Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold737
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: 33586
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Found at i:1319 original size:40 final size:39
Alignment explanation
Indices: 1275--1449 Score: 184
Period size: 40 Copynumber: 4.6 Consensus size: 39
1265 GCCACTAGCT
*
1275 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTTGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TATAGTAACTCGCA
*
1315 CAAATGCCTTCGGGACTTAG--C-AT-TA-TAA-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTATAGTAACTCGCA
* *
1348 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAGCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTA-TAGTAACTCGCA
* ** * *
1388 CAAATGCCTTCGGGACTTAGCCCGGAATTAGCCACTAGCT
1 CAAATGCCTTCGGGACTTAGCCCGGTA-TAGTAACTCGCA
1428 CAAATG-CTCTCGGGACTTAGCC
1 CAAATGCCT-TCGGGACTTAGCC
1450 TTATCATCCG
Statistics
Matches: 117, Mismatches: 10, Indels: 16
0.82 0.07 0.11
Matches are distributed among these distances:
33 24 0.21
34 3 0.03
35 3 0.03
36 1 0.01
38 3 0.03
39 4 0.03
40 79 0.68
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAGCCCGGTATAGTAACTCGCA
Found at i:9361 original size:39 final size:39
Alignment explanation
Indices: 9276--9460 Score: 228
Period size: 40 Copynumber: 4.7 Consensus size: 39
9266 GCCACTAGCT
*
9276 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTTGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TATAGTAACTCGCA
* *
9316 CAAATGCCTTCGGGACTTAGCTCGGTATAATAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTATAGTAACTCGCA
* * *
9355 CAAATGCCTTCGGGACTTAGCCCAGAATTAGTAGCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTA-TAGTAACTCGCA
* ** * *
9395 CAAATGCCTTCGGGACTTAGCCCGGAATTAGCCACTAGCT
1 CAAATGCCTTCGGGACTTAGCCCGGTA-TAGTAACTCGCA
9435 CAAATG-CTCTCGGGACTTAGCCCGGT
1 CAAATGCCT-TCGGGACTTAGCCCGGT
9461 TATCATCCGA
Statistics
Matches: 128, Mismatches: 15, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
39 38 0.30
40 90 0.70
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAGCCCGGTATAGTAACTCGCA
Found at i:9899 original size:18 final size:18
Alignment explanation
Indices: 9876--9910 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
9866 TACACAATGG
9876 TCATGCGCATTTTTAATA
1 TCATGCGCATTTTTAATA
9894 TCATGCGCATTTTTAAT
1 TCATGCGCATTTTTAAT
9911 CACATTAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.26, C:0.17, G:0.11, T:0.46
Consensus pattern (18 bp):
TCATGCGCATTTTTAATA
Found at i:18441 original size:28 final size:28
Alignment explanation
Indices: 18361--18444 Score: 98
Period size: 28 Copynumber: 3.0 Consensus size: 28
18351 GTGAGCATGA
* * *
18361 ATATGAATGTGACTGGGCCTAACGGTCC
1 ATATGAATGTGATTGGGCCTAATGGGCC
18389 ATAT-AGATGTGATTTGGGCCTAATGGGCC
1 ATATGA-ATGTGA-TTGGGCCTAATGGGCC
* *
18418 ATATGAATATGATTGGGCTTAATGGGC
1 ATATGAATGTGATTGGGCCTAATGGGC
18445 TAGATACAGG
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
27 1 0.02
28 24 0.50
29 22 0.46
30 1 0.02
ACGTcount: A:0.26, C:0.14, G:0.30, T:0.30
Consensus pattern (28 bp):
ATATGAATGTGATTGGGCCTAATGGGCC
Found at i:25539 original size:28 final size:28
Alignment explanation
Indices: 25474--25594 Score: 179
Period size: 28 Copynumber: 4.3 Consensus size: 28
25464 GAGATTGGCG
* * * *
25474 CTAAGTGTGCGGGTTTAAATTGTACAGCA
1 CTAAGTGTGCGAGTTT-GATTATATAGCA
25503 CTAAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
25531 CTAAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
25559 CTAAGTGTGCGAGTTTGATTACATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
25587 CTGAGTGT
1 CTAAGTGT
25595 ACGGACTTAA
Statistics
Matches: 86, Mismatches: 6, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
28 71 0.83
29 15 0.17
ACGTcount: A:0.27, C:0.12, G:0.26, T:0.34
Consensus pattern (28 bp):
CTAAGTGTGCGAGTTTGATTATATAGCA
Found at i:32799 original size:8 final size:8
Alignment explanation
Indices: 32786--32828 Score: 52
Period size: 8 Copynumber: 5.2 Consensus size: 8
32776 ATTAAACCGC
32786 TTTTTATT
1 TTTTTATT
32794 TTTTTATT
1 TTTTTATT
32802 TTATTT-TT
1 TT-TTTATT
*
32810 TTTTTTTT
1 TTTTTATT
32818 TTTTTAATT
1 TTTTT-ATT
32827 TT
1 TT
32829 ATGATCATCG
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
7 3 0.10
8 21 0.68
9 7 0.23
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTTTATT
Found at i:32805 original size:13 final size:13
Alignment explanation
Indices: 32787--32830 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
32777 TTAAACCGCT
32787 TTTTATTTTTTTA
1 TTTTATTTTTTTA
32800 TTTTATTTTTTT-
1 TTTTATTTTTTTA
32812 TTTT-TTTTTTTAA
1 TTTTATTTTTTT-A
32825 TTTTAT
1 TTTTAT
32831 GATCATCGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
11 7 0.25
12 4 0.14
13 16 0.57
14 1 0.04
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTTATTTTTTTA
Done.