Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024503.1 Corchorus olitorius cultivar O-4 contig24536, 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: 27215
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32


Found at i:5054 original size:20 final size:20

Alignment explanation


    Indices: 5017--5055  Score: 53
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       5007 TAAAAAATTT

                         *      
       5017 ATATATTTTATATTTTTTAA
          1 ATATATTTTATATCTTTTAA

                                
       5037 ATATACTTTTATA-CTTTTA
          1 ATATA-TTTTATATCTTTTA

       5056 CCTAACTAAA


Statistics
Matches: 17,  Mismatches: 1, Indels: 2
        0.85            0.05        0.10

Matches are distributed among these distances:
  20   10  0.59
  21    7  0.41

ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62


Consensus pattern (20 bp):   
ATATATTTTATATCTTTTAA

Found at i:7424 original size:22 final size:23

Alignment explanation


    Indices: 7381--7424  Score: 63
    Period size: 24  Copynumber: 1.9  Consensus size: 23

       7371 GTTTATAATA

                *                   
       7381 TTCTTGGGTCATTACCGGGTTAAC
          1 TTCTCGGGTCATTA-CGGGTTAAC

                                 
       7405 TTCTCGGGTCATT-CGGGTTA
          1 TTCTCGGGTCATTACGGGTTA

       7425 CGGGTGTCGG


Statistics
Matches: 19,  Mismatches: 1, Indels: 2
        0.86            0.05        0.09

Matches are distributed among these distances:
  22    7  0.37
  24   12  0.63

ACGTcount: A:0.14, C:0.20, G:0.27, T:0.39


Consensus pattern (23 bp):   
TTCTCGGGTCATTACGGGTTAAC

Found at i:8190 original size:1 final size:1

Alignment explanation


    Indices: 8184--8209  Score: 52
    Period size: 1  Copynumber: 26.0  Consensus size: 1

       8174 CTCGATCTAG

                                      
       8184 TTTTTTTTTTTTTTTTTTTTTTTTTT
          1 TTTTTTTTTTTTTTTTTTTTTTTTTT

       8210 CCATCAAAGA


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   25  1.00

ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00


Consensus pattern (1 bp):   
T

Found at i:11695 original size:12 final size:12

Alignment explanation


    Indices: 11665--11701  Score: 51
    Period size: 12  Copynumber: 3.2  Consensus size: 12

      11655 AAGCAAACAG

                       *
      11665 AATAATTAA-AG
          1 AATAATTAAGAA

                        
      11676 AA-AATTAAGAA
          1 AATAATTAAGAA

                        
      11687 AATAATTAAGAA
          1 AATAATTAAGAA

               
      11699 AAT
          1 AAT

      11702 TAAAGGAAAA


Statistics
Matches: 23,  Mismatches: 1, Indels: 3
        0.85            0.04        0.11

Matches are distributed among these distances:
  10    6  0.26
  11    5  0.22
  12   12  0.52

ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24


Consensus pattern (12 bp):   
AATAATTAAGAA

Found at i:13016 original size:27 final size:27

Alignment explanation


    Indices: 12980--13041  Score: 115
    Period size: 27  Copynumber: 2.3  Consensus size: 27

      12970 AAAGCTCCAA

                        *              
      12980 TCTTCAATTCTTGCTTCTTAAAATAAT
          1 TCTTCAATTCTTACTTCTTAAAATAAT

                                       
      13007 TCTTCAATTCTTACTTCTTAAAATAAT
          1 TCTTCAATTCTTACTTCTTAAAATAAT

                    
      13034 TCTTCAAT
          1 TCTTCAAT

      13042 GATCTTCAAA


Statistics
Matches: 34,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  27   34  1.00

ACGTcount: A:0.31, C:0.19, G:0.02, T:0.48


Consensus pattern (27 bp):   
TCTTCAATTCTTACTTCTTAAAATAAT

Found at i:25817 original size:2 final size:2

Alignment explanation


    Indices: 25810--25835  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

      25800 TTTACTGCAC

                                                  
      25810 AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT

      25836 TCATGATTGA


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

Matches are distributed among these distances:
   2   24  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Done.