Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01004519.1 Corchorus olitorius cultivar O-4 contig04535, 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, 820

Length: 1368
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.38


Found at i:119 original size:21 final size:21

Alignment explanation


    Indices: 48--110  Score: 117
    Period size: 21  Copynumber: 3.0  Consensus size: 21

         38 GGTAAGCCTA

                                 
         48 TTTATTTCTGGTTCTAAGAGT
          1 TTTATTTCTGGTTCTAAGAGT

                             *   
         69 TTTATTTCTGGTTCTAAAAGT
          1 TTTATTTCTGGTTCTAAGAGT

                                 
         90 TTTATTTCTGGTTCTAAGAGT
          1 TTTATTTCTGGTTCTAAGAGT

        111 AGTAGTTCTA


Statistics
Matches: 40,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  21   40  1.00

ACGTcount: A:0.21, C:0.10, G:0.17, T:0.52


Consensus pattern (21 bp):   
TTTATTTCTGGTTCTAAGAGT

Found at i:634 original size:21 final size:22

Alignment explanation


    Indices: 601--648  Score: 80
    Period size: 21  Copynumber: 2.2  Consensus size: 22

        591 TATTATTATT

                                  
        601 TAAATATATATAAACGGAATAA
          1 TAAATATATATAAACGGAATAA

                          *       
        623 TAAATA-ATATAAATGGAATAA
          1 TAAATATATATAAACGGAATAA

                 
        644 TAAAT
          1 TAAAT

        649 TTAAATATAT


Statistics
Matches: 25,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  21   19  0.76
  22    6  0.24

ACGTcount: A:0.60, C:0.02, G:0.08, T:0.29


Consensus pattern (22 bp):   
TAAATATATATAAACGGAATAA

Found at i:697 original size:29 final size:28

Alignment explanation


    Indices: 655--711  Score: 96
    Period size: 29  Copynumber: 2.0  Consensus size: 28

        645 AAATTTAAAT

                     *                   
        655 ATATATGTACTAATTGTAATAGTAATTAA
          1 ATATATGTAATAATTGTAATAGT-ATTAA

                                        
        684 ATATATGTAATAATTGTAATAGTATTAA
          1 ATATATGTAATAATTGTAATAGTATTAA

        712 TAATAATAGA


Statistics
Matches: 27,  Mismatches: 1, Indels: 1
        0.93            0.03        0.03

Matches are distributed among these distances:
  28    5  0.19
  29   22  0.81

ACGTcount: A:0.46, C:0.02, G:0.11, T:0.42


Consensus pattern (28 bp):   
ATATATGTAATAATTGTAATAGTATTAA

Found at i:752 original size:18 final size:18

Alignment explanation


    Indices: 726--763  Score: 58
    Period size: 18  Copynumber: 2.1  Consensus size: 18

        716 AATAGAGTAT

                              
        726 TATTCATATAAATGAATA
          1 TATTCATATAAATGAATA

                *        *    
        744 TATTTATATAAATTAATA
          1 TATTCATATAAATGAATA

              
        762 TA
          1 TA

        764 ATAATATAGA


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  18   18  1.00

ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45


Consensus pattern (18 bp):   
TATTCATATAAATGAATA

Found at i:770 original size:18 final size:18

Alignment explanation


    Indices: 731--792  Score: 56
    Period size: 18  Copynumber: 3.4  Consensus size: 18

        721 AGTATTATTC

                    *      * *
        731 ATATAAATGAATATATTT
          1 ATATAAATTAATATAATA

                              
        749 ATATAAATTAATATAATA
          1 ATATAAATTAATATAATA

                                 
        767 ATATAGAATATTAATAT-ATA
          1 ATAT--AA-ATTAATATAATA

                   
        787 A-ATAAA
          1 ATATAAA

        793 ATATGCATTA


Statistics
Matches: 38,  Mismatches: 3, Indels: 8
        0.78            0.06        0.16

Matches are distributed among these distances:
  16    1  0.03
  17    2  0.05
  18   19  0.50
  19    2  0.05
  20    6  0.16
  21    8  0.21

ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39


Consensus pattern (18 bp):   
ATATAAATTAATATAATA

Found at i:781 original size:21 final size:19

Alignment explanation


    Indices: 755--796  Score: 57
    Period size: 19  Copynumber: 2.1  Consensus size: 19

        745 ATTTATATAA

                             *   
        755 ATTAATATAATAATATAGAAT
          1 ATTAATAT-ATAA-ATAAAAT

                               
        776 ATTAATATATAAATAAAAT
          1 ATTAATATATAAATAAAAT

              
        795 AT
          1 AT

        797 GCATTATATA


Statistics
Matches: 20,  Mismatches: 1, Indels: 2
        0.87            0.04        0.09

Matches are distributed among these distances:
  19    8  0.40
  20    4  0.20
  21    8  0.40

ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38


Consensus pattern (19 bp):   
ATTAATATATAAATAAAAT
Done.