Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01007386.1 Corchorus olitorius cultivar O-4 contig07411, 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: 2914
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34


Found at i:48 original size:2 final size:2

Alignment explanation


    Indices: 3--35  Score: 57
    Period size: 2  Copynumber: 16.5  Consensus size: 2

          1 AT

                                             *               
          3 GA GA GA GA GA GA GA GA GA GA GA AA GA GA GA GA G
          1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G

         36 CTTTGTAGAG


Statistics
Matches: 29,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   2   29  1.00

ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00


Consensus pattern (2 bp):   
GA

Found at i:1597 original size:118 final size:118

Alignment explanation


    Indices: 1389--1619  Score: 426
    Period size: 118  Copynumber: 2.0  Consensus size: 118

       1379 TGTTAACGTG

                 *                                                           
       1389 TTTGGGATCTAAGAATTAAGGAGTAATTTATACTATTTTTATTGGAAGAGTTGGTTTGAAGTGGA
          1 TTTGGAATCTAAGAATTAAGGAGTAATTTATACTATTTTTATTGGAAGAGTTGGTTTGAAGTGGA

                           *                                     
       1454 AAATTCAAGGACTTGGAATTCCTCAAAACAATATTCATGGTTATGGTGGAGCA
         66 AAATTCAAGGACTTGAAATTCCTCAAAACAATATTCATGGTTATGGTGGAGCA

                                                                             
       1507 TTTGGAATCTAAGAATTAAGGAGTAATTTATACTATTTTTATTGGAAGAGTTGGTTTGAAGTGGA
          1 TTTGGAATCTAAGAATTAAGGAGTAATTTATACTATTTTTATTGGAAGAGTTGGTTTGAAGTGGA

                 *                                    *     
       1572 AAATTTAAGGACTTGAAATTCCTCAAAACAATATTCATGGTTTTGGTG
         66 AAATTCAAGGACTTGAAATTCCTCAAAACAATATTCATGGTTATGGTG

       1620 AATGTTCTTC


Statistics
Matches: 109,  Mismatches: 4, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
 118  109  1.00

ACGTcount: A:0.33, C:0.08, G:0.23, T:0.36


Consensus pattern (118 bp):   
TTTGGAATCTAAGAATTAAGGAGTAATTTATACTATTTTTATTGGAAGAGTTGGTTTGAAGTGGA
AAATTCAAGGACTTGAAATTCCTCAAAACAATATTCATGGTTATGGTGGAGCA

Found at i:2506 original size:18 final size:17

Alignment explanation


    Indices: 2483--2520  Score: 67
    Period size: 18  Copynumber: 2.2  Consensus size: 17

       2473 CCCAAATTAC

                              
       2483 TTATGGAAATTAGGGAAA
          1 TTATGGAAATTA-GGAAA

                             
       2501 TTATGGAAATTAGGAAA
          1 TTATGGAAATTAGGAAA

               
       2518 TTA
          1 TTA

       2521 AATGAATTAA


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

Matches are distributed among these distances:
  17    8  0.40
  18   12  0.60

ACGTcount: A:0.45, C:0.00, G:0.24, T:0.32


Consensus pattern (17 bp):   
TTATGGAAATTAGGAAA

Found at i:2518 original size:8 final size:9

Alignment explanation


    Indices: 2487--2520  Score: 52
    Period size: 9  Copynumber: 3.9  Consensus size: 9

       2477 AATTACTTAT

                     
       2487 GGAAATTAG
          1 GGAAATTAG

                    *
       2496 GGAAATTAT
          1 GGAAATTAG

                     
       2505 GGAAATTA-
          1 GGAAATTAG

                    
       2513 GGAAATTA
          1 GGAAATTA

       2521 AATGAATTAA


Statistics
Matches: 24,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
   8    8  0.33
   9   16  0.67

ACGTcount: A:0.47, C:0.00, G:0.26, T:0.26


Consensus pattern (9 bp):   
GGAAATTAG
Done.