Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023314.1 Corchorus olitorius cultivar O-4 contig23347, 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: 14263
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31


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

Alignment explanation


    Indices: 1--96  Score: 183
    Period size: 3  Copynumber: 32.0  Consensus size: 3

                                                    *                      
          1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA CAA TAA TAA TAA TAA TAA
          1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA

                                                                           
         49 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
          1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA

         97 GGAGATTAAA


Statistics
Matches: 91,  Mismatches: 2, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
   3   91  1.00

ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32


Consensus pattern (3 bp):   
TAA

Found at i:1318 original size:12 final size:12

Alignment explanation


    Indices: 1266--1323  Score: 57
    Period size: 12  Copynumber: 4.8  Consensus size: 12

       1256 TCCGTTGAGG

                        
       1266 AAATGTTTTAAT
          1 AAATGTTTTAAT

              *           
       1278 -ACTGCTTTTATAT
          1 AAATG-TTTTA-AT

                 *      
       1291 AAATGCTTT-AT
          1 AAATGTTTTAAT

                         
       1302 AAAATGTTTTAAT
          1 -AAATGTTTTAAT

                     
       1315 AAATGTTTT
          1 AAATGTTTT

       1324 GGGTGCATAA


Statistics
Matches: 37,  Mismatches: 4, Indels: 10
        0.73            0.08        0.20

Matches are distributed among these distances:
  11    5  0.14
  12   22  0.59
  13    7  0.19
  14    3  0.08

ACGTcount: A:0.36, C:0.05, G:0.09, T:0.50


Consensus pattern (12 bp):   
AAATGTTTTAAT

Found at i:8593 original size:21 final size:21

Alignment explanation


    Indices: 8569--8620  Score: 104
    Period size: 21  Copynumber: 2.5  Consensus size: 21

       8559 TAATTACACA

                                 
       8569 TTCTTCCCCTCTTAGCCTTTT
          1 TTCTTCCCCTCTTAGCCTTTT

                                 
       8590 TTCTTCCCCTCTTAGCCTTTT
          1 TTCTTCCCCTCTTAGCCTTTT

                      
       8611 TTCTTCCCCT
          1 TTCTTCCCCT

       8621 TAAAATTAAA


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  21   31  1.00

ACGTcount: A:0.04, C:0.40, G:0.04, T:0.52


Consensus pattern (21 bp):   
TTCTTCCCCTCTTAGCCTTTT

Found at i:12522 original size:24 final size:24

Alignment explanation


    Indices: 12494--12541  Score: 78
    Period size: 24  Copynumber: 2.0  Consensus size: 24

      12484 AGAAGAATCA

                 *                  
      12494 AATACTAAGCATACAGCAGTTTGG
          1 AATACGAAGCATACAGCAGTTTGG

                  *                 
      12518 AATACGGAGCATACAGCAGTTTGG
          1 AATACGAAGCATACAGCAGTTTGG

      12542 GATGATTTTA


Statistics
Matches: 22,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  24   22  1.00

ACGTcount: A:0.35, C:0.17, G:0.25, T:0.23


Consensus pattern (24 bp):   
AATACGAAGCATACAGCAGTTTGG
Done.