Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008529.1 Corchorus capsularis cultivar CVL-1 contig08550, 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: 11764
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Found at i:7223 original size:2 final size:2
Alignment explanation
Indices: 7216--7249 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
7206 TAGTATGTAC
7216 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7250 TAAAATTCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7389 original size:30 final size:31
Alignment explanation
Indices: 7353--7425 Score: 121
Period size: 31 Copynumber: 2.4 Consensus size: 31
7343 CCTCATTGCG
*
7353 CACCAGGGGAGGCT-CCCCCCTACCAGCACA
1 CACCAGGGGAGACTCCCCCCCTACCAGCACA
*
7383 CACCAGGGGAGACTCCCCCCCTTCCAGCACA
1 CACCAGGGGAGACTCCCCCCCTACCAGCACA
7414 CACCAGGGGAGA
1 CACCAGGGGAGA
7426 ACCCCCAACT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
30 13 0.32
31 27 0.68
ACGTcount: A:0.25, C:0.44, G:0.25, T:0.07
Consensus pattern (31 bp):
CACCAGGGGAGACTCCCCCCCTACCAGCACA
Found at i:7453 original size:9 final size:10
Alignment explanation
Indices: 7437--7464 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
7427 CCCCCAACTA
7437 TAAAAAAAAT
1 TAAAAAAAAT
7447 TAAAAAAAAT
1 TAAAAAAAAT
7457 TAAAAAAA
1 TAAAAAAA
7465 GGCAAAAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (10 bp):
TAAAAAAAAT
Found at i:8363 original size:16 final size:16
Alignment explanation
Indices: 8338--8372 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
8328 TCTACCCTAA
*
8338 TCACCCAGTACAATAC
1 TCACCCAGTACAACAC
*
8354 TCACCTAGTACAACAC
1 TCACCCAGTACAACAC
8370 TCA
1 TCA
8373 TACTCACCCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.37, C:0.37, G:0.06, T:0.20
Consensus pattern (16 bp):
TCACCCAGTACAACAC
Found at i:9109 original size:31 final size:31
Alignment explanation
Indices: 9074--9150 Score: 109
Period size: 31 Copynumber: 2.5 Consensus size: 31
9064 GCCAAATTAG
*
9074 CAATTTGAGCCTAAACCTTTCAAAAATTGCT
1 CAATTTGAGCCTAAACATTTCAAAAATTGCT
* * *
9105 CAATTTAAGGCTGAACATTTCAAAAATTGCT
1 CAATTTGAGCCTAAACATTTCAAAAATTGCT
*
9136 CAATTTGAGTCTAAA
1 CAATTTGAGCCTAAA
9151 AACAGAATAA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (31 bp):
CAATTTGAGCCTAAACATTTCAAAAATTGCT
Found at i:9363 original size:29 final size:29
Alignment explanation
Indices: 9289--9387 Score: 78
Period size: 31 Copynumber: 3.3 Consensus size: 29
9279 AATTTATACC
* *
9289 CAAATTGGTGCATTTTGATAAGGTTTAGACT
1 CAAATTGGT-CA-GTTGAAAAGGTTTAGACT
* *
9320 CAATTTGGTTCAGTT-TAAAGGTTTAGACT
1 CAAATTGG-TCAGTTGAAAAGGTTTAGACT
9349 CAAATTGAG-CAAGTTGGAAAAGGTTTAGAC-
1 CAAATTG-GTC-AGTT-GAAAAGGTTTAGACT
9379 CAAAATTGG
1 C-AAATTGG
9388 ATATTAGGTC
Statistics
Matches: 56, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
28 1 0.02
29 22 0.39
30 5 0.09
31 27 0.48
32 1 0.02
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (29 bp):
CAAATTGGTCAGTTGAAAAGGTTTAGACT
Found at i:10330 original size:20 final size:20
Alignment explanation
Indices: 10305--10344 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
10295 ATTTAATTTA
*
10305 ATATGGATATTTACGGATAT
1 ATATGGATATTTACGAATAT
10325 ATATGGATATTTACGAATAT
1 ATATGGATATTTACGAATAT
10345 CACGGATACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.05, G:0.17, T:0.40
Consensus pattern (20 bp):
ATATGGATATTTACGAATAT
Found at i:11037 original size:19 final size:18
Alignment explanation
Indices: 10995--11057 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 18
10985 ATAATTTTCC
*
10995 TATATAATTATATATATC
1 TATATAATTATATATATA
*
11013 TAATATTATTATATATATGA
1 T-ATATAATTATATATAT-A
*
11033 TATATATTTA-AT-TATA
1 TATATAATTATATATATA
11049 TATAATAAT
1 TAT-ATAAT
11058 ATTCGGTTGG
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
16 4 0.11
17 7 0.19
18 3 0.08
19 22 0.59
20 1 0.03
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (18 bp):
TATATAATTATATATATA
Done.