Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01005860.1 Corchorus olitorius cultivar O-4 contig05885, 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, 616

Length: 1028
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.33


Found at i:383 original size:18 final size:18

Alignment explanation


    Indices: 362--400  Score: 78
    Period size: 18  Copynumber: 2.2  Consensus size: 18

        352 GGTATCAACC

                              
        362 AGATTAATATTTTCAATT
          1 AGATTAATATTTTCAATT

                              
        380 AGATTAATATTTTCAATT
          1 AGATTAATATTTTCAATT

               
        398 AGA
          1 AGA

        401 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:477 original size:9 final size:10

Alignment explanation


    Indices: 455--493  Score: 71
    Period size: 10  Copynumber: 4.0  Consensus size: 10

        445 CAGGCTCCGT

                      
        455 TTAGAAAAAC
          1 TTAGAAAAAC

                      
        465 TTAGAAAAA-
          1 TTAGAAAAAC

                      
        474 TTAGAAAAAC
          1 TTAGAAAAAC

                      
        484 TTAGAAAAAC
          1 TTAGAAAAAC

        494 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:479 original size:19 final size:19

Alignment explanation


    Indices: 455--492  Score: 76
    Period size: 19  Copynumber: 2.0  Consensus size: 19

        445 CAGGCTCCGT

                               
        455 TTAGAAAAACTTAGAAAAA
          1 TTAGAAAAACTTAGAAAAA

                               
        474 TTAGAAAAACTTAGAAAAA
          1 TTAGAAAAACTTAGAAAAA

        493 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:877 original size:22 final size:21

Alignment explanation


    Indices: 844--907  Score: 119
    Period size: 21  Copynumber: 3.0  Consensus size: 21

        834 TTGAATCCCA

                                 
        844 ATAGTAAAAAAATAGATCAAT
          1 ATAGTAAAAAAATAGATCAAT

                                  
        865 ATAGTAAAAAAAATAGATCAAT
          1 ATAGT-AAAAAAATAGATCAAT

                                 
        887 ATAGTAAAAAAATAGATCAAT
          1 ATAGTAAAAAAATAGATCAAT

        908 GTAAAAGTTT


Statistics
Matches: 42,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
  21   21  0.50
  22   21  0.50

ACGTcount: A:0.62, C:0.05, G:0.09, T:0.23


Consensus pattern (21 bp):   
ATAGTAAAAAAATAGATCAAT
Done.