Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006490.1 Corchorus capsularis cultivar CVL-1 contig06511, 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, 886

Length: 1478
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.35


Found at i:281 original size:154 final size:154

Alignment explanation


    Indices: 1--858  Score: 1181
    Period size: 154  Copynumber: 5.6  Consensus size: 154

                                  *   *                                    * 
          1 GCTGTTTTTGAATCGTCTTCGATTTTAGCAAACCACTAAAGC-TTTCTTTCAATTGTTTAC-GAC
          1 GCTG-TTTTGAATCGTCTTC-AATTTGGCAAACCAC-AAAGCTTTTCTTTCAATTGTTTACGGCC

                                          *             *       *            
         64 TAACTAT-ATTATTTTGATGAGATTAGTCCATTGTGAAGTTTTTTGCTCATTTAGAACACTTGTT
         63 TAACTATAATTATTTTGATGAGATTAGTCCTTTGTGAAGTTTTTAGCTCATTCAGAACACTTGTT

                                       
        128 ATTTCGGGCCTTTCGGGGCCCATTAGT
        128 ATTTCGGGCCTTTCGGGGCCCATTAGT

                              *                            *            *    
        155 GCTGTTTTGAATCGTCTTAAATTTGGCAAACCACAAAGCTTTTCTTTTAATTGTTTACGGGCTAA
          1 GCTGTTTTGAATCGTCTTCAATTTGGCAAACCACAAAGCTTTTCTTTCAATTGTTTACGGCCTAA

                   *                                    *                    
        220 CTATAATCATTTTTG-TGAGATTAGTCCTTTGTGAAGTTTTTAGGTCATTCAGAACACTTGTTAT
         66 CTATAATTA-TTTTGATGAGATTAGTCCTTTGTGAAGTTTTTAGCTCATTCAGAACACTTGTTAT

                                     
        284 TTCGGGCCTTTCGGGGCCCATTAGT
        130 TTCGGGCCTTTCGGGGCCCATTAGT

                               *     *             *                   *     
        309 GCTGTTTTGAATCGTCTTCTATTTGCCAAACCACAAAGCATTTCTTTCAATTGTTTACGACCTAA
          1 GCTGTTTTGAATCGTCTTCAATTTGGCAAACCACAAAGCTTTTCTTTCAATTGTTTACGGCCTAA

                   *      *             *                   *                
        374 CTATAATCATTTTGGTGAGATTAGTCCTCTGTGAAGTTTTTAGCTCATCCAGAACACTTGTTATT
         66 CTATAATTATTTTGATGAGATTAGTCCTTTGTGAAGTTTTTAGCTCATTCAGAACACTTGTTATT

              *         *    * *    
        439 TCAGGCCTTTCGAGGCCGAATAGT
        131 TCGGGCCTTTCGGGGCCCATTAGT

                          *                                            *     
        463 GCTGTTTTGAATCGGCTTCAATTTGGCAAACCACAAAGCTTTTCTTTCAATTGTTTACGACCTAA
          1 GCTGTTTTGAATCGTCTTCAATTTGGCAAACCACAAAGCTTTTCTTTCAATTGTTTACGGCCT-A

                                     *                    *                  
        528 AC-ATAATTATTTTGATGAGATTAGACCATTT-TGAAGTTTTTAGCACATTCAGAACACTTGTTA
         65 ACTATAATTATTTTGATGAGATTAGTCC-TTTGTGAAGTTTTTAGCTCATTCAGAACACTTGTTA

                *       *           * 
        591 TTTCAGGCCTTTTGGGGCCCATTACT
        129 TTTCGGGCCTTTCGGGGCCCATTAGT

               *               *    *                                  * *   
        617 GCTATTTTGAATCGTCTTCGATTTAGCAAACCACAAAGCTTTTCTTTCAATTGTTTACGACGTAA
          1 GCTGTTTTGAATCGTCTTCAATTTGGCAAACCACAAAGCTTTTCTTTCAATTGTTTACGGCCTAA

                 *                     *    *                         *   *  
        682 CTATAGTTATTTTGATGAGATTAGTCCATTGTAAAGTTTTTAGCTCATTCAGAACACTAGTTTTT
         66 CTATAATTATTTTGATGAGATTAGTCCTTTGTGAAGTTTTTAGCTCATTCAGAACACTTGTTATT

                         * *      * 
        747 TCGGGCCTTTCGGAGACCATTACT
        131 TCGGGCCTTTCGGGGCCCATTAGT

                              **                                *     *      
        771 GCTGTTTTGAATCGTCTTTGATTTGGCAAACCACAAAGCTTTTCTTTTC-ATAGTTTATGGCCTA
          1 GCTGTTTTGAATCGTCTTCAATTTGGCAAACCACAAAGCTTTTC-TTTCAATTGTTTACGGCCTA

                                    
        835 ACTATAATTATTTTGATGAGATTA
         65 ACTATAATTATTTTGATGAGATTA

        859 CCTAGTGATG


Statistics
Matches: 631,  Mismatches: 63, Indels: 20
        0.88            0.09        0.03

Matches are distributed among these distances:
 151    5  0.01
 152   30  0.05
 153   33  0.05
 154  549  0.87
 155   14  0.02

ACGTcount: A:0.25, C:0.18, G:0.17, T:0.40


Consensus pattern (154 bp):   
GCTGTTTTGAATCGTCTTCAATTTGGCAAACCACAAAGCTTTTCTTTCAATTGTTTACGGCCTAA
CTATAATTATTTTGATGAGATTAGTCCTTTGTGAAGTTTTTAGCTCATTCAGAACACTTGTTATT
TCGGGCCTTTCGGGGCCCATTAGT

Found at i:914 original size:33 final size:32

Alignment explanation


    Indices: 877--973  Score: 113
    Period size: 33  Copynumber: 2.9  Consensus size: 32

        867 TGACCGGTTA

                       *                     
        877 TGGCCGGACATGTCCATGTCGCGTGGCCGGTGT
          1 TGGCCGGACATCTCCA-GTCGCGTGGCCGGTGT

                   *            *            
        910 TGGCCGGGCATCTCCGAGTCACGTGGCCGGTGT
          1 TGGCCGGACATCTCC-AGTCGCGTGGCCGGTGT

                 *   *            *        
        943 TGGCCAGACTTCTCCAAGTCGCATGGCCGGT
          1 TGGCCGGACATCTCC-AGTCGCGTGGCCGGT

        974 CACTAGTGCT


Statistics
Matches: 54,  Mismatches: 9, Indels: 2
        0.83            0.14        0.03

Matches are distributed among these distances:
  33   53  0.98
  34    1  0.02

ACGTcount: A:0.11, C:0.30, G:0.36, T:0.23


Consensus pattern (32 bp):   
TGGCCGGACATCTCCAGTCGCGTGGCCGGTGT
Done.