Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020019.1 Corchorus olitorius cultivar O-4 contig20052, 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: 4766
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34


Found at i:756 original size:252 final size:255

Alignment explanation


    Indices: 303--814  Score: 895
    Period size: 252  Copynumber: 2.0  Consensus size: 255

        293 AATGGTTCAC

                            **       *                               *       
        303 TTTTAGGTAAAAGTACTTGGGAGGTTCCTGTACTATACGAAATGTTGATTTTGGTCCTTGTACTT
          1 TTTTAGGTAAAAGTACCCGGGAGGTCCCTGTACTATACGAAATGTTGATTTTGGTCCCTGTAC-T

                                  *                                         *
        368 TTTTTTTTGCTACAAATTCGTCTCTCTACTATCAGAACCTATCACCCGAAGTCCCTCACGTTAGT
         65 TTTTTTTTGCTACAAATTCGTCCCTCTACTATCAGAACCTATCACCCGAAGTCCCTCACGTTAGC

            *                                                                
        433 GTGCCGTGACAGACCCGTCAAATATGCTGACGTGGCACTAACACCGTCTTTTTTGCTGACGTGGC
        130 ATGCCGTGACAGACCCGTCAAATATGCTGACGTGGCACTAACACCGTCTTTTTTGCTGACGTGGC

                                                           *             
        498 AGGTGACACGTGGAATAAAAATTAAATATTTTTTTAATATATTTTATTTTATTGAAATTTA
        195 AGGTGACACGTGGAATAAAAATTAAATATTTTTTTAATATATTTTATGTTATTGAAATTTA

                                                                             
        559 TTTT-GGTAAAAGTACCCGGGAGGTCCCTGTACTATACGAAATGTTGATTTTGGTCCCTGTAC-T
          1 TTTTAGGTAAAAGTACCCGGGAGGTCCCTGTACTATACGAAATGTTGATTTTGGTCCCTGTACTT

                                                            *        *       
        622 TTTTTTT-CTACAAATTCGTCCCTCTACTATCAGAACCTATCACCCGAGGTCCCTCATGTTAGCA
         66 TTTTTTTGCTACAAATTCGTCCCTCTACTATCAGAACCTATCACCCGAAGTCCCTCACGTTAGCA

                                                                             
        686 TGCCGTGACAGACCCGTCAAATATGCTGACGTGGCACTAACACCGTCTTTTTTGCTGACGTGGCA
        131 TGCCGTGACAGACCCGTCAAATATGCTGACGTGGCACTAACACCGTCTTTTTTGCTGACGTGGCA

                                                                       *
        751 GGTGACACGTGGAATAAAAATTAAATATTTTTTTAATATATTTTATGTTATTGAAATTTG
        196 GGTGACACGTGGAATAAAAATTAAATATTTTTTTAATATATTTTATGTTATTGAAATTTA

                
        811 TTTT
          1 TTTT

        815 TAAAAAAATA


Statistics
Matches: 245,  Mismatches: 11, Indels: 4
        0.94            0.04        0.02

Matches are distributed among these distances:
 252  179  0.73
 253    8  0.03
 255   54  0.22
 256    4  0.02

ACGTcount: A:0.26, C:0.19, G:0.18, T:0.37


Consensus pattern (255 bp):   
TTTTAGGTAAAAGTACCCGGGAGGTCCCTGTACTATACGAAATGTTGATTTTGGTCCCTGTACTT
TTTTTTTGCTACAAATTCGTCCCTCTACTATCAGAACCTATCACCCGAAGTCCCTCACGTTAGCA
TGCCGTGACAGACCCGTCAAATATGCTGACGTGGCACTAACACCGTCTTTTTTGCTGACGTGGCA
GGTGACACGTGGAATAAAAATTAAATATTTTTTTAATATATTTTATGTTATTGAAATTTA

Found at i:3122 original size:17 final size:17

Alignment explanation


    Indices: 3088--3133  Score: 51
    Period size: 17  Copynumber: 2.8  Consensus size: 17

       3078 TTCCAACACC

                        * *  
       3088 TATATAT-ATATTATTA
          1 TATATATAATATAAGTA

                             
       3104 TATATATAATATAAGTA
          1 TATATATAATATAAGTA

                          
       3121 TATA-ACTAATATA
          1 TATATA-TAATATA

       3134 GTAGCTTTTA


Statistics
Matches: 26,  Mismatches: 2, Indels: 3
        0.84            0.06        0.10

Matches are distributed among these distances:
  16    8  0.31
  17   18  0.69

ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46


Consensus pattern (17 bp):   
TATATATAATATAAGTA
Done.