Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012973.1 Corchorus olitorius cultivar O-4 contig13006, 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: 22807
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.30


Found at i:2100 original size:26 final size:26

Alignment explanation


    Indices: 2071--2122  Score: 70
    Period size: 26  Copynumber: 2.0  Consensus size: 26

       2061 TTTTCTTAAA

                   *                   
       2071 CTATTTTCTT-AATCTCTAGTTTAATT
          1 CTATTTTATTGAAT-TCTAGTTTAATT

                       *              
       2097 CTATTTTATTGTATTCTAGTTTAATT
          1 CTATTTTATTGAATTCTAGTTTAATT

       2123 TGTCTATTTT


Statistics
Matches: 23,  Mismatches: 2, Indels: 2
        0.85            0.07        0.07

Matches are distributed among these distances:
  26   21  0.91
  27    2  0.09

ACGTcount: A:0.23, C:0.12, G:0.06, T:0.60


Consensus pattern (26 bp):   
CTATTTTATTGAATTCTAGTTTAATT

Found at i:6046 original size:30 final size:30

Alignment explanation


    Indices: 6010--6067  Score: 82
    Period size: 30  Copynumber: 1.9  Consensus size: 30

       6000 ATTCTTGCTC

                               *           
       6010 CTTGAAATAATTCTTCAA-TGATCTTCAAGT
          1 CTTGAAATAA-TCTTCAACAGATCTTCAAGT

                    *                   
       6040 CTTGAAATTATCTTCAACAGATCTTCAA
          1 CTTGAAATAATCTTCAACAGATCTTCAA

       6068 ACACGAGTTT


Statistics
Matches: 25,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  29    7  0.28
  30   18  0.72

ACGTcount: A:0.34, C:0.19, G:0.09, T:0.38


Consensus pattern (30 bp):   
CTTGAAATAATCTTCAACAGATCTTCAAGT

Found at i:22163 original size:25 final size:23

Alignment explanation


    Indices: 22135--22196  Score: 63
    Period size: 25  Copynumber: 2.6  Consensus size: 23

      22125 ATTAGATGTG

                    *  *             
      22135 TAAATTAATTATTAATATATATTAT
          1 TAAATTAAATAATAA-ATATATT-T

                                   
      22160 TAAA-TAAATAATAAATATATTT
          1 TAAATTAAATAATAAATATATTT

                           
      22182 TAAATGATAAATAAT
          1 TAAAT--TAAATAAT

      22197 GAGTTCAAAA


Statistics
Matches: 32,  Mismatches: 2, Indels: 6
        0.80            0.05        0.15

Matches are distributed among these distances:
  22    5  0.16
  23    7  0.22
  24    8  0.25
  25   12  0.38

ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44


Consensus pattern (23 bp):   
TAAATTAAATAATAAATATATTT
Done.