Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold761
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: 110815
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:160 original size:11 final size:11
Alignment explanation
Indices: 129--162 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
119 GCATAAAGAC
129 GTTCACACCAT
1 GTTCACACCAT
*
140 GTTCA-GCCAT
1 GTTCACACCAT
150 GTTCACACCAT
1 GTTCACACCAT
161 GT
1 GT
163 GGCTCTTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.24, C:0.32, G:0.15, T:0.29
Consensus pattern (11 bp):
GTTCACACCAT
Found at i:1461 original size:18 final size:18
Alignment explanation
Indices: 1423--1462 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1413 TAATCGAAAG
* **
1423 AAAAGAAAAAGAGATTGA
1 AAAAGAAAAAGAAATAAA
1441 AAAAGAAAAAGAAATAAA
1 AAAAGAAAAAGAAATAAA
1459 AAAA
1 AAAA
1463 AGAGTGAGGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAATAAA
Found at i:6656 original size:20 final size:19
Alignment explanation
Indices: 6621--6658 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
6611 GAGTTAAGAC
*
6621 GAGCTCAATGAGCTGAATT
1 GAGCTCAATAAGCTGAATT
6640 GAGCTCGAATAAGCTGAAT
1 GAGCTC-AATAAGCTGAAT
6659 CGAAAATGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.34, C:0.16, G:0.26, T:0.24
Consensus pattern (19 bp):
GAGCTCAATAAGCTGAATT
Found at i:9069 original size:23 final size:22
Alignment explanation
Indices: 9017--9069 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
9007 TCCACGTCTT
*
9017 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
9039 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
9062 TTTCTTTT
1 TTTCTTTT
9070 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:16648 original size:23 final size:23
Alignment explanation
Indices: 16619--16671 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
16609 ATGGTATTGT
*
16619 AAAAAAA-TAAAAAAAAAACTTGA
1 AAAAAAATTAAAAAAAAAA-TTCA
*
16642 AAAAAAATTCAAAAAAAAATTCA
1 AAAAAAATTAAAAAAAAAATTCA
16665 AAAAAAA
1 AAAAAAA
16672 AATTTTGTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 17 0.63
24 10 0.37
ACGTcount: A:0.79, C:0.06, G:0.02, T:0.13
Consensus pattern (23 bp):
AAAAAAATTAAAAAAAAAATTCA
Found at i:16675 original size:13 final size:12
Alignment explanation
Indices: 16619--16672 Score: 67
Period size: 12 Copynumber: 4.6 Consensus size: 12
16609 ATGGTATTGT
*
16619 AAAAAAA-TAAA
1 AAAAAAATTCAA
*
16630 AAAAAAACTT-GA
1 AAAAAAA-TTCAA
16642 AAAAAAATTCAA
1 AAAAAAATTCAA
16654 AAAAAAATTCAA
1 AAAAAAATTCAA
16666 AAAAAAA
1 AAAAAAA
16673 ATTTTGTATT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
11 9 0.24
12 28 0.74
13 1 0.03
ACGTcount: A:0.80, C:0.06, G:0.02, T:0.13
Consensus pattern (12 bp):
AAAAAAATTCAA
Found at i:16738 original size:14 final size:13
Alignment explanation
Indices: 16713--16769 Score: 51
Period size: 13 Copynumber: 4.0 Consensus size: 13
16703 ATTTAGTATT
*
16713 GAAGGAAAAAAAA
1 GAAGAAAAAAAAA
16726 GAAGAAGAAAAAATTCA
1 GAAGAA-AAAAAA---A
*
16743 GAATTAAAAAAAAA
1 GAA-GAAAAAAAAA
16757 GAAGAAAAAAAAA
1 GAAGAAAAAAAAA
16770 TCGAAATTGA
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
13 14 0.39
14 10 0.28
17 10 0.28
18 2 0.06
ACGTcount: A:0.75, C:0.02, G:0.16, T:0.07
Consensus pattern (13 bp):
GAAGAAAAAAAAA
Found at i:16782 original size:28 final size:30
Alignment explanation
Indices: 16718--16786 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 30
16708 GTATTGAAGG
*
16718 AAAAAAAAGAAGAAGAAAAAATTCAGAATT
1 AAAAAAAAGAAGAAGAAAAAAATCAGAATT
16748 AAAAAAAAAGAAGAA-AAAAAAATC-GAAATT
1 -AAAAAAAAGAAGAAGAAAAAAATCAG-AATT
16778 GAAAAAAAA
1 -AAAAAAAA
16787 AGAGTGATTG
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
29 1 0.03
30 20 0.57
31 14 0.40
ACGTcount: A:0.75, C:0.03, G:0.12, T:0.10
Consensus pattern (30 bp):
AAAAAAAAGAAGAAGAAAAAAATCAGAATT
Found at i:16789 original size:28 final size:31
Alignment explanation
Indices: 16718--16789 Score: 103
Period size: 31 Copynumber: 2.3 Consensus size: 31
16708 GTATTGAAGG
*
16718 AAAAAAAAGAAGAAGAAAAAATTCAGAATTA
1 AAAAAAAAGAAGAAGAAAAAAATCAGAATTA
16749 AAAAAAAAGAAGAA-AAAAAAATC-GAAATTGA
1 AAAAAAAAGAAGAAGAAAAAAATCAG-AATT-A
16780 AAAAAAAAGA
1 AAAAAAAAGA
16790 GTGATTGAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
29 1 0.03
30 12 0.32
31 25 0.66
ACGTcount: A:0.75, C:0.03, G:0.12, T:0.10
Consensus pattern (31 bp):
AAAAAAAAGAAGAAGAAAAAAATCAGAATTA
Found at i:30082 original size:89 final size:89
Alignment explanation
Indices: 29977--30147 Score: 324
Period size: 89 Copynumber: 1.9 Consensus size: 89
29967 CATTTAATGA
29977 TACGGGGTTGCGCGCGGACCAAGATCGAGTTGCCAAGTCACGGGAAACTCCTACGAAAACCCTAA
1 TACGGGGTTGCGCGCGGACCAAGATCGAGTTGCCAAGTCACGGGAAACTCCTACGAAAACCCTAA
30042 ACAATCAGATCCGAAACAAAATAG
66 ACAATCAGATCCGAAACAAAATAG
*
30066 TACGGGGTTGCGCGCGGACCAAGATCGAGTTGCCAAGTCACGGGAAACTCCTATGAAAACCCTAA
1 TACGGGGTTGCGCGCGGACCAAGATCGAGTTGCCAAGTCACGGGAAACTCCTACGAAAACCCTAA
*
30131 ACAATTAGATCCGAAAC
66 ACAATCAGATCCGAAAC
30148 GAAACAGAAA
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
89 80 1.00
ACGTcount: A:0.35, C:0.26, G:0.24, T:0.16
Consensus pattern (89 bp):
TACGGGGTTGCGCGCGGACCAAGATCGAGTTGCCAAGTCACGGGAAACTCCTACGAAAACCCTAA
ACAATCAGATCCGAAACAAAATAG
Found at i:32023 original size:48 final size:48
Alignment explanation
Indices: 31967--32071 Score: 128
Period size: 48 Copynumber: 2.2 Consensus size: 48
31957 TTGTCTTTTC
*
31967 TTTC-TTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
32014 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
32062 TTTCTTTTTC
1 TTTCTTTTTC
32072 CATGACACTC
Statistics
Matches: 51, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
47 4 0.08
48 35 0.69
49 8 0.16
50 4 0.08
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:33128 original size:21 final size:21
Alignment explanation
Indices: 33080--33135 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
33070 GCAAGACTTT
*
33080 TCACTTTTTTTTTCTTCTTTTT
1 TCAC-TTTTTTTTCTTCTTTTC
*
33102 TTACTTTTTTTTCTT-TTTTGC
1 TCACTTTTTTTTCTTCTTTT-C
33123 TCACTTCTTTTTT
1 TCACTT-TTTTTT
33136 TTCGAATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 4 0.14
21 16 0.55
22 9 0.31
ACGTcount: A:0.05, C:0.18, G:0.02, T:0.75
Consensus pattern (21 bp):
TCACTTTTTTTTCTTCTTTTC
Found at i:34697 original size:20 final size:20
Alignment explanation
Indices: 34654--34697 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
34644 GGGTTAAGAT
*
34654 TGAGTTGAATTGAGCTTGAA
1 TGAGTTGAATTGAGCTCGAA
* *
34674 TGAGTTGACTTGAGCTCGAG
1 TGAGTTGAATTGAGCTCGAA
34694 TGAG
1 TGAG
34698 CTGGAAACAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.25, C:0.09, G:0.34, T:0.32
Consensus pattern (20 bp):
TGAGTTGAATTGAGCTCGAA
Found at i:38124 original size:17 final size:18
Alignment explanation
Indices: 38102--38138 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
38092 TGGAATAAAC
38102 TTAGTTAA-TTAAATAAG
1 TTAGTTAATTTAAATAAG
*
38119 TTAGTTAATTTAATTAAG
1 TTAGTTAATTTAAATAAG
38137 TT
1 TT
38139 CAGCTCAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.49
Consensus pattern (18 bp):
TTAGTTAATTTAAATAAG
Found at i:40835 original size:23 final size:23
Alignment explanation
Indices: 40806--40865 Score: 111
Period size: 23 Copynumber: 2.6 Consensus size: 23
40796 TTAATAAGTG
*
40806 TTTTAATGTGTTTAATAAACTCA
1 TTTTAATGTGTTTAATAAAATCA
40829 TTTTAATGTGTTTAATAAAATCA
1 TTTTAATGTGTTTAATAAAATCA
40852 TTTTAATGTGTTTA
1 TTTTAATGTGTTTA
40866 TTGCAGGTGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.33, C:0.05, G:0.10, T:0.52
Consensus pattern (23 bp):
TTTTAATGTGTTTAATAAAATCA
Found at i:42696 original size:14 final size:14
Alignment explanation
Indices: 42677--42703 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
42667 TGCATCTCCC
42677 CATGCATGAATCTA
1 CATGCATGAATCTA
42691 CATGCATGAATCT
1 CATGCATGAATCT
42704 GCCCAATGTA
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:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (14 bp):
CATGCATGAATCTA
Found at i:49349 original size:22 final size:22
Alignment explanation
Indices: 49319--49362 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
49309 TTTGGTATTT
49319 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
49341 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
49363 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:66328 original size:61 final size:61
Alignment explanation
Indices: 66230--66360 Score: 212
Period size: 61 Copynumber: 2.1 Consensus size: 61
66220 TGTCTCTAGA
66230 TTTTTTTACGGATCTTTCACGTCTTTTCGTCCGCACCTAAACCGTATGC-TTTTTTTTC-T
1 TTTTTTTACGGATCTTTCACGTCTTTTCGTCCGCACCTAAACCGTATGCATTTTTTTTCAT
66289 TTTTTTTACGGATCTTTCACGTTCTTTTTCGTCCGCACCTAAACCGTATGCAATTTTTTTTCAAT
1 TTTTTTTACGGATCTTTCACG-TC-TTTTCGTCCGCACCTAAACCGTATGC-ATTTTTTTTC-AT
66354 TTTTTTT
1 TTTTTTT
66361 TTCAATTTTT
Statistics
Matches: 66, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
59 21 0.32
60 2 0.03
61 26 0.39
63 9 0.14
65 8 0.12
ACGTcount: A:0.15, C:0.23, G:0.11, T:0.51
Consensus pattern (61 bp):
TTTTTTTACGGATCTTTCACGTCTTTTCGTCCGCACCTAAACCGTATGCATTTTTTTTCAT
Found at i:66360 original size:13 final size:13
Alignment explanation
Indices: 66342--66387 Score: 92
Period size: 13 Copynumber: 3.5 Consensus size: 13
66332 CCGTATGCAA
66342 TTTTTTTTCAATT
1 TTTTTTTTCAATT
66355 TTTTTTTTCAATT
1 TTTTTTTTCAATT
66368 TTTTTTTTCAATT
1 TTTTTTTTCAATT
66381 TTTTTTT
1 TTTTTTT
66388 ACGTACCTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 33 1.00
ACGTcount: A:0.13, C:0.07, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTTTTCAATT
Found at i:66714 original size:21 final size:21
Alignment explanation
Indices: 66685--66726 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
66675 TTTGGTATTT
66685 GGGAATTGGTACGAAATGGTA
1 GGGAATTGGTACGAAATGGTA
*
66706 GGGATTTGGTACGAAATGGTA
1 GGGAATTGGTACGAAATGGTA
66727 ATGGTTCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.05, G:0.38, T:0.26
Consensus pattern (21 bp):
GGGAATTGGTACGAAATGGTA
Found at i:71076 original size:20 final size:20
Alignment explanation
Indices: 71053--71099 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
71043 GGGTTAAGAT
*
71053 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
71073 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
71093 TGAGCTG
1 TGAGCTG
71100 GAAACAAGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:72817 original size:48 final size:48
Alignment explanation
Indices: 72762--72867 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
72752 TTGTCTTTTC
*
72762 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
72810 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
72858 TTTCTTTTTC
1 TTTCTTTTTC
72868 CATGACACTC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:75385 original size:12 final size:11
Alignment explanation
Indices: 75362--75406 Score: 58
Period size: 11 Copynumber: 4.2 Consensus size: 11
75352 CTCGCAAGAC
*
75362 TTTTCACTTTT
1 TTTTTACTTTT
75373 TTTTT-CTTCTT
1 TTTTTACTT-TT
75384 TTTTTACTTTT
1 TTTTTACTTTT
75395 TTTTT-CTTTT
1 TTTTTACTTTT
75405 TT
1 TT
75407 GCTCGCTTCT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
10 10 0.32
11 18 0.58
12 3 0.10
ACGTcount: A:0.04, C:0.13, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTTTACTTTT
Found at i:75392 original size:22 final size:21
Alignment explanation
Indices: 75362--75406 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
75352 CTCGCAAGAC
75362 TTTTCACTTTTTTTTTCTTCTT
1 TTTTCACTTTTTTTTTCTT-TT
*
75384 TTTTTACTTTTTTTTTCTTTT
1 TTTTCACTTTTTTTTTCTTTT
75405 TT
1 TT
75407 GCTCGCTTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.04, C:0.13, G:0.00, T:0.82
Consensus pattern (21 bp):
TTTTCACTTTTTTTTTCTTTT
Found at i:76960 original size:20 final size:19
Alignment explanation
Indices: 76918--76963 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
76908 GGGTTAAGAT
* *
76918 TGAGCTGATTGAGCTTGAA
1 TGAGCTGATTGAACTCGAA
*
76937 TGAGCTGACTTGAACTCGAG
1 TGAGCTGA-TTGAACTCGAA
76957 TGAGCTG
1 TGAGCTG
76964 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.24, C:0.15, G:0.33, T:0.28
Consensus pattern (19 bp):
TGAGCTGATTGAACTCGAA
Found at i:77551 original size:4 final size:4
Alignment explanation
Indices: 77542--77569 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
77532 AAGTTTTATT
77542 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
77570 CTTAGTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:83276 original size:12 final size:12
Alignment explanation
Indices: 83259--83283 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
83249 TTTCACTCTT
83259 CTCTTTTTCAAA
1 CTCTTTTTCAAA
83271 CTCTTTTTCAAA
1 CTCTTTTTCAAA
83283 C
1 C
83284 CCTCTCTCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.28, G:0.00, T:0.48
Consensus pattern (12 bp):
CTCTTTTTCAAA
Found at i:84312 original size:12 final size:12
Alignment explanation
Indices: 84297--84366 Score: 54
Period size: 11 Copynumber: 5.6 Consensus size: 12
84287 TTTTGCTTGA
*
84297 TTTTTTTTC-AC
1 TTTTTTTTCAAT
*
84308 TTTTTTTTGAAT
1 TTTTTTTTCAAT
84320 TTTTTTTTCAAACAAT
1 TTTTTTTT----CAAT
84336 TTTTTTTTCGAAT
1 TTTTTTTTC-AAT
*
84349 TTTTTTTT-GAT
1 TTTTTTTTCAAT
84360 TTTTTTT
1 TTTTTTT
84367 GTTACTCCAA
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
11 17 0.35
12 10 0.20
13 11 0.22
16 11 0.22
ACGTcount: A:0.16, C:0.07, G:0.04, T:0.73
Consensus pattern (12 bp):
TTTTTTTTCAAT
Found at i:84324 original size:13 final size:13
Alignment explanation
Indices: 84308--84366 Score: 50
Period size: 12 Copynumber: 4.5 Consensus size: 13
84298 TTTTTTTCAC
84308 TTTTTTTTGAATT
1 TTTTTTTTGAATT
**
84321 TTTTTTTCAAACAATT
1 TTTTTTT---TGAATT
*
84337 TTTTTTTCGAA-T
1 TTTTTTTTGAATT
84349 TTTTTTTTG-ATT
1 TTTTTTTTGAATT
84361 TTTTTT
1 TTTTTT
84367 GTTACTCCAA
Statistics
Matches: 37, Mismatches: 5, Indels: 9
0.73 0.10 0.18
Matches are distributed among these distances:
11 1 0.03
12 16 0.43
13 9 0.24
16 11 0.30
ACGTcount: A:0.17, C:0.05, G:0.05, T:0.73
Consensus pattern (13 bp):
TTTTTTTTGAATT
Found at i:85849 original size:20 final size:20
Alignment explanation
Indices: 85826--85872 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
85816 GGGTTAAGAT
*
85826 TGAGCTGAATTGAGCTCGAA
1 TGAGCTGAATTGAACTCGAA
* *
85846 TGAGCTGACTTGAACTCGAG
1 TGAGCTGAATTGAACTCGAA
85866 TGAGCTG
1 TGAGCTG
85873 GAAACGAGCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.26, C:0.17, G:0.32, T:0.26
Consensus pattern (20 bp):
TGAGCTGAATTGAACTCGAA
Found at i:91659 original size:24 final size:26
Alignment explanation
Indices: 91621--91679 Score: 86
Period size: 24 Copynumber: 2.3 Consensus size: 26
91611 CCGTATGCAA
91621 TTTTTTTTCATTTTTTTTTTCAAAAT-
1 TTTTTTTTCA-TTTTTTTTTCAAAATC
*
91647 TTTTTTTTC-TTTTTTTTTCAAACTC
1 TTTTTTTTCATTTTTTTTTCAAAATC
91672 TTTTTTTT
1 TTTTTTTT
91680 ACGTACCTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
24 14 0.45
25 8 0.26
26 9 0.29
ACGTcount: A:0.14, C:0.10, G:0.00, T:0.76
Consensus pattern (26 bp):
TTTTTTTTCATTTTTTTTTCAAAATC
Found at i:92031 original size:22 final size:22
Alignment explanation
Indices: 91980--92045 Score: 80
Period size: 21 Copynumber: 3.0 Consensus size: 22
91970 GGTATTTGGG
* *
91980 AATTGGTTCGAAATAGTATGG-
1 AATTGGTACGAAATGGTATGGT
92001 AATTGGTACGAAATGGTATGGT
1 AATTGGTACGAAATGGTATGGT
* *
92023 ATTTGGTACGAATTGGTAATGGT
1 AATTGGTACGAAATGGT-ATGGT
92046 TGAAAAGGAC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 19 0.49
22 15 0.38
23 5 0.13
ACGTcount: A:0.30, C:0.05, G:0.30, T:0.35
Consensus pattern (22 bp):
AATTGGTACGAAATGGTATGGT
Found at i:94070 original size:20 final size:20
Alignment explanation
Indices: 94047--94093 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
94037 GGGTTAAGAT
*
94047 TGAGCTGAATTGAGCTCGAA
1 TGAGCTGAATTGAACTCGAA
* *
94067 TGAGCTGACTTGAACTCGAG
1 TGAGCTGAATTGAACTCGAA
94087 TGAGCTG
1 TGAGCTG
94094 GAAACGAGCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.26, C:0.17, G:0.32, T:0.26
Consensus pattern (20 bp):
TGAGCTGAATTGAACTCGAA
Found at i:97998 original size:22 final size:22
Alignment explanation
Indices: 97970--98013 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
97960 TTTTGAACCA
97970 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
97992 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
98014 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:98331 original size:14 final size:14
Alignment explanation
Indices: 98312--98362 Score: 61
Period size: 14 Copynumber: 3.6 Consensus size: 14
98302 ATAGGTACGT
98312 AAAAAAAAATTTGA
1 AAAAAAAAATTTGA
98326 AAAAAAAAATTTTTTG-
1 AAAAAAAAA---TTTGA
98342 AAAAAAAAA-TTGA
1 AAAAAAAAATTTGA
98355 AAAAAAAA
1 AAAAAAAA
98363 TTGCATACGG
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
12 3 0.09
13 8 0.24
14 9 0.27
16 9 0.27
17 4 0.12
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.22
Consensus pattern (14 bp):
AAAAAAAAATTTGA
Found at i:98334 original size:17 final size:17
Alignment explanation
Indices: 98312--98350 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
98302 ATAGGTACGT
98312 AAAAAAAAATTTGAAAA
1 AAAAAAAAATTTGAAAA
***
98329 AAAAAATTTTTTGAAAA
1 AAAAAAAAATTTGAAAA
98346 AAAAA
1 AAAAA
98351 TTGAAAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (17 bp):
AAAAAAAAATTTGAAAA
Found at i:98362 original size:12 final size:12
Alignment explanation
Indices: 98339--98365 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
98329 AAAAAATTTT
98339 TTGAAAAAAAAA
1 TTGAAAAAAAAA
98351 TTGAAAAAAAAA
1 TTGAAAAAAAAA
98363 TTG
1 TTG
98366 CATACGGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.11, T:0.22
Consensus pattern (12 bp):
TTGAAAAAAAAA
Found at i:98433 original size:67 final size:66
Alignment explanation
Indices: 98352--98479 Score: 238
Period size: 67 Copynumber: 1.9 Consensus size: 66
98342 AAAAAAAAAT
98352 TGAAAAAAAAATTGCATACGGTTTAGGTGCGGACAAAAAGAACGTGAAAGATCCGTAAAAAGAAC
1 TGAAAAAAAAATTGCATACGGTTTAGGTGCGGACAAAAAGAACGTGAAAGATCCGTAAAAAGAAC
98417 G
66 G
*
98418 TGAACAAAAAAATTGCATACGGTTTAGGTGCGGACGAAAAGAACGTGAAAGATCCGTAAAAA
1 TGAA-AAAAAAATTGCATACGGTTTAGGTGCGGACAAAAAGAACGTGAAAGATCCGTAAAAA
98480 AAAAGAGTCT
Statistics
Matches: 60, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
66 4 0.07
67 56 0.93
ACGTcount: A:0.46, C:0.12, G:0.24, T:0.17
Consensus pattern (66 bp):
TGAAAAAAAAATTGCATACGGTTTAGGTGCGGACAAAAAGAACGTGAAAGATCCGTAAAAAGAAC
G
Done.