Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012916.1 Corchorus olitorius cultivar O-4 contig12949, 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: 28353
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32


Found at i:2140 original size:38 final size:39

Alignment explanation


    Indices: 2081--2160  Score: 110
    Period size: 38  Copynumber: 2.1  Consensus size: 39

       2071 CGGTCCAATC

                            *             *        
       2081 TTTGTAGTTTCAGGTTTGGTTTGTATCAATTAAGGGG-G
          1 TTTGTAGTTTCAGGTTCGGTTTGTATCAATAAAGGGGCG

                                        *           
       2119 TTTGTAGTTTC-GTGTTCGGTTTGTATCCATAAAGGGGCG
          1 TTTGTAGTTTCAG-GTTCGGTTTGTATCAATAAAGGGGCG

               
       2158 TTT
          1 TTT

       2161 TCCGGCTTGG


Statistics
Matches: 37,  Mismatches: 3, Indels: 3
        0.86            0.07        0.07

Matches are distributed among these distances:
  37    1  0.03
  38   32  0.86
  39    4  0.11

ACGTcount: A:0.16, C:0.09, G:0.30, T:0.45


Consensus pattern (39 bp):   
TTTGTAGTTTCAGGTTCGGTTTGTATCAATAAAGGGGCG

Found at i:16165 original size:13 final size:12

Alignment explanation


    Indices: 16143--16178  Score: 54
    Period size: 13  Copynumber: 2.9  Consensus size: 12

      16133 ACTACCGGCC

                        
      16143 CTGCTTGCTTAT
          1 CTGCTTGCTTAT

              *          
      16155 CTTCTTTGCTTAT
          1 CTGC-TTGCTTAT

                       
      16168 CTGCTTGCTTA
          1 CTGCTTGCTTA

      16179 GTATGGAACT


Statistics
Matches: 21,  Mismatches: 2, Indels: 2
        0.84            0.08        0.08

Matches are distributed among these distances:
  12   10  0.48
  13   11  0.52

ACGTcount: A:0.08, C:0.25, G:0.14, T:0.53


Consensus pattern (12 bp):   
CTGCTTGCTTAT

Found at i:22343 original size:15 final size:15

Alignment explanation


    Indices: 22306--22356  Score: 75
    Period size: 15  Copynumber: 3.3  Consensus size: 15

      22296 CCTTTGAAAC

                   *  *    
      22306 CTAAAATTCTAAATA
          1 CTAAAATGCTGAATA

                            
      22321 CTTAAAATGCTGAATA
          1 C-TAAAATGCTGAATA

                           
      22337 CTAAAATGCTGAATA
          1 CTAAAATGCTGAATA

                 
      22352 CTAAA
          1 CTAAA

      22357 GCGCTGGAAA


Statistics
Matches: 33,  Mismatches: 2, Indels: 2
        0.89            0.05        0.05

Matches are distributed among these distances:
  15   20  0.61
  16   13  0.39

ACGTcount: A:0.49, C:0.14, G:0.08, T:0.29


Consensus pattern (15 bp):   
CTAAAATGCTGAATA

Found at i:22362 original size:15 final size:15

Alignment explanation


    Indices: 22317--22362  Score: 56
    Period size: 15  Copynumber: 3.0  Consensus size: 15

      22307 TAAAATTCTA

                       *    
      22317 AATACTTAAAATGCTG
          1 AATAC-TAAAACGCTG

                      *    
      22333 AATACTAAAATGCTG
          1 AATACTAAAACGCTG

                     *     
      22348 AATACTAAAGCGCTG
          1 AATACTAAAACGCTG

      22363 GAAAGTTATC


Statistics
Matches: 28,  Mismatches: 2, Indels: 1
        0.90            0.06        0.03

Matches are distributed among these distances:
  15   23  0.82
  16    5  0.18

ACGTcount: A:0.43, C:0.15, G:0.15, T:0.26


Consensus pattern (15 bp):   
AATACTAAAACGCTG
Done.