Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010620.1 Corchorus capsularis cultivar CVL-1 contig10641, 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: 4255
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30


Found at i:96 original size:19 final size:20

Alignment explanation


    Indices: 50--97  Score: 62
    Period size: 22  Copynumber: 2.4  Consensus size: 20

         40 TGTGGCACGC

                                 *
         50 CACATGTACCAAAAAGTCGTGC
          1 CACATGTACCAAAAA--CGTGA

                                
         72 CACATGTACCAAAAA-GTGA
          1 CACATGTACCAAAAACGTGA

                   
         91 CACATGT
          1 CACATGT

         98 CACGCCACGT


Statistics
Matches: 25,  Mismatches: 1, Indels: 3
        0.86            0.03        0.10

Matches are distributed among these distances:
  19   10  0.40
  22   15  0.60

ACGTcount: A:0.40, C:0.25, G:0.17, T:0.19


Consensus pattern (20 bp):   
CACATGTACCAAAAACGTGA

Found at i:102 original size:53 final size:53

Alignment explanation


    Indices: 17--119  Score: 161
    Period size: 53  Copynumber: 1.9  Consensus size: 53

          7 GACGTGGCAC

                 *                 **                            
         17 GCCACGTGTACCAAAAAGTGACATGTGGCACGCCACATGTACCAAAAAGTCGT
          1 GCCACATGTACCAAAAAGTGACACATGGCACGCCACATGTACCAAAAAGTCGT

                                       *        *             
         70 GCCACATGTACCAAAAAGTGACACATGTCACGCCACGTGTACCAAAAAGT
          1 GCCACATGTACCAAAAAGTGACACATGGCACGCCACATGTACCAAAAAGT

        120 GACACGTGAC


Statistics
Matches: 45,  Mismatches: 5, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  53   45  1.00

ACGTcount: A:0.36, C:0.27, G:0.20, T:0.17


Consensus pattern (53 bp):   
GCCACATGTACCAAAAAGTGACACATGGCACGCCACATGTACCAAAAAGTCGT

Found at i:136 original size:31 final size:31

Alignment explanation


    Indices: 69--167  Score: 117
    Period size: 31  Copynumber: 3.2  Consensus size: 31

         59 CAAAAAGTCG

                                     *  *  
         69 TGCCACATGTACCAAAAAGTGACACATGTCA
          1 TGCCACATGTACCAAAAAGTGACACGTGACA

            *     *                        
        100 CGCCACGTGTACCAAAAAGTGACACGTGACA
          1 TGCCACATGTACCAAAAAGTGACACGTGACA

                      **      *  *      *  
        131 TGCCACATGTTTCAAAAAATGGCACGTGGCA
          1 TGCCACATGTACCAAAAAGTGACACGTGACA

                  
        162 TGCCAC
          1 TGCCAC

        168 GTGCACAAAA


Statistics
Matches: 57,  Mismatches: 11, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  31   57  1.00

ACGTcount: A:0.34, C:0.27, G:0.20, T:0.18


Consensus pattern (31 bp):   
TGCCACATGTACCAAAAAGTGACACGTGACA

Found at i:4127 original size:30 final size:29

Alignment explanation


    Indices: 4058--4131  Score: 105
    Period size: 29  Copynumber: 2.5  Consensus size: 29

       4048 GTAGCGTTTA

                                          
       4058 GACGTTTTGTCCCCC-GAACTTCAATCTTG
          1 GACGTTTTG-CCCCCTGAACTTCAATCTTG

               *                     *    
       4087 GACATTTTGCCCCCTGAACTTCAATTTTGG
          1 GACGTTTTGCCCCCTGAACTTCAATCTT-G

                           
       4117 GACGTTTTGCCCCCT
          1 GACGTTTTGCCCCCT

       4132 CAACCTAACG


Statistics
Matches: 40,  Mismatches: 3, Indels: 3
        0.87            0.07        0.07

Matches are distributed among these distances:
  28    5  0.12
  29   20  0.50
  30   15  0.38

ACGTcount: A:0.16, C:0.31, G:0.18, T:0.35


Consensus pattern (29 bp):   
GACGTTTTGCCCCCTGAACTTCAATCTTG
Done.