Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021352.1 Corchorus olitorius cultivar O-4 contig21385, 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: 36625
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35


Found at i:4773 original size:23 final size:23

Alignment explanation


    Indices: 4739--4785  Score: 76
    Period size: 23  Copynumber: 2.0  Consensus size: 23

       4729 TTAGCAGGAA

                   *               
       4739 AATTTGATCAATGTATGAAACTT
          1 AATTTGACCAATGTATGAAACTT

                        *          
       4762 AATTTGACCAATTTATGAAACTT
          1 AATTTGACCAATGTATGAAACTT

             
       4785 A
          1 A

       4786 TTCGTTCATT


Statistics
Matches: 22,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  23   22  1.00

ACGTcount: A:0.40, C:0.11, G:0.11, T:0.38


Consensus pattern (23 bp):   
AATTTGACCAATGTATGAAACTT

Found at i:23401 original size:12 final size:13

Alignment explanation


    Indices: 23384--23419  Score: 56
    Period size: 12  Copynumber: 2.8  Consensus size: 13

      23374 CATCGATACC

                         
      23384 TCGATATATCCG-
          1 TCGATATATCCGT

                         
      23396 TCGATATATCCGT
          1 TCGATATATCCGT

              *        
      23409 TCAATATATCC
          1 TCGATATATCC

      23420 ATGGATATTT


Statistics
Matches: 22,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  12   12  0.55
  13   10  0.45

ACGTcount: A:0.28, C:0.25, G:0.11, T:0.36


Consensus pattern (13 bp):   
TCGATATATCCGT

Found at i:36468 original size:2 final size:2

Alignment explanation


    Indices: 36461--36497  Score: 74
    Period size: 2  Copynumber: 18.5  Consensus size: 2

      36451 TTTGATCCAA

                                                                   
      36461 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
          1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T

      36498 TTCTTCTTTA


Statistics
Matches: 35,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   35  1.00

ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51


Consensus pattern (2 bp):   
TC

Done.