Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01002408.1 Corchorus capsularis cultivar CVL-1 contig02414, 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, 816

Length: 1361
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39


Found at i:417 original size:20 final size:19

Alignment explanation


    Indices: 389--426  Score: 67
    Period size: 20  Copynumber: 1.9  Consensus size: 19

        379 ATATTGAATA

                               
        389 TATAATATATATAAGTAAG
          1 TATAATATATATAAGTAAG

                               
        408 TATAAGTATATATAAGTAA
          1 TATAA-TATATATAAGTAA

        427 TTAAACATAA


Statistics
Matches: 18,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  19    5  0.28
  20   13  0.72

ACGTcount: A:0.53, C:0.00, G:0.11, T:0.37


Consensus pattern (19 bp):   
TATAATATATATAAGTAAG

Found at i:493 original size:20 final size:20

Alignment explanation


    Indices: 468--529  Score: 94
    Period size: 20  Copynumber: 3.2  Consensus size: 20

        458 CATGGATTCC

                                
        468 TTTTATAGATAATGTCTAAT
          1 TTTTATAGATAATGTCTAAT

                                
        488 TTTTATAGATAATGTCTAA-
          1 TTTTATAGATAATGTCTAAT

                                
        507 --TTATAGATAATGTCTAAT
          1 TTTTATAGATAATGTCTAAT

                 
        525 GTTTT
          1 -TTTT

        530 GTTATAATTG


Statistics
Matches: 38,  Mismatches: 0, Indels: 7
        0.84            0.00        0.16

Matches are distributed among these distances:
  17   17  0.45
  20   19  0.50
  21    2  0.05

ACGTcount: A:0.34, C:0.05, G:0.11, T:0.50


Consensus pattern (20 bp):   
TTTTATAGATAATGTCTAAT

Found at i:512 original size:17 final size:17

Alignment explanation


    Indices: 470--524  Score: 83
    Period size: 17  Copynumber: 3.1  Consensus size: 17

        460 TGGATTCCTT

                             
        470 TTATAGATAATGTCTAA
          1 TTATAGATAATGTCTAA

                                
        487 TTTTTATAGATAATGTCTAA
          1 ---TTATAGATAATGTCTAA

                             
        507 TTATAGATAATGTCTAA
          1 TTATAGATAATGTCTAA

             
        524 T
          1 T

        525 GTTTTGTTAT


Statistics
Matches: 35,  Mismatches: 0, Indels: 3
        0.92            0.00        0.08

Matches are distributed among these distances:
  17   18  0.51
  20   17  0.49

ACGTcount: A:0.38, C:0.05, G:0.11, T:0.45


Consensus pattern (17 bp):   
TTATAGATAATGTCTAA
Done.