Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01006526.1 Corchorus olitorius cultivar O-4 contig06551, 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: 16210
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33


Found at i:13612 original size:24 final size:23

Alignment explanation


    Indices: 13575--13619  Score: 63
    Period size: 24  Copynumber: 1.9  Consensus size: 23

      13565 AACTAGTATC

                     *     *       
      13575 CTTCAAAAAGAAAAAGTATCATT
          1 CTTCAAAAAAAAAAAATATCATT

                                  
      13598 CTTCAAAAAAAAAAAAATATCA
          1 CTTC-AAAAAAAAAAAATATCA

      13620 ACTAGTTACA


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  23    4  0.21
  24   15  0.79

ACGTcount: A:0.60, C:0.13, G:0.04, T:0.22


Consensus pattern (23 bp):   
CTTCAAAAAAAAAAAATATCATT

Found at i:14774 original size:7 final size:7

Alignment explanation


    Indices: 14758--14820  Score: 69
    Period size: 7  Copynumber: 9.0  Consensus size: 7

      14748 CTTATCTTAC

                 * 
      14758 TATATGT
          1 TATATAT

                   
      14765 TATATA-
          1 TATATAT

                   
      14771 T-TATAT
          1 TATATAT

                   
      14777 TATATAT
          1 TATATAT

                   
      14784 TATATAT
          1 TATATAT

                   
      14791 TATAT-T
          1 TATATAT

                     
      14797 ATATTATAT
          1 -TA-TATAT

                   
      14806 TATATAT
          1 TATATAT

                    
      14813 ATATATAT
          1 -TATATAT

      14821 ACTATATAAA


Statistics
Matches: 49,  Mismatches: 1, Indels: 11
        0.80            0.02        0.18

Matches are distributed among these distances:
   5    4  0.08
   6    3  0.06
   7   29  0.59
   8   12  0.24
   9    1  0.02

ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57


Consensus pattern (7 bp):   
TATATAT

Found at i:14775 original size:5 final size:5

Alignment explanation


    Indices: 14767--14827  Score: 72
    Period size: 5  Copynumber: 12.0  Consensus size: 5

      14757 CTATATGTTA

                                                                         
      14767 TATAT TATAT TATA- TAT-T ATATAT TATAT TATAT TATAT TATAT ATATAT
          1 TATAT TATAT TATAT TATAT -TATAT TATAT TATAT TATAT TATAT -TATAT

                 *      
      14817 ATATAC TATAT
          1 -TATAT TATAT

      14828 AAAATCACGA


Statistics
Matches: 50,  Mismatches: 2, Indels: 8
        0.83            0.03        0.13

Matches are distributed among these distances:
   4    3  0.06
   5   36  0.72
   6   11  0.22

ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56


Consensus pattern (5 bp):   
TATAT

Found at i:14782 original size:2 final size:2

Alignment explanation


    Indices: 14765--14828  Score: 70
    Period size: 2  Copynumber: 35.0  Consensus size: 2

      14755 TACTATATGT

                                                                          
      14765 TA TA TA T- TA TA T- TA TA TA T- TA TA TA T- TA TA T- TA TA T-
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

                                                      
      14801 TA TA T- TA TA TA TA TA TA TA TA CTA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA

      14829 AAATCACGAA


Statistics
Matches: 54,  Mismatches: 0, Indels: 16
        0.77            0.00        0.23

Matches are distributed among these distances:
   1    7  0.13
   2   45  0.83
   3    2  0.04

ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55


Consensus pattern (2 bp):   
TA

Done.