Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014735.1 Corchorus olitorius cultivar O-4 contig14768, 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: 20108
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34


Found at i:4631 original size:118 final size:118

Alignment explanation


    Indices: 4423--4655  Score: 457
    Period size: 118  Copynumber: 2.0  Consensus size: 118

       4413 ATATAATTAT

                                                                             
       4423 TTATTGTTAATTTGGGGCTAAACCTGATGTTTAACTGAGAAAGTGGTGTGAAGTGGTGTGAATGA
          1 TTATTGTTAATTTGGGGCTAAACCTGATGTTTAACTGAGAAAGTGGTGTGAAGTGGTGTGAATGA

                                                                 
       4488 TATTACCACGTAATGCCTAAGATACCACTAACCAAACATAACCTTAGAAATAA
         66 TATTACCACGTAATGCCTAAGATACCACTAACCAAACATAACCTTAGAAATAA

                                                 *                           
       4541 TTATTGTTAATTTGGGGCTAAACCTGATGTTTAACTGGGAAAGTGGTGTGAAGTGGTGTGAATGA
          1 TTATTGTTAATTTGGGGCTAAACCTGATGTTTAACTGAGAAAGTGGTGTGAAGTGGTGTGAATGA

                                                              
       4606 TATTACCACGTAATGCCTAAGATACCACTAACCAAACATAACCTTAGAAA
         66 TATTACCACGTAATGCCTAAGATACCACTAACCAAACATAACCTTAGAAA

       4656 AGTGTTCAAC


Statistics
Matches: 114,  Mismatches: 1, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
 118  114  1.00

ACGTcount: A:0.35, C:0.15, G:0.21, T:0.30


Consensus pattern (118 bp):   
TTATTGTTAATTTGGGGCTAAACCTGATGTTTAACTGAGAAAGTGGTGTGAAGTGGTGTGAATGA
TATTACCACGTAATGCCTAAGATACCACTAACCAAACATAACCTTAGAAATAA

Found at i:4710 original size:35 final size:35

Alignment explanation


    Indices: 4664--4733  Score: 131
    Period size: 35  Copynumber: 2.0  Consensus size: 35

       4654 AAAGTGTTCA

                                   *           
       4664 ACGTAATGCCTAAGATACCACTACCAAACATAACC
          1 ACGTAATGCCTAAGATACCACTAACAAACATAACC

                                               
       4699 ACGTAATGCCTAAGATACCACTAACAAACATAACC
          1 ACGTAATGCCTAAGATACCACTAACAAACATAACC

       4734 TTATAAAATA


Statistics
Matches: 34,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  35   34  1.00

ACGTcount: A:0.44, C:0.30, G:0.09, T:0.17


Consensus pattern (35 bp):   
ACGTAATGCCTAAGATACCACTAACAAACATAACC

Found at i:4745 original size:28 final size:29

Alignment explanation


    Indices: 4713--4770  Score: 100
    Period size: 29  Copynumber: 2.0  Consensus size: 29

       4703 AATGCCTAAG

                                     *   
       4713 ATACCACTAA-CAAACATAACCTTATAAA
          1 ATACCACTAACCAAACATAACCTTAGAAA

                                         
       4741 ATACCACTAACCAAACATAACCTTAGAAA
          1 ATACCACTAACCAAACATAACCTTAGAAA

             
       4770 A
          1 A

       4771 GTGTTCAATG


Statistics
Matches: 28,  Mismatches: 1, Indels: 1
        0.93            0.03        0.03

Matches are distributed among these distances:
  28   10  0.36
  29   18  0.64

ACGTcount: A:0.53, C:0.26, G:0.02, T:0.19


Consensus pattern (29 bp):   
ATACCACTAACCAAACATAACCTTAGAAA

Found at i:8562 original size:16 final size:16

Alignment explanation


    Indices: 8541--8572  Score: 64
    Period size: 16  Copynumber: 2.0  Consensus size: 16

       8531 TCCCATCCGG

                            
       8541 TATCTAGGGCAAATGA
          1 TATCTAGGGCAAATGA

                            
       8557 TATCTAGGGCAAATGA
          1 TATCTAGGGCAAATGA

       8573 CTAATTCGGA


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

Matches are distributed among these distances:
  16   16  1.00

ACGTcount: A:0.38, C:0.12, G:0.25, T:0.25


Consensus pattern (16 bp):   
TATCTAGGGCAAATGA

Found at i:9508 original size:13 final size:13

Alignment explanation


    Indices: 9490--9514  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       9480 ATTGAGTTGT

                         
       9490 CTCTGTTTCTTCA
          1 CTCTGTTTCTTCA

                        
       9503 CTCTGTTTCTTC
          1 CTCTGTTTCTTC

       9515 TCAGGAAATC


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.04, C:0.32, G:0.08, T:0.56


Consensus pattern (13 bp):   
CTCTGTTTCTTCA

Found at i:15266 original size:40 final size:39

Alignment explanation


    Indices: 15174--15279  Score: 113
    Period size: 39  Copynumber: 2.7  Consensus size: 39

      15164 AAGGATTGGT

                        *               *          *
      15174 AAACTAATGTGGAAAATAAAATAAGTAGTAAGATTTAAGT
          1 AAACT-ATGTGGGAAATAAAATAAGTAGCAAGATTTAAGA

                *  *              *  *          *   
      15214 AAACCATATGGGAAATAAAATATGTTGCAAGATTTACGCA
          1 AAACTATGTGGGAAATAAAATAAGTAGCAAGATTTAAG-A

                             *        
      15254 AAACTATGTGGGAAATATAATAAGTA
          1 AAACTATGTGGGAAATAAAATAAGTA

      15280 ATACTCCCTT


Statistics
Matches: 52,  Mismatches: 13, Indels: 2
        0.78            0.19        0.03

Matches are distributed among these distances:
  39   27  0.52
  40   25  0.48

ACGTcount: A:0.49, C:0.07, G:0.18, T:0.26


Consensus pattern (39 bp):   
AAACTATGTGGGAAATAAAATAAGTAGCAAGATTTAAGA
Done.