Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001345.1 Corchorus olitorius cultivar O-4 contig01345, 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: 1795
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29


Found at i:1114 original size:50 final size:50

Alignment explanation


    Indices: 1039--1145  Score: 169
    Period size: 50  Copynumber: 2.1  Consensus size: 50

       1029 AGACCATGGG

                                           *         *        
       1039 CCCAACATGATGGCCCAAGTGGAAACAAAAAGGAAATAGATTGAAATAAA
          1 CCCAACATGATGGCCCAAGTGGAAACAAAAAAGAAATAGATGGAAATAAA

                         *                                 * *
       1089 CCCAACATGATGGGCCAAGTGGAAACAAAAAAGAAATAGATGGAAATGAG
          1 CCCAACATGATGGCCCAAGTGGAAACAAAAAAGAAATAGATGGAAATAAA

                   
       1139 CCCAACA
          1 CCCAACA

       1146 ACACAAGAAA


Statistics
Matches: 52,  Mismatches: 5, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  50   52  1.00

ACGTcount: A:0.49, C:0.18, G:0.21, T:0.12


Consensus pattern (50 bp):   
CCCAACATGATGGCCCAAGTGGAAACAAAAAAGAAATAGATGGAAATAAA

Found at i:1546 original size:39 final size:39

Alignment explanation


    Indices: 1503--1736  Score: 249
    Period size: 39  Copynumber: 6.0  Consensus size: 39

       1493 TGTTTTTTTT

                    *            *   *       **    
       1503 CTTAAATGAAAACTCTAAATATAGATCTAAGCAAATTTA
          1 CTTAAATGGAAACTCTAAATAGAGACCTAAGCAGGTTTA

                                                *  
       1542 CTTAAATGGAAACTCTAAATAGAGACCTAAGCAGGTATA
          1 CTTAAATGGAAACTCTAAATAGAGACCTAAGCAGGTTTA

                                *                   
       1581 CTTAAAATGG-AACTCTAAACAGAGACCTAAGCAGGTTTA
          1 CTT-AAATGGAAACTCTAAATAGAGACCTAAGCAGGTTTA

                          *  * * * *      *        
       1620 CTTAAATGGAAACTTTAGACAAAAACCTAAACAGGTTTA
          1 CTTAAATGGAAACTCTAAATAGAGACCTAAGCAGGTTTA

                          *    *  *                
       1659 CTTAAATGGAAACTTTAAACAGGGACCTAAGCAGGTTTA
          1 CTTAAATGGAAACTCTAAATAGAGACCTAAGCAGGTTTA

               *            *  *                     
       1698 CTTGAAT-GATTAA-TTTAGATAGAGACCTAAGCAGGTTTA
          1 CTTAAATGGA--AACTCTAAATAGAGACCTAAGCAGGTTTA

       1737 TTGAAACGGA


Statistics
Matches: 169,  Mismatches: 22, Indels: 8
        0.85            0.11        0.04

Matches are distributed among these distances:
  38    8  0.05
  39  153  0.91
  40    8  0.05

ACGTcount: A:0.42, C:0.15, G:0.16, T:0.27


Consensus pattern (39 bp):   
CTTAAATGGAAACTCTAAATAGAGACCTAAGCAGGTTTA

Done.