Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019281.1 Corchorus olitorius cultivar O-4 contig19314, 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: 5073
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32


Found at i:1980 original size:62 final size:62

Alignment explanation


    Indices: 1863--2224  Score: 591
    Period size: 62  Copynumber: 5.8  Consensus size: 62

       1853 CAATCTTAGG

                        *       *                                            
       1863 ATGACAACTTCTAGTGTCAATAATTTCCTCAGCATGACAACTTCTGGTGTCAAGATAATAATTTG
          1 ATGACAACTTCTGGTGTCAAAAATTT--T---CATGACAACTTCTGGTGTCAAGATAATAATTTG

            * 
       1928 CT
         61 AT

                                                                          
       1930 ATGACAACTTCTGGTGTCAAAAATTTTCATGACAACTTCTGGTGTCAAGATAATAATTTGAT
          1 ATGACAACTTCTGGTGTCAAAAATTTTCATGACAACTTCTGGTGTCAAGATAATAATTTGAT

                                *                                       * 
       1992 ATGACAACTTCTGGTGTCAATAATTTTCATGACAACTTCTGGTGTCAAGATAATAATTTGCT
          1 ATGACAACTTCTGGTGTCAAAAATTTTCATGACAACTTCTGGTGTCAAGATAATAATTTGAT

                        *                                                 
       2054 ATGACAACTTCTAGTGTCAAAAATTTTCATGACAACTTCTGGTGTCAAGATAATAATTTGAT
          1 ATGACAACTTCTGGTGTCAAAAATTTTCATGACAACTTCTGGTGTCAAGATAATAATTTGAT

                                                                          
       2116 ATGACAACTTCTGGTGTCAAAAATTTTCATGACAACTTCTGGTGTCAAGATAATAATTTGAT
          1 ATGACAACTTCTGGTGTCAAAAATTTTCATGACAACTTCTGGTGTCAAGATAATAATTTGAT

                                *        *                  
       2178 ATGACAACTTCTGGTGTCAATAA-TTTCTGTGACAACTTCTGGTGTCA
          1 ATGACAACTTCTGGTGTCAAAAATTTTC-ATGACAACTTCTGGTGTCA

       2225 TTTGTAAGAC


Statistics
Matches: 283,  Mismatches: 11, Indels: 7
        0.94            0.04        0.02

Matches are distributed among these distances:
  61    4  0.01
  62  254  0.90
  65    1  0.00
  67   24  0.08

ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36


Consensus pattern (62 bp):   
ATGACAACTTCTGGTGTCAAAAATTTTCATGACAACTTCTGGTGTCAAGATAATAATTTGAT

Found at i:2243 original size:30 final size:30

Alignment explanation


    Indices: 2207--2292  Score: 172
    Period size: 30  Copynumber: 2.9  Consensus size: 30

       2197 ATAATTTCTG

                                          
       2207 TGACAACTTCTGGTGTCATTTGTAAGACCA
          1 TGACAACTTCTGGTGTCATTTGTAAGACCA

                                          
       2237 TGACAACTTCTGGTGTCATTTGTAAGACCA
          1 TGACAACTTCTGGTGTCATTTGTAAGACCA

                                      
       2267 TGACAACTTCTGGTGTCATTTGTAAG
          1 TGACAACTTCTGGTGTCATTTGTAAG

       2293 TAGAATAAAT


Statistics
Matches: 56,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  30   56  1.00

ACGTcount: A:0.26, C:0.19, G:0.21, T:0.35


Consensus pattern (30 bp):   
TGACAACTTCTGGTGTCATTTGTAAGACCA

Found at i:3475 original size:22 final size:24

Alignment explanation


    Indices: 3440--3498  Score: 61
    Period size: 22  Copynumber: 2.5  Consensus size: 24

       3430 ATAAATGTTG

                            *      *
       3440 CTGATAA-TCTTCT-CTTTTATCT
          1 CTGATAATTCTTCTCCATTTATCA

                                    
       3462 CTGATAATTC-TCTCCATTTATCA
          1 CTGATAATTCTTCTCCATTTATCA

                          
       3485 CTTGATAATATCTT
          1 C-TGATAAT-TCTT

       3499 GCCAGATAAA


Statistics
Matches: 30,  Mismatches: 2, Indels: 6
        0.79            0.05        0.16

Matches are distributed among these distances:
  22   10  0.33
  23   10  0.33
  24    7  0.23
  25    2  0.07
  26    1  0.03

ACGTcount: A:0.24, C:0.22, G:0.05, T:0.49


Consensus pattern (24 bp):   
CTGATAATTCTTCTCCATTTATCA
Done.