Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022926.1 Corchorus olitorius cultivar O-4 contig22959, 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: 2734
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.38


Found at i:441 original size:204 final size:208

Alignment explanation


    Indices: 70--486  Score: 736
    Period size: 204  Copynumber: 2.0  Consensus size: 208

         60 GCTTAATAAC

                                                   *      *                  
         70 TTTATCAATGGTGAATGATTATTAATTTTTTAAGTCTAAGATTAATTTAACAAAGTTGTAGTGAA
          1 TTTATCAATGGTGAATGATTATTAATTTTTTAAGTCTAAAATTAATCTAACAAAGTTGTAGTGAA

                             *                                               
        135 TAAGATACAACACATTATTATTATATATAAAAACTTATACCAAAAAAAAATTAGTTGAACATTAG
         66 TAAGATACAACACATTACTATTATATATAAAAACTTATACCAAAAAAAAATTAGTTGAACATTAG

                                                                             
        200 TGGTTCATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTA
        131 TGGTTCATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTA

                 *       
        265 AAGATTCGATTTA
        196 AAGATCCGATTTA

                                                                             
        278 TTTATCAATGGTGAATG-TTATTAATTTTTTAAGTCTAAAATT-A-CTAACAAAGTTGTAGTGAA
          1 TTTATCAATGGTGAATGATTATTAATTTTTTAAGTCTAAAATTAATCTAACAAAGTTGTAGTGAA

                                           *                                 
        340 TAAGATACAACACATTACTATTATATATATAGAAC-TATACC-AAAAAAAATTAGTTGAACATTA
         66 TAAGATACAACACATTACTATTATATATA-AAAACTTATACCAAAAAAAAATTAGTTGAACATTA

                  *                                                          
        403 GTGGTTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATT
        130 GTGGTTCATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATT

                          
        468 AAAGATCCGATTTA
        195 AAAGATCCGATTTA

                 
        482 TTTAT
          1 TTTAT

        487 TATTAAGGAA


Statistics
Matches: 202,  Mismatches: 6, Indels: 6
        0.94            0.03        0.03

Matches are distributed among these distances:
 204  104  0.51
 205   52  0.26
 206    5  0.02
 207   24  0.12
 208   17  0.08

ACGTcount: A:0.45, C:0.08, G:0.10, T:0.37


Consensus pattern (208 bp):   
TTTATCAATGGTGAATGATTATTAATTTTTTAAGTCTAAAATTAATCTAACAAAGTTGTAGTGAA
TAAGATACAACACATTACTATTATATATAAAAACTTATACCAAAAAAAAATTAGTTGAACATTAG
TGGTTCATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTA
AAGATCCGATTTA

Found at i:615 original size:17 final size:17

Alignment explanation


    Indices: 590--649  Score: 54
    Period size: 17  Copynumber: 3.5  Consensus size: 17

        580 AAAGAATACC

                *            
        590 TAAGAATTTAATTAATG
          1 TAAGTATTTAATTAATG

                       *      
        607 TAAGTATTTCAGTT-AT-
          1 TAAGTATTT-AATTAATG

                               
        623 TATAGTA-TTACATTAATG
          1 TA-AGTATTTA-ATTAATG

                     
        641 TAAGTATTT
          1 TAAGTATTT

        650 TAGTTATTAT


Statistics
Matches: 34,  Mismatches: 3, Indels: 11
        0.71            0.06        0.23

Matches are distributed among these distances:
  15    1  0.03
  16    6  0.18
  17   20  0.59
  18    7  0.21

ACGTcount: A:0.38, C:0.03, G:0.12, T:0.47


Consensus pattern (17 bp):   
TAAGTATTTAATTAATG

Found at i:1805 original size:16 final size:16

Alignment explanation


    Indices: 1784--1815  Score: 55
    Period size: 16  Copynumber: 2.0  Consensus size: 16

       1774 AAAAGGAGAT

                            
       1784 TAATATAATGAATTTA
          1 TAATATAATGAATTTA

                       *    
       1800 TAATATAATGACTTTA
          1 TAATATAATGAATTTA

       1816 ATACCAATCA


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  16   15  1.00

ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44


Consensus pattern (16 bp):   
TAATATAATGAATTTA
Done.