Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023465.1 Corchorus olitorius cultivar O-4 contig23498, 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: 11095
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.32


Found at i:1755 original size:21 final size:21

Alignment explanation


    Indices: 1722--1770  Score: 55
    Period size: 21  Copynumber: 2.3  Consensus size: 21

       1712 AAGAATTGTA

                          **     
       1722 GCTT-CTTGGAAATGGCTCTT
          1 GCTTCCTTGGAAATCCCTCTT

                    *            
       1742 GCTTCCTTTGAAATCCCTCTT
          1 GCTTCCTTGGAAATCCCTCTT

                    
       1763 GCATTCCT
          1 GC-TTCCT

       1771 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:2879 original size:13 final size:13

Alignment explanation


    Indices: 2861--2890  Score: 51
    Period size: 13  Copynumber: 2.3  Consensus size: 13

       2851 TAAACTAAAG

                         
       2861 AAAAAATAAAACA
          1 AAAAAATAAAACA

                       * 
       2874 AAAAAATAAAAGA
          1 AAAAAATAAAACA

                
       2887 AAAA
          1 AAAA

       2891 GAAAAATAAC


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  13   16  1.00

ACGTcount: A:0.87, C:0.03, G:0.03, T:0.07


Consensus pattern (13 bp):   
AAAAAATAAAACA

Found at i:2904 original size:16 final size:17

Alignment explanation


    Indices: 2875--2912  Score: 51
    Period size: 16  Copynumber: 2.3  Consensus size: 17

       2865 AATAAAACAA

                             
       2875 AAAAATAAAAGAAAAAG
          1 AAAAATAAAAGAAAAAG

                     *      *
       2892 AAAAAT-AACGAAAAAT
          1 AAAAATAAAAGAAAAAG

                 
       2908 AAAAA
          1 AAAAA

       2913 GATAAGGGTA


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  16   13  0.68
  17    6  0.32

ACGTcount: A:0.82, C:0.03, G:0.08, T:0.08


Consensus pattern (17 bp):   
AAAAATAAAAGAAAAAG

Found at i:4642 original size:76 final size:76

Alignment explanation


    Indices: 4492--4632  Score: 171
    Period size: 76  Copynumber: 1.9  Consensus size: 76

       4482 ACAAGGACCC

                  *                                            *           * 
       4492 CGACTCTACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCTTGAGAACCCAGGT
          1 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT

                       
       4557 AGGCAGTGTCA
         66 AGGCAGTGTCA

                    *                    *                            **     
       4568 CGACTCCAGCTGGGCGCCCACATGGTTTGTC-TGAAG-ACCCATGT-GTTTCGCCTGATCACCCA
          1 CGACTCCACCTGGGCGCCCACATGG-TTGCCTTG-AGCACCCATGTGGTTT-GCCTGAGAACCCA

               
       4630 GAT
         63 GAT

       4633 GGGTTGTGTC


Statistics
Matches: 55,  Mismatches: 7, Indels: 6
        0.81            0.10        0.09

Matches are distributed among these distances:
  75    4  0.07
  76   45  0.82
  77    6  0.11

ACGTcount: A:0.18, C:0.30, G:0.27, T:0.24


Consensus pattern (76 bp):   
CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
AGGCAGTGTCA

Found at i:10637 original size:31 final size:31

Alignment explanation


    Indices: 10602--10698  Score: 167
    Period size: 31  Copynumber: 3.1  Consensus size: 31

      10592 AAGGGACTGA

                                           
      10602 TTTGTCCCAAAAGAAAAACATAAGGGATTTT
          1 TTTGTCCCAAAAGAAAAACATAAGGGATTTT

                                           
      10633 TTTGTCCCAAAAGAAAAACATAAGGGATTTT
          1 TTTGTCCCAAAAGAAAAACATAAGGGATTTT

                              *       *     
      10664 TTTGTCCCAAAAGAAAAATATAAGAGAATTTT
          1 TTTGTCCCAAAAGAAAAACATAAG-GGATTTT

               
      10696 TTT
          1 TTT

      10699 AGTATTTAGT


Statistics
Matches: 63,  Mismatches: 2, Indels: 1
        0.95            0.03        0.02

Matches are distributed among these distances:
  31   54  0.86
  32    9  0.14

ACGTcount: A:0.42, C:0.11, G:0.14, T:0.32


Consensus pattern (31 bp):   
TTTGTCCCAAAAGAAAAACATAAGGGATTTT
Done.