Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012899.1 Corchorus capsularis cultivar CVL-1 contig12920, 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: 15216
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33


Found at i:416 original size:167 final size:165

Alignment explanation


    Indices: 36--476  Score: 598
    Period size: 167  Copynumber: 2.6  Consensus size: 165

         26 GTCATTTGTC

                                                                             
         36 AATTGAGAAATGACCAAAAAGTTTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAAGACATTTA
          1 AATTGAGAAATGACCAAAAAG-TTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAAGACATTTA

                                                         *    ** *   *       
        101 AGTAATCTGCCAAGTA-GATAAAGACGAAAAAAATTAGTTCTCTAGCTCATCATCAATCCTTGAT
         65 AGTAATCTGCCAAGTAGGA-AAAGACGAAAAAAATTAGTTCTCTAACTCAAAAGCAAGCCTTGAT

            *           *                  *    *
        165 GGGGATCTTTTATTAATTCCACTACTCTATTCAAGTC
        129 AGGGATCTTTTAGTAATTCCACTACTCTATTAAAGTA

            *                    *   *              *               *        
        202 CATTGAGAAATGACCAAAAAAATTACTTATTTAATCCCCTTAAGAATCAAAAGTTATGACATTTA
          1 AATTGAGAAATGACC-AAAAAGTTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAAGACATTTA

                    *                         *      *                     * 
        267 AGTAATCTACCAAGTAGGAAAAGACGAAAAAAATAAGTTCTTTAACTCCAAAAGCAAGCCTTGGT
         65 AGTAATCTGCCAAGTAGGAAAAGACGAAAAAAATTAGTTCTCTAACT-CAAAAGCAAGCCTTGAT

                                      *          
        332 AGGGATCTTTTAGTAATTCCACTACTTTATTAAAGTA
        129 AGGGATCTTTTAGTAATTCCACTACTCTATTAAAGTA

                                                *                   * *      
        369 AATTGAGAAATGACCAAAAAGTCTAGTTATTTAATCACCTCAAGAATCAAAAGTTAGGGCATTTA
          1 AATTGAGAAATGACCAAAAAGT-TAGTTATTTAATCCCCTCAAGAATCAAAAGTTAAGACATTTA

                   * *                                  
        434 AGTAATCGGTCAAGT-GTGAAAAGACGAAAAAAATTAGTTCTCT
         65 AGTAATCTGCCAAGTAG-GAAAAGACGAAAAAAATTAGTTCTCT

        477 CGCTCCTCAT


Statistics
Matches: 239,  Mismatches: 31, Indels: 9
        0.86            0.11        0.03

Matches are distributed among these distances:
 166  101  0.42
 167  138  0.58

ACGTcount: A:0.41, C:0.16, G:0.14, T:0.29


Consensus pattern (165 bp):   
AATTGAGAAATGACCAAAAAGTTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAAGACATTTAA
GTAATCTGCCAAGTAGGAAAAGACGAAAAAAATTAGTTCTCTAACTCAAAAGCAAGCCTTGATAG
GGATCTTTTAGTAATTCCACTACTCTATTAAAGTA

Found at i:1255 original size:167 final size:165

Alignment explanation


    Indices: 875--1315  Score: 598
    Period size: 167  Copynumber: 2.6  Consensus size: 165

        865 GTCATTTGTC

                                                                             
        875 AATTGAGAAATGACCAAAAAGTTTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAAGACATTTA
          1 AATTGAGAAATGACCAAAAAG-TTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAAGACATTTA

                                                         *    ** *   *       
        940 AGTAATCTGCCAAGTA-GATAAAGACGAAAAAAATTAGTTCTCTAGCTCATCATCAATCCTTGAT
         65 AGTAATCTGCCAAGTAGGA-AAAGACGAAAAAAATTAGTTCTCTAACTCAAAAGCAAGCCTTGAT

            *           *                  *    *
       1004 GGGGATCTTTTATTAATTCCACTACTCTATTCAAGTC
        129 AGGGATCTTTTAGTAATTCCACTACTCTATTAAAGTA

            *                    *   *              *               *        
       1041 CATTGAGAAATGACCAAAAAAATTACTTATTTAATCCCCTTAAGAATCAAAAGTTATGACATTTA
          1 AATTGAGAAATGACC-AAAAAGTTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAAGACATTTA

                    *                         *      *                     * 
       1106 AGTAATCTACCAAGTAGGAAAAGACGAAAAAAATAAGTTCTTTAACTCCAAAAGCAAGCCTTGGT
         65 AGTAATCTGCCAAGTAGGAAAAGACGAAAAAAATTAGTTCTCTAACT-CAAAAGCAAGCCTTGAT

                                      *          
       1171 AGGGATCTTTTAGTAATTCCACTACTTTATTAAAGTA
        129 AGGGATCTTTTAGTAATTCCACTACTCTATTAAAGTA

                                                *                   * *      
       1208 AATTGAGAAATGACCAAAAAGTCTAGTTATTTAATCACCTCAAGAATCAAAAGTTAGGGCATTTA
          1 AATTGAGAAATGACCAAAAAGT-TAGTTATTTAATCCCCTCAAGAATCAAAAGTTAAGACATTTA

                   * *                                  
       1273 AGTAATCGGTCAAGT-GTGAAAAGACGAAAAAAATTAGTTCTCT
         65 AGTAATCTGCCAAGTAG-GAAAAGACGAAAAAAATTAGTTCTCT

       1316 CGCTCCTCAT


Statistics
Matches: 239,  Mismatches: 31, Indels: 9
        0.86            0.11        0.03

Matches are distributed among these distances:
 166  101  0.42
 167  138  0.58

ACGTcount: A:0.41, C:0.16, G:0.14, T:0.29


Consensus pattern (165 bp):   
AATTGAGAAATGACCAAAAAGTTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAAGACATTTAA
GTAATCTGCCAAGTAGGAAAAGACGAAAAAAATTAGTTCTCTAACTCAAAAGCAAGCCTTGATAG
GGATCTTTTAGTAATTCCACTACTCTATTAAAGTA

Found at i:13882 original size:2 final size:2

Alignment explanation


    Indices: 13875--13910  Score: 72
    Period size: 2  Copynumber: 18.0  Consensus size: 2

      13865 CGGTTGCCAC

                                                                 
      13875 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

      13911 CACACACCCT


Statistics
Matches: 34,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   34  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Done.