Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019506.1 Corchorus olitorius cultivar O-4 contig19539, 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: 4558
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34


Found at i:117 original size:13 final size:13

Alignment explanation


    Indices: 99--123  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

         89 TTTTTACCAC

                         
         99 CTTAAAATTATTG
          1 CTTAAAATTATTG

                        
        112 CTTAAAATTATT
          1 CTTAAAATTATT

        124 TTTTGGCAAA


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.40, C:0.08, G:0.04, T:0.48


Consensus pattern (13 bp):   
CTTAAAATTATTG

Found at i:2307 original size:3 final size:3

Alignment explanation


    Indices: 2299--2337  Score: 78
    Period size: 3  Copynumber: 13.0  Consensus size: 3

       2289 ATCTCCTAAC

                                                               
       2299 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
          1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT

       2338 TGCAAAAATA


Statistics
Matches: 36,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   36  1.00

ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33


Consensus pattern (3 bp):   
AAT

Found at i:3170 original size:45 final size:45

Alignment explanation


    Indices: 3106--3196  Score: 182
    Period size: 45  Copynumber: 2.0  Consensus size: 45

       3096 TTCATATACT

                                                         
       3106 GTAATATTTACAAAATATAAAACATTGTGGCATATGTTGACATCA
          1 GTAATATTTACAAAATATAAAACATTGTGGCATATGTTGACATCA

                                                         
       3151 GTAATATTTACAAAATATAAAACATTGTGGCATATGTTGACATCA
          1 GTAATATTTACAAAATATAAAACATTGTGGCATATGTTGACATCA

             
       3196 G
          1 G

       3197 CATCATTTGA


Statistics
Matches: 46,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  45   46  1.00

ACGTcount: A:0.42, C:0.11, G:0.14, T:0.33


Consensus pattern (45 bp):   
GTAATATTTACAAAATATAAAACATTGTGGCATATGTTGACATCA
Done.