Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010189.1 Corchorus olitorius cultivar O-4 contig10221, 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: 19367
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34


Found at i:13 original size:2 final size:2

Alignment explanation


    Indices: 7--33  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

          1 AACTAG

                                                    
          7 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

         34 TATGAAGTAA


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:1891 original size:22 final size:22

Alignment explanation


    Indices: 1866--1912  Score: 69
    Period size: 22  Copynumber: 2.1  Consensus size: 22

       1856 TATCCTTATA

                     *             
       1866 ACTATTTTATTTTTATCA-TTTT
          1 ACTATTTTACTTTTAT-AGTTTT

                                  
       1888 ACTATTTTACTTTTATAGTTTT
          1 ACTATTTTACTTTTATAGTTTT

               
       1910 ACT
          1 ACT

       1913 CAACTAAAAA


Statistics
Matches: 23,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  21    1  0.04
  22   22  0.96

ACGTcount: A:0.23, C:0.11, G:0.02, T:0.64


Consensus pattern (22 bp):   
ACTATTTTACTTTTATAGTTTT

Found at i:1908 original size:93 final size:93

Alignment explanation


    Indices: 1805--1973  Score: 302
    Period size: 93  Copynumber: 1.8  Consensus size: 93

       1795 TTGTTTAAAT

                         *                                                   
       1805 TTTTATAGTTTCAGTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
          1 TTTTATAGTTTCACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA

                                        
       1870 TTTTATTTTTATCATTTTACTATTTTAC
         66 TTTTATTTTTATCATTTTACTATTTTAC

                       *                                *                *   
       1898 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTATATCTAATATCCTTATACCTA
          1 TTTTATAGTTTCACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA

                       
       1963 TTTTATTTTTA
         66 TTTTATTTTTA

       1974 CGATATTATT


Statistics
Matches: 72,  Mismatches: 4, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  93   72  1.00

ACGTcount: A:0.32, C:0.13, G:0.02, T:0.53


Consensus pattern (93 bp):   
TTTTATAGTTTCACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
TTTTATTTTTATCATTTTACTATTTTAC

Found at i:5610 original size:22 final size:21

Alignment explanation


    Indices: 5585--5645  Score: 52
    Period size: 22  Copynumber: 2.8  Consensus size: 21

       5575 TATAGTTAGG

                                  *
       5585 TTATTAAAGTTTCATATGG-AAT
          1 TTATTAAA-TTTCATA-GGTAAA

                *       *         
       5607 TTATCACAATTTTATAGGTAAA
          1 TTATTA-AATTTCATAGGTAAA

                             
       5629 TTATTAAAATTTCATAG
          1 TTATT-AAATTTCATAG

       5646 CATGGTTATC


Statistics
Matches: 31,  Mismatches: 5, Indels: 6
        0.74            0.12        0.14

Matches are distributed among these distances:
  21    2  0.06
  22   26  0.84
  23    3  0.10

ACGTcount: A:0.39, C:0.07, G:0.10, T:0.44


Consensus pattern (21 bp):   
TTATTAAATTTCATAGGTAAA

Found at i:5654 original size:22 final size:22

Alignment explanation


    Indices: 5629--5688  Score: 75
    Period size: 22  Copynumber: 2.7  Consensus size: 22

       5619 TATAGGTAAA

                *               * 
       5629 TTATTAAAATTTCATAGCATGG
          1 TTATCAAAATTTCATAGCATAG

                     *  *    *    
       5651 TTATCAAAAATTAATAGGATAG
          1 TTATCAAAATTTCATAGCATAG

                            
       5673 TTATCAAAATTTCATA
          1 TTATCAAAATTTCATA

       5689 AAAATAGATG


Statistics
Matches: 31,  Mismatches: 7, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  22   31  1.00

ACGTcount: A:0.43, C:0.08, G:0.10, T:0.38


Consensus pattern (22 bp):   
TTATCAAAATTTCATAGCATAG
Done.