Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023041.1 Corchorus olitorius cultivar O-4 contig23074, 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: 23506
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31


Found at i:1365 original size:3 final size:3

Alignment explanation


    Indices: 1357--1417  Score: 122
    Period size: 3  Copynumber: 20.3  Consensus size: 3

       1347 AAAATTAATT

                                                                           
       1357 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
          1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA

                             
       1405 TAA TAA TAA TAA T
          1 TAA TAA TAA TAA T

       1418 CATCATTACC


Statistics
Matches: 58,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   58  1.00

ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34


Consensus pattern (3 bp):   
TAA

Found at i:1816 original size:13 final size:13

Alignment explanation


    Indices: 1798--1823  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

       1788 TAACGTGACT

                         
       1798 TTTTTTAATAATA
          1 TTTTTTAATAATA

                         
       1811 TTTTTTAATAATA
          1 TTTTTTAATAATA

       1824 ATAAAATATT


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

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62


Consensus pattern (13 bp):   
TTTTTTAATAATA

Found at i:20979 original size:5 final size:5

Alignment explanation


    Indices: 20969--20996  Score: 56
    Period size: 5  Copynumber: 5.6  Consensus size: 5

      20959 AGTTCAATAG

                                             
      20969 AATTA AATTA AATTA AATTA AATTA AAT
          1 AATTA AATTA AATTA AATTA AATTA AAT

      20997 CATATATAAA


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   5   23  1.00

ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39


Consensus pattern (5 bp):   
AATTA

Found at i:21875 original size:177 final size:177

Alignment explanation


    Indices: 21587--21922  Score: 473
    Period size: 177  Copynumber: 1.9  Consensus size: 177

      21577 CCGATTAAGG

                 *      *                        *               *        *  
      21587 TGATTTAAGTGTTTATTAAAAGATTGTTCCATGATCTTCAACTTTCATGAAGGCCTCGAAAATTA
          1 TGATTCAAGTGTCTATTAAAAGATTGTTCCATGATCTACAACTTTCATGAAGGACTCGAAAACTA

                                            *      *        *                
      21652 AATTAAATGTTTCAAGTATAAAAAATGCTTCCGAAAATTTGTTGTTTCGGTTAAC-GAGAATAGA
         66 AATTAAATGTTTCAAGTATAAAAAATGCTTCCAAAAATTAGTTGTTTCAGTTAACGGA-AATAGA

                             *                               
      21716 CGGTCCACTTAATATTATATAACTTT-TGCTCTAGATGTATGATTGAGA
        130 CGGTCCACTTAATATTACATAA-TTTGTGCTCTAGATGTATGATTGAGA

                          *  *    *                                 *        
      21764 TGATTCAAGTGTCTCTTGAAAGGTTGTTCCATGATCTACAACTTTCATG-AGGACTTGAAAACTA
          1 TGATTCAAGTGTCTATTAAAAGATTGTTCCATGATCTACAACTTTCATGAAGGACTCGAAAACTA

                *                                                            
      21828 AATTTAATG-TTCAAGGTATAAAAAATGCTTCCAAAGAATTAGTTGTTTCAGTTAACGGAAATAG
         66 AATTAAATGTTTCAA-GTATAAAAAATGCTTCCAAA-AATTAGTTGTTTCAGTTAACGGAAATAG

                  *                        
      21892 ACGGTCTACTTAATATTACATAATTTGTGCT
        129 ACGGTCCACTTAATATTACATAATTTGTGCT

      21923 TATGGTGGAA


Statistics
Matches: 140,  Mismatches: 15, Indels: 8
        0.86            0.09        0.05

Matches are distributed among these distances:
 175    5  0.04
 176   42  0.30
 177   91  0.65
 178    2  0.01

ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36


Consensus pattern (177 bp):   
TGATTCAAGTGTCTATTAAAAGATTGTTCCATGATCTACAACTTTCATGAAGGACTCGAAAACTA
AATTAAATGTTTCAAGTATAAAAAATGCTTCCAAAAATTAGTTGTTTCAGTTAACGGAAATAGAC
GGTCCACTTAATATTACATAATTTGTGCTCTAGATGTATGATTGAGA

Found at i:21938 original size:24 final size:24

Alignment explanation


    Indices: 21911--21958  Score: 96
    Period size: 24  Copynumber: 2.0  Consensus size: 24

      21901 TTAATATTAC

                                    
      21911 ATAATTTGTGCTTATGGTGGAAAT
          1 ATAATTTGTGCTTATGGTGGAAAT

                                    
      21935 ATAATTTGTGCTTATGGTGGAAAT
          1 ATAATTTGTGCTTATGGTGGAAAT

      21959 TTGACCCACA


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  24   24  1.00

ACGTcount: A:0.29, C:0.04, G:0.25, T:0.42


Consensus pattern (24 bp):   
ATAATTTGTGCTTATGGTGGAAAT

Done.