Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01002508.1 Corchorus olitorius cultivar O-4 contig02508, 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, 809

Length: 1349
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.29

Warning! 2 characters in sequence are not A, C, G, or T


Found at i:408 original size:27 final size:27

Alignment explanation


    Indices: 378--629  Score: 432
    Period size: 27  Copynumber: 9.3  Consensus size: 27

        368 TAAAAAAATG

                            *          
        378 CGATGATACCAATACTCTTACTAATAC
          1 CGATGATACCAATACTTTTACTAATAC

                                *      
        405 CGATGATACCAATACTTTTATTAATAC
          1 CGATGATACCAATACTTTTACTAATAC

                      *      *         
        432 CGATGATACCGATACTTATACTAATAC
          1 CGATGATACCAATACTTTTACTAATAC

                      *      *         
        459 CGATGATACCGATACTTATACTAATAC
          1 CGATGATACCAATACTTTTACTAATAC

                                       
        486 CGATGATACCAATACTTTTACTAATAC
          1 CGATGATACCAATACTTTTACTAATAC

                                       
        513 CGATGATACCAATACTTTTACTAATAC
          1 CGATGATACCAATACTTTTACTAATAC

                                       
        540 CGATGATACCAATACTTTTACTAATAC
          1 CGATGATACCAATACTTTTACTAATAC

                            *          
        567 CGATGATACCAATACTCTTACTAATAC
          1 CGATGATACCAATACTTTTACTAATAC

                                *      
        594 CGATGATACCAATACTTTTATTAATAC
          1 CGATGATACCAATACTTTTACTAATAC

                     
        621 CGATGATAC
          1 CGATGATAC

        630 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:656 original size:21 final size:21

Alignment explanation


    Indices: 630--678  Score: 80
    Period size: 21  Copynumber: 2.3  Consensus size: 21

        620 CCGATGATAC

                        *        
        630 TGATAATACCAATAATCCTAA
          1 TGATAATACCAAGAATCCTAA

                                 
        651 TGATAATACCAAGAATCCTAA
          1 TGATAATACCAAGAATCCTAA

            *      
        672 AGATAAT
          1 TGATAAT

        679 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:678 original size:27 final size:27

Alignment explanation


    Indices: 648--710  Score: 92
    Period size: 27  Copynumber: 2.3  Consensus size: 27

        638 CCAATAATCC

                                        
        648 TAATGATAAT-ACCAAGAATCCTAAAGA
          1 TAATGATAATGA-CAAGAATCCTAAAGA

                   *                *  
        675 TAATGATGATGACAAGAATCCTAATGA
          1 TAATGATAATGACAAGAATCCTAAAGA

                     
        702 TAATGATAA
          1 TAATGATAA

        711 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:987 original size:36 final size:36

Alignment explanation


    Indices: 944--1012  Score: 138
    Period size: 36  Copynumber: 1.9  Consensus size: 36

        934 AAGTAAAAAG

                                                
        944 AAAGAATCACAAATTTCTAATAATACAGAAAACAAA
          1 AAAGAATCACAAATTTCTAATAATACAGAAAACAAA

                                             
        980 AAAGAATCACAAATTTCTAATAATACAGAAAAC
          1 AAAGAATCACAAATTTCTAATAATACAGAAAAC

       1013 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.