Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015096.1 Corchorus capsularis cultivar CVL-1 contig15117, 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: 18198
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31


Found at i:630 original size:20 final size:20

Alignment explanation


    Indices: 605--653  Score: 89
    Period size: 20  Copynumber: 2.4  Consensus size: 20

        595 CAAAGCTACT

                                
        605 ACCCAAAAGCCCAAGTTTAA
          1 ACCCAAAAGCCCAAGTTTAA

                                
        625 ACCCAAAAGCCCAAGTTTAA
          1 ACCCAAAAGCCCAAGTTTAA

                     
        645 AGCCCAAAA
          1 A-CCCAAAA

        654 TGATAGCAAA


Statistics
Matches: 28,  Mismatches: 0, Indels: 1
        0.97            0.00        0.03

Matches are distributed among these distances:
  20   21  0.75
  21    7  0.25

ACGTcount: A:0.47, C:0.31, G:0.10, T:0.12


Consensus pattern (20 bp):   
ACCCAAAAGCCCAAGTTTAA

Found at i:4116 original size:41 final size:41

Alignment explanation


    Indices: 4006--4200  Score: 205
    Period size: 41  Copynumber: 4.7  Consensus size: 41

       3996 GTAATTCAAG

                   *              *       *         ** 
       4006 GTGACAATTTCTGGTGTGTCAACAGTAATTATAATTTACCGGA
          1 GTGACAACTTCT-G-GTGTCAAAAGTAATTTTAATTTACCAAA

              *        *     *  **                   
       4049 GTAAC-ACTTCCGGTGTTAATGGTAATTTTAATTTACCAAA
          1 GTGACAACTTCTGGTGTCAAAAGTAATTTTAATTTACCAAA

                                  *                  
       4089 GTGACAACTTCTGGTGTCAAAAATAATTTTAATTTACC-AA
          1 GTGACAACTTCTGGTGTCAAAAGTAATTTTAATTTACCAAA

                         *      **            *       
       4129 GATGACAACTTCTAGTGTCAGTAGTAATTTTAATATACCAAA
          1 G-TGACAACTTCTGGTGTCAAAAGTAATTTTAATTTACCAAA

                                 *        
       4171 GTGACAACTTCTGGTGTCAAAGGTAATTTT
          1 GTGACAACTTCTGGTGTCAAAAGTAATTTT

       4201 CAATATTATT


Statistics
Matches: 125,  Mismatches: 24, Indels: 8
        0.80            0.15        0.05

Matches are distributed among these distances:
  40   29  0.23
  41   85  0.68
  42    7  0.06
  43    4  0.03

ACGTcount: A:0.33, C:0.14, G:0.17, T:0.35


Consensus pattern (41 bp):   
GTGACAACTTCTGGTGTCAAAAGTAATTTTAATTTACCAAA

Found at i:12849 original size:145 final size:145

Alignment explanation


    Indices: 12586--12857  Score: 517
    Period size: 145  Copynumber: 1.9  Consensus size: 145

      12576 CTCCCTTGAC

                                                *                            
      12586 ACATATCCTCAACTCCAAGTTGGTTTTTAATGGAGTTTCTCAACTGCCCTGTAACGTTAGCAGAA
          1 ACATATCCTCAACTCCAAGTTGGTTTTTAATGGAGTCTCTCAACTGCCCTGTAACGTTAGCAGAA

                                                                             
      12651 AAATAGACAGCAGATGTGGTGAAGTTAACCATCTGCCCTGTAGCACTTTTAAACTTATCAAGGAT
         66 AAATAGACAGCAGATGTGGTGAAGTTAACCATCTGCCCTGTAGCACTTTTAAACTTATCAAGGAT

                           
      12716 AGAAAGAATTGTATT
        131 AGAAAGAATTGTATT

                                                                             
      12731 ACATATCCTCAACTCCAAGTTGGTTTTTAATGGAGTCTCTCAACTGCCCTGTAACGTTAGCAGAA
          1 ACATATCCTCAACTCCAAGTTGGTTTTTAATGGAGTCTCTCAACTGCCCTGTAACGTTAGCAGAA

                           *                             *                
      12796 AAATAGACAGCAGATTTGGTGAAGTTAACCATCTGCCCTGTAGCATTTTTAAACTTATCAAG
         66 AAATAGACAGCAGATGTGGTGAAGTTAACCATCTGCCCTGTAGCACTTTTAAACTTATCAAG

      12858 ATAACAAGAA


Statistics
Matches: 124,  Mismatches: 3, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
 145  124  1.00

ACGTcount: A:0.32, C:0.20, G:0.18, T:0.31


Consensus pattern (145 bp):   
ACATATCCTCAACTCCAAGTTGGTTTTTAATGGAGTCTCTCAACTGCCCTGTAACGTTAGCAGAA
AAATAGACAGCAGATGTGGTGAAGTTAACCATCTGCCCTGTAGCACTTTTAAACTTATCAAGGAT
AGAAAGAATTGTATT

Found at i:13122 original size:28 final size:28

Alignment explanation


    Indices: 13091--13149  Score: 66
    Period size: 28  Copynumber: 2.1  Consensus size: 28

      13081 TTTTTTTTAT

                                         
      13091 TATTAATATATTT-ATAAATTTATAATAA
          1 TATTAATAT-TTTCATAAATTTATAATAA

                 *       *   *      *   
      13119 TATTATTATTTTCTTAATTTTATATTAA
          1 TATTAATATTTTCATAAATTTATAATAA

               
      13147 TAT
          1 TAT

      13150 GTATTTTATT


Statistics
Matches: 26,  Mismatches: 4, Indels: 2
        0.81            0.12        0.06

Matches are distributed among these distances:
  27    3  0.12
  28   23  0.88

ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58


Consensus pattern (28 bp):   
TATTAATATTTTCATAAATTTATAATAA
Done.