Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012335.1 Corchorus olitorius cultivar O-4 contig12368, 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: 29525
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.34


Found at i:17594 original size:1 final size:1

Alignment explanation


    Indices: 17588--17618  Score: 62
    Period size: 1  Copynumber: 31.0  Consensus size: 1

      17578 AGATTCATTC

                                           
      17588 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
          1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT

      17619 CTGCAGGTAT


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   30  1.00

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


Consensus pattern (1 bp):   
T

Found at i:21133 original size:27 final size:29

Alignment explanation


    Indices: 21095--21156  Score: 92
    Period size: 27  Copynumber: 2.2  Consensus size: 29

      21085 TTTCCTTTTC

                            *            
      21095 TTTTTCTTTTTTGCCAGA-AAA-TTAGGG
          1 TTTTTCTTTTTTGCCACATAAAGTTAGGG

                 *                       
      21122 TTTTTTTTTTTTGCCACATAAAGTTAGGG
          1 TTTTTCTTTTTTGCCACATAAAGTTAGGG

                  
      21151 TTTTTC
          1 TTTTTC

      21157 GGTTCCTTGA


Statistics
Matches: 30,  Mismatches: 3, Indels: 2
        0.86            0.09        0.06

Matches are distributed among these distances:
  27   16  0.53
  28    3  0.10
  29   11  0.37

ACGTcount: A:0.19, C:0.11, G:0.16, T:0.53


Consensus pattern (29 bp):   
TTTTTCTTTTTTGCCACATAAAGTTAGGG

Found at i:21327 original size:7 final size:6

Alignment explanation


    Indices: 21292--21345  Score: 58
    Period size: 6  Copynumber: 9.2  Consensus size: 6

      21282 TAAATTTACA

                            *      *                             *  
      21292 TTTC-T TTTCTT TTCCTT TTCCTT TTTCTT TTGTCTT TTT-TT TTTTTT
          1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TT-TCTT TTTCTT TTTCTT

                    
      21339 TTTCTT T
          1 TTTCTT T

      21346 CCAAATTTAA


Statistics
Matches: 43,  Mismatches: 3, Indels: 5
        0.84            0.06        0.10

Matches are distributed among these distances:
   5    9  0.21
   6   28  0.65
   7    6  0.14

ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81


Consensus pattern (6 bp):   
TTTCTT

Found at i:24603 original size:31 final size:31

Alignment explanation


    Indices: 24568--24658  Score: 155
    Period size: 31  Copynumber: 2.9  Consensus size: 31

      24558 GTGTCCGACG

                                           
      24568 TGGCACGCCAGGTGTACCAAAAAGCGACATA
          1 TGGCACGCCAGGTGTACCAAAAAGCGACATA

                                          *
      24599 TGGCACGCCAGGTGTACCAAAAAGCGACATG
          1 TGGCACGCCAGGTGTACCAAAAAGCGACATA

                      *             *    
      24630 TGGCACGCCACGTGTACCAAAAAGTGACA
          1 TGGCACGCCAGGTGTACCAAAAAGCGACA

      24659 CGTTGTTAGG


Statistics
Matches: 57,  Mismatches: 3, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  31   57  1.00

ACGTcount: A:0.34, C:0.26, G:0.26, T:0.13


Consensus pattern (31 bp):   
TGGCACGCCAGGTGTACCAAAAAGCGACATA
Done.