Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016536.1 Corchorus olitorius cultivar O-4 contig16569, 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: 15948
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35


Found at i:557 original size:17 final size:17

Alignment explanation


    Indices: 531--564  Score: 59
    Period size: 17  Copynumber: 2.0  Consensus size: 17

        521 TAATCTTATT

                 *           
        531 TAATATTTATTCATATA
          1 TAATAATTATTCATATA

                             
        548 TAATAATTATTCATATA
          1 TAATAATTATTCATATA

        565 ATGAAGTTTA


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  17   16  1.00

ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50


Consensus pattern (17 bp):   
TAATAATTATTCATATA

Found at i:10079 original size:31 final size:34

Alignment explanation


    Indices: 10003--10092  Score: 114
    Period size: 37  Copynumber: 2.6  Consensus size: 34

       9993 TAAGTTGGGC

                                           **  
      10003 AATAAGAGTAGAATATGTACCATGATAATTATTAT
          1 AATAAGAGTAGAATATGTACCATGATAA-TAGCAT

                                                
      10038 AGAATAAGAGTAGAATATGTACCATGAT-A-AGCAT
          1 --AATAAGAGTAGAATATGTACCATGATAATAGCAT

                                  
      10072 -ATAAGAGTAGAATATGTACCA
          1 AATAAGAGTAGAATATGTACCA

      10093 ACTTATATAT


Statistics
Matches: 51,  Mismatches: 2, Indels: 6
        0.86            0.03        0.10

Matches are distributed among these distances:
  31   21  0.41
  34    3  0.06
  36    1  0.02
  37   26  0.51

ACGTcount: A:0.47, C:0.08, G:0.18, T:0.28


Consensus pattern (34 bp):   
AATAAGAGTAGAATATGTACCATGATAATAGCAT

Found at i:12254 original size:31 final size:30

Alignment explanation


    Indices: 12216--12320  Score: 113
    Period size: 31  Copynumber: 3.5  Consensus size: 30

      12206 TTGGCTAATC

                         *                 
      12216 GCTCAAATAAGGGTCTAATGTTTGTCAAAAT
          1 GCTCAAATAAGGGCCTAATGTTT-TCAAAAT

                           *   *       ** 
      12247 GCTCAAATAAGGGCCCAATCTTTT-AATTT
          1 GCTCAAATAAGGGCCTAATGTTTTCAAAAT

             *                    *        
      12276 GGTCAAATAAGGGCCTAATGTTATCGAAAAT
          1 GCTCAAATAAGGGCCTAATGTTTTC-AAAAT

             *            
      12307 GTTCAAATAAGGGC
          1 GCTCAAATAAGGGC

      12321 TTGGTGTCAG


Statistics
Matches: 60,  Mismatches: 12, Indels: 4
        0.79            0.16        0.05

Matches are distributed among these distances:
  29   23  0.38
  30    1  0.02
  31   36  0.60

ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30


Consensus pattern (30 bp):   
GCTCAAATAAGGGCCTAATGTTTTCAAAAT
Done.