Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004336.1 Corchorus capsularis cultivar CVL-1 contig04344, 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, 766

Length: 1278
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.32


Found at i:91 original size:13 final size:13

Alignment explanation


    Indices: 73--98  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

         63 TTTTCACAAA

                         
         73 ATTATCAACTAAT
          1 ATTATCAACTAAT

                         
         86 ATTATCAACTAAT
          1 ATTATCAACTAAT

         99 CATAATGGTT


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.46, C:0.15, G:0.00, T:0.38


Consensus pattern (13 bp):   
ATTATCAACTAAT

Found at i:369 original size:26 final size:26

Alignment explanation


    Indices: 304--382  Score: 74
    Period size: 26  Copynumber: 3.0  Consensus size: 26

        294 AGAAATATTC

                                  *      
        304 GAAATATATAAATAAATTAGAAAATATAG
          1 GAAAT-TATAAAT-AATTA-AATATATAG

                                       
        333 GAAATT-T-AATAATTTAAATATATA-
          1 GAAATTATAAATAA-TTAAATATATAG

            *                         
        357 TAAATTATAAATAGATTAAATATATA
          1 GAAATTATAAATA-ATTAAATATATA

        383 ATTATAATAT


Statistics
Matches: 44,  Mismatches: 2, Indels: 11
        0.77            0.04        0.19

Matches are distributed among these distances:
  24    5  0.11
  25   10  0.23
  26   21  0.48
  27    2  0.05
  28    1  0.02
  29    5  0.11

ACGTcount: A:0.58, C:0.00, G:0.06, T:0.35


Consensus pattern (26 bp):   
GAAATTATAAATAATTAAATATATAG

Found at i:396 original size:20 final size:23

Alignment explanation


    Indices: 352--396  Score: 60
    Period size: 20  Copynumber: 2.0  Consensus size: 23

        342 TAATTTAAAT

                                    
        352 ATATATAAATTATAAATAGATTAA
          1 ATATATAAATTATAAATA-ATTAA

                                   
        376 ATATAT-AATTAT-AAT-ATTAA
          1 ATATATAAATTATAAATAATTAA

             
        396 A
          1 A

        397 CAGTAATATA


Statistics
Matches: 21,  Mismatches: 0, Indels: 4
        0.84            0.00        0.16

Matches are distributed among these distances:
  20    6  0.29
  22    3  0.14
  23    6  0.29
  24    6  0.29

ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40


Consensus pattern (23 bp):   
ATATATAAATTATAAATAATTAA
Done.