Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015370.1 Corchorus olitorius cultivar O-4 contig15403, 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: 32368
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29


Found at i:687 original size:40 final size:40

Alignment explanation


    Indices: 625--700  Score: 116
    Period size: 40  Copynumber: 1.9  Consensus size: 40

        615 ACTTGACTCT

                             *         *            
        625 CCTAATAATTAAGGAAATAAATTAAATTCAGGTTTAACCC
          1 CCTAATAATTAAGGAAAGAAATTAAATCCAGGTTTAACCC

                   *      *                     
        665 CCTAATAGTTAAGGTAAGAAATTAAATCCAGGTTTA
          1 CCTAATAATTAAGGAAAGAAATTAAATCCAGGTTTA

        701 GCTCCTAGTT


Statistics
Matches: 32,  Mismatches: 4, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  40   32  1.00

ACGTcount: A:0.43, C:0.13, G:0.13, T:0.30


Consensus pattern (40 bp):   
CCTAATAATTAAGGAAAGAAATTAAATCCAGGTTTAACCC

Found at i:969 original size:141 final size:141

Alignment explanation


    Indices: 712--991  Score: 445
    Period size: 141  Copynumber: 2.0  Consensus size: 141

        702 CTCCTAGTTA

                                        *                         *          
        712 TAAATATGGAGAGTTTGCAGGGTAAATCTCGTGATTTTAGGCTATTATTGAATAGGGTTTTAAAA
          1 TAAATATGGAGAGTTTGCAGGGTAAATCCCGTGATTTTAGGCTATTATTGAATAAGGTTTTAAAA

                  *                                       *                * 
        777 ATTATAGTAACTTTTCCAATGACACGTTAGGAGGGTCAAGTGGAGGGACAAATTGGAGGATCAGG
         66 ATTATAATAACTTTTCCAATGACACGTTAGGAGGGTCAAGTGGAGGAACAAATTGGAGGATCAAG

                       
        842 TAGCAATACTC
        131 TAGCAATACTC

                                          *                               *  
        853 TAAATATGGAGAGTTTGCAGGGTAAATCCCTTGATTTTAGGCTATTATTGAATAAGGTTTTAGAA
          1 TAAATATGGAGAGTTTGCAGGGTAAATCCCGTGATTTTAGGCTATTATTGAATAAGGTTTTAAAA

                      *     *         *                                 *    
        918 ATTATAATAAGTTTTCTAAT-ATCACTTTAGGAGGGTCAAGTGGAGGAACAAATTGGAGGGTCAA
         66 ATTATAATAACTTTTCCAATGA-CACGTTAGGAGGGTCAAGTGGAGGAACAAATTGGAGGATCAA

                      
        982 GTAGCAATAC
        130 GTAGCAATAC

        992 ACTTAGTCAA


Statistics
Matches: 127,  Mismatches: 11, Indels: 2
        0.91            0.08        0.01

Matches are distributed among these distances:
 140    1  0.01
 141  126  0.99

ACGTcount: A:0.34, C:0.10, G:0.25, T:0.31


Consensus pattern (141 bp):   
TAAATATGGAGAGTTTGCAGGGTAAATCCCGTGATTTTAGGCTATTATTGAATAAGGTTTTAAAA
ATTATAATAACTTTTCCAATGACACGTTAGGAGGGTCAAGTGGAGGAACAAATTGGAGGATCAAG
TAGCAATACTC

Found at i:25175 original size:41 final size:41

Alignment explanation


    Indices: 25118--25218  Score: 157
    Period size: 41  Copynumber: 2.5  Consensus size: 41

      25108 TTAGTGTTGC

                      *                *             
      25118 CCAAGCCCGGTCCATTTATAAAACGGGTCTCAAACTTTTGT
          1 CCAAGCCCGGCCCATTTATAAAACGGGCCTCAAACTTTTGT

                     *                      *        
      25159 CCAAGCCCGACCCATTTATAAAACGGGCCTCAGACTTTTGT
          1 CCAAGCCCGGCCCATTTATAAAACGGGCCTCAAACTTTTGT

                *              
      25200 CCAAACCCGGCCCATTTAT
          1 CCAAGCCCGGCCCATTTAT

      25219 CAAATACTTA


Statistics
Matches: 54,  Mismatches: 6, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  41   54  1.00

ACGTcount: A:0.27, C:0.32, G:0.16, T:0.26


Consensus pattern (41 bp):   
CCAAGCCCGGCCCATTTATAAAACGGGCCTCAAACTTTTGT
Done.