Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014578.1 Corchorus olitorius cultivar O-4 contig14611, 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: 35305
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32


Found at i:15804 original size:32 final size:32

Alignment explanation


    Indices: 15763--15828  Score: 123
    Period size: 32  Copynumber: 2.1  Consensus size: 32

      15753 AATACGACTC

                                            
      15763 AATTCTAAATTAATTAGATTTAAAAAAACAAA
          1 AATTCTAAATTAATTAGATTTAAAAAAACAAA

                        *                   
      15795 AATTCTAAATTAGTTAGATTTAAAAAAACAAA
          1 AATTCTAAATTAATTAGATTTAAAAAAACAAA

              
      15827 AA
          1 AA

      15829 CGAAAACGAA


Statistics
Matches: 33,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  32   33  1.00

ACGTcount: A:0.59, C:0.06, G:0.05, T:0.30


Consensus pattern (32 bp):   
AATTCTAAATTAATTAGATTTAAAAAAACAAA

Found at i:22816 original size:3 final size:3

Alignment explanation


    Indices: 22808--22835  Score: 56
    Period size: 3  Copynumber: 9.3  Consensus size: 3

      22798 ATTCATTTCC

                                                 
      22808 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
          1 CTT CTT CTT CTT CTT CTT CTT CTT CTT C

      22836 AGTTTCATCC


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

Matches are distributed among these distances:
   3   25  1.00

ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64


Consensus pattern (3 bp):   
CTT

Found at i:25359 original size:21 final size:20

Alignment explanation


    Indices: 25308--25371  Score: 85
    Period size: 21  Copynumber: 3.1  Consensus size: 20

      25298 TTGATACTGT

                                 
      25308 TTAACAACTGTACAGATGAGA
          1 TTAAC-ACTGTACAGATGAGA

                            *   
      25329 TT-ACACTGTACAGATTAGA
          1 TTAACACTGTACAGATGAGA

                 *               
      25348 TTAGATACTGTACAGATGAGA
          1 TTA-ACACTGTACAGATGAGA

               
      25369 TTA
          1 TTA

      25372 TTAGAGCAAC


Statistics
Matches: 38,  Mismatches: 3, Indels: 4
        0.84            0.07        0.09

Matches are distributed among these distances:
  19   16  0.42
  20    2  0.05
  21   20  0.53

ACGTcount: A:0.39, C:0.12, G:0.19, T:0.30


Consensus pattern (20 bp):   
TTAACACTGTACAGATGAGA

Found at i:26891 original size:226 final size:225

Alignment explanation


    Indices: 26592--27007  Score: 661
    Period size: 226  Copynumber: 1.8  Consensus size: 225

      26582 AATACTTAAA

                                                         *    *              
      26592 AGGCAAATTATACAATACACCGGCGATGGAGTTTAGCAGACTACATAAACGGGTCCTGAAGGGTG
          1 AGGCAAATTATACAATACACCGGCGATGGAGTTTAGCAGACTACACAAACAGGTCCTGAAGGGTG

                              *                          *            * *    
      26657 ACATGTGTCCTCTAGGGATTAGATTGAAATATTTAAAACTTAATTGATTAAAAAAATATATATGT
         66 ACATGTGTCCTCTAGGGACTAGATTGAAATATTTAAAACTTAATTAATT-AAAAAATAGACATGT

                                        *                                    
      26722 GTCAACTCCATAACCCGCTTGTGGAGTCTAAAATTTACACCGCCGGTGTATCAAATAATTATCAT
        130 GTCAACTCCATAACCCGCTTGTGGAGTCCAAAATTTACACCGCCGGTGTATCAAATAATTATCAT

                                           
      26787 ACTTAAAATCATTGAATAATTGAAAAATAAT
        195 ACTTAAAATCATTGAATAATTGAAAAATAAT

                        *            *                      *      * *       
      26818 AGGCAAATTATATAATACACCGGCGGTGGAGTTTAGCAGACTACACAAGCAGGTCTTTAAGGGTG
          1 AGGCAAATTATACAATACACCGGCGATGGAGTTTAGCAGACTACACAAACAGGTCCTGAAGGGTG

             *         *               *                            *        
      26883 ATATGTGTCCTTTAGGGACTAGATTGAGATATTTAAAACTTAATTAATTAAAAAATGGACATGTG
         66 ACATGTGTCCTCTAGGGACTAGATTGAAATATTTAAAACTTAATTAATTAAAAAATAGACATGTG

                            *                        *                  
      26948 TCAACTCCATAACCCGTTTGTGGAGTCCAAAATTTACACCGTCGGTGTATCAAATAATTA
        131 TCAACTCCATAACCCGCTTGTGGAGTCCAAAATTTACACCGCCGGTGTATCAAATAATTA

      27008 CCCAAAATAA


Statistics
Matches: 172,  Mismatches: 18, Indels: 1
        0.90            0.09        0.01

Matches are distributed among these distances:
 225   70  0.41
 226  102  0.59

ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29


Consensus pattern (225 bp):   
AGGCAAATTATACAATACACCGGCGATGGAGTTTAGCAGACTACACAAACAGGTCCTGAAGGGTG
ACATGTGTCCTCTAGGGACTAGATTGAAATATTTAAAACTTAATTAATTAAAAAATAGACATGTG
TCAACTCCATAACCCGCTTGTGGAGTCCAAAATTTACACCGCCGGTGTATCAAATAATTATCATA
CTTAAAATCATTGAATAATTGAAAAATAAT
Done.