Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013609.1 Corchorus olitorius cultivar O-4 contig13642, 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: 17247
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31


Found at i:2936 original size:29 final size:29

Alignment explanation


    Indices: 2849--2927  Score: 149
    Period size: 29  Copynumber: 2.7  Consensus size: 29

       2839 TCTTGGTGTA

                                         
       2849 TCAAGTGCGGGTTGTGCACTTGTGTTTGT
          1 TCAAGTGCGGGTTGTGCACTTGTGTTTGT

                    *                    
       2878 TCAAGTGCTGGTTGTGCACTTGTGTTTGT
          1 TCAAGTGCGGGTTGTGCACTTGTGTTTGT

                                 
       2907 TCAAGTGCGGGTTGTGCACTT
          1 TCAAGTGCGGGTTGTGCACTT

       2928 CGGATTGTTG


Statistics
Matches: 48,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  29   48  1.00

ACGTcount: A:0.11, C:0.15, G:0.33, T:0.41


Consensus pattern (29 bp):   
TCAAGTGCGGGTTGTGCACTTGTGTTTGT

Found at i:2961 original size:24 final size:27

Alignment explanation


    Indices: 2852--2962  Score: 70
    Period size: 29  Copynumber: 4.0  Consensus size: 27

       2842 TGGTGTATCA

                                   *     *
       2852 AGTGCGGGTTGTGCACTT-GTGTTTGTTCA
          1 AGTGCGGGTTGTGCACTTCG-G-ATGTT-G

                 *                 *     *
       2881 AGTGCTGGTTGTGCACTT-GTGTTTGTTCA
          1 AGTGCGGGTTGTGCACTTCG-G-ATGTT-G

                                        
       2910 AGTGCGGGTTGTGCACTTCGGATTGTTG
          1 AGTGCGGGTTGTGCACTTCGGA-TGTTG

                *                      
       2938 AGTGTGGGTT-TGCA-TTCGG-TGTTG
          1 AGTGCGGGTTGTGCACTTCGGATGTTG

             
       2962 A
          1 A

       2963 AGTTTCAGTT


Statistics
Matches: 75,  Mismatches: 5, Indels: 9
        0.84            0.06        0.10

Matches are distributed among these distances:
  24    6  0.08
  26    5  0.07
  27    4  0.05
  28    9  0.12
  29   50  0.67
  30    1  0.01

ACGTcount: A:0.11, C:0.13, G:0.36, T:0.41


Consensus pattern (27 bp):   
AGTGCGGGTTGTGCACTTCGGATGTTG
Done.