Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000237.1 Corchorus olitorius cultivar O-4 contig00237, 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: 1847
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36


Found at i:421 original size:138 final size:138

Alignment explanation


    Indices: 138--390  Score: 355
    Period size: 138  Copynumber: 1.8  Consensus size: 138

        128 ATTTTTTTAA

                 *                                                        *  
        138 TTAAATTAGTAAAATGGTAAAAATAAAATAGGTATAAATATTAGATTTAATTAAATAAAAATGGA
          1 TTAAAATAGTAAAATGGTAAAAATAAAATAGGTATAAATATTAGATTTAATTAAATAAAAATAGA

                                                   * **                 **   
        203 GCATTTTAGTTGAGTAAAACTATAAAAGTATATTTAAAAGATTCTAATATATATAAGTTTTTCAA
         66 GCATTTTAGTTGAGTAAAACTATAAAAGTATATTTAAAAAAAACTAATATATATAAGTTTAACAA

                    
        268 TTAAAAAT
        131 TTAAAAAT

                                    *      *                                 
        276 TTAAAATAGTAAAATGGTAAAAATTAAATAGTTATAAGGATATTAGATTTAATTAAATAAAAATA
          1 TTAAAATAGTAAAATGGTAAAAATAAAATAGGTATAA--ATATTAGATTTAATTAAATAAAAATA

                *                          *                   
        341 GAG-TTTTTAGTTGAGTAAAACTATAAAAGTTTATTTCTCAAAAAAAACTA
         64 GAGCATTTTAGTTGAGTAAAACTATAAAAGTATA-TT-T-AAAAAAAACTA

        391 TAAAAATTTA


Statistics
Matches: 101,  Mismatches: 9, Indels: 6
        0.87            0.08        0.05

Matches are distributed among these distances:
 138   34  0.34
 139   28  0.28
 140   30  0.30
 141    1  0.01
 142    8  0.08

ACGTcount: A:0.50, C:0.03, G:0.11, T:0.36


Consensus pattern (138 bp):   
TTAAAATAGTAAAATGGTAAAAATAAAATAGGTATAAATATTAGATTTAATTAAATAAAAATAGA
GCATTTTAGTTGAGTAAAACTATAAAAGTATATTTAAAAAAAACTAATATATATAAGTTTAACAA
TTAAAAAT

Found at i:1226 original size:36 final size:35

Alignment explanation


    Indices: 1155--1260  Score: 160
    Period size: 35  Copynumber: 3.0  Consensus size: 35

       1145 GAATTTCATC

                     *                 *       
       1155 AAGTTTTTTTAATTGGGAAAGTTCCCACCAGTTTT
          1 AAGTTTTTTAAATTGGGAAAGTTCCCATCAGTTTT

                                                
       1190 AAGTTTTTTAAATTGGGAAAGTTCCCATCAGCTTTT
          1 AAGTTTTTTAAATTGGGAAAGTTCCCATCAG-TTTT

                    *                           
       1226 AAG-TTTTCAAATTGGGAAAGTTCCCATTCAGTTTT
          1 AAGTTTTTTAAATTGGGAAAGTTCCCA-TCAGTTTT

       1261 TCAAAGTTCT


Statistics
Matches: 66,  Mismatches: 3, Indels: 4
        0.90            0.04        0.05

Matches are distributed among these distances:
  35   55  0.83
  36   11  0.17

ACGTcount: A:0.27, C:0.14, G:0.17, T:0.42


Consensus pattern (35 bp):   
AAGTTTTTTAAATTGGGAAAGTTCCCATCAGTTTT
Done.