Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015728.1 Corchorus capsularis cultivar CVL-1 contig15749, 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: 13685
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.33
Found at i:7469 original size:74 final size:74
Alignment explanation
Indices: 7348--7495 Score: 287
Period size: 74 Copynumber: 2.0 Consensus size: 74
7338 CTTTCTCCTT
*
7348 GAAGTCACCACAATCTTGAATTTCATGCCCCAAACCATGATATGGGCATACCTTATTCATTTCTT
1 GAAGTCACCACAATCCTGAATTTCATGCCCCAAACCATGATATGGGCATACCTTATTCATTTCTT
7413 CTCCTCCAA
66 CTCCTCCAA
7422 GAAGTCACCACAATCCTGAATTTCATGCCCCAAACCATGATATGGGCATACCTTATTCATTTCTT
1 GAAGTCACCACAATCCTGAATTTCATGCCCCAAACCATGATATGGGCATACCTTATTCATTTCTT
7487 CTCCTCCAA
66 CTCCTCCAA
7496 ATTCTCCAGG
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
74 73 1.00
ACGTcount: A:0.28, C:0.30, G:0.11, T:0.30
Consensus pattern (74 bp):
GAAGTCACCACAATCCTGAATTTCATGCCCCAAACCATGATATGGGCATACCTTATTCATTTCTT
CTCCTCCAA
Found at i:12125 original size:17 final size:19
Alignment explanation
Indices: 12093--12130 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
12083 TGCAAAATGC
*
12093 AAAGCGAAAGAAC-AAAGA
1 AAAGCGAAACAACAAAAGA
12111 AAAGC-AAACAACAAAAGA
1 AAAGCGAAACAACAAAAGA
12129 AA
1 AA
12131 TTAGTTAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.71, C:0.13, G:0.16, T:0.00
Consensus pattern (19 bp):
AAAGCGAAACAACAAAAGA
Found at i:13364 original size:15 final size:15
Alignment explanation
Indices: 13346--13376 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
13336 TTACTTTTGC
*
13346 TACTTTTATCATTTT
1 TACTTTTACCATTTT
13361 TACTTTTACCATTTT
1 TACTTTTACCATTTT
13376 T
1 T
13377 CTTACTCTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.16, G:0.00, T:0.65
Consensus pattern (15 bp):
TACTTTTACCATTTT
Found at i:13376 original size:24 final size:24
Alignment explanation
Indices: 13332--13403 Score: 63
Period size: 24 Copynumber: 2.9 Consensus size: 24
13322 ATTGATTACA
* * *
13332 ATTTTTACTTTTGCTACTTTTATC
1 ATTTTTACTTTTACCATTTTTATC
* *
13356 ATTTTTACTTTTACCATTTTTCTT
1 ATTTTTACTTTTACCATTTTTATC
*
13380 ACTCTTTTACTTAATACCATTTTT
1 A-T-TTTTACTT-TTACCATTTTT
13404 TTTAAAAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
24 20 0.51
25 1 0.03
26 8 0.21
27 10 0.26
ACGTcount: A:0.19, C:0.18, G:0.01, T:0.61
Consensus pattern (24 bp):
ATTTTTACTTTTACCATTTTTATC
Found at i:13490 original size:26 final size:26
Alignment explanation
Indices: 13453--13524 Score: 126
Period size: 26 Copynumber: 2.8 Consensus size: 26
13443 AATACCATAC
*
13453 TTTACTTGATACCATTTTTGACCCTT
1 TTTACTTAATACCATTTTTGACCCTT
*
13479 TTTACTTAATACCATTTTTGACCTTT
1 TTTACTTAATACCATTTTTGACCCTT
13505 TTTACTTAATACCATTTTTG
1 TTTACTTAATACCATTTTTG
13525 CTTAATACCA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 44 1.00
ACGTcount: A:0.22, C:0.19, G:0.06, T:0.53
Consensus pattern (26 bp):
TTTACTTAATACCATTTTTGACCCTT
Found at i:13533 original size:42 final size:40
Alignment explanation
Indices: 13477--13565 Score: 126
Period size: 42 Copynumber: 2.2 Consensus size: 40
13467 TTTTTGACCC
*
13477 TTTTTACTTAATACCATTTTTGAC-CTTTTTTACTTAATACCA
1 TTTTTACTTAATACCATTTTT-ACTCTTTTGT--TTAATACCA
*
13519 TTTTTGCTTAATACCATTTTTACTCTTTTGTTTAATACCA
1 TTTTTACTTAATACCATTTTTACTCTTTTGTTTAATACCA
13559 TTTTTAC
1 TTTTTAC
13566 CTTTTTTACT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
40 15 0.35
41 2 0.05
42 26 0.60
ACGTcount: A:0.24, C:0.18, G:0.03, T:0.55
Consensus pattern (40 bp):
TTTTTACTTAATACCATTTTTACTCTTTTGTTTAATACCA
Found at i:13538 original size:15 final size:16
Alignment explanation
Indices: 13503--13542 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
13493 TTTTTGACCT
13503 TTTTTACTTAATACCA
1 TTTTTACTTAATACCA
*
13519 TTTTTGCTTAATACCA
1 TTTTTACTTAATACCA
13535 TTTTTACT
1 TTTTTACT
13543 CTTTTGTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.25, C:0.17, G:0.03, T:0.55
Consensus pattern (16 bp):
TTTTTACTTAATACCA
Found at i:13563 original size:25 final size:23
Alignment explanation
Indices: 13520--13635 Score: 102
Period size: 24 Copynumber: 5.1 Consensus size: 23
13510 TTAATACCAT
*
13520 TTTTGCTTAATACCATTTTTACTC
1 TTTTGTTTAATACCATTTTTAC-C
13544 TTTTGTTTAATACCATTTTTACC
1 TTTTGTTTAATACCATTTTTACC
* *
13567 TTTTTTACTTAATACCATCTTTA-C
1 TTTTGT--TTAATACCATTTTTACC
13591 ------TTAATACCATTTTTTACTC
1 TTTTGTTTAATACCA-TTTTTAC-C
13610 TTTTGTTTAATACCATTTTTGACC
1 TTTTGTTTAATACCATTTTT-ACC
13634 TT
1 TT
13636 AATACCATCT
Statistics
Matches: 76, Mismatches: 4, Indels: 24
0.73 0.04 0.23
Matches are distributed among these distances:
16 9 0.12
17 5 0.07
19 1 0.01
23 6 0.08
24 30 0.39
25 25 0.33
ACGTcount: A:0.22, C:0.19, G:0.03, T:0.55
Consensus pattern (23 bp):
TTTTGTTTAATACCATTTTTACC
Found at i:13582 original size:16 final size:16
Alignment explanation
Indices: 13563--13608 Score: 65
Period size: 16 Copynumber: 2.8 Consensus size: 16
13553 ATACCATTTT
13563 TACCTTTTTTACTTAA
1 TACCTTTTTTACTTAA
* *
13579 TACCATCTTTACTTAA
1 TACCTTTTTTACTTAA
13595 TACCATTTTTTACT
1 TACC-TTTTTTACT
13609 CTTTTGTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
16 18 0.72
17 7 0.28
ACGTcount: A:0.26, C:0.22, G:0.00, T:0.52
Consensus pattern (16 bp):
TACCTTTTTTACTTAA
Found at i:13582 original size:65 final size:66
Alignment explanation
Indices: 13415--13635 Score: 322
Period size: 66 Copynumber: 3.3 Consensus size: 66
13405 TTAAAAAAAA
* * *
13415 TTAATACCATTTTTTGACC-TTCTTACTTAATACCATACTTTACTTGATACCATTTTTGACCCTT
1 TTAATACCA-TTTTTGACCTTTTTTACTTAATACCAT-CTTTACTTAATACCATTTTT-ACTCTT
13479 TT-T
63 TTGT
* *
13482 ACTTAATACCATTTTTGACCTTTTTTACTTAATACCATTTTTGCTTAATACCATTTTTACTCTTT
1 --TTAATACCATTTTTGACCTTTTTTACTTAATACCATCTTTACTTAATACCATTTTTACTCTTT
13547 TGT
64 TGT
13550 TTAATACCATTTTT-ACCTTTTTTACTTAATACCATCTTTACTTAATACCATTTTTTACTCTTTT
1 TTAATACCATTTTTGACCTTTTTTACTTAATACCATCTTTACTTAATACCA-TTTTTACTCTTTT
13614 GT
65 GT
13616 TTAATACCATTTTTGACCTT
1 TTAATACCATTTTTGACCTT
13636 AATACCATCT
Statistics
Matches: 141, Mismatches: 7, Indels: 10
0.89 0.04 0.06
Matches are distributed among these distances:
65 34 0.24
66 43 0.30
67 12 0.09
68 27 0.19
69 25 0.18
ACGTcount: A:0.24, C:0.20, G:0.04, T:0.52
Consensus pattern (66 bp):
TTAATACCATTTTTGACCTTTTTTACTTAATACCATCTTTACTTAATACCATTTTTACTCTTTTG
T
Found at i:13603 original size:41 final size:42
Alignment explanation
Indices: 13550--13650 Score: 127
Period size: 41 Copynumber: 2.4 Consensus size: 42
13540 ACTCTTTTGT
*
13550 TTAATACCATTTTTAC-CTTTTTTACTTAATACCATCTTT-A-C
1 TTAATACCATTTTTACTCTTTTGT--TTAATACCATCTTTGACC
*
13591 TTAATACCATTTTTTACTCTTTTGTTTAATACCATTTTTGACC
1 TTAATACCA-TTTTTACTCTTTTGTTTAATACCATCTTTGACC
*
13634 TTAATACCATCTTTACT
1 TTAATACCATTTTTACT
13651 TGATACCATT
Statistics
Matches: 53, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
41 22 0.42
42 15 0.28
43 16 0.30
ACGTcount: A:0.26, C:0.21, G:0.02, T:0.51
Consensus pattern (42 bp):
TTAATACCATTTTTACTCTTTTGTTTAATACCATCTTTGACC
Found at i:13639 original size:18 final size:16
Alignment explanation
Indices: 13616--13662 Score: 58
Period size: 18 Copynumber: 2.8 Consensus size: 16
13606 ACTCTTTTGT
13616 TTAATACCATTTTTGACC
1 TTAATACCATTTTT-A-C
*
13634 TTAATACCATCTTTAC
1 TTAATACCATTTTTAC
*
13650 TTGATACCATTTT
1 TTAATACCATTTT
13663 ACTCTCCATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
16 12 0.46
17 1 0.04
18 13 0.50
ACGTcount: A:0.28, C:0.21, G:0.04, T:0.47
Consensus pattern (16 bp):
TTAATACCATTTTTAC
Done.