Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015839.1 Corchorus olitorius cultivar O-4 contig15872, 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: 15015
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35


Found at i:302 original size:19 final size:19

Alignment explanation


    Indices: 278--314  Score: 65
    Period size: 19  Copynumber: 1.9  Consensus size: 19

        268 AGTGGCTTCT

                               
        278 TATTCATGGATGGAAATCA
          1 TATTCATGGATGGAAATCA

                         *    
        297 TATTCATGGATGGGAATC
          1 TATTCATGGATGGAAATC

        315 GGCAATAGGT


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  19   17  1.00

ACGTcount: A:0.32, C:0.11, G:0.24, T:0.32


Consensus pattern (19 bp):   
TATTCATGGATGGAAATCA

Found at i:789 original size:2 final size:2

Alignment explanation


    Indices: 782--811  Score: 60
    Period size: 2  Copynumber: 15.0  Consensus size: 2

        772 ACGTTTTCCA

                                                        
        782 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

        812 TTGTATCTTG


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   28  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:5503 original size:14 final size:13

Alignment explanation


    Indices: 5467--5505  Score: 51
    Period size: 14  Copynumber: 2.8  Consensus size: 13

       5457 ATTTTATATT

                        * 
       5467 TATAATTATATTTA
          1 TATAATTA-ATTAA

                         
       5481 TATAATTAATTAA
          1 TATAATTAATTAA

                        
       5494 TATAATTTAATT
          1 TATAA-TTAATT

       5506 CTTAAAATAA


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

Matches are distributed among these distances:
  13    9  0.39
  14   14  0.61

ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54


Consensus pattern (13 bp):   
TATAATTAATTAA

Found at i:8345 original size:12 final size:12

Alignment explanation


    Indices: 8328--8359  Score: 55
    Period size: 12  Copynumber: 2.7  Consensus size: 12

       8318 TACCCTATGT

                        
       8328 AAACACGACACG
          1 AAACACGACACG

                        
       8340 AAACACGACACG
          1 AAACACGACACG

               *    
       8352 AAATACGA
          1 AAACACGA

       8360 ATTACCAGGT


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  12   19  1.00

ACGTcount: A:0.53, C:0.28, G:0.16, T:0.03


Consensus pattern (12 bp):   
AAACACGACACG

Found at i:8991 original size:11 final size:11

Alignment explanation


    Indices: 8975--9009  Score: 54
    Period size: 11  Copynumber: 3.3  Consensus size: 11

       8965 TATAGTGTTT

                       
       8975 TATATTATATA
          1 TATATTATATA

                   *   
       8986 TATATTAAATA
          1 TATATTATATA

                       
       8997 TATA-TATATA
          1 TATATTATATA

               
       9007 TAT
          1 TAT

       9010 TCCTAAAAAA


Statistics
Matches: 22,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  10    8  0.36
  11   14  0.64

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


Consensus pattern (11 bp):   
TATATTATATA
Done.