAATT
1 AAAATT
169665 TAAATTTATT
Statistics
Matches: 48, Mismatches: 12, Indels: 10
0.69 0.17 0.14
Matches are distributed among these distances:
28 3 0.06
29 25 0.52
30 17 0.35
31 3 0.06
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (29 bp):
AAAATTATAATAATAATAATTAATATTTT
Found at i:170502 original size:18 final size:18
Alignment explanation
Indices: 170476--170510 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
170466 TATATATCCT
*
170476 GTGATAAAATATGATAAC
1 GTGACAAAATATGATAAC
170494 GTGACAAAATATGATAA
1 GTGACAAAATATGATAA
170511 TGGAGACACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.51, C:0.06, G:0.17, T:0.26
Consensus pattern (18 bp):
GTGACAAAATATGATAAC
Found at i:176556 original size:26 final size:27
Alignment explanation
Indices: 176541--176676 Score: 75
Period size: 30 Copynumber: 4.7 Consensus size: 27
176531 TATTTAGTGT
176541 AATATA-AAATATATAAATTTAATATA
1 AATATATAAATATATAAATTTAATATA
*
176567 AATATATAAATATTTTAAAATTTAA-ATA
1 AATATATAAATA-TAT-AAATTTAATATA
* ** *
176595 ACATAAATTATTAATATATAAAAATAATTTA
1 A-AT--A-TATAAATATATAAATTTAATATA
176626 AATATAATAATAATATGATAAAATTT-ATA-A
1 AATAT-AT-A-AATAT-AT-AAATTTAATATA
176656 ATATAATATAAATATA-AAATT
1 A-AT-ATATAAATATATAAATT
176677 ATTAAATCTG
Statistics
Matches: 85, Mismatches: 10, Indels: 30
0.68 0.08 0.24
Matches are distributed among these distances:
26 11 0.13
27 6 0.07
28 10 0.12
29 15 0.18
30 16 0.19
31 14 0.16
32 13 0.15
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.39
Consensus pattern (27 bp):
AATATATAAATATATAAATTTAATATA
Found at i:176573 original size:8 final size:8
Alignment explanation
Indices: 176541--176616 Score: 50
Period size: 8 Copynumber: 9.2 Consensus size: 8
176531 TATTTAGTGT
176541 AATATA-A
1 AATATATA
176548 AATATATA
1 AATATATA
176556 AATTTAATATA
1 AA--T-ATATA
176567 AATATATA
1 AATATATA
*
176575 AATATTTTA
1 AATA-TATA
*
176584 AA-ATTTA
1 AATATATA
*
176591 AATAACATA
1 AAT-ATATA
*
176600 AAT-TATT
1 AATATATA
176607 AATATATA
1 AATATATA
176615 AA
1 AA
176617 AATAATTTAA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
7 17 0.31
8 18 0.33
9 12 0.22
10 1 0.02
11 7 0.13
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.39
Consensus pattern (8 bp):
AATATATA
Found at i:176585 original size:28 final size:26
Alignment explanation
Indices: 176541--176595 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 26
176531 TATTTAGTGT
176541 AATATAAAATATAT-AAATTTAATATA
1 AATATAAAATATATAAAATTTAA-ATA
*
176567 AATATATAAATATTTTAAAATTTAAATA
1 AATATA-AAATA-TATAAAATTTAAATA
176595 A
1 A
176596 CATAAATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
26 6 0.24
27 5 0.20
28 6 0.24
29 8 0.32
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (26 bp):
AATATAAAATATATAAAATTTAAATA
Found at i:176619 original size:17 final size:17
Alignment explanation
Indices: 176605--176639 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
176595 ACATAAATTA
176605 TTAATATATAAAAATAAT
1 TTAA-ATATAAAAATAAT
*
176623 TTAAATATAATAATAAT
1 TTAAATATAAAAATAAT
176640 ATGATAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TTAAATATAAAAATAAT
Found at i:176663 original size:29 final size:26
Alignment explanation
Indices: 176624--176676 Score: 79
Period size: 29 Copynumber: 1.9 Consensus size: 26
176614 AAAAATAATT
176624 TAAATATAATAATAATATGATAAAATTTA
1 TAAATATAAT-ATAA-AT-ATAAAATTTA
176653 TAAATATAATATAAATATAAAATT
1 TAAATATAATATAAATATAAAATT
176677 ATTAAATCTG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 8 0.33
27 2 0.08
28 4 0.17
29 10 0.42
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (26 bp):
TAAATATAATATAAATATAAAATTTA
Found at i:176666 original size:20 final size:20
Alignment explanation
Indices: 176540--176675 Score: 76
Period size: 19 Copynumber: 7.0 Consensus size: 20
176530 ATATTTAGTG
*
176540 TAATATAAAATATATAAATT
1 TAATATAAAATATATAAATA
176560 TAATAT-AAATATATAAATA
1 TAATATAAAATATATAAATA
* *
176579 T--TTTAAAATTTAAATAACATA
1 TAATATAAAA--TATATAA-ATA
* *
176600 -AAT-TATTAATATATAAAAA
1 TAATATA-AAATATATAAATA
*
176619 TAAT-TTAAATATA-ATAATA
1 TAATATAAAATATATA-AATA
*
176638 -ATATGATAAAATTTATAAATA
1 TA-AT-ATAAAATATATAAATA
176659 TAATAT-AAATATA-AAAT
1 TAATATAAAATATATAAAT
176676 TATTAAATCT
Statistics
Matches: 90, Mismatches: 12, Indels: 30
0.68 0.09 0.23
Matches are distributed among these distances:
17 2 0.02
18 9 0.10
19 32 0.36
20 24 0.27
21 18 0.20
22 5 0.06
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.39
Consensus pattern (20 bp):
TAATATAAAATATATAAATA
Found at i:176670 original size:59 final size:58
Alignment explanation
Indices: 176540--176671 Score: 135
Period size: 59 Copynumber: 2.2 Consensus size: 58
176530 ATATTTAGTG
** **
176540 TAATATAAAATATATAAATTTAATATAAATATATAAATATTTTAAAATTTAAATAACATA
1 TAATAT-AAATATATAAAAATAATATAAATATATAAATATGATAAAATTT-AATAACATA
* *
176600 -AATTATTAATATATAAAAATAATTTAAATATAATAATAATATGATAAAATTT-ATAA-ATA
1 TAA-TATAAATATATAAAAATAATATAAATAT-AT-A-AATATGATAAAATTTAATAACATA
176659 TAATATAAATATA
1 TAATATAAATATA
176672 AAATTATTAA
Statistics
Matches: 60, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
59 35 0.58
60 11 0.18
61 1 0.02
62 13 0.22
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (58 bp):
TAATATAAATATATAAAAATAATATAAATATATAAATATGATAAAATTTAATAACATA
Found at i:176682 original size:26 final size:28
Alignment explanation
Indices: 176622--176683 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 28
176612 ATAAAAATAA
176622 TTTAAATATAATAATAATATGATAAAAT
1 TTTAAATATAATAATAATATGATAAAAT
176650 TTATAAATATAAT-ATAA-AT-ATAAAAT
1 TT-TAAATATAATAATAATATGATAAAAT
176676 TATTAAAT
1 T-TTAAAT
176684 CTGAAAGATT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
26 13 0.41
27 3 0.09
28 6 0.19
29 10 0.31
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (28 bp):
TTTAAATATAATAATAATATGATAAAAT
Found at i:177835 original size:29 final size:29
Alignment explanation
Indices: 177771--177859 Score: 142
Period size: 29 Copynumber: 3.0 Consensus size: 29
177761 ATTCAATTAT
*
177771 ATTAAAAATTTATTTAAGTATAAATTAAA
1 ATTAAAAATTTATTTAAATATAAATTAAA
*
177800 ATTTAAAAATATATTTAAATATAAATTAAA
1 A-TTAAAAATTTATTTAAATATAAATTAAA
*
177830 ATTAAAAATTTATTTAAATGTAAATTAAA
1 ATTAAAAATTTATTTAAATATAAATTAAA
177859 A
1 A
177860 ATTATTTATT
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
29 28 0.51
30 27 0.49
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (29 bp):
ATTAAAAATTTATTTAAATATAAATTAAA
Found at i:177871 original size:30 final size:30
Alignment explanation
Indices: 177771--177863 Score: 143
Period size: 30 Copynumber: 3.1 Consensus size: 30
177761 ATTCAATTAT
*
177771 ATTAAAAATTTATTTAAGTATAAATTAAAA
1 ATTAAAAATTTATTTAAATATAAATTAAAA
* *
177801 TTTAAAAATATATTTAAATATAAATT-AAA
1 ATTAAAAATTTATTTAAATATAAATTAAAA
*
177830 ATTAAAAATTTATTTAAATGTAAATTAAAA
1 ATTAAAAATTTATTTAAATATAAATTAAAA
177860 ATTA
1 ATTA
177864 TTTATTTAGA
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
29 26 0.46
30 30 0.54
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (30 bp):
ATTAAAAATTTATTTAAATATAAATTAAAA
Found at i:178531 original size:20 final size:20
Alignment explanation
Indices: 178494--178543 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
178484 TTGAATTTAA
*
178494 TTTA-TTTAA-AAAATTA-T
1 TTTATTTTAATAATATTATT
178511 TTTATTTTTAATAATATTATT
1 TTTA-TTTTAATAATATTATT
178532 TTTATTTTAATA
1 TTTATTTTAATA
178544 TTTATATATT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 4 0.14
19 5 0.18
20 14 0.50
21 5 0.18
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTATTTTAATAATATTATT
Found at i:178601 original size:21 final size:22
Alignment explanation
Indices: 178577--178626 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
178567 TTATATAAAA
178577 TAATTTTAATTATTA-AATAA-T
1 TAATTTTAATT-TTATAATAATT
* *
178598 TAATTATAATTTTATTATAATT
1 TAATTTTAATTTTATAATAATT
178620 TAATTTT
1 TAATTTT
178627 TATGTGCAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 3 0.12
21 14 0.58
22 7 0.29
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
TAATTTTAATTTTATAATAATT
Found at i:183920 original size:31 final size:30
Alignment explanation
Indices: 183830--183920 Score: 78
Period size: 31 Copynumber: 3.0 Consensus size: 30
183820 TAAAAGTAAA
* *
183830 AATT-AATATTTTTAATTTAATATTAATAAT
1 AATTAAATATTTTTAA-TTATTTTTAATAAT
* ***
183860 ATATTAAAT-GTAAAAATTATTTTTAAATAAT
1 A-ATTAAATATTTTTAATTATTTTT-AATAAT
183891 AATTAAATATTTTTAATCTATTTTTAATAA
1 AATTAAATATTTTTAAT-TATTTTTAATAA
183921 ACATGGTTAA
Statistics
Matches: 46, Mismatches: 10, Indels: 9
0.71 0.15 0.14
Matches are distributed among these distances:
30 14 0.30
31 22 0.48
32 10 0.22
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (30 bp):
AATTAAATATTTTTAATTATTTTTAATAAT
Found at i:184485 original size:27 final size:26
Alignment explanation
Indices: 184449--184548 Score: 86
Period size: 20 Copynumber: 4.0 Consensus size: 26
184439 AATTATTTTT
184449 ACTTAAATAAATTAATTTTTATATAAA
1 ACTTAAAT-AATTAATTTTTATATAAA
*
184476 ACTTTAATAATTAA---TT-T-TAAA
1 ACTTAAATAATTAATTTTTATATAAA
*
184497 A-TTAAATAATTAAATTTTATATAAA
1 ACTTAAATAATTAATTTTTATATAAA
* * *
184522 CCTTAATTAAATTAAATTTTTTTATAA
1 ACTTAAAT-AATT-AATTTTTATATAA
184549 TTTAAGTTAG
Statistics
Matches: 59, Mismatches: 6, Indels: 15
0.74 0.08 0.19
Matches are distributed among these distances:
20 11 0.19
21 5 0.08
22 1 0.02
23 4 0.07
24 1 0.02
25 4 0.07
26 11 0.19
27 11 0.19
28 11 0.19
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (26 bp):
ACTTAAATAATTAATTTTTATATAAA
Done.