Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024395.1 Corchorus olitorius cultivar O-4 contig24428, 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: 5540
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.30


Found at i:930 original size:22 final size:22

Alignment explanation


    Indices: 904--952  Score: 73
    Period size: 22  Copynumber: 2.2  Consensus size: 22

        894 GACGCAGAAA

                                   
        904 CAAAAAAATTTTTTTTAT-GACG
          1 CAAAAAAATTTTTTTT-TCGACG

                  *               
        926 CAAAAATATTTTTTTTTCGACG
          1 CAAAAAAATTTTTTTTTCGACG

                 
        948 CAAAA
          1 CAAAA

        953 CACAAAACTT


Statistics
Matches: 25,  Mismatches: 1, Indels: 2
        0.89            0.04        0.07

Matches are distributed among these distances:
  21    1  0.04
  22   24  0.96

ACGTcount: A:0.41, C:0.12, G:0.08, T:0.39


Consensus pattern (22 bp):   
CAAAAAAATTTTTTTTTCGACG

Found at i:3806 original size:27 final size:27

Alignment explanation


    Indices: 3755--3806  Score: 86
    Period size: 27  Copynumber: 1.9  Consensus size: 27

       3745 TCAAGAATCT

                                *      
       3755 AGGGGCATTTTAGTCATTTGCAGTTTC
          1 AGGGGCATTTTAGTCATTTGAAGTTTC

                               *     
       3782 AGGGGCATTTTAGTCATTTTAAGTT
          1 AGGGGCATTTTAGTCATTTGAAGTT

       3807 CACATTTTAT


Statistics
Matches: 23,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  27   23  1.00

ACGTcount: A:0.21, C:0.12, G:0.25, T:0.42


Consensus pattern (27 bp):   
AGGGGCATTTTAGTCATTTGAAGTTTC

Found at i:5165 original size:15 final size:16

Alignment explanation


    Indices: 5137--5166  Score: 53
    Period size: 15  Copynumber: 1.9  Consensus size: 16

       5127 TTTCCCAAAG

                            
       5137 AGTTACAGAGAGAAAC
          1 AGTTACAGAGAGAAAC

                           
       5153 AGTTACA-AGAGAAA
          1 AGTTACAGAGAGAAA

       5167 GAAAAGGATA


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  15    7  0.50
  16    7  0.50

ACGTcount: A:0.53, C:0.10, G:0.23, T:0.13


Consensus pattern (16 bp):   
AGTTACAGAGAGAAAC
Done.