Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018887.1 Corchorus olitorius cultivar O-4 contig18920, 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: 26289
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31


Found at i:11787 original size:16 final size:16

Alignment explanation


    Indices: 11757--11786  Score: 53
    Period size: 16  Copynumber: 1.9  Consensus size: 16

      11747 TTTTAAAGGT

                            
      11757 TTTCTTTTTACTTTTA
          1 TTTCTTTTTACTTTTA

                           
      11773 TTTCTTTTTA-TTTT
          1 TTTCTTTTTACTTTT

      11787 TCTTTTTCTG


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

Matches are distributed among these distances:
  15    4  0.29
  16   10  0.71

ACGTcount: A:0.10, C:0.10, G:0.00, T:0.80


Consensus pattern (16 bp):   
TTTCTTTTTACTTTTA

Found at i:23814 original size:165 final size:166

Alignment explanation


    Indices: 23622--23950  Score: 525
    Period size: 168  Copynumber: 2.0  Consensus size: 166

      23612 TCATTTTGTT

                     *                  *          *                      *  
      23622 TTTTTTTTTCTTATTATAAAAAACCATATTAGGTAGAAGTGAAATT-AAAAAAAATGGCCTATAG
          1 TTTTTTTTTATTATTATAAAAAACCATAATAGGTAGAAGCGAAATTAAAAAAAAATGGCCTAAAG

                         *      *    *                                       
      23686 ATGGAGAGTTTAGGATCCAAGATTTTTGGTGAATTTTATCGATCTCTAACCATCCTAGTAGTTAA
         66 ATGGAGAGTTTAGAATCCAAAATTTATGGTGAATTTTATCGATCTCTAACCATCCTAGTAGTTAA

                                                
      23751 TTAGGAGAGTAATTCATTAAAATATATGATATTTGC
        131 TTAGGAGAGTAATTCATTAAAATATATGATATTTGC

                                                       *                *    
      23787 TTTTTTTTTATTATTATAAAAAACCATAATAGGTAGAAGCGAAGTTACGAAAAAAAATGGTCTAA
          1 TTTTTTTTTATTATTATAAAAAACCATAATAGGTAGAAGCGAAATTA--AAAAAAAATGGCCTAA

                                                               *             
      23852 AGATGGAGAGTTTAGAATCCAAAATTTATGGTGAATTTTATCGATCTCTAAGCATCCTAGTAGTT
         64 AGATGGAGAGTTTAGAATCCAAAATTTATGGTGAATTTTATCGATCTCTAACCATCCTAGTAGTT

                     *           *            
      23917 AATTAGGAGGGTAATTCATTACAATATATGATAT
        129 AATTAGGAGAGTAATTCATTAAAATATATGATAT

      23951 CATTATTTAT


Statistics
Matches: 149,  Mismatches: 12, Indels: 3
        0.91            0.07        0.02

Matches are distributed among these distances:
 165   42  0.28
 168  107  0.72

ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36


Consensus pattern (166 bp):   
TTTTTTTTTATTATTATAAAAAACCATAATAGGTAGAAGCGAAATTAAAAAAAAATGGCCTAAAG
ATGGAGAGTTTAGAATCCAAAATTTATGGTGAATTTTATCGATCTCTAACCATCCTAGTAGTTAA
TTAGGAGAGTAATTCATTAAAATATATGATATTTGC

Found at i:24870 original size:11 final size:11

Alignment explanation


    Indices: 24827--24864  Score: 51
    Period size: 11  Copynumber: 3.5  Consensus size: 11

      24817 TTCCTATATA

                *      
      24827 AAATAAATTAT
          1 AAATTAATTAT

                        
      24838 CAAA-TAATTAT
          1 -AAATTAATTAT

                       
      24849 AAATTAATTAT
          1 AAATTAATTAT

                 
      24860 AAATT
          1 AAATT

      24865 TGTTATGAAT


Statistics
Matches: 24,  Mismatches: 1, Indels: 3
        0.86            0.04        0.11

Matches are distributed among these distances:
  10    3  0.12
  11   18  0.75
  12    3  0.12

ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39


Consensus pattern (11 bp):   
AAATTAATTAT

Found at i:25629 original size:84 final size:84

Alignment explanation


    Indices: 25488--25656  Score: 338
    Period size: 84  Copynumber: 2.0  Consensus size: 84

      25478 ATTATGCCGC

                                                                             
      25488 ATTATTTTCATTATTTAATTATCTTTTAGGTTATGAAGAAATTTAATGTATTAATGTTGATATGA
          1 ATTATTTTCATTATTTAATTATCTTTTAGGTTATGAAGAAATTTAATGTATTAATGTTGATATGA

                               
      25553 TCTAATCCAAATAATTTTA
         66 TCTAATCCAAATAATTTTA

                                                                             
      25572 ATTATTTTCATTATTTAATTATCTTTTAGGTTATGAAGAAATTTAATGTATTAATGTTGATATGA
          1 ATTATTTTCATTATTTAATTATCTTTTAGGTTATGAAGAAATTTAATGTATTAATGTTGATATGA

                               
      25637 TCTAATCCAAATAATTTTA
         66 TCTAATCCAAATAATTTTA

             
      25656 A
          1 A

      25657 GGAAAGATTC


Statistics
Matches: 85,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  84   85  1.00

ACGTcount: A:0.36, C:0.06, G:0.09, T:0.49


Consensus pattern (84 bp):   
ATTATTTTCATTATTTAATTATCTTTTAGGTTATGAAGAAATTTAATGTATTAATGTTGATATGA
TCTAATCCAAATAATTTTA

Found at i:26083 original size:2 final size:2

Alignment explanation


    Indices: 26076--26117  Score: 84
    Period size: 2  Copynumber: 21.0  Consensus size: 2

      26066 TTTCTCAATA

                                                                          
      26076 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

      26118 CCAAGCCATT


Statistics
Matches: 40,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   40  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:26192 original size:15 final size:15

Alignment explanation


    Indices: 26172--26202  Score: 53
    Period size: 15  Copynumber: 2.1  Consensus size: 15

      26162 TACGTCAGTG

                    *      
      26172 TAATAAATGAATAAA
          1 TAATAAATAAATAAA

                           
      26187 TAATAAATAAATAAA
          1 TAATAAATAAATAAA

             
      26202 T
          1 T

      26203 CAAAAAGTGA


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  15   15  1.00

ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29


Consensus pattern (15 bp):   
TAATAAATAAATAAA
Done.