Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001109.1 Corchorus olitorius cultivar O-4 contig01109, 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, 909

Length: 1515
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33


Found at i:592 original size:24 final size:24

Alignment explanation


    Indices: 565--611  Score: 67
    Period size: 24  Copynumber: 2.0  Consensus size: 24

        555 CTAACGTTAA

                    *         *     
        565 CGTTTCTATGGCTATGGTTTGGGT
          1 CGTTTCTAAGGCTATGGTGTGGGT

                         *         
        589 CGTTTCTAAGGCTGTGGTGTGGG
          1 CGTTTCTAAGGCTATGGTGTGGG

        612 ACCCAACAAT


Statistics
Matches: 20,  Mismatches: 3, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  24   20  1.00

ACGTcount: A:0.09, C:0.13, G:0.38, T:0.40


Consensus pattern (24 bp):   
CGTTTCTAAGGCTATGGTGTGGGT

Found at i:860 original size:83 final size:82

Alignment explanation


    Indices: 721--890  Score: 322
    Period size: 83  Copynumber: 2.1  Consensus size: 82

        711 CCCCACTAAA

                                                                             
        721 TATGATAAAATCCAGAAAATTATAGTAAAAAGCTAAATAATTTATACATCAACTCCAAAGTCCAA
          1 TATGATAAAATCCAGAAAATTATAGTAAAAAGCTAAATAATTTATACATCAACTCCAAAGTCCAA

                             
        786 ACACAATAGTTATTTTC
         66 ACACAATAGTTATTTTC

                                                                             
        803 TTATGATAAAATCCAGAAAATTATAGTAAAAAGCTAAATAATTTATACATCAACTCCAAAGTCCA
          1 -TATGATAAAATCCAGAAAATTATAGTAAAAAGCTAAATAATTTATACATCAACTCCAAAGTCCA

                    *         
        868 AACACAATGGTTATTTTC
         65 AACACAATAGTTATTTTC

                 
        886 TATGA
          1 TATGA

        891 CTAATCCCAC


Statistics
Matches: 86,  Mismatches: 1, Indels: 1
        0.98            0.01        0.01

Matches are distributed among these distances:
  82    5  0.06
  83   81  0.94

ACGTcount: A:0.46, C:0.15, G:0.08, T:0.30


Consensus pattern (82 bp):   
TATGATAAAATCCAGAAAATTATAGTAAAAAGCTAAATAATTTATACATCAACTCCAAAGTCCAA
ACACAATAGTTATTTTC

Found at i:1077 original size:25 final size:24

Alignment explanation


    Indices: 1038--1085  Score: 87
    Period size: 25  Copynumber: 2.0  Consensus size: 24

       1028 TCGAGGGATC

                                    
       1038 TCCAATCATGAATTGAGACTAATA
          1 TCCAATCATGAATTGAGACTAATA

                                    
       1062 TCCAATCAATGAATTGAGACTAAT
          1 TCCAATC-ATGAATTGAGACTAAT

       1086 CACTTTTGGA


Statistics
Matches: 23,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  24    7  0.30
  25   16  0.70

ACGTcount: A:0.42, C:0.17, G:0.12, T:0.29


Consensus pattern (24 bp):   
TCCAATCATGAATTGAGACTAATA
Done.