Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020431.1 Corchorus olitorius cultivar O-4 contig20464, 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: 13395
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31


Found at i:3911 original size:24 final size:24

Alignment explanation


    Indices: 3879--3933  Score: 110
    Period size: 24  Copynumber: 2.3  Consensus size: 24

       3869 TGCCTCCTTC

                                    
       3879 CTGCAGGAAGAGAAAAATATCTCT
          1 CTGCAGGAAGAGAAAAATATCTCT

                                    
       3903 CTGCAGGAAGAGAAAAATATCTCT
          1 CTGCAGGAAGAGAAAAATATCTCT

                   
       3927 CTGCAGG
          1 CTGCAGG

       3934 GCAGAGGGCG


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  24   31  1.00

ACGTcount: A:0.38, C:0.18, G:0.24, T:0.20


Consensus pattern (24 bp):   
CTGCAGGAAGAGAAAAATATCTCT

Found at i:4167 original size:19 final size:19

Alignment explanation


    Indices: 4143--4180  Score: 58
    Period size: 19  Copynumber: 2.0  Consensus size: 19

       4133 TGGGATTTTT

                               
       4143 AATAATAATTATTCAATAA
          1 AATAATAATTATTCAATAA

                  *      *     
       4162 AATAATTATTATTTAATAA
          1 AATAATAATTATTCAATAA

       4181 TTAATTAATT


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  19   17  1.00

ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42


Consensus pattern (19 bp):   
AATAATAATTATTCAATAA

Found at i:4563 original size:13 final size:13

Alignment explanation


    Indices: 4545--4570  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

       4535 AAAGTAACAA

                         
       4545 CAAAAATCATCAC
          1 CAAAAATCATCAC

                         
       4558 CAAAAATCATCAC
          1 CAAAAATCATCAC

       4571 TCATGCCAAG


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.54, C:0.31, G:0.00, T:0.15


Consensus pattern (13 bp):   
CAAAAATCATCAC

Found at i:6141 original size:22 final size:22

Alignment explanation


    Indices: 6092--6142  Score: 59
    Period size: 22  Copynumber: 2.3  Consensus size: 22

       6082 AAATATTACC

                             **   
       6092 ATAATTATTTTTGACAGCCATA
          1 ATAATTATTTTTGACAGAAATA

                         *         
       6114 ATAATTATTTTTGCCAAGAAATA
          1 ATAATTATTTTTGAC-AGAAATA

                   
       6137 A-AATTA
          1 ATAATTA

       6143 GGGAATAATT


Statistics
Matches: 25,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  22   19  0.76
  23    6  0.24

ACGTcount: A:0.43, C:0.10, G:0.08, T:0.39


Consensus pattern (22 bp):   
ATAATTATTTTTGACAGAAATA
Done.