Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022790.1 Corchorus olitorius cultivar O-4 contig22823, 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: 20232
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.30


Found at i:11065 original size:12 final size:12

Alignment explanation


    Indices: 11048--11072  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

      11038 GAACAACCTC

                        
      11048 AGACTCCTTCAG
          1 AGACTCCTTCAG

                        
      11060 AGACTCCTTCAG
          1 AGACTCCTTCAG

             
      11072 A
          1 A

      11073 TGACAAAAAA


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   13  1.00

ACGTcount: A:0.28, C:0.32, G:0.16, T:0.24


Consensus pattern (12 bp):   
AGACTCCTTCAG

Found at i:16989 original size:1 final size:1

Alignment explanation


    Indices: 16983--17008  Score: 52
    Period size: 1  Copynumber: 26.0  Consensus size: 1

      16973 AAGGAACCTG

                                      
      16983 AAAAAAAAAAAAAAAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAA

      17009 CACCCAAGAT


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   25  1.00

ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00


Consensus pattern (1 bp):   
A

Found at i:19223 original size:54 final size:54

Alignment explanation


    Indices: 19141--19247  Score: 205
    Period size: 54  Copynumber: 2.0  Consensus size: 54

      19131 CTTTGTCTGT

                                                                  
      19141 TTCTGTTGATGATCCAACCCCAAACCCTCTCAAGAAACCTCGGCTTCATCAGAA
          1 TTCTGTTGATGATCCAACCCCAAACCCTCTCAAGAAACCTCGGCTTCATCAGAA

                                                          *      
      19195 TTCTGTTGATGATCCAACCCCAAACCCTCTCAAGAAACCTCGGCTTGATCAGA
          1 TTCTGTTGATGATCCAACCCCAAACCCTCTCAAGAAACCTCGGCTTCATCAGA

      19248 CTATTGGTAA


Statistics
Matches: 52,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  54   52  1.00

ACGTcount: A:0.29, C:0.33, G:0.14, T:0.24


Consensus pattern (54 bp):   
TTCTGTTGATGATCCAACCCCAAACCCTCTCAAGAAACCTCGGCTTCATCAGAA

Found at i:19452 original size:18 final size:18

Alignment explanation


    Indices: 19429--19482  Score: 99
    Period size: 18  Copynumber: 3.0  Consensus size: 18

      19419 CCGAAATCCA

                     *        
      19429 ACCTCTTGCGCAACTTCC
          1 ACCTCTTGCCCAACTTCC

                              
      19447 ACCTCTTGCCCAACTTCC
          1 ACCTCTTGCCCAACTTCC

                              
      19465 ACCTCTTGCCCAACTTCC
          1 ACCTCTTGCCCAACTTCC

      19483 TGATGTGGAA


Statistics
Matches: 35,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  18   35  1.00

ACGTcount: A:0.17, C:0.48, G:0.07, T:0.28


Consensus pattern (18 bp):   
ACCTCTTGCCCAACTTCC
Done.