Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010805.1 Corchorus olitorius cultivar O-4 contig10837, 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: 3786
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32


Found at i:2605 original size:15 final size:15

Alignment explanation


    Indices: 2585--2647  Score: 63
    Period size: 15  Copynumber: 4.0  Consensus size: 15

       2575 CACCAGATGA

                    *      
       2585 TGTTTCTGCAACGGT
          1 TGTTTCTGAAACGGT

                            
       2600 TGTTTCTGAAACGGAT
          1 TGTTTCTGAAACGG-T

                   *  *  *   
       2616 GATGTTTTTGCAATGGT
          1 --TGTTTCTGAAACGGT

                           
       2633 TGTTTCTGAAACGGT
          1 TGTTTCTGAAACGGT

       2648 GCCAATTTTT


Statistics
Matches: 38,  Mismatches: 7, Indels: 6
        0.75            0.14        0.12

Matches are distributed among these distances:
  15   25  0.66
  16    1  0.03
  17    1  0.03
  18   11  0.29

ACGTcount: A:0.19, C:0.13, G:0.27, T:0.41


Consensus pattern (15 bp):   
TGTTTCTGAAACGGT

Found at i:2617 original size:33 final size:33

Alignment explanation


    Indices: 2580--2646  Score: 116
    Period size: 33  Copynumber: 2.0  Consensus size: 33

       2570 TTCTGCACCA

                                             
       2580 GATGATGTTTCTGCAACGGTTGTTTCTGAAACG
          1 GATGATGTTTCTGCAACGGTTGTTTCTGAAACG

                      *     *                
       2613 GATGATGTTTTTGCAATGGTTGTTTCTGAAACG
          1 GATGATGTTTCTGCAACGGTTGTTTCTGAAACG

             
       2646 G
          1 G

       2647 TGCCAATTTT


Statistics
Matches: 32,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  33   32  1.00

ACGTcount: A:0.21, C:0.12, G:0.28, T:0.39


Consensus pattern (33 bp):   
GATGATGTTTCTGCAACGGTTGTTTCTGAAACG

Found at i:2744 original size:27 final size:27

Alignment explanation


    Indices: 2706--2878  Score: 319
    Period size: 27  Copynumber: 6.4  Consensus size: 27

       2696 AAACGGCCAT

                                       
       2706 CCACTTGGGGTTGCGGATGAAGCGCAG
          1 CCACTTGGGGTTGCGGATGAAGCGCAG

                                 *     
       2733 CCACTTGGGGTTGCGGATGAAACGCAG
          1 CCACTTGGGGTTGCGGATGAAGCGCAG

                                       
       2760 CCACTTGGGGTTGCGGATGAAGCGCAG
          1 CCACTTGGGGTTGCGGATGAAGCGCAG

                                       
       2787 CCACTTGGGGTTGCGGATGAAGCGCAG
          1 CCACTTGGGGTTGCGGATGAAGCGCAG

             *                        *
       2814 CTACTTGGGGTTGCGGATGAAGCGCAA
          1 CCACTTGGGGTTGCGGATGAAGCGCAG

                                       
       2841 CCACTTGGGGTTGCGGATGAAGCGCAG
          1 CCACTTGGGGTTGCGGATGAAGCGCAG

                       
       2868 CCACTTGGGGT
          1 CCACTTGGGGT

       2879 GGCACCACAT


Statistics
Matches: 140,  Mismatches: 6, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  27  140  1.00

ACGTcount: A:0.19, C:0.22, G:0.39, T:0.20


Consensus pattern (27 bp):   
CCACTTGGGGTTGCGGATGAAGCGCAG

Done.