Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015307.1 Corchorus capsularis cultivar CVL-1 contig15328, 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: 42017
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Found at i:239 original size:12 final size:14
Alignment explanation
Indices: 222--254 Score: 52
Period size: 12 Copynumber: 2.5 Consensus size: 14
212 GACCCGTACT
222 CTTCTTCTT-AAC-
1 CTTCTTCTTCAACG
234 CTTCTTCTTCAACG
1 CTTCTTCTTCAACG
248 CTTCTTC
1 CTTCTTC
255 CCTCTGCCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 9 0.47
13 3 0.16
14 7 0.37
ACGTcount: A:0.12, C:0.36, G:0.03, T:0.48
Consensus pattern (14 bp):
CTTCTTCTTCAACG
Found at i:2159 original size:20 final size:20
Alignment explanation
Indices: 2134--2172 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2124 AAAAAGACCA
2134 CCAATTTGCAAATCAAATGT
1 CCAATTTGCAAATCAAATGT
*
2154 CCAATTTGTAAATCAAATG
1 CCAATTTGCAAATCAAATG
2173 CCTTGTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.31
Consensus pattern (20 bp):
CCAATTTGCAAATCAAATGT
Found at i:2387 original size:14 final size:14
Alignment explanation
Indices: 2368--2397 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
2358 TGATAGTAAT
2368 CTAAATGGACTAAA
1 CTAAATGGACTAAA
2382 CTAAATGGACTAAA
1 CTAAATGGACTAAA
2396 CT
1 CT
2398 TAATATGCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.47, C:0.17, G:0.13, T:0.23
Consensus pattern (14 bp):
CTAAATGGACTAAA
Found at i:3760 original size:33 final size:32
Alignment explanation
Indices: 3663--3767 Score: 129
Period size: 33 Copynumber: 3.2 Consensus size: 32
3653 TTGAAGAGAG
*
3663 TGTTTTAGATGTTGTTTGCGATGATACTAAACC
1 TGTTTTAG-TGTTGTTTGCGATGATACTAAATC
* * * *
3696 TAATTTGAGTGTTGTTTGCAATGACACTAAATC
1 T-GTTTTAGTGTTGTTTGCGATGATACTAAATC
*
3729 TGTTTTAAGTGTTGTTTGTGATGATACTAAATC
1 TGTTTT-AGTGTTGTTTGCGATGATACTAAATC
3762 TGTTTT
1 TGTTTT
3768 GGATGCTAAT
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
32 3 0.05
33 52 0.87
34 5 0.08
ACGTcount: A:0.25, C:0.10, G:0.20, T:0.46
Consensus pattern (32 bp):
TGTTTTAGTGTTGTTTGCGATGATACTAAATC
Found at i:3830 original size:33 final size:33
Alignment explanation
Indices: 3783--3868 Score: 127
Period size: 33 Copynumber: 2.6 Consensus size: 33
3773 CTAATTGTGA
* * *
3783 TGAAAACAAATCTGTTTTGGTTGATCATAGCAT
1 TGAAAATAATTCTGTTTTGGTTGATCATAACAT
* *
3816 TGCAAATAATTCTGTTTTGGTTGATCATAATAT
1 TGAAAATAATTCTGTTTTGGTTGATCATAACAT
3849 TGAAAATAATTCTGTTTTGG
1 TGAAAATAATTCTGTTTTGG
3869 GTGAAAAGAA
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.31, C:0.09, G:0.17, T:0.42
Consensus pattern (33 bp):
TGAAAATAATTCTGTTTTGGTTGATCATAACAT
Found at i:24736 original size:8 final size:8
Alignment explanation
Indices: 24723--24764 Score: 56
Period size: 8 Copynumber: 5.8 Consensus size: 8
24713 CAAAAATTGC
24723 CGTGTCGA
1 CGTGTCGA
24731 CGTGTC--
1 CGTGTCGA
24737 CGTGTCGA
1 CGTGTCGA
24745 CGTGTC--
1 CGTGTCGA
24751 CGTGTCGA
1 CGTGTCGA
24759 CGTGTC
1 CGTGTC
24765 CGTGTCGTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
6 12 0.40
8 18 0.60
ACGTcount: A:0.07, C:0.29, G:0.36, T:0.29
Consensus pattern (8 bp):
CGTGTCGA
Found at i:24741 original size:14 final size:14
Alignment explanation
Indices: 24722--24771 Score: 100
Period size: 14 Copynumber: 3.6 Consensus size: 14
24712 TCAAAAATTG
24722 CCGTGTCGACGTGT
1 CCGTGTCGACGTGT
24736 CCGTGTCGACGTGT
1 CCGTGTCGACGTGT
24750 CCGTGTCGACGTGT
1 CCGTGTCGACGTGT
24764 CCGTGTCG
1 CCGTGTCG
24772 TGTCATATTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 36 1.00
ACGTcount: A:0.06, C:0.30, G:0.36, T:0.28
Consensus pattern (14 bp):
CCGTGTCGACGTGT
Found at i:41903 original size:1 final size:1
Alignment explanation
Indices: 41897--41924 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
41887 ACTTTTCTGC
41897 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
41925 CTTTGCAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Done.