Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012756.1 Corchorus olitorius cultivar O-4 contig12789, 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: 5314
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.31


Found at i:4070 original size:29 final size:29

Alignment explanation


    Indices: 3998--4071  Score: 96
    Period size: 28  Copynumber: 2.6  Consensus size: 29

       3988 GGGTCACTTA

                                 *  *    
       3998 AGGGGGCATTTTGGTCATTCTGCATATCC
          1 AGGGGGCATTTTGGTCATTCTACACATCC

                       *       *        *
       4027 A-GGGGCATTTCGGTCATTTTACACATCT
          1 AGGGGGCATTTTGGTCATTCTACACATCC

                             
       4055 AGGGGGCATTTTGGTCA
          1 AGGGGGCATTTTGGTCA

       4072 CTTCAAGTGC


Statistics
Matches: 38,  Mismatches: 6, Indels: 2
        0.83            0.13        0.04

Matches are distributed among these distances:
  28   23  0.61
  29   15  0.39

ACGTcount: A:0.19, C:0.19, G:0.28, T:0.34


Consensus pattern (29 bp):   
AGGGGGCATTTTGGTCATTCTACACATCC

Found at i:4453 original size:22 final size:22

Alignment explanation


    Indices: 4426--4475  Score: 75
    Period size: 22  Copynumber: 2.3  Consensus size: 22

       4416 TTAGTAATAG

                                   
       4426 TTGCATTTTTGCAT-GTCACCTT
          1 TTGCATTTTTGCATGGT-ACCTT

                              *   
       4448 TTGCATTTTTGCATGGTATCTT
          1 TTGCATTTTTGCATGGTACCTT

                  
       4470 TTGCAT
          1 TTGCAT

       4476 CCATCCTTTT


Statistics
Matches: 26,  Mismatches: 1, Indels: 2
        0.90            0.03        0.07

Matches are distributed among these distances:
  22   24  0.92
  23    2  0.08

ACGTcount: A:0.14, C:0.18, G:0.16, T:0.52


Consensus pattern (22 bp):   
TTGCATTTTTGCATGGTACCTT
Done.