Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold105
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: 2918491
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.33
Warning! 41655 characters in sequence are not A, C, G, or T
File 10 of 16
Found at i:1542285 original size:29 final size:29
Alignment explanation
Indices: 1542252--1542365 Score: 108
Period size: 29 Copynumber: 3.9 Consensus size: 29
1542242 ATATGAAATT
1542252 TATTTAGATATAAATTAAAAATTAAGTTA
1 TATTTAGATATAAATTAAAAATTAAGTTA
* *
1542281 TATTT-GAATATAAATTAAAAAGTAAAATTTA
1 TATTTAG-ATATAAATTAAAAA-T-TAAGTTA
* *
1542312 TTTATTTAGATAT-AATTAAAGATTAAGATA
1 --TATTTAGATATAAATTAAAAATTAAGTTA
* *
1542342 TACTTA-ATATAAATTAAAAGTTAA
1 TATTTAGATATAAATTAAAAATTAA
1542366 AACTTGTGTG
Statistics
Matches: 69, Mismatches: 9, Indels: 15
0.74 0.10 0.16
Matches are distributed among these distances:
27 4 0.06
28 17 0.25
29 19 0.28
30 5 0.07
31 6 0.09
32 8 0.12
33 9 0.13
34 1 0.01
ACGTcount: A:0.52, C:0.01, G:0.07, T:0.40
Consensus pattern (29 bp):
TATTTAGATATAAATTAAAAATTAAGTTA
Found at i:1555544 original size:12 final size:13
Alignment explanation
Indices: 1555523--1555551 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1555513 TTTGTTTTTA
1555523 TTTTATTTTATTT
1 TTTTATTTTATTT
1555536 TTTTA-TTTATTT
1 TTTTATTTTATTT
1555548 TTTT
1 TTTT
1555552 CTTTGAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTTATTTTATTT
Found at i:1557017 original size:3 final size:3
Alignment explanation
Indices: 1557009--1557044 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
1556999 TGATTCAGCC
*
1557009 TTA TTA TTA TTG TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1557045 GGGTTAAAGT
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:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1558526 original size:3 final size:3
Alignment explanation
Indices: 1558518--1558543 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1558508 ACTCTTTCAC
1558518 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
1558544 CTCCTTGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:1559069 original size:41 final size:38
Alignment explanation
Indices: 1559014--1559094 Score: 99
Period size: 41 Copynumber: 2.1 Consensus size: 38
1559004 ATTTTGGTAT
*
1559014 AAATATATGAATATAATATTTATAAAATTATTAAAATATA
1 AAATATATAAATATAATATTTA-AAAATTA-TAAAATATA
* * *
1559054 AAATAATATAAATATATTATTTAAAATTTATATAATATA
1 AAAT-ATATAAATATAATATTTAAAAATTATAAAATATA
1559093 AA
1 AA
1559095 TTATTAATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
39 10 0.28
40 10 0.28
41 16 0.44
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (38 bp):
AAATATATAAATATAATATTTAAAAATTATAAAATATA
Found at i:1559079 original size:39 final size:40
Alignment explanation
Indices: 1559014--1559094 Score: 96
Period size: 39 Copynumber: 2.0 Consensus size: 40
1559004 ATTTTGGTAT
*
1559014 AAATATATGAATATAATATTTATAAAA-TTATTAAAATATA
1 AAATATATAAATATAATATTTATAAAATTTA-TAAAATATA
* *
1559054 AAATAATATAAATATATTA-TT-TAAAATTTATATAATATA
1 AAAT-ATATAAATATAATATTTATAAAATTTATAAAATATA
1559093 AA
1 AA
1559095 TTATTAATAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
39 15 0.42
40 9 0.25
41 12 0.33
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (40 bp):
AAATATATAAATATAATATTTATAAAATTTATAAAATATA
Found at i:1559106 original size:25 final size:24
Alignment explanation
Indices: 1559059--1559112 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 24
1559049 ATATAAAATA
*
1559059 ATATAAATATATTATTTAAAATTT
1 ATATAAATAAATTATTTAAAATTT
1559083 ATATAATATAAATTA-TTAATAATTT
1 ATATAA-ATAAATTATTTAA-AATTT
1559108 ATATA
1 ATATA
1559113 TATTGTTATA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 10 0.37
25 17 0.63
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
ATATAAATAAATTATTTAAAATTT
Found at i:1559161 original size:19 final size:19
Alignment explanation
Indices: 1559134--1559195 Score: 69
Period size: 18 Copynumber: 3.4 Consensus size: 19
1559124 ATATTTGTAT
*
1559134 TAATCATAAAAATTTAAATA
1 TAAT-ATAAAATTTTAAATA
1559154 TAATAT-AAATTATTAAATA
1 TAATATAAAATT-TTAAATA
1559173 T-AT-TAAAATTTTAAA-A
1 TAATATAAAATTTTAAATA
1559189 TAATATA
1 TAATATA
1559196 TAAGATAAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
16 2 0.05
17 8 0.22
18 13 0.35
19 10 0.27
20 4 0.11
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (19 bp):
TAATATAAAATTTTAAATA
Found at i:1559186 original size:17 final size:17
Alignment explanation
Indices: 1559139--1559193 Score: 67
Period size: 19 Copynumber: 3.2 Consensus size: 17
1559129 TGTATTAATC
*
1559139 ATAAAAATTTAAATATA
1 ATAAAATTTTAAATATA
1559156 ATATAAATTATTAAATATA
1 ATA-AAATT-TTAAATATA
*
1559175 TTAAAATTTTAAA-ATA
1 ATAAAATTTTAAATATA
1559191 ATA
1 ATA
1559194 TATAAGATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
16 5 0.15
17 8 0.24
18 9 0.27
19 11 0.33
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
ATAAAATTTTAAATATA
Found at i:1559238 original size:3 final size:3
Alignment explanation
Indices: 1559230--1559275 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
1559220 CTAAACAAAG
1559230 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1559276 AAAGGAGATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1559549 original size:2 final size:2
Alignment explanation
Indices: 1559542--1559567 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1559532 TATGAGATTA
1559542 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
1559568 TAAAAAAAGC
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:1561074 original size:18 final size:19
Alignment explanation
Indices: 1561031--1561076 Score: 51
Period size: 18 Copynumber: 2.4 Consensus size: 19
1561021 AATTAAGATG
*
1561031 ATATTAAATAATAAATTTT
1 ATATTAAATAATAAATTAT
1561050 ATAATTAAA-AA-AAATTAAT
1 AT-ATTAAATAATAAATT-AT
1561069 ATATTAAA
1 ATATTAAA
1561077 CGTAAAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
18 11 0.46
19 7 0.29
20 6 0.25
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
ATATTAAATAATAAATTAT
Found at i:1561923 original size:14 final size:14
Alignment explanation
Indices: 1561901--1562009 Score: 66
Period size: 14 Copynumber: 7.6 Consensus size: 14
1561891 CTCGAGCTTA
*
1561901 AAATATAAATAATT
1 AAATTTAAATAATT
1561915 AAATTT-AA-AATT
1 AAATTTAAATAATT
* *
1561927 AAATATAAAAAATT
1 AAATTTAAATAATT
1561941 AAATTT--ATAATT
1 AAATTTAAATAATT
1561953 AAATTAATAAATTTAATT
1 AAATT--TAAA--TAATT
* * *
1561971 AAATCT-ACTCAAAT
1 AAATTTAAAT-AATT
1561985 AAATTTAAATAATTT
1 AAATTTAAATAA-TT
1562000 AAAATTTAAA
1 -AAATTTAAA
1562010 GTAAAATTTG
Statistics
Matches: 73, Mismatches: 10, Indels: 22
0.70 0.10 0.21
Matches are distributed among these distances:
12 19 0.26
13 5 0.07
14 25 0.34
15 4 0.05
16 11 0.15
18 9 0.12
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.39
Consensus pattern (14 bp):
AAATTTAAATAATT
Found at i:1561931 original size:26 final size:26
Alignment explanation
Indices: 1561901--1562009 Score: 94
Period size: 26 Copynumber: 3.9 Consensus size: 26
1561891 CTCGAGCTTA
1561901 AAATATAAATAATTAAATTTAAAATT
1 AAATATAAATAATTAAATTTAAAATT
* *
1561927 AAATATAAAAAATTAAATTTATAATT
1 AAATATAAATAATTAAATTTAAAATT
*
1561953 AAATTAATAAATTTAATTAAATCTACTCAAA-T
1 AAA-T-ATAAA--TAATTAAAT-T--TAAAATT
*
1561985 AAATTTAAATAATTTAAAATTTAAA
1 AAATATAAATAA-TT-AAATTTAAA
1562010 GTAAAATTTG
Statistics
Matches: 67, Mismatches: 7, Indels: 17
0.74 0.08 0.19
Matches are distributed among these distances:
26 27 0.40
27 4 0.06
28 8 0.12
29 3 0.04
30 16 0.24
31 2 0.03
32 4 0.06
33 3 0.04
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.39
Consensus pattern (26 bp):
AAATATAAATAATTAAATTTAAAATT
Found at i:1561939 original size:21 final size:21
Alignment explanation
Indices: 1561898--1561940 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
1561888 TTACTCGAGC
**
1561898 TTAAAATATAAATAATTAAAT
1 TTAAAATATAAATAAAAAAAT
1561919 TTAAAAT-TAAATATAAAAAAT
1 TTAAAATATAAATA-AAAAAAT
1561940 T
1 T
1561941 AAATTTATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
TTAAAATATAAATAAAAAAAT
Found at i:1561962 original size:12 final size:12
Alignment explanation
Indices: 1561908--1561972 Score: 60
Period size: 12 Copynumber: 5.2 Consensus size: 12
1561898 TTAAAATATA
1561908 AATAATTAAATTT
1 AATAATTAAA-TT
1561921 AA-AATTAAATAT
1 AATAATTAAAT-T
*
1561933 AAAAAATTAAATT
1 -AATAATTAAATT
*
1561946 TATAATTAAATT
1 AATAATTAAATT
*
1561958 AATAAATTTAATT
1 AAT-AATTAAATT
1561971 AA
1 AA
1561973 ATCTACTCAA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
11 1 0.02
12 20 0.45
13 15 0.34
14 8 0.18
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
AATAATTAAATT
Found at i:1562036 original size:7 final size:7
Alignment explanation
Indices: 1562021--1562068 Score: 53
Period size: 7 Copynumber: 7.0 Consensus size: 7
1562011 TAAAATTTGA
1562021 TTAAATT
1 TTAAATT
*
1562028 TTAATTT
1 TTAAATT
*
1562035 TTAAATA
1 TTAAATT
1562042 TT-AATT
1 TTAAATT
*
1562048 TTAATTT
1 TTAAATT
*
1562055 TTAAATA
1 TTAAATT
1562062 TTAAATT
1 TTAAATT
1562069 AAACTCAAAT
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
6 5 0.16
7 27 0.84
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (7 bp):
TTAAATT
Found at i:1562049 original size:20 final size:20
Alignment explanation
Indices: 1562024--1562065 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
1562014 AATTTGATTA
1562024 AATTTTAATTTTTAAATATT
1 AATTTTAATTTTTAAATATT
1562044 AATTTTAATTTTTAAATATT
1 AATTTTAATTTTTAAATATT
1562064 AA
1 AA
1562066 ATTAAACTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
AATTTTAATTTTTAAATATT
Found at i:1562681 original size:6 final size:6
Alignment explanation
Indices: 1562672--1562700 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
1562662 TTTTTTTTTT
1562672 TTTTCC TTTTCC TTTTCC TTTTCC TTTTC
1 TTTTCC TTTTCC TTTTCC TTTTCC TTTTC
1562701 AGTGGGTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTTCC
Found at i:1576582 original size:20 final size:20
Alignment explanation
Indices: 1576556--1576611 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
1576546 TAGGGTACTC
*
1576556 AATTTTAAAATTTAATATTA
1 AATTTTAAAATTTAATAATA
* * *
1576576 TATTTTAAAAATAAATAATA
1 AATTTTAAAATTTAATAATA
1576596 AATTTTAAAAGTTTAA
1 AATTTTAAAA-TTTAA
1576612 ATTTTTCATT
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
20 25 0.89
21 3 0.11
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.45
Consensus pattern (20 bp):
AATTTTAAAATTTAATAATA
Found at i:1576750 original size:18 final size:18
Alignment explanation
Indices: 1576682--1576750 Score: 65
Period size: 18 Copynumber: 3.9 Consensus size: 18
1576672 TATTTAAGTT
*
1576682 ATTTT-ATATTTATATAA
1 ATTTTAATATATATATAA
1576699 ATTTTAATATAT-TA-ATA
1 ATTTTAATATATATATA-A
*
1576716 ATATTTCATAT-TATATAA
1 AT-TTTAATATATATATAA
*
1576734 ATTTTAAAATATATATA
1 ATTTTAATATATATATA
1576751 TGAAATTAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
16 1 0.02
17 17 0.40
18 23 0.55
19 1 0.02
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.52
Consensus pattern (18 bp):
ATTTTAATATATATATAA
Found at i:1576792 original size:43 final size:42
Alignment explanation
Indices: 1576680--1576802 Score: 99
Period size: 43 Copynumber: 2.8 Consensus size: 42
1576670 CGTATTTAAG
* *
1576680 TTATTTTATATTTATATAAATTTTAATATATTAATAATATTTCATA
1 TTATATTATATTTATAT-AA--TT-ATATATAAATAATATTTCATA
* * *
1576726 TTATA-TAAATTT-TAAAATATATATATGAAATTAATATTTTAT-
1 TTATATTATATTTATATAAT-TATATAT-AAA-TAATATTTCATA
*
1576768 TTATATTATATTTATATAATTATATTTAAAATAAT
1 TTATATTATATTTATATAATTATATAT-AAATAAT
1576803 CATATTTAAT
Statistics
Matches: 63, Mismatches: 9, Indels: 14
0.73 0.10 0.16
Matches are distributed among these distances:
41 7 0.11
42 12 0.19
43 27 0.43
44 7 0.11
45 6 0.10
46 4 0.06
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.54
Consensus pattern (42 bp):
TTATATTATATTTATATAATTATATATAAATAATATTTCATA
Found at i:1576801 original size:15 final size:15
Alignment explanation
Indices: 1576772--1576811 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
1576762 TTTTATTTAT
*
1576772 ATTATATTT-ATATA
1 ATTATATTTAAAATA
1576786 ATTATATTTAAAATA
1 ATTATATTTAAAATA
*
1576801 ATCATATTTAA
1 ATTATATTTAA
1576812 TTTTATTACT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 9 0.39
15 14 0.61
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTATATTTAAAATA
Found at i:1577723 original size:17 final size:19
Alignment explanation
Indices: 1577703--1577747 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
1577693 TAATTAAATT
1577703 ATAATATAATATAA-A-AA
1 ATAATATAATATAACATAA
1577720 ATAATATAAATATAACATAA
1 ATAATAT-AATATAACATAA
1577740 ATAA-ATAA
1 ATAATATAA
1577748 GAATGTCTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 7 0.28
18 9 0.36
19 3 0.12
20 6 0.24
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (19 bp):
ATAATATAATATAACATAA
Found at i:1577733 original size:28 final size:27
Alignment explanation
Indices: 1577688--1577744 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 27
1577678 ATACGATACG
*
1577688 AAAAATAATTAAATTATAATATAATATA
1 AAAAATAATTAAATTATAACATAA-ATA
1577716 AAAAATAATATAAA-TATAACATAAATA
1 AAAAATAAT-TAAATTATAACATAAATA
1577743 AA
1 AA
1577745 TAAGAATGTC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 5 0.19
28 18 0.67
29 4 0.15
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (27 bp):
AAAAATAATTAAATTATAACATAAATA
Found at i:1577739 original size:11 final size:11
Alignment explanation
Indices: 1577705--1577746 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
1577695 ATTAAATTAT
1577705 AATATAATATAA
1 AATATAATAT-A
*
1577717 AAAATAATATA
1 AATATAATATA
*
1577728 AATATAACATA
1 AATATAATATA
1577739 AATA-AATA
1 AATATAATA
1577747 AGAATGTCTC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
10 3 0.12
11 14 0.54
12 9 0.35
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (11 bp):
AATATAATATA
Found at i:1577924 original size:13 final size:13
Alignment explanation
Indices: 1577906--1577934 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1577896 AAATTTGTTC
1577906 AATTATGTAATTT
1 AATTATGTAATTT
1577919 AATTATGTAATTT
1 AATTATGTAATTT
1577932 AAT
1 AAT
1577935 GAATATAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (13 bp):
AATTATGTAATTT
Found at i:1578764 original size:18 final size:17
Alignment explanation
Indices: 1578723--1578768 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
1578713 TAAAATTTAT
1578723 TTTATTTTTTAATAAAA
1 TTTATTTTTTAATAAAA
* *
1578740 TTTATTTTTTACTCAAA
1 TTTATTTTTTAATAAAA
*
1578757 TTTAATTTTTAA
1 TTTATTTTTTAA
1578769 ATCTAATATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTATTTTTTAATAAAA
Found at i:1579169 original size:18 final size:19
Alignment explanation
Indices: 1579128--1579169 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1579118 TGATTTTTAA
**
1579128 AAAAATTATCATTTAATTT
1 AAAAATTATCATTTAAAAT
*
1579147 AAAAATTATTATTTAAAAT
1 AAAAATTATCATTTAAAAT
1579166 AAAA
1 AAAA
1579170 TAAAATAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (19 bp):
AAAAATTATCATTTAAAAT
Found at i:1579939 original size:27 final size:27
Alignment explanation
Indices: 1579883--1579963 Score: 80
Period size: 27 Copynumber: 3.1 Consensus size: 27
1579873 TGATACTTTT
*
1579883 TAAAATTATTATGTAATAATTAACTAA
1 TAAAATTATTATGTAATAATTAAATAA
*
1579910 TAAAATTATTTAT-TATTATATTAAAT-A
1 TAAAATTA-TTATGTAATA-ATTAAATAA
* *
1579937 TAAAATTAAT-TGTTATAA-TAAATAA
1 TAAAATTATTATGTAATAATTAAATAA
1579962 TA
1 TA
1579964 TATTAATTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
24 5 0.11
25 5 0.11
26 4 0.09
27 21 0.47
28 10 0.22
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.44
Consensus pattern (27 bp):
TAAAATTATTATGTAATAATTAAATAA
Found at i:1580497 original size:20 final size:22
Alignment explanation
Indices: 1580472--1580513 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
1580462 TTATTATTTT
1580472 TATTTTATAAT-A-TAATAAAA
1 TATTTTATAATAATTAATAAAA
*
1580492 TATTTTATTATAATTAATAAAA
1 TATTTTATAATAATTAATAAAA
1580514 AACCTTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 10 0.53
21 1 0.05
22 8 0.42
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TATTTTATAATAATTAATAAAA
Found at i:1581361 original size:2 final size:2
Alignment explanation
Indices: 1581354--1581378 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1581344 AAATATGTTC
1581354 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
1581379 CATAGGGATC
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:1582063 original size:33 final size:33
Alignment explanation
Indices: 1582021--1582104 Score: 93
Period size: 33 Copynumber: 2.6 Consensus size: 33
1582011 AATAATTAAA
* *
1582021 ATATAATATAAATATATTTATAT-TTCATAATTT
1 ATATAATATAAATATATTTACATATT-AAAATTT
*
1582054 ATATAATATAAAT-TATTAACATATTAAAATTT
1 ATATAATATAAATATATTTACATATTAAAATTT
*
1582086 TTATAAATATAAA-ATATTT
1 ATAT-AATATAAATATATTT
1582105 TAAATACATT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
32 16 0.37
33 27 0.63
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (33 bp):
ATATAATATAAATATATTTACATATTAAAATTT
Found at i:1582110 original size:16 final size:17
Alignment explanation
Indices: 1582050--1582110 Score: 56
Period size: 17 Copynumber: 3.6 Consensus size: 17
1582040 ATATTTCATA
*
1582050 ATTTATATAATATAAATT
1 ATTTATA-AATATAAAAT
*
1582068 A-TTA-ACATATTAAAAT
1 ATTTATAAATA-TAAAAT
*
1582084 TTTTATAAATATAAAAT
1 ATTTATAAATATAAAAT
1582101 ATTT-TAAATA
1 ATTTATAAATA
1582111 CATTATAACA
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
15 3 0.09
16 12 0.34
17 15 0.43
18 5 0.14
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (17 bp):
ATTTATAAATATAAAAT
Found at i:1582158 original size:29 final size:28
Alignment explanation
Indices: 1582121--1582176 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
1582111 CATTATAACA
*
1582121 TAATAAAATATAT-AAATTTAATTTAAAT
1 TAATAAAAT-TATCAAATTTAAATTAAAT
1582149 TAATATAAATTATCAAATTTAAATTAAA
1 TAATA-AAATTATCAAATTTAAATTAAA
1582177 GTATTTAGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 8 0.32
29 17 0.68
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (28 bp):
TAATAAAATTATCAAATTTAAATTAAAT
Found at i:1582597 original size:2 final size:2
Alignment explanation
Indices: 1582590--1582617 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1582580 CACTCAATTT
1582590 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
1582618 AGTGTAATAT
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:1582678 original size:24 final size:25
Alignment explanation
Indices: 1582651--1582711 Score: 72
Period size: 24 Copynumber: 2.4 Consensus size: 25
1582641 GTTTTAATAA
*
1582651 ATTTATATTATTTATGTT-TGTTTT
1 ATTTATATTATTTATGTTATATTTT
*
1582675 ATTTA-ATTATTTTATTTTATATTTT
1 ATTTATATTA-TTTATGTTATATTTT
1582700 ATTTATAATTAT
1 ATTTAT-ATTAT
1582712 ATAAATTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
23 4 0.13
24 12 0.39
25 10 0.32
26 1 0.03
27 4 0.13
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (25 bp):
ATTTATATTATTTATGTTATATTTT
Found at i:1582699 original size:12 final size:13
Alignment explanation
Indices: 1582671--1582704 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
1582661 TTTATGTTTG
1582671 TTTTATTTAATTA
1 TTTTATTTAATTA
*
1582684 TTTTATTTTA-TA
1 TTTTATTTAATTA
1582696 TTTTATTTA
1 TTTTATTTA
1582705 TAATTATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTTATTTAATTA
Found at i:1584842 original size:20 final size:20
Alignment explanation
Indices: 1584808--1584845 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1584798 TTATTTAATT
1584808 TAATAAATTTAAAATTATAA
1 TAATAAATTTAAAATTATAA
1584828 TAATATAATTT-AAATTAT
1 TAATA-AATTTAAAATTAT
1584846 TATTTAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TAATAAATTTAAAATTATAA
Found at i:1584855 original size:20 final size:20
Alignment explanation
Indices: 1584805--1584855 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 20
1584795 TATTTATTTA
1584805 ATTTAATAAATTTAAAATTAT
1 ATTTAAT-AATTTAAAATTAT
* *
1584826 AATAATATAATTT-AAATTATT
1 ATTTA-ATAATTTAAAATTA-T
1584847 ATTTAATAA
1 ATTTAATAA
1584856 ATAAAATATA
Statistics
Matches: 24, Mismatches: 4, Indels: 5
0.73 0.12 0.15
Matches are distributed among these distances:
20 10 0.42
21 12 0.50
22 2 0.08
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
ATTTAATAATTTAAAATTAT
Found at i:1585061 original size:3 final size:3
Alignment explanation
Indices: 1585053--1585093 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
1585043 CAATGAATAG
1585053 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1585094 CATTGCTTTT
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1590261 original size:2 final size:2
Alignment explanation
Indices: 1590254--1590286 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1590244 TTCACACCAT
1590254 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 T
1590287 TTACTAGTAC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1592311 original size:27 final size:26
Alignment explanation
Indices: 1592281--1592377 Score: 99
Period size: 27 Copynumber: 3.5 Consensus size: 26
1592271 TGTAGCTTTC
1592281 ATTATATTTAATAATTTATGTATTTAT
1 ATTATATTTAATAATTTAT-TATTTAT
*
1592308 ATTATATTTATATATTTTATTATATTAT
1 ATTATATTTA-ATAATTTATTAT-TTAT
*
1592336 AATTATATTTAA-AATATTTTATATTTAT
1 -ATTATATTTAATAAT-TTAT-TATTTAT
1592364 ATTA-ATTTTAATAA
1 ATTATA-TTTAATAA
1592378 AATAATAATT
Statistics
Matches: 60, Mismatches: 3, Indels: 13
0.79 0.04 0.17
Matches are distributed among these distances:
26 1 0.02
27 24 0.40
28 22 0.37
29 13 0.22
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (26 bp):
ATTATATTTAATAATTTATTATTTAT
Found at i:1592314 original size:5 final size:5
Alignment explanation
Indices: 1592304--1592481 Score: 83
Period size: 5 Copynumber: 36.6 Consensus size: 5
1592294 ATTTATGTAT
* * * *
1592304 TTATA TTATA TT-TA -TATA TTTTA TTATA TTATAA TTATA TTTAAA ATATT
1 TTATA TTATA TTATA TTATA TTATA TTATA TTAT-A TTATA -TTATA TTATA
* * * * *
1592354 TTATA TTTATA TTA-A TTTTAA TAAAA TAATAA TTAATA ATATA TTA-A
1 TTATA -TTATA TTATA TTAT-A TTATA TTAT-A TT-ATA TTATA TTATA
* **
1592401 TTTTA AAATA -TATA TTATA TTATA TTATA TTATA TTATA TT-T- TTATAA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTAT-A
* *
1592449 TTTTA -TATA TT-TT TTAT- TTATA -TA-A TTATA TTA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTA
1592482 AATATTATTA
Statistics
Matches: 130, Mismatches: 24, Indels: 38
0.68 0.12 0.20
Matches are distributed among these distances:
3 4 0.03
4 29 0.22
5 72 0.55
6 23 0.18
7 2 0.02
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
TTATA
Found at i:1592723 original size:16 final size:15
Alignment explanation
Indices: 1592698--1592731 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
1592688 ATATTATTTT
1592698 ATATTTTAAATATTA
1 ATATTTTAAATATTA
*
1592713 ATATTTATAAATTTTA
1 ATATTT-TAAATATTA
1592729 ATA
1 ATA
1592732 ATTAATAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
ATATTTTAAATATTA
Found at i:1592735 original size:23 final size:22
Alignment explanation
Indices: 1592692--1592743 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 22
1592682 TATTATATAT
*
1592692 TATTTTATATTTTAAATATTAA
1 TATTTTAAATTTTAAATATTAA
1592714 TATTTATAAATTTT-AATAATTAA
1 TATTT-TAAATTTTAAAT-ATTAA
1592737 TAATTTT
1 T-ATTTT
1592744 TATTATATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 8 0.31
23 14 0.54
24 4 0.15
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
TATTTTAAATTTTAAATATTAA
Found at i:1592757 original size:15 final size:16
Alignment explanation
Indices: 1592739--1592789 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 16
1592729 ATAATTAATA
1592739 ATTTTTATTATATTA-
1 ATTTTTATTATATTAT
1592754 A-TTTTA-TATATTTAT
1 ATTTTTATTATA-TTAT
*
1592769 ATATTTAATTATATTAT
1 AT-TTTTATTATATTAT
1592786 ATTT
1 ATTT
1592790 ATTTTTTTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 9
0.75 0.03 0.22
Matches are distributed among these distances:
13 4 0.13
14 8 0.27
15 2 0.07
16 2 0.07
17 10 0.33
18 4 0.13
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
ATTTTTATTATATTAT
Found at i:1592780 original size:31 final size:30
Alignment explanation
Indices: 1592687--1592789 Score: 88
Period size: 31 Copynumber: 3.4 Consensus size: 30
1592677 TCACTTATTA
1592687 TATATT-ATTTTATAT-TTTAA-ATATTAAT
1 TATATTAATTTTATATATTTAATAT-TTAAT
* * * *
1592715 ATTTATAAATTTTA-ATAATTAATAATTTTTAT
1 -TATATTAATTTTATATATTTAAT-A-TTTAAT
1592747 TATATTAATTTTATATATTTATATATTTAAT
1 TATATTAATTTTATATATTTA-ATATTTAAT
1592778 TATATTATATTT
1 TATATTA-ATTT
1592790 ATTTTTTTAT
Statistics
Matches: 58, Mismatches: 8, Indels: 13
0.73 0.10 0.16
Matches are distributed among these distances:
29 6 0.10
30 10 0.17
31 23 0.40
32 16 0.28
33 3 0.05
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (30 bp):
TATATTAATTTTATATATTTAATATTTAAT
Found at i:1596633 original size:2 final size:2
Alignment explanation
Indices: 1596628--1596662 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1596618 ATCTCATCTT
*
1596628 TC TC TC TC TT TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1596663 AATACACACT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (2 bp):
TC
Found at i:1606037 original size:2 final size:2
Alignment explanation
Indices: 1606030--1606082 Score: 92
Period size: 2 Copynumber: 27.5 Consensus size: 2
1606020 AAAAGTAAAG
1606030 GA GA GA GA GA GA GA GA G- GA GA G- 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
1606070 GA GA GA GA GA GA G
1 GA GA GA GA GA GA G
1606083 GAAGTAATGT
Statistics
Matches: 49, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.04
2 47 0.96
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1609437 original size:24 final size:24
Alignment explanation
Indices: 1609388--1609437 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
1609378 TGCAAACATG
* **
1609388 AATACTGCTTATTGTTTTTTTTAT
1 AATACTGCATATTGTTTTTTGAAT
1609412 AATA-TGCATATTGTATTTTTGAAT
1 AATACTGCATATTGT-TTTTTGAAT
1609436 AA
1 AA
1609438 GAACTTATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 9 0.41
24 13 0.59
ACGTcount: A:0.30, C:0.06, G:0.10, T:0.54
Consensus pattern (24 bp):
AATACTGCATATTGTTTTTTGAAT
Found at i:1609582 original size:2 final size:2
Alignment explanation
Indices: 1609575--1609613 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
1609565 CTGAATCCTA
* * *
1609575 AT AT AT AT AT AT AT AT AT AT AT AT GT AT TT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1609614 CTCTTTCCTC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1611443 original size:2 final size:2
Alignment explanation
Indices: 1611436--1611504 Score: 70
Period size: 2 Copynumber: 34.5 Consensus size: 2
1611426 GAAAATTTAT
* * * *
1611436 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG GA GTT TCA -A T- TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA T-A TA TA TA
1611478 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
1611505 TATTAGTGTA
Statistics
Matches: 56, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
1 2 0.04
2 54 0.96
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1612417 original size:2 final size:2
Alignment explanation
Indices: 1612412--1612438 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1612402 ATATATATAT
1612412 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1612439 TAAAAAAGTA
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1614975 original size:30 final size:30
Alignment explanation
Indices: 1614915--1614975 Score: 72
Period size: 29 Copynumber: 2.0 Consensus size: 30
1614905 TTGTAAAAAA
*
1614915 ATTAATATTAATAAAAATAATTTTATTTTT
1 ATTAATATTAATAAAAATAATTTTACTTTT
*
1614945 ATTAAT-TT-ATAAATAGTAATTTTAGCTTTT
1 ATTAATATTAATAAA-AATAATTTTA-CTTTT
1614975 A
1 A
1614976 AGTCAAGTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 5 0.19
29 11 0.41
30 11 0.41
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (30 bp):
ATTAATATTAATAAAAATAATTTTACTTTT
Found at i:1619457 original size:18 final size:17
Alignment explanation
Indices: 1619421--1619472 Score: 52
Period size: 18 Copynumber: 3.0 Consensus size: 17
1619411 CGGTTGAGTG
*
1619421 GAAAAAAATATTAAAAA
1 GAAAAAAATATAAAAAA
1619438 GATAAAAAAT-TAAAAGAA
1 GA-AAAAAATATAAAA-AA
* *
1619456 GAAAAAAGTGTAAAAAA
1 GAAAAAAATATAAAAAA
1619473 TAGAAAATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
17 14 0.47
18 16 0.53
ACGTcount: A:0.73, C:0.00, G:0.12, T:0.15
Consensus pattern (17 bp):
GAAAAAAATATAAAAAA
Found at i:1619810 original size:20 final size:20
Alignment explanation
Indices: 1619775--1619842 Score: 77
Period size: 21 Copynumber: 3.5 Consensus size: 20
1619765 ATTTAAAATT
*
1619775 CTTTTTT-TAT-TTTTTTCA
1 CTTTTTTATATATCTTTTCA
*
1619793 CTTTTTTATCTATCTTTTCA
1 CTTTTTTATATATCTTTTCA
* *
1619813 CTTTTTTTATATATCTTCTAA
1 C-TTTTTTATATATCTTTTCA
1619834 CTTTTTTAT
1 CTTTTTTAT
1619843 TTTCGTATAC
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
18 7 0.17
19 2 0.05
20 16 0.38
21 17 0.40
ACGTcount: A:0.16, C:0.15, G:0.00, T:0.69
Consensus pattern (20 bp):
CTTTTTTATATATCTTTTCA
Found at i:1623221 original size:26 final size:28
Alignment explanation
Indices: 1623157--1623239 Score: 83
Period size: 22 Copynumber: 3.2 Consensus size: 28
1623147 TAAAGTTTTA
* *
1623157 ATTTTTAAAATAAACTTT-TT-TAAATT
1 ATTTTTAAAATAAAATTTATTATAATTT
1623183 A-TTTT---ATAAAATTTA-TAT-ATTT
1 ATTTTTAAAATAAAATTTATTATAATTT
*
1623205 ATTTTTAAAATAAAATTTATTTTAATTT
1 ATTTTTAAAATAAAATTTATTATAATTT
1623233 ATTTTTA
1 ATTTTTA
1623240 TATTTAAAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 14
0.73 0.05 0.22
Matches are distributed among these distances:
22 13 0.28
23 5 0.11
25 4 0.09
26 11 0.24
27 2 0.04
28 11 0.24
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (28 bp):
ATTTTTAAAATAAAATTTATTATAATTT
Found at i:1626384 original size:18 final size:18
Alignment explanation
Indices: 1626361--1626398 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
1626351 TGTTTCTATG
1626361 AAAAAAAATT-ATATTATT
1 AAAAAAAATTAATA-TATT
1626379 AAAAAAAATTAATATATT
1 AAAAAAAATTAATATATT
1626397 AA
1 AA
1626399 TTACTCTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 16 0.84
19 3 0.16
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
AAAAAAAATTAATATATT
Found at i:1626980 original size:25 final size:26
Alignment explanation
Indices: 1626922--1626985 Score: 96
Period size: 25 Copynumber: 2.5 Consensus size: 26
1626912 TGAAAATACT
*
1626922 TAATATATAATATATATTTTTAAATA
1 TAATATATAATATATATTATTAAATA
*
1626948 T-TTATATAATATATATTATTAAATA
1 TAATATATAATATATATTATTAAATA
1626973 TAAT-TATAATATA
1 TAATATATAATATA
1626986 ATAAAATATA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
25 32 0.94
26 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (26 bp):
TAATATATAATATATATTATTAAATA
Found at i:1626984 original size:21 final size:19
Alignment explanation
Indices: 1626951--1626995 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 19
1626941 TTAAATATTT
* *
1626951 ATATAATATATATTATTAA
1 ATATAATATATATAATAAA
1626970 ATATAATTATAATATAATAAA
1 ATATAA-TAT-ATATAATAAA
1626991 ATATA
1 ATATA
1626996 TAAATATGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 6 0.27
20 3 0.14
21 13 0.59
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
ATATAATATATATAATAAA
Found at i:1627153 original size:2 final size:2
Alignment explanation
Indices: 1627146--1627182 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1627136 AGCAACAATT
1627146 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1627183 TAAGAAAGGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1627368 original size:18 final size:18
Alignment explanation
Indices: 1627341--1627396 Score: 67
Period size: 18 Copynumber: 3.1 Consensus size: 18
1627331 CGTTCATTGA
*
1627341 ATTTTAAAAAATTATTTT
1 ATTTTTAAAAATTATTTT
**
1627359 ATTTTTAAAAATTATTAA
1 ATTTTTAAAAATTATTTT
* *
1627377 AATATTAAAAATTATTTT
1 ATTTTTAAAAATTATTTT
1627395 AT
1 AT
1627397 ATAATATTTA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
ATTTTTAAAAATTATTTT
Found at i:1627450 original size:24 final size:24
Alignment explanation
Indices: 1627419--1627468 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1627409 ATTAAAATTT
* *
1627419 TAAAAATATTTTTATTAATT-AAA
1 TAAAAATAATTTAATTAATTCAAA
1627442 TAAATAATAATTTAATTAATTCAAA
1 TAAA-AATAATTTAATTAATTCAAA
1627467 TA
1 TA
1627469 TTTACATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 4 0.17
24 14 0.61
25 5 0.22
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (24 bp):
TAAAAATAATTTAATTAATTCAAA
Found at i:1627520 original size:25 final size:24
Alignment explanation
Indices: 1627486--1627566 Score: 78
Period size: 25 Copynumber: 3.3 Consensus size: 24
1627476 ATTAAAAATA
1627486 TAAA-TTAATATATAAATTGATAAT
1 TAAATTTAATATATAAATT-ATAAT
*
1627510 TAAATTTAATATAT--TTTATAATT
1 TAAATTTAATATATAAATTATAA-T
* *
1627533 TAATATTTAAAAATAAAAATTATAAT
1 TAA-ATTT-AATATATAAATTATAAT
1627559 TAAATTTA
1 TAAATTTA
1627567 TATTAATAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
22 4 0.09
23 6 0.13
24 9 0.19
25 18 0.38
26 4 0.09
27 6 0.13
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (24 bp):
TAAATTTAATATATAAATTATAAT
Found at i:1627574 original size:27 final size:27
Alignment explanation
Indices: 1627544--1627615 Score: 71
Period size: 27 Copynumber: 2.7 Consensus size: 27
1627534 AATATTTAAA
1627544 AATAAAAATTATAATTA-AATTTATATT
1 AATAAAAATTATAATTATAATTTA-ATT
*
1627571 AATAATATAA-TAT-ATTATTATTTAATT
1 AATAA-A-AATTATAATTATAATTTAATT
1627598 AATAAAAA-TATATATTAT
1 AATAAAAATTATA-ATTAT
1627616 CGTTATTAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
25 5 0.13
26 1 0.03
27 22 0.56
28 9 0.23
29 2 0.05
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (27 bp):
AATAAAAATTATAATTATAATTTAATT
Found at i:1627600 original size:24 final size:24
Alignment explanation
Indices: 1627564--1627615 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
1627554 ATAATTAAAT
*
1627564 TTATATTAATAAT-ATAATATATTA
1 TTATATTAATAATAAAAATATA-TA
1627588 TTAT-TTAATTAATAAAAATATATA
1 TTATATTAA-TAATAAAAATATATA
1627612 TTAT
1 TTAT
1627616 CGTTATTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
23 4 0.16
24 14 0.56
25 7 0.28
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
TTATATTAATAATAAAAATATATA
Found at i:1628355 original size:15 final size:16
Alignment explanation
Indices: 1628327--1628368 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
1628317 ATGATTCCAA
1628327 TTTTAATTTAATT-AT
1 TTTTAATTTAATTAAT
* *
1628342 TTTTATTTTTATTAAT
1 TTTTAATTTAATTAAT
1628358 TTTTAAATTTA
1 TTTT-AATTTA
1628369 TTTTATTATT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
15 11 0.52
16 6 0.29
17 4 0.19
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TTTTAATTTAATTAAT
Found at i:1628420 original size:21 final size:21
Alignment explanation
Indices: 1628345--1628450 Score: 72
Period size: 22 Copynumber: 4.7 Consensus size: 21
1628335 TAATTATTTT
*
1628345 TATTTT-TATTAATTTTTAAA
1 TATTTTATATTAATATTTAAA
* *
1628365 TTTATTTTATTATTAAAAAATTAAAAA
1 --TATTTTA-TATT--AATATT-TAAA
1628392 TACTTTTATATTAATATTTAAA
1 TA-TTTTATATTAATATTTAAA
1628414 TATTTTATAATTAA-ATTTAAA
1 TATTTTAT-ATTAATATTTAAA
*
1628435 TACTATTTTTATTAAT
1 TA-T-TTTATATTAAT
1628451 TAAATAATAT
Statistics
Matches: 68, Mismatches: 6, Indels: 19
0.73 0.06 0.20
Matches are distributed among these distances:
21 15 0.22
22 22 0.32
23 9 0.13
24 4 0.06
25 6 0.09
26 9 0.13
27 3 0.04
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (21 bp):
TATTTTATATTAATATTTAAA
Found at i:1628426 original size:22 final size:21
Alignment explanation
Indices: 1628389--1628456 Score: 79
Period size: 21 Copynumber: 3.2 Consensus size: 21
1628379 AAAAAATTAA
1628389 AAATACTTTTATATTAATATTT
1 AAATACTTTTATATTAA-ATTT
1628411 AAATA-TTTTATAATTAAATTT
1 AAATACTTTTAT-ATTAAATTT
*
1628432 AAATACTATTTTTATT-AA-TT
1 AAATACT-TTTATATTAAATTT
1628452 AAATA
1 AAATA
1628457 ATATTTTTTA
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
20 7 0.17
21 17 0.40
22 14 0.33
23 4 0.10
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (21 bp):
AAATACTTTTATATTAAATTT
Found at i:1628464 original size:21 final size:23
Alignment explanation
Indices: 1628347--1628466 Score: 74
Period size: 21 Copynumber: 5.3 Consensus size: 23
1628337 ATTATTTTTA
* *
1628347 TTTTTATTAATTTTTAAAT-TTAT
1 TTTTTATTAA-ATTTAAATAATAT
*
1628370 TTTATTATTAAAAAATTAAA-AATACT
1 TTT-TTATT--AAATTTAAATAATA-T
*
1628396 TTTATATTAATATTTAAAT-AT-T
1 TTTTTATTAA-ATTTAAATAATAT
* * *
1628418 TTATAATTAAATTTAAATACTA-
1 TTTTTATTAAATTTAAATAATAT
1628440 TTTTTATT-AA-TTAAATAATAT
1 TTTTTATTAAATTTAAATAATAT
1628461 TTTTTA
1 TTTTTA
1628467 AAAAAATCAA
Statistics
Matches: 75, Mismatches: 12, Indels: 22
0.69 0.11 0.20
Matches are distributed among these distances:
20 9 0.12
21 16 0.21
22 15 0.20
23 5 0.07
24 13 0.17
25 11 0.15
26 6 0.08
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (23 bp):
TTTTTATTAAATTTAAATAATAT
Found at i:1629402 original size:15 final size:16
Alignment explanation
Indices: 1629382--1629416 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
1629372 ATTCACTTAG
1629382 TTTTTTGTTGGTT-TT
1 TTTTTTGTTGGTTATT
*
1629397 TTTTTTTTTGGTTATT
1 TTTTTTGTTGGTTATT
1629413 TTTT
1 TTTT
1629417 CCGTTGTCTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.03, C:0.00, G:0.14, T:0.83
Consensus pattern (16 bp):
TTTTTTGTTGGTTATT
Found at i:1635323 original size:5 final size:5
Alignment explanation
Indices: 1635290--1635380 Score: 50
Period size: 5 Copynumber: 18.4 Consensus size: 5
1635280 GATTTGATAA
* *
1635290 ATTAT ATT-T -TTAT ATCAT ATT-T -TTAT ATTTT ATTAT ATTAT AATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT -ATTAT
* * *
1635337 ATTTAA AATAT TTTAT ATT-T A-TAT ATTGAT AAATTAT ATTAT AT
1 A-TTAT ATTAT ATTAT ATTAT ATTAT ATT-AT --ATTAT ATTAT AT
1635381 ATAAATTTTA
Statistics
Matches: 65, Mismatches: 10, Indels: 22
0.67 0.10 0.23
Matches are distributed among these distances:
3 5 0.08
4 8 0.12
5 36 0.55
6 11 0.17
7 2 0.03
8 3 0.05
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.59
Consensus pattern (5 bp):
ATTAT
Found at i:1635323 original size:13 final size:13
Alignment explanation
Indices: 1635290--1635340 Score: 57
Period size: 13 Copynumber: 3.7 Consensus size: 13
1635280 GATTTGATAA
1635290 ATTATATTTTTAT
1 ATTATATTTTTAT
*
1635303 ATCATATTTTTAT
1 ATTATATTTTTAT
*
1635316 ATTTTATTATATTAT
1 ATTATATT-T-TTAT
1635331 AATTATATTT
1 -ATTATATTT
1635341 AAAATATTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
13 18 0.58
14 1 0.03
15 5 0.16
16 7 0.23
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (13 bp):
ATTATATTTTTAT
Found at i:1635378 original size:26 final size:23
Alignment explanation
Indices: 1635321--1635394 Score: 69
Period size: 22 Copynumber: 3.1 Consensus size: 23
1635311 TTTATATTTT
*
1635321 ATTATATTATAATTATATTTAAA
1 ATTATATTATATTTATATTTAAA
*
1635344 A-TATTTTATATTTATATATTGATAA
1 ATTATATTATATTTATAT-TT-A-AA
* *
1635369 ATTATATTATATATAAATTTTAAA
1 ATTATATTATATTTATA-TTTAAA
1635393 AT
1 AT
1635395 GTGTATAATA
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
22 14 0.34
23 3 0.07
24 5 0.12
25 4 0.10
26 14 0.34
27 1 0.02
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (23 bp):
ATTATATTATATTTATATTTAAA
Found at i:1635603 original size:2 final size:2
Alignment explanation
Indices: 1635596--1635633 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1635586 CCTCCCCAAA
*
1635596 AT AT AT AT AT AT AT AT AT AT GT 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
1635634 TTATCACCCA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1643753 original size:29 final size:29
Alignment explanation
Indices: 1643716--1643785 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
1643706 AAAAAAAAGA
* * *
1643716 AAATTAAAAAAAAATGAGTCCATAAAATT-
1 AAATAAAAAAAAAAGGA-TCCACAAAATTG
*
1643745 AAATAAAAAATAAAGGATCCACAAAATTG
1 AAATAAAAAAAAAAGGATCCACAAAATTG
*
1643774 AAAGAAAAAAAA
1 AAATAAAAAAAA
1643786 GAACCTCAGA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
28 10 0.29
29 24 0.71
ACGTcount: A:0.67, C:0.07, G:0.09, T:0.17
Consensus pattern (29 bp):
AAATAAAAAAAAAAGGATCCACAAAATTG
Found at i:1643765 original size:28 final size:29
Alignment explanation
Indices: 1643720--1643785 Score: 82
Period size: 28 Copynumber: 2.3 Consensus size: 29
1643710 AAAAGAAAAT
* *
1643720 TAAAAAAAAATGAGTCCATAAAATT-AAA
1 TAAAAAAAAAGGAGTCCACAAAATTGAAA
1643748 TAAAAAATAAAGGA-TCCACAAAATTGAAA
1 TAAAAAA-AAAGGAGTCCACAAAATTGAAA
*
1643777 GAAAAAAAA
1 TAAAAAAAA
1643786 GAACCTCAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 19 0.58
29 14 0.42
ACGTcount: A:0.67, C:0.08, G:0.09, T:0.17
Consensus pattern (29 bp):
TAAAAAAAAAGGAGTCCACAAAATTGAAA
Found at i:1644492 original size:2 final size:2
Alignment explanation
Indices: 1644487--1644528 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
1644477 AATTGGAAAA
* *
1644487 AG AG AG AG AG AG TG AG AG TG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1644529 TTTGGGGTTG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.45, C:0.00, G:0.50, T:0.05
Consensus pattern (2 bp):
AG
Found at i:1645296 original size:2 final size:2
Alignment explanation
Indices: 1645289--1645314 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1645279 AACATATTAC
1645289 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
1645315 GCCCTTTTTA
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:1645509 original size:15 final size:17
Alignment explanation
Indices: 1645469--1645514 Score: 60
Period size: 15 Copynumber: 2.8 Consensus size: 17
1645459 TATTTTGTAT
1645469 TTAAATTATGTTAAATAA
1 TTAAATTA-GTTAAATAA
*
1645487 TTATATTA-TTAAA-AA
1 TTAAATTAGTTAAATAA
1645502 TTAAATTAGTTAA
1 TTAAATTAGTTAA
1645515 TTTACAACGT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 9 0.36
16 9 0.36
18 7 0.28
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (17 bp):
TTAAATTAGTTAAATAA
Found at i:1657044 original size:17 final size:17
Alignment explanation
Indices: 1657022--1657054 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1657012 TAATATATTT
*
1657022 AAATTTCAAAAAGAAAG
1 AAATTTAAAAAAGAAAG
1657039 AAATTTAAAAAAGAAA
1 AAATTTAAAAAAGAAA
1657055 AAGAAAAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.70, C:0.03, G:0.09, T:0.18
Consensus pattern (17 bp):
AAATTTAAAAAAGAAAG
Found at i:1657723 original size:24 final size:24
Alignment explanation
Indices: 1657690--1657741 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
1657680 ACTACGAAAC
1657690 TAAA-TGATAAGTGC-GTGGACTTA
1 TAAACTGATAAGT-CAGTGGACTTA
*
1657713 TAAACTGATAAGTCAGTGTACTTA
1 TAAACTGATAAGTCAGTGGACTTA
1657737 TAAAC
1 TAAAC
1657742 GTAATTAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 5 0.19
24 21 0.81
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (24 bp):
TAAACTGATAAGTCAGTGGACTTA
Found at i:1658650 original size:21 final size:22
Alignment explanation
Indices: 1658616--1658656 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1658606 AAAAATTAAA
1658616 TAAACAATTATTAACATTAATT
1 TAAACAATTATTAACATTAATT
* *
1658638 TAAACTATT-TTAATATTAA
1 TAAACAATTATTAACATTAA
1658657 CTAAAATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (22 bp):
TAAACAATTATTAACATTAATT
Found at i:1659514 original size:27 final size:26
Alignment explanation
Indices: 1659484--1659611 Score: 82
Period size: 28 Copynumber: 4.5 Consensus size: 26
1659474 TTAGGTAATT
1659484 ATAAAATATTTAAAATATATGATATAA
1 ATAAAATATTTAAAATATAT-ATATAA
*
1659511 AT-AAATTTTTAAAATTTATATAATATAA
1 ATAAAATATTTAAAA--TATAT-ATATAA
* *
1659539 ATTATTAATATATTAAAATTTATATA-AA
1 A-TA-AAATAT-TTAAAATATATATATAA
1659567 TATAAAATATTTTAAACATA-ATTATTATATA
1 -ATAAAATA-TTTAAA-ATATA-TA-TATA-A
*
1659598 ATAAAATATATAAA
1 ATAAAATATTTAAA
1659612 TAAAAATAAA
Statistics
Matches: 80, Mismatches: 8, Indels: 24
0.71 0.07 0.21
Matches are distributed among these distances:
26 11 0.14
27 12 0.15
28 21 0.26
29 12 0.15
30 13 0.16
31 5 0.06
32 6 0.08
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (26 bp):
ATAAAATATTTAAAATATATATATAA
Found at i:1659522 original size:26 final size:25
Alignment explanation
Indices: 1659487--1659553 Score: 75
Period size: 24 Copynumber: 2.7 Consensus size: 25
1659477 GGTAATTATA
*
1659487 AAATATTTAAAATATATGATATAA-AT
1 AAATTTTTAAAATAT-T-ATATAATAT
1659513 AAATTTTTAAAAT-TTATATAATAT
1 AAATTTTTAAAATATTATATAATAT
* *
1659537 AAATTATTAATATATTA
1 AAATTTTTAAAATATTA
1659554 AAATTTATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
23 6 0.17
24 14 0.39
25 4 0.11
26 12 0.33
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (25 bp):
AAATTTTTAAAATATTATATAATAT
Found at i:1659572 original size:17 final size:17
Alignment explanation
Indices: 1659520--1659574 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
1659510 AATAAATTTT
1659520 TAAAATTTATAT-AATA
1 TAAAATTTATATAAATA
1659536 T-AAA-TTAT-TAATATA
1 TAAAATTTATATAA-ATA
1659551 TTAAAATTTATATAAATA
1 -TAAAATTTATATAAATA
1659569 TAAAAT
1 TAAAAT
1659575 ATTTTAAACA
Statistics
Matches: 33, Mismatches: 0, Indels: 11
0.75 0.00 0.25
Matches are distributed among these distances:
13 1 0.03
14 5 0.15
15 6 0.18
16 2 0.06
17 9 0.27
18 7 0.21
19 3 0.09
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAAATTTATATAAATA
Found at i:1659907 original size:20 final size:21
Alignment explanation
Indices: 1659884--1659925 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
1659874 AAAATGTGCT
*
1659884 TGATAGG-ATAAAAAGTAAAA
1 TGATAGGAAGAAAAAGTAAAA
1659904 TGATAGGTAAGAAAAAGTAAAA
1 TGATAGG-AAGAAAAAGTAAAA
1659926 AATTAGGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 7 0.37
22 12 0.63
ACGTcount: A:0.60, C:0.00, G:0.21, T:0.19
Consensus pattern (21 bp):
TGATAGGAAGAAAAAGTAAAA
Found at i:1662895 original size:15 final size:15
Alignment explanation
Indices: 1662875--1662923 Score: 53
Period size: 17 Copynumber: 3.0 Consensus size: 15
1662865 TATATTATAA
1662875 TTATATTTAAAAATT
1 TTATATTTAAAAATT
1662890 TTATATTTATATAAATT
1 TTATATTTA-A-AAATT
*
1662907 TTAATATATTAATAATT
1 TT-ATAT-TTAAAAATT
1662924 AATTTTATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
15 9 0.31
16 1 0.03
17 11 0.38
18 5 0.17
19 3 0.10
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TTATATTTAAAAATT
Found at i:1662916 original size:20 final size:20
Alignment explanation
Indices: 1662885--1662934 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 20
1662875 TTATATTTAA
1662885 AAATTTTATAT-TT-AT-AT
1 AAATTTTATATATTAATAAT
1662902 AAATTTTAATATATTAATAAT
1 AAATTTT-ATATATTAATAAT
*
1662923 TAATTTTATATA
1 AAATTTTATATA
1662935 AATTATAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 7 0.25
18 4 0.14
19 2 0.07
20 7 0.25
21 8 0.29
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
AAATTTTATATATTAATAAT
Found at i:1664020 original size:8 final size:8
Alignment explanation
Indices: 1664004--1664098 Score: 62
Period size: 8 Copynumber: 12.5 Consensus size: 8
1663994 TACTATACGG
*
1664004 TAAAAATA
1 TAAATATA
1664012 TAAATATA
1 TAAATATA
1664020 TAAATATAA
1 TAAATAT-A
*
1664029 TAAAATTTA
1 T-AAATATA
1664038 TAAA-A-A
1 TAAATATA
1664044 TAAA-ATA
1 TAAATATA
*
1664051 TTAATATA
1 TAAATATA
1664059 TACAA-ATA
1 TA-AATATA
**
1664067 TTTATATA
1 TAAATATA
1664075 T-AAT-TA
1 TAAATATA
1664081 T-AATATA
1 TAAATATA
1664088 TAAAT-TA
1 TAAATATA
1664095 TAAA
1 TAAA
1664099 GTAAAATCAC
Statistics
Matches: 71, Mismatches: 8, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
6 12 0.17
7 16 0.23
8 32 0.45
9 6 0.08
10 5 0.07
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (8 bp):
TAAATATA
Found at i:1664026 original size:14 final size:14
Alignment explanation
Indices: 1664007--1664098 Score: 59
Period size: 14 Copynumber: 6.6 Consensus size: 14
1663997 TATACGGTAA
1664007 AAATATAAATATAT
1 AAATATAAATATAT
1664021 AAATAT-AATA-A-
1 AAATATAAATATAT
* *
1664032 AATTTATAAAAATA-
1 AA-ATATAAATATAT
*
1664046 AAATATTAATATATAC
1 AAATA-TAA-ATATAT
**
1664062 AAATATTTATATAT
1 AAATATAAATATAT
*
1664076 AATTAT-AATATAT
1 AAATATAAATATAT
1664089 AAATTATAAA
1 AAA-TATAAA
1664099 GTAAAATCAC
Statistics
Matches: 60, Mismatches: 10, Indels: 15
0.71 0.12 0.18
Matches are distributed among these distances:
11 2 0.03
12 4 0.07
13 17 0.28
14 25 0.42
15 7 0.12
16 5 0.08
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (14 bp):
AAATATAAATATAT
Found at i:1664039 original size:18 final size:19
Alignment explanation
Indices: 1664008--1664066 Score: 57
Period size: 18 Copynumber: 3.1 Consensus size: 19
1663998 ATACGGTAAA
*
1664008 AATATAAATATATAAATAT
1 AATATAAATATATAAAAAT
*
1664027 AATA-AAATTTATAAAAAT
1 AATATAAATATATAAAAAT
* *
1664045 AAAATATTAATATATACAAAT
1 --AATATAAATATATAAAAAT
1664066 A
1 A
1664067 TTTATATATA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
18 12 0.38
19 5 0.16
20 4 0.12
21 11 0.34
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (19 bp):
AATATAAATATATAAAAAT
Found at i:1664070 original size:33 final size:34
Alignment explanation
Indices: 1664004--1664097 Score: 97
Period size: 33 Copynumber: 2.7 Consensus size: 34
1663994 TACTATACGG
1664004 TAAAAATATAAATATATAAATATAATAAAATTTA
1 TAAAAATATAAATATATAAATATAATAAAATTTA
*
1664038 TAAAAATA-AAATAT-TAATATATACA-AATATTTA
1 TAAAAATATAAATATATAA-ATATA-ATAAAATTTA
*
1664071 TATATAAT-TATAATATATAAATTATAA
1 TA-AAAATATA-AATATATAAA-TATAA
1664098 AGTAAAATCA
Statistics
Matches: 51, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
32 3 0.06
33 20 0.39
34 14 0.27
35 7 0.14
36 7 0.14
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (34 bp):
TAAAAATATAAATATATAAATATAATAAAATTTA
Found at i:1664624 original size:33 final size:34
Alignment explanation
Indices: 1664581--1664644 Score: 89
Period size: 33 Copynumber: 1.9 Consensus size: 34
1664571 TTTATAATAA
1664581 TTTATATATTTT-ATAATTAAATTT-AAATAAAAAT
1 TTTATATATTTTAATAA-T-AATTTAAAATAAAAAT
1664615 TTTAT-TATTTTAATAATAATTTAAAATAAA
1 TTTATATATTTTAATAATAATTTAAAATAAA
1664645 TATGTTCAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
32 5 0.18
33 14 0.50
34 9 0.32
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (34 bp):
TTTATATATTTTAATAATAATTTAAAATAAAAAT
Found at i:1666002 original size:24 final size:26
Alignment explanation
Indices: 1665961--1666012 Score: 72
Period size: 24 Copynumber: 2.1 Consensus size: 26
1665951 TTATTTTTGT
**
1665961 TTTTTAAATTTATTATT-A-TTTTAA
1 TTTTTAAATTTAAAATTAATTTTTAA
1665985 TTTTTAAATTTAAAATTAATTTTTAA
1 TTTTTAAATTTAAAATTAATTTTTAA
1666011 TT
1 TT
1666013 GTTTCGTTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 15 0.62
25 1 0.04
26 8 0.33
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (26 bp):
TTTTTAAATTTAAAATTAATTTTTAA
Found at i:1666294 original size:21 final size:20
Alignment explanation
Indices: 1666268--1666321 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 20
1666258 ATTTATTGAT
1666268 TTTAATCTTATTAATATAATA
1 TTTAAT-TTATTAATATAATA
* * *
1666289 TTTAATTTTAATATTATGATA
1 TTTAA-TTTATTAATATAATA
*
1666310 ATTAATTTATTA
1 TTTAATTTATTA
1666322 TTATTAAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
20 6 0.22
21 20 0.74
22 1 0.04
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (20 bp):
TTTAATTTATTAATATAATA
Found at i:1667717 original size:22 final size:22
Alignment explanation
Indices: 1667692--1667747 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
1667682 TACTTGTGTC
1667692 AATAATTAAAATATATTTAAAA
1 AATAATTAAAATATATTTAAAA
** *
1667714 AAT-ATATATCATATTTTTAAAA
1 AATAAT-TAAAATATATTTAAAA
1667736 AATAAATTAAAA
1 AAT-AATTAAAA
1667748 ATTTAAAATA
Statistics
Matches: 26, Mismatches: 5, Indels: 5
0.72 0.14 0.14
Matches are distributed among these distances:
21 2 0.08
22 19 0.73
23 3 0.12
24 2 0.08
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (22 bp):
AATAATTAAAATATATTTAAAA
Found at i:1667751 original size:22 final size:21
Alignment explanation
Indices: 1667695--1667763 Score: 59
Period size: 20 Copynumber: 3.2 Consensus size: 21
1667685 TTGTGTCAAT
1667695 AATTAAAATATATTTAAAAAATA
1 AATTAAAA-AT-TTTAAAAAATA
* * * *
1667718 TATATCATATTTTTAAAAAATA
1 AAT-TAAAAATTTTAAAAAATA
*
1667740 AATTAAAAA-TTTAAAATATA
1 AATTAAAAATTTTAAAAAATA
1667760 AATT
1 AATT
1667764 TCAGTAAATA
Statistics
Matches: 36, Mismatches: 9, Indels: 5
0.72 0.18 0.10
Matches are distributed among these distances:
20 14 0.39
21 3 0.08
22 13 0.36
23 3 0.08
24 3 0.08
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.39
Consensus pattern (21 bp):
AATTAAAAATTTTAAAAAATA
Found at i:1668274 original size:21 final size:20
Alignment explanation
Indices: 1668250--1668289 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
1668240 CACATCAAGC
*
1668250 TTTGTTTATTTTATGAATTTG
1 TTTGTTTATTGT-TGAATTTG
1668271 TTTGTTTATTGTTGAATTT
1 TTTGTTTATTGTTGAATTT
1668290 TTTTCTTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.17, C:0.00, G:0.15, T:0.68
Consensus pattern (20 bp):
TTTGTTTATTGTTGAATTTG
Found at i:1668349 original size:16 final size:15
Alignment explanation
Indices: 1668324--1668353 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1668314 AGAGAATTAA
1668324 AAAAATAAAATAAAT
1 AAAAATAAAATAAAT
1668339 AAAAATAAAAATAAA
1 AAAAAT-AAAATAAA
1668354 AGAGTTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (15 bp):
AAAAATAAAATAAAT
Found at i:1668565 original size:19 final size:18
Alignment explanation
Indices: 1668543--1668588 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
1668533 AGAATTGAGA
*
1668543 ATTTTTTTAAAATATTTAT
1 ATTTTTATAAAA-ATTTAT
1668562 A-TTTTATAAAAATTTAT
1 ATTTTTATAAAAATTTAT
1668579 ATATTTTATA
1 AT-TTTTATA
1668589 TTTATAATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 7 0.29
18 9 0.38
19 8 0.33
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
ATTTTTATAAAAATTTAT
Found at i:1669609 original size:2 final size:2
Alignment explanation
Indices: 1669602--1669635 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1669592 ATCTACATAC
1669602 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
1669636 TCCCATGTAT
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:1674949 original size:2 final size:2
Alignment explanation
Indices: 1674910--1674937 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1674900 TTTGAGTTCA
1674910 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
1674938 GCATACATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1675166 original size:27 final size:28
Alignment explanation
Indices: 1675096--1675166 Score: 74
Period size: 28 Copynumber: 2.5 Consensus size: 28
1675086 TTAATAATTT
*
1675096 ATATTATATAAATTTTAATATATATATAA
1 ATATT-TATATATTTTAATATATATATAA
* *
1675125 ATTTTTATTTATTTTAATAT-TATATCAA
1 ATATTTATATATTTTAATATATATAT-AA
*
1675153 A-ATTTATATGTTTT
1 ATATTTATATATTTT
1675167 TTTGTTCGTA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
27 15 0.43
28 16 0.46
29 4 0.11
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (28 bp):
ATATTTATATATTTTAATATATATATAA
Found at i:1675167 original size:28 final size:28
Alignment explanation
Indices: 1675107--1675168 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 28
1675097 TATTATATAA
* *
1675107 ATTTTAATATATATATAAATTTTTATTT
1 ATTTTAATATATATATAAATTTATATGT
1675135 ATTTTAATAT-TATATCAAAATTTATATGT
1 ATTTTAATATATATAT--AAATTTATATGT
*
1675164 TTTTT
1 ATTTT
1675169 TGTTCGTATC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 5 0.17
28 10 0.34
29 14 0.48
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (28 bp):
ATTTTAATATATATATAAATTTATATGT
Found at i:1675168 original size:29 final size:28
Alignment explanation
Indices: 1675107--1675161 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 28
1675097 TATTATATAA
*
1675107 ATTTTAATATATATATAAATTTTTATTT
1 ATTTTAATATATATATAAATTTATATTT
1675135 ATTTTAATAT-TATATCAAAATTTATAT
1 ATTTTAATATATATAT--AAATTTATAT
1675162 GTTTTTTTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 5 0.21
28 10 0.42
29 9 0.38
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (28 bp):
ATTTTAATATATATATAAATTTATATTT
Found at i:1677908 original size:30 final size:30
Alignment explanation
Indices: 1677874--1677930 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
1677864 AAAGTTACAC
*
1677874 ATATATCAATTTTTTAA-TTATATTTTAAGG
1 ATATATCAATTTATTAATTTA-ATTTTAAGG
*
1677904 ATATATCACTTTATTAATTTAATTTTA
1 ATATATCAATTTATTAATTTAATTTTA
1677931 CATGTGAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 21 0.88
31 3 0.12
ACGTcount: A:0.37, C:0.05, G:0.04, T:0.54
Consensus pattern (30 bp):
ATATATCAATTTATTAATTTAATTTTAAGG
Found at i:1678655 original size:14 final size:14
Alignment explanation
Indices: 1678636--1678663 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1678626 TTTGAAAGGG
1678636 GCATTGATTGAGAT
1 GCATTGATTGAGAT
1678650 GCATTGATTGAGAT
1 GCATTGATTGAGAT
1678664 TTGAGGGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.07, G:0.29, T:0.36
Consensus pattern (14 bp):
GCATTGATTGAGAT
Found at i:1678928 original size:15 final size:16
Alignment explanation
Indices: 1678908--1678939 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
1678898 TGGCACGTTT
1678908 CATTTGCTTT-TCTGC
1 CATTTGCTTTGTCTGC
1678923 CATTTGCTTTGTCTGC
1 CATTTGCTTTGTCTGC
1678939 C
1 C
1678940 TTGATGATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.06, C:0.28, G:0.16, T:0.50
Consensus pattern (16 bp):
CATTTGCTTTGTCTGC
Found at i:1679141 original size:23 final size:23
Alignment explanation
Indices: 1679096--1679141 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1679086 TTTATTATTA
* * *
1679096 TTTATATTTATAAATTATTAAAT
1 TTTATATTTAAAAAATATAAAAT
*
1679119 TTTATTTTTAAAAAATATAAAAT
1 TTTATATTTAAAAAATATAAAAT
1679142 ATATTAAAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TTTATATTTAAAAAATATAAAAT
Found at i:1679150 original size:19 final size:19
Alignment explanation
Indices: 1679126--1679166 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1679116 AATTTTATTT
1679126 TTAAAAAATAT-AAAATATA
1 TTAAAAAA-ATCAAAATATA
*
1679145 TTAAAAAAATCAAATTATA
1 TTAAAAAAATCAAAATATA
1679164 TTA
1 TTA
1679167 TAATTATCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 2 0.10
19 18 0.90
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34
Consensus pattern (19 bp):
TTAAAAAAATCAAAATATA
Found at i:1682690 original size:24 final size:23
Alignment explanation
Indices: 1682663--1682709 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
1682653 TCAAACATTT
*
1682663 TATATAATCAATTATATTTAAAAA
1 TATAT-ATCAAATATATTTAAAAA
*
1682687 TATATATTAAATATATTTAAAAA
1 TATATATCAAATATATTTAAAAA
1682710 AAATTATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 16 0.76
24 5 0.24
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (23 bp):
TATATATCAAATATATTTAAAAA
Found at i:1682730 original size:26 final size:26
Alignment explanation
Indices: 1682682--1682732 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
1682672 AATTATATTT
*
1682682 AAAAATATATATTAAATATATTTAAA
1 AAAAATATATATTAAATAAATTTAAA
*
1682708 AAAAAT-TATATTGAATAAAATTTAA
1 AAAAATATATATTAAAT-AAATTTAA
1682733 GATTTAATCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 9 0.41
26 13 0.59
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (26 bp):
AAAAATATATATTAAATAAATTTAAA
Found at i:1686086 original size:26 final size:23
Alignment explanation
Indices: 1686032--1686088 Score: 64
Period size: 22 Copynumber: 2.4 Consensus size: 23
1686022 ACCAAGTAGT
1686032 ATTA-ATTTATTTAGATTTAATA
1 ATTATATTTATTTAGATTTAATA
*
1686054 ATT-TATTTATTTATATTATATTATA
1 ATTATATTTATTTAGATT-TA--ATA
1686079 ATTATATTTA
1 ATTATATTTA
1686089 AAATATTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
22 15 0.52
23 2 0.07
25 6 0.21
26 6 0.21
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.60
Consensus pattern (23 bp):
ATTATATTTATTTAGATTTAATA
Found at i:1686150 original size:33 final size:32
Alignment explanation
Indices: 1686057--1686168 Score: 86
Period size: 33 Copynumber: 3.4 Consensus size: 32
1686047 TTTAATAATT
* *
1686057 TATTTATTTATATTATATTATA-ATTATATTTAA
1 TATTTA-TTATATTAT-TTATATATTAAATTTTA
* *
1686090 AATATT-TTATATT-TTTATAAATTTTAAATTTTA
1 TAT-TTATTATATTATTTAT--ATATTAAATTTTA
*
1686123 TATTTATTATATTATGTTATATATTAAATATTA
1 TATTTATTATATTAT-TTATATATTAAATTTTA
*
1686156 TATATATATATAT
1 TATTTAT-TATAT
1686169 ATCATATTTA
Statistics
Matches: 63, Mismatches: 8, Indels: 15
0.73 0.09 0.17
Matches are distributed among these distances:
30 4 0.06
31 1 0.02
32 10 0.16
33 36 0.57
34 8 0.13
35 4 0.06
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (32 bp):
TATTTATTATATTATTTATATATTAAATTTTA
Found at i:1690437 original size:2 final size:2
Alignment explanation
Indices: 1690430--1690467 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1690420 ACTTTCTAAA
1690430 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1690468 GGCAAGGAAG
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1691265 original size:28 final size:28
Alignment explanation
Indices: 1691221--1691280 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 28
1691211 TCACCGTGAG
* * *
1691221 ATTGTATGAAGTGACATAGTGAACTTGT
1 ATTGTATGAAATCACATAGTAAACTTGT
1691249 ATTGTATGAAATCACATAGTAAACTTGT
1 ATTGTATGAAATCACATAGTAAACTTGT
1691277 ATTG
1 ATTG
1691281 CCACCAAAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.35, C:0.08, G:0.20, T:0.37
Consensus pattern (28 bp):
ATTGTATGAAATCACATAGTAAACTTGT
Found at i:1698332 original size:18 final size:18
Alignment explanation
Indices: 1698309--1698343 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1698299 CCCTACACCC
1698309 AAAAAAA-AAAAGTTAAAG
1 AAAAAAACAAAA-TTAAAG
1698327 AAAAAAACAAAATTAAA
1 AAAAAAACAAAATTAAA
1698344 ACAACAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.80, C:0.03, G:0.06, T:0.11
Consensus pattern (18 bp):
AAAAAAACAAAATTAAAG
Found at i:1699422 original size:17 final size:17
Alignment explanation
Indices: 1699400--1699435 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
1699390 TAAATTAAAT
1699400 AAATA-TTATTAATAATA
1 AAATATTTA-TAATAATA
1699417 AAATATTTATAATAATA
1 AAATATTTATAATAATA
1699434 AA
1 AA
1699436 TTGAAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 15 0.83
18 3 0.17
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AAATATTTATAATAATA
Done.