Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01005594.1 Corchorus olitorius cultivar O-4 contig05618, 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, 634

Length: 1057
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.36


Found at i:173 original size:57 final size:57

Alignment explanation


    Indices: 85--200  Score: 189
    Period size: 57  Copynumber: 2.0  Consensus size: 57

         75 TATCAGTTTC

                 *               *                                    
         85 CTTTCGCACAATAAATGTTATGATAAATCATATCCCCTC-TATCTCTACTTAATTATT
          1 CTTTCACACAATAAATGTTATAATAAATCATATCCCC-CATATCTCTACTTAATTATT

                                                      *              
        142 CTTTCACACAATAAATGTTATAATAAATCATATCCCCCATATTTCTACTTAATTATT
          1 CTTTCACACAATAAATGTTATAATAAATCATATCCCCCATATCTCTACTTAATTATT

              
        199 CT
          1 CT

        201 ACAAAATAAA


Statistics
Matches: 55,  Mismatches: 3, Indels: 2
        0.92            0.05        0.03

Matches are distributed among these distances:
  56    1  0.02
  57   54  0.98

ACGTcount: A:0.34, C:0.22, G:0.03, T:0.41


Consensus pattern (57 bp):   
CTTTCACACAATAAATGTTATAATAAATCATATCCCCCATATCTCTACTTAATTATT

Found at i:290 original size:21 final size:21

Alignment explanation


    Indices: 266--332  Score: 57
    Period size: 21  Copynumber: 3.2  Consensus size: 21

        256 AAGGCTTAGG

                                 
        266 ATTTGAGTTGAGTATTTCTTA
          1 ATTTGAGTTGAGTATTTCTTA

                   ***  *         *
        287 ATTT-A-CAAAGAATTTTCTATG
          1 ATTTGAGTTGAGTA-TTTCT-TA

                                 
        308 ATTTGAGTTGAGTATTTCTTA
          1 ATTTGAGTTGAGTATTTCTTA

                
        329 ATTT
          1 ATTT

        333 ACAGAGAATT


Statistics
Matches: 32,  Mismatches: 10, Indels: 8
        0.64            0.20        0.16

Matches are distributed among these distances:
  19    3  0.09
  20    6  0.19
  21   14  0.44
  22    6  0.19
  23    3  0.09

ACGTcount: A:0.28, C:0.06, G:0.15, T:0.51


Consensus pattern (21 bp):   
ATTTGAGTTGAGTATTTCTTA

Found at i:324 original size:42 final size:42

Alignment explanation


    Indices: 265--345  Score: 153
    Period size: 42  Copynumber: 1.9  Consensus size: 42

        255 TAAGGCTTAG

                                                      
        265 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
          1 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT

                                         *         
        307 GATTTGAGTTGAGTATTTCTTAATTTACAGAGAATTTTC
          1 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTC

        346 AAGATTTAGC


Statistics
Matches: 38,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  42   38  1.00

ACGTcount: A:0.30, C:0.07, G:0.16, T:0.47


Consensus pattern (42 bp):   
GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
Done.