Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01004102.1 Corchorus olitorius cultivar O-4 contig04115, 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, 694

Length: 1158
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31


Found at i:339 original size:18 final size:18

Alignment explanation


    Indices: 318--356  Score: 78
    Period size: 18  Copynumber: 2.2  Consensus size: 18

        308 GGTATCAACC

                              
        318 AGATTAATATTTTCAATT
          1 AGATTAATATTTTCAATT

                              
        336 AGATTAATATTTTCAATT
          1 AGATTAATATTTTCAATT

               
        354 AGA
          1 AGA

        357 ATGCTTTATG


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   21  1.00

ACGTcount: A:0.41, C:0.05, G:0.08, T:0.46


Consensus pattern (18 bp):   
AGATTAATATTTTCAATT

Found at i:433 original size:9 final size:10

Alignment explanation


    Indices: 411--449  Score: 71
    Period size: 10  Copynumber: 4.0  Consensus size: 10

        401 CAGGCTCCGT

                      
        411 TTAGAAAAAC
          1 TTAGAAAAAC

                      
        421 TTAGAAAAA-
          1 TTAGAAAAAC

                      
        430 TTAGAAAAAC
          1 TTAGAAAAAC

                      
        440 TTAGAAAAAC
          1 TTAGAAAAAC

        450 CCAATTGGTA


Statistics
Matches: 28,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
   9    9  0.32
  10   19  0.68

ACGTcount: A:0.62, C:0.08, G:0.10, T:0.21


Consensus pattern (10 bp):   
TTAGAAAAAC

Found at i:435 original size:19 final size:19

Alignment explanation


    Indices: 411--448  Score: 76
    Period size: 19  Copynumber: 2.0  Consensus size: 19

        401 CAGGCTCCGT

                               
        411 TTAGAAAAACTTAGAAAAA
          1 TTAGAAAAACTTAGAAAAA

                               
        430 TTAGAAAAACTTAGAAAAA
          1 TTAGAAAAACTTAGAAAAA

        449 CCCAATTGGT


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  19   19  1.00

ACGTcount: A:0.63, C:0.05, G:0.11, T:0.21


Consensus pattern (19 bp):   
TTAGAAAAACTTAGAAAAA

Found at i:825 original size:21 final size:20

Alignment explanation


    Indices: 796--856  Score: 113
    Period size: 20  Copynumber: 3.0  Consensus size: 20

        786 TTGAATCCCA

                                
        796 ATGAAAAAAAATAGATCAAT
          1 ATGAAAAAAAATAGATCAAT

                                
        816 ATGAAAAAAAATAGATCAAT
          1 ATGAAAAAAAATAGATCAAT

                                 
        836 ATGAAAAAAAACTAGATCAAT
          1 ATGAAAAAAAA-TAGATCAAT

        857 GAAAAGTTTG


Statistics
Matches: 40,  Mismatches: 0, Indels: 1
        0.98            0.00        0.02

Matches are distributed among these distances:
  20   31  0.77
  21    9  0.22

ACGTcount: A:0.64, C:0.07, G:0.10, T:0.20


Consensus pattern (20 bp):   
ATGAAAAAAAATAGATCAAT

Found at i:905 original size:21 final size:22

Alignment explanation


    Indices: 876--917  Score: 77
    Period size: 21  Copynumber: 2.0  Consensus size: 22

        866 GTGCGATAAG

                                  
        876 TTTAGCAAAATTTTTTTCTATA
          1 TTTAGCAAAATTTTTTTCTATA

                                 
        898 TTTA-CAAAATTTTTTTCTAT
          1 TTTAGCAAAATTTTTTTCTAT

        918 CTTATAGGAA


Statistics
Matches: 20,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  21   16  0.80
  22    4  0.20

ACGTcount: A:0.31, C:0.10, G:0.02, T:0.57


Consensus pattern (22 bp):   
TTTAGCAAAATTTTTTTCTATA
Done.