Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004205.1 Corchorus capsularis cultivar CVL-1 contig04213, 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, 622

Length: 1037
ACGTcount: A:0.38, C:0.14, G:0.23, T:0.25


Found at i:70 original size:32 final size:33

Alignment explanation


    Indices: 10--79  Score: 99
    Period size: 32  Copynumber: 2.2  Consensus size: 33

          1 ATAATCGGT

                                             
         10 AAAGAGTAAAATGGTAAAATGGTAATTAAATCC
          1 AAAGAGTAAAATGGTAAAATGGTAATTAAATCC

                                    *       * 
         43 AAAGAGTAAAAT-G-ACAAATGGTGATTAAATTC
          1 AAAGAGTAAAATGGTA-AAATGGTAATTAAATCC

                 
         75 AAAGA
          1 AAAGA

         80 ATGAAAATAG


Statistics
Matches: 34,  Mismatches: 2, Indels: 3
        0.87            0.05        0.08

Matches are distributed among these distances:
  31    1  0.03
  32   21  0.62
  33   12  0.35

ACGTcount: A:0.53, C:0.06, G:0.19, T:0.23


Consensus pattern (33 bp):   
AAAGAGTAAAATGGTAAAATGGTAATTAAATCC

Found at i:95 original size:26 final size:25

Alignment explanation


    Indices: 52--119  Score: 64
    Period size: 26  Copynumber: 2.6  Consensus size: 25

         42 CAAAGAGTAA

                      *  *             
         52 AATGACAAATGGTGATTAAATTCAAAG
          1 AATGA-AAATAGTAATTAAATTC-AAG

                              *      
         79 AATGAAAATAGTAATTAAGTTCAAG
          1 AATGAAAATAGTAATTAAATTCAAG

             **             
        104 AGGGTAAAATAGTAAT
          1 AATG-AAAATAGTAAT

        120 CAGTAAAGAG


Statistics
Matches: 35,  Mismatches: 5, Indels: 3
        0.81            0.12        0.07

Matches are distributed among these distances:
  25    5  0.14
  26   25  0.71
  27    5  0.14

ACGTcount: A:0.50, C:0.04, G:0.19, T:0.26


Consensus pattern (25 bp):   
AATGAAAATAGTAATTAAATTCAAG

Found at i:152 original size:14 final size:14

Alignment explanation


    Indices: 114--283  Score: 65
    Period size: 14  Copynumber: 12.4  Consensus size: 14

        104 AGGGTAAAAT

                          
        114 AGTAATCAGTAAAG
          1 AGTAATCAGTAAAG

              *  **       
        128 AGGAAAAAGTAAAG
          1 AGTAATCAGTAAAG

                          
        142 AGTAATCAGTAAA-
          1 AGTAATCAGTAAAG

                 **    *    
        155 AGTAAAAATGGCAAAG
          1 AGTAATCA--GTAAAG

                         *
        171 AG---T-AGTAAAA
          1 AGTAATCAGTAAAG

                          *
        181 AGTAATCAGGT-AAT
          1 AGTAATCA-GTAAAG

                          
        195 AGTAATCAGTAAA-
          1 AGTAATCAGTAAAG

                        *  
        208 AGGTAATCAGT-CAG
          1 A-GTAATCAGTAAAG

                          **
        222 AGTAAAAT-AGTAATC
          1 AGT--AATCAGTAAAG

                  *         
        237 AGTAA-GAGCTAAATG
          1 AGTAATCAG-TAAA-G

                  *     * 
        252 -GTAATTAGTAAGG
          1 AGTAATCAGTAAAG

                          
        265 AGTAATCAGTAAAG
          1 AGTAATCAGTAAAG

                 
        279 AGTAA
          1 AGTAA

        284 AAGGTGATCA


Statistics
Matches: 114,  Mismatches: 23, Indels: 38
        0.65            0.13        0.22

Matches are distributed among these distances:
  10    6  0.05
  12    1  0.01
  13   18  0.16
  14   73  0.64
  15   14  0.12
  16    2  0.02

ACGTcount: A:0.51, C:0.06, G:0.22, T:0.21


Consensus pattern (14 bp):   
AGTAATCAGTAAAG
Done.