Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023122.1 Corchorus olitorius cultivar O-4 contig23155, 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: 8780
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.36


Found at i:1103 original size:48 final size:48

Alignment explanation


    Indices: 979--1120  Score: 146
    Period size: 49  Copynumber: 3.0  Consensus size: 48

        969 CAAGCAATCC

                *                       *     **          *  
        979 TTTACTTTTCA-CTGCACTTTTTCTCAAATTTTACTACAAAATTGAAAT
          1 TTTAATTTTCATC-GCACTTTTTCTCAATTTTTAAGACAAAATTGATAT

                     *   *                                  * 
       1027 TTT-ATTTTTACTTGCATCTTTTTCTCAATTTTTAAGACAAAATTGATCT
          1 TTTAATTTTCA-TCGCA-CTTTTTCTCAATTTTTAAGACAAAATTGATAT

                                  *          *            
       1076 TTTAATTTTCATCGCACTTTTTATCAATTTTT-TGACAAAATTGAT
          1 TTTAATTTTCATCGCACTTTTTCTCAATTTTTAAGACAAAATTGAT

       1121 TGGCACGCTC


Statistics
Matches: 78,  Mismatches: 12, Indels: 9
        0.79            0.12        0.09

Matches are distributed among these distances:
  47   17  0.22
  48   21  0.27
  49   34  0.44
  50    6  0.08

ACGTcount: A:0.29, C:0.15, G:0.06, T:0.50


Consensus pattern (48 bp):   
TTTAATTTTCATCGCACTTTTTCTCAATTTTTAAGACAAAATTGATAT

Found at i:2804 original size:25 final size:24

Alignment explanation


    Indices: 2750--2807  Score: 73
    Period size: 25  Copynumber: 2.4  Consensus size: 24

       2740 ATCAGTCTTG

                                *   
       2750 AATTT-TTTAATGTTTAATTCTTA
          1 AATTTATTTAATGTTTAATTATTA

                                     *
       2773 AATTTTATTTAATGTCTTAATTATTC
          1 AA-TTTATTTAATGT-TTAATTATTA

                     
       2799 AATTTATTT
          1 AATTTATTT

       2808 TACAATCCAC


Statistics
Matches: 30,  Mismatches: 2, Indels: 4
        0.83            0.06        0.11

Matches are distributed among these distances:
  23    2  0.07
  24    3  0.10
  25   15  0.50
  26   10  0.33

ACGTcount: A:0.31, C:0.05, G:0.03, T:0.60


Consensus pattern (24 bp):   
AATTTATTTAATGTTTAATTATTA

Found at i:2809 original size:26 final size:24

Alignment explanation


    Indices: 2752--2809  Score: 71
    Period size: 26  Copynumber: 2.3  Consensus size: 24

       2742 CAGTCTTGAA

                             *      
       2752 TTTTTTAATGTTTAATTCTTAAAT
          1 TTTTTTAATGTTTAATTATTAAAT

                                  *   
       2776 TTTATTTAATGTCTTAATTATTCAAT
          1 TTT-TTTAATGT-TTAATTATTAAAT

                    
       2802 TTATTTTA
          1 TT-TTTTA

       2810 CAATCCACTA


Statistics
Matches: 29,  Mismatches: 2, Indels: 4
        0.83            0.06        0.11

Matches are distributed among these distances:
  24    3  0.10
  25    8  0.28
  26   17  0.59
  27    1  0.03

ACGTcount: A:0.29, C:0.05, G:0.03, T:0.62


Consensus pattern (24 bp):   
TTTTTTAATGTTTAATTATTAAAT

Found at i:4286 original size:4 final size:4

Alignment explanation


    Indices: 4277--4327  Score: 93
    Period size: 4  Copynumber: 12.5  Consensus size: 4

       4267 TTAATATATT

                                                                        
       4277 ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTAA ATTA ATTA ATTA ATTA
          1 ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATT-A ATTA ATTA ATTA ATTA

              
       4326 AT
          1 AT

       4328 ACCAATAGAA


Statistics
Matches: 46,  Mismatches: 0, Indels: 2
        0.96            0.00        0.04

Matches are distributed among these distances:
   4   42  0.91
   5    4  0.09

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (4 bp):   
ATTA

Done.