Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022558.1 Corchorus olitorius cultivar O-4 contig22591, 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: 6914
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34


Found at i:33 original size:2 final size:2

Alignment explanation


    Indices: 21--54  Score: 50
    Period size: 2  Copynumber: 16.5  Consensus size: 2

         11 GTTTAGTACT

                               *                              
         21 TA TA TA GTA TA TA GA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA T

         55 TTACTTACTG


Statistics
Matches: 29,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
   2   27  0.93
   3    2  0.07

ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47


Consensus pattern (2 bp):   
TA

Found at i:5558 original size:24 final size:24

Alignment explanation


    Indices: 5528--5578  Score: 75
    Period size: 24  Copynumber: 2.1  Consensus size: 24

       5518 TATTTTTACG

                    *             * 
       5528 TTAAACATTTTATCATTATAATTA
          1 TTAAACATCTTATCATTATAATAA

                         *          
       5552 TTAAACATCTTATTATTATAATAA
          1 TTAAACATCTTATCATTATAATAA

               
       5576 TTA
          1 TTA

       5579 TTAGTAGTAG


Statistics
Matches: 24,  Mismatches: 3, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  24   24  1.00

ACGTcount: A:0.43, C:0.08, G:0.00, T:0.49


Consensus pattern (24 bp):   
TTAAACATCTTATCATTATAATAA

Found at i:5803 original size:3 final size:3

Alignment explanation


    Indices: 5795--5825  Score: 53
    Period size: 3  Copynumber: 10.3  Consensus size: 3

       5785 TACTTCTTAC

                                 *                   
       5795 AAT AAT AAT AAT AAT AGT AAT AAT AAT AAT A
          1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A

       5826 GTAAAATTAT


Statistics
Matches: 26,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   3   26  1.00

ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32


Consensus pattern (3 bp):   
AAT

Found at i:5817 original size:15 final size:15

Alignment explanation


    Indices: 5797--5829  Score: 66
    Period size: 15  Copynumber: 2.2  Consensus size: 15

       5787 CTTCTTACAA

                           
       5797 TAATAATAATAATAG
          1 TAATAATAATAATAG

                           
       5812 TAATAATAATAATAG
          1 TAATAATAATAATAG

               
       5827 TAA
          1 TAA

       5830 AATTATTATT


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   18  1.00

ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33


Consensus pattern (15 bp):   
TAATAATAATAATAG
Done.