Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2803
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: 34782
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Found at i:1385 original size:39 final size:40
Alignment explanation
Indices: 1308--1454 Score: 120
Period size: 40 Copynumber: 3.7 Consensus size: 40
1298 TAGCTCCTCG
* * *
1308 TTCAAGTGCCTTCGGGACATAGCCCGG-TTATAGTAACTCA
1 TTCAA-TGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
* *
1348 TTCAATGCCTTCGGGACTTAACCCGGATTTTA-AAACTCG
1 TTCAATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
** * * * *
1387 CACGAATGCCTTCGGGACTTAACCCGGAAT-TAGTATCTCG
1 TTC-AATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
** *
1427 CACAAAGGCCTTCGGGACTTAACCCGGA
1 TTC-AATGCCTTCGGGACTTAACCCGGA
1455 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:1465 original size:80 final size:80
Alignment explanation
Indices: 1354--1534 Score: 219
Period size: 80 Copynumber: 2.3 Consensus size: 80
1344 CTCATTCAAT
* * *
1354 GCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAATGCCTTCGGGA-CTTAACCCGGA-AT
1 GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTC-GGATCTTAACCCGGATA-
*
1417 TAGT-A-TCTCGCACAAA
64 TAGTCACT-TAGCACAAA
**
1433 GGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACAAATACCTTCGGATCTTAGTCCGGATA
1 -GCCTTCGGGACTTAACCCGGATATTAA-AACTCGCACAAATACCTTCGGATCTTAACCCGGATA
1497 TAGTCACTTAGCACAAA
64 TAGTCACTTAGCACAAA
*
1514 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
1535 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:1494 original size:40 final size:40
Alignment explanation
Indices: 1351--1534 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
1341 TAACTCATTC
* *
1351 AATGCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA
* *
1391 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
*
1431 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
* ** * * *
1471 AATACCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAATAAC-TCGCACA
*
1512 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
1535 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
Found at i:9241 original size:39 final size:40
Alignment explanation
Indices: 9164--9310 Score: 120
Period size: 40 Copynumber: 3.7 Consensus size: 40
9154 TAGCTCCTCG
* * *
9164 TTCAAGTGCCTTCGGGACATAGCCCGG-TTATAGTAACTCA
1 TTCAA-TGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
* *
9204 TTCAATGCCTTCGGGACTTAACCCGGATTTTA-AAACTCG
1 TTCAATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
** * * * *
9243 CACGAATGCCTTCGGGACTTAACCCGGAAT-TAGTATCTCG
1 TTC-AATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
** *
9283 CACAAAGGCCTTCGGGACTTAACCCGGA
1 TTC-AATGCCTTCGGGACTTAACCCGGA
9311 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:9321 original size:80 final size:80
Alignment explanation
Indices: 9210--9390 Score: 219
Period size: 80 Copynumber: 2.3 Consensus size: 80
9200 CTCATTCAAT
* * *
9210 GCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAATGCCTTCGGGA-CTTAACCCGGA-AT
1 GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTC-GGATCTTAACCCGGATA-
*
9273 TAGT-A-TCTCGCACAAA
64 TAGTCACT-TAGCACAAA
**
9289 GGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACAAATACCTTCGGATCTTAGTCCGGATA
1 -GCCTTCGGGACTTAACCCGGATATTAA-AACTCGCACAAATACCTTCGGATCTTAACCCGGATA
9353 TAGTCACTTAGCACAAA
64 TAGTCACTTAGCACAAA
*
9370 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
9391 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:9350 original size:40 final size:40
Alignment explanation
Indices: 9207--9390 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
9197 TAACTCATTC
* *
9207 AATGCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA
* *
9247 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
*
9287 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
* ** * * *
9327 AATACCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAATAAC-TCGCACA
*
9368 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
9391 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
Found at i:11869 original size:11 final size:11
Alignment explanation
Indices: 11854--11884 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
11844 ATTTTCTTTT
11854 ATTTTTTTCAA
1 ATTTTTTTCAA
*
11865 TTTTTTTTCAA
1 ATTTTTTTCAA
11876 ATTTTTTTC
1 ATTTTTTTC
11885 TATCTTCCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.19, C:0.10, G:0.00, T:0.71
Consensus pattern (11 bp):
ATTTTTTTCAA
Found at i:11870 original size:12 final size:12
Alignment explanation
Indices: 11855--11883 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
11845 TTTTCTTTTA
11855 TTTTTTTC-AAT
1 TTTTTTTCAAAT
11866 TTTTTTTCAAAT
1 TTTTTTTCAAAT
11878 TTTTTT
1 TTTTTT
11884 CTATCTTCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 8 0.47
12 9 0.53
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTTTTCAAAT
Found at i:25306 original size:27 final size:27
Alignment explanation
Indices: 25269--25473 Score: 259
Period size: 27 Copynumber: 7.6 Consensus size: 27
25259 TAAATTGTAC
25269 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
25296 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
25323 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
25349 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
25377 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
25405 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
25432 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
25459 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
25474 GACTCAATAT
Statistics
Matches: 156, Mismatches: 19, Indels: 6
0.86 0.10 0.03
Matches are distributed among these distances:
27 133 0.85
28 23 0.15
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:25408 original size:109 final size:108
Alignment explanation
Indices: 25270--25473 Score: 320
Period size: 109 Copynumber: 1.9 Consensus size: 108
25260 AAATTGTACA
* *
25270 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGT
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGATTTGACTACGTAGCACTAAGTGT
25335 GCGAAATGAATATGAT-GCACTAAGTGTGCGAATTGACCATGCG
66 GCGAAATGAATAT-ATAGCACTAAGTGTGCGAATTGACCATGCG
*
25378 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGATTTGACTACGTAGCACTAAGTG
** * *
25443 TGCGAGTTGATTATATAGCACTGAGTGTGCG
65 TGCGAAATGAATATATAGCACTAAGTGTGCG
25474 GACTCAATAT
Statistics
Matches: 87, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
108 17 0.20
109 70 0.80
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.30
Consensus pattern (108 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGATTTGACTACGTAGCACTAAGTGT
GCGAAATGAATATATAGCACTAAGTGTGCGAATTGACCATGCG
Found at i:33302 original size:27 final size:27
Alignment explanation
Indices: 33265--33469 Score: 259
Period size: 27 Copynumber: 7.6 Consensus size: 27
33255 TAAATTGTAC
33265 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
33292 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
33319 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
33345 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
33373 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
33401 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
33428 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
33455 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
33470 GACTCAATAT
Statistics
Matches: 156, Mismatches: 19, Indels: 6
0.86 0.10 0.03
Matches are distributed among these distances:
27 133 0.85
28 23 0.15
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:33404 original size:109 final size:108
Alignment explanation
Indices: 33266--33469 Score: 320
Period size: 109 Copynumber: 1.9 Consensus size: 108
33256 AAATTGTACA
* *
33266 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGT
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGATTTGACTACGTAGCACTAAGTGT
33331 GCGAAATGAATATGAT-GCACTAAGTGTGCGAATTGACCATGCG
66 GCGAAATGAATAT-ATAGCACTAAGTGTGCGAATTGACCATGCG
*
33374 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGATTTGACTACGTAGCACTAAGTG
** * *
33439 TGCGAGTTGATTATATAGCACTGAGTGTGCG
65 TGCGAAATGAATATATAGCACTAAGTGTGCG
33470 GACTCAATAT
Statistics
Matches: 87, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
108 17 0.20
109 70 0.80
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.30
Consensus pattern (108 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGATTTGACTACGTAGCACTAAGTGT
GCGAAATGAATATATAGCACTAAGTGTGCGAATTGACCATGCG
Done.