Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021910.1 Corchorus olitorius cultivar O-4 contig21943, 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: 15638
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.33


Found at i:80 original size:13 final size:13

Alignment explanation


    Indices: 62--86  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

         52 ACTCGGTTCT

                         
         62 TATTTTTGTATTC
          1 TATTTTTGTATTC

                        
         75 TATTTTTGTATT
          1 TATTTTTGTATT

         87 GTATCACTTT


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.16, C:0.04, G:0.08, T:0.72


Consensus pattern (13 bp):   
TATTTTTGTATTC

Found at i:241 original size:16 final size:16

Alignment explanation


    Indices: 220--251  Score: 64
    Period size: 16  Copynumber: 2.0  Consensus size: 16

        210 TATATTCTAT

                            
        220 ATTAGCTAGAAATGTA
          1 ATTAGCTAGAAATGTA

                            
        236 ATTAGCTAGAAATGTA
          1 ATTAGCTAGAAATGTA

        252 TTTTTTTTCA


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  16   16  1.00

ACGTcount: A:0.44, C:0.06, G:0.19, T:0.31


Consensus pattern (16 bp):   
ATTAGCTAGAAATGTA

Found at i:2038 original size:18 final size:18

Alignment explanation


    Indices: 2015--2049  Score: 70
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       2005 TATCTATAGG

                              
       2015 TTTAAACATAGAAGTAGT
          1 TTTAAACATAGAAGTAGT

                             
       2033 TTTAAACATAGAAGTAG
          1 TTTAAACATAGAAGTAG

       2050 GAAAAGGAAA


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   17  1.00

ACGTcount: A:0.46, C:0.06, G:0.17, T:0.31


Consensus pattern (18 bp):   
TTTAAACATAGAAGTAGT

Found at i:4913 original size:37 final size:37

Alignment explanation


    Indices: 4863--4947  Score: 143
    Period size: 37  Copynumber: 2.3  Consensus size: 37

       4853 CCCGTTGAGG

                             *                *  
       4863 AAAATGTTTTATTACTGTTTTTATTTAAATGCTTTAT
          1 AAAATGTTTTATTACTGATTTTATTTAAATGCTTAAT

                                                 
       4900 AAAATGTTTTATTACTGATTTTATTTAAATGCTTAAT
          1 AAAATGTTTTATTACTGATTTTATTTAAATGCTTAAT

                 *     
       4937 AAAATATTTTA
          1 AAAATGTTTTA

       4948 ATAAATTATT


Statistics
Matches: 45,  Mismatches: 3, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  37   45  1.00

ACGTcount: A:0.35, C:0.05, G:0.07, T:0.53


Consensus pattern (37 bp):   
AAAATGTTTTATTACTGATTTTATTTAAATGCTTAAT

Found at i:7080 original size:41 final size:41

Alignment explanation


    Indices: 7023--7110  Score: 140
    Period size: 41  Copynumber: 2.1  Consensus size: 41

       7013 TATTTACTCG

                                                     
       7023 TGTATGTTTTGGAACTATATCACCTGACATATGAAACTTAA
          1 TGTATGTTTTGGAACTATATCACCTGACATATGAAACTTAA

                                *     **       *     
       7064 TGTATGTTTTGGAACTATATTACCTGTTATATGAACCTTAA
          1 TGTATGTTTTGGAACTATATCACCTGACATATGAAACTTAA

                  
       7105 TGTATG
          1 TGTATG

       7111 GCTTTTTCTG


Statistics
Matches: 43,  Mismatches: 4, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  41   43  1.00

ACGTcount: A:0.31, C:0.12, G:0.16, T:0.41


Consensus pattern (41 bp):   
TGTATGTTTTGGAACTATATCACCTGACATATGAAACTTAA

Found at i:14645 original size:76 final size:76

Alignment explanation


    Indices: 14494--14638  Score: 170
    Period size: 76  Copynumber: 1.9  Consensus size: 76

      14484 ACAAGGACCC

                                                               *           * 
      14494 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCTTGAGAACCCAGGT
          1 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT

                       
      14559 GGGCAGTGTCA
         66 GGGCAGTGTCA

                 *  *     *              *                            **     
      14570 CGACTTCAGCTGGGTGCCCACATGGTTTGTC-TGAAG-ACCCATGT-GTTTCGCCTGATCACCCA
          1 CGACTCCACCTGGGCGCCCACATGG-TTGCCTTG-AGCACCCATGTGGTTT-GCCTGAGAACCCA

                   
      14632 GATGGGC
         63 GATGGGC

      14639 GATGTCATAG


Statistics
Matches: 58,  Mismatches: 8, Indels: 6
        0.81            0.11        0.08

Matches are distributed among these distances:
  75    4  0.07
  76   48  0.83
  77    6  0.10

ACGTcount: A:0.17, C:0.30, G:0.29, T:0.24


Consensus pattern (76 bp):   
CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
GGGCAGTGTCA
Done.