Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015360.1 Corchorus olitorius cultivar O-4 contig15393, 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: 10095
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.32


Found at i:737 original size:19 final size:18

Alignment explanation


    Indices: 713--748  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

        703 TGAAGATTTA

                   *           
        713 TTGAAGATAATTTGAAGAT
          1 TTGAAGACAA-TTGAAGAT

                             
        732 TTGAAGACAATTGAAGA
          1 TTGAAGACAATTGAAGA

        749 ATTATCTCAA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    7  0.44
  19    9  0.56

ACGTcount: A:0.44, C:0.03, G:0.22, T:0.31


Consensus pattern (18 bp):   
TTGAAGACAATTGAAGAT

Found at i:2579 original size:32 final size:33

Alignment explanation


    Indices: 2524--2587  Score: 103
    Period size: 32  Copynumber: 2.0  Consensus size: 33

       2514 CGTTTTTAAT

                           *                 
       2524 TTTTGTGTCTTGGCGTTTTTGAAAAAAAAATTG
          1 TTTTGTGTCTTGGCGATTTTGAAAAAAAAATTG

                       *                    
       2557 TTTTGTGT-TTTGCGATTTTGAAAAAAAAATT
          1 TTTTGTGTCTTGGCGATTTTGAAAAAAAAATT

       2588 CAATTTTGCG


Statistics
Matches: 29,  Mismatches: 2, Indels: 1
        0.91            0.06        0.03

Matches are distributed among these distances:
  32   21  0.72
  33    8  0.28

ACGTcount: A:0.30, C:0.05, G:0.19, T:0.47


Consensus pattern (33 bp):   
TTTTGTGTCTTGGCGATTTTGAAAAAAAAATTG

Found at i:6676 original size:21 final size:21

Alignment explanation


    Indices: 6627--6669  Score: 86
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       6617 CAAAGTCTTG

                                 
       6627 TAAGTTTTCTCATGCCACTCA
          1 TAAGTTTTCTCATGCCACTCA

                                 
       6648 TAAGTTTTCTCATGCCACTCA
          1 TAAGTTTTCTCATGCCACTCA

             
       6669 T
          1 T

       6670 GGATTTTAGG


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  21   22  1.00

ACGTcount: A:0.23, C:0.28, G:0.09, T:0.40


Consensus pattern (21 bp):   
TAAGTTTTCTCATGCCACTCA
Done.