Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01003992.1 Corchorus capsularis cultivar CVL-1 contig04000, 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, 777

Length: 1295
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30


Found at i:161 original size:27 final size:28

Alignment explanation


    Indices: 84--162  Score: 92
    Period size: 27  Copynumber: 2.9  Consensus size: 28

         74 TTGAAAAGGC

                                         
         84 AATCAGTAAAGAGTAAAATGGTAAAAAGT
          1 AATCAGTAAAGAGT-AAATGGTAAAAAGT

               *     **                  
        113 AATGA-TAATCAGTAAA-GAGTAAAAAGT
          1 AATCAGTAAAGAGTAAATG-GTAAAAAGT

                                    
        140 AATCAGTAAAGAG-AAATGGTAAA
          1 AATCAGTAAAGAGTAAATGGTAAA

        163 GAGTTATAGA


Statistics
Matches: 41,  Mismatches: 6, Indels: 8
        0.75            0.11        0.15

Matches are distributed among these distances:
  26    1  0.02
  27   24  0.59
  28   12  0.29
  29    4  0.10

ACGTcount: A:0.56, C:0.04, G:0.20, T:0.20


Consensus pattern (28 bp):   
AATCAGTAAAGAGTAAATGGTAAAAAGT

Found at i:165 original size:69 final size:71

Alignment explanation


    Indices: 89--243  Score: 176
    Period size: 69  Copynumber: 2.2  Consensus size: 71

         79 AAGGCAATCA

                                        *   *                                
         89 GTAAAGAGTAAAATG-GTAAA-AAGTAATG-ATAATCAGTAAAGAGTAAAAAGTAATCAGTAAAG
          1 GTAAAGAGTAAAATGAG-AAATAAGTAAAGAAAAAT-AGTAAAGAGTAAAAAGTAATCAGTAAAG

              *     
        151 -AGAAATG
         64 AAAAAATG

                     * *         *             *                             
        158 GTAAAGAGTTATA-GAGAAATCAGTAAAGAAAAATGGTAAAGAGTAAAAAGTAATCAGTAAAGAA
          1 GTAAAGAGTAAAATGAGAAATAAGTAAAGAAAAATAGTAAAGAGTAAAAAGTAATCAGTAAAG--

                    
        222 AAAAAATG
         64 AAAAAATG

                          
        230 GTAAAGAGTAAAAT
          1 GTAAAGAGTAAAAT

        244 ATTAATCAGT


Statistics
Matches: 70,  Mismatches: 9, Indels: 10
        0.79            0.10        0.11

Matches are distributed among these distances:
  68    4  0.06
  69   45  0.64
  70    4  0.06
  72   17  0.24

ACGTcount: A:0.57, C:0.03, G:0.21, T:0.19


Consensus pattern (71 bp):   
GTAAAGAGTAAAATGAGAAATAAGTAAAGAAAAATAGTAAAGAGTAAAAAGTAATCAGTAAAGAA
AAAATG

Found at i:183 original size:35 final size:35

Alignment explanation


    Indices: 124--265  Score: 166
    Period size: 35  Copynumber: 4.0  Consensus size: 35

        114 ATGATAATCA

                                         *     
        124 GTAAAGAG-TAAAAAGTAATCAGTAAAGAGAAATG
          1 GTAAAGAGTTAAAAAGTAATCAGTAAAGAAAAATG

                       * *  *                  
        158 GTAAAGAGTTATAGAGAAATCAGTAAAGAAAAATG
          1 GTAAAGAGTTAAAAAGTAATCAGTAAAGAAAAATG

                                                  
        193 GTAAAGAG-TAAAAAGTAATCAGTAAAGAAAAAAAATG
          1 GTAAAGAGTTAAAAAGTAATCAGTAAAG---AAAAATG

                            *                    
        230 GTAAAGAG-TAAAATATTAATCAGTAAA-AAGAAATG
          1 GTAAAGAGTTAAAA-AGTAATCAGTAAAGAA-AAATG

             
        265 G
          1 G

        266 CAATCAATAA


Statistics
Matches: 94,  Mismatches: 8, Indels: 11
        0.83            0.07        0.10

Matches are distributed among these distances:
  34   26  0.28
  35   36  0.38
  37   20  0.21
  38   12  0.13

ACGTcount: A:0.57, C:0.03, G:0.21, T:0.19


Consensus pattern (35 bp):   
GTAAAGAGTTAAAAAGTAATCAGTAAAGAAAAATG

Found at i:235 original size:16 final size:17

Alignment explanation


    Indices: 186--242  Score: 53
    Period size: 16  Copynumber: 3.1  Consensus size: 17

        176 ATCAGTAAAG

                              
        186 AAAAATGGTAAAGAGTAA
          1 AAAAATGGTAAAGAG-AA

                     *          
        204 AAAGTAATCAGTAAAGA-AA
          1 AAA--AAT-GGTAAAGAGAA

                              
        223 AAAAATGGTAAAGAGTAA
          1 AAAAATGGTAAAGAG-AA

              
        241 AA
          1 AA

        243 TATTAATCAG


Statistics
Matches: 32,  Mismatches: 2, Indels: 10
        0.73            0.05        0.23

Matches are distributed among these distances:
  16    7  0.22
  17    3  0.09
  18    7  0.22
  19    5  0.16
  20    3  0.09
  21    7  0.22

ACGTcount: A:0.63, C:0.02, G:0.19, T:0.16


Consensus pattern (17 bp):   
AAAAATGGTAAAGAGAA
Done.