Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023003.1 Corchorus olitorius cultivar O-4 contig23036, 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: 9641
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33


Found at i:9 original size:2 final size:2

Alignment explanation


    Indices: 3--37  Score: 70
    Period size: 2  Copynumber: 17.5  Consensus size: 2

          1 AC

                                                                
          3 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

         38 TTGATTACTG


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   33  1.00

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (2 bp):   
TA

Found at i:3155 original size:16 final size:17

Alignment explanation


    Indices: 3136--3181  Score: 51
    Period size: 16  Copynumber: 2.8  Consensus size: 17

       3126 TCTAGGTTAT

                             
       3136 GGGTCATTTGGGTCT-C
          1 GGGTCATTTGGGTCTAC

                 * *   *     
       3152 GGGTCCTATGGAT-TAC
          1 GGGTCATTTGGGTCTAC

                          
       3168 GGGTCATTTGGGTC
          1 GGGTCATTTGGGTC

       3182 GTGGGTTTAT


Statistics
Matches: 22,  Mismatches: 6, Indels: 3
        0.71            0.19        0.10

Matches are distributed among these distances:
  15    1  0.05
  16   21  0.95

ACGTcount: A:0.11, C:0.17, G:0.37, T:0.35


Consensus pattern (17 bp):   
GGGTCATTTGGGTCTAC

Found at i:4358 original size:109 final size:109

Alignment explanation


    Indices: 4167--4477  Score: 550
    Period size: 109  Copynumber: 2.9  Consensus size: 109

       4157 GAAATCTTTT

                                                                         *   
       4167 ATCTTTTACTAATAGAAGAAGATATTTCAATGAATCCTATTAAAATCACTAGCTCAACTTGAAAT
          1 ATCTTTTACTAATAGAAGAAGATATTTCAATGAATCCTATTAAAATCACTAGCTCAACTTGGAAT

                                                        
       4232 GAAATTTATATATAATTTAAATCATCATGGGTCTCGTTTAAGAA
         66 GAAATTTATATATAATTTAAATCATCATGGGTCTCGTTTAAGAA

                                                                             
       4276 ATCTTTTACTAATAGAAGAAGATATTTCAATGAATCCTATTAAAATCACTAGCTCAACTTGGAAT
          1 ATCTTTTACTAATAGAAGAAGATATTTCAATGAATCCTATTAAAATCACTAGCTCAACTTGGAAT

                                        *               
       4341 GAAATTTATATATAATTTAAATCATCATTGGTCTCGTTTAAGAA
         66 GAAATTTATATATAATTTAAATCATCATGGGTCTCGTTTAAGAA

                                  *    *             *                       
       4385 ATCTTTTACTAATAGAAGAAGAGATTTTAATGAATCCTATTGAAATCACTAGCTCAACTTGGAAT
          1 ATCTTTTACTAATAGAAGAAGATATTTCAATGAATCCTATTAAAATCACTAGCTCAACTTGGAAT

                * *  *                  
       4450 GAAAATGATTTATAATTTAAATCATCAT
         66 GAAATTTATATATAATTTAAATCATCAT

       4478 CATCTTATTT


Statistics
Matches: 194,  Mismatches: 8, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
 109  194  1.00

ACGTcount: A:0.40, C:0.13, G:0.11, T:0.36


Consensus pattern (109 bp):   
ATCTTTTACTAATAGAAGAAGATATTTCAATGAATCCTATTAAAATCACTAGCTCAACTTGGAAT
GAAATTTATATATAATTTAAATCATCATGGGTCTCGTTTAAGAA

Found at i:6874 original size:14 final size:14

Alignment explanation


    Indices: 6855--6888  Score: 59
    Period size: 14  Copynumber: 2.4  Consensus size: 14

       6845 GCGGCTTGAG

                          
       6855 CCGGTTTGGCCGGA
          1 CCGGTTTGGCCGGA

                     *    
       6869 CCGGTTTGGTCGGA
          1 CCGGTTTGGCCGGA

                  
       6883 CCGGTT
          1 CCGGTT

       6889 CGATCCGGTC


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  14   19  1.00

ACGTcount: A:0.06, C:0.26, G:0.41, T:0.26


Consensus pattern (14 bp):   
CCGGTTTGGCCGGA
Done.