Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017930.1 Corchorus olitorius cultivar O-4 contig17963, 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: 15089
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31


Found at i:7634 original size:32 final size:32

Alignment explanation


    Indices: 7593--7658  Score: 132
    Period size: 32  Copynumber: 2.1  Consensus size: 32

       7583 CCTAACTCTT

                                            
       7593 TCTTTACCAACTTTTCCACTACACAAACAAAA
          1 TCTTTACCAACTTTTCCACTACACAAACAAAA

                                            
       7625 TCTTTACCAACTTTTCCACTACACAAACAAAA
          1 TCTTTACCAACTTTTCCACTACACAAACAAAA

              
       7657 TC
          1 TC

       7659 ATTAGTTTTC


Statistics
Matches: 34,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  32   34  1.00

ACGTcount: A:0.39, C:0.32, G:0.00, T:0.29


Consensus pattern (32 bp):   
TCTTTACCAACTTTTCCACTACACAAACAAAA

Found at i:11131 original size:19 final size:18

Alignment explanation


    Indices: 11098--11133  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

      11088 TTGAAATAAT

                              
      11098 TCTTCAATGATCTTCAAA
          1 TCTTCAATGATCTTCAAA

                     *        
      11116 TCTTCAAATTATCTTCAA
          1 TCTTC-AATGATCTTCAA

      11134 TAAGTCCTCA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    5  0.31
  19   11  0.69

ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42


Consensus pattern (18 bp):   
TCTTCAATGATCTTCAAA

Found at i:13166 original size:21 final size:21

Alignment explanation


    Indices: 13140--13180  Score: 66
    Period size: 21  Copynumber: 2.0  Consensus size: 21

      13130 TTGAAGCCCT

                                  
      13140 ATTGGATAC-AAGTGGTACTAA
          1 ATTGGAT-CTAAGTGGTACTAA

                                
      13161 ATTGGATCTAAGTGGTACTA
          1 ATTGGATCTAAGTGGTACTA

      13181 GGGTTTCTAA


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

Matches are distributed among these distances:
  20    1  0.05
  21   18  0.95

ACGTcount: A:0.34, C:0.10, G:0.24, T:0.32


Consensus pattern (21 bp):   
ATTGGATCTAAGTGGTACTAA

Found at i:14561 original size:24 final size:24

Alignment explanation


    Indices: 14524--14649  Score: 175
    Period size: 24  Copynumber: 5.2  Consensus size: 24

      14514 CAAATCTAGG

                   *                
      14524 AGGCCACATGCAGTCCCACCCTCA
          1 AGGCCACCTGCAGTCCCACCCTCA

                     *              
      14548 AGGCCACCTTCAGTCCCACCCTCA
          1 AGGCCACCTGCAGTCCCACCCTCA

              *           *         
      14572 AGACCACCTGCAGTTCCA-CCT-A
          1 AGGCCACCTGCAGTCCCACCCTCA

                                      
      14594 GGAGGCCACCTGCAGTCCCACCCTCA
          1 --AGGCCACCTGCAGTCCCACCCTCA

             *                      
      14620 ATGCCACCTGCAGTCCCACCCTCA
          1 AGGCCACCTGCAGTCCCACCCTCA

                  
      14644 AGGCCA
          1 AGGCCA

      14650 GAAGGACATC


Statistics
Matches: 89,  Mismatches: 9, Indels: 8
        0.84            0.08        0.08

Matches are distributed among these distances:
  22    1  0.01
  23    3  0.03
  24   81  0.91
  25    3  0.03
  26    1  0.01

ACGTcount: A:0.23, C:0.46, G:0.17, T:0.14


Consensus pattern (24 bp):   
AGGCCACCTGCAGTCCCACCCTCA

Found at i:14590 original size:12 final size:12

Alignment explanation


    Indices: 14575--14639  Score: 53
    Period size: 12  Copynumber: 5.4  Consensus size: 12

      14565 ACCCTCAAGA

                       *
      14575 CCACCTGCAGTT
          1 CCACCTGCAGTC

                    *   *
      14587 CCACCTAGGAG-G
          1 CCACCT-GCAGTC

                        
      14599 CCACCTGCAGTC
          1 CCACCTGCAGTC

                      * *
      14611 CCACCCT-CAATG
          1 CCA-CCTGCAGTC

                        
      14623 CCACCTGCAGTC
          1 CCACCTGCAGTC

                 
      14635 CCACC
          1 CCACC

      14640 CTCAAGGCCA


Statistics
Matches: 41,  Mismatches: 8, Indels: 8
        0.72            0.14        0.14

Matches are distributed among these distances:
  11    6  0.15
  12   29  0.71
  13    6  0.15

ACGTcount: A:0.20, C:0.48, G:0.17, T:0.15


Consensus pattern (12 bp):   
CCACCTGCAGTC

Done.