Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017108.1 Corchorus olitorius cultivar O-4 contig17141, 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: 21690
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29


Found at i:7 original size:2 final size:2

Alignment explanation


    Indices: 1--38  Score: 51
    Period size: 2  Copynumber: 19.0  Consensus size: 2

                                                              *      
          1 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AGT AT AG AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT

         39 GTGTGTGTAC


Statistics
Matches: 32,  Mismatches: 2, Indels: 4
        0.84            0.05        0.11

Matches are distributed among these distances:
   1    1  0.03
   2   29  0.91
   3    2  0.06

ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47


Consensus pattern (2 bp):   
AT

Found at i:2749 original size:65 final size:64

Alignment explanation


    Indices: 2628--2749  Score: 156
    Period size: 65  Copynumber: 1.9  Consensus size: 64

       2618 TTTCCCCCCA

                            *              *   *     **                     
       2628 AACTTTTAATTTGGAATTTTCACTTCTTAAATTATGAAAATTTAGACAATATCCCCCTGAACTG
          1 AACTTTTAATTTGGAACTTTCACTTCTTAAACTATCAAAATCGAGACAATATCCCCCTGAACTG

                                                         *      *      
       2692 AACTTTTAATTTGGAACTTTCACCCTT-TTAAACTATCAAAATCGGGACAATTTCCCCC
          1 AACTTTTAATTTGGAACTTTCA--CTTCTTAAACTATCAAAATCGAGACAATATCCCCC

       2750 AGGCTATTAA


Statistics
Matches: 49,  Mismatches: 7, Indels: 3
        0.83            0.12        0.05

Matches are distributed among these distances:
  64   21  0.43
  65   25  0.51
  66    3  0.06

ACGTcount: A:0.33, C:0.21, G:0.09, T:0.37


Consensus pattern (64 bp):   
AACTTTTAATTTGGAACTTTCACTTCTTAAACTATCAAAATCGAGACAATATCCCCCTGAACTG

Found at i:19643 original size:42 final size:42

Alignment explanation


    Indices: 19580--19672  Score: 123
    Period size: 42  Copynumber: 2.2  Consensus size: 42

      19570 TCAAATCTAG

                         *  *                     *    
      19580 CAAATCCGACAACGAGGAATAACAAGCCTTCAGCCATTTCTCT
          1 CAAATCC-ACAACAAGAAATAACAAGCCTTCAGCCATTCCTCT

                                         **           
      19623 CAAATCCACAACAAGAAATAACAAGCCTTTGGCCATTCCTCT
          1 CAAATCCACAACAAGAAATAACAAGCCTTCAGCCATTCCTCT

              *     
      19665 CATATCCA
          1 CAAATCCA

      19673 TTTCATCGAG


Statistics
Matches: 44,  Mismatches: 6, Indels: 1
        0.86            0.12        0.02

Matches are distributed among these distances:
  42   37  0.84
  43    7  0.16

ACGTcount: A:0.37, C:0.31, G:0.11, T:0.22


Consensus pattern (42 bp):   
CAAATCCACAACAAGAAATAACAAGCCTTCAGCCATTCCTCT

Found at i:20234 original size:20 final size:20

Alignment explanation


    Indices: 20209--20255  Score: 94
    Period size: 20  Copynumber: 2.4  Consensus size: 20

      20199 CTGTCCTAGA

                                
      20209 TCCACTTACCAAGGGTGGAC
          1 TCCACTTACCAAGGGTGGAC

                                
      20229 TCCACTTACCAAGGGTGGAC
          1 TCCACTTACCAAGGGTGGAC

                   
      20249 TCCACTT
          1 TCCACTT

      20256 CCTTCAGAAA


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  20   27  1.00

ACGTcount: A:0.23, C:0.32, G:0.21, T:0.23


Consensus pattern (20 bp):   
TCCACTTACCAAGGGTGGAC
Done.