Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012905.1 Corchorus olitorius cultivar O-4 contig12938, 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: 37393
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33


Found at i:16 original size:3 final size:3

Alignment explanation


    Indices: 10--131  Score: 212
    Period size: 3  Copynumber: 41.0  Consensus size: 3

          1 AAATAATAT

                                                                           
         10 TTA TTA TTA TTA -TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
          1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA

                                    *                                   
         57 TTA TTA TTA TTA TTA TTA ATA TTAA TTA TTA TTA -TA TTA TTA TTA
          1 TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA

                                                   
        102 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
          1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA

        132 CAAGTGGATT


Statistics
Matches: 114,  Mismatches: 2, Indels: 6
        0.93            0.02        0.05

Matches are distributed among these distances:
   2    4  0.04
   3  107  0.94
   4    3  0.03

ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65


Consensus pattern (3 bp):   
TTA

Found at i:723 original size:6 final size:6

Alignment explanation


    Indices: 714--746  Score: 66
    Period size: 6  Copynumber: 5.5  Consensus size: 6

        704 TATATCTATT

                                                  
        714 TATTAG TATTAG TATTAG TATTAG TATTAG TAT
          1 TATTAG TATTAG TATTAG TATTAG TATTAG TAT

        747 ATATATATTT


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   27  1.00

ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52


Consensus pattern (6 bp):   
TATTAG

Found at i:13263 original size:17 final size:17

Alignment explanation


    Indices: 13241--13273  Score: 66
    Period size: 17  Copynumber: 1.9  Consensus size: 17

      13231 GAGGGAGTAG

                             
      13241 CCTCGAAGACGTGGCTC
          1 CCTCGAAGACGTGGCTC

                            
      13258 CCTCGAAGACGTGGCT
          1 CCTCGAAGACGTGGCT

      13274 AGAGGATGAA


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   16  1.00

ACGTcount: A:0.18, C:0.33, G:0.30, T:0.18


Consensus pattern (17 bp):   
CCTCGAAGACGTGGCTC

Found at i:14236 original size:27 final size:27

Alignment explanation


    Indices: 14201--14253  Score: 79
    Period size: 27  Copynumber: 2.0  Consensus size: 27

      14191 AACTCAGTGT

                *              *       
      14201 TCCAGCCAATAAAATTGACTCCCAAAC
          1 TCCAACCAATAAAATTGACGCCCAAAC

                       *              
      14228 TCCAACCAATACAATTGACGCCCAAA
          1 TCCAACCAATAAAATTGACGCCCAAA

      14254 TTCCTAGAGG


Statistics
Matches: 23,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  27   23  1.00

ACGTcount: A:0.42, C:0.34, G:0.08, T:0.17


Consensus pattern (27 bp):   
TCCAACCAATAAAATTGACGCCCAAAC

Found at i:20650 original size:20 final size:20

Alignment explanation


    Indices: 20625--20663  Score: 60
    Period size: 20  Copynumber: 1.9  Consensus size: 20

      20615 TGAACGAATA

                    *    *      
      20625 AAAATTTTTGGATTATAAAT
          1 AAAATTTTGGGATAATAAAT

                               
      20645 AAAATTTTGGGATAATAAA
          1 AAAATTTTGGGATAATAAA

      20664 CAATTTTTAG


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  20   17  1.00

ACGTcount: A:0.49, C:0.00, G:0.13, T:0.38


Consensus pattern (20 bp):   
AAAATTTTGGGATAATAAAT
Done.