Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2403
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: 21358
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Found at i:1204 original size:39 final size:39
Alignment explanation
Indices: 1089--1335 Score: 231
Period size: 40 Copynumber: 6.3 Consensus size: 39
1079 AAATCACGTA
* * * **
1089 CCTTCGGAATTTAACCGGATATAGCT-ACTCGTTCAAATG
1 CCTTCGGGACTTAACCGGATTTAG-TAACTCGCACAAATG
* *
1128 CCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTA-ACCGGATT-TAGTAACTCGCACAAATG
1168 CCTTCGGGACTTAACCGGATTTAGTAACTCGCACAAATG
1 CCTTCGGGACTTAACCGGATTTAGTAACTCGCACAAATG
1207 CCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAATATG
1 CCTTCGGGACTTAA-CCGGATTTAGTAACTCGCACAA-ATG
* * *
1248 CCTTC-GG-C-T-GCCGGAATTAGTATCTCGCACAAATG
1 CCTTCGGGACTTAACCGGATTTAGTAACTCGCACAAATG
* * * * *
1283 CCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCACAAA-G
1 CCTTCGGGA-CTTA-ACCGGATTTAGTAAC-TCGCACAAATG
1323 CCTTCGGGACTTA
1 CCTTCGGGACTTA
1336 GCCCGGACAT
Statistics
Matches: 176, Mismatches: 19, Indels: 25
0.80 0.09 0.11
Matches are distributed among these distances:
35 10 0.06
36 20 0.11
37 1 0.01
38 2 0.01
39 49 0.28
40 75 0.43
41 19 0.11
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.27
Consensus pattern (39 bp):
CCTTCGGGACTTAACCGGATTTAGTAACTCGCACAAATG
Found at i:1225 original size:79 final size:79
Alignment explanation
Indices: 1089--1335 Score: 258
Period size: 79 Copynumber: 3.2 Consensus size: 79
1079 AAATCACGTA
* * * ** *
1089 CCTTCGGAATTTAACCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGCCCGGTTATAG
1 CCTTCGGGACTTAACCGGATTTAG-TAACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAG
1153 TAACTCGCACAAATG
65 TAACTCGCACAAATG
*
1168 CCTTCGGGACTTAACCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATT-TAG
1 CCTTCGGGACTTAACCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG-TTATAG
1232 TAACTCGCACAATATG
65 TAACTCGCACAA-ATG
* * * * * *
1248 CCTTC-GG-C-T-GCCGGAATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGGATATGG
1 CCTTCGGGACTTAACCGGATTTAGTAACTCGCACAAATGCCTTCGGGA-CTTAGCCCGGTTATAG
* *
1308 TCACTTAGCACAAA-G
65 TAAC-TCGCACAAATG
1323 CCTTCGGGACTTA
1 CCTTCGGGACTTA
1336 GCCCGGACAT
Statistics
Matches: 142, Mismatches: 16, Indels: 20
0.80 0.09 0.11
Matches are distributed among these distances:
75 10 0.07
76 44 0.31
77 9 0.06
78 3 0.02
79 66 0.46
80 10 0.07
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.27
Consensus pattern (79 bp):
CCTTCGGGACTTAACCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGT
AACTCGCACAAATG
Found at i:9036 original size:40 final size:40
Alignment explanation
Indices: 8999--9223 Score: 278
Period size: 40 Copynumber: 5.7 Consensus size: 40
8989 GCTACTCGTT
* *
8999 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
9039 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
9079 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * * *
9119 CCAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** * * * *
9158 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
9199 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
9224 CATCATTCGA
Statistics
Matches: 165, Mismatches: 15, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
38 2 0.01
39 32 0.19
40 118 0.72
41 13 0.08
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:9183 original size:119 final size:120
Alignment explanation
Indices: 9001--9223 Score: 301
Period size: 119 Copynumber: 1.9 Consensus size: 120
8991 TACTCGTTCA
*
9001 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
* *
9066 TTAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
66 ATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
* * **
9121 AATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGG
1 AATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
* * *
9183 ATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
64 ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGA
9224 CATCATTCGA
Statistics
Matches: 90, Mismatches: 10, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
118 4 0.04
119 66 0.73
120 20 0.22
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (120 bp):
AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
ATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
Found at i:10415 original size:56 final size:56
Alignment explanation
Indices: 10348--10467 Score: 222
Period size: 56 Copynumber: 2.1 Consensus size: 56
10338 TATTAGTTTA
*
10348 TTGCCCATGCTTCTTATTTTATTATTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTATTCCATTAACACAACATGTTTCATGACATGCT
*
10404 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGCT
1 TTGCCCATGCTTCTTATTTTATTATTCCATTAACACAACATGTTTCATGACATGCT
10460 TTGCCCAT
1 TTGCCCAT
10468 CATCCCTTGT
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 62 1.00
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.44
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTATTCCATTAACACAACATGTTTCATGACATGCT
Found at i:17504 original size:29 final size:29
Alignment explanation
Indices: 17462--17522 Score: 106
Period size: 29 Copynumber: 2.1 Consensus size: 29
17452 AAAACCAACT
17462 TTTCGCAACCAGAACTCAC-ATTTACTAAA
1 TTTCGCAACCAGAACTCACAATTT-CTAAA
17491 TTTCGCAACCAGAACTCACAATTTCTAAA
1 TTTCGCAACCAGAACTCACAATTTCTAAA
17520 TTT
1 TTT
17523 TGTATACAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 27 0.87
30 4 0.13
ACGTcount: A:0.36, C:0.26, G:0.07, T:0.31
Consensus pattern (29 bp):
TTTCGCAACCAGAACTCACAATTTCTAAA
Done.