Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014166.1 Corchorus olitorius cultivar O-4 contig14199, 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: 5693
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29


Found at i:298 original size:25 final size:25

Alignment explanation


    Indices: 262--309  Score: 64
    Period size: 27  Copynumber: 1.9  Consensus size: 25

        252 TCCTTCTATT

                                     
        262 CATCTATCATC-AAG-TTTTTCATC
          1 CATCTATCATCAAAGATTTTTCATC

                                     
        285 CATCTCATCCATCAAAGATTTTTCA
          1 CATCT-AT-CATCAAAGATTTTTCA

        310 AATTTTCAAG


Statistics
Matches: 21,  Mismatches: 0, Indels: 4
        0.84            0.00        0.16

Matches are distributed among these distances:
  23    5  0.24
  24    2  0.10
  25    4  0.19
  26    3  0.14
  27    7  0.33

ACGTcount: A:0.29, C:0.27, G:0.04, T:0.40


Consensus pattern (25 bp):   
CATCTATCATCAAAGATTTTTCATC

Found at i:5419 original size:162 final size:163

Alignment explanation


    Indices: 5135--5527  Score: 700
    Period size: 162  Copynumber: 2.4  Consensus size: 163

       5125 TGACAGAAAG

                   *  *         *     *                                      
       5135 ACGCCGCCATATTAATATATGGAGGGTGAGATTTTTTTTCTCCTTTTTTTGGAGGGAAAAATTCC
          1 ACGCCGCTATTTTAATATATCGAGGGAGAGATTTTTTTTC-CCTTTTTTTGGAGGGAAAAATTCC

                             *                                               
       5200 CTCCCCACTAAAACAAAGAAAGTTTACAACTCTACACCTATAATATATAGCGGCGTTTGGAACTC
         65 CTCCCCACTAAAACAAAAAAAGTTTACAACTCTACACCTATAATATATAGCGGCGTTTGGAACTC

                                              
       5265 AGACGCCGCTAATCAGTGGCGTCTAGAGAAGCAA
        130 AGACGCCGCTAATCAGTGGCGTCTAGAGAAGCAA

                                                                             
       5299 ACGCCGCTATTTTAATATATCGAGGGAGAGATTTTTTTTCCCTTTTTTTGGAGGGAAAAATTCCC
          1 ACGCCGCTATTTTAATATATCGAGGGAGAGATTTTTTTTCCCTTTTTTTGGAGGGAAAAATTCCC

                                                                             
       5364 TCCCC-CTAAAACAAAAAAAGTTTACAACTCTACACCTATAATATATAGCGGCGTTTGGAACTCA
         66 TCCCCACTAAAACAAAAAAAGTTTACAACTCTACACCTATAATATATAGCGGCGTTTGGAACTCA

                                             
       5428 GACGCCGCTAATCAGTGGCGTCTAGAGAAGCAA
        131 GACGCCGCTAATCAGTGGCGTCTAGAGAAGCAA

              *                           *                                  
       5461 ACTCCGCTATTTTAATATATCGAGGGAGAGGTTTTTTTTCCC-TTTTTTGGAGGGAAAAATTCCC
          1 ACGCCGCTATTTTAATATATCGAGGGAGAGATTTTTTTTCCCTTTTTTTGGAGGGAAAAATTCCC

               
       5525 TCC
         66 TCC

       5528 TCCATAATAA


Statistics
Matches: 222,  Mismatches: 7, Indels: 3
        0.96            0.03        0.01

Matches are distributed among these distances:
 161   25  0.11
 162  131  0.59
 163   30  0.14
 164   36  0.16

ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30


Consensus pattern (163 bp):   
ACGCCGCTATTTTAATATATCGAGGGAGAGATTTTTTTTCCCTTTTTTTGGAGGGAAAAATTCCC
TCCCCACTAAAACAAAAAAAGTTTACAACTCTACACCTATAATATATAGCGGCGTTTGGAACTCA
GACGCCGCTAATCAGTGGCGTCTAGAGAAGCAA
Done.