Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010590.1 Corchorus capsularis cultivar CVL-1 contig10611, 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: 19314
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31


Found at i:2319 original size:15 final size:15

Alignment explanation


    Indices: 2270--2315  Score: 51
    Period size: 14  Copynumber: 3.1  Consensus size: 15

       2260 TTTTTTTCTA

                             
       2270 ATTTACTT-ATTACCAT
          1 ATTTACTTAATTA--AT

                     *     
       2286 ATTTACTTATTTAAT
          1 ATTTACTTAATTAAT

                           
       2301 ATTTA-TTAATTAAT
          1 ATTTACTTAATTAAT

             
       2315 A
          1 A

       2316 ATTTCTTCAA


Statistics
Matches: 27,  Mismatches: 2, Indels: 4
        0.82            0.06        0.12

Matches are distributed among these distances:
  14    9  0.33
  15    7  0.26
  16    8  0.30
  17    3  0.11

ACGTcount: A:0.37, C:0.09, G:0.00, T:0.54


Consensus pattern (15 bp):   
ATTTACTTAATTAAT

Found at i:7598 original size:13 final size:13

Alignment explanation


    Indices: 7563--7603  Score: 50
    Period size: 13  Copynumber: 3.2  Consensus size: 13

       7553 AAGCTTCTTC

                          
       7563 GGAAGAAAGAAAA-
          1 GGAA-AAAGAAAAG

                         
       7576 -GAAAAAGAAAAG
          1 GGAAAAAGAAAAG

                  *      
       7588 GGAAAATGAAAAG
          1 GGAAAAAGAAAAG

               
       7601 GGA
          1 GGA

       7604 CTTTTTTATA


Statistics
Matches: 25,  Mismatches: 1, Indels: 4
        0.83            0.03        0.13

Matches are distributed among these distances:
  11    8  0.32
  12    3  0.12
  13   14  0.56

ACGTcount: A:0.66, C:0.00, G:0.32, T:0.02


Consensus pattern (13 bp):   
GGAAAAAGAAAAG

Found at i:13331 original size:111 final size:111

Alignment explanation


    Indices: 13137--13369  Score: 412
    Period size: 111  Copynumber: 2.1  Consensus size: 111

      13127 AAGGTATTGT

                   *                                                         
      13137 GGATTGGAAGTTATCATAGAATAAGAAGTATTGTTATCTAAAGGGATATCTTCAGGTAAAGAAGA
          1 GGATTGGTAGTTATCATAGAATAAGAAGTATTGTTATCTAAAGGGATATCTTCAGGTAAAGAAGA

                     *            *                       
      13202 AGAATCCTCGTTTTGGGTATTTGAGTTCTCAGGAAAGGAGATTAAA
         66 AGAATCCTCATTTTGGGTATTTAAGTTCTCAGGAAAGGAGATTAAA

                                               *           *                 
      13248 GGATTGGTAGTTATCATAGAATAAGAAGTATTGTTTTCTAAAGGGATGTCTTCAGGTAAAGAAGA
          1 GGATTGGTAGTTATCATAGAATAAGAAGTATTGTTATCTAAAGGGATATCTTCAGGTAAAGAAGA

                                                  *       
      13313 AGAATCCTCATTTTGGGTATTTAAGTTCTCAGGAAAGGTGATTAAA
         66 AGAATCCTCATTTTGGGTATTTAAGTTCTCAGGAAAGGAGATTAAA

                       
      13359 GGATTGGTAGT
          1 GGATTGGTAGT

      13370 AGAGGGGATA


Statistics
Matches: 116,  Mismatches: 6, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
 111  116  1.00

ACGTcount: A:0.34, C:0.08, G:0.26, T:0.32


Consensus pattern (111 bp):   
GGATTGGTAGTTATCATAGAATAAGAAGTATTGTTATCTAAAGGGATATCTTCAGGTAAAGAAGA
AGAATCCTCATTTTGGGTATTTAAGTTCTCAGGAAAGGAGATTAAA

Found at i:17505 original size:44 final size:44

Alignment explanation


    Indices: 17455--17546  Score: 184
    Period size: 44  Copynumber: 2.1  Consensus size: 44

      17445 CAATCTGATA

                                                        
      17455 CAAACAAACAGCATAAAGATTAAGATCAACTCATACTCATACCG
          1 CAAACAAACAGCATAAAGATTAAGATCAACTCATACTCATACCG

                                                        
      17499 CAAACAAACAGCATAAAGATTAAGATCAACTCATACTCATACCG
          1 CAAACAAACAGCATAAAGATTAAGATCAACTCATACTCATACCG

                
      17543 CAAA
          1 CAAA

      17547 ATAAAAGATA


Statistics
Matches: 48,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  44   48  1.00

ACGTcount: A:0.49, C:0.25, G:0.09, T:0.17


Consensus pattern (44 bp):   
CAAACAAACAGCATAAAGATTAAGATCAACTCATACTCATACCG

Done.