Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009749.1 Corchorus olitorius cultivar O-4 contig09781, 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: 2041
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.34

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:1540 original size:22 final size:22

Alignment explanation


    Indices: 1515--1591  Score: 102
    Period size: 22  Copynumber: 3.5  Consensus size: 22

       1505 TATTTTTATG

                                 *
       1515 AAATTTTGATAATTACCCTATT
          1 AAATTTTGATAATTACCCTATA

                        **   *    
       1537 AAATTTTGATAACCACCATATA
          1 AAATTTTGATAATTACCCTATA

                                  
       1559 AAATTTTGATAATTA-CCTATA
          1 AAATTTTGATAATTACCCTATA

                 *      
       1580 AAATTGTGATAA
          1 AAATTTTGATAA

       1592 ACTCCATATG


Statistics
Matches: 47,  Mismatches: 8, Indels: 1
        0.84            0.14        0.02

Matches are distributed among these distances:
  21   16  0.34
  22   31  0.66

ACGTcount: A:0.43, C:0.12, G:0.06, T:0.39


Consensus pattern (22 bp):   
AAATTTTGATAATTACCCTATA

Found at i:1599 original size:43 final size:44

Alignment explanation


    Indices: 1515--1613  Score: 137
    Period size: 43  Copynumber: 2.3  Consensus size: 44

       1505 TATTTTTATG

                                 *     *      *         
       1515 AAATTTTGATAATTACCCTATTAAATTTTGATAACCACCATATA
          1 AAATTTTGATAATTACCCTATAAAATTGTGATAAACACCATATA

                                                *      *
       1559 AAATTTTGATAATTA-CCTATAAAATTGTGATAAACTCCATATG
          1 AAATTTTGATAATTACCCTATAAAATTGTGATAAACACCATATA

               *        
       1602 AAACTTTGATAA
          1 AAATTTTGATAA

       1614 CCTAACTATG


Statistics
Matches: 49,  Mismatches: 6, Indels: 1
        0.88            0.11        0.02

Matches are distributed among these distances:
  43   34  0.69
  44   15  0.31

ACGTcount: A:0.42, C:0.13, G:0.07, T:0.37


Consensus pattern (44 bp):   
AAATTTTGATAATTACCCTATAAAATTGTGATAAACACCATATA

Found at i:1664 original size:20 final size:21

Alignment explanation


    Indices: 1560--1707  Score: 79
    Period size: 22  Copynumber: 6.9  Consensus size: 21

       1550 CACCATATAA

                          *      *
       1560 AATTTTGATAAT-TACCTATAA
          1 AATTTTGATAATCTTCCTAT-G

                *      *          
       1581 AATTGTGATAAAC-TCCATATG
          1 AATTTTGATAATCTTCC-TATG

               *        *  **     
       1602 AAACTTTGATAACCTAACTATG
          1 -AATTTTGATAATCTTCCTATG

                   *    *          
       1624 AAATTTTAATAAACTTTCCTATG
          1 -AATTTTGATAATC-TTCCTATG

                                 
       1647 AATTTTG-TAATCTTCCTATG
          1 AATTTTGATAATCTTCCTATG

             *                 *  
       1667 ATTTTTGATAATC-TCTCTGTG
          1 AATTTTGATAATCTTC-CTATG

                    *      *    
       1688 AGATTTTGTTAATCTCCCTA
          1 A-ATTTTGATAATCTTCCTA

       1708 CAATTTTTTA


Statistics
Matches: 96,  Mismatches: 22, Indels: 17
        0.71            0.16        0.13

Matches are distributed among these distances:
  20   16  0.17
  21   26  0.27
  22   46  0.48
  23    8  0.08

ACGTcount: A:0.33, C:0.15, G:0.09, T:0.43


Consensus pattern (21 bp):   
AATTTTGATAATCTTCCTATG

Found at i:1680 original size:21 final size:20

Alignment explanation


    Indices: 1639--1707  Score: 68
    Period size: 20  Copynumber: 3.3  Consensus size: 20

       1629 TTAATAAACT

                                
       1639 TTCCTATGAATTTTGTAATC
          1 TTCCTATGAATTTTGTAATC

                     *           
       1659 TTCCTATGATTTTTGATAATC
          1 TTCCTATGAATTTTG-TAATC

                  *                
       1680 -TCTCTGTGAGATTTTGTTAATC
          1 TTC-CTATGA-ATTTTG-TAATC

             *    
       1702 TCCCTA
          1 TTCCTA

       1708 CAATTTTTTA


Statistics
Matches: 39,  Mismatches: 6, Indels: 6
        0.76            0.12        0.12

Matches are distributed among these distances:
  20   16  0.41
  21   10  0.26
  22   12  0.31
  23    1  0.03

ACGTcount: A:0.22, C:0.17, G:0.12, T:0.49


Consensus pattern (20 bp):   
TTCCTATGAATTTTGTAATC
Done.