Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016276.1 Corchorus olitorius cultivar O-4 contig16309, 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: 2273
ACGTcount: A:0.43, C:0.13, G:0.10, T:0.34


Found at i:1611 original size:15 final size:16

Alignment explanation


    Indices: 1591--1620  Score: 53
    Period size: 16  Copynumber: 1.9  Consensus size: 16

       1581 ATTCTTATTA

                            
       1591 TAAACT-CCAATACAT
          1 TAAACTACCAATACAT

                           
       1606 TAAACTACCAATACA
          1 TAAACTACCAATACA

       1621 CACTCCAAAA


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

Matches are distributed among these distances:
  15    6  0.43
  16    8  0.57

ACGTcount: A:0.50, C:0.27, G:0.00, T:0.23


Consensus pattern (16 bp):   
TAAACTACCAATACAT

Found at i:1682 original size:16 final size:15

Alignment explanation


    Indices: 1650--1679  Score: 51
    Period size: 15  Copynumber: 2.0  Consensus size: 15

       1640 AGGTTAATCA

                  *        
       1650 AAATAATTAAATTTT
          1 AAATAAATAAATTTT

                           
       1665 AAATAAATAAATTTT
          1 AAATAAATAAATTTT

       1680 TAACTTAATT


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

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43


Consensus pattern (15 bp):   
AAATAAATAAATTTT

Found at i:2094 original size:131 final size:131

Alignment explanation


    Indices: 1949--2263  Score: 560
    Period size: 131  Copynumber: 2.4  Consensus size: 131

       1939 AAATATATTC

                   *                                                         
       1949 AAAAATTATAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATAAAATAGGTATA
          1 AAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATAAAATAGGTATA

                                      *     *                                
       2014 AGGATATTAGATTTAATTAAATAAAAGTAGACTTTTTAGTT-GAATAAAACTGTAACAGTATACT
         66 AGGATATTAGATTTAATTAAATAAAAATAGA-GTTTTAGTTAGAATAAAACTGTAACAGTATACT

              
       2078 TA
        130 TA

                                 *                                 *         
       2080 AAAAATTCTAATATATATAAGGTTTTTAATTAAAATAGTAAAATGGTAAAAATAAGATAGGTATA
          1 AAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATAAAATAGGTATA

                                                                          *  
       2145 AGGATATTAGATTTAATTAAATAAAAATAGAGTTTTAGTTAGAATAAAACTGTAACAGTATATTT
         66 AGGATATTAGATTTAATTAAATAAAAATAGAGTTTTAGTTAGAATAAAACTGTAACAGTATACTT

             
       2210 A
        131 A

                                                                 
       2211 AAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAAT
          1 AAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAAT

       2264 TATAAAGATA


Statistics
Matches: 176,  Mismatches: 7, Indels: 2
        0.95            0.04        0.01

Matches are distributed among these distances:
 130    8  0.05
 131  168  0.95

ACGTcount: A:0.50, C:0.03, G:0.11, T:0.36


Consensus pattern (131 bp):   
AAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATAAAATAGGTATA
AGGATATTAGATTTAATTAAATAAAAATAGAGTTTTAGTTAGAATAAAACTGTAACAGTATACTT
A
Done.