Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011556.1 Corchorus capsularis cultivar CVL-1 contig11577, 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: 6203
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36


Found at i:3127 original size:64 final size:64

Alignment explanation


    Indices: 3048--3177  Score: 215
    Period size: 64  Copynumber: 2.0  Consensus size: 64

       3038 GATGCAGACA

                                    *                                       
       3048 GTAAATAATCTTTTCAAGCGATTTTTGATGCCATTAGATTTCTTTTATATAGTTTTAAGCATAT
          1 GTAAATAATCTTTTCAAGCGATTTCTGATGCCATTAGATTTCTTTTATATAGTTTTAAGCATAT

                  *          * *                *                           
       3112 GTAAATCATCTTTTCAATCTATTTCTGATGCCATTATATTTCTTTTATATAGTTTTAAGCATAT
          1 GTAAATAATCTTTTCAAGCGATTTCTGATGCCATTAGATTTCTTTTATATAGTTTTAAGCATAT

              
       3176 GT
          1 GT

       3178 TGCTATAAGG


Statistics
Matches: 61,  Mismatches: 5, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  64   61  1.00

ACGTcount: A:0.28, C:0.12, G:0.11, T:0.48


Consensus pattern (64 bp):   
GTAAATAATCTTTTCAAGCGATTTCTGATGCCATTAGATTTCTTTTATATAGTTTTAAGCATAT

Found at i:6163 original size:53 final size:53

Alignment explanation


    Indices: 6078--6180  Score: 152
    Period size: 53  Copynumber: 1.9  Consensus size: 53

       6068 GACGTGGCAC

                 *                 **                            
       6078 GCCACGTGTACCAAAAAGTGACATGTGGCACGCCACATATACCAAAAAGTCGT
          1 GCCACATGTACCAAAAAGTGACACATGGCACGCCACATATACCAAAAAGTCGT

                                       *        * *           
       6131 GCCACATGTACCAAAAAGTGACACATGTCACGCCACGTGTACCAAAAAGT
          1 GCCACATGTACCAAAAAGTGACACATGGCACGCCACATATACCAAAAAGT

       6181 GACATGTGGC


Statistics
Matches: 44,  Mismatches: 6, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  53   44  1.00

ACGTcount: A:0.37, C:0.27, G:0.19, T:0.17


Consensus pattern (53 bp):   
GCCACATGTACCAAAAAGTGACACATGGCACGCCACATATACCAAAAAGTCGT

Found at i:6197 original size:31 final size:31

Alignment explanation


    Indices: 6130--6201  Score: 99
    Period size: 31  Copynumber: 2.3  Consensus size: 31

       6120 CAAAAAGTCG

                                        *  
       6130 TGCCACATGTACCAAAAAGTGACACATGTCA
          1 TGCCACATGTACCAAAAAGTGACACATGGCA

            *     *                 **     
       6161 CGCCACGTGTACCAAAAAGTGACATGTGGCA
          1 TGCCACATGTACCAAAAAGTGACACATGGCA

                      
       6192 TGCCACATGT
          1 TGCCACATGT

       6202 TT


Statistics
Matches: 34,  Mismatches: 7, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  31   34  1.00

ACGTcount: A:0.33, C:0.26, G:0.21, T:0.19


Consensus pattern (31 bp):   
TGCCACATGTACCAAAAAGTGACACATGGCA
Done.