Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013320.1 Corchorus olitorius cultivar O-4 contig13353, 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: 10195
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32


Found at i:1354 original size:58 final size:58

Alignment explanation


    Indices: 1254--1583  Score: 434
    Period size: 58  Copynumber: 5.7  Consensus size: 58

       1244 TCATACTCAT

                         *      *                                     
       1254 CCTTAATC-TAAAGT-TTTTGGGAACTGTCTTCAGATCCATCTGTGAGCTGTCTTCAG
          1 CCTTAATCTTAAAATCTTTTAGGAACTGTCTTCAGATCCATCTGTGAGCTGTCTTCAG

                                     *            *                   
       1310 CCTTAATCTTAAAATCTTTTAGGAATTGTCTTCAGATCTATCTGTGAGCTGTCTTCAG
          1 CCTTAATCTTAAAATCTTTTAGGAACTGTCTTCAGATCCATCTGTGAGCTGTCTTCAG

             *                 *                       *             *
       1368 CTTTAATCTTAAAATCTTTCAGGAACTGTCTTCAGATCCATCTATGAGCTGTCTTCAA
          1 CCTTAATCTTAAAATCTTTTAGGAACTGTCTTCAGATCCATCTGTGAGCTGTCTTCAG

            *  *                *    *  *           *   *              
       1426 TCTCAATCTTAAAATC-TTTCGAGAGCTATCTTCAGATCCGTCTATGAGCTGTCTTCAG
          1 CCTTAATCTTAAAATCTTTTAG-GAACTGTCTTCAGATCCATCTGTGAGCTGTCTTCAG

            *  *               *    *                                 
       1484 TCTCAATCTTAAAATCTTTCAGGAGCTGTCTTCAGATCCATCTGTGAGCTGTCTTCAG
          1 CCTTAATCTTAAAATCTTTTAGGAACTGTCTTCAGATCCATCTGTGAGCTGTCTTCAG

                                                       
       1542 CCTTAATCTTAAAAT-TTTTCAGGAACTGTCTTCAGAATCCAT
          1 CCTTAATCTTAAAATCTTTT-AGGAACTGTCTTCAG-ATCCAT

       1584 TTCTGATGAA


Statistics
Matches: 240,  Mismatches: 28, Indels: 9
        0.87            0.10        0.03

Matches are distributed among these distances:
  56    8  0.03
  57   11  0.05
  58  212  0.88
  59    9  0.04

ACGTcount: A:0.25, C:0.22, G:0.15, T:0.38


Consensus pattern (58 bp):   
CCTTAATCTTAAAATCTTTTAGGAACTGTCTTCAGATCCATCTGTGAGCTGTCTTCAG

Found at i:9197 original size:39 final size:38

Alignment explanation


    Indices: 9105--9372  Score: 194
    Period size: 39  Copynumber: 6.8  Consensus size: 38

       9095 GAAATCTTTA

                                                   ** 
       9105 ATGGGATCTTTCCCCT-AATTGAAAACTTTGAAAAAGACCAG
          1 ATGGGATCTTT-CCCTAAATT-AAAACTTTG-AAAA-ACTTG

                    *                              
       9146 ATGGGA-CCTTCCCTAAATTAAAACTTCTGAAAAACTTG
          1 ATGGGATCTTTCCCTAAATTAAAACTT-TGAAAAACTTG

                                           *        * 
       9184 ATGGGATCTTTCCCTAAATTAAAGACTTTAAAAAGAAACTGG
          1 ATGGGATCTTTCCCTAAATTAAA-ACTTT--GAA-AAACTTG

                                *         *          
       9226 ATGGGATCTTTCCCTAAATCGAAAGAC-TTAAACAAACTTG
          1 ATGGGATCTTTCCCTAAAT-TAAA-ACTTTGAA-AAACTTG

                  *                            *    
       9266 ATGGGACCTTTCCC--AATTAGAAA-TCTTG-AAAGCTTG
          1 ATGGGATCTTTCCCTAAATTA-AAACT-TTGAAAAACTTG

                            *                        
       9302 ATGGGATCTTTCCCTATATTAAAAAC-TTGAGAAATAC-TG
          1 ATGGGATCTTTCCCTAAATT-AAAACTTTGA-AAA-ACTTG

            *                *      *       
       9341 GTGGGATCTTTCCCTAATTTGAAATCTTTGAA
          1 ATGGGATCTTTCCCTAAATT-AAAACTTTGAA

       9373 TTGAAAACTT


Statistics
Matches: 187,  Mismatches: 21, Indels: 40
        0.75            0.08        0.16

Matches are distributed among these distances:
  36   19  0.10
  37    6  0.03
  38   22  0.12
  39   59  0.32
  40   40  0.21
  41    8  0.04
  42   27  0.14
  43    6  0.03

ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31


Consensus pattern (38 bp):   
ATGGGATCTTTCCCTAAATTAAAACTTTGAAAAACTTG

Done.