Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01004511.1 Corchorus olitorius cultivar O-4 contig04527, 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, 810

Length: 1351
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31


Found at i:489 original size:76 final size:71

Alignment explanation


    Indices: 409--557  Score: 235
    Period size: 76  Copynumber: 2.0  Consensus size: 71

        399 CCAATTTGAA

                                                                  *          
        409 ATTGTGAAAGAGGAAGAGATAGGAAGGAGATCAGACTTTTTTTTTTTTTTCGTCGTGGAAAGAGG
          1 ATTGTGAAAGAGGAAGAGATAGGAAGGAGATCAGA----TTTTTTTTTTT-GTCCTGGAAAGAGG

                       
        474 AGATGAAGAAG
         61 AGATGAAGAAG

                                           *                                 
        485 ATTGTGAAAGAGGAAGAGATAGGAAGGAGATGAGATTTTTTTTTTTGTCCTGGAAAGAGGAGATG
          1 ATTGTGAAAGAGGAAGAGATAGGAAGGAGATCAGATTTTTTTTTTTGTCCTGGAAAGAGGAGATG

                  
        550 AAGAAG
         66 AAGAAG

              
        556 AT
          1 AT

        558 AAGAAAACAT


Statistics
Matches: 71,  Mismatches: 2, Indels: 5
        0.91            0.03        0.06

Matches are distributed among these distances:
  71   26  0.37
  72   11  0.15
  76   34  0.48

ACGTcount: A:0.36, C:0.04, G:0.32, T:0.28


Consensus pattern (71 bp):   
ATTGTGAAAGAGGAAGAGATAGGAAGGAGATCAGATTTTTTTTTTTGTCCTGGAAAGAGGAGATG
AAGAAG

Found at i:768 original size:16 final size:16

Alignment explanation


    Indices: 741--793  Score: 52
    Period size: 16  Copynumber: 3.3  Consensus size: 16

        731 TGTAATTGCA

                   *    *   
        741 TATTCAACTCCCTCCT
          1 TATTCAATTCCCACCT

             *              
        757 TTTTCAATTCCCACCT
          1 TATTCAATTCCCACCT

               *       *  * 
        773 TATGCAATTCCTACTT
          1 TATTCAATTCCCACCT

                 
        789 TATTC
          1 TATTC

        794 CACCGAATTT


Statistics
Matches: 29,  Mismatches: 8, Indels: 0
        0.78            0.22        0.00

Matches are distributed among these distances:
  16   29  1.00

ACGTcount: A:0.21, C:0.34, G:0.02, T:0.43


Consensus pattern (16 bp):   
TATTCAATTCCCACCT

Found at i:1079 original size:17 final size:17

Alignment explanation


    Indices: 1034--1081  Score: 69
    Period size: 17  Copynumber: 2.8  Consensus size: 17

       1024 CATATCACAT

                       *     
       1034 GACTAGTAATGGTTTAG
          1 GACTAGTAATGTTTTAG

                            *
       1051 GACTAGTAATGTTTTAT
          1 GACTAGTAATGTTTTAG

            *             
       1068 TACTAGTAATGTTT
          1 GACTAGTAATGTTT

       1082 CTCAAATCTT


Statistics
Matches: 28,  Mismatches: 3, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  17   28  1.00

ACGTcount: A:0.29, C:0.06, G:0.21, T:0.44


Consensus pattern (17 bp):   
GACTAGTAATGTTTTAG
Done.