Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012693.1 Corchorus capsularis cultivar CVL-1 contig12714, 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: 4887
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


Found at i:514 original size:13 final size:12

Alignment explanation


    Indices: 491--533  Score: 77
    Period size: 12  Copynumber: 3.5  Consensus size: 12

        481 TTAATACAGG

                        
        491 TATCGACGGATA
          1 TATCGACGGATA

                         
        503 TATCGAACGGATA
          1 TATCG-ACGGATA

                        
        516 TATCGACGGATA
          1 TATCGACGGATA

                  
        528 TATCGA
          1 TATCGA

        534 TATATCGATG


Statistics
Matches: 30,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
  12   18  0.60
  13   12  0.40

ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26


Consensus pattern (12 bp):   
TATCGACGGATA

Found at i:1635 original size:50 final size:49

Alignment explanation


    Indices: 1608--1954  Score: 522
    Period size: 48  Copynumber: 7.1  Consensus size: 49

       1598 GAAGAAACAA

                    **                                       
       1608 ATAAAAATTGGTGCCTTCCGTCCGGGAAGGGCATTTTGGGAAATAGCAG
          1 ATAAAAATAAGTGCCTTCCGTCCGGGAAGGGCATTTTGGGAAATAGCAG

                 * **     *       *                          
       1657 ATAAAGACGAGTGCATTCCGTCTGGGAAGGGCATTTTGGGAAATAGCAG
          1 ATAAAAATAAGTGCCTTCCGTCCGGGAAGGGCATTTTGGGAAATAGCAG

                             *                      *         
       1706 ATAAAAATAAGTGCCTTTCGTCCGGGAAGGGCATTTTAGGAAAATAGCAG
          1 ATAAAAATAAGTGCCTTCCGTCCGGGAAGGGCATTTT-GGGAAATAGCAG

                   *                                         
       1756 ATAAAAACAAGTGCCTTCCGTCCGGGAAGGGCATTTTGGGAAATAGCAG
          1 ATAAAAATAAGTGCCTTCCGTCCGGGAAGGGCATTTTGGGAAATAGCAG

                                                        *    
       1805 AT--AAATAAGTGCCTTCCGTCCGGGAAGGGCATTTTGGGAAATGGCAG
          1 ATAAAAATAAGTGCCTTCCGTCCGGGAAGGGCATTTTGGGAAATAGCAG

                                           *                 
       1852 AT-AAAATAAGTGCCTTCCGTCCGGGAAGGGTATTTTGGGAAATAGCAG
          1 ATAAAAATAAGTGCCTTCCGTCCGGGAAGGGCATTTTGGGAAATAGCAG

                         *         *       *                 
       1900 AT-AAAATAAGTGTCTTCCGTCCCGGAAGGGTATTTTGGGAAATAGCAG
          1 ATAAAAATAAGTGCCTTCCGTCCGGGAAGGGCATTTTGGGAAATAGCAG

                   
       1948 ATAAAAA
          1 ATAAAAA

       1955 CCGAAAATTG


Statistics
Matches: 273,  Mismatches: 22, Indels: 6
        0.91            0.07        0.02

Matches are distributed among these distances:
  47   45  0.16
  48   91  0.33
  49   91  0.33
  50   46  0.17

ACGTcount: A:0.32, C:0.15, G:0.29, T:0.24


Consensus pattern (49 bp):   
ATAAAAATAAGTGCCTTCCGTCCGGGAAGGGCATTTTGGGAAATAGCAG

Found at i:1783 original size:99 final size:97

Alignment explanation


    Indices: 1618--1955  Score: 536
    Period size: 99  Copynumber: 3.5  Consensus size: 97

       1608 ATAAAAATTG

                                                        *  *     *       *   
       1618 GTGCCTTCCGTCCGGGAAGGGCATTTTGGGAAATAGCAGATAAAGACGAGTGCATTCCGTCTGGG
          1 GTGCCTTCCGTCCGGGAAGGGCATTTTGGGAAATAGCAGATAAAAACAAGTGCCTTCCGTCCGGG

                                             
       1683 AAGGGCATTTTGGGAAATAGCAGATAAAAATAA
         66 AAGGGCATTTTGGGAAATAGCAGAT-AAAATAA

                   *                      *                                  
       1716 GTGCCTTTCGTCCGGGAAGGGCATTTTAGGAAAATAGCAGATAAAAACAAGTGCCTTCCGTCCGG
          1 GTGCCTTCCGTCCGGGAAGGGCATTTT-GGGAAATAGCAGATAAAAACAAGTGCCTTCCGTCCGG

                                             
       1781 GAAGGGCATTTTGGGAAATAGCAGAT-AAATAA
         65 GAAGGGCATTTTGGGAAATAGCAGATAAAATAA

                                              *           *                  
       1813 GTGCCTTCCGTCCGGGAAGGGCATTTTGGGAAATGGCAGAT-AAAATAAGTGCCTTCCGTCCGGG
          1 GTGCCTTCCGTCCGGGAAGGGCATTTTGGGAAATAGCAGATAAAAACAAGTGCCTTCCGTCCGGG

                 *                          
       1877 AAGGGTATTTTGGGAAATAGCAGATAAAATAA
         66 AAGGGCATTTTGGGAAATAGCAGATAAAATAA

               *         *       *                         
       1909 GTGTCTTCCGTCCCGGAAGGGTATTTTGGGAAATAGCAGATAAAAAC
          1 GTGCCTTCCGTCCGGGAAGGGCATTTTGGGAAATAGCAGATAAAAAC

       1956 CGAAAATTGA


Statistics
Matches: 221,  Mismatches: 16, Indels: 7
        0.91            0.07        0.03

Matches are distributed among these distances:
  95   46  0.21
  96   55  0.25
  97   36  0.16
  98   26  0.12
  99   58  0.26

ACGTcount: A:0.31, C:0.16, G:0.29, T:0.23


Consensus pattern (97 bp):   
GTGCCTTCCGTCCGGGAAGGGCATTTTGGGAAATAGCAGATAAAAACAAGTGCCTTCCGTCCGGG
AAGGGCATTTTGGGAAATAGCAGATAAAATAA

Done.