Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018218.1 Corchorus olitorius cultivar O-4 contig18251, 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: 4628
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29


Found at i:1398 original size:21 final size:21

Alignment explanation


    Indices: 1372--1413  Score: 75
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       1362 AAAAATCAGA

                     *           
       1372 ACAACTCCTGCCCAGGACTTG
          1 ACAACTCCTACCCAGGACTTG

                                 
       1393 ACAACTCCTACCCAGGACTTG
          1 ACAACTCCTACCCAGGACTTG

       1414 GTCTGTTGAA


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  21   20  1.00

ACGTcount: A:0.26, C:0.38, G:0.17, T:0.19


Consensus pattern (21 bp):   
ACAACTCCTACCCAGGACTTG

Found at i:1442 original size:71 final size:71

Alignment explanation


    Indices: 1321--1463  Score: 214
    Period size: 71  Copynumber: 2.0  Consensus size: 71

       1311 CTAAAAATAG

                 *    *                      *                        *      
       1321 GACAAGTCCTGCCCAGGACCTGGTCTGTTGAAAGACGGAAGAAAAATCAGAACAACTCCTGCCCA
          1 GACAACTCCTACCCAGGACCTGGTCTGTTGAAAAACGGAAGAAAAATCAGAACAACTCATGCCCA

                  
       1386 GGACTT
         66 GGACTT

                               *                         *         *     *   
       1392 GACAACTCCTACCCAGGACTTGGTCTGTTGAAAAACGGAAGAAAATTCAGAACAAGTCATGTCCA
          1 GACAACTCCTACCCAGGACCTGGTCTGTTGAAAAACGGAAGAAAAATCAGAACAACTCATGCCCA

                  
       1457 GGACTT
         66 GGACTT

             
       1463 G
          1 G

       1464 TTGCGGAAAA


Statistics
Matches: 64,  Mismatches: 8, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  71   64  1.00

ACGTcount: A:0.34, C:0.24, G:0.23, T:0.19


Consensus pattern (71 bp):   
GACAACTCCTACCCAGGACCTGGTCTGTTGAAAAACGGAAGAAAAATCAGAACAACTCATGCCCA
GGACTT

Found at i:2682 original size:57 final size:57

Alignment explanation


    Indices: 2616--2789  Score: 321
    Period size: 57  Copynumber: 3.1  Consensus size: 57

       2606 AACTACTTAT

                                             *                       
       2616 AAAGCTCGCTAAGTTGAAAATCCTGCAAAGGACAGCTTAGGCAAAAGTTAGAGCACA
          1 AAAGCTCGCTAAGTTGAAAATCCTGCAAAGGACGGCTTAGGCAAAAGTTAGAGCACA

                                                                     
       2673 AAAGCTCGCTAAGTTGAAAATCCTGCAAAGGACGGCTTAGGCAAAAGTTAGAGCACA
          1 AAAGCTCGCTAAGTTGAAAATCCTGCAAAGGACGGCTTAGGCAAAAGTTAGAGCACA

                                                      *            * 
       2730 AAAGCTCGCTAAGTTGAAAATCCTGCAAAGGACGGCTTAGGCGAAAGTTAGAGCAAA
          1 AAAGCTCGCTAAGTTGAAAATCCTGCAAAGGACGGCTTAGGCAAAAGTTAGAGCACA

               
       2787 AAA
          1 AAA

       2790 AAACAAAAAA


Statistics
Matches: 114,  Mismatches: 3, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  57  114  1.00

ACGTcount: A:0.40, C:0.18, G:0.24, T:0.17


Consensus pattern (57 bp):   
AAAGCTCGCTAAGTTGAAAATCCTGCAAAGGACGGCTTAGGCAAAAGTTAGAGCACA

Found at i:2799 original size:9 final size:10

Alignment explanation


    Indices: 2783--2808  Score: 52
    Period size: 10  Copynumber: 2.6  Consensus size: 10

       2773 AAAGTTAGAG

                      
       2783 CAAAAAAAAA
          1 CAAAAAAAAA

                      
       2793 CAAAAAAAAA
          1 CAAAAAAAAA

                  
       2803 CAAAAA
          1 CAAAAA

       2809 CCAAAGAACT


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   16  1.00

ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00


Consensus pattern (10 bp):   
CAAAAAAAAA
Done.