Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015348.1 Corchorus olitorius cultivar O-4 contig15381, 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: 23196
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.30


Found at i:5474 original size:41 final size:42

Alignment explanation


    Indices: 5398--5477  Score: 119
    Period size: 41  Copynumber: 1.9  Consensus size: 42

       5388 ATCTGTCCAT

                                                       
       5398 GTCATCTGTCCACGTGGCTCAAAAAGCCACGTGGCCAAACCAC
          1 GTCATCTGTCCACGTGGC-CAAAAAGCCACGTGGCCAAACCAC

                                         *         
       5441 GTCATCT-TCCCACGTGG-CAAAAAGCCATGTGGCCAAA
          1 GTCATCTGT-CCACGTGGCCAAAAAGCCACGTGGCCAAA

       5478 ATATTGTGGG


Statistics
Matches: 35,  Mismatches: 1, Indels: 4
        0.88            0.03        0.10

Matches are distributed among these distances:
  41   19  0.54
  42    1  0.03
  43   15  0.43

ACGTcount: A:0.29, C:0.33, G:0.21, T:0.17


Consensus pattern (42 bp):   
GTCATCTGTCCACGTGGCCAAAAAGCCACGTGGCCAAACCAC

Found at i:10514 original size:52 final size:52

Alignment explanation


    Indices: 10417--10515  Score: 130
    Period size: 52  Copynumber: 1.9  Consensus size: 52

      10407 AAAATTTTAA

                                                 ** *           
      10417 ATTTTTTTACTGAAAATTTAATATTTTTCTGGGAAAATTTTTTTTGGGTTTT
          1 ATTTTTTTACTGAAAATTTAATATTTTTCTGGGAAAAAATATTTTGGGTTTT

                    *                                        
      10469 ATTTTTTTCCTGAAAATTTAA-ACTTTTT-TGGGGAAAAAATATTTTGG
          1 ATTTTTTTACTGAAAATTTAATA-TTTTTCT-GGGAAAAAATATTTTGG

      10516 CCACGTGGCT


Statistics
Matches: 41,  Mismatches: 4, Indels: 4
        0.84            0.08        0.08

Matches are distributed among these distances:
  51    2  0.05
  52   39  0.95

ACGTcount: A:0.28, C:0.05, G:0.14, T:0.53


Consensus pattern (52 bp):   
ATTTTTTTACTGAAAATTTAATATTTTTCTGGGAAAAAATATTTTGGGTTTT

Found at i:10556 original size:41 final size:42

Alignment explanation


    Indices: 10511--10594  Score: 127
    Period size: 41  Copynumber: 2.0  Consensus size: 42

      10501 GAAAAAATAT

                                                       
      10511 TTTGGCCACGTGGCTTTTT-GCCACGTGGGA-AGATGACGTGG
          1 TTTGGCCACGTGGCTTTTTAGCCACGT-GGACAGATGACGTGG

                                                  *    
      10552 TTTGGCCACGTGGCTTTTTGAGCCACGTGGACAGATGATGTGG
          1 TTTGGCCACGTGGCTTTTT-AGCCACGTGGACAGATGACGTGG

      10595 ACAAATTTGA


Statistics
Matches: 39,  Mismatches: 1, Indels: 4
        0.89            0.02        0.09

Matches are distributed among these distances:
  41   19  0.49
  42    3  0.08
  43   17  0.44

ACGTcount: A:0.15, C:0.19, G:0.36, T:0.30


Consensus pattern (42 bp):   
TTTGGCCACGTGGCTTTTTAGCCACGTGGACAGATGACGTGG

Found at i:17839 original size:109 final size:109

Alignment explanation


    Indices: 17648--17863  Score: 369
    Period size: 109  Copynumber: 2.0  Consensus size: 109

      17638 CTATTATATA

                     *                                         *             
      17648 TATTATTATTAATTGTGTGGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAACAATA
          1 TATTATTATCAATTGTGTGGTTTATTCAATTGAACCTATTAAATAAGCACAAATACCAAACAATA

                                  *       *             
      17713 CAAAATGCAATGAACTATTGGATTTAAAGACAAATACAAGCACC
         66 CAAAATGCAATGAACTATTGGACTTAAAGAAAAATACAAGCACC

                              *                                    *         
      17757 TATTATTATCAATTGTGTTGTTTATTCAATTGAACCTATTAAATAAGCACAAATATCAAACAATA
          1 TATTATTATCAATTGTGTGGTTTATTCAATTGAACCTATTAAATAAGCACAAATACCAAACAATA

                *                                     
      17822 CAAAGTGCAATGAACTATTGGACTTAAAGAAAAATACAAGCA
         66 CAAAATGCAATGAACTATTGGACTTAAAGAAAAATACAAGCA

      17864 TCAAAATGAC


Statistics
Matches: 100,  Mismatches: 7, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
 109  100  1.00

ACGTcount: A:0.44, C:0.14, G:0.11, T:0.31


Consensus pattern (109 bp):   
TATTATTATCAATTGTGTGGTTTATTCAATTGAACCTATTAAATAAGCACAAATACCAAACAATA
CAAAATGCAATGAACTATTGGACTTAAAGAAAAATACAAGCACC
Done.