Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2280
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: 26823
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Found at i:85 original size:52 final size:52
Alignment explanation
Indices: 2--116 Score: 203
Period size: 52 Copynumber: 2.2 Consensus size: 52
1 G
*
2 CAGGCAAATTTGCCCAGATATATCGATACACTATGAAATGTATCGATACATA
1 CAGGTAAATTTGCCCAGATATATCGATACACTATGAAATGTATCGATACATA
* *
54 CAGGTAAATTTGCCCAGATGTATCGATACACTATGAAATGTATCGATACATG
1 CAGGTAAATTTGCCCAGATATATCGATACACTATGAAATGTATCGATACATA
106 CAGGTAAATTT
1 CAGGTAAATTT
117 TCATAATTCG
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 60 1.00
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (52 bp):
CAGGTAAATTTGCCCAGATATATCGATACACTATGAAATGTATCGATACATA
Found at i:5757 original size:15 final size:15
Alignment explanation
Indices: 5735--5769 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
5725 AAAAAATTAT
5735 AATT-TAAAATAAAA
1 AATTATAAAATAAAA
*
5749 AATTATAAAATTAAA
1 AATTATAAAATAAAA
5764 AATTAT
1 AATTAT
5770 TTAATATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 4 0.21
15 15 0.79
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
AATTATAAAATAAAA
Found at i:5760 original size:22 final size:20
Alignment explanation
Indices: 5725--5766 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
5715 AATAAATATA
*
5725 AAAAAATTATAATTTAAAAT
1 AAAAAATTATAATTAAAAAT
5745 AAAAAATTATAAAATTAAAAAT
1 AAAAAATTAT--AATTAAAAAT
5767 TATTTAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 10 0.53
22 9 0.47
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (20 bp):
AAAAAATTATAATTAAAAAT
Found at i:5762 original size:21 final size:22
Alignment explanation
Indices: 5710--5764 Score: 71
Period size: 21 Copynumber: 2.6 Consensus size: 22
5700 AAGAATTTTA
5710 TATAAAA-TAAATATAAAAAAAT
1 TATAAAATTAAA-ATAAAAAAAT
*
5732 TAT-AATTTAAAAT-AAAAAAT
1 TATAAAATTAAAATAAAAAAAT
5752 TATAAAATTAAAA
1 TATAAAATTAAAA
5765 ATTATTTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
20 10 0.34
21 12 0.41
22 7 0.24
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (22 bp):
TATAAAATTAAAATAAAAAAAT
Found at i:6647 original size:22 final size:23
Alignment explanation
Indices: 6622--6671 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
6612 GCTAATGGAG
*
6622 ATATTT-AAATTTTATAATTTAT
1 ATATTTGAAATTATATAATTTAT
* *
6644 ATATTTGTAATTATATATTTTAT
1 ATATTTGAAATTATATAATTTAT
6667 -TATTT
1 ATATTT
6672 TATAAATTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 11 0.46
23 13 0.54
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (23 bp):
ATATTTGAAATTATATAATTTAT
Found at i:6739 original size:32 final size:33
Alignment explanation
Indices: 6700--6765 Score: 91
Period size: 32 Copynumber: 2.0 Consensus size: 33
6690 TATTTTATAT
*
6700 TTATAT-AAATTTTGATATATTCATA-ATTAATA
1 TTATATAAAATTTT-AGATATTCATATATTAATA
*
6732 TTATATAAAATTTTAGATATTCATATATTCATA
1 TTATATAAAATTTTAGATATTCATATATTAATA
6765 T
1 T
6766 AATTTATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
32 16 0.53
33 14 0.47
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.50
Consensus pattern (33 bp):
TTATATAAAATTTTAGATATTCATATATTAATA
Found at i:6775 original size:15 final size:16
Alignment explanation
Indices: 6755--6791 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
6745 TAGATATTCA
6755 TATATTCATATAAT-T
1 TATATTCATATAATAT
*
6770 TATATTCATATTATAT
1 TATATTCATATAATAT
6786 TATATT
1 TATATT
6792 ATTTTTATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (16 bp):
TATATTCATATAATAT
Found at i:12683 original size:57 final size:57
Alignment explanation
Indices: 12544--13055 Score: 202
Period size: 58 Copynumber: 8.9 Consensus size: 57
12534 ATATGGTGAA
* * * ** * *
12544 ATAATAATTTTCGGACCTTTGACAATGGTCATGTTCTTAAAAC--TGGCAATAG-AGAG
1 ATAATAATTTT-AGACCTTTGACAATGGTCAAGTTCTTGAGCCTTTAGCAATGGTAG-G
* * ** * ** *
12600 ACAATAACTTTAGACCTTAAAGAATGGTTGAGTGCTTGAGCCTTTAGCAATGGTAGG
1 ATAATAATTTTAGACCTTTGACAATGGTCAAGTTCTTGAGCCTTTAGCAATGGTAGG
* * ** * * **
12657 ATAATAATTTTAGACCTTTGTCAATGGTCAAATTCTCAAGCCTTTAGTAATTGTAAA
1 ATAATAATTTTAGACCTTTGACAATGGTCAAGTTCTTGAGCCTTTAGCAATGGTAGG
* * * * * *
12714 ATAATAACTTTAGACCTTAGAGAATGGTCCAAGTTCTTGAACCTTTAACAATGG-CGAG
1 ATAATAATTTTAGACCTTTGACAATGGT-CAAGTTCTTGAGCCTTTAGCAATGGTAG-G
* * * * *
12772 ATAATGATTTTAGACCTTTGACAGTGGTCAAATTCTTAAGCCTTT-GACAATGG-CGAG
1 ATAATAATTTTAGACCTTTGACAATGGTCAAGTTCTTGAGCCTTTAG-CAATGGTAG-G
* * * * * ** * * * * *
12829 ATAATAACTTTGGACCTTAGGCAATAG-CCCGATTCTTAAGCCCTTGGTAATAGT-GAG
1 ATAATAATTTTAGACCTTTGACAATGGTCAAG-TTCTTGAGCCTTTAGCAATGGTAG-G
* * * * * *
12886 ATAATAATCTTTAAACCGTAGGCAATGGTCGAA-TTCTTAAGCCTTTGGCAAT-G-ACGAG
1 ATAATAAT-TTTAGACCTTTGACAATGGTC-AAGTTCTTGAGCCTTTAGCAATGGTA-G-G
* * * * * ** * * *
12944 ATAATAATATTTGGACCTTAGATAATGGTTAAATTCTCAAGCCTTTGGCAATGGCAAG
1 ATAATAAT-TTTAGACCTTTGACAATGGTCAAGTTCTTGAGCCTTTAGCAATGGTAGG
* * ** *
13002 ATAATAATTTTTGGACCTTT-AGCAATGGTCAAATTCTCAAGCCTTTGGCAATGG
1 ATAATAA-TTTTAGACCTTTGA-CAATGGTCAAGTTCTTGAGCCTTTAGCAATGG
13056 CGAGATCACA
Statistics
Matches: 349, Mismatches: 88, Indels: 36
0.74 0.19 0.08
Matches are distributed among these distances:
55 20 0.06
56 10 0.03
57 147 0.42
58 168 0.48
59 3 0.01
60 1 0.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (57 bp):
ATAATAATTTTAGACCTTTGACAATGGTCAAGTTCTTGAGCCTTTAGCAATGGTAGG
Found at i:12833 original size:115 final size:113
Alignment explanation
Indices: 12544--13667 Score: 641
Period size: 115 Copynumber: 9.8 Consensus size: 113
12534 ATATGGTGAA
* ** ** * * *
12544 ATAATAATTTTCGGACCTTTGACAATGGTCATGTTCTTAAAAC--TGGCAATAGAGAGACAATAA
1 ATAATAATTTT-AGACCTTTGACAATGGTCAAATTCTTAAGCCTTTGGCAATGGCGAGATAATAA
* * * * * * * *
12607 CTTTAGACCTTAAAGAATGGTTGAGTGCTTGAGCCTTTAGCAATGG-TAGG
65 CTTTGGACCTTAGAGAATGG-TCAATTCTTGAACCTTTGGCAATGGCGA-G
* * * * * ** *
12657 ATAATAATTTTAGACCTTTGTCAATGGTCAAATTCTCAAGCCTTTAGTAATTGTAAAATAATAAC
1 ATAATAATTTTAGACCTTTGACAATGGTCAAATTCTTAAGCCTTTGGCAATGGCGAGATAATAAC
* **
12722 TTTAGACCTTAGAGAATGGTCCAAGTTCTTGAACCTTTAACAATGGCGAG
66 TTTGGACCTTAGAGAATGGT-CAA-TTCTTGAACCTTTGGCAATGGCGAG
* * *
12772 ATAATGATTTTAGACCTTTGACAGTGGTCAAATTCTTAAGCCTTTGACAATGGCGAGATAATAAC
1 ATAATAATTTTAGACCTTTGACAATGGTCAAATTCTTAAGCCTTTGGCAATGGCGAGATAATAAC
** * * * * *
12837 TTTGGACCTTAG-GCAATAGCCCGATTCTT-AAGCCCTTGGTAATAGTGAG
66 TTTGGACCTTAGAG-AAT-GGTCAATTCTTGAA-CCTTTGGCAATGGCGAG
* * * * * *
12886 ATAATAATCTTTAAACCGTAGGCAATGGTCGAATTCTTAAGCCTTTGGCAATGACGAGATAATAA
1 ATAATAAT-TTTAGACCTTTGACAATGGTCAAATTCTTAAGCCTTTGGCAATGGCGAGATAATAA
* * * * *
12951 TATTTGGACCTTAGATAATGGTTAAATTC-TCAAGCCTTTGGCAATGGCAAG
65 -CTTTGGACCTTAGAGAATGG-TCAATTCTTGAA-CCTTTGGCAATGGCGAG
* * * *
13002 ATAATAATTTTTGGACCTTT-AGCAATGGTCAAATTCTCAAGCCTTTGGCAATGGCGAGATCACA
1 ATAATAA-TTTTAGACCTTTGA-CAATGGTCAAATTCTTAAGCCTTTGGCAATGGCGAGATAATA
* * * * * * * *
13066 ACTTTAGACCTTAGAGAATGATAGAATTTTTAAAACTTTGACAATGGAGAG
64 ACTTTGGACCTTAGAGAATGGT-CAATTCTTGAACCTTTGGCAATGGCGAG
* * * * * * * *
13117 ATAACAATCTTTGGACTTTATG-TAGTGGT-AGAATTCTCAAACCTTTGGCAATGACGAGATAAT
1 ATAATAAT-TTTAGACCTT-TGACAATGGTCA-AATTCTTAAGCCTTTGGCAATGGCGAGATAAT
* * * * * * *
13180 AACTTCGGACCTTAAAGAATTGTCTACTTC-TCAAGCTATTGGTAATGGCGAG
63 AACTTTGGACCTTAGAGAATGGTC-AATTCTTGAACCT-TTGGCAATGGCGAG
* * * * * * *
13232 ATAATAATCATTA-AACTTTAAGGAATGGTCAAATTCTTAAGCCTTTGGTAATGGTGAGATTATA
1 ATAATAAT-TTTAGACCTTTGA-CAATGGTCAAATTCTTAAGCCTTTGGCAATGGCGAGATAATA
* * * * ** *
13296 ACTTTTGACCTTAGAGAATGGTCGAGTTCTCGAGCCTTCAGCAATGGTGAG
64 ACTTTGGACCTTAGAGAATGGTC-AATTCTTGAACCTTTGGCAATGGCGAG
* * * * ** * *
13347 ATGATAATTTCAAAACTTT-AGCAATTATCAAATTCTTAAGCCTTTGGTAATGGCAAGATAATAA
1 ATAATAATTTTAGACCTTTGA-CAATGGTCAAATTCTTAAGCCTTTGGCAATGGCGAGATAATAA
* ** *
13411 TTTTGGACCTTA-AGCAATGGTCGAATTCTT-AAGTTTTGGCAATAGCGAG
65 CTTTGGACCTTAGAG-AATGGTC-AATTCTTGAACCTTTGGCAATGGCGAG
* * * * * ** * *
13460 ATAATAACTTTGGA-CTTTAAAGAATAGTTGAA-TCTTAA-CCTTTTAGCAATGGTGAGATAATA
1 ATAATAATTTTAGACCTTT-GACAATGGTCAAATTCTTAAGCC-TTTGGCAATGGCGAGATAATA
* * * * * * *
13522 ATCTTTGAACTTTAG-GCAAGGGTCGAATTCCT-AAGCCTTTGGTAATGGCAAT
64 A-CTTTGGACCTTAGAG-AATGGTC-AATTCTTGAA-CCTTTGGCAATGGCGAG
* * ** * ** * * *
13574 ATAATAATTTTGGATCTCAGAGAATGGTTGAGTTCTTAAGCCTTTAGCAATGGCGAGATAATAAT
1 ATAATAATTTTAGACCTTTGACAATGGTCAAATTCTTAAGCCTTTGGCAATGGCGAGATAATAAC
* *
13639 TTTGGACTTTTG-GCAATGGTCGAATTCTT
66 TTTGGACCTTAGAG-AATGGTC-AATTCTT
13668 AAGCCCTTGA
Statistics
Matches: 784, Mismatches: 189, Indels: 75
0.75 0.18 0.07
Matches are distributed among these distances:
111 2 0.00
112 52 0.07
113 70 0.09
114 192 0.24
115 369 0.47
116 98 0.12
117 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.33
Consensus pattern (113 bp):
ATAATAATTTTAGACCTTTGACAATGGTCAAATTCTTAAGCCTTTGGCAATGGCGAGATAATAAC
TTTGGACCTTAGAGAATGGTCAATTCTTGAACCTTTGGCAATGGCGAG
Found at i:13427 original size:57 final size:57
Alignment explanation
Indices: 12638--13699 Score: 641
Period size: 57 Copynumber: 18.5 Consensus size: 57
12628 TGAGTGCTTG
* * * * *
12638 AGCCTTTAGCAATGG-TAGGATAATAATTTTAGACCTT-TGTCAATGGTCAAATTCTCA
1 AGCCTTTGGCAATGGCGA-GATAATAATTTTGGACCTTAAG-CAATGGTCAAATTCTTA
* * * ** * * * *
12695 AGCCTTTAGTAATTGTAAAATAATAACTTTAGACCTTAGAG-AATGGTCCAAGTTCTTGA
1 AGCCTTTGGCAATGGCGAGATAATAATTTTGGACCTTA-AGCAATGGT-CAAATTCTT-A
** * * * *
12754 A-CCTTTAACAATGGCGAGATAATGATTTTAGACCTT-TGACAGTGGTCAAATTCTTA
1 AGCCTTTGGCAATGGCGAGATAATAATTTTGGACCTTAAG-CAATGGTCAAATTCTTA
* * * * * **
12810 AGCCTTTGACAATGGCGAGATAATAACTTTGGACCTTAGGCAATAGCCCGATTCTTA
1 AGCCTTTGGCAATGGCGAGATAATAATTTTGGACCTTAAGCAATGGTCAAATTCTTA
* * * * ** * * *
12867 AGCCCTTGGTAATAGTGAGATAATAATCTTTAAACCGTAGGCAATGGTCGAATTCTTA
1 AGCCTTTGGCAATGGCGAGATAATAAT-TTTGGACCTTAAGCAATGGTCAAATTCTTA
* * * *
12925 AGCCTTTGGCAATGACGAGATAATAATATTTGGACCTT-AGATAATGGTTAAATTCTCA
1 AGCCTTTGGCAATGGCGAGATAATAAT-TTTGGACCTTAAG-CAATGGTCAAATTCTTA
* * *
12983 AGCCTTTGGCAATGGCAAGATAATAATTTTTGGACCTTTAGCAATGGTCAAATTCTCA
1 AGCCTTTGGCAATGGCGAGATAATAA-TTTTGGACCTTAAGCAATGGTCAAATTCTTA
* * * * * *
13041 AGCCTTTGGCAATGGCGAGATCACAACTTTAGACCTTAGAG-AATGAT-AGAATTTTTA
1 AGCCTTTGGCAATGGCGAGATAATAATTTTGGACCTTA-AGCAATGGTCA-AATTCTTA
** * * * * * * * *
13098 AAACTTTGACAATGGAGAGATAACAATCTTTGGACTTTATGTAGTGGT-AGAATTCTCA
1 AGCCTTTGGCAATGGCGAGATAATAAT-TTTGGACCTTAAGCAATGGTCA-AATTCTTA
* * * * * * * *
13156 AACCTTTGGCAATGACGAGATAATAACTTCGGACCTTAAAG-AATTGTCTACTTCTCA
1 AGCCTTTGGCAATGGCGAGATAATAATTTTGGACCTT-AAGCAATGGTCAAATTCTTA
* * ** * *
13213 AG-CTATTGGTAATGGCGAGATAATAATCATTAAACTTTAAGGAATGGTCAAATTCTTA
1 AGCCT-TTGGCAATGGCGAGATAATAAT-TTTGGACCTTAAGCAATGGTCAAATTCTTA
* * * * * **
13271 AGCCTTTGGTAATGGTGAGATTATAACTTTT-GACCTTAGAG-AATGGTCGAGTTCTCG
1 AGCCTTTGGCAATGGCGAGATAATAA-TTTTGGACCTTA-AGCAATGGTCAAATTCTTA
** * * *** * * **
13328 AGCCTTCAGCAATGGTGAGATGATAATTTCAAAACTTTAGCAATTATCAAATTCTTA
1 AGCCTTTGGCAATGGCGAGATAATAATTTTGGACCTTAAGCAATGGTCAAATTCTTA
* * *
13385 AGCCTTTGGTAATGGCAAGATAATAATTTTGGACCTTAAGCAATGGTCGAATTCTTA
1 AGCCTTTGGCAATGGCGAGATAATAATTTTGGACCTTAAGCAATGGTCAAATTCTTA
* * * * * **
13442 AG-TTTTGGCAATAGCGAGATAATAACTTTGGACTTTAAAG-AATAGTTGAA-TCTTA
1 AGCCTTTGGCAATGGCGAGATAATAATTTTGGACCTT-AAGCAATGGTCAAATTCTTA
* * * * * * * *
13497 A-CCTTTTAGCAATGGTGAGATAATAATCTTTGAACTTTAGGCAAGGGTCGAATTCCTA
1 AGCC-TTTGGCAATGGCGAGATAATAAT-TTTGGACCTTAAGCAATGGTCAAATTCTTA
* * * * * ** *
13555 AGCCTTTGGTAATGGCAATATAATAATTTTGGATCTCAGAG-AATGGTTGAGTTCTTA
1 AGCCTTTGGCAATGGCGAGATAATAATTTTGGACCTTA-AGCAATGGTCAAATTCTTA
* * ** *
13612 AGCCTTTAGCAATGGCGAGATAATAATTTTGGACTTTTGGCAATGGTCGAATTCTTA
1 AGCCTTTGGCAATGGCGAGATAATAATTTTGGACCTTAAGCAATGGTCAAATTCTTA
* * * *
13669 AGCCCTTGACAATTGG-AAGATAACAATTTTG
1 AGCCTTTGGCAA-TGGCGAGATAATAATTTTG
13700 AAGGCATGAT
Statistics
Matches: 774, Mismatches: 194, Indels: 74
0.74 0.19 0.07
Matches are distributed among these distances:
55 6 0.01
56 69 0.09
57 395 0.51
58 293 0.38
59 11 0.01
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.33
Consensus pattern (57 bp):
AGCCTTTGGCAATGGCGAGATAATAATTTTGGACCTTAAGCAATGGTCAAATTCTTA
Found at i:20479 original size:19 final size:19
Alignment explanation
Indices: 20436--20508 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 19
20426 CACACCCAGA
*
20436 TGTATCGATACAT-TATGCTT
1 TGTATCGATACATGT-T-CAT
20456 TGTATCGATACATGTTCAT
1 TGTATCGATACATGTTCAT
**
20475 TGTATCGATACATGGACAAT
1 TGTATCGATACATGTTC-AT
20495 TGTATCGATACATG
1 TGTATCGATACATG
20509 AAACTGGCAG
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
19 17 0.35
20 30 0.62
21 1 0.02
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.38
Consensus pattern (19 bp):
TGTATCGATACATGTTCAT
Found at i:20570 original size:13 final size:13
Alignment explanation
Indices: 20549--20578 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
20539 CGATACATGG
*
20549 TACATTGTATCGA
1 TACAATGTATCGA
20562 TACAATGTATCGA
1 TACAATGTATCGA
20575 TACA
1 TACA
20579 TGATTAATAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (13 bp):
TACAATGTATCGA
Found at i:24286 original size:23 final size:23
Alignment explanation
Indices: 24237--24286 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
24227 CATACATGTT
* * *
24237 TTATTTTAATTATATAATATTAT
1 TTATTTTAATAATATAATATAAA
24260 TTATTTTAATAATA-AATAATAAA
1 TTATTTTAATAATATAAT-ATAAA
24283 TTAT
1 TTAT
24287 AAATATAATG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 3 0.13
23 20 0.87
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
TTATTTTAATAATATAATATAAA
Found at i:24666 original size:21 final size:19
Alignment explanation
Indices: 24641--24681 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
24631 TTTTACACTA
*
24641 AATATTACTATTTGAAATATT
1 AATATTAATA-TT-AAATATT
24662 AATATTAATATTAAATATT
1 AATATTAATATTAAATATT
24681 A
1 A
24682 GTAGTTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 8 0.42
20 2 0.11
21 9 0.47
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.46
Consensus pattern (19 bp):
AATATTAATATTAAATATT
Found at i:25324 original size:24 final size:24
Alignment explanation
Indices: 25280--25326 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
25270 ATTATTATTT
* *
25280 TATTATTTTTAATTTGTATAAATA
1 TATTATTATTAATTTGAATAAATA
25304 TATTATTATTAATTAT-AATAAAT
1 TATTATTATTAATT-TGAATAAAT
25327 TTAATCTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 19 0.95
25 1 0.05
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (24 bp):
TATTATTATTAATTTGAATAAATA
Found at i:26440 original size:16 final size:15
Alignment explanation
Indices: 26358--26439 Score: 56
Period size: 16 Copynumber: 5.1 Consensus size: 15
26348 TGTTAAATCT
* *
26358 AAATAATTTGAAATTG
1 AAATAATTT-AATTTA
*
26374 AAATAACTTAAATTTA
1 AAATAA-TTTAATTTA
* * * *
26390 AAATTATTTGGACTTG
1 AAATAATTT-AATTTA
26406 AAATAATTTAATTTA
1 AAATAATTTAATTTA
26421 AAATAAATTTAATTCTA
1 AAAT-AATTTAATT-TA
26438 AA
1 AA
26440 TTATCAAAAA
Statistics
Matches: 50, Mismatches: 12, Indels: 7
0.72 0.17 0.10
Matches are distributed among these distances:
15 9 0.18
16 35 0.70
17 6 0.12
ACGTcount: A:0.50, C:0.04, G:0.06, T:0.40
Consensus pattern (15 bp):
AAATAATTTAATTTA
Found at i:26508 original size:15 final size:15
Alignment explanation
Indices: 26470--26499 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
26460 TAGAAATTTA
26470 AAATTTAAAATAATT
1 AAATTTAAAATAATT
26485 AAATTTAAAATAATT
1 AAATTTAAAATAATT
26500 TATTTTAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
AAATTTAAAATAATT
Done.