Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011173.1 Corchorus capsularis cultivar CVL-1 contig11194, 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: 37004
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32


Found at i:7059 original size:6 final size:6

Alignment explanation


    Indices: 7050--7089  Score: 53
    Period size: 6  Copynumber: 6.5  Consensus size: 6

       7040 TCTTTAATTT

                                   *          *           
       7050 TTTTTC TTTTTC TTTTTC TTGTTC TTCTTTT TTTTTC TTT
          1 TTTTTC TTTTTC TTTTTC TTTTTC TT-TTTC TTTTTC TTT

       7090 AACGTTTTTA


Statistics
Matches: 29,  Mismatches: 4, Indels: 2
        0.83            0.11        0.06

Matches are distributed among these distances:
   6   25  0.86
   7    4  0.14

ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82


Consensus pattern (6 bp):   
TTTTTC

Found at i:8245 original size:14 final size:13

Alignment explanation


    Indices: 8210--8256  Score: 53
    Period size: 14  Copynumber: 3.6  Consensus size: 13

       8200 ACAAGCCCCT

                      *  
       8210 ATATATATTTTTA
          1 ATATATATTTATA

                         
       8223 ATA-AT-TTTATA
          1 ATATATATTTATA

                           
       8234 ATAATATATTTAATA
          1 AT-ATATATTT-ATA

                    
       8249 ATATATAT
          1 ATATATAT

       8257 CTTACTTAAA


Statistics
Matches: 29,  Mismatches: 1, Indels: 7
        0.78            0.03        0.19

Matches are distributed among these distances:
  11    7  0.24
  12    3  0.10
  13    5  0.17
  14    9  0.31
  15    5  0.17

ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53


Consensus pattern (13 bp):   
ATATATATTTATA

Found at i:8249 original size:12 final size:12

Alignment explanation


    Indices: 8214--8254  Score: 50
    Period size: 12  Copynumber: 3.5  Consensus size: 12

       8204 GCCCCTATAT

                *       
       8214 ATATTTTTAATA
          1 ATATATTTAATA

                         
       8226 AT-T-TTATAATA
          1 ATATATT-TAATA

                        
       8237 ATATATTTAATA
          1 ATATATTTAATA

                  
       8249 ATATAT
          1 ATATAT

       8255 ATCTTACTTA


Statistics
Matches: 26,  Mismatches: 0, Indels: 6
        0.81            0.00        0.19

Matches are distributed among these distances:
  10    2  0.08
  11    8  0.31
  12   14  0.54
  13    2  0.08

ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54


Consensus pattern (12 bp):   
ATATATTTAATA

Found at i:8288 original size:21 final size:23

Alignment explanation


    Indices: 8248--8292  Score: 76
    Period size: 21  Copynumber: 2.0  Consensus size: 23

       8238 TATATTTAAT

                                   
       8248 AATATATATCTTACTTAAATTAC
          1 AATATATATCTTACTTAAATTAC

                                   
       8271 AATA-ATATCTTA-TTAAATTAC
          1 AATATATATCTTACTTAAATTAC

             
       8292 A
          1 A

       8293 GATTTGTATA


Statistics
Matches: 22,  Mismatches: 0, Indels: 2
        0.92            0.00        0.08

Matches are distributed among these distances:
  21   10  0.45
  22    8  0.36
  23    4  0.18

ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42


Consensus pattern (23 bp):   
AATATATATCTTACTTAAATTAC

Found at i:15662 original size:50 final size:50

Alignment explanation


    Indices: 15587--15687  Score: 202
    Period size: 50  Copynumber: 2.0  Consensus size: 50

      15577 AGTTGAAATA

                                                              
      15587 CAAAATGTGTAGAATGCTACAAATGAATGACTGAGTAAAAAGTCCAAGTT
          1 CAAAATGTGTAGAATGCTACAAATGAATGACTGAGTAAAAAGTCCAAGTT

                                                              
      15637 CAAAATGTGTAGAATGCTACAAATGAATGACTGAGTAAAAAGTCCAAGTT
          1 CAAAATGTGTAGAATGCTACAAATGAATGACTGAGTAAAAAGTCCAAGTT

             
      15687 C
          1 C

      15688 CATAGTGGAA


Statistics
Matches: 51,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  50   51  1.00

ACGTcount: A:0.44, C:0.13, G:0.20, T:0.24


Consensus pattern (50 bp):   
CAAAATGTGTAGAATGCTACAAATGAATGACTGAGTAAAAAGTCCAAGTT

Found at i:27662 original size:14 final size:14

Alignment explanation


    Indices: 27645--27671  Score: 54
    Period size: 14  Copynumber: 1.9  Consensus size: 14

      27635 GAATAATATC

                          
      27645 ATTTGACCTAACAT
          1 ATTTGACCTAACAT

                         
      27659 ATTTGACCTAACA
          1 ATTTGACCTAACA

      27672 CCTAAGATTT


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   13  1.00

ACGTcount: A:0.37, C:0.22, G:0.07, T:0.33


Consensus pattern (14 bp):   
ATTTGACCTAACAT
Done.