Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005470.1 Corchorus capsularis cultivar CVL-1 contig05488, 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: 19834
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36


Found at i:10854 original size:36 final size:36

Alignment explanation


    Indices: 10807--10878  Score: 144
    Period size: 36  Copynumber: 2.0  Consensus size: 36

      10797 TCACTGGGTT

                                                
      10807 TATTTGTAATTTGTTTATTTATGTATTTGGTAGGTA
          1 TATTTGTAATTTGTTTATTTATGTATTTGGTAGGTA

                                                
      10843 TATTTGTAATTTGTTTATTTATGTATTTGGTAGGTA
          1 TATTTGTAATTTGTTTATTTATGTATTTGGTAGGTA

      10879 GGTAGTTTAT


Statistics
Matches: 36,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  36   36  1.00

ACGTcount: A:0.22, C:0.00, G:0.19, T:0.58


Consensus pattern (36 bp):   
TATTTGTAATTTGTTTATTTATGTATTTGGTAGGTA

Found at i:11736 original size:6 final size:6

Alignment explanation


    Indices: 11725--11757  Score: 66
    Period size: 6  Copynumber: 5.5  Consensus size: 6

      11715 TGAGTGTGTG

                                                  
      11725 TATCTT TATCTT TATCTT TATCTT TATCTT TAT
          1 TATCTT TATCTT TATCTT TATCTT TATCTT TAT

      11758 ACTCTATAAT


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   27  1.00

ACGTcount: A:0.18, C:0.15, G:0.00, T:0.67


Consensus pattern (6 bp):   
TATCTT

Found at i:16785 original size:19 final size:20

Alignment explanation


    Indices: 16758--16803  Score: 76
    Period size: 19  Copynumber: 2.4  Consensus size: 20

      16748 GATACGAAAA

                                
      16758 TTAGTAACCATTGGATT-TT
          1 TTAGTAACCATTGGATTCTT

              *                 
      16777 TTTGTAACCATTGGATTCTT
          1 TTAGTAACCATTGGATTCTT

                   
      16797 TTAGTAA
          1 TTAGTAA

      16804 TTTTAAATAA


Statistics
Matches: 24,  Mismatches: 2, Indels: 1
        0.89            0.07        0.04

Matches are distributed among these distances:
  19   16  0.67
  20    8  0.33

ACGTcount: A:0.26, C:0.11, G:0.15, T:0.48


Consensus pattern (20 bp):   
TTAGTAACCATTGGATTCTT

Found at i:17032 original size:21 final size:21

Alignment explanation


    Indices: 16993--17032  Score: 55
    Period size: 21  Copynumber: 1.9  Consensus size: 21

      16983 ATTGATAAAA

                         *       
      16993 GTATAACATTTTTCATAATCG
          1 GTATAACATTTTTAATAATCG

                                
      17014 GTATAAC-TTTTTAAGTAAT
          1 GTATAACATTTTTAA-TAAT

      17033 ACTCCATCTA


Statistics
Matches: 17,  Mismatches: 1, Indels: 2
        0.85            0.05        0.10

Matches are distributed among these distances:
  20    6  0.35
  21   11  0.65

ACGTcount: A:0.35, C:0.10, G:0.10, T:0.45


Consensus pattern (21 bp):   
GTATAACATTTTTAATAATCG
Done.