Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006147.1 Corchorus capsularis cultivar CVL-1 contig06165, 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: 11275
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32


Found at i:1710 original size:6 final size:6

Alignment explanation


    Indices: 1699--1735  Score: 74
    Period size: 6  Copynumber: 6.2  Consensus size: 6

       1689 AGAGATCTAG

                                                       
       1699 TAAATA TAAATA TAAATA TAAATA TAAATA TAAATA T
          1 TAAATA TAAATA TAAATA TAAATA TAAATA TAAATA T

       1736 GGGTAATAAT


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   31  1.00

ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35


Consensus pattern (6 bp):   
TAAATA

Found at i:2381 original size:18 final size:17

Alignment explanation


    Indices: 2354--2387  Score: 68
    Period size: 17  Copynumber: 2.0  Consensus size: 17

       2344 AAGTTACAGA

                             
       2354 TTTTTCAAAAAATAATC
          1 TTTTTCAAAAAATAATC

                             
       2371 TTTTTCAAAAAATAATC
          1 TTTTTCAAAAAATAATC

       2388 AACAAAGTCA


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:0.47, C:0.12, G:0.00, T:0.41


Consensus pattern (17 bp):   
TTTTTCAAAAAATAATC

Found at i:3009 original size:167 final size:165

Alignment explanation


    Indices: 2533--3013  Score: 628
    Period size: 167  Copynumber: 2.9  Consensus size: 165

       2523 TAAGTCATTT

                            *                                *               
       2533 GTCAATTGAGAAATGATCAAAAAGTTTAGTTATTTAATCCCCTCAAGAACCAAAAGTTAGGACAT
          1 GTCAATTGAGAAATGACCAAAAAG-TTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT

                                 *     *      *                *             
       2598 TTAAGTAATCTGCCAAGTAGGTAAAGAGGAAAAAGATTAGTTCTCTAACTCATCATCAATCCTTG
         65 TTAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAATTAGTTCTCTAACTCCTCATCAATCCTTG

              *           *                  *  
       2663 ATGGGGATCTTTTATTAATTCCACTACTCTATTCAA
        130 ATAGGGATCTTTTAGTAATTCCACTACTCTATTAAA

               *            **                                               
       2699 GTCCATTGAGAAATGAGAAAAAAGTTACG-TATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
          1 GTCAATTGAGAAATGACCAAAAAGTTA-GTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT

                                                 *      *        ** *   *    
       2763 TTAAGTAATCTGCCAAGTAGGAAAAGAC-AAAAAAA-AAGTTCTATAACTCCAAAAGCAAGCCTT
         65 TTAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAATTAGTTCTCTAACTCC-TCATCAATCCTT

                                                   
       2826 GATAGGGATCTTTTAGTAATTCCACTACTCTATATTAAA
        129 GATAGGGATCTTTTAGTAATTCCACTACTC--TATTAAA

                                                   *                         
       2865 GTCAATTGAGAAATGACCAAAAAGTCTAGTTATTTAATCACCTCAAGAATCAAAAGTTAGGACAT
          1 GTCAATTGAGAAATGACCAAAAAGT-TAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT

                      * *     *                           **        *     ** 
       2930 TTAAGTAATCGGTCAAGTGGGAAAAGACGAAAAAAATTAGTTCTCTCGCTCCTCATTAATCCGGG
         65 TTAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAATTAGTTCTCTAACTCCTCATCAATCCTTG

            *                   
       2995 GTAGGGAT-TTTTAGTAATT
        130 ATAGGGATCTTTTAGTAATT

       3014 TACATATGTT


Statistics
Matches: 271,  Mismatches: 36, Indels: 15
        0.84            0.11        0.05

Matches are distributed among these distances:
 163   12  0.04
 164   42  0.15
 165   63  0.23
 166   51  0.19
 167   72  0.27
 168   20  0.07
 169   11  0.04

ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29


Consensus pattern (165 bp):   
GTCAATTGAGAAATGACCAAAAAGTTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACATT
TAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAATTAGTTCTCTAACTCCTCATCAATCCTTGA
TAGGGATCTTTTAGTAATTCCACTACTCTATTAAA

Found at i:10197 original size:8 final size:8

Alignment explanation


    Indices: 10184--10217  Score: 50
    Period size: 8  Copynumber: 4.1  Consensus size: 8

      10174 CACCTTCTTG

                    
      10184 AAAAATTC
          1 AAAAATTC

                    
      10192 AAAAATTC
          1 AAAAATTC

                 *   
      10200 AGAAACTTC
          1 A-AAAATTC

                    
      10209 AAAAATTC
          1 AAAAATTC

             
      10217 A
          1 A

      10218 TAGCCGATTC


Statistics
Matches: 23,  Mismatches: 2, Indels: 2
        0.85            0.07        0.07

Matches are distributed among these distances:
   8   16  0.70
   9    7  0.30

ACGTcount: A:0.59, C:0.15, G:0.03, T:0.24


Consensus pattern (8 bp):   
AAAAATTC
Done.