Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018624.1 Corchorus olitorius cultivar O-4 contig18657, 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: 12201
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34


Found at i:34 original size:17 final size:17

Alignment explanation


    Indices: 11--59  Score: 55
    Period size: 17  Copynumber: 2.8  Consensus size: 17

          1 ATAATCACTA

                             
         11 AAATACTTAATTAAATG
          1 AAATACTTAATTAAATG

            *              *  
         28 TAATACTATAA-TAACTG
          1 AAATACT-TAATTAAATG

                           
         45 AAATACTTACATTAA
          1 AAATACTTA-ATTAA

         60 TTAAATTCTT


Statistics
Matches: 26,  Mismatches: 3, Indels: 5
        0.76            0.09        0.15

Matches are distributed among these distances:
  16    2  0.08
  17   18  0.69
  18    6  0.23

ACGTcount: A:0.51, C:0.10, G:0.04, T:0.35


Consensus pattern (17 bp):   
AAATACTTAATTAAATG

Found at i:92 original size:25 final size:24

Alignment explanation


    Indices: 56--102  Score: 85
    Period size: 25  Copynumber: 1.9  Consensus size: 24

         46 AATACTTACA

                                    
         56 TTAATTAAATTCTTAGGTATTTTT
          1 TTAATTAAATTCTTAGGTATTTTT

                                   
         80 TTAATTCAAATTCTTAGGTATTT
          1 TTAATT-AAATTCTTAGGTATTT

        103 GTGCAAACGT


Statistics
Matches: 22,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  24    6  0.27
  25   16  0.73

ACGTcount: A:0.30, C:0.06, G:0.09, T:0.55


Consensus pattern (24 bp):   
TTAATTAAATTCTTAGGTATTTTT

Found at i:958 original size:36 final size:36

Alignment explanation


    Indices: 904--973  Score: 104
    Period size: 36  Copynumber: 1.9  Consensus size: 36

        894 GAGATTTTGG

                       * *      *               
        904 AGAAATATGATTATCAAAATTACAAAAAATGTAATA
          1 AGAAATATGATAACCAAAATCACAAAAAATGTAATA

                                       *      
        940 AGAAATATGATAACCAAAATCACAAAAGATGTAA
          1 AGAAATATGATAACCAAAATCACAAAAAATGTAA

        974 GCTTATTGAA


Statistics
Matches: 30,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  36   30  1.00

ACGTcount: A:0.59, C:0.09, G:0.10, T:0.23


Consensus pattern (36 bp):   
AGAAATATGATAACCAAAATCACAAAAAATGTAATA

Found at i:7944 original size:42 final size:42

Alignment explanation


    Indices: 7885--7967  Score: 148
    Period size: 42  Copynumber: 2.0  Consensus size: 42

       7875 GTTAAGTCTT

                                                      
       7885 GAAAATTCTCTGTAAATTAAAAAATACTCAACTCAAATCATA
          1 GAAAATTCTCTGTAAATTAAAAAATACTCAACTCAAATCATA

                     *          *                    
       7927 GAAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATCAT
          1 GAAAATTCTCTGTAAATTAAAAAATACTCAACTCAAATCAT

       7968 GATCCTTAGC


Statistics
Matches: 39,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  42   39  1.00

ACGTcount: A:0.48, C:0.16, G:0.06, T:0.30


Consensus pattern (42 bp):   
GAAAATTCTCTGTAAATTAAAAAATACTCAACTCAAATCATA

Found at i:8101 original size:55 final size:56

Alignment explanation


    Indices: 8031--8142  Score: 190
    Period size: 56  Copynumber: 2.0  Consensus size: 56

       8021 TTTATTTTGT

                                                                    
       8031 AGAATAATTAAGTAGAAATA-GGGGATAGGATTTATTATAACATTTATTGAGTGAA
          1 AGAATAATTAAGTAGAAATAGGGGGATAGGATTTATTATAACATTTATTGAGTGAA

                            *        *                        *     
       8086 AGAATAATTAAGTAGAGATAGGGGGGTAGGATTTATTATAACATTTATTGTGTGAA
          1 AGAATAATTAAGTAGAAATAGGGGGATAGGATTTATTATAACATTTATTGAGTGAA

             
       8142 A
          1 A

       8143 AGGAAACACA


Statistics
Matches: 53,  Mismatches: 3, Indels: 1
        0.93            0.05        0.02

Matches are distributed among these distances:
  55   19  0.36
  56   34  0.64

ACGTcount: A:0.41, C:0.02, G:0.24, T:0.33


Consensus pattern (56 bp):   
AGAATAATTAAGTAGAAATAGGGGGATAGGATTTATTATAACATTTATTGAGTGAA

Done.