Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001322.1 Corchorus olitorius cultivar O-4 contig01322, 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, 689

Length: 1149
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.35


Found at i:661 original size:147 final size:147

Alignment explanation


    Indices: 394--688  Score: 581
    Period size: 147  Copynumber: 2.0  Consensus size: 147

        384 TTATAGGGGA

                                                                             
        394 TGGAAATCACCTACTTCCAATTTCGCGTCCTACTCCATGTTCTATTTATCAAATTATACTATATA
          1 TGGAAATCACCTACTTCCAATTTCGCGTCCTACTCCATGTTCTATTTATCAAATTATACTATATA

                                                                             
        459 TGTTCCTTGTATTATATTTACAAGTTTTAACAAATAACATTAATATAAAAAATAGAATAAAAATC
         66 TGTTCCTTGTATTATATTTACAAGTTTTAACAAATAACATTAATATAAAAAATAGAATAAAAATC

                             
        524 CCATATAAACACAAGGT
        131 CCATATAAACACAAGGT

                                                                     *       
        541 TGGAAATCACCTACTTCCAATTTCGCGTCCTACTCCATGTTCTATTTATCAAATTATGCTATATA
          1 TGGAAATCACCTACTTCCAATTTCGCGTCCTACTCCATGTTCTATTTATCAAATTATACTATATA

                                                                             
        606 TGTTCCTTGTATTATATTTACAAGTTTTAACAAATAACATTAATATAAAAAATAGAATAAAAATC
         66 TGTTCCTTGTATTATATTTACAAGTTTTAACAAATAACATTAATATAAAAAATAGAATAAAAATC

                             
        671 CCATATAAACACAAGGT
        131 CCATATAAACACAAGGT

             
        688 T
          1 T

        689 TAGCGCCAAA


Statistics
Matches: 147,  Mismatches: 1, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
 147  147  1.00

ACGTcount: A:0.39, C:0.18, G:0.08, T:0.36


Consensus pattern (147 bp):   
TGGAAATCACCTACTTCCAATTTCGCGTCCTACTCCATGTTCTATTTATCAAATTATACTATATA
TGTTCCTTGTATTATATTTACAAGTTTTAACAAATAACATTAATATAAAAAATAGAATAAAAATC
CCATATAAACACAAGGT

Found at i:1025 original size:46 final size:45

Alignment explanation


    Indices: 953--1046  Score: 161
    Period size: 46  Copynumber: 2.1  Consensus size: 45

        943 ATATTTTGAT

                  *                                      
        953 TTATTTTAGGGAAAAAAGTTCATTCTTTTTAATCATGTTCATTAA
          1 TTATTTGAGGGAAAAAAGTTCATTCTTTTTAATCATGTTCATTAA

                                              *           
        998 TTATTTGAGGGAAAAAAAGTTCATTCTTTTTAATTATGTTCATTAA
          1 TTATTTGAGGG-AAAAAAGTTCATTCTTTTTAATCATGTTCATTAA

               
       1044 TTA
          1 TTA

       1047 ATAGAGATTA


Statistics
Matches: 46,  Mismatches: 2, Indels: 1
        0.94            0.04        0.02

Matches are distributed among these distances:
  45   10  0.22
  46   36  0.78

ACGTcount: A:0.34, C:0.07, G:0.12, T:0.47


Consensus pattern (45 bp):   
TTATTTGAGGGAAAAAAGTTCATTCTTTTTAATCATGTTCATTAA
Done.