Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012444.1 Corchorus olitorius cultivar O-4 contig12477, 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: 8409
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33


Found at i:122 original size:2 final size:2

Alignment explanation


    Indices: 117--143  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

        107 ATAAGTTTAT

                                                    
        117 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

        144 TTAGTAGTTT


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:252 original size:26 final size:22

Alignment explanation


    Indices: 195--252  Score: 53
    Period size: 26  Copynumber: 2.4  Consensus size: 22

        185 AATTGTGATC

                *                 
        195 ATTATTATATAAATTTTATTAT
          1 ATTAATATATAAATTTTATTAT

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

                    
        245 ATTAATAT
          1 ATTAATAT

        253 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:321 original size:6 final size:6

Alignment explanation


    Indices: 313--360  Score: 53
    Period size: 6  Copynumber: 8.2  Consensus size: 6

        303 TCAAATTATT

                 *     *                            *          *   
        313 TCGGGT TCGGCC TCGGGC TCGGGC TCGGG- TCGGGT TCGGGC TCAGGC
          1 TCGGGC TCGGGC TCGGGC TCGGGC TCGGGC TCGGGC TCGGGC TCGGGC

             
        360 T
          1 T

        361 GCCTCGGGTA


Statistics
Matches: 36,  Mismatches: 5, Indels: 2
        0.84            0.12        0.05

Matches are distributed among these distances:
   5    5  0.14
   6   31  0.86

ACGTcount: A:0.02, C:0.29, G:0.46, T:0.23


Consensus pattern (6 bp):   
TCGGGC

Found at i:3032 original size:25 final size:26

Alignment explanation


    Indices: 3004--3053  Score: 84
    Period size: 25  Copynumber: 1.9  Consensus size: 26

       2994 CTTACCCTTA

                                      
       3004 TCTTTTATTTTCG-TATTTTTCTTTT
          1 TCTTTTATTTTCGTTATTTTTCTTTT

                                     
       3029 TCTTTTATTTTCGTTTATTTTTCTT
          1 TCTTTTATTTTCG-TTATTTTTCTT

       3054 AGTTACTTTT


Statistics
Matches: 23,  Mismatches: 0, Indels: 2
        0.92            0.00        0.08

Matches are distributed among these distances:
  25   13  0.57
  27   10  0.43

ACGTcount: A:0.08, C:0.12, G:0.04, T:0.76


Consensus pattern (26 bp):   
TCTTTTATTTTCGTTATTTTTCTTTT
Done.