Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009205.1 Corchorus capsularis cultivar CVL-1 contig09226, 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: 62948
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33


Found at i:5321 original size:25 final size:25

Alignment explanation


    Indices: 5292--5343  Score: 104
    Period size: 25  Copynumber: 2.1  Consensus size: 25

       5282 TATGACAAAT

                                     
       5292 TTATTAGCAAAGGAAAAAGGAAGAA
          1 TTATTAGCAAAGGAAAAAGGAAGAA

                                     
       5317 TTATTAGCAAAGGAAAAAGGAAGAA
          1 TTATTAGCAAAGGAAAAAGGAAGAA

              
       5342 TT
          1 TT

       5344 GAACAAGGAC


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  25   27  1.00

ACGTcount: A:0.54, C:0.04, G:0.23, T:0.19


Consensus pattern (25 bp):   
TTATTAGCAAAGGAAAAAGGAAGAA

Found at i:12855 original size:3 final size:3

Alignment explanation


    Indices: 12847--12875  Score: 58
    Period size: 3  Copynumber: 9.7  Consensus size: 3

      12837 TGAAGCGTTT

                                                  
      12847 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
          1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT

      12876 TGTGTCTTTG


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   26  1.00

ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69


Consensus pattern (3 bp):   
TTA

Found at i:28926 original size:24 final size:24

Alignment explanation


    Indices: 28886--28934  Score: 82
    Period size: 25  Copynumber: 2.0  Consensus size: 24

      28876 ATAGTAGTAC

                                     
      28886 TTCAAAAAAAAATGTTTTACCATTA
          1 TTCAAAAAAAAATGTTTTACC-TTA

                                    
      28911 TTCAAAAAAAAA-GTTTTACCTTA
          1 TTCAAAAAAAAATGTTTTACCTTA

             
      28934 T
          1 T

      28935 ATATGTATAT


Statistics
Matches: 24,  Mismatches: 0, Indels: 2
        0.92            0.00        0.08

Matches are distributed among these distances:
  23    4  0.17
  24    8  0.33
  25   12  0.50

ACGTcount: A:0.47, C:0.12, G:0.04, T:0.37


Consensus pattern (24 bp):   
TTCAAAAAAAAATGTTTTACCTTA

Found at i:50592 original size:32 final size:32

Alignment explanation


    Indices: 50551--50650  Score: 200
    Period size: 32  Copynumber: 3.1  Consensus size: 32

      50541 GCCGTGGTTG

                                            
      50551 AGCCTCCCCAGTGGGGCGGCTTCGCCACGGTA
          1 AGCCTCCCCAGTGGGGCGGCTTCGCCACGGTA

                                            
      50583 AGCCTCCCCAGTGGGGCGGCTTCGCCACGGTA
          1 AGCCTCCCCAGTGGGGCGGCTTCGCCACGGTA

                                            
      50615 AGCCTCCCCAGTGGGGCGGCTTCGCCACGGTA
          1 AGCCTCCCCAGTGGGGCGGCTTCGCCACGGTA

                
      50647 AGCC
          1 AGCC

      50651 GCCCTCTTGG


Statistics
Matches: 68,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  32   68  1.00

ACGTcount: A:0.13, C:0.38, G:0.34, T:0.15


Consensus pattern (32 bp):   
AGCCTCCCCAGTGGGGCGGCTTCGCCACGGTA

Found at i:51990 original size:13 final size:13

Alignment explanation


    Indices: 51972--51997  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

      51962 TTGGGGTATC

                         
      51972 TTTTTTGTTTTTT
          1 TTTTTTGTTTTTT

                         
      51985 TTTTTTGTTTTTT
          1 TTTTTTGTTTTTT

      51998 GATAAAAGGG


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92


Consensus pattern (13 bp):   
TTTTTTGTTTTTT
Done.