Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005680.1 Corchorus capsularis cultivar CVL-1 contig05698, 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: 1938
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28


Found at i:152 original size:14 final size:15

Alignment explanation


    Indices: 135--167  Score: 50
    Period size: 15  Copynumber: 2.3  Consensus size: 15

        125 GAAAACAGGG

                      *    
        135 ATTATGAA-ATAACA
          1 ATTATGAAGAAAACA

                           
        149 ATTATGAAGAAAACA
          1 ATTATGAAGAAAACA

                
        164 ATTA
          1 ATTA

        168 AACTAAAAAT


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  14    8  0.47
  15    9  0.53

ACGTcount: A:0.58, C:0.06, G:0.09, T:0.27


Consensus pattern (15 bp):   
ATTATGAAGAAAACA

Found at i:197 original size:6 final size:6

Alignment explanation


    Indices: 188--214  Score: 54
    Period size: 6  Copynumber: 4.5  Consensus size: 6

        178 AAAGCAAAGC

                                           
        188 AAATCT AAATCT AAATCT AAATCT AAA
          1 AAATCT AAATCT AAATCT AAATCT AAA

        215 GCAGATTATA


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   21  1.00

ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30


Consensus pattern (6 bp):   
AAATCT

Found at i:226 original size:12 final size:13

Alignment explanation


    Indices: 211--255  Score: 74
    Period size: 13  Copynumber: 3.5  Consensus size: 13

        201 AATCTAAATC

                         
        211 TAAAGCAGATT-A
          1 TAAAGCAGATTAA

                   *     
        223 TAAAGCAAATTAA
          1 TAAAGCAGATTAA

                         
        236 TAAAGCAGATTAA
          1 TAAAGCAGATTAA

                   
        249 TAAAGCA
          1 TAAAGCA

        256 AACAATAATT


Statistics
Matches: 30,  Mismatches: 2, Indels: 1
        0.91            0.06        0.03

Matches are distributed among these distances:
  12   10  0.33
  13   20  0.67

ACGTcount: A:0.56, C:0.09, G:0.13, T:0.22


Consensus pattern (13 bp):   
TAAAGCAGATTAA

Found at i:262 original size:25 final size:25

Alignment explanation


    Indices: 211--263  Score: 81
    Period size: 25  Copynumber: 2.1  Consensus size: 25

        201 AATCTAAATC

                                  *  
        211 TAAAGCAGATTATAAAGCAAATTAA
          1 TAAAGCAGATTATAAAGCAAATCAA

                                      
        236 TAAAGCAGATTAATAAAGCAAA-CAA
          1 TAAAGCAGATT-ATAAAGCAAATCAA

               
        261 TAA
          1 TAA

        264 TTAAAAAGCA


Statistics
Matches: 26,  Mismatches: 1, Indels: 2
        0.90            0.03        0.07

Matches are distributed among these distances:
  25   16  0.62
  26   10  0.38

ACGTcount: A:0.58, C:0.09, G:0.11, T:0.21


Consensus pattern (25 bp):   
TAAAGCAGATTATAAAGCAAATCAA

Found at i:1456 original size:94 final size:94

Alignment explanation


    Indices: 1306--1494  Score: 360
    Period size: 94  Copynumber: 2.0  Consensus size: 94

       1296 CGGGCCTAAA

                      *                                                      
       1306 ACGGACATATGAGCAGAAAGTTATGGCCTTTTTACCGAGACTGCGCTGAATCCTAGTCCAAATAG
          1 ACGGACATATAAGCAGAAAGTTATGGCCTTTTTACCGAGACTGCGCTGAATCCTAGTCCAAATAG

                                         
       1371 GACTAGTTGCGGGAAATTACGGGATTTGG
         66 GACTAGTTGCGGGAAATTACGGGATTTGG

                    *                                                        
       1400 ACGGACATCTAAGCAGAAAGTTATGGCCTTTTTACCGAGACTGCGCTGAATCCTAGTCCAAATAG
          1 ACGGACATATAAGCAGAAAGTTATGGCCTTTTTACCGAGACTGCGCTGAATCCTAGTCCAAATAG

                                         
       1465 GACTAGTTGCGGGAAATTACGGGATTTGG
         66 GACTAGTTGCGGGAAATTACGGGATTTGG

             
       1494 A
          1 A

       1495 TATTTCCTTG


Statistics
Matches: 93,  Mismatches: 2, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  94   93  1.00

ACGTcount: A:0.29, C:0.19, G:0.27, T:0.25


Consensus pattern (94 bp):   
ACGGACATATAAGCAGAAAGTTATGGCCTTTTTACCGAGACTGCGCTGAATCCTAGTCCAAATAG
GACTAGTTGCGGGAAATTACGGGATTTGG

Found at i:1711 original size:11 final size:11

Alignment explanation


    Indices: 1691--1724  Score: 50
    Period size: 11  Copynumber: 3.1  Consensus size: 11

       1681 TTGATCTTCA

                 *     
       1691 AATCTCCAAAT
          1 AATCTTCAAAT

            *          
       1702 TATCTTCAAAT
          1 AATCTTCAAAT

                       
       1713 AATCTTCAAAT
          1 AATCTTCAAAT

             
       1724 A
          1 A

       1725 CGAACTTCGA


Statistics
Matches: 20,  Mismatches: 3, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  11   20  1.00

ACGTcount: A:0.44, C:0.21, G:0.00, T:0.35


Consensus pattern (11 bp):   
AATCTTCAAAT
Done.