Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005058.1 Corchorus capsularis cultivar CVL-1 contig05076, 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: 9560
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35


Found at i:523 original size:23 final size:23

Alignment explanation


    Indices: 476--524  Score: 57
    Period size: 23  Copynumber: 2.1  Consensus size: 23

        466 AAAGTAGCAT

                                *  
        476 AGAAAGGGAATGAGACACAGGAG
          1 AGAAAGGGAATGAGACACAGAAG

                                     
        499 AGAAGAGGGAA-GAGACA-ATGAAG
          1 AGAA-AGGGAATGAGACACA-GAAG

               
        522 AGA
          1 AGA

        525 GAAAGAGGGA


Statistics
Matches: 23,  Mismatches: 1, Indels: 4
        0.82            0.04        0.14

Matches are distributed among these distances:
  22    1  0.04
  23   16  0.70
  24    6  0.26

ACGTcount: A:0.51, C:0.06, G:0.39, T:0.04


Consensus pattern (23 bp):   
AGAAAGGGAATGAGACACAGAAG

Found at i:2341 original size:28 final size:28

Alignment explanation


    Indices: 2295--2349  Score: 74
    Period size: 28  Copynumber: 2.0  Consensus size: 28

       2285 GTATTTCATC

                       * **      *      
       2295 TTCTGTTGTAATGGCATAAGTCTTGATG
          1 TTCTGTTGTAAAGAAATAAGTATTGATG

                                       
       2323 TTCTGTTGTAAAGAAATAAGTATTGAT
          1 TTCTGTTGTAAAGAAATAAGTATTGAT

       2350 TCTTAAGTGA


Statistics
Matches: 23,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  28   23  1.00

ACGTcount: A:0.29, C:0.07, G:0.22, T:0.42


Consensus pattern (28 bp):   
TTCTGTTGTAAAGAAATAAGTATTGATG

Found at i:5878 original size:11 final size:11

Alignment explanation


    Indices: 5862--5886  Score: 50
    Period size: 11  Copynumber: 2.3  Consensus size: 11

       5852 ATGGTTCTTA

                       
       5862 TTTAAGTAGTC
          1 TTTAAGTAGTC

                       
       5873 TTTAAGTAGTC
          1 TTTAAGTAGTC

               
       5884 TTT
          1 TTT

       5887 TTTTTTAATC


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

Matches are distributed among these distances:
  11   14  1.00

ACGTcount: A:0.24, C:0.08, G:0.16, T:0.52


Consensus pattern (11 bp):   
TTTAAGTAGTC

Found at i:7473 original size:33 final size:33

Alignment explanation


    Indices: 7436--7503  Score: 118
    Period size: 33  Copynumber: 2.1  Consensus size: 33

       7426 TTTCAAGGAG

                     *                       
       7436 GAGTTAAAAGCCGAGATTATGCTGGAGTTTCGA
          1 GAGTTAAAAACCGAGATTATGCTGGAGTTTCGA

                       *                     
       7469 GAGTTAAAAACTGAGATTATGCTGGAGTTTCGA
          1 GAGTTAAAAACCGAGATTATGCTGGAGTTTCGA

              
       7502 GA
          1 GA

       7504 TATGTTGGAG


Statistics
Matches: 33,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  33   33  1.00

ACGTcount: A:0.32, C:0.10, G:0.29, T:0.28


Consensus pattern (33 bp):   
GAGTTAAAAACCGAGATTATGCTGGAGTTTCGA
Done.