Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019624.1 Corchorus olitorius cultivar O-4 contig19657, 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: 13389
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


Found at i:7760 original size:29 final size:30

Alignment explanation


    Indices: 7710--7766  Score: 89
    Period size: 29  Copynumber: 1.9  Consensus size: 30

       7700 AAAAACTCTC

                             *            
       7710 TTTTTTTTTTCAAAAACGCAAC-ACAAATT
          1 TTTTTTTTTTCAAAAACACAACAACAAATT

                            *           
       7739 TTTTTTTTTTCAAAAATACAACAACAAA
          1 TTTTTTTTTTCAAAAACACAACAACAAA

       7767 ACAATTTTTT


Statistics
Matches: 25,  Mismatches: 2, Indels: 1
        0.89            0.07        0.04

Matches are distributed among these distances:
  29   20  0.80
  30    5  0.20

ACGTcount: A:0.42, C:0.16, G:0.02, T:0.40


Consensus pattern (30 bp):   
TTTTTTTTTTCAAAAACACAACAACAAATT

Found at i:7974 original size:29 final size:30

Alignment explanation


    Indices: 7933--8035  Score: 172
    Period size: 30  Copynumber: 3.4  Consensus size: 30

       7923 AGTCTATTTT

                                           
       7933 CCTTCCCCTGGCAAAAACAAGAAAAAGTT-C
          1 CCTTCCCC-GGCAAAAACAAGAAAAAGTTAC

                             *            
       7963 CCTTCCCCGGCAAAAACCAGAAAAAGTTAC
          1 CCTTCCCCGGCAAAAACAAGAAAAAGTTAC

                             *            
       7993 CCTTCCCCGGCAAAAACTAGAAAAAGTTAC
          1 CCTTCCCCGGCAAAAACAAGAAAAAGTTAC

                         
       8023 CCTTCCCCGGCAA
          1 CCTTCCCCGGCAA

       8036 CGGCGCCAAA


Statistics
Matches: 70,  Mismatches: 2, Indels: 2
        0.95            0.03        0.03

Matches are distributed among these distances:
  29   19  0.27
  30   51  0.73

ACGTcount: A:0.37, C:0.34, G:0.14, T:0.16


Consensus pattern (30 bp):   
CCTTCCCCGGCAAAAACAAGAAAAAGTTAC

Found at i:9035 original size:12 final size:13

Alignment explanation


    Indices: 9010--9035  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

       9000 CCCTTTGCCT

                         
       9010 AAAAACTAGAAAA
          1 AAAAACTAGAAAA

                         
       9023 AAAAACTAGAAAA
          1 AAAAACTAGAAAA

       9036 TAAATCTAAA


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.77, C:0.08, G:0.08, T:0.08


Consensus pattern (13 bp):   
AAAAACTAGAAAA
Done.