Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024039.1 Corchorus olitorius cultivar O-4 contig24072, 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: 4185
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.33


Found at i:222 original size:35 final size:35

Alignment explanation


    Indices: 51--222  Score: 204
    Period size: 34  Copynumber: 4.8  Consensus size: 35

         41 TCAATCTTCG

                                      *        
         51 AAGTTTTCAAATTGGGAAAGTTCCCACCAGGTTTT
          1 AAGTTTTCAAATTGGGAAAGTTCCCATCAGGTTTT

                   *                  *    *    
         86 -AGTTTTTAAATTGGGAAAGTTCCCAACAAGTTTTT
          1 AAGTTTTCAAATTGGGAAAGTTCCCATC-AGGTTTT

                                           *    
        121 AAGTTTTCAAATTGGGAAAGTTCCCATTCAGTTTTT
          1 AAGTTTTCAAATTGGGAAAGTTCCCA-TCAGGTTTT

                *    *                           
        157 CAAAATTTTTAAATTGGGAAAGTTCCCATCAGGTTTT
          1 --AAGTTTTCAAATTGGGAAAGTTCCCATCAGGTTTT

                      *             *     
        194 -AGTTTTCAATTTAGGGAAAGTTCTCATCA
          1 AAGTTTTCAAATT-GGGAAAGTTCCCATCA

        223 TTTTCAGTTT


Statistics
Matches: 119,  Mismatches: 12, Indels: 12
        0.83            0.08        0.08

Matches are distributed among these distances:
  34   34  0.29
  35   21  0.18
  36   31  0.26
  37    9  0.08
  38   24  0.20

ACGTcount: A:0.30, C:0.14, G:0.17, T:0.38


Consensus pattern (35 bp):   
AAGTTTTCAAATTGGGAAAGTTCCCATCAGGTTTT

Found at i:249 original size:74 final size:75

Alignment explanation


    Indices: 81--260  Score: 192
    Period size: 74  Copynumber: 2.4  Consensus size: 75

         71 TTCCCACCAG

                                          *    *                             
         81 GTTTTAGTTTTTAAATTGGGAAAGTTCCCAACAAGTTTTTAAGTTTTCAAATTGGGAAAGTTCCC
          1 GTTTTAG--TTTAAATTGGGAAAGTTCCCATCAAGGTTTTAAGTTTTCAAATTGGGAAAGTTCCC

                         
        146 ATTCAGTTTTTCA
         64 ATTCAG-TTTTCA

            ***                                             *             *  
        159 AAATT--TTTAAATTGGGAAAGTTCCCATC-AGGTTTT-AGTTTTCAATTTAGGGAAAGTTCTCA
          1 GTTTTAGTTTAAATTGGGAAAGTTCCCATCAAGGTTTTAAGTTTTCAAATT-GGGAAAGTTCCCA

                       
        220 -TCA-TTTTCA
         65 TTCAGTTTTCA

                           *                
        229 GTTTTAGTTTCCAAAGTGGGAAAGTTCCCATC
          1 GTTTTAGTTT--AAATTGGGAAAGTTCCCATC

        261 GAAAATCAGT


Statistics
Matches: 86,  Mismatches: 11, Indels: 14
        0.77            0.10        0.13

Matches are distributed among these distances:
  70    8  0.09
  72   17  0.20
  73   18  0.21
  74   41  0.48
  78    2  0.02

ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41


Consensus pattern (75 bp):   
GTTTTAGTTTAAATTGGGAAAGTTCCCATCAAGGTTTTAAGTTTTCAAATTGGGAAAGTTCCCAT
TCAGTTTTCA

Found at i:279 original size:108 final size:107

Alignment explanation


    Indices: 51--280  Score: 241
    Period size: 108  Copynumber: 2.1  Consensus size: 107

         41 TCAATCTTCG

                   *                                 *                       
         51 AAGTTTTCAAATTGGGAAAGTTCCCACCAGGTTTTAGTTTTTAAATTGGGAAAGTTCCCAACAAG
          1 AAGTTTTAAAATTGGGAAAGTTCCCACCAGGTTTTAGTTTTCAAATTGGGAAAGTTCCCAACAAG

                       *    *                   ****  
        116 TTTTTAAGTTTTCAAATTGGGAAAGTTCCCATTCAGTTTTTC
         66 TTTTTAAGTTTCCAAAGTGGGAAAGTTCCCATTCAGAAAATC

               *    *                  *                 *             *  *  
        158 AAAATTTTTAAATTGGGAAAGTTCCCATCAGGTTTTAGTTTTCAATTTAGGGAAAGTTCTCATCA
          1 -AAGTTTTAAAATTGGGAAAGTTCCCACCAGGTTTTAGTTTTCAAATT-GGGAAAGTTCCCAACA

            **        *                                    
        223 TTTTCAGTTTTAGTTTCCAAAGTGGGAAAGTTCCCA-TC-GAAAATC
         64 AGTT---TTTAAGTTTCCAAAGTGGGAAAGTTCCCATTCAGAAAATC

                          
        268 -AGTTTTAAAATTG
          1 AAGTTTTAAAATTG

        281 AGTCGTTTTA


Statistics
Matches: 100,  Mismatches: 18, Indels: 8
        0.79            0.14        0.06

Matches are distributed among these distances:
 108   53  0.53
 109   16  0.16
 110    3  0.03
 111    2  0.02
 112   26  0.26

ACGTcount: A:0.30, C:0.14, G:0.17, T:0.38


Consensus pattern (107 bp):   
AAGTTTTAAAATTGGGAAAGTTCCCACCAGGTTTTAGTTTTCAAATTGGGAAAGTTCCCAACAAG
TTTTTAAGTTTCCAAAGTGGGAAAGTTCCCATTCAGAAAATC
Done.