Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012844.1 Corchorus olitorius cultivar O-4 contig12877, 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: 15208
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.37


Found at i:8 original size:3 final size:3

Alignment explanation


    Indices: 1--112  Score: 170
    Period size: 3  Copynumber: 36.0  Consensus size: 3

                                                                           
          1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
          1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT

                                            *                     *      
         49 AAT AAT AAT AAT AAT AAT AAT AAT GAT AAAT AAT AAAT AAT TAT AAT
          1 AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT -AAT AAT AAT AAT

                                 
         96 AAT AAAT AAT AAAT AAT
          1 AAT -AAT AAT -AAT AAT

        113 TTCTCCAAAA


Statistics
Matches: 101,  Mismatches: 4, Indels: 8
        0.89            0.04        0.07

Matches are distributed among these distances:
   3   90  0.89
   4   11  0.11

ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33


Consensus pattern (3 bp):   
AAT

Found at i:2493 original size:8 final size:8

Alignment explanation


    Indices: 2482--2516  Score: 56
    Period size: 8  Copynumber: 4.6  Consensus size: 8

       2472 AATAGAATTC

                    
       2482 AATATTTT
          1 AATATTTT

                    
       2490 AATATTTT
          1 AATATTTT

                    
       2498 --TATTTT
          1 AATATTTT

                    
       2504 AATATTTT
          1 AATATTTT

                 
       2512 AATAT
          1 AATAT

       2517 ATAAGTTTAT


Statistics
Matches: 25,  Mismatches: 0, Indels: 4
        0.86            0.00        0.14

Matches are distributed among these distances:
   6    6  0.24
   8   19  0.76

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


Consensus pattern (8 bp):   
AATATTTT

Found at i:2503 original size:14 final size:14

Alignment explanation


    Indices: 2484--2511  Score: 56
    Period size: 14  Copynumber: 2.0  Consensus size: 14

       2474 TAGAATTCAA

                          
       2484 TATTTTAATATTTT
          1 TATTTTAATATTTT

                          
       2498 TATTTTAATATTTT
          1 TATTTTAATATTTT

       2512 AATATATAAG


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

Matches are distributed among these distances:
  14   14  1.00

ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71


Consensus pattern (14 bp):   
TATTTTAATATTTT

Found at i:2834 original size:18 final size:18

Alignment explanation


    Indices: 2811--2849  Score: 69
    Period size: 18  Copynumber: 2.2  Consensus size: 18

       2801 GTATAGTAGT

                              
       2811 ATACTATATACTATACTA
          1 ATACTATATACTATACTA

                      *       
       2829 ATACTATATATTATACTA
          1 ATACTATATACTATACTA

               
       2847 ATA
          1 ATA

       2850 TTTATGGGTA


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  18   20  1.00

ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41


Consensus pattern (18 bp):   
ATACTATATACTATACTA
Done.