Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold692
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: 28653
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
Found at i:661 original size:21 final size:21
Alignment explanation
Indices: 610--663 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 21
600 ATTAAGTTAA
* *
610 TTTTAATATTAAATAAATAAT
1 TTTTAAAATAAAATAAATAAT
* * * *
631 TATTATAATAAAATATATGAT
1 TTTTAAAATAAAATAAATAAT
652 TTTTAAAATAAA
1 TTTTAAAATAAA
664 TTTAAATATT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (21 bp):
TTTTAAAATAAAATAAATAAT
Found at i:5647 original size:2 final size:2
Alignment explanation
Indices: 5640--5681 Score: 52
Period size: 2 Copynumber: 21.5 Consensus size: 2
5630 CGAATATAAC
*
5640 AT AT AT AT AT AT AT AT AT AT AA AT AT AT CAT AT A- AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT
5681 A
1 A
5682 ATTATTATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
1 2 0.06
2 31 0.89
3 2 0.06
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:6618 original size:17 final size:18
Alignment explanation
Indices: 6573--6618 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
6563 CAAGTGGGTG
* *
6573 AAAAAATATTTTTTTTTA
1 AAAAAATATTATATTTTA
6591 AAAAAATATTATATTTT-
1 AAAAAATATTATATTTTA
6608 AAAAAATATTA
1 AAAAAATATTA
6619 AAATATAAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 11 0.42
18 15 0.58
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
AAAAAATATTATATTTTA
Found at i:6930 original size:15 final size:16
Alignment explanation
Indices: 6910--6943 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
6900 GTATTAATAA
6910 AATGAATAG-ATTTTT
1 AATGAATAGTATTTTT
6925 AATGAATAGTTATTTTT
1 AATGAATAG-TATTTTT
6942 AA
1 AA
6944 AAAATTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
17 8 0.47
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (16 bp):
AATGAATAGTATTTTT
Found at i:7225 original size:17 final size:18
Alignment explanation
Indices: 7191--7226 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
7181 ATATCCTTGA
*
7191 TTAATTTATTATTAATTT
1 TTAATTTATTAATAATTT
7209 TTAATTT-TTAATAATTT
1 TTAATTTATTAATAATTT
7226 T
1 T
7227 ATCAACTAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TTAATTTATTAATAATTT
Found at i:8039 original size:18 final size:19
Alignment explanation
Indices: 8016--8054 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
8006 TGATCAAATT
*
8016 ATTTATTTAA-ATTTAAAA
1 ATTTATATAATATTTAAAA
8034 ATTTATATAATATTTAAAA
1 ATTTATATAATATTTAAAA
8053 AT
1 AT
8055 ATTTGAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATTTATATAATATTTAAAA
Found at i:8847 original size:2 final size:2
Alignment explanation
Indices: 8840--8878 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
8830 CCTTTCAATC
8840 AT AT AT AT AT AT 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 AT AT AT AT AT AT A
8879 GAATAGGGAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:8991 original size:22 final size:23
Alignment explanation
Indices: 8966--9021 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
8956 TATCAAGAAT
*
8966 TTAAATTTTT-TTAAATTTTA-TA
1 TTAAATTTTTATT-AATTTAAGTA
8988 TTAAATTTATTATTAATTTAAGTA
1 TTAAATTT-TTATTAATTTAAGTA
9012 -TAAATTTTTA
1 TTAAATTTTTA
9022 AATATTTATT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
22 11 0.37
23 15 0.50
24 4 0.13
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (23 bp):
TTAAATTTTTATTAATTTAAGTA
Found at i:9001 original size:12 final size:11
Alignment explanation
Indices: 8966--9003 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
8956 TATCAAGAAT
8966 TTAAATTTTT-
1 TTAAATTTTTA
8976 TTAAATTTTATA
1 TTAAATTTT-TA
8988 TTAAATTTATTA
1 TTAAATTT-TTA
9000 TTAA
1 TTAA
9004 TTTAAGTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 9 0.36
11 1 0.04
12 14 0.56
13 1 0.04
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
TTAAATTTTTA
Found at i:9607 original size:10 final size:9
Alignment explanation
Indices: 9576--9606 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
9566 TCCCACCATC
*
9576 AAAAGAAAA
1 AAAATAAAA
9585 AAAATAAAA
1 AAAATAAAA
9594 AAAATAAAA
1 AAAATAAAA
9603 AAAA
1 AAAA
9607 AAGATAAAGA
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:0.90, C:0.00, G:0.03, T:0.06
Consensus pattern (9 bp):
AAAATAAAA
Found at i:10249 original size:13 final size:13
Alignment explanation
Indices: 10201--10254 Score: 54
Period size: 13 Copynumber: 3.9 Consensus size: 13
10191 TTTAACTCAA
10201 TATTAAATTTTAT
1 TATTAAATTTTAT
* * *
10214 CAATATATTTTCATT
1 TATTAAATTTT-A-T
10229 TAATTAAATTTTAT
1 T-ATTAAATTTTAT
10243 TATTAAATTTTA
1 TATTAAATTTTA
10255 ATTTTTTATT
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
13 19 0.59
14 3 0.09
15 2 0.06
16 8 0.25
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (13 bp):
TATTAAATTTTAT
Found at i:10263 original size:18 final size:19
Alignment explanation
Indices: 10235--10271 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
10225 CATTTAATTA
10235 AATTTTATTATTAAATTTT
1 AATTTTATTATTAAATTTT
10254 AATTTT-TTATTAAATTTT
1 AATTTTATTATTAAATTTT
10272 TTCTCTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
AATTTTATTATTAAATTTT
Found at i:10284 original size:31 final size:31
Alignment explanation
Indices: 10201--10271 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 31
10191 TTTAACTCAA
* * * *
10201 TATTAAATTTTATCAATATATTTTCA--TTT
1 TATTAAATTTTATTATTAAATTTTAATTTTT
*
10230 AATTAAATTTTATTATTAAATTTTAATTTTT
1 TATTAAATTTTATTATTAAATTTTAATTTTT
10261 TATTAAATTTT
1 TATTAAATTTT
10272 TTCTCTTAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 21 0.62
31 13 0.38
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (31 bp):
TATTAAATTTTATTATTAAATTTTAATTTTT
Found at i:10438 original size:17 final size:18
Alignment explanation
Indices: 10416--10450 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
10406 CCTTTAACCC
10416 TATTTAATAT-AATAATA
1 TATTTAATATAAATAATA
*
10433 TATTTATTATAAATAATA
1 TATTTAATATAAATAATA
10451 AATATATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TATTTAATATAAATAATA
Found at i:10448 original size:21 final size:22
Alignment explanation
Indices: 10416--10458 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
10406 CCTTTAACCC
10416 TATTTAATATAAT-AATATATT
1 TATTTAATATAATAAATATATT
10437 TATTATAA-ATAATAAATATATT
1 TATT-TAATATAATAAATATATT
10459 AACTAATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
TATTTAATATAATAAATATATT
Found at i:11384 original size:20 final size:21
Alignment explanation
Indices: 11347--11387 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
11337 AAGTATGCCA
*
11347 CAAAATTAATTATAAATTATT
1 CAAAATAAATTATAAATTATT
11368 CAAAATAAATT-TAAATTATT
1 CAAAATAAATTATAAATTATT
11388 TATCATTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (21 bp):
CAAAATAAATTATAAATTATT
Found at i:16615 original size:7 final size:7
Alignment explanation
Indices: 16603--16638 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
16593 AGATAGATTT
16603 CTGGAAC
1 CTGGAAC
16610 CTGGAAC
1 CTGGAAC
16617 CTGGAAC
1 CTGGAAC
*
16624 CAGGAAC
1 CTGGAAC
*
16631 CAGGAAC
1 CTGGAAC
16638 C
1 C
16639 ATGTCAAGTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.33, C:0.31, G:0.28, T:0.08
Consensus pattern (7 bp):
CTGGAAC
Found at i:17204 original size:2 final size:2
Alignment explanation
Indices: 17197--17233 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
17187 AGGTCTGTTA
17197 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
17234 TACTCAGCCC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:19642 original size:2 final size:2
Alignment explanation
Indices: 19635--19671 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
19625 ATGATTTACT
19635 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
19672 TTTTTGTTAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:20543 original size:15 final size:15
Alignment explanation
Indices: 20523--20569 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
20513 TTATTATAAT
*
20523 TTAAAAACATAAAAA
1 TTAAAAATATAAAAA
* *
20538 TT-AAAATATTAAAT
1 TTAAAAATATAAAAA
20552 TTAAAAATATAAAAA
1 TTAAAAATATAAAAA
20567 TTA
1 TTA
20570 GAATATTTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
14 11 0.42
15 15 0.58
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (15 bp):
TTAAAAATATAAAAA
Found at i:20557 original size:29 final size:30
Alignment explanation
Indices: 20514--20576 Score: 101
Period size: 29 Copynumber: 2.1 Consensus size: 30
20504 TATTTTTATT
20514 TATTATAATTTAAAAACATAAAAATTAAAA
1 TATTATAATTTAAAAACATAAAAATTAAAA
* *
20544 TATTA-AATTTAAAAATATAAAAATTAGAA
1 TATTATAATTTAAAAACATAAAAATTAAAA
20573 TATT
1 TATT
20577 TTATTTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 26 0.84
30 5 0.16
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (30 bp):
TATTATAATTTAAAAACATAAAAATTAAAA
Found at i:20574 original size:14 final size:14
Alignment explanation
Indices: 20526--20575 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
20516 TTATAATTTA
*
20526 AAAACATAAAAATT
1 AAAATATAAAAATT
* *
20540 AAAATATTAAATTT
1 AAAATATAAAAATT
20554 AAAAATATAAAAATT
1 -AAAATATAAAAATT
*
20569 AGAATAT
1 AAAATAT
20576 TTTATTTATT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
14 17 0.59
15 12 0.41
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (14 bp):
AAAATATAAAAATT
Found at i:20582 original size:29 final size:29
Alignment explanation
Indices: 20514--20599 Score: 100
Period size: 29 Copynumber: 2.9 Consensus size: 29
20504 TATTTTTATT
*
20514 TATTATAATTTAAAAACATAAAAATTAAAA
1 TATTA-AATTTAAAAATATAAAAATTAAAA
*
20544 TATTAAATTTAAAAATATAAAAATTAGAA
1 TATTAAATTTAAAAATATAAAAATTAAAA
** *
20573 TATTTTATTTATTATAATATAAAAATT
1 TATTAAATTTA--AAAATATAAAAATT
20600 TTTAATAATT
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
29 31 0.63
30 5 0.10
31 13 0.27
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (29 bp):
TATTAAATTTAAAAATATAAAAATTAAAA
Found at i:21127 original size:22 final size:23
Alignment explanation
Indices: 21102--21157 Score: 55
Period size: 22 Copynumber: 2.6 Consensus size: 23
21092 TAAAATATTG
21102 AAAAAATATATTTAA-AAAAATA
1 AAAAAATATATTTAATAAAAATA
** *
21124 AAAATTTATA-TAAATAAAAATA
1 AAAAAATATATTTAATAAAAATA
*
21146 ATAAAAT-TATTT
1 AAAAAATATATTT
21158 TATCTTTTAA
Statistics
Matches: 25, Mismatches: 7, Indels: 4
0.69 0.19 0.11
Matches are distributed among these distances:
21 5 0.20
22 20 0.80
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (23 bp):
AAAAAATATATTTAATAAAAATA
Found at i:21128 original size:20 final size:21
Alignment explanation
Indices: 21103--21142 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
21093 AAAATATTGA
*
21103 AAAAATATATTTAAA-AAAAT
1 AAAAATATATATAAATAAAAT
*
21123 AAAAATTTATATAAATAAAA
1 AAAAATATATATAAATAAAA
21143 ATAATAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (21 bp):
AAAAATATATATAAATAAAAT
Found at i:21130 original size:16 final size:16
Alignment explanation
Indices: 21111--21144 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
21101 GAAAAAATAT
21111 ATTTAAAAAAATAAAA
1 ATTTAAAAAAATAAAA
* *
21127 ATTTATATAAATAAAA
1 ATTTAAAAAAATAAAA
21143 AT
1 AT
21145 AATAAAATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
ATTTAAAAAAATAAAA
Found at i:23071 original size:17 final size:17
Alignment explanation
Indices: 23051--23085 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
23041 TATATTGTTA
23051 ATATTTATATATTATAT
1 ATATTTATATATTATAT
* *
23068 ATATTTATTTTTTATAT
1 ATATTTATATATTATAT
23085 A
1 A
23086 ATAAAAATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
ATATTTATATATTATAT
Found at i:23106 original size:21 final size:22
Alignment explanation
Indices: 23080--23126 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
23070 ATTTATTTTT
23080 TATAT-AATA-AAAATTACATAA
1 TATATAAATATAAAATTA-ATAA
23101 TATATAAATATAAAATTAATAA
1 TATATAAATATAAAATTAATAA
23123 -ATAT
1 TATAT
23127 TATATAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 9 0.38
22 8 0.33
23 7 0.29
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (22 bp):
TATATAAATATAAAATTAATAA
Found at i:23135 original size:18 final size:17
Alignment explanation
Indices: 23084--23137 Score: 51
Period size: 18 Copynumber: 3.2 Consensus size: 17
23074 ATTTTTTATA
*
23084 TAATAAAAATTACATAA-
1 TAATAAATATTA-ATAAT
23101 TATATAAATA-TAA-AAT
1 TA-ATAAATATTAATAAT
23117 TAATAAATATTATATAAT
1 TAATAAATATTA-ATAAT
23135 TAA
1 TAA
23138 AAACGGATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
15 9 0.29
16 5 0.16
17 5 0.16
18 12 0.39
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (17 bp):
TAATAAATATTAATAAT
Found at i:27382 original size:23 final size:23
Alignment explanation
Indices: 27350--27393 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
27340 CAATCATATC
27350 AAAAACATAATTAAAATATAATA
1 AAAAACATAATTAAAATATAATA
* *
27373 AAAAATATAATTATAATATAA
1 AAAAACATAATTAAAATATAA
27394 ATATATTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (23 bp):
AAAAACATAATTAAAATATAATA
Found at i:27388 original size:29 final size:32
Alignment explanation
Indices: 27356--27422 Score: 88
Period size: 29 Copynumber: 2.2 Consensus size: 32
27346 TATCAAAAAC
27356 ATAATTA-AAATATAATAAAAA-ATA-TAATT
1 ATAATTATAAATATAATAAAAATATATTAATT
*
27385 ATAA-TATAAATATATTAAAAATATATTAATT
1 ATAATTATAAATATAATAAAAATATATTAATT
27416 ATTAATT
1 A-TAATT
27423 TATTAAAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
28 2 0.06
29 17 0.53
30 3 0.09
31 6 0.19
32 3 0.09
33 1 0.03
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (32 bp):
ATAATTATAAATATAATAAAAATATATTAATT
Found at i:27440 original size:26 final size:25
Alignment explanation
Indices: 27356--27440 Score: 64
Period size: 26 Copynumber: 3.2 Consensus size: 25
27346 TATCAAAAAC
*
27356 ATAATTA-AAATATAATAAAAAATAT
1 ATAATTATAAATAT-ATTAAAAATAT
*
27381 AATTATAATATAAATATATTAAAAATAT
1 -A-TA-ATTATAAATATATTAAAAATAT
* * *
27409 ATTAATTATTAATTTATTAAAATTTAT
1 A-TAATTATAAATATATTAAAA-ATAT
27436 ATAAT
1 ATAAT
27441 ATTTTAAATA
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
26 20 0.41
27 10 0.20
28 13 0.27
29 6 0.12
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (25 bp):
ATAATTATAAATATATTAAAAATAT
Found at i:28171 original size:29 final size:29
Alignment explanation
Indices: 28105--28169 Score: 87
Period size: 29 Copynumber: 2.3 Consensus size: 29
28095 CATTTGTATC
*
28105 TAAATAAATTTTTAACTTTAACTTATATC
1 TAAATAAATTTTTAACTTTAACTTATATA
* * *
28134 TAAATAAATTTTTAATTTTTA-TTATTTA
1 TAAATAAATTTTTAACTTTAACTTATATA
28162 TAAATAAA
1 TAAATAAA
28170 ATCTTAATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 13 0.41
29 19 0.59
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.51
Consensus pattern (29 bp):
TAAATAAATTTTTAACTTTAACTTATATA
Done.