Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012490.1 Corchorus olitorius cultivar O-4 contig12523, 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: 18384
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32


Found at i:6038 original size:22 final size:22

Alignment explanation


    Indices: 6006--6080  Score: 141
    Period size: 22  Copynumber: 3.4  Consensus size: 22

       5996 TTGGGCGGAC

                                  
       6006 GTCGGAGATAAGGGAAAGAGAT
          1 GTCGGAGATAAGGGAAAGAGAT

               *                  
       6028 GTCAGAGATAAGGGAAAGAGAT
          1 GTCGGAGATAAGGGAAAGAGAT

                                  
       6050 GTCGGAGATAAGGGAAAGAGAT
          1 GTCGGAGATAAGGGAAAGAGAT

                     
       6072 GTCGGAGAT
          1 GTCGGAGAT

       6081 GGCCCGTCTC


Statistics
Matches: 51,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  22   51  1.00

ACGTcount: A:0.40, C:0.05, G:0.40, T:0.15


Consensus pattern (22 bp):   
GTCGGAGATAAGGGAAAGAGAT

Found at i:7192 original size:19 final size:18

Alignment explanation


    Indices: 7168--7205  Score: 58
    Period size: 19  Copynumber: 2.1  Consensus size: 18

       7158 TTTGAAGACC

                               
       7168 ACTTGAAGATAATTTGAAG
          1 ACTTGAAGAT-ATTTGAAG

                      *       
       7187 ACTTGAAGATTTTTGAAG
          1 ACTTGAAGATATTTGAAG

             
       7205 A
          1 A

       7206 ATTATTTCAA


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  18    8  0.44
  19   10  0.56

ACGTcount: A:0.39, C:0.05, G:0.21, T:0.34


Consensus pattern (18 bp):   
ACTTGAAGATATTTGAAG

Found at i:9006 original size:24 final size:22

Alignment explanation


    Indices: 8971--9021  Score: 66
    Period size: 24  Copynumber: 2.2  Consensus size: 22

       8961 TTTTTTTTAT

                        *         
       8971 AAAAAAAAGTTTTTGCGTCAAA
          1 AAAAAAAAGTTTCTGCGTCAAA

                                  * 
       8993 AAAAAAAATTGTTTCTGCGTCATA
          1 AAAAAAAA--GTTTCTGCGTCAAA

                 
       9017 AAAAA
          1 AAAAA

       9022 TATTTTCCTT


Statistics
Matches: 25,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  22    8  0.32
  24   17  0.68

ACGTcount: A:0.51, C:0.10, G:0.12, T:0.27


Consensus pattern (22 bp):   
AAAAAAAAGTTTCTGCGTCAAA

Found at i:12241 original size:21 final size:20

Alignment explanation


    Indices: 12179--12246  Score: 64
    Period size: 21  Copynumber: 3.2  Consensus size: 20

      12169 CCACTACCAA

                 *                
      12179 GCCACAACCGGCCATACACCGT
          1 GCCACCACCGGCCAT-C-CCGT

                        **       
      12201 GCCACCACCGGTTAATCCCGT
          1 GCCACCACCGG-CCATCCCGT

                                *
      12222 GCCACCACCGGCCATGCCCGA
          1 GCCACCACCGGCCAT-CCCGT

                
      12243 GCCA
          1 GCCA

      12247 TCGCCATTCC


Statistics
Matches: 38,  Mismatches: 6, Indels: 5
        0.78            0.12        0.10

Matches are distributed among these distances:
  20    2  0.05
  21   23  0.61
  22   11  0.29
  23    2  0.05

ACGTcount: A:0.22, C:0.47, G:0.21, T:0.10


Consensus pattern (20 bp):   
GCCACCACCGGCCATCCCGT
Done.