Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01000432.1 Corchorus capsularis cultivar CVL-1 contig00432, 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, 976

Length: 1627
ACGTcount: A:0.35, C:0.13, G:0.21, T:0.30


Found at i:77 original size:52 final size:51

Alignment explanation


    Indices: 1--121  Score: 163
    Period size: 52  Copynumber: 2.3  Consensus size: 51

                         * *                            *    * 
          1 AAGATCAAGCAAACAAAGTAAAATGATGAGCCTACA-TTCAAGTTAGAGGG
          1 AAGATCAAGCAAATACAGTAAAATGATGAGCCTACATTTCAAGTCAGAGAG

                                                *                 
         51 AAGATCCAAGCCAAATACAGTAAAATGATGAGCCTAGATTTTCAAGTCAGAGAG
          1 AAGAT-CAAG-CAAATACAGTAAAATGATGAGCCTACA-TTTCAAGTCAGAGAG

                             
        105 AAGATCAAGCAAATACA
          1 AAGATCAAGCAAATACA

        122 TGCATTAACA


Statistics
Matches: 62,  Mismatches: 5, Indels: 6
        0.85            0.07        0.08

Matches are distributed among these distances:
  50    5  0.08
  51    4  0.06
  52   32  0.52
  53    4  0.06
  54   17  0.27

ACGTcount: A:0.46, C:0.16, G:0.20, T:0.18


Consensus pattern (51 bp):   
AAGATCAAGCAAATACAGTAAAATGATGAGCCTACATTTCAAGTCAGAGAG

Found at i:1182 original size:12 final size:11

Alignment explanation


    Indices: 1139--1190  Score: 52
    Period size: 12  Copynumber: 4.6  Consensus size: 11

       1129 TTATATTAAT

                    *  
       1139 AAAAAAAAGAA
          1 AAAAAAAACAA

                       *
       1150 AAAGAAAAAC-T
          1 AAA-AAAAACAA

               *       
       1161 AAACAAAACAA
          1 AAAAAAAACAA

                        
       1172 AACAAAAAACAA
          1 AA-AAAAAACAA

                   
       1184 AAAAAAA
          1 AAAAAAA

       1191 GGAAAAAAGA


Statistics
Matches: 33,  Mismatches: 5, Indels: 6
        0.75            0.11        0.14

Matches are distributed among these distances:
  10    5  0.15
  11   13  0.39
  12   15  0.45

ACGTcount: A:0.85, C:0.10, G:0.04, T:0.02


Consensus pattern (11 bp):   
AAAAAAAACAA

Found at i:1211 original size:15 final size:14

Alignment explanation


    Indices: 1188--1218  Score: 53
    Period size: 14  Copynumber: 2.2  Consensus size: 14

       1178 AAACAAAAAA

                 *        
       1188 AAAGGAAAAAAGAG
          1 AAAGGGAAAAAGAG

                          
       1202 AAAGGGAAAAAGAG
          1 AAAGGGAAAAAGAG

               
       1216 AAA
          1 AAA

       1219 AATAAATTTG


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  14   16  1.00

ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00


Consensus pattern (14 bp):   
AAAGGGAAAAAGAG
Done.