Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022284.1 Corchorus olitorius cultivar O-4 contig22317, 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: 8630
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34


Found at i:7 original size:2 final size:2

Alignment explanation


    Indices: 1--34  Score: 68
    Period size: 2  Copynumber: 17.0  Consensus size: 2

                                                              
          1 AT AT 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 AT AT

         35 TTAGTAGTTT


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   32  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:143 original size:26 final size:22

Alignment explanation


    Indices: 86--143  Score: 53
    Period size: 26  Copynumber: 2.4  Consensus size: 22

         76 AATTGTGATC

                *                 
         86 ATTATTATATAAATTTTATTAT
          1 ATTAATATATAAATTTTATTAT

                                        
        108 ATTCATATATATAATAGTTTTATTTAAT
          1 ATT-A-ATATATAA-A-TTTTA-TT-AT

                    
        136 ATTAATAT
          1 ATTAATAT

        144 GTTTTTTTTC


Statistics
Matches: 29,  Mismatches: 1, Indels: 8
        0.76            0.03        0.21

Matches are distributed among these distances:
  22    3  0.10
  23    1  0.03
  24    7  0.24
  25    1  0.03
  26    9  0.31
  27    3  0.10
  28    5  0.17

ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55


Consensus pattern (22 bp):   
ATTAATATATAAATTTTATTAT

Found at i:233 original size:23 final size:22

Alignment explanation


    Indices: 203--258  Score: 76
    Period size: 23  Copynumber: 2.5  Consensus size: 22

        193 TCAAATTATT

                            *    **
        203 TCGGGTTCGGGCTCGGTCTCGGG
          1 TCGGGTTCGGGCTCGGGCT-GCC

                                  
        226 TCGGGTTCGGGCTCGGGCTGCC
          1 TCGGGTTCGGGCTCGGGCTGCC

                       
        248 TCGGGTTCGGG
          1 TCGGGTTCGGG

        259 TATTTTCAGG


Statistics
Matches: 30,  Mismatches: 3, Indels: 1
        0.88            0.09        0.03

Matches are distributed among these distances:
  22   12  0.40
  23   18  0.60

ACGTcount: A:0.00, C:0.27, G:0.48, T:0.25


Consensus pattern (22 bp):   
TCGGGTTCGGGCTCGGGCTGCC

Found at i:242 original size:12 final size:12

Alignment explanation


    Indices: 203--242  Score: 57
    Period size: 12  Copynumber: 3.4  Consensus size: 12

        193 TCAAATTATT

                        
        203 TCGGGTTCGGGC
          1 TCGGGTTCGGGC

                         
        215 TC-GGTCTCGGG-
          1 TCGGGT-TCGGGC

                        
        226 TCGGGTTCGGGC
          1 TCGGGTTCGGGC

                 
        238 TCGGG
          1 TCGGG

        243 CTGCCTCGGG


Statistics
Matches: 25,  Mismatches: 0, Indels: 6
        0.81            0.00        0.19

Matches are distributed among these distances:
  11   10  0.40
  12   15  0.60

ACGTcount: A:0.00, C:0.25, G:0.50, T:0.25


Consensus pattern (12 bp):   
TCGGGTTCGGGC

Found at i:243 original size:6 final size:6

Alignment explanation


    Indices: 203--244  Score: 50
    Period size: 6  Copynumber: 7.2  Consensus size: 6

        193 TCAAATTATT

                 *            *              *                
        203 TCGGGT TCGGGC TCGGTC TCGGG- TCGGGT TCGGGC TCGGGC T
          1 TCGGGC TCGGGC TCGGGC TCGGGC TCGGGC TCGGGC TCGGGC T

        245 GCCTCGGGTT


Statistics
Matches: 31,  Mismatches: 4, Indels: 2
        0.84            0.11        0.05

Matches are distributed among these distances:
   5    5  0.16
   6   26  0.84

ACGTcount: A:0.00, C:0.26, G:0.48, T:0.26


Consensus pattern (6 bp):   
TCGGGC
Done.