Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011989.1 Corchorus capsularis cultivar CVL-1 contig12010, 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: 54332
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:19386 original size:4 final size:4

Alignment explanation


    Indices: 19379--19427  Score: 61
    Period size: 4  Copynumber: 13.2  Consensus size: 4

      19369 GTTGGTTGGC

                              *                                        
      19379 TAAT TAAT T-AT T-AG TAA- TAA- TAAT TAAT TAAT TAAT TAAT TAAT
          1 TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT

                  
      19423 TAAT T
          1 TAAT T

      19428 GTTGTTGCAG


Statistics
Matches: 42,  Mismatches: 1, Indels: 4
        0.89            0.02        0.09

Matches are distributed among these distances:
   3   11  0.26
   4   31  0.74

ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49


Consensus pattern (4 bp):   
TAAT

Found at i:28782 original size:2 final size:2

Alignment explanation


    Indices: 28775--28803  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

      28765 CATTCAATGC

                                                       
      28775 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

      28804 ACTAAAAAAT


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   27  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:36019 original size:2 final size:2

Alignment explanation


    Indices: 36012--36043  Score: 64
    Period size: 2  Copynumber: 16.0  Consensus size: 2

      36002 ATTTATAGAG

                                                           
      36012 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

      36044 GTCTTGTCTC


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   30  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:36885 original size:105 final size:108

Alignment explanation


    Indices: 36754--36970  Score: 289
    Period size: 109  Copynumber: 2.0  Consensus size: 108

      36744 TTTGCTTCTA

                        *                                            *      *
      36754 TAATCATATCATTTGTAAAGAGAAATTATT-A-AAAT-TATAATCTCATTC-AGGGATGGATCTT
          1 TAATCATATCATGTGTAAAGAGAAATTATTGAGAAATATATAATCTCA-TCAAGGGACGGATCTC

                     *                                  
      36815 GATATATAAGTTTGATGAGTAATATAAATTACCTTAAGTAAAAT
         65 GATATATAACTTTGATGAGTAATATAAATTACCTTAAGTAAAAT

                      *          *            **                             
      36859 TAATCATATCCTGTGTAAAGATAAATTATTGATGCTATATATAATCTCATCAAGGGACGGATCTC
          1 TAATCATATCATGTGTAAAGAGAAATTATTGA-GAAATATATAATCTCATCAAGGGACGGATCTC

                                 *          *   *       
      36924 GATATATAACTTTGATGAGTATTATAAATTACTTTATGTAAAAT
         65 GATATATAACTTTGATGAGTAATATAAATTACCTTAAGTAAAAT

               
      36968 TAA
          1 TAA

      36971 CCCAAGTAAA


Statistics
Matches: 96,  Mismatches: 11, Indels: 6
        0.85            0.10        0.05

Matches are distributed among these distances:
 105   27  0.28
 106    1  0.01
 108    4  0.04
 109   64  0.67

ACGTcount: A:0.40, C:0.09, G:0.13, T:0.37


Consensus pattern (108 bp):   
TAATCATATCATGTGTAAAGAGAAATTATTGAGAAATATATAATCTCATCAAGGGACGGATCTCG
ATATATAACTTTGATGAGTAATATAAATTACCTTAAGTAAAAT
Done.