Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010909.1 Corchorus capsularis cultivar CVL-1 contig10930, 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: 6606
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32


Found at i:222 original size:24 final size:24

Alignment explanation


    Indices: 195--241  Score: 69
    Period size: 24  Copynumber: 2.0  Consensus size: 24

        185 GAAATTGGTA

                                     
        195 ATTAAAGTAGA-AATTAAGATTCAT
          1 ATTAAAGT-GATAATTAAGATTCAT

                           *       
        219 ATTAAAGTGATAATTGAGATTCA
          1 ATTAAAGTGATAATTAAGATTCA

        242 AAGTAAGAGA


Statistics
Matches: 21,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  23    2  0.10
  24   19  0.90

ACGTcount: A:0.47, C:0.04, G:0.15, T:0.34


Consensus pattern (24 bp):   
ATTAAAGTGATAATTAAGATTCAT

Found at i:475 original size:30 final size:34

Alignment explanation


    Indices: 441--505  Score: 84
    Period size: 32  Copynumber: 2.0  Consensus size: 34

        431 GGTGATCAAT

                           *                  
        441 AGAAAA-AGAGAGT-GAAAATGGT-ATT-AAGTA
          1 AGAAAAGAGAGAGTAAAAAATGGTAATTAAAGTA

                   *                          
        471 AGAAAAGGGAGAGTAAAAAATGGTAATTAAAGTA
          1 AGAAAAGAGAGAGTAAAAAATGGTAATTAAAGTA

             
        505 A
          1 A

        506 AAGAGTAAAA


Statistics
Matches: 29,  Mismatches: 2, Indels: 4
        0.83            0.06        0.11

Matches are distributed among these distances:
  30    6  0.21
  31    6  0.21
  32    8  0.28
  33    3  0.10
  34    6  0.21

ACGTcount: A:0.55, C:0.00, G:0.26, T:0.18


Consensus pattern (34 bp):   
AGAAAAGAGAGAGTAAAAAATGGTAATTAAAGTA

Found at i:514 original size:27 final size:27

Alignment explanation


    Indices: 480--551  Score: 85
    Period size: 26  Copynumber: 2.7  Consensus size: 27

        470 AAGAAAAGGG

                                        
        480 AGAGTAAAAAATGGTAATTAAAGTA-AA
          1 AGAGTAAAAAATGGTAATT-AAGTACAA

                     **        *      *
        507 AGAGTAAAATTTGGTAA-TCAGTACAG
          1 AGAGTAAAAAATGGTAATTAAGTACAA

                               
        533 AGAGTAAAAAATGGTAATT
          1 AGAGTAAAAAATGGTAATT

        552 GGCAATCAAA


Statistics
Matches: 37,  Mismatches: 6, Indels: 4
        0.79            0.13        0.09

Matches are distributed among these distances:
  25    4  0.11
  26   17  0.46
  27   16  0.43

ACGTcount: A:0.51, C:0.03, G:0.21, T:0.25


Consensus pattern (27 bp):   
AGAGTAAAAAATGGTAATTAAGTACAA

Found at i:3422 original size:22 final size:22

Alignment explanation


    Indices: 3397--3446  Score: 91
    Period size: 22  Copynumber: 2.3  Consensus size: 22

       3387 ATTAGCTCAT

                                  
       3397 TAAATTGTGTAATTCAATTTCA
          1 TAAATTGTGTAATTCAATTTCA

                                  
       3419 TAAATTGTGTAATTCAATTTCA
          1 TAAATTGTGTAATTCAATTTCA

            *     
       3441 GAAATT
          1 TAAATT

       3447 CGAATGAGCT


Statistics
Matches: 27,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  22   27  1.00

ACGTcount: A:0.38, C:0.08, G:0.10, T:0.44


Consensus pattern (22 bp):   
TAAATTGTGTAATTCAATTTCA
Done.