Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007679.1 Corchorus capsularis cultivar CVL-1 contig07700, 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: 5999
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.31


Found at i:1126 original size:33 final size:32

Alignment explanation


    Indices: 1049--1153  Score: 102
    Period size: 33  Copynumber: 3.2  Consensus size: 32

       1039 TTGCGAAGAA

                                           * 
       1049 TGTTTTAGATGTTGTTTGCAATGATACTAAACC
          1 TGTTTTAG-TGTTGTTTGCAATGATACTAAATC

              * * *      *          *        
       1082 TAATGTGAGTGTTCTTTGCAATGAAACTAAATC
          1 T-GTTTTAGTGTTGTTTGCAATGATACTAAATC

                              **             
       1115 TGTTTTAAGTGTTGTTTGTGATGATACTAAATC
          1 TGTTTT-AGTGTTGTTTGCAATGATACTAAATC

             *    
       1148 TTTTTT
          1 TGTTTT

       1154 GGATGCTAAT


Statistics
Matches: 56,  Mismatches: 14, Indels: 4
        0.76            0.19        0.05

Matches are distributed among these distances:
  32    2  0.04
  33   50  0.89
  34    4  0.07

ACGTcount: A:0.27, C:0.10, G:0.18, T:0.46


Consensus pattern (32 bp):   
TGTTTTAGTGTTGTTTGCAATGATACTAAATC

Found at i:3388 original size:33 final size:33

Alignment explanation


    Indices: 3344--3427  Score: 114
    Period size: 33  Copynumber: 2.5  Consensus size: 33

       3334 TTTCAATACC

                          *                  
       3344 ATCAACCAAAACAGGATTATTTGCAATGCTATG
          1 ATCAACCAAAACAGAATTATTTGCAATGCTATG

                  *      *        **         
       3377 ATCAACAAAAACAAAATTATTTTTAATGCTATG
          1 ATCAACCAAAACAGAATTATTTGCAATGCTATG

            *                 
       3410 TTCAACCAAAACAGAATT
          1 ATCAACCAAAACAGAATT

       3428 GTTTTCATAA


Statistics
Matches: 43,  Mismatches: 8, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  33   43  1.00

ACGTcount: A:0.45, C:0.17, G:0.10, T:0.29


Consensus pattern (33 bp):   
ATCAACCAAAACAGAATTATTTGCAATGCTATG

Found at i:3467 original size:33 final size:32

Alignment explanation


    Indices: 3414--3521  Score: 92
    Period size: 33  Copynumber: 3.3  Consensus size: 32

       3404 GCTATGTTCA

                       *                ** * 
       3414 ACCAAAACAGAATT-GTTTTCATAACAATTAGC
          1 ACCAAAACAGATTTAG-TTTCATAACAAACAAC

                                   *         
       3446 ATCCAAAACAGATTTAGTTTCATCACAAACAAC
          1 A-CCAAAACAGATTTAGTTTCATAACAAACAAC

                              *    **        
       3479 ACCTAAAACAGATTTAGTGTCATTGCAAACAAC
          1 ACC-AAAACAGATTTAGTTTCATAACAAACAAC

               *      
       3512 ATCTAAAACA
          1 A-CCAAAACA

       3522 CTCTTTTCAA


Statistics
Matches: 63,  Mismatches: 9, Indels: 7
        0.80            0.11        0.09

Matches are distributed among these distances:
  32    3  0.05
  33   58  0.92
  34    2  0.03

ACGTcount: A:0.45, C:0.21, G:0.08, T:0.25


Consensus pattern (32 bp):   
ACCAAAACAGATTTAGTTTCATAACAAACAAC
Done.