Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007819.1 Corchorus capsularis cultivar CVL-1 contig07840, 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: 13740
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Found at i:108 original size:14 final size:14
Alignment explanation
Indices: 86--121 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
76 TAAACACTTA
* *
86 CCAAGCTCCAAAGT
1 CCAATCTCCAAACT
100 CCAATCTCCAAACT
1 CCAATCTCCAAACT
114 CCAATCTC
1 CCAATCTC
122 TTATCCAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.33, C:0.42, G:0.06, T:0.19
Consensus pattern (14 bp):
CCAATCTCCAAACT
Found at i:1226 original size:13 final size:12
Alignment explanation
Indices: 1196--1238 Score: 68
Period size: 12 Copynumber: 3.5 Consensus size: 12
1186 CATCGATACC
1196 TCGATATATCCG
1 TCGATATATCCG
1208 TCGATATATCCG
1 TCGATATATCCG
*
1220 TTCGATATATTCG
1 -TCGATATATCCG
1233 TCGATA
1 TCGATA
1239 CCTGTATTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
12 18 0.62
13 11 0.38
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (12 bp):
TCGATATATCCG
Found at i:5948 original size:17 final size:17
Alignment explanation
Indices: 5912--5953 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
5902 CGAAAGTGAA
* *
5912 CCCGAACCCGACCCGGG
1 CCCGAACCCGACACGAG
*
5929 CCCGAACCCGACATGAG
1 CCCGAACCCGACACGAG
5946 CCCGAACC
1 CCCGAACC
5954 TGAAAATACC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.24, C:0.50, G:0.24, T:0.02
Consensus pattern (17 bp):
CCCGAACCCGACACGAG
Found at i:5988 original size:16 final size:16
Alignment explanation
Indices: 5946--6002 Score: 64
Period size: 16 Copynumber: 3.6 Consensus size: 16
5936 CCGACATGAG
*
5946 CCCGAACCTGAAAATA
1 CCCGAACCCGAAAATA
5962 CCCGGAA-CCGAAAATA
1 CCC-GAACCCGAAAATA
*
5978 CCCGAACCCG-AAGTA
1 CCCGAACCCGAAAATA
*
5993 CCTGAACCCG
1 CCCGAACCCG
6003 CCCAATTGCC
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
15 16 0.44
16 17 0.47
17 3 0.08
ACGTcount: A:0.37, C:0.37, G:0.18, T:0.09
Consensus pattern (16 bp):
CCCGAACCCGAAAATA
Found at i:6868 original size:133 final size:132
Alignment explanation
Indices: 6731--6996 Score: 394
Period size: 134 Copynumber: 2.0 Consensus size: 132
6721 ATTTAAGAAA
** *
6731 TATATTTTTAAAATTCTAATATATCTAAG-TTTTTTAATTA-AATTAATAAAATGATAAAAA-TA
1 TATATTTAAAAAATTCTAATATATATAAGTTTTTTTAATTATAA-TAATAAAATGATAAAAAGT-
* *
6793 AAATAGGTATAAGGATATTAGATTTAATTAAATAAAAAAATATAGTTTTTAGTTGAGTAAAACTA
64 AAATAGGTATAAGAATATTAGATTTAATTAAAT--AAAAATAGAGTTTTTAGTTGAGTAAAACTA
6858 TAAAAG
127 TAAAAG
* *
6864 TATATTTAAAAAATTCTAATATATATAAGTTTTTTTAATTATAATAGTAAAATGGTAAAAAGTAA
1 TATATTTAAAAAATTCTAATATATATAAGTTTTTTTAATTATAATAATAAAATGATAAAAAGTAA
* *
6929 ATAGTTATAAGAATATTAGATTTAATTAAATAAAAATAGGGTTTTTAGTTGAGTAAAACTATAAA
66 ATAGGTATAAGAATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAA
6994 AG
131 AG
6996 T
1 T
6997 TTAAACAAAG
Statistics
Matches: 121, Mismatches: 9, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
132 35 0.29
133 26 0.21
134 57 0.47
135 3 0.02
ACGTcount: A:0.49, C:0.02, G:0.10, T:0.39
Consensus pattern (132 bp):
TATATTTAAAAAATTCTAATATATATAAGTTTTTTTAATTATAATAATAAAATGATAAAAAGTAA
ATAGGTATAAGAATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAA
AG
Done.