Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021890.1 Corchorus olitorius cultivar O-4 contig21923, 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: 19394
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33


Found at i:897 original size:15 final size:15

Alignment explanation


    Indices: 877--926  Score: 91
    Period size: 15  Copynumber: 3.3  Consensus size: 15

        867 GATCTTGGAT

                           
        877 GTTTGAGTCAGTTTA
          1 GTTTGAGTCAGTTTA

                           
        892 GTTTGAGTCAGTTTA
          1 GTTTGAGTCAGTTTA

                         * 
        907 GTTTGAGTCAGTTGA
          1 GTTTGAGTCAGTTTA

                 
        922 GTTTG
          1 GTTTG

        927 TCGAGTTAGA


Statistics
Matches: 34,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  15   34  1.00

ACGTcount: A:0.18, C:0.06, G:0.30, T:0.46


Consensus pattern (15 bp):   
GTTTGAGTCAGTTTA

Found at i:5251 original size:11 final size:11

Alignment explanation


    Indices: 5235--5259  Score: 50
    Period size: 11  Copynumber: 2.3  Consensus size: 11

       5225 ATATGAGAAA

                       
       5235 ATATGAATAAG
          1 ATATGAATAAG

                       
       5246 ATATGAATAAG
          1 ATATGAATAAG

               
       5257 ATA
          1 ATA

       5260 AGTAGATAAC


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   14  1.00

ACGTcount: A:0.56, C:0.00, G:0.16, T:0.28


Consensus pattern (11 bp):   
ATATGAATAAG

Found at i:8685 original size:201 final size:201

Alignment explanation


    Indices: 8340--8730  Score: 710
    Period size: 201  Copynumber: 1.9  Consensus size: 201

       8330 ATTATGAGCA

                                        *                                    
       8340 TTTCCAGGCTGATCCTAAGACTTTTGCTTAGTGCATCGACAGTCTCATAAGAACACTCAAGAATA
          1 TTTCCAGGCTGATCCTAAGACTTTTGCTGAGTGCATCGACAGTCTCATAAGAACACTCAAGAATA

                                                    *                        
       8405 ACAGAGTCATCTCTTTTACTTCCATAGCTCCATTTGATGATGATGATCTTCAAAGCCATTACAAA
         66 ACAGAGTCATCTCTTTTACTTCCATAGCTCCATTTGATGACGATGATCTTCAAAGCCATTACAAA

                                                                             
       8470 GCCTTGTGGAAAACCTATGGTGACCTCATAAACTATTTGAACTTCCAATTTTACGCCTATGATCC
        131 GCCTTGTGGAAAACCTATGGTGACCTCATAAACTATTTGAACTTCCAATTTTACGCCTATGATCC

                  
       8535 TGAGAC
        196 TGAGAC

                            *                     *                          
       8541 TTTCCAGGCTGATCCTGAGACTTTTGCTGAGTGCATCGGCAGTCTCATAAGAACACTCAAGAATA
          1 TTTCCAGGCTGATCCTAAGACTTTTGCTGAGTGCATCGACAGTCTCATAAGAACACTCAAGAATA

              *                                            *                 
       8606 ACGGAGTCATCTCTTTTACTTCCATAGCTCCATTTGATGACGATGATGTTCAAAGCCATTACAAA
         66 ACAGAGTCATCTCTTTTACTTCCATAGCTCCATTTGATGACGATGATCTTCAAAGCCATTACAAA

                                          *                *            
       8671 GCCTTGTGGAAAACCTATGGTGACCTCATAGACTATTTGAACTTCCAGTTTTACGCCTAT
        131 GCCTTGTGGAAAACCTATGGTGACCTCATAAACTATTTGAACTTCCAATTTTACGCCTAT

       8731 CATCAAGGAA


Statistics
Matches: 182,  Mismatches: 8, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
 201  182  1.00

ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31


Consensus pattern (201 bp):   
TTTCCAGGCTGATCCTAAGACTTTTGCTGAGTGCATCGACAGTCTCATAAGAACACTCAAGAATA
ACAGAGTCATCTCTTTTACTTCCATAGCTCCATTTGATGACGATGATCTTCAAAGCCATTACAAA
GCCTTGTGGAAAACCTATGGTGACCTCATAAACTATTTGAACTTCCAATTTTACGCCTATGATCC
TGAGAC

Found at i:11020 original size:27 final size:27

Alignment explanation


    Indices: 10990--11067  Score: 113
    Period size: 27  Copynumber: 2.9  Consensus size: 27

      10980 GAATTAGGGT

                            *          
      10990 CATCTAGGGGCATTTTAGTCATTTGCA
          1 CATCTAGGGGCATTTTGGTCATTTGCA

                *                      
      11017 CATCCAGGGGCATTTTGGTCATTTGCA
          1 CATCTAGGGGCATTTTGGTCATTTGCA

            *                        
      11044 TAT-TCAGGGGCATTTTGGTCATTT
          1 CATCT-AGGGGCATTTTGGTCATTT

      11068 CAAGTTCACT


Statistics
Matches: 46,  Mismatches: 4, Indels: 2
        0.88            0.08        0.04

Matches are distributed among these distances:
  27   46  1.00

ACGTcount: A:0.19, C:0.18, G:0.24, T:0.38


Consensus pattern (27 bp):   
CATCTAGGGGCATTTTGGTCATTTGCA
Done.