Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold497
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: 23852
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Found at i:3688 original size:39 final size:40
Alignment explanation
Indices: 3645--3901 Score: 253
Period size: 39 Copynumber: 6.6 Consensus size: 40
3635 TCCTCGTTCA
* * * *
3645 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACG
*
3684 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACG
3724 AATGCCTTCGGGACTTAACCCGGA-TT--T-ACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACG
* *
3760 AATGCCTTC-GGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACG
* * * * *
3799 AAGGCCTTCGGGGCTTAACCCGGACTT-GTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACG
** * * * *
3838 AATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCACG
* *
3878 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
3902 CAGCATTCAA
Statistics
Matches: 186, Mismatches: 22, Indels: 19
0.82 0.10 0.08
Matches are distributed among these distances:
35 14 0.08
36 20 0.11
37 1 0.01
38 3 0.02
39 81 0.44
40 59 0.32
41 8 0.04
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACG
Found at i:3795 original size:75 final size:76
Alignment explanation
Indices: 3643--3902 Score: 265
Period size: 75 Copynumber: 3.4 Consensus size: 76
3633 GCTCCTCGTT
* * * ** *
3643 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACTTAACCCGGA
1 CAAAGGCCTTCGGGACTTAACCCGGACTT-GT-ACTCGCACAATGCCTTC-GGACTTAACCCGGA
3708 TTTAATAACTCGCA
63 TTTAATAACTCGCA
* *
3722 CGAATGCCTTCGGGACTTAACCCGGA-TT-TACTCGCACGAATGCCTTCGGACTTAACCCGGATT
1 CAAAGGCCTTCGGGACTTAACCCGGACTTGTACTCGCAC-AATGCCTTCGGACTTAACCCGGATT
* *
3785 TAGTATCTCGCA
65 TAATAACTCGCA
* **
3797 CAAAGGCCTTCGGGGCTTAACCCGGACTTGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGGA
1 CAAAGGCCTTCGGGACTTAACCCGGACTTGTA-CTCGCAC-AATGCCTTCGGA-CTTAACCCGGA
* * * *
3862 TATATTCACTTAGCA
63 TTTAATAAC-TCGCA
*
3877 CAAA-GCCTTCGGGACTTAGCCCGGAC
1 CAAAGGCCTTCGGGACTTAACCCGGAC
3903 AGCATTCAAT
Statistics
Matches: 155, Mismatches: 20, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
75 56 0.36
76 12 0.08
77 2 0.01
78 21 0.14
79 56 0.36
80 8 0.05
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.25
Consensus pattern (76 bp):
CAAAGGCCTTCGGGACTTAACCCGGACTTGTACTCGCACAATGCCTTCGGACTTAACCCGGATTT
AATAACTCGCA
Found at i:3910 original size:41 final size:41
Alignment explanation
Indices: 3833--3910 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
3823 CTTGTATCTC
* * *
3833 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
3874 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
3911 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:4054 original size:13 final size:14
Alignment explanation
Indices: 4030--4059 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
4020 ACACATAGAG
4030 CATGATTTTAATCA
1 CATGATTTTAATCA
4044 CATGA-TTTAATCA
1 CATGATTTTAATCA
4057 CAT
1 CAT
4060 CGTAATTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.37, C:0.17, G:0.07, T:0.40
Consensus pattern (14 bp):
CATGATTTTAATCA
Found at i:11232 original size:34 final size:34
Alignment explanation
Indices: 11183--11265 Score: 98
Period size: 34 Copynumber: 2.4 Consensus size: 34
11173 TTGTACTAAA
* * *
11183 ATGGGCTAAGGCCCACACTGATACTGTTACTG-T
1 ATGGGTTAAGGCCCACACAGATACTGTGACTGAT
*
11216 ATTGGGTTAAGGCCCACAGAGATACTGTGACTGAT
1 A-TGGGTTAAGGCCCACACAGATACTGTGACTGAT
11251 ATGGGCTT-AGGCCCA
1 ATGGG-TTAAGGCCCA
11266 GACTATTCAA
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
33 1 0.02
34 38 0.88
35 4 0.09
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (34 bp):
ATGGGTTAAGGCCCACACAGATACTGTGACTGAT
Found at i:16252 original size:40 final size:40
Alignment explanation
Indices: 16050--16252 Score: 238
Period size: 40 Copynumber: 5.1 Consensus size: 40
16040 CGGAATTTAA
** *
16050 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
16090 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
16130 CCGGAT-TAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
16168 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
16208 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
16248 CCGGA
1 CCGGA
16253 CATCATTCAA
Statistics
Matches: 141, Mismatches: 14, Indels: 16
0.82 0.08 0.09
Matches are distributed among these distances:
38 12 0.09
39 49 0.35
40 68 0.48
41 12 0.09
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Done.