Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01008691.1 Corchorus olitorius cultivar O-4 contig08718, 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: 2936
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32


Found at i:2441 original size:16 final size:17

Alignment explanation


    Indices: 2409--2466  Score: 77
    Period size: 16  Copynumber: 3.6  Consensus size: 17

       2399 TACCCGAGAT

                 *           
       2409 CGAACTCGA-AAATACC
          1 CGAACCCGACAAATACC

                       *     
       2425 CGAACCCGACATA-ACC
          1 CGAACCCGACAAATACC

                             
       2441 CGAACCCGA-AAATACC
          1 CGAACCCGACAAATACC

                      
       2457 CGAACCCGAC
          1 CGAACCCGAC

       2467 TGATAAGTGT


Statistics
Matches: 36,  Mismatches: 3, Indels: 5
        0.82            0.07        0.11

Matches are distributed among these distances:
  15    2  0.06
  16   32  0.89
  17    2  0.06

ACGTcount: A:0.40, C:0.40, G:0.14, T:0.07


Consensus pattern (17 bp):   
CGAACCCGACAAATACC

Found at i:2876 original size:69 final size:69

Alignment explanation


    Indices: 2732--2936  Score: 306
    Period size: 69  Copynumber: 3.0  Consensus size: 69

       2722 CAGATCTTGG

                         *       *           **      *             *         
       2732 CCAAGTCCTGTCCAGGACTTGGGCTGTTGAGGAATGCAAAAATACAGGACAAGACATGGGCAGGA
          1 CCAAGTCCTGTCCCGGACTTGTGCTGTTGAGGAGCGC-AAATTACAGGACAAGACCTGGGCAGGA

                 
       2797 GTTAC
         65 GTTAC

                                *         *                             *    
       2802 CCAAGTCCTGTCCCGGACTTCTGCTGTTGAAGAGCGCAAATTACAGGACAAGACCTGGGCGGGAG
          1 CCAAGTCCTGTCCCGGACTTGTGCTGTTGAGGAGCGCAAATTACAGGACAAGACCTGGGCAGGAG

                
       2867 TTAC
         66 TTAC

                                                                             
       2871 CCAAGTCCTGTCCCGGACTTGTGC--TTGAGGAGCGCAAATTACAGGACAAGACCTGGGCAGGAG
          1 CCAAGTCCTGTCCCGGACTTGTGCTGTTGAGGAGCGCAAATTACAGGACAAGACCTGGGCAGGAG

               
       2934 TTA
         66 TTA


Statistics
Matches: 123,  Mismatches: 12, Indels: 3
        0.89            0.09        0.02

Matches are distributed among these distances:
  67   40  0.33
  69   52  0.42
  70   31  0.25

ACGTcount: A:0.27, C:0.23, G:0.30, T:0.20


Consensus pattern (69 bp):   
CCAAGTCCTGTCCCGGACTTGTGCTGTTGAGGAGCGCAAATTACAGGACAAGACCTGGGCAGGAG
TTAC

Done.