Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016763.1 Corchorus olitorius cultivar O-4 contig16796, 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: 15605
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31


Found at i:7314 original size:17 final size:17

Alignment explanation


    Indices: 7275--7317  Score: 61
    Period size: 18  Copynumber: 2.5  Consensus size: 17

       7265 CGGGAAATTC

                     *       
       7275 AAAA-AAATGAAAATAA
          1 AAAACAAATAAAAATAA

                              
       7291 AACAACAAATAAAAATAA
          1 AA-AACAAATAAAAATAA

                     
       7309 AAAACAAAT
          1 AAAACAAAT

       7318 CCAAGTTCAA


Statistics
Matches: 24,  Mismatches: 1, Indels: 3
        0.86            0.04        0.11

Matches are distributed among these distances:
  16    2  0.08
  17    9  0.38
  18   13  0.54

ACGTcount: A:0.79, C:0.07, G:0.02, T:0.12


Consensus pattern (17 bp):   
AAAACAAATAAAAATAA

Found at i:7944 original size:12 final size:12

Alignment explanation


    Indices: 7923--7954  Score: 55
    Period size: 12  Copynumber: 2.7  Consensus size: 12

       7913 AAAAACCTAT

                 *      
       7923 TATATATATATA
          1 TATATTTATATA

                        
       7935 TATATTTATATA
          1 TATATTTATATA

                    
       7947 TATATTTA
          1 TATATTTA

       7955 GATGAGATGA


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  12   19  1.00

ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56


Consensus pattern (12 bp):   
TATATTTATATA

Found at i:8117 original size:40 final size:40

Alignment explanation


    Indices: 8062--8143  Score: 164
    Period size: 40  Copynumber: 2.0  Consensus size: 40

       8052 AACCATGACA

                                                    
       8062 TGAAAGTTAAGGGAGATATAATAATCAAATATGTAGTTTT
          1 TGAAAGTTAAGGGAGATATAATAATCAAATATGTAGTTTT

                                                    
       8102 TGAAAGTTAAGGGAGATATAATAATCAAATATGTAGTTTT
          1 TGAAAGTTAAGGGAGATATAATAATCAAATATGTAGTTTT

              
       8142 TG
          1 TG

       8144 TCTAAGTTAA


Statistics
Matches: 42,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  40   42  1.00

ACGTcount: A:0.41, C:0.02, G:0.21, T:0.35


Consensus pattern (40 bp):   
TGAAAGTTAAGGGAGATATAATAATCAAATATGTAGTTTT
Done.