Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013631.1 Corchorus capsularis cultivar CVL-1 contig13652, 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: 13901
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28


Found at i:355 original size:7 final size:7

Alignment explanation


    Indices: 343--368  Score: 52
    Period size: 7  Copynumber: 3.7  Consensus size: 7

        333 AAACATGCTT

                   
        343 AATGAGA
          1 AATGAGA

                   
        350 AATGAGA
          1 AATGAGA

                   
        357 AATGAGA
          1 AATGAGA

                 
        364 AATGA
          1 AATGA

        369 ACATGAATAT


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   7   19  1.00

ACGTcount: A:0.58, C:0.00, G:0.27, T:0.15


Consensus pattern (7 bp):   
AATGAGA

Found at i:644 original size:27 final size:27

Alignment explanation


    Indices: 575--650  Score: 89
    Period size: 27  Copynumber: 2.8  Consensus size: 27

        565 AAAATGGATT

                *     *     *       *  
        575 TAAAGATGACTAAAATCCCCCTTAGTG
          1 TAAAAATGACCAAAATGCCCCTTAATG

              *       *                
        602 TACAAATGACGAAAATGCCCCTTAATG
          1 TAAAAATGACCAAAATGCCCCTTAATG

                       *          
        629 TAAAAATGACCTAAATGCCCCT
          1 TAAAAATGACCAAAATGCCCCT

        651 GGATGACCTT


Statistics
Matches: 41,  Mismatches: 8, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  27   41  1.00

ACGTcount: A:0.39, C:0.24, G:0.13, T:0.24


Consensus pattern (27 bp):   
TAAAAATGACCAAAATGCCCCTTAATG

Found at i:6213 original size:17 final size:19

Alignment explanation


    Indices: 6186--6223  Score: 53
    Period size: 17  Copynumber: 2.1  Consensus size: 19

       6176 TACTAACTAA

                       *       
       6186 TTTCTTTTGTTGTTT-GCT
          1 TTTCTTTTGTTCTTTCGCT

                               
       6204 TTTC-TTTGTTCTTTCGCT
          1 TTTCTTTTGTTCTTTCGCT

              
       6222 TT
          1 TT

       6224 GCATTTTGCA


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  17    9  0.50
  18    9  0.50

ACGTcount: A:0.00, C:0.16, G:0.13, T:0.71


Consensus pattern (19 bp):   
TTTCTTTTGTTCTTTCGCT
Done.