Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010618.1 Corchorus olitorius cultivar O-4 contig10650, 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: 2385
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.30


Found at i:78 original size:50 final size:50

Alignment explanation


    Indices: 3--113  Score: 204
    Period size: 50  Copynumber: 2.2  Consensus size: 50

          1 AC

                                                              
          3 TCGTTTCCATACGAGTCAATTATCAACATAGGCTTTTCCACAAGCCAAAT
          1 TCGTTTCCATACGAGTCAATTATCAACATAGGCTTTTCCACAAGCCAAAT

                                                           *  
         53 TCGTTTCCATACGAGTCAATTATCAACATAGGCTTTTCCACAAGCCACAT
          1 TCGTTTCCATACGAGTCAATTATCAACATAGGCTTTTCCACAAGCCAAAT

            *          
        103 CCGTTTCCATA
          1 TCGTTTCCATA

        114 AGGTGCATTA


Statistics
Matches: 59,  Mismatches: 2, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  50   59  1.00

ACGTcount: A:0.30, C:0.28, G:0.12, T:0.31


Consensus pattern (50 bp):   
TCGTTTCCATACGAGTCAATTATCAACATAGGCTTTTCCACAAGCCAAAT

Found at i:358 original size:50 final size:50

Alignment explanation


    Indices: 124--356  Score: 387
    Period size: 50  Copynumber: 4.7  Consensus size: 50

        114 AGGTGCATTA

                                                              
        124 CCTTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGT
          1 CCTTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGT

                                                              
        174 CCTTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGT
          1 CCTTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGT

                                                              
        224 CCTTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGT
          1 CCTTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGT

             *                               *                
        274 CTTTTTAAGATTGAATTGGTAGACAGTTCAAAGAATAAGCGGAAGACGGT
          1 CCTTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGT

            *     * *           *     *       
        324 TCTTTTGATATT-AGATTGGAAGACAATTCAAAG
          1 CCTTTTAAGATTGA-ATTGGTAGACAGTTCAAAG

        357 AAGTTGATCG


Statistics
Matches: 174,  Mismatches: 8, Indels: 2
        0.95            0.04        0.01

Matches are distributed among these distances:
  49    1  0.01
  50  173  0.99

ACGTcount: A:0.35, C:0.11, G:0.26, T:0.28


Consensus pattern (50 bp):   
CCTTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGT

Found at i:633 original size:26 final size:26

Alignment explanation


    Indices: 600--670  Score: 115
    Period size: 26  Copynumber: 2.7  Consensus size: 26

        590 GGTCACCTAG

                                      
        600 GGGCATTTTGGTCATTTGTGCACCCA
          1 GGGCATTTTGGTCATTTGTGCACCCA

                    *             *   
        626 GGGCATTTCGGTCATTTGTGCATCCA
          1 GGGCATTTTGGTCATTTGTGCACCCA

                               
        652 GAGGCATTTTGGTCATTTG
          1 G-GGCATTTTGGTCATTTG

        671 GTCACTTTAC


Statistics
Matches: 41,  Mismatches: 3, Indels: 1
        0.91            0.07        0.02

Matches are distributed among these distances:
  26   25  0.61
  27   16  0.39

ACGTcount: A:0.15, C:0.20, G:0.28, T:0.37


Consensus pattern (26 bp):   
GGGCATTTTGGTCATTTGTGCACCCA

Found at i:998 original size:27 final size:27

Alignment explanation


    Indices: 924--998  Score: 114
    Period size: 27  Copynumber: 2.8  Consensus size: 27

        914 TTAGGGTCAC

                              *    *   
        924 CCAGGGGCATTTTGGTAAATTGCGCAT
          1 CCAGGGGCATTTTGGTAATTTGCACAT

                                     * 
        951 CCAGGGGCATTTTGGTAATTTGCACGT
          1 CCAGGGGCATTTTGGTAATTTGCACAT

                            *    
        978 CCAGGGGCATTTTGGTCATTT
          1 CCAGGGGCATTTTGGTAATTT

        999 TTAAGTTCAC


Statistics
Matches: 44,  Mismatches: 4, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  27   44  1.00

ACGTcount: A:0.19, C:0.19, G:0.29, T:0.33


Consensus pattern (27 bp):   
CCAGGGGCATTTTGGTAATTTGCACAT
Done.