Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011467.1 Corchorus capsularis cultivar CVL-1 contig11488, 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: 11635
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34


Found at i:747 original size:22 final size:22

Alignment explanation


    Indices: 713--755  Score: 61
    Period size: 22  Copynumber: 2.0  Consensus size: 22

        703 CATGGTTTTT

                                  
        713 ATGGGTAATAGGAAATCTGTTG
          1 ATGGGTAATAGGAAATCTGTTG

                           *      
        735 ATGGGTTAA-AGGAACTCTGTT
          1 ATGGG-TAATAGGAAATCTGTT

        756 TTAGGATTTT


Statistics
Matches: 19,  Mismatches: 1, Indels: 2
        0.86            0.05        0.09

Matches are distributed among these distances:
  22   16  0.84
  23    3  0.16

ACGTcount: A:0.30, C:0.07, G:0.30, T:0.33


Consensus pattern (22 bp):   
ATGGGTAATAGGAAATCTGTTG

Found at i:3622 original size:22 final size:22

Alignment explanation


    Indices: 3588--3633  Score: 60
    Period size: 22  Copynumber: 2.1  Consensus size: 22

       3578 ATAATACAAT

                                   
       3588 ATTATATATATAATA-TACTATA
          1 ATTATATATATAATATTA-TATA

                                   
       3610 ATTAT-TATAATAATATTATATA
          1 ATTATATAT-ATAATATTATATA

              
       3632 AT
          1 AT

       3634 AAAAATATAC


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

Matches are distributed among these distances:
  21    3  0.14
  22   17  0.77
  23    2  0.09

ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48


Consensus pattern (22 bp):   
ATTATATATATAATATTATATA

Found at i:4172 original size:6 final size:6

Alignment explanation


    Indices: 4161--4199  Score: 64
    Period size: 6  Copynumber: 6.8  Consensus size: 6

       4151 TATTCAGATA

                                                           
       4161 TATAAT TATAAT TATAAT TATAAT TAT-AT TAT-AT TATAA
          1 TATAAT TATAAT TATAAT TATAAT TATAAT TATAAT TATAA

       4200 AGAACAATAA


Statistics
Matches: 32,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   5   10  0.31
   6   22  0.69

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (6 bp):   
TATAAT

Found at i:8968 original size:17 final size:16

Alignment explanation


    Indices: 8928--8978  Score: 57
    Period size: 17  Copynumber: 3.1  Consensus size: 16

       8918 CATGTAATCT

                    **      
       8928 TTGATCACCGGTGATC
          1 TTGATCACTAGTGATC

                             
       8944 TTGCATCACTAGTGATC
          1 TTG-ATCACTAGTGATC

                         *   
       8961 TTAGATCACTAGTTATC
          1 TT-GATCACTAGTGATC

             
       8978 T
          1 T

       8979 GGGGGGTAAT


Statistics
Matches: 30,  Mismatches: 3, Indels: 3
        0.83            0.08        0.08

Matches are distributed among these distances:
  16    3  0.10
  17   26  0.87
  18    1  0.03

ACGTcount: A:0.24, C:0.22, G:0.18, T:0.37


Consensus pattern (16 bp):   
TTGATCACTAGTGATC

Found at i:9465 original size:25 final size:25

Alignment explanation


    Indices: 9436--9491  Score: 94
    Period size: 25  Copynumber: 2.2  Consensus size: 25

       9426 ATTTAATGGT

                                     
       9436 GTAATTAAATTTAAAGTCAAATATA
          1 GTAATTAAATTTAAAGTCAAATATA

                  *                  
       9461 GTAATTCAATTTAAAGTCAAATATA
          1 GTAATTAAATTTAAAGTCAAATATA

            *     
       9486 TTAATT
          1 GTAATT

       9492 GATTACAGAA


Statistics
Matches: 29,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  25   29  1.00

ACGTcount: A:0.48, C:0.05, G:0.07, T:0.39


Consensus pattern (25 bp):   
GTAATTAAATTTAAAGTCAAATATA

Found at i:9883 original size:26 final size:25

Alignment explanation


    Indices: 9849--9920  Score: 90
    Period size: 26  Copynumber: 2.8  Consensus size: 25

       9839 TTTTTCCCCA

                                     
       9849 AGGGTATTTTGGTCATTTTCACTTC
          1 AGGGTATTTTGGTCATTTTCACTTC

                 *        *       *   
       9874 GAGGGCATTTTGGTTATTTTCATTTC
          1 -AGGGTATTTTGGTCATTTTCACTTC

                                 
       9900 AGGGGTATTTTGGTCACTTTT
          1 A-GGGTATTTTGGTCA-TTTT

       9921 AGGGGGATAA


Statistics
Matches: 39,  Mismatches: 5, Indels: 3
        0.83            0.11        0.06

Matches are distributed among these distances:
  25    1  0.03
  26   34  0.87
  27    4  0.10

ACGTcount: A:0.15, C:0.12, G:0.24, T:0.49


Consensus pattern (25 bp):   
AGGGTATTTTGGTCATTTTCACTTC

Found at i:10861 original size:28 final size:28

Alignment explanation


    Indices: 10799--10871  Score: 96
    Period size: 28  Copynumber: 2.6  Consensus size: 28

      10789 GGTCACATAA

                                     *  
      10799 GGGCATTTTGGTCA-TTTTCATGTTCAG
          1 GGGCATTTTGGTCATTTTTCATGTTAAG

                                         
      10826 GGGCATTTTGGTCATTTTTGCAT-TTAAG
          1 GGGCATTTTGGTCATTTTT-CATGTTAAG

              **              
      10854 GGTTATTTTGGTCATTTT
          1 GGGCATTTTGGTCATTTT

      10872 AAGTTCACTT


Statistics
Matches: 41,  Mismatches: 3, Indels: 3
        0.87            0.06        0.06

Matches are distributed among these distances:
  27   14  0.34
  28   24  0.59
  29    3  0.07

ACGTcount: A:0.15, C:0.11, G:0.25, T:0.49


Consensus pattern (28 bp):   
GGGCATTTTGGTCATTTTTCATGTTAAG
Done.