Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01005192.1 Corchorus olitorius cultivar O-4 contig05214, 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, 685

Length: 1142
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.30


Found at i:781 original size:13 final size:13

Alignment explanation


    Indices: 763--788  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

        753 CTTTCACAAA

                         
        763 ATTATCAACTAAT
          1 ATTATCAACTAAT

                         
        776 ATTATCAACTAAT
          1 ATTATCAACTAAT

        789 CATAATGGTT


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.46, C:0.15, G:0.00, T:0.38


Consensus pattern (13 bp):   
ATTATCAACTAAT

Found at i:1000 original size:10 final size:10

Alignment explanation


    Indices: 984--1019  Score: 56
    Period size: 10  Copynumber: 3.7  Consensus size: 10

        974 AATAGAAATA

                      
        984 AGAAATAATT
          1 AGAAATAATT

            *         
        994 CGAAATAA-T
          1 AGAAATAATT

                      
       1003 AGAAATAATT
          1 AGAAATAATT

                   
       1013 AGAAATA
          1 AGAAATA

       1020 TAGAATTAAT


Statistics
Matches: 23,  Mismatches: 2, Indels: 2
        0.85            0.07        0.07

Matches are distributed among these distances:
   9    8  0.35
  10   15  0.65

ACGTcount: A:0.61, C:0.03, G:0.11, T:0.25


Consensus pattern (10 bp):   
AGAAATAATT

Found at i:1006 original size:19 final size:18

Alignment explanation


    Indices: 976--1029  Score: 74
    Period size: 19  Copynumber: 3.0  Consensus size: 18

        966 GAAAATAAAA

                              
        976 TAGAAATA-AGAAATAAT
          1 TAGAAATATAGAAATAAT

             *                 
        993 TCGAAATAATAGAAATAAT
          1 TAGAAAT-ATAGAAATAAT

                         *    
       1012 TAGAAATATAGAATTAAT
          1 TAGAAATATAGAAATAAT

       1030 AATTAATATA


Statistics
Matches: 32,  Mismatches: 3, Indels: 3
        0.84            0.08        0.08

Matches are distributed among these distances:
  17    6  0.19
  18   11  0.34
  19   15  0.47

ACGTcount: A:0.59, C:0.02, G:0.11, T:0.28


Consensus pattern (18 bp):   
TAGAAATATAGAAATAAT

Found at i:1046 original size:20 final size:21

Alignment explanation


    Indices: 1006--1055  Score: 59
    Period size: 20  Copynumber: 2.5  Consensus size: 21

        996 AAATAATAGA

                                 
       1006 AATAATTAGAAATATAGAATT
          1 AATAATTAGAAATATAGAATT

                      *     *    
       1027 AATAATTA-ATATATATAATT
          1 AATAATTAGAAATATAGAATT

                 *    
       1047 -ATAAATAGA
          1 AATAATTAGA

       1056 TTAAATACTA


Statistics
Matches: 25,  Mismatches: 3, Indels: 3
        0.81            0.10        0.10

Matches are distributed among these distances:
  19    6  0.24
  20   11  0.44
  21    8  0.32

ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36


Consensus pattern (21 bp):   
AATAATTAGAAATATAGAATT

Found at i:1059 original size:24 final size:23

Alignment explanation


    Indices: 1027--1071  Score: 65
    Period size: 24  Copynumber: 1.9  Consensus size: 23

       1017 ATATAGAATT

                                    
       1027 AATAATTAATATA-TATAATTATA
          1 AATAATTAA-ATACTATAATTATA

                                  
       1050 AATAGATTAAATACTATAATTA
          1 AATA-ATTAAATACTATAATTA

       1072 GAATATTAAA


Statistics
Matches: 20,  Mismatches: 0, Indels: 3
        0.87            0.00        0.13

Matches are distributed among these distances:
  23    7  0.35
  24   13  0.65

ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40


Consensus pattern (23 bp):   
AATAATTAAATACTATAATTATA
Done.