Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022667.1 Corchorus olitorius cultivar O-4 contig22700, 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: 8013
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29


Found at i:3107 original size:29 final size:28

Alignment explanation


    Indices: 3039--3115  Score: 95
    Period size: 29  Copynumber: 2.8  Consensus size: 28

       3029 TGTGAATTTA

                                        
       3039 AAATGACCAAAATGCCCCT-GAATATGC
          1 AAATGACCAAAATGCCCCTAGAATATGC

                   *              *  *   
       3066 AAATGACTAAAATGCCCCTAGATTCTTG-
          1 AAATGACCAAAATGCCCCTAGAAT-ATGC

                                  
       3094 AGAATGACCAAAATGCCCCTAG
          1 A-AATGACCAAAATGCCCCTAG

       3116 TTGATCCTAA


Statistics
Matches: 43,  Mismatches: 4, Indels: 4
        0.84            0.08        0.08

Matches are distributed among these distances:
  27   18  0.42
  28    4  0.09
  29   21  0.49

ACGTcount: A:0.39, C:0.25, G:0.16, T:0.21


Consensus pattern (28 bp):   
AAATGACCAAAATGCCCCTAGAATATGC

Found at i:6189 original size:10 final size:10

Alignment explanation


    Indices: 6174--6199  Score: 52
    Period size: 10  Copynumber: 2.6  Consensus size: 10

       6164 CACCAAAGGA

                      
       6174 TAAGAAGTAT
          1 TAAGAAGTAT

                      
       6184 TAAGAAGTAT
          1 TAAGAAGTAT

                  
       6194 TAAGAA
          1 TAAGAA

       6200 TTTAGCTACT


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   16  1.00

ACGTcount: A:0.54, C:0.00, G:0.19, T:0.27


Consensus pattern (10 bp):   
TAAGAAGTAT

Found at i:7120 original size:21 final size:21

Alignment explanation


    Indices: 7076--7130  Score: 65
    Period size: 21  Copynumber: 2.6  Consensus size: 21

       7066 GGCTTTGAAT

                             *** 
       7076 GGTGATGGCACGGGCATGGTC
          1 GGTGATGGCACGGGCATAACC

                           *     
       7097 GGTGATGGCACGGGCTTAACC
          1 GGTGATGGCACGGGCATAACC

                *        
       7118 GGTGGTGGCACGG
          1 GGTGATGGCACGG

       7131 TGGTGGGTGC


Statistics
Matches: 29,  Mismatches: 5, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  21   29  1.00

ACGTcount: A:0.15, C:0.20, G:0.47, T:0.18


Consensus pattern (21 bp):   
GGTGATGGCACGGGCATAACC
Done.