Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012102.1 Corchorus capsularis cultivar CVL-1 contig12123, 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: 5468
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:532 original size:69 final size:70
Alignment explanation
Indices: 264--675 Score: 649
Period size: 69 Copynumber: 6.0 Consensus size: 70
254 CCTCTTTACA
* * *
264 ATTACAACAGGTCCACCTTGTCGCAAGGCAATGGTTGATTGAGCATTATGTCTCTCACCTTGTC-
1 ATTACAAAAGGTCCACTTTGTGGCAAGGCAATGGTTGATTGAGCATTATGTCTCTCACCTTGTCT
328 -T-TT
66 TTATT
331 ATTACAAAAGGTCCACTTTGTGGCAAGGCAATGGTTGATTGAGCATTATGTCTCTCACCTTGTCT
1 ATTACAAAAGGTCCACTTTGTGGCAAGGCAATGGTTGATTGAGCATTATGTCTCTCACCTTGTCT
396 TTA-T
66 TTATT
*
400 A-TACAAAAGGTCCACTTTGTGGCAAGGCAATGGTTGATTGAGCATTATGTCTCTTACCTTGTCT
1 ATTACAAAAGGTCCACTTTGTGGCAAGGCAATGGTTGATTGAGCATTATGTCTCTCACCTTGTCT
464 TTATT
66 TTATT
* * *
469 ATTACAAAAGGTCCACTTTGTGGCAAGGCAGTGG-TAATTGAGCATTATGTCTCTTACCTTGTCT
1 ATTACAAAAGGTCCACTTTGTGGCAAGGCAATGGTTGATTGAGCATTATGTCTCTCACCTTGTCT
533 TTATT
66 TTATT
* *
538 ATTACAAAAGGTCCACTTTGTGGCAAGGCATTGGATGATTGAGCATTATGTCTCTCACCTTGTCT
1 ATTACAAAAGGTCCACTTTGTGGCAAGGCAATGGTTGATTGAGCATTATGTCTCTCACCTTGTCT
*
603 TTACT
66 TTATT
* * * *
608 ATTACAAAAGGTCCACTTTGTGTCAAGGCATTGG-TAATTGAGCATTATGTCTCTTACCTTGTCT
1 ATTACAAAAGGTCCACTTTGTGGCAAGGCAATGGTTGATTGAGCATTATGTCTCTCACCTTGTCT
672 TTAT
66 TTAT
676 ACTATTCTAT
Statistics
Matches: 325, Mismatches: 14, Indels: 10
0.93 0.04 0.03
Matches are distributed among these distances:
67 61 0.19
68 65 0.20
69 103 0.32
70 96 0.30
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.37
Consensus pattern (70 bp):
ATTACAAAAGGTCCACTTTGTGGCAAGGCAATGGTTGATTGAGCATTATGTCTCTCACCTTGTCT
TTATT
Found at i:588 original size:139 final size:139
Alignment explanation
Indices: 264--675 Score: 672
Period size: 139 Copynumber: 3.0 Consensus size: 139
254 CCTCTTTACA
* * *
264 ATTACAACAGGTCCACCTTGTCGCAAGGCAATGGTTGATTGAGCATTATGTCTCTCACCTTGTC-
1 ATTACAAAAGGTCCACTTTGTGGCAAGGCAATGGTTGATTGAGCATTATGTCTCTCACCTTGTCT
* *
328 -T-TTATTACAAAAGGTCCACTTTGTGGCAAGGCAATGGTTGATTGAGCATTATGTCTCTCACCT
66 TTATTATTACAAAAGGTCCACTTTGTGGCAAGGCAATGG-TAATTGAGCATTATGTCTCTTACCT
391 TGTCTTTA-T
130 TGTCTTTATT
*
400 A-TACAAAAGGTCCACTTTGTGGCAAGGCAATGGTTGATTGAGCATTATGTCTCTTACCTTGTCT
1 ATTACAAAAGGTCCACTTTGTGGCAAGGCAATGGTTGATTGAGCATTATGTCTCTCACCTTGTCT
*
464 TTATTATTACAAAAGGTCCACTTTGTGGCAAGGCAGTGGTAATTGAGCATTATGTCTCTTACCTT
66 TTATTATTACAAAAGGTCCACTTTGTGGCAAGGCAATGGTAATTGAGCATTATGTCTCTTACCTT
529 GTCTTTATT
131 GTCTTTATT
* *
538 ATTACAAAAGGTCCACTTTGTGGCAAGGCATTGGATGATTGAGCATTATGTCTCTCACCTTGTCT
1 ATTACAAAAGGTCCACTTTGTGGCAAGGCAATGGTTGATTGAGCATTATGTCTCTCACCTTGTCT
* * *
603 TTACTATTACAAAAGGTCCACTTTGTGTCAAGGCATTGGTAATTGAGCATTATGTCTCTTACCTT
66 TTATTATTACAAAAGGTCCACTTTGTGGCAAGGCAATGGTAATTGAGCATTATGTCTCTTACCTT
668 GTCTTTAT
131 GTCTTTAT
676 ACTATTCTAT
Statistics
Matches: 258, Mismatches: 13, Indels: 7
0.93 0.05 0.03
Matches are distributed among these distances:
135 58 0.22
136 1 0.00
137 32 0.12
138 37 0.14
139 130 0.50
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.37
Consensus pattern (139 bp):
ATTACAAAAGGTCCACTTTGTGGCAAGGCAATGGTTGATTGAGCATTATGTCTCTCACCTTGTCT
TTATTATTACAAAAGGTCCACTTTGTGGCAAGGCAATGGTAATTGAGCATTATGTCTCTTACCTT
GTCTTTATT
Found at i:1955 original size:21 final size:21
Alignment explanation
Indices: 1929--1981 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
1919 GCACTAGAGT
* * *
1929 ACATGGGTCGCGAGGCAAACC
1 ACATGGGGCGCCAAGCAAACC
1950 ACATGGGGCGCCAAGCAAACC
1 ACATGGGGCGCCAAGCAAACC
1971 ACAT-GGGCGCC
1 ACATGGGGCGCC
1982 CAGCGCTAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 7 0.24
21 22 0.76
ACGTcount: A:0.28, C:0.32, G:0.32, T:0.08
Consensus pattern (21 bp):
ACATGGGGCGCCAAGCAAACC
Done.