Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021909.1 Corchorus olitorius cultivar O-4 contig21942, 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: 14717
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34


Found at i:1778 original size:12 final size:13

Alignment explanation


    Indices: 1746--1792  Score: 53
    Period size: 13  Copynumber: 3.6  Consensus size: 13

       1736 CTATTTTATT

                         
       1746 ATTGTTTTATTAA
          1 ATTGTTTTATTAA

                         
       1759 ATTGTTTTA-TAA
          1 ATTGTTTTATTAA

                       *   
       1771 A-TGTTTTTAAATAA
          1 ATTG-TTTT-ATTAA

                    
       1785 ATTGTTTT
          1 ATTGTTTT

       1793 GGGTGCATGA


Statistics
Matches: 30,  Mismatches: 0, Indels: 7
        0.81            0.00        0.19

Matches are distributed among these distances:
  11    2  0.07
  12    8  0.27
  13   10  0.33
  14    8  0.27
  15    2  0.07

ACGTcount: A:0.32, C:0.00, G:0.09, T:0.60


Consensus pattern (13 bp):   
ATTGTTTTATTAA

Found at i:5676 original size:52 final size:53

Alignment explanation


    Indices: 5598--5726  Score: 251
    Period size: 53  Copynumber: 2.5  Consensus size: 53

       5588 CAATTTTAAT

                                                                 
       5598 AAATTTGGGACCAACTCATTCGGCGATATTTATGAAG-AAAAAAAATTGTGAC
          1 AAATTTGGGACCAACTCATTCGGCGATATTTATGAAGAAAAAAAAATTGTGAC

                                                                 
       5650 AAATTTGGGACCAACTCATTCGGCGATATTTATGAAGAAAAAAAAATTGTGAC
          1 AAATTTGGGACCAACTCATTCGGCGATATTTATGAAGAAAAAAAAATTGTGAC

                                    
       5703 AAATTTGGGACCAACTCATTCGGC
          1 AAATTTGGGACCAACTCATTCGGC

       5727 AAAAAAAGTT


Statistics
Matches: 76,  Mismatches: 0, Indels: 1
        0.99            0.00        0.01

Matches are distributed among these distances:
  52   37  0.49
  53   39  0.51

ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26


Consensus pattern (53 bp):   
AAATTTGGGACCAACTCATTCGGCGATATTTATGAAGAAAAAAAAATTGTGAC

Found at i:5948 original size:32 final size:31

Alignment explanation


    Indices: 5908--5968  Score: 77
    Period size: 32  Copynumber: 1.9  Consensus size: 31

       5898 TACTTAGTAA

                           *      *        
       5908 CCAATCCAGTCCAGATGATTAGGTCCATTGT
          1 CCAATCCAGTCCAGACGATTAGATCCATTGT

                       *   *              
       5939 CCAAGTCCAGTTCAGGCGATTAGATCCATT
          1 CCAA-TCCAGTCCAGACGATTAGATCCATT

       5969 ATTCAAGACC


Statistics
Matches: 25,  Mismatches: 4, Indels: 1
        0.83            0.13        0.03

Matches are distributed among these distances:
  31    4  0.16
  32   21  0.84

ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28


Consensus pattern (31 bp):   
CCAATCCAGTCCAGACGATTAGATCCATTGT

Found at i:11881 original size:17 final size:20

Alignment explanation


    Indices: 11859--11898  Score: 59
    Period size: 17  Copynumber: 2.1  Consensus size: 20

      11849 AACATTGAAG

                                
      11859 TTATAACCT-TA-A-TTTTT
          1 TTATAACCTCTATAGTTTTT

                                
      11876 TTATAACCTCTATAGTTTTT
          1 TTATAACCTCTATAGTTTTT

               
      11896 TTA
          1 TTA

      11899 GTGACCTTAT


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

Matches are distributed among these distances:
  17    9  0.45
  18    2  0.10
  19    1  0.05
  20    8  0.40

ACGTcount: A:0.28, C:0.12, G:0.03, T:0.57


Consensus pattern (20 bp):   
TTATAACCTCTATAGTTTTT

Found at i:13921 original size:24 final size:24

Alignment explanation


    Indices: 13889--13938  Score: 73
    Period size: 24  Copynumber: 2.1  Consensus size: 24

      13879 AATTCCTGTT

                       *            
      13889 AAATCTTCATCTAAAAAGTCCAAG
          1 AAATCTTCATCCAAAAAGTCCAAG

                *          *        
      13913 AAATTTTCATCCAAAGAGTCCAAG
          1 AAATCTTCATCCAAAAAGTCCAAG

              
      13937 AA
          1 AA

      13939 GAAAGTTTTT


Statistics
Matches: 23,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  24   23  1.00

ACGTcount: A:0.46, C:0.20, G:0.10, T:0.24


Consensus pattern (24 bp):   
AAATCTTCATCCAAAAAGTCCAAG

Found at i:14284 original size:15 final size:15

Alignment explanation


    Indices: 14264--14294  Score: 62
    Period size: 15  Copynumber: 2.1  Consensus size: 15

      14254 TTTTTTTTAA

                           
      14264 AACATGTATATATGT
          1 AACATGTATATATGT

                           
      14279 AACATGTATATATGT
          1 AACATGTATATATGT

             
      14294 A
          1 A

      14295 TATATATGCA


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   16  1.00

ACGTcount: A:0.42, C:0.06, G:0.13, T:0.39


Consensus pattern (15 bp):   
AACATGTATATATGT

Found at i:14293 original size:8 final size:8

Alignment explanation


    Indices: 14267--14299  Score: 50
    Period size: 8  Copynumber: 4.2  Consensus size: 8

      14257 TTTTTAAAAC

                    
      14267 ATGTATAT
          1 ATGTATAT

                   *
      14275 ATGTA-AC
          1 ATGTATAT

                    
      14282 ATGTATAT
          1 ATGTATAT

                    
      14290 ATGTATAT
          1 ATGTATAT

              
      14298 AT
          1 AT

      14300 ATGCACATTG


Statistics
Matches: 22,  Mismatches: 2, Indels: 2
        0.85            0.08        0.08

Matches are distributed among these distances:
   7    6  0.27
   8   16  0.73

ACGTcount: A:0.39, C:0.03, G:0.12, T:0.45


Consensus pattern (8 bp):   
ATGTATAT
Done.