Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01006000.1 Corchorus olitorius cultivar O-4 contig06025, 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: 2006
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.38


Found at i:192 original size:32 final size:33

Alignment explanation


    Indices: 137--210  Score: 87
    Period size: 32  Copynumber: 2.3  Consensus size: 33

        127 TGCTGGAAAA

                   *          *          *   
        137 TAGCGGCCTCTACCGAAGCAAACGCC-CTTATT
          1 TAGCGGCGTCTACCGAAGAAAACGCCGCTAATT

                        **                   
        169 TAGCGGCGTCTATTGAAGAAAACGCCGCTAATT
          1 TAGCGGCGTCTACCGAAGAAAACGCCGCTAATT

               *     
        202 TAGTGGCGT
          1 TAGCGGCGT

        211 TTTAAGCCTC


Statistics
Matches: 35,  Mismatches: 6, Indels: 1
        0.83            0.14        0.02

Matches are distributed among these distances:
  32   22  0.63
  33   13  0.37

ACGTcount: A:0.26, C:0.26, G:0.24, T:0.24


Consensus pattern (33 bp):   
TAGCGGCGTCTACCGAAGAAAACGCCGCTAATT

Found at i:210 original size:33 final size:31

Alignment explanation


    Indices: 151--244  Score: 93
    Period size: 33  Copynumber: 2.9  Consensus size: 31

        141 GGCCTCTACC

                           *      *          
        151 GAAGCAAACGCC-CTTATTTAGCGGCGTCTATT
          1 GAAGCAAACGCCGCTAATTTAGTGGCGT-T-TT

                *                          
        183 GAAGAAAACGCCGCTAATTTAGTGGCGTTTT
          1 GAAGCAAACGCCGCTAATTTAGTGGCGTTTT

                     *                      
        214 -AAGCCTCATACGCCGCTAATTTAGTGGCGTT
          1 GAAG---CAAACGCCGCTAATTTAGTGGCGTT

        245 GTTAGTCTAA


Statistics
Matches: 53,  Mismatches: 5, Indels: 7
        0.82            0.08        0.11

Matches are distributed among these distances:
  30    3  0.06
  31    2  0.04
  32   12  0.23
  33   36  0.68

ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29


Consensus pattern (31 bp):   
GAAGCAAACGCCGCTAATTTAGTGGCGTTTT

Found at i:260 original size:33 final size:33

Alignment explanation


    Indices: 190--264  Score: 107
    Period size: 33  Copynumber: 2.3  Consensus size: 33

        180 ATTGAAGAAA

                                          * *
        190 ACGCCGCTAATTTAGTGGCGTTTTAAGCCTCAT
          1 ACGCCGCTAATTTAGTGGCGTTTTAAGCCTAAG

                                        *     
        223 ACGCCGCTAATTTAGTGGCGTTGTT-AGTCTAAG
          1 ACGCCGCTAATTTAGTGGCGTT-TTAAGCCTAAG

                     
        256 ACGCCGCTA
          1 ACGCCGCTA

        265 TATATAATCA


Statistics
Matches: 38,  Mismatches: 3, Indels: 2
        0.88            0.07        0.05

Matches are distributed among these distances:
  33   36  0.95
  34    2  0.05

ACGTcount: A:0.21, C:0.24, G:0.24, T:0.31


Consensus pattern (33 bp):   
ACGCCGCTAATTTAGTGGCGTTTTAAGCCTAAG
Done.