Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009337.1 Corchorus olitorius cultivar O-4 contig09367, 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, 604

Length: 1008
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31


Found at i:284 original size:153 final size:154

Alignment explanation


    Indices: 5--286  Score: 449
    Period size: 153  Copynumber: 1.8  Consensus size: 154

          1 AGCC

                      *                     * ** *                           
          5 TTGAGGTTTGTCAAATCCAAGACGATTCAAAATGTCACTAATGGGCCCCGATAGGCCCAAAATAA
          1 TTGAGGTTTGCCAAATCCAAGACGATTCAAAACGGAAATAATGGGCCCCGATAGGCCCAAAATAA

                                 *  *                    *                   
         70 CAAGTGTTCCAAATGAGCTAAGAACTTCACAGTGGACTAATCTCATCAAAATGATTATAGTTAGG
         66 CAAGTGTTCCAAATGAGCTAAAAAATTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGG

                                    
        135 CCATAAACAACTTACAGAAAAGCT
        131 CCATAAACAACTTACAGAAAAGCT

                             *                        **           *         
        159 TTGAGGTTTGCCAAATCGAAGACGATTC-AAACGGAAATAATTTGCCCCGATAGGTCCAAAATAA
          1 TTGAGGTTTGCCAAATCCAAGACGATTCAAAACGGAAATAATGGGCCCCGATAGGCCCAAAATAA

                                                                            
        223 CAAGTGTTCCAAATGAGCTAAAAAATTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAG
         66 CAAGTGTTCCAAATGAGCTAAAAAATTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAG

        287 TCTGATGCGC


Statistics
Matches: 116,  Mismatches: 12, Indels: 1
        0.90            0.09        0.01

Matches are distributed among these distances:
 153   90  0.78
 154   26  0.22

ACGTcount: A:0.39, C:0.19, G:0.18, T:0.24


Consensus pattern (154 bp):   
TTGAGGTTTGCCAAATCCAAGACGATTCAAAACGGAAATAATGGGCCCCGATAGGCCCAAAATAA
CAAGTGTTCCAAATGAGCTAAAAAATTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGG
CCATAAACAACTTACAGAAAAGCT

Found at i:415 original size:21 final size:21

Alignment explanation


    Indices: 391--465  Score: 114
    Period size: 21  Copynumber: 3.6  Consensus size: 21

        381 AAGATGCTAG

                                 
        391 AAGTTCATTGGAGAAGGTTCC
          1 AAGTTCATTGGAGAAGGTTCC

                                 
        412 AAGTTCATTGGAGAAGGTTCC
          1 AAGTTCATTGGAGAAGGTTCC

              **               * 
        433 AAAATCATTGGAGAAGGTTTC
          1 AAGTTCATTGGAGAAGGTTCC

               *        
        454 AAGCTCATTGGA
          1 AAGTTCATTGGA

        466 ATTGCCTAAG


Statistics
Matches: 49,  Mismatches: 5, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  21   49  1.00

ACGTcount: A:0.32, C:0.13, G:0.27, T:0.28


Consensus pattern (21 bp):   
AAGTTCATTGGAGAAGGTTCC
Done.