Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021369.1 Corchorus olitorius cultivar O-4 contig21402, 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: 10658
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33


Found at i:7025 original size:177 final size:180

Alignment explanation


    Indices: 6713--7069  Score: 562
    Period size: 177  Copynumber: 2.0  Consensus size: 180

       6703 ACGATTATAC

                                         *            *     *  *             
       6713 CCTTATTTTTCGATTATATTTCTTAAATGGCATTGTTTAAATTTTTTATAGTTTTTACTCAATTA
          1 CCTTATTTTTCGATTATATTTCTTAAATGCCATTGTTTAAATCTTTTACAGATTTTACTCAATTA

                                 **                                          
       6778 AAAACTCAATTTTTTTTAATTTTAATCTAATATATTTATAAATATTTTATTTTTACCACTTTACT
         66 AAAACTCAATTTTTTTTAATTCAAATCTAATATATTTATAAATATTTTATTTTTACCACTTTACT

                           *                                   
       6843 ATTTTAATTAGAAAACTTAGATATATTAGAATTTTTTAAATATATTTCTTA
        131 ATTTTAATTA-AAAAATTAGATATATTAGAATTTTTTAAATATATTTCTTA

                       *                                                     
       6894 CCTTATTTTT-TA-TATATTTCTTAAATGCCATTGTTTAAA-CTTTTACA-ATTTTACTCAATTA
          1 CCTTATTTTTCGATTATATTTCTTAAATGCCATTGTTTAAATCTTTTACAGATTTTACTCAATTA

                   *                                  *                *     
       6955 AAAACTCTATTTTTATTTAA-TCAAATCTAATATATTTATAACTATTTTATTTTTACCATTTTAC
         66 AAAACTCAATTTTT-TTTAATTCAAATCTAATATATTTATAAATATTTTATTTTTACCACTTTAC

                                                               
       7019 TATTTTAATTAAAAAATTAGATATATTAGAATTTTTTAAATATATTTCTTA
        130 TATTTTAATTAAAAAATTAGATATATTAGAATTTTTTAAATATATTTCTTA

       7070 AATGACATTA


Statistics
Matches: 164,  Mismatches: 11, Indels: 7
        0.90            0.06        0.04

Matches are distributed among these distances:
 176   39  0.24
 177   77  0.47
 178   11  0.07
 179   26  0.16
 180    1  0.01
 181   10  0.06

ACGTcount: A:0.35, C:0.10, G:0.03, T:0.52


Consensus pattern (180 bp):   
CCTTATTTTTCGATTATATTTCTTAAATGCCATTGTTTAAATCTTTTACAGATTTTACTCAATTA
AAAACTCAATTTTTTTTAATTCAAATCTAATATATTTATAAATATTTTATTTTTACCACTTTACT
ATTTTAATTAAAAAATTAGATATATTAGAATTTTTTAAATATATTTCTTA

Found at i:7397 original size:32 final size:31

Alignment explanation


    Indices: 7314--7396  Score: 107
    Period size: 31  Copynumber: 2.7  Consensus size: 31

       7304 ACTAAATACT

                            *          *    
       7314 AAAAAAAT-CTCTTATATTTTTCTTTTGGGAC
          1 AAAAAAATCCT-TTATGTTTTTCTTTTAGGAC

                                           
       7345 AAAAAAATCCTTTATGTTTTTCTTTTAGGAC
          1 AAAAAAATCCTTTATGTTTTTCTTTTAGGAC

                   *              
       7376 GAAAAAATTCC-TTATGTTTTT
          1 -AAAAAAATCCTTTATGTTTTT

       7397 TTTGGATAAA


Statistics
Matches: 47,  Mismatches: 3, Indels: 4
        0.87            0.06        0.07

Matches are distributed among these distances:
  31   36  0.77
  32   11  0.23

ACGTcount: A:0.33, C:0.12, G:0.10, T:0.46


Consensus pattern (31 bp):   
AAAAAAATCCTTTATGTTTTTCTTTTAGGAC

Found at i:8117 original size:23 final size:23

Alignment explanation


    Indices: 8091--8135  Score: 54
    Period size: 23  Copynumber: 2.0  Consensus size: 23

       8081 TTCGCGCGTT

                             *     
       8091 TTTTACTACTAAAATTTTTTTTG
          1 TTTTACTACTAAAATTTCTTTTG

                **  *             
       8114 TTTTTGTATTAAAATTTCTTTT
          1 TTTTACTACTAAAATTTCTTTT

       8136 ATCATGGCGC


Statistics
Matches: 18,  Mismatches: 4, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  23   18  1.00

ACGTcount: A:0.24, C:0.07, G:0.04, T:0.64


Consensus pattern (23 bp):   
TTTTACTACTAAAATTTCTTTTG

Found at i:9019 original size:22 final size:22

Alignment explanation


    Indices: 8993--9046  Score: 54
    Period size: 28  Copynumber: 2.2  Consensus size: 22

       8983 ATACAATTAC

                                  
       8993 ACCAAATGATAATCAATTCCAT
          1 ACCAAATGATAATCAATTCCAT

                                        
       9015 ACCAATTACAAATGATAATCAATTCCAT
          1 A-C-----CAAATGATAATCAATTCCAT

                
       9043 ACCA
          1 ACCA

       9047 TCCTAGAGCT


Statistics
Matches: 26,  Mismatches: 0, Indels: 12
        0.68            0.00        0.32

Matches are distributed among these distances:
  22    3  0.12
  23    1  0.04
  27    1  0.04
  28   21  0.81

ACGTcount: A:0.46, C:0.24, G:0.04, T:0.26


Consensus pattern (22 bp):   
ACCAAATGATAATCAATTCCAT

Found at i:9678 original size:2 final size:2

Alignment explanation


    Indices: 9671--9698  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

       9661 GACACTTATC

                                                     
       9671 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       9699 TGGATTATAA


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   26  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Done.