Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001146.1 Corchorus olitorius cultivar O-4 contig01146, 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, 664

Length: 1108
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.41


Found at i:395 original size:21 final size:22

Alignment explanation


    Indices: 371--411  Score: 57
    Period size: 21  Copynumber: 1.9  Consensus size: 22

        361 GTTTATAATA

                *                 
        371 TTCTTGGGTCA-TCGGGTTATC
          1 TTCTCGGGTCATTCGGGTTATC

                     *          
        392 TTCTCGGGTTATTCGGGTTA
          1 TTCTCGGGTCATTCGGGTTA

        412 CGAGTTTGTC


Statistics
Matches: 17,  Mismatches: 2, Indels: 1
        0.85            0.10        0.05

Matches are distributed among these distances:
  21    9  0.53
  22    8  0.47

ACGTcount: A:0.10, C:0.17, G:0.29, T:0.44


Consensus pattern (22 bp):   
TTCTCGGGTCATTCGGGTTATC

Found at i:838 original size:105 final size:102

Alignment explanation


    Indices: 698--903  Score: 326
    Period size: 105  Copynumber: 2.0  Consensus size: 102

        688 CTTAAATTTT

                                                *                            
        698 TATAGTTTTACTCAACTAAAAACTCTATTTTTATTTGATTAAATCTAATATCCTTGTAAGTA-CT
          1 TATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCC-T-T-A-TACCT

                                                *     
        762 ATTTTATTTTTACCATTTTACT-ATTTTAATTAAAATACTTC
         62 ATTTTATTTTTACCATTTTACTAATTTT-ATTAAAAAACTTC

                                                                             
        803 TATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACCTATTT
          1 TATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACCTATTT

                    *                           
        868 TATTTTTATCATTTTACTAATTTTATTAAAAAACTT
         66 TATTTTTACCATTTTACTAATTTTATTAAAAAACTT

        904 AGATATATTA


Statistics
Matches: 96,  Mismatches: 3, Indels: 7
        0.91            0.03        0.07

Matches are distributed among these distances:
 101    2  0.02
 102   35  0.36
 103    6  0.06
 104    1  0.01
 105   52  0.54

ACGTcount: A:0.34, C:0.13, G:0.02, T:0.50


Consensus pattern (102 bp):   
TATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACCTATTT
TATTTTTACCATTTTACTAATTTTATTAAAAAACTTC

Found at i:845 original size:23 final size:26

Alignment explanation


    Indices: 786--845  Score: 63
    Period size: 23  Copynumber: 2.4  Consensus size: 26

        776 ATTTTACTAT

                                       
        786 TTTAATTAAAATACTTCTATAGTTTTA
          1 TTTAATTAAAATACTTCTATA-TTTTA

            * *  *                    
        813 CTCAACTAAAA-AC-TCTAT-TTTTA
          1 TTTAATTAAAATACTTCTATATTTTA

                      
        836 TTTAATTAAA
          1 TTTAATTAAA

        846 TCTAATATCC


Statistics
Matches: 27,  Mismatches: 6, Indels: 4
        0.73            0.16        0.11

Matches are distributed among these distances:
  23   12  0.44
  25    5  0.19
  26    2  0.07
  27    8  0.30

ACGTcount: A:0.40, C:0.12, G:0.02, T:0.47


Consensus pattern (26 bp):   
TTTAATTAAAATACTTCTATATTTTA

Found at i:877 original size:23 final size:23

Alignment explanation


    Indices: 851--894  Score: 54
    Period size: 23  Copynumber: 1.9  Consensus size: 23

        841 TTAAATCTAA

                *                   
        851 TATCCTTATACCT-ATTTTATTTT
          1 TATCATTATA-CTAATTTTATTTT

                   *             
        874 TATCATTTTACTAATTTTATT
          1 TATCATTATACTAATTTTATT

        895 AAAAAACTTA


Statistics
Matches: 18,  Mismatches: 2, Indels: 2
        0.82            0.09        0.09

Matches are distributed among these distances:
  22    2  0.11
  23   16  0.89

ACGTcount: A:0.25, C:0.14, G:0.00, T:0.61


Consensus pattern (23 bp):   
TATCATTATACTAATTTTATTTT
Done.