Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021598.1 Corchorus olitorius cultivar O-4 contig21631, 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: 18399
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Found at i:268 original size:31 final size:31
Alignment explanation
Indices: 233--331 Score: 132
Period size: 31 Copynumber: 3.3 Consensus size: 31
223 AATAGGACTG
*
233 AATTGAGCGATCGCTCAAAGGTTTAGGATCA
1 AATTGAGCGATCGCTCAAAGGTTTAGGACCA
* * *
264 AATTG-GTC-A-GGTTTAAAGGTTTAGGACCA
1 AATTGAG-CGATCGCTCAAAGGTTTAGGACCA
293 AATTGAGCGATCGCTCAAAGGTTTAGGACCA
1 AATTGAGCGATCGCTCAAAGGTTTAGGACCA
324 AATTGAGC
1 AATTGAGC
332 ATTTAGCCTT
Statistics
Matches: 57, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
29 22 0.39
30 4 0.07
31 31 0.54
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.26
Consensus pattern (31 bp):
AATTGAGCGATCGCTCAAAGGTTTAGGACCA
Found at i:4474 original size:2 final size:2
Alignment explanation
Indices: 4467--4505 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
4457 TTTTCTCAAA
4467 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4506 GATAGATAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:7526 original size:7 final size:7
Alignment explanation
Indices: 7516--7546 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
7506 AAACTTTAAA
7516 ACTCCCC
1 ACTCCCC
7523 ACTCCCC
1 ACTCCCC
7530 ACTCCCC
1 ACTCCCC
7537 ACTCCCC
1 ACTCCCC
7544 ACT
1 ACT
7547 GACAGTTGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.16, C:0.68, G:0.00, T:0.16
Consensus pattern (7 bp):
ACTCCCC
Found at i:15145 original size:17 final size:19
Alignment explanation
Indices: 15125--15167 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
15115 CTTCCCCGCG
15125 CCTCTCT-C-CTTCTTCTT
1 CCTCTCTCCTCTTCTTCTT
15142 CCTCCTCTCCTCTTCTTCTT
1 CCT-CTCTCCTCTTCTTCTT
15162 CCTCTC
1 CCTCTC
15168 CTCGACGCCG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 3 0.13
18 4 0.17
19 4 0.17
20 12 0.52
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (19 bp):
CCTCTCTCCTCTTCTTCTT
Found at i:15168 original size:17 final size:17
Alignment explanation
Indices: 15128--15170 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
15118 CCCCGCGCCT
15128 CTCTCCTTCTTCTTCCTC
1 CTCTCC-TCTTCTTCCTC
*
15146 CTCTCCTCTTCTTCTTC
1 CTCTCCTCTTCTTCCTC
15163 CTCTCCTC
1 CTCTCCTC
15171 GACGCCGCCT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 18 0.75
18 6 0.25
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (17 bp):
CTCTCCTCTTCTTCCTC
Found at i:17948 original size:21 final size:21
Alignment explanation
Indices: 17924--17992 Score: 113
Period size: 21 Copynumber: 3.3 Consensus size: 21
17914 CTTAGACAAT
*
17924 TCCAATGAGCTTGAAACCTTC
1 TCCAATGAGCTTGGAACCTTC
17945 TCCAATGAGCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
17966 TCCAATGAGCTTGGAA-CTTGC
1 TCCAATGAGCTTGGAACCTT-C
17987 TCCAAT
1 TCCAAT
17993 AATCTCCTAG
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
20 3 0.07
21 43 0.93
ACGTcount: A:0.26, C:0.28, G:0.17, T:0.29
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACCTTC
Found at i:18338 original size:8 final size:8
Alignment explanation
Indices: 18325--18360 Score: 72
Period size: 8 Copynumber: 4.5 Consensus size: 8
18315 CAACAATGTG
18325 TTTTGTTT
1 TTTTGTTT
18333 TTTTGTTT
1 TTTTGTTT
18341 TTTTGTTT
1 TTTTGTTT
18349 TTTTGTTT
1 TTTTGTTT
18357 TTTT
1 TTTT
18361 TGCTTCTTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (8 bp):
TTTTGTTT
Found at i:18370 original size:24 final size:24
Alignment explanation
Indices: 18325--18370 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
18315 CAACAATGTG
* *
18325 TTTTGTTTTTTTGTTTTTTTGTTT
1 TTTTGTTTTTTTGTCTTCTTGTTT
18349 TTTTGTTTTTTT-TGCTTCTTGT
1 TTTTGTTTTTTTGT-CTTCTTGT
18371 AAAAAAGGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 1 0.05
24 18 0.95
ACGTcount: A:0.00, C:0.04, G:0.13, T:0.83
Consensus pattern (24 bp):
TTTTGTTTTTTTGTCTTCTTGTTT
Done.