Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016356.1 Corchorus olitorius cultivar O-4 contig16389, 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: 22167
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31


Found at i:2513 original size:30 final size:31

Alignment explanation


    Indices: 2477--2542  Score: 91
    Period size: 32  Copynumber: 2.1  Consensus size: 31

       2467 TTAAGGGGGG

                             *              
       2477 TTAAAACATA-CTT-TAGGGTATGTGAGATAT
          1 TTAAAACA-AGCTTATAAGGTATGTGAGATAT

                                            
       2507 TTAAAACAAGCTTGATAAGGTATGTGAGATAT
          1 TTAAAACAAGCTT-ATAAGGTATGTGAGATAT

                
       2539 TTAA
          1 TTAA

       2543 GCAGTGGACT


Statistics
Matches: 32,  Mismatches: 1, Indels: 4
        0.86            0.03        0.11

Matches are distributed among these distances:
  29    1  0.03
  30   11  0.34
  32   20  0.62

ACGTcount: A:0.39, C:0.06, G:0.20, T:0.35


Consensus pattern (31 bp):   
TTAAAACAAGCTTATAAGGTATGTGAGATAT

Found at i:4116 original size:98 final size:98

Alignment explanation


    Indices: 3947--4126  Score: 288
    Period size: 98  Copynumber: 1.8  Consensus size: 98

       3937 CCAAAATATT

                                   *          *    *                         
       3947 TTCAAAACTACAAAACTCAAATATTATAACTATTTTTCTTACCCTATTCATCAAATTTTACAGAA
          1 TTCAAAACTACAAAACTCAAATACTATAACTATTATTCTAACCCTATTCATCAAATTTTACAGAA

                     *                       
       4012 CAATAGCACTTTTTCATTAAAATTAGAATTTAA
         66 CAATAGCACCTTTTCATTAAAATTAGAATTTAA

                     *     *                         *      *                
       4045 TTCAAAACTGCAAAAGTCAAATACTATAACTATTATTCTAATCCTATTTATCAAATTTTACAGAA
          1 TTCAAAACTACAAAACTCAAATACTATAACTATTATTCTAACCCTATTCATCAAATTTTACAGAA

                             
       4110 CAATAGCACCTTTTCAT
         66 CAATAGCACCTTTTCAT

       4127 AAAGATCAAA


Statistics
Matches: 74,  Mismatches: 8, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  98   74  1.00

ACGTcount: A:0.41, C:0.18, G:0.04, T:0.37


Consensus pattern (98 bp):   
TTCAAAACTACAAAACTCAAATACTATAACTATTATTCTAACCCTATTCATCAAATTTTACAGAA
CAATAGCACCTTTTCATTAAAATTAGAATTTAA

Found at i:9756 original size:20 final size:20

Alignment explanation


    Indices: 9731--9769  Score: 78
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       9721 GTTTAATATA

                                
       9731 TATAATATATATGTATAATG
          1 TATAATATATATGTATAATG

                               
       9751 TATAATATATATGTATAAT
          1 TATAATATATATGTATAAT

       9770 TTGGTGGAAT


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  20   19  1.00

ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46


Consensus pattern (20 bp):   
TATAATATATATGTATAATG

Found at i:10872 original size:18 final size:17

Alignment explanation


    Indices: 10840--10873  Score: 50
    Period size: 17  Copynumber: 1.9  Consensus size: 17

      10830 ATCAAGTATT

                    *        
      10840 ATAATTAAGAGAAGAGC
          1 ATAATTAACAGAAGAGC

                             
      10857 ATAATTAATCAGAAGAG
          1 ATAATTAA-CAGAAGAG

      10874 ATCAAAGAGA


Statistics
Matches: 15,  Mismatches: 1, Indels: 1
        0.88            0.06        0.06

Matches are distributed among these distances:
  17    8  0.53
  18    7  0.47

ACGTcount: A:0.53, C:0.06, G:0.21, T:0.21


Consensus pattern (17 bp):   
ATAATTAACAGAAGAGC

Found at i:14664 original size:20 final size:21

Alignment explanation


    Indices: 14639--14677  Score: 62
    Period size: 21  Copynumber: 1.9  Consensus size: 21

      14629 GAGCTGATCA

                                 
      14639 GCTGAAAA-TTCCTCAGTTCG
          1 GCTGAAAAGTTCCTCAGTTCG

                       *       
      14659 GCTGAAAAGTTGCTCAGTT
          1 GCTGAAAAGTTCCTCAGTT

      14678 TGGCGAAGTT


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  20    8  0.47
  21    9  0.53

ACGTcount: A:0.26, C:0.21, G:0.23, T:0.31


Consensus pattern (21 bp):   
GCTGAAAAGTTCCTCAGTTCG

Found at i:21623 original size:10 final size:11

Alignment explanation


    Indices: 21603--21632  Score: 51
    Period size: 11  Copynumber: 2.7  Consensus size: 11

      21593 CCTAACCTAA

                       
      21603 TCAATTTTTTT
          1 TCAATTTTTTT

                       
      21614 TCAATTTTTTT
          1 TCAATTTTTTT

             *      
      21625 TTAATTTT
          1 TCAATTTT

      21633 CAAAATTTTC


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  11   18  1.00

ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73


Consensus pattern (11 bp):   
TCAATTTTTTT

Found at i:22010 original size:2 final size:2

Alignment explanation


    Indices: 22003--22051  Score: 62
    Period size: 2  Copynumber: 24.5  Consensus size: 2

      21993 CATCACCTTC

                                                   *     *     *     *    
      22003 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT GT AT GT AT GT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

                      
      22045 AT AT AT A
          1 AT AT AT A

      22052 AGTTTGGCCA


Statistics
Matches: 39,  Mismatches: 8, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
   2   39  1.00

ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49


Consensus pattern (2 bp):   
AT

Done.