Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011998.1 Corchorus olitorius cultivar O-4 contig12031, 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: 18889
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.33


Found at i:5071 original size:21 final size:21

Alignment explanation


    Indices: 5045--5115  Score: 108
    Period size: 21  Copynumber: 3.4  Consensus size: 21

       5035 TGCTAGGAGA

                            *     
       5045 TCATTGGAGCAA-GTTCCAAGC
          1 TCATTGGAG-AAGGTTTCAAGC

                            *    
       5066 TCATTGGAGAAGGTTTTAAGC
          1 TCATTGGAGAAGGTTTCAAGC

                                 
       5087 TCATTGGAGAAGGTTTCAAGC
          1 TCATTGGAGAAGGTTTCAAGC

                    
       5108 TCATTGGA
          1 TCATTGGA

       5116 ATTGCCTAAG


Statistics
Matches: 46,  Mismatches: 3, Indels: 2
        0.90            0.06        0.04

Matches are distributed among these distances:
  20    2  0.04
  21   44  0.96

ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30


Consensus pattern (21 bp):   
TCATTGGAGAAGGTTTCAAGC

Found at i:15378 original size:10 final size:10

Alignment explanation


    Indices: 15365--15400  Score: 54
    Period size: 10  Copynumber: 3.5  Consensus size: 10

      15355 GTAGAACTTG

                      
      15365 GAAAAGTAAA
          1 GAAAAGTAAA

                  *   
      15375 GAAAAGAAAA
          1 GAAAAGTAAA

                       
      15385 GAAAAAGTAAA
          1 G-AAAAGTAAA

                 
      15396 GAAAA
          1 GAAAA

      15401 TATACCTTGA


Statistics
Matches: 23,  Mismatches: 2, Indels: 2
        0.85            0.07        0.07

Matches are distributed among these distances:
  10   14  0.61
  11    9  0.39

ACGTcount: A:0.75, C:0.00, G:0.19, T:0.06


Consensus pattern (10 bp):   
GAAAAGTAAA

Found at i:18322 original size:20 final size:20

Alignment explanation


    Indices: 18294--18347  Score: 58
    Period size: 20  Copynumber: 2.7  Consensus size: 20

      18284 GCCAAAAATA

                                 
      18294 TGATAATAAA-TAATACATAT
          1 TGATAATAAATTAATAC-TAT

                *               
      18314 TGATTATAAATTAATACTAT
          1 TGATAATAAATTAATACTAT

                 *         
      18334 T-ATAGTAATATTAA
          1 TGATAATAA-ATTAA

      18348 ATATAGGACA


Statistics
Matches: 29,  Mismatches: 3, Indels: 4
        0.81            0.08        0.11

Matches are distributed among these distances:
  19    5  0.17
  20   18  0.62
  21    6  0.21

ACGTcount: A:0.50, C:0.04, G:0.06, T:0.41


Consensus pattern (20 bp):   
TGATAATAAATTAATACTAT

Found at i:18719 original size:21 final size:21

Alignment explanation


    Indices: 18673--18798  Score: 123
    Period size: 21  Copynumber: 6.0  Consensus size: 21

      18663 CATTTAACAT

                                *
      18673 GGTTTGACTATCAAACTTT-A
          1 GGTTTGACTATCAAACTTTGG

                                  
      18693 GGTTTGACTATCGAAA-TTTGG
          1 GGTTTGACTATC-AAACTTTGG

                   *   *        *
      18714 GGTTTGAATATTAAACTTTGA
          1 GGTTTGACTATCAAACTTTGG

             *                    
      18735 GATTTGA-TCATCAAACTTTGG
          1 GGTTTGACT-ATCAAACTTTGG

                 *  *      *     
      18756 GGTTTAACCATCAAAATTTGG
          1 GGTTTGACTATCAAACTTTGG

                    *      *     
      18777 GGTTTGACAATCAAAATTTGG
          1 GGTTTGACTATCAAACTTTGG

             
      18798 G
          1 G

      18799 CAAAAACACG


Statistics
Matches: 88,  Mismatches: 13, Indels: 9
        0.80            0.12        0.08

Matches are distributed among these distances:
  20   19  0.22
  21   69  0.78

ACGTcount: A:0.30, C:0.11, G:0.21, T:0.37


Consensus pattern (21 bp):   
GGTTTGACTATCAAACTTTGG

Found at i:18730 original size:41 final size:42

Alignment explanation


    Indices: 18673--18760  Score: 110
    Period size: 41  Copynumber: 2.1  Consensus size: 42

      18663 CATTTAACAT

                   *              *                     
      18673 GGTTTGACTATCAAACTTT-AGGTTTGA-CTATCGAAA-TTTGG
          1 GGTTTGAATATCAAACTTTGAGATTTGATC-ATC-AAACTTTGG

                       *                              
      18714 GGTTTGAATATTAAACTTTGAGATTTGATCATCAAACTTTGG
          1 GGTTTGAATATCAAACTTTGAGATTTGATCATCAAACTTTGG

                 
      18756 GGTTT
          1 GGTTT

      18761 AACCATCAAA


Statistics
Matches: 41,  Mismatches: 3, Indels: 5
        0.84            0.06        0.10

Matches are distributed among these distances:
  41   20  0.49
  42   20  0.49
  43    1  0.02

ACGTcount: A:0.27, C:0.10, G:0.22, T:0.41


Consensus pattern (42 bp):   
GGTTTGAATATCAAACTTTGAGATTTGATCATCAAACTTTGG
Done.