Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01016371.1 Corchorus capsularis cultivar CVL-1 contig16392, 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: 9907
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29


Found at i:118 original size:13 final size:13

Alignment explanation


    Indices: 79--111  Score: 57
    Period size: 13  Copynumber: 2.5  Consensus size: 13

         69 GACGAGGAGG

                      *  
         79 AAGAAAAGAAGAA
          1 AAGAAAAGAAAAA

                         
         92 AAGAAAAGAAAAA
          1 AAGAAAAGAAAAA

                   
        105 AAGAAAA
          1 AAGAAAA

        112 TATAAAAGGA


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  13   19  1.00

ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00


Consensus pattern (13 bp):   
AAGAAAAGAAAAA

Found at i:918 original size:35 final size:35

Alignment explanation


    Indices: 877--1362  Score: 637
    Period size: 35  Copynumber: 13.9  Consensus size: 35

        867 GTAAATCAGT

                      *                         
        877 AGTAATCAACCTAATTCAGGGTAATTAAGTGAGTT-
          1 AGTAATCAACTTAATTCAGGGTAATTAAGT-AGTTC

             *                             *   
        912 AATAATCAACTTAATTCAGGGTAATTAAGTAATTC
          1 AGTAATCAACTTAATTCAGGGTAATTAAGTAGTTC

                 *                             *
        947 AGTTAGT-AACTTAATTCAGGGTAATTAAGTAGTTT
          1 AG-TAATCAACTTAATTCAGGGTAATTAAGTAGTTC

             *   *                               
        982 AATGAGT-AACTTAATTCAGGGTAATTAAGTGAG-TC
          1 AGT-AATCAACTTAATTCAGGGTAATTAAGT-AGTTC

            *                                   
       1017 GGTAATCAACTTAATTCAGGGTAATTAAGTAAGTT-
          1 AGTAATCAACTTAATTCAGGGTAATTAAGT-AGTTC

                                                
       1052 AGTAATCAACTTAATTCAGGGTAATTAAGTAAG-TC
          1 AGTAATCAACTTAATTCAGGGTAATTAAGT-AGTTC

                            *              *   
       1087 AGTAATCAACTTAATTTAGGGTAATTAAGTAATTC
          1 AGTAATCAACTTAATTCAGGGTAATTAAGTAGTTC

                  *                        *   
       1122 AGTAATTAACTTAATTCAGGGTAATTAAGTAATTC
          1 AGTAATCAACTTAATTCAGGGTAATTAAGTAGTTC

                  *                        *   
       1157 AGTAATTAACTTAATTCAGGGTAATTAAGTAATTC
          1 AGTAATCAACTTAATTCAGGGTAATTAAGTAGTTC

                                           *   
       1192 AGTAATCAACTTAATTCAGGGTAATTAAGTAATTC
          1 AGTAATCAACTTAATTCAGGGTAATTAAGTAGTTC

                  *                        *   
       1227 AGTAATTAACTTAATTCAGGGTAATTAAGTAATTC
          1 AGTAATCAACTTAATTCAGGGTAATTAAGTAGTTC

                            *                   
       1262 AGTAATCAACTTAATTTAGGGTAATTAAGTGAG-TC
          1 AGTAATCAACTTAATTCAGGGTAATTAAGT-AGTTC

                             **                 
       1297 AGTAATCAACTTTAATTTGGGGTAATTAAGTAGTTC
          1 AGTAATCAAC-TTAATTCAGGGTAATTAAGTAGTTC

             *                    *        
       1333 AATAAGT-AACTTAATTCAGGGCAATTAAGT
          1 AGTAA-TCAACTTAATTCAGGGTAATTAAGT

       1363 TTAGTAAGCA


Statistics
Matches: 411,  Mismatches: 28, Indels: 24
        0.89            0.06        0.05

Matches are distributed among these distances:
  34    8  0.02
  35  367  0.89
  36   35  0.09
  37    1  0.00

ACGTcount: A:0.39, C:0.09, G:0.17, T:0.35


Consensus pattern (35 bp):   
AGTAATCAACTTAATTCAGGGTAATTAAGTAGTTC

Found at i:5839 original size:8 final size:8

Alignment explanation


    Indices: 5826--5853  Score: 56
    Period size: 8  Copynumber: 3.5  Consensus size: 8

       5816 CATCCAAATA

                    
       5826 AAAATAAT
          1 AAAATAAT

                    
       5834 AAAATAAT
          1 AAAATAAT

                    
       5842 AAAATAAT
          1 AAAATAAT

                
       5850 AAAA
          1 AAAA

       5854 AAGAGAAGAA


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   8   20  1.00

ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21


Consensus pattern (8 bp):   
AAAATAAT

Found at i:7809 original size:34 final size:35

Alignment explanation


    Indices: 7724--7814  Score: 112
    Period size: 35  Copynumber: 2.6  Consensus size: 35

       7714 GTTACTCGAG

                               *    *        * 
       7724 CCAGGGCGATCTTTCTTCAGTTAATTTCAATGGGT
          1 CCAGGGCGATCTTTCTTCAATTAACTTCAATGGAT

                       *          *            
       7759 CCAGGGCGATCATTCTTCAATTTACTTCAAT-GAT
          1 CCAGGGCGATCTTTCTTCAATTAACTTCAATGGAT

                  * *             
       7793 CCAGGGTGGTCTTTCTTCAATT
          1 CCAGGGCGATCTTTCTTCAATT

       7815 CTCAAATTAT


Statistics
Matches: 48,  Mismatches: 8, Indels: 1
        0.84            0.14        0.02

Matches are distributed among these distances:
  34   21  0.44
  35   27  0.56

ACGTcount: A:0.21, C:0.22, G:0.20, T:0.37


Consensus pattern (35 bp):   
CCAGGGCGATCTTTCTTCAATTAACTTCAATGGAT
Done.