Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3614
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: 54944
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:8656 original size:30 final size:30
Alignment explanation
Indices: 8622--8718 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
8612 AGCTCACTCC
8622 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
8652 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
8682 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
8712 TAGCTCA
1 TAGCTCA
8719 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:10414 original size:12 final size:12
Alignment explanation
Indices: 10399--10437 Score: 69
Period size: 12 Copynumber: 3.2 Consensus size: 12
10389 AAAAAAAAAA
*
10399 AAAAAAAAATTG
1 AAAAAAAAATTC
10411 AAAAAAAAATTC
1 AAAAAAAAATTC
10423 AAAAAAAAATTC
1 AAAAAAAAATTC
10435 AAA
1 AAA
10438 TTGAAGAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.77, C:0.05, G:0.03, T:0.15
Consensus pattern (12 bp):
AAAAAAAAATTC
Found at i:10419 original size:24 final size:25
Alignment explanation
Indices: 10380--10453 Score: 76
Period size: 30 Copynumber: 2.7 Consensus size: 25
10370 AGCATATTGT
*
10380 AATTGAAAAAAAAAAAAAAAAAAAAA
1 AATTG-AAAAAAAAAAAAAAAAAATA
10406 AATTGAAAAAAAAATTCAAAAAAAAATTCA
1 AATTGAAAAAAAAA---AAAAAAAAA-T-A
*
10436 AATTGAAGAAAAAAAAAA
1 AATTGAAAAAAAAAAAAA
10454 GTGAAAAGTC
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
25 9 0.22
26 5 0.12
27 4 0.10
28 9 0.22
30 14 0.34
ACGTcount: A:0.78, C:0.03, G:0.05, T:0.14
Consensus pattern (25 bp):
AATTGAAAAAAAAAAAAAAAAAATA
Found at i:10427 original size:30 final size:31
Alignment explanation
Indices: 10393--10450 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
10383 TGAAAAAAAA
10393 AAAAAAAAAAAAAAATTGAA-AAAAAAATTC
1 AAAAAAAAAAAAAAATTGAAGAAAAAAATTC
***
10423 AAAAAAAAATTCAAATTGAAGAAAAAAA
1 AAAAAAAAAAAAAAATTGAAGAAAAAAA
10451 AAAGTGAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 17 0.71
31 7 0.29
ACGTcount: A:0.78, C:0.03, G:0.05, T:0.14
Consensus pattern (31 bp):
AAAAAAAAAAAAAAATTGAAGAAAAAAATTC
Found at i:11351 original size:5 final size:5
Alignment explanation
Indices: 11341--11400 Score: 61
Period size: 5 Copynumber: 12.0 Consensus size: 5
11331 AAGAGAAAAC
* * *
11341 AAAGA AAAGA AAAGA AAAAA AAAG- CAAGA GAAGA AAAGA AAATGA AATA-A
1 AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAA-GA AA-AGA
11391 AAAGA AAAGA
1 AAAGA AAAGA
11401 GAGGCAAGAG
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
4 4 0.09
5 37 0.80
6 4 0.09
7 1 0.02
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.03
Consensus pattern (5 bp):
AAAGA
Found at i:11480 original size:11 final size:12
Alignment explanation
Indices: 11448--11478 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
11438 TTGAGAGAAC
11448 TTGAAAAAGCCT
1 TTGAAAAAGCCT
11460 TTGAAAAAGCCT
1 TTGAAAAAGCCT
11472 TTGAAAA
1 TTGAAAA
11479 GCAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:13631 original size:30 final size:30
Alignment explanation
Indices: 13597--13692 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
13587 AGCTCACTCC
13597 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
13627 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
*
13657 CAGCTCAACTTTAGCTCACGAGCTAAA-CT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
13686 TAGCTCA
1 TAGCTCA
13693 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 3
0.75 0.21 0.04
Matches are distributed among these distances:
29 9 0.18
30 42 0.82
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:16837 original size:20 final size:20
Alignment explanation
Indices: 16814--16860 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
16804 GGGTTAAGAT
*
16814 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
16834 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
16854 TGAGCTG
1 TGAGCTG
16861 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:18583 original size:48 final size:48
Alignment explanation
Indices: 18528--18633 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
18518 TTGTCTTTTC
*
18528 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
18576 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
18624 TTTCTTTTTC
1 TTTCTTTTTC
18634 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:21271 original size:20 final size:20
Alignment explanation
Indices: 21248--21294 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
21238 GGGTTAAGAT
*
21248 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
21268 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
21288 TGAGCTG
1 TGAGCTG
21295 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:23926 original size:20 final size:20
Alignment explanation
Indices: 23903--23949 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
23893 GGGTTAAGAT
*
23903 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
23923 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
23943 TGAGCTG
1 TGAGCTG
23950 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:28108 original size:16 final size:16
Alignment explanation
Indices: 28087--28142 Score: 98
Period size: 15 Copynumber: 3.6 Consensus size: 16
28077 TATCTTCTTC
28087 TTTTTTTTCACGAAAT
1 TTTTTTTTCACGAAAT
28103 TTTTTTTTCAC-AAAT
1 TTTTTTTTCACGAAAT
28118 TTTTTTTTCACG-AAT
1 TTTTTTTTCACGAAAT
28133 TTTTTTTTCA
1 TTTTTTTTCA
28143 ACTTGATATC
Statistics
Matches: 39, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
15 28 0.72
16 11 0.28
ACGTcount: A:0.21, C:0.12, G:0.04, T:0.62
Consensus pattern (16 bp):
TTTTTTTTCACGAAAT
Found at i:28200 original size:10 final size:10
Alignment explanation
Indices: 28185--28211 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
28175 AACCAAATTT
28185 TTTTTTTGAA
1 TTTTTTTGAA
28195 TTTTTTTGAA
1 TTTTTTTGAA
28205 TTTTTTT
1 TTTTTTT
28212 TCGAGAAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.15, C:0.00, G:0.07, T:0.78
Consensus pattern (10 bp):
TTTTTTTGAA
Found at i:28583 original size:46 final size:46
Alignment explanation
Indices: 28530--28623 Score: 154
Period size: 46 Copynumber: 2.0 Consensus size: 46
28520 CAAAGAAAAG
* *
28530 ACCTCGACCCACTATCTA-GAATGATAGGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAATG-ATGATAAGAACCTTGGTATATGATGA
28576 ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATATGATGA
28622 AC
1 AC
28624 GCCACACTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
46 44 0.98
47 1 0.02
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (46 bp):
ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATATGATGA
Found at i:32121 original size:30 final size:30
Alignment explanation
Indices: 32081--32153 Score: 114
Period size: 30 Copynumber: 2.5 Consensus size: 30
32071 CGAGTTTAAA
*
32081 CTAAA-ATGAGCTAAGTTTTAGCTCGTGAG
1 CTAAATATGAGCTAAGGTTTAGCTCGTGAG
32110 CTAAAGT-TGAGCTAAGGTTTAGCTCGTGAG
1 CTAAA-TATGAGCTAAGGTTTAGCTCGTGAG
32140 CTAAATATGAGCTA
1 CTAAATATGAGCTA
32154 GGAGTGAGCT
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
29 6 0.15
30 34 0.85
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.30
Consensus pattern (30 bp):
CTAAATATGAGCTAAGGTTTAGCTCGTGAG
Found at i:32164 original size:30 final size:30
Alignment explanation
Indices: 32100--32165 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
32090 GCTAAGTTTT
* *
32100 AGCTCGTGAGCTAAAGTTGAGCTAAGGTTT
1 AGCTCGTGAGCTAAAGTTGAGCTAAGGGTG
32130 AGCTCGTGAGCTAAA-TATGAGCT-AGGAGTG
1 AGCTCGTGAGCTAAAGT-TGAGCTAAGG-GTG
32160 AGCTCG
1 AGCTCG
32166 GTTTAGCTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 4 0.12
30 28 0.88
ACGTcount: A:0.27, C:0.15, G:0.32, T:0.26
Consensus pattern (30 bp):
AGCTCGTGAGCTAAAGTTGAGCTAAGGGTG
Found at i:34333 original size:12 final size:12
Alignment explanation
Indices: 34318--34348 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
34308 TTCTTTTTGC
34318 TTTTCAAAGGCT
1 TTTTCAAAGGCT
34330 TTTTCAAAGGCT
1 TTTTCAAAGGCT
34342 TTTTCAA
1 TTTTCAA
34349 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:34425 original size:6 final size:6
Alignment explanation
Indices: 34409--34458 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
34399 TTTCTTTTTA
*
34409 TTTCAT TTTCTT TTTCTT CTCTTGCTT TTTCTT TTTC-T TTTC-T TTTCTT
1 TTTCTT TTTCTT TTTCTT -T-TT-CTT TTTCTT TTTCTT TTTCTT TTTCTT
34458 T
1 T
34459 GTTTTCTCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
5 10 0.26
6 20 0.51
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (6 bp):
TTTCTT
Found at i:34441 original size:37 final size:37
Alignment explanation
Indices: 34398--34468 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
34388 CTTGCCTCTC
34398 TTTTCTTTTT-ATTTCATTTTCTTT-TTCTTCTCTTGCT
1 TTTTCTTTTTCATTTC-TTTTCTTTGTT-TTCTCTTGCT
*
34435 TTTTCTTTTTCTTTTCTTTTCTTTGTTTTCTCTT
1 TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTT
34469 TACAAGAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 25 0.81
38 6 0.19
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (37 bp):
TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTTGCT
Found at i:34469 original size:16 final size:16
Alignment explanation
Indices: 34394--34454 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
34384 GCCTCTTGCC
*
34394 TCTCTTTTCTTTTTAT
1 TCTCTTTTCTTTTTCT
34410 T-TCATTTTCTTTTTCT
1 TCTC-TTTTCTTTTTCT
*
34426 TCTC-TTGCTTTTTCTT
1 TCTCTTTTCTTTTTC-T
*
34442 TTTCTTTTCTTTT
1 TCTCTTTTCTTTT
34455 CTTTGTTTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
15 11 0.30
16 17 0.46
17 9 0.24
ACGTcount: A:0.03, C:0.20, G:0.02, T:0.75
Consensus pattern (16 bp):
TCTCTTTTCTTTTTCT
Found at i:35391 original size:11 final size:11
Alignment explanation
Indices: 35374--35403 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
35364 TTCAAAATTT
35374 ATTTTTTTTG-
1 ATTTTTTTTGA
35384 ATTTTTTTTGA
1 ATTTTTTTTGA
35395 ATTTTTTTT
1 ATTTTTTTT
35404 TCAAATTTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.13, C:0.00, G:0.07, T:0.80
Consensus pattern (11 bp):
ATTTTTTTTGA
Found at i:37142 original size:30 final size:30
Alignment explanation
Indices: 37102--37174 Score: 114
Period size: 30 Copynumber: 2.5 Consensus size: 30
37092 CGAGTTTAAA
*
37102 CTAAA-ATGAGCTAAGTTTTAGCTCGTGAG
1 CTAAATATGAGCTAAGGTTTAGCTCGTGAG
37131 CTAAAGT-TGAGCTAAGGTTTAGCTCGTGAG
1 CTAAA-TATGAGCTAAGGTTTAGCTCGTGAG
37161 CTAAATATGAGCTA
1 CTAAATATGAGCTA
37175 GGAGTGAGCT
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
29 6 0.15
30 34 0.85
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.30
Consensus pattern (30 bp):
CTAAATATGAGCTAAGGTTTAGCTCGTGAG
Found at i:37185 original size:30 final size:30
Alignment explanation
Indices: 37121--37186 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
37111 GCTAAGTTTT
* *
37121 AGCTCGTGAGCTAAAGTTGAGCTAAGGTTT
1 AGCTCGTGAGCTAAAGTTGAGCTAAGGGTG
37151 AGCTCGTGAGCTAAA-TATGAGCT-AGGAGTG
1 AGCTCGTGAGCTAAAGT-TGAGCTAAGG-GTG
37181 AGCTCG
1 AGCTCG
37187 GTTTAGCTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 4 0.12
30 28 0.88
ACGTcount: A:0.27, C:0.15, G:0.32, T:0.26
Consensus pattern (30 bp):
AGCTCGTGAGCTAAAGTTGAGCTAAGGGTG
Found at i:39860 original size:67 final size:69
Alignment explanation
Indices: 39749--39882 Score: 218
Period size: 67 Copynumber: 2.0 Consensus size: 69
39739 TGAATTAAAT
39749 CAGCAGCAATAAAGGAGGTGTTGGCCGAATTTAATGTAAAGCATAGACATGCATTTAAGGTGATG
1 CAGCAGCAAT-AAGGAGGTGTTGGCCGAATTTAATGTAAAGCATAGACATGCATTTAAGGTGATG
39814 TTCAA
65 TTCAA
* * *
39819 CAGCAGCAAT-A-GAGGTTTTGGCCGAATTTAATGTAAAGCATAGACATGTATTTAAGGTGCTGT
1 CAGCAGCAATAAGGAGGTGTTGGCCGAATTTAATGTAAAGCATAGACATGCATTTAAGGTGATGT
39882 T
66 T
39883 GGGCATGCAA
Statistics
Matches: 61, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
67 50 0.82
68 1 0.02
70 10 0.16
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.28
Consensus pattern (69 bp):
CAGCAGCAATAAGGAGGTGTTGGCCGAATTTAATGTAAAGCATAGACATGCATTTAAGGTGATGT
TCAA
Found at i:40854 original size:21 final size:21
Alignment explanation
Indices: 40828--40890 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
40818 TTGGTATTTG
40828 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
40849 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
40870 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
40891 ATGGTTCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 22 0.59
22 15 0.41
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:50206 original size:22 final size:22
Alignment explanation
Indices: 50175--50239 Score: 103
Period size: 22 Copynumber: 2.9 Consensus size: 22
50165 ACCTTTTTGA
50175 ACCATTACCATTTCGTACCAAAT
1 ACCA-TACCATTTCGTACCAAAT
*
50198 ACCATACCATTTCGTACCAACT
1 ACCATACCATTTCGTACCAAAT
*
50220 TCCATACCATTTCGTACCAA
1 ACCATACCATTTCGTACCAA
50240 TTCCTAAATA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
22 36 0.90
23 4 0.10
ACGTcount: A:0.32, C:0.34, G:0.05, T:0.29
Consensus pattern (22 bp):
ACCATACCATTTCGTACCAAAT
Found at i:50560 original size:10 final size:10
Alignment explanation
Indices: 50545--50605 Score: 72
Period size: 10 Copynumber: 6.2 Consensus size: 10
50535 AGTAGACTTG
50545 TGAAAAAAAT
1 TGAAAAAAAT
50555 TGAAAAAAAAT
1 TG-AAAAAAAT
*
50566 TGAAAAAAAA
1 TGAAAAAAAT
*
50576 T-AAAAAATT
1 TGAAAAAAAT
50585 TG-AAAAAAT
1 TGAAAAAAAT
*
50594 TAAAAAAAAT
1 TGAAAAAAAT
50604 TG
1 TG
50606 TATACGGTCT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
9 14 0.33
10 18 0.43
11 10 0.24
ACGTcount: A:0.70, C:0.00, G:0.08, T:0.21
Consensus pattern (10 bp):
TGAAAAAAAT
Found at i:50563 original size:11 final size:11
Alignment explanation
Indices: 50547--50605 Score: 67
Period size: 11 Copynumber: 5.9 Consensus size: 11
50537 TAGACTTGTG
50547 AAAAAAATTGA
1 AAAAAAATTGA
50558 AAAAAAATTGA
1 AAAAAAATTGA
50569 AAAAAAA-T--
1 AAAAAAATTGA
*
50577 AAAAAATTTG-
1 AAAAAAATTGA
50587 -AAAAAATT-A
1 AAAAAAATTGA
50596 AAAAAAATTG
1 AAAAAAATTG
50606 TATACGGTCT
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
8 6 0.15
9 8 0.20
10 9 0.22
11 18 0.44
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (11 bp):
AAAAAAATTGA
Found at i:50580 original size:19 final size:18
Alignment explanation
Indices: 50558--50601 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
50548 AAAAAATTGA
50558 AAAAAAATTGAAAAAAAAT
1 AAAAAAATTG-AAAAAAAT
* *
50577 AAAAAATTTGAAAAAATT
1 AAAAAAATTGAAAAAAAT
50595 AAAAAAA
1 AAAAAAA
50602 ATTGTATACG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 13 0.59
19 9 0.41
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (18 bp):
AAAAAAATTGAAAAAAAT
Found at i:52837 original size:20 final size:20
Alignment explanation
Indices: 52812--52856 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
52802 GCGAAAATAC
*
52812 AAAAGAAAAGAAAAATGAAA
1 AAAAGAAAAGAAAAATCAAA
*
52832 AAAAG-AAAGAAAATTCAAA
1 AAAAGAAAAGAAAAATCAAA
52851 AAAAGA
1 AAAAGA
52857 GAATGAAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.78, C:0.02, G:0.13, T:0.07
Consensus pattern (20 bp):
AAAAGAAAAGAAAAATCAAA
Found at i:52904 original size:14 final size:15
Alignment explanation
Indices: 52875--52904 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
52865 AGAGAGCGAG
52875 AAAAGAAAAAGATGA
1 AAAAGAAAAAGATGA
52890 AAAAGAAAAAG-TGA
1 AAAAGAAAAAGATGA
52904 A
1 A
52905 TGAAAAATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.73, C:0.00, G:0.20, T:0.07
Consensus pattern (15 bp):
AAAAGAAAAAGATGA
Done.