Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010369.1 Corchorus olitorius cultivar O-4 contig10401, 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: 6363
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.30


Found at i:2552 original size:31 final size:30

Alignment explanation


    Indices: 2512--2606  Score: 72
    Period size: 31  Copynumber: 3.2  Consensus size: 30

       2502 CCATTTGAAG

                *                         *
       2512 CAAATTGTCCAAAATTTGAAAGCTAAGGGGT
          1 CAAAATGTCCAAAATTTGAAAG-TAAGGGGA

                              *            
       2543 CAAAATGTCCCAAAA---AAAAGTAAGGGGA
          1 CAAAATGT-CCAAAATTTGAAAGTAAGGGGA

                        **                 *
       2571 CAAAATGT-CAATTTTTGAAAAGGTAAGGGGG
          1 CAAAATGTCCAAAATTTG-AAA-GTAAGGGGA

                 
       2602 CAAAA
          1 CAAAA

       2607 GGGCATTTAA


Statistics
Matches: 51,  Mismatches: 7, Indels: 12
        0.73            0.10        0.17

Matches are distributed among these distances:
  26    3  0.06
  28   15  0.29
  29    4  0.08
  30    3  0.06
  31   20  0.39
  32    6  0.12

ACGTcount: A:0.45, C:0.12, G:0.23, T:0.20


Consensus pattern (30 bp):   
CAAAATGTCCAAAATTTGAAAGTAAGGGGA

Found at i:2892 original size:21 final size:24

Alignment explanation


    Indices: 2863--2913  Score: 72
    Period size: 22  Copynumber: 2.2  Consensus size: 24

       2853 TTTTGAACTC

                                     
       2863 ATTATT-TATTATTTAA-AATATAT
          1 ATTATTAT-TTATTTAATAATATAT

                                    
       2886 -TTATTATTTATTTAATAATATAT
          1 ATTATTATTTATTTAATAATATAT

                 
       2909 ATTAT
          1 ATTAT

       2914 ATCTAAGATA


Statistics
Matches: 25,  Mismatches: 0, Indels: 5
        0.83            0.00        0.17

Matches are distributed among these distances:
  22   13  0.52
  23    8  0.32
  24    4  0.16

ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59


Consensus pattern (24 bp):   
ATTATTATTTATTTAATAATATAT

Found at i:2908 original size:25 final size:25

Alignment explanation


    Indices: 2863--2911  Score: 64
    Period size: 25  Copynumber: 2.0  Consensus size: 25

       2853 TTTTGAACTC

                        *            
       2863 ATTATTTATTATTTAAAATATATTT
          1 ATTATTTATTATATAAAATATATTT

                             *       
       2888 ATTATTTATT-TAATAATATATATT
          1 ATTATTTATTAT-ATAAAATATATT

       2912 ATATCTAAGA


Statistics
Matches: 21,  Mismatches: 2, Indels: 2
        0.84            0.08        0.08

Matches are distributed among these distances:
  24    1  0.05
  25   20  0.95

ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59


Consensus pattern (25 bp):   
ATTATTTATTATATAAAATATATTT
Done.