Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017003.1 Corchorus olitorius cultivar O-4 contig17036, 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: 18513
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32


Found at i:3402 original size:9 final size:9

Alignment explanation


    Indices: 3390--3415  Score: 52
    Period size: 9  Copynumber: 2.9  Consensus size: 9

       3380 AATTTATTGT

                     
       3390 CAATTAACA
          1 CAATTAACA

                     
       3399 CAATTAACA
          1 CAATTAACA

                    
       3408 CAATTAAC
          1 CAATTAAC

       3416 TTAATTGTGT


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   9   17  1.00

ACGTcount: A:0.54, C:0.23, G:0.00, T:0.23


Consensus pattern (9 bp):   
CAATTAACA

Found at i:6427 original size:19 final size:19

Alignment explanation


    Indices: 6390--6427  Score: 51
    Period size: 19  Copynumber: 2.0  Consensus size: 19

       6380 TATTTTTGCG

                    *          
       6390 TTAATTTTTTTTTCTGTTT
          1 TTAATTTTATTTTCTGTTT

                                
       6409 TTAATTTTAATTTTC-GTTT
          1 TTAATTTT-ATTTTCTGTTT

       6428 AAGAACTTTT


Statistics
Matches: 17,  Mismatches: 1, Indels: 2
        0.85            0.05        0.10

Matches are distributed among these distances:
  19   12  0.71
  20    5  0.29

ACGTcount: A:0.16, C:0.05, G:0.05, T:0.74


Consensus pattern (19 bp):   
TTAATTTTATTTTCTGTTT

Found at i:11969 original size:13 final size:13

Alignment explanation


    Indices: 11951--11976  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

      11941 CTTGGCATGA

                         
      11951 GTGATGATTTTTG
          1 GTGATGATTTTTG

                         
      11964 GTGATGATTTTTG
          1 GTGATGATTTTTG

      11977 TTGTTACCTT


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.15, C:0.00, G:0.31, T:0.54


Consensus pattern (13 bp):   
GTGATGATTTTTG

Found at i:14362 original size:31 final size:31

Alignment explanation


    Indices: 14327--14409  Score: 157
    Period size: 31  Copynumber: 2.7  Consensus size: 31

      14317 ATCAACTTTT

                                           
      14327 TTGGGTACATATGAAAACCATGGACTTGAAA
          1 TTGGGTACATATGAAAACCATGGACTTGAAA

                 *                         
      14358 TTGGGCACATATGAAAACCATGGACTTGAAA
          1 TTGGGTACATATGAAAACCATGGACTTGAAA

                                 
      14389 TTGGGTACATATGAAAACCAT
          1 TTGGGTACATATGAAAACCAT

      14410 TGGCACCTCC


Statistics
Matches: 50,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  31   50  1.00

ACGTcount: A:0.39, C:0.14, G:0.22, T:0.25


Consensus pattern (31 bp):   
TTGGGTACATATGAAAACCATGGACTTGAAA

Found at i:15086 original size:21 final size:21

Alignment explanation


    Indices: 15056--15116  Score: 77
    Period size: 21  Copynumber: 2.9  Consensus size: 21

      15046 CCTCCTGTTT

                *                
      15056 AGCAAGGAGGGTATTCTGACA
          1 AGCATGGAGGGTATTCTGACA

             *          *    *  *
      15077 ATCATGGAGGGTTTTCTAACC
          1 AGCATGGAGGGTATTCTGACA

                               
      15098 AGCATGGAGGGTATTCTGA
          1 AGCATGGAGGGTATTCTGA

      15117 AGAACAAGTA


Statistics
Matches: 32,  Mismatches: 8, Indels: 0
        0.80            0.20        0.00

Matches are distributed among these distances:
  21   32  1.00

ACGTcount: A:0.28, C:0.15, G:0.31, T:0.26


Consensus pattern (21 bp):   
AGCATGGAGGGTATTCTGACA

Found at i:16174 original size:22 final size:21

Alignment explanation


    Indices: 16149--16202  Score: 60
    Period size: 19  Copynumber: 2.6  Consensus size: 21

      16139 GAAGTTCGTG

                                  
      16149 TTTGAAGACTTATTGAAGATAA
          1 TTTGAAGA-TTATTGAAGATAA

                               * 
      16171 TTTGAAGA-T-TTGAAGATCA
          1 TTTGAAGATTATTGAAGATAA

                          
      16190 -TTGAAGAATTATT
          1 TTTGAAG-ATTATT

      16203 TCAAGAAGCA


Statistics
Matches: 28,  Mismatches: 1, Indels: 7
        0.78            0.03        0.19

Matches are distributed among these distances:
  18    6  0.21
  19   10  0.36
  20    2  0.07
  21    2  0.07
  22    8  0.29

ACGTcount: A:0.39, C:0.04, G:0.19, T:0.39


Consensus pattern (21 bp):   
TTTGAAGATTATTGAAGATAA

Done.