Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016990.1 Corchorus olitorius cultivar O-4 contig17023, 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: 32811
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.34


Found at i:10768 original size:21 final size:21

Alignment explanation


    Indices: 10742--10802  Score: 86
    Period size: 21  Copynumber: 2.9  Consensus size: 21

      10732 GATAGGCCGC

                         *       
      10742 GACCTTGGACGCGTGCGGGCA
          1 GACCTTGGACGCGCGCGGGCA

                        *   *    
      10763 GACCTTGGACGCACGCCGGCA
          1 GACCTTGGACGCGCGCGGGCA

              *                
      10784 GATCTTGGACGCGCGCGGG
          1 GACCTTGGACGCGCGCGGG

      10803 TGAGCACCGA


Statistics
Matches: 34,  Mismatches: 6, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  21   34  1.00

ACGTcount: A:0.15, C:0.31, G:0.41, T:0.13


Consensus pattern (21 bp):   
GACCTTGGACGCGCGCGGGCA

Found at i:20401 original size:8 final size:8

Alignment explanation


    Indices: 20385--20420  Score: 63
    Period size: 8  Copynumber: 4.5  Consensus size: 8

      20375 ATCTTTCATA

                *   
      20385 CTTTCATT
          1 CTTTGATT

                    
      20393 CTTTGATT
          1 CTTTGATT

                    
      20401 CTTTGATT
          1 CTTTGATT

                    
      20409 CTTTGATT
          1 CTTTGATT

                
      20417 CTTT
          1 CTTT

      20421 CTTTTATTAA


Statistics
Matches: 27,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
   8   27  1.00

ACGTcount: A:0.11, C:0.17, G:0.08, T:0.64


Consensus pattern (8 bp):   
CTTTGATT

Found at i:20404 original size:16 final size:16

Alignment explanation


    Indices: 20371--20421  Score: 68
    Period size: 16  Copynumber: 3.2  Consensus size: 16

      20361 ACTGGAATTA

                       *  * 
      20371 TTTCA-TCTTTCATAC
          1 TTTCATTCTTTGATTC

                            
      20386 TTTCATTCTTTGATTC
          1 TTTCATTCTTTGATTC

               *            
      20402 TTTGATTCTTTGATTC
          1 TTTCATTCTTTGATTC

                
      20418 TTTC
          1 TTTC

      20422 TTTTATTAAT


Statistics
Matches: 31,  Mismatches: 4, Indels: 1
        0.86            0.11        0.03

Matches are distributed among these distances:
  15    5  0.16
  16   26  0.84

ACGTcount: A:0.14, C:0.20, G:0.06, T:0.61


Consensus pattern (16 bp):   
TTTCATTCTTTGATTC

Found at i:31532 original size:14 final size:15

Alignment explanation


    Indices: 31513--31541  Score: 51
    Period size: 14  Copynumber: 2.0  Consensus size: 15

      31503 ATAGTTAGTT

                           
      31513 TTTCTTTTTC-TTTA
          1 TTTCTTTTTCGTTTA

                           
      31527 TTTCTTTTTCGTTTA
          1 TTTCTTTTTCGTTTA

      31542 GCATTTAGTT


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

Matches are distributed among these distances:
  14   10  0.71
  15    4  0.29

ACGTcount: A:0.07, C:0.14, G:0.03, T:0.76


Consensus pattern (15 bp):   
TTTCTTTTTCGTTTA

Found at i:31573 original size:18 final size:18

Alignment explanation


    Indices: 31552--31587  Score: 54
    Period size: 18  Copynumber: 2.0  Consensus size: 18

      31542 GCATTTAGTT

                 *   *        
      31552 TACATTTAGTTTGCATTG
          1 TACATGTAGATTGCATTG

                              
      31570 TACATGTAGATTGCATTG
          1 TACATGTAGATTGCATTG

      31588 CATTTAACTT


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  18   16  1.00

ACGTcount: A:0.25, C:0.11, G:0.19, T:0.44


Consensus pattern (18 bp):   
TACATGTAGATTGCATTG
Done.