Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01005148.1 Corchorus olitorius cultivar O-4 contig05169, 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, 640

Length: 1067
ACGTcount: A:0.39, C:0.16, G:0.15, T:0.29


Found at i:286 original size:27 final size:27

Alignment explanation


    Indices: 256--507  Score: 432
    Period size: 27  Copynumber: 9.3  Consensus size: 27

        246 TTAAAAAAAG

                            *          
        256 CGATGATACCAATACTCTTACTAATAC
          1 CGATGATACCAATACTTTTACTAATAC

                                *      
        283 CGATGATACCAATACTTTTATTAATAC
          1 CGATGATACCAATACTTTTACTAATAC

                      *      *         
        310 CGATGATACCGATACTTATACTAATAC
          1 CGATGATACCAATACTTTTACTAATAC

                      *      *         
        337 CGATGATACCGATACTTATACTAATAC
          1 CGATGATACCAATACTTTTACTAATAC

                                       
        364 CGATGATACCAATACTTTTACTAATAC
          1 CGATGATACCAATACTTTTACTAATAC

                                       
        391 CGATGATACCAATACTTTTACTAATAC
          1 CGATGATACCAATACTTTTACTAATAC

                                       
        418 CGATGATACCAATACTTTTACTAATAC
          1 CGATGATACCAATACTTTTACTAATAC

                            *          
        445 CGATGATACCAATACTCTTACTAATAC
          1 CGATGATACCAATACTTTTACTAATAC

                                *      
        472 CGATGATACCAATACTTTTATTAATAC
          1 CGATGATACCAATACTTTTACTAATAC

                     
        499 CGATGATAC
          1 CGATGATAC

        508 TGATAATACC


Statistics
Matches: 215,  Mismatches: 10, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  27  215  1.00

ACGTcount: A:0.37, C:0.22, G:0.09, T:0.32


Consensus pattern (27 bp):   
CGATGATACCAATACTTTTACTAATAC

Found at i:534 original size:21 final size:21

Alignment explanation


    Indices: 508--556  Score: 80
    Period size: 21  Copynumber: 2.3  Consensus size: 21

        498 CCGATGATAC

                        *        
        508 TGATAATACCAATAATCCTAA
          1 TGATAATACCAAGAATCCTAA

                                 
        529 TGATAATACCAAGAATCCTAA
          1 TGATAATACCAAGAATCCTAA

            *      
        550 AGATAAT
          1 TGATAAT

        557 GATGATGACA


Statistics
Matches: 26,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  21   26  1.00

ACGTcount: A:0.49, C:0.16, G:0.08, T:0.27


Consensus pattern (21 bp):   
TGATAATACCAAGAATCCTAA

Found at i:556 original size:27 final size:27

Alignment explanation


    Indices: 526--588  Score: 92
    Period size: 27  Copynumber: 2.3  Consensus size: 27

        516 CCAATAATCC

                                        
        526 TAATGATAAT-ACCAAGAATCCTAAAGA
          1 TAATGATAATGA-CAAGAATCCTAAAGA

                   *                *  
        553 TAATGATGATGACAAGAATCCTAATGA
          1 TAATGATAATGACAAGAATCCTAAAGA

                     
        580 TAATGATAA
          1 TAATGATAA

        589 ACTAGAGGAA


Statistics
Matches: 32,  Mismatches: 3, Indels: 2
        0.86            0.08        0.05

Matches are distributed among these distances:
  27   31  0.97
  28    1  0.03

ACGTcount: A:0.49, C:0.11, G:0.14, T:0.25


Consensus pattern (27 bp):   
TAATGATAATGACAAGAATCCTAAAGA

Found at i:882 original size:36 final size:36

Alignment explanation


    Indices: 839--907  Score: 138
    Period size: 36  Copynumber: 1.9  Consensus size: 36

        829 AAGTAAAAAG

                                                
        839 AAAGAATCACAAATTTCTAATAATACAGAAAACAAA
          1 AAAGAATCACAAATTTCTAATAATACAGAAAACAAA

                                             
        875 AAAGAATCACAAATTTCTAATAATACAGAAAAC
          1 AAAGAATCACAAATTTCTAATAATACAGAAAAC

        908 GATAGAGACG


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  36   33  1.00

ACGTcount: A:0.59, C:0.14, G:0.06, T:0.20


Consensus pattern (36 bp):   
AAAGAATCACAAATTTCTAATAATACAGAAAACAAA
Done.