Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018744.1 Corchorus olitorius cultivar O-4 contig18777, 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: 10500
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.33


Found at i:1282 original size:12 final size:11

Alignment explanation


    Indices: 1254--1282  Score: 58
    Period size: 11  Copynumber: 2.6  Consensus size: 11

       1244 GAATTTTTTT

                       
       1254 TATTTTTGAAA
          1 TATTTTTGAAA

                       
       1265 TATTTTTGAAA
          1 TATTTTTGAAA

                   
       1276 TATTTTT
          1 TATTTTT

       1283 CGATTGAACT


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   18  1.00

ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62


Consensus pattern (11 bp):   
TATTTTTGAAA

Found at i:2334 original size:21 final size:21

Alignment explanation


    Indices: 2310--2426  Score: 182
    Period size: 21  Copynumber: 5.6  Consensus size: 21

       2300 CTTAGGCAAT

                    *    *       
       2310 TCCAATGAGCTTGAAACCTTC
          1 TCCAATGAACTTGGAACCTTC

                    *            
       2331 TCCAATGATCTTGGAACCTTC
          1 TCCAATGAACTTGGAACCTTC

                                 
       2352 TCCAATGAACTTGGAACCTTC
          1 TCCAATGAACTTGGAACCTTC

                                 
       2373 TCCAATGAACTTGGAACCTTC
          1 TCCAATGAACTTGGAACCTTC

                    *             
       2394 TCCAATGAGCTTGGAA-CTTGC
          1 TCCAATGAACTTGGAACCTT-C

                        
       2415 TCCAATGAACTT
          1 TCCAATGAACTT

       2427 CTAGCATCTT


Statistics
Matches: 90,  Mismatches: 5, Indels: 2
        0.93            0.05        0.02

Matches are distributed among these distances:
  20    3  0.03
  21   87  0.97

ACGTcount: A:0.27, C:0.27, G:0.15, T:0.30


Consensus pattern (21 bp):   
TCCAATGAACTTGGAACCTTC

Found at i:7139 original size:34 final size:34

Alignment explanation


    Indices: 7092--7204  Score: 95
    Period size: 34  Copynumber: 3.2  Consensus size: 34

       7082 ATTGGAGAAA

                    *     *       *            
       7092 TTAGGGTTTTAAAATTTGAGG-CTTTTATTTCGGT
          1 TTAGGGTTCTAAAAATTG-GGAATTTTATTTCGGT

                                              
       7126 TTAGGGTTCTAAAAATTGGGAATTTTATTTCGGT
          1 TTAGGGTTCTAAAAATTGGGAATTTTATTTCGGT

             *  **  *              *              
       7160 TGAGTCTTTTATGTAAAATTGGGGATTTTAATTT-GGT
          1 TTAGGGTTCTA---AAAATTGGGAATTTT-ATTTCGGT

                    
       7197 TTAGGGTT
          1 TTAGGGTT

       7205 TTATGTCAAA


Statistics
Matches: 63,  Mismatches: 11, Indels: 7
        0.78            0.14        0.09

Matches are distributed among these distances:
  33    2  0.03
  34   35  0.56
  37   22  0.35
  38    4  0.06

ACGTcount: A:0.23, C:0.04, G:0.25, T:0.48


Consensus pattern (34 bp):   
TTAGGGTTCTAAAAATTGGGAATTTTATTTCGGT

Found at i:7188 original size:37 final size:37

Alignment explanation


    Indices: 7137--7230  Score: 111
    Period size: 37  Copynumber: 2.6  Consensus size: 37

       7127 TAGGGTTCTA

                                        *         
       7137 AAAATTGGGAATTTT-ATTTCGGTTGAGTCTTTTATGT
          1 AAAATTGGGAATTTTAATTT-GGTTGAGGCTTTTATGT

                     *              *   *        
       7174 AAAATTGGGGATTTTAATTTGGTTTAGGGTTTTATGT
          1 AAAATTGGGAATTTTAATTTGGTTGAGGCTTTTATGT

            *          *         
       7211 CAAATT-GGAAATTTAATTTG
          1 AAAATTGGGAATTTTAATTTG

       7231 CTGATATTGT


Statistics
Matches: 49,  Mismatches: 7, Indels: 3
        0.83            0.12        0.05

Matches are distributed among these distances:
  36   12  0.24
  37   33  0.67
  38    4  0.08

ACGTcount: A:0.28, C:0.03, G:0.22, T:0.47


Consensus pattern (37 bp):   
AAAATTGGGAATTTTAATTTGGTTGAGGCTTTTATGT
Done.