Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01000225.1 Corchorus capsularis cultivar CVL-1 contig00225, 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: 4746
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.34


Found at i:2465 original size:24 final size:24

Alignment explanation


    Indices: 2407--2465  Score: 73
    Period size: 24  Copynumber: 2.5  Consensus size: 24

       2397 ATGTGGCAGC

                              * * * 
       2407 ATGGTGCTTAACTTCTGCGGTAGA
          1 ATGGTGCTTAACTTCTGCCGCAAA

              *   *                 
       2431 ATTGTGATTAACTTCTGCCGCAAA
          1 ATGGTGCTTAACTTCTGCCGCAAA

                       
       2455 ATGGTGCTTAA
          1 ATGGTGCTTAA

       2466 GATTGGTAGT


Statistics
Matches: 28,  Mismatches: 7, Indels: 0
        0.80            0.20        0.00

Matches are distributed among these distances:
  24   28  1.00

ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34


Consensus pattern (24 bp):   
ATGGTGCTTAACTTCTGCCGCAAA

Found at i:2824 original size:27 final size:27

Alignment explanation


    Indices: 2792--2879  Score: 90
    Period size: 27  Copynumber: 3.3  Consensus size: 27

       2782 TGCCTTGGTG

                  *  *                  
       2792 ATTTTGTCTTGTTGCAGGG-TTCTTGCA
          1 ATTTTGGCTAGTTGC-GGGATTCTTGCA

                                 *   * 
       2819 ATTTTGGCTAGTTGCGGGATTTTTGTA
          1 ATTTTGGCTAGTTGCGGGATTCTTGCA

                              * *       
       2846 ATTTTGGCTAGTTGCGGCAAGT-TTGCA
          1 ATTTTGGCTAGTTGCGG-GATTCTTGCA

                   
       2873 ATTTTGG
          1 ATTTTGG

       2880 GTTGATACGG


Statistics
Matches: 52,  Mismatches: 7, Indels: 4
        0.83            0.11        0.06

Matches are distributed among these distances:
  26    3  0.06
  27   47  0.90
  28    2  0.04

ACGTcount: A:0.15, C:0.11, G:0.28, T:0.45


Consensus pattern (27 bp):   
ATTTTGGCTAGTTGCGGGATTCTTGCA

Found at i:2938 original size:47 final size:46

Alignment explanation


    Indices: 2848--2944  Score: 115
    Period size: 47  Copynumber: 2.1  Consensus size: 46

       2838 TTTTTGTAAT

                *                        *              * 
       2848 TTTGGCTAGTTGCGGCAAGTTTGCAATTTTGGGTTGATACGGCATC
          1 TTTGACTAGTTGCGGCAAGTTTGCAATTTGGGGTTGATACGGCAAC

                        *                         * *       
       2894 TTTGACTAGTTGTGGCAA-TTGTGGCAATTTGGGGTTGCTGCGGCAAC
          1 TTTGACTAGTTGCGGCAAGTT-T-GCAATTTGGGGTTGATACGGCAAC

                
       2941 TTTG
          1 TTTG

       2945 CAATTCTAGG


Statistics
Matches: 43,  Mismatches: 6, Indels: 3
        0.83            0.12        0.06

Matches are distributed among these distances:
  45    2  0.05
  46   17  0.40
  47   24  0.56

ACGTcount: A:0.16, C:0.14, G:0.32, T:0.37


Consensus pattern (46 bp):   
TTTGACTAGTTGCGGCAAGTTTGCAATTTGGGGTTGATACGGCAAC
Done.