Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012439.1 Corchorus capsularis cultivar CVL-1 contig12460, 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: 37573
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32


Found at i:4626 original size:20 final size:20

Alignment explanation


    Indices: 4598--4636  Score: 69
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       4588 GAGTACAGGT

                *               
       4598 AAATGACTCTATCATATCAC
          1 AAATAACTCTATCATATCAC

                               
       4618 AAATAACTCTATCATATCA
          1 AAATAACTCTATCATATCA

       4637 AGATTGCCTC


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  20   18  1.00

ACGTcount: A:0.44, C:0.23, G:0.03, T:0.31


Consensus pattern (20 bp):   
AAATAACTCTATCATATCAC

Found at i:26772 original size:31 final size:31

Alignment explanation


    Indices: 26713--26806  Score: 107
    Period size: 31  Copynumber: 3.0  Consensus size: 31

      26703 GTACCAAAAA

                *            *  *  *       
      26713 GTACAAAAAAGTGACACATGTCACGCCACGT
          1 GTACCAAAAAGTGACACGTGGCATGCCACGT

                                         * 
      26744 GTACCAAAAAGTGACACGTGGCATGCCACAT
          1 GTACCAAAAAGTGACACGTGGCATGCCACGT

              **      *  *                 
      26775 GTTTCAAAAAATGGCACGTGGCATGCCACGT
          1 GTACCAAAAAGTGACACGTGGCATGCCACGT

             
      26806 G
          1 G

      26807 CACAAAAGGA


Statistics
Matches: 53,  Mismatches: 10, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  31   53  1.00

ACGTcount: A:0.34, C:0.24, G:0.23, T:0.18


Consensus pattern (31 bp):   
GTACCAAAAAGTGACACGTGGCATGCCACGT

Found at i:35262 original size:4 final size:4

Alignment explanation


    Indices: 35248--35306  Score: 100
    Period size: 4  Copynumber: 14.8  Consensus size: 4

      35238 TATGTATATA

                   *          *                                        
      35248 TATG TAAG TATG TATT TATG TATG TATG TATG TATG TATG TATG TATG
          1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG

                         
      35296 TATG TATG TAT
          1 TATG TATG TAT

      35307 ACACACACGC


Statistics
Matches: 51,  Mismatches: 4, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   4   51  1.00

ACGTcount: A:0.27, C:0.00, G:0.22, T:0.51


Consensus pattern (4 bp):   
TATG

Found at i:35619 original size:31 final size:30

Alignment explanation


    Indices: 35584--35646  Score: 81
    Period size: 30  Copynumber: 2.1  Consensus size: 30

      35574 ATTTTGTTCC

                             *             
      35584 GTTGTAACAGTTGGGGTCTCAATTTGAATTT
          1 GTTGTAACAGTT-GGGTATCAATTTGAATTT

                   *          **          
      35615 GTTGTAATAGTTGGGTATGGATTTGAATTT
          1 GTTGTAACAGTTGGGTATCAATTTGAATTT

              
      35645 GT
          1 GT

      35647 AGTTGCTTTA


Statistics
Matches: 28,  Mismatches: 4, Indels: 1
        0.85            0.12        0.03

Matches are distributed among these distances:
  30   17  0.61
  31   11  0.39

ACGTcount: A:0.22, C:0.05, G:0.29, T:0.44


Consensus pattern (30 bp):   
GTTGTAACAGTTGGGTATCAATTTGAATTT

Found at i:37109 original size:31 final size:31

Alignment explanation


    Indices: 37066--37156  Score: 101
    Period size: 31  Copynumber: 2.9  Consensus size: 31

      37056 GACAAAAAAT

                                   *       
      37066 AACACGTGGCATGCCACGTGCCATTTTTTGA
          1 AACACGTGGCATGCCACGTGCCACTTTTTGA

                *               *         *
      37097 AACATGTGGCATGCCACGTGTCACTTTTTGG
          1 AACACGTGGCATGCCACGTGCCACTTTTTGA

            *         *  *  *   *        
      37128 TACACGTGGCGTGACATGTGTCACTTTTT
          1 AACACGTGGCATGCCACGTGCCACTTTTT

      37157 CGTACATGTG


Statistics
Matches: 51,  Mismatches: 9, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  31   51  1.00

ACGTcount: A:0.20, C:0.23, G:0.24, T:0.33


Consensus pattern (31 bp):   
AACACGTGGCATGCCACGTGCCACTTTTTGA

Found at i:37181 original size:53 final size:53

Alignment explanation


    Indices: 37119--37222  Score: 154
    Period size: 53  Copynumber: 2.0  Consensus size: 53

      37109 GCCACGTGTC

                                     **                 *        
      37119 ACTTTTTGGTACACGTGGCGTGACATGTGTCACTTTTTCGTACATGTGGCACG
          1 ACTTTTTGGTACACGTGGCGTGACACATGTCACTTTTTCGTACACGTGGCACG

                         *        *               *            
      37172 ACTTTTTGGTACATGTGGCGTGTCACATGTCACTTTTTGGTACACGTGGCA
          1 ACTTTTTGGTACACGTGGCGTGACACATGTCACTTTTTCGTACACGTGGCA

      37223 TGCCACGTCG


Statistics
Matches: 45,  Mismatches: 6, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  53   45  1.00

ACGTcount: A:0.17, C:0.20, G:0.26, T:0.37


Consensus pattern (53 bp):   
ACTTTTTGGTACACGTGGCGTGACACATGTCACTTTTTCGTACACGTGGCACG
Done.