Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024173.1 Corchorus olitorius cultivar O-4 contig24206, 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: 37039
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32


Found at i:2106 original size:57 final size:57

Alignment explanation


    Indices: 2018--2132  Score: 221
    Period size: 57  Copynumber: 2.0  Consensus size: 57

       2008 CCTTTAGGAA

                                                        *            
       2018 AAGCTTATGTAATCCACTTTGGATGGTGTAGCAACAATGTTGGAGAAGAAAATGAGC
          1 AAGCTTATGTAATCCACTTTGGATGGTGTAGCAACAATGTTGGAAAAGAAAATGAGC

                                                                     
       2075 AAGCTTATGTAATCCACTTTGGATGGTGTAGCAACAATGTTGGAAAAGAAAATGAGC
          1 AAGCTTATGTAATCCACTTTGGATGGTGTAGCAACAATGTTGGAAAAGAAAATGAGC

             
       2132 A
          1 A

       2133 CCAATTTGTA


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

Matches are distributed among these distances:
  57   57  1.00

ACGTcount: A:0.37, C:0.12, G:0.25, T:0.26


Consensus pattern (57 bp):   
AAGCTTATGTAATCCACTTTGGATGGTGTAGCAACAATGTTGGAAAAGAAAATGAGC

Found at i:2171 original size:20 final size:20

Alignment explanation


    Indices: 2133--2173  Score: 64
    Period size: 20  Copynumber: 2.0  Consensus size: 20

       2123 AAAATGAGCA

                          *     
       2133 CCAATTTGTAAACCGAATGC
          1 CCAATTTGTAAACCAAATGC

                        *       
       2153 CCAATTTGTAAATCAAATGC
          1 CCAATTTGTAAACCAAATGC

             
       2173 C
          1 C

       2174 TTTTATTTTC


Statistics
Matches: 19,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  20   19  1.00

ACGTcount: A:0.37, C:0.24, G:0.12, T:0.27


Consensus pattern (20 bp):   
CCAATTTGTAAACCAAATGC

Found at i:8840 original size:10 final size:10

Alignment explanation


    Indices: 8821--8861  Score: 64
    Period size: 10  Copynumber: 4.1  Consensus size: 10

       8811 TAAATATCCA

                      
       8821 ATTCCCGCAT
          1 ATTCCCGCAT

                **    
       8831 ATTCTTGCAT
          1 ATTCCCGCAT

                      
       8841 ATTCCCGCAT
          1 ATTCCCGCAT

                      
       8851 ATTCCCGCAT
          1 ATTCCCGCAT

             
       8861 A
          1 A

       8862 CTAGTCCTAG


Statistics
Matches: 27,  Mismatches: 4, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  10   27  1.00

ACGTcount: A:0.22, C:0.34, G:0.10, T:0.34


Consensus pattern (10 bp):   
ATTCCCGCAT

Found at i:10326 original size:23 final size:22

Alignment explanation


    Indices: 10280--10327  Score: 60
    Period size: 23  Copynumber: 2.1  Consensus size: 22

      10270 TTTCTTGTTT

                     *         *  
      10280 TTGCGTTTTGTTCTAAAAACAA
          1 TTGCGTTTTCTTCTAAAAAAAA

                         *         
      10302 TTGCGTTTTCTATTTAAAAAAAA
          1 TTGCGTTTTCT-TCTAAAAAAAA

               
      10325 TTG
          1 TTG

      10328 TTTTTGCGTT


Statistics
Matches: 22,  Mismatches: 3, Indels: 1
        0.85            0.12        0.04

Matches are distributed among these distances:
  22   10  0.45
  23   12  0.55

ACGTcount: A:0.33, C:0.10, G:0.12, T:0.44


Consensus pattern (22 bp):   
TTGCGTTTTCTTCTAAAAAAAA

Found at i:30262 original size:76 final size:76

Alignment explanation


    Indices: 30056--30226  Score: 308
    Period size: 76  Copynumber: 2.2  Consensus size: 76

      30046 ATCTGGGTGA

                                                                         *   
      30056 TCAAGCGAAA-CACATGGGTCTTCAGACAAACCATGTGGGCACCCAGCTGGAGTCGTGACATTGC
          1 TCAAGC-AAACCACATGGGTCTTCAGACAAACCATGTGGGCACCCAGCTGGAGTCGTGACACTGC

                        
      30120 CCACCTGGGTTC
         65 CCACCTGGGTTC

                                                          *                  
      30132 TCAAGCAAACCACATGGGTCTTCAGACAAACCATGTGGGCACCCAGTTGGAGTCGTGACACTGCC
          1 TCAAGCAAACCACATGGGTCTTCAGACAAACCATGTGGGCACCCAGCTGGAGTCGTGACACTGCC

                       
      30197 CACCTGGGTTC
         66 CACCTGGGTTC

                               
      30208 TCAAGCAAACCACATGGGT
          1 TCAAGCAAACCACATGGGT

      30227 GCTCAAGGCA


Statistics
Matches: 92,  Mismatches: 2, Indels: 2
        0.96            0.02        0.02

Matches are distributed among these distances:
  75    3  0.03
  76   89  0.97

ACGTcount: A:0.26, C:0.29, G:0.25, T:0.19


Consensus pattern (76 bp):   
TCAAGCAAACCACATGGGTCTTCAGACAAACCATGTGGGCACCCAGCTGGAGTCGTGACACTGCC
CACCTGGGTTC
Done.