Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024103.1 Corchorus olitorius cultivar O-4 contig24136, 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: 13463
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33


Found at i:6288 original size:17 final size:16

Alignment explanation


    Indices: 6240--6288  Score: 55
    Period size: 17  Copynumber: 3.0  Consensus size: 16

       6230 CAATGGAGAT

                     *      
       6240 CATGGAAAGGATG-AG
          1 CATGGAAAGCATGAAG

                   *         
       6255 CATGGAATGCATGGAAG
          1 CATGGAAAGCAT-GAAG

                             
       6272 CATGGAGAAGCATGAAG
          1 CATGGA-AAGCATGAAG

       6289 ATGATGGAGA


Statistics
Matches: 28,  Mismatches: 3, Indels: 4
        0.80            0.09        0.11

Matches are distributed among these distances:
  15   10  0.36
  16    1  0.04
  17   12  0.43
  18    5  0.18

ACGTcount: A:0.39, C:0.10, G:0.37, T:0.14


Consensus pattern (16 bp):   
CATGGAAAGCATGAAG

Found at i:7470 original size:27 final size:27

Alignment explanation


    Indices: 7440--7513  Score: 89
    Period size: 27  Copynumber: 2.7  Consensus size: 27

       7430 GATGTGAAAC

                           *             
       7440 TTTAAAATGGTT-AACAAGGATGACAA-T
          1 TTTAAAATGGTTGAAAAAGGA-GA-AAGT

                               *       
       7467 TTTAAAATGGTTGAAAAAGTAGAAAGT
          1 TTTAAAATGGTTGAAAAAGGAGAAAGT

                          *     
       7494 TTTAAAATGGTTGATAAAGG
          1 TTTAAAATGGTTGAAAAAGG

       7514 TTGAAAATTT


Statistics
Matches: 41,  Mismatches: 4, Indels: 4
        0.84            0.08        0.08

Matches are distributed among these distances:
  26    2  0.05
  27   33  0.80
  28    6  0.15

ACGTcount: A:0.45, C:0.03, G:0.22, T:0.31


Consensus pattern (27 bp):   
TTTAAAATGGTTGAAAAAGGAGAAAGT

Found at i:11237 original size:82 final size:82

Alignment explanation


    Indices: 11129--11295  Score: 334
    Period size: 82  Copynumber: 2.0  Consensus size: 82

      11119 AAGAGAAAAG

                                                                             
      11129 AGAGAAGAATTGAGATGGAGCAGAAGAATAATGGAAGGAGACGGAGAGGGAGAAGAAACGCAGAG
          1 AGAGAAGAATTGAGATGGAGCAGAAGAATAATGGAAGGAGACGGAGAGGGAGAAGAAACGCAGAG

                             
      11194 GTGGACAGATGGAGAGA
         66 GTGGACAGATGGAGAGA

                                                                             
      11211 AGAGAAGAATTGAGATGGAGCAGAAGAATAATGGAAGGAGACGGAGAGGGAGAAGAAACGCAGAG
          1 AGAGAAGAATTGAGATGGAGCAGAAGAATAATGGAAGGAGACGGAGAGGGAGAAGAAACGCAGAG

                             
      11276 GTGGACAGATGGAGAGA
         66 GTGGACAGATGGAGAGA

               
      11293 AGA
          1 AGA

      11296 CTTCAACGTG


Statistics
Matches: 85,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  82   85  1.00

ACGTcount: A:0.44, C:0.06, G:0.41, T:0.08


Consensus pattern (82 bp):   
AGAGAAGAATTGAGATGGAGCAGAAGAATAATGGAAGGAGACGGAGAGGGAGAAGAAACGCAGAG
GTGGACAGATGGAGAGA
Done.