Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023517.1 Corchorus olitorius cultivar O-4 contig23550, 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: 16183
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31


Found at i:2438 original size:104 final size:104

Alignment explanation


    Indices: 2308--2517  Score: 411
    Period size: 104  Copynumber: 2.0  Consensus size: 104

       2298 TAATATGCCT

                                                                             
       2308 TGCAGCAGGTGGAAAACTTGATAGTAGCAACACAGCTCCTTGAATTGCTAAAAGCACCAGAAAAT
          1 TGCAGCAGGTGGAAAACTTGATAGTAGCAACACAGCTCCTTGAATTGCTAAAAGCACCAGAAAAT

                                                   
       2373 AATTAATTAAACAGAAACTATATCCAACATAAAGCAAAC
         66 AATTAATTAAACAGAAACTATATCCAACATAAAGCAAAC

                                                                             
       2412 TGCAGCAGGTGGAAAACTTGATAGTAGCAACACAGCTCCTTGAATTGCTAAAAGCACCAGAAAAT
          1 TGCAGCAGGTGGAAAACTTGATAGTAGCAACACAGCTCCTTGAATTGCTAAAAGCACCAGAAAAT

                       *                           
       2477 AATTAATTAAATAGAAACTATATCCAACATAAAGCAAAC
         66 AATTAATTAAACAGAAACTATATCCAACATAAAGCAAAC

              
       2516 TG
          1 TG

       2518 ACCAGATTCT


Statistics
Matches: 105,  Mismatches: 1, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
 104  105  1.00

ACGTcount: A:0.45, C:0.19, G:0.16, T:0.21


Consensus pattern (104 bp):   
TGCAGCAGGTGGAAAACTTGATAGTAGCAACACAGCTCCTTGAATTGCTAAAAGCACCAGAAAAT
AATTAATTAAACAGAAACTATATCCAACATAAAGCAAAC

Found at i:7469 original size:29 final size:29

Alignment explanation


    Indices: 7424--7482  Score: 100
    Period size: 29  Copynumber: 2.0  Consensus size: 29

       7414 ATTTATTACA

                        *         *      
       7424 ATTTCATAGTTAGATTATCAAAGTTTCAT
          1 ATTTCATAGTTAAATTATCAAAATTTCAT

                                         
       7453 ATTTCATAGTTAAATTATCAAAATTTCAT
          1 ATTTCATAGTTAAATTATCAAAATTTCAT

             
       7482 A
          1 A

       7483 ACGTGGTTAT


Statistics
Matches: 28,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  29   28  1.00

ACGTcount: A:0.39, C:0.10, G:0.07, T:0.44


Consensus pattern (29 bp):   
ATTTCATAGTTAAATTATCAAAATTTCAT

Found at i:7527 original size:22 final size:22

Alignment explanation


    Indices: 7467--7520  Score: 72
    Period size: 22  Copynumber: 2.5  Consensus size: 22

       7457 CATAGTTAAA

                        *       **
       7467 TTATCAAAATTTCATAACGTGG
          1 TTATCAAAATTTAATAACGTAC

                             *    
       7489 TTATCAAAATTTAATAAGGTAC
          1 TTATCAAAATTTAATAACGTAC

                      
       7511 TTATCAAAAT
          1 TTATCAAAAT

       7521 CTTATAAAAA


Statistics
Matches: 28,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  22   28  1.00

ACGTcount: A:0.43, C:0.11, G:0.09, T:0.37


Consensus pattern (22 bp):   
TTATCAAAATTTAATAACGTAC

Found at i:13219 original size:42 final size:42

Alignment explanation


    Indices: 13171--13253  Score: 157
    Period size: 42  Copynumber: 2.0  Consensus size: 42

      13161 CAAAGAACTT

                   *                                  
      13171 TTTATTAGTTGAAAAATTCACTCAACAAGAACAAGAACAATA
          1 TTTATTAATTGAAAAATTCACTCAACAAGAACAAGAACAATA

                                                     
      13213 TTTATTAATTGAAAAATTCACTCAACAAGAACAAGAACAAT
          1 TTTATTAATTGAAAAATTCACTCAACAAGAACAAGAACAAT

      13254 TTTGATGGAG


Statistics
Matches: 40,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  42   40  1.00

ACGTcount: A:0.51, C:0.14, G:0.08, T:0.27


Consensus pattern (42 bp):   
TTTATTAATTGAAAAATTCACTCAACAAGAACAAGAACAATA
Done.