Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3701
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: 49763
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.31
Found at i:1297 original size:82 final size:80
Alignment explanation
Indices: 1120--1340 Score: 292
Period size: 82 Copynumber: 2.8 Consensus size: 80
1110 ACCCAAGTAT
* * *
1120 CTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAAT-CCTTCGGGTCTTAGCCCGGATATAG
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
**
1182 TCACTAGCATGAATGC
65 TCACTAGCACAAATGC
1198 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGG-TATAG-
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
1261 CAACTACTCGCACAAATGC
66 C-ACTA---GCACAAATGC
* *
1280 CTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATGCCTTC-GGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGATAT
1341 CATCCGAATA
Statistics
Matches: 128, Mismatches: 7, Indels: 12
0.87 0.05 0.08
Matches are distributed among these distances:
78 13 0.10
79 30 0.23
80 19 0.15
81 13 0.10
82 53 0.41
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (80 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
CACTAGCACAAATGC
Found at i:1339 original size:39 final size:40
Alignment explanation
Indices: 1120--1340 Score: 297
Period size: 40 Copynumber: 5.5 Consensus size: 40
1110 ACCCAAGTAT
* * *
1120 CTTCGGGATTTAG-CCGGATATAGCAACTCGCACAAAT-C
1 CTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGC
* * **
1158 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCATGAATGC
1 CTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGC
*
1198 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGC
*
1238 CTTCGGGACTTAGCCCGG-TATAGCAACTACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTAACTA---GCACAAATGC
*
1280 CTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGC
1320 CTTC-GGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
1341 CATCCGAATA
Statistics
Matches: 163, Mismatches: 14, Indels: 11
0.87 0.07 0.06
Matches are distributed among these distances:
38 11 0.07
39 45 0.28
40 70 0.43
42 28 0.17
43 9 0.06
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGC
Found at i:9410 original size:40 final size:40
Alignment explanation
Indices: 9332--9511 Score: 212
Period size: 40 Copynumber: 4.5 Consensus size: 40
9322 ACCCAAGTAT
* *
9332 CTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* **
9371 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCATGAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
9411 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
*
9451 CTTCGGGACTTAGCCCGGGTATAG-CAACTACTCGCACAAA---
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTA---GCACAAATGC
9491 -TTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
9512 CATCCGAATA
Statistics
Matches: 125, Mismatches: 10, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
39 32 0.26
40 85 0.68
41 1 0.01
43 7 0.06
ACGTcount: A:0.26, C:0.27, G:0.24, T:0.24
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:42086 original size:39 final size:40
Alignment explanation
Indices: 42009--42155 Score: 120
Period size: 40 Copynumber: 3.7 Consensus size: 40
41999 TAGCTCCTCG
* * *
42009 TTCAAGTGCCTTCGGGACATAGCCCGG-TTATAGTAACTCA
1 TTCAA-TGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
* *
42049 TTCAATGCCTTCGGGACTTAACCCGGATTTTA-AAACTCG
1 TTCAATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
** * * * *
42088 CACGAATGCCTTCGGGACTTAACCCGGAAT-TAGTATCTCG
1 TTC-AATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
** *
42128 CACAAAGGCCTTCGGGACTTAACCCGGA
1 TTC-AATGCCTTCGGGACTTAACCCGGA
42156 ATTAATAACT
Statistics
Matches: 92, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
39 27 0.29
40 65 0.71
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
TTCAATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
Found at i:42166 original size:80 final size:80
Alignment explanation
Indices: 42055--42235 Score: 219
Period size: 80 Copynumber: 2.3 Consensus size: 80
42045 CTCATTCAAT
* * *
42055 GCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAATGCCTTCGGGA-CTTAACCCGGA-AT
1 GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTC-GGATCTTAACCCGGATA-
*
42118 TAGT-A-TCTCGCACAAA
64 TAGTCACT-TAGCACAAA
**
42134 GGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACAAATACCTTCGGATCTTAGTCCGGATA
1 -GCCTTCGGGACTTAACCCGGATATTAA-AACTCGCACAAATACCTTCGGATCTTAACCCGGATA
42198 TAGTCACTTAGCACAAA
64 TAGTCACTTAGCACAAA
*
42215 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
42236 CAGCATTCAA
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
79 7 0.08
80 71 0.80
81 10 0.11
82 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.24
Consensus pattern (80 bp):
GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTCGGATCTTAACCCGGATATA
GTCACTTAGCACAAA
Found at i:42195 original size:40 final size:40
Alignment explanation
Indices: 42052--42235 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
42042 TAACTCATTC
* *
42052 AATGCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA
* *
42092 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
*
42132 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
* ** * * *
42172 AATACCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAATAAC-TCGCACA
*
42213 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
42236 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 16, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
39 8 0.07
40 103 0.84
41 11 0.09
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
Done.