Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005176.1 Corchorus capsularis cultivar CVL-1 contig05194, 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: 2673
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34


Found at i:199 original size:113 final size:113

Alignment explanation


    Indices: 1--399  Score: 663
    Period size: 113  Copynumber: 3.5  Consensus size: 113

                                                                             
          1 ATAGCGGCGTCTAGGCCCTAAACGCCGCTAAATAGTGGCGTCTTATGTCCCGGACGCCGCCATAA
          1 ATAGCGGCGTCTAGGCCCTAAACGCCGCTAAATAGTGGCGTCTTATGTCCCGGACGCCGCCATAA

                        *                                   
         66 TTAATTTTTTCGAAGAAATGCAAATTGAGTAAAAATGAAGCCTAACAA
         66 TTAATTTTTTCGGAGAAATGCAAATTGAGTAAAAATGAAGCCTAACAA

                                                                      ***    
        114 ATAGCGGCGTCTAGGCCCTAAACGCCGCTAAATAGTGGCGTCTTATGTCCCGGACGCCATTATAA
          1 ATAGCGGCGTCTAGGCCCTAAACGCCGCTAAATAGTGGCGTCTTATGTCCCGGACGCCGCCATAA

                                                            
        179 TTAATTTTTTCGGAGAAATGCAAATTGAGTAAAAATGAAGCCTAACAA
         66 TTAATTTTTTCGGAGAAATGCAAATTGAGTAAAAATGAAGCCTAACAA

                                                             ***        *    
        227 ATAGCGGCGTCTAGGCCCTAAACGCCGCTAAATAGTGGCGTCTTATGTCAAAGACGCCGCGATAA
          1 ATAGCGGCGTCTAGGCCCTAAACGCCGCTAAATAGTGGCGTCTTATGTCCCGGACGCCGCCATAA

                                   *                *       
        292 TTAATTTTTTCGGAGAAATGCAATTTGAGTAAAAATGAAGTCTAACAA
         66 TTAATTTTTTCGGAGAAATGCAAATTGAGTAAAAATGAAGCCTAACAA

                         *                            **     * *        
        340 ATAGCGGCGTCTATGCCCTAAACGCCGCTAAATAGTGGCGTCCGATGTCACAGACGCCGC
          1 ATAGCGGCGTCTAGGCCCTAAACGCCGCTAAATAGTGGCGTCTTATGTCCCGGACGCCGC

        400 TAAATAGTGG


Statistics
Matches: 270,  Mismatches: 16, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
 113  270  1.00

ACGTcount: A:0.32, C:0.22, G:0.22, T:0.24


Consensus pattern (113 bp):   
ATAGCGGCGTCTAGGCCCTAAACGCCGCTAAATAGTGGCGTCTTATGTCCCGGACGCCGCCATAA
TTAATTTTTTCGGAGAAATGCAAATTGAGTAAAAATGAAGCCTAACAA

Found at i:402 original size:32 final size:32

Alignment explanation


    Indices: 361--438  Score: 156
    Period size: 32  Copynumber: 2.4  Consensus size: 32

        351 TATGCCCTAA

                                            
        361 ACGCCGCTAAATAGTGGCGTCCGATGTCACAG
          1 ACGCCGCTAAATAGTGGCGTCCGATGTCACAG

                                            
        393 ACGCCGCTAAATAGTGGCGTCCGATGTCACAG
          1 ACGCCGCTAAATAGTGGCGTCCGATGTCACAG

                          
        425 ACGCCGCTAAATAG
          1 ACGCCGCTAAATAG

        439 AGTCGTCTCT


Statistics
Matches: 46,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  32   46  1.00

ACGTcount: A:0.27, C:0.28, G:0.27, T:0.18


Consensus pattern (32 bp):   
ACGCCGCTAAATAGTGGCGTCCGATGTCACAG
Done.