Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023733.1 Corchorus olitorius cultivar O-4 contig23766, 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: 32491
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:12155 original size:19 final size:18

Alignment explanation


    Indices: 12118--12165  Score: 57
    Period size: 16  Copynumber: 2.8  Consensus size: 18

      12108 CTGAAATTAT

                              
      12118 TAATTATTTATTAAATAA
          1 TAATTATTTATTAAATAA

                         * *  
      12136 TAATTATTT-TT-CAGAA
          1 TAATTATTTATTAAATAA

                           
      12152 TAATTA-TTATTAAA
          1 TAATTATTTATTAAA

      12166 ATTCCCTTCA


Statistics
Matches: 25,  Mismatches: 3, Indels: 5
        0.76            0.09        0.15

Matches are distributed among these distances:
  15    2  0.08
  16   11  0.44
  17    3  0.12
  18    9  0.36

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


Consensus pattern (18 bp):   
TAATTATTTATTAAATAA

Found at i:14338 original size:6 final size:6

Alignment explanation


    Indices: 14331--14366  Score: 54
    Period size: 6  Copynumber: 6.0  Consensus size: 6

      14321 GAGGAGCTCG

                 *      *                            
      14331 AACTCG AACTCG AACTCA AACTCA AACTCA AACTCA
          1 AACTCA AACTCA AACTCA AACTCA AACTCA AACTCA

      14367 TCGTTAGGAG


Statistics
Matches: 29,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
   6   29  1.00

ACGTcount: A:0.44, C:0.33, G:0.06, T:0.17


Consensus pattern (6 bp):   
AACTCA

Found at i:14344 original size:12 final size:12

Alignment explanation


    Indices: 14327--14365  Score: 60
    Period size: 12  Copynumber: 3.2  Consensus size: 12

      14317 CTATGAGGAG

                     *  
      14327 CTCGAACTCGAA
          1 CTCGAACTCAAA

                        
      14339 CTCGAACTCAAA
          1 CTCGAACTCAAA

               *        
      14351 CTCAAACTCAAA
          1 CTCGAACTCAAA

               
      14363 CTC
          1 CTC

      14366 ATCGTTAGGA


Statistics
Matches: 25,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  12   25  1.00

ACGTcount: A:0.38, C:0.36, G:0.08, T:0.18


Consensus pattern (12 bp):   
CTCGAACTCAAA

Found at i:17250 original size:2 final size:2

Alignment explanation


    Indices: 17245--17285  Score: 82
    Period size: 2  Copynumber: 20.5  Consensus size: 2

      17235 TGTGTGTGTC

                                                                         
      17245 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

      17286 TANGTTTTCA


Statistics
Matches: 39,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   39  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:22320 original size:36 final size:36

Alignment explanation


    Indices: 22273--22346  Score: 96
    Period size: 36  Copynumber: 2.1  Consensus size: 36

      22263 CTTGCGTTTC

                 *                          *    
      22273 TTTTAGATTT-CCTGAATTCCTAATCATAACCTTAGT
          1 TTTTAAATTTCCCT-AATTCCTAATCATAACCATAGT

                                  *      *      
      22309 TTTTAAATTTCCCTAATTCCTAGTCATAATCATAGT
          1 TTTTAAATTTCCCTAATTCCTAATCATAACCATAGT

              
      22345 TT
          1 TT

      22347 ATTCTCTATA


Statistics
Matches: 33,  Mismatches: 4, Indels: 2
        0.85            0.10        0.05

Matches are distributed among these distances:
  36   30  0.91
  37    3  0.09

ACGTcount: A:0.28, C:0.19, G:0.07, T:0.46


Consensus pattern (36 bp):   
TTTTAAATTTCCCTAATTCCTAATCATAACCATAGT

Found at i:23830 original size:16 final size:15

Alignment explanation


    Indices: 23792--23833  Score: 66
    Period size: 15  Copynumber: 2.7  Consensus size: 15

      23782 ACAGAGATTG

                   *       
      23792 ACAGAAAGCAATTAA
          1 ACAGAAAACAATTAA

                           
      23807 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                        
      23822 ACTAGAAAACAA
          1 AC-AGAAAACAA

      23834 AGCAAAGTAA


Statistics
Matches: 25,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  15   16  0.64
  16    9  0.36

ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12


Consensus pattern (15 bp):   
ACAGAAAACAATTAA
Done.