Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01007102.1 Corchorus olitorius cultivar O-4 contig07127, 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: 2005
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.28


Found at i:1510 original size:6 final size:6

Alignment explanation


    Indices: 1499--1533  Score: 56
    Period size: 6  Copynumber: 6.2  Consensus size: 6

       1489 TCCGGCAAAG

                                                       
       1499 AAGAAA AAGAAA AAGAAA AA-AAA AA-AAA AAGAAA A
          1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA A

       1534 GAAGGAAGAG


Statistics
Matches: 28,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
   5   10  0.36
   6   18  0.64

ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00


Consensus pattern (6 bp):   
AAGAAA

Found at i:1515 original size:15 final size:14

Alignment explanation


    Indices: 1495--1533  Score: 53
    Period size: 14  Copynumber: 2.8  Consensus size: 14

       1485 CTGTTCCGGC

                           
       1495 AAAGAAGAAAAAGAA
          1 AAAGAAGAAAAA-AA

                          
       1510 AAAGAA-AAAAAAA
          1 AAAGAAGAAAAAAA

               *       
       1523 AAAAAAGAAAA
          1 AAAGAAGAAAA

       1534 GAAGGAAGAG


Statistics
Matches: 22,  Mismatches: 1, Indels: 3
        0.85            0.04        0.12

Matches are distributed among these distances:
  13    7  0.32
  14    9  0.41
  15    6  0.27

ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00


Consensus pattern (14 bp):   
AAAGAAGAAAAAAA

Found at i:1527 original size:16 final size:16

Alignment explanation


    Indices: 1502--1533  Score: 55
    Period size: 16  Copynumber: 2.0  Consensus size: 16

       1492 GGCAAAGAAG

                 *          
       1502 AAAAAGAAAAAGAAAA
          1 AAAAAAAAAAAGAAAA

                            
       1518 AAAAAAAAAAAGAAAA
          1 AAAAAAAAAAAGAAAA

       1534 GAAGGAAGAG


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  16   15  1.00

ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00


Consensus pattern (16 bp):   
AAAAAAAAAAAGAAAA

Found at i:1723 original size:6 final size:6

Alignment explanation


    Indices: 1623--1716  Score: 106
    Period size: 6  Copynumber: 16.2  Consensus size: 6

       1613 CCAAGAAAAG

                 *                                                 
       1623 AAAGAG AAA-AA AAAG-A AAAG-A AAA-AA AAAGAA AAAGAA AAAGAA
          1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA

                                           *      *       *     *   
       1667 AAAGAA AAAGAA AAAGAA AAAGGAA AAGGAA AAGGAA AAATAA AATGAA
          1 AAAGAA AAAGAA AAAGAA AAA-GAA AAAGAA AAAGAA AAAGAA AAAGAA

             
       1716 A
          1 A

       1717 TGAAAATAAT


Statistics
Matches: 78,  Mismatches: 6, Indels: 8
        0.85            0.07        0.09

Matches are distributed among these distances:
   5   17  0.22
   6   56  0.72
   7    5  0.06

ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02


Consensus pattern (6 bp):   
AAAGAA
Done.