Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024025.1 Corchorus olitorius cultivar O-4 contig24058, 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: 13195
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29


Found at i:3340 original size:15 final size:15

Alignment explanation


    Indices: 3322--3351  Score: 51
    Period size: 15  Copynumber: 2.0  Consensus size: 15

       3312 TTTGTTCCTA

                     *     
       3322 GTTTAATTGTTTTCT
          1 GTTTAATTGCTTTCT

                           
       3337 GTTTAATTGCTTTCT
          1 GTTTAATTGCTTTCT

       3352 TTCAACCTCT


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.13, C:0.10, G:0.13, T:0.63


Consensus pattern (15 bp):   
GTTTAATTGCTTTCT

Found at i:3568 original size:41 final size:41

Alignment explanation


    Indices: 3511--3775  Score: 318
    Period size: 41  Copynumber: 6.3  Consensus size: 41

       3501 CGACCGATCA

                    *                              *  
       3511 ATAACACAAAGGCATCTATATCAAAGTCC-CAAAACACAATT
          1 ATAACACAGAGGCATCTATATCAAAGTCCTC-AAACACATTT

                     *       *                         
       3552 ATAACACAGGGGCATCTCTAATCCAAAGTCCTCAAACACATTT
          1 ATAACACAGAGGCATCTAT-AT-CAAAGTCCTCAAACACATTT

                                         *           
       3595 ATAACACAGAGGCATCTATATCAAAGTCCCCAAACACATTT
          1 ATAACACAGAGGCATCTATATCAAAGTCCTCAAACACATTT

                     *         * * *                   
       3636 ATAACACAGGGGCAATTCTCTCTAAAAGTCCTCAAACACATTT
          1 ATAACACAGAGGC-A-TCTATATCAAAGTCCTCAAACACATTT

                            *                         
       3679 ATAACACAGAGGCATCCATA-CTAAAGTCCTCAAACACATTT
          1 ATAACACAGAGGCATCTATATC-AAAGTCCTCAAACACATTT

                     *           *                      
       3720 ATAACACAGGGGCACCTCTATCTCAAAAGTCCTCAAACACATTT
          1 ATAACACAGAGGCA--TCTATATC-AAAGTCCTCAAACACATTT

               *        
       3764 ATAGCACAGAGG
          1 ATAACACAGAGG

       3776 TACTTCTCTT


Statistics
Matches: 192,  Mismatches: 23, Indels: 15
        0.83            0.10        0.07

Matches are distributed among these distances:
  41   82  0.43
  42    6  0.03
  43   73  0.38
  44   31  0.16

ACGTcount: A:0.40, C:0.26, G:0.11, T:0.22


Consensus pattern (41 bp):   
ATAACACAGAGGCATCTATATCAAAGTCCTCAAACACATTT

Found at i:3664 original size:84 final size:84

Alignment explanation


    Indices: 3511--3775  Score: 383
    Period size: 84  Copynumber: 3.1  Consensus size: 84

       3501 CGACCGATCA

                    *                     *       *                       *  
       3511 ATAACACAAAGGCATCTATATCAAAGTCCCAAAACACAATTATAACACAGGGGC-ATCTCTAATC
          1 ATAACACAGAGGCATCTATATCAAAGTCCCCAAACACATTTATAACACAGGGGCAATCTCT-CTC

            *                   
       3575 CAAAGTCCTCAAACACATTT
         65 AAAAGTCCTCAAACACATTT

                                                                             
       3595 ATAACACAGAGGCATCTATATCAAAGTCCCCAAACACATTTATAACACAGGGGCAAT-TCTCTCT
          1 ATAACACAGAGGCATCTATATCAAAGTCCCCAAACACATTTATAACACAGGGGCAATCTCTCTC-

                                
       3659 AAAAGTCCTCAAACACATTT
         65 AAAAGTCCTCAAACACATTT

                            *             *                          *   *   
       3679 ATAACACAGAGGCATCCATA-CTAAAGTCCTCAAACACATTTATAACACAGGGGCACCTCTATCT
          1 ATAACACAGAGGCATCTATATC-AAAGTCCCCAAACACATTTATAACACAGGGGCA-ATCTCTCT

                                 
       3743 CAAAAGTCCTCAAACACATTT
         64 CAAAAGTCCTCAAACACATTT

               *        
       3764 ATAGCACAGAGG
          1 ATAACACAGAGG

       3776 TACTTCTCTT


Statistics
Matches: 166,  Mismatches: 10, Indels: 9
        0.90            0.05        0.05

Matches are distributed among these distances:
  83    3  0.02
  84  124  0.75
  85   34  0.20
  86    5  0.03

ACGTcount: A:0.40, C:0.26, G:0.11, T:0.22


Consensus pattern (84 bp):   
ATAACACAGAGGCATCTATATCAAAGTCCCCAAACACATTTATAACACAGGGGCAATCTCTCTCA
AAAGTCCTCAAACACATTT

Found at i:3847 original size:2 final size:2

Alignment explanation


    Indices: 3840--3874  Score: 70
    Period size: 2  Copynumber: 17.5  Consensus size: 2

       3830 ATTCCTATCT

                                                                
       3840 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

       3875 GTAACAAGGG


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   33  1.00

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (2 bp):   
TA

Found at i:12388 original size:25 final size:25

Alignment explanation


    Indices: 12354--12402  Score: 98
    Period size: 25  Copynumber: 2.0  Consensus size: 25

      12344 AAATTATGGT

                                     
      12354 ATATTTTAAGATTATGATGCATGCC
          1 ATATTTTAAGATTATGATGCATGCC

                                    
      12379 ATATTTTAAGATTATGATGCATGC
          1 ATATTTTAAGATTATGATGCATGC

      12403 AGACTCTTTA


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  25   24  1.00

ACGTcount: A:0.33, C:0.10, G:0.16, T:0.41


Consensus pattern (25 bp):   
ATATTTTAAGATTATGATGCATGCC
Done.