Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3046
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: 29371
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Found at i:320 original size:20 final size:17
Alignment explanation
Indices: 278--323 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
268 GATTAAATTA
278 CGGTCGCGGTCGCGTTTT
1 CGGTCGC-GTCGCGTTTT
*
296 CGGTCGCGTCGCGTTGT
1 CGGTCGCGTCGCGTTTT
313 -GGTCG-GTCGCG
1 CGGTCGCGTCGCG
324 GACATAACGG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 6 0.22
16 5 0.19
17 9 0.33
18 7 0.26
ACGTcount: A:0.00, C:0.28, G:0.43, T:0.28
Consensus pattern (17 bp):
CGGTCGCGTCGCGTTTT
Found at i:14007 original size:138 final size:138
Alignment explanation
Indices: 13831--14090 Score: 475
Period size: 138 Copynumber: 1.9 Consensus size: 138
13821 GAAAAAGGAA
* *
13831 AATTGCTGATTAGACCTTGAACTTTTACTATCTATGCAATCTAACCCTAGTAAGTTTGTAGGGTT
1 AATTGCTGATTAGACCTTGAACTTTTACTATCTATGCAATCTAACCCTAGTAAGTTCGTACGGTT
13896 TAAATTAGAATAATTTGTAATGTTATATTTGACTCGTGGATTATGATTTGTTGAATAATCAGCAA
66 TAAATTAGAATAATTTGTAATGTTATATTTGACTCGTGGATTATGATTTGTTGAATAATCAGCAA
13961 TTACAAAT
131 TTACAAAT
* *
13969 AATTGCTGATTAGACCTTGAACTTTTACTATCTCTGCAATCTAACCCTTGTAAGTTCGTACGGTT
1 AATTGCTGATTAGACCTTGAACTTTTACTATCTATGCAATCTAACCCTAGTAAGTTCGTACGGTT
*
14034 TAAATTAGAATAATTTGTAATGTTATATTTGACTTGTGGATTATGATTTGTTGAATA
66 TAAATTAGAATAATTTGTAATGTTATATTTGACTCGTGGATTATGATTTGTTGAATA
14091 TTCGTATTTT
Statistics
Matches: 117, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
138 117 1.00
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.41
Consensus pattern (138 bp):
AATTGCTGATTAGACCTTGAACTTTTACTATCTATGCAATCTAACCCTAGTAAGTTCGTACGGTT
TAAATTAGAATAATTTGTAATGTTATATTTGACTCGTGGATTATGATTTGTTGAATAATCAGCAA
TTACAAAT
Found at i:16603 original size:25 final size:25
Alignment explanation
Indices: 16574--16632 Score: 91
Period size: 25 Copynumber: 2.4 Consensus size: 25
16564 GAAAAATATG
*
16574 TATTGGGTTGGATTGAATCCTAAAA
1 TATTGGGTTGGATTGAATCATAAAA
* *
16599 TATTGGGTTGGATTGAATTATAAAG
1 TATTGGGTTGGATTGAATCATAAAA
16624 TATTGGGTT
1 TATTGGGTT
16633 AAAAGTACAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.29, C:0.03, G:0.27, T:0.41
Consensus pattern (25 bp):
TATTGGGTTGGATTGAATCATAAAA
Found at i:17539 original size:70 final size:70
Alignment explanation
Indices: 17342--17517 Score: 255
Period size: 70 Copynumber: 2.5 Consensus size: 70
17332 ACATATCGAT
* * *
17342 AATCTCTACTAAT-TTAAAGCCCTGATTGAGTTTCGTGTCACTAGTCAAGTGAGACCAACTCAAT
1 AATCTCTACTAATATTAAAGCCCTGATTGAGTTTGGTGTCACAAGTCAAGTGACACCAACTCAAT
17406 TAATA
66 TAATA
* * * *
17411 AATCTCTACTAATATTAAAGCCCTGATTAAGTTTGATGTCACAAGTCAAGAGACACCAACTTAAT
1 AATCTCTACTAATATTAAAGCCCTGATTGAGTTTGGTGTCACAAGTCAAGTGACACCAACTCAAT
17476 TAATA
66 TAATA
* * *
17481 AATCTCTACTAATATTAAGGCCTTGACTGAGTTTGGT
1 AATCTCTACTAATATTAAAGCCCTGATTGAGTTTGGT
17518 ATTAGGAGTT
Statistics
Matches: 94, Mismatches: 12, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
69 13 0.14
70 81 0.86
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.32
Consensus pattern (70 bp):
AATCTCTACTAATATTAAAGCCCTGATTGAGTTTGGTGTCACAAGTCAAGTGACACCAACTCAAT
TAATA
Found at i:19261 original size:15 final size:15
Alignment explanation
Indices: 19241--19275 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
19231 TATTTTAATA
19241 TATTATCATCATTAT
1 TATTATCATCATTAT
*
19256 TATTATCATTATTAT
1 TATTATCATCATTAT
19271 TATTA
1 TATTA
19276 ACCTTATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.57
Consensus pattern (15 bp):
TATTATCATCATTAT
Found at i:19271 original size:12 final size:12
Alignment explanation
Indices: 19241--19273 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
19231 TATTTTAATA
*
19241 TATTATCATCAT
1 TATTATTATCAT
19253 TATTATTATCAT
1 TATTATTATCAT
19265 TATTATTAT
1 TATTATTAT
19274 TAACCTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.33, C:0.09, G:0.00, T:0.58
Consensus pattern (12 bp):
TATTATTATCAT
Found at i:19282 original size:15 final size:15
Alignment explanation
Indices: 19241--19287 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
19231 TATTTTAATA
* *
19241 TATTATCATCATTAT
1 TATTAACATTATTAT
*
19256 TATTATCATTATTAT
1 TATTAACATTATTAT
*
19271 TATTAACCTTATTAT
1 TATTAACATTATTAT
19286 TA
1 TA
19288 CTAGTAACCA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.34, C:0.11, G:0.00, T:0.55
Consensus pattern (15 bp):
TATTAACATTATTAT
Done.