Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015493.1 Corchorus capsularis cultivar CVL-1 contig15514, 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: 7509
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.32


Found at i:743 original size:33 final size:33

Alignment explanation


    Indices: 693--816  Score: 135
    Period size: 33  Copynumber: 3.7  Consensus size: 33

        683 CCGCGCAACA

                                              *
        693 CCGGCCACAAGACCGGCCACGCGACATGGACATGT
          1 CCGGCCAC-A-ACCGGCCACGCGACATGGACATGC

                                             *
        728 CCGGCCATC-ACCGGCCACGCGACATGGACATGG
          1 CCGGCCA-CAACCGGCCACGCGACATGGACATGC

                 *      *    **         *     
        761 CCGGCTACAACCCGCCAAACGAC-TCGGCCATGC
          1 CCGGCCACAACCGGCCACGCGACAT-GGACATGC

                                   
        794 CCGGCCACAACCGGCCACGCGAC
          1 CCGGCCACAACCGGCCACGCGAC

        817 CCTTTGTCTA


Statistics
Matches: 75,  Mismatches: 11, Indels: 8
        0.80            0.12        0.09

Matches are distributed among these distances:
  32    2  0.03
  33   65  0.87
  35    7  0.09
  36    1  0.01

ACGTcount: A:0.23, C:0.43, G:0.27, T:0.07


Consensus pattern (33 bp):   
CCGGCCACAACCGGCCACGCGACATGGACATGC

Found at i:3738 original size:32 final size:32

Alignment explanation


    Indices: 3697--3794  Score: 144
    Period size: 32  Copynumber: 3.1  Consensus size: 32

       3687 TTGGGGTATA

                        *                   
       3697 CCCTTATATAGCCGCGTCTAAAGAACAAAGCG
          1 CCCTTATATAGCGGCGTCTAAAGAACAAAGCG

                               *           *
       3729 CCCTTATATAGCGGCGTCTGAAGAACAAAGCA
          1 CCCTTATATAGCGGCGTCTAAAGAACAAAGCG

                          *                  
       3761 CCCTTATATAGCGGTGTCTAAAGTAACAAA-CG
          1 CCCTTATATAGCGGCGTCTAAAG-AACAAAGCG

              
       3793 CC
          1 CC

       3795 GCTATATTTA


Statistics
Matches: 59,  Mismatches: 6, Indels: 2
        0.88            0.09        0.03

Matches are distributed among these distances:
  32   53  0.90
  33    6  0.10

ACGTcount: A:0.34, C:0.27, G:0.19, T:0.20


Consensus pattern (32 bp):   
CCCTTATATAGCGGCGTCTAAAGAACAAAGCG

Found at i:3878 original size:24 final size:24

Alignment explanation


    Indices: 3849--3981  Score: 203
    Period size: 24  Copynumber: 5.5  Consensus size: 24

       3839 AGGTGGCGGG

                       *        *   
       3849 GTCTGGACGCCCCCAAATAGTGGC
          1 GTCTGGACGCCGCCAAATAGGGGC

                         *          
       3873 GTCTGGACGCCGCGAAATAGGGGC
          1 GTCTGGACGCCGCCAAATAGGGGC

                         *          
       3897 GTCTGGACGCCGCAAAATAGGGGC
          1 GTCTGGACGCCGCCAAATAGGGGC

                        *           
       3921 GTCTGGACGCCGTCAAATAGGGGC
          1 GTCTGGACGCCGCCAAATAGGGGC

                        *           
       3945 GTCTGGACGCCGTCAAATAGGGGC
          1 GTCTGGACGCCGCCAAATAGGGGC

               *         
       3969 GTCCGGACGCCGC
          1 GTCTGGACGCCGC

       3982 AATATGCTTT


Statistics
Matches: 101,  Mismatches: 8, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  24  101  1.00

ACGTcount: A:0.20, C:0.29, G:0.37, T:0.14


Consensus pattern (24 bp):   
GTCTGGACGCCGCCAAATAGGGGC

Found at i:4383 original size:24 final size:25

Alignment explanation


    Indices: 4330--4377  Score: 89
    Period size: 25  Copynumber: 2.0  Consensus size: 25

       4320 TTTAAATAGC

                                     
       4330 AACGCCGCTATATGGTAAAAAAAAA
          1 AACGCCGCTATATGGTAAAAAAAAA

                                    
       4355 AACGCCGCTATAT-GTAAAAAAAA
          1 AACGCCGCTATATGGTAAAAAAAA

       4378 TGACGCTATT


Statistics
Matches: 23,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  24   10  0.43
  25   13  0.57

ACGTcount: A:0.52, C:0.17, G:0.15, T:0.17


Consensus pattern (25 bp):   
AACGCCGCTATATGGTAAAAAAAAA

Found at i:6932 original size:11 final size:11

Alignment explanation


    Indices: 6916--6943  Score: 56
    Period size: 11  Copynumber: 2.5  Consensus size: 11

       6906 CAAGAAATAA

                       
       6916 ATATTATTATT
          1 ATATTATTATT

                       
       6927 ATATTATTATT
          1 ATATTATTATT

                  
       6938 ATATTA
          1 ATATTA

       6944 GAAATAGGGT


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   17  1.00

ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61


Consensus pattern (11 bp):   
ATATTATTATT

Found at i:7275 original size:27 final size:27

Alignment explanation


    Indices: 7244--7299  Score: 96
    Period size: 27  Copynumber: 2.1  Consensus size: 27

       7234 ACTCCCTCAG

                                        
       7244 TTCCTTTTTAATTGTCTC-TTTCCCTTA
          1 TTCCTTTTTAATTGTC-CATTTCCCTTA

                                       
       7271 TTCCTTTTTAATTGTCCATTTCCCTTA
          1 TTCCTTTTTAATTGTCCATTTCCCTTA

              
       7298 TT
          1 TT

       7300 TTCCAGAAAT


Statistics
Matches: 28,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
  26    1  0.04
  27   27  0.96

ACGTcount: A:0.12, C:0.25, G:0.04, T:0.59


Consensus pattern (27 bp):   
TTCCTTTTTAATTGTCCATTTCCCTTA
Done.