Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008317.1 Corchorus capsularis cultivar CVL-1 contig08338, 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: 10805
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.31


Found at i:6919 original size:3 final size:3

Alignment explanation


    Indices: 6913--6953  Score: 73
    Period size: 3  Copynumber: 13.3  Consensus size: 3

       6903 CAAAAAAAGT

                                                                  
       6913 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA CATA A
          1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA A

       6954 ATACATACAT


Statistics
Matches: 37,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
   3   34  0.92
   4    3  0.08

ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32


Consensus pattern (3 bp):   
ATA

Found at i:6961 original size:12 final size:12

Alignment explanation


    Indices: 6942--7003  Score: 83
    Period size: 12  Copynumber: 5.3  Consensus size: 12

       6932 TAATAATAAT

                        
       6942 AATA-ATACATA
          1 AATACATACATA

                        
       6953 AATACATACATA
          1 AATACATACATA

            *           
       6965 CATACATACATA
          1 AATACATACATA

            *           
       6977 CATACATACATA
          1 AATACATACATA

            *           
       6989 CATACATACA-A
          1 AATACATACATA

                
       7000 AATA
          1 AATA

       7004 TTTAGTTACA


Statistics
Matches: 48,  Mismatches: 2, Indels: 2
        0.92            0.04        0.04

Matches are distributed among these distances:
  11    8  0.17
  12   40  0.83

ACGTcount: A:0.56, C:0.19, G:0.00, T:0.24


Consensus pattern (12 bp):   
AATACATACATA

Found at i:7017 original size:4 final size:4

Alignment explanation


    Indices: 6946--6998  Score: 97
    Period size: 4  Copynumber: 13.2  Consensus size: 4

       6936 AATAATAATA

                    *                                                  
       6946 ATAC ATAA ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
          1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC

                  
       6994 ATAC A
          1 ATAC A

       6999 AAATATTTAG


Statistics
Matches: 47,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
   4   47  1.00

ACGTcount: A:0.53, C:0.23, G:0.00, T:0.25


Consensus pattern (4 bp):   
ATAC
Done.