Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021955.1 Corchorus olitorius cultivar O-4 contig21988, 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: 2890
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28


Found at i:692 original size:112 final size:108

Alignment explanation


    Indices: 355--705  Score: 533
    Period size: 108  Copynumber: 3.2  Consensus size: 108

        345 CCAATCAACG

                                                                             
        355 TTGAAGAGAGAGTGAAAGGAAAGGAATTTCCTATAGAATAAAACAAACAAAAATTTATTCCT-TG
          1 TTGAAGAGAGAGTGAAAGGAAAGGAATTTCCTATAGAATAAAACAAACAAAAATTTATT-CTATG

              **                                         
        419 CAACTTCTAAAATAAGAATCAAACGAAAGGAAATTTAAAGAGAGA
         65 -ATTTTCTAAAATAAGAATCAAACGAAAGGAAATTTAAAGAGAGA

                         *                                              *   *
        464 TTGAAGAGAGAGTTAAAGGAAAGGAATTTCCTATAGAATAAAACAAACAAAAATTTATTCAATGT
          1 TTGAAGAGAGAGTGAAAGGAAAGGAATTTCCTATAGAATAAAACAAACAAAAATTTATTCTATGA

                                                       
        529 TTTTCTAAAATAAGAATCAAACGAAAGGAAATTTAAAGAGAGA
         66 TTTTCTAAAATAAGAATCAAACGAAAGGAAATTTAAAGAGAGA

                                            * *                     *        
        572 TTGAAGAGAGAGTGAAAGGAAAGGAATTTCCTTTCGAATAAAACAAACAAAAATTAAAGGTTCTT
          1 TTGAAGAGAGAGTGAAAGGAAAGGAATTTCCTATAGAATAAAACAAACAAAAATT-TA--TTC-T

               *                **                         
        637 ATGGTTTTCTAAAATAAGAAAAAAACGAAAGGAAATTTAAAGAGAGA
         62 ATGATTTTCTAAAATAAGAATCAAACGAAAGGAAATTTAAAGAGAGA

              *                   
        684 TTAAAGAGAGAGTGAAAGGAAA
          1 TTGAAGAGAGAGTGAAAGGAAA

        706 TTTACCAGGT


Statistics
Matches: 223,  Mismatches: 14, Indels: 7
        0.91            0.06        0.03

Matches are distributed among these distances:
 108   94  0.42
 109   61  0.27
 111    3  0.01
 112   65  0.29

ACGTcount: A:0.51, C:0.08, G:0.19, T:0.23


Consensus pattern (108 bp):   
TTGAAGAGAGAGTGAAAGGAAAGGAATTTCCTATAGAATAAAACAAACAAAAATTTATTCTATGA
TTTTCTAAAATAAGAATCAAACGAAAGGAAATTTAAAGAGAGA

Found at i:2122 original size:21 final size:21

Alignment explanation


    Indices: 2096--2135  Score: 62
    Period size: 21  Copynumber: 1.9  Consensus size: 21

       2086 AAACATTAAG

                  *  *           
       2096 ATATTCTATTAAACATTTGTA
          1 ATATTCCATAAAACATTTGTA

                               
       2117 ATATTCCATAAAACATTTG
          1 ATATTCCATAAAACATTTG

       2136 AAACCAACAA


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  21   17  1.00

ACGTcount: A:0.40, C:0.12, G:0.05, T:0.42


Consensus pattern (21 bp):   
ATATTCCATAAAACATTTGTA
Done.