Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014065.1 Corchorus olitorius cultivar O-4 contig14098, 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: 3631
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.37


Found at i:138 original size:18 final size:20

Alignment explanation


    Indices: 117--165  Score: 66
    Period size: 21  Copynumber: 2.5  Consensus size: 20

        107 ATTTTACCAC

                                
        117 TAATAATAA-TTAAT-ATAA
          1 TAATAATAAGTTAATAATAA

                               * 
        135 TAATAATAAGTTTAATAATTA
          1 TAATAATAAG-TTAATAATAA

                      
        156 TAATAATAAG
          1 TAATAATAAG

        166 AGGTTTAACG


Statistics
Matches: 27,  Mismatches: 1, Indels: 3
        0.87            0.03        0.10

Matches are distributed among these distances:
  18    9  0.33
  20    5  0.19
  21   13  0.48

ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39


Consensus pattern (20 bp):   
TAATAATAAGTTAATAATAA

Found at i:150 original size:15 final size:14

Alignment explanation


    Indices: 117--160  Score: 52
    Period size: 15  Copynumber: 3.0  Consensus size: 14

        107 ATTTTACCAC

                           
        117 TAATAATAATTAATA
          1 TAATAATAA-TAATA

                          *
        132 TAATAATAATAAGTT
          1 TAATAATAATAA-TA

                   *      
        147 TAATAATTATAATA
          1 TAATAATAATAATA

        161 ATAAGAGGTT


Statistics
Matches: 25,  Mismatches: 3, Indels: 3
        0.81            0.10        0.10

Matches are distributed among these distances:
  14    4  0.16
  15   21  0.84

ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41


Consensus pattern (14 bp):   
TAATAATAATAATA

Found at i:526 original size:55 final size:53

Alignment explanation


    Indices: 445--553  Score: 182
    Period size: 55  Copynumber: 2.0  Consensus size: 53

        435 ACTTATATAG

                                *                                
        445 TATATAGATATAGATATAATTACATATTCAATTACACAAAACCATTTGATTAA
          1 TATATAGATATAGATATAATGACATATTCAATTACACAAAACCATTTGATTAA

                  *                                                
        498 TATATATATATATGTATATAATGACATATTCAATTACACAAAACCATTTGATTAA
          1 TATATAGATATA-G-ATATAATGACATATTCAATTACACAAAACCATTTGATTAA

             
        553 T
          1 T

        554 TAGCTATAGC


Statistics
Matches: 52,  Mismatches: 2, Indels: 2
        0.93            0.04        0.04

Matches are distributed among these distances:
  53   11  0.21
  54    1  0.02
  55   40  0.77

ACGTcount: A:0.46, C:0.11, G:0.06, T:0.38


Consensus pattern (53 bp):   
TATATAGATATAGATATAATGACATATTCAATTACACAAAACCATTTGATTAA
Done.