Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020473.1 Corchorus olitorius cultivar O-4 contig20506, 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: 13849
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31


Found at i:750 original size:18 final size:19

Alignment explanation


    Indices: 727--766  Score: 64
    Period size: 19  Copynumber: 2.2  Consensus size: 19

        717 CTCTTGAGAT

                               
        727 AATTCTTC-AATGATCTTC
          1 AATTCTTCAAATGATCTTC

                        *      
        745 AATTCTTCAAATTATCTTC
          1 AATTCTTCAAATGATCTTC

               
        764 AAT
          1 AAT

        767 AAGTCTTCCA


Statistics
Matches: 20,  Mismatches: 1, Indels: 1
        0.91            0.05        0.05

Matches are distributed among these distances:
  18    8  0.40
  19   12  0.60

ACGTcount: A:0.33, C:0.20, G:0.03, T:0.45


Consensus pattern (19 bp):   
AATTCTTCAAATGATCTTC

Found at i:1886 original size:18 final size:18

Alignment explanation


    Indices: 1851--1885  Score: 54
    Period size: 18  Copynumber: 2.0  Consensus size: 18

       1841 CTCCTCTTGC

                     *        
       1851 ATGAAAACACTTCTTTTT
          1 ATGAAAACAATTCTTTTT

                              
       1869 ATGAAAACAATT-TTTTT
          1 ATGAAAACAATTCTTTTT

       1886 TTAAAAACTA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  17    5  0.31
  18   11  0.69

ACGTcount: A:0.37, C:0.11, G:0.06, T:0.46


Consensus pattern (18 bp):   
ATGAAAACAATTCTTTTT

Found at i:6406 original size:18 final size:19

Alignment explanation


    Indices: 6383--6419  Score: 67
    Period size: 18  Copynumber: 2.0  Consensus size: 19

       6373 CACCCTAGCC

                               
       6383 CTAAAACTAGAAGA-AAAA
          1 CTAAAACTAGAAGAGAAAA

                               
       6401 CTAAAACTAGAAGAGAAAA
          1 CTAAAACTAGAAGAGAAAA

       6420 AGAAGAAGAG


Statistics
Matches: 18,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  18   14  0.78
  19    4  0.22

ACGTcount: A:0.65, C:0.11, G:0.14, T:0.11


Consensus pattern (19 bp):   
CTAAAACTAGAAGAGAAAA

Found at i:8000 original size:18 final size:19

Alignment explanation


    Indices: 7977--8016  Score: 64
    Period size: 19  Copynumber: 2.2  Consensus size: 19

       7967 CTCTTGATAT

                               
       7977 AATTCTTC-AATGATCTTC
          1 AATTCTTCAAATGATCTTC

                        *      
       7995 AATTCTTCAAATTATCTTC
          1 AATTCTTCAAATGATCTTC

               
       8014 AAT
          1 AAT

       8017 AAGTCTTCCA


Statistics
Matches: 20,  Mismatches: 1, Indels: 1
        0.91            0.05        0.05

Matches are distributed among these distances:
  18    8  0.40
  19   12  0.60

ACGTcount: A:0.33, C:0.20, G:0.03, T:0.45


Consensus pattern (19 bp):   
AATTCTTCAAATGATCTTC

Done.