Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020926.1 Corchorus olitorius cultivar O-4 contig20959, 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: 8083
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.32


Found at i:5184 original size:28 final size:30

Alignment explanation


    Indices: 5141--5217  Score: 90
    Period size: 28  Copynumber: 2.7  Consensus size: 30

       5131 CAAGGTTAAA

                       *                  
       5141 AAGGGTAAAACTGTAAATTTAAC-C-TTCT
          1 AAGGGTAAAACGGTAAATTTAACTCATTCT

                                          
       5169 AAGGGTAAAACGGT-AATTT-ACTCATTCT
          1 AAGGGTAAAACGGTAAATTTAACTCATTCT

            *       *       *    
       5197 TAGGGTAAGACGGTAATTTTA
          1 AAGGGTAAAACGGTAAATTTA

       5218 TGCCTATACA


Statistics
Matches: 41,  Mismatches: 4, Indels: 6
        0.80            0.08        0.12

Matches are distributed among these distances:
  26    2  0.05
  27    6  0.15
  28   29  0.71
  29    4  0.10

ACGTcount: A:0.36, C:0.12, G:0.19, T:0.32


Consensus pattern (30 bp):   
AAGGGTAAAACGGTAAATTTAACTCATTCT

Found at i:7830 original size:2 final size:2

Alignment explanation


    Indices: 7823--7870  Score: 89
    Period size: 2  Copynumber: 24.5  Consensus size: 2

       7813 TGATTTGTCT

                                                                          
       7823 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

                      
       7864 TA TA TA T
          1 TA TA TA T

       7871 CCATAATCAT


Statistics
Matches: 45,  Mismatches: 0, Indels: 2
        0.96            0.00        0.04

Matches are distributed among these distances:
   1    1  0.02
   2   44  0.98

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Done.