Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01008670.1 Corchorus olitorius cultivar O-4 contig08697, 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: 5674
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.33


Found at i:415 original size:21 final size:19

Alignment explanation


    Indices: 390--429  Score: 62
    Period size: 21  Copynumber: 2.0  Consensus size: 19

        380 ACGCTAAATT

                                 
        390 CTTCTTACAAAGAACTAGAAC
          1 CTTCTTACAAA-AAC-AGAAC

                               
        411 CTTCTTACAAAAACAGAAC
          1 CTTCTTACAAAAACAGAAC

        430 AGAACAGAAC


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

Matches are distributed among these distances:
  19    5  0.26
  20    3  0.16
  21   11  0.58

ACGTcount: A:0.45, C:0.25, G:0.07, T:0.23


Consensus pattern (19 bp):   
CTTCTTACAAAAACAGAAC

Found at i:432 original size:5 final size:5

Alignment explanation


    Indices: 422--448  Score: 54
    Period size: 5  Copynumber: 5.4  Consensus size: 5

        412 TTCTTACAAA

                                            
        422 AACAG AACAG AACAG AACAG AACAG AA
          1 AACAG AACAG AACAG AACAG AACAG AA

        449 ATAAACAGAA


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

Matches are distributed among these distances:
   5   22  1.00

ACGTcount: A:0.63, C:0.19, G:0.19, T:0.00


Consensus pattern (5 bp):   
AACAG

Found at i:455 original size:15 final size:15

Alignment explanation


    Indices: 420--458  Score: 53
    Period size: 15  Copynumber: 2.6  Consensus size: 15

        410 CCTTCTTACA

                           
        420 AAAACAGAACAGAAC
          1 AAAACAGAACAGAAC

             *             
        435 AGAACAGAACAGAA-
          1 AAAACAGAACAGAAC

                      
        449 ATAAACAGAA
          1 A-AAACAGAA

        459 TTTGAAACTA


Statistics
Matches: 21,  Mismatches: 2, Indels: 2
        0.84            0.08        0.08

Matches are distributed among these distances:
  14    1  0.05
  15   20  0.95

ACGTcount: A:0.67, C:0.15, G:0.15, T:0.03


Consensus pattern (15 bp):   
AAAACAGAACAGAAC
Done.