Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008492.1 Corchorus capsularis cultivar CVL-1 contig08513, whole genome shotgun sequence
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: 16639
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Found at i:2000 original size:10 final size:12
Alignment explanation
Indices: 1982--2012 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
1972 AAAAGACCAG
*
1982 GAAAAAAAAAAA
1 GAAAAAAAACAA
1994 GAAAAAAAACAA
1 GAAAAAAAACAA
2006 GAAAAAA
1 GAAAAAA
2013 GGAAACGCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.87, C:0.03, G:0.10, T:0.00
Consensus pattern (12 bp):
GAAAAAAAACAA
Found at i:2284 original size:2 final size:2
Alignment explanation
Indices: 2277--2306 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2267 GATACACTAT
*
2277 TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2307 ATTAGTCATC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:4312 original size:28 final size:28
Alignment explanation
Indices: 4281--4344 Score: 85
Period size: 28 Copynumber: 2.3 Consensus size: 28
4271 ACGACTCTCA
4281 CTCTCTCTGTTTA-TACGTCTCTCACTCT
1 CTCTCTCTGTTTATTACGTCT-TCACTCT
* *
4309 CTCTCTCTGTTTATTGCTTCTTCACTCT
1 CTCTCTCTGTTTATTACGTCTTCACTCT
*
4337 CTTTCTCT
1 CTCTCTCT
4345 CCCTCTCTGT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
28 27 0.84
29 5 0.16
ACGTcount: A:0.08, C:0.34, G:0.06, T:0.52
Consensus pattern (28 bp):
CTCTCTCTGTTTATTACGTCTTCACTCT
Found at i:7610 original size:17 final size:17
Alignment explanation
Indices: 7581--7613 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
7571 CTAGATTGAC
7581 ACTTATTATTTTCTTTA
1 ACTTATTATTTTCTTTA
7598 ACTT-TTATGTTTCTTT
1 ACTTATTAT-TTTCTTT
7614 TTCCATCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.18, C:0.12, G:0.03, T:0.67
Consensus pattern (17 bp):
ACTTATTATTTTCTTTA
Found at i:14202 original size:13 final size:13
Alignment explanation
Indices: 14166--14194 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
14156 TTTCTTGGTA
14166 CATTCTACTTTTC
1 CATTCTACTTTTC
14179 CATTCTACTTTTC
1 CATTCTACTTTTC
14192 CAT
1 CAT
14195 ATTGCTTTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.31, G:0.00, T:0.52
Consensus pattern (13 bp):
CATTCTACTTTTC
Found at i:16426 original size:7 final size:7
Alignment explanation
Indices: 16410--16639 Score: 303
Period size: 7 Copynumber: 34.9 Consensus size: 7
16400 GTCCATTTAG
*
16410 TTAGGTT
1 TTAGGGT
16417 TTAGGGT
1 TTAGGGT
16424 TTAGGGT
1 TTAGGGT
16431 TTAGGGTT
1 TTAGGG-T
16439 TTAGGG-
1 TTAGGGT
16445 TTAGGG-
1 TTAGGGT
16451 TTAGGGT
1 TTAGGGT
16458 TTAGGG-
1 TTAGGGT
16464 TTAGGGT
1 TTAGGGT
16471 TTAGGGT
1 TTAGGGT
16478 TTAGGGT
1 TTAGGGT
16485 TTAGGG-
1 TTAGGGT
16491 TTAGGG-
1 TTAGGGT
16497 TTAGGGT
1 TTAGGGT
*
16504 TGAGGGT
1 TTAGGGT
*
16511 TGAGGGT
1 TTAGGGT
16518 TTAGGG-
1 TTAGGGT
16524 TTAGGG-
1 TTAGGGT
16530 TTAGGG-
1 TTAGGGT
16536 TTAGGGT
1 TTAGGGT
16543 TTAGGGT
1 TTAGGGT
16550 TTAGGG-
1 TTAGGGT
16556 TTAGGG-
1 TTAGGGT
16562 TTAGGG-
1 TTAGGGT
16568 TTAGGGT
1 TTAGGGT
16575 TTAGGG-
1 TTAGGGT
16581 TTAGGGT
1 TTAGGGT
16588 TTAGGGT
1 TTAGGGT
16595 TTAGGG-
1 TTAGGGT
16601 TTAGGG-
1 TTAGGGT
16607 TTAGGG-
1 TTAGGGT
16613 TTAGGGT
1 TTAGGGT
16620 TTAGGG-
1 TTAGGGT
16626 TTAGGGTT
1 TTAGGG-T
16634 TTAGGG
1 TTAGGG
Statistics
Matches: 210, Mismatches: 3, Indels: 19
0.91 0.01 0.08
Matches are distributed among these distances:
6 96 0.46
7 101 0.48
8 13 0.06
ACGTcount: A:0.15, C:0.00, G:0.46, T:0.39
Consensus pattern (7 bp):
TTAGGGT
Found at i:16450 original size:6 final size:6
Alignment explanation
Indices: 16417--16633 Score: 281
Period size: 6 Copynumber: 33.3 Consensus size: 6
16407 TAGTTAGGTT
16417 TTAGGG TTTAGGG TTTAGGG TTTTAGGG TTAGGG TTAGGG TTTAGGG TTAGGG
1 TTAGGG -TTAGGG -TTAGGG --TTAGGG TTAGGG TTAGGG -TTAGGG TTAGGG
16470 TTTAGGG TTTAGGG TTTAGGG TTAGGG TTAGGG TTGAGGG TTGAGGG TTTAGGG
1 -TTAGGG -TTAGGG -TTAGGG TTAGGG TTAGGG TT-AGGG TT-AGGG -TTAGGG
16524 TTAGGG TTAGGG TTAGGG TTTAGGG TTTAGGG TTAGGG TTAGGG TTAGGG
1 TTAGGG TTAGGG TTAGGG -TTAGGG -TTAGGG TTAGGG TTAGGG TTAGGG
16574 TTTAGGG TTAGGG TTTAGGG TTTAGGG TTAGGG TTAGGG TTAGGG TTTAGGG
1 -TTAGGG TTAGGG -TTAGGG -TTAGGG TTAGGG TTAGGG TTAGGG -TTAGGG
16626 TTAGGG TT
1 TTAGGG TT
16634 TTAGGG
Statistics
Matches: 201, Mismatches: 0, Indels: 19
0.91 0.00 0.09
Matches are distributed among these distances:
6 100 0.50
7 92 0.46
8 9 0.04
ACGTcount: A:0.15, C:0.00, G:0.47, T:0.38
Consensus pattern (6 bp):
TTAGGG
Found at i:16634 original size:13 final size:13
Alignment explanation
Indices: 16409--16633 Score: 295
Period size: 13 Copynumber: 17.2 Consensus size: 13
16399 GGTCCATTTA
*
16409 GTTAGGTTTTAGG
1 GTTAGGGTTTAGG
16422 GTTTAGGGTTTAGG
1 G-TTAGGGTTTAGG
16436 GTTTTAGGG-TTAGG
1 G--TTAGGGTTTAGG
16450 GTTAGGGTTTAGG
1 GTTAGGGTTTAGG
16463 GTTAGGGTTTAGG
1 GTTAGGGTTTAGG
16476 GTTTAGGGTTTAGG
1 G-TTAGGGTTTAGG
16490 GTTAGGG-TTAGG
1 GTTAGGGTTTAGG
*
16502 GTTGAGGGTTGAGG
1 GTT-AGGGTTTAGG
16516 GTTTAGGG-TTAGG
1 G-TTAGGGTTTAGG
16529 GTTAGGG-TTAGG
1 GTTAGGGTTTAGG
16541 GTTTAGGGTTTAGG
1 G-TTAGGGTTTAGG
16555 GTTAGGG-TTAGG
1 GTTAGGGTTTAGG
16567 GTTAGGGTTTAGG
1 GTTAGGGTTTAGG
16580 GTTAGGGTTTAGG
1 GTTAGGGTTTAGG
16593 GTTTAGGG-TTAGG
1 G-TTAGGGTTTAGG
16606 GTTAGGG-TTAGG
1 GTTAGGGTTTAGG
16618 GTTTAGGG-TTAGG
1 G-TTAGGGTTTAGG
16631 GTT
1 GTT
16634 TTAGGG
Statistics
Matches: 197, Mismatches: 3, Indels: 25
0.88 0.01 0.11
Matches are distributed among these distances:
12 52 0.26
13 84 0.43
14 52 0.26
15 9 0.05
ACGTcount: A:0.15, C:0.00, G:0.46, T:0.39
Consensus pattern (13 bp):
GTTAGGGTTTAGG
Done.