Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2286
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: 72843
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:5537 original size:18 final size:18
Alignment explanation
Indices: 5458--5551 Score: 131
Period size: 18 Copynumber: 5.4 Consensus size: 18
5448 CAAGGTCACG
*
5458 ATCAATAGCGTCACTATC
1 ATCAATATCGTCACTATC
* *
5476 ATCAATAGCGTCACTAGC
1 ATCAATATCGTCACTATC
*
5494 ATCAATATCGTCACTAGC
1 ATCAATATCGTCACTATC
5512 ATCAATATCGTCACTATC
1 ATCAATATCGTCACTATC
5530 ATCAATATCG--A-TATC
1 ATCAATATCGTCACTATC
5545 ATCAATA
1 ATCAATA
5552 AGAAAACCTT
Statistics
Matches: 73, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
15 11 0.15
16 1 0.01
18 61 0.84
ACGTcount: A:0.36, C:0.26, G:0.10, T:0.29
Consensus pattern (18 bp):
ATCAATATCGTCACTATC
Found at i:5538 original size:9 final size:9
Alignment explanation
Indices: 5458--5538 Score: 54
Period size: 9 Copynumber: 9.0 Consensus size: 9
5448 CAAGGTCACG
*
5458 ATCAATAGC
1 ATCAATATC
* *
5467 GTCACTATC
1 ATCAATATC
*
5476 ATCAATAGC
1 ATCAATATC
* * *
5485 GTCACTAGC
1 ATCAATATC
5494 ATCAATATC
1 ATCAATATC
* * *
5503 GTCACTAGC
1 ATCAATATC
5512 ATCAATATC
1 ATCAATATC
* *
5521 GTCACTATC
1 ATCAATATC
5530 ATCAATATC
1 ATCAATATC
5539 GATATCATCA
Statistics
Matches: 51, Mismatches: 21, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
9 51 1.00
ACGTcount: A:0.35, C:0.27, G:0.10, T:0.28
Consensus pattern (9 bp):
ATCAATATC
Found at i:7941 original size:21 final size:21
Alignment explanation
Indices: 7911--7999 Score: 90
Period size: 21 Copynumber: 4.1 Consensus size: 21
7901 CTCACAAAGA
* *
7911 AAAAAG-GAAGTGAGTTAGAC
1 AAAAAGAGAAGTAACTTAGAC
* *
7931 AAAAAGAGAAGCAACTTGGAC
1 AAAAAGAGAAGTAACTTAGAC
*
7952 AAAAAGAGAAGTAACTTGGAC
1 AAAAAGAGAAGTAACTTAGAC
*
7973 AAAAAGAAACGAAGTGACTTAGAC
1 AAAAAG--A-GAAGTAACTTAGAC
7997 AAA
1 AAA
8000 TCTTTTTTGT
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
20 6 0.10
21 36 0.62
23 1 0.02
24 15 0.26
ACGTcount: A:0.54, C:0.10, G:0.24, T:0.12
Consensus pattern (21 bp):
AAAAAGAGAAGTAACTTAGAC
Found at i:7992 original size:24 final size:21
Alignment explanation
Indices: 7911--7979 Score: 95
Period size: 21 Copynumber: 3.3 Consensus size: 21
7901 CTCACAAAGA
* * *
7911 AAAAAG-GAAGTGAGTTAGAC
1 AAAAAGAGAAGTAACTTGGAC
*
7931 AAAAAGAGAAGCAACTTGGAC
1 AAAAAGAGAAGTAACTTGGAC
7952 AAAAAGAGAAGTAACTTGGAC
1 AAAAAGAGAAGTAACTTGGAC
7973 AAAAAGA
1 AAAAAGA
7980 AACGAAGTGA
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
20 6 0.14
21 37 0.86
ACGTcount: A:0.55, C:0.09, G:0.25, T:0.12
Consensus pattern (21 bp):
AAAAAGAGAAGTAACTTGGAC
Found at i:12156 original size:14 final size:14
Alignment explanation
Indices: 12137--12165 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
12127 TACAATATAT
12137 ATAAGAATTATACG
1 ATAAGAATTATACG
12151 ATAAGAATTATACG
1 ATAAGAATTATACG
12165 A
1 A
12166 ATCCATCTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.07, G:0.14, T:0.28
Consensus pattern (14 bp):
ATAAGAATTATACG
Found at i:14946 original size:13 final size:15
Alignment explanation
Indices: 14921--14960 Score: 66
Period size: 13 Copynumber: 2.8 Consensus size: 15
14911 TATTTTATTA
14921 AATAAATATTAAATT
1 AATAAATATTAAATT
14936 AA-AAA-ATTAAATT
1 AATAAATATTAAATT
14949 AATAAATATTAA
1 AATAAATATTAA
14961 TAAATTAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 10 0.43
14 6 0.26
15 7 0.30
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
AATAAATATTAAATT
Found at i:26715 original size:12 final size:12
Alignment explanation
Indices: 26698--26722 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
26688 CAGAGGCTAT
26698 TAACAATATTTA
1 TAACAATATTTA
26710 TAACAATATTTA
1 TAACAATATTTA
26722 T
1 T
26723 GTTATAAAAT
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:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (12 bp):
TAACAATATTTA
Found at i:29272 original size:21 final size:20
Alignment explanation
Indices: 29243--29281 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
29233 ACGCCTACGA
29243 AAAGATCGCTTGGATTTAAG
1 AAAGATCGCTTGGATTTAAG
29263 AAAGAGTCGCTTGGATTTA
1 AAAGA-TCGCTTGGATTTA
29282 TCCATGATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.33, C:0.10, G:0.26, T:0.31
Consensus pattern (20 bp):
AAAGATCGCTTGGATTTAAG
Found at i:29481 original size:15 final size:15
Alignment explanation
Indices: 29461--29499 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
29451 TATCATTTCA
29461 ATATATAATTAAAAT
1 ATATATAATTAAAAT
*
29476 ATATATAAATTTAAAT
1 ATATAT-AATTAAAAT
29492 ATAT-TAAT
1 ATATATAAT
29500 AATATTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 3 0.14
15 7 0.32
16 12 0.55
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATATATAATTAAAAT
Found at i:29517 original size:18 final size:18
Alignment explanation
Indices: 29467--29518 Score: 56
Period size: 16 Copynumber: 3.0 Consensus size: 18
29457 TTCAATATAT
*
29467 AATTAAAATAT-AT-ATA
1 AATTTAAATATAATAATA
*
29483 AATTTAAATATATTAATA
1 AATTTAAATATAATAATA
29501 ATATTTAAATA-AATAATA
1 A-ATTTAAATATAATAATA
29519 TTAATAATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 10 0.33
17 1 0.03
18 10 0.33
19 9 0.30
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AATTTAAATATAATAATA
Found at i:31258 original size:13 final size:13
Alignment explanation
Indices: 31240--31273 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
31230 ACCTCCTTGG
31240 ATTAAATTATTAA
1 ATTAAATTATTAA
31253 ATTAAAATTATTAA
1 ATT-AAATTATTAA
31267 A-TAAATT
1 ATTAAATT
31274 GAAATTAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 5 0.25
13 4 0.20
14 11 0.55
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATTAAATTATTAA
Found at i:38527 original size:17 final size:17
Alignment explanation
Indices: 38507--38540 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
38497 TTCGTATATT
*
38507 ATACTAATTATATCTAA
1 ATACTAAGTATATCTAA
38524 ATACTAAGTATATCTAA
1 ATACTAAGTATATCTAA
38541 GCGAATCTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.47, C:0.12, G:0.03, T:0.38
Consensus pattern (17 bp):
ATACTAAGTATATCTAA
Found at i:43185 original size:20 final size:19
Alignment explanation
Indices: 43115--43198 Score: 70
Period size: 20 Copynumber: 4.4 Consensus size: 19
43105 ATAGATAAGA
43115 AATAGATAAATAATATAA-A-
1 AATA-ATAAAT-ATATAATAG
*
43134 AATAATACTAATATATATTAG
1 AATAATA--AATATATAATAG
43155 AAT-AT--ATATATAATAG
1 AATAATAAATATATAATAG
43171 AATAGATAAATATATAATAG
1 AATA-ATAAATATATAATAG
43191 AATTAATA
1 AA-TAATA
43199 TTCTAACATC
Statistics
Matches: 54, Mismatches: 2, Indels: 17
0.74 0.03 0.23
Matches are distributed among these distances:
16 13 0.24
18 5 0.09
19 9 0.17
20 22 0.41
21 5 0.09
ACGTcount: A:0.60, C:0.01, G:0.06, T:0.33
Consensus pattern (19 bp):
AATAATAAATATATAATAG
Found at i:46642 original size:15 final size:15
Alignment explanation
Indices: 46622--46652 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
46612 CTGTATCAGT
46622 AATGAATCAGAGCAC
1 AATGAATCAGAGCAC
46637 AATGAATCAGAGCAC
1 AATGAATCAGAGCAC
46652 A
1 A
46653 CGGAACCGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.48, C:0.19, G:0.19, T:0.13
Consensus pattern (15 bp):
AATGAATCAGAGCAC
Found at i:51398 original size:18 final size:18
Alignment explanation
Indices: 51377--51419 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
51367 CCTTTCCCCC
*
51377 TTCTTTCATTTGTTTATT
1 TTCTTTCATTTATTTATT
*
51395 TTCTTTCGTTTATTTATT
1 TTCTTTCATTTATTTATT
*
51413 TGCTTTC
1 TTCTTTC
51420 TTTTTATGCG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.09, C:0.14, G:0.07, T:0.70
Consensus pattern (18 bp):
TTCTTTCATTTATTTATT
Found at i:52061 original size:15 final size:17
Alignment explanation
Indices: 52041--52072 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
52031 ACGTTTCATT
52041 TATATAA-T-CATAAAA
1 TATATAACTGCATAAAA
52056 TATATAACTGCATAAAA
1 TATATAACTGCATAAAA
52073 AGATTTTGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 1 0.07
17 7 0.47
ACGTcount: A:0.56, C:0.09, G:0.03, T:0.31
Consensus pattern (17 bp):
TATATAACTGCATAAAA
Found at i:52154 original size:31 final size:31
Alignment explanation
Indices: 52119--52178 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
52109 AACTAAATAG
*
52119 AAATAAATTTAATCTATATTAAATCTATTCA
1 AAATAAATTGAATCTATATTAAATCTATTCA
52150 AAATAAATTGAATCTATATTAAATCTATT
1 AAATAAATTGAATCTATATTAAATCTATT
52179 AAATCGATCG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.48, C:0.08, G:0.02, T:0.42
Consensus pattern (31 bp):
AAATAAATTGAATCTATATTAAATCTATTCA
Found at i:52261 original size:17 final size:17
Alignment explanation
Indices: 52239--52277 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
52229 AATTTAGATG
*
52239 TAAAATATACTA-AAATA
1 TAAAATAAACTAGAAA-A
52256 TAAAATAAACTAGAAAA
1 TAAAATAAACTAGAAAA
52273 TAAAA
1 TAAAA
52278 ATGGAGTCAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 17 0.85
18 3 0.15
ACGTcount: A:0.69, C:0.05, G:0.03, T:0.23
Consensus pattern (17 bp):
TAAAATAAACTAGAAAA
Found at i:52354 original size:9 final size:9
Alignment explanation
Indices: 52340--52370 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
52330 TATAAAAAAG
52340 ATATTAAAT
1 ATATTAAAT
52349 ATATTAAAT
1 ATATTAAAT
*
52358 ATATAAAAT
1 ATATTAAAT
52367 ATAT
1 ATAT
52371 AGATAAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
ATATTAAAT
Found at i:52371 original size:9 final size:9
Alignment explanation
Indices: 52329--52371 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
52319 TATAACTAAG
*
52329 ATATAAAAA
1 ATATATAAA
* *
52338 AGATATTAA
1 ATATATAAA
*
52347 ATATATTAA
1 ATATATAAA
52356 ATATATAAA
1 ATATATAAA
52365 ATATATA
1 ATATATA
52372 GATAAATAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (9 bp):
ATATATAAA
Found at i:52387 original size:19 final size:21
Alignment explanation
Indices: 52353--52396 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 21
52343 TTAAATATAT
52353 TAAATATATAAAATATATAGA
1 TAAATATATAAAATATATAGA
*
52374 TAAATA-AT-AAATATATATA
1 TAAATATATAAAATATATAGA
52393 TAAA
1 TAAA
52397 ATTTTAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 14 0.64
20 2 0.09
21 6 0.27
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (21 bp):
TAAATATATAAAATATATAGA
Found at i:52566 original size:13 final size:13
Alignment explanation
Indices: 52550--52577 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
52540 ATTCGAGTCT
52550 ATAATTCATATTA
1 ATAATTCATATTA
52563 ATAATTCATATTA
1 ATAATTCATATTA
52576 AT
1 AT
52578 TATGAATAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.46
Consensus pattern (13 bp):
ATAATTCATATTA
Found at i:53003 original size:25 final size:25
Alignment explanation
Indices: 52975--53082 Score: 69
Period size: 25 Copynumber: 4.2 Consensus size: 25
52965 TATTTAATAT
52975 TATATTCAATTTATTTATATATCTA
1 TATATTCAATTTATTTATATATCTA
*
53000 TATA-TCTATTTTATTATATATATTCTA
1 TATATTC-AATTTATT-TATATA-TCTA
* ** * * *
53027 AATATTTTATATATTTTTATATTTA
1 TATATTCAATTTATTTATATATCTA
* *
53052 TATATTAATATTCTTTTTATATAT-TA
1 TATATTCA-ATT-TATTTATATATCTA
53078 T-TATT
1 TATATT
53083 ATATATATTT
Statistics
Matches: 63, Mismatches: 14, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
24 2 0.03
25 23 0.37
26 16 0.25
27 21 0.33
28 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (25 bp):
TATATTCAATTTATTTATATATCTA
Found at i:53051 original size:16 final size:17
Alignment explanation
Indices: 52986--53094 Score: 75
Period size: 16 Copynumber: 6.4 Consensus size: 17
52976 ATATTCAATT
52986 TATTTATATATCTATATA
1 TATTTATATAT-TATATA
*
53004 TCTATT-T-TATTATATA
1 TAT-TTATATATTATATA
* *
53020 TATTCTAAATATTTTATA
1 TATT-TATATATTATATA
*
53038 TATTTTTATATT-TATA
1 TATTTATATATTATATA
* * *
53054 TATTAATAT-TCTTTTTA
1 TATTTATATAT-TATATA
53071 TATATTAT-TATTATATA
1 TAT-TTATATATTATATA
53088 TATTTAT
1 TATTTAT
53095 TTCTATTTTT
Statistics
Matches: 71, Mismatches: 12, Indels: 18
0.70 0.12 0.18
Matches are distributed among these distances:
15 2 0.03
16 25 0.35
17 23 0.32
18 19 0.27
19 2 0.03
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (17 bp):
TATTTATATATTATATA
Found at i:53083 original size:25 final size:26
Alignment explanation
Indices: 53018--53088 Score: 76
Period size: 25 Copynumber: 2.8 Consensus size: 26
53008 TTTTATTATA
* * *
53018 TATATTCTAAATATTTTATA-TATTTT
1 TATATT-TATATATTATATATTCTTTT
53044 TATATTTATATATTA-ATATTCTTTT
1 TATATTTATATATTATATATTCTTTT
53069 TATATATTAT-TATTATATAT
1 TATAT-TTATATATTATATAT
53089 ATTTATTTCT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
24 3 0.08
25 22 0.56
26 14 0.36
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (26 bp):
TATATTTATATATTATATATTCTTTT
Found at i:54387 original size:14 final size:14
Alignment explanation
Indices: 54365--54398 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
54355 AATAGAAAAC
*
54365 TTTTCATCACTTTT
1 TTTTTATCACTTTT
54379 TTTTTATCACTTTT
1 TTTTTATCACTTTT
*
54393 TCTTTA
1 TTTTTA
54399 GCCTCCGGGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.15, C:0.18, G:0.00, T:0.68
Consensus pattern (14 bp):
TTTTTATCACTTTT
Found at i:55737 original size:16 final size:16
Alignment explanation
Indices: 55716--55766 Score: 93
Period size: 16 Copynumber: 3.2 Consensus size: 16
55706 AAGAAAGAGC
55716 AAATACGCTAGTAAAT
1 AAATACGCTAGTAAAT
55732 AAATACGCTAGTAAAT
1 AAATACGCTAGTAAAT
*
55748 AAACACGCTAGTAAAT
1 AAATACGCTAGTAAAT
55764 AAA
1 AAA
55767 ATACTAGAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.53, C:0.14, G:0.12, T:0.22
Consensus pattern (16 bp):
AAATACGCTAGTAAAT
Found at i:56705 original size:16 final size:17
Alignment explanation
Indices: 56684--56717 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
56674 AATTAGAGAA
56684 TTCTATTTAA-TTCTAT
1 TTCTATTTAATTTCTAT
56700 TTCTATTTAATTTCTAT
1 TTCTATTTAATTTCTAT
56717 T
1 T
56718 AAATCCATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.65
Consensus pattern (17 bp):
TTCTATTTAATTTCTAT
Found at i:57410 original size:15 final size:15
Alignment explanation
Indices: 57392--57422 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
57382 ATAACTAAAG
57392 AAAAAATAGATAGAT
1 AAAAAATAGATAGAT
57407 AAAAAATAGATAGAT
1 AAAAAATAGATAGAT
57422 A
1 A
57423 GATGAGAGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.13, T:0.19
Consensus pattern (15 bp):
AAAAAATAGATAGAT
Found at i:63136 original size:23 final size:22
Alignment explanation
Indices: 63110--63154 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
63100 AATATTCAGA
63110 ATATTAAGTA-ATTAATAATATTT
1 ATATT-AGTATATTAAT-ATATTT
*
63133 ATATTATTATATTAATATATTT
1 ATATTAGTATATTAATATATTT
63155 CGATTTATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (22 bp):
ATATTAGTATATTAATATATTT
Found at i:63142 original size:8 final size:8
Alignment explanation
Indices: 63131--63352 Score: 79
Period size: 8 Copynumber: 28.2 Consensus size: 8
63121 TTAATAATAT
63131 TTATATTA
1 TTATATTA
63139 TTATATTA
1 TTATATTA
*
63147 ATATATTTCGA
1 TTATA-TT--A
*
63158 TT-TATAAA
1 TTATAT-TA
63166 TCTATATT-
1 T-TATATTA
63174 TCTATATTA
1 T-TATATTA
63183 TT-TATT-
1 TTATATTA
*
63189 TTATTATTC
1 TTA-TATTA
*
63198 TATCTATTA
1 T-TATATTA
63207 TTATATTA
1 TTATATTA
*
63215 -TCTATTA
1 TTATATTA
63222 TTATATTA
1 TTATATTA
63230 TCTAT-TTA
1 T-TATATTA
*
63238 TAAT-TTA
1 TTATATTA
63245 -TATATTA
1 TTATATTA
63252 TT-T-TTA
1 TTATATTA
63258 -TAT-TTA
1 TTATATTA
*
63264 TAAT-TTA
1 TTATATTA
63271 TATATTATTA
1 T-TA-TATTA
63281 TTATATATA
1 TTATAT-TA
63290 TT-T-TTA
1 TTATATTA
63296 TATATATTA
1 T-TATATTA
*
63305 -TATATTT
1 TTATATTA
*
63312 TTATTTCTA
1 TTATAT-TA
63321 TT-TAGTTA
1 TTATA-TTA
63329 TTAT-TTA
1 TTATATTA
63336 TT-TAGTTA
1 TTATA-TTA
63344 TTAT-TTA
1 TTATATTA
63351 TT
1 TT
63353 TTTATTTCTA
Statistics
Matches: 166, Mismatches: 17, Indels: 63
0.67 0.07 0.26
Matches are distributed among these distances:
5 1 0.01
6 15 0.09
7 43 0.26
8 65 0.39
9 30 0.18
10 10 0.06
11 2 0.01
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.63
Consensus pattern (8 bp):
TTATATTA
Found at i:63196 original size:15 final size:15
Alignment explanation
Indices: 63178--63399 Score: 81
Period size: 15 Copynumber: 14.3 Consensus size: 15
63168 TATATTTCTA
63178 TATTATTTATTTTAT
1 TATTATTTATTTTAT
*
63193 TATTCTATCTATTATTA-
1 TA-T-TATTTATT-TTAT
*
63210 TATTATCTATTATTATAT
1 TATTA--T-TTATTTTAT
63228 TATCTATTTATAATTTAT
1 TAT-TATTTAT--TTTAT
*
63246 ATATTATTT-TTATATT
1 -TATTATTTATTTTA-T
*
63262 TATAATTTATATATTAT
1 TATTATTTAT-T-TTAT
*
63279 TATTATATATATTT-T
1 TATTATTTAT-TTTAT
*
63294 TATATATATTA-TATAT
1 TAT-TAT-TTATTTTAT
* *
63310 TTTTATTTCTATTTAGT
1 TATTATTTAT-TTTA-T
63327 TATTATTTA-TTTAGT
1 TATTATTTATTTTA-T
63342 TATTATTTA-TTT-T
1 TATTATTTATTTTAT
*
63355 TATT-TCTATTTT-T
1 TATTATTTATTTTAT
*
63368 TATT-TCTA-TTTAGT
1 TATTATTTATTTTA-T
*
63382 TATTATTTA-GTTAT
1 TATTATTTATTTTAT
63396 TATT
1 TATT
63400 TATATTTAGT
Statistics
Matches: 163, Mismatches: 19, Indels: 51
0.70 0.08 0.22
Matches are distributed among these distances:
12 6 0.04
13 17 0.10
14 12 0.07
15 47 0.29
16 19 0.12
17 36 0.22
18 21 0.13
19 5 0.03
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.66
Consensus pattern (15 bp):
TATTATTTATTTTAT
Found at i:63235 original size:27 final size:30
Alignment explanation
Indices: 63190--63347 Score: 116
Period size: 26 Copynumber: 5.3 Consensus size: 30
63180 TTATTTATTT
* *
63190 TATTATTCTATCTATTA-TTAT-A-TTATC
1 TATTATTATATCTATTATTTATAATTTATA
63217 TATTATTATAT-TATCTATTTATAATTTATA
1 TATTATTATATCTAT-TATTTATAATTTATA
63247 TATTATT-T-T-TA-TATTTATAATTTATA
1 TATTATTATATCTATTATTTATAATTTATA
* *
63273 TATTATTATTATATATATTTTTATATATATTATA
1 TATTATTA-TATCTAT-TATTTATA-AT-TTATA
* * * * *
63307 TATTTTTATTTCTATTTAGTTATTATTTATT
1 TATTATTATATCTA-TTATTTATAATTTATA
63338 TAGTTATTAT
1 TA-TTATTAT
63348 TTATTTTTAT
Statistics
Matches: 106, Mismatches: 11, Indels: 23
0.76 0.08 0.16
Matches are distributed among these distances:
26 25 0.24
27 12 0.11
28 8 0.08
29 3 0.03
30 13 0.12
31 6 0.06
32 15 0.14
33 11 0.10
34 13 0.12
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.63
Consensus pattern (30 bp):
TATTATTATATCTATTATTTATAATTTATA
Found at i:63243 original size:7 final size:6
Alignment explanation
Indices: 63222--63324 Score: 68
Period size: 6 Copynumber: 16.5 Consensus size: 6
63212 TTATCTATTA
* *
63222 TTATAT TATCTAT TTATAAT TTATAT ATTATTT TTATAT TTATAAT TTATAT
1 TTATAT T-TATAT TTAT-AT TTATAT -TTATAT TTATAT TTAT-AT TTATAT
* * * *
63274 ATTAT-T ATTATA- -TATAT TTTTAT ATATAT TATATAT TTTTAT TTCTAT
1 -TTATAT -TTATAT TTATAT TTATAT TTATAT T-TATAT TTATAT TTATAT
63322 TTA
1 TTA
63325 GTTATTATTT
Statistics
Matches: 77, Mismatches: 11, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
4 4 0.05
6 41 0.53
7 32 0.42
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (6 bp):
TTATAT
Found at i:63300 original size:51 final size:48
Alignment explanation
Indices: 63227--63434 Score: 122
Period size: 55 Copynumber: 4.1 Consensus size: 48
63217 TATTATTATA
*
63227 TTATCTATTTATAATTTATATATTATTTTTATATTTATAATTTATATATTA-
1 TTAT-TATTTAT-TTTTATATATTATTTTTATATTT-TAATTTATAT-TTAG
* * *
63278 TTATTATATATATTTTTATATA-TA-TTATATATTTTTATTTCTATTTAG
1 TTATTAT-T-TATTTTTATATATTATTTTTATATTTTAATTTATATTTAG
* *
63326 TTATTATTTATTTAGTTAT-TATTTATTTTTATTTCTATTTTTTATTTCTATTTAG
1 TTATTATTTATTT--TTATATA-TTATTTTTA----TA-TTTTAATTTATATTTAG
* * * *
63381 TTATTATTTAGTTATTATTTA-TATTTAGTATATTTAGAATTTATTATTTA-
1 TTATTATTTA-TTTTTATATATTATTT-TTATATTT-TAATTTA-TATTTAG
63431 TTAT
1 TTAT
63435 AATATTTAAT
Statistics
Matches: 129, Mismatches: 10, Indels: 37
0.73 0.06 0.21
Matches are distributed among these distances:
46 5 0.04
47 6 0.05
48 19 0.15
49 14 0.11
50 19 0.15
51 19 0.15
52 3 0.02
53 5 0.04
54 8 0.06
55 29 0.22
56 2 0.02
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.65
Consensus pattern (48 bp):
TTATTATTTATTTTTATATATTATTTTTATATTTTAATTTATATTTAG
Found at i:63324 original size:80 final size:84
Alignment explanation
Indices: 63182--63354 Score: 191
Period size: 80 Copynumber: 2.1 Consensus size: 84
63172 TTTCTATATT
* * *
63182 ATTTATTTTATTATTCTATCTATTATTATATTATCTATTATTATATTATCTATTTATAATTTA-T
1 ATTTATTTTATTATTATATATATTATTATATTATATATTATTATATTATCTATTTATAATTTAGT
*
63246 ATATTATTT-TTATATTTATA
66 -TATTATTTATT-TAGTTATA
* *
63266 ATTTATATATTATTATTATATATATT-TT-TA-TATATATTA-TATATT-TTTATTTCT-ATTTA
1 ATTTAT-T-TTATTATTATATATATTATTATATTATATATTATTATATTATCTATTTATAATTTA
*
63325 GTTATTATTTATTTAGTTATT
64 GTTATTATTTATTTAGTTATA
63346 ATTTATTTT
1 ATTTATTTT
63355 TATTTCTATT
Statistics
Matches: 78, Mismatches: 7, Indels: 14
0.79 0.07 0.14
Matches are distributed among these distances:
78 2 0.03
79 1 0.01
80 25 0.32
81 10 0.13
82 6 0.08
83 8 0.10
84 8 0.10
85 3 0.04
86 15 0.19
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.65
Consensus pattern (84 bp):
ATTTATTTTATTATTATATATATTATTATATTATATATTATTATATTATCTATTTATAATTTAGT
TATTATTTATTTAGTTATA
Found at i:63351 original size:7 final size:7
Alignment explanation
Indices: 63178--63434 Score: 121
Period size: 7 Copynumber: 35.9 Consensus size: 7
63168 TATATTTCTA
63178 TATTATT
1 TATTATT
63185 TA-T-TT
1 TATTATT
63190 TATTATT
1 TATTATT
63197 CTATCTA-T
1 -TAT-TATT
63205 TATTATAT
1 TATTAT-T
63213 TATCTA-T
1 TAT-TATT
63220 TATTATAT
1 TATTAT-T
63228 TATCTATT
1 TAT-TATT
*
63236 TATAATT
1 TATTATT
63243 TA-TATAT
1 TATTAT-T
63250 TATT-TT
1 TATTATT
63256 TA-TATT
1 TATTATT
*
63262 TATAATT
1 TATTATT
63269 TA-TATAT
1 TATTAT-T
63276 TATTATT
1 TATTATT
63283 ATATATATT
1 -TAT-TATT
63292 T-TTATAT
1 TATTAT-T
*
63299 ATATTATA
1 -TATTATT
63307 TATT-TT
1 TATTATT
*
63313 TATT-TC
1 TATTATT
*
63319 TATTTAGT
1 TA-TTATT
63327 TATTATT
1 TATTATT
*
63334 TATTTAGT
1 TA-TTATT
63342 TATTATT
1 TATTATT
63349 TATT-TT
1 TATTATT
63355 TATTTCTATT
1 TA--T-TATT
*
63365 TTTTATT
1 TATTATT
*
63372 T-CTATT
1 TATTATT
63378 TAGTTA-T
1 TA-TTATT
*
63385 TATTTAGT
1 TA-TTATT
63393 TATTATT
1 TATTATT
63400 TA-TATT
1 TATTATT
63406 TAGTATATT
1 TA-T-TATT
**
63415 TAGAATT
1 TATTATT
63422 TATTATT
1 TATTATT
63429 TATTAT
1 TATTAT
63435 AATATTTAAT
Statistics
Matches: 195, Mismatches: 21, Indels: 68
0.69 0.07 0.24
Matches are distributed among these distances:
5 5 0.03
6 43 0.22
7 82 0.42
8 40 0.21
9 22 0.11
10 3 0.02
ACGTcount: A:0.30, C:0.03, G:0.02, T:0.65
Consensus pattern (7 bp):
TATTATT
Found at i:63351 original size:55 final size:52
Alignment explanation
Indices: 63219--63399 Score: 158
Period size: 55 Copynumber: 3.4 Consensus size: 52
63209 ATATTATCTA
* * *
63219 TTATTATATTATCTATTTATAATTTATA-TA-TTAT-TTTTATATTTATAATTTA-
1 TTATTAT-TTATTTA-TTATTATTTATATTATTTATATTTT-TATTTCT-ATTTAG
63271 TATATTA-TTATTATATATATT-TTTATATATATTATATATTTTTATTTCTATTTAG
1 T-TATTATTTATT-TAT-TATTATTTATAT-TATT-TATATTTTTATTTCTATTTAG
* *
63326 TTATTATTTATTTAGTTATTATTTATTTTTATTTCTATTTTTTATTTCTATTTAG
1 TTATTATTTATTTA-TTATTATTTA-TATTATTTATA-TTTTTATTTCTATTTAG
*
63381 TTATTATTTAGTTATTATT
1 TTATTATTTATTTATTATT
63400 TATATTTAGT
Statistics
Matches: 109, Mismatches: 6, Indels: 26
0.77 0.04 0.18
Matches are distributed among these distances:
51 11 0.10
52 6 0.06
53 7 0.06
54 25 0.23
55 54 0.50
56 6 0.06
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.66
Consensus pattern (52 bp):
TTATTATTTATTTATTATTATTTATATTATTTATATTTTTATTTCTATTTAG
Found at i:63364 original size:19 final size:18
Alignment explanation
Indices: 63178--63378 Score: 97
Period size: 19 Copynumber: 10.6 Consensus size: 18
63168 TATATTTCTA
63178 TATTATTTATTTTATTATT
1 TATT-TTTATTTTATTATT
* * *
63197 CTATCTATTATTATATTATC
1 -TAT-TTTTATTTTATTATT
* *
63217 TA---TTATTATATTATC
1 TATTTTTATTTTATTATT
* *
63232 TATTTATAATTTA-TATAT
1 TATTTTTATTTTATTAT-T
*
63250 TATTTTTATATTTATAATT
1 TATTTTTAT-TTTATTATT
* *
63269 TATATATTATTATTA-TATA
1 TAT-TTTTATT-TTATTATT
* *
63288 TATTTTTATATATATTATA
1 TATTTTTAT-TTTATTATT
*
63307 TATTTTTATTTCTATTTAGT
1 TATTTTTATTT-TA-TTATT
63327 TATTATTTATTTAGTTATTATT
1 TATT-TTTA-TT--TTATTATT
*
63349 TATTTTTATTTCTATTTTT
1 TATTTTTATTT-TATTATT
*
63368 TATTTCTATTT
1 TATTTTTATTT
63379 AGTTATTATT
Statistics
Matches: 142, Mismatches: 21, Indels: 37
0.71 0.10 0.19
Matches are distributed among these distances:
15 15 0.11
17 3 0.02
18 21 0.15
19 48 0.34
20 33 0.23
21 9 0.06
22 10 0.07
23 2 0.01
24 1 0.01
ACGTcount: A:0.29, C:0.03, G:0.01, T:0.66
Consensus pattern (18 bp):
TATTTTTATTTTATTATT
Found at i:63390 original size:11 final size:10
Alignment explanation
Indices: 63178--63402 Score: 121
Period size: 11 Copynumber: 22.0 Consensus size: 10
63168 TATATTTCTA
63178 TATTATTTAT
1 TATTATTTAT
63188 T-TTA-TTAT
1 TATTATTTAT
* *
63196 T-CTATCTAT
1 TATTATTTAT
63205 TATTATATTAT
1 TATTAT-TTAT
63216 CTATTATTATAT
1 -TATTATT-TAT
63228 TATCTATTTA-
1 TAT-TATTTAT
63238 TA--ATTTAT
1 TATTATTTAT
63246 ATATTATTT-T
1 -TATTATTTAT
63256 TA-TATTTAT
1 TATTATTTAT
* *
63265 AATTTATATAT
1 TA-TTATTTAT
63276 TATTATTATAT
1 TATTATT-TAT
*
63287 ATATTTTTATAT
1 -TATTATT-TAT
*
63299 ATATTATATAT
1 -TATTATTTAT
* *
63310 TTTTATTT-C
1 TATTATTTAT
*
63319 TATTTAGTTAT
1 TA-TTATTTAT
63330 TATTTATTTAGT
1 TA-TTATTTA-T
63342 TATTATTTAT
1 TATTATTTAT
* *
63352 TTTTATTT-C
1 TATTATTTAT
*
63361 TATTTTTTAT
1 TATTATTTAT
63371 T-TCTATTTAGT
1 TAT-TATTTA-T
63382 TATTATTTAGT
1 TATTATTTA-T
63393 TATTATTTAT
1 TATTATTTAT
63403 ATTTAGTATA
Statistics
Matches: 169, Mismatches: 24, Indels: 44
0.71 0.10 0.19
Matches are distributed among these distances:
7 5 0.03
8 12 0.07
9 21 0.12
10 37 0.22
11 61 0.36
12 33 0.20
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.66
Consensus pattern (10 bp):
TATTATTTAT
Found at i:63430 original size:29 final size:30
Alignment explanation
Indices: 63308--63431 Score: 99
Period size: 29 Copynumber: 4.4 Consensus size: 30
63298 TATATTATAT
*
63308 ATTT-TTATTTCTATTTAGTTATTATTT--
1 ATTTATTATTTATATTTAGTTATTATTTAG
* **
63335 ATTTAGTTA--T-TATTTA-TTTTTATTTCT
1 ATTTA-TTATTTATATTTAGTTATTATTTAG
* *
63362 ATTTTTTATTTCTATTTAGTTATTATTTAG
1 ATTTATTATTTATATTTAGTTATTATTTAG
63392 --TTATTATTTATATTTAG-TA-TATTTAG
1 ATTTATTATTTATATTTAGTTATTATTTAG
63418 AATTTATTATTTAT
1 -ATTTATTATTTAT
63432 TATAATATTT
Statistics
Matches: 79, Mismatches: 7, Indels: 20
0.75 0.07 0.19
Matches are distributed among these distances:
25 8 0.10
26 16 0.20
27 11 0.14
28 16 0.20
29 20 0.25
30 8 0.10
ACGTcount: A:0.26, C:0.02, G:0.05, T:0.67
Consensus pattern (30 bp):
ATTTATTATTTATATTTAGTTATTATTTAG
Found at i:63459 original size:40 final size:40
Alignment explanation
Indices: 63381--63459 Score: 92
Period size: 40 Copynumber: 2.0 Consensus size: 40
63371 TTCTATTTAG
**
63381 TTATTATTTAGTTATTATTTATATTTAGTATATTTAGAAT
1 TTATTATTTAGTTATTATTTATATTTAGTATAAATAGAAT
63421 TTATTATTTA-TTATAATATTTA-ATTTAAGT-TAAATAGAA
1 TTATTATTTAGTTAT--TATTTATATTT-AGTATAAATAGAA
63460 AAATTAATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
39 4 0.12
40 21 0.62
41 9 0.26
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (40 bp):
TTATTATTTAGTTATTATTTATATTTAGTATAAATAGAAT
Found at i:63473 original size:31 final size:32
Alignment explanation
Indices: 63434--63508 Score: 93
Period size: 31 Copynumber: 2.4 Consensus size: 32
63424 TTATTTATTA
63434 TAAT-ATTTAATTTAAGT-TAAATAGAAA-AAT
1 TAATAATTTAATTTAAGTATAAATA-AAACAAT
*
63464 TAATAATTTAATTTAAGTATAATTAAAATCAAT
1 TAATAATTTAATTTAAGTATAAATAAAA-CAAT
*
63497 TATTAATTTAAT
1 TAATAATTTAAT
63509 AATTTTTCAT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
30 4 0.10
31 16 0.41
32 5 0.13
33 14 0.36
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.44
Consensus pattern (32 bp):
TAATAATTTAATTTAAGTATAAATAAAACAAT
Done.