Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001377.1 Corchorus olitorius cultivar O-4 contig01377, 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: 3424
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.32


Found at i:300 original size:98 final size:98

Alignment explanation


    Indices: 184--368  Score: 318
    Period size: 98  Copynumber: 1.9  Consensus size: 98

        174 AAATTGATAA

                                                                             
        184 TCTTCTTGCATCAGAGATCGATAACCTCCTTAATTGATTAATATTTAACTTCGTTCTTTAATAGC
          1 TCTTCTTGCATCAGAGATCGATAACCTCCTTAATTGATTAATATTTAACTTCGTTC-TTAATAGC

                                              
        249 CCTGTAG-TTTTTTAGTAAATTCTTTCTTCTTCT
         65 CCTGTAGTTTTTTTAGTAAATTCTTTCTTCTTCT

                                       *              *                    * 
        282 TCTTCTTGCATCAGAGATCGATAACCTTCTTAATTGATTAATGTTTAACTTCGTTCTTAATAGTC
          1 TCTTCTTGCATCAGAGATCGATAACCTCCTTAATTGATTAATATTTAACTTCGTTCTTAATAGCC

            *                     
        347 TTGTAGTTTTTTTAGTAAATTC
         66 CTGTAGTTTTTTTAGTAAATTC

        369 AAATAAGAAA


Statistics
Matches: 82,  Mismatches: 4, Indels: 2
        0.93            0.05        0.02

Matches are distributed among these distances:
  97   13  0.16
  98   69  0.84

ACGTcount: A:0.24, C:0.17, G:0.11, T:0.47


Consensus pattern (98 bp):   
TCTTCTTGCATCAGAGATCGATAACCTCCTTAATTGATTAATATTTAACTTCGTTCTTAATAGCC
CTGTAGTTTTTTTAGTAAATTCTTTCTTCTTCT

Found at i:607 original size:2 final size:2

Alignment explanation


    Indices: 600--635  Score: 63
    Period size: 2  Copynumber: 18.0  Consensus size: 2

        590 CTTTAACTAG

                                                      *          
        600 TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

        636 AATTTTAGTA


Statistics
Matches: 32,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   2   32  1.00

ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47


Consensus pattern (2 bp):   
TA

Found at i:1220 original size:82 final size:84

Alignment explanation


    Indices: 1077--1239  Score: 267
    Period size: 82  Copynumber: 2.0  Consensus size: 84

       1067 TCGAGGAGCT

                                                       *      *     *        
       1077 AAGAAGTGACTATTCCAAGTAAATGGGGATCCATCCTAACCCCGTAGTTGCACATCTAAGTAAAG
          1 AAGAAGTGACTATTCCAAGTAAATGGGGATCCATCCTAACCCCATAGTTGAACATCCAAGTAAAG

                               
       1142 AGATCAACTT-TTAAGCAA
         66 AGATCAACTTCTTAAGCAA

                                                         *                  *
       1160 AAGAAGTGACTATTCCAAG-AAATGGGGATCCATCCTAACCCCATGGTTGAACATCCAAGTAAAT
          1 AAGAAGTGACTATTCCAAGTAAATGGGGATCCATCCTAACCCCATAGTTGAACATCCAAGTAAAG

                            
       1224 AGATCAACTTCTTAAG
         66 AGATCAACTTCTTAAG

       1240 TAAGAAATCC


Statistics
Matches: 74,  Mismatches: 5, Indels: 2
        0.91            0.06        0.02

Matches are distributed among these distances:
  82   50  0.68
  83   24  0.32

ACGTcount: A:0.37, C:0.21, G:0.18, T:0.24


Consensus pattern (84 bp):   
AAGAAGTGACTATTCCAAGTAAATGGGGATCCATCCTAACCCCATAGTTGAACATCCAAGTAAAG
AGATCAACTTCTTAAGCAA
Done.