Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1888
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: 15349
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.33
Found at i:2882 original size:35 final size:35
Alignment explanation
Indices: 2843--2913 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
2833 TATGGCTATG
2843 AAATTAAATGGTTAAGGGATTTAAATTTTAATTTT
1 AAATTAAATGGTTAAGGGATTTAAATTTTAATTTT
2878 AAATTAAATGGTTAAGGGATTTAAATTTTAATTTT
1 AAATTAAATGGTTAAGGGATTTAAATTTTAATTTT
2913 A
1 A
2914 CCATTTATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.41, C:0.00, G:0.14, T:0.45
Consensus pattern (35 bp):
AAATTAAATGGTTAAGGGATTTAAATTTTAATTTT
Found at i:6340 original size:20 final size:20
Alignment explanation
Indices: 6311--6354 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
6301 TAAATATAAA
* *
6311 TAAAACTTATAATTATTTTT
1 TAAAACTTATAATGAATTTT
* *
6331 TAAAATTTATTATGAATTTT
1 TAAAACTTATAATGAATTTT
6351 TAAA
1 TAAA
6355 GTCAGAACAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (20 bp):
TAAAACTTATAATGAATTTT
Found at i:7365 original size:46 final size:46
Alignment explanation
Indices: 7219--7389 Score: 188
Period size: 46 Copynumber: 3.7 Consensus size: 46
7209 AACCCGCCCC
* * * *
7219 TAAGTGAACTCGGACTCAACTCAATGAGCTCGG-CGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
* * * *
7264 TAAATGAACTCGGACTCAACTCAACGAGTTCGATGCCTAGTTACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCG--GAC-ATTTGCATCCA
* *
7311 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
*
7356 TAAGTGAACTCGGACTCAACTCAAAGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
7390 TGCTCAACCA
Statistics
Matches: 104, Mismatches: 15, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
43 6 0.06
44 3 0.03
45 31 0.30
46 55 0.53
47 3 0.03
48 2 0.02
49 4 0.04
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
Found at i:7385 original size:92 final size:92
Alignment explanation
Indices: 7224--7392 Score: 268
Period size: 92 Copynumber: 1.8 Consensus size: 92
7214 GCCCCTAAGT
* * *
7224 GAACTCGGACTCAACTCAATGAGCTCGGCGTTCGCATCCATAAATGAACTCGGACTCAACTCAAC
1 GAACTCGGACTCAACTCAACGAGCTCGGCATTCGCATCCATAAATGAACTCGGACTCAACTCAAA
7289 GAGTTC-GATGCCTAGTTACATCTCAC
66 GAGTTCGGATGCCTAGTTACATCTCAC
* * *
7315 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGG-CATTCGCATCCATAAATGAACTCGGACTCAACTCAA
7380 AGAGTTCGGATGC
65 AGAGTTCGGATGC
7393 TCAACCATCC
Statistics
Matches: 70, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
91 26 0.37
92 39 0.56
93 5 0.07
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (92 bp):
GAACTCGGACTCAACTCAACGAGCTCGGCATTCGCATCCATAAATGAACTCGGACTCAACTCAAA
GAGTTCGGATGCCTAGTTACATCTCAC
Found at i:14452 original size:93 final size:93
Alignment explanation
Indices: 14293--14463 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
14283 CCCCCTAAGT
* *
14293 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAATGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
14358 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
* * *
14386 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
14451 CGAGTTCGGATGC
66 CGAGTTCGGATGC
14464 TCAACCATCC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:14460 original size:46 final size:46
Alignment explanation
Indices: 14288--14460 Score: 208
Period size: 46 Copynumber: 3.7 Consensus size: 46
14278 TAACCCCCCC
* * * *
14288 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
* * *
14334 TAAATGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-ATTTGCATCCA
* *
14382 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
14427 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
14461 TGCTCAACCA
Statistics
Matches: 107, Mismatches: 13, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
43 6 0.06
44 2 0.02
45 2 0.02
46 60 0.56
47 29 0.27
48 2 0.02
49 2 0.02
50 4 0.04
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
Done.