Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020804.1 Corchorus olitorius cultivar O-4 contig20837, 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: 26758
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33


Found at i:3735 original size:17 final size:18

Alignment explanation


    Indices: 3708--3743  Score: 56
    Period size: 17  Copynumber: 2.1  Consensus size: 18

       3698 TAAATTGTGT

                       *      
       3708 AATTATATATAGTAATTA
          1 AATTATATATAATAATTA

                              
       3726 AATTAT-TATAATAATTA
          1 AATTATATATAATAATTA

             
       3743 A
          1 A

       3744 CTCACTTTTC


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  17   11  0.65
  18    6  0.35

ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44


Consensus pattern (18 bp):   
AATTATATATAATAATTA

Found at i:4530 original size:14 final size:15

Alignment explanation


    Indices: 4511--4539  Score: 51
    Period size: 14  Copynumber: 2.0  Consensus size: 15

       4501 TTTTTTGATA

                           
       4511 AAAAAATAA-TTTTT
          1 AAAAAATAAGTTTTT

                           
       4525 AAAAAATAAGTTTTT
          1 AAAAAATAAGTTTTT

       4540 TTGAAAAAAA


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

Matches are distributed among these distances:
  14    9  0.64
  15    5  0.36

ACGTcount: A:0.55, C:0.00, G:0.03, T:0.41


Consensus pattern (15 bp):   
AAAAAATAAGTTTTT

Found at i:7189 original size:2 final size:2

Alignment explanation


    Indices: 7182--7220  Score: 78
    Period size: 2  Copynumber: 19.5  Consensus size: 2

       7172 GTTTTGAACA

                                                                      
       7182 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

       7221 ATGGGTTAAA


Statistics
Matches: 37,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   37  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:10460 original size:6 final size:6

Alignment explanation


    Indices: 10449--10474  Score: 52
    Period size: 6  Copynumber: 4.3  Consensus size: 6

      10439 AAATGTTCTT

                                          
      10449 CCAAAG CCAAAG CCAAAG CCAAAG CC
          1 CCAAAG CCAAAG CCAAAG CCAAAG CC

      10475 CCAATGCCAA


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   20  1.00

ACGTcount: A:0.46, C:0.38, G:0.15, T:0.00


Consensus pattern (6 bp):   
CCAAAG

Found at i:24744 original size:26 final size:26

Alignment explanation


    Indices: 24708--24760  Score: 88
    Period size: 26  Copynumber: 2.0  Consensus size: 26

      24698 GCATTTTCAA

                            *         
      24708 ATCCTAACACATAAGGGAAAGAAAAC
          1 ATCCTAACACATAAGGAAAAGAAAAC

                 *                    
      24734 ATCCTGACACATAAGGAAAAGAAAAC
          1 ATCCTAACACATAAGGAAAAGAAAAC

             
      24760 A
          1 A

      24761 ACAACATTAG


Statistics
Matches: 25,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  26   25  1.00

ACGTcount: A:0.55, C:0.19, G:0.15, T:0.11


Consensus pattern (26 bp):   
ATCCTAACACATAAGGAAAAGAAAAC
Done.