Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023780.1 Corchorus olitorius cultivar O-4 contig23813, 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: 14681
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.34


Found at i:5492 original size:22 final size:22

Alignment explanation


    Indices: 5462--5504  Score: 68
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       5452 AAAATTCAGA

                *     *           
       5462 ACAAGTCCTGTCCAGGACTTGG
          1 ACAACTCCTGCCCAGGACTTGG

                                 
       5484 ACAACTCCTGCCCAGGACTTG
          1 ACAACTCCTGCCCAGGACTTG

       5505 TTGCGGAAAA


Statistics
Matches: 19,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  22   19  1.00

ACGTcount: A:0.23, C:0.33, G:0.23, T:0.21


Consensus pattern (22 bp):   
ACAACTCCTGCCCAGGACTTGG

Found at i:10804 original size:12 final size:12

Alignment explanation


    Indices: 10787--10811  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

      10777 ACAATTAAAG

                        
      10787 AAAATTAAGAAA
          1 AAAATTAAGAAA

                        
      10799 AAAATTAAGAAA
          1 AAAATTAAGAAA

             
      10811 A
          1 A

      10812 TTAAAAAAAA


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

Matches are distributed among these distances:
  12   13  1.00

ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16


Consensus pattern (12 bp):   
AAAATTAAGAAA

Found at i:10804 original size:22 final size:22

Alignment explanation


    Indices: 10774--10828  Score: 76
    Period size: 21  Copynumber: 2.5  Consensus size: 22

      10764 CAAAGCAAAC

                *                *
      10774 AAAACAATTAAAGAAAATTAAG
          1 AAAAAAATTAAAGAAAATTAAA

                                  
      10796 AAAAAAATT-AAGAAAATTAAA
          1 AAAAAAATTAAAGAAAATTAAA

                        
      10817 AAAAACAATTAA
          1 AAAAA-AATTAA

      10829 TCAGAGAGCA


Statistics
Matches: 29,  Mismatches: 2, Indels: 3
        0.85            0.06        0.09

Matches are distributed among these distances:
  21   16  0.55
  22   12  0.41
  23    1  0.03

ACGTcount: A:0.73, C:0.04, G:0.05, T:0.18


Consensus pattern (22 bp):   
AAAAAAATTAAAGAAAATTAAA

Found at i:12577 original size:39 final size:39

Alignment explanation


    Indices: 12446--12664  Score: 246
    Period size: 38  Copynumber: 5.7  Consensus size: 39

      12436 GGCTGTGCAT

                     *               *             
      12446 AGTGGACCCATACCTCAGGGGGTTAGACTGA-TGGTAAG
          1 AGTGGACCCGTACCTCAGGGGGTTAAACTGATTGGTAAG

                              *       *     *      
      12484 AGTGGACCCGTACCTCAGAGGGTTAATCTGA-CGGTAAG
          1 AGTGGACCCGTACCTCAGGGGGTTAAACTGATTGGTAAG

               *   *   *      *                    
      12522 AGTAGACTCGTGCCTCAGTGGGTTAAACTGATTGGTAAG
          1 AGTGGACCCGTACCTCAGGGGGTTAAACTGATTGGTAAG

             *        *                            
      12561 ACTGGACCCGCACCTCAGGGGGTTAAACTGATTGGTAAG
          1 AGTGGACCCGTACCTCAGGGGGTTAAACTGATTGGTAAG

            *    *    **   *           *           
      12600 GGTGGCCCCGCGCCTTAGGGGGTTAAATTG-TTGGTAAG
          1 AGTGGACCCGTACCTCAGGGGGTTAAACTGATTGGTAAG

                       *               
      12638 AGTGGACCCGTGCCTCAGGGGGGTTAA
          1 AGTGGACCCGTACCTCA-GGGGGTTAA

      12665 TTATTGGCTA


Statistics
Matches: 152,  Mismatches: 27, Indels: 3
        0.84            0.15        0.02

Matches are distributed among these distances:
  38   80  0.53
  39   72  0.47

ACGTcount: A:0.23, C:0.20, G:0.34, T:0.23


Consensus pattern (39 bp):   
AGTGGACCCGTACCTCAGGGGGTTAAACTGATTGGTAAG

Found at i:12584 original size:77 final size:78

Alignment explanation


    Indices: 12458--12665  Score: 251
    Period size: 77  Copynumber: 2.7  Consensus size: 78

      12448 TGGACCCATA

                         *                               *                   
      12458 CCTCAGGGGGTTAGACTGA-TGGTAAGAGTGGACCCGTACCTCAGAGGGTTAATCTGA-CGGTAA
          1 CCTCAGGGGGTTAAACTGATTGGTAAGAGTGGACCCGTACCTCAGGGGGTTAATCTGATCGGTAA

                    *  * 
      12521 GAGTAGACTCGTG
         66 GAGTAGACCCGCG

                  *                     *        *               *     *     
      12534 CCTCAGTGGGTTAAACTGATTGGTAAGACTGGACCCGCACCTCAGGGGGTTAAACTGATTGGTAA
          1 CCTCAGGGGGTTAAACTGATTGGTAAGAGTGGACCCGTACCTCAGGGGGTTAATCTGATCGGTAA

             *  * *      
      12599 GGGTGGCCCCGCG
         66 GAGTAGACCCGCG

               *           *                      *                
      12612 CCTTAGGGGGTTAAATTG-TTGGTAAGAGTGGACCCGTGCCTCAGGGGGGTTAAT
          1 CCTCAGGGGGTTAAACTGATTGGTAAGAGTGGACCCGTACCTCA-GGGGGTTAAT

      12666 TATTGGCTAG


Statistics
Matches: 110,  Mismatches: 19, Indels: 4
        0.83            0.14        0.03

Matches are distributed among these distances:
  76   17  0.15
  77   56  0.51
  78   37  0.34

ACGTcount: A:0.23, C:0.19, G:0.35, T:0.24


Consensus pattern (78 bp):   
CCTCAGGGGGTTAAACTGATTGGTAAGAGTGGACCCGTACCTCAGGGGGTTAATCTGATCGGTAA
GAGTAGACCCGCG
Done.