Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold7015.1
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: 8558
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.29
Found at i:6474 original size:79 final size:79
Alignment explanation
Indices: 6290--6514 Score: 240
Period size: 79 Copynumber: 2.8 Consensus size: 79
6280 GCTCCTCGTT
* * * * *
6290 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA-CAAATGCCTTCAGGACTTAACCCG
1 CAAATGCCTTCGGGACTTAACCCGGATATAGTAACTCGCACCAAA-GCCTTC-GGGCTTAGCCCG
* *
6354 GATTTAGTAACTCGTA
64 GAATTAGTAACTCGCA
* *
6370 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACCAAGGCCTTCGGGCTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGATATAGTAACTCGCACCAAAGCCTTCGGGCTTAGCCCGGA
*
6435 ATTAGTATCTCGCA
66 ATTAGTAACTCGCA
* ** * * *
6449 CAAATGTCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA-CAAAGCCTTCGGGACTTAGCCC
1 CAAATGCCTTCGGGA-CTTAACCCGGATATAGTAAC-TCGCACCAAAGCCTTCGGG-CTTAGCCC
6512 GGA
63 GGA
6515 CATCATTCAA
Statistics
Matches: 123, Mismatches: 18, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
78 3 0.02
79 60 0.49
80 57 0.46
81 3 0.02
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAACCCGGATATAGTAACTCGCACCAAAGCCTTCGGGCTTAGCCCGGA
ATTAGTAACTCGCA
Found at i:6474 original size:119 final size:120
Alignment explanation
Indices: 6295--6514 Score: 277
Period size: 119 Copynumber: 1.8 Consensus size: 120
6285 TCGTTCAAAT
* *
6295 GCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCAGGACTTAACCCGGATTTA
1 GCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCAGGACTTAACCCGGATATA
* *
6360 GTAAC-TCGTACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACCAAG
66 GTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACCAAG
* * * **
6415 GCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATGTCTTC-GGATCTTAGTCCGGATA
1 GCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCAGGA-CTTAACCCGGATA
* * *
6477 TGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
64 TAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGA
6515 CATCATTCAA
Statistics
Matches: 85, Mismatches: 12, Indels: 7
0.82 0.12 0.07
Matches are distributed among these distances:
118 4 0.05
119 65 0.76
120 16 0.19
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (120 bp):
GCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCAGGACTTAACCCGGATATA
GTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACCAAG
Found at i:6514 original size:40 final size:40
Alignment explanation
Indices: 6290--6514 Score: 251
Period size: 40 Copynumber: 5.7 Consensus size: 40
6280 GCTCCTCGTT
* *
6290 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* * * *
6330 CAAATGCCTTCAGGACTTAACCCGGATTTAGTAACTCGTA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
6370 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* * *
6410 CCAAGGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * * *
6449 CAAATGTCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
6490 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
6515 CATCATTCAA
Statistics
Matches: 156, Mismatches: 23, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
38 2 0.01
39 29 0.19
40 113 0.72
41 12 0.08
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:8124 original size:53 final size:53
Alignment explanation
Indices: 8055--8161 Score: 196
Period size: 53 Copynumber: 2.0 Consensus size: 53
8045 TCCAGCACAA
* *
8055 CAAAAGTATAGCATTCATGTAGCTAAACGGATAATTTCATATGCACAATTTTT
1 CAAAAGTATAGCATTCATATAGCTAAACGGATAATTTCATATGCACAAATTTT
8108 CAAAAGTATAGCATTCATATAGCTAAACGGATAATTTCATATGCACAAATTTT
1 CAAAAGTATAGCATTCATATAGCTAAACGGATAATTTCATATGCACAAATTTT
8161 C
1 C
8162 GATATCATAC
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.33
Consensus pattern (53 bp):
CAAAAGTATAGCATTCATATAGCTAAACGGATAATTTCATATGCACAAATTTT
Found at i:8526 original size:39 final size:40
Alignment explanation
Indices: 8411--8554 Score: 179
Period size: 40 Copynumber: 3.6 Consensus size: 40
8401 TACTCGTTCA
*
8411 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA-C
1 AATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCACC
*
8450 AATTGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
1 AA-TGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACC
* * *
8491 AATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACC
*
8530 AATGCCTTC-GGATCTTAGTCCGGAT
1 AATGCCTTCGGGA-CTTAGCCCGGAT
8555 ATGG
Statistics
Matches: 92, Mismatches: 8, Indels: 9
0.84 0.07 0.08
Matches are distributed among these distances:
38 2 0.02
39 34 0.37
40 51 0.55
41 5 0.05
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.26
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACC
Done.