Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020528.1 Corchorus olitorius cultivar O-4 contig20561, 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: 15550
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30


Found at i:3125 original size:17 final size:17

Alignment explanation


    Indices: 3103--3136  Score: 52
    Period size: 17  Copynumber: 2.0  Consensus size: 17

       3093 AAACTAGGGA

                              
       3103 AAAGAGA-ACAAACGGTG
          1 AAAGAGAGA-AAACGGTG

                             
       3120 AAAGAGAGAAAACGGTG
          1 AAAGAGAGAAAACGGTG

       3137 TAAAAACAAT


Statistics
Matches: 16,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  17   15  0.94
  18    1  0.06

ACGTcount: A:0.53, C:0.09, G:0.32, T:0.06


Consensus pattern (17 bp):   
AAAGAGAGAAAACGGTG

Found at i:7032 original size:14 final size:16

Alignment explanation


    Indices: 7008--7041  Score: 54
    Period size: 15  Copynumber: 2.2  Consensus size: 16

       6998 AAAAAACTTT

                            
       7008 AAAAAATAAAAAT-AC
          1 AAAAAATAAAAATGAC

                            
       7023 AAAAAA-AAAAATGAC
          1 AAAAAATAAAAATGAC

                
       7038 AAAA
          1 AAAA

       7042 GGGTTCTCAC


Statistics
Matches: 18,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  14    6  0.33
  15   12  0.67

ACGTcount: A:0.82, C:0.06, G:0.03, T:0.09


Consensus pattern (16 bp):   
AAAAAATAAAAATGAC

Found at i:10751 original size:11 final size:11

Alignment explanation


    Indices: 10735--10760  Score: 52
    Period size: 11  Copynumber: 2.4  Consensus size: 11

      10725 CTAGCCCTAA

                       
      10735 AAAACTAGAAG
          1 AAAACTAGAAG

                       
      10746 AAAACTAGAAG
          1 AAAACTAGAAG

                
      10757 AAAA
          1 AAAA

      10761 GAAATTATCT


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   15  1.00

ACGTcount: A:0.69, C:0.08, G:0.15, T:0.08


Consensus pattern (11 bp):   
AAAACTAGAAG

Found at i:11775 original size:341 final size:341

Alignment explanation


    Indices: 11152--11833  Score: 1303
    Period size: 341  Copynumber: 2.0  Consensus size: 341

      11142 CTTGTTAGGA

                                                                             
      11152 CTAGAATCAGGAATCTACGGGATTTTGATATTTCCTTGGATTTAGGAGTCATTAATTGAGATTTG
          1 CTAGAATCAGGAATCTACGGGATTTTGATATTTCCTTGGATTTAGGAGTCATTAATTGAGATTTG

                                                                             
      11217 AATTCCAATTAATATCTTATATGGGCTGAGTATTTTCCCATATAAATTATCCATAAATACCAAAG
         66 AATTCCAATTAATATCTTATATGGGCTGAGTATTTTCCCATATAAATTATCCATAAATACCAAAG

                                               *                             
      11282 CTTAAGGGCTTATCCATGGCTTGTCTTCAATTAAAGCTCCAATTCTTCAATTCTTCCTCTTGAAA
        131 CTTAAGGGCTTATCCATGGCTTGTCTTCAATTAAAACTCCAATTCTTCAATTCTTCCTCTTGAAA

                 *                                                           
      11347 TAAATTTTCAATGGTCTTCAAGTCTCCAATTTATCTTCAAATGGTCTTCAAACACGAACTTCGAA
        196 TAAATCTTCAATGGTCTTCAAGTCTCCAATTTATCTTCAAATGGTCTTCAAACACGAACTTCGAA

                                                       *                     
      11412 TCTCCAAATCTATGCTCAAAATTGCTTTGCTCAAATCTGTGTATAAAGTCATCAAAATAACTCCA
        261 TCTCCAAATCTATGCTCAAAATTGCTTTGCTCAAATCTGTGTAAAAAGTCATCAAAATAACTCCA

                            
      11477 AAAAATAGTGAAAAAT
        326 AAAAATAGTGAAAAAT

                    *                                                        
      11493 CTAGAATCGGGAAT-TCACGGGATTTTGATATTTCCTTGGATTTAGGAGTCATTAATTGAGATTT
          1 CTAGAATCAGGAATCT-ACGGGATTTTGATATTTCCTTGGATTTAGGAGTCATTAATTGAGATTT

                                                   *                         
      11557 GAATTCCAATTAATATCTTATATGGGCTGAGTATTTTCCTATATAAATTATCCATAAATACCAAA
         65 GAATTCCAATTAATATCTTATATGGGCTGAGTATTTTCCCATATAAATTATCCATAAATACCAAA

                                                                             
      11622 GCTTAAGGGCTTATCCATGGCTTGTCTTCAATTAAAACTCCAATTCTTCAATTCTTCCTCTTGAA
        130 GCTTAAGGGCTTATCCATGGCTTGTCTTCAATTAAAACTCCAATTCTTCAATTCTTCCTCTTGAA

                                                                             
      11687 ATAAATCTTCAATGGTCTTCAAGTCTCCAATTTATCTTCAAATGGTCTTCAAACACGAACTTCGA
        195 ATAAATCTTCAATGGTCTTCAAGTCTCCAATTTATCTTCAAATGGTCTTCAAACACGAACTTCGA

                                                                             
      11752 ATCTCCAAATCTATGCTCAAAATTGCTTTGCTCAAATCTGTGTAAAAAGTCATCAAAATAACTCC
        260 ATCTCCAAATCTATGCTCAAAATTGCTTTGCTCAAATCTGTGTAAAAAGTCATCAAAATAACTCC

                             
      11817 AAAAAATAGTGAAAAAT
        325 AAAAAATAGTGAAAAAT

      11834 AACAATTTAT


Statistics
Matches: 335,  Mismatches: 5, Indels: 2
        0.98            0.01        0.01

Matches are distributed among these distances:
 340    1  0.00
 341  334  1.00

ACGTcount: A:0.34, C:0.18, G:0.13, T:0.35


Consensus pattern (341 bp):   
CTAGAATCAGGAATCTACGGGATTTTGATATTTCCTTGGATTTAGGAGTCATTAATTGAGATTTG
AATTCCAATTAATATCTTATATGGGCTGAGTATTTTCCCATATAAATTATCCATAAATACCAAAG
CTTAAGGGCTTATCCATGGCTTGTCTTCAATTAAAACTCCAATTCTTCAATTCTTCCTCTTGAAA
TAAATCTTCAATGGTCTTCAAGTCTCCAATTTATCTTCAAATGGTCTTCAAACACGAACTTCGAA
TCTCCAAATCTATGCTCAAAATTGCTTTGCTCAAATCTGTGTAAAAAGTCATCAAAATAACTCCA
AAAAATAGTGAAAAAT

Found at i:13478 original size:16 final size:16

Alignment explanation


    Indices: 13457--13487  Score: 53
    Period size: 16  Copynumber: 1.9  Consensus size: 16

      13447 AGGAATAGGC

                            
      13457 AATCAATCAAAGCAAT
          1 AATCAATCAAAGCAAT

                     *     
      13473 AATCAATCAGAGCAA
          1 AATCAATCAAAGCAA

      13488 AACAATGCAA


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  16   14  1.00

ACGTcount: A:0.55, C:0.19, G:0.10, T:0.16


Consensus pattern (16 bp):   
AATCAATCAAAGCAAT
Done.