Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019963.1 Corchorus olitorius cultivar O-4 contig19996, 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, 1000

Length: 4919
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35


Found at i:85 original size:42 final size:43

Alignment explanation


    Indices: 3--86  Score: 100
    Period size: 42  Copynumber: 2.0  Consensus size: 43

          1 TA

                  *               *         **          
          3 ATTTAACTTTTTTATTAATTATGGAAAGATATTGTAAATCCAAT
          1 ATTTAAATTTTTTA-TAATTATAGAAAGATATAATAAATCCAAT

                                                      
         47 ATTTAAATTTTTTA-AATTATAGAAAGATATAA-ATAATCCA
          1 ATTTAAATTTTTTATAATTATAGAAAGATATAATA-AATCCA

         87 CTATAATTGT


Statistics
Matches: 35,  Mismatches: 4, Indels: 4
        0.81            0.09        0.09

Matches are distributed among these distances:
  41    1  0.03
  42   21  0.60
  44   13  0.37

ACGTcount: A:0.44, C:0.06, G:0.07, T:0.43


Consensus pattern (43 bp):   
ATTTAAATTTTTTATAATTATAGAAAGATATAATAAATCCAAT

Found at i:151 original size:15 final size:16

Alignment explanation


    Indices: 126--155  Score: 53
    Period size: 15  Copynumber: 1.9  Consensus size: 16

        116 AATAATTATT

                            
        126 TTTAGATTATAATATA
          1 TTTAGATTATAATATA

                           
        142 TTTA-ATTATAATAT
          1 TTTAGATTATAATAT

        156 TATTATTTAT


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  15   10  0.71
  16    4  0.29

ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53


Consensus pattern (16 bp):   
TTTAGATTATAATATA

Found at i:3295 original size:35 final size:36

Alignment explanation


    Indices: 3251--3331  Score: 121
    Period size: 36  Copynumber: 2.2  Consensus size: 36

       3241 GCCTGGCGCA

                                                  
       3251 GCCCAAGCGCCCAGGCC-AG-GCGCGGGCCAGCGCATG
          1 GCCC-AGCGCCCAGGCCTAGTGCGCGGGCCAGC-CATG

                             *                  
       3287 GCCCAGCGCCCAGGCCTGGTGCGCGGGCCAGCCATG
          1 GCCCAGCGCCCAGGCCTAGTGCGCGGGCCAGCCATG

                     
       3323 GCCCAGCGC
          1 GCCCAGCGC

       3332 TCAAGCTTGG


Statistics
Matches: 42,  Mismatches: 1, Indels: 4
        0.89            0.02        0.09

Matches are distributed among these distances:
  35   12  0.29
  36   18  0.43
  37   12  0.29

ACGTcount: A:0.14, C:0.43, G:0.38, T:0.05


Consensus pattern (36 bp):   
GCCCAGCGCCCAGGCCTAGTGCGCGGGCCAGCCATG

Done.