Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020769.1 Corchorus olitorius cultivar O-4 contig20802, 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: 3664
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33


Found at i:18 original size:1 final size:1

Alignment explanation


    Indices: 13--64  Score: 104
    Period size: 1  Copynumber: 52.0  Consensus size: 1

          3 TTCTTACGTC

                                                                
         13 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
          1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT

         65 AAATTGATGC


Statistics
Matches: 51,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   51  1.00

ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00


Consensus pattern (1 bp):   
T

Found at i:854 original size:9 final size:9

Alignment explanation


    Indices: 840--866  Score: 54
    Period size: 9  Copynumber: 3.0  Consensus size: 9

        830 TTCATTACAA

                     
        840 GAAACAGAG
          1 GAAACAGAG

                     
        849 GAAACAGAG
          1 GAAACAGAG

                     
        858 GAAACAGAG
          1 GAAACAGAG

        867 CAATGGCAAT


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   9   18  1.00

ACGTcount: A:0.56, C:0.11, G:0.33, T:0.00


Consensus pattern (9 bp):   
GAAACAGAG

Found at i:3210 original size:16 final size:16

Alignment explanation


    Indices: 3183--3241  Score: 57
    Period size: 16  Copynumber: 3.7  Consensus size: 16

       3173 TTTGGTTGAG

                            
       3183 AGGAAA-GAAATAAGA
          1 AGGAAAGGAAATAAGA

                           * 
       3198 AGGAAAGGAAATAACAA
          1 AGGAAAGGAAATAA-GA

                 *       * *
       3215 AGGAAGGGAAATAGGG
          1 AGGAAAGGAAATAAGA

                 *     
       3231 AGGAAGGGAAA
          1 AGGAAAGGAAA

       3242 GGGAGTTATA


Statistics
Matches: 37,  Mismatches: 5, Indels: 3
        0.82            0.11        0.07

Matches are distributed among these distances:
  15    6  0.16
  16   18  0.49
  17   13  0.35

ACGTcount: A:0.58, C:0.02, G:0.36, T:0.05


Consensus pattern (16 bp):   
AGGAAAGGAAATAAGA

Found at i:3219 original size:17 final size:16

Alignment explanation


    Indices: 3183--3227  Score: 56
    Period size: 17  Copynumber: 2.8  Consensus size: 16

       3173 TTTGGTTGAG

                          * 
       3183 AGGAAA-GAAATAAGA
          1 AGGAAAGGAAATAAAA

                             
       3198 AGGAAAGGAAATAACAA
          1 AGGAAAGGAAATAA-AA

                 *       
       3215 AGGAAGGGAAATA
          1 AGGAAAGGAAATA

       3228 GGGAGGAAGG


Statistics
Matches: 26,  Mismatches: 2, Indels: 2
        0.87            0.07        0.07

Matches are distributed among these distances:
  15    6  0.23
  16    7  0.27
  17   13  0.50

ACGTcount: A:0.62, C:0.02, G:0.29, T:0.07


Consensus pattern (16 bp):   
AGGAAAGGAAATAAAA
Done.