Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001662.1 Corchorus olitorius cultivar O-4 contig01662, 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: 7522
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34


Found at i:7397 original size:11 final size:11

Alignment explanation


    Indices: 7378--7449  Score: 50
    Period size: 10  Copynumber: 7.2  Consensus size: 11

       7368 ACTTTATCAA

                       
       7378 ATTTT-TATAT
          1 ATTTTATATAT

                       
       7388 ATTTTATATA-
          1 ATTTTATATAT

             *   *     
       7398 AATTTGTA-AT
          1 ATTTTATATAT

               *       
       7408 -TTCT-TATAT
          1 ATTTTATATAT

                    *  
       7417 ATTTTATAAAT
          1 ATTTTATATAT

                *      
       7428 ATTTCATAT-T
          1 ATTTTATATAT

                       
       7438 A-TTTATATAT
          1 ATTTTATATAT

              
       7448 AT
          1 AT

       7450 AATGACTAAA


Statistics
Matches: 46,  Mismatches: 9, Indels: 13
        0.68            0.13        0.19

Matches are distributed among these distances:
   8    2  0.04
   9   11  0.24
  10   18  0.39
  11   15  0.33

ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60


Consensus pattern (11 bp):   
ATTTTATATAT

Found at i:7443 original size:29 final size:28

Alignment explanation


    Indices: 7377--7447  Score: 83
    Period size: 29  Copynumber: 2.5  Consensus size: 28

       7367 AACTTTATCA

                                      * 
       7377 AATTTTTATATATTTTATATAAATTTGT
          1 AATTTTTATATATTTTATATAAATTTAT

                                           
       7405 AATTTCTTATATATTTTATA-AATATTTCAT
          1 AATTT-TTATATATTTTATATAA-ATTT-AT

                          
       7435 -ATTATTTATATAT
          1 AATT-TTTATATAT

       7448 ATAATGACTA


Statistics
Matches: 38,  Mismatches: 1, Indels: 7
        0.83            0.02        0.15

Matches are distributed among these distances:
  28    7  0.18
  29   29  0.76
  30    2  0.05

ACGTcount: A:0.37, C:0.03, G:0.01, T:0.59


Consensus pattern (28 bp):   
AATTTTTATATATTTTATATAAATTTAT

Found at i:7502 original size:2 final size:2

Alignment explanation


    Indices: 7495--7521  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

       7485 AGTTTACCTC

                                                    
       7495 TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA T

       7522 T


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   25  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Done.