Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022112.1 Corchorus olitorius cultivar O-4 contig22145, 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, 841

Length: 1402
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.30


Found at i:734 original size:25 final size:26

Alignment explanation


    Indices: 701--792  Score: 100
    Period size: 25  Copynumber: 3.5  Consensus size: 26

        691 GAAAAACGCA

                                 *    
        701 AAAACTTTTTTTTATGACGCAGAAAC
          1 AAAACTTTTTTTTATGACGCAAAAAC

                                     *
        727 AAAA-TTTTTTTTATGACGCAAAAAT
          1 AAAACTTTTTTTTATGACGCAAAAAC

                             *            
        752 ATATATA-TTTTTTTT-CGACGCAAAACAC
          1 A-A-A-ACTTTTTTTTATGACGCAAAA-AC

                         
        780 AAAACTTTTTTTT
          1 AAAACTTTTTTTT

        793 CTTTGACGCA


Statistics
Matches: 57,  Mismatches: 4, Indels: 10
        0.80            0.06        0.14

Matches are distributed among these distances:
  25   21  0.37
  26   14  0.25
  27   11  0.19
  28   11  0.19

ACGTcount: A:0.38, C:0.13, G:0.08, T:0.41


Consensus pattern (26 bp):   
AAAACTTTTTTTTATGACGCAAAAAC

Found at i:1250 original size:16 final size:15

Alignment explanation


    Indices: 1213--1253  Score: 73
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       1203 CAGAGGTTGG

                           
       1213 CAGAAAACAATTAAA
          1 CAGAAAACAATTAAA

                           
       1228 CAGAAAACAATTAAA
          1 CAGAAAACAATTAAA

                       
       1243 CTAGAAAACAA
          1 C-AGAAAACAA

       1254 AGCAAAGTAA


Statistics
Matches: 25,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  15   16  0.64
  16    9  0.36

ACGTcount: A:0.66, C:0.15, G:0.07, T:0.12


Consensus pattern (15 bp):   
CAGAAAACAATTAAA
Done.