Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021601.1 Corchorus olitorius cultivar O-4 contig21634, 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: 3686
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30


Found at i:473 original size:16 final size:15

Alignment explanation


    Indices: 435--476  Score: 75
    Period size: 15  Copynumber: 2.7  Consensus size: 15

        425 ACAGAGGTTG

                           
        435 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                           
        450 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                        
        465 ACTAGAAAACAA
          1 AC-AGAAAACAA

        477 AACAAAGTAA


Statistics
Matches: 26,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  15   17  0.65
  16    9  0.35

ACGTcount: A:0.67, C:0.14, G:0.07, T:0.12


Consensus pattern (15 bp):   
ACAGAAAACAATTAA

Found at i:2737 original size:22 final size:23

Alignment explanation


    Indices: 2694--2743  Score: 59
    Period size: 22  Copynumber: 2.2  Consensus size: 23

       2684 ATGCTGTGTC

                *                  
       2694 AAAACCTTTTATTTCTGTTTTT-
          1 AAAATCTTTTATTTCTGTTTTTG

                       *            
       2716 AAAATCTTTTACTT-TGTTTTTTG
          1 AAAATCTTTTATTTCTG-TTTTTG

                 
       2739 AAAAT
          1 AAAAT

       2744 TCCCATTTTA


Statistics
Matches: 24,  Mismatches: 2, Indels: 3
        0.83            0.07        0.10

Matches are distributed among these distances:
  21    2  0.08
  22   17  0.71
  23    5  0.21

ACGTcount: A:0.28, C:0.10, G:0.06, T:0.56


Consensus pattern (23 bp):   
AAAATCTTTTATTTCTGTTTTTG

Found at i:2743 original size:23 final size:22

Alignment explanation


    Indices: 2694--2736  Score: 61
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       2684 ATGCTGTGTC

                *                 
       2694 AAAACCTTTTATTTCTGTTTTT
          1 AAAATCTTTTATTTCTGTTTTT

                       *          
       2716 AAAATCTTTTACTT-TGTTTTT
          1 AAAATCTTTTATTTCTGTTTTT

       2737 TGAAAATTCC


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  21    7  0.37
  22   12  0.63

ACGTcount: A:0.23, C:0.12, G:0.05, T:0.60


Consensus pattern (22 bp):   
AAAATCTTTTATTTCTGTTTTT
Done.