Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold953
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: 189922
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.30
Found at i:45 original size:2 final size:2
Alignment explanation
Indices: 38--67 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
28 ACTATAAAGG
38 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
68 ACACATTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:575 original size:13 final size:13
Alignment explanation
Indices: 542--582 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
532 ATATTTATAT
542 TTAAATAT--ATA
1 TTAAATATAAATA
553 TTAATTATATAAATA
1 TTAA--ATATAAATA
568 TTAAATATAAATA
1 TTAAATATAAATA
581 TT
1 TT
583 TTTAAAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
11 4 0.15
13 15 0.58
15 7 0.27
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TTAAATATAAATA
Found at i:1668 original size:20 final size:21
Alignment explanation
Indices: 1627--1666 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1617 CAGGGTAAAA
*
1627 TTTTTTATTTAATTTAATTTC
1 TTTTTTATTTAAATTAATTTC
1648 TTTTTT-TTTAAAATTAATT
1 TTTTTTATTT-AAATTAATT
1667 CTAAAAATCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTTTTATTTAAATTAATTTC
Found at i:7084 original size:17 final size:17
Alignment explanation
Indices: 7062--7096 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
7052 TCATTACACA
7062 TGGGAATTTGAAGGGCT
1 TGGGAATTTGAAGGGCT
*
7079 TGGGAATTTTAAGGGCT
1 TGGGAATTTGAAGGGCT
7096 T
1 T
7097 AGATCAAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.23, C:0.06, G:0.37, T:0.34
Consensus pattern (17 bp):
TGGGAATTTGAAGGGCT
Found at i:9013 original size:12 final size:13
Alignment explanation
Indices: 8990--9018 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
8980 TATCAAATAT
8990 AATTAGTTAAAAA
1 AATTAGTTAAAAA
9003 AATTA-TTAAAAA
1 AATTAGTTAAAAA
9015 AATT
1 AATT
9019 GAAAAAAATA
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:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (13 bp):
AATTAGTTAAAAA
Found at i:9033 original size:16 final size:17
Alignment explanation
Indices: 9012--9044 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
9002 AAATTATTAA
*
9012 AAAAATTGAA-AAAAAT
1 AAAAATTAAACAAAAAT
9028 AAAAATTAAACAAAAAT
1 AAAAATTAAACAAAAAT
9045 GGTTGAGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.18
Consensus pattern (17 bp):
AAAAATTAAACAAAAAT
Found at i:9480 original size:12 final size:13
Alignment explanation
Indices: 9429--9482 Score: 51
Period size: 12 Copynumber: 4.3 Consensus size: 13
9419 ATCAAAAAAA
*
9429 TTATAAATTTATT
1 TTATAAATTAATT
*
9442 TAAT-AA-TAATT
1 TTATAAATTAATT
*
9453 TTATGAATTAAATT
1 TTATAAATT-AATT
9467 TTA-AAATTAATT
1 TTATAAATTAATT
9479 TTAT
1 TTAT
9483 TTTTCTGAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
11 7 0.21
12 11 0.33
13 8 0.24
14 7 0.21
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (13 bp):
TTATAAATTAATT
Found at i:15917 original size:22 final size:22
Alignment explanation
Indices: 15891--15943 Score: 81
Period size: 22 Copynumber: 2.4 Consensus size: 22
15881 ATAAGGAATG
15891 AAATAATTA-AAATATAATATAA
1 AAAT-ATTATAAATATAATATAA
15913 AAATATTATAAATATAATATAA
1 AAATATTATAAATATAATATAA
*
15935 ATATATTAT
1 AAATATTAT
15944 TTAAGTTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 4 0.14
22 25 0.86
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
AAATATTATAAATATAATATAA
Found at i:15922 original size:11 final size:11
Alignment explanation
Indices: 15891--15935 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
15881 ATAAGGAATG
15891 AAATAAT-TAA
1 AAATAATATAA
15901 AATATAATATAA
1 AA-ATAATATAA
*
15913 AAATATTATAA
1 AAATAATATAA
*
15924 ATATAATATAA
1 AAATAATATAA
15935 A
1 A
15936 TATATTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
10 2 0.07
11 23 0.77
12 5 0.17
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
AAATAATATAA
Found at i:15936 original size:11 final size:11
Alignment explanation
Indices: 15900--15939 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
15890 GAAATAATTA
15900 AAATATAATAT
1 AAATATAATAT
* *
15911 AAAAATATTAT
1 AAATATAATAT
15922 AAATATAATAT
1 AAATATAATAT
15933 AAATATA
1 AAATATA
15940 TTATTTAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
AAATATAATAT
Found at i:16683 original size:10 final size:10
Alignment explanation
Indices: 16668--16706 Score: 53
Period size: 10 Copynumber: 3.8 Consensus size: 10
16658 TATTTCATTC
16668 AATTAATTTA
1 AATTAATTTA
16678 AATTAATTT-
1 AATTAATTTA
16687 AATTAATTTTAA
1 AATTAA-TTT-A
16699 AATTAATT
1 AATTAATT
16707 GATTTATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 6 0.23
10 12 0.46
11 2 0.08
12 6 0.23
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (10 bp):
AATTAATTTA
Found at i:16692 original size:9 final size:9
Alignment explanation
Indices: 16654--16742 Score: 65
Period size: 9 Copynumber: 9.7 Consensus size: 9
16644 AATTGGTAGA
*
16654 AATTTATTT
1 AATTTAATT
* *
16663 CATTCAATT
1 AATTTAATT
16672 AATTTAAATT
1 AATTT-AATT
16682 AATTTAATT
1 AATTTAATT
16691 AATTTTAAAATT
1 AA-TTT--AATT
*
16703 AA-TTGATT
1 AATTTAATT
* *
16711 TATTTTATT
1 AATTTAATT
16720 AATTTAATT
1 AATTTAATT
*
16729 AA-TTATTT
1 AATTTAATT
16737 AATTTA
1 AATTTA
16743 GAATTTAATA
Statistics
Matches: 63, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
8 11 0.17
9 32 0.51
10 14 0.22
12 6 0.10
ACGTcount: A:0.40, C:0.02, G:0.01, T:0.56
Consensus pattern (9 bp):
AATTTAATT
Found at i:16734 original size:21 final size:21
Alignment explanation
Indices: 16675--16736 Score: 65
Period size: 21 Copynumber: 2.9 Consensus size: 21
16665 TTCAATTAAT
16675 TTAAATTAATTTAATTAATTTTA
1 TTAAATTAA-TTAATT-ATTTTA
*
16698 --AAATTAATTGATTTATTTTA
1 TTAAATTAATT-AATTATTTTA
*
16718 TTAATTTAATTAATTATTT
1 TTAAATTAATTAATTATTT
16737 AATTTAGAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
20 8 0.24
21 17 0.52
22 8 0.24
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (21 bp):
TTAAATTAATTAATTATTTTA
Found at i:16853 original size:18 final size:18
Alignment explanation
Indices: 16830--16872 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
16820 GGAAGGAAAT
16830 TCATGCTGTCAACTAAAG
1 TCATGCTGTCAACTAAAG
16848 TCATGCTGTCAACTAAAG
1 TCATGCTGTCAACTAAAG
16866 TCATGCT
1 TCATGCT
16873 CAACCACTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.30
Consensus pattern (18 bp):
TCATGCTGTCAACTAAAG
Found at i:16983 original size:14 final size:14
Alignment explanation
Indices: 16964--16996 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
16954 CTTTTTTTTT
16964 TTAAATCTCGTTGA
1 TTAAATCTCGTTGA
16978 TTAAATCTCGTTGA
1 TTAAATCTCGTTGA
16992 -TAAAT
1 TTAAAT
16997 ACTCACTAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 5 0.26
14 14 0.74
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.42
Consensus pattern (14 bp):
TTAAATCTCGTTGA
Found at i:18580 original size:15 final size:15
Alignment explanation
Indices: 18560--18590 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
18550 AACTTGACGG
18560 TTCTTTTTCTTTAAT
1 TTCTTTTTCTTTAAT
*
18575 TTCTTTTTTTTTAAT
1 TTCTTTTTCTTTAAT
18590 T
1 T
18591 GCAAGTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.10, G:0.00, T:0.77
Consensus pattern (15 bp):
TTCTTTTTCTTTAAT
Found at i:21485 original size:2 final size:2
Alignment explanation
Indices: 21478--21507 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
21468 TGTAGTTAAA
21478 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
21508 TTATGTGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23190 original size:6 final size:6
Alignment explanation
Indices: 23179--23203 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
23169 TCATCTTCCC
23179 CGTTGG CGTTGG CGTTGG CGTTGG C
1 CGTTGG CGTTGG CGTTGG CGTTGG C
23204 TGATCTTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.20, G:0.48, T:0.32
Consensus pattern (6 bp):
CGTTGG
Found at i:30119 original size:6 final size:6
Alignment explanation
Indices: 30108--30141 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
30098 AAATCATTCA
*
30108 TTTTGT TTTTGT TTTTGT TTTT-T TTTTTT TTTTG
1 TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT TTTTG
30142 GAGTTGAGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (6 bp):
TTTTGT
Found at i:30125 original size:12 final size:12
Alignment explanation
Indices: 30108--30141 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
30098 AAATCATTCA
30108 TTTTGTTTTTGT
1 TTTTGTTTTTGT
30120 TTTTGTTTTT-T
1 TTTTGTTTTTGT
*
30131 TTTTTTTTTTG
1 TTTTGTTTTTG
30142 GAGTTGAGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (12 bp):
TTTTGTTTTTGT
Found at i:30133 original size:17 final size:18
Alignment explanation
Indices: 30108--30141 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
30098 AAATCATTCA
30108 TTTTGTTTTTGTTTTTGT
1 TTTTGTTTTTGTTTTTGT
*
30126 TTTT-TTTTTTTTTTTG
1 TTTTGTTTTTGTTTTTG
30142 GAGTTGAGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (18 bp):
TTTTGTTTTTGTTTTTGT
Found at i:33007 original size:30 final size:30
Alignment explanation
Indices: 32973--33030 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
32963 AATCTAGGCT
**
32973 CAGCACAGACAATCGAGAGAAAGCAAGAGC
1 CAGCACAGACAAGAGAGAGAAAGCAAGAGC
* *
33003 CAGCACTGACAAGAGAGAGAAATCAAGA
1 CAGCACAGACAAGAGAGAGAAAGCAAGA
33031 AAGAGCTTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.48, C:0.21, G:0.26, T:0.05
Consensus pattern (30 bp):
CAGCACAGACAAGAGAGAGAAAGCAAGAGC
Found at i:49516 original size:43 final size:42
Alignment explanation
Indices: 49460--49631 Score: 117
Period size: 37 Copynumber: 4.1 Consensus size: 42
49450 ATAAATTTTG
* *
49460 ATAATTTTTATATATTATATTATTTTATATTAATTATGTAAAT
1 ATAAATTTAATATATTATATTATTTTATATTAATTAT-TAAAT
* *
49503 ATAAATTTAATATA--AT-TTATTATA-ATTTATT-TTAAAT
1 ATAAATTTAATATATTATATTATTTTATATTAATTATTAAAT
* ** * *
49540 ATAAATATAATATTATTATTAAACATATTATGTTAATTCAATTTAAAT
1 ATAAATTTAATA-TATTA-T-ATTATTTTATATTAATT--A-TTAAAT
*
49588 ATATAATATT-ATATATTATATTATTTT-TA-TATTTATTAAAT
1 ATA-AAT-TTAATATATTATATTATTTTATATTAATTATTAAAT
49629 ATA
1 ATA
49632 TTTTATTTAT
Statistics
Matches: 99, Mismatches: 17, Indels: 28
0.69 0.12 0.19
Matches are distributed among these distances:
37 16 0.16
38 3 0.03
39 6 0.06
40 8 0.08
41 12 0.12
42 1 0.01
43 16 0.16
44 9 0.09
45 1 0.01
46 5 0.05
47 1 0.01
48 14 0.14
49 6 0.06
50 1 0.01
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (42 bp):
ATAAATTTAATATATTATATTATTTTATATTAATTATTAAAT
Found at i:49804 original size:14 final size:15
Alignment explanation
Indices: 49785--49814 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
49775 TTAAATAAAT
49785 ATTTTAA-TAATTTA
1 ATTTTAATTAATTTA
49799 ATTTTAATTAATTTA
1 ATTTTAATTAATTTA
49814 A
1 A
49815 ATTATTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
ATTTTAATTAATTTA
Found at i:49912 original size:37 final size:36
Alignment explanation
Indices: 49809--49912 Score: 104
Period size: 37 Copynumber: 2.8 Consensus size: 36
49799 ATTTTAATTA
* *
49809 ATTTAAATTATTTTTATATAAT-AAATAAATATTTTT
1 ATTTAAATTA-TTTTAAATAATAAAATAAAAATTTTT
* * *
49845 ATTTAAATTTAATTATAAATATTAATATAAAAATTATTT
1 ATTTAAA-TT-ATTTTAAATAATAAAATAAAAATT-TTT
49884 -TTTAATATTATTTTAAATAATAAAATAAA
1 ATTTAA-ATTATTTTAAATAATAAAATAAA
49913 TTTTTAAATC
Statistics
Matches: 55, Mismatches: 8, Indels: 9
0.76 0.11 0.12
Matches are distributed among these distances:
36 7 0.13
37 27 0.49
38 17 0.31
39 4 0.07
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (36 bp):
ATTTAAATTATTTTAAATAATAAAATAAAAATTTTT
Found at i:51583 original size:17 final size:16
Alignment explanation
Indices: 51558--51591 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
51548 AAATTAATAT
51558 TAAATAAATATTATTA
1 TAAATAAATATTATTA
*
51574 TAAATAAAATTTTATTA
1 TAAAT-AAATATTATTA
51591 T
1 T
51592 CTTTTTATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TAAATAAATATTATTA
Found at i:51676 original size:14 final size:15
Alignment explanation
Indices: 51654--51689 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
51644 AAATTAAAGA
51654 TTTAA-TTTTTTTAT
1 TTTAATTTTTTTTAT
*
51668 TTTACTTTTTTTTAT
1 TTTAATTTTTTTTAT
51683 TTTAATT
1 TTTAATT
51690 GAGTTTACGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
14 4 0.21
15 15 0.79
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTAATTTTTTTTAT
Found at i:52013 original size:31 final size:30
Alignment explanation
Indices: 51976--52044 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 30
51966 AAATATAGAT
51976 TGTAATAAATAA-ATAATTAAAAATATAATAA
1 TGTAATAAA-AATATAATTAAAAAT-TAATAA
* *
52007 TGTAATAAAAATTTACTTAAAAATTAATAA
1 TGTAATAAAAATATAATTAAAAATTAATAA
*
52037 TTTAATAA
1 TGTAATAA
52045 TTTACTTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
30 15 0.44
31 19 0.56
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.36
Consensus pattern (30 bp):
TGTAATAAAAATATAATTAAAAATTAATAA
Found at i:52046 original size:27 final size:30
Alignment explanation
Indices: 51992--52051 Score: 81
Period size: 27 Copynumber: 2.1 Consensus size: 30
51982 AAATAAATAA
51992 TTAAAAATATAATAATGTAATAAAAATTTAC
1 TTAAAAATATAATAATGT-ATAAAAATTTAC
*
52023 TTAAAAAT-TAATAAT-T-TAATAATTTAC
1 TTAAAAATATAATAATGTATAAAAATTTAC
52050 TT
1 TT
52052 TTTAAGGATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 12 0.43
29 1 0.04
30 7 0.25
31 8 0.29
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (30 bp):
TTAAAAATATAATAATGTATAAAAATTTAC
Found at i:52201 original size:16 final size:16
Alignment explanation
Indices: 52159--52224 Score: 51
Period size: 16 Copynumber: 4.1 Consensus size: 16
52149 AAACTCGAAT
* * *
52159 AAGCTTGAACCCGAAT
1 AAGCTCGAACCCAAAA
* *
52175 AAGCCCAAACCCAAAA
1 AAGCTCGAACCCAAAA
* *
52191 AAGTTCGAACCCAAAT
1 AAGCTCGAACCCAAAA
* *
52207 AAGCTCGAGCTCAAAA
1 AAGCTCGAACCCAAAA
52223 AA
1 AA
52225 ATCTAAACTC
Statistics
Matches: 37, Mismatches: 13, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.47, C:0.27, G:0.14, T:0.12
Consensus pattern (16 bp):
AAGCTCGAACCCAAAA
Found at i:52380 original size:16 final size:15
Alignment explanation
Indices: 52357--52399 Score: 59
Period size: 16 Copynumber: 2.8 Consensus size: 15
52347 TAATATTAAA
52357 TTTAATTTTTAATAT
1 TTTAATTTTTAATAT
*
52372 TTATAATTTTTCATAT
1 TT-TAATTTTTAATAT
*
52388 TTTATTTTTTAA
1 TTTAATTTTTAA
52400 GTCTGTATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTAATTTTTAATAT
Found at i:52823 original size:18 final size:19
Alignment explanation
Indices: 52788--52834 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
52778 GACTTGTTCA
*
52788 AAATTTAAGATATTTATTT-
1 AAATTTAA-ATATATATTTG
52807 AAATTTAAATATATATTTG
1 AAATTTAAATATATATTTG
*
52826 ATATTTAAA
1 AAATTTAAA
52835 AATTTTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (19 bp):
AAATTTAAATATATATTTG
Found at i:52850 original size:14 final size:15
Alignment explanation
Indices: 52830--52875 Score: 53
Period size: 14 Copynumber: 3.3 Consensus size: 15
52820 TATTTGATAT
* *
52830 TTAAAAATTTTTAAA
1 TTAAAAATATTAAAA
52845 -TAAAAATATTAAAA
1 TTAAAAATATTAAAA
52859 TTAAAAA-A-TAAAA
1 TTAAAAATATTAAAA
52872 TTAA
1 TTAA
52876 TTTAAAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 9 0.32
14 13 0.46
15 6 0.21
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
TTAAAAATATTAAAA
Found at i:52882 original size:18 final size:19
Alignment explanation
Indices: 52852--52907 Score: 80
Period size: 18 Copynumber: 3.1 Consensus size: 19
52842 AAATAAAAAT
*
52852 ATTAAAATTAAAAAATAAA
1 ATTAAACTTAAAAAATAAA
*
52871 ATT-AATTTAAAAAAT-AA
1 ATTAAACTTAAAAAATAAA
52888 ATTAAACTTAAAAAATAAA
1 ATTAAACTTAAAAAATAAA
52907 A
1 A
52908 ATTTACTAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
17 5 0.15
18 22 0.67
19 6 0.18
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.29
Consensus pattern (19 bp):
ATTAAACTTAAAAAATAAA
Found at i:53934 original size:14 final size:13
Alignment explanation
Indices: 53915--53945 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
53905 ATTGGTATGA
53915 ATTTTTTAATATAT
1 ATTTTTTAATAT-T
53929 ATTTTTTAATATT
1 ATTTTTTAATATT
53942 ATTT
1 ATTT
53946 ATATTTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.29
14 12 0.71
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
ATTTTTTAATATT
Found at i:54676 original size:20 final size:19
Alignment explanation
Indices: 54606--54678 Score: 60
Period size: 20 Copynumber: 3.6 Consensus size: 19
54596 TTAATAATTT
54606 ATTTATATATTTATATTATAA
1 ATTTATATATTTATA-TA-AA
*
54627 TTATTTA-ATAATTATATATAAT
1 --ATTTATAT-ATT-TATATAAA
54649 ATTT-TATATTTATATAAA
1 ATTTATATATTTATATAAA
54667 ATTTAATATATT
1 ATTT-ATATATT
54679 AATTTATATC
Statistics
Matches: 43, Mismatches: 2, Indels: 13
0.74 0.03 0.22
Matches are distributed among these distances:
18 11 0.26
19 3 0.07
20 12 0.28
22 3 0.07
23 10 0.23
24 4 0.09
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
ATTTATATATTTATATAAA
Found at i:54685 original size:30 final size:31
Alignment explanation
Indices: 54606--54687 Score: 80
Period size: 30 Copynumber: 2.7 Consensus size: 31
54596 TTAATAATTT
* * *
54606 ATTT-ATATATTTATATTATAATTATTTAATA
1 ATTTAATATATTAAT-TTATATTTATATAATA
* *
54637 A-TTATATATAATATTTTATATTTATATAA-A
1 ATTTA-ATATATTAATTTATATTTATATAATA
54667 ATTTAATATATTAATTTATAT
1 ATTTAATATATTAATTTATAT
54688 CCTATAATAT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
30 18 0.44
31 16 0.39
32 7 0.17
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (31 bp):
ATTTAATATATTAATTTATATTTATATAATA
Found at i:54731 original size:47 final size:47
Alignment explanation
Indices: 54643--54732 Score: 114
Period size: 47 Copynumber: 1.9 Consensus size: 47
54633 AATAATTATA
*
54643 TATAATATTTTATATTTATATAAAATTTAATATATTAATTTATATCC
1 TATAATATTGTATATTTATATAAAATTTAATATATTAATTTATATCC
*
54690 TATAATATTGTAT-TTTA-A-AATATTTATATCATATTATATTTAT
1 TATAATATTGTATATTTATATAAAATTTA-AT-ATATTA-ATTTAT
54733 TTAAATTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
44 7 0.18
45 3 0.08
46 10 0.26
47 18 0.47
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.54
Consensus pattern (47 bp):
TATAATATTGTATATTTATATAAAATTTAATATATTAATTTATATCC
Found at i:55461 original size:22 final size:22
Alignment explanation
Indices: 55434--55476 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
55424 AATTTAAAAA
*
55434 ATAT-TTTTAT-ATTAATTTTT
1 ATATATTTTATAATTAAATTTT
55454 ATATATTTTATAATTAAATTTT
1 ATATATTTTATAATTAAATTTT
55476 A
1 A
55477 ATAAAAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 4 0.20
21 6 0.30
22 10 0.50
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
ATATATTTTATAATTAAATTTT
Found at i:55516 original size:28 final size:27
Alignment explanation
Indices: 55456--55510 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 27
55446 TAATTTTTAT
**
55456 ATATTTTATAATTAAATTTTAATAAAA
1 ATATTTTATAATTAAATAATAATAAAA
*
55483 ATATTTT-TAATTAAATAATAATATAA
1 ATATTTTATAATTAAATAATAATAAAA
55509 AT
1 AT
55511 TAATTTAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
26 18 0.72
27 7 0.28
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (27 bp):
ATATTTTATAATTAAATAATAATAAAA
Found at i:56044 original size:24 final size:23
Alignment explanation
Indices: 56012--56061 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 23
56002 TAGAACCGAA
*
56012 TTAATATTATTAGATATATCATAT
1 TTAATATTATTAAATATAT-ATAT
*
56036 TTAATATTATTAAATTTATATAT
1 TTAATATTATTAAATATATATAT
56059 TTA
1 TTA
56062 TCATTTATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 7 0.29
24 17 0.71
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (23 bp):
TTAATATTATTAAATATATATAT
Found at i:56644 original size:13 final size:13
Alignment explanation
Indices: 56626--56656 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
56616 AATATATTCA
56626 TGATAATTTATTT
1 TGATAATTTATTT
56639 TGATAATTTATTT
1 TGATAATTTATTT
56652 TGATA
1 TGATA
56657 GGGAAAATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.10, T:0.58
Consensus pattern (13 bp):
TGATAATTTATTT
Found at i:57785 original size:4 final size:4
Alignment explanation
Indices: 57778--57807 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
57768 TCAATCAACA
57778 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
57808 TTGTCTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:58187 original size:12 final size:12
Alignment explanation
Indices: 58170--58212 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
58160 GCCTAACTAG
58170 TTTTATTCTTTA
1 TTTTATTCTTTA
***
58182 TTTTATGAATTA
1 TTTTATTCTTTA
58194 GTTTTATTCTTTA
1 -TTTTATTCTTTA
58207 TTTTAT
1 TTTTAT
58213 GAATTATAAA
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
12 15 0.62
13 9 0.38
ACGTcount: A:0.21, C:0.05, G:0.05, T:0.70
Consensus pattern (12 bp):
TTTTATTCTTTA
Found at i:58200 original size:25 final size:25
Alignment explanation
Indices: 58167--58218 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
58157 TATGCCTAAC
58167 TAGTTTTATTCTTTATTTTATGAAT
1 TAGTTTTATTCTTTATTTTATGAAT
58192 TAGTTTTATTCTTTATTTTATGAAT
1 TAGTTTTATTCTTTATTTTATGAAT
58217 TA
1 TA
58219 TAAAAAGAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.25, C:0.04, G:0.08, T:0.63
Consensus pattern (25 bp):
TAGTTTTATTCTTTATTTTATGAAT
Found at i:61571 original size:2 final size:2
Alignment explanation
Indices: 61564--61596 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
61554 CTTCAGAATG
61564 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
61597 TGTTAAAAGC
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:63196 original size:242 final size:245
Alignment explanation
Indices: 62875--63371 Score: 869
Period size: 242 Copynumber: 2.0 Consensus size: 245
62865 TTTGAACTAA
*
62875 AATT-AATTTAGTGAAAATAAATAATTGAAAATTTTCATTAACAAGTGTTTTAAAAACACTTACT
1 AATTGAATTAAGTGAAAATAAATAATT-AAAATTTTCATTAACAAGTGTTTTAAAAACACTTACT
* * *
62939 AAAATTAATAAATTATTATTTGTAACAATATTTTACATTAAATATAATAATTAATAATCAATTTA
65 AAAATTAACAAATTATTATTTATAACAATATTTTAAATTAAATATAATAATTAATAATCAATTTA
*
63004 ATAATTCTTAATATGTGAAAAATTGTAATTTATTT-TTAAAAAAATGAATTAAAGTCTTTGTTAG
130 ATAATTCTTAATATGTGAAAAATTATAATTTATTTCTT-AAAAAATGAATTAAAGTCTTTGTTAG
63068 -AAAAAAAATGAGGTGGGGCAAAGCACAAATATTGGAAATTTGGAGACCCAG
194 AAAAAAAAATGAGGTGGGGCAAAGCACAAATATTGGAAATTTGGAGACCCAG
*
63119 AATTGAATTAAGTGAAAATAAATCATT-AAA-TTTCATTAACAAGTGTTTTAAAAACACTTACTA
1 AATTGAATTAAGTGAAAATAAATAATTAAAATTTTCATTAACAAGTGTTTTAAAAACACTTACTA
*
63182 AAATTAACAAATTATTATTTATAATAATATTTTAAATTAAATATAATAATTAATAATCAATTTAA
66 AAATTAACAAATTATTATTTATAACAATATTTTAAATTAAATATAATAATTAATAATCAATTTAA
*
63247 TAATTCTTAATATGTGAAAAATTATAATTTATTTCTTAAAAAATGATTTAAAGTCTTTGTTAGAA
131 TAATTCTTAATATGTGAAAAATTATAATTTATTTCTTAAAAAATGAATTAAAGTCTTTGTTAGAA
63312 AAAAAAATGAGGTGGGGCAAAGCACAAATATTGGAAATTTGGAGACCCAG
196 AAAAAAATGAGGTGGGGCAAAGCACAAATATTGGAAATTTGGAGACCCAG
63362 AATTGAATTA
1 AATTGAATTA
63372 TGAAAAGCAA
Statistics
Matches: 242, Mismatches: 8, Indels: 7
0.94 0.03 0.03
Matches are distributed among these distances:
242 152 0.63
243 66 0.27
244 4 0.02
245 20 0.08
ACGTcount: A:0.47, C:0.07, G:0.11, T:0.36
Consensus pattern (245 bp):
AATTGAATTAAGTGAAAATAAATAATTAAAATTTTCATTAACAAGTGTTTTAAAAACACTTACTA
AAATTAACAAATTATTATTTATAACAATATTTTAAATTAAATATAATAATTAATAATCAATTTAA
TAATTCTTAATATGTGAAAAATTATAATTTATTTCTTAAAAAATGAATTAAAGTCTTTGTTAGAA
AAAAAAATGAGGTGGGGCAAAGCACAAATATTGGAAATTTGGAGACCCAG
Found at i:72202 original size:13 final size:13
Alignment explanation
Indices: 72184--72208 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
72174 TTACAAATAT
72184 ACTAAAATGGAAA
1 ACTAAAATGGAAA
72197 ACTAAAATGGAA
1 ACTAAAATGGAA
72209 TATTAGAAAC
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:0.60, C:0.08, G:0.16, T:0.16
Consensus pattern (13 bp):
ACTAAAATGGAAA
Found at i:77219 original size:2 final size:2
Alignment explanation
Indices: 77212--77242 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
77202 AATTCCCCCA
77212 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
77243 AGAAAAAAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:85646 original size:2 final size:2
Alignment explanation
Indices: 85639--85683 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
85629 TGAACACTTT
*
85639 TA TA TA TA TA TA TA TA TA TA TA TA TC TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
85681 TA T
1 TA T
85684 TGTATAGTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:88267 original size:2 final size:2
Alignment explanation
Indices: 88260--88289 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
88250 TTATCACATG
*
88260 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
88290 GTAAAGTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:88559 original size:36 final size:36
Alignment explanation
Indices: 88519--88588 Score: 122
Period size: 36 Copynumber: 1.9 Consensus size: 36
88509 ATTCCATTTC
* *
88519 GACTAGGATCGATGGTAACATTTGCCTGGATTCCGA
1 GACTAGGATCAATGATAACATTTGCCTGGATTCCGA
88555 GACTAGGATCAATGATAACATTTGCCTGGATTCC
1 GACTAGGATCAATGATAACATTTGCCTGGATTCC
88589 AAGAATTTGG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (36 bp):
GACTAGGATCAATGATAACATTTGCCTGGATTCCGA
Found at i:91397 original size:21 final size:21
Alignment explanation
Indices: 91371--91415 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
91361 AGACAGTGCA
91371 CATTTTGATATAGTTTGTTGG
1 CATTTTGATATAGTTTGTTGG
91392 CATTTTGATATAGTTTGTTGG
1 CATTTTGATATAGTTTGTTGG
91413 CAT
1 CAT
91416 CGAAATTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.20, C:0.07, G:0.22, T:0.51
Consensus pattern (21 bp):
CATTTTGATATAGTTTGTTGG
Found at i:94174 original size:11 final size:11
Alignment explanation
Indices: 94158--94182 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
94148 TTAAATACAT
94158 AAAAAAATTAA
1 AAAAAAATTAA
94169 AAAAAAATTAA
1 AAAAAAATTAA
94180 AAA
1 AAA
94183 TACTCATATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAAAAATTAA
Found at i:94939 original size:13 final size:12
Alignment explanation
Indices: 94921--94962 Score: 50
Period size: 13 Copynumber: 3.5 Consensus size: 12
94911 TTACGTGTTG
94921 AAATATTAATAT
1 AAATATTAATAT
*
94933 CAAATATAAATAT
1 -AAATATTAATAT
*
94946 ATAT-TTAATAT
1 AAATATTAATAT
94957 AAATAT
1 AAATAT
94963 ATTTAATTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
11 9 0.38
12 4 0.17
13 11 0.46
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (12 bp):
AAATATTAATAT
Found at i:95501 original size:60 final size:60
Alignment explanation
Indices: 95408--95527 Score: 222
Period size: 60 Copynumber: 2.0 Consensus size: 60
95398 AGGTACTTAT
*
95408 ATATGGTAAACGAGTCAATCGATGATATAAAGTCATGAAAGAATAACATAAACTGCTAAC
1 ATATGGTAAACGAGTCAATCGATGATATAAAGTCATGAAAGAATAACATAAACTGATAAC
*
95468 ATATGGTAAACGAGTCAATCGATGATATAAAGTCATGTAAGAATAACATAAACTGATAAC
1 ATATGGTAAACGAGTCAATCGATGATATAAAGTCATGAAAGAATAACATAAACTGATAAC
95528 CTGTTAAGAG
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 58 1.00
ACGTcount: A:0.47, C:0.12, G:0.17, T:0.24
Consensus pattern (60 bp):
ATATGGTAAACGAGTCAATCGATGATATAAAGTCATGAAAGAATAACATAAACTGATAAC
Found at i:96435 original size:16 final size:17
Alignment explanation
Indices: 96404--96438 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
96394 CACACACCTA
*
96404 ATCTCATGCATGCATAC
1 ATCTCATGCATACATAC
96421 ATCTC-TGCATACATAC
1 ATCTCATGCATACATAC
96437 AT
1 AT
96439 ACATAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.31, C:0.29, G:0.09, T:0.31
Consensus pattern (17 bp):
ATCTCATGCATACATAC
Found at i:100349 original size:15 final size:15
Alignment explanation
Indices: 100329--100366 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
100319 GTAGGAAGAG
100329 AAATAATAAAGCC-GA
1 AAATAA-AAAGCCGGA
*
100344 AAATAAACAGCCGGA
1 AAATAAAAAGCCGGA
100359 AAATAAAA
1 AAATAAAA
100367 TATTTTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 5 0.25
15 15 0.75
ACGTcount: A:0.63, C:0.13, G:0.13, T:0.11
Consensus pattern (15 bp):
AAATAAAAAGCCGGA
Found at i:102445 original size:2 final size:2
Alignment explanation
Indices: 102433--102471 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
102423 ATACATCGGT
*
102433 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
102472 TCGAAACAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:105917 original size:4 final size:4
Alignment explanation
Indices: 105908--105933 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
105898 AAGTGATTAG
105908 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
105934 AATAATGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:110927 original size:32 final size:32
Alignment explanation
Indices: 110870--110944 Score: 84
Period size: 33 Copynumber: 2.4 Consensus size: 32
110860 ACAAAGAGGG
* *
110870 AAAAACATGAAAACAAGTAAATGAAAAAGCAAA
1 AAAAACACGAAAACAAGTAAATGAAAAA-AAAA
*
110903 AAAAGCACGAAAA-AAG-AAATTGAAAAAAAAA
1 AAAAACACGAAAACAAGTAAA-TGAAAAAAAAA
110934 AAAAA-ACGAAA
1 AAAAACACGAAA
110945 CTGAAAGAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
30 6 0.16
31 10 0.27
32 10 0.27
33 11 0.30
ACGTcount: A:0.73, C:0.08, G:0.12, T:0.07
Consensus pattern (32 bp):
AAAAACACGAAAACAAGTAAATGAAAAAAAAA
Found at i:110935 original size:31 final size:32
Alignment explanation
Indices: 110870--110944 Score: 84
Period size: 30 Copynumber: 2.4 Consensus size: 32
110860 ACAAAGAGGG
*
110870 AAAAACATGAAAACAAGTAAATGAAAAAGCAAA
1 AAAAACACGAAAACAAGTAAATGAAAAAG-AAA
*
110903 AAAAGCACGAAAA-AAG-AAATTGAAAAA-AAA
1 AAAAACACGAAAACAAGTAAA-TGAAAAAGAAA
*
110933 AAAAAAACGAAA
1 AAAAACACGAAA
110945 CTGAAAGAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
30 13 0.35
31 3 0.08
32 10 0.27
33 11 0.30
ACGTcount: A:0.73, C:0.08, G:0.12, T:0.07
Consensus pattern (32 bp):
AAAAACACGAAAACAAGTAAATGAAAAAGAAA
Found at i:110938 original size:23 final size:23
Alignment explanation
Indices: 110912--110955 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
110902 AAAAAGCACG
*
110912 AAAAAAGAAATTGAAAAAAAAAA
1 AAAAAAGAAACTGAAAAAAAAAA
* *
110935 AAAAACGAAACTGAAAGAAAA
1 AAAAAAGAAACTGAAAAAAAA
110956 TGTTTCGCTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.77, C:0.05, G:0.11, T:0.07
Consensus pattern (23 bp):
AAAAAAGAAACTGAAAAAAAAAA
Found at i:114572 original size:18 final size:18
Alignment explanation
Indices: 114549--114585 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
114539 GATCATGGCC
* *
114549 AGAAAGAGAGAGGGAGAG
1 AGAAAGAGAAAGAGAGAG
114567 AGAAAGAGAAAGAGAGAG
1 AGAAAGAGAAAGAGAGAG
114585 A
1 A
114586 TTATAAGGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (18 bp):
AGAAAGAGAAAGAGAGAG
Found at i:123037 original size:24 final size:24
Alignment explanation
Indices: 123010--123058 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
123000 ATAAAATAAT
123010 TCATATCCATATCATGGTTGATAC
1 TCATATCCATATCATGGTTGATAC
*
123034 TCATATCCGTATCATGGTTGATAC
1 TCATATCCATATCATGGTTGATAC
123058 T
1 T
123059 TGATCCTCCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.39
Consensus pattern (24 bp):
TCATATCCATATCATGGTTGATAC
Found at i:128123 original size:18 final size:18
Alignment explanation
Indices: 128081--128128 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
128071 AAAAAAGCGT
128081 AAAAAAA-GAAAATGAAA
1 AAAAAAACGAAAATGAAA
* *
128098 AAAAAAACGAAACTGAAC
1 AAAAAAACGAAAATGAAA
128116 AAAAAAACTGAAA
1 AAAAAAAC-GAAA
128129 GAAAATGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
17 7 0.26
18 16 0.59
19 4 0.15
ACGTcount: A:0.75, C:0.08, G:0.10, T:0.06
Consensus pattern (18 bp):
AAAAAAACGAAAATGAAA
Found at i:129739 original size:2 final size:2
Alignment explanation
Indices: 129732--129784 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
129722 AGATAGCAGC
*
129732 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA AA 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
129774 GA GA GA GA GA G
1 GA GA GA GA GA G
129785 CGATAAGATT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
GA
Found at i:138071 original size:11 final size:11
Alignment explanation
Indices: 138043--138093 Score: 54
Period size: 11 Copynumber: 4.9 Consensus size: 11
138033 TTCTAAGCTG
*
138043 ATATAATTTTG
1 ATATAATTTTA
138054 AT-T-ATTTTA
1 ATATAATTTTA
138063 ATATAATTTTA
1 ATATAATTTTA
*
138074 ATA-AATTTTT
1 ATATAATTTTA
*
138084 ATACAATTTT
1 ATATAATTTT
138094 GATAACTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
9 7 0.20
10 11 0.31
11 17 0.49
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (11 bp):
ATATAATTTTA
Found at i:138091 original size:21 final size:21
Alignment explanation
Indices: 138057--138103 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
138047 AATTTTGATT
*
138057 ATTTTAATATAATTTTAATAA
1 ATTTTAATACAATTTTAATAA
* *
138078 ATTTTTATACAATTTTGATAA
1 ATTTTAATACAATTTTAATAA
*
138099 CTTTT
1 ATTTT
138104 GATATGATAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.55
Consensus pattern (21 bp):
ATTTTAATACAATTTTAATAA
Found at i:138169 original size:21 final size:20
Alignment explanation
Indices: 138145--138225 Score: 67
Period size: 21 Copynumber: 3.9 Consensus size: 20
138135 GATTATCTTA
*
138145 GATAATTTTTTATATAATTT
1 GATAATCTTTTATATAATTT
138165 CGATAA-CTTTTATATAAATTT
1 -GATAATCTTTTATAT-AATTT
*
138186 GAGTAATCTTTCATATAAATATT
1 GA-TAATCTTTTATAT-AAT-TT
* *
138209 -ATGATCTTTAATATAAT
1 GATAATCTTTTATATAAT
138226 ATTAGCAGCC
Statistics
Matches: 52, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
20 13 0.25
21 24 0.46
22 13 0.25
23 2 0.04
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.49
Consensus pattern (20 bp):
GATAATCTTTTATATAATTT
Found at i:138180 original size:22 final size:20
Alignment explanation
Indices: 138152--138205 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 20
138142 TTAGATAATT
138152 TTTTATAT-AATTTCGATAAC
1 TTTTATATAAATTT-GATAAC
138172 TTTTATATAAATTTGAGTAATC
1 TTTTATATAAATTTGA-TAA-C
*
138194 TTTCATATAAAT
1 TTTTATATAAAT
138206 ATTATGATCT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 10 0.33
21 8 0.27
22 12 0.40
ACGTcount: A:0.37, C:0.07, G:0.06, T:0.50
Consensus pattern (20 bp):
TTTTATATAAATTTGATAAC
Found at i:138228 original size:20 final size:21
Alignment explanation
Indices: 138191--138229 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
138181 AATTTGAGTA
*
138191 ATCTTTCATATAAATATTATG
1 ATCTTTAATATAAATATTATG
138212 ATCTTTAATAT-AATATTA
1 ATCTTTAATATAAATATTA
138230 GCAGCCTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.41, C:0.08, G:0.03, T:0.49
Consensus pattern (21 bp):
ATCTTTAATATAAATATTATG
Found at i:138277 original size:21 final size:21
Alignment explanation
Indices: 138239--138310 Score: 63
Period size: 21 Copynumber: 3.4 Consensus size: 21
138229 AGCAGCCTTT
* *
138239 ATAATTTTGGTGACATTTGTA
1 ATAATTTTGGTAACATTTATA
* * *
138260 ATAATTTTTGTAATATTTATT
1 ATAATTTTGGTAACATTTATA
* * *
138281 ATAATTTTGATAAAATTAATA
1 ATAATTTTGGTAACATTTATA
*
138302 ATAAATTTG
1 ATAATTTTG
138311 ATAATTTTTT
Statistics
Matches: 40, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.39, C:0.01, G:0.10, T:0.50
Consensus pattern (21 bp):
ATAATTTTGGTAACATTTATA
Found at i:138472 original size:19 final size:19
Alignment explanation
Indices: 138441--138478 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
138431 TTTTTATTTA
138441 AAATTTAATTATAAAATAT
1 AAATTTAATTATAAAATAT
138460 AAATATTAA-TATAAAATAT
1 AAAT-TTAATTATAAAATAT
138479 TTAATTTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
AAATTTAATTATAAAATAT
Found at i:138628 original size:21 final size:21
Alignment explanation
Indices: 138597--138713 Score: 83
Period size: 21 Copynumber: 5.5 Consensus size: 21
138587 TGAACACCTC
138597 TAATTATTGATAACCTTTAATA
1 TAATT-TTGATAACCTTTAATA
**
138619 TAATTTTGATAATATTATAA-A
1 TAATTTTGATAACCTT-TAATA
* * * *
138640 TGATTTTAACAACCTTTATTA
1 TAATTTTGATAACCTTTAATA
* *
138661 TAATTTTAATAACCTTTAATG
1 TAATTTTGATAACCTTTAATA
* * ** *
138682 TAGTTGTGATAATATTTCATA
1 TAATTTTGATAACCTTTAATA
*
138703 TAATTTGGATA
1 TAATTTTGATA
138714 TATTTACTAC
Statistics
Matches: 71, Mismatches: 22, Indels: 5
0.72 0.22 0.05
Matches are distributed among these distances:
20 2 0.03
21 61 0.86
22 8 0.11
ACGTcount: A:0.38, C:0.07, G:0.08, T:0.47
Consensus pattern (21 bp):
TAATTTTGATAACCTTTAATA
Found at i:146208 original size:2 final size:2
Alignment explanation
Indices: 146201--146225 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
146191 TCATGGCCAC
146201 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 A
146226 TTATAAAGGC
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:148575 original size:28 final size:28
Alignment explanation
Indices: 148522--148604 Score: 132
Period size: 28 Copynumber: 3.0 Consensus size: 28
148512 TACCTCAAGC
148522 CTGTACTTCCT-GCAAAGCATCAGGAAA
1 CTGTACTTCCTGGCAAAGCATCAGGAAA
* *
148549 CTGTATTTCCTGGCAAAGCATCGGGAAA
1 CTGTACTTCCTGGCAAAGCATCAGGAAA
*
148577 CTGTACTTCCTGGTAAAGCATCAGGAAA
1 CTGTACTTCCTGGCAAAGCATCAGGAAA
148605 TGGAGATCGG
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
27 10 0.20
28 40 0.80
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.24
Consensus pattern (28 bp):
CTGTACTTCCTGGCAAAGCATCAGGAAA
Found at i:155177 original size:26 final size:26
Alignment explanation
Indices: 155143--155195 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
155133 CTAGGGTTTA
155143 TTAATTATTACTTTATTATAACAAGT
1 TTAATTATTACTTTATTATAACAAGT
155169 TTAATTATTACTTTATTATAACAAGT
1 TTAATTATTACTTTATTATAACAAGT
155195 T
1 T
155196 CAGAAAATAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.38, C:0.08, G:0.04, T:0.51
Consensus pattern (26 bp):
TTAATTATTACTTTATTATAACAAGT
Found at i:159603 original size:29 final size:29
Alignment explanation
Indices: 159561--159618 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
159551 GAGTAAAATA
159561 TGGTACACCACAGGCAAGAAAAACTAGCC
1 TGGTACACCACAGGCAAGAAAAACTAGCC
159590 TGGTACACCACAGGCAAGAAAAACTAGCC
1 TGGTACACCACAGGCAAGAAAAACTAGCC
159619 CAGAAACTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.41, C:0.28, G:0.21, T:0.10
Consensus pattern (29 bp):
TGGTACACCACAGGCAAGAAAAACTAGCC
Found at i:165073 original size:13 final size:13
Alignment explanation
Indices: 165055--165080 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
165045 CCACTAACCA
165055 GCTGACTTGATTT
1 GCTGACTTGATTT
165068 GCTGACTTGATTT
1 GCTGACTTGATTT
165081 TTAATGTGAA
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:0.15, C:0.15, G:0.23, T:0.46
Consensus pattern (13 bp):
GCTGACTTGATTT
Found at i:165676 original size:28 final size:28
Alignment explanation
Indices: 165636--165719 Score: 141
Period size: 28 Copynumber: 3.0 Consensus size: 28
165626 TACCTCAAGC
165636 CTGTACTTCCTGGCAAAGCATCAGGAAA
1 CTGTACTTCCTGGCAAAGCATCAGGAAA
* *
165664 CTGTATTTCCTGGCAAAGCATCGGGAAA
1 CTGTACTTCCTGGCAAAGCATCAGGAAA
*
165692 CTGTACTTCCTGGTAAAGCATCAGGAAA
1 CTGTACTTCCTGGCAAAGCATCAGGAAA
165720 TGGAGATCGG
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 51 1.00
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.24
Consensus pattern (28 bp):
CTGTACTTCCTGGCAAAGCATCAGGAAA
Found at i:172299 original size:26 final size:26
Alignment explanation
Indices: 172265--172317 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
172255 CTAGGGTTTA
172265 TTAATTATTACTTTATTATAACAAGT
1 TTAATTATTACTTTATTATAACAAGT
172291 TTAATTATTACTTTATTATAACAAGT
1 TTAATTATTACTTTATTATAACAAGT
172317 T
1 T
172318 CAGAAAATAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.38, C:0.08, G:0.04, T:0.51
Consensus pattern (26 bp):
TTAATTATTACTTTATTATAACAAGT
Found at i:179290 original size:21 final size:22
Alignment explanation
Indices: 179264--179305 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
179254 AGTTTCTCAA
*
179264 TATTTTAAT-TTCAAAATATTT
1 TATTTTAATACTCAAAATATTT
*
179285 TATTTTTATACTCAAAATATT
1 TATTTTAATACTCAAAATATT
179306 AAAATATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (22 bp):
TATTTTAATACTCAAAATATTT
Found at i:179384 original size:22 final size:21
Alignment explanation
Indices: 179359--179437 Score: 59
Period size: 22 Copynumber: 3.3 Consensus size: 21
179349 ATCTAAATTA
179359 AAAAATTTATTTAAATATAAAT
1 AAAAATTTATTT-AATATAAAT
*
179381 AAAAATTAAAAATTATTTTAATAAAAATT
1 AAAAA-T-----TTA-TTTAATATAAA-T
179410 AAAAATTTATTTAATATAAAT
1 AAAAATTTATTTAATATAAAT
*
179431 TAAAATT
1 AAAAATT
179438 ATTGACTTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 17
0.70 0.05 0.26
Matches are distributed among these distances:
21 7 0.15
22 15 0.33
23 4 0.09
28 11 0.24
29 9 0.20
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
AAAAATTTATTTAATATAAAT
Found at i:179391 original size:28 final size:27
Alignment explanation
Indices: 179360--179438 Score: 87
Period size: 28 Copynumber: 3.0 Consensus size: 27
179350 TCTAAATTAA
179360 AAAATTTATTTAAATATAAATAAAAATT
1 AAAATTTATTT-AATATAAATAAAAATT
*
179388 AAAAATTA-TT--T-T-AATAAAAATT
1 AAAATTTATTTAATATAAATAAAAATT
*
179410 AAAAATTTATTTAATATAAATTAAAATT
1 -AAAATTTATTTAATATAAATAAAAATT
179438 A
1 A
179439 TTGACTTTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 13
0.72 0.05 0.22
Matches are distributed among these distances:
22 10 0.24
23 8 0.19
24 3 0.07
26 1 0.02
27 4 0.10
28 16 0.38
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (27 bp):
AAAATTTATTTAATATAAATAAAAATT
Found at i:179401 original size:29 final size:30
Alignment explanation
Indices: 179353--179416 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 30
179343 TTTTATATCT
*
179353 AAATTAAAAAATTTATTTAAATATAAA-TAA
1 AAATTAAAAAATTTATTT-AATAAAAATTAA
179383 AAATT-AAAAA-TTATTTTAATAAAAATTAA
1 AAATTAAAAAATTTA-TTTAATAAAAATTAA
179412 AAATT
1 AAATT
179417 TATTTAATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
28 10 0.32
29 16 0.52
30 5 0.16
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (30 bp):
AAATTAAAAAATTTATTTAATAAAAATTAA
Found at i:179407 original size:23 final size:22
Alignment explanation
Indices: 179378--179440 Score: 94
Period size: 22 Copynumber: 2.9 Consensus size: 22
179368 TTTAAATATA
179378 AATAAAAATTAAAAATTATTTT
1 AATAAAAATTAAAAATTATTTT
179400 AATAAAAATTAAAAATT-TATTT
1 AATAAAAATTAAAAATTAT-TTT
*
179422 AATATAAATT-AAAATTATT
1 AATAAAAATTAAAAATTATT
179441 GACTTTTTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
21 8 0.21
22 30 0.79
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
AATAAAAATTAAAAATTATTTT
Found at i:179791 original size:22 final size:22
Alignment explanation
Indices: 179766--179810 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
179756 TAGATTTTGT
* *
179766 TTTATTTTATTAATAATTTTTA
1 TTTATTTTATAAATAATATTTA
179788 TTTATTTTATAAATAATATTTA
1 TTTATTTTATAAATAATATTTA
179810 T
1 T
179811 ATTACTTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
TTTATTTTATAAATAATATTTA
Found at i:179867 original size:14 final size:14
Alignment explanation
Indices: 179850--179876 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
179840 TTCTACTATT
179850 ATTATTTTTTTATA
1 ATTATTTTTTTATA
179864 ATTATTTTTTTAT
1 ATTATTTTTTTAT
179877 TTCATAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
ATTATTTTTTTATA
Found at i:183352 original size:236 final size:229
Alignment explanation
Indices: 182938--183394 Score: 652
Period size: 237 Copynumber: 2.0 Consensus size: 229
182928 CGAAAATCGA
182938 TTGCTTCATTATCTTCCACTTGGCCTATCTAACAAACTAAAAGAAGGCAAGCAGAATACAATATA
1 TTGCTTCATTATCTTCCACTTGGCCTATCTAACAAACTAAAAGAAGGCAAGCAGAATACAATATA
* *
183003 AAAAAGAAACCTTTTAAAACTAAAATAAAAAAGACTGGAACACCAAGGCCAACCCAGGACCTTGC
66 AAAAAGAAACCTTTTAAAACTAAAATAAAAAAGACTAGAACACCAAGGCCAACCCAGCACCTTGC
* * *
183068 TTAATTACTCTAAATCAATTGGGTTCATAAAAAGAATAGCTCGGAAATGGACA-ATCATTCAAAA
131 CTAATTACCCTAAATCAATTGGGTTCATAAAAAGAACAGCTCGGAAATGGACATATCATTCAAAA
183132 AAACTCTTTCACCAGTATCCTTTCTAGAGCTGGT
196 AAACTCTTTCACCAGTATCCTTTCTAGAGCTGGT
* *
183166 TTGCTTCATTGTCTTCCACTTGGCCTATCTACCAAACTACAGGAAGACAAGAAGGCAAGCAGAAT
1 TTGCTTCATTATCTTCCACTTGGCCTATCTAACAAACT------A-A-AAGAAGGCAAGCAGAAT
* * *
183231 ACATTAT-AAAAAGAAACCTTTTAAAATTAAAAT-AAAAAGAATCTAGAACACCAAGGCCAAATC
58 ACAATATAAAAAAGAAACCTTTTAAAACTAAAATAAAAAAG-A-CTAGAACACCAAGGCC-AACC
* * *
183294 CATCACCTTGCCTAGTTACCCTAAATCAATTGGGTTCAT-AAAAGAACAGCTTGGAAATGGACAT
120 CAGCACCTTGCCTAATTACCCTAAATCAATTGGGTTCATAAAAAGAACAGCTCGGAAATGGACAT
* *
183358 ATCATTCAAAAAACCTCTTTCACCAGTTTCCTTTCTA
185 ATCATTCAAAAAAACTCTTTCACCAGTATCCTTTCTA
183395 AAAACTGGTT
Statistics
Matches: 202, Mismatches: 15, Indels: 15
0.87 0.06 0.06
Matches are distributed among these distances:
228 36 0.18
234 7 0.03
235 27 0.13
236 60 0.30
237 72 0.36
ACGTcount: A:0.40, C:0.21, G:0.13, T:0.26
Consensus pattern (229 bp):
TTGCTTCATTATCTTCCACTTGGCCTATCTAACAAACTAAAAGAAGGCAAGCAGAATACAATATA
AAAAAGAAACCTTTTAAAACTAAAATAAAAAAGACTAGAACACCAAGGCCAACCCAGCACCTTGC
CTAATTACCCTAAATCAATTGGGTTCATAAAAAGAACAGCTCGGAAATGGACATATCATTCAAAA
AAACTCTTTCACCAGTATCCTTTCTAGAGCTGGT
Done.