Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024213.1 Corchorus olitorius cultivar O-4 contig24246, 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: 8272
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34


Found at i:364 original size:22 final size:22

Alignment explanation


    Indices: 336--465  Score: 98
    Period size: 22  Copynumber: 5.5  Consensus size: 22

        326 CAACAAGAAG

                                  
        336 TGCTCTGCAAAGTGGAAAATAA
          1 TGCTCTGCAAAGTGGAAAATAA

                             ***     
        358 TGCTCTGCAAAGATGTTTCCAATAA
          1 TGCTCTGCAAAG-TG--GAAAATAA

               ***   *                
        383 TGCAAAGCTGAAGTTGAAGAAAATAA
          1 TGCTCTGC-AAAG-TG--GAAAATAA

                                    
        409 TGCACTCTGCAAAGTGGAAAATAA
          1 TG--CTCTGCAAAGTGGAAAATAA

                         **       
        433 TGCTCTGCAAAGTATAAAATAA
          1 TGCTCTGCAAAGTGGAAAATAA

                       
        455 TGCTCTGCAAA
          1 TGCTCTGCAAA

        466 AATGTTTCCA


Statistics
Matches: 83,  Mismatches: 19, Indels: 12
        0.73            0.17        0.11

Matches are distributed among these distances:
  22   41  0.49
  23    2  0.02
  24   10  0.12
  25   10  0.12
  26   14  0.17
  27    3  0.04
  28    3  0.04

ACGTcount: A:0.41, C:0.15, G:0.19, T:0.25


Consensus pattern (22 bp):   
TGCTCTGCAAAGTGGAAAATAA

Found at i:844 original size:27 final size:27

Alignment explanation


    Indices: 812--865  Score: 74
    Period size: 27  Copynumber: 2.0  Consensus size: 27

        802 CTTATTTCTT

                                        
        812 AAATATATTTCTAAAT-TGACATTATTA
          1 AAATATATTT-TAAATATGACATTATTA

                         *    *        
        839 AAATATATTTTAATTATGTCATTATTA
          1 AAATATATTTTAAATATGACATTATTA

        866 TTAAAAATAT


Statistics
Matches: 24,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  26    4  0.17
  27   20  0.83

ACGTcount: A:0.43, C:0.06, G:0.04, T:0.48


Consensus pattern (27 bp):   
AAATATATTTTAAATATGACATTATTA

Found at i:930 original size:43 final size:45

Alignment explanation


    Indices: 840--930  Score: 141
    Period size: 43  Copynumber: 2.0  Consensus size: 45

        830 ACATTATTAA

                                   *                       
        840 AATATATTTTAATTATGTCATTATTATTAAAAATATATAAAATTGCC
          1 AATATATTTTAATTATGTC--TACTATTAAAAATATATAAAATTGCC

                                                         
        887 AATATATTTTAATTATGTC-ACTATT-AAAATATATAAAATTGCC
          1 AATATATTTTAATTATGTCTACTATTAAAAATATATAAAATTGCC

             
        930 A
          1 A

        931 TTATTAAAAT


Statistics
Matches: 43,  Mismatches: 1, Indels: 4
        0.90            0.02        0.08

Matches are distributed among these distances:
  43   19  0.44
  44    5  0.12
  47   19  0.44

ACGTcount: A:0.45, C:0.08, G:0.04, T:0.43


Consensus pattern (45 bp):   
AATATATTTTAATTATGTCTACTATTAAAAATATATAAAATTGCC

Found at i:1838 original size:22 final size:22

Alignment explanation


    Indices: 1813--1917  Score: 70
    Period size: 22  Copynumber: 4.8  Consensus size: 22

       1803 TCATACGGAG

                               *  
       1813 GTTATCAAAATTTCATAGTTTA
          1 GTTATCAAAATTTCATAGTGTA

                   **       *   * 
       1835 GTTATCAGTATTTCATTG-GGA
          1 GTTATCAAAATTTCATAGTGTA

                    *            *  
       1856 GTTTATCACAATTTCATA-TAATA
          1 G-TTATCAAAATTTCATAGT-GTA

            * *     *            *
       1879 ATCATCAACATTTCATAGTGTG
          1 GTTATCAAAATTTCATAGTGTA

                    *        
       1901 GTTATCAACATTTCATA
          1 GTTATCAAAATTTCATA

       1918 AAAATATTTA


Statistics
Matches: 61,  Mismatches: 18, Indels: 8
        0.70            0.21        0.09

Matches are distributed among these distances:
  21    2  0.03
  22   57  0.93
  23    2  0.03

ACGTcount: A:0.33, C:0.13, G:0.11, T:0.42


Consensus pattern (22 bp):   
GTTATCAAAATTTCATAGTGTA

Found at i:1983 original size:2 final size:2

Alignment explanation


    Indices: 1976--2002  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

       1966 CTAAAACTAG

                                                    
       1976 TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA T

       2003 TGGTTGGTTT


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   25  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:6243 original size:15 final size:14

Alignment explanation


    Indices: 6218--6247  Score: 51
    Period size: 15  Copynumber: 2.1  Consensus size: 14

       6208 AGTTGGAAGG

                          
       6218 TGAACTTTTTTTTT
          1 TGAACTTTTTTTTT

                           
       6232 TGAACGTTTTTTTTT
          1 TGAAC-TTTTTTTTT

             
       6247 T
          1 T

       6248 TTTGTATTTG


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

Matches are distributed among these distances:
  14    5  0.33
  15   10  0.67

ACGTcount: A:0.13, C:0.07, G:0.10, T:0.70


Consensus pattern (14 bp):   
TGAACTTTTTTTTT
Done.