Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018615.1 Corchorus olitorius cultivar O-4 contig18648, 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: 10887
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.32


Found at i:89 original size:50 final size:50

Alignment explanation


    Indices: 4--374  Score: 706
    Period size: 50  Copynumber: 7.4  Consensus size: 50

          1 GAA

                *              *          *                   
          4 TTTGCCTTGTGGAAAAGCCTATGTTGATAACTGACTCGTATGGAAACGAG
          1 TTTGGCTTGTGGAAAAGCCCATGTTGATAATTGACTCGTATGGAAACGAG

                                                              
         54 TTTGGCTTGTGGAAAAGCCCATGTTGATAATTGACTCGTATGGAAACGAG
          1 TTTGGCTTGTGGAAAAGCCCATGTTGATAATTGACTCGTATGGAAACGAG

                                                              
        104 TTTGGCTTGTGGAAAAGCCCATGTTGATAATTGACTCGTATGGAAACGAG
          1 TTTGGCTTGTGGAAAAGCCCATGTTGATAATTGACTCGTATGGAAACGAG

                                                              
        154 TTTGGCTTGTGGAAAAGCCCATGTTGATAATTGACTCGTATGGAAACGAG
          1 TTTGGCTTGTGGAAAAGCCCATGTTGATAATTGACTCGTATGGAAACGAG

                                                              
        204 TTTGGCTTGTGGAAAAGCCCATGTTGATAATTGACTCGTATGGAAACGAG
          1 TTTGGCTTGTGGAAAAGCCCATGTTGATAATTGACTCGTATGGAAACGAG

                                                              
        254 TTTGGCTTGTGGAAAAGCCCATGTTGATAATTGACTCGTATGGAAACGAG
          1 TTTGGCTTGTGGAAAAGCCCATGTTGATAATTGACTCGTATGGAAACGAG

                                                              
        304 TTTGGCTTGTGGAAAAGCCCATGTTGATAATTGACTCGTATGGAAACGAG
          1 TTTGGCTTGTGGAAAAGCCCATGTTGATAATTGACTCGTATGGAAACGAG

                *                
        354 TTTGTCTTGTGGAAAAGCCCA
          1 TTTGGCTTGTGGAAAAGCCCA

        375 AAGCATTCGG


Statistics
Matches: 317,  Mismatches: 4, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
  50  317  1.00

ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30


Consensus pattern (50 bp):   
TTTGGCTTGTGGAAAAGCCCATGTTGATAATTGACTCGTATGGAAACGAG

Found at i:1086 original size:50 final size:50

Alignment explanation


    Indices: 1032--1180  Score: 167
    Period size: 50  Copynumber: 3.0  Consensus size: 50

       1022 CTTAAATGCC

                                 *   *        **       *       
       1032 CTTTGAAAAGCGAATTTTGATATTGGACTCACAACTAG-AATGCAATCTTA
          1 CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAAGAGAAAT-AAATCTTA

                              *            *    *             
       1082 CTTTGAAAAGCGAATTTTAATCTTGAACTCATAAAGGGAAATAAATCTTA
          1 CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAAGAGAAATAAATCTTA

            *                              *          *       
       1132 TTTTGAAAAGCGAATTTTGATCTTGAACTCATAAATG-GAAAGAAATCTT
          1 CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAA-GAGAAATAAATCTT

       1181 GTTATAAAAC


Statistics
Matches: 86,  Mismatches: 11, Indels: 4
        0.85            0.11        0.04

Matches are distributed among these distances:
  50   82  0.95
  51    4  0.05

ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33


Consensus pattern (50 bp):   
CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAAGAGAAATAAATCTTA

Found at i:1780 original size:14 final size:14

Alignment explanation


    Indices: 1763--1822  Score: 60
    Period size: 11  Copynumber: 4.7  Consensus size: 14

       1753 TTTGATTTGA

                      *   
       1763 TATTTTTTTTTATG
          1 TATTTTTTTTGATG

                          
       1777 TATTTTTTTTGATG
          1 TATTTTTTTTGATG

                          
       1791 -A--TTTTTTGATG
          1 TATTTTTTTTGATG

                         *
       1802 -A-TTTTTTT-ATT
          1 TATTTTTTTTGATG

                      
       1813 TATTTTTTTT
          1 TATTTTTTTT

       1823 TTAAAATTTC


Statistics
Matches: 41,  Mismatches: 2, Indels: 7
        0.82            0.04        0.14

Matches are distributed among these distances:
  11   13  0.32
  12    7  0.17
  13    8  0.20
  14   13  0.32

ACGTcount: A:0.15, C:0.00, G:0.08, T:0.77


Consensus pattern (14 bp):   
TATTTTTTTTGATG

Found at i:1784 original size:12 final size:12

Alignment explanation


    Indices: 1767--1821  Score: 60
    Period size: 12  Copynumber: 4.6  Consensus size: 12

       1757 ATTTGATATT

                        
       1767 TTTTTTTATGTA
          1 TTTTTTTATGTA

                          
       1779 TTTTTTT-TGATGA
          1 TTTTTTTATG-T-A

                  *     
       1792 TTTTTTGATG-A
          1 TTTTTTTATGTA

                     *  
       1803 TTTTTTTATTTA
          1 TTTTTTTATGTA

                   
       1815 TTTTTTT
          1 TTTTTTT

       1822 TTTAAAATTT


Statistics
Matches: 36,  Mismatches: 3, Indels: 8
        0.77            0.06        0.17

Matches are distributed among these distances:
  11   11  0.31
  12   16  0.44
  13    7  0.19
  14    2  0.06

ACGTcount: A:0.15, C:0.00, G:0.09, T:0.76


Consensus pattern (12 bp):   
TTTTTTTATGTA

Found at i:4308 original size:21 final size:22

Alignment explanation


    Indices: 4275--4315  Score: 57
    Period size: 21  Copynumber: 1.9  Consensus size: 22

       4265 CTAAAGTTTA

                *         *       
       4275 ATGGGATGTATGAATGAATGCC
          1 ATGGCATGTATGAAAGAATGCC

                                
       4297 ATGGCATG-ATGAAAGAATG
          1 ATGGCATGTATGAAAGAATG

       4316 TATGAGGCAA


Statistics
Matches: 17,  Mismatches: 2, Indels: 1
        0.85            0.10        0.05

Matches are distributed among these distances:
  21   10  0.59
  22    7  0.41

ACGTcount: A:0.37, C:0.07, G:0.32, T:0.24


Consensus pattern (22 bp):   
ATGGCATGTATGAAAGAATGCC
Done.