Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012705.1 Corchorus capsularis cultivar CVL-1 contig12726, 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: 14602
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31


Found at i:777 original size:158 final size:159

Alignment explanation


    Indices: 485--795  Score: 536
    Period size: 158  Copynumber: 2.0  Consensus size: 159

        475 AATTTTTTTG

                                           *                                 
        485 TTTCCTTCTCTTCGATTCATTCCCTAATTTCTAAAACCCTAATTTTTCTCTTCGGTTCCTTTCCC
          1 TTTCCTTCTCTTCGATTCATTCCCTAATTTCGAAAACCCTAATTTTTCTCTTCGGTTCCTTTCCC

                                    *                   *    *       *       
        550 TTCGCATTTTTTGTTTAATTTTCTCAATTTTTTGTTTAATTTTTTGTTTTTTCTGAATCATATCG
         66 TTCGCATTTTTTGTTTAATTTTCTAAATTTTTTGTTTAATTTTTCGTTTCTTCTGAAGCATATCG

                                         
        615 ACACATTGGTGGATTCTTAACTGGAGTAC
        131 ACACATTGGTGGATTCTTAACTGGAGTAC

                                            *                                
        644 TTTCCTTCTCTTCGATTCATTCCCTAATTTCGGAAACCCTGAATTTTTCTCTTCGGTTCCTTTCC
          1 TTTCCTTCTCTTCGATTCATTCCCTAATTTCGAAAACCCT-AATTTTTCTCTTCGGTTCCTTTCC

                                                                       *     
        709 CTTCGCA-TTTTT-TTTAATTTTCTAAATTTTTTGTTTAATTTTTCGTTTCTTCTGAAGGATATC
         65 CTTCGCATTTTTTGTTTAATTTTCTAAATTTTTTGTTTAATTTTTCGTTTCTTCTGAAGCATATC

                                    
        772 GACACATTGGTGGATTCTTAACTG
        130 GACACATTGGTGGATTCTTAACTG

        796 CGTTCCTCCT


Statistics
Matches: 144,  Mismatches: 7, Indels: 3
        0.94            0.05        0.02

Matches are distributed among these distances:
 158   70  0.49
 159   43  0.30
 160   31  0.22

ACGTcount: A:0.18, C:0.21, G:0.11, T:0.50


Consensus pattern (159 bp):   
TTTCCTTCTCTTCGATTCATTCCCTAATTTCGAAAACCCTAATTTTTCTCTTCGGTTCCTTTCCC
TTCGCATTTTTTGTTTAATTTTCTAAATTTTTTGTTTAATTTTTCGTTTCTTCTGAAGCATATCG
ACACATTGGTGGATTCTTAACTGGAGTAC

Found at i:2051 original size:54 final size:53

Alignment explanation


    Indices: 1970--2077  Score: 162
    Period size: 54  Copynumber: 2.0  Consensus size: 53

       1960 CCCCATTGAT

                               *                                  
       1970 GCTGCAAATAGAGACGATGTTCATGTTCCGACTCTCCCCACTTCGACCCAAGAA
          1 GCTGCAAATAGAGACGATGCTCATGTTCCGACTCTCCCCACTTCGACCC-AGAA

                     *    *       *       *                      
       2024 GCTGCAAATGGAGAGGATGCTCCTGTTCCGGCTCTCCCCACTTCGACCCAGAA
          1 GCTGCAAATAGAGACGATGCTCATGTTCCGACTCTCCCCACTTCGACCCAGAA

             
       2077 G
          1 G

       2078 TGGATCCTCC


Statistics
Matches: 49,  Mismatches: 5, Indels: 1
        0.89            0.09        0.02

Matches are distributed among these distances:
  53    5  0.10
  54   44  0.90

ACGTcount: A:0.24, C:0.32, G:0.22, T:0.21


Consensus pattern (53 bp):   
GCTGCAAATAGAGACGATGCTCATGTTCCGACTCTCCCCACTTCGACCCAGAA

Found at i:2944 original size:30 final size:30

Alignment explanation


    Indices: 2858--2945  Score: 113
    Period size: 30  Copynumber: 2.8  Consensus size: 30

       2848 GGATCCATTC

                        *             * *    
       2858 GCCGGTTGTGGCTGGTTGATGCCCCAAGCGATG
          1 GCCGGTTGTGGCCGG-T--TGCCCCATGAGATG

                                          
       2891 GCCGGTTGTGGCCGGTTGCCCCATGAGATG
          1 GCCGGTTGTGGCCGGTTGCCCCATGAGATG

               *                     
       2921 GCCTGTTGTGGCCGGTTGCCCCATG
          1 GCCGGTTGTGGCCGGTTGCCCCATG

       2946 CAATAGCGCA


Statistics
Matches: 51,  Mismatches: 4, Indels: 3
        0.88            0.07        0.05

Matches are distributed among these distances:
  30   36  0.71
  32    1  0.02
  33   14  0.27

ACGTcount: A:0.09, C:0.27, G:0.39, T:0.25


Consensus pattern (30 bp):   
GCCGGTTGTGGCCGGTTGCCCCATGAGATG

Found at i:9430 original size:33 final size:31

Alignment explanation


    Indices: 9393--9475  Score: 114
    Period size: 30  Copynumber: 2.6  Consensus size: 31

       9383 AAGGATCCAT

                                             
       9393 TGGCCGGTTGTGGCCGGTTGATGCCCCATGCGA
          1 TGGCCGGTTGTGGCCGGTT--TGCCCCATGCGA

                           *               
       9426 TGGCCGGTTGTGGCCAG-TTGCCCCATGCGA
          1 TGGCCGGTTGTGGCCGGTTTGCCCCATGCGA

                                
       9456 TGGCCGGTCATGTGGCCGGT
          1 TGGCCGGT--TGTGGCCGGT

       9476 GTTACGTGGC


Statistics
Matches: 45,  Mismatches: 2, Indels: 6
        0.85            0.04        0.11

Matches are distributed among these distances:
  30   20  0.44
  32    9  0.20
  33   16  0.36

ACGTcount: A:0.08, C:0.28, G:0.40, T:0.24


Consensus pattern (31 bp):   
TGGCCGGTTGTGGCCGGTTTGCCCCATGCGA

Found at i:11008 original size:19 final size:18

Alignment explanation


    Indices: 10975--11010  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

      10965 TTGAAATAAT

                              
      10975 TCTTCAATGATCTTCAAA
          1 TCTTCAATGATCTTCAAA

                     *        
      10993 TCTTCAAATTATCTTCAA
          1 TCTTC-AATGATCTTCAA

      11011 GAAATCTTCA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    5  0.31
  19   11  0.69

ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42


Consensus pattern (18 bp):   
TCTTCAATGATCTTCAAA
Done.