Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017816.1 Corchorus olitorius cultivar O-4 contig17849, 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: 10715
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31


Found at i:8846 original size:7 final size:7

Alignment explanation


    Indices: 8830--8907  Score: 56
    Period size: 7  Copynumber: 11.1  Consensus size: 7

       8820 ACCGTTTTTT

                   
       8830 TTAATAA
          1 TTAATAA

                 * 
       8837 TTAATTA
          1 TTAATAA

               *   
       8844 TTATTAA
          1 TTAATAA

            *      
       8851 GT-ATAA
          1 TTAATAA

                   
       8857 TTAA-AA
          1 TTAATAA

                *  
       8863 -TAACAA
          1 TTAATAA

                      
       8869 TTTAAATTAA
          1 -TT-AA-TAA

                   
       8879 -TAATAA
          1 TTAATAA

                   
       8885 TTAATAA
          1 TTAATAA

                    
       8892 TTAAATAA
          1 TT-AATAA

                   
       8900 TTAATAA
          1 TTAATAA

             
       8907 T
          1 T

       8908 AATTAAAAAA


Statistics
Matches: 56,  Mismatches: 7, Indels: 16
        0.71            0.09        0.20

Matches are distributed among these distances:
   5    3  0.05
   6   11  0.20
   7   29  0.52
   8    9  0.16
   9    2  0.04
  10    2  0.04

ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42


Consensus pattern (7 bp):   
TTAATAA

Found at i:8900 original size:18 final size:18

Alignment explanation


    Indices: 8853--8914  Score: 67
    Period size: 18  Copynumber: 3.5  Consensus size: 18

       8843 ATTATTAAGT

                         *    *
       8853 ATAATTAAAATAACAATTT
          1 ATAATT-AAATAATAATTA

                              
       8872 A-AATT-AATAATAATTA
          1 ATAATTAAATAATAATTA

                               
       8888 ATAATTAAATAATTAA-TA
          1 ATAATTAAATAA-TAATTA

                     
       8906 ATAATTAAA
          1 ATAATTAAA

       8915 AAAATAAAAA


Statistics
Matches: 38,  Mismatches: 2, Indels: 7
        0.81            0.04        0.15

Matches are distributed among these distances:
  16   10  0.26
  17    4  0.11
  18   20  0.53
  19    4  0.11

ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37


Consensus pattern (18 bp):   
ATAATTAAATAATAATTA

Done.