Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022655.1 Corchorus olitorius cultivar O-4 contig22688, 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: 18782
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28


Found at i:16975 original size:2 final size:2

Alignment explanation


    Indices: 16963--17003  Score: 73
    Period size: 2  Copynumber: 20.5  Consensus size: 2

      16953 CTGGTACTCG

                  *                                                      
      16963 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

      17004 CAAATTCCTT


Statistics
Matches: 37,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
   2   37  1.00

ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49


Consensus pattern (2 bp):   
TA

Found at i:17755 original size:50 final size:50

Alignment explanation


    Indices: 17696--17869  Score: 253
    Period size: 50  Copynumber: 3.5  Consensus size: 50

      17686 ATCCAGAAAT

                                                            * 
      17696 GTGAATTGGAAGACAGTTCAAAGGATAGGCGGGAGACGGTCCTTTTAAGA
          1 GTGAATTGGAAGACAGTTCAAAGGATAGGCGGGAGACGGTCCTTTTAATA

                                                              
      17746 GTGAATTGGAAGACAGTTCAAAGGATAGGCGGGAGACGGTCCTTTTAATA
          1 GTGAATTGGAAGACAGTTCAAAGGATAGGCGGGAGACGGTCCTTTTAATA

              *                         *    *             *   
      17796 -TTATATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTTATA
          1 GTGA-ATTGGAAGACAGTTCAAAGGATAGGCGGGAGACGGTCCTTTTAATA

             *                       
      17846 TTTGAATTGGAAGAC-GATTCAAAG
          1 -GTGAATTGGAAGACAG-TTCAAAG

      17870 TAGTTGATTC


Statistics
Matches: 114,  Mismatches: 6, Indels: 7
        0.90            0.05        0.06

Matches are distributed among these distances:
  49    2  0.02
  50   93  0.82
  51   17  0.15
  52    2  0.02

ACGTcount: A:0.33, C:0.11, G:0.29, T:0.26


Consensus pattern (50 bp):   
GTGAATTGGAAGACAGTTCAAAGGATAGGCGGGAGACGGTCCTTTTAATA

Found at i:17911 original size:27 final size:26

Alignment explanation


    Indices: 17847--17941  Score: 81
    Period size: 26  Copynumber: 3.7  Consensus size: 26

      17837 CTTTTTATAT

                                      
      17847 TTGAATTGGAAGACGATTCAAAGTAG
          1 TTGAATTGGAAGACGATTCAAAGTAG

                                          
      17873 TTG-ATTCGGAAGACGATTCCCCAAAG-A-
          1 TTGAATT-GGAAGACGATT---CAAAGTAG

                          *   **   *  
      17900 TTGAATTGGAAGACAATTTGAAGAAG
          1 TTGAATTGGAAGACGATTCAAAGTAG

                     *       
      17926 TTG-ATTGGGAGACGAT
          1 TTGAATTGGAAGACGAT

      17942 CCATTTCAAA


Statistics
Matches: 57,  Mismatches: 5, Indels: 15
        0.74            0.06        0.19

Matches are distributed among these distances:
  24    3  0.05
  25   15  0.26
  26   17  0.30
  27   13  0.23
  28    4  0.07
  29    5  0.09

ACGTcount: A:0.36, C:0.11, G:0.27, T:0.26


Consensus pattern (26 bp):   
TTGAATTGGAAGACGATTCAAAGTAG

Found at i:18184 original size:28 final size:28

Alignment explanation


    Indices: 18142--18210  Score: 111
    Period size: 28  Copynumber: 2.5  Consensus size: 28

      18132 TTTACTTCTT

                      *          *      
      18142 ATTTTGGTCAGTTTGCATGTCTAGGGGC
          1 ATTTTGGTCATTTTGCATGTCCAGGGGC

                                       *
      18170 ATTTTGGTCATTTTGCATGTCCAGGGGT
          1 ATTTTGGTCATTTTGCATGTCCAGGGGC

                         
      18198 ATTTTGGTCATTT
          1 ATTTTGGTCATTT

      18211 GTACATCTAG


Statistics
Matches: 38,  Mismatches: 3, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  28   38  1.00

ACGTcount: A:0.14, C:0.13, G:0.28, T:0.45


Consensus pattern (28 bp):   
ATTTTGGTCATTTTGCATGTCCAGGGGC

Found at i:18224 original size:28 final size:27

Alignment explanation


    Indices: 18141--18223  Score: 78
    Period size: 28  Copynumber: 3.0  Consensus size: 27

      18131 ATTTACTTCT

                            * **        
      18141 TATTTTGGTCAGTTTGCATGTCTAGGGG
          1 TATTTTGGTCA-TTTGTACATCTAGGGG

            *               *      *     
      18169 CATTTTGGTCATTT-TGCATGTCCAGGGG
          1 TATTTTGGTCATTTGTACA--TCTAGGGG

                                       
      18197 TATTTTGGTCATTTGTACATCTAGGGG
          1 TATTTTGGTCATTTGTACATCTAGGGG

      18224 GGGGGGCATT


Statistics
Matches: 43,  Mismatches: 9, Indels: 7
        0.73            0.15        0.12

Matches are distributed among these distances:
  27   10  0.23
  28   30  0.70
  29    3  0.07

ACGTcount: A:0.16, C:0.13, G:0.29, T:0.42


Consensus pattern (27 bp):   
TATTTTGGTCATTTGTACATCTAGGGG
Done.