Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012745.1 Corchorus olitorius cultivar O-4 contig12778, 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: 12585
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32


Found at i:2861 original size:9 final size:9

Alignment explanation


    Indices: 2849--2875  Score: 54
    Period size: 9  Copynumber: 3.0  Consensus size: 9

       2839 CAATAAACAT

                     
       2849 CAAAACAAA
          1 CAAAACAAA

                     
       2858 CAAAACAAA
          1 CAAAACAAA

                     
       2867 CAAAACAAA
          1 CAAAACAAA

       2876 GCAATCTTTT


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   9   18  1.00

ACGTcount: A:0.78, C:0.22, G:0.00, T:0.00


Consensus pattern (9 bp):   
CAAAACAAA

Found at i:6912 original size:27 final size:27

Alignment explanation


    Indices: 6854--6926  Score: 101
    Period size: 27  Copynumber: 2.7  Consensus size: 27

       6844 AAGTGAACTT

                 *       *             
       6854 AAAATTACCAAAACGCCCCTGAATGCA
          1 AAAATGACCAAAATGCCCCTGAATGCA

            *                        * 
       6881 CAAATGACCAAAATGCCCCTGAATGTA
          1 AAAATGACCAAAATGCCCCTGAATGCA

                    *          
       6908 AAAATGACTAAAATGCCCC
          1 AAAATGACCAAAATGCCCC

       6927 CTATGTGACT


Statistics
Matches: 40,  Mismatches: 6, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  27   40  1.00

ACGTcount: A:0.44, C:0.27, G:0.12, T:0.16


Consensus pattern (27 bp):   
AAAATGACCAAAATGCCCCTGAATGCA

Found at i:7023 original size:21 final size:21

Alignment explanation


    Indices: 6997--7038  Score: 84
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       6987 AATGTGTGTC

                                 
       6997 TACAATACCCATGAGCGGTTA
          1 TACAATACCCATGAGCGGTTA

                                 
       7018 TACAATACCCATGAGCGGTTA
          1 TACAATACCCATGAGCGGTTA

       7039 CCTCATGAAC


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  21   21  1.00

ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24


Consensus pattern (21 bp):   
TACAATACCCATGAGCGGTTA

Found at i:7380 original size:26 final size:26

Alignment explanation


    Indices: 7351--7404  Score: 72
    Period size: 26  Copynumber: 2.1  Consensus size: 26

       7341 TACAGTCATC

                  * *                 
       7351 CAGGGGGATTTTGGTCATTTATACTT
          1 CAGGGGCACTTTGGTCATTTATACTT

                            *   *     
       7377 CAGGGGCACTTTGGTCTTTTGTACTT
          1 CAGGGGCACTTTGGTCATTTATACTT

              
       7403 CA
          1 CA

       7405 TTACTAGCTT


Statistics
Matches: 24,  Mismatches: 4, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  26   24  1.00

ACGTcount: A:0.17, C:0.17, G:0.26, T:0.41


Consensus pattern (26 bp):   
CAGGGGCACTTTGGTCATTTATACTT
Done.