Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016867.1 Corchorus olitorius cultivar O-4 contig16900, 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: 16765
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.32


Found at i:7 original size:1 final size:1

Alignment explanation


    Indices: 2--27  Score: 52
    Period size: 1  Copynumber: 26.0  Consensus size: 1

          1 G

                                      
          2 TTTTTTTTTTTTTTTTTTTTTTTTTT
          1 TTTTTTTTTTTTTTTTTTTTTTTTTT

         28 GTTGTTGTTG


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

Matches are distributed among these distances:
   1   25  1.00

ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00


Consensus pattern (1 bp):   
T

Found at i:821 original size:28 final size:28

Alignment explanation


    Indices: 787--884  Score: 124
    Period size: 28  Copynumber: 3.5  Consensus size: 28

        777 GCACTTGAAG

                                        
        787 TGACCAAAATGCCCTTGGATATGCAAAA
          1 TGACCAAAATGCCCTTGGATATGCAAAA

             *            *             
        815 TAACCAAAATGCCCCTGGATATGCAAAA
          1 TGACCAAAATGCCCTTGGATATGCAAAA

                     **        *    *  *
        843 TGACCAAAACACCCTTGGACATGCGAAG
          1 TGACCAAAATGCCCTTGGATATGCAAAA

                  *       
        871 TGACCAGAATGCCC
          1 TGACCAAAATGCCC

        885 CCTTAAGTGA


Statistics
Matches: 58,  Mismatches: 12, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  28   58  1.00

ACGTcount: A:0.38, C:0.27, G:0.18, T:0.17


Consensus pattern (28 bp):   
TGACCAAAATGCCCTTGGATATGCAAAA

Found at i:1621 original size:35 final size:35

Alignment explanation


    Indices: 1142--1620  Score: 711
    Period size: 35  Copynumber: 13.9  Consensus size: 35

       1132 CGAGTTCATA

                                          **   
       1142 TTGAAGATGCTACACCGAGTCATCTGAATTCATCT
          1 TTGAAGATGCTACACCGAGTCATCTGAATTTGTCT

                                               
       1177 TTGAAGATGCTACACCGAGTCATCTGAATTTGTCT
          1 TTGAAGATGCTACACCGAGTCATCTGAATTTGTCT

                           *       *      **   
       1212 TTGAAGATGCTACACTGAGTCATATGAATTCATCT
          1 TTGAAGATGCTACACCGAGTCATCTGAATTTGTCT

                      **                       
       1247 TTGAAGATGCCGCACCGAGTCATCTGAATTTGTCT
          1 TTGAAGATGCTACACCGAGTCATCTGAATTTGTCT

                              *           **   
       1282 TTGAAGATGCTACACCGACTCATCTGAATTCATCT
          1 TTGAAGATGCTACACCGAGTCATCTGAATTTGTCT

                       *                       
       1317 TTGAAGATGCTGCACCGAGTCATCTGAATTTGTCT
          1 TTGAAGATGCTACACCGAGTCATCTGAATTTGTCT

                                   *           
       1352 TTGAAGATGCTACACCGAGTCATTTGAATTTGTCT
          1 TTGAAGATGCTACACCGAGTCATCTGAATTTGTCT

                                               
       1387 TTGAAGA---T---CCGAGTCATCTGAATTTGTCT
          1 TTGAAGATGCTACACCGAGTCATCTGAATTTGTCT

                       *                       
       1416 TTGAAGATGCTGCACCGAGTCATCTGAATTTGTCT
          1 TTGAAGATGCTACACCGAGTCATCTGAATTTGTCT

                 *                             
       1451 TTGAATATGCTACACCGAGTCATCTGAATTTGTCT
          1 TTGAAGATGCTACACCGAGTCATCTGAATTTGTCT

                       *                       
       1486 TTGAAGATGCTGCACCGAGTCATCTGAATTTGTCT
          1 TTGAAGATGCTACACCGAGTCATCTGAATTTGTCT

                       *             *    **   
       1521 TTGAAGATGCTCCACCGAGTCATCTAAATTCATCT
          1 TTGAAGATGCTACACCGAGTCATCTGAATTTGTCT

                                     *          
       1556 TTGAAGATGCTACACCGAGTCATCTAAATTCT-TCT
          1 TTGAAGATGCTACACCGAGTCATCTGAATT-TGTCT

                                          
       1591 TTGAAGATGCTACACCGAGTCATCTGAATT
          1 TTGAAGATGCTACACCGAGTCATCTGAATT

       1621 CCCGAGAATT


Statistics
Matches: 402,  Mismatches: 35, Indels: 14
        0.89            0.08        0.03

Matches are distributed among these distances:
  29   27  0.07
  32    2  0.00
  35  373  0.93

ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34


Consensus pattern (35 bp):   
TTGAAGATGCTACACCGAGTCATCTGAATTTGTCT

Found at i:2560 original size:1 final size:1

Alignment explanation


    Indices: 2512--2543  Score: 64
    Period size: 1  Copynumber: 32.0  Consensus size: 1

       2502 TTAGGCTGAG

                                            
       2512 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
          1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT

       2544 AAAGCATAAT


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   31  1.00

ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00


Consensus pattern (1 bp):   
T
Done.