Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009852.1 Corchorus capsularis cultivar CVL-1 contig09873, 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: 28326
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33


Found at i:3513 original size:17 final size:17

Alignment explanation


    Indices: 3493--3526  Score: 68
    Period size: 17  Copynumber: 2.0  Consensus size: 17

       3483 TAAGTTACAG

                             
       3493 ATTTTTCAAAAAATAAT
          1 ATTTTTCAAAAAATAAT

                             
       3510 ATTTTTCAAAAAATAAT
          1 ATTTTTCAAAAAATAAT

       3527 CGACGGAAAA


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   17  1.00

ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41


Consensus pattern (17 bp):   
ATTTTTCAAAAAATAAT

Found at i:3905 original size:165 final size:165

Alignment explanation


    Indices: 3688--4131  Score: 554
    Period size: 168  Copynumber: 2.7  Consensus size: 165

       3678 TGAGTCATTT

                                                                             
       3688 GTCAATTGAGAAATGA-CAAAAAAGTTTAATTATTTAATTCCCTCAAGAATCAAAAGTTAGGACA
          1 GTCAATTGAGAAATGACCAAAAAA--TTAATTATTTAA-TCCCTCAAGAATCAAAAGTTAGGACA

                                  *     *      *       *          ** *   *   
       3752 TTTAAGTAATCTGCCAAGTAGGTAAAGAGGAAAAAGATTAGTTTTCTAACT-CATCATCAATCCT
         63 TTTAAGTAATCTGCCAAGTAGGAAAAGAAGAAAAAAATTAGTTCTCTAACTCCAAAAGCAAGCCT

                *           *                  *  
       3816 TGATGGGGATCTTTTATTAATTCCACTACTCTATTCAA
        128 TGATAGGGATCTTTTAGTAATTCCACTACTCTATTAAA

               *                       *              *                     *
       3854 GTCCATTGAGAAATGACCAAAAAATTACTTATTTAATCCTCTGAAGAATCAAAAGTTAGGACATC
          1 GTCAATTGAGAAATGACCAAAAAATTAATTATTTAATCC-CTCAAGAATCAAAAGTTAGGACATT

                                         *        *                          
       3919 TAAGTAATCTGCCAAGTAGGAAAAGACCAAAAAAAAATAAGTTCTCTAACTCCAAAAGCAAGCCT
         65 TAAGTAATCTGCCAAGTAGGAAAAGA--AGAAAAAAATTAGTTCTCTAACTCCAAAAGCAAGCCT

              *                    *              
       3984 TGGTAGGGATCTTTTAGTAATTCGACTACTCTATTAAA
        128 TGATAGGGATCTTTTAGTAATTCCACTACTCTATTAAA

                                   *    *                                  * 
       4022 GTCAATTGAGAAATGACCAAAAAGTCTAGTTATTTAATCACCTCAAGAATCAAAAGTTAAGG-TA
          1 GTCAATTGAGAAATGACCAAAAAAT-TAATTATTTAATC-CCTCAAGAATCAAAAGTT-AGGACA

                       * *              *                  
       4086 TTTAAGTAA-CGGTCAAGTAGGAAAAGACGAAAAAAATTAGTTCTCT
         63 TTTAAGTAATCTGCCAAGTAGGAAAAGAAGAAAAAAATTAGTTCTCT

       4132 CGCTCCTCAT


Statistics
Matches: 240,  Mismatches: 30, Indels: 16
        0.84            0.10        0.06

Matches are distributed among these distances:
 164    3  0.01
 165   59  0.25
 166   31  0.13
 167   25  0.10
 168   81  0.34
 169   37  0.15
 170    4  0.02

ACGTcount: A:0.41, C:0.15, G:0.15, T:0.29


Consensus pattern (165 bp):   
GTCAATTGAGAAATGACCAAAAAATTAATTATTTAATCCCTCAAGAATCAAAAGTTAGGACATTT
AAGTAATCTGCCAAGTAGGAAAAGAAGAAAAAAATTAGTTCTCTAACTCCAAAAGCAAGCCTTGA
TAGGGATCTTTTAGTAATTCCACTACTCTATTAAA

Found at i:17822 original size:24 final size:24

Alignment explanation


    Indices: 17790--17838  Score: 89
    Period size: 24  Copynumber: 2.0  Consensus size: 24

      17780 AGTGAAGCTG

                         *          
      17790 CAGTCAACCTTCCTAGACAAGATT
          1 CAGTCAACCTTCCAAGACAAGATT

                                    
      17814 CAGTCAACCTTCCAAGACAAGATT
          1 CAGTCAACCTTCCAAGACAAGATT

             
      17838 C
          1 C

      17839 TGATTCATCA


Statistics
Matches: 24,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  24   24  1.00

ACGTcount: A:0.35, C:0.31, G:0.12, T:0.22


Consensus pattern (24 bp):   
CAGTCAACCTTCCAAGACAAGATT

Found at i:23902 original size:25 final size:25

Alignment explanation


    Indices: 23847--23893  Score: 78
    Period size: 25  Copynumber: 1.9  Consensus size: 25

      23837 AAGCCTACCC

                                     
      23847 AAAAAAAAACATAAGAATTTGAAAA
          1 AAAAAAAAACATAAGAATTTGAAAA

                        *          
      23872 AAAAAAAAACATGA-AATTTGAA
          1 AAAAAAAAACATAAGAATTTGAA

      23894 GAATCAAAAG


Statistics
Matches: 21,  Mismatches: 1, Indels: 1
        0.91            0.04        0.04

Matches are distributed among these distances:
  24    8  0.38
  25   13  0.62

ACGTcount: A:0.70, C:0.04, G:0.09, T:0.17


Consensus pattern (25 bp):   
AAAAAAAAACATAAGAATTTGAAAA

Found at i:24765 original size:3 final size:3

Alignment explanation


    Indices: 24757--24796  Score: 53
    Period size: 3  Copynumber: 13.3  Consensus size: 3

      24747 TTCAGTGAAA

                            *           *         *              
      24757 AAT AAT AAT AAT GAT AAT AAT TAT AAT AAC AAT AAT AAT A
          1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A

      24797 GTTAAGTTGT


Statistics
Matches: 31,  Mismatches: 6, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
   3   31  1.00

ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33


Consensus pattern (3 bp):   
AAT

Done.