Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009499.1 Corchorus capsularis cultivar CVL-1 contig09520, 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: 6349
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32


Found at i:4822 original size:122 final size:119

Alignment explanation


    Indices: 4599--4839  Score: 428
    Period size: 122  Copynumber: 2.0  Consensus size: 119

       4589 TCATAAAAGT

                                          *                                  
       4599 TTAAGTGTGCAATTTGCAATTTTGGAAGTTGAAGTGCTAATTTGTCTCTTTTTAAAAGTTCAGGG
          1 TTAAGTGTGCAATTTGCAATTTTGGAAGTTAAAGTGCTAATTTGTCTCTTTTTAAAAGTTCAGGG

               *                       *                            
       4664 GTAGAATGTCTAATAAGCCGAATTATAGCTAGTACCATATTCCTAATTTCCTTTAG
         66 GTAAAATGTCTAATAAGCCGAATTATAACTAGTACC--ATTCCTAATTTCCTTTAG

                                                                             
       4720 TTAAGTGTGCAATTTGCAATTTTGGAAGTTAAAGTGCTAATTTGTCTCTTTTTTAAAAGTTCAGG
          1 TTAAGTGTGCAATTTGCAATTTTGGAAGTTAAAGTGCTAATTTGTCTC-TTTTTAAAAGTTCAGG

                                                                   
       4785 GGTAAAATGTCTAATAAGCCGAATTATAACTAGTACCATTCCTAATTTCCTTTAG
         65 GGTAAAATGTCTAATAAGCCGAATTATAACTAGTACCATTCCTAATTTCCTTTAG

       4840 CTTATTAGAC


Statistics
Matches: 116,  Mismatches: 3, Indels: 3
        0.95            0.02        0.02

Matches are distributed among these distances:
 120   18  0.16
 121   47  0.41
 122   51  0.44

ACGTcount: A:0.30, C:0.13, G:0.18, T:0.39


Consensus pattern (119 bp):   
TTAAGTGTGCAATTTGCAATTTTGGAAGTTAAAGTGCTAATTTGTCTCTTTTTAAAAGTTCAGGG
GTAAAATGTCTAATAAGCCGAATTATAACTAGTACCATTCCTAATTTCCTTTAG

Found at i:6160 original size:61 final size:61

Alignment explanation


    Indices: 6095--6211  Score: 180
    Period size: 61  Copynumber: 1.9  Consensus size: 61

       6085 GCGTGCCATT

                                   *                                     
       6095 TTTTGAAACATGTGGCATACCACGTGTCACTTTTTGGTACACGTGGCGTGACACGTGTCAC
          1 TTTTGAAACATGTGGCATACCACATGTCACTTTTTGGTACACGTGGCGTGACACGTGTCAC

                 **         * *                               *     
       6156 TTTTGGTACATGTGGCGTGCCACATGTCACTTTTTGGTACACGTGGCGTGCCACGT
          1 TTTTGAAACATGTGGCATACCACATGTCACTTTTTGGTACACGTGGCGTGACACGT

       6212 CGGACACCGT


Statistics
Matches: 50,  Mismatches: 6, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  61   50  1.00

ACGTcount: A:0.18, C:0.23, G:0.26, T:0.32


Consensus pattern (61 bp):   
TTTTGAAACATGTGGCATACCACATGTCACTTTTTGGTACACGTGGCGTGACACGTGTCAC

Found at i:6162 original size:30 final size:31

Alignment explanation


    Indices: 6072--6211  Score: 165
    Period size: 31  Copynumber: 4.5  Consensus size: 31

       6062 TCCTTTTGTG

                    *    *    *  *      ** 
       6072 CACGTGGCATGCCGCGTGCCATTTTTTGAAA
          1 CACGTGGCGTGCCACGTGTCACTTTTTGGTA

              *     * *                    
       6103 CATGTGGCATACCACGTGTCACTTTTTGGTA
          1 CACGTGGCGTGCCACGTGTCACTTTTTGGTA

                       *                   
       6134 CACGTGGCGTGACACGTGTCAC-TTTTGGTA
          1 CACGTGGCGTGCCACGTGTCACTTTTTGGTA

              *            *               
       6164 CATGTGGCGTGCCACATGTCACTTTTTGGTA
          1 CACGTGGCGTGCCACGTGTCACTTTTTGGTA

                             
       6195 CACGTGGCGTGCCACGT
          1 CACGTGGCGTGCCACGT

       6212 CGGACACCGT


Statistics
Matches: 92,  Mismatches: 16, Indels: 2
        0.84            0.15        0.02

Matches are distributed among these distances:
  30   27  0.29
  31   65  0.71

ACGTcount: A:0.17, C:0.25, G:0.27, T:0.31


Consensus pattern (31 bp):   
CACGTGGCGTGCCACGTGTCACTTTTTGGTA
Done.