Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016174.1 Corchorus olitorius cultivar O-4 contig16207, 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: 21456
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32


Found at i:666 original size:30 final size:30

Alignment explanation


    Indices: 609--672  Score: 85
    Period size: 30  Copynumber: 2.1  Consensus size: 30

        599 TACATGTACT

                             *  *         
        609 AAAACTTGAACCTGAAGTTGGGCAAAAAAA
          1 AAAACTTGAACCTGAAGATGCGCAAAAAAA

                                 *         
        639 AAAACTTGAACCTGAAGAT-CTCTAAAAAAA
          1 AAAACTTGAACCTGAAGATGCGC-AAAAAAA

                
        669 AAAA
          1 AAAA

        673 ATTTAATTAA


Statistics
Matches: 30,  Mismatches: 3, Indels: 2
        0.86            0.09        0.06

Matches are distributed among these distances:
  29    1  0.03
  30   29  0.97

ACGTcount: A:0.55, C:0.14, G:0.14, T:0.17


Consensus pattern (30 bp):   
AAAACTTGAACCTGAAGATGCGCAAAAAAA

Found at i:1786 original size:29 final size:29

Alignment explanation


    Indices: 1739--1795  Score: 78
    Period size: 29  Copynumber: 2.0  Consensus size: 29

       1729 ATAAGTAAAT

                     *   *       *       
       1739 GGACAATTTGCACTATAAACTTTAATTTC
          1 GGACAATTTACACCATAAACTATAATTTC

                          *             
       1768 GGACAATTTACACCCTAAACTATAATTT
          1 GGACAATTTACACCATAAACTATAATTT

       1796 ATGGGCAACT


Statistics
Matches: 24,  Mismatches: 4, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  29   24  1.00

ACGTcount: A:0.37, C:0.19, G:0.09, T:0.35


Consensus pattern (29 bp):   
GGACAATTTACACCATAAACTATAATTTC

Found at i:7525 original size:22 final size:25

Alignment explanation


    Indices: 7492--7543  Score: 58
    Period size: 23  Copynumber: 2.2  Consensus size: 25

       7482 AAATGTTGCC

                          *      *   
       7492 GATAA-TCTTCT-CTTTTATCTC-T
          1 GATAATTCTTCTCCATTTATCACTT

                                     
       7514 GATAATTC-TCTCCATTTATCACTT
          1 GATAATTCTTCTCCATTTATCACTT

                  
       7538 GATAAT
          1 GATAAT

       7544 ATCTAGCCAG


Statistics
Matches: 25,  Mismatches: 2, Indels: 4
        0.81            0.06        0.13

Matches are distributed among these distances:
  22    8  0.32
  23   10  0.40
  24    7  0.28

ACGTcount: A:0.25, C:0.21, G:0.06, T:0.48


Consensus pattern (25 bp):   
GATAATTCTTCTCCATTTATCACTT

Found at i:11733 original size:30 final size:30

Alignment explanation


    Indices: 11697--12201  Score: 696
    Period size: 30  Copynumber: 16.7  Consensus size: 30

      11687 AAGGTAAAAT

                                          
      11697 CATGACAACTTCTGGTGTCAATTGCAAGAG
          1 CATGACAACTTCTGGTGTCAATTGCAAGAG

                                          
      11727 CATGACAACTTCTGGTGTCAATTGCAAGAG
          1 CATGACAACTTCTGGTGTCAATTGCAAGAG

                              *          *
      11757 CATGACAACTTCTGGTGTGAATTGCAAGAA
          1 CATGACAACTTCTGGTGTCAATTGCAAGAG

                                       *  
      11787 CATGACAACTTCTGGTGTCAATTGCAACAG
          1 CATGACAACTTCTGGTGTCAATTGCAAGAG

                                       *  
      11817 CATGACAACTTCTGGTGTCAATTGCAACAG
          1 CATGACAACTTCTGGTGTCAATTGCAAGAG

                    *                  *  
      11847 CATGACAAGTTCTGGTGTCAATTGCAACAG
          1 CATGACAACTTCTGGTGTCAATTGCAAGAG

                    *            *    *   
      11877 CATGACAATTTCTGGTGTCAACTGCAGGAG
          1 CATGACAACTTCTGGTGTCAATTGCAAGAG

                    *                    *
      11907 CATGACAATTTCTGGTGTCAATTGCAAGAT
          1 CATGACAACTTCTGGTGTCAATTGCAAGAG

                                           
      11937 CATTGACAACTTCTGGTGTCAATTGCAAG-G
          1 CA-TGACAACTTCTGGTGTCAATTGCAAGAG

             *                       *    *
      11967 TTATGACAACTTCTGGTGTCAATTGTAAGAC
          1 -CATGACAACTTCTGGTGTCAATTGCAAGAG

                                    *    *
      11998 CATGACAACTTCTGGTGTCAATTGTAAGAT
          1 CATGACAACTTCTGGTGTCAATTGCAAGAG

                                     *    *
      12028 CATTGACAACTTCTGGTGTCAATTGTAAGAC
          1 CA-TGACAACTTCTGGTGTCAATTGCAAGAG

                                          
      12059 CATGACAACTTCTGGTGTCAATTGCAAG-G
          1 CATGACAACTTCTGGTGTCAATTGCAAGAG

                                 *         
      12088 CCATGACAACTTCTGGTGTCATTTGCAAG-G
          1 -CATGACAACTTCTGGTGTCAATTGCAAGAG

                    **                     
      12118 CCATGACAGGTTCTGGTGTCAATTGCAAG-G
          1 -CATGACAACTTCTGGTGTCAATTGCAAGAG

              *                  *         
      12148 CCTTGACAACTTCTGGTGTCATTTGCAAG-G
          1 -CATGACAACTTCTGGTGTCAATTGCAAGAG

                                    
      12178 TCATTGACAACTTCTGGTGTCAAT
          1 -CA-TGACAACTTCTGGTGTCAAT

      12202 ATATACTAGC


Statistics
Matches: 435,  Mismatches: 34, Indels: 11
        0.91            0.07        0.02

Matches are distributed among these distances:
  30  361  0.83
  31   74  0.17

ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30


Consensus pattern (30 bp):   
CATGACAACTTCTGGTGTCAATTGCAAGAG

Found at i:13334 original size:22 final size:24

Alignment explanation


    Indices: 13299--13352  Score: 60
    Period size: 22  Copynumber: 2.3  Consensus size: 24

      13289 ATAAATGTTG

                            *      *
      13299 CTGATAA-TCTTCT-CTTTTATCT
          1 CTGATAATTCTTCTCCATTTATCA

                                    
      13321 CTGATAATTC-TCTCCATTTATCA
          1 CTGATAATTCTTCTCCATTTATCA

                     
      13344 CTTGATAAT
          1 C-TGATAAT

      13353 ATCTACCCAG


Statistics
Matches: 27,  Mismatches: 2, Indels: 4
        0.82            0.06        0.12

Matches are distributed among these distances:
  22   10  0.37
  23   10  0.37
  24    7  0.26

ACGTcount: A:0.24, C:0.22, G:0.06, T:0.48


Consensus pattern (24 bp):   
CTGATAATTCTTCTCCATTTATCA
Done.