Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01000684.1 Corchorus capsularis cultivar CVL-1 contig00684, 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: 8721
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34


Found at i:446 original size:16 final size:17

Alignment explanation


    Indices: 405--473  Score: 54
    Period size: 16  Copynumber: 4.2  Consensus size: 17

        395 TTAAACGGTA

                             
        405 AAAAAGAAATTAAA-AG
          1 AAAAAGAAATTAAATAG

            *  ***           
        421 GAATTTAAATTAAAT-G
          1 AAAAAGAAATTAAATAG

                             *
        437 AAAAAGAAA-TAAATACA
          1 AAAAAGAAATTAAATA-G

                           * 
        454 AAAAAGAAATTAAATGG
          1 AAAAAGAAATTAAATAG

               
        471 AAA
          1 AAA

        474 TTAAATAAAA


Statistics
Matches: 38,  Mismatches: 11, Indels: 7
        0.68            0.20        0.12

Matches are distributed among these distances:
  15    5  0.13
  16   16  0.42
  17   12  0.32
  18    5  0.13

ACGTcount: A:0.68, C:0.01, G:0.12, T:0.19


Consensus pattern (17 bp):   
AAAAAGAAATTAAATAG

Found at i:8691 original size:2 final size:2

Alignment explanation


    Indices: 8669--8720  Score: 77
    Period size: 2  Copynumber: 26.0  Consensus size: 2

       8659 AATGGACCCC

                     *        *     *                                     
       8669 AT AT AT CT AT AT CT AT TT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

                          
       8711 AT AT AT AT AT
          1 AT AT AT AT AT

       8721 T


Statistics
Matches: 44,  Mismatches: 6, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
   2   44  1.00

ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52


Consensus pattern (2 bp):   
AT

Done.