Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013583.1 Corchorus olitorius cultivar O-4 contig13616, 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: 20657
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32


Found at i:1408 original size:19 final size:19

Alignment explanation


    Indices: 1384--1421  Score: 67
    Period size: 19  Copynumber: 2.0  Consensus size: 19

       1374 CTAGTTAATT

                               
       1384 AGGTTTTCATCGACAGATA
          1 AGGTTTTCATCGACAGATA

                          *    
       1403 AGGTTTTCATCGACGGATA
          1 AGGTTTTCATCGACAGATA

       1422 GCGAATCTAA


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  19   18  1.00

ACGTcount: A:0.29, C:0.16, G:0.24, T:0.32


Consensus pattern (19 bp):   
AGGTTTTCATCGACAGATA

Found at i:3669 original size:30 final size:30

Alignment explanation


    Indices: 3633--3701  Score: 93
    Period size: 30  Copynumber: 2.3  Consensus size: 30

       3623 CCCCCCAAAT

                        *       *         
       3633 TTTTAAAATCTCGACGTTTTGCTCCTAAAC
          1 TTTTAAAATCTCAACGTTTTACTCCTAAAC

                   *   *  *               
       3663 TTTTAAATTCTTAATGTTTTACTCCTAAAC
          1 TTTTAAAATCTCAACGTTTTACTCCTAAAC

                     
       3693 TTTTAAAAT
          1 TTTTAAAAT

       3702 TTTGTTGACA


Statistics
Matches: 33,  Mismatches: 6, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  30   33  1.00

ACGTcount: A:0.30, C:0.17, G:0.06, T:0.46


Consensus pattern (30 bp):   
TTTTAAAATCTCAACGTTTTACTCCTAAAC

Found at i:13032 original size:7 final size:7

Alignment explanation


    Indices: 12978--13004  Score: 54
    Period size: 7  Copynumber: 3.9  Consensus size: 7

      12968 GAGAACAATT

                   
      12978 CTTTTTA
          1 CTTTTTA

                   
      12985 CTTTTTA
          1 CTTTTTA

                   
      12992 CTTTTTA
          1 CTTTTTA

                  
      12999 CTTTTT
          1 CTTTTT

      13005 TATATTTTAC


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   7   20  1.00

ACGTcount: A:0.11, C:0.15, G:0.00, T:0.74


Consensus pattern (7 bp):   
CTTTTTA

Found at i:13038 original size:29 final size:29

Alignment explanation


    Indices: 12980--13038  Score: 68
    Period size: 29  Copynumber: 2.0  Consensus size: 29

      12970 GAACAATTCT

                                     *   
      12980 TTTTACTTTTTACTTTTTACTTTTTTATA
          1 TTTTACTTTTTACTTTTTACTTTTTCATA

                         *                 
      13009 TTTTACATTTTT-GTTTTT-CTTTTTCCATA
          1 TTTTAC-TTTTTACTTTTTACTTTTT-CATA

             
      13038 T
          1 T

      13039 CATCTGGAGT


Statistics
Matches: 26,  Mismatches: 2, Indels: 4
        0.81            0.06        0.12

Matches are distributed among these distances:
  28    6  0.23
  29   15  0.58
  30    5  0.19

ACGTcount: A:0.15, C:0.12, G:0.02, T:0.71


Consensus pattern (29 bp):   
TTTTACTTTTTACTTTTTACTTTTTCATA

Found at i:14352 original size:16 final size:16

Alignment explanation


    Indices: 14310--14340  Score: 53
    Period size: 16  Copynumber: 1.9  Consensus size: 16

      14300 ATTCTCCTGC

                            
      14310 ACAGATAAACAATTAA
          1 ACAGATAAACAATTAA

                 *         
      14326 ACAGACAAACAATTA
          1 ACAGATAAACAATTA

      14341 CTACAATAAA


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  16   14  1.00

ACGTcount: A:0.61, C:0.16, G:0.06, T:0.16


Consensus pattern (16 bp):   
ACAGATAAACAATTAA
Done.