Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1574
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: 53604
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Found at i:143 original size:2 final size:2
Alignment explanation
Indices: 134--175 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
124 AAATATATCA
134 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
175 A
1 A
176 AAAGAATGCC
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:786 original size:2 final size:2
Alignment explanation
Indices: 779--807 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
769 ACAAGATCCC
779 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 A
808 AAATGAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1304 original size:24 final size:24
Alignment explanation
Indices: 1277--1332 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 24
1267 AGTTTATCTA
1277 AAAATTTATTT-TATTATTTAAAAT
1 AAAATTTATTTATATTATTT-AAAT
*
1301 AAAA-ATATTTATATTATTTAAAT
1 AAAATTTATTTATATTATTTAAAT
1324 AATAATTTA
1 AA-AATTTA
1333 AATTTATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 11 0.41
24 14 0.52
25 2 0.07
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
AAAATTTATTTATATTATTTAAAT
Found at i:1343 original size:10 final size:10
Alignment explanation
Indices: 1314--1356 Score: 59
Period size: 10 Copynumber: 4.1 Consensus size: 10
1304 AATATTTATA
1314 TTATTTAAAT
1 TTATTTAAAT
*
1324 AATAATTTAAAT
1 --TTATTTAAAT
1336 TTATTTAAAT
1 TTATTTAAAT
1346 TTATTTAAAT
1 TTATTTAAAT
1356 T
1 T
1357 AAAAATATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
10 20 0.69
12 9 0.31
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (10 bp):
TTATTTAAAT
Found at i:5427 original size:33 final size:33
Alignment explanation
Indices: 5390--5454 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
5380 TAACTGTTAT
* *
5390 ATTAATTATGTAATATTAAAGTATTCATATTAA
1 ATTAATTATATAATATTAAAATATTCATATTAA
* *
5423 ATTAATTTTATAATATTAAAATATTTATATTA
1 ATTAATTATATAATATTAAAATATTCATATTA
5455 TTTTTATATC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (33 bp):
ATTAATTATATAATATTAAAATATTCATATTAA
Found at i:15875 original size:17 final size:17
Alignment explanation
Indices: 15849--15883 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
15839 TTGGGAGACC
15849 ATAAAAAAAAGAAAATA
1 ATAAAAAAAAGAAAATA
* *
15866 ATAAATAAAATAAAATA
1 ATAAAAAAAAGAAAATA
15883 A
1 A
15884 AATAAGGTTT
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:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (17 bp):
ATAAAAAAAAGAAAATA
Found at i:21201 original size:10 final size:10
Alignment explanation
Indices: 21186--21228 Score: 59
Period size: 10 Copynumber: 4.1 Consensus size: 10
21176 ATATATTTTT
21186 AATTTAAATA
1 AATTTAAATA
21196 AATTTAAATA
1 AATTTAAATA
21206 AATTTAAATTA
1 AATTTAAA-TA
*
21217 TTATTTAAATA
1 -AATTTAAATA
21228 A
1 A
21229 TATAAATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
10 18 0.62
11 4 0.14
12 7 0.24
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (10 bp):
AATTTAAATA
Found at i:21210 original size:27 final size:26
Alignment explanation
Indices: 21171--21268 Score: 76
Period size: 27 Copynumber: 3.7 Consensus size: 26
21161 GAGCTAAAAT
* *
21171 TTTATATATATTTTTAATTTAAATAAA
1 TTTAAATAAATTTTTAATTTAAAT-AA
21198 TTTAAATAAATTTAAATTATTATTTAAATAA
1 TTTAAATAAATTT---TTA--ATTTAAATAA
* *
21229 TATAAAT--ATTTTTATTTTAAATAA
1 TTTAAATAAATTTTTAATTTAAATAA
*
21253 -TAAAATAAATTTTTAA
1 TTTAAATAAATTTTTAA
21269 ATAAACTCAA
Statistics
Matches: 57, Mismatches: 7, Indels: 16
0.71 0.09 0.20
Matches are distributed among these distances:
23 4 0.07
24 9 0.16
25 7 0.12
26 3 0.05
27 11 0.19
29 4 0.07
30 3 0.05
31 8 0.14
32 8 0.14
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (26 bp):
TTTAAATAAATTTTTAATTTAAATAA
Found at i:21265 original size:24 final size:24
Alignment explanation
Indices: 21210--21265 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 24
21200 TAAATAAATT
21210 TAAATTATTATTTAAATAATATAAA
1 TAAATT-TTATTTAAATAATATAAA
*
21235 T-ATTTTTATTTTAAATAATA-AAA
1 TAAATTTTA-TTTAAATAATATAAA
21258 TAAATTTT
1 TAAATTTT
21266 TAAATAAACT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 7 0.26
24 19 0.70
25 1 0.04
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
TAAATTTTATTTAAATAATATAAA
Found at i:21740 original size:2 final size:2
Alignment explanation
Indices: 21733--21769 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
21723 CGTTTTTCAT
21733 TA TA TA TA TA 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 TA TA TA TA TA T
21770 GGGATCTTGT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:22424 original size:2 final size:2
Alignment explanation
Indices: 22373--22416 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
22363 GGCATTCTTT
22373 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
22414 TA T
1 TA T
22417 TGATATATTT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:22788 original size:26 final size:25
Alignment explanation
Indices: 22726--22788 Score: 63
Period size: 26 Copynumber: 2.4 Consensus size: 25
22716 CATAATTATT
* * *
22726 TTTATTTAAATTTTTATTGATTTTAA
1 TTTATATAAATTTTTATTTA-ATTAA
* *
22752 ATTATAAAAATTTTTATTTAATTAA
1 TTTATATAAATTTTTATTTAATTAA
22777 TTTAATATAAAT
1 TTT-ATATAAAT
22789 AAAACGACTG
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
25 6 0.21
26 23 0.79
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (25 bp):
TTTATATAAATTTTTATTTAATTAA
Found at i:23319 original size:29 final size:28
Alignment explanation
Indices: 23281--23349 Score: 68
Period size: 29 Copynumber: 2.4 Consensus size: 28
23271 TTAAATTTAA
* *
23281 AATTTTAATTTATT-ATTTAAAATAATAAT
1 AATTTAAATTTATTGAATTAAAATAAT--T
*
23310 AATTTAAATTAAATTGAATTAAAATAATT
1 AATTTAAATT-TATTGAATTAAAATAATT
*
23339 AATATAAATTT
1 AATTTAAATTT
23350 TAAATTTAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
29 19 0.58
30 3 0.09
31 11 0.33
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.46
Consensus pattern (28 bp):
AATTTAAATTTATTGAATTAAAATAATT
Found at i:24026 original size:3 final size:3
Alignment explanation
Indices: 24018--24048 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
24008 GATGTAGATG
24018 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
24049 ACATTGATTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:25580 original size:22 final size:20
Alignment explanation
Indices: 25550--25591 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
25540 ATAGTTTGGG
25550 GATTAAAATTTATAAATATTGT
1 GATTAAAATTT-TAAAT-TTGT
*
25572 GATTCAAATTTTAAATTTGT
1 GATTAAAATTTTAAATTTGT
25592 TAAATATCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 4 0.21
21 5 0.26
22 10 0.53
ACGTcount: A:0.40, C:0.02, G:0.10, T:0.48
Consensus pattern (20 bp):
GATTAAAATTTTAAATTTGT
Found at i:29036 original size:12 final size:11
Alignment explanation
Indices: 29010--29047 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
29000 AACAGTATTT
29010 TAAA-AAAATAA
1 TAAATAAAA-AA
29021 TAAATAATAAAA
1 TAAATAA-AAAA
29033 TAAATAAAAAA
1 TAAATAAAAAA
29044 TAAA
1 TAAA
29048 ACAATGGAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 12 0.48
12 11 0.44
13 2 0.08
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (11 bp):
TAAATAAAAAA
Found at i:29037 original size:19 final size:18
Alignment explanation
Indices: 29010--29046 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
29000 AACAGTATTT
*
29010 TAAAAAAATAATAAATAA
1 TAAAAAAATAAAAAATAA
29028 TAAAATAAATAAAAAATAA
1 TAAAA-AAATAAAAAATAA
29047 AACAATGGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (18 bp):
TAAAAAAATAAAAAATAA
Found at i:29038 original size:16 final size:15
Alignment explanation
Indices: 29014--29048 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
29004 GTATTTTAAA
*
29014 AAAATAATAAATAAT
1 AAAATAATAAAAAAT
29029 AAAATAAATAAAAAAT
1 AAAAT-AATAAAAAAT
29045 AAAA
1 AAAA
29049 CAATGGAGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (15 bp):
AAAATAATAAAAAAT
Found at i:29863 original size:14 final size:14
Alignment explanation
Indices: 29835--29884 Score: 57
Period size: 14 Copynumber: 3.4 Consensus size: 14
29825 ATATTAAAAT
29835 TTAAATATTAAATTTA
1 TTAAATATT--ATTTA
29851 TTAAATATTATTTA
1 TTAAATATTATTTA
*
29865 TTAAA-AATATTTA
1 TTAAATATTATTTA
29878 TATAAAT
1 T-TAAAT
29885 TAATAGAGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
13 8 0.26
14 14 0.45
16 9 0.29
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TTAAATATTATTTA
Found at i:29877 original size:13 final size:14
Alignment explanation
Indices: 29846--29889 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
29836 TAAATATTAA
*
29846 ATTTATTAAATATT
1 ATTTATTAAATAAT
29860 ATTTATTAAA-AAT
1 ATTTATTAAATAAT
29873 ATTTATATAAATTAAT
1 ATTTAT-TAAA-TAAT
29889 A
1 A
29890 GAGTTAAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
13 8 0.31
14 14 0.54
16 4 0.15
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
ATTTATTAAATAAT
Found at i:29889 original size:16 final size:16
Alignment explanation
Indices: 29819--29889 Score: 50
Period size: 14 Copynumber: 4.9 Consensus size: 16
29809 ATAAAAAAAA
* *
29819 TTATATATATTAAAAT
1 TTATATAAATTAATAT
*
29835 TTA-A-ATATTAA-AT
1 TTATATAAATTAATAT
*
29848 TTAT-TAAA-TATTAT
1 TTATATAAATTAATAT
29862 TTAT-TAAA--AATAT
1 TTATATAAATTAATAT
29875 TTATATAAATTAATA
1 TTATATAAATTAATA
29890 GAGTTAAACT
Statistics
Matches: 46, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
13 15 0.33
14 23 0.50
15 1 0.02
16 7 0.15
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TTATATAAATTAATAT
Found at i:30091 original size:2 final size:2
Alignment explanation
Indices: 30084--30115 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
30074 CATGAAAGTG
30084 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30116 TATGTTTTGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30665 original size:2 final size:2
Alignment explanation
Indices: 30658--30697 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
30648 AAGCTTTCTT
*
30658 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TC TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
30698 AAGAAAGCTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:32045 original size:24 final size:26
Alignment explanation
Indices: 31990--32046 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 26
31980 TTATTTACTT
* *
31990 TTATTTTATTTTTATATAAATATTTA
1 TTATTTTATATTTATATAAATATCTA
**
32016 AAATTTTA-ATTT-TATAAATATCTA
1 TTATTTTATATTTATATAAATATCTA
32040 TTATTTT
1 TTATTTT
32047 TACCATATAT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
24 16 0.64
25 3 0.12
26 6 0.24
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (26 bp):
TTATTTTATATTTATATAAATATCTA
Found at i:32497 original size:22 final size:23
Alignment explanation
Indices: 32472--32538 Score: 75
Period size: 22 Copynumber: 2.9 Consensus size: 23
32462 AATTTGAATC
*
32472 ATTTTAA-ATTTAAATTAATTAA
1 ATTTTAATATTTAAATTAATAAA
32494 A-TTTAATATTTAAATTAATAAA
1 ATTTTAATATTTAAATTAATAAA
* *
32516 ATTTGAATTAATTAAATATAATA
1 ATTTTAA-TATTTAAAT-TAATA
32539 TTTAGATTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
21 5 0.13
22 16 0.42
23 4 0.11
24 8 0.21
25 5 0.13
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.46
Consensus pattern (23 bp):
ATTTTAATATTTAAATTAATAAA
Found at i:32518 original size:37 final size:37
Alignment explanation
Indices: 32476--32558 Score: 123
Period size: 37 Copynumber: 2.2 Consensus size: 37
32466 TGAATCATTT
*
32476 TAAATTTAAATTAATTAAATTTAATATTTA-AATTAA
1 TAAATTTAAATTAATTAAATATAATATTTAGAATTAA
* *
32512 TAAAATTTGAATTAATTAAATATAATATTTAGATTTAA
1 T-AAATTTAAATTAATTAAATATAATATTTAGAATTAA
32550 TAAATTTAA
1 TAAATTTAA
32559 TTATTTTGAG
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
36 1 0.02
37 34 0.83
38 6 0.15
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (37 bp):
TAAATTTAAATTAATTAAATATAATATTTAGAATTAA
Found at i:32541 original size:22 final size:22
Alignment explanation
Indices: 32511--32564 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 22
32501 ATTTAAATTA
*
32511 ATAAAATTT-GAATTAATTAAAT
1 ATAATATTTAGAATTAA-TAAAT
*
32533 ATAATATTTAGATTTAATAAAT
1 ATAATATTTAGAATTAATAAAT
*
32555 TTAATTATTT
1 ATAA-TATTT
32565 TGAGTTCAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 16 0.59
23 11 0.41
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (22 bp):
ATAATATTTAGAATTAATAAAT
Found at i:33705 original size:23 final size:24
Alignment explanation
Indices: 33679--33729 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
33669 AAAATAAAAA
33679 ATTATAA-ATTATAAATATTAAAT
1 ATTATAATATTATAAATATTAAAT
* **
33702 ATTA-AATTTTATATTTATTAAAT
1 ATTATAATATTATAAATATTAAAT
33725 ATTAT
1 ATTAT
33730 TTCTTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
22 2 0.09
23 21 0.91
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
ATTATAATATTATAAATATTAAAT
Found at i:41721 original size:2 final size:2
Alignment explanation
Indices: 41714--41756 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
41704 AATTCTTGCA
*
41714 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AA AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
41756 A
1 A
41757 AAGAATGGAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:42718 original size:14 final size:14
Alignment explanation
Indices: 42663--42761 Score: 87
Period size: 14 Copynumber: 7.1 Consensus size: 14
42653 TGTTAGGTAA
42663 CTGTGTCAAAAGTAC
1 CTGTGTC-AAAGTAC
* *
42678 CTGTG-CTAAAATGC
1 CTGTGTC-AAAGTAC
* *
42692 CTATATC-AAGTAC
1 CTGTGTCAAAGTAC
*
42705 CTATGTCAAAGTAC
1 CTGTGTCAAAGTAC
* *
42719 TTGTGTCAAAGTGC
1 CTGTGTCAAAGTAC
*
42733 CTGTG-CCAAGTAC
1 CTGTGTCAAAGTAC
42746 CTGTGTCAAAGTAC
1 CTGTGTCAAAGTAC
42760 CT
1 CT
42762 ACGCCAGGCA
Statistics
Matches: 66, Mismatches: 15, Indels: 7
0.75 0.17 0.08
Matches are distributed among these distances:
13 21 0.32
14 39 0.59
15 6 0.09
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.29
Consensus pattern (14 bp):
CTGTGTCAAAGTAC
Found at i:42727 original size:27 final size:27
Alignment explanation
Indices: 42663--42762 Score: 85
Period size: 27 Copynumber: 3.6 Consensus size: 27
42653 TGTTAGGTAA
* * *
42663 CTGTGTCAAAAGTACCTGTGCTAAAATGC
1 CTGTGTC-AAAGTACCTATGC-AAAGTAC
* *
42692 CTATATC-AAGTACCTATGTCAAAGTAC
1 CTGTGTCAAAGTACCTATG-CAAAGTAC
* * * *
42719 TTGTGTCAAAGTGCCTGTGCCAAGTAC
1 CTGTGTCAAAGTACCTATGCAAAGTAC
42746 CTGTGTCAAAGTACCTA
1 CTGTGTCAAAGTACCTA
42763 CGCCAGGCAC
Statistics
Matches: 55, Mismatches: 14, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
27 40 0.73
28 10 0.18
29 5 0.09
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (27 bp):
CTGTGTCAAAGTACCTATGCAAAGTAC
Found at i:42734 original size:41 final size:41
Alignment explanation
Indices: 42666--42761 Score: 113
Period size: 41 Copynumber: 2.3 Consensus size: 41
42656 TAGGTAACTG
*
42666 TGTCAAAAGTACCTGTGCTAAAATGCCTATATCAAGTACCTA
1 TGTC-AAAGTACCTGTGCTAAAATGCCTATACCAAGTACCTA
* * * * *
42708 TGTCAAAGTACTTGTG-TCAAAGTGCCTGTGCCAAGTACCTG
1 TGTCAAAGTACCTGTGCT-AAAATGCCTATACCAAGTACCTA
42749 TGTCAAAGTACCT
1 TGTCAAAGTACCT
42762 ACGCCAGGCA
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
40 1 0.02
41 41 0.89
42 4 0.09
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (41 bp):
TGTCAAAGTACCTGTGCTAAAATGCCTATACCAAGTACCTA
Found at i:42767 original size:27 final size:27
Alignment explanation
Indices: 42699--42795 Score: 104
Period size: 27 Copynumber: 3.6 Consensus size: 27
42689 TGCCTATATC
*
42699 AAGTACCTATGTCAAAGTACTTGTGTCA
1 AAGTACCTATG-CCAAGTACTTGTGTCA
* * *
42727 AAGTGCCTGTGCCAAGTACCTGTGTCA
1 AAGTACCTATGCCAAGTACTTGTGTCA
* * * *
42754 AAGTACCTACGCCAGGCACTTGTGCCA
1 AAGTACCTATGCCAAGTACTTGTGTCA
*
42781 AAGTACCTGTGCCAA
1 AAGTACCTATGCCAA
42796 AGAGTATTAT
Statistics
Matches: 55, Mismatches: 14, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
27 46 0.84
28 9 0.16
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.25
Consensus pattern (27 bp):
AAGTACCTATGCCAAGTACTTGTGTCA
Found at i:42793 original size:14 final size:14
Alignment explanation
Indices: 42699--42797 Score: 85
Period size: 14 Copynumber: 7.2 Consensus size: 14
42689 TGCCTATATC
* *
42699 AAGTACCTATGTCA
1 AAGTACCTGTGCCA
* *
42713 AAGTACTTGTGTCA
1 AAGTACCTGTGCCA
*
42727 AAGTGCCTGTGCC-
1 AAGTACCTGTGCCA
*
42740 AAGTACCTGTGTCA
1 AAGTACCTGTGCCA
**
42754 AAGTACCTACGCC-
1 AAGTACCTGTGCCA
* * *
42767 AGGCACTTGTGCCA
1 AAGTACCTGTGCCA
42781 AAGTACCTGTGCCA
1 AAGTACCTGTGCCA
42795 AAG
1 AAG
42798 AGTATTATGG
Statistics
Matches: 65, Mismatches: 18, Indels: 4
0.75 0.21 0.05
Matches are distributed among these distances:
13 19 0.29
14 46 0.71
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.24
Consensus pattern (14 bp):
AAGTACCTGTGCCA
Found at i:43374 original size:14 final size:14
Alignment explanation
Indices: 43357--43395 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 14
43347 CCCACGAGGC
43357 ATTATCCGTAAGGT
1 ATTATCCGTAAGGT
43371 ATTATTCACTGTAAGGT
1 ATTA-TC-C-GTAAGGT
43388 ATTATCCG
1 ATTATCCG
43396 CGAGATAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 5 0.23
15 3 0.14
16 3 0.14
17 11 0.50
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.38
Consensus pattern (14 bp):
ATTATCCGTAAGGT
Found at i:43649 original size:16 final size:17
Alignment explanation
Indices: 43628--43662 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
43618 TTTTTTTTTA
43628 AACTT-ATAAAATATAT
1 AACTTAATAAAATATAT
43644 AACTTAAATAAAATATAT
1 AACTT-AATAAAATATAT
43662 A
1 A
43663 TAGAATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.29
18 12 0.71
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (17 bp):
AACTTAATAAAATATAT
Found at i:52548 original size:210 final size:207
Alignment explanation
Indices: 52123--52746 Score: 976
Period size: 210 Copynumber: 3.0 Consensus size: 207
52113 AAAATATTTT
* * * *
52123 AGATTCAAATTACTTTGATTTAAATTATTATTTAATTAA-TAAAATATAATTTTATTTAAATTTT
1 AGATTCAAATTAATCTGATTTAAAGTATTATTTAATTAATTAAAA-ATATTTTTATTTAAATTTT
* *
52187 ATT--AAAA-AT-AAAATTAATATAAAGATATAATTTTAATATTTAATAAATTTTAAACAATAAA
65 ATTAAAAAATATAAAAATTTATATAAAAATATAATTTTAATATTTAATAAATTTTAAACAATAAA
* *
52248 ATAAGTTTTCAAAATCAACAAACATTTTG-TATATACATTTTTTTTATATAAGAACCTAACCAAA
130 ATAAGTTTTCAAAATCAACAAACATTTTGATAAATACATTTTTTTTATATAGGAACCTAACCAAA
*
52312 TATAAATATAACT
195 TATAAATATAACC
52325 AGATTCAAATTAATCTGATTTAAAGTATTATTTAATTAATTAAAAATATTTTTATTTAAATTTTA
1 AGATTCAAATTAATCTGATTTAAAGTATTATTTAATTAATTAAAAATATTTTTATTTAAATTTTA
*
52390 TTAAAAAATATAAAAATTTATATAAAAATATAATTTTAATATTTTAATAAATTTTAAATAATAAA
66 TTAAAAAATATAAAAATTTATATAAAAATATAATTTTAATA-TTTAATAAATTTTAAACAATAAA
52455 ATAAGTTTTCAAAATCAACAAAACATTTTGAATAAATACATTTTTTTTATATAGGAACCTAACCA
130 ATAAGTTTTCAAAATCAAC-AAACATTTTG-ATAAATACATTTTTTTTATATAGGAACCTAACCA
52520 AATATAAATATAACC
193 AATATAAATATAACC
* *
52535 AGATTCTAATTAATCTGATTTAAAGTATTATTTAATTAATAAAAAATATTTTTATTTAAATTTTA
1 AGATTCAAATTAATCTGATTTAAAGTATTATTTAATTAATTAAAAATATTTTTATTTAAATTTTA
*
52600 TTAAAAAACATATAAAAATTAATATAAAAAAATATAATTTTAATATTTAATAAATTTTAAACAAT
66 TT-AAAAA-ATATAAAAATT--TATATAAAAATATAATTTTAATATTTAATAAATTTTAAACAAT
* *
52665 AAAATAAGTTTTCAAAATCAACAAACA-TTTGAGTAAATACA-TTTTTTTCTGTAGGAACCTAAC
127 AAAATAAGTTTTCAAAATCAACAAACATTTTGA-TAAATACATTTTTTTTATATAGGAACCTAAC
52728 CAAATATAAATATAACC
191 CAAATATAAATATAACC
52745 AG
1 AG
52747 TAATGCTACC
Statistics
Matches: 392, Mismatches: 16, Indels: 20
0.92 0.04 0.05
Matches are distributed among these distances:
202 57 0.15
203 5 0.01
204 4 0.01
205 2 0.01
206 27 0.07
207 41 0.10
208 10 0.03
210 150 0.38
211 17 0.04
212 16 0.04
213 41 0.10
214 22 0.06
ACGTcount: A:0.49, C:0.07, G:0.04, T:0.40
Consensus pattern (207 bp):
AGATTCAAATTAATCTGATTTAAAGTATTATTTAATTAATTAAAAATATTTTTATTTAAATTTTA
TTAAAAAATATAAAAATTTATATAAAAATATAATTTTAATATTTAATAAATTTTAAACAATAAAA
TAAGTTTTCAAAATCAACAAACATTTTGATAAATACATTTTTTTTATATAGGAACCTAACCAAAT
ATAAATATAACC
Found at i:52642 original size:21 final size:23
Alignment explanation
Indices: 52591--52645 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 23
52581 TATTTTTATT
52591 TAAATTTT-AT-TAAAAAACATA
1 TAAATTTTAATATAAAAAACATA
**
52612 TAAAAATTAATATAAAAAA-ATA
1 TAAATTTTAATATAAAAAACATA
52634 T-AATTTTAATAT
1 TAAATTTTAATAT
52646 TTAATAAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 15 0.54
22 6 0.21
23 7 0.25
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (23 bp):
TAAATTTTAATATAAAAAACATA
Found at i:53165 original size:25 final size:22
Alignment explanation
Indices: 53137--53197 Score: 63
Period size: 21 Copynumber: 2.7 Consensus size: 22
53127 ATTAAATTTG
53137 ATAATATTAAAAATAATTAACATAT
1 ATAATA-TAAAAATAATTAA-A-AT
53162 ATAATA-ATAAAA-AATTAAAAT
1 ATAATATA-AAAATAATTAAAAT
*
53183 ATAATATAAGAATAA
1 ATAATATAAAAATAA
53198 ATAATAAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
21 11 0.34
22 4 0.12
23 7 0.22
24 4 0.12
25 6 0.19
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (22 bp):
ATAATATAAAAATAATTAAAAT
Found at i:53181 original size:33 final size:33
Alignment explanation
Indices: 53142--53205 Score: 87
Period size: 33 Copynumber: 1.9 Consensus size: 33
53132 ATTTGATAAT
53142 ATTAAAA-ATAAT-TAACATATATAATAATAAAAA
1 ATTAAAATATAATATAACA-ATA-AATAATAAAAA
*
53175 ATTAAAATATAATATAAGAATAAATAATAAA
1 ATTAAAATATAATATAACAATAAATAATAAA
53206 TATTTTAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 16 0.57
34 8 0.29
35 4 0.14
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (33 bp):
ATTAAAATATAATATAACAATAAATAATAAAAA
Found at i:53184 original size:23 final size:25
Alignment explanation
Indices: 53137--53202 Score: 66
Period size: 23 Copynumber: 2.7 Consensus size: 25
53127 ATTAAATTTG
* *
53137 ATAATATTAAAAATAATTAACATAT
1 ATAATAATAAAAATAATTAAAATAT
53162 ATAATAAT-AAAA-AATTAAAATAT
1 ATAATAATAAAAATAATTAAAATAT
*
53185 A-ATATAAGAATAAATAAT
1 ATA-ATAATAA-AAATAAT
53203 AAATATTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
22 1 0.03
23 15 0.44
24 5 0.15
25 10 0.29
26 3 0.09
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (25 bp):
ATAATAATAAAAATAATTAAAATAT
Done.