Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013236.1 Corchorus capsularis cultivar CVL-1 contig13257, 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: 55627
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32


Found at i:7 original size:2 final size:2

Alignment explanation


    Indices: 1--38  Score: 76
    Period size: 2  Copynumber: 19.0  Consensus size: 2

                                                                    
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

         39 CTAGTTAAGG


Statistics
Matches: 36,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   36  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:1086 original size:15 final size:15

Alignment explanation


    Indices: 1046--1077  Score: 55
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       1036 ATAATTTATA

                            
       1046 AATATAATGAAATAAT
          1 AATATAAT-AAATAAT

                           
       1062 AATATAATAAATAAT
          1 AATATAATAAATAAT

             
       1077 A
          1 A

       1078 TATGTATAAT


Statistics
Matches: 16,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  15    8  0.50
  16    8  0.50

ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31


Consensus pattern (15 bp):   
AATATAATAAATAAT

Found at i:18415 original size:13 final size:13

Alignment explanation


    Indices: 18394--18436  Score: 68
    Period size: 13  Copynumber: 3.3  Consensus size: 13

      18384 TTAACCTTAG

                         
      18394 TTAAAAATTAGGA
          1 TTAAAAATTAGGA

                *        
      18407 TTAACAATTAGGA
          1 TTAAAAATTAGGA

                    *    
      18420 TTAAAAATCAGGA
          1 TTAAAAATTAGGA

                
      18433 TTAA
          1 TTAA

      18437 TTATTTAAAA


Statistics
Matches: 27,  Mismatches: 3, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  13   27  1.00

ACGTcount: A:0.51, C:0.05, G:0.14, T:0.30


Consensus pattern (13 bp):   
TTAAAAATTAGGA

Found at i:32306 original size:12 final size:12

Alignment explanation


    Indices: 32291--32315  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

      32281 AAACTTCTTT

                        
      32291 AGCTGCTCCTTC
          1 AGCTGCTCCTTC

                        
      32303 AGCTGCTCCTTC
          1 AGCTGCTCCTTC

             
      32315 A
          1 A

      32316 CAATTTGCTC


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

Matches are distributed among these distances:
  12   13  1.00

ACGTcount: A:0.12, C:0.40, G:0.16, T:0.32


Consensus pattern (12 bp):   
AGCTGCTCCTTC

Found at i:36023 original size:32 final size:31

Alignment explanation


    Indices: 35965--36024  Score: 75
    Period size: 32  Copynumber: 1.9  Consensus size: 31

      35955 GCTACATGGC

                            *              
      35965 ATTTTTGTCCAACATGTCACTACCACGTGGT
          1 ATTTTTGTCCAACATGACACTACCACGTGGT

                          *     * *      
      35996 ATTTTTAGTCCAACGTGACATTGCCACGT
          1 ATTTTT-GTCCAACATGACACTACCACGT

      36025 CAGCAATACC


Statistics
Matches: 24,  Mismatches: 4, Indels: 1
        0.83            0.14        0.03

Matches are distributed among these distances:
  31    6  0.25
  32   18  0.75

ACGTcount: A:0.23, C:0.25, G:0.17, T:0.35


Consensus pattern (31 bp):   
ATTTTTGTCCAACATGACACTACCACGTGGT

Found at i:39460 original size:78 final size:78

Alignment explanation


    Indices: 39367--39536  Score: 252
    Period size: 78  Copynumber: 2.2  Consensus size: 78

      39357 GTTTTTTAAT

                                                                             
      39367 TAAAATAGTAAAATGG-TAAAATATAATAGTTACAAGGATATTAGATTTAATTATAAAAAAAAAA
          1 TAAAATAGTAAAATGGTTAAAATATAATAGTTACAAGGATATTAGATTTAATTAT-AAAAAAAAA

                          
      39431 GAGTTTTTAGTGAG
         65 GAGTTTTTAGTGAG

                                     **      *           *          *     *  
      39445 TAAAATAGTAAAATGGTTAAAATATTTTAGTTATAAGGATATTAGCTTTAATTATATAAAAATAG
          1 TAAAATAGTAAAATGGTTAAAATATAATAGTTACAAGGATATTAGATTTAATTATAAAAAAAAAG

                    *    
      39510 AGTTTTTATTGAG
         66 AGTTTTTAGTGAG

                  *       
      39523 TAAAATGGTAAAAT
          1 TAAAATAGTAAAAT

      39537 AAAATAGTTA


Statistics
Matches: 83,  Mismatches: 8, Indels: 2
        0.89            0.09        0.02

Matches are distributed among these distances:
  78   49  0.59
  79   34  0.41

ACGTcount: A:0.48, C:0.01, G:0.15, T:0.36


Consensus pattern (78 bp):   
TAAAATAGTAAAATGGTTAAAATATAATAGTTACAAGGATATTAGATTTAATTATAAAAAAAAAG
AGTTTTTAGTGAG

Found at i:39564 original size:69 final size:71

Alignment explanation


    Indices: 39451--39597  Score: 208
    Period size: 69  Copynumber: 2.1  Consensus size: 71

      39441 TGAGTAAAAT

                              ***         *        *        *                
      39451 AGTAAAATGGTTAAAATATTTTAGTTATAAGGATATTAGCTTTAATTATATAAAAATAGAGTTTT
          1 AGTAAAATGGTTAAAATAAAATAGTTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTT

                  
      39516 TA-TTG
         66 TATTTG

                                                  *                          
      39521 AGTAAAATGG-TAAAATAAAATAGTTATAAAGATATTATATTTAATTAAATAAAAATAGAGTTTT
          1 AGTAAAATGGTTAAAATAAAATAGTTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTT

                  
      39585 TATTTG
         66 TATTTG

             *     
      39591 ACTAAAA
          1 AGTAAAA

      39598 CTATAAAAAG


Statistics
Matches: 68,  Mismatches: 8, Indels: 2
        0.87            0.10        0.03

Matches are distributed among these distances:
  69   49  0.72
  70   19  0.28

ACGTcount: A:0.47, C:0.01, G:0.12, T:0.39


Consensus pattern (71 bp):   
AGTAAAATGGTTAAAATAAAATAGTTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTT
TATTTG
Done.