Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011391.1 Corchorus olitorius cultivar O-4 contig11424, 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: 23497
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32


Found at i:10508 original size:19 final size:18

Alignment explanation


    Indices: 10484--10519  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

      10474 TGAAGATTTA

                               
      10484 TTGAAGACAATTTGAAGAT
          1 TTGAAGACAA-TTGAAGAT

                    *        
      10503 TTGAAGACCATTGAAGA
          1 TTGAAGACAATTGAAGA

      10520 ATAATTTTAA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    7  0.44
  19    9  0.56

ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28


Consensus pattern (18 bp):   
TTGAAGACAATTGAAGAT

Found at i:16691 original size:18 final size:18

Alignment explanation


    Indices: 16654--16691  Score: 58
    Period size: 18  Copynumber: 2.1  Consensus size: 18

      16644 CTAGCCCTAA

                          **  
      16654 AACTAGAAGAAAAACTAG
          1 AACTAGAAGAAAAAAAAG

                              
      16672 AACTAGAAGAAAAAAAAG
          1 AACTAGAAGAAAAAAAAG

              
      16690 AA
          1 AA

      16692 GAGAAAATTA


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  18   18  1.00

ACGTcount: A:0.68, C:0.08, G:0.16, T:0.08


Consensus pattern (18 bp):   
AACTAGAAGAAAAAAAAG

Found at i:20068 original size:32 final size:32

Alignment explanation


    Indices: 20009--20070  Score: 81
    Period size: 32  Copynumber: 1.9  Consensus size: 32

      19999 GATCCCTTAG

                             *              
      20009 TTAGTCGACAAACTTAATTCAAAACTTGCTCT
          1 TTAGTCGACAAACTTAAGTCAAAACTTGCTCT

                                 * *       
      20041 TTAGTCGAC-AACTTCAAGTCGACACTTGCT
          1 TTAGTCGACAAACTT-AAGTCAAAACTTGCT

      20071 TTGTCGATTT


Statistics
Matches: 26,  Mismatches: 3, Indels: 2
        0.84            0.10        0.06

Matches are distributed among these distances:
  31    5  0.19
  32   21  0.81

ACGTcount: A:0.31, C:0.24, G:0.13, T:0.32


Consensus pattern (32 bp):   
TTAGTCGACAAACTTAAGTCAAAACTTGCTCT

Found at i:20830 original size:6 final size:6

Alignment explanation


    Indices: 20819--20845  Score: 54
    Period size: 6  Copynumber: 4.5  Consensus size: 6

      20809 AATTAGTGTA

                                           
      20819 AAAATT AAAATT AAAATT AAAATT AAA
          1 AAAATT AAAATT AAAATT AAAATT AAA

      20846 TATGCAAAGA


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   21  1.00

ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30


Consensus pattern (6 bp):   
AAAATT

Done.