Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012019.1 Corchorus capsularis cultivar CVL-1 contig12040, 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: 31706
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.30


Found at i:883 original size:107 final size:105

Alignment explanation


    Indices: 652--909  Score: 335
    Period size: 107  Copynumber: 2.5  Consensus size: 105

        642 TAATTTTAAT

                           *                 *                           *   
        652 TTAGTG-AATTAGTTATATATTTTATTTCTAAAGCCCTATAACAAT--ATTATTAATTATGGAAT
          1 TTAGTGAAATTAGTTTTATATTTTATTTCTAAAACCCTATAACAATAAATTATTAATTATGAAAT

                     *                       *      
        714 TTACCCTTACAATAAAAAACAAATTAATTTGGGGCTAAAC
         66 TTACCCTTAAAATAAAAAACAAATTAATTTGGGACTAAAC

               *             *          *      *                      *      
        754 TTAATGAAATTAGTTTTGTATTTTATTTTTAAAACGCTATAACAATAAATTATTAATTTTGAAAT
          1 TTAGTGAAATTAGTTTTATATTTTATTTCTAAAACCCTATAACAATAAATTATTAATTATGAAAT

                 *                           *         
        819 TTACCTTTAAAATAAAAATA-AAATTTTAATTTTGGACTAAAC
         66 TTACCCTTAAAATAAAAA-ACAAA--TTAATTTGGGACTAAAC

                                               *      *      
        861 TTAGTGAAATTAGTTTTATATTTTATTTCTAAAACTCTATAATAATAAA
          1 TTAGTGAAATTAGTTTTATATTTTATTTCTAAAACCCTATAACAATAAA

        910 AAAAATGACA


Statistics
Matches: 133,  Mismatches: 17, Indels: 7
        0.85            0.11        0.04

Matches are distributed among these distances:
 102    5  0.04
 103   34  0.26
 105   34  0.26
 106    1  0.01
 107   59  0.44

ACGTcount: A:0.41, C:0.09, G:0.08, T:0.42


Consensus pattern (105 bp):   
TTAGTGAAATTAGTTTTATATTTTATTTCTAAAACCCTATAACAATAAATTATTAATTATGAAAT
TTACCCTTAAAATAAAAAACAAATTAATTTGGGACTAAAC

Found at i:19992 original size:30 final size:30

Alignment explanation


    Indices: 19956--20015  Score: 111
    Period size: 30  Copynumber: 2.0  Consensus size: 30

      19946 CAAAGGATCA

                                          
      19956 AATGGCATATTTGGTGCGATTCCTCCATCC
          1 AATGGCATATTTGGTGCGATTCCTCCATCC

                    *                     
      19986 AATGGCATCTTTGGTGCGATTCCTCCATCC
          1 AATGGCATATTTGGTGCGATTCCTCCATCC

      20016 TTTGATGTCT


Statistics
Matches: 29,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  30   29  1.00

ACGTcount: A:0.18, C:0.28, G:0.20, T:0.33


Consensus pattern (30 bp):   
AATGGCATATTTGGTGCGATTCCTCCATCC

Found at i:20027 original size:30 final size:30

Alignment explanation


    Indices: 19956--20035  Score: 97
    Period size: 30  Copynumber: 2.7  Consensus size: 30

      19946 CAAAGGATCA

                *   *                     
      19956 AATGGCATATTTGGTGCGATTCCTCCATCC
          1 AATGACATCTTTGGTGCGATTCCTCCATCC

                *                         
      19986 AATGGCATCTTTGGTGCGATTCCTCCATCC
          1 AATGACATCTTTGGTGCGATTCCTCCATCC

            **   **             
      20016 TTTGATGTCTTTGGTGCGAT
          1 AATGACATCTTTGGTGCGAT

      20036 CCCATCTCCT


Statistics
Matches: 44,  Mismatches: 6, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  30   44  1.00

ACGTcount: A:0.16, C:0.24, G:0.23, T:0.38


Consensus pattern (30 bp):   
AATGACATCTTTGGTGCGATTCCTCCATCC

Found at i:22917 original size:30 final size:30

Alignment explanation


    Indices: 22881--22938  Score: 107
    Period size: 30  Copynumber: 1.9  Consensus size: 30

      22871 GGCATCTTAA

                           *              
      22881 TGGCATCTCCATGAGGCTTTGCGATTCCAT
          1 TGGCATCTCCATGAGACTTTGCGATTCCAT

                                        
      22911 TGGCATCTCCATGAGACTTTGCGATTCC
          1 TGGCATCTCCATGAGACTTTGCGATTCC

      22939 TTCCTCTCCT


Statistics
Matches: 27,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  30   27  1.00

ACGTcount: A:0.17, C:0.28, G:0.22, T:0.33


Consensus pattern (30 bp):   
TGGCATCTCCATGAGACTTTGCGATTCCAT
Done.