Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000196.1 Corchorus olitorius cultivar O-4 contig00196, 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, 822

Length: 1370
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.29


Found at i:382 original size:18 final size:18

Alignment explanation


    Indices: 352--430  Score: 81
    Period size: 18  Copynumber: 4.3  Consensus size: 18

        342 ACCAAAATGC

                            *  
        352 ATAAATAAAAGCCCAAGTA
          1 ATAAAT-AAAGCCCAAATA

                             *
        371 ATAAATAAAGCCCAAATT
          1 ATAAATAAAGCCCAAATA

                               
        389 ATAAATAAAG-CCAAATTA
          1 ATAAATAAAGCCCAAA-TA

             *                *
        407 AGAAA-ACAAGCCCAAATC
          1 ATAAATA-AAGCCCAAATA

                  
        425 ATAAAT
          1 ATAAAT

        431 GGTACCCAAT


Statistics
Matches: 50,  Mismatches: 6, Indels: 8
        0.78            0.09        0.12

Matches are distributed among these distances:
  17    6  0.12
  18   33  0.66
  19   11  0.22

ACGTcount: A:0.58, C:0.16, G:0.08, T:0.18


Consensus pattern (18 bp):   
ATAAATAAAGCCCAAATA

Found at i:418 original size:36 final size:37

Alignment explanation


    Indices: 346--430  Score: 102
    Period size: 36  Copynumber: 2.3  Consensus size: 37

        336 ACAAAAACCA

                               *      *           
        346 AAATGCATAAATAAAAGCCCAAGTAATAAATAAAGCCC
          1 AAAT-CATAAATAAAAGCCAAAGTAAGAAATAAAGCCC

                *                *                
        384 AAATTATAAAT-AAAGCCAAATTAAGAAA-ACAAGCCC
          1 AAATCATAAATAAAAGCCAAAGTAAGAAATA-AAGCCC

                       
        420 AAATCATAAAT
          1 AAATCATAAAT

        431 GGTACCCAAT


Statistics
Matches: 41,  Mismatches: 5, Indels: 4
        0.82            0.10        0.08

Matches are distributed among these distances:
  35    1  0.02
  36   30  0.73
  37    6  0.15
  38    4  0.10

ACGTcount: A:0.58, C:0.16, G:0.08, T:0.18


Consensus pattern (37 bp):   
AAATCATAAATAAAAGCCAAAGTAAGAAATAAAGCCC
Done.