Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01007389.1 Corchorus olitorius cultivar O-4 contig07414, 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, 849

Length: 1415
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35


Found at i:814 original size:35 final size:34

Alignment explanation


    Indices: 763--910  Score: 156
    Period size: 35  Copynumber: 4.2  Consensus size: 34

        753 ATCATGTTCA

                    *                 *       
        763 AAGTTTTTTAATTGGGAAAGTTCCCACCAATTTT
          1 AAGTTTTTAAATTGGGAAAGTTCCCATCAATTTT

                                            *    
        797 AAGTTTTTCAAATTGGGAAAGTTCCCATTCAGTTTTT
          1 AAGTTTTT-AAATTGGGAAAGTTCCCA-TCA-ATTTT

                                                 
        834 CAAAGTTTTTAAATTGGGAAAGTTCCCATCAAGTTTT
          1 --AAGTTTTTAAATTGGGAAAGTTCCCATCAA-TTTT

                   *  *               *        
        871 -AGTTTTCAATTTAGGGAAAGTTCCCGTC-ATTTT
          1 AAGTTTTTAAATT-GGGAAAGTTCCCATCAATTTT

            *      
        904 CAGTTTT
          1 AAGTTTT

        911 AGTTTTCAAA


Statistics
Matches: 99,  Mismatches: 7, Indels: 16
        0.81            0.06        0.13

Matches are distributed among these distances:
  33    4  0.04
  34   25  0.25
  35   31  0.31
  36    2  0.02
  37   11  0.11
  38   18  0.18
  39    8  0.08

ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42


Consensus pattern (34 bp):   
AAGTTTTTAAATTGGGAAAGTTCCCATCAATTTT

Found at i:857 original size:38 final size:37

Alignment explanation


    Indices: 759--870  Score: 149
    Period size: 38  Copynumber: 3.0  Consensus size: 37

        749 TTTCATCATG

                        *                 *   *  
        759 TTCAAAGTTTTTTAATTGGGAAAGTTCCCACCA-ATT
          1 TTCAAAGTTTTTAAATTGGGAAAGTTCCCATCAGTTT

                                                   
        795 TT--AAGTTTTTCAAATTGGGAAAGTTCCCATTCAGTTT
          1 TTCAAAGTTTTT-AAATTGGGAAAGTTCCCA-TCAGTTT

                                                  
        832 TTCAAAGTTTTTAAATTGGGAAAGTTCCCATCAAGTTT
          1 TTCAAAGTTTTTAAATTGGGAAAGTTCCCATC-AGTTT

             
        870 T
          1 T

        871 AGTTTTCAAT


Statistics
Matches: 67,  Mismatches: 3, Indels: 10
        0.84            0.04        0.12

Matches are distributed among these distances:
  34    8  0.12
  35   17  0.25
  36    4  0.06
  37    6  0.09
  38   24  0.36
  39    8  0.12

ACGTcount: A:0.29, C:0.14, G:0.15, T:0.41


Consensus pattern (37 bp):   
TTCAAAGTTTTTAAATTGGGAAAGTTCCCATCAGTTT

Found at i:888 original size:73 final size:73

Alignment explanation


    Indices: 759--895  Score: 215
    Period size: 73  Copynumber: 1.9  Consensus size: 73

        749 TTTCATCATG

                        *                                                    
        759 TTCAAAGTTTTTTAATTGGGAAAGTTCCCACCAATTTTAAGTTTTTCAAATTGGGAAAGTTCCCA
          1 TTCAAAGTTTTTAAATTGGGAAAGTTCCCACCAATTTTAAGTTTTTCAAATTGGGAAAGTTCCCA

                    
        824 TTCAGTTT
         66 TTCAGTTT

                                          *                   *              
        832 TTCAAAGTTTTTAAATTGGGAAAGTTCCCATCAAGTTTT-AG-TTTTCAATTTAGGGAAAGTTCC
          1 TTCAAAGTTTTTAAATTGGGAAAGTTCCCACCAA-TTTTAAGTTTTTCAAATT-GGGAAAGTTCC

             
        895 C
         64 C

        896 GTCATTTTCA


Statistics
Matches: 59,  Mismatches: 3, Indels: 4
        0.89            0.05        0.06

Matches are distributed among these distances:
  72    9  0.15
  73   46  0.78
  74    4  0.07

ACGTcount: A:0.29, C:0.15, G:0.16, T:0.40


Consensus pattern (73 bp):   
TTCAAAGTTTTTAAATTGGGAAAGTTCCCACCAATTTTAAGTTTTTCAAATTGGGAAAGTTCCCA
TTCAGTTT

Found at i:934 original size:74 final size:71

Alignment explanation


    Indices: 775--937  Score: 181
    Period size: 74  Copynumber: 2.2  Consensus size: 71

        765 GTTTTTTAAT

                          *                                                  
        775 TGGGAAAGTTCCCACCAATTTTAAGTTTTTCAAATTGGGAAAGTTCCCATTCAGTTTTTCAAAGT
          1 TGGGAAAGTTCCCATCAATTTTAAGTTTTTCAAATTGGGAAAGTTCCCATTCAGTTTTT--AAGT

               *   *
        840 TTTTAAAT
         64 TTTCAAAA

                                              *                              
        848 TGGGAAAGTTCCCATCAAGTTTT-AG-TTTTCAATTTAGGGAAAGTTCCCGTCATTTTCAG-TTT
          1 TGGGAAAGTTCCCATCAA-TTTTAAGTTTTTCAAATT-GGGAAAGTT-CC--CA--TTCAGTTTT

                         
        910 T-AGTTTTCAAAA
         59 TAAGTTTTCAAAA

                            
        922 TGGGAAAGTTCCCATC
          1 TGGGAAAGTTCCCATC

        938 CAAAGCATTT


Statistics
Matches: 79,  Mismatches: 4, Indels: 13
        0.82            0.04        0.14

Matches are distributed among these distances:
  72    9  0.11
  73   28  0.35
  74   31  0.39
  76    2  0.03
  77    4  0.05
  78    5  0.06

ACGTcount: A:0.28, C:0.16, G:0.17, T:0.39


Consensus pattern (71 bp):   
TGGGAAAGTTCCCATCAATTTTAAGTTTTTCAAATTGGGAAAGTTCCCATTCAGTTTTTAAGTTT
TCAAAA
Done.