Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013822.1 Corchorus olitorius cultivar O-4 contig13855, 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: 2269
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31


Found at i:369 original size:33 final size:33

Alignment explanation


    Indices: 332--402  Score: 117
    Period size: 33  Copynumber: 2.2  Consensus size: 33

        322 CAAGCAGCGT

                                             
        332 TGGGCCGCGCTGCTGGCCAGCTGGGCAGCACGC
          1 TGGGCCGCGCTGCTGGCCAGCTGGGCAGCACGC

                            **               
        365 TGGGCCGCGCTGCTGGTTAGCTGGGCAGCACGC
          1 TGGGCCGCGCTGCTGGCCAGCTGGGCAGCACGC

                  
        398 -GGGCC
          1 TGGGCC

        403 TAGCTGTGCT


Statistics
Matches: 36,  Mismatches: 2, Indels: 1
        0.92            0.05        0.03

Matches are distributed among these distances:
  32    5  0.14
  33   31  0.86

ACGTcount: A:0.08, C:0.34, G:0.44, T:0.14


Consensus pattern (33 bp):   
TGGGCCGCGCTGCTGGCCAGCTGGGCAGCACGC

Found at i:488 original size:23 final size:23

Alignment explanation


    Indices: 457--500  Score: 61
    Period size: 23  Copynumber: 1.9  Consensus size: 23

        447 TAGGCCCAAC

                     *   *         
        457 AAAAAAAAATGAATGATGAAATG
          1 AAAAAAAAAAGAAAGATGAAATG

                *                
        480 AAAAGAAAAAGAAAGATGAAA
          1 AAAAAAAAAAGAAAGATGAAA

        501 GGGAGGATGA


Statistics
Matches: 18,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  23   18  1.00

ACGTcount: A:0.70, C:0.00, G:0.18, T:0.11


Consensus pattern (23 bp):   
AAAAAAAAAAGAAAGATGAAATG

Found at i:833 original size:26 final size:26

Alignment explanation


    Indices: 778--834  Score: 62
    Period size: 26  Copynumber: 2.2  Consensus size: 26

        768 TTGTAAGAAT

                   *                 *
        778 GTAAATTTCCGTTTTACCCATAAATG
          1 GTAAATTACCGTTTTACCCATAAATA

                                *   *  
        804 GTAAATTACC-TTATTACCCCTAACTA
          1 GTAAATTACCGTT-TTACCCATAAATA

                 
        830 GTAAA
          1 GTAAA

        835 AGTGTACTAA


Statistics
Matches: 26,  Mismatches: 4, Indels: 2
        0.81            0.12        0.06

Matches are distributed among these distances:
  25    2  0.08
  26   24  0.92

ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35


Consensus pattern (26 bp):   
GTAAATTACCGTTTTACCCATAAATA
Done.