Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011995.1 Corchorus olitorius cultivar O-4 contig12028, 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: 20569
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32


Found at i:5691 original size:19 final size:20

Alignment explanation


    Indices: 5652--5692  Score: 57
    Period size: 19  Copynumber: 2.1  Consensus size: 20

       5642 AGAGTGCAAG

                            *   
       5652 GAAGCATGGAAAATCATGGA
          1 GAAGCATGGAAAATCAAGGA

                       *        
       5672 GAAGCAT-GAAGATCAAGGA
          1 GAAGCATGGAAAATCAAGGA

              
       5691 GA
          1 GA

       5693 TGTCACACAA


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  19   12  0.63
  20    7  0.37

ACGTcount: A:0.46, C:0.10, G:0.32, T:0.12


Consensus pattern (20 bp):   
GAAGCATGGAAAATCAAGGA

Found at i:9754 original size:13 final size:13

Alignment explanation


    Indices: 9736--9761  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

       9726 TCAAGGAGAT

                         
       9736 CATGGAGATCAAG
          1 CATGGAGATCAAG

                         
       9749 CATGGAGATCAAG
          1 CATGGAGATCAAG

       9762 GGCTTATCAT


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:0.38, C:0.15, G:0.31, T:0.15


Consensus pattern (13 bp):   
CATGGAGATCAAG

Found at i:10045 original size:21 final size:21

Alignment explanation


    Indices: 9994--10045  Score: 50
    Period size: 21  Copynumber: 2.5  Consensus size: 21

       9984 AACTCATCTT

                 *               
       9994 GAAGACTTGAAGACCATTGAA
          1 GAAGAATTGAAGACCATTGAA

             ***           *     
      10015 GTTCAATTGAAGACCTTTGAA
          1 GAAGAATTGAAGACCATTGAA

                 *    
      10036 GAAGATTTGA
          1 GAAGAATTGA

      10046 GCAAAGAAGA


Statistics
Matches: 22,  Mismatches: 9, Indels: 0
        0.71            0.29        0.00

Matches are distributed among these distances:
  21   22  1.00

ACGTcount: A:0.38, C:0.12, G:0.23, T:0.27


Consensus pattern (21 bp):   
GAAGAATTGAAGACCATTGAA

Found at i:13664 original size:21 final size:21

Alignment explanation


    Indices: 13638--13679  Score: 84
    Period size: 21  Copynumber: 2.0  Consensus size: 21

      13628 TAAGGAAGAA

                                 
      13638 GTTTCAAGCTCATCGGAGTTG
          1 GTTTCAAGCTCATCGGAGTTG

                                 
      13659 GTTTCAAGCTCATCGGAGTTG
          1 GTTTCAAGCTCATCGGAGTTG

      13680 CCTAAGATGC


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  21   21  1.00

ACGTcount: A:0.19, C:0.19, G:0.29, T:0.33


Consensus pattern (21 bp):   
GTTTCAAGCTCATCGGAGTTG

Found at i:14832 original size:14 final size:14

Alignment explanation


    Indices: 14822--14851  Score: 60
    Period size: 14  Copynumber: 2.1  Consensus size: 14

      14812 TAATAAATTT

                          
      14822 TACTAAATAAATAA
          1 TACTAAATAAATAA

                          
      14836 TACTAAATAAATAA
          1 TACTAAATAAATAA

              
      14850 TA
          1 TA

      14852 TATAAATACA


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

Matches are distributed among these distances:
  14   16  1.00

ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30


Consensus pattern (14 bp):   
TACTAAATAAATAA

Found at i:14859 original size:15 final size:15

Alignment explanation


    Indices: 14825--14878  Score: 58
    Period size: 15  Copynumber: 3.7  Consensus size: 15

      14815 TAAATTTTAC

                          *
      14825 TAAATAAATAATA-C
          1 TAAATAAATAATATA

                           
      14839 TAAATAAATAATATA
          1 TAAATAAATAATATA

                  *         
      14854 TAAATACATAGA-ATA
          1 TAAATAAATA-ATATA

            *         
      14869 AAAATAAATA
          1 TAAATAAATA

      14879 TTTATATATA


Statistics
Matches: 34,  Mismatches: 4, Indels: 3
        0.83            0.10        0.07

Matches are distributed among these distances:
  14   13  0.38
  15   20  0.59
  16    1  0.03

ACGTcount: A:0.67, C:0.04, G:0.02, T:0.28


Consensus pattern (15 bp):   
TAAATAAATAATATA
Done.