Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023706.1 Corchorus olitorius cultivar O-4 contig23739, 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: 7203
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32


Found at i:838 original size:201 final size:199

Alignment explanation


    Indices: 328--956  Score: 907
    Period size: 197  Copynumber: 3.2  Consensus size: 199

        318 GGGCATGACA

                             *   *                                           
        328 GCACGTGCGGGGTTTAAAGGTTGACATGTGTCCCCTTA-GGGAATATGTATTAATATTAAATATA
          1 GCACGTGCGGGGTTTAAGGGTCGACATGTGTCCCC-TAGGGGAATATGTATTAATATT-AATATA

               **                *                                *          
        392 TTTTCTTAATTATGAAATGGGTTATGTGTCAACTTCTTAACCAGCTTATGGAGTTCAAAATTTAC
         64 TTTAATTAATTATGAAATGGGGTATGTGTCAACTTCTTAACC-GCTTATGGAGTCCAAAATTTAC

                   *                                  *                      
        457 ACTGACAGTGTATTGTATAATAATCCTATAAGAAAAATTATAAAATACACCGTCACTGGAGTTTA
        128 ACTGACAATGTATTGTATAATAATCCTATAAGAAAAATTATACAATACACCGTCACTGGAGTTTA

               *   
        522 GCATACT
        193 GCAGACT

                                  *                                          
        529 GCA----CGGGGTTTAAGGGTCAACATGTGTCCCCTAGGGGAATATGTATTAATATTGAATATAT
          1 GCACGTGCGGGGTTTAAGGGTCGACATGTGTCCCCTAGGGGAATATGTATTAATATT-AATATAT

                                                                           * 
        590 TTAATTAATTATGAAATGGGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTATA
         65 TTAATTAATTATGAAATGGGGTATGTGTCAACTTCTTAA-CCGCTTATGGAGTCCAAAATTTACA

             *                                                               
        655 CGGACAATGTATTGTATAATAATCCTATAAGAAAAATTATACAATACACCGTCACTGGAGTTTAG
        129 CTGACAATGTATTGTATAATAATCCTATAAGAAAAATTATACAATACACCGTCACTGGAGTTTAG

                  
        720 CAGACT
        194 CAGACT

                                                                             
        726 GCACGTGCGGGGTTTAAGGGTCGACATGTGTCCCCTAGGGGAATATGTATTAATATTAACTATAT
          1 GCACGTGCGGGGTTTAAGGGTCGACATGTGTCCCCTAGGGGAATATGTATTAATATTAA-TATAT

                        *                                    *               
        791 TTAATTAATTATAAAATGGGGTATGTGTCAACTTCTTAACTCGCTTATGTAGTCCAAAATTTACA
         65 TTAATTAATTATGAAATGGGGTATGTGTCAACTTCTTAAC-CGCTTATGGAGTCCAAAATTTACA

            *                             *                   *   *          
        856 TTGACAATGTATTGTATAATAATCCTA-AAAAAAAATTATAC---ACACCATCAGTGGAGTTTAG
        129 CTGACAATGTATTGTATAATAATCCTATAAGAAAAATTATACAATACACCGTCACTGGAGTTTAG

                * 
        917 CAGATT
        194 CAGACT

               * **  *           *       *    
        923 GCATGCACGAGGTTTAAGGGTTGACATGTTTCCC
          1 GCACGTGCGGGGTTTAAGGGTCGACATGTGTCCC

        957 TTTAGGAAAT


Statistics
Matches: 391,  Mismatches: 29, Indels: 20
        0.89            0.07        0.05

Matches are distributed among these distances:
 196    2  0.01
 197  229  0.59
 198    2  0.01
 200   16  0.04
 201  142  0.36

ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33


Consensus pattern (199 bp):   
GCACGTGCGGGGTTTAAGGGTCGACATGTGTCCCCTAGGGGAATATGTATTAATATTAATATATT
TAATTAATTATGAAATGGGGTATGTGTCAACTTCTTAACCGCTTATGGAGTCCAAAATTTACACT
GACAATGTATTGTATAATAATCCTATAAGAAAAATTATACAATACACCGTCACTGGAGTTTAGCA
GACT

Found at i:2436 original size:21 final size:21

Alignment explanation


    Indices: 2412--2482  Score: 72
    Period size: 21  Copynumber: 3.4  Consensus size: 21

       2402 TCTAACAATG

                                 
       2412 TTAATAAGGTCACTAAAAAAC
          1 TTAATAAGGTCACTAAAAAAC

                    *  *    *     
       2433 TTAA-AGAAGTTACTATAAAAC
          1 TTAATA-AGGTCACTAAAAAAC

                **            *  
       2454 TTAACGAGGTCACTAAAATAC
          1 TTAATAAGGTCACTAAAAAAC

                    
       2475 TTAATAAG
          1 TTAATAAG

       2483 ATTAAGATTT


Statistics
Matches: 38,  Mismatches: 10, Indels: 4
        0.73            0.19        0.08

Matches are distributed among these distances:
  20    1  0.03
  21   37  0.97

ACGTcount: A:0.49, C:0.13, G:0.11, T:0.27


Consensus pattern (21 bp):   
TTAATAAGGTCACTAAAAAAC

Found at i:2690 original size:20 final size:20

Alignment explanation


    Indices: 2654--2691  Score: 51
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       2644 CTAAAAAGGT

                        *       
       2654 TTAATAAAGTTAGTACAATA
          1 TTAATAAAGTTACTACAATA

                               
       2674 TTAATAACA-TTACTACAA
          1 TTAATAA-AGTTACTACAA

       2692 ATCATCAAGG


Statistics
Matches: 16,  Mismatches: 1, Indels: 2
        0.84            0.05        0.11

Matches are distributed among these distances:
  20   15  0.94
  21    1  0.06

ACGTcount: A:0.50, C:0.11, G:0.05, T:0.34


Consensus pattern (20 bp):   
TTAATAAAGTTACTACAATA

Found at i:4165 original size:20 final size:22

Alignment explanation


    Indices: 4142--4182  Score: 68
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       4132 TCGAGCTCGG

                                  
       4142 CTCGAA-TTTTC-CGAGTCGAA
          1 CTCGAATTTTTCTCGAGTCGAA

                                 
       4162 CTCGAATTTTTCTCGAGTCGA
          1 CTCGAATTTTTCTCGAGTCGA

       4183 GCCCAAGTAG


Statistics
Matches: 19,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  20    6  0.32
  21    5  0.26
  22    8  0.42

ACGTcount: A:0.22, C:0.24, G:0.20, T:0.34


Consensus pattern (22 bp):   
CTCGAATTTTTCTCGAGTCGAA

Found at i:5947 original size:13 final size:14

Alignment explanation


    Indices: 5931--5959  Score: 51
    Period size: 14  Copynumber: 2.1  Consensus size: 14

       5921 TTATTGTTAG

                          
       5931 CTTTTA-TTAATTT
          1 CTTTTATTTAATTT

                          
       5944 CTTTTATTTAATTT
          1 CTTTTATTTAATTT

              
       5958 CT
          1 CT

       5960 AAATAACTAT


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  13    6  0.40
  14    9  0.60

ACGTcount: A:0.21, C:0.10, G:0.00, T:0.69


Consensus pattern (14 bp):   
CTTTTATTTAATTT
Done.