Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022239.1 Corchorus olitorius cultivar O-4 contig22272, 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: 19655
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.32


Found at i:4274 original size:19 final size:19

Alignment explanation


    Indices: 4247--4283  Score: 56
    Period size: 19  Copynumber: 1.9  Consensus size: 19

       4237 AGGAACTTTT

                *        *     
       4247 AAAAGAAAATTATTAATAG
          1 AAAAAAAAATTATAAATAG

                              
       4266 AAAAAAAAATTATAAATA
          1 AAAAAAAAATTATAAATA

       4284 CATAAAAATC


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

Matches are distributed among these distances:
  19   16  1.00

ACGTcount: A:0.70, C:0.00, G:0.05, T:0.24


Consensus pattern (19 bp):   
AAAAAAAAATTATAAATAG

Found at i:4290 original size:19 final size:19

Alignment explanation


    Indices: 4247--4291  Score: 54
    Period size: 19  Copynumber: 2.4  Consensus size: 19

       4237 AGGAACTTTT

                *        *    *
       4247 AAAAGAAAATTATTAATAG
          1 AAAAAAAAATTATAAATAC

                               
       4266 AAAAAAAAATTATAAATAC
          1 AAAAAAAAATTATAAATAC

             *     
       4285 ATAAAAA
          1 AAAAAAA

       4292 TCTTAACGAA


Statistics
Matches: 22,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  19   22  1.00

ACGTcount: A:0.71, C:0.02, G:0.04, T:0.22


Consensus pattern (19 bp):   
AAAAAAAAATTATAAATAC

Found at i:4579 original size:2 final size:2

Alignment explanation


    Indices: 4572--4596  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

       4562 AGACCTAAGC

                                                 
       4572 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 T

       4597 TGTAATATAA


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:10102 original size:21 final size:21

Alignment explanation


    Indices: 10076--10118  Score: 86
    Period size: 21  Copynumber: 2.0  Consensus size: 21

      10066 TTATACTCTA

                                 
      10076 ACAATTTATTTAAACTGACGT
          1 ACAATTTATTTAAACTGACGT

                                 
      10097 ACAATTTATTTAAACTGACGT
          1 ACAATTTATTTAAACTGACGT

             
      10118 A
          1 A

      10119 AGGGTTAAAA


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  21   22  1.00

ACGTcount: A:0.40, C:0.14, G:0.09, T:0.37


Consensus pattern (21 bp):   
ACAATTTATTTAAACTGACGT

Found at i:10164 original size:26 final size:26

Alignment explanation


    Indices: 10135--10187  Score: 106
    Period size: 26  Copynumber: 2.0  Consensus size: 26

      10125 AAAATAACAC

                                      
      10135 AGGCATTTTTATACAAATTCAATTTT
          1 AGGCATTTTTATACAAATTCAATTTT

                                      
      10161 AGGCATTTTTATACAAATTCAATTTT
          1 AGGCATTTTTATACAAATTCAATTTT

             
      10187 A
          1 A

      10188 ACTTATCTAA


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  26   27  1.00

ACGTcount: A:0.36, C:0.11, G:0.08, T:0.45


Consensus pattern (26 bp):   
AGGCATTTTTATACAAATTCAATTTT
Done.