Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011292.1 Corchorus capsularis cultivar CVL-1 contig11313, 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, 767

Length: 1279
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.30


Found at i:1047 original size:55 final size:55

Alignment explanation


    Indices: 969--1275  Score: 490
    Period size: 55  Copynumber: 5.6  Consensus size: 55

        959 TAAAAAGGGG

                        *                                          
        969 CAATCAGT-AATAAGTAAAAAGAGATTAATCAGAGTCAAGGTGATGGTAATCAGT
          1 CAATCAGTAAATCAGTAAAAAGAGATTAATCAGAGTCAAGGTGATGGTAATCAGT

                *       *    *              *                      
       1023 CAATTAGTAAATTAGTAGAAAGAGATTAATCAAAGTCAAGGTGATGGTAATCAGT
          1 CAATCAGTAAATCAGTAAAAAGAGATTAATCAGAGTCAAGGTGATGGTAATCAGT

                          *  *              *                      
       1078 CAATCAGTAAATCAATAGAAAGAGATTAATCAAAGTCAAGGTGATGGTAATCAGT
          1 CAATCAGTAAATCAGTAAAAAGAGATTAATCAGAGTCAAGGTGATGGTAATCAGT

            *                              *        *               
       1133 AAATCAGTAAATCAGTAAAAAGAGATTAATCGGAGTACAAAGTGATGGTAATCAGT
          1 CAATCAGTAAATCAGTAAAAAGAGATTAATCAGAGT-CAAGGTGATGGTAATCAGT

                                                                   
       1189 CAATCAGTAAATCAGTAAAAAGAGATTAATCAGAGTCAAGGTGATGGTAATCAGT
          1 CAATCAGTAAATCAGTAAAAAGAGATTAATCAGAGTCAAGGTGATGGTAATCAGT

                                  *         
       1244 CAATCAGTAAATCAGTAAAAAGGGATTAATCA
          1 CAATCAGTAAATCAGTAAAAAGAGATTAATCA

       1276 AGAG


Statistics
Matches: 234,  Mismatches: 17, Indels: 3
        0.92            0.07        0.01

Matches are distributed among these distances:
  54    7  0.03
  55  175  0.75
  56   52  0.22

ACGTcount: A:0.45, C:0.10, G:0.21, T:0.24


Consensus pattern (55 bp):   
CAATCAGTAAATCAGTAAAAAGAGATTAATCAGAGTCAAGGTGATGGTAATCAGT

Found at i:1139 original size:8 final size:8

Alignment explanation


    Indices: 1126--1151  Score: 52
    Period size: 8  Copynumber: 3.2  Consensus size: 8

       1116 AGGTGATGGT

                    
       1126 AATCAGTA
          1 AATCAGTA

                    
       1134 AATCAGTA
          1 AATCAGTA

                    
       1142 AATCAGTA
          1 AATCAGTA

              
       1150 AA
          1 AA

       1152 AAGAGATTAA


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   8   18  1.00

ACGTcount: A:0.54, C:0.12, G:0.12, T:0.23


Consensus pattern (8 bp):   
AATCAGTA

Found at i:1219 original size:111 final size:110

Alignment explanation


    Indices: 969--1276  Score: 492
    Period size: 111  Copynumber: 2.8  Consensus size: 110

        959 TAAAAAGGGG

                        *                                              *     
        969 CAATCAGT-AATAAGTAAAAAGAGATTAATCAGAGTCAAGGTGATGGTAATCAGTCAATTAGTAA
          1 CAATCAGTAAATCAGTAAAAAGAGATTAATCAGAGTCAAGGTGATGGTAATCAGTCAATCAGTAA

              *    *                     *               
       1033 ATTAGTAGAAAGAGATTAATCAAAGTCAAGGTGATGGTAATCAGT
         66 ATCAGTAAAAAGAGATTAATCAAAGTCAAAGTGATGGTAATCAGT

                          *  *              *                      *         
       1078 CAATCAGTAAATCAATAGAAAGAGATTAATCAAAGTCAAGGTGATGGTAATCAGTAAATCAGTAA
          1 CAATCAGTAAATCAGTAAAAAGAGATTAATCAGAGTCAAGGTGATGGTAATCAGTCAATCAGTAA

                                 **                       
       1143 ATCAGTAAAAAGAGATTAATCGGAGTACAAAGTGATGGTAATCAGT
         66 ATCAGTAAAAAGAGATTAATCAAAGT-CAAAGTGATGGTAATCAGT

                                                                             
       1189 CAATCAGTAAATCAGTAAAAAGAGATTAATCAGAGTCAAGGTGATGGTAATCAGTCAATCAGTAA
          1 CAATCAGTAAATCAGTAAAAAGAGATTAATCAGAGTCAAGGTGATGGTAATCAGTCAATCAGTAA

                        *          
       1254 ATCAGTAAAAAGGGATTAATCAA
         66 ATCAGTAAAAAGAGATTAATCAA

       1277 GAG


Statistics
Matches: 179,  Mismatches: 18, Indels: 2
        0.90            0.09        0.01

Matches are distributed among these distances:
 109    8  0.04
 110   72  0.40
 111   99  0.55

ACGTcount: A:0.45, C:0.10, G:0.21, T:0.24


Consensus pattern (110 bp):   
CAATCAGTAAATCAGTAAAAAGAGATTAATCAGAGTCAAGGTGATGGTAATCAGTCAATCAGTAA
ATCAGTAAAAAGAGATTAATCAAAGTCAAAGTGATGGTAATCAGT

Found at i:1254 original size:166 final size:164

Alignment explanation


    Indices: 970--1276  Score: 506
    Period size: 166  Copynumber: 1.9  Consensus size: 164

        960 AAAAAGGGGC

                                                 *                   *       
        970 AATCAGTAATAAGTAAAAAGAGATTAATCAGAGTCAAGGTGATGGTAATCAGTCAATTAGTAAAT
          1 AATCAGTAATAAGTAAAAAGAGATTAATCAGAGTCAAAGTGATGGTAATCAGTCAATCAGTAAAT

            *    *                                                      *    
       1035 TAGTAGAAAGAGATTAATCAAAGTCAAGGTGATGGTAATCAGTCAATCAGTAAATCAATAGAAAG
         66 CAGTAAAAAGAGATTAATCAAAGTCAAGGTGATGGTAATCAGTCAATCAGTAAATCAATAAAAAG

                                              
       1100 AGATTAATCAAAGTCAAGGTGATGGTAATCAGTA
        131 AGATTAATCAAAGTCAAGGTGATGGTAATCAGTA

                       *                  *                                  
       1134 AATCAGTAAATCAGTAAAAAGAGATTAATCGGAGTACAAAGTGATGGTAATCAGTCAATCAGTAA
          1 AATCAGT-AATAAGTAAAAAGAGATTAATCAGAGT-CAAAGTGATGGTAATCAGTCAATCAGTAA

                                  *                                    *     
       1199 ATCAGTAAAAAGAGATTAATCAGAGTCAAGGTGATGGTAATCAGTCAATCAGTAAATCAGTAAAA
         64 ATCAGTAAAAAGAGATTAATCAAAGTCAAGGTGATGGTAATCAGTCAATCAGTAAATCAATAAAA

              *          
       1264 AGGGATTAATCAA
        129 AGAGATTAATCAA

       1277 GAG


Statistics
Matches: 131,  Mismatches: 10, Indels: 2
        0.92            0.07        0.01

Matches are distributed among these distances:
 164    7  0.05
 165   25  0.19
 166   99  0.76

ACGTcount: A:0.46, C:0.09, G:0.21, T:0.24


Consensus pattern (164 bp):   
AATCAGTAATAAGTAAAAAGAGATTAATCAGAGTCAAAGTGATGGTAATCAGTCAATCAGTAAAT
CAGTAAAAAGAGATTAATCAAAGTCAAGGTGATGGTAATCAGTCAATCAGTAAATCAATAAAAAG
AGATTAATCAAAGTCAAGGTGATGGTAATCAGTA
Done.