Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010611.1 Corchorus capsularis cultivar CVL-1 contig10632, 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: 9859
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34


Found at i:2679 original size:29 final size:29

Alignment explanation


    Indices: 2622--2680  Score: 68
    Period size: 29  Copynumber: 2.0  Consensus size: 29

       2612 AGTTATTTAG

                              *     *    
       2622 TTTATGCTTTATCTTTAATTTTCCTTTAA
          1 TTTATGCTTTATCTTTAAGTTTCCATTAA

                                           
       2651 TTTATGTCTTTAT-TTTCAAGTTT-CATTAA
          1 TTTATG-CTTTATCTTT-AAGTTTCCATTAA

             
       2680 T
          1 T

       2681 AAACTATCTA


Statistics
Matches: 26,  Mismatches: 2, Indels: 4
        0.81            0.06        0.12

Matches are distributed among these distances:
  29   15  0.58
  30   11  0.42

ACGTcount: A:0.22, C:0.12, G:0.05, T:0.61


Consensus pattern (29 bp):   
TTTATGCTTTATCTTTAAGTTTCCATTAA

Found at i:5546 original size:15 final size:16

Alignment explanation


    Indices: 5526--5559  Score: 52
    Period size: 16  Copynumber: 2.2  Consensus size: 16

       5516 GATTGCTCTC

                         *  
       5526 TTAGTTA-ATTTACTT
          1 TTAGTTAGATTTAATT

                            
       5541 TTAGTTAGATTTAATT
          1 TTAGTTAGATTTAATT

               
       5557 TTA
          1 TTA

       5560 AATTCTTCTT


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  15    7  0.41
  16   10  0.59

ACGTcount: A:0.29, C:0.03, G:0.09, T:0.59


Consensus pattern (16 bp):   
TTAGTTAGATTTAATT

Found at i:8133 original size:15 final size:14

Alignment explanation


    Indices: 8105--8135  Score: 53
    Period size: 14  Copynumber: 2.1  Consensus size: 14

       8095 AAAGTTACTC

                          
       8105 ATTTAATTTTAATT
          1 ATTTAATTTTAATT

                           
       8119 ATTTAATTATTAATT
          1 ATTTAATT-TTAATT

              
       8134 AT
          1 AT

       8136 AATGTAAAAA


Statistics
Matches: 16,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  14    8  0.50
  15    8  0.50

ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61


Consensus pattern (14 bp):   
ATTTAATTTTAATT
Done.