Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_1914
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: 26630
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32
Found at i:1369 original size:48 final size:48
Alignment explanation
Indices: 1314--1419 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
1304 TTGTCTTTTC
*
1314 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
1362 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
1410 TTTCTTTTTC
1 TTTCTTTTTC
1420 CATGACACTC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:2327 original size:27 final size:26
Alignment explanation
Indices: 2303--2354 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
2293 TTCATTTCTT
2303 CTTTTTGGCTTGATTTTTTTTTTTCAG
1 CTTTTT-GCTTGATTTTTTTTTTTCAG
** *
2330 CTTTTTTTTTGAATTTTTTTTTTCA
1 CTTTTTGCTTGATTTTTTTTTTTCA
2355 ATCAATTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 16 0.73
27 6 0.27
ACGTcount: A:0.10, C:0.10, G:0.10, T:0.71
Consensus pattern (26 bp):
CTTTTTGCTTGATTTTTTTTTTTCAG
Found at i:2334 original size:13 final size:13
Alignment explanation
Indices: 2318--2379 Score: 54
Period size: 13 Copynumber: 4.5 Consensus size: 13
2308 TGGCTTGATT
*
2318 TTTTTTTTTCAGC
1 TTTTTTTTTCAAC
* *
2331 TTTTTTTTTGAAT
1 TTTTTTTTTCAAC
2344 TTTTTTTTTCAATC
1 TTTTTTTTTCAA-C
2358 AATTTTTTTTTCGAA-
1 --TTTTTTTTTC-AAC
2373 TTTTTTT
1 TTTTTTT
2380 CGAATATTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
13 28 0.70
16 10 0.25
17 2 0.05
ACGTcount: A:0.15, C:0.08, G:0.05, T:0.73
Consensus pattern (13 bp):
TTTTTTTTTCAAC
Found at i:9497 original size:20 final size:20
Alignment explanation
Indices: 9474--9527 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
9464 AACTAAGAAG
9474 GAGCTGAATGAGCTAAGGA-T
1 GAGCTGAATGAGCT-AGGATT
* *
9494 GAGCTCAATGAGCTATGATT
1 GAGCTGAATGAGCTAGGATT
9514 GAGCTGAATGAGCT
1 GAGCTGAATGAGCT
9528 TGAAGTAGAG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 3 0.10
20 27 0.90
ACGTcount: A:0.31, C:0.13, G:0.31, T:0.24
Consensus pattern (20 bp):
GAGCTGAATGAGCTAGGATT
Found at i:17163 original size:13 final size:13
Alignment explanation
Indices: 17145--17169 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17135 TGTAGCTTCG
17145 AAAAAAAAAGTTA
1 AAAAAAAAAGTTA
17158 AAAAAAAAAGTT
1 AAAAAAAAAGTT
17170 TCGAAAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (13 bp):
AAAAAAAAAGTTA
Found at i:21041 original size:23 final size:22
Alignment explanation
Indices: 20994--21047 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
20984 GAGTGATAAA
*
20994 AAAAGAGAGAGTGATTCAAAAG
1 AAAAGAAAGAGTGATTCAAAAG
*
21016 AAAAGAAACGAGTGA-TGAAAATG
1 AAAAGAAA-GAGTGATTCAAAA-G
21039 AAAA-AAAGA
1 AAAAGAAAGA
21048 ATTTGTTGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
21 2 0.07
22 15 0.54
23 11 0.39
ACGTcount: A:0.61, C:0.04, G:0.24, T:0.11
Consensus pattern (22 bp):
AAAAGAAAGAGTGATTCAAAAG
Done.