Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014320.1 Corchorus olitorius cultivar O-4 contig14353, 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: 18787
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32


Found at i:4434 original size:11 final size:11

Alignment explanation


    Indices: 4418--4475  Score: 73
    Period size: 11  Copynumber: 5.1  Consensus size: 11

       4408 CAGCGCAACA

                       
       4418 AAAACAAAACG
          1 AAAACAAAACG

                      *
       4429 AAAACAAAACA
          1 AAAACAAAACG

                       
       4440 AAAACAAAAC-
          1 AAAACAAAACG

                         
       4450 AAAACAAAAACAG
          1 AAAAC-AAAAC-G

                        
       4463 AAAACGAAAACG
          1 AAAAC-AAAACG

             
       4475 A
          1 A

       4476 TGCCAAACGA


Statistics
Matches: 42,  Mismatches: 2, Indels: 5
        0.86            0.04        0.10

Matches are distributed among these distances:
  10    5  0.12
  11   25  0.60
  12    2  0.05
  13   10  0.24

ACGTcount: A:0.76, C:0.17, G:0.07, T:0.00


Consensus pattern (11 bp):   
AAAACAAAACG

Found at i:4439 original size:16 final size:17

Alignment explanation


    Indices: 4418--4473  Score: 80
    Period size: 16  Copynumber: 3.3  Consensus size: 17

       4408 CAGCGCAACA

                             
       4418 AAAAC-AAAACGAAAAC
          1 AAAACAAAAACGAAAAC

                             
       4434 AAAACAAAAAC-AAAAC
          1 AAAACAAAAACGAAAAC

                              
       4450 AAAACAAAAACAGAAAAC
          1 AAAACAAAAAC-GAAAAC

                  
       4468 GAAAAC
          1 -AAAAC

       4474 GATGCCAAAC


Statistics
Matches: 36,  Mismatches: 0, Indels: 5
        0.88            0.00        0.12

Matches are distributed among these distances:
  16   21  0.58
  17    5  0.14
  18    5  0.14
  19    5  0.14

ACGTcount: A:0.77, C:0.18, G:0.05, T:0.00


Consensus pattern (17 bp):   
AAAACAAAAACGAAAAC

Found at i:4475 original size:6 final size:5

Alignment explanation


    Indices: 4418--4458  Score: 64
    Period size: 5  Copynumber: 7.8  Consensus size: 5

       4408 CAGCGCAACA

                                                            
       4418 AAAAC AAAAC GAAAAC AAAAC AAAAAC AAAAC AAAAC AAAA
          1 AAAAC AAAAC -AAAAC AAAAC -AAAAC AAAAC AAAAC AAAA

       4459 ACAGAAAACG


Statistics
Matches: 34,  Mismatches: 0, Indels: 4
        0.89            0.00        0.11

Matches are distributed among these distances:
   5   24  0.71
   6   10  0.29

ACGTcount: A:0.80, C:0.17, G:0.02, T:0.00


Consensus pattern (5 bp):   
AAAAC

Found at i:12654 original size:2 final size:2

Alignment explanation


    Indices: 12647--12675  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

      12637 TGAGTACAAA

                                                       
      12647 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 A

      12676 AAATACGTTC


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

Matches are distributed among these distances:
   2   27  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:13017 original size:18 final size:18

Alignment explanation


    Indices: 12986--13023  Score: 58
    Period size: 18  Copynumber: 2.1  Consensus size: 18

      12976 AAAAAACTTA

                     *        
      12986 TATATATTAGAATTTTTT
          1 TATATATTACAATTTTTT

                 *            
      13004 TATATTTTACAATTTTTT
          1 TATATATTACAATTTTTT

              
      13022 TA
          1 TA

      13024 GAAATAAACT


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

Matches are distributed among these distances:
  18   18  1.00

ACGTcount: A:0.32, C:0.03, G:0.03, T:0.63


Consensus pattern (18 bp):   
TATATATTACAATTTTTT
Done.