Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014620.1 Corchorus capsularis cultivar CVL-1 contig14641, 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: 2770
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.36
Found at i:1297 original size:44 final size:44
Alignment explanation
Indices: 1261--1349 Score: 153
Period size: 44 Copynumber: 2.0 Consensus size: 44
1251 ACCATTTTAC
1261 CTTTTTACT-CTTAATATTTCACTCTTTACTGATTACCTTCTTA
1 CTTTTTACTGCTTAATATTTCACTCTTTACTGATTACCTTCTTA
* *
1304 CTTTTTACTGGTTACTATTTCACTCTTTACTGATTACCTTCTTA
1 CTTTTTACTGCTTAATATTTCACTCTTTACTGATTACCTTCTTA
1348 CT
1 CT
1350 CTTACTGATT
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
43 9 0.21
44 34 0.79
ACGTcount: A:0.19, C:0.24, G:0.04, T:0.53
Consensus pattern (44 bp):
CTTTTTACTGCTTAATATTTCACTCTTTACTGATTACCTTCTTA
Found at i:1311 original size:22 final size:22
Alignment explanation
Indices: 1285--1362 Score: 90
Period size: 22 Copynumber: 3.6 Consensus size: 22
1275 TATTTCACTC
1285 TTTACTGATTACCTTCTTACTT
1 TTTACTGATTACCTTCTTACTT
* *
1307 TTTACTGGTTA-CTAT-TTCACTC
1 TTTACTGATTACCT-TCTT-ACTT
1329 TTTACTGATTACCTTCTTAC-T
1 TTTACTGATTACCTTCTTACTT
*
1350 CTTACTGATTACC
1 TTTACTGATTACC
1363 CTTTACTCTT
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
21 16 0.34
22 27 0.57
23 4 0.09
ACGTcount: A:0.19, C:0.24, G:0.06, T:0.50
Consensus pattern (22 bp):
TTTACTGATTACCTTCTTACTT
Found at i:1365 original size:22 final size:20
Alignment explanation
Indices: 1281--1372 Score: 87
Period size: 22 Copynumber: 4.3 Consensus size: 20
1271 TTAATATTTC
1281 ACTCTTTACTGATTACCTTCTT
1 ACTC-TTACTGATTACCTT-TT
* *
1303 ACTTTTTACTGGTTA-CTATTT
1 AC-TCTTACTGATTACCT-TTT
1324 CACTCTTTACTGATTACCTTCTT
1 -ACTC-TTACTGATTACCTT-TT
*
1347 ACTCTTACTGATTACCCTTT
1 ACTCTTACTGATTACCTTTT
1367 ACTCTT
1 ACTCTT
1373 TATCATTCTT
Statistics
Matches: 59, Mismatches: 5, Indels: 14
0.76 0.06 0.18
Matches are distributed among these distances:
20 8 0.14
21 18 0.31
22 28 0.47
23 5 0.08
ACGTcount: A:0.18, C:0.26, G:0.05, T:0.50
Consensus pattern (20 bp):
ACTCTTACTGATTACCTTTT
Found at i:1367 original size:35 final size:34
Alignment explanation
Indices: 1328--1410 Score: 85
Period size: 35 Copynumber: 2.4 Consensus size: 34
1318 CTATTTCACT
* *
1328 CTTTACTGATTACCTTCTTACTCTTACTGATTACC
1 CTTTACTGATTACATTCTTACT-TTACTCATTACC
** * *
1363 CTTTACTCTTTATCATTCTTCCTTTACTCATTACT
1 CTTTACTGATTA-CATTCTTACTTTACTCATTACC
*
1398 CTTTGCTGATTAC
1 CTTTACTGATTAC
1411 TTTTACCTGA
Statistics
Matches: 38, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
34 1 0.03
35 29 0.76
36 8 0.21
ACGTcount: A:0.18, C:0.28, G:0.05, T:0.49
Consensus pattern (34 bp):
CTTTACTGATTACATTCTTACTTTACTCATTACC
Found at i:1465 original size:14 final size:14
Alignment explanation
Indices: 1448--1488 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
1438 TTTGCCATTT
*
1448 TTACTTTTTATTGA
1 TTACTTTTTACTGA
*
1462 TTACTCTTTACTGA
1 TTACTTTTTACTGA
1476 TTACTATTTTACT
1 TTACT-TTTTACT
1489 CTCTTGAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
14 17 0.74
15 6 0.26
ACGTcount: A:0.22, C:0.15, G:0.05, T:0.59
Consensus pattern (14 bp):
TTACTTTTTACTGA
Found at i:1509 original size:26 final size:25
Alignment explanation
Indices: 1475--1572 Score: 97
Period size: 26 Copynumber: 3.6 Consensus size: 25
1465 CTCTTTACTG
1475 ATTACTATTTTACTCTCTTGAATTTA
1 ATTACTATTTTACTCT-TTGAATTTA
1501 ATTACTATTTTCACTCTTTGAATTTA
1 ATTACTATTTT-ACTCTTTGAATTTA
*
1527 ATCACCATTTGTCATTTTACTCTTTGAATTTA
1 ATTA-C-----T-ATTTTACTCTTTGAATTTA
*
1559 ATTACCATTTTACT
1 ATTACTATTTTACT
1573 ATTTTACTCT
Statistics
Matches: 61, Mismatches: 3, Indels: 17
0.75 0.04 0.21
Matches are distributed among these distances:
25 8 0.13
26 23 0.38
27 6 0.10
31 1 0.02
32 18 0.30
33 5 0.08
ACGTcount: A:0.27, C:0.17, G:0.04, T:0.52
Consensus pattern (25 bp):
ATTACTATTTTACTCTTTGAATTTA
Found at i:1582 original size:33 final size:33
Alignment explanation
Indices: 1502--1584 Score: 125
Period size: 32 Copynumber: 2.5 Consensus size: 33
1492 TTGAATTTAA
1502 TTACTATTTTCACTCTTTGAATTTAATCACCATT
1 TTACTATTTT-ACTCTTTGAATTTAATCACCATT
*
1536 TGT-C-ATTTTACTCTTTGAATTTAATTACCATT
1 T-TACTATTTTACTCTTTGAATTTAATCACCATT
1568 TTACTATTTTACTCTTT
1 TTACTATTTTACTCTTT
1585 ACCGATTACT
Statistics
Matches: 45, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
31 1 0.02
32 24 0.53
33 17 0.38
34 2 0.04
35 1 0.02
ACGTcount: A:0.24, C:0.18, G:0.04, T:0.54
Consensus pattern (33 bp):
TTACTATTTTACTCTTTGAATTTAATCACCATT
Done.