Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012631.1 Corchorus capsularis cultivar CVL-1 contig12652, 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: 11731
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.31


Found at i:9327 original size:25 final size:24

Alignment explanation


    Indices: 9299--9376  Score: 65
    Period size: 25  Copynumber: 3.2  Consensus size: 24

       9289 TCCTATATTT

                                     
       9299 TGTTTCCTAGTTTAAGTTAGACTTA
          1 TGTTTCCTAGTTTAA-TTAGACTTA

                  *                   
       9324 TGTTTCTTAGGTCTTAATT---C-TA
          1 TGTTTCCTA-GT-TTAATTAGACTTA

            * *                      
       9346 GGATTCCTAGTTTAAATTAGACTTA
          1 TGTTTCCTAGTTT-AATTAGACTTA

                  
       9371 TGTTTC
          1 TGTTTC

       9377 TTGGGTCTTA


Statistics
Matches: 40,  Mismatches: 6, Indels: 14
        0.67            0.10        0.23

Matches are distributed among these distances:
  20    2  0.05
  21    6  0.15
  22    8  0.20
  23    1  0.03
  24    1  0.03
  25   14  0.35
  26    4  0.10
  27    4  0.10

ACGTcount: A:0.23, C:0.13, G:0.15, T:0.49


Consensus pattern (24 bp):   
TGTTTCCTAGTTTAATTAGACTTA

Found at i:9371 original size:47 final size:46

Alignment explanation


    Indices: 9302--9444  Score: 232
    Period size: 47  Copynumber: 3.0  Consensus size: 46

       9292 TATATTTTGT

                                                           
       9302 TTCCTAGTTTAAGTTAGACTTATGTTTCTTAGGTCTTAATTCTAGGA
          1 TTCCTAGTTTAAGTTAGACTTATGTTTCTT-GGTCTTAATTCTAGGA

                        *                                  
       9349 TTCCTAGTTTAAATTAGACTTATGTTTCTTGGGTCTTAATTCTAGGA
          1 TTCCTAGTTTAAGTTAGACTTATGTTTCTT-GGTCTTAATTCTAGGA

                              *              *             
       9396 TTCCTAGTTTAAGTTAGATTTATGTTTCTTGTGCCTTAATTCTAGGA
          1 TTCCTAGTTTAAGTTAGACTTATGTTTCTTG-GTCTTAATTCTAGGA

              
       9443 TT
          1 TT

       9445 ATATTCTAGT


Statistics
Matches: 90,  Mismatches: 5, Indels: 2
        0.93            0.05        0.02

Matches are distributed among these distances:
  46    1  0.01
  47   89  0.99

ACGTcount: A:0.22, C:0.13, G:0.17, T:0.48


Consensus pattern (46 bp):   
TTCCTAGTTTAAGTTAGACTTATGTTTCTTGGTCTTAATTCTAGGA
Done.