Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011388.1 Corchorus olitorius cultivar O-4 contig11421, 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: 14398
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.30


Found at i:14025 original size:16 final size:16

Alignment explanation


    Indices: 14006--14049  Score: 63
    Period size: 16  Copynumber: 2.8  Consensus size: 16

      13996 ACCCGTCCGA

                             
      14006 ACCCGAACCC-AAAATT
          1 ACCCGAACCCGAAAA-T

                  *         
      14022 ACCCGAGCCCGAAAAT
          1 ACCCGAACCCGAAAAT

                        
      14038 ACCCGAACCCGA
          1 ACCCGAACCCGA

      14050 GGCAGCCCGA


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

Matches are distributed among these distances:
  16   21  0.84
  17    4  0.16

ACGTcount: A:0.39, C:0.41, G:0.14, T:0.07


Consensus pattern (16 bp):   
ACCCGAACCCGAAAAT

Found at i:14105 original size:23 final size:23

Alignment explanation


    Indices: 14055--14106  Score: 68
    Period size: 23  Copynumber: 2.3  Consensus size: 23

      14045 CCCGAGGCAG

                                   
      14055 CCCGAACCCGACTCGAGACCAAA
          1 CCCGAACCCGACTCGAGACCAAA

            *    *           *  *  
      14078 TCCGAGCCCGACTCGAGCCCGAA
          1 CCCGAACCCGACTCGAGACCAAA

                  
      14101 CCCGAA
          1 CCCGAA

      14107 ATAATTTGAA


Statistics
Matches: 23,  Mismatches: 6, Indels: 0
        0.79            0.21        0.00

Matches are distributed among these distances:
  23   23  1.00

ACGTcount: A:0.29, C:0.44, G:0.21, T:0.06


Consensus pattern (23 bp):   
CCCGAACCCGACTCGAGACCAAA

Found at i:14242 original size:26 final size:25

Alignment explanation


    Indices: 14176--14242  Score: 68
    Period size: 26  Copynumber: 2.7  Consensus size: 25

      14166 TATTTCCTTT

                                     
      14176 TAAT-ATTAAATAAAATATTATATA
          1 TAATGATTAAATAAAATATTATATA

                  *                    
      14200 T-ATGAATATAATAAAAT-TTATATAA
          1 TAATGATTA-AATAAAATATTATAT-A

                         *    
      14225 TAATGATTACAATTAAAT
          1 TAATGATTA-AATAAAAT

      14243 GATTCATTAA


Statistics
Matches: 35,  Mismatches: 4, Indels: 6
        0.78            0.09        0.13

Matches are distributed among these distances:
  23    2  0.06
  24   10  0.29
  25   10  0.29
  26   13  0.37

ACGTcount: A:0.55, C:0.01, G:0.03, T:0.40


Consensus pattern (25 bp):   
TAATGATTAAATAAAATATTATATA

Found at i:14289 original size:2 final size:2

Alignment explanation


    Indices: 14282--14309  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

      14272 AAACTACTAA

                                                     
      14282 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT

      14310 TTAAAACTAA


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   26  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Done.