Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012706.1 Corchorus capsularis cultivar CVL-1 contig12727, 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: 14399
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32


Found at i:3325 original size:32 final size:32

Alignment explanation


    Indices: 3257--3318  Score: 88
    Period size: 32  Copynumber: 1.9  Consensus size: 32

       3247 TGATTTGGGG

                   *       *         *      
       3257 TATATAGTGGCATCTGAAGAACAAAGCGCCCT
          1 TATATAGCGGCATCTAAAGAACAAAACGCCCT

                       *                  
       3289 TATATAGCGGCGTCTAAAGAACAAAACGCC
          1 TATATAGCGGCATCTAAAGAACAAAACGCC

       3319 GCTATATTTA


Statistics
Matches: 26,  Mismatches: 4, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  32   26  1.00

ACGTcount: A:0.37, C:0.23, G:0.21, T:0.19


Consensus pattern (32 bp):   
TATATAGCGGCATCTAAAGAACAAAACGCCCT

Found at i:3434 original size:24 final size:24

Alignment explanation


    Indices: 3373--3436  Score: 92
    Period size: 24  Copynumber: 2.7  Consensus size: 24

       3363 TGCAGGTAGC

                   *     **        *
       3373 GGCGTCTTGACGCCCCCAAATAGT
          1 GGCGTCTGGACGCTGCCAAATAGG

                                    
       3397 GGCGTCTGGACGCTGCCAAATAGG
          1 GGCGTCTGGACGCTGCCAAATAGG

                            
       3421 GGCGTCTGGACGCTGC
          1 GGCGTCTGGACGCTGC

       3437 AATATGCTAT


Statistics
Matches: 36,  Mismatches: 4, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  24   36  1.00

ACGTcount: A:0.17, C:0.30, G:0.34, T:0.19


Consensus pattern (24 bp):   
GGCGTCTGGACGCTGCCAAATAGG

Found at i:6192 original size:2 final size:2

Alignment explanation


    Indices: 6185--6234  Score: 82
    Period size: 2  Copynumber: 25.0  Consensus size: 2

       6175 TGATTAAAAC

                              *                    *                      
       6185 AT AT AT AT AT AT GT AT AT AT AT AT AT CT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

                       
       6227 AT AT AT AT
          1 AT AT AT AT

       6235 GTGAATCAAT


Statistics
Matches: 44,  Mismatches: 4, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
   2   44  1.00

ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:11290 original size:67 final size:68

Alignment explanation


    Indices: 11178--11338  Score: 260
    Period size: 67  Copynumber: 2.4  Consensus size: 68

      11168 AGACAGAAGG

                                       *                                     
      11178 TTATTAATTCAGTATTATCCC-A-AT-GT-ATTAGTTTGGGTGAGTGAATTAAAAATATTTTAAA
          1 TTATTAATTCAGTATTATCCCAATATATTAATTAGTTTGGGTGAGTGAATTAAAAATATTTTAAA

               
      11239 ATA
         66 ATA

                                                    *                        
      11242 TTATTAATT-AGTATTATCCCAATATATTAATTAGTTTGGTTGAGTGAATTAAAAATATTTTAAA
          1 TTATTAATTCAGTATTATCCCAATATATTAATTAGTTTGGGTGAGTGAATTAAAAATATTTTAAA

               
      11306 ATA
         66 ATA

                              *           
      11309 TTATTAATTCAGTATTATTCCAATATATTA
          1 TTATTAATTCAGTATTATCCCAATATATTA

      11339 TTTTAAGCAA


Statistics
Matches: 89,  Mismatches: 3, Indels: 6
        0.91            0.03        0.06

Matches are distributed among these distances:
  63   11  0.12
  64   10  0.11
  65    2  0.02
  66    1  0.01
  67   46  0.52
  68   19  0.21

ACGTcount: A:0.39, C:0.06, G:0.11, T:0.45


Consensus pattern (68 bp):   
TTATTAATTCAGTATTATCCCAATATATTAATTAGTTTGGGTGAGTGAATTAAAAATATTTTAAA
ATA

Found at i:12081 original size:24 final size:24

Alignment explanation


    Indices: 12028--12081  Score: 58
    Period size: 24  Copynumber: 2.2  Consensus size: 24

      12018 ATACCCTTTA

                                *   
      12028 CTATATAATGGCGTTTAAAGGACG
          1 CTATATAATGGCGTTTAAAGCACG

             *                        
      12052 CAATATAGA-GGCGTTTAAA-CACTG
          1 CTATATA-ATGGCGTTTAAAGCAC-G

                  
      12076 CTATAT
          1 CTATAT

      12082 TTAACTTAAT


Statistics
Matches: 25,  Mismatches: 3, Indels: 4
        0.78            0.09        0.12

Matches are distributed among these distances:
  23    2  0.08
  24   22  0.88
  25    1  0.04

ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30


Consensus pattern (24 bp):   
CTATATAATGGCGTTTAAAGCACG
Done.