Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024543.1 Corchorus olitorius cultivar O-4 contig24576, 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: 18786
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.31


Found at i:686 original size:2 final size:2

Alignment explanation


    Indices: 679--744  Score: 55
    Period size: 2  Copynumber: 33.5  Consensus size: 2

        669 TGAAATTGTA

                                                *  *  *  *    *       *    
        679 AT AT AT AT AT AT AT AT AT AT AT AT GT GT GT GT GAA AT -T GT A-
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT

                                                 
        720 AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT A

        745 AACGTTAGGG


Statistics
Matches: 56,  Mismatches: 5, Indels: 6
        0.84            0.07        0.09

Matches are distributed among these distances:
   1    2  0.04
   2   54  0.96

ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47


Consensus pattern (2 bp):   
AT

Found at i:835 original size:22 final size:21

Alignment explanation


    Indices: 785--835  Score: 57
    Period size: 22  Copynumber: 2.3  Consensus size: 21

        775 TTCTCCACAA

                                  
        785 TTAATAAGAGCTAATTATTCCC
          1 TTAA-AAGAGCTAATTATTCCC

              *                 *  
        807 TAAAAAAGAGCTAATTATATTCC
          1 T-TAAAAGAGCTAATTAT-TCCC

                  
        830 TTAAAA
          1 TTAAAA

        836 AATCAAGGGG


Statistics
Matches: 24,  Mismatches: 3, Indels: 4
        0.77            0.10        0.13

Matches are distributed among these distances:
  22   18  0.75
  23    6  0.25

ACGTcount: A:0.45, C:0.14, G:0.08, T:0.33


Consensus pattern (21 bp):   
TTAAAAGAGCTAATTATTCCC

Found at i:3223 original size:25 final size:25

Alignment explanation


    Indices: 3189--3259  Score: 142
    Period size: 25  Copynumber: 2.8  Consensus size: 25

       3179 CCCCCTGATC

                                     
       3189 ACCCCTCTAAGGGTGATCTGGTGGT
          1 ACCCCTCTAAGGGTGATCTGGTGGT

                                     
       3214 ACCCCTCTAAGGGTGATCTGGTGGT
          1 ACCCCTCTAAGGGTGATCTGGTGGT

                                 
       3239 ACCCCTCTAAGGGTGATCTGG
          1 ACCCCTCTAAGGGTGATCTGG

       3260 ATTACCACCA


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

Matches are distributed among these distances:
  25   46  1.00

ACGTcount: A:0.17, C:0.25, G:0.31, T:0.27


Consensus pattern (25 bp):   
ACCCCTCTAAGGGTGATCTGGTGGT

Found at i:3326 original size:17 final size:16

Alignment explanation


    Indices: 3286--3336  Score: 66
    Period size: 17  Copynumber: 3.1  Consensus size: 16

       3276 CATGTAATCT

                    *       
       3286 TTGATCACCGGTGATC
          1 TTGATCACTGGTGATC

                             
       3302 TTGCATCACTGGTGATC
          1 TTG-ATCACTGGTGATC

                      *      
       3319 TTAGATCACTAGTGATC
          1 TT-GATCACTGGTGATC

             
       3336 T
          1 T

       3337 GGGGGTGATC


Statistics
Matches: 31,  Mismatches: 2, Indels: 3
        0.86            0.06        0.08

Matches are distributed among these distances:
  16    3  0.10
  17   27  0.87
  18    1  0.03

ACGTcount: A:0.22, C:0.22, G:0.22, T:0.35


Consensus pattern (16 bp):   
TTGATCACTGGTGATC
Done.