Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014524.1 Corchorus olitorius cultivar O-4 contig14557, 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: 26357
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32


Found at i:202 original size:26 final size:26

Alignment explanation


    Indices: 173--262  Score: 74
    Period size: 26  Copynumber: 3.3  Consensus size: 26

        163 CTAATCCAAA

                *                     
        173 TTAAGAAATTACCTTAAATAACCTAC
          1 TTAACAAATTACCTTAAATAACCTAC

                       ** *            * *
        199 TTAACAAA-TAGATGAGAATCTAACCCAAA
          1 TTAACAAATTACCTTA-AA--TAA-CCTAC

                *                     
        228 TTAAGAAATTACCTTAAATAACCTAC
          1 TTAACAAATTACCTTAAATAACCTAC

                     
        254 TTAACAAAT
          1 TTAACAAAT

        263 AAATAAATAA


Statistics
Matches: 46,  Mismatches: 13, Indels: 10
        0.67            0.19        0.14

Matches are distributed among these distances:
  25    4  0.09
  26   20  0.43
  27    3  0.07
  28    3  0.07
  29   12  0.26
  30    4  0.09

ACGTcount: A:0.49, C:0.18, G:0.06, T:0.28


Consensus pattern (26 bp):   
TTAACAAATTACCTTAAATAACCTAC

Found at i:221 original size:55 final size:55

Alignment explanation


    Indices: 155--263  Score: 209
    Period size: 55  Copynumber: 2.0  Consensus size: 55

        145 GAACATCTAA

                        *                                          
        155 ATGAGAATCTAATCCAAATTAAGAAATTACCTTAAATAACCTACTTAACAAATAG
          1 ATGAGAATCTAACCCAAATTAAGAAATTACCTTAAATAACCTACTTAACAAATAG

                                                                  
        210 ATGAGAATCTAACCCAAATTAAGAAATTACCTTAAATAACCTACTTAACAAATA
          1 ATGAGAATCTAACCCAAATTAAGAAATTACCTTAAATAACCTACTTAACAAATA

        264 AATAAATAAA


Statistics
Matches: 53,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  55   53  1.00

ACGTcount: A:0.50, C:0.17, G:0.06, T:0.27


Consensus pattern (55 bp):   
ATGAGAATCTAACCCAAATTAAGAAATTACCTTAAATAACCTACTTAACAAATAG

Found at i:8533 original size:35 final size:35

Alignment explanation


    Indices: 8487--8555  Score: 102
    Period size: 35  Copynumber: 2.0  Consensus size: 35

       8477 AGACTTCTCG

                                               
       8487 TGAGTTAACTTATGTTACACGGATTCTTCACTTTC
          1 TGAGTTAACTTATGTTACACGGATTCTTCACTTTC

                            *** *             
       8522 TGAGTTAACTTATGTTGTGCTGATTCTTCACTTT
          1 TGAGTTAACTTATGTTACACGGATTCTTCACTTT

       8556 ATGATATTCG


Statistics
Matches: 30,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  35   30  1.00

ACGTcount: A:0.20, C:0.17, G:0.16, T:0.46


Consensus pattern (35 bp):   
TGAGTTAACTTATGTTACACGGATTCTTCACTTTC

Found at i:11675 original size:33 final size:33

Alignment explanation


    Indices: 11633--11699  Score: 134
    Period size: 33  Copynumber: 2.0  Consensus size: 33

      11623 TAATTTTGCC

                                             
      11633 CAAAAGTTAGTTAGGGACAGGAAAAGCAACTTA
          1 CAAAAGTTAGTTAGGGACAGGAAAAGCAACTTA

                                             
      11666 CAAAAGTTAGTTAGGGACAGGAAAAGCAACTTA
          1 CAAAAGTTAGTTAGGGACAGGAAAAGCAACTTA

             
      11699 C
          1 C

      11700 CATGTCACGC


Statistics
Matches: 34,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  33   34  1.00

ACGTcount: A:0.45, C:0.13, G:0.24, T:0.18


Consensus pattern (33 bp):   
CAAAAGTTAGTTAGGGACAGGAAAAGCAACTTA
Done.