Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012783.1 Corchorus olitorius cultivar O-4 contig12816, 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: 19272
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33


Found at i:2220 original size:21 final size:21

Alignment explanation


    Indices: 2187--2235  Score: 55
    Period size: 21  Copynumber: 2.3  Consensus size: 21

       2177 AAGAATTGTA

                          **     
       2187 GCTT-CTTGGAAATGGCTCTT
          1 GCTTCCTTGGAAATCCCTCTT

                    *            
       2207 GCTTCCTTTGAAATCCCTCTT
          1 GCTTCCTTGGAAATCCCTCTT

                    
       2228 GCATTCCT
          1 GC-TTCCT

       2236 AAAGCATTGA


Statistics
Matches: 24,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  20    4  0.17
  21   15  0.62
  22    5  0.21

ACGTcount: A:0.14, C:0.29, G:0.16, T:0.41


Consensus pattern (21 bp):   
GCTTCCTTGGAAATCCCTCTT

Found at i:4991 original size:21 final size:21

Alignment explanation


    Indices: 4962--5007  Score: 58
    Period size: 21  Copynumber: 2.2  Consensus size: 21

       4952 CACCTGGGTG

                                * 
       4962 CCCACATGG-TTGCCTTGAGCA
          1 CCCACATGGTTTG-CTTGAGAA

                *                
       4983 CCCATATGGTTTGCTTGAGAA
          1 CCCACATGGTTTGCTTGAGAA

                
       5004 CCCA
          1 CCCA

       5008 GGTGGGCAGT


Statistics
Matches: 22,  Mismatches: 2, Indels: 2
        0.85            0.08        0.08

Matches are distributed among these distances:
  21   19  0.86
  22    3  0.14

ACGTcount: A:0.22, C:0.30, G:0.22, T:0.26


Consensus pattern (21 bp):   
CCCACATGGTTTGCTTGAGAA

Found at i:5083 original size:76 final size:76

Alignment explanation


    Indices: 4946--5096  Score: 182
    Period size: 76  Copynumber: 2.0  Consensus size: 76

       4936 ACAAGGACCC

                                                               *           * 
       4946 CGACTCCACCTGGGTGCCCACATGGTTGCCTTGAGCACCCATATGGTTTGCTTGAGAACCCAGGT
          1 CGACTCCACCTGGGTGCCCACATGGTTGCCTTGAGCACCCATATGGTTTGCCTGAGAACCCAGAT

                       
       5011 GGGCAGTGTCA
         66 GGGCAGTGTCA

                    *                    *              *             **     
       5022 CGACTCCAGCTGGGTGCCCACATGGTTTGTC-TGAAG-ACCCATGT-GTTTCGCCTGATCACCCA
          1 CGACTCCACCTGGGTGCCCACATGG-TTGCCTTG-AGCACCCATATGGTTT-GCCTGAGAACCCA

                   *     
       5084 GATGGGCTGTGTC
         63 GATGGGCAGTGTC

       5097 TTAGCTCATC


Statistics
Matches: 64,  Mismatches: 8, Indels: 6
        0.82            0.10        0.08

Matches are distributed among these distances:
  75    4  0.06
  76   54  0.84
  77    6  0.09

ACGTcount: A:0.17, C:0.29, G:0.28, T:0.25


Consensus pattern (76 bp):   
CGACTCCACCTGGGTGCCCACATGGTTGCCTTGAGCACCCATATGGTTTGCCTGAGAACCCAGAT
GGGCAGTGTCA

Found at i:18191 original size:20 final size:21

Alignment explanation


    Indices: 18160--18198  Score: 62
    Period size: 20  Copynumber: 1.9  Consensus size: 21

      18150 TCTTACATAA

                                 
      18160 GATTATTGAAAAAGCTATACT
          1 GATTATTGAAAAAGCTATACT

                        *      
      18181 GATTA-TGAAAATGCTATA
          1 GATTATTGAAAAAGCTATA

      18199 TTGTTATCAA


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  20   12  0.71
  21    5  0.29

ACGTcount: A:0.44, C:0.08, G:0.15, T:0.33


Consensus pattern (21 bp):   
GATTATTGAAAAAGCTATACT

Done.