Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022923.1 Corchorus olitorius cultivar O-4 contig22956, 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: 4622
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.32


Found at i:7 original size:2 final size:2

Alignment explanation


    Indices: 1--42  Score: 84
    Period size: 2  Copynumber: 21.0  Consensus size: 2

                                                                          
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

         43 GTGTAAAAGA


Statistics
Matches: 40,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   40  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:1106 original size:18 final size:19

Alignment explanation


    Indices: 1083--1125  Score: 61
    Period size: 18  Copynumber: 2.3  Consensus size: 19

       1073 ATGGTTTTAA

                               
       1083 TTCTATCCAAAAT-AATTT
          1 TTCTATCCAAAATCAATTT

                  **           
       1101 TTCTATTGAAAATCAATTT
          1 TTCTATCCAAAATCAATTT

                  
       1120 TTCTAT
          1 TTCTAT

       1126 GAACACGGAG


Statistics
Matches: 22,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  18   11  0.50
  19   11  0.50

ACGTcount: A:0.35, C:0.14, G:0.02, T:0.49


Consensus pattern (19 bp):   
TTCTATCCAAAATCAATTT

Found at i:3763 original size:19 final size:19

Alignment explanation


    Indices: 3711--3768  Score: 62
    Period size: 19  Copynumber: 3.0  Consensus size: 19

       3701 CTTTTTTTTA

                       *        
       3711 TTCGGACCGGGTCAAACCGG
          1 TTCGGACC-GGCCAAACCGG

             *   *   *         
       3731 TCCGGTCCGACCAAACCGG
          1 TTCGGACCGGCCAAACCGG

                          *    
       3750 TTCGGACCGGCCAAGCCGG
          1 TTCGGACCGGCCAAACCGG

       3769 CTCGAGCCGA


Statistics
Matches: 30,  Mismatches: 8, Indels: 1
        0.77            0.21        0.03

Matches are distributed among these distances:
  19   24  0.80
  20    6  0.20

ACGTcount: A:0.19, C:0.36, G:0.33, T:0.12


Consensus pattern (19 bp):   
TTCGGACCGGCCAAACCGG
Done.