Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018012.1 Corchorus olitorius cultivar O-4 contig18045, 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: 23756
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33


Found at i:13604 original size:38 final size:39

Alignment explanation


    Indices: 13468--13618  Score: 218
    Period size: 39  Copynumber: 3.9  Consensus size: 39

      13458 GGCTGTGCAT

                                           *        
      13468 AGTGGACCCGTACCTCAGGGGGGTTAAACTGATGGTAAAG
          1 AGTGGACCCGTACCTCAGGGGGGTTAAACTGTTGGT-AAG

                     *    *                        
      13508 AGTGGACCCATACCACA-GGGGGTTAAACTGTTGGTAAG
          1 AGTGGACCCGTACCTCAGGGGGGTTAAACTGTTGGTAAG

                        *                           
      13546 AGTGGACCCCGTGCCTCA-GGGGGTTAAACTGTTGGTAAG
          1 AGTGGA-CCCGTACCTCAGGGGGGTTAAACTGTTGGTAAG

                       *                       
      13585 AGTGGACCCGTGCCTCAGGGGGGTT-AACTGTTGG
          1 AGTGGACCCGTACCTCAGGGGGGTTAAACTGTTGG

      13619 CTAGACTCGA


Statistics
Matches: 103,  Mismatches: 6, Indels: 6
        0.90            0.05        0.05

Matches are distributed among these distances:
  38   29  0.28
  39   59  0.57
  40   15  0.15

ACGTcount: A:0.23, C:0.19, G:0.36, T:0.22


Consensus pattern (39 bp):   
AGTGGACCCGTACCTCAGGGGGGTTAAACTGTTGGTAAG

Found at i:13658 original size:6 final size:6

Alignment explanation


    Indices: 13648--13703  Score: 94
    Period size: 6  Copynumber: 9.3  Consensus size: 6

      13638 CGTTAACGGA

                 *                                                *
      13648 TGATTA TGATTG TGATTG TGATTG TGATTG TGATTG TGATTG TGATTA
          1 TGATTG TGATTG TGATTG TGATTG TGATTG TGATTG TGATTG TGATTG

                     
      13696 TGATTG TG
          1 TGATTG TG

      13704 GTGCAGCCTG


Statistics
Matches: 47,  Mismatches: 3, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   6   47  1.00

ACGTcount: A:0.20, C:0.00, G:0.30, T:0.50


Consensus pattern (6 bp):   
TGATTG

Found at i:17159 original size:38 final size:38

Alignment explanation


    Indices: 17060--17207  Score: 226
    Period size: 38  Copynumber: 3.9  Consensus size: 38

      17050 GGCTGTGCAT

                                          *        
      17060 AGTGGACCCGTACCTCAGGGGGTTAAACTGATGGTAAAG
          1 AGTGGACCCGTACCTCAGGGGGTTAAACTGTTGGT-AAG

                     *    *  *                    
      17099 AGTGGACCCATACCACAAGGGGTTAAACTGTTGGTAAG
          1 AGTGGACCCGTACCTCAGGGGGTTAAACTGTTGGTAAG

                       *                          
      17137 AGTGGACCCGTGCCTCAGGGGGTTAAACTGTTGGTAAG
          1 AGTGGACCCGTACCTCAGGGGGTTAAACTGTTGGTAAG

                       *                      
      17175 AGTGGACCCGTGCCTCAGGGGGTT-AACTGTTGG
          1 AGTGGACCCGTACCTCAGGGGGTTAAACTGTTGG

      17208 CTAGACTCGA


Statistics
Matches: 101,  Mismatches: 8, Indels: 2
        0.91            0.07        0.02

Matches are distributed among these distances:
  37    9  0.09
  38   61  0.60
  39   31  0.31

ACGTcount: A:0.24, C:0.19, G:0.34, T:0.22


Consensus pattern (38 bp):   
AGTGGACCCGTACCTCAGGGGGTTAAACTGTTGGTAAG

Found at i:17247 original size:6 final size:6

Alignment explanation


    Indices: 17237--17292  Score: 94
    Period size: 6  Copynumber: 9.3  Consensus size: 6

      17227 CGTTAACGGA

                 *                                                *
      17237 TGATTA TGATTG TGATTG TGATTG TGATTG TGATTG TGATTG TGATTA
          1 TGATTG TGATTG TGATTG TGATTG TGATTG TGATTG TGATTG TGATTG

                     
      17285 TGATTG TG
          1 TGATTG TG

      17293 GTGCAGCCTG


Statistics
Matches: 47,  Mismatches: 3, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   6   47  1.00

ACGTcount: A:0.20, C:0.00, G:0.30, T:0.50


Consensus pattern (6 bp):   
TGATTG

Found at i:21815 original size:19 final size:18

Alignment explanation


    Indices: 21791--21826  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

      21781 TGAAGATTTA

                               
      21791 TTGAAGATAATTTGAAGAT
          1 TTGAAGATAA-TTGAAGAT

                    *        
      21810 TTGAAGATCATTGAAGA
          1 TTGAAGATAATTGAAGA

      21827 ATTATCTCAA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    7  0.44
  19    9  0.56

ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33


Consensus pattern (18 bp):   
TTGAAGATAATTGAAGAT
Done.