Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021948.1 Corchorus olitorius cultivar O-4 contig21981, 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: 10218
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36


Found at i:3871 original size:24 final size:25

Alignment explanation


    Indices: 3837--3887  Score: 77
    Period size: 24  Copynumber: 2.1  Consensus size: 25

       3827 ATTGGAGTAT

                           *         
       3837 TTATTTATCTTGTTTCTTAATTTTA
          1 TTATTTATCTTGTTTATTAATTTTA

                              *      
       3862 TTATTT-TCTTGTTTATTTATTTTA
          1 TTATTTATCTTGTTTATTAATTTTA

              
       3886 TT
          1 TT

       3888 GTTACTCTAT


Statistics
Matches: 24,  Mismatches: 2, Indels: 1
        0.89            0.07        0.04

Matches are distributed among these distances:
  24   18  0.75
  25    6  0.25

ACGTcount: A:0.18, C:0.06, G:0.04, T:0.73


Consensus pattern (25 bp):   
TTATTTATCTTGTTTATTAATTTTA

Found at i:5540 original size:45 final size:45

Alignment explanation


    Indices: 5489--5585  Score: 167
    Period size: 45  Copynumber: 2.2  Consensus size: 45

       5479 AAAATCTGAG

                                                         
       5489 GCTACCCAGCCCCGGGTGACCCAAGAAGCTTAAATACTAAGATAC
          1 GCTACCCAGCCCCGGGTGACCCAAGAAGCTTAAATACTAAGATAC

                                  *            *         
       5534 GCTACCCAGCCCCGGGTGACCCCAGAAGCTTAAATGCTAAGATAC
          1 GCTACCCAGCCCCGGGTGACCCAAGAAGCTTAAATACTAAGATAC

            *      
       5579 CCTACCC
          1 GCTACCC

       5586 GCGGCCGGGC


Statistics
Matches: 49,  Mismatches: 3, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  45   49  1.00

ACGTcount: A:0.30, C:0.35, G:0.20, T:0.15


Consensus pattern (45 bp):   
GCTACCCAGCCCCGGGTGACCCAAGAAGCTTAAATACTAAGATAC

Found at i:8556 original size:24 final size:25

Alignment explanation


    Indices: 8522--8575  Score: 92
    Period size: 24  Copynumber: 2.2  Consensus size: 25

       8512 ATTGAAGTAT

                                     
       8522 TTATTTATCTTGTTTATTAATTTTA
          1 TTATTTATCTTGTTTATTAATTTTA

                              *      
       8547 TTATTT-TCTTGTTTATTTATTTTA
          1 TTATTTATCTTGTTTATTAATTTTA

                 
       8571 TTATT
          1 TTATT

       8576 ACTCTATTCA


Statistics
Matches: 28,  Mismatches: 1, Indels: 1
        0.93            0.03        0.03

Matches are distributed among these distances:
  24   22  0.79
  25    6  0.21

ACGTcount: A:0.20, C:0.04, G:0.04, T:0.72


Consensus pattern (25 bp):   
TTATTTATCTTGTTTATTAATTTTA

Found at i:8575 original size:12 final size:13

Alignment explanation


    Indices: 8521--8566  Score: 53
    Period size: 12  Copynumber: 3.7  Consensus size: 13

       8511 GATTGAAGTA

                         
       8521 TTTATTTATCTTG
          1 TTTATTTATCTTG

                  *      
       8534 TTTATTAAT-TT-
          1 TTTATTTATCTTG

                          
       8545 TATTATTT-TCTTG
          1 T-TTATTTATCTTG

                     
       8558 TTTATTTAT
          1 TTTATTTAT

       8567 TTTATTATTA


Statistics
Matches: 27,  Mismatches: 2, Indels: 8
        0.73            0.05        0.22

Matches are distributed among these distances:
  11    2  0.07
  12   15  0.56
  13   10  0.37

ACGTcount: A:0.20, C:0.04, G:0.04, T:0.72


Consensus pattern (13 bp):   
TTTATTTATCTTG

Found at i:9161 original size:15 final size:15

Alignment explanation


    Indices: 9143--9176  Score: 59
    Period size: 15  Copynumber: 2.3  Consensus size: 15

       9133 AAAAGGGAGG

                         * 
       9143 AAGAAGAAGAAGAGA
          1 AAGAAGAAGAAGAAA

                           
       9158 AAGAAGAAGAAGAAA
          1 AAGAAGAAGAAGAAA

                
       9173 AAGA
          1 AAGA

       9177 GGGTTCCATT


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

Matches are distributed among these distances:
  15   18  1.00

ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00


Consensus pattern (15 bp):   
AAGAAGAAGAAGAAA

Found at i:9523 original size:27 final size:27

Alignment explanation


    Indices: 9493--9550  Score: 98
    Period size: 27  Copynumber: 2.1  Consensus size: 27

       9483 CATTTACATG

                                       
       9493 TCCAAGGGCATTTTGGTCAATTGCACA
          1 TCCAAGGGCATTTTGGTCAATTGCACA

                *              *       
       9520 TCCAGGGGCATTTTGGTCATTTGCACA
          1 TCCAAGGGCATTTTGGTCAATTGCACA

                
       9547 TCCA
          1 TCCA

       9551 TGAAACGATC


Statistics
Matches: 29,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  27   29  1.00

ACGTcount: A:0.22, C:0.24, G:0.22, T:0.31


Consensus pattern (27 bp):   
TCCAAGGGCATTTTGGTCAATTGCACA
Done.