Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021696.1 Corchorus olitorius cultivar O-4 contig21729, 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: 14467
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32


Found at i:1767 original size:13 final size:13

Alignment explanation


    Indices: 1749--1775  Score: 54
    Period size: 13  Copynumber: 2.1  Consensus size: 13

       1739 GATTATGTAT

                         
       1749 TTTATTTAATATA
          1 TTTATTTAATATA

                         
       1762 TTTATTTAATATA
          1 TTTATTTAATATA

             
       1775 T
          1 T

       1776 GATATATAAA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   14  1.00

ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63


Consensus pattern (13 bp):   
TTTATTTAATATA

Found at i:3753 original size:15 final size:15

Alignment explanation


    Indices: 3735--3774  Score: 80
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       3725 AGTTTTTCTA

                           
       3735 TAGAAAGTTTAGGAC
          1 TAGAAAGTTTAGGAC

                           
       3750 TAGAAAGTTTAGGAC
          1 TAGAAAGTTTAGGAC

                      
       3765 TAGAAAGTTT
          1 TAGAAAGTTT

       3775 TTTCTTATGA


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

Matches are distributed among these distances:
  15   25  1.00

ACGTcount: A:0.40, C:0.05, G:0.25, T:0.30


Consensus pattern (15 bp):   
TAGAAAGTTTAGGAC

Found at i:3953 original size:48 final size:48

Alignment explanation


    Indices: 3877--4005  Score: 152
    Period size: 49  Copynumber: 2.7  Consensus size: 48

       3867 GAGCGTGCCA

                        **         *                         
       3877 ATCAATTTTGTCCAAAAAATTGATAAAAAGTGCAACAAAAAGTAAA-AG
          1 ATCAATTTTGTCTTAAAAATTGAGAAAAAGTGCAACAAAAA-TAAAGAG

                                              * *          * 
       3925 ATCAATTTTGTCTTAAAAATTGAGAAAAAGGTGCGAGAAAAATAAAGGG
          1 ATCAATTTTGTCTTAAAAATTGAGAAAAA-GTGCAACAAAAATAAAGAG

            *        * *                    
       3974 TTCAATTTTATATTAAAAATTGAGAAAAAGTG
          1 ATCAATTTTGTCTTAAAAATTGAGAAAAAGTG

       4006 TAGGAAATGA


Statistics
Matches: 70,  Mismatches: 9, Indels: 4
        0.84            0.11        0.05

Matches are distributed among these distances:
  48   33  0.47
  49   37  0.53

ACGTcount: A:0.50, C:0.07, G:0.16, T:0.27


Consensus pattern (48 bp):   
ATCAATTTTGTCTTAAAAATTGAGAAAAAGTGCAACAAAAATAAAGAG

Found at i:7891 original size:18 final size:18

Alignment explanation


    Indices: 7842--7893  Score: 59
    Period size: 18  Copynumber: 2.9  Consensus size: 18

       7832 AAGTGTGGTA

                       *      
       7842 ATTTGGTGCGGAGCGAAC
          1 ATTTGGTGCGGTGCGAAC

             *      **      * 
       7860 AATTGGTGTTGTGCGACC
          1 ATTTGGTGCGGTGCGAAC

                            
       7878 ATTTGGTGCGGTGCGA
          1 ATTTGGTGCGGTGCGA

       7894 TTTGTTGTTG


Statistics
Matches: 26,  Mismatches: 8, Indels: 0
        0.76            0.24        0.00

Matches are distributed among these distances:
  18   26  1.00

ACGTcount: A:0.17, C:0.15, G:0.38, T:0.29


Consensus pattern (18 bp):   
ATTTGGTGCGGTGCGAAC

Found at i:8503 original size:48 final size:48

Alignment explanation


    Indices: 8427--8555  Score: 152
    Period size: 49  Copynumber: 2.7  Consensus size: 48

       8417 AAGCGTGCCA

                        **         *           *             
       8427 ATCAATTTTGTCCAAAAAATTGATAAAAAGTGCAATAAAAAGTAAA-AG
          1 ATCAATTTTGTCTTAAAAATTGAGAAAAAGTGCAAGAAAAA-TAAAGAG

                                              *            * 
       8475 ATCAATTTTGTCTTAAAAATTGAGAAAAAGGTGCGAGAAAAATAAAGGG
          1 ATCAATTTTGTCTTAAAAATTGAGAAAAA-GTGCAAGAAAAATAAAGAG

            *        * *                    
       8524 TTCAATTTTATATTAAAAATTGAGAAAAAGTG
          1 ATCAATTTTGTCTTAAAAATTGAGAAAAAGTG

       8556 TAGGAAATGA


Statistics
Matches: 70,  Mismatches: 9, Indels: 4
        0.84            0.11        0.05

Matches are distributed among these distances:
  48   33  0.47
  49   37  0.53

ACGTcount: A:0.50, C:0.06, G:0.16, T:0.28


Consensus pattern (48 bp):   
ATCAATTTTGTCTTAAAAATTGAGAAAAAGTGCAAGAAAAATAAAGAG

Done.