Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011902.1 Corchorus capsularis cultivar CVL-1 contig11923, 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: 9716
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31


Found at i:4956 original size:30 final size:30

Alignment explanation


    Indices: 4922--4995  Score: 94
    Period size: 30  Copynumber: 2.5  Consensus size: 30

       4912 GGTAATGGTG

                  *           *           
       4922 ATGGTGCAGAAGTTAATGGTCCAAAAGTTA
          1 ATGGTGAAGAAGTTAATGCTCCAAAAGTTA

                        *       *  *  *   
       4952 ATGGTGAAGAAGCTAATGCTGCAGAATTTA
          1 ATGGTGAAGAAGTTAATGCTCCAAAAGTTA

                          
       4982 ATGGTGAAGAAGTT
          1 ATGGTGAAGAAGTT

       4996 GAGGATGATG


Statistics
Matches: 37,  Mismatches: 7, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  30   37  1.00

ACGTcount: A:0.36, C:0.08, G:0.28, T:0.27


Consensus pattern (30 bp):   
ATGGTGAAGAAGTTAATGCTCCAAAAGTTA

Found at i:4968 original size:15 final size:15

Alignment explanation


    Indices: 4922--4995  Score: 78
    Period size: 15  Copynumber: 4.9  Consensus size: 15

       4912 GGTAATGGTG

                  *        
       4922 ATGGTGCAGAAGTTA
          1 ATGGTGAAGAAGTTA

                  *         
       4937 ATGGTCCAA-AAGTTA
          1 ATGGT-GAAGAAGTTA

                        *  
       4952 ATGGTGAAGAAGCTA
          1 ATGGTGAAGAAGTTA

               *  *    *   
       4967 ATGCTGCAGAATTTA
          1 ATGGTGAAGAAGTTA

                          
       4982 ATGGTGAAGAAGTT
          1 ATGGTGAAGAAGTT

       4996 GAGGATGATG


Statistics
Matches: 46,  Mismatches: 11, Indels: 4
        0.75            0.18        0.07

Matches are distributed among these distances:
  14    2  0.04
  15   43  0.93
  16    1  0.02

ACGTcount: A:0.36, C:0.08, G:0.28, T:0.27


Consensus pattern (15 bp):   
ATGGTGAAGAAGTTA

Found at i:5062 original size:15 final size:15

Alignment explanation


    Indices: 5044--5073  Score: 51
    Period size: 15  Copynumber: 2.0  Consensus size: 15

       5034 ACAACAAGCA

                    *      
       5044 CCTGAAGAGGTTATT
          1 CCTGAAGAAGTTATT

                           
       5059 CCTGAAGAAGTTATT
          1 CCTGAAGAAGTTATT

       5074 GCAGATGGTG


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.30, C:0.13, G:0.23, T:0.33


Consensus pattern (15 bp):   
CCTGAAGAAGTTATT

Found at i:7948 original size:44 final size:45

Alignment explanation


    Indices: 7900--7990  Score: 148
    Period size: 44  Copynumber: 2.0  Consensus size: 45

       7890 AGATATGGGC

                                                *        
       7900 AAATTATGGGTGTCTAAATTTATTTTGG-ATGGTTATGCTGGACA
          1 AAATTATGGGTGTCTAAATTTATTTTGGAATGGTTAAGCTGGACA

                           *                              
       7944 AAATTATGGGTGTCTGAATTTATTTTGGATATGGTTAAGCTGGACA
          1 AAATTATGGGTGTCTAAATTTATTTTGGA-ATGGTTAAGCTGGACA

             
       7990 A
          1 A

       7991 GTTATGAGTT


Statistics
Matches: 43,  Mismatches: 2, Indels: 2
        0.91            0.04        0.04

Matches are distributed among these distances:
  44   27  0.63
  46   16  0.37

ACGTcount: A:0.29, C:0.07, G:0.25, T:0.40


Consensus pattern (45 bp):   
AAATTATGGGTGTCTAAATTTATTTTGGAATGGTTAAGCTGGACA

Found at i:9467 original size:39 final size:40

Alignment explanation


    Indices: 9394--9474  Score: 146
    Period size: 39  Copynumber: 2.0  Consensus size: 40

       9384 TGGTGATTCC

                       *                            
       9394 AAGCTCACCTGCAACAATAAACAGTAGTAGCCATGTCAAG
          1 AAGCTCACCTGAAACAATAAACAGTAGTAGCCATGTCAAG

                                                    
       9434 AAGCTCACCTGAAACAAT-AACAGTAGTAGCCATGTCAAG
          1 AAGCTCACCTGAAACAATAAACAGTAGTAGCCATGTCAAG

              
       9473 AA
          1 AA

       9475 ACATGCCATG


Statistics
Matches: 40,  Mismatches: 1, Indels: 1
        0.95            0.02        0.02

Matches are distributed among these distances:
  39   23  0.57
  40   17  0.43

ACGTcount: A:0.42, C:0.23, G:0.17, T:0.17


Consensus pattern (40 bp):   
AAGCTCACCTGAAACAATAAACAGTAGTAGCCATGTCAAG
Done.