Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005572.1 Corchorus capsularis cultivar CVL-1 contig05590, 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: 4170
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.33


Found at i:375 original size:22 final size:21

Alignment explanation


    Indices: 318--375  Score: 53
    Period size: 22  Copynumber: 2.6  Consensus size: 21

        308 ATCTTATAAC

                         *         
        318 TTCACCTTCCTTTCACTTTCATT
          1 TTCA-CTT-CTTTTACTTTCATT

                 *  *              
        341 TTCAAATTTTTTTACTTTCAGTT
          1 TTC-ACTTCTTTTACTTTCA-TT

                        
        364 TTCACTTCTTTT
          1 TTCACTTCTTTT

        376 CTCTTCTCTT


Statistics
Matches: 28,  Mismatches: 5, Indels: 5
        0.74            0.13        0.13

Matches are distributed among these distances:
  22   17  0.61
  23   10  0.36
  24    1  0.04

ACGTcount: A:0.16, C:0.24, G:0.02, T:0.59


Consensus pattern (21 bp):   
TTCACTTCTTTTACTTTCATT

Found at i:375 original size:23 final size:22

Alignment explanation


    Indices: 318--376  Score: 57
    Period size: 23  Copynumber: 2.6  Consensus size: 22

        308 ATCTTATAAC

                     *             
        318 TTCACCTTCCTTTCACTTTCATT
          1 TTCA-CTTCTTTTCACTTTCATT

                 *       *          
        341 TTCAAATT-TTTTTACTTTCAGTT
          1 TTC-ACTTCTTTTCACTTTCA-TT

                         
        364 TTCACTTCTTTTC
          1 TTCACTTCTTTTC

        377 TCTTCTCTTC


Statistics
Matches: 28,  Mismatches: 5, Indels: 6
        0.72            0.13        0.15

Matches are distributed among these distances:
  22   13  0.46
  23   14  0.50
  24    1  0.04

ACGTcount: A:0.15, C:0.25, G:0.02, T:0.58


Consensus pattern (22 bp):   
TTCACTTCTTTTCACTTTCATT

Found at i:3454 original size:51 final size:51

Alignment explanation


    Indices: 3378--3540  Score: 265
    Period size: 51  Copynumber: 3.2  Consensus size: 51

       3368 TTTTTGGCAA

                                                                
       3378 ATAAAAATTAAATCTTTATGTAGTAAGGGTTGAGTTCTAGTGATATTT-ATC
          1 ATAAAAATTAAATCTTTATGTAGTAAGGGTTGAGTTCTAGTGAT-TTTAATC

                                                               
       3429 ATAAAAATTAAATCTTTATGTAGTAAGGGTTGAGTTCTAGTGATTTTAATC
          1 ATAAAAATTAAATCTTTATGTAGTAAGGGTTGAGTTCTAGTGATTTTAATC

                                       *        *    *       * 
       3480 ATAAAAATTAAATCTTTATGTAGTAAGAGTTGAGTTTTAGTAATTTTAAAC
          1 ATAAAAATTAAATCTTTATGTAGTAAGGGTTGAGTTCTAGTGATTTTAATC

                      
       3531 AATAAAAATT
          1 -ATAAAAATT

       3541 GAATATTGAT


Statistics
Matches: 106,  Mismatches: 4, Indels: 3
        0.94            0.04        0.03

Matches are distributed among these distances:
  50    3  0.03
  51   94  0.89
  52    9  0.08

ACGTcount: A:0.39, C:0.05, G:0.15, T:0.40


Consensus pattern (51 bp):   
ATAAAAATTAAATCTTTATGTAGTAAGGGTTGAGTTCTAGTGATTTTAATC
Done.