Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019965.1 Corchorus olitorius cultivar O-4 contig19998, 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: 5108
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.35


Found at i:2808 original size:33 final size:33

Alignment explanation


    Indices: 2764--2828  Score: 94
    Period size: 33  Copynumber: 2.0  Consensus size: 33

       2754 TTCAATAACC

                         *  *   *            
       2764 TTACATCTTTTGTGATTTTGGTTATCATATTTA
          1 TTACATCTTTTGTAATCTTGATTATCATATTTA

                  *                         
       2797 TTACATTTTTTGTAATCTTGATTATCATATTT
          1 TTACATCTTTTGTAATCTTGATTATCATATTT

       2829 CTCCAAAATC


Statistics
Matches: 28,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  33   28  1.00

ACGTcount: A:0.23, C:0.09, G:0.09, T:0.58


Consensus pattern (33 bp):   
TTACATCTTTTGTAATCTTGATTATCATATTTA

Found at i:3713 original size:39 final size:40

Alignment explanation


    Indices: 3659--3739  Score: 137
    Period size: 39  Copynumber: 2.0  Consensus size: 40

       3649 ATACCTAAGA

                                             *      
       3659 ATTTAATTAATGTAAGTATTTCAGTTATTATA-GTATTAC
          1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC

                                 *                  
       3698 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
          1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC

              
       3738 AT
          1 AT

       3740 AGGAATTAAA


Statistics
Matches: 39,  Mismatches: 2, Indels: 1
        0.93            0.05        0.02

Matches are distributed among these distances:
  39   31  0.79
  40    8  0.21

ACGTcount: A:0.37, C:0.04, G:0.09, T:0.51


Consensus pattern (40 bp):   
ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC

Found at i:4911 original size:7 final size:7

Alignment explanation


    Indices: 4899--4926  Score: 56
    Period size: 7  Copynumber: 4.0  Consensus size: 7

       4889 GAAAGAGGCA

                   
       4899 GGTGCCC
          1 GGTGCCC

                   
       4906 GGTGCCC
          1 GGTGCCC

                   
       4913 GGTGCCC
          1 GGTGCCC

                   
       4920 GGTGCCC
          1 GGTGCCC

       4927 CCTCCCAAAT


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   7   21  1.00

ACGTcount: A:0.00, C:0.43, G:0.43, T:0.14


Consensus pattern (7 bp):   
GGTGCCC

Found at i:5034 original size:18 final size:17

Alignment explanation


    Indices: 4995--5034  Score: 53
    Period size: 18  Copynumber: 2.3  Consensus size: 17

       4985 GATTCAATCT

                             
       4995 AAAACCCCCCAAAAGCC
          1 AAAACCCCCCAAAAGCC

            *             *   
       5012 CAAACCCACCCAAATGCC
          1 AAAACCC-CCCAAAAGCC

                 
       5030 AAAAC
          1 AAAAC

       5035 ATTAAAAAAC


Statistics
Matches: 19,  Mismatches: 3, Indels: 1
        0.83            0.13        0.04

Matches are distributed among these distances:
  17    6  0.32
  18   13  0.68

ACGTcount: A:0.47, C:0.45, G:0.05, T:0.03


Consensus pattern (17 bp):   
AAAACCCCCCAAAAGCC
Done.