Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006349.1 Corchorus capsularis cultivar CVL-1 contig06370, 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: 7200
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.30


Found at i:3149 original size:71 final size:71

Alignment explanation


    Indices: 3054--3185  Score: 169
    Period size: 71  Copynumber: 1.9  Consensus size: 71

       3044 GGACTGGTCT

                  *                                                          
       3054 TCTTCAGTTTCAGACCTCAAACAGGTCCCCCTT-AATTTCAAAAGCGACCACAGACTGGTCTCTT
          1 TCTTCAATTTCAGACCTCAAACAGGT-CCCCTTCAATTTCAAAAGCGACCACAGACTGGTCTCTT

                   
       3118 TCTCATA
         65 TCTCATA

                                *       **    *       * *                 
       3125 TCTTCAATTCTCA-ACCTCAGACAGGTCTTCTTCGATTTCAACATCGACCACAGACTGGTCT
          1 TCTTCAATT-TCAGACCTCAAACAGGTCCCCTTCAATTTCAAAAGCGACCACAGACTGGTCT

       3186 TCTCCAAAAT


Statistics
Matches: 52,  Mismatches: 7, Indels: 4
        0.83            0.11        0.06

Matches are distributed among these distances:
  70    4  0.08
  71   45  0.87
  72    3  0.06

ACGTcount: A:0.26, C:0.31, G:0.13, T:0.30


Consensus pattern (71 bp):   
TCTTCAATTTCAGACCTCAAACAGGTCCCCTTCAATTTCAAAAGCGACCACAGACTGGTCTCTTT
CTCATA

Found at i:3253 original size:33 final size:33

Alignment explanation


    Indices: 3087--3254  Score: 107
    Period size: 33  Copynumber: 5.1  Consensus size: 33

       3077 GGTCCCCCTT

                    * *                   *    
       3087 AATTTCAAAAGCGACCACAGACTGGTCTCTTTCTC
          1 AATTTCAATATCGACCACAGACTGGTCT-TCT-TC

                        *  *   *     *          
       3122 ATATCTTCAATTCTCAACCTCAGACAGGTCTTCTTC
          1 A-AT-TTCAA-TATCGACCACAGACTGGTCTTCTTC

            *       *                      * 
       3158 GATTTCAACATCGACCACAGACTGGTCTTCTCC
          1 AATTTCAATATCGACCACAGACTGGTCTTCTTC

                            **   **           
       3191 AA----AAT-T-GACCTTAGAAAGGTCTT-TCTC
          1 AATTTCAATATCGACCACAGACTGGTCTTCT-TC

                                             
       3218 AATTTCAATATCGACCACAGACTGGTCTTCTTC
          1 AATTTCAATATCGACCACAGACTGGTCTTCTTC

                
       3251 AATT
          1 AATT

       3255 CCAGACCTCA


Statistics
Matches: 97,  Mismatches: 25, Indels: 24
        0.66            0.17        0.16

Matches are distributed among these distances:
  26    1  0.01
  27   16  0.16
  28    1  0.01
  29    2  0.02
  31    3  0.03
  32    1  0.01
  33   39  0.40
  34    6  0.06
  35    3  0.03
  36    4  0.04
  37    7  0.07
  38   14  0.14

ACGTcount: A:0.28, C:0.27, G:0.12, T:0.32


Consensus pattern (33 bp):   
AATTTCAATATCGACCACAGACTGGTCTTCTTC
Done.