Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012107.1 Corchorus capsularis cultivar CVL-1 contig12128, 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: 13504
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30


Found at i:1184 original size:33 final size:33

Alignment explanation


    Indices: 1167--1320  Score: 195
    Period size: 33  Copynumber: 4.7  Consensus size: 33

       1157 CGACTTGGAG

                               *  * *         
       1167 ATGCCCGGCCA-ACACCGGTCATGTGACATGACC
          1 ATGCCCGGCCACA-ACCGGCCACGCGACATGACC

                                             
       1200 ATGCCCGGCCACAACCGGCCACGCGACATGACC
          1 ATGCCCGGCCACAACCGGCCACGCGACATGACC

                                             
       1233 ATGCCCGGCCACAACCGGCCACGCGACATGACC
          1 ATGCCCGGCCACAACCGGCCACGCGACATGACC

            *                 *   **       *  
       1266 TTGCCCGGCCACAACCGGTCACATGAC-TCGGCC
          1 ATGCCCGGCCACAACCGGCCACGCGACAT-GACC

             *                    
       1299 AAGCCCGGCCACAACCGGCCAC
          1 ATGCCCGGCCACAACCGGCCAC

       1321 ATGATCCTTT


Statistics
Matches: 108,  Mismatches: 11, Indels: 4
        0.88            0.09        0.03

Matches are distributed among these distances:
  32    1  0.01
  33  106  0.98
  34    1  0.01

ACGTcount: A:0.23, C:0.44, G:0.24, T:0.09


Consensus pattern (33 bp):   
ATGCCCGGCCACAACCGGCCACGCGACATGACC

Found at i:11112 original size:30 final size:30

Alignment explanation


    Indices: 11078--11147  Score: 131
    Period size: 30  Copynumber: 2.3  Consensus size: 30

      11068 CAAAGGATCA

                       *                  
      11078 AATGGCATCTTTGGTGCGATTCCATCACCT
          1 AATGGCATCTTAGGTGCGATTCCATCACCT

                                          
      11108 AATGGCATCTTAGGTGCGATTCCATCACCT
          1 AATGGCATCTTAGGTGCGATTCCATCACCT

                      
      11138 AATGGCATCT
          1 AATGGCATCT

      11148 CCATTGTATT


Statistics
Matches: 39,  Mismatches: 1, Indels: 0
        0.98            0.03        0.00

Matches are distributed among these distances:
  30   39  1.00

ACGTcount: A:0.23, C:0.26, G:0.20, T:0.31


Consensus pattern (30 bp):   
AATGGCATCTTAGGTGCGATTCCATCACCT

Found at i:11324 original size:30 final size:30

Alignment explanation


    Indices: 11283--11345  Score: 83
    Period size: 30  Copynumber: 2.1  Consensus size: 30

      11273 TCTTCAAGGG

                *                          
      11283 GGAGGGAATGATGCACCCAAGG-CATATCAT
          1 GGAGAGAATGATGC-CCCAAGGACATATCAT

                          *        *      
      11313 GGAGAGAATGATGCGCCAAGGACTTATCAT
          1 GGAGAGAATGATGCCCCAAGGACATATCAT

               
      11343 GGA
          1 GGA

      11346 CTTGAAGATG


Statistics
Matches: 29,  Mismatches: 3, Indels: 2
        0.85            0.09        0.06

Matches are distributed among these distances:
  29    6  0.21
  30   23  0.79

ACGTcount: A:0.33, C:0.17, G:0.32, T:0.17


Consensus pattern (30 bp):   
GGAGAGAATGATGCCCCAAGGACATATCAT

Found at i:12257 original size:54 final size:54

Alignment explanation


    Indices: 12103--12263  Score: 241
    Period size: 55  Copynumber: 3.0  Consensus size: 54

      12093 GAAATCTTTC

                                   * *  *            *            
      12103 TTCAAGGAACACTGGAGATCACGAAAATTTCAAGCGAGTGTTAGCATTGAAGCT
          1 TTCAAGGAACACTGGAGATCACGGAGATCTCAAGCGAGTGTCAGCATTGAAGCT

                                   *                               
      12157 TTCAAGGAACACTGGGAGATCACTGAGATCTCAAGCGAGTGTCAGCATTGAAGCT
          1 TTCAAGGAACACT-GGAGATCACGGAGATCTCAAGCGAGTGTCAGCATTGAAGCT

                            *               *     *             
      12212 TTCAAGGAACACTGGAAATCACGGAGATCTCAGGCGAGCGTCAGCATTGAAG
          1 TTCAAGGAACACTGGAGATCACGGAGATCTCAAGCGAGTGTCAGCATTGAAG

      12264 ATTGATAAGA


Statistics
Matches: 97,  Mismatches: 9, Indels: 2
        0.90            0.08        0.02

Matches are distributed among these distances:
  54   48  0.49
  55   49  0.51

ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21


Consensus pattern (54 bp):   
TTCAAGGAACACTGGAGATCACGGAGATCTCAAGCGAGTGTCAGCATTGAAGCT
Done.