Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017384.1 Corchorus olitorius cultivar O-4 contig17417, 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: 15862
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30


Found at i:227 original size:24 final size:23

Alignment explanation


    Indices: 200--251  Score: 59
    Period size: 23  Copynumber: 2.2  Consensus size: 23

        190 AGGTTGCGCA

                      *             
        200 AACTTCAGGGTTCAACCTGGCCCC
          1 AACTTCAGGGCT-AACCTGGCCCC

                 *        **       
        224 AACTTGAGGGCTAAGTTGGCCCC
          1 AACTTCAGGGCTAACCTGGCCCC

                 
        247 AACTT
          1 AACTT

        252 AGAGTTCGTT


Statistics
Matches: 24,  Mismatches: 4, Indels: 1
        0.83            0.14        0.03

Matches are distributed among these distances:
  23   14  0.58
  24   10  0.42

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


Consensus pattern (23 bp):   
AACTTCAGGGCTAACCTGGCCCC

Found at i:2043 original size:23 final size:23

Alignment explanation


    Indices: 2016--2067  Score: 70
    Period size: 23  Copynumber: 2.3  Consensus size: 23

       2006 AATGTAATGC

                    *               
       2016 ATGCAAACTTAAGAAAAG-AAAAA
          1 ATGCAAACATAA-AAAAGAAAAAA

                           *       
       2039 ATGCAAACATAAAAAGGAAAAAA
          1 ATGCAAACATAAAAAAGAAAAAA

                  
       2062 ATGCAA
          1 ATGCAA

       2068 TTTCTTTAAC


Statistics
Matches: 26,  Mismatches: 2, Indels: 2
        0.87            0.07        0.07

Matches are distributed among these distances:
  22    4  0.15
  23   22  0.85

ACGTcount: A:0.65, C:0.10, G:0.13, T:0.12


Consensus pattern (23 bp):   
ATGCAAACATAAAAAAGAAAAAA

Found at i:4471 original size:24 final size:23

Alignment explanation


    Indices: 4444--4495  Score: 59
    Period size: 23  Copynumber: 2.2  Consensus size: 23

       4434 AGGTTGCGCA

                      *             
       4444 AACTTCAGGGTTCAACCTGGCCCC
          1 AACTTCAGGGGT-AACCTGGCCCC

                 *        **       
       4468 AACTTGAGGGGTAAGTTGGCCCC
          1 AACTTCAGGGGTAACCTGGCCCC

                 
       4491 AACTT
          1 AACTT

       4496 AGAGTTCGTT


Statistics
Matches: 24,  Mismatches: 4, Indels: 1
        0.83            0.14        0.03

Matches are distributed among these distances:
  23   14  0.58
  24   10  0.42

ACGTcount: A:0.23, C:0.29, G:0.25, T:0.23


Consensus pattern (23 bp):   
AACTTCAGGGGTAACCTGGCCCC

Found at i:9019 original size:38 final size:38

Alignment explanation


    Indices: 8976--9052  Score: 154
    Period size: 38  Copynumber: 2.0  Consensus size: 38

       8966 AATTTTCAAT

                                                  
       8976 TGTGAATAGACAGAATACGGCATGATGTTAATTGGAGA
          1 TGTGAATAGACAGAATACGGCATGATGTTAATTGGAGA

                                                  
       9014 TGTGAATAGACAGAATACGGCATGATGTTAATTGGAGA
          1 TGTGAATAGACAGAATACGGCATGATGTTAATTGGAGA

             
       9052 T
          1 T

       9053 CCAAATTCAC


Statistics
Matches: 39,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  38   39  1.00

ACGTcount: A:0.36, C:0.08, G:0.29, T:0.27


Consensus pattern (38 bp):   
TGTGAATAGACAGAATACGGCATGATGTTAATTGGAGA

Found at i:14368 original size:11 final size:11

Alignment explanation


    Indices: 14352--14377  Score: 52
    Period size: 11  Copynumber: 2.4  Consensus size: 11

      14342 CCTTGCCTAA

                       
      14352 AAAACTAGAAG
          1 AAAACTAGAAG

                       
      14363 AAAACTAGAAG
          1 AAAACTAGAAG

                
      14374 AAAA
          1 AAAA

      14378 GAAATTATCT


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   15  1.00

ACGTcount: A:0.69, C:0.08, G:0.15, T:0.08


Consensus pattern (11 bp):   
AAAACTAGAAG
Done.