Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017660.1 Corchorus olitorius cultivar O-4 contig17693, 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: 7333
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32


Found at i:3457 original size:20 final size:20

Alignment explanation


    Indices: 3418--3457  Score: 55
    Period size: 20  Copynumber: 2.0  Consensus size: 20

       3408 TTGTAATCTC

                           *    
       3418 TGATTATTGATTAATGAAAG
          1 TGATTATTGATTAATAAAAG

                                 
       3438 TGATTATTTGATTAA-AAAAG
          1 TGATTA-TTGATTAATAAAAG

       3458 GTGTAATGAC


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  20   10  0.56
  21    8  0.44

ACGTcount: A:0.42, C:0.00, G:0.17, T:0.40


Consensus pattern (20 bp):   
TGATTATTGATTAATAAAAG

Found at i:3851 original size:271 final size:276

Alignment explanation


    Indices: 3325--3870  Score: 868
    Period size: 271  Copynumber: 2.0  Consensus size: 276

       3315 GTAAATAAAA

                                                      *             *       *
       3325 AAGCCAATGTATTTGCACATTCTCTAACTAATTAAGATTGAGTTGGATAATCGTGTGGTGCGCAT
          1 AAGCCAATGTATTTGCACATTCTCTAAC--A-TAAGATTGAGCTGGATAATCGTGTAGT-CGCAG

                         *                      *                       *    
       3390 GACTATTACTCACGGCATTTGTAATCTCTGATTATTGATTAATGAAAGTGATTATTTGATTAAAA
         62 GACTATTACTCACAGCATTTGTAATCTCTGATTATTAATTAATGAAAGTGATTATTTGATAAAAA

              *                                            *                 
       3455 AAGGTGTAATGACTAAAATAGATCATATTGATAATTATAGTAAAAATTATCTATTCTAAATTAAT
        127 AAAGTGTAATGACTAAAATAGA-CATATTGATAATTATAGTAAAAATCATCTATTCTAAATTAAT

                          *        *                                         
       3520 AATTGAAGGTATTTGTGAAATTTTTCATTCTAAATTAAGTGTAATGACTAATAGAATGGATATTG
        191 AATTGAAGGTATTTATGAAATTTCTCATTCTAAATTAAGTGTAATGACTAATAGAATGGATATTG

               *      *          
       3585 GGATATAGTGGGTCATGATAT
        256 GGACATAGTGAGTCATGATAT

                                      *                                      
       3606 AAGCCAATGTATTTGCACATTCTCTAGC-TAAGATTGAGCTGGATAATCGTGTAGT-GCAGGACT
          1 AAGCCAATGTATTTGCACATTCTCTAACATAAGATTGAGCTGGATAATCGTGTAGTCGCAGGACT

                        *                                                    
       3669 ATTACTCACAGCGTTTGTAATCTCTGATTATTAATTAATGAAAGTGATTATTTGATAAAAAAAAG
         66 ATTACTCACAGCATTTGTAATCTCTGATTATTAATTAATGAAAGTGATTATTTGATAAAAAAAAG

                              *                                              
       3734 TGTAATGACTAAAA-AG-GATATTGATAATTATAGTAAAAATCATCTA-TCTAAATTAATAATTG
        131 TGTAATGACTAAAATAGACATATTGATAATTATAGTAAAAATCATCTATTCTAAATTAATAATTG

                                                                        *    
       3796 AAGGTATTTATGAAATTTCTCATTCTAAATTAAGTGTAATGACTAATAGAATGGATATTGTGACA
        196 AAGGTATTTATGAAATTTCTCATTCTAAATTAAGTGTAATGACTAATAGAATGGATATTGGGACA

                      
       3861 TAGTGAGTCA
        261 TAGTGAGTCA

       3871 CGATGTATCT


Statistics
Matches: 249,  Mismatches: 16, Indels: 10
        0.91            0.06        0.04

Matches are distributed among these distances:
 271   86  0.35
 272   28  0.11
 274    2  0.01
 275   81  0.33
 277   25  0.10
 281   27  0.11

ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36


Consensus pattern (276 bp):   
AAGCCAATGTATTTGCACATTCTCTAACATAAGATTGAGCTGGATAATCGTGTAGTCGCAGGACT
ATTACTCACAGCATTTGTAATCTCTGATTATTAATTAATGAAAGTGATTATTTGATAAAAAAAAG
TGTAATGACTAAAATAGACATATTGATAATTATAGTAAAAATCATCTATTCTAAATTAATAATTG
AAGGTATTTATGAAATTTCTCATTCTAAATTAAGTGTAATGACTAATAGAATGGATATTGGGACA
TAGTGAGTCATGATAT

Found at i:6626 original size:17 final size:16

Alignment explanation


    Indices: 6588--6629  Score: 50
    Period size: 17  Copynumber: 2.6  Consensus size: 16

       6578 GAGGAGGCTC

                            
       6588 TTTTTTTGTCCTTTGT
          1 TTTTTTTGTCCTTTGT

             *    *          
       6604 CCTTTTCTGTCCTTT-T
          1 -TTTTTTTGTCCTTTGT

                      
       6620 TTTTTTTGTC
          1 TTTTTTTGTC

       6630 TTTTCTCACT


Statistics
Matches: 21,  Mismatches: 4, Indels: 2
        0.78            0.15        0.07

Matches are distributed among these distances:
  15    8  0.38
  16    1  0.05
  17   12  0.57

ACGTcount: A:0.00, C:0.19, G:0.10, T:0.71


Consensus pattern (16 bp):   
TTTTTTTGTCCTTTGT

Found at i:6959 original size:27 final size:27

Alignment explanation


    Indices: 6926--6979  Score: 108
    Period size: 27  Copynumber: 2.0  Consensus size: 27

       6916 GTGGTATATG

                                       
       6926 CTATATATGCTCAATGTTAATAGTATA
          1 CTATATATGCTCAATGTTAATAGTATA

                                       
       6953 CTATATATGCTCAATGTTAATAGTATA
          1 CTATATATGCTCAATGTTAATAGTATA

       6980 ACCTTTTAAA


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  27   27  1.00

ACGTcount: A:0.37, C:0.11, G:0.11, T:0.41


Consensus pattern (27 bp):   
CTATATATGCTCAATGTTAATAGTATA
Done.