Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022043.1 Corchorus olitorius cultivar O-4 contig22076, 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: 9567
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27


Found at i:4236 original size:2 final size:2

Alignment explanation


    Indices: 4229--4253  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

       4219 AAGTTTTATC

                                                 
       4229 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 T

       4254 TTTTTCTTTT


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:5185 original size:5 final size:5

Alignment explanation


    Indices: 5176--5217  Score: 52
    Period size: 5  Copynumber: 8.8  Consensus size: 5

       5166 AAATAACATA

                  *                                      *      
       5176 AAAAC CAAAC -AAAC -AAAC AAAAC AAAAC AAAAC AAAGC AAAA
          1 AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAA

       5218 GATTGCGACG


Statistics
Matches: 33,  Mismatches: 3, Indels: 2
        0.87            0.08        0.05

Matches are distributed among these distances:
   4    8  0.24
   5   25  0.76

ACGTcount: A:0.76, C:0.21, G:0.02, T:0.00


Consensus pattern (5 bp):   
AAAAC

Found at i:5523 original size:12 final size:15

Alignment explanation


    Indices: 5490--5522  Score: 52
    Period size: 13  Copynumber: 2.3  Consensus size: 15

       5480 AAAAAAAGAG

                           
       5490 AAAAAATAATAATAA
          1 AAAAAATAATAATAA

                           
       5505 AAAAAAT-A-AATAA
          1 AAAAAATAATAATAA

                 
       5518 AAAAA
          1 AAAAA

       5523 TCAGCCTAAA


Statistics
Matches: 18,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  13   10  0.56
  14    1  0.06
  15    7  0.39

ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15


Consensus pattern (15 bp):   
AAAAAATAATAATAA

Found at i:6736 original size:58 final size:58

Alignment explanation


    Indices: 6641--6906  Score: 371
    Period size: 58  Copynumber: 4.6  Consensus size: 58

       6631 AAAGAATTCA

                   *              *                                    
       6641 TCACAGACGGATCTGAAGACAGATCCT-AATAGATTTTAAGATTAAGACTGAAGACAGC
          1 TCACAGATGGATCTGAAGACAGTTCCTGAA-AGATTTTAAGATTAAGACTGAAGACAGC

                                            *      *      *           
       6699 TCACAGATGGATCTGAAGACAGTTCCTGAAAGTTTTTAAAATTAAGGCTGAAGACAGC
          1 TCACAGATGGATCTGAAGACAGTTCCTGAAAGATTTTAAGATTAAGACTGAAGACAGC

                                                                       
       6757 TCACAGATGGATCTGAAGACAGTTCCTGAAAGATTTTAAGATTAA-AGCTGAAGACAGC
          1 TCACAGATGGATCTGAAGACAGTTCCTGAAAGATTTTAAGATTAAGA-CTGAAGACAGC

                                           *            *              
       6815 TCACAGATGGATCTGAAGACAGTTCCT-AAAAATTTTTAAGATTGAGACTGAAGACAGC
          1 TCACAGATGGATCTGAAGACAGTTCCTGAAAGA-TTTTAAGATTAAGACTGAAGACAGC

                                    *  *        
       6873 TCAC-GA-GTGATTCTGAAGACAGATCATGAAAGAT
          1 TCACAGATG-GA-TCTGAAGACAGTTCCTGAAAGAT

       6907 GTCGACAGAT


Statistics
Matches: 188,  Mismatches: 13, Indels: 14
        0.87            0.06        0.07

Matches are distributed among these distances:
  56    1  0.01
  57    8  0.04
  58  172  0.91
  59    7  0.04

ACGTcount: A:0.38, C:0.16, G:0.22, T:0.24


Consensus pattern (58 bp):   
TCACAGATGGATCTGAAGACAGTTCCTGAAAGATTTTAAGATTAAGACTGAAGACAGC

Done.