Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01000982.1 Corchorus capsularis cultivar CVL-1 contig00982, 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, 695

Length: 1159
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.33


Found at i:990 original size:107 final size:107

Alignment explanation


    Indices: 851--1120  Score: 330
    Period size: 107  Copynumber: 2.5  Consensus size: 107

        841 TTAATGACCC

                            *                                 *              
        851 AGGGTGGTTACTT-TTAAGTTCAGTTCGGAATGATCGAGGGTGGTCGTTCCTCAGTTTATTTCAG
          1 AGGGTGGTTA-TTCTTCAGTTCAGTTCGGAATGATCGAGGGTGGTCGTTCTTCAGTTTATTTCAG

                   * *        *        *                
        915 TTGACCCGGGGTGGTCTTTCTTCAATTCG-AGTCAGAATGATCG
         65 TTGACCCAGAGTGGTCTTCCTTCAATTAGCA-TCAGAATGATCG

                                *   *                                    *   
        958 AGGGTGGTTATTCTTCAGTTTAGTCCGGAATGATCGAGGGTGGTCGTTCTTCAGTTTATTTTAGT
          1 AGGGTGGTTATTCTTCAGTTCAGTTCGGAATGATCGAGGGTGGTCGTTCTTCAGTTTATTTCAGT

                *                  *        *        *
       1023 TGACTCAGAGTGGTCTTCCTTCAGTTAGCATCGGAATGATCT
         66 TGACCCAGAGTGGTCTTCCTTCAATTAGCATCAGAATGATCG

                           *      *   *         *         *          
       1065 AGGGTGGTCT-TTCTCCAGTTCGGTTTGGAATGATCTAGGGTGGTCTTTCTTCAGTT
          1 AGGGTGGT-TATTCTTCAGTTCAGTTCGGAATGATCGAGGGTGGTCGTTCTTCAGTT

       1121 ACTTATTTTA


Statistics
Matches: 140,  Mismatches: 20, Indels: 6
        0.84            0.12        0.04

Matches are distributed among these distances:
 106    2  0.01
 107  136  0.97
 108    2  0.01

ACGTcount: A:0.17, C:0.16, G:0.29, T:0.38


Consensus pattern (107 bp):   
AGGGTGGTTATTCTTCAGTTCAGTTCGGAATGATCGAGGGTGGTCGTTCTTCAGTTTATTTCAGT
TGACCCAGAGTGGTCTTCCTTCAATTAGCATCAGAATGATCG

Found at i:1011 original size:36 final size:36

Alignment explanation


    Indices: 867--1120  Score: 189
    Period size: 36  Copynumber: 7.1  Consensus size: 36

        857 GTTACTTTTA

                *                        *   *  
        867 AGTTCAGTTCGGAATGATCGAGGGTGGTCGTTCCTC
          1 AGTTTAGTTCGGAATGATCGAGGGTGGTCTTTCTTC

                  *   *  *    *                  
        903 AGTTTATTTCAG-TTGACCCG-GGGTGGTCTTTCTTC
          1 AGTTTAGTTCGGAATGA-TCGAGGGTGGTCTTTCTTC

             *   *     *                          
        938 AATTCGAG-TCAGAATGATCGAGGGTGGT-TATTCTTC
          1 AGTT-TAGTTCGGAATGATCGAGGGTGGTCT-TTCTTC

                    *                    *      
        974 AGTTTAGTCCGGAATGATCGAGGGTGGTCGTTCTTC
          1 AGTTTAGTTCGGAATGATCGAGGGTGGTCTTTCTTC

                  *  **  *         *        *    
       1010 AGTTTATTTTAG-TTGACTC-AGAGTGGTCTTCCTTC
          1 AGTTTAGTTCGGAATGA-TCGAGGGTGGTCTTTCTTC

                    *           *              * 
       1045 AG-TTAGCATCGGAATGATCTAGGGTGGTCTTTCTCC
          1 AGTTTAG-TTCGGAATGATCGAGGGTGGTCTTTCTTC

                **   *         *                
       1081 AGTTCGGTTTGGAATGATCTAGGGTGGTCTTTCTTC
          1 AGTTTAGTTCGGAATGATCGAGGGTGGTCTTTCTTC

                
       1117 AGTT
          1 AGTT

       1121 ACTTATTTTA


Statistics
Matches: 168,  Mismatches: 38, Indels: 24
        0.73            0.17        0.10

Matches are distributed among these distances:
  34    3  0.02
  35   50  0.30
  36  113  0.67
  37    2  0.01

ACGTcount: A:0.17, C:0.17, G:0.28, T:0.37


Consensus pattern (36 bp):   
AGTTTAGTTCGGAATGATCGAGGGTGGTCTTTCTTC
Done.