Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015890.1 Corchorus olitorius cultivar O-4 contig15923, 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: 4167
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34


Found at i:562 original size:15 final size:15

Alignment explanation


    Indices: 529--570  Score: 57
    Period size: 15  Copynumber: 2.7  Consensus size: 15

        519 TTACTTTGCT

                          * 
        529 TTGTTTTCTAGTTTCA
          1 TTGTTTTCT-GTTTAA

                           
        545 TTGTTTTCTGTTTAA
          1 TTGTTTTCTGTTTAA

               *       
        560 TTGCTTTCTGT
          1 TTGTTTTCTGT

        571 CAACCTCTGT


Statistics
Matches: 24,  Mismatches: 2, Indels: 1
        0.89            0.07        0.04

Matches are distributed among these distances:
  15   15  0.62
  16    9  0.38

ACGTcount: A:0.10, C:0.12, G:0.14, T:0.64


Consensus pattern (15 bp):   
TTGTTTTCTGTTTAA

Found at i:2668 original size:24 final size:24

Alignment explanation


    Indices: 2613--2668  Score: 67
    Period size: 24  Copynumber: 2.3  Consensus size: 24

       2603 AGTATGGTGC

                *    *          *   
       2613 TTGAATTCTGCTGTAGAATAGTGA
          1 TTGACTTCTACTGTAGAATAATGA

                                   *
       2637 TTGACTTCTACTGTAGAATAATGG
          1 TTGACTTCTACTGTAGAATAATGA

               *    
       2661 TTGGCTTC
          1 TTGACTTC

       2669 CTTCCACAGG


Statistics
Matches: 27,  Mismatches: 5, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  24   27  1.00

ACGTcount: A:0.25, C:0.12, G:0.23, T:0.39


Consensus pattern (24 bp):   
TTGACTTCTACTGTAGAATAATGA

Found at i:2870 original size:27 final size:26

Alignment explanation


    Indices: 2839--2927  Score: 81
    Period size: 27  Copynumber: 3.3  Consensus size: 26

       2829 CGTAGTTGAC

                         *     *       
       2839 ACTCATGCTGAAATTCCAGAAGTTGGG
          1 ACTCATGCTGAAACTCC-GCAGTTGGG

                 *   *                  
       2866 ACTCACGC-CAAAGCCTCCGCAGTTGGG
          1 ACTCATGCTGAAA--CTCCGCAGTTGGG

                      * *              
       2893 ACTCATGCTGCAGCTCCCGCAGTTGGG
          1 ACTCATGCTGAAACT-CCGCAGTTGGG

                    
       2920 ACTCATGC
          1 ACTCATGC

       2928 CAAAGCCTCT


Statistics
Matches: 50,  Mismatches: 8, Indels: 8
        0.76            0.12        0.12

Matches are distributed among these distances:
  26    5  0.10
  27   41  0.82
  28    4  0.08

ACGTcount: A:0.22, C:0.30, G:0.26, T:0.21


Consensus pattern (26 bp):   
ACTCATGCTGAAACTCCGCAGTTGGG

Found at i:2943 original size:27 final size:27

Alignment explanation


    Indices: 2859--2945  Score: 104
    Period size: 27  Copynumber: 3.2  Consensus size: 27

       2849 AAATTCCAGA

                        *              
       2859 AGTTGGGACTCACGCCAAAGCCTCCGC
          1 AGTTGGGACTCATGCCAAAGCCTCCGC

                           ***          
       2886 AGTTGGGACTCATGCTGCAG-CTCCCGC
          1 AGTTGGGACTCATGCCAAAGCCT-CCGC

                                    * *
       2913 AGTTGGGACTCATGCCAAAGCCTCTGT
          1 AGTTGGGACTCATGCCAAAGCCTCCGC

                  
       2940 AGTTGG
          1 AGTTGG

       2946 CACTTTTGCT


Statistics
Matches: 49,  Mismatches: 9, Indels: 4
        0.79            0.15        0.06

Matches are distributed among these distances:
  26    2  0.04
  27   45  0.92
  28    2  0.04

ACGTcount: A:0.20, C:0.30, G:0.29, T:0.22


Consensus pattern (27 bp):   
AGTTGGGACTCATGCCAAAGCCTCCGC
Done.