Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01000700.1 Corchorus capsularis cultivar CVL-1 contig00700, 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: 1980
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.37


Found at i:369 original size:167 final size:162

Alignment explanation


    Indices: 48--494  Score: 558
    Period size: 167  Copynumber: 2.7  Consensus size: 162

         38 TCCCCACCCT

                 *    *    *                          *                      
         48 GGATTAATGACGAGCGAGAGAACTAATTTTTTCGTCTTTTCCCACTTGGCAGATTACTTAAATGT
          1 GGATTGATGATGAGCTAGAGAACTAATTTTTTCGTCTTTTCCTACTTGGCAGATTACTTAAATGT

                                                                       *     
        113 -CTCAACTTTTGATTCTTGAGGGGATTAAATAAAT-ATGCTTTTTGGTCATTTCTCAATTGACTT
         66 CCT-AACTTTTGATTCTTGAGGGGATTAAATAAATAAT-CTTTTTGGTCATTTCTCAATAGACTT

            *    *             *                 
        176 TAATATAGTAATAGAATTACTAAAAGATCCCTACCAA
        129 GAATAGAGTAATAGAATTAATAAAAGAT--C-ACCAA

              *   * **     *         *           *                           
        213 GGCTTGCTTTTGGAGTTAGAGAACTTATTTTTTCCGTTTTTTCCTACTTGGCAGATTACTTAAAT
          1 GGATTGATGAT-GAGCTAGAGAACTAATTTTTT-CGTCTTTTCCTACTTGGCAGATTACTTAAAT

                                              *     *                        
        278 GTCCTAACTTTTGATTCTTGAGGGGATTAAATAAGTAATCGTTTTGGTCATTTCTCAATAGACTT
         64 GTCCTAACTTTTGATTCTTGAGGGGATTAAATAAATAATCTTTTTGGTCATTTCTCAATAGACTT

                     ** *                 *   
        343 GAATAGAGTGGTGGAATTAATAAAAGATCATCAA
        129 GAATAGAGTAATAGAATTAATAAAAGATCACCAA

                                                    *                        
        377 GGATTGATGATGAGCTAGAGAACTAATCTTTTTCGTCTTTACCTACTTGGCAGATTACTTAAATG
          1 GGATTGATGATGAGCTAGAGAACTAAT-TTTTTCGTCTTTTCCTACTTGGCAGATTACTTAAATG

                   *        *  *             *   *                
        442 TCCT-ACCTTTGATTCCTGGGGGGATTAAATAACTAAACTTTTTGGTCATTTCT
         65 TCCTAACTTTTGATTCTTGAGGGGATTAAATAAATAATCTTTTTGGTCATTTCT

        495 TAATTGACAA


Statistics
Matches: 242,  Mismatches: 35, Indels: 13
        0.83            0.12        0.04

Matches are distributed among these distances:
 162   43  0.18
 163   48  0.20
 164   16  0.07
 165    6  0.02
 166   18  0.07
 167  107  0.44
 168    4  0.02

ACGTcount: A:0.29, C:0.15, G:0.18, T:0.38


Consensus pattern (162 bp):   
GGATTGATGATGAGCTAGAGAACTAATTTTTTCGTCTTTTCCTACTTGGCAGATTACTTAAATGT
CCTAACTTTTGATTCTTGAGGGGATTAAATAAATAATCTTTTTGGTCATTTCTCAATAGACTTGA
ATAGAGTAATAGAATTAATAAAAGATCACCAA
Done.