Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1575
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: 39888
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.35
Found at i:8107 original size:21 final size:20
Alignment explanation
Indices: 8081--8153 Score: 69
Period size: 21 Copynumber: 3.5 Consensus size: 20
8071 ACATATATGT
8081 ATAATAATGATGAAAATAATA
1 ATAATAAT-ATGAAAATAATA
8102 ATAATAATAGTGAAAATAAATA
1 ATAATAATA-TGAAAAT-AATA
8124 AT-ATAATAAT-AAATATAATA
1 ATAATAAT-ATGAAA-ATAATA
* *
8144 GTAACAATAT
1 ATAATAATAT
8154 TAGTAATATG
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
20 11 0.24
21 27 0.60
22 7 0.16
ACGTcount: A:0.62, C:0.01, G:0.07, T:0.30
Consensus pattern (20 bp):
ATAATAATATGAAAATAATA
Found at i:8125 original size:16 final size:15
Alignment explanation
Indices: 8096--8138 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
8086 AATGATGAAA
8096 ATAATAAT-AATAAT
1 ATAATAATAAATAAT
8110 AGTGAA-AATAAATAAT
1 A-T-AATAATAAATAAT
8126 ATAATAATAAATA
1 ATAATAATAAATA
8139 TAATAGTAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
14 3 0.12
15 13 0.52
16 9 0.36
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (15 bp):
ATAATAATAAATAAT
Found at i:9363 original size:17 final size:17
Alignment explanation
Indices: 9341--9374 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
9331 GACGGGTTAT
9341 TGGGTTGTTTGGTTTAG
1 TGGGTTGTTTGGTTTAG
9358 TGGGTTGTTTGGTTTAG
1 TGGGTTGTTTGGTTTAG
9375 GGCCCAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.06, C:0.00, G:0.41, T:0.53
Consensus pattern (17 bp):
TGGGTTGTTTGGTTTAG
Found at i:11811 original size:60 final size:60
Alignment explanation
Indices: 11747--11872 Score: 137
Period size: 60 Copynumber: 2.1 Consensus size: 60
11737 ATCCAAAATA
* * ** * * * *
11747 TAAAAAAATCAACAAAATTAGCTCTC-ATGTTTACAAAATTTGTCATTTTAGTTCTAATTC
1 TAAAAAAATCAACAAAATTAACACTCAACATTTACAAAATCTGTCA-ATTAGTCCTAACTC
* * *
11807 TAAAAAATTCAATAAATTTAACACTCAACATTTACAAAATCTGTCAATTAGTCCTAACTC
1 TAAAAAAATCAACAAAATTAACACTCAACATTTACAAAATCTGTCAATTAGTCCTAACTC
11867 TAAAAA
1 TAAAAA
11873 GTTAATTTTT
Statistics
Matches: 54, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
60 38 0.70
61 16 0.30
ACGTcount: A:0.44, C:0.17, G:0.05, T:0.34
Consensus pattern (60 bp):
TAAAAAAATCAACAAAATTAACACTCAACATTTACAAAATCTGTCAATTAGTCCTAACTC
Found at i:12797 original size:7 final size:6
Alignment explanation
Indices: 12743--12796 Score: 74
Period size: 6 Copynumber: 8.8 Consensus size: 6
12733 AGAGAGAAGC
*
12743 GAAAAG GAAAAG GAAAAG GAAAAT G-AAAG GAAAAGG GAAAAG GAAAAAG
1 GAAAAG GAAAAG GAAAAG GAAAAG GAAAAG GAAAA-G GAAAAG G-AAAAG
12792 GAAAA
1 GAAAA
12797 AAAAAAGTGC
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
5 4 0.09
6 27 0.63
7 12 0.28
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.02
Consensus pattern (6 bp):
GAAAAG
Found at i:19371 original size:3 final size:3
Alignment explanation
Indices: 19365--19409 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
19355 GAAGACTTCT
19365 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
19410 AAGGTAAGAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:28136 original size:15 final size:15
Alignment explanation
Indices: 28116--28146 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
28106 TTTACTATAC
28116 TACTTATTTTCTGGT
1 TACTTATTTTCTGGT
28131 TACTTATTTTCTGGT
1 TACTTATTTTCTGGT
28146 T
1 T
28147 TTTTGTTGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.13, C:0.13, G:0.13, T:0.61
Consensus pattern (15 bp):
TACTTATTTTCTGGT
Found at i:30949 original size:178 final size:177
Alignment explanation
Indices: 30650--30991 Score: 535
Period size: 178 Copynumber: 1.9 Consensus size: 177
30640 GGGAAGTGAT
* * * *
30650 GCTTATTATTGAAGAAAAGTTGGCAAAATAAAAACAAAAAAAATCCTTATTTGTATGTGTTTGTA
1 GCTTATTATTAAAGAAAAGCTGGAAAAATAAAAAC-AAAAAAATCCTCATTTGTATGTGTTTGTA
*
30715 TTTAAGATGTGTTGCATTTGATTCTAATAGGTCTCATGATTTTATCACTTTGAAGTGGTTAATTC
65 TTAAAGATGTGTTGCATTTGATTCTAATAGGTCTCATGATTTTATCACTTTGAAGTGGTTAATTC
* *
30780 CCTATTATTAGATCAGCTCTGAGAGTGTGTTTCTCTAACTTTTATAAA
130 CCTATGATTAGATCACCTCTGAGAGTGTGTTTCTCTAACTTTTATAAA
*
30828 GCTTATTATTAAAGCAAAGCTGGAAAAATAAAAAC-AAAAAATCCTCATTTGTATAGATGTTTGT
1 GCTTATTATTAAAGAAAAGCTGGAAAAATAAAAACAAAAAAATCCTCATTTGTAT-G-TGTTTGT
* *
30892 ATTAAAGAT-TGATTGCATTTGATTCTAATAGGTCTCATGGTTTTATCACTTTGAAGTGGTTCAT
64 ATTAAAGATGTG-TTGCATTTGATTCTAATAGGTCTCATGATTTTATCACTTTGAAGTGGTTAAT
*
30956 TCCCTATGATTGGATCACCTCTGAGAGTGTGTTTCT
128 TCCCTATGATTAGATCACCTCTGAGAGTGTGTTTCT
30992 TAGACTTCTA
Statistics
Matches: 150, Mismatches: 11, Indels: 6
0.90 0.07 0.04
Matches are distributed among these distances:
176 18 0.12
177 3 0.02
178 129 0.86
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.39
Consensus pattern (177 bp):
GCTTATTATTAAAGAAAAGCTGGAAAAATAAAAACAAAAAAATCCTCATTTGTATGTGTTTGTAT
TAAAGATGTGTTGCATTTGATTCTAATAGGTCTCATGATTTTATCACTTTGAAGTGGTTAATTCC
CTATGATTAGATCACCTCTGAGAGTGTGTTTCTCTAACTTTTATAAA
Done.