Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012360.1 Corchorus capsularis cultivar CVL-1 contig12381, 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: 5232
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32


Found at i:1438 original size:27 final size:27

Alignment explanation


    Indices: 1387--1456  Score: 97
    Period size: 27  Copynumber: 2.6  Consensus size: 27

       1377 GCCCAAGGGT

                             *          
       1387 ATTTTGGGTCATTTTTGTAGCCAGGGGC
          1 ATTTT-GGTCATTTTTGCAGCCAGGGGC

                                        
       1415 ATTTTGGTCATTTTTGCA-CTCAGGGGC
          1 ATTTTGGTCATTTTTGCAGC-CAGGGGC

                 *         
       1442 ATTTTAGTCATTTTT
          1 ATTTTGGTCATTTTT

       1457 AGGTTCACCT


Statistics
Matches: 39,  Mismatches: 2, Indels: 3
        0.89            0.05        0.07

Matches are distributed among these distances:
  26    1  0.03
  27   33  0.85
  28    5  0.13

ACGTcount: A:0.16, C:0.14, G:0.24, T:0.46


Consensus pattern (27 bp):   
ATTTTGGTCATTTTTGCAGCCAGGGGC

Found at i:2141 original size:16 final size:16

Alignment explanation


    Indices: 2120--2153  Score: 50
    Period size: 16  Copynumber: 2.1  Consensus size: 16

       2110 ATTTGGACCT

                            
       2120 TGCAAAGAAAAAGAAA
          1 TGCAAAGAAAAAGAAA

                   * *      
       2136 TGCAAAGCACAAGAAA
          1 TGCAAAGAAAAAGAAA

              
       2152 TG
          1 TG

       2154 TTCCCCAAGG


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  16   16  1.00

ACGTcount: A:0.59, C:0.12, G:0.21, T:0.09


Consensus pattern (16 bp):   
TGCAAAGAAAAAGAAA

Found at i:2944 original size:27 final size:27

Alignment explanation


    Indices: 2914--2965  Score: 86
    Period size: 27  Copynumber: 1.9  Consensus size: 27

       2904 GCATTGGGGT

                      *                
       2914 CGCCCAAGGGTATTTTGGTCATTTTCG
          1 CGCCCAAGGGCATTTTGGTCATTTTCG

                  *                  
       2941 CGCCCATGGGCATTTTGGTCATTTT
          1 CGCCCAAGGGCATTTTGGTCATTTT

       2966 TACACTCGGG


Statistics
Matches: 23,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  27   23  1.00

ACGTcount: A:0.13, C:0.23, G:0.25, T:0.38


Consensus pattern (27 bp):   
CGCCCAAGGGCATTTTGGTCATTTTCG

Found at i:5104 original size:51 final size:51

Alignment explanation


    Indices: 4932--5232  Score: 399
    Period size: 51  Copynumber: 5.9  Consensus size: 51

       4922 CCTCGCAAAA

                                      *                         
       4932 AAAAATGTCATCTTTGGGTAAAAGATGGAATTTTTAAGAGTAATTAGTAAAT
          1 AAAAATGTCATCTTTGGGTAAAAGATTGAATTTTT-AGAGTAATTAGTAAAT

                                      *                         
       4984 AAAAATGTCATCTTTGGGTAAAAGATGGAATTTTTAAGAGTAATTAGTAAAT
          1 AAAAATGTCATCTTTGGGTAAAAGATTGAATTTTT-AGAGTAATTAGTAAAT

                        *                         *            
       5036 AAAAATGTCATCCTTGGGTAAAAGATTGAATTTTTAGATTAATTAGTAAAT
          1 AAAAATGTCATCTTTGGGTAAAAGATTGAATTTTTAGAGTAATTAGTAAAT

            *                              *    *            * 
       5087 GAAAATGTCATCTTTGGGTAAAAGATTGAATCTTTAAAGTAATTAGTAAGT
          1 AAAAATGTCATCTTTGGGTAAAAGATTGAATTTTTAGAGTAATTAGTAAAT

               *  * * *     **           *               *      
       5138 AAAGATTTAACCTTTGAATAAAAGATTTGGATTTTT-GAGTAATTGGTAAAT
          1 AAAAATGTCATCTTTGGGTAAAAGA-TTGAATTTTTAGAGTAATTAGTAAAT

                                            *            
       5189 AAAAATGTCGA-CTTTGGGTAAAAGATTGAATCTTTAGAGTAATT
          1 AAAAATGTC-ATCTTTGGGTAAAAGATTGAATTTTTAGAGTAATT


Statistics
Matches: 218,  Mismatches: 28, Indels: 7
        0.86            0.11        0.03

Matches are distributed among these distances:
  50    8  0.04
  51  116  0.53
  52   94  0.43

ACGTcount: A:0.41, C:0.05, G:0.19, T:0.36


Consensus pattern (51 bp):   
AAAAATGTCATCTTTGGGTAAAAGATTGAATTTTTAGAGTAATTAGTAAAT

Done.