Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022093.1 Corchorus olitorius cultivar O-4 contig22126, 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: 12456
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32


Found at i:2655 original size:21 final size:21

Alignment explanation


    Indices: 2631--2675  Score: 54
    Period size: 21  Copynumber: 2.1  Consensus size: 21

       2621 GTGACACTGC

                *     *          
       2631 CCACCTGGGTTCTCAAGCAAA
          1 CCACATGGGTGCTCAAGCAAA

                         *   *   
       2652 CCACATGGGTGCTTAAGGAAA
          1 CCACATGGGTGCTCAAGCAAA

               
       2673 CCA
          1 CCA

       2676 TGTGGGCGCC


Statistics
Matches: 20,  Mismatches: 4, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  21   20  1.00

ACGTcount: A:0.31, C:0.29, G:0.22, T:0.18


Consensus pattern (21 bp):   
CCACATGGGTGCTCAAGCAAA

Found at i:4504 original size:21 final size:21

Alignment explanation


    Indices: 4474--4513  Score: 55
    Period size: 21  Copynumber: 1.9  Consensus size: 21

       4464 TTAAGTGATA

                      *          
       4474 CAAATTAACTGAA-TATAAAT
          1 CAAATTAACTCAACTATAAAT

                                
       4494 CAAATTTAACTCAACTATAA
          1 CAAA-TTAACTCAACTATAA

       4514 TTTAATTAAA


Statistics
Matches: 17,  Mismatches: 1, Indels: 2
        0.85            0.05        0.10

Matches are distributed among these distances:
  20    4  0.24
  21    8  0.47
  22    5  0.29

ACGTcount: A:0.53, C:0.15, G:0.03, T:0.30


Consensus pattern (21 bp):   
CAAATTAACTCAACTATAAAT

Found at i:5834 original size:31 final size:32

Alignment explanation


    Indices: 5787--5847  Score: 115
    Period size: 31  Copynumber: 1.9  Consensus size: 32

       5777 GAGCAGTTGG

                                            
       5787 GTTTGCCATTTTTTTTTTTACTTGATGAAATT
          1 GTTTGCCATTTTTTTTTTTACTTGATGAAATT

                                          
       5819 GTTTGCCA-TTTTTTTTTTACTTGATGAAA
          1 GTTTGCCATTTTTTTTTTTACTTGATGAAA

       5848 CTATATGTTG


Statistics
Matches: 29,  Mismatches: 0, Indels: 1
        0.97            0.00        0.03

Matches are distributed among these distances:
  31   21  0.72
  32    8  0.28

ACGTcount: A:0.20, C:0.10, G:0.13, T:0.57


Consensus pattern (32 bp):   
GTTTGCCATTTTTTTTTTTACTTGATGAAATT

Found at i:9389 original size:10 final size:10

Alignment explanation


    Indices: 9374--9404  Score: 62
    Period size: 10  Copynumber: 3.1  Consensus size: 10

       9364 TATCTGAATT

                      
       9374 AGCTCAAATG
          1 AGCTCAAATG

                      
       9384 AGCTCAAATG
          1 AGCTCAAATG

                      
       9394 AGCTCAAATG
          1 AGCTCAAATG

             
       9404 A
          1 A

       9405 AGTGTGAACT


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

Matches are distributed among these distances:
  10   21  1.00

ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19


Consensus pattern (10 bp):   
AGCTCAAATG

Found at i:10909 original size:199 final size:199

Alignment explanation


    Indices: 10568--10965  Score: 778
    Period size: 199  Copynumber: 2.0  Consensus size: 199

      10558 CTCCCTAACT

                                                                             
      10568 TTGCCTTTAAAAAAGCAAAAGAACAACTATTTATAATCAAGGTTAAAATGAATGAATACAATGTC
          1 TTGCCTTTAAAAAAGCAAAAGAACAACTATTTATAATCAAGGTTAAAATGAATGAATACAATGTC

                                                                         *   
      10633 AACATATATAAATTTATTAGTTTTGTAACTAATTCGATTTTTTGAAAAAAAATTACGGCCGTGAC
         66 AACATATATAAATTTATTAGTTTTGTAACTAATTCGATTTTTTGAAAAAAAATTACGGCCGCGAC

                 *                                                           
      10698 ACCCGTGATGCTTTACGTTCGCGACACCAGCAACCGCGACACCGTGACCGAGTCCGCGACCGCGA
        131 ACCCGCGATGCTTTACGTTCGCGACACCAGCAACCGCGACACCGTGACCGAGTCCGCGACCGCGA

                
      10763 TTTA
        196 TTTA

                                                                             
      10767 TTGCCTTTAAAAAAGCAAAAGAACAACTATTTATAATCAAGGTTAAAATGAATGAATACAATGTC
          1 TTGCCTTTAAAAAAGCAAAAGAACAACTATTTATAATCAAGGTTAAAATGAATGAATACAATGTC

                                                                             
      10832 AACATATATAAATTTATTAGTTTTGTAACTAATTCGATTTTTTGAAAAAAAATTACGGCCGCGAC
         66 AACATATATAAATTTATTAGTTTTGTAACTAATTCGATTTTTTGAAAAAAAATTACGGCCGCGAC

                                                                             
      10897 ACCCGCGATGCTTTACGTTCGCGACACCAGCAACCGCGACACCGTGACCGAGTCCGCGACCGCGA
        131 ACCCGCGATGCTTTACGTTCGCGACACCAGCAACCGCGACACCGTGACCGAGTCCGCGACCGCGA

                
      10962 TTTA
        196 TTTA

      10966 ATACTATGAG


Statistics
Matches: 197,  Mismatches: 2, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
 199  197  1.00

ACGTcount: A:0.36, C:0.21, G:0.17, T:0.27


Consensus pattern (199 bp):   
TTGCCTTTAAAAAAGCAAAAGAACAACTATTTATAATCAAGGTTAAAATGAATGAATACAATGTC
AACATATATAAATTTATTAGTTTTGTAACTAATTCGATTTTTTGAAAAAAAATTACGGCCGCGAC
ACCCGCGATGCTTTACGTTCGCGACACCAGCAACCGCGACACCGTGACCGAGTCCGCGACCGCGA
TTTA
Done.