Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015831.1 Corchorus capsularis cultivar CVL-1 contig15852, 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, 909

Length: 1515
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.30


Found at i:540 original size:38 final size:39

Alignment explanation


    Indices: 484--559  Score: 91
    Period size: 38  Copynumber: 2.0  Consensus size: 39

        474 GTTCTTAAAT

                    *           *       *          
        484 AAAAAGCAGAAACAGAAAA-TAAAAATATATTTTTTTTA
          1 AAAAAGCAAAAACAGAAAAGGAAAAATAAATTTTTTTTA

                  *      *           *            
        522 AAAAAGGAAAAACGGAAAAGGAAAATTAAATTTTTTTT
          1 AAAAAGCAAAAACAGAAAAGGAAAAATAAATTTTTTTT

        560 TTAAAGAAAA


Statistics
Matches: 31,  Mismatches: 6, Indels: 1
        0.82            0.16        0.03

Matches are distributed among these distances:
  38   16  0.52
  39   15  0.48

ACGTcount: A:0.57, C:0.04, G:0.12, T:0.28


Consensus pattern (39 bp):   
AAAAAGCAAAAACAGAAAAGGAAAAATAAATTTTTTTTA

Found at i:997 original size:6 final size:6

Alignment explanation


    Indices: 986--1012  Score: 54
    Period size: 6  Copynumber: 4.5  Consensus size: 6

        976 AAAGCAAAGC

                                           
        986 AAATCT AAATCT AAATCT AAATCT AAA
          1 AAATCT AAATCT AAATCT AAATCT AAA

       1013 GCAAATTAAT


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   21  1.00

ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30


Consensus pattern (6 bp):   
AAATCT

Found at i:1027 original size:13 final size:13

Alignment explanation


    Indices: 1009--1043  Score: 61
    Period size: 13  Copynumber: 2.7  Consensus size: 13

        999 AATCTAAATC

                         
       1009 TAAAGCAAATTAA
          1 TAAAGCAAATTAA

                    *    
       1022 TAAAGCAATTTAA
          1 TAAAGCAAATTAA

                     
       1035 TAAAGCAAA
          1 TAAAGCAAA

       1044 CAATAATTAT


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  13   20  1.00

ACGTcount: A:0.60, C:0.09, G:0.09, T:0.23


Consensus pattern (13 bp):   
TAAAGCAAATTAA
Done.