Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013125.1 Corchorus olitorius cultivar O-4 contig13158, 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: 10682
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.32


Found at i:848 original size:10 final size:10

Alignment explanation


    Indices: 833--863  Score: 53
    Period size: 10  Copynumber: 3.1  Consensus size: 10

        823 CAGAGAAAGA

                      
        833 AAAACAGAGG
          1 AAAACAGAGG

                     *
        843 AAAACAGAGA
          1 AAAACAGAGG

                      
        853 AAAACAGAGG
          1 AAAACAGAGG

             
        863 A
          1 A

        864 GAGTTTATTC


Statistics
Matches: 19,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  10   19  1.00

ACGTcount: A:0.65, C:0.10, G:0.26, T:0.00


Consensus pattern (10 bp):   
AAAACAGAGG

Found at i:1238 original size:22 final size:21

Alignment explanation


    Indices: 1196--1238  Score: 50
    Period size: 22  Copynumber: 2.0  Consensus size: 21

       1186 TTCTTTTCTT

                        *        
       1196 TTTTCCTTTTTCTACTGATAG
          1 TTTTCCTTTTTCCACTGATAG

                 *           *    
       1217 TTTTCTTTTCTTCCACTTATAG
          1 TTTTCCTTT-TTCCACTGATAG

       1239 CATACTCAGG


Statistics
Matches: 18,  Mismatches: 3, Indels: 1
        0.82            0.14        0.05

Matches are distributed among these distances:
  21    8  0.44
  22   10  0.56

ACGTcount: A:0.14, C:0.21, G:0.07, T:0.58


Consensus pattern (21 bp):   
TTTTCCTTTTTCCACTGATAG

Found at i:9059 original size:21 final size:22

Alignment explanation


    Indices: 8907--9072  Score: 114
    Period size: 22  Copynumber: 7.7  Consensus size: 22

       8897 TGAATATTTT

                            *   *  
       8907 TATGAAATTTTGAT-AGCTACCC
          1 TATGAAATTTTGATAACCT-TCC

               *               *  
       8929 TATTAAATTTTGATAACC-ACC
          1 TATGAAATTTTGATAACCTTCC

                                   
       8950 -ATGAAATTTTGATAA--TTACC
          1 TATGAAATTTTGATAACCTT-CC

               *     *      *     
       8970 TATAAAATTGTGATAAAC-TCC
          1 TATGAAATTTTGATAACCTTCC

               *    *           ** 
       8991 ATAAGAAACTTTGATAACCTAAC
          1 -TATGAAATTTTGATAACCTTCC

                       *      *    
       9014 TATGAAATTTTAATAAACTTTCC
          1 TATGAAATTTTGAT-AACCTTCC

                                  
       9037 TATGAAATTTTG-TAACCTTCC
          1 TATGAAATTTTGATAACCTTCC

                  *         
       9058 TATG-ATTTTTGATAA
          1 TATGAAATTTTGATAA

       9073 TCTCTCTGTG


Statistics
Matches: 111,  Mismatches: 23, Indels: 21
        0.72            0.15        0.14

Matches are distributed among these distances:
  20   22  0.20
  21   31  0.28
  22   39  0.35
  23   19  0.17

ACGTcount: A:0.38, C:0.14, G:0.09, T:0.39


Consensus pattern (22 bp):   
TATGAAATTTTGATAACCTTCC
Done.