Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022857.1 Corchorus olitorius cultivar O-4 contig22890, 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: 16494
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.31


Found at i:4163 original size:21 final size:21

Alignment explanation


    Indices: 4137--4177  Score: 57
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       4127 TTTAAACCCT

                                  
       4137 ATTGGAGAC-AAGTGGTACTAA
          1 ATTGGA-ACTAAGTGGTACTAA

                  *             
       4158 ATTGGATCTAAGTGGTACTA
          1 ATTGGAACTAAGTGGTACTA

       4178 GGGTTTTTTA


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  20    1  0.06
  21   17  0.94

ACGTcount: A:0.34, C:0.10, G:0.27, T:0.29


Consensus pattern (21 bp):   
ATTGGAACTAAGTGGTACTAA

Found at i:11232 original size:33 final size:33

Alignment explanation


    Indices: 11134--11264  Score: 127
    Period size: 33  Copynumber: 3.8  Consensus size: 33

      11124 AAAAACTGAA

                              *            ****
      11134 TGGGAACTTTCCCAATTTGAAAACTTAAAAGTTAA
          1 TGGGAACTTTCCCAA-TTAAAAACTT-AAAGCCGG

                                           *    
      11169 TGGGAACTTTCCCAATTTTTAAAAACTTAAATCCGG
          1 TGGGAACTTTCCCAA---TTAAAAACTTAAAGCCGG

                *        *        *       *  
      11205 TGGGGACTTTCCCGATTAAAAATTTAAAGCTGG
          1 TGGGAACTTTCCCAATTAAAAACTTAAAGCCGG

                                       
      11238 TGGGAACTTTCCCAATTAAAAACTTAA
          1 TGGGAACTTTCCCAATTAAAAACTTAA

      11265 TGAAATTCTT


Statistics
Matches: 80,  Mismatches: 14, Indels: 6
        0.80            0.14        0.06

Matches are distributed among these distances:
  33   39  0.49
  35   15  0.19
  36   16  0.20
  37   10  0.12

ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31


Consensus pattern (33 bp):   
TGGGAACTTTCCCAATTAAAAACTTAAAGCCGG

Found at i:11304 original size:18 final size:19

Alignment explanation


    Indices: 11281--11316  Score: 56
    Period size: 19  Copynumber: 1.9  Consensus size: 19

      11271 TCTTTTTTGA

                               
      11281 TTTTTG-AGTTTTGAAAAT
          1 TTTTTGTAGTTTTGAAAAT

                    *         
      11299 TTTTTGTATTTTTGAAAA
          1 TTTTTGTAGTTTTGAAAA

      11317 CCTTTTTATT


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

Matches are distributed among these distances:
  18    6  0.38
  19   10  0.62

ACGTcount: A:0.28, C:0.00, G:0.14, T:0.58


Consensus pattern (19 bp):   
TTTTTGTAGTTTTGAAAAT

Found at i:11326 original size:18 final size:19

Alignment explanation


    Indices: 11289--11326  Score: 51
    Period size: 19  Copynumber: 2.1  Consensus size: 19

      11279 GATTTTTGAG

                     **        
      11289 TTTTGAAAATTTTTTGTAT
          1 TTTTGAAAACCTTTTGTAT

                               
      11308 TTTTGAAAACCTTTT-TAT
          1 TTTTGAAAACCTTTTGTAT

             
      11326 T
          1 T

      11327 AATTTTGAAA


Statistics
Matches: 17,  Mismatches: 2, Indels: 1
        0.85            0.10        0.05

Matches are distributed among these distances:
  18    4  0.24
  19   13  0.76

ACGTcount: A:0.26, C:0.05, G:0.08, T:0.61


Consensus pattern (19 bp):   
TTTTGAAAACCTTTTGTAT
Done.