Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017361.1 Corchorus olitorius cultivar O-4 contig17394, 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: 13597
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32


Found at i:4597 original size:19 final size:19

Alignment explanation


    Indices: 4551--4597  Score: 58
    Period size: 19  Copynumber: 2.5  Consensus size: 19

       4541 TCAGACCGGG

                          *    
       4551 TCAAACCGGTCCGGTCCGA
          1 TCAAACCGGTCCGGACCGA

            *         *        
       4570 CCAAACCGGTTCGGACCGA
          1 TCAAACCGGTCCGGACCGA

                *    
       4589 TCAAGCCGG
          1 TCAAACCGG

       4598 CTCGAGCAGG


Statistics
Matches: 23,  Mismatches: 5, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  19   23  1.00

ACGTcount: A:0.23, C:0.36, G:0.28, T:0.13


Consensus pattern (19 bp):   
TCAAACCGGTCCGGACCGA

Found at i:10109 original size:36 final size:36

Alignment explanation


    Indices: 10062--10130  Score: 138
    Period size: 36  Copynumber: 1.9  Consensus size: 36

      10052 AATTATGGGC

                                                
      10062 TAAATTTTTGAATATCATTCCATGCATATTGATTAG
          1 TAAATTTTTGAATATCATTCCATGCATATTGATTAG

                                             
      10098 TAAATTTTTGAATATCATTCCATGCATATTGAT
          1 TAAATTTTTGAATATCATTCCATGCATATTGAT

      10131 CCCTATAATG


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  36   33  1.00

ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45


Consensus pattern (36 bp):   
TAAATTTTTGAATATCATTCCATGCATATTGATTAG

Found at i:10538 original size:19 final size:19

Alignment explanation


    Indices: 10509--10553  Score: 63
    Period size: 19  Copynumber: 2.4  Consensus size: 19

      10499 GGGTGCGCAT

                *           *  
      10509 CACCCACCGAAACCGATGC
          1 CACCGACCGAAACCGACGC

             *                 
      10528 CTCCGACCGAAACCGACGC
          1 CACCGACCGAAACCGACGC

                   
      10547 CACCGAC
          1 CACCGAC

      10554 GTGCGTCGGC


Statistics
Matches: 22,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  19   22  1.00

ACGTcount: A:0.29, C:0.49, G:0.18, T:0.04


Consensus pattern (19 bp):   
CACCGACCGAAACCGACGC

Found at i:11908 original size:175 final size:175

Alignment explanation


    Indices: 11706--12032  Score: 555
    Period size: 175  Copynumber: 1.9  Consensus size: 175

      11696 TTTATTTAGC

                     *        *              *                               
      11706 TAGCATGTTTAATCAATTTAGTTTTTTGCTAACGTAATTACTAATTGATTGATTTATTTATGGTA
          1 TAGCATGTTCAATCAATTGAGTTTTTTGCTAACATAATTACTAATTGATTGATTTATTTATGGTA

                        *  *                                                 
      11771 AAATTAAATAATTATGAATAAATTATAACTTTGATTGGCAAAGTTAACTAACGACTAACTTGATT
         66 AAATTAAATAATCATCAATAAATTATAACTTTGATTGGCAAAGTTAACTAACGACTAACTTGATT

            *      *                                     
      11836 TATTTATTTATTTAGCATGTTCTTTTTTTTTGGCATCAATTTATT
        131 CATTTATCTATTTAGCATGTTCTTTTTTTTTGGCATCAATTTATT

                                *                                            
      11881 TAGCATGTTCAATCAATTGATTTTTTTGCTAACATAATTACTAATTGATTGATTTATTTATGGTA
          1 TAGCATGTTCAATCAATTGAGTTTTTTGCTAACATAATTACTAATTGATTGATTTATTTATGGTA

                               *                               *             
      11946 AAATTAAATAATCATCAATTAATTATAACTTTGATTGGCAAAGTTAACTAATGACTAACTTGATT
         66 AAATTAAATAATCATCAATAAATTATAACTTTGATTGGCAAAGTTAACTAACGACTAACTTGATT

                 *                
      12011 CATTTGTCTATTTAGCATGTTC
        131 CATTTATCTATTTAGCATGTTC

      12033 AATAATTAAT


Statistics
Matches: 141,  Mismatches: 11, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
 175  141  1.00

ACGTcount: A:0.33, C:0.10, G:0.11, T:0.46


Consensus pattern (175 bp):   
TAGCATGTTCAATCAATTGAGTTTTTTGCTAACATAATTACTAATTGATTGATTTATTTATGGTA
AAATTAAATAATCATCAATAAATTATAACTTTGATTGGCAAAGTTAACTAACGACTAACTTGATT
CATTTATCTATTTAGCATGTTCTTTTTTTTTGGCATCAATTTATT

Found at i:12957 original size:127 final size:129

Alignment explanation


    Indices: 12714--12960  Score: 363
    Period size: 130  Copynumber: 1.9  Consensus size: 129

      12704 AATTACAACT

                                             *                              *
      12714 TTTGATTGGCAAAATTAACTAACGACTAACTTGTTTCATTTATTTATTTAGCATGTTCAAACAAT
          1 TTTGATTGGCAAAATTAACTAACGACTAACTTGGTTCATTTATTTATTTAGCATGTTCAAACAAG

                             *                                               
      12779 TTTATTTTTTTGCTAACGTAATTACTAATTGATTCATTTATTTATGCCAAAATTATAGGAGTAAC
         66 TTTA-TTTTTTGCTAACATAATTACTAATTGATTCATTTATTTATGCCAAAATTATAGGAGTAAC

                     *   *  *   * *                  *               *  *    
      12844 TTTGATTGGTAAAGTTGACTTAGGACTAACTTGGTTCATTTGTTTATTTAGCATGTTGAATC-AG
          1 TTTGATTGGCAAAATTAACTAACGACTAACTTGGTTCATTTATTTATTTAGCATGTTCAAACAAG

                                                         *        
      12908 TTTA-TTTTTGCTAACATAATTACTAATTGATTCATTTATTTATGGCAAAATTA
         66 TTTATTTTTTGCTAACATAATTACTAATTGATTCATTTATTTATGCCAAAATTA

      12961 AATAATCATT


Statistics
Matches: 105,  Mismatches: 12, Indels: 3
        0.88            0.10        0.03

Matches are distributed among these distances:
 127   47  0.45
 129    5  0.05
 130   53  0.50

ACGTcount: A:0.31, C:0.11, G:0.13, T:0.45


Consensus pattern (129 bp):   
TTTGATTGGCAAAATTAACTAACGACTAACTTGGTTCATTTATTTATTTAGCATGTTCAAACAAG
TTTATTTTTTGCTAACATAATTACTAATTGATTCATTTATTTATGCCAAAATTATAGGAGTAAC
Done.