Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021055.1 Corchorus olitorius cultivar O-4 contig21088, 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: 3035
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28


Found at i:2291 original size:15 final size:16

Alignment explanation


    Indices: 2257--2297  Score: 50
    Period size: 15  Copynumber: 2.7  Consensus size: 16

       2247 CTTATTTTCC

                            
       2257 CCTTTTT-TTTTCCTT
          1 CCTTTTTCTTTTCCTT

                            
       2272 CCTTTTTCTTTT-CTT
          1 CCTTTTTCTTTTCCTT

            *     *    
       2287 TCTTTTCCTTT
          1 CCTTTTTCTTT

       2298 CTATTTTTCT


Statistics
Matches: 23,  Mismatches: 2, Indels: 2
        0.85            0.07        0.07

Matches are distributed among these distances:
  15   19  0.83
  16    4  0.17

ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73


Consensus pattern (16 bp):   
CCTTTTTCTTTTCCTT

Found at i:2311 original size:13 final size:13

Alignment explanation


    Indices: 2274--2320  Score: 67
    Period size: 13  Copynumber: 3.5  Consensus size: 13

       2264 TTTTCCTTCC

                        *
       2274 TTTTTCTTTTCTT
          1 TTTTTCTTTTCTA

                   *      
       2287 TCTTTTCCTTTCTA
          1 T-TTTTCTTTTCTA

                         
       2301 TTTTTCTTTTCTA
          1 TTTTTCTTTTCTA

                   
       2314 TTTTTCT
          1 TTTTTCT

       2321 CCCTTTTTGG


Statistics
Matches: 30,  Mismatches: 3, Indels: 2
        0.86            0.09        0.06

Matches are distributed among these distances:
  13   19  0.63
  14   11  0.37

ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77


Consensus pattern (13 bp):   
TTTTTCTTTTCTA

Found at i:2477 original size:46 final size:46

Alignment explanation


    Indices: 2427--2515  Score: 151
    Period size: 46  Copynumber: 1.9  Consensus size: 46

       2417 CTAGGACCCA

                                                 *        
       2427 ACGCTGCCCATTGGCAGCAGCGTGGCCCAGCACTGGCTAGGCCCGC
          1 ACGCTGCCCATTGGCAGCAGCGTGGCCCAGCACTGGCCAGGCCCGC

                                *          *           
       2473 ACGCTGCCCATTGGCAGCAGTGTGGCCCAGCGCTGGCCAGGCC
          1 ACGCTGCCCATTGGCAGCAGCGTGGCCCAGCACTGGCCAGGCC

       2516 TGCTTAGCAG


Statistics
Matches: 40,  Mismatches: 3, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  46   40  1.00

ACGTcount: A:0.15, C:0.38, G:0.34, T:0.13


Consensus pattern (46 bp):   
ACGCTGCCCATTGGCAGCAGCGTGGCCCAGCACTGGCCAGGCCCGC
Done.