Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013593.1 Corchorus olitorius cultivar O-4 contig13626, 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: 1861
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32


Found at i:1135 original size:29 final size:31

Alignment explanation


    Indices: 1077--1153  Score: 113
    Period size: 29  Copynumber: 2.5  Consensus size: 31

       1067 ATACCGTACA

                                           
       1077 GGTCCCTCTACTTATAAAAAAGGATCAATTT
          1 GGTCCCTCTACTTATAAAAAAGGATCAATTT

                 *              **         
       1108 GGTCCTTCTAC-TATAAAAACTG-TCAATTT
          1 GGTCCCTCTACTTATAAAAAAGGATCAATTT

                             
       1137 GGTCCCTCTACTTATAA
          1 GGTCCCTCTACTTATAA

       1154 TTTGGTGTCA


Statistics
Matches: 41,  Mismatches: 4, Indels: 3
        0.85            0.08        0.06

Matches are distributed among these distances:
  29   17  0.41
  30   14  0.34
  31   10  0.24

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


Consensus pattern (31 bp):   
GGTCCCTCTACTTATAAAAAAGGATCAATTT

Found at i:1484 original size:29 final size:31

Alignment explanation


    Indices: 1449--1522  Score: 116
    Period size: 29  Copynumber: 2.5  Consensus size: 31

       1439 CACCAAATTG

                                           
       1449 TAAGTAGAGGGACCAAATTGA-CAGTTTTTA
          1 TAAGTAGAGGGACCAAATTGATCAGTTTTTA

                                   **      
       1479 T-AGTAGAGGGACCAAATTGATCCTTTTTTA
          1 TAAGTAGAGGGACCAAATTGATCAGTTTTTA

                          
       1509 TAAGTAGAGGGACC
          1 TAAGTAGAGGGACC

       1523 TGTAGGGTAT


Statistics
Matches: 40,  Mismatches: 2, Indels: 3
        0.89            0.04        0.07

Matches are distributed among these distances:
  29   19  0.47
  30    9  0.22
  31   12  0.30

ACGTcount: A:0.34, C:0.12, G:0.24, T:0.30


Consensus pattern (31 bp):   
TAAGTAGAGGGACCAAATTGATCAGTTTTTA

Found at i:1616 original size:58 final size:58

Alignment explanation


    Indices: 1540--1861  Score: 540
    Period size: 58  Copynumber: 5.5  Consensus size: 58

       1530 TATTTTGACC

                  *                 *                                 
       1540 TAGGAAGTGTCTTCAGATCCATCTGTGAGCTGTCTTCAGTCTCAATCTTAAAATCTTT
          1 TAGGAACTGTCTTCAGATCCATCTATGAGCTGTCTTCAGTCTCAATCTTAAAATCTTT

                         *                                            
       1598 TAGGAACTGTCTTTAGATCCATCTATGAGCTGTCTTCAGTCTCAATCTTAAAATCTTT
          1 TAGGAACTGTCTTCAGATCCATCTATGAGCTGTCTTCAGTCTCAATCTTAAAATCTTT

                                                   *  *               
       1656 TAGGAACTGTCTTCAGATCCATCTATGAGCTGTCTTCAGCCTTAATCTTAAAATCTTT
          1 TAGGAACTGTCTTCAGATCCATCTATGAGCTGTCTTCAGTCTCAATCTTAAAATCTTT

                *                 *                                     
       1714 TAGGGACTGTCTTCAGATCTACTTCTATGAGCTGTCTTCAGTCTCAATCTT-AAATCTTT
          1 TAGGAACTGTCTTCAGATC--CATCTATGAGCTGTCTTCAGTCTCAATCTTAAAATCTTT

                                                                       
       1773 TAGGAACTGTCTTACAGATCCATCTATGAGCTGTCTTCAGTCTCAATCTTAAAATC-TT
          1 TAGGAACTGTCTT-CAGATCCATCTATGAGCTGTCTTCAGTCTCAATCTTAAAATCTTT

                                           
       1831 TAGGAACTGTCTTCAGATCCATCTATGAGCT
          1 TAGGAACTGTCTTCAGATCCATCTATGAGCT


Statistics
Matches: 248,  Mismatches: 12, Indels: 9
        0.92            0.04        0.03

Matches are distributed among these distances:
  57   18  0.07
  58  172  0.69
  59   25  0.10
  60   33  0.13

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


Consensus pattern (58 bp):   
TAGGAACTGTCTTCAGATCCATCTATGAGCTGTCTTCAGTCTCAATCTTAAAATCTTT

Done.