Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022377.1 Corchorus olitorius cultivar O-4 contig22410, 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: 29773
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31


Found at i:22379 original size:21 final size:21

Alignment explanation


    Indices: 22354--22394  Score: 66
    Period size: 21  Copynumber: 2.0  Consensus size: 21

      22344 TTAGAAACCC

                                  
      22354 TAGTACCACTTAG-ATCCAATT
          1 TAGTACCACTT-GTATCCAATT

                                
      22375 TAGTACCACTTGTATCCAAT
          1 TAGTACCACTTGTATCCAAT

      22395 AGGGCTTCAA


Statistics
Matches: 19,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  20    1  0.05
  21   18  0.95

ACGTcount: A:0.32, C:0.24, G:0.10, T:0.34


Consensus pattern (21 bp):   
TAGTACCACTTGTATCCAATT

Found at i:26539 original size:25 final size:26

Alignment explanation


    Indices: 26488--26539  Score: 63
    Period size: 27  Copynumber: 2.0  Consensus size: 26

      26478 TAAGGTTACT

                               **     
      26488 AAAAAAGTTATAGTTGATTGCTGTAA
          1 AAAAAAGTTATAGTTGATTAATGTAA

                                       
      26514 AAAAAGAGTTATAGTTGA-TAAT-TAA
          1 AAAAA-AGTTATAGTTGATTAATGTAA

             
      26539 A
          1 A

      26540 GATATATTAT


Statistics
Matches: 23,  Mismatches: 2, Indels: 3
        0.82            0.07        0.11

Matches are distributed among these distances:
  25    4  0.17
  26    7  0.30
  27   12  0.52

ACGTcount: A:0.48, C:0.02, G:0.17, T:0.33


Consensus pattern (26 bp):   
AAAAAAGTTATAGTTGATTAATGTAA

Found at i:27018 original size:71 final size:71

Alignment explanation


    Indices: 26902--27044  Score: 268
    Period size: 71  Copynumber: 2.0  Consensus size: 71

      26892 AAAACTAATG

                                                                      *      
      26902 AAGAATATTTTATTGATCTACAAACCAAATTGTAATTTTTTGGAAACAAAAAATTGAACTTTTAA
          1 AAGAATATTTTATTGATCTACAAACCAAATTGTAATTTTTTGGAAACAAAAAATTGAAATTTTAA

                  
      26967 TATTTA
         66 TATTTA

                                     *                                       
      26973 AAGAATATTTTATTGATCTACAAACGAAATTGTAATTTTTTGGAAACAAAAAATTGAAATTTTAA
          1 AAGAATATTTTATTGATCTACAAACCAAATTGTAATTTTTTGGAAACAAAAAATTGAAATTTTAA

                  
      27038 TATTTA
         66 TATTTA

             
      27044 A
          1 A

      27045 TACTTATTGT


Statistics
Matches: 70,  Mismatches: 2, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  71   70  1.00

ACGTcount: A:0.45, C:0.07, G:0.09, T:0.39


Consensus pattern (71 bp):   
AAGAATATTTTATTGATCTACAAACCAAATTGTAATTTTTTGGAAACAAAAAATTGAAATTTTAA
TATTTA

Found at i:28866 original size:6 final size:6

Alignment explanation


    Indices: 28855--28885  Score: 53
    Period size: 6  Copynumber: 5.2  Consensus size: 6

      28845 AGAGTATAAA

                                    *           
      28855 AAAGAT AAAGAT AAAGAT AAAAAT AAAGAT A
          1 AAAGAT AAAGAT AAAGAT AAAGAT AAAGAT A

      28886 TATATATATA


Statistics
Matches: 23,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
   6   23  1.00

ACGTcount: A:0.71, C:0.00, G:0.13, T:0.16


Consensus pattern (6 bp):   
AAAGAT

Found at i:29741 original size:2 final size:2

Alignment explanation


    Indices: 29730--29770  Score: 75
    Period size: 2  Copynumber: 21.0  Consensus size: 2

      29720 AACAAATCCC

                                                                          
      29730 TA TA -A 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 TA TA

      29771 CTA


Statistics
Matches: 38,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
   1    1  0.03
   2   37  0.97

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


Consensus pattern (2 bp):   
TA

Done.