Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2054
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: 70443
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.36
Found at i:5369 original size:14 final size:14
Alignment explanation
Indices: 5350--5377 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5340 AGAAAGAAGG
5350 GTAGCCAGCTGCAA
1 GTAGCCAGCTGCAA
5364 GTAGCCAGCTGCAA
1 GTAGCCAGCTGCAA
5378 AAAACAAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.29, G:0.29, T:0.14
Consensus pattern (14 bp):
GTAGCCAGCTGCAA
Found at i:9770 original size:6 final size:6
Alignment explanation
Indices: 9761--9793 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
9751 AAATTCAAAG
9761 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAA
9794 TAGGGGAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:10396 original size:13 final size:13
Alignment explanation
Indices: 10375--10457 Score: 52
Period size: 13 Copynumber: 6.6 Consensus size: 13
10365 GATAATTTAT
*
10375 TTATTTATAT-TA
1 TTATATATATATA
10387 -TATATATATATA
1 TTATATATATATA
* *
10399 TTA-ATTTTATATG
1 TTATA-TATATATA
10412 TTATA-AT-TATA
1 TTATATATATATA
10423 TTGATATATTATATA
1 TT-ATATA-TATATA
* *
10438 TT-TATATAAATT
1 TTATATATATATA
10450 TTATATAT
1 TTATATAT
10458 TAATAATTTA
Statistics
Matches: 55, Mismatches: 7, Indels: 17
0.70 0.09 0.22
Matches are distributed among these distances:
11 13 0.24
12 13 0.24
13 21 0.38
14 2 0.04
15 6 0.11
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (13 bp):
TTATATATATATA
Found at i:10428 original size:60 final size:58
Alignment explanation
Indices: 10358--10514 Score: 162
Period size: 60 Copynumber: 2.7 Consensus size: 58
10348 TTATTTAATT
*
10358 TAAATA-TGATAATTTATTTATTTATATTATATATATATATATTAAT-TTTATATGTTA
1 TAAATATTGATAATTTATATATTTATATTATAT-TATATATATTAATATTTATATGTTA
* * *
10415 TAATTATATTGAT-ATATTATATATTTATA-TAAATTTTATATATTAATAATTTATATTTTA
1 TAA--ATATTGATAAT-TTATATATTTATATTATATTATATATATTAAT-ATTTATATGTTA
* * *
10475 TAAATTTTGATATATTTATATATTCATATTTTATT-TATAT
1 TAAATATTGATA-ATTTATATATTTATATTATATTATATAT
10515 TATTTTTCGT
Statistics
Matches: 83, Mismatches: 8, Indels: 16
0.78 0.07 0.15
Matches are distributed among these distances:
57 3 0.04
58 19 0.23
59 26 0.31
60 35 0.42
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.57
Consensus pattern (58 bp):
TAAATATTGATAATTTATATATTTATATTATATTATATATATTAATATTTATATGTTA
Found at i:10431 original size:47 final size:47
Alignment explanation
Indices: 10380--10471 Score: 134
Period size: 47 Copynumber: 2.0 Consensus size: 47
10370 TTTATTTATT
* *
10380 TATATTATATATATATATATTAATTTTATATGTT-ATAA-TTATATTGA
1 TATATTATATAT-T-TATATAAATTTTATATATTAATAATTTATATTGA
10427 TATATTATATATTTATATAAATTTTATATATTAATAATTTATATT
1 TATATTATATATTTATATAAATTTTATATATTAATAATTTATATT
10472 TTATAAATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
45 17 0.41
46 5 0.12
47 19 0.46
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (47 bp):
TATATTATATATTTATATAAATTTTATATATTAATAATTTATATTGA
Found at i:10454 original size:32 final size:31
Alignment explanation
Indices: 10418--10508 Score: 87
Period size: 32 Copynumber: 2.8 Consensus size: 31
10408 TATGTTATAA
10418 TTATAT-TG-ATATATTATATATTTATATAAATT
1 TTATATATGAATA-ATT-TATATTT-TATAAATT
*
10450 TTATATATTAATAATTTATATTTTATAAATT
1 TTATATATGAATAATTTATATTTTATAAATT
** *
10481 TTGATATATTTATATATTCATATTTTAT
1 TT-ATATATGAATA-ATTTATATTTTAT
10509 TTATATTATT
Statistics
Matches: 52, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
31 10 0.19
32 23 0.44
33 16 0.31
34 3 0.06
ACGTcount: A:0.38, C:0.01, G:0.02, T:0.58
Consensus pattern (31 bp):
TTATATATGAATAATTTATATTTTATAAATT
Found at i:10456 original size:26 final size:27
Alignment explanation
Indices: 10423--10503 Score: 83
Period size: 31 Copynumber: 2.8 Consensus size: 27
10413 TATAATTATA
10423 TTGATATATTATATATTTATATAAATT
1 TTGATATATTATATATTTATATAAATT
*
10450 TT-ATATATTAATAATTTATATTTTATAAATT
1 TTGATATATT-AT-A--TAT-TTATATAAATT
*
10481 TTGATATATTTATATATTCATAT
1 TTGATATA-TTATATATTTATAT
10504 TTTATTTATA
Statistics
Matches: 44, Mismatches: 3, Indels: 13
0.73 0.05 0.22
Matches are distributed among these distances:
26 7 0.16
27 4 0.09
28 5 0.11
29 3 0.07
30 3 0.07
31 13 0.30
32 7 0.16
33 2 0.05
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.57
Consensus pattern (27 bp):
TTGATATATTATATATTTATATAAATT
Found at i:10463 original size:17 final size:17
Alignment explanation
Indices: 10431--10490 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 17
10421 TATTGATATA
10431 TTATATATTTATATAAATT
1 TTATATA-TTA-ATAAATT
10450 TTATATATTAAT-AA-T
1 TTATATATTAATAAATT
*
10465 TTATAT-TTTATAAATT
1 TTATATATTAATAAATT
10481 TTGATATATT
1 TT-ATATATT
10491 TATATATTCA
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
14 4 0.11
15 9 0.25
16 5 0.14
17 6 0.17
18 5 0.14
19 7 0.19
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (17 bp):
TTATATATTAATAAATT
Found at i:10487 original size:58 final size:58
Alignment explanation
Indices: 10393--10503 Score: 154
Period size: 58 Copynumber: 1.9 Consensus size: 58
10383 ATTATATATA
*
10393 TATATATTAATTTTATATGTTATAATTATATTGATATA-TTATATATTTATATAAATTT
1 TATATATTAATTTTATATGTTATAA-TATATTGATATATTTATATATTCATATAAATTT
* *
10451 TATATATTAATAATTTATATTTTATAA-ATTTTGATATATTTATATATTCATAT
1 TATATATTAAT--TTTATATGTTATAATATATTGATATATTTATATATTCATAT
10504 TTTATTTATA
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
58 21 0.45
59 13 0.28
60 13 0.28
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.57
Consensus pattern (58 bp):
TATATATTAATTTTATATGTTATAATATATTGATATATTTATATATTCATATAAATTT
Found at i:10531 original size:28 final size:28
Alignment explanation
Indices: 10495--10548 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
10485 TATATTTATA
**
10495 TATTCATATTTTATTTATATTATTTTTCG
1 TATTCATATAATATTTA-ATTATTTTTCG
*
10524 TATT-ATATAATATTTAATTTTTTTT
1 TATTCATATAATATTTAATTATTTTT
10549 TCACATATGT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 8 0.36
28 10 0.45
29 4 0.18
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.67
Consensus pattern (28 bp):
TATTCATATAATATTTAATTATTTTTCG
Found at i:11314 original size:8 final size:9
Alignment explanation
Indices: 11287--11321 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
11277 ACATATCTTT
*
11287 TAAATATAA
1 TAAAAATAA
11296 TAAAAATAA
1 TAAAAATAA
11305 TAAAAA-AA
1 TAAAAATAA
11313 TAAAAATAA
1 TAAAAATAA
11322 AATATATGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
8 8 0.33
9 16 0.67
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (9 bp):
TAAAAATAA
Found at i:11612 original size:2 final size:2
Alignment explanation
Indices: 11605--11634 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
11595 AAAACAGCCC
11605 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
11635 TTTCTTTTTT
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):
CT
Found at i:12801 original size:2 final size:2
Alignment explanation
Indices: 12794--12820 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
12784 CTTGTAGATT
12794 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 T
12821 TTTTTAAGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:13370 original size:17 final size:18
Alignment explanation
Indices: 13348--13387 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
13338 TATATGACTT
*
13348 AAATTATTTAAATAT-TA
1 AAATTATATAAATATATA
13365 AAATTATATAAATATATA
1 AAATTATATAAATATATA
13383 AAATT
1 AAATT
13388 TAAAACATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
AAATTATATAAATATATA
Found at i:13428 original size:22 final size:25
Alignment explanation
Indices: 13388--13439 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
13378 ATATAAAATT
*
13388 TAAAACATGATTATGATAAAA-AAA
1 TAAAACATGATTATAATAAAAGAAA
13412 TAAAAC-T-ATTATAATAAAAGTAAA
1 TAAAACATGATTATAATAAAAG-AAA
13436 TAAA
1 TAAA
13440 TTATTAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 11 0.44
23 1 0.04
24 13 0.52
ACGTcount: A:0.63, C:0.04, G:0.06, T:0.27
Consensus pattern (25 bp):
TAAAACATGATTATAATAAAAGAAA
Found at i:13458 original size:16 final size:17
Alignment explanation
Indices: 13437--13477 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
13427 AAAAGTAAAT
* *
13437 AAATTATTAA-ATTTAA
1 AAATTAATAATATATAA
13453 AAATTAATAATATATAA
1 AAATTAATAATATATAA
13470 AAA-TAATA
1 AAATTAATA
13478 TTTAGTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 14 0.64
17 8 0.36
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
AAATTAATAATATATAA
Found at i:20133 original size:35 final size:35
Alignment explanation
Indices: 20088--20154 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
20078 CATCTTTTAA
*
20088 TATATTTATATATTTATATTATATTTTAAATTTTTT
1 TATATTTATATAATTATATTATA-TTTAAATTTTTT
*
20124 TATA-TTATATAATTATATTTTATTTAAATTT
1 TATATTTATATAATTATATTATATTTAAATTT
20155 ATCAAATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 9 0.31
35 16 0.55
36 4 0.14
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (35 bp):
TATATTTATATAATTATATTATATTTAAATTTTTT
Found at i:20904 original size:38 final size:36
Alignment explanation
Indices: 20847--20924 Score: 95
Period size: 38 Copynumber: 2.1 Consensus size: 36
20837 ATGATGAGTT
*
20847 TAAATTTTTAATTTTATATTAAAAATTATATTATTTTA
1 TAAATTTTTAATTTAATATT-AAAATTA-ATTATTTTA
* * *
20885 TAAATTTTTTATTTAATATTTAAATTAATTTTTTTA
1 TAAATTTTTAATTTAATATTAAAATTAATTATTTTA
20921 -AAAT
1 TAAAT
20925 AATCTATTCA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
35 4 0.11
36 8 0.22
37 6 0.17
38 18 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (36 bp):
TAAATTTTTAATTTAATATTAAAATTAATTATTTTA
Found at i:21292 original size:17 final size:17
Alignment explanation
Indices: 21262--21339 Score: 70
Period size: 17 Copynumber: 4.4 Consensus size: 17
21252 TTGATATATG
*
21262 TATATATATTTTATATTT
1 TATAT-TATATTATATTT
*
21280 TATATTATATTATGTTT
1 TATATTATATTATATTT
21297 ATATTATTATTATTATATTAT
1 -TA-TATTA-TATTATATT-T
*
21318 TAT-TTTTATTATATTT
1 TATATTATATTATATTT
21334 TA-ATTA
1 TATATTA
21340 ATTTTTTAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
16 5 0.10
17 19 0.38
18 9 0.18
19 6 0.12
20 10 0.20
21 1 0.02
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.65
Consensus pattern (17 bp):
TATATTATATTATATTT
Found at i:21306 original size:3 final size:3
Alignment explanation
Indices: 21282--21329 Score: 50
Period size: 3 Copynumber: 17.0 Consensus size: 3
21272 TTATATTTTA
*
21282 TAT TA- TAT TAT GT-T TA- TAT TAT TAT TAT TA- TAT TAT TAT TTT
1 TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
21324 TAT TAT
1 TAT TAT
21330 ATTTTAATTA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
2 7 0.18
3 30 0.79
4 1 0.03
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:21309 original size:11 final size:11
Alignment explanation
Indices: 21262--21332 Score: 62
Period size: 11 Copynumber: 6.5 Consensus size: 11
21252 TTGATATATG
21262 TATATATATT-T
1 TATAT-TATTAT
*
21273 TATATTTTATAT
1 TATATTAT-TAT
21285 TATATTATGT-T
1 TATATTAT-TAT
21296 TATATTATTAT
1 TATATTATTAT
21307 TAT-TATATTAT
1 TATAT-TATTAT
21318 TAT-TT-TTAT
1 TATATTATTAT
21327 TATATT
1 TATATT
21333 TTAATTAATT
Statistics
Matches: 52, Mismatches: 3, Indels: 11
0.79 0.05 0.17
Matches are distributed among these distances:
9 7 0.13
10 7 0.13
11 29 0.56
12 9 0.17
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.66
Consensus pattern (11 bp):
TATATTATTAT
Found at i:21332 original size:14 final size:14
Alignment explanation
Indices: 21266--21326 Score: 70
Period size: 14 Copynumber: 4.2 Consensus size: 14
21256 TATATGTATA
21266 TATATT-TTATATTT
1 TATATTATTAT-TTT
*
21280 TATATTATATTATGTT
1 TATA-T-TATTATTTT
*
21296 TATATTATTATTAT
1 TATATTATTATTTT
21310 TATATTATTATTTT
1 TATATTATTATTTT
21324 TAT
1 TAT
21327 TATATTTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
14 27 0.68
15 2 0.05
16 7 0.17
17 4 0.10
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (14 bp):
TATATTATTATTTT
Found at i:21333 original size:11 final size:11
Alignment explanation
Indices: 21266--21345 Score: 54
Period size: 11 Copynumber: 6.8 Consensus size: 11
21256 TATATGTATA
21266 TATATTTTATAT
1 TATATTTT-TAT
* *
21278 TTTATATTATAT
1 TATAT-TTTTAT
* *
21290 TATGTTTATAT
1 TATATTTTTAT
21301 TATTATTATTATAT
1 TA-TATT-TT-TAT
21315 TATTATTTTTAT
1 TA-TATTTTTAT
*
21327 TATATTTTAAT
1 TATATTTTTAT
21338 TA-ATTTTT
1 TATATTTTT
21346 TAAAATTATT
Statistics
Matches: 56, Mismatches: 8, Indels: 10
0.76 0.11 0.14
Matches are distributed among these distances:
10 5 0.09
11 18 0.32
12 18 0.32
13 5 0.09
14 10 0.18
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.68
Consensus pattern (11 bp):
TATATTTTTAT
Found at i:21618 original size:11 final size:11
Alignment explanation
Indices: 21602--21698 Score: 67
Period size: 11 Copynumber: 8.9 Consensus size: 11
21592 GCCATAATTT
21602 TAAATATAATA
1 TAAATATAATA
21613 TAAATATAATA
1 TAAATATAATA
21624 TAAA-ATTAA-A
1 TAAATA-TAATA
*
21634 TATAATTTAATA
1 TA-AATATAATA
*
21646 TAAATA-AATG
1 TAAATATAATA
* * *
21656 TATATTAAAATT
1 TA-AATATAATA
* *
21668 TATATAAAATA
1 TAAATATAATA
21679 TAAA-ATAATA
1 TAAATATAATA
*
21689 GAAATATAAT
1 TAAATATAAT
21699 TATTGTATAA
Statistics
Matches: 68, Mismatches: 11, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
10 17 0.25
11 43 0.63
12 8 0.12
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (11 bp):
TAAATATAATA
Found at i:21625 original size:16 final size:16
Alignment explanation
Indices: 21604--21698 Score: 76
Period size: 16 Copynumber: 6.2 Consensus size: 16
21594 CATAATTTTA
21604 AATATAATATAAATAT
1 AATATAATATAAATAT
*
21620 AATATAAAATTAAATAT
1 AATATAATA-TAAATAT
*
21637 AATTTAATATAAATA-
1 AATATAATATAAATAT
*
21652 AATGT-ATATTAAA-AT
1 AATATAATA-TAAATAT
*
21667 -TTAT-ATA-AAATAT
1 AATATAATATAAATAT
* *
21680 AAAATAATAGAAATAT
1 AATATAATATAAATAT
21696 AAT
1 AAT
21699 TATTGTATAA
Statistics
Matches: 63, Mismatches: 9, Indels: 14
0.73 0.10 0.16
Matches are distributed among these distances:
12 3 0.05
13 2 0.03
14 11 0.17
15 11 0.17
16 22 0.35
17 14 0.22
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (16 bp):
AATATAATATAAATAT
Found at i:21635 original size:28 final size:26
Alignment explanation
Indices: 21601--21653 Score: 79
Period size: 28 Copynumber: 2.0 Consensus size: 26
21591 TGCCATAATT
21601 TTAAATATAATATAAATATAATATAAAA
1 TTAAATATAAT-TAAATATAA-ATAAAA
*
21629 TTAAATATAATTTAATATAAATAAA
1 TTAAATATAATTAAATATAAATAAA
21654 TGTATATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 5 0.21
27 8 0.33
28 11 0.46
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (26 bp):
TTAAATATAATTAAATATAAATAAAA
Found at i:22453 original size:4 final size:4
Alignment explanation
Indices: 22444--22473 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
22434 TGAACTCGTT
22444 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
22474 ATCATTTCAT
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:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:23485 original size:17 final size:17
Alignment explanation
Indices: 23459--23499 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
23449 TATTTATTAG
* *
23459 ATATTAAATATAAATAT
1 ATATTTAATAAAAATAT
23476 ATATTTAATAAAAATAT
1 ATATTTAATAAAAATAT
23493 ATTATTT
1 A-TATTT
23500 TTTAAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 16 0.76
18 5 0.24
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATTTAATAAAAATAT
Found at i:23797 original size:14 final size:15
Alignment explanation
Indices: 23764--23805 Score: 59
Period size: 14 Copynumber: 2.8 Consensus size: 15
23754 ATCACATGTA
23764 AAAAATATAAAATAAT
1 AAAAAT-TAAAATAAT
23780 AAAAATTAAAAT-AT
1 AAAAATTAAAATAAT
*
23794 AAAAAATAAAAT
1 AAAAATTAAAAT
23806 TATTTTATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 13 0.52
15 6 0.24
16 6 0.24
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
AAAAATTAAAATAAT
Found at i:23871 original size:20 final size:21
Alignment explanation
Indices: 23816--23892 Score: 70
Period size: 20 Copynumber: 3.7 Consensus size: 21
23806 TATTTTATTT
23816 TAAAAA-TA-AATTTCAAATTA
1 TAAAAATTATAATTT-AAATTA
* *
23836 TAAAATTTTTTAATTTAAATTA
1 TAAAA-ATTATAATTTAAATTA
* *
23858 T-CAAATTATAATTTTAATTA
1 TAAAAATTATAATTTAAATTA
*
23878 TAAAAATTAAAATTT
1 TAAAAATTATAATTT
23893 TTTATCCATT
Statistics
Matches: 45, Mismatches: 8, Indels: 7
0.75 0.13 0.12
Matches are distributed among these distances:
20 19 0.42
21 13 0.29
22 8 0.18
23 5 0.11
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (21 bp):
TAAAAATTATAATTTAAATTA
Found at i:24684 original size:32 final size:32
Alignment explanation
Indices: 24648--24715 Score: 102
Period size: 32 Copynumber: 2.1 Consensus size: 32
24638 TAATGTTGAT
*
24648 TAAATTTTTATCATTGAA-AAATTATTTAAATG
1 TAAATTTTTATCATT-AAGAAATTATTTAAATA
*
24680 TAAATTTTTATTATTAAGAAATTATTTAAATA
1 TAAATTTTTATCATTAAGAAATTATTTAAATA
24712 TAAA
1 TAAA
24716 CTTTCAAACT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
31 2 0.06
32 31 0.94
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (32 bp):
TAAATTTTTATCATTAAGAAATTATTTAAATA
Found at i:25554 original size:21 final size:22
Alignment explanation
Indices: 25518--25583 Score: 98
Period size: 22 Copynumber: 3.0 Consensus size: 22
25508 TTCTACATTT
*
25518 AATATATAATTATTTTAAATAA
1 AATATATAAATATTTTAAATAA
* *
25540 AATATA-ACATATTTTAACTAA
1 AATATATAAATATTTTAAATAA
25561 AATATATAAATATTTTAAATAA
1 AATATATAAATATTTTAAATAA
25583 A
1 A
25584 CTATTTTAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
21 18 0.47
22 20 0.53
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (22 bp):
AATATATAAATATTTTAAATAA
Found at i:25590 original size:36 final size:38
Alignment explanation
Indices: 25539--25641 Score: 99
Period size: 36 Copynumber: 2.7 Consensus size: 38
25529 ATTTTAAATA
*
25539 AAATATAACATATTTTAACTAAAATATAT-AAATATTTT
1 AAATATAACATATTTTAAATAAAATATATAAAATA-TTT
**
25577 AAATA-AAC-TATTTTAAATTTAATATATAAAATATTT
1 AAATATAACATATTTTAAATAAAATATATAAAATATTT
25613 AAATTAATATATCATA-TTTAAA-AAAATAT
1 AAA-T-ATA-A-CATATTTTAAATAAAATAT
25642 TTTAATTATA
Statistics
Matches: 53, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
36 22 0.42
37 9 0.17
38 6 0.11
39 1 0.02
40 6 0.11
41 7 0.13
42 2 0.04
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (38 bp):
AAATATAACATATTTTAAATAAAATATATAAAATATTT
Found at i:25621 original size:21 final size:23
Alignment explanation
Indices: 25579--25624 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 23
25569 AATATTTTAA
*
25579 ATAAACTATTTTAAATTTAATAT
1 ATAAAATATTTTAAATTTAATAT
25602 ATAAAATA-TTTAAA-TTAATAT
1 ATAAAATATTTTAAATTTAATAT
25623 AT
1 AT
25625 CATATTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 9 0.41
22 6 0.27
23 7 0.32
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (23 bp):
ATAAAATATTTTAAATTTAATAT
Found at i:25629 original size:19 final size:21
Alignment explanation
Indices: 25579--25634 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 21
25569 AATATTTTAA
25579 ATAAACTATTTTAAATTTAATAT
1 ATAAA-TA-TTTAAATTTAATAT
25602 ATAAAATATTTAAA-TTAATAT
1 AT-AAATATTTAAATTTAATAT
*
25623 AT-CATATTTAAA
1 ATAAATATTTAAA
25635 AAAATATTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
19 9 0.29
21 9 0.29
22 6 0.19
23 4 0.13
24 3 0.10
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.45
Consensus pattern (21 bp):
ATAAATATTTAAATTTAATAT
Found at i:27264 original size:15 final size:16
Alignment explanation
Indices: 27228--27267 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
27218 TTTAATATTT
*
27228 ATAAAATTTTTAATTAA
1 ATAAAA-TTATAATTAA
27245 ATAAAATTATAATT-A
1 ATAAAATTATAATTAA
27260 ATAAAATT
1 ATAAAATT
27268 TATTTAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.41
16 7 0.32
17 6 0.27
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATAAAATTATAATTAA
Found at i:27270 original size:16 final size:17
Alignment explanation
Indices: 27228--27270 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
27218 TTTAATATTT
*
27228 ATAAAATTTTTAATTAA
1 ATAAAATTTATAATTAA
27245 ATAAAA-TTATAATT-A
1 ATAAAATTTATAATTAA
27260 ATAAAATTTAT
1 ATAAAATTTAT
27271 TTAAAAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 7 0.29
16 11 0.46
17 6 0.25
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATAAAATTTATAATTAA
Found at i:28365 original size:20 final size:19
Alignment explanation
Indices: 28340--28387 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
28330 GAACACATAA
28340 TTTTTTT-TGCTTTGTCTATC
1 TTTTTTTCT-CTTTGT-TATC
*
28360 TTTTTTTCTCTTTGTTTTC
1 TTTTTTTCTCTTTGTTATC
28379 TTTTTTTCT
1 TTTTTTTCT
28388 TTCATTTCCT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 12 0.46
20 13 0.50
21 1 0.04
ACGTcount: A:0.02, C:0.15, G:0.06, T:0.77
Consensus pattern (19 bp):
TTTTTTTCTCTTTGTTATC
Found at i:29069 original size:33 final size:32
Alignment explanation
Indices: 29001--29069 Score: 88
Period size: 33 Copynumber: 2.1 Consensus size: 32
28991 AACACATAAA
29001 TTTTTTCTCTTTTTCTTTCTTTCCTTTTTCATT
1 TTTTTTCTCTTTTTCTTTCTTTCCTTTTT-ATT
*
29034 TTTTTTC-CTTATTTCTTTCTTTCTCTCTTT-TT
1 TTTTTTCTCTT-TTTCTTTCTTTC-CTTTTTATT
29066 TTTT
1 TTTT
29070 CACCTCTGCC
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
32 9 0.27
33 19 0.58
34 5 0.15
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (32 bp):
TTTTTTCTCTTTTTCTTTCTTTCCTTTTTATT
Found at i:31026 original size:54 final size:54
Alignment explanation
Indices: 30944--31072 Score: 224
Period size: 54 Copynumber: 2.4 Consensus size: 54
30934 TGTTTAGTGT
* *
30944 TATACCTGTACCTTAGAAGTAGCTAAATCAAAGTTAA-CATTTAGCATGTACCAA
1 TATACCTTTACCTTAGAAGTGGCTAAATCAAAGTTAATC-TTTAGCATGTACCAA
30998 TATACCTTTACCTTAGAAGTGGCTAAATCAAAGTTAATCTTTAGCATGTACCAA
1 TATACCTTTACCTTAGAAGTGGCTAAATCAAAGTTAATCTTTAGCATGTACCAA
31052 TATACCTTTACCTTAGAAGTG
1 TATACCTTTACCTTAGAAGTG
31073 CCCATCTCCA
Statistics
Matches: 72, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
54 71 0.99
55 1 0.01
ACGTcount: A:0.36, C:0.19, G:0.13, T:0.33
Consensus pattern (54 bp):
TATACCTTTACCTTAGAAGTGGCTAAATCAAAGTTAATCTTTAGCATGTACCAA
Found at i:31656 original size:36 final size:36
Alignment explanation
Indices: 31609--31681 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
31599 TCCTCGTCCT
31609 ACCCCAAGTGCAGGACAACAAGCTTATACCATGTCA
1 ACCCCAAGTGCAGGACAACAAGCTTATACCATGTCA
31645 ACCCCAAGTGCAGGACAACAAGCTTATACCATGTCA
1 ACCCCAAGTGCAGGACAACAAGCTTATACCATGTCA
31681 A
1 A
31682 TTTTCATCCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.37, C:0.30, G:0.16, T:0.16
Consensus pattern (36 bp):
ACCCCAAGTGCAGGACAACAAGCTTATACCATGTCA
Found at i:34640 original size:26 final size:26
Alignment explanation
Indices: 34591--34640 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
34581 TGACATAATT
* * * *
34591 TTTTTATATTAATATAGTTTTTTTAA
1 TTTTAATATCAATATAATTATTTTAA
34617 TTTTAATATCAATATAATTATTTT
1 TTTTAATATCAATATAATTATTTT
34641 CATTGAATAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (26 bp):
TTTTAATATCAATATAATTATTTTAA
Found at i:36306 original size:2 final size:2
Alignment explanation
Indices: 36299--36325 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
36289 TACCCTGATA
36299 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
36326 AAGTTTGATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39762 original size:2 final size:2
Alignment explanation
Indices: 39755--39799 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
39745 AACTGAAGTT
* *
39755 TA TA TA TA TA TA CA TA CA TA TA TA TA 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
39797 TA T
1 TA T
39800 GGAAAATTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:41647 original size:14 final size:11
Alignment explanation
Indices: 41617--41642 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
41607 ATTTTAATTT
41617 TATTAACATAA
1 TATTAACATAA
41628 TATTAACATAA
1 TATTAACATAA
41639 TATT
1 TATT
41643 TTTAATAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (11 bp):
TATTAACATAA
Found at i:42435 original size:13 final size:13
Alignment explanation
Indices: 42417--42449 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
42407 TTAATATTAT
42417 ATAATTAAAAATG
1 ATAATTAAAAATG
*
42430 ATAATT-CAAATG
1 ATAATTAAAAATG
42442 ATAATTAA
1 ATAATTAA
42450 TATTGTTTGG
Statistics
Matches: 17, Mismatches: 2, Indels: 2
0.81 0.10 0.10
Matches are distributed among these distances:
12 11 0.65
13 6 0.35
ACGTcount: A:0.58, C:0.03, G:0.06, T:0.33
Consensus pattern (13 bp):
ATAATTAAAAATG
Found at i:43106 original size:12 final size:13
Alignment explanation
Indices: 43089--43119 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
43079 TTATTGAGAA
43089 TTAAATAATA-TT
1 TTAAATAATATTT
43101 TTAAATAATATTT
1 TTAAATAATATTT
43114 TTAAAT
1 TTAAAT
43120 TCAAAATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 10 0.56
13 8 0.44
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TTAAATAATATTT
Found at i:43974 original size:14 final size:14
Alignment explanation
Indices: 43920--44042 Score: 66
Period size: 14 Copynumber: 8.1 Consensus size: 14
43910 TTAAGTATTT
*
43920 AAATGCATTCATTC
1 AAATACATTCATTC
* *
43934 AAAAATTCATTCATCC
1 --AAATACATTCATTC
*
43950 AAATGCATTCATTC
1 AAATACATTCATTC
*
43964 AAATACGTTCATTTATC
1 AAATACATTCA--T-TC
**
43981 TAAATGTATTCATTC
1 -AAATACATTCATTC
43996 AAATACATTCATTC
1 AAATACATTCATTC
* *
44010 ATCCAACTATATTCATTT
1 A---AA-TACATTCATTC
*
44028 AAATAAATTCATTC
1 AAATACATTCATTC
44042 A
1 A
44043 TTCATTTAAA
Statistics
Matches: 84, Mismatches: 15, Indels: 18
0.72 0.13 0.15
Matches are distributed among these distances:
14 44 0.52
15 4 0.05
16 14 0.17
17 4 0.05
18 18 0.21
ACGTcount: A:0.39, C:0.20, G:0.03, T:0.38
Consensus pattern (14 bp):
AAATACATTCATTC
Found at i:43986 original size:32 final size:32
Alignment explanation
Indices: 43919--44043 Score: 146
Period size: 32 Copynumber: 4.0 Consensus size: 32
43909 TTTAAGTATT
43919 TAAATGCATTCATTCAAA-A-ATTCATTCATC
1 TAAATGCATTCATTCAAATACATTCATTCATC
* * *
43949 CAAATGCATTCATTCAAATACGTTCATTTATC
1 TAAATGCATTCATTCAAATACATTCATTCATC
*
43981 TAAATGTATTCATTCAAATACATTCATTCATC
1 TAAATGCATTCATTCAAATACATTCATTCATC
* * ** * *
44013 CAACTATATTCATTTAAATAAATTCATTCAT
1 TAAATGCATTCATTCAAATACATTCATTCAT
44044 TCATTTAAAT
Statistics
Matches: 81, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
30 17 0.21
31 1 0.01
32 63 0.78
ACGTcount: A:0.38, C:0.19, G:0.03, T:0.39
Consensus pattern (32 bp):
TAAATGCATTCATTCAAATACATTCATTCATC
Found at i:44023 original size:18 final size:18
Alignment explanation
Indices: 43925--44026 Score: 53
Period size: 18 Copynumber: 6.2 Consensus size: 18
43915 TATTTAAATG
*
43925 CATTCATTCAAA-A-ATT
1 CATTCATCCAAATACATT
*
43941 CATTCATCCAAATGCATT
1 CATTCATCCAAATACATT
*
43959 CA-T--T-CAAATACGTT
1 CATTCATCCAAATACATT
* * *
43973 CATTTATCTAAAT---GT
1 CATTCATCCAAATACATT
*
43988 -ATTCATTCAAATACATT
1 CATTCATCCAAATACATT
* *
44005 CATTCATCCAACTATATT
1 CATTCATCCAAATACATT
44023 CATT
1 CATT
44027 TAAATAAATT
Statistics
Matches: 63, Mismatches: 13, Indels: 18
0.67 0.14 0.19
Matches are distributed among these distances:
14 19 0.30
15 3 0.05
16 11 0.17
17 3 0.05
18 27 0.43
ACGTcount: A:0.36, C:0.22, G:0.03, T:0.39
Consensus pattern (18 bp):
CATTCATCCAAATACATT
Found at i:49509 original size:41 final size:40
Alignment explanation
Indices: 49453--49537 Score: 109
Period size: 41 Copynumber: 2.1 Consensus size: 40
49443 ATTTTAATTT
*
49453 TATTAAATTAAATTTAATTTTAATTTAGATATTAATAAAATA
1 TATTAAATTAAATTTAATTTTAATTTAGAAATT--TAAAATA
* * *
49495 TATT-AATTTAATTTAATTTTTATTTATAAATTTAAAATA
1 TATTAAATTAAATTTAATTTTAATTTAGAAATTTAAAATA
49534 TATT
1 TATT
49538 TATTAAAATT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
39 11 0.28
41 24 0.62
42 4 0.10
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (40 bp):
TATTAAATTAAATTTAATTTTAATTTAGAAATTTAAAATA
Found at i:52331 original size:11 final size:11
Alignment explanation
Indices: 52315--52366 Score: 65
Period size: 10 Copynumber: 4.9 Consensus size: 11
52305 GGGGGAGGAG
52315 AAGAAAAAAGA
1 AAGAAAAAAGA
52326 AAG-AAAAAG-
1 AAGAAAAAAGA
*
52335 AAGAAAAAAGG
1 AAGAAAAAAGA
52346 AAGAAAAAAAGA
1 AAG-AAAAAAGA
52358 AA-AAAAAAG
1 AAGAAAAAAG
52367 TAAGGGGAGA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
9 3 0.08
10 19 0.51
11 6 0.16
12 9 0.24
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (11 bp):
AAGAAAAAAGA
Found at i:52338 original size:20 final size:20
Alignment explanation
Indices: 52313--52366 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
52303 AGGGGGGAGG
52313 AGAAGAAAAAAGAAAGAAAA
1 AGAAGAAAAAAGAAAGAAAA
*
52333 AGAAGAAAAAAGGAAGAAAA
1 AGAAGAAAAAAGAAAGAAAA
52353 A-AAGAAAAAA-AAAG
1 AGAAGAAAAAAGAAAG
52367 TAAGGGGAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
18 3 0.09
19 9 0.28
20 20 0.62
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (20 bp):
AGAAGAAAAAAGAAAGAAAA
Found at i:62248 original size:21 final size:22
Alignment explanation
Indices: 62214--62262 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
62204 ATTATATACA
* *
62214 CTTTAACTTGTTCTGATTTT-TG
1 CTTTGACTTATTCT-ATTTTATG
62236 -TTTGACTTATTCTATTTTATG
1 CTTTGACTTATTCTATTTTATG
62257 CTTTGA
1 CTTTGA
62263 TTGCTTTTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 5 0.22
21 13 0.57
22 5 0.22
ACGTcount: A:0.16, C:0.12, G:0.12, T:0.59
Consensus pattern (22 bp):
CTTTGACTTATTCTATTTTATG
Found at i:70410 original size:13 final size:13
Alignment explanation
Indices: 70394--70418 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
70384 ATAACATCAT
70394 TATATATATATTA
1 TATATATATATTA
70407 TATATATATATT
1 TATATATATATT
70419 TGAATTAGTA
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TATATATATATTA
Done.