genome.fa.s11996.2.7.7.80.10.50.1000.txt.html

Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011996.1 Corchorus olitorius cultivar O-4 contig12029, 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: 19689
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30


Found at i:458 original size:205 final size:201

Alignment explanation


    Indices: 69--479  Score: 725
    Period size: 205  Copynumber: 2.0  Consensus size: 201

         59 TGCTTAATAC

                                *                                            
         69 TTTATAAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
          1 TTTATAAATGGTGAATGTTAATAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA

                          *              *                                   
        134 GATACAACACATTATTATTATATATAAAACTATACCAAAAAAAGTAGTTGAACATTAGTGGTTGA
         66 GATACAACACATTACTATTATATATAAAAATATACCAAAAAAAGTAGTTGAACATTAGTGGTTGA

                                                                             
        199 TTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATCC
        131 TTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATT-AAGATCC

                   
        264 G-ATTTA
        195 GAATTTA

                 *                                                           
        270 TTTATCAATGGTGAATGTTAATAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
          1 TTTATAAATGGTGAATGTTAATAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA

                                                           *                 
        335 GATACAACACATTACTATTATATATATAGAAATATACCAAAAAAAAATTAGTTGAACATTAGTGG
         66 GATACAACACATTACTATTATATATA-A-AAATATACC--AAAAAAAGTAGTTGAACATTAGTGG

                                                                             
        400 TTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGA
        127 TTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGA

                      
        465 TCCGAATTTA
        192 TCCGAATTTA

                 
        475 TTTAT
          1 TTTAT

        480 TATTAAGAAA


Statistics
Matches: 200,  Mismatches: 5, Indels: 6
        0.95            0.02        0.03

Matches are distributed among these distances:
 201   88  0.44
 202    1  0.00
 203    8  0.04
 204    8  0.04
 205   95  0.47

ACGTcount: A:0.45, C:0.08, G:0.11, T:0.36


Consensus pattern (201 bp):   
TTTATAAATGGTGAATGTTAATAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
GATACAACACATTACTATTATATATAAAAATATACCAAAAAAAGTAGTTGAACATTAGTGGTTGA
TTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGATCCG
AATTTA

Found at i:10866 original size:13 final size:13

Alignment explanation


    Indices: 10848--10873  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

      10838 CTAATATATA

                         
      10848 GACCCAATTAATT
          1 GACCCAATTAATT

                         
      10861 GACCCAATTAATT
          1 GACCCAATTAATT

      10874 ATATAGACCC


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.38, C:0.23, G:0.08, T:0.31


Consensus pattern (13 bp):   
GACCCAATTAATT
Done.