Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021394.1 Corchorus olitorius cultivar O-4 contig21427, 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: 4947
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32


Found at i:410 original size:27 final size:27

Alignment explanation


    Indices: 380--450  Score: 106
    Period size: 27  Copynumber: 2.6  Consensus size: 27

        370 AATGTACTTG

                                *      
        380 AAATGACTAAAATGCCCCTGGACGAGC
          1 AAATGACTAAAATGCCCCTGAACGAGC

                   *              * *  
        407 AAATGACCAAAATGCCCCTGAATGTGC
          1 AAATGACTAAAATGCCCCTGAACGAGC

                             
        434 AAATGACTAAAATGCCC
          1 AAATGACTAAAATGCCC

        451 TTAGACTTTG


Statistics
Matches: 39,  Mismatches: 5, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  27   39  1.00

ACGTcount: A:0.39, C:0.25, G:0.18, T:0.17


Consensus pattern (27 bp):   
AAATGACTAAAATGCCCCTGAACGAGC

Found at i:828 original size:35 final size:35

Alignment explanation


    Indices: 789--1057  Score: 373
    Period size: 35  Copynumber: 7.7  Consensus size: 35

        779 TGTGTTCATA

                                                 
        789 TTGAAGATGCTACACCGTA-TCATCTGAATT-ATTCT
          1 TTGAAGATGCTACACCG-AGTCATCTGAATTCA-TCT

                    *     *            *       
        824 TTGAAGATTCTACATCGAGTCATCTGAGTTCATCT
          1 TTGAAGATGCTACACCGAGTCATCTGAATTCATCT

                                            *  
        859 TTGAAGATGCTACACCGAGTCATCTGAATTCAACT
          1 TTGAAGATGCTACACCGAGTCATCTGAATTCATCT

                                            *  
        894 TTGAAGATGCTACACCGAGTCATCTGAATTCAACT
          1 TTGAAGATGCTACACCGAGTCATCTGAATTCATCT

             *                         *   * * 
        929 TGGAAGATGCTACACCGAGTCATCTGAGTTCGTTT
          1 TTGAAGATGCTACACCGAGTCATCTGAATTCATCT

                                    *  **    * 
        964 TTGAAGATGCTACACCGAGTCATCCGAGGTCATTT
          1 TTGAAGATGCTACACCGAGTCATCTGAATTCATCT

                                            *  
        999 TTGAAGATGCTACACCGAGTCATCTG-ATTCAACT
          1 TTGAAGATGCTACACCGAGTCATCTGAATTCATCT

                                     
       1033 TTGAAGATGCTACACCGAGTCATCT
          1 TTGAAGATGCTACACCGAGTCATCT

       1058 CTGGAAAACA


Statistics
Matches: 211,  Mismatches: 21, Indels: 5
        0.89            0.09        0.02

Matches are distributed among these distances:
  34   30  0.14
  35  180  0.85
  36    1  0.00

ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31


Consensus pattern (35 bp):   
TTGAAGATGCTACACCGAGTCATCTGAATTCATCT

Found at i:1229 original size:92 final size:91

Alignment explanation


    Indices: 1067--1241  Score: 251
    Period size: 92  Copynumber: 1.9  Consensus size: 91

       1057 TCTGGAAAAC

                                  *                *          **       **    
       1067 AACTCTGAATCTGATGTTGTAATTGAAAACTTCTTGATTGATGATGAAAGGGGACCAATTTGCGG
          1 AACTCTGAATCTGATGTTGTAACTGAAAACTTCTTGATTAATGATGAAAGAAGACCAATGCGCGG

                                       
       1132 CCAACTTTGAAAAACAACTTGAAGAAT
         66 CCAAC-TTGAAAAACAACTTGAAGAAT

                    *                                               *        
       1159 AACTCTGAGTCTGATGTTGTAACTGAAAACTTCTTGATTAATGATGAAAGAAGACCGATGCGCGG
          1 AACTCTGAATCTGATGTTGTAACTGAAAACTTCTTGATTAATGATGAAAGAAGACCAATGCGCGG

            *            *    
       1224 TCAACTTGAAAAATAACT
         66 CCAACTTGAAAAACAACT

       1242 CTGAGTCTGA


Statistics
Matches: 73,  Mismatches: 10, Indels: 1
        0.87            0.12        0.01

Matches are distributed among these distances:
  91   12  0.16
  92   61  0.84

ACGTcount: A:0.36, C:0.15, G:0.21, T:0.29


Consensus pattern (91 bp):   
AACTCTGAATCTGATGTTGTAACTGAAAACTTCTTGATTAATGATGAAAGAAGACCAATGCGCGG
CCAACTTGAAAAACAACTTGAAGAAT

Found at i:1781 original size:50 final size:50

Alignment explanation


    Indices: 1727--1873  Score: 231
    Period size: 50  Copynumber: 2.9  Consensus size: 50

       1717 CTTAAATGCC

                                                              
       1727 CTTTGAAAAGCGAATTTTGATCTTGGACTCACAAATGGAATGCAATCCTA
          1 CTTTGAAAAGCGAATTTTGATCTTGGACTCACAAATGGAATGCAATCCTA

                                     *   *          *     **  
       1777 CTTTGAAAAGCGAATTTTGATCTTGAACTTACAAATGGAAAGCAATTTTA
          1 CTTTGAAAAGCGAATTTTGATCTTGGACTCACAAATGGAATGCAATCCTA

                                      **                   
       1827 CTTTGAAAAGCGAATTTTGATCTTGGGTTCACAAATGGAATGCAATC
          1 CTTTGAAAAGCGAATTTTGATCTTGGACTCACAAATGGAATGCAATC

       1874 TTATTGTAAA


Statistics
Matches: 86,  Mismatches: 11, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  50   86  1.00

ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32


Consensus pattern (50 bp):   
CTTTGAAAAGCGAATTTTGATCTTGGACTCACAAATGGAATGCAATCCTA

Found at i:2262 original size:19 final size:19

Alignment explanation


    Indices: 2235--2276  Score: 59
    Period size: 20  Copynumber: 2.2  Consensus size: 19

       2225 TCTAAAACCT

                              *
       2235 TTTTGAAAAAC-ATTTTTC
          1 TTTTGAAAAACGATTTTTA

                                
       2253 TTTTGCAAAAACGATTTTTA
          1 TTTTG-AAAAACGATTTTTA

                
       2273 TTTT
          1 TTTT

       2277 AGGAACAATC


Statistics
Matches: 21,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  18    5  0.24
  19    6  0.29
  20   10  0.48

ACGTcount: A:0.31, C:0.10, G:0.07, T:0.52


Consensus pattern (19 bp):   
TTTTGAAAAACGATTTTTA

Done.