Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013212.1 Corchorus olitorius cultivar O-4 contig13245, 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: 27740
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32


Found at i:31 original size:6 final size:6

Alignment explanation


    Indices: 2--67  Score: 53
    Period size: 6  Copynumber: 10.7  Consensus size: 6

          1 G

                *               *                         *      *   
          2 AAAGGA AAA-AA AAAGAGG AAAGAA AAAGAA AAAGGAA AATGAA AAGGAA
          1 AAAGAA AAAGAA AAAGA-A AAAGAA AAAGAA AAA-GAA AAAGAA AAAGAA

                       *       
         51 AAAGAA AGAAAAA AAAG
          1 AAAGAA A-AAGAA AAAG

         68 TAAATAAATA


Statistics
Matches: 48,  Mismatches: 8, Indels: 8
        0.75            0.12        0.12

Matches are distributed among these distances:
   5    4  0.08
   6   29  0.60
   7   15  0.31

ACGTcount: A:0.76, C:0.00, G:0.23, T:0.02


Consensus pattern (6 bp):   
AAAGAA

Found at i:35 original size:12 final size:12

Alignment explanation


    Indices: 2--67  Score: 53
    Period size: 13  Copynumber: 5.3  Consensus size: 12

          1 G

                *       
          2 AAAGGAAAA-AA
          1 AAAGAAAAAGAA

                  *      
         13 AAAGAGGAAAGAA
          1 AAAGA-AAAAGAA

                         
         26 AAAGAAAAAGGAA
          1 AAAGAAAAA-GAA

              *     *   
         39 AATGAAAAGGAA
          1 AAAGAAAAAGAA

                      *  
         51 AAAGAAAGAAAAA
          1 AAAGAAA-AAGAA

                
         64 AAAG
          1 AAAG

         68 TAAATAAATA


Statistics
Matches: 43,  Mismatches: 8, Indels: 6
        0.75            0.14        0.11

Matches are distributed among these distances:
  11    4  0.09
  12   15  0.35
  13   24  0.56

ACGTcount: A:0.76, C:0.00, G:0.23, T:0.02


Consensus pattern (12 bp):   
AAAGAAAAAGAA

Found at i:364 original size:26 final size:26

Alignment explanation


    Indices: 309--365  Score: 62
    Period size: 26  Copynumber: 2.2  Consensus size: 26

        299 TCGTAAGAAC

                   *                 *
        309 GTAAATTCCCGTTTTACCCATAAGTG
          1 GTAAATTACCGTTTTACCCATAAGTA

                                *   *  
        335 GTAAATTACC-TTATTACCCCTAATTA
          1 GTAAATTACCGTT-TTACCCATAAGTA

                 
        361 GTAAA
          1 GTAAA

        366 AGCGTACTAA


Statistics
Matches: 26,  Mismatches: 4, Indels: 2
        0.81            0.12        0.06

Matches are distributed among these distances:
  25    2  0.08
  26   24  0.92

ACGTcount: A:0.33, C:0.21, G:0.11, T:0.35


Consensus pattern (26 bp):   
GTAAATTACCGTTTTACCCATAAGTA

Found at i:6206 original size:33 final size:33

Alignment explanation


    Indices: 6169--6231  Score: 126
    Period size: 33  Copynumber: 1.9  Consensus size: 33

       6159 AAAGATACGA

                                             
       6169 AGTATTAAGAATTTAGCTACTCATGGATTTTTC
          1 AGTATTAAGAATTTAGCTACTCATGGATTTTTC

                                          
       6202 AGTATTAAGAATTTAGCTACTCATGGATTT
          1 AGTATTAAGAATTTAGCTACTCATGGATTT

       6232 GGAAAAATCC


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  33   30  1.00

ACGTcount: A:0.32, C:0.11, G:0.16, T:0.41


Consensus pattern (33 bp):   
AGTATTAAGAATTTAGCTACTCATGGATTTTTC

Found at i:18056 original size:68 final size:69

Alignment explanation


    Indices: 17970--18106  Score: 240
    Period size: 68  Copynumber: 2.0  Consensus size: 69

      17960 TGCACATGTG

                                       *                                     
      17970 TAAAAGTGTGGTTTCAAAAATAAATGTGCTAATGAGAGACTTGACTCAAAAAGAAAGTGTCGACC
          1 TAAAAGTGTGGTTTCAAAAATAAATGTCCTAATGAGAGACTTGACTCAAAAAGAAAGTGTCGACC

                
      18035 CAAT
         66 CAAT

                                          *                 *                
      18039 TAAAAGTGTGG-TTCAAAAATAAATGTCCTTATGAGAGACTTGACTCACAAAGAAAGTGTCGACC
          1 TAAAAGTGTGGTTTCAAAAATAAATGTCCTAATGAGAGACTTGACTCAAAAAGAAAGTGTCGACC

                
      18103 CAAT
         66 CAAT

      18107 CAAGTAATTC


Statistics
Matches: 65,  Mismatches: 3, Indels: 1
        0.94            0.04        0.01

Matches are distributed among these distances:
  68   54  0.83
  69   11  0.17

ACGTcount: A:0.41, C:0.15, G:0.20, T:0.25


Consensus pattern (69 bp):   
TAAAAGTGTGGTTTCAAAAATAAATGTCCTAATGAGAGACTTGACTCAAAAAGAAAGTGTCGACC
CAAT
Done.