Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01006901.1 Corchorus olitorius cultivar O-4 contig06926, 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, 708

Length: 1181
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.38


Found at i:393 original size:16 final size:16

Alignment explanation


    Indices: 374--415  Score: 75
    Period size: 16  Copynumber: 2.6  Consensus size: 16

        364 GGGCTGCCTT

                       *    
        374 GGGTTCGGGTATTTTC
          1 GGGTTCGGGTAATTTC

                            
        390 GGGTTCGGGTAATTTC
          1 GGGTTCGGGTAATTTC

                      
        406 GGGTTCGGGT
          1 GGGTTCGGGT

        416 TCGGGCGGGT


Statistics
Matches: 25,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  16   25  1.00

ACGTcount: A:0.07, C:0.12, G:0.43, T:0.38


Consensus pattern (16 bp):   
GGGTTCGGGTAATTTC

Found at i:656 original size:29 final size:31

Alignment explanation


    Indices: 624--690  Score: 111
    Period size: 31  Copynumber: 2.2  Consensus size: 31

        614 ATGCAATTTG

                                           
        624 GGATATAACGTTAC-AAAA-CAAGCAATTAA
          1 GGATATAACGTTACGAAAAGCAAGCAATTAA

                                 *         
        653 GGATATAACGTTACGAAAAGCGAGCAATTAA
          1 GGATATAACGTTACGAAAAGCAAGCAATTAA

                   
        684 GGATATA
          1 GGATATA

        691 GTCCGTTAGA


Statistics
Matches: 35,  Mismatches: 1, Indels: 2
        0.92            0.03        0.05

Matches are distributed among these distances:
  29   14  0.40
  30    4  0.11
  31   17  0.49

ACGTcount: A:0.48, C:0.12, G:0.19, T:0.21


Consensus pattern (31 bp):   
GGATATAACGTTACGAAAAGCAAGCAATTAA

Found at i:944 original size:31 final size:30

Alignment explanation


    Indices: 819--955  Score: 141
    Period size: 31  Copynumber: 4.5  Consensus size: 30

        809 GCCTAACTGA

                      *                    
        819 TTATATCCTTGATTGCTTGAAATAGGAAACG
          1 TTATATCCTTAATTGCTTGAAATA-GAAACG

             *                             
        850 TCATATCCTTAATTGCTTGAAATAGAAAACG
          1 TTATATCCTTAATTGCTTGAAATAG-AAACG

                   *            ** * *    
        881 TTATATCATTAATTGCTTG-TTTTGTAACG
          1 TTATATCCTTAATTGCTTGAAATAGAAACG

                               ** *        
        910 TTATATCCTTAATTGCTTGTGACAGCAAACG
          1 TTATATCCTTAATTGCTTGAAATAG-AAACG

                     *     
        941 TTATATCCTAAATTG
          1 TTATATCCTTAATTG

        956 ATTATTTGAC


Statistics
Matches: 88,  Mismatches: 15, Indels: 6
        0.81            0.14        0.06

Matches are distributed among these distances:
  29   22  0.25
  30    4  0.05
  31   62  0.70

ACGTcount: A:0.31, C:0.15, G:0.15, T:0.39


Consensus pattern (30 bp):   
TTATATCCTTAATTGCTTGAAATAGAAACG
Done.