Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013384.1 Corchorus olitorius cultivar O-4 contig13417, 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: 13615
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33


Found at i:7650 original size:66 final size:67

Alignment explanation


    Indices: 7580--7704  Score: 191
    Period size: 66  Copynumber: 1.9  Consensus size: 67

       7570 AAATAAAATT

                     *                         *                             
       7580 AAAAAAAAATTGGCCCTTTCCCTTCCCCGGCTG-AGCTTCCGGCCT-CCCCAGAAAAGGTAACAT
          1 AAAAAAAAAATGGCCCTTTCCCTTCCCCGGCTGCACCTT-CGGCCTCCCCCAGAAAAGGTAACAT

               
       7643 AAA
         65 AAA

                                              *    *                   
       7646 AAAAAAAAAATGGCCCTTTCCCTTCCCCGGCTGCCCCTTTGGCCTCCCCCAGAAAAGGT
          1 AAAAAAAAAATGGCCCTTTCCCTTCCCCGGCTGCACCTTCGGCCTCCCCCAGAAAAGGT

       7705 TAATTTTTGA


Statistics
Matches: 53,  Mismatches: 4, Indels: 3
        0.88            0.07        0.05

Matches are distributed among these distances:
  66   37  0.70
  67   16  0.30

ACGTcount: A:0.29, C:0.34, G:0.17, T:0.20


Consensus pattern (67 bp):   
AAAAAAAAAATGGCCCTTTCCCTTCCCCGGCTGCACCTTCGGCCTCCCCCAGAAAAGGTAACATA
AA

Found at i:10657 original size:14 final size:15

Alignment explanation


    Indices: 10627--10659  Score: 50
    Period size: 15  Copynumber: 2.3  Consensus size: 15

      10617 TTAAATCTAA

                           
      10627 TATTTATACCTATTT
          1 TATTTATACCTATTT

                 *         
      10642 TATTTTTACC-ATTT
          1 TATTTATACCTATTT

                
      10656 TATT
          1 TATT

      10660 AATTTAATTA


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  14    8  0.47
  15    9  0.53

ACGTcount: A:0.24, C:0.12, G:0.00, T:0.64


Consensus pattern (15 bp):   
TATTTATACCTATTT

Found at i:12854 original size:25 final size:25

Alignment explanation


    Indices: 12806--12858  Score: 70
    Period size: 25  Copynumber: 2.1  Consensus size: 25

      12796 TATAATATCT

                           ** **     
      12806 AAATTTATGTTCTTTTTTTTTAGAA
          1 AAATTTATGTTCTTTCCTAATAGAA

                                     
      12831 AAATTTATGTTCTTTCCTAATAGAA
          1 AAATTTATGTTCTTTCCTAATAGAA

               
      12856 AAA
          1 AAA

      12859 ATTGTCAAGA


Statistics
Matches: 24,  Mismatches: 4, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  25   24  1.00

ACGTcount: A:0.36, C:0.08, G:0.08, T:0.49


Consensus pattern (25 bp):   
AAATTTATGTTCTTTCCTAATAGAA
Done.