Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015365.1 Corchorus olitorius cultivar O-4 contig15398, 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: 3587
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35


Found at i:191 original size:33 final size:33

Alignment explanation


    Indices: 116--179  Score: 92
    Period size: 33  Copynumber: 1.9  Consensus size: 33

        106 GCGTCCCTAG

                          *                  
        116 AGGGCGCCCCACCATGGTGGAAGGCATCCCCAA
          1 AGGGCGCCCCACCACGGTGGAAGGCATCCCCAA

             *  *               *          
        149 AAGGTGCCCCACCACGGTGGGAGGCATCCCC
          1 AGGGCGCCCCACCACGGTGGAAGGCATCCCC

        180 GGGGGGCGCC


Statistics
Matches: 27,  Mismatches: 4, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  33   27  1.00

ACGTcount: A:0.22, C:0.38, G:0.31, T:0.09


Consensus pattern (33 bp):   
AGGGCGCCCCACCACGGTGGAAGGCATCCCCAA

Found at i:2129 original size:69 final size:69

Alignment explanation


    Indices: 2056--2193  Score: 276
    Period size: 69  Copynumber: 2.0  Consensus size: 69

       2046 CACATATTCA

                                                                             
       2056 ATTGCAAACTTTCTCGCTATTGGTGTTTCATCCCATATTTTTAGTTTTGCTCTTCTTAATAGTTC
          1 ATTGCAAACTTTCTCGCTATTGGTGTTTCATCCCATATTTTTAGTTTTGCTCTTCTTAATAGTTC

                
       2121 AACC
         66 AACC

                                                                             
       2125 ATTGCAAACTTTCTCGCTATTGGTGTTTCATCCCATATTTTTAGTTTTGCTCTTCTTAATAGTTC
          1 ATTGCAAACTTTCTCGCTATTGGTGTTTCATCCCATATTTTTAGTTTTGCTCTTCTTAATAGTTC

                
       2190 AACC
         66 AACC

       2194 TTAGCACTCT


Statistics
Matches: 69,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  69   69  1.00

ACGTcount: A:0.20, C:0.22, G:0.12, T:0.46


Consensus pattern (69 bp):   
ATTGCAAACTTTCTCGCTATTGGTGTTTCATCCCATATTTTTAGTTTTGCTCTTCTTAATAGTTC
AACC

Found at i:2529 original size:7 final size:7

Alignment explanation


    Indices: 2509--2555  Score: 62
    Period size: 7  Copynumber: 7.0  Consensus size: 7

       2499 ATCCACAAGG

                   
       2509 AAACAAA
          1 AAACAAA

             *     
       2516 ACA-AAA
          1 AAACAAA

                   
       2522 AAAC-AA
          1 AAACAAA

                   
       2528 AAACAAA
          1 AAACAAA

                   
       2535 AAACAAA
          1 AAACAAA

              *    
       2542 AACCAAA
          1 AAACAAA

                   
       2549 AAACAAA
          1 AAACAAA

       2556 CTTCTCTTTT


Statistics
Matches: 34,  Mismatches: 4, Indels: 4
        0.81            0.10        0.10

Matches are distributed among these distances:
   6   11  0.32
   7   23  0.68

ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00


Consensus pattern (7 bp):   
AAACAAA

Found at i:2532 original size:14 final size:13

Alignment explanation


    Indices: 2509--2555  Score: 69
    Period size: 13  Copynumber: 3.5  Consensus size: 13

       2499 ATCCACAAGG

                          
       2509 AAAC-AAAACAAAA
          1 AAACAAAAAC-AAA

                         
       2522 AAACAAAAACAAA
          1 AAACAAAAACAAA

                          
       2535 AAACAAAAACCAAA
          1 AAACAAAAA-CAAA

                   
       2549 AAACAAA
          1 AAACAAA

       2556 CTTCTCTTTT


Statistics
Matches: 32,  Mismatches: 0, Indels: 3
        0.91            0.00        0.09

Matches are distributed among these distances:
  13   16  0.50
  14   16  0.50

ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00


Consensus pattern (13 bp):   
AAACAAAAACAAA
Done.