Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01016398.1 Corchorus capsularis cultivar CVL-1 contig16419, 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, 967

Length: 1613
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32


Found at i:562 original size:300 final size:302

Alignment explanation


    Indices: 6--669  Score: 1057
    Period size: 300  Copynumber: 2.2  Consensus size: 302

          1 GGTTG

                                                 * *                         
          6 TATGCAAAACATCATTTTTAGCGAAAGGCTCATTCCAAACGCATTTTTTGCGTCAACGAGTGCTC
          1 TATGCAAAACATCATTTTTAGCGAAAGGCTCATTCCAGATGCATTTTTTGCG-CAACGAGTGCTC

                     *                         * *                 *         
         71 AAATGAACGTGCGTCAAAGTGCGATGAGATTGTTGGATAGCCCTGTGCACAAACAGAGCATGTTA
         65 AAATGAACGGGCGTCAAAGTGCGATGAGATTGTTGCACAGCCCTGTGCACAAACAAAGCATGTTA

                                                                        *    
        136 GGCAGCGATATGCACAAACTAAAGCTCTCCTCGATGTCCAAAACATCAACTTTGCGAGTTTGTAT
        130 GGCAGCGATATGCACAAACTAAAGCTCTCCTCGATGTCCAAAACATCAACTTTGCGAGTTCGTAT

                *              *                                             
        201 GCAACACATCGTTCTTACCGGTTTGTCGGAGTGAGATGAACTTTTTGGACAGCGCTGTGCAGAAA
        195 GCAAAACATCGTTCTTACCAGTTTGTCGGAGTGAGATGAACTTTTTGGACAGCGCTGTGCAGAAA

                                                       
        266 CAAAGCTTTCCTAAAAGCCCAAAACCTCAACTTTGAGCAGTTC
        260 CAAAGCTTTCCTAAAAGCCCAAAACCTCAACTTTGAGCAGTTC

                                 *  *             *                          
        309 TATGCAAAACATCATTTTTAGTGACAGGCTCATTCCAGTTGCATTTTTTGCGCAACGAGTGCTCA
          1 TATGCAAAACATCATTTTTAGCGAAAGGCTCATTCCAGATGCATTTTTTGCGCAACGAGTGCTCA

                 *        *                  *                        *      
        374 AATG-TCGGGCGTCGAAGTGCGATGAGATTGTTTCACAGCCCTGTGCACAAACAAAGCTTGTTAG
         66 AATGAACGGGCGTCAAAGTGCGATGAGATTGTTGCACAGCCCTGTGCACAAACAAAGCATGTTAG

                  *                                  *                       
        438 GCAGCGCTATGCACAAAC-AAAGCTCTCCTCGATGTCCAAAGCATCAACTTTGCGCA-TTCGTAT
        131 GCAGCGATATGCACAAACTAAAGCTCTCCTCGATGTCCAAAACATCAACTTTGCG-AGTTCGTAT

                             *                               *               
        501 GCAAAACATCGTTCTTAGCAGTTTGTCGGAGTGAGATGAACTTTTTGGATAGC-CATGTGCAGAA
        195 GCAAAACATCGTTCTTACCAGTTTGTCGGAGTGAGATGAACTTTTTGGACAGCGC-TGTGCAGAA

                          *                        *   *
        565 ACAAAGCTTTCCTAGAAGCCCAAAACCTCAACTTTGAGCGGTTG
        259 ACAAAGCTTTCCTAAAAGCCCAAAACCTCAACTTTGAGCAGTTC

                                                  *                      
        609 TATGCAAAACATCATTTTTAGCGAAAGGCTCATTCCAGGTGCATTTTTTGCGCAACGAGTG
          1 TATGCAAAACATCATTTTTAGCGAAAGGCTCATTCCAGATGCATTTTTTGCGCAACGAGTG

        670 TGATCGAGCT


Statistics
Matches: 333,  Mismatches: 26, Indels: 7
        0.91            0.07        0.02

Matches are distributed among these distances:
 299    1  0.00
 300  198  0.59
 301   70  0.21
 302   17  0.05
 303   47  0.14

ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27


Consensus pattern (302 bp):   
TATGCAAAACATCATTTTTAGCGAAAGGCTCATTCCAGATGCATTTTTTGCGCAACGAGTGCTCA
AATGAACGGGCGTCAAAGTGCGATGAGATTGTTGCACAGCCCTGTGCACAAACAAAGCATGTTAG
GCAGCGATATGCACAAACTAAAGCTCTCCTCGATGTCCAAAACATCAACTTTGCGAGTTCGTATG
CAAAACATCGTTCTTACCAGTTTGTCGGAGTGAGATGAACTTTTTGGACAGCGCTGTGCAGAAAC
AAAGCTTTCCTAAAAGCCCAAAACCTCAACTTTGAGCAGTTC
Done.