Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01002834.1 Corchorus capsularis cultivar CVL-1 contig02842, 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, 892

Length: 1487
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35


Found at i:128 original size:30 final size:32

Alignment explanation


    Indices: 92--160  Score: 90
    Period size: 30  Copynumber: 2.2  Consensus size: 32

         82 CTCGTCACCT

                            *                
         92 AAAACA-GATTTATTTTCAATGC-T-ATCAACC
          1 AAAACAGGA-TTATTTCCAATGCATAATCAACC

                                             
        122 AAAACAGGATTATTTCCAATGCTATAATCAACC
          1 AAAACAGGATTATTTCCAATGC-ATAATCAACC

                  
        155 AAAACA
          1 AAAACA

        161 TAATTGTTTT


Statistics
Matches: 34,  Mismatches: 1, Indels: 5
        0.85            0.03        0.12

Matches are distributed among these distances:
  30   18  0.53
  31    2  0.06
  32    1  0.03
  33   13  0.38

ACGTcount: A:0.45, C:0.20, G:0.07, T:0.28


Consensus pattern (32 bp):   
AAAACAGGATTATTTCCAATGCATAATCAACC

Found at i:187 original size:34 final size:34

Alignment explanation


    Indices: 139--204  Score: 114
    Period size: 34  Copynumber: 1.9  Consensus size: 34

        129 GATTATTTCC

                                              
        139 AATGCTATAATCAACCAAAACATAATTGTTTTTT
          1 AATGCTATAATCAACCAAAACATAATTGTTTTTT

                    **                      
        173 AATGCTATGTTCAACCAAAACATAATTGTTTT
          1 AATGCTATAATCAACCAAAACATAATTGTTTT

        205 CATCACAATT


Statistics
Matches: 30,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  34   30  1.00

ACGTcount: A:0.39, C:0.15, G:0.08, T:0.38


Consensus pattern (34 bp):   
AATGCTATAATCAACCAAAACATAATTGTTTTTT

Found at i:758 original size:8 final size:8

Alignment explanation


    Indices: 745--778  Score: 50
    Period size: 8  Copynumber: 4.1  Consensus size: 8

        735 CCTTCTTCAA

                    
        745 AAAAATTC
          1 AAAAATTC

                    
        753 AAAAATTC
          1 AAAAATTC

                 *   
        761 AGAAACTTC
          1 A-AAAATTC

                    
        770 AAAAATTC
          1 AAAAATTC

             
        778 A
          1 A

        779 TAGCTGATTC


Statistics
Matches: 23,  Mismatches: 2, Indels: 2
        0.85            0.07        0.07

Matches are distributed among these distances:
   8   16  0.70
   9    7  0.30

ACGTcount: A:0.59, C:0.15, G:0.03, T:0.24


Consensus pattern (8 bp):   
AAAAATTC
Done.