Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012094.1 Corchorus capsularis cultivar CVL-1 contig12115, 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: 20819
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32


Found at i:606 original size:40 final size:40

Alignment explanation


    Indices: 548--629  Score: 155
    Period size: 40  Copynumber: 2.0  Consensus size: 40

        538 ATTCTCTTCA

                                                    
        548 AGTTTAAGTTTATACTAATGGCTCAACCAAATTCCGCATC
          1 AGTTTAAGTTTATACTAATGGCTCAACCAAATTCCGCATC

                         *                          
        588 AGTTTAAGTTTATGCTAATGGCTCAACCAAATTCCGCATC
          1 AGTTTAAGTTTATACTAATGGCTCAACCAAATTCCGCATC

              
        628 AG
          1 AG

        630 GTATGTCTAA


Statistics
Matches: 41,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  40   41  1.00

ACGTcount: A:0.32, C:0.22, G:0.15, T:0.32


Consensus pattern (40 bp):   
AGTTTAAGTTTATACTAATGGCTCAACCAAATTCCGCATC

Found at i:3671 original size:18 final size:18

Alignment explanation


    Indices: 3644--3678  Score: 52
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       3634 GTCACGGTTG

                 *            
       3644 ATGTTTCTTTACCCATAA
          1 ATGTTCCTTTACCCATAA

                       *     
       3662 ATGTTCCTTTATCCATA
          1 ATGTTCCTTTACCCATA

       3679 CCTAATCAAA


Statistics
Matches: 15,  Mismatches: 2, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  18   15  1.00

ACGTcount: A:0.26, C:0.23, G:0.06, T:0.46


Consensus pattern (18 bp):   
ATGTTCCTTTACCCATAA

Found at i:20707 original size:14 final size:14

Alignment explanation


    Indices: 20669--20710  Score: 57
    Period size: 14  Copynumber: 3.0  Consensus size: 14

      20659 TTTTACGTTA

                          
      20669 TTTTCCTTTTCTTT
          1 TTTTCCTTTTCTTT

             *    *       
      20683 TCTTCCCTTTCTTT
          1 TTTTCCTTTTCTTT

                 *        
      20697 TTTTCGTTTTCTTT
          1 TTTTCCTTTTCTTT

      20711 GCTTCGTTTG


Statistics
Matches: 23,  Mismatches: 5, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  14   23  1.00

ACGTcount: A:0.00, C:0.24, G:0.02, T:0.74


Consensus pattern (14 bp):   
TTTTCCTTTTCTTT

Found at i:20716 original size:14 final size:14

Alignment explanation


    Indices: 20675--20719  Score: 54
    Period size: 14  Copynumber: 3.2  Consensus size: 14

      20665 GTTATTTTCC

                         *
      20675 TTTTCTTTTCTTCC
          1 TTTTCTTTTCTTCG

            *        *    
      20689 CTTTCTTTTTTTCG
          1 TTTTCTTTTCTTCG

                    *     
      20703 TTTTCTTTGCTTCG
          1 TTTTCTTTTCTTCG

               
      20717 TTT
          1 TTT

      20720 GCTGCACTTG


Statistics
Matches: 25,  Mismatches: 6, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  14   25  1.00

ACGTcount: A:0.00, C:0.22, G:0.07, T:0.71


Consensus pattern (14 bp):   
TTTTCTTTTCTTCG
Done.