Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012427.1 Corchorus olitorius cultivar O-4 contig12460, 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: 7536
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.36


Found at i:644 original size:30 final size:31

Alignment explanation


    Indices: 582--651  Score: 97
    Period size: 30  Copynumber: 2.3  Consensus size: 31

        572 TTGTTTTTAG

                                     *     
        582 CCTGAATTGACACAACCCGATAACGTTATAT
          1 CCTGAATTGACACAACCCGATAACGGTATAT

                           **          *   
        613 CCTGAATTGACACAAGTCG-TAACGGTGTAT
          1 CCTGAATTGACACAACCCGATAACGGTATAT

                     
        643 CCTGAATTG
          1 CCTGAATTG

        652 CATTTTCACC


Statistics
Matches: 35,  Mismatches: 4, Indels: 1
        0.88            0.10        0.03

Matches are distributed among these distances:
  30   18  0.51
  31   17  0.49

ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27


Consensus pattern (31 bp):   
CCTGAATTGACACAACCCGATAACGGTATAT

Found at i:1204 original size:42 final size:42

Alignment explanation


    Indices: 1145--1225  Score: 153
    Period size: 42  Copynumber: 1.9  Consensus size: 42

       1135 TAAGGATCAG

                                                      
       1145 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
          1 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT

                                         *         
       1187 GATTTGAGTTGAGTATTTCTTAATTTACAGAGAATTTTC
          1 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTC

       1226 AAGACTTAAC


Statistics
Matches: 38,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  42   38  1.00

ACGTcount: A:0.30, C:0.07, G:0.16, T:0.47


Consensus pattern (42 bp):   
GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT

Found at i:3289 original size:21 final size:20

Alignment explanation


    Indices: 3257--3297  Score: 64
    Period size: 21  Copynumber: 2.0  Consensus size: 20

       3247 TGGTCGATTA

                                
       3257 TTATATTATATAAAATATAT
          1 TTATATTATATAAAATATAT

                         *       
       3277 TTATATATATATATAATATAT
          1 TTATAT-TATATAAAATATAT

       3298 AATAAATTAT


Statistics
Matches: 19,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  20    6  0.32
  21   13  0.68

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (20 bp):   
TTATATTATATAAAATATAT

Found at i:4765 original size:22 final size:22

Alignment explanation


    Indices: 4737--4780  Score: 79
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       4727 CTTTTCTTGC

                      *           
       4737 GTGCTTGCTTTTGTCAGTTTGT
          1 GTGCTTGCTTCTGTCAGTTTGT

                                  
       4759 GTGCTTGCTTCTGTCAGTTTGT
          1 GTGCTTGCTTCTGTCAGTTTGT

       4781 TTTAGGGTCA


Statistics
Matches: 21,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  22   21  1.00

ACGTcount: A:0.05, C:0.16, G:0.27, T:0.52


Consensus pattern (22 bp):   
GTGCTTGCTTCTGTCAGTTTGT
Done.