Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006973.1 Corchorus capsularis cultivar CVL-1 contig06994, 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: 11657
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33


Found at i:1984 original size:27 final size:29

Alignment explanation


    Indices: 1938--1997  Score: 97
    Period size: 27  Copynumber: 2.1  Consensus size: 29

       1928 TTAAAAAACT

                                         
       1938 TATTCTTCACTTAACAAATCATTATCTCA
          1 TATTCTTCACTTAACAAATCATTATCTCA

                    *                    
       1967 TATT-TTCCCTTAA-AAATCATTATCTCA
          1 TATTCTTCACTTAACAAATCATTATCTCA

                
       1994 TATT
          1 TATT

       1998 AATGTATATT


Statistics
Matches: 30,  Mismatches: 1, Indels: 2
        0.91            0.03        0.06

Matches are distributed among these distances:
  27   18  0.60
  28    8  0.27
  29    4  0.13

ACGTcount: A:0.33, C:0.22, G:0.00, T:0.45


Consensus pattern (29 bp):   
TATTCTTCACTTAACAAATCATTATCTCA

Found at i:4221 original size:36 final size:39

Alignment explanation


    Indices: 4171--4246  Score: 122
    Period size: 36  Copynumber: 2.0  Consensus size: 39

       4161 GGCACATCGT

                                               *   
       4171 ATAAGGAAAGATGGATGCAGAATAC-A-ACTTGGTGCTA
          1 ATAAGGAAAGATGGATGCAGAATACTATACTTGGTCCTA

                                                   
       4208 ATAAGG-AAGATGGATGCAGAATACTATACTTGGTCCTA
          1 ATAAGGAAAGATGGATGCAGAATACTATACTTGGTCCTA

             
       4246 A
          1 A

       4247 GGACTAAGGA


Statistics
Matches: 36,  Mismatches: 1, Indels: 3
        0.90            0.03        0.08

Matches are distributed among these distances:
  36   18  0.50
  37    7  0.19
  38   11  0.31

ACGTcount: A:0.39, C:0.12, G:0.25, T:0.24


Consensus pattern (39 bp):   
ATAAGGAAAGATGGATGCAGAATACTATACTTGGTCCTA

Found at i:7819 original size:31 final size:31

Alignment explanation


    Indices: 7757--7831  Score: 89
    Period size: 31  Copynumber: 2.4  Consensus size: 31

       7747 GAAGAAGCAA

                                  *  *     
       7757 TCAATTTAGTCCATTATACTCATAAGATGGG
          1 TCAATTTAGTCCATTATACTCACAAAATGGG

                           *                
       7788 TCAATTTAGTCCA-TGTACTCACAAAATTGGG
          1 TCAATTTAGTCCATTATACTCACAAAA-TGGG

             *    *      
       7819 TAAATTGAGTCCA
          1 TCAATTTAGTCCA

       7832 ATCGATAACG


Statistics
Matches: 38,  Mismatches: 5, Indels: 2
        0.84            0.11        0.04

Matches are distributed among these distances:
  30   10  0.26
  31   28  0.74

ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33


Consensus pattern (31 bp):   
TCAATTTAGTCCATTATACTCACAAAATGGG
Done.