Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015311.1 Corchorus olitorius cultivar O-4 contig15344, 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: 15491
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


Found at i:1934 original size:15 final size:15

Alignment explanation


    Indices: 1914--1944  Score: 62
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       1904 TTTACTTTTG

                           
       1914 ATCAAAACATTAAAA
          1 ATCAAAACATTAAAA

                           
       1929 ATCAAAACATTAAAA
          1 ATCAAAACATTAAAA

             
       1944 A
          1 A

       1945 GATCAAAAAT


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

Matches are distributed among these distances:
  15   16  1.00

ACGTcount: A:0.68, C:0.13, G:0.00, T:0.19


Consensus pattern (15 bp):   
ATCAAAACATTAAAA

Found at i:8517 original size:18 final size:19

Alignment explanation


    Indices: 8496--8537  Score: 52
    Period size: 18  Copynumber: 2.3  Consensus size: 19

       8486 ATAAAAGAAA

                               
       8496 AGAAAAGAAAA-AAAAAAT
          1 AGAAAAGAAAACAAAAAAT

                         *     
       8514 AG-AAAGAAAACAGAAAAT
          1 AGAAAAGAAAACAAAAAAT

             *    
       8532 ACAAAA
          1 AGAAAA

       8538 AACGAAAAAC


Statistics
Matches: 20,  Mismatches: 2, Indels: 3
        0.80            0.08        0.12

Matches are distributed among these distances:
  17    8  0.40
  18    9  0.45
  19    3  0.15

ACGTcount: A:0.79, C:0.05, G:0.12, T:0.05


Consensus pattern (19 bp):   
AGAAAAGAAAACAAAAAAT

Found at i:8552 original size:14 final size:14

Alignment explanation


    Indices: 8520--8571  Score: 54
    Period size: 15  Copynumber: 3.6  Consensus size: 14

       8510 AAATAGAAAG

                            
       8520 AAAACAGAAAATACAA
          1 AAAAC-GAAAA-ACAA

                           
       8536 AAAACGAAAAACGAA
          1 AAAACGAAAAAC-AA

                           
       8551 AAAA-GAAGAAA-AA
          1 AAAACGAA-AAACAA

                    
       8564 AAAACGAA
          1 AAAACGAA

       8572 GCTCTTTTTC


Statistics
Matches: 33,  Mismatches: 0, Indels: 8
        0.80            0.00        0.20

Matches are distributed among these distances:
  13    6  0.18
  14    8  0.24
  15   14  0.42
  16    5  0.15

ACGTcount: A:0.77, C:0.10, G:0.12, T:0.02


Consensus pattern (14 bp):   
AAAACGAAAAACAA

Found at i:8572 original size:14 final size:15

Alignment explanation


    Indices: 8532--8572  Score: 52
    Period size: 14  Copynumber: 2.9  Consensus size: 15

       8522 AACAGAAAAT

                           
       8532 ACAAAAAACGAA-AA
          1 ACAAAAAACGAAGAA

                            
       8546 ACGAAAAAA-GAAGAA
          1 AC-AAAAAACGAAGAA

                         
       8561 A-AAAAAACGAAG
          1 ACAAAAAACGAAG

       8573 CTCTTTTTCT


Statistics
Matches: 24,  Mismatches: 0, Indels: 6
        0.80            0.00        0.20

Matches are distributed among these distances:
  13    6  0.25
  14    9  0.38
  15    9  0.38

ACGTcount: A:0.76, C:0.10, G:0.15, T:0.00


Consensus pattern (15 bp):   
ACAAAAAACGAAGAA

Found at i:10769 original size:16 final size:16

Alignment explanation


    Indices: 10746--10788  Score: 52
    Period size: 16  Copynumber: 2.8  Consensus size: 16

      10736 TCCGAACCGA

                            
      10746 AACC-GAAATGACTCG
          1 AACCTGAAATGACTCG

                     **     
      10761 AACCTGAAACAACTCG
          1 AACCTGAAATGACTCG

              *         
      10777 AAGCTGAAATGA
          1 AACCTGAAATGA

      10789 TCCAAACCCG


Statistics
Matches: 22,  Mismatches: 5, Indels: 1
        0.79            0.18        0.04

Matches are distributed among these distances:
  15    4  0.18
  16   18  0.82

ACGTcount: A:0.44, C:0.23, G:0.19, T:0.14


Consensus pattern (16 bp):   
AACCTGAAATGACTCG

Found at i:11202 original size:49 final size:48

Alignment explanation


    Indices: 11108--11249  Score: 191
    Period size: 49  Copynumber: 3.0  Consensus size: 48

      11098 GAGCGTGCCA

                        *         *                         
      11108 ATCAATTTTGTCAAAAAATTGATAAAAAGTGCAA-TAAAAAGTAAAAG
          1 ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAAGTAAAAAGTAAAAG

                                                              
      11155 ATCAATTTTGTCTTAAAAATTGAGAAAAAGATGCAAGTAAAAA-TAAAAG
          1 ATCAATTTTGTC-TAAAAATTGAGAAAAAG-TGCAAGTAAAAAGTAAAAG

            *           *               *                  
      11204 TTCAATTTTGTAGTAAAAATTGAGAAAAGGTGC-AGTAAAAAGTAAA
          1 ATCAATTTTGT-CTAAAAATTGAGAAAAAGTGCAAGTAAAAAGTAAA

      11250 GGATTGCTTG


Statistics
Matches: 85,  Mismatches: 5, Indels: 9
        0.86            0.05        0.09

Matches are distributed among these distances:
  47   20  0.24
  48   22  0.26
  49   37  0.44
  50    6  0.07

ACGTcount: A:0.52, C:0.06, G:0.15, T:0.27


Consensus pattern (48 bp):   
ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAAGTAAAAAGTAAAAG
Done.