Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017581.1 Corchorus olitorius cultivar O-4 contig17614, 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: 19774
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32


Found at i:404 original size:41 final size:41

Alignment explanation


    Indices: 359--441  Score: 148
    Period size: 41  Copynumber: 2.0  Consensus size: 41

        349 GAGTGAAAGG

                                                *    
        359 TTTCCTAATTCCTAAAAAAGTAAAAAACGAGAATGATCTGA
          1 TTTCCTAATTCCTAAAAAAGTAAAAAACGAGAATGACCTGA

                         *                           
        400 TTTCCTAATTCCTGAAAAAGTAAAAAACGAGAATGACCTGA
          1 TTTCCTAATTCCTAAAAAAGTAAAAAACGAGAATGACCTGA

             
        441 T
          1 T

        442 GACTGACAAA


Statistics
Matches: 40,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  41   40  1.00

ACGTcount: A:0.45, C:0.16, G:0.13, T:0.27


Consensus pattern (41 bp):   
TTTCCTAATTCCTAAAAAAGTAAAAAACGAGAATGACCTGA

Found at i:735 original size:56 final size:56

Alignment explanation


    Indices: 654--761  Score: 182
    Period size: 56  Copynumber: 1.9  Consensus size: 56

        644 GCATTTTCTC

                                                                     
        654 TTTTTTCCTACCTCAAATATTTACAAGAAATTATTAATT-TCATTTAAAAAAATTTT
          1 TTTTTTCCTACCTCAAATATTTACAAGAAATTATT-ATTGTCATTTAAAAAAATTTT

                     * *                                        
        710 TTTTTTCCTTCTTCAAATATTTACAAGAAATTATTATTGTCATTTAAAAAAA
          1 TTTTTTCCTACCTCAAATATTTACAAGAAATTATTATTGTCATTTAAAAAAA

        762 AAAAGAGTTA


Statistics
Matches: 49,  Mismatches: 2, Indels: 2
        0.92            0.04        0.04

Matches are distributed among these distances:
  55    3  0.06
  56   46  0.94

ACGTcount: A:0.39, C:0.12, G:0.03, T:0.46


Consensus pattern (56 bp):   
TTTTTTCCTACCTCAAATATTTACAAGAAATTATTATTGTCATTTAAAAAAATTTT

Found at i:862 original size:26 final size:26

Alignment explanation


    Indices: 826--877  Score: 95
    Period size: 26  Copynumber: 2.0  Consensus size: 26

        816 TCCATTTTTT

                *                     
        826 CCTTGATATATAACTATGCCAAAATC
          1 CCTTAATATATAACTATGCCAAAATC

                                      
        852 CCTTAATATATAACTATGCCAAAATC
          1 CCTTAATATATAACTATGCCAAAATC

        878 ACATGGAGTA


Statistics
Matches: 25,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  26   25  1.00

ACGTcount: A:0.40, C:0.23, G:0.06, T:0.31


Consensus pattern (26 bp):   
CCTTAATATATAACTATGCCAAAATC

Found at i:4691 original size:29 final size:28

Alignment explanation


    Indices: 4659--4713  Score: 101
    Period size: 29  Copynumber: 1.9  Consensus size: 28

       4649 ACCAAAGTCC

                                         
       4659 AAACCCGCCATTCTTTTCAACCCAAAAAA
          1 AAACCCGCCATTCTTTTCAA-CCAAAAAA

                                      
       4688 AAACCCGCCATTCTTTTCAACCAAAA
          1 AAACCCGCCATTCTTTTCAACCAAAA

       4714 GCAGCGTTTT


Statistics
Matches: 26,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  28    6  0.23
  29   20  0.77

ACGTcount: A:0.40, C:0.35, G:0.04, T:0.22


Consensus pattern (28 bp):   
AAACCCGCCATTCTTTTCAACCAAAAAA

Found at i:15165 original size:5 final size:5

Alignment explanation


    Indices: 15153--15182  Score: 51
    Period size: 5  Copynumber: 6.0  Consensus size: 5

      15143 AGAGACCTTC

                     *                         
      15153 CTTTT CTTCT CTTTT CTTTT CTTTT CTTTT
          1 CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT

      15183 TATTTATTTT


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

Matches are distributed among these distances:
   5   23  1.00

ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77


Consensus pattern (5 bp):   
CTTTT

Done.