Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012939.1 Corchorus olitorius cultivar O-4 contig12972, 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: 8544
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.33


Found at i:1007 original size:11 final size:11

Alignment explanation


    Indices: 983--1017  Score: 52
    Period size: 11  Copynumber: 3.2  Consensus size: 11

        973 TTGATAGCGC

                       
        983 AACAAAAACAA
          1 AACAAAAACAA

               *     * 
        994 AACGAAAACGA
          1 AACAAAAACAA

                       
       1005 AACAAAAACAA
          1 AACAAAAACAA

              
       1016 AA
          1 AA

       1018 AACAGAAAAA


Statistics
Matches: 20,  Mismatches: 4, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  11   20  1.00

ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00


Consensus pattern (11 bp):   
AACAAAAACAA

Found at i:1106 original size:24 final size:24

Alignment explanation


    Indices: 1079--1127  Score: 89
    Period size: 24  Copynumber: 2.0  Consensus size: 24

       1069 TAGACATTGG

                                    
       1079 ACTCTTGTTCAACACCCCACCACC
          1 ACTCTTGTTCAACACCCCACCACC

                       *            
       1103 ACTCTTGTTCAGCACCCCACCACC
          1 ACTCTTGTTCAACACCCCACCACC

             
       1127 A
          1 A

       1128 GCCACTAGTG


Statistics
Matches: 24,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  24   24  1.00

ACGTcount: A:0.24, C:0.49, G:0.06, T:0.20


Consensus pattern (24 bp):   
ACTCTTGTTCAACACCCCACCACC

Found at i:2045 original size:56 final size:56

Alignment explanation


    Indices: 1979--2092  Score: 219
    Period size: 56  Copynumber: 2.0  Consensus size: 56

       1969 TAGTAGCGTC

                                                                    
       1979 ATCAATTGCGTTCACATTCCTCAAATTAAAAGCTACTATATATCTAGCTCGTTAAT
          1 ATCAATTGCGTTCACATTCCTCAAATTAAAAGCTACTATATATCTAGCTCGTTAAT

                         *                                          
       2035 ATCAATTGCGTTCGCATTCCTCAAATTAAAAGCTACTATATATCTAGCTCGTTAAT
          1 ATCAATTGCGTTCACATTCCTCAAATTAAAAGCTACTATATATCTAGCTCGTTAAT

              
       2091 AT
          1 AT

       2093 AAAGTAATCA


Statistics
Matches: 57,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  56   57  1.00

ACGTcount: A:0.33, C:0.21, G:0.10, T:0.36


Consensus pattern (56 bp):   
ATCAATTGCGTTCACATTCCTCAAATTAAAAGCTACTATATATCTAGCTCGTTAAT

Found at i:7272 original size:14 final size:13

Alignment explanation


    Indices: 7253--7293  Score: 59
    Period size: 14  Copynumber: 3.2  Consensus size: 13

       7243 CACGGCTAAC

                          
       7253 AAAAGAAAGAAAGA
          1 AAAAGAAAGAAA-A

                         
       7267 AAAAGAAAGAAAA
          1 AAAAGAAAGAAAA

                         
       7280 AAAA-AAA-AAAA
          1 AAAAGAAAGAAAA

               
       7291 AAA
          1 AAA

       7294 GCTAAAAGGA


Statistics
Matches: 27,  Mismatches: 0, Indels: 3
        0.90            0.00        0.10

Matches are distributed among these distances:
  11    7  0.26
  12    3  0.11
  13    5  0.19
  14   12  0.44

ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00


Consensus pattern (13 bp):   
AAAAGAAAGAAAA
Done.