Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023316.1 Corchorus olitorius cultivar O-4 contig23349, 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: 23785
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36


Found at i:1030 original size:14 final size:14

Alignment explanation


    Indices: 1013--1046  Score: 59
    Period size: 14  Copynumber: 2.4  Consensus size: 14

       1003 CCCATCACCC

                          
       1013 CAAAAAAAAAAAAA
          1 CAAAAAAAAAAAAA

                    *     
       1027 CAAAAAAACAAAAA
          1 CAAAAAAAAAAAAA

                  
       1041 CAAAAA
          1 CAAAAA

       1047 CACTAGAGTT


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  14   19  1.00

ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00


Consensus pattern (14 bp):   
CAAAAAAAAAAAAA

Found at i:2379 original size:257 final size:247

Alignment explanation


    Indices: 1927--2403  Score: 717
    Period size: 257  Copynumber: 1.9  Consensus size: 247

       1917 TTACCAATTA

                 *                                                           
       1927 CAAACTTGAAGTTGTAAAAAAAAGGACAAATTAACCATTTTGAATGGAAATTGGTTAAATTTCGT
          1 CAAACCTGAAGTTGTAAAAAAAAGGACAAATTAACCATTTTGAATGGAAATTGGTTAAATTTCGT

                        *                   *                                
       1992 TAACGATGGAAATTAGCTGGAGAGAAATTGGTGTGACTCTAATAAATTTCGTTCAATTCCTGTCC
         66 TAACGATGGAAAGTAGCTGGAGAGAAATTGGTATGACTCTAATAAATTTCGTTCAATTCCTGTCC

                                           *     *                           
       2057 AATTATTAGCATAATTTAACCAATTTCGGTCCAAAAAGGATAATTTGTCCATTTTTTACAAGTTC
        131 AATTATTAGCATAATTTAACCAATTTCGGTCAAAAAAAGATAATTTGTCCATTTTTTACAAGTTC

             *                                                  
       2122 ATATATGCAAATGACAATTTTGAAAGTTGTAAAATGGATAAATTGCCGATTG
        196 AGATATGCAAATGACAATTTTGAAAGTTGTAAAATGGATAAATTGCCGATTG

                             *               *                             * 
       2174 CAAACCTGAAGTTGTAACAAAAAGGACAAATTAGCCATTTT-AGATGGAAATTGGTTAAATTTTG
          1 CAAACCTGAAGTTGTAAAAAAAAGGACAAATTAACCATTTTGA-ATGGAAATTGGTTAAATTTCG

                                                                             
       2238 TTAACAATTGGATGGAAAGTAGCCTTTTTGGAGAGAAATTGGTATGACTCTAATAAATTTCGTTC
         65 TTAAC-----GATGGAAAGTAG-C----TGGAGAGAAATTGGTATGACTCTAATAAATTTCGTTC

                **                                                           
       2303 AATTTTTGTCCAATTATTAGCA-AATTTTAACCAATTTCGGT-AAAAAATAGATAATTTGTCCAT
        120 AATTCCTGTCCAATTATTAGCATAA-TTTAACCAATTTCGGTCAAAAAA-AGATAATTTGTCCAT

                                                  
       2366 TTTTTACAAGTTCAGATATGCAAATGACAATTTTGAAA
        183 TTTTTACAAGTTCAGATATGCAAATGACAATTTTGAAA

       2404 ATTCAAGGAT


Statistics
Matches: 206,  Mismatches: 11, Indels: 16
        0.88            0.05        0.07

Matches are distributed among these distances:
 246    1  0.00
 247   63  0.31
 252   11  0.05
 253    1  0.00
 256    7  0.03
 257  123  0.60

ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34


Consensus pattern (247 bp):   
CAAACCTGAAGTTGTAAAAAAAAGGACAAATTAACCATTTTGAATGGAAATTGGTTAAATTTCGT
TAACGATGGAAAGTAGCTGGAGAGAAATTGGTATGACTCTAATAAATTTCGTTCAATTCCTGTCC
AATTATTAGCATAATTTAACCAATTTCGGTCAAAAAAAGATAATTTGTCCATTTTTTACAAGTTC
AGATATGCAAATGACAATTTTGAAAGTTGTAAAATGGATAAATTGCCGATTG

Found at i:12436 original size:15 final size:16

Alignment explanation


    Indices: 12403--12442  Score: 55
    Period size: 15  Copynumber: 2.6  Consensus size: 16

      12393 TTACTTTGCT

                            
      12403 TTGTTTTCTAGTATAA
          1 TTGTTTTCTAGTATAA

                        *   
      12419 TTGTTTTCT-GTTTAA
          1 TTGTTTTCTAGTATAA

               *     
      12434 TTGCTTTCT
          1 TTGTTTTCT

      12443 TTCAACCTCT


Statistics
Matches: 22,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  15   13  0.59
  16    9  0.41

ACGTcount: A:0.15, C:0.10, G:0.12, T:0.62


Consensus pattern (16 bp):   
TTGTTTTCTAGTATAA

Found at i:18267 original size:13 final size:13

Alignment explanation


    Indices: 18246--18277  Score: 55
    Period size: 13  Copynumber: 2.5  Consensus size: 13

      18236 TTACTAACAA

                         
      18246 TTTTCTTTTGAGT
          1 TTTTCTTTTGAGT

                *        
      18259 TTTTTTTTTGAGT
          1 TTTTCTTTTGAGT

                  
      18272 TTTTCT
          1 TTTTCT

      18278 AGGAAGCTGC


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  13   17  1.00

ACGTcount: A:0.06, C:0.06, G:0.12, T:0.75


Consensus pattern (13 bp):   
TTTTCTTTTGAGT
Done.