Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021399.1 Corchorus olitorius cultivar O-4 contig21432, 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: 2424
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30


Found at i:548 original size:18 final size:18

Alignment explanation


    Indices: 519--660  Score: 187
    Period size: 18  Copynumber: 7.9  Consensus size: 18

        509 AAGTGTGGCA

                              
        519 ACTTGGTGCGGTGCGACC
          1 ACTTGGTGCGGTGCGACC

                               
        537 AC-TGGATGCGGTGCGACC
          1 ACTTGG-TGCGGTGCGACC

                    *         
        555 ACTTGGTGTGGTGCGACC
          1 ACTTGGTGCGGTGCGACC

             *              **
        573 ATTTGGTGCGGTGCGAAT
          1 ACTTGGTGCGGTGCGACC

                              
        591 ACTTGGTGCGGTGCGACC
          1 ACTTGGTGCGGTGCGACC

                    *         
        609 ACTTGGTGTGGTGCGACC
          1 ACTTGGTGCGGTGCGACC

             *              **
        627 ATTTGGTGCGGTGCGAAT
          1 ACTTGGTGCGGTGCGACC

                    *       
        645 ACTTGGTGTGGTGCGA
          1 ACTTGGTGCGGTGCGA

        661 TTTGTTGTTG


Statistics
Matches: 107,  Mismatches: 15, Indels: 4
        0.85            0.12        0.03

Matches are distributed among these distances:
  17    3  0.03
  18  101  0.94
  19    3  0.03

ACGTcount: A:0.13, C:0.20, G:0.39, T:0.27


Consensus pattern (18 bp):   
ACTTGGTGCGGTGCGACC

Found at i:588 original size:54 final size:54

Alignment explanation


    Indices: 521--660  Score: 228
    Period size: 54  Copynumber: 2.6  Consensus size: 54

        511 GTGTGGCAAC

                          *                                        
        521 TTGGTGCGGTGCGACCAC-TGGATGCGGTGCGACCACTTGGTGTGGTGCGACCAT
          1 TTGGTGCGGTGCGAACACTTGG-TGCGGTGCGACCACTTGGTGTGGTGCGACCAT

                           *                                      
        575 TTGGTGCGGTGCGAATACTTGGTGCGGTGCGACCACTTGGTGTGGTGCGACCAT
          1 TTGGTGCGGTGCGAACACTTGGTGCGGTGCGACCACTTGGTGTGGTGCGACCAT

                           *        *       
        629 TTGGTGCGGTGCGAATACTTGGTGTGGTGCGA
          1 TTGGTGCGGTGCGAACACTTGGTGCGGTGCGA

        661 TTTGTTGTTG


Statistics
Matches: 82,  Mismatches: 3, Indels: 2
        0.94            0.03        0.02

Matches are distributed among these distances:
  54   79  0.96
  55    3  0.04

ACGTcount: A:0.13, C:0.20, G:0.40, T:0.27


Consensus pattern (54 bp):   
TTGGTGCGGTGCGAACACTTGGTGCGGTGCGACCACTTGGTGTGGTGCGACCAT

Found at i:1309 original size:50 final size:48

Alignment explanation


    Indices: 1196--1336  Score: 135
    Period size: 50  Copynumber: 2.9  Consensus size: 48

       1186 CGTGCCAATC

                      *         *             *    *      *   
       1196 AATTTTGTC-AAAAAATTGATAAAAAGTGC-GATGAAAATTAAAAGATC-
          1 AATTTTGTCGTAAAAATTGAGAAAAAGTGCAG-TAAAAAAT-AAAGTTCA

                     *                                        
       1243 AATTTTGTCTTAAAAATTGAGAAAAAGATGCAAGTAAAAAATAAAGTTCA
          1 AATTTTGTCGTAAAAATTGAGAAAAAG-TGC-AGTAAAAAATAAAGTTCA

                    *          *             *    *     
       1293 AATTTTGTGGTAAAAATTGTGAAAAAGTGCAGTGAAAAGTAAAG
          1 AATTTTGTCGTAAAAATTGAGAAAAAGTGCAGTAAAAAATAAAG

       1337 GATTGCTTTA


Statistics
Matches: 79,  Mismatches: 10, Indels: 9
        0.81            0.10        0.09

Matches are distributed among these distances:
  47    9  0.11
  48   27  0.34
  49   12  0.15
  50   30  0.38
  51    1  0.01

ACGTcount: A:0.50, C:0.05, G:0.18, T:0.28


Consensus pattern (48 bp):   
AATTTTGTCGTAAAAATTGAGAAAAAGTGCAGTAAAAAATAAAGTTCA
Done.