Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023522.1 Corchorus olitorius cultivar O-4 contig23555, 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: 10354
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32


Found at i:13 original size:2 final size:2

Alignment explanation


    Indices: 7--44  Score: 67
    Period size: 2  Copynumber: 18.5  Consensus size: 2

          1 TGGATG

                                                                    
          7 AT AT AT AT AT GAT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT A

         45 GAGAGAGAGA


Statistics
Matches: 35,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
   2   33  0.94
   3    2  0.06

ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47


Consensus pattern (2 bp):   
AT

Found at i:941 original size:11 final size:11

Alignment explanation


    Indices: 925--980  Score: 112
    Period size: 11  Copynumber: 5.1  Consensus size: 11

        915 ATAAATCATT

                       
        925 AACACACGTGC
          1 AACACACGTGC

                       
        936 AACACACGTGC
          1 AACACACGTGC

                       
        947 AACACACGTGC
          1 AACACACGTGC

                       
        958 AACACACGTGC
          1 AACACACGTGC

                       
        969 AACACACGTGC
          1 AACACACGTGC

             
        980 A
          1 A

        981 TTTGTTCTAA


Statistics
Matches: 45,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   45  1.00

ACGTcount: A:0.38, C:0.36, G:0.18, T:0.09


Consensus pattern (11 bp):   
AACACACGTGC

Found at i:1630 original size:21 final size:21

Alignment explanation


    Indices: 1587--1630  Score: 54
    Period size: 21  Copynumber: 2.1  Consensus size: 21

       1577 GTTCTTTCCA

                  *           *  
       1587 TTTTTCTTTGTTCTTAACGTT
          1 TTTTTCATTGTTCTTAACCTT

                                  
       1608 TTTTTCATTGTT-TTAATCCTT
          1 TTTTTCATTGTTCTTAA-CCTT

              
       1629 TT
          1 TT

       1631 GAACCCAACA


Statistics
Matches: 20,  Mismatches: 2, Indels: 2
        0.83            0.08        0.08

Matches are distributed among these distances:
  20    4  0.20
  21   16  0.80

ACGTcount: A:0.11, C:0.14, G:0.07, T:0.68


Consensus pattern (21 bp):   
TTTTTCATTGTTCTTAACCTT
Done.