Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold7613.1
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: 6513
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Found at i:422 original size:13 final size:13
Alignment explanation
Indices: 404--443 Score: 71
Period size: 13 Copynumber: 3.1 Consensus size: 13
394 TAAGTAGATT
404 TTTGAAAAAAAAA
1 TTTGAAAAAAAAA
417 TTTGAAAAAAAAA
1 TTTGAAAAAAAAA
*
430 ATTGAAAAAAAAA
1 TTTGAAAAAAAAA
443 T
1 T
444 CAAAAAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (13 bp):
TTTGAAAAAAAAA
Found at i:426 original size:12 final size:11
Alignment explanation
Indices: 409--464 Score: 58
Period size: 11 Copynumber: 4.7 Consensus size: 11
399 AGATTTTTGA
409 AAAAAAAATTTG
1 AAAAAAAA-TTG
421 AAAAAAAAAATTG
1 --AAAAAAAATTG
* *
434 AAAAAAAAATC
1 AAAAAAAATTG
445 AAAAAAAATTG
1 AAAAAAAATTG
456 AAAAGAAAA
1 AAAA-AAAA
465 AAAATTGTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
11 22 0.59
12 4 0.11
13 3 0.08
14 8 0.22
ACGTcount: A:0.77, C:0.02, G:0.07, T:0.14
Consensus pattern (11 bp):
AAAAAAAATTG
Found at i:448 original size:22 final size:23
Alignment explanation
Indices: 423--465 Score: 79
Period size: 22 Copynumber: 1.9 Consensus size: 23
413 AAAATTTGAA
423 AAAAAAAATTGAAAA-AAAAATC
1 AAAAAAAATTGAAAAGAAAAATC
445 AAAAAAAATTGAAAAGAAAAA
1 AAAAAAAATTGAAAAGAAAAA
466 AAATTGTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.79, C:0.02, G:0.07, T:0.12
Consensus pattern (23 bp):
AAAAAAAATTGAAAAGAAAAATC
Found at i:464 original size:13 final size:12
Alignment explanation
Indices: 405--465 Score: 72
Period size: 12 Copynumber: 5.0 Consensus size: 12
395 AAGTAGATTT
405 TTGAAAAAAAAA
1 TTGAAAAAAAAA
417 TTTGAAAAAAAAAA
1 -TTG-AAAAAAAAA
431 TTGAAAAAAAAA
1 TTGAAAAAAAAA
*
443 -T-CAAAAAAAA
1 TTGAAAAAAAAA
453 TTGAAAAGAAAAA
1 TTGAAAA-AAAAA
466 AAATTGTATA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
10 8 0.19
11 2 0.05
12 12 0.29
13 11 0.26
14 9 0.21
ACGTcount: A:0.74, C:0.02, G:0.08, T:0.16
Consensus pattern (12 bp):
TTGAAAAAAAAA
Found at i:4853 original size:84 final size:84
Alignment explanation
Indices: 4712--4879 Score: 318
Period size: 84 Copynumber: 2.0 Consensus size: 84
4702 TTCGTCCAAA
*
4712 GACTTAGTTGGCTTATCTACTAGTTAGTGGCGTCAACCTTTGTACTTTGCATCCCGAACTTATCA
1 GACTTAGTTGGCTTATCTACTAGTTAGTGGCATCAACCTTTGTACTTTGCATCCCGAACTTATCA
4777 CTTTCACCCAAAGTGTGGC
66 CTTTCACCCAAAGTGTGGC
*
4796 GACTTAGTTGGCTTATCTACTAGTTAGTGGCATCAACCTTTGTTCTTTGCATCCCGAACTTATCA
1 GACTTAGTTGGCTTATCTACTAGTTAGTGGCATCAACCTTTGTACTTTGCATCCCGAACTTATCA
4861 CTTTCACCCAAAGTGTGGC
66 CTTTCACCCAAAGTGTGGC
4880 ATTCATTTGA
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 82 1.00
ACGTcount: A:0.21, C:0.25, G:0.18, T:0.35
Consensus pattern (84 bp):
GACTTAGTTGGCTTATCTACTAGTTAGTGGCATCAACCTTTGTACTTTGCATCCCGAACTTATCA
CTTTCACCCAAAGTGTGGC
Done.