Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021960.1 Corchorus olitorius cultivar O-4 contig21993, 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: 12771
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35


Found at i:4180 original size:16 final size:16

Alignment explanation


    Indices: 4159--4189  Score: 53
    Period size: 16  Copynumber: 1.9  Consensus size: 16

       4149 CTGCGACGGA

                  *         
       4159 TTTGTAGGTCGCATTT
          1 TTTGTACGTCGCATTT

                           
       4175 TTTGTACGTCGCATT
          1 TTTGTACGTCGCATT

       4190 AGACATGTTT


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  16   14  1.00

ACGTcount: A:0.13, C:0.16, G:0.23, T:0.48


Consensus pattern (16 bp):   
TTTGTACGTCGCATTT

Found at i:8839 original size:3 final size:3

Alignment explanation


    Indices: 8831--8855  Score: 50
    Period size: 3  Copynumber: 8.3  Consensus size: 3

       8821 TACTTGTGTG

                                             
       8831 TAA TAA TAA TAA TAA TAA TAA TAA T
          1 TAA TAA TAA TAA TAA TAA TAA TAA T

       8856 GATGCAATAA


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   22  1.00

ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36


Consensus pattern (3 bp):   
TAA

Found at i:9240 original size:20 final size:20

Alignment explanation


    Indices: 9215--9252  Score: 67
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       9205 CCTTTCCTGA

                     *          
       9215 AGAAATCTTTGTTCAATACT
          1 AGAAATCTTGGTTCAATACT

                              
       9235 AGAAATCTTGGTTCAATA
          1 AGAAATCTTGGTTCAATA

       9253 TTCTGGTCTT


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  20   17  1.00

ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37


Consensus pattern (20 bp):   
AGAAATCTTGGTTCAATACT
Done.