Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1256
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: 36995
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Found at i:1276 original size:39 final size:39
Alignment explanation
Indices: 1202--1424 Score: 270
Period size: 39 Copynumber: 5.6 Consensus size: 39
1192 GCTACTCGTT
*
1202 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTC-GGACTTAGCCCGGATT-TAGTAACTCGCA
*
1242 CAAATGCCTTCGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
1281 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
1320 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
1359 CAAATGCCTTCGGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
1400 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTC-GGACTTAGCCCGGA
1425 CATCATTCAA
Statistics
Matches: 164, Mismatches: 15, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
39 110 0.67
40 43 0.26
41 11 0.07
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (39 bp):
CAAATGCCTTCGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:9321 original size:79 final size:79
Alignment explanation
Indices: 9210--9433 Score: 283
Period size: 79 Copynumber: 2.8 Consensus size: 79
9200 GCTACTCGTT
* * *
9210 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGG-CTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
* *
9275 ATTTAGTAACTCGCA
65 AATTAGTAACTCACA
*
9290 CAAATGCCTTCGGGCTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTCGGG-CTTAGCCCGG
1 CAAATGCCTTCGGGCTTAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
*
9353 AATTAGTATCTCACA
65 AATTAGTAACTCACA
* * * * *
9368 CAAATGCCTTCGGATCTTAGTCCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGG-GCTTAGCCCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGCCCG
9432 GA
64 GA
9434 CATCATTCAA
Statistics
Matches: 126, Mismatches: 13, Indels: 10
0.85 0.09 0.07
Matches are distributed among these distances:
78 35 0.28
79 57 0.45
80 34 0.27
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (79 bp):
CAAATGCCTTCGGGCTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGA
ATTAGTAACTCACA
Found at i:9327 original size:39 final size:40
Alignment explanation
Indices: 9210--9433 Score: 271
Period size: 40 Copynumber: 5.7 Consensus size: 40
9200 GCTACTCGTT
* *
9210 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCA
* *
9250 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
*
9290 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
* *
9329 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCACA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
* * * *
9368 CAAATGCCTTC-GGATCTTAGTCCGG-ATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGAAT-TAGTAAC-TCGCA
9409 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
9434 CATCATTCAA
Statistics
Matches: 164, Mismatches: 13, Indels: 13
0.86 0.07 0.07
Matches are distributed among these distances:
38 2 0.01
39 73 0.45
40 77 0.47
41 12 0.07
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
Found at i:15830 original size:17 final size:17
Alignment explanation
Indices: 15810--15843 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
15800 TTCGTATATT
* *
15810 ATACTAATTATATCTAA
1 ATACTAAGTATACCTAA
15827 ATACTAAGTATACCTAA
1 ATACTAAGTATACCTAA
15844 GCGAGTCTAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.15, G:0.03, T:0.35
Consensus pattern (17 bp):
ATACTAAGTATACCTAA
Found at i:22291 original size:32 final size:32
Alignment explanation
Indices: 22255--22316 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
22245 AGCTTTTGGT
22255 TTTTTCATGTTGTCAAAGAGTTGAACAATGGA
1 TTTTTCATGTTGTCAAAGAGTTGAACAATGGA
*
22287 TTTTTCGTGTTGTCAAAGAGTTGAACAATG
1 TTTTTCATGTTGTCAAAGAGTTGAACAATG
22317 AAAATAGATG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.29, C:0.10, G:0.23, T:0.39
Consensus pattern (32 bp):
TTTTTCATGTTGTCAAAGAGTTGAACAATGGA
Found at i:34212 original size:14 final size:14
Alignment explanation
Indices: 34193--34221 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
34183 ACAGATGGAT
34193 TCGTATAATTCTTA
1 TCGTATAATTCTTA
34207 TCGTATAATTCTTA
1 TCGTATAATTCTTA
34221 T
1 T
34222 ATATATTGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.14, G:0.07, T:0.52
Consensus pattern (14 bp):
TCGTATAATTCTTA
Done.