Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005206.1 Corchorus capsularis cultivar CVL-1 contig05224, 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: 2814
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33


Found at i:474 original size:22 final size:22

Alignment explanation


    Indices: 445--553  Score: 102
    Period size: 22  Copynumber: 5.2  Consensus size: 22

        435 TGATAACCTC

                                  
        445 ATAACCACACTATGAAATTTTG
          1 ATAACCACACTATGAAATTTTG

            *              *  *   
        467 GTAACCACACTATGAGATGTTG
          1 ATAACCACACTATGAAATTTTG

                  *               
        489 ATAA-CTC-CTATGAAATTTTG
          1 ATAACCACACTATGAAATTTTG

                *                *
        509 ATAATCACA-T-T-AAATTTTA
          1 ATAACCACACTATGAAATTTTG

                   *    * *       
        528 ATAACCATACTAAGGAATTTTG
          1 ATAACCACACTATGAAATTTTG

                
        550 ATAA
          1 ATAA

        554 TTACAAATTC


Statistics
Matches: 68,  Mismatches: 14, Indels: 10
        0.74            0.15        0.11

Matches are distributed among these distances:
  19   14  0.21
  20   17  0.25
  21    5  0.07
  22   32  0.47

ACGTcount: A:0.40, C:0.15, G:0.11, T:0.34


Consensus pattern (22 bp):   
ATAACCACACTATGAAATTTTG

Found at i:2590 original size:24 final size:25

Alignment explanation


    Indices: 2544--2594  Score: 77
    Period size: 24  Copynumber: 2.1  Consensus size: 25

       2534 TCAACTTCCC

                    *                
       2544 GAGTCAGACGAAACAGAAGAAGATG
          1 GAGTCAGAAGAAACAGAAGAAGATG

                       *             
       2569 GAGTCAGAAGAGA-AGAAGAAGATG
          1 GAGTCAGAAGAAACAGAAGAAGATG

              
       2593 GA
          1 GA

       2595 TTCTTTAACT


Statistics
Matches: 24,  Mismatches: 2, Indels: 1
        0.89            0.07        0.04

Matches are distributed among these distances:
  24   13  0.54
  25   11  0.46

ACGTcount: A:0.49, C:0.08, G:0.35, T:0.08


Consensus pattern (25 bp):   
GAGTCAGAAGAAACAGAAGAAGATG
Done.