Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007179.1 Corchorus capsularis cultivar CVL-1 contig07200, 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: 35205
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


Found at i:17044 original size:2 final size:2

Alignment explanation


    Indices: 17039--17073  Score: 70
    Period size: 2  Copynumber: 17.5  Consensus size: 2

      17029 AAAAAAAAAA

                                                                
      17039 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
          1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A

      17074 AGAAGAAAGA


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   33  1.00

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


Consensus pattern (2 bp):   
AG

Found at i:17090 original size:10 final size:10

Alignment explanation


    Indices: 17037--17090  Score: 54
    Period size: 10  Copynumber: 5.2  Consensus size: 10

      17027 TTAAAAAAAA

                      
      17037 AAAGAGAGAG
          1 AAAGAGAGAG

             *        
      17047 AGAGAGAGAG
          1 AAAGAGAGAG

             *        
      17057 AGAGAGAGAG
          1 AAAGAGAGAG

             *          
      17067 AGAGAGAAGAAG
          1 AAAGAG-AG-AG

                 *    
      17079 AAAGAAAGAG
          1 AAAGAGAGAG

              
      17089 AA
          1 AA

      17091 GCCCGCGAAG


Statistics
Matches: 39,  Mismatches: 3, Indels: 4
        0.85            0.07        0.09

Matches are distributed among these distances:
  10   29  0.74
  11    4  0.10
  12    6  0.15

ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00


Consensus pattern (10 bp):   
AAAGAGAGAG

Found at i:28546 original size:24 final size:24

Alignment explanation


    Indices: 28503--28549  Score: 62
    Period size: 24  Copynumber: 2.0  Consensus size: 24

      28493 ATGGTTATCA

                                    
      28503 TATATAATATAATTCTAAGTATAC
          1 TATATAATATAATTCTAAGTATAC

                                     
      28527 TATA-AATA-AATTACTAAAGTATA
          1 TATATAATATAATT-CT-AAGTATA

      28550 TATTAAGTTG


Statistics
Matches: 21,  Mismatches: 0, Indels: 4
        0.84            0.00        0.16

Matches are distributed among these distances:
  22    4  0.19
  23    6  0.29
  24   11  0.52

ACGTcount: A:0.51, C:0.06, G:0.04, T:0.38


Consensus pattern (24 bp):   
TATATAATATAATTCTAAGTATAC

Found at i:30725 original size:2 final size:2

Alignment explanation


    Indices: 30702--30754  Score: 72
    Period size: 2  Copynumber: 27.0  Consensus size: 2

      30692 AATTCATTAT

                   *        *                                        *    
      30702 TA TA TG TA TA TG TA TA TA -A TA TA TA TA TA TA TA TA TA CA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

                             
      30743 TA TA TA TA TA TA
          1 TA TA TA TA TA TA

      30755 AATGTTGAGC


Statistics
Matches: 44,  Mismatches: 6, Indels: 2
        0.85            0.12        0.04

Matches are distributed among these distances:
   1    1  0.02
   2   43  0.98

ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47


Consensus pattern (2 bp):   
TA

Found at i:32240 original size:17 final size:17

Alignment explanation


    Indices: 32218--32250  Score: 66
    Period size: 17  Copynumber: 1.9  Consensus size: 17

      32208 AACTTAAAGA

                             
      32218 AAGTAGAACAATTGGCG
          1 AAGTAGAACAATTGGCG

                            
      32235 AAGTAGAACAATTGGC
          1 AAGTAGAACAATTGGC

      32251 AGCTCCAGCA


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   16  1.00

ACGTcount: A:0.42, C:0.12, G:0.27, T:0.18


Consensus pattern (17 bp):   
AAGTAGAACAATTGGCG

Found at i:34677 original size:17 final size:17

Alignment explanation


    Indices: 34655--34689  Score: 52
    Period size: 17  Copynumber: 2.1  Consensus size: 17

      34645 AGCATTTCTC

                    *   *    
      34655 TTTACTCTTTTTTAAGT
          1 TTTACTCTCTTTAAAGT

                             
      34672 TTTACTCTCTTTAAAGT
          1 TTTACTCTCTTTAAAGT

             
      34689 T
          1 T

      34690 GAAATGAAGT


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  17   16  1.00

ACGTcount: A:0.20, C:0.14, G:0.06, T:0.60


Consensus pattern (17 bp):   
TTTACTCTCTTTAAAGT
Done.