Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022301.1 Corchorus olitorius cultivar O-4 contig22334, 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: 2839
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.35


Found at i:159 original size:79 final size:79

Alignment explanation


    Indices: 64--218  Score: 292
    Period size: 79  Copynumber: 2.0  Consensus size: 79

         54 TGAATTCATG

                                                                             
         64 TGGAAAACTTGGCTTATGGAAAAGCCCATGTTGCTTGGATGGAACCAAAGCTTAAACTGACTCGT
          1 TGGAAAACTTGGCTTATGGAAAAGCCCATGTTGCTTGGATGGAACCAAAGCTTAAACTGACTCGT

                          
        129 ATGGAAACGAGCTT
         66 ATGGAAACGAGCTT

                                       *                    *                
        143 TGGAAAACTTGGCTTATGGAAAAGCCCGTGTTGCTTGGATGGAACCAAGGCTTAAACTGACTCGT
          1 TGGAAAACTTGGCTTATGGAAAAGCCCATGTTGCTTGGATGGAACCAAAGCTTAAACTGACTCGT

                       
        208 ATGGAAACGAG
         66 ATGGAAACGAG

        219 TTTAGTCTTG


Statistics
Matches: 74,  Mismatches: 2, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  79   74  1.00

ACGTcount: A:0.31, C:0.17, G:0.27, T:0.25


Consensus pattern (79 bp):   
TGGAAAACTTGGCTTATGGAAAAGCCCATGTTGCTTGGATGGAACCAAAGCTTAAACTGACTCGT
ATGGAAACGAGCTT

Found at i:212 original size:50 final size:50

Alignment explanation


    Indices: 157--313  Score: 130
    Period size: 50  Copynumber: 3.2  Consensus size: 50

        147 AAACTTGGCT

                                                              
        157 TATGGAAAAGCCCGTGTTGCTTGGATGGAACCAAGGCTTAAACTGACTCG
          1 TATGGAAAAGCCCGTGTTGCTTGGATGGAACCAAGGCTTAAACTGACTCG

                       **               *     *     * * *      *    
        207 TATGG-AAA-CGAGT-TTAGTCTTGGA-AG-ACTGAATTGTCATGAACTTGGCT--
          1 TATGGAAAAGCCCGTGTT-G-CTTGGATGGAAC-CAA--GGCTTAAAC-TGACTCG

                         *                                    
        256 TATGGAAAAGCCCATGTTGCTTGGATGGAACCAAGGCTTAAACTGACTCG
          1 TATGGAAAAGCCCGTGTTGCTTGGATGGAACCAAGGCTTAAACTGACTCG

                    
        306 TATGGAAA
          1 TATGGAAA

        314 TGAGCTTGAC


Statistics
Matches: 77,  Mismatches: 17, Indels: 26
        0.64            0.14        0.22

Matches are distributed among these distances:
  47    4  0.05
  48   11  0.14
  49   20  0.26
  50   28  0.36
  51   10  0.13
  52    4  0.05

ACGTcount: A:0.30, C:0.17, G:0.27, T:0.27


Consensus pattern (50 bp):   
TATGGAAAAGCCCGTGTTGCTTGGATGGAACCAAGGCTTAAACTGACTCG

Found at i:2404 original size:14 final size:13

Alignment explanation


    Indices: 2366--2405  Score: 53
    Period size: 14  Copynumber: 2.8  Consensus size: 13

       2356 CTAGTTTCTG

                          
       2366 GAAAATCCTTTTTT
          1 GAAAA-CCTTTTTT

                          
       2380 GAAAACACTTTTTT
          1 GAAAAC-CTTTTTT

                        
       2394 GAAAAGCCTTTT
          1 GAAAA-CCTTTT

       2406 GTTTTGAAAA


Statistics
Matches: 24,  Mismatches: 0, Indels: 4
        0.86            0.00        0.14

Matches are distributed among these distances:
  13    1  0.04
  14   22  0.92
  15    1  0.04

ACGTcount: A:0.33, C:0.15, G:0.10, T:0.42


Consensus pattern (13 bp):   
GAAAACCTTTTTT
Done.