Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012717.1 Corchorus olitorius cultivar O-4 contig12750, 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: 10480
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30


Found at i:6010 original size:25 final size:25

Alignment explanation


    Indices: 5976--6025  Score: 100
    Period size: 25  Copynumber: 2.0  Consensus size: 25

       5966 TTGGTTGGAA

                                     
       5976 TTTAATCCTAAATTACCTTAATTAG
          1 TTTAATCCTAAATTACCTTAATTAG

                                     
       6001 TTTAATCCTAAATTACCTTAATTAG
          1 TTTAATCCTAAATTACCTTAATTAG

       6026 ATAAAGCTCT


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  25   25  1.00

ACGTcount: A:0.36, C:0.16, G:0.04, T:0.44


Consensus pattern (25 bp):   
TTTAATCCTAAATTACCTTAATTAG

Found at i:7181 original size:22 final size:21

Alignment explanation


    Indices: 7129--7183  Score: 62
    Period size: 19  Copynumber: 2.7  Consensus size: 21

       7119 GCTTCTTGGA

                                  
       7129 AATAATTCTTC-AATGGTCTTC
          1 AATAA-TCTTCAAATGGTCTTC

                          *      
       7150 -A-AATCTTCAAATTGTCTTC
          1 AATAATCTTCAAATGGTCTTC

                           
       7169 AATAAGTCTTCAAAT
          1 AATAA-TCTTCAAAT

       7184 ACGAACTTCG


Statistics
Matches: 29,  Mismatches: 1, Indels: 7
        0.78            0.03        0.19

Matches are distributed among these distances:
  18    5  0.17
  19   11  0.38
  20    2  0.07
  21    2  0.07
  22    9  0.31

ACGTcount: A:0.35, C:0.18, G:0.07, T:0.40


Consensus pattern (21 bp):   
AATAATCTTCAAATGGTCTTC

Found at i:8725 original size:30 final size:28

Alignment explanation


    Indices: 8686--8742  Score: 87
    Period size: 30  Copynumber: 2.0  Consensus size: 28

       8676 GTTTATTAAT

                *                         
       8686 GAAACTTGAAAATTAAAGACATAAGATAAA
          1 GAAAATTGAAAATTAAAG-CATAA-ATAAA

                                       
       8716 GAAAATTGAAAATTAAAGCATAAATAA
          1 GAAAATTGAAAATTAAAGCATAAATAA

       8743 CTAATCCTAA


Statistics
Matches: 26,  Mismatches: 1, Indels: 2
        0.90            0.03        0.07

Matches are distributed among these distances:
  28    4  0.15
  29    5  0.19
  30   17  0.65

ACGTcount: A:0.61, C:0.05, G:0.12, T:0.21


Consensus pattern (28 bp):   
GAAAATTGAAAATTAAAGCATAAATAAA
Done.