Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020604.1 Corchorus olitorius cultivar O-4 contig20637, 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: 4049
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.32


Found at i:235 original size:16 final size:16

Alignment explanation


    Indices: 216--258  Score: 50
    Period size: 16  Copynumber: 2.7  Consensus size: 16

        206 TGTCTCCGTC

                            
        216 TCTGTATGTCTATGTA
          1 TCTGTATGTCTATGTA

                 *   *     *
        232 TCTGTCTGTTTATGTG
          1 TCTGTATGTCTATGTA

                 *     
        248 TCTGTGTGTCT
          1 TCTGTATGTCT

        259 GTGTCTTCCT


Statistics
Matches: 22,  Mismatches: 5, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  16   22  1.00

ACGTcount: A:0.09, C:0.14, G:0.23, T:0.53


Consensus pattern (16 bp):   
TCTGTATGTCTATGTA

Found at i:788 original size:35 final size:35

Alignment explanation


    Indices: 742--944  Score: 291
    Period size: 35  Copynumber: 5.8  Consensus size: 35

        732 ATCAATGTGA

                                *              
        742 AGATCAACTCTGATCATTAAGAACTTCTTGAAACG
          1 AGATCAACTCTGATCATTAAAAACTTCTTGAAACG

                             *                 
        777 AGATCAACTCTGATCATAAAAAACTTCTTGAAACG
          1 AGATCAACTCTGATCATTAAAAACTTCTTGAAACG

                *           ***              * 
        812 AGATTAACTCTGATCAACGAAAACTTCTTGAAAGG
          1 AGATCAACTCTGATCATTAAAAACTTCTTGAAACG

                            ***              * 
        847 AGATCAACTCTGATCAACGAAAACTTCTTGAAAGG
          1 AGATCAACTCTGATCATTAAAAACTTCTTGAAACG

                                             * 
        882 AGATCAACTCTGATCATTAAAAACTTCTTGAAATG
          1 AGATCAACTCTGATCATTAAAAACTTCTTGAAACG

                                         
        917 AGATCAACTCTGATCA-TAAAAACTTCTT
          1 AGATCAACTCTGATCATTAAAAACTTCTT

        945 TGAACGACCG


Statistics
Matches: 156,  Mismatches: 12, Indels: 1
        0.92            0.07        0.01

Matches are distributed among these distances:
  34   12  0.08
  35  144  0.92

ACGTcount: A:0.40, C:0.19, G:0.13, T:0.28


Consensus pattern (35 bp):   
AGATCAACTCTGATCATTAAAAACTTCTTGAAACG

Found at i:1018 original size:54 final size:54

Alignment explanation


    Indices: 935--1072  Score: 177
    Period size: 54  Copynumber: 2.6  Consensus size: 54

        925 TCTGATCATA

                     *    *    *    *                        *    
        935 AAAACTTCTTTGAACGACCGCACTAGGTCAACTTAAGATCAACTTAGATTTCTG
          1 AAAACTTCTATGAAAGACCACACTGGGTCAACTTAAGATCAACTTAGATCTCTG

                                          *         ***           
        989 AAAACTTCTATGAAAGACCACACTGGGTCATCTTAAGATCTGTTTAGATCTCTG
          1 AAAACTTCTATGAAAGACCACACTGGGTCAACTTAAGATCAACTTAGATCTCTG

                           *      *       
       1043 AAAACTTCTATGAAAAACCACATTGGGTCA
          1 AAAACTTCTATGAAAGACCACACTGGGTCA

       1073 TTTTAAACAC


Statistics
Matches: 73,  Mismatches: 11, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  54   73  1.00

ACGTcount: A:0.35, C:0.21, G:0.15, T:0.29


Consensus pattern (54 bp):   
AAAACTTCTATGAAAGACCACACTGGGTCAACTTAAGATCAACTTAGATCTCTG

Done.