Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010263.1 Corchorus olitorius cultivar O-4 contig10295, 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: 7530
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33


Found at i:2255 original size:34 final size:34

Alignment explanation


    Indices: 2212--2282  Score: 106
    Period size: 34  Copynumber: 2.1  Consensus size: 34

       2202 AAACACTGAC

                              *         *     
       2212 ATATTTTGTATATCTTGTTTAGTTGGGATACCTG
          1 ATATTTTGTATATCTTGTGTAGTTGGGAAACCTG

                         *                *   
       2246 ATATTTTGTATATGTTGTGTAGTTGGGAAATCTG
          1 ATATTTTGTATATCTTGTGTAGTTGGGAAACCTG

               
       2280 ATA
          1 ATA

       2283 GTTTAGGGTA


Statistics
Matches: 33,  Mismatches: 4, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  34   33  1.00

ACGTcount: A:0.24, C:0.06, G:0.23, T:0.48


Consensus pattern (34 bp):   
ATATTTTGTATATCTTGTGTAGTTGGGAAACCTG

Found at i:2302 original size:21 final size:22

Alignment explanation


    Indices: 2273--2318  Score: 76
    Period size: 21  Copynumber: 2.1  Consensus size: 22

       2263 TGTAGTTGGG

                                  
       2273 AAATCTGATAGTTTAGGGTACC
          1 AAATCTGATAGTTTAGGGTACC

                     *            
       2295 AAAT-TGATGGTTTAGGGTACC
          1 AAATCTGATAGTTTAGGGTACC

               
       2316 AAA
          1 AAA

       2319 ACAATGTTGT


Statistics
Matches: 23,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  21   19  0.83
  22    4  0.17

ACGTcount: A:0.35, C:0.11, G:0.24, T:0.30


Consensus pattern (22 bp):   
AAATCTGATAGTTTAGGGTACC

Found at i:6752 original size:30 final size:30

Alignment explanation


    Indices: 6718--7092  Score: 412
    Period size: 30  Copynumber: 12.7  Consensus size: 30

       6708 AATCTCCAAA

                                          
       6718 TGACACCAGAAGTTGTCATGATCTTGCAAT
          1 TGACACCAGAAGTTGTCATGATCTTGCAAT

                 *              *     *   
       6748 TGACATCAGAAGTTGTCATGGTCTTGTAAT
          1 TGACACCAGAAGTTGTCATGATCTTGCAAT

                                     *    
       6778 TGACACCAGAAGTTGTCATGATCTTCCAAT
          1 TGACACCAGAAGTTGTCATGATCTTGCAAT

                                *         
       6808 TGACACCAGAAGTTGTCATGCTCTTGCAAT
          1 TGACACCAGAAGTTGTCATGATCTTGCAAT

                            *   *         
       6838 TGACACCAGAAGTTGTTATGCTCTTGCAAT
          1 TGACACCAGAAGTTGTCATGATCTTGCAAT

                                     *    
       6868 TGACACCAGAAGTTGTCATGATCTTCCAAT
          1 TGACACCAGAAGTTGTCATGATCTTGCAAT

                                  *  *    
       6898 TGACACCAGAAGTTGTCATGATTTTACAAT
          1 TGACACCAGAAGTTGTCATGATCTTGCAAT

                    *            *    *    
       6928 TGACACCAAAAGTTGTCAATGGTCTTACAAT
          1 TGACACCAGAAGTTGTC-ATGATCTTGCAAT

                                     *  *    
       6959 TG--ACCAGAAGTTGTCATGATAAATTTTCAAT
          1 TGACACCAGAAGTTGTCATGAT---CTTGCAAT

            *     **    *         *       
       6990 AGACACTTGAAGATGTCAT-A-ATT-CAAT
          1 TGACACCAGAAGTTGTCATGATCTTGCAAT

                                  *       
       7017 TGACACCAGAAGTTGTCAT-A-ATT-CAAT
          1 TGACACCAGAAGTTGTCATGATCTTGCAAT

                                  *     * 
       7044 TGACACCAGAAGTTGTCAT-A-ATT-CAGT
          1 TGACACCAGAAGTTGTCATGATCTTGCAAT

            *          *          
       7071 GGACACCAGAATTTGTCATGAT
          1 TGACACCAGAAGTTGTCATGAT

       7093 TTTACCTTTC


Statistics
Matches: 303,  Mismatches: 34, Indels: 17
        0.86            0.10        0.05

Matches are distributed among these distances:
  27   70  0.23
  28    7  0.02
  29   12  0.04
  30  181  0.60
  31   20  0.07
  32    1  0.00
  33   12  0.04

ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31


Consensus pattern (30 bp):   
TGACACCAGAAGTTGTCATGATCTTGCAAT

Found at i:7022 original size:27 final size:27

Alignment explanation


    Indices: 6984--7089  Score: 149
    Period size: 27  Copynumber: 3.9  Consensus size: 27

       6974 ATGATAAATT

                  *     **    *        
       6984 TTCAATAGACACTTGAAGATGTCATAA
          1 TTCAATTGACACCAGAAGTTGTCATAA

                                       
       7011 TTCAATTGACACCAGAAGTTGTCATAA
          1 TTCAATTGACACCAGAAGTTGTCATAA

                                       
       7038 TTCAATTGACACCAGAAGTTGTCATAA
          1 TTCAATTGACACCAGAAGTTGTCATAA

                * *          *       
       7065 TTCAGTGGACACCAGAATTTGTCAT
          1 TTCAATTGACACCAGAAGTTGTCAT

       7090 GATTTTACCT


Statistics
Matches: 72,  Mismatches: 7, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  27   72  1.00

ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30


Consensus pattern (27 bp):   
TTCAATTGACACCAGAAGTTGTCATAA

Done.