Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009702.1 Corchorus olitorius cultivar O-4 contig09734, 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: 6212
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32


Found at i:2669 original size:27 final size:27

Alignment explanation


    Indices: 2527--2665  Score: 188
    Period size: 27  Copynumber: 5.1  Consensus size: 27

       2517 AATGAACTTA

                   *    *         *    
       2527 AAATGACCAAAACGCCCCTGAATATGC
          1 AAATGACTAAAATGCCCCTGAACATGC

                    *    **      *  *   
       2554 AAAATGACCAAAACACCCCTGGACGTGC
          1 -AAATGACTAAAATGCCCCTGAACATGC

                                       
       2582 AAATGACTAAAATGCCCCTGAACATGC
          1 AAATGACTAAAATGCCCCTGAACATGC

                                       
       2609 AAATGACTAAAATGCCCCTGAACATGC
          1 AAATGACTAAAATGCCCCTGAACATGC

               *                       
       2636 AAACGACTAAAATGCCCCTGAACATGC
          1 AAATGACTAAAATGCCCCTGAACATGC

               
       2663 AAA
          1 AAA

       2666 CGACCCGAAA


Statistics
Matches: 101,  Mismatches: 10, Indels: 1
        0.90            0.09        0.01

Matches are distributed among these distances:
  27   78  0.77
  28   23  0.23

ACGTcount: A:0.42, C:0.28, G:0.15, T:0.15


Consensus pattern (27 bp):   
AAATGACTAAAATGCCCCTGAACATGC

Found at i:4400 original size:16 final size:16

Alignment explanation


    Indices: 4379--4432  Score: 51
    Period size: 16  Copynumber: 3.5  Consensus size: 16

       4369 TATAATTATT

                            
       4379 TATATATTAATAATAA
          1 TATATATTAATAATAA

                     *   *  
       4395 TATATATTATTAACAA
          1 TATATATTAATAATAA

              *              
       4411 -AAAGTATTAA-AATAA
          1 TATA-TATTAATAATAA

                    
       4426 TA-ATATT
          1 TATATATT

       4433 CTATTATCTA


Statistics
Matches: 31,  Mismatches: 5, Indels: 6
        0.74            0.12        0.14

Matches are distributed among these distances:
  14    4  0.13
  15    7  0.23
  16   20  0.65

ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41


Consensus pattern (16 bp):   
TATATATTAATAATAA

Found at i:6102 original size:2 final size:2

Alignment explanation


    Indices: 6095--6133  Score: 78
    Period size: 2  Copynumber: 19.5  Consensus size: 2

       6085 TCTACCCCAA

                                                                      
       6095 AT AT AT AT AT AT AT 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 AT A

       6134 CTAAATATTA


Statistics
Matches: 37,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   37  1.00

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (2 bp):   
AT

Done.