Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01006680.1 Corchorus olitorius cultivar O-4 contig06705, 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, 739

Length: 1232
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.31


Found at i:575 original size:15 final size:15

Alignment explanation


    Indices: 557--586  Score: 60
    Period size: 15  Copynumber: 2.0  Consensus size: 15

        547 TGATATAAGT

                           
        557 TGTCCTGATGGTGTG
          1 TGTCCTGATGGTGTG

                           
        572 TGTCCTGATGGTGTG
          1 TGTCCTGATGGTGTG

        587 CTATTTCTTT


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   15  1.00

ACGTcount: A:0.07, C:0.13, G:0.40, T:0.40


Consensus pattern (15 bp):   
TGTCCTGATGGTGTG

Found at i:780 original size:27 final size:27

Alignment explanation


    Indices: 754--847  Score: 143
    Period size: 27  Copynumber: 3.5  Consensus size: 27

        744 ATCATCTCAT

                           *          *
        754 GACCATCGGGATCAATCTTGGCATCAT
          1 GACCATCGGGATCAACCTTGGCATCAC

                                     * 
        781 GACCATCGGGATCAACCTTGGCATCCC
          1 GACCATCGGGATCAACCTTGGCATCAC

                                     * 
        808 GACCATCGGGATCAACCTTGGCATCCC
          1 GACCATCGGGATCAACCTTGGCATCAC

                   *     
        835 GACCATCAGGATC
          1 GACCATCGGGATC

        848 CAATATCATC


Statistics
Matches: 63,  Mismatches: 4, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  27   63  1.00

ACGTcount: A:0.24, C:0.33, G:0.22, T:0.20


Consensus pattern (27 bp):   
GACCATCGGGATCAACCTTGGCATCAC

Found at i:788 original size:54 final size:54

Alignment explanation


    Indices: 724--861  Score: 138
    Period size: 54  Copynumber: 2.6  Consensus size: 54

        714 CCAAATTGCA

                                         *               *        
        724 CATGACCATCGGGACCAAAAATCATCTCATGACCATCGGGATCAATCTTGGCAT
          1 CATGACCATCGGGACCAAAAATCATCTCACGACCATCGGGATCAACCTTGGCAT

                          *   ***                                   
        778 CATGACCATCGGGATCAACCTTGGCATC-C-CGACCATCGGGATCAACCTTGGCAT
          1 CATGACCATCGGGACCAAAAAT--CATCTCACGACCATCGGGATCAACCTTGGCAT

             **       *         *          
        832 CCCGACCATCAGGATCC-AATATCATCTCAC
          1 CATGACCATCGGGA-CCAAAAATCATCTCAC

        862 ATCATCAGGA


Statistics
Matches: 66,  Mismatches: 13, Indels: 10
        0.74            0.15        0.11

Matches are distributed among these distances:
  52    4  0.06
  53    1  0.02
  54   55  0.83
  55    2  0.03
  56    4  0.06

ACGTcount: A:0.28, C:0.33, G:0.18, T:0.21


Consensus pattern (54 bp):   
CATGACCATCGGGACCAAAAATCATCTCACGACCATCGGGATCAACCTTGGCAT
Done.