Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024693.1 Corchorus olitorius cultivar O-4 contig24726, 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: 16524
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31


Found at i:3202 original size:13 final size:13

Alignment explanation


    Indices: 3184--3213  Score: 51
    Period size: 13  Copynumber: 2.3  Consensus size: 13

       3174 AACCGTTAAT

                         
       3184 ATCAAAATCATAA
          1 ATCAAAATCATAA

                  *      
       3197 ATCAAAGTCATAA
          1 ATCAAAATCATAA

                
       3210 ATCA
          1 ATCA

       3214 GAGTAAAACC


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

Matches are distributed among these distances:
  13   16  1.00

ACGTcount: A:0.57, C:0.17, G:0.03, T:0.23


Consensus pattern (13 bp):   
ATCAAAATCATAA

Found at i:4306 original size:2 final size:2

Alignment explanation


    Indices: 4299--4346  Score: 64
    Period size: 2  Copynumber: 24.5  Consensus size: 2

       4289 CTTCATTTAT

                                                             *             
       4299 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TCA -A AA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA

                      
       4340 TA TA TA T
          1 TA TA TA T

       4347 TTTACGGTCT


Statistics
Matches: 42,  Mismatches: 1, Indels: 6
        0.86            0.02        0.12

Matches are distributed among these distances:
   1    2  0.05
   2   39  0.93
   3    1  0.02

ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48


Consensus pattern (2 bp):   
TA

Found at i:4809 original size:106 final size:106

Alignment explanation


    Indices: 4590--4781  Score: 271
    Period size: 106  Copynumber: 1.8  Consensus size: 106

       4580 TAGTAAAATG

                                                                       *     
       4590 GTAAAAATAAAATAGGTAGAAGGATATTAGATTTAATTAAATAAAAAATAGAGTTTTTATTTGAG
          1 GTAAAAATAAAATAGGTAGAAGGATATTAGATTTAATTAAATAAAAAATAGAGTTTTTAGTTGAG

                 *            ***           *        
       4655 TAAAATTATAAAAGTATATTTAAAAATTCTAATATATAAAA
         66 TAAAACTATAAAAGTATAAACAAAAATTCTAAAATATAAAA

                    *      *  *                            *                 
       4696 GTAAAAATTAAATAGTTATAAGGATATTAGATTTAATTAAAT-AAAATTAGAGTTTTTAGTTGAG
          1 GTAAAAATAAAATAGGTAGAAGGATATTAGATTTAATTAAATAAAAAATAGAGTTTTTAGTTGAG

                           *       
       4760 T-AAACTATAAAAGTTTAAACAA
         66 TAAAACTATAAAAGTATAAACAA

       4782 TGACATTTAA


Statistics
Matches: 76,  Mismatches: 10, Indels: 2
        0.86            0.11        0.02

Matches are distributed among these distances:
 104   16  0.21
 105   21  0.28
 106   39  0.51

ACGTcount: A:0.51, C:0.02, G:0.12, T:0.35


Consensus pattern (106 bp):   
GTAAAAATAAAATAGGTAGAAGGATATTAGATTTAATTAAATAAAAAATAGAGTTTTTAGTTGAG
TAAAACTATAAAAGTATAAACAAAAATTCTAAAATATAAAA

Found at i:6298 original size:19 final size:18

Alignment explanation


    Indices: 6267--6303  Score: 56
    Period size: 19  Copynumber: 2.0  Consensus size: 18

       6257 GGGTCTTTAA

                    *         
       6267 CTATAGTATTAATTAATT
          1 CTATAGTAATAATTAATT

                               
       6285 CTATAAGTAATAATTAATT
          1 CTAT-AGTAATAATTAATT

       6304 AACTATTTAT


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  18    4  0.24
  19   13  0.76

ACGTcount: A:0.43, C:0.05, G:0.05, T:0.46


Consensus pattern (18 bp):   
CTATAGTAATAATTAATT

Found at i:15647 original size:31 final size:31

Alignment explanation


    Indices: 15624--15690  Score: 82
    Period size: 31  Copynumber: 2.1  Consensus size: 31

      15614 CCGAACCTGC

                                            
      15624 ATGACGCTAAATCCAGCAGACCCGAGACCCGA
          1 ATGAC-CTAAATCCAGCAGACCCGAGACCCGA

                   *            *    *      
      15656 ATGACCTGAATCCAG-ATGAGCCGAAACCCGA
          1 ATGACCTAAATCCAGCA-GACCCGAGACCCGA

                
      15687 ATGA
          1 ATGA

      15691 TCTGAGAAAA


Statistics
Matches: 31,  Mismatches: 3, Indels: 3
        0.84            0.08        0.08

Matches are distributed among these distances:
  30    1  0.03
  31   25  0.81
  32    5  0.16

ACGTcount: A:0.36, C:0.30, G:0.22, T:0.12


Consensus pattern (31 bp):   
ATGACCTAAATCCAGCAGACCCGAGACCCGA
Done.