Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold538
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: 178739
ACGTcount: A:0.18, C:0.10, G:0.10, T:0.18
Warning! 79664 characters in sequence are not A, C, G, or T
Found at i:5070 original size:14 final size:14
Alignment explanation
Indices: 5051--5078 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5041 TATATTAGTA
5051 TTTTCTATTCTATT
1 TTTTCTATTCTATT
5065 TTTTCTATTCTATT
1 TTTTCTATTCTATT
5079 AGTATTAGAT
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:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTCTATTCTATT
Found at i:5090 original size:5 final size:6
Alignment explanation
Indices: 5075--5125 Score: 56
Period size: 6 Copynumber: 9.2 Consensus size: 6
5065 TTTTCTATTC
* *
5075 TATTAG TATTAG -ATTAG TATT-C TATT-C TATTAG TATTAG -ATTAG
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
5119 TATTAG T
1 TATTAG T
5126 TAGTCATCCT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
5 19 0.47
6 21 0.52
ACGTcount: A:0.31, C:0.04, G:0.14, T:0.51
Consensus pattern (6 bp):
TATTAG
Found at i:5090 original size:11 final size:12
Alignment explanation
Indices: 5075--5125 Score: 56
Period size: 11 Copynumber: 4.6 Consensus size: 12
5065 TTTTCTATTC
5075 TATTAGTATTAG
1 TATTAGTATTAG
*
5087 -ATTAGTATT-C
1 TATTAGTATTAG
*
5097 TATT-CTATTAG
1 TATTAGTATTAG
5108 TATTAG-ATTAG
1 TATTAGTATTAG
5119 TATTAGT
1 TATTAGT
5126 TAGTCATCCT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
10 4 0.13
11 27 0.87
ACGTcount: A:0.31, C:0.04, G:0.14, T:0.51
Consensus pattern (12 bp):
TATTAGTATTAG
Found at i:5097 original size:27 final size:27
Alignment explanation
Indices: 5067--5122 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
5057 ATTCTATTTT
5067 TTCTATTCTATTAGTATTAGATTAGTA
1 TTCTATTCTATTAGTATTAGATTAGTA
5094 TTCTATTCTATTAGTATTAGATTAGTA
1 TTCTATTCTATTAGTATTAGATTAGTA
5121 TT
1 TT
5123 AGTTAGTCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.29, C:0.07, G:0.11, T:0.54
Consensus pattern (27 bp):
TTCTATTCTATTAGTATTAGATTAGTA
Found at i:8293 original size:20 final size:22
Alignment explanation
Indices: 8256--8305 Score: 70
Period size: 20 Copynumber: 2.4 Consensus size: 22
8246 AAATGATGAG
8256 AAAATACAAATGAAATGT-CCT
1 AAAATACAAATGAAATGTACCT
*
8277 AAAATACAACT-AAATGTACCT
1 AAAATACAAATGAAATGTACCT
8298 -AAATACAA
1 AAAATACAA
8306 GCAATTAGCT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 14 0.52
21 13 0.48
ACGTcount: A:0.56, C:0.16, G:0.06, T:0.22
Consensus pattern (22 bp):
AAAATACAAATGAAATGTACCT
Found at i:10418 original size:30 final size:30
Alignment explanation
Indices: 10351--10432 Score: 87
Period size: 30 Copynumber: 2.8 Consensus size: 30
10341 CCACTAATTA
***
10351 GTACCTAAAC-TTTTTTTTTTCCTATCTTG
1 GTACCTAAACTTTTTTTTTTTCCTAAAATG
*
10380 GTAACTAAACTTTTTTTTTTGTCCTAAAATG
1 GTACCTAAACTTTTTTTTTT-TCCTAAAATG
**
10411 GT-CCTAAACTACTTTTTTTTCC
1 GTACCTAAACTTTTTTTTTTTCC
10433 CAAGTTTGTA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
29 12 0.27
30 23 0.52
31 9 0.20
ACGTcount: A:0.22, C:0.20, G:0.07, T:0.51
Consensus pattern (30 bp):
GTACCTAAACTTTTTTTTTTTCCTAAAATG
Found at i:13818 original size:20 final size:22
Alignment explanation
Indices: 13781--13830 Score: 70
Period size: 20 Copynumber: 2.4 Consensus size: 22
13771 AAATGATGAG
13781 AAAATACAAATGAAATGT-CCT
1 AAAATACAAATGAAATGTACCT
*
13802 AAAATACAACT-AAATGTACCT
1 AAAATACAAATGAAATGTACCT
13823 -AAATACAA
1 AAAATACAA
13831 GCAATTAGCT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 14 0.52
21 13 0.48
ACGTcount: A:0.56, C:0.16, G:0.06, T:0.22
Consensus pattern (22 bp):
AAAATACAAATGAAATGTACCT
Found at i:15764 original size:30 final size:29
Alignment explanation
Indices: 15707--15784 Score: 84
Period size: 29 Copynumber: 2.6 Consensus size: 29
15697 TAATTAGTAC
***
15707 CTAAACTTTTTTTTTTCCTATCTTGGTAA
1 CTAAACTTTTTTTTTTCCTAAAATGGTAA
* *
15736 CTAAACTTTTTTTTTTGTCTAAAATGGTAC
1 CTAAACTTTTTTTTTT-CCTAAAATGGTAA
*
15766 CTAAACTACTTTTTTTTCC
1 CTAAACT-TTTTTTTTTCC
15785 CAAGTTTGTA
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
29 16 0.40
30 16 0.40
31 8 0.20
ACGTcount: A:0.23, C:0.18, G:0.06, T:0.53
Consensus pattern (29 bp):
CTAAACTTTTTTTTTTCCTAAAATGGTAA
Found at i:17749 original size:18 final size:18
Alignment explanation
Indices: 17728--17763 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
17718 AGTTATATAT
17728 GACATTTAATATAATAGA
1 GACATTTAATATAATAGA
*
17746 GACATTTAATATTATAGA
1 GACATTTAATATAATAGA
17764 ATTTTATCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.11, T:0.36
Consensus pattern (18 bp):
GACATTTAATATAATAGA
Found at i:31296 original size:26 final size:26
Alignment explanation
Indices: 31254--31329 Score: 109
Period size: 26 Copynumber: 2.9 Consensus size: 26
31244 CTGTAATGAT
*
31254 AACCTTTGTGGCATAATATGAAAGAA
1 AACCTTTGTGGCGTAATATGAAAGAA
31280 AGA-CTTTGTGGCGTAATATGAAAGAA
1 A-ACCTTTGTGGCGTAATATGAAAGAA
*
31306 AACCCTTTGTGGCGGAATATGAAA
1 AA-CCTTTGTGGCGTAATATGAAA
31330 AGAACGCCTT
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
25 1 0.02
26 24 0.53
27 20 0.44
ACGTcount: A:0.38, C:0.12, G:0.24, T:0.26
Consensus pattern (26 bp):
AACCTTTGTGGCGTAATATGAAAGAA
Found at i:31324 original size:27 final size:27
Alignment explanation
Indices: 31256--31346 Score: 107
Period size: 27 Copynumber: 3.4 Consensus size: 27
31246 GTAATGATAA
*
31256 CCTTTGTGGCATAATATGAAAGAAAGA-
1 CCTTTGTGGCGTAATATGAAAGAAA-AC
31283 -CTTTGTGGCGTAATATGAAAGAAAAC
1 CCTTTGTGGCGTAATATGAAAGAAAAC
* *
31309 CCTTTGTGGCGGAATATGAAA-AGAAC
1 CCTTTGTGGCGTAATATGAAAGAAAAC
*
31335 GCCTTTATGGCG
1 -CCTTTGTGGCG
31347 AATTATAGAG
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
25 1 0.02
26 27 0.47
27 29 0.51
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.26
Consensus pattern (27 bp):
CCTTTGTGGCGTAATATGAAAGAAAAC
Found at i:33184 original size:36 final size:35
Alignment explanation
Indices: 33061--33188 Score: 143
Period size: 35 Copynumber: 3.6 Consensus size: 35
33051 TACTCTCTAT
* * *
33061 TTGGTGTGTTTCGAG-TGAACTAGCTCTTATGAGCA
1 TTGGTGTGTTTCG-GTTGGATTGGCTCTTATGAGCA
* * *
33096 TTGGTGTGTTCCGG-AGGTATTAGCTCTTATGAGCA
1 TTGGTGTGTTTCGGTTGG-ATTGGCTCTTATGAGCA
*
33131 TTGGTGTGTTTCAGTTGGATTGGCTCTTATGAGCA
1 TTGGTGTGTTTCGGTTGGATTGGCTCTTATGAGCA
*
33166 TCTGGTGTGTTTTGGTTGGATTG
1 T-TGGTGTGTTTCGGTTGGATTG
33189 ACGATGTACT
Statistics
Matches: 80, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
34 2 0.03
35 57 0.71
36 21 0.26
ACGTcount: A:0.15, C:0.12, G:0.32, T:0.41
Consensus pattern (35 bp):
TTGGTGTGTTTCGGTTGGATTGGCTCTTATGAGCA
Found at i:35450 original size:21 final size:21
Alignment explanation
Indices: 35425--35464 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
35415 CATTCTTGAT
* *
35425 AATAATTAATAATATTGATTA
1 AATAATAAATAATAGTGATTA
35446 AATAATAAATAATAGTGAT
1 AATAATAAATAATAGTGAT
35465 ATTTTAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (21 bp):
AATAATAAATAATAGTGATTA
Found at i:35585 original size:54 final size:54
Alignment explanation
Indices: 35510--35619 Score: 166
Period size: 54 Copynumber: 2.0 Consensus size: 54
35500 GAAATATAAG
* * *
35510 TATGTGTGAATATGAGCGTATTCATAGAGATTAGTAAAAATCGATAAATAAGGA
1 TATGTGTGAATACGAGCGTATTCACAGAGATCAGTAAAAATCGATAAATAAGGA
* * *
35564 TATGTGTGAATACGAGTGTATTCACAGAGATCGGTAAAAATCGGTAAATAAGGA
1 TATGTGTGAATACGAGCGTATTCACAGAGATCAGTAAAAATCGATAAATAAGGA
35618 TA
1 TA
35620 CCAAGTAAGT
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 50 1.00
ACGTcount: A:0.41, C:0.07, G:0.24, T:0.28
Consensus pattern (54 bp):
TATGTGTGAATACGAGCGTATTCACAGAGATCAGTAAAAATCGATAAATAAGGA
Found at i:36314 original size:14 final size:15
Alignment explanation
Indices: 36290--36318 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
36280 TGTGATTATT
36290 ATGATGATTGATATG
1 ATGATGATTGATATG
36305 ATGA-GATTGATATG
1 ATGATGATTGATATG
36319 TTAATATGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.34, C:0.00, G:0.28, T:0.38
Consensus pattern (15 bp):
ATGATGATTGATATG
Found at i:37311 original size:11 final size:11
Alignment explanation
Indices: 37295--37335 Score: 73
Period size: 11 Copynumber: 3.7 Consensus size: 11
37285 GGTCCTGAAT
37295 TGTTTCTAAGG
1 TGTTTCTAAGG
37306 TGTTTCTAAGG
1 TGTTTCTAAGG
37317 TGTTTCTAAGG
1 TGTTTCTAAGG
*
37328 TATTTCTA
1 TGTTTCTA
37336 GGGCCTCGAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.20, C:0.10, G:0.22, T:0.49
Consensus pattern (11 bp):
TGTTTCTAAGG
Found at i:37384 original size:14 final size:15
Alignment explanation
Indices: 37365--37404 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
37355 AAGGGACGAT
*
37365 ATGTATGTGAATG-A
1 ATGTATGTAAATGAA
37379 ATGTAT-TAAATGAA
1 ATGTATGTAAATGAA
37393 ATGTATG-AAATG
1 ATGTATGTAAATG
37405 TATGAATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
13 5 0.22
14 18 0.78
ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (15 bp):
ATGTATGTAAATGAA
Found at i:43252 original size:25 final size:25
Alignment explanation
Indices: 43217--43282 Score: 78
Period size: 25 Copynumber: 2.6 Consensus size: 25
43207 CCATAACTCG
* *
43217 TGAGAGTATACCGATTTACAGCTTA
1 TGAGAGCATACCGATTTACAGCTCA
* *
43242 TGAGAGCATACCAATTTATAGCTCA
1 TGAGAGCATACCGATTTACAGCTCA
* *
43267 TGTGAGCATACAGATT
1 TGAGAGCATACCGATT
43283 CATAGCTCGT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (25 bp):
TGAGAGCATACCGATTTACAGCTCA
Found at i:43287 original size:25 final size:25
Alignment explanation
Indices: 43208--43290 Score: 69
Period size: 25 Copynumber: 3.3 Consensus size: 25
43198 CGTTTCGACC
* * * *
43208 CATAACTCGTGAGAGTATACCGATT
1 CATAGCTCATGAGAGCATACCAATT
* * *
43233 TACAGCTTATGAGAGCATACCAATT
1 CATAGCTCATGAGAGCATACCAATT
* *
43258 TATAGCTCATGTGAGCATA-CAGATT
1 CATAGCTCATGAGAGCATACCA-ATT
43283 CATAGCTC
1 CATAGCTC
43291 GTATAAGCAT
Statistics
Matches: 46, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
24 2 0.04
25 44 0.96
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (25 bp):
CATAGCTCATGAGAGCATACCAATT
Found at i:55784 original size:45 final size:45
Alignment explanation
Indices: 55727--55893 Score: 194
Period size: 45 Copynumber: 3.7 Consensus size: 45
55717 TCATCTTGCC
* * *
55727 ATAGTTTCTTTCAACTATTGTCTTACAT-GTTTGAATCATGATGCT
1 ATAGTGTCTTTCAACTATGGTCTTAC-TCGTTTGAATCGTGATGCT
* *
55772 ATAGTGTCTTTCATCTATGGTCTTACTCGTTTGAATTGTGATG-T
1 ATAGTGTCTTTCAACTATGGTCTTACTCGTTTGAATCGTGATGCT
** * * *
55816 CATAACGTCTTTCAGCTATGGTCTTACTCATTTGAATCGTGATGCC
1 -ATAGTGTCTTTCAACTATGGTCTTACTCGTTTGAATCGTGATGCT
* *
55862 ATTGTGTCTTTCCACTATGGTCTTACTCGTTT
1 ATAGTGTCTTTCAACTATGGTCTTACTCGTTT
55894 TTCAACCAAC
Statistics
Matches: 102, Mismatches: 17, Indels: 6
0.82 0.14 0.05
Matches are distributed among these distances:
44 2 0.02
45 100 0.98
ACGTcount: A:0.20, C:0.19, G:0.17, T:0.45
Consensus pattern (45 bp):
ATAGTGTCTTTCAACTATGGTCTTACTCGTTTGAATCGTGATGCT
Found at i:88701 original size:22 final size:22
Alignment explanation
Indices: 88674--88728 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
88664 CTATTTCCAT
88674 TTTCGTACCAAATCCATTACCA
1 TTTCGTACCAAATCCATTACCA
** * *
88696 TTTCGTTTCAAATCCCTTACCG
1 TTTCGTACCAAATCCATTACCA
*
88718 TTTCATACCAA
1 TTTCGTACCAA
88729 TTCCCAAATA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.27, C:0.31, G:0.05, T:0.36
Consensus pattern (22 bp):
TTTCGTACCAAATCCATTACCA
Found at i:93677 original size:20 final size:20
Alignment explanation
Indices: 93641--93678 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
93631 CGGTGAGGTT
*
93641 TGTTAAGTTTTCTTTTTGAG
1 TGTTAAGTTTTCGTTTTGAG
93661 TGTTAAGTGTTT-GTTTTG
1 TGTTAAGT-TTTCGTTTTG
93679 CAGGTTTGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.81
21 3 0.19
ACGTcount: A:0.13, C:0.03, G:0.24, T:0.61
Consensus pattern (20 bp):
TGTTAAGTTTTCGTTTTGAG
Found at i:95827 original size:20 final size:19
Alignment explanation
Indices: 95772--95816 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
95762 CATTTCATTG
*
95772 AGCTCCAATTAGCTCATTTCC
1 AGCTCC-ATGAGCTCATTT-C
*
95793 AGCTCCATGAACTCATTTC
1 AGCTCCATGAGCTCATTTC
95812 AGCTC
1 AGCTC
95817 ATTTGAGCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 6 0.27
20 10 0.45
21 6 0.27
ACGTcount: A:0.24, C:0.33, G:0.11, T:0.31
Consensus pattern (19 bp):
AGCTCCATGAGCTCATTTC
Found at i:97132 original size:21 final size:21
Alignment explanation
Indices: 97106--97168 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
97096 TTGGTATTTG
97106 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
97127 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
97148 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
97169 ATGGTTCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 22 0.59
22 15 0.41
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:104408 original size:11 final size:10
Alignment explanation
Indices: 104383--104443 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
104373 ACCAATAAAA
104383 TAAA-TGAGC
1 TAAATTGAGC
*
104392 TGAATTGTAGC
1 TAAATTG-AGC
104403 TAAATTGAGC
1 TAAATTGAGC
**
104413 TTGATTGAGC
1 TAAATTGAGC
104423 TGAAA-TGAGC
1 T-AAATTGAGC
*
104433 TCAATTGAGC
1 TAAATTGAGC
104443 T
1 T
104444 GGTCGGAGCT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.11, G:0.25, T:0.31
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:104444 original size:20 final size:20
Alignment explanation
Indices: 104384--104444 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
104374 CCAATAAAAT
*
104384 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
**
104404 AAATTGAGCTTGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
104425 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
104445 GTCGGAGCTG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
20 22 0.63
21 13 0.37
ACGTcount: A:0.33, C:0.11, G:0.26, T:0.30
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:104453 original size:30 final size:30
Alignment explanation
Indices: 104388--104464 Score: 84
Period size: 30 Copynumber: 2.5 Consensus size: 30
104378 TAAAATAAAT
* *
104388 GAGCTGAATTGTAGCTAAATTGAGCTTGATT
1 GAGCTGAAATG-AGCTAAATTGAGCTTGATG
* *
104419 GAGCTGAAATGAGCTCAATTGAGC-TGGTCG
1 GAGCTGAAATGAGCTAAATTGAGCTTGAT-G
*
104449 GAGCTGAAACGAGCTA
1 GAGCTGAAATGAGCTA
104465 GAAAAGCTAA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
29 3 0.08
30 26 0.67
31 10 0.26
ACGTcount: A:0.30, C:0.14, G:0.30, T:0.26
Consensus pattern (30 bp):
GAGCTGAAATGAGCTAAATTGAGCTTGATG
Found at i:117794 original size:20 final size:20
Alignment explanation
Indices: 117765--117834 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
117755 CAATTTATCT
*
117765 ACATTACTGGTAGTTTGTCC
1 ACATTACTGGTAGCTTGTCC
* * *
117785 ACAATACTGGCAGCTTGTCT
1 ACATTACTGGTAGCTTGTCC
*
117805 ACATTACTAGT-GACTTGTCC
1 ACATTACTGGTAG-CTTGTCC
117825 ACATTACTGG
1 ACATTACTGG
117835 CAATTTGTCT
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
19 1 0.03
20 39 0.98
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.34
Consensus pattern (20 bp):
ACATTACTGGTAGCTTGTCC
Found at i:117842 original size:20 final size:20
Alignment explanation
Indices: 117749--117843 Score: 73
Period size: 20 Copynumber: 4.8 Consensus size: 20
117739 AAGGATGAAG
* * *
117749 TACTAGCAATTTATCTACAT
1 TACTGGCAATTTGTCCACAT
* * *
117769 TACTGGTAGTTTGTCCACAA
1 TACTGGCAATTTGTCCACAT
** *
117789 TACTGGCAGCTTGTCTACAT
1 TACTGGCAATTTGTCCACAT
* ** *
117809 TACTAGTGACTTGTCCACAT
1 TACTGGCAATTTGTCCACAT
117829 TACTGGCAATTTGTC
1 TACTGGCAATTTGTC
117844 TGAAAATTTG
Statistics
Matches: 56, Mismatches: 19, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 56 1.00
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (20 bp):
TACTGGCAATTTGTCCACAT
Found at i:117843 original size:40 final size:40
Alignment explanation
Indices: 117749--117844 Score: 113
Period size: 40 Copynumber: 2.4 Consensus size: 40
117739 AAGGATGAAG
* * * *
117749 TACTAGCAATTTATCTACATTACTGGTAGTTTGTCCACAA
1 TACTGGCAATTTGTCTACATTACTAGTAGCTTGTCCACAA
** *
117789 TACTGGCAGCTTGTCTACATTACTAGT-GACTTGTCCACAT
1 TACTGGCAATTTGTCTACATTACTAGTAG-CTTGTCCACAA
117829 TACTGGCAATTTGTCT
1 TACTGGCAATTTGTCT
117845 GAAAATTTGG
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
39 1 0.02
40 45 0.98
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.38
Consensus pattern (40 bp):
TACTGGCAATTTGTCTACATTACTAGTAGCTTGTCCACAA
Found at i:119389 original size:51 final size:51
Alignment explanation
Indices: 119322--119422 Score: 202
Period size: 51 Copynumber: 2.0 Consensus size: 51
119312 TATACGAAAG
119322 ATATTAATGTAATTCATGAATAGTTTTATTAACCAATCTGTTCGAAAAAAA
1 ATATTAATGTAATTCATGAATAGTTTTATTAACCAATCTGTTCGAAAAAAA
119373 ATATTAATGTAATTCATGAATAGTTTTATTAACCAATCTGTTCGAAAAAA
1 ATATTAATGTAATTCATGAATAGTTTTATTAACCAATCTGTTCGAAAAAA
119423 CTATAAGTGT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.38
Consensus pattern (51 bp):
ATATTAATGTAATTCATGAATAGTTTTATTAACCAATCTGTTCGAAAAAAA
Done.