Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018632.1 Corchorus olitorius cultivar O-4 contig18665, 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: 6148
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32


Found at i:178 original size:32 final size:32

Alignment explanation


    Indices: 16--258  Score: 336
    Period size: 32  Copynumber: 7.6  Consensus size: 32

          6 ATTGAAATAT

                                               
         16 AAAGACCTGTCTGAGGTCGAAATTTAAAAGCTGAG
          1 AAAGACCTGTCTGAGGTCGAAA--TAAAA-CTGAG

                              *              
         51 AAAGACCTGTCTGAGGTCAAAATAAAAACTGAG
          1 AAAGACCTGTCTGAGGTCGAAAT-AAAACTGAG

                   *                          
         84 AAAGACCCGTCTGAGGTCGAAATAAAAAGCTGAG
          1 AAAGACCTGTCTGAGGTCGAAAT-AAAA-CTGAG

                                            
        118 AAAGACCTGTCTGAGGTCG-----AAACTGAG
          1 AAAGACCTGTCTGAGGTCGAAATAAAACTGAG

                        *                   
        145 AAAGACCTGTCTAAGGTCGAAATAAAACTGAG
          1 AAAGACCTGTCTGAGGTCGAAATAAAACTGAG

                               *            
        177 AAAGACCTGTCTGAGGTCGGAATAAAACTGAG
          1 AAAGACCTGTCTGAGGTCGAAATAAAACTGAG

                                            *
        209 AAAGACCTGTCTGAGGTC-ACAATAAAACTGAT
          1 AAAGACCTGTCTGAGGTCGA-AATAAAACTGAG

                              
        241 AAAGACCTGTCTGAGGTC
          1 AAAGACCTGTCTGAGGTC

        259 TGGAACTTCG


Statistics
Matches: 191,  Mismatches: 9, Indels: 19
        0.87            0.04        0.09

Matches are distributed among these distances:
  27   23  0.12
  28    3  0.02
  32   85  0.45
  33   32  0.17
  34   27  0.14
  35   21  0.11

ACGTcount: A:0.39, C:0.17, G:0.25, T:0.19


Consensus pattern (32 bp):   
AAAGACCTGTCTGAGGTCGAAATAAAACTGAG

Found at i:192 original size:93 final size:92

Alignment explanation


    Indices: 46--226  Score: 301
    Period size: 93  Copynumber: 2.0  Consensus size: 92

         36 AATTTAAAAG

                             *                                               
         46 CTGAGAAAGACCTGTCTGAGGTCAAAATAAAAACTGAGAAAGACCCGTCTGAGGTCGAAATAAAA
          1 CTGAGAAAGACCTGTCTAAGGTCAAAATAAAAACTGAGAAAGACCCGTCTGAGGTCGAAAT-AAA

                                         
        111 AGCTGAGAAAGACCTGTCTGAGGTCGAAA
         65 A-CTGAGAAAGACCTGTCTGAGGTCGAAA

                                   *                     *           *       
        140 CTGAGAAAGACCTGTCTAAGGTCGAAAT-AAAACTGAGAAAGACCTGTCTGAGGTCGGAATAAAA
          1 CTGAGAAAGACCTGTCTAAGGTCAAAATAAAAACTGAGAAAGACCCGTCTGAGGTCGAAATAAAA

                                   
        204 CTGAGAAAGACCTGTCTGAGGTC
         66 CTGAGAAAGACCTGTCTGAGGTC

        227 ACAATAAAAC


Statistics
Matches: 83,  Mismatches: 4, Indels: 3
        0.92            0.04        0.03

Matches are distributed among these distances:
  91   23  0.28
  92    4  0.05
  93   30  0.36
  94   26  0.31

ACGTcount: A:0.39, C:0.17, G:0.26, T:0.18


Consensus pattern (92 bp):   
CTGAGAAAGACCTGTCTAAGGTCAAAATAAAAACTGAGAAAGACCCGTCTGAGGTCGAAATAAAA
CTGAGAAAGACCTGTCTGAGGTCGAAA

Done.