Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013054.1 Corchorus olitorius cultivar O-4 contig13087, 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: 18051
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31


Found at i:1918 original size:4 final size:4

Alignment explanation


    Indices: 1909--1934  Score: 52
    Period size: 4  Copynumber: 6.5  Consensus size: 4

       1899 AATTTTTTTA

                                            
       1909 ATTT ATTT ATTT ATTT ATTT ATTT AT
          1 ATTT ATTT ATTT ATTT ATTT ATTT AT

       1935 GGGAAAGCGA


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   4   22  1.00

ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73


Consensus pattern (4 bp):   
ATTT

Found at i:12281 original size:15 final size:16

Alignment explanation


    Indices: 12248--12287  Score: 55
    Period size: 15  Copynumber: 2.6  Consensus size: 16

      12238 TTACTTTGCT

                            
      12248 TTGTTTTCTAGTATAA
          1 TTGTTTTCTAGTATAA

                        *   
      12264 TTGTTTTCT-GTTTAA
          1 TTGTTTTCTAGTATAA

               *     
      12279 TTGCTTTCT
          1 TTGTTTTCT

      12288 TTCAACCTCT


Statistics
Matches: 22,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  15   13  0.59
  16    9  0.41

ACGTcount: A:0.15, C:0.10, G:0.12, T:0.62


Consensus pattern (16 bp):   
TTGTTTTCTAGTATAA

Found at i:16315 original size:26 final size:26

Alignment explanation


    Indices: 16267--16318  Score: 68
    Period size: 26  Copynumber: 2.0  Consensus size: 26

      16257 AAAATAGGCA

                              *       
      16267 AATTAAACTAGAAAACAATAAAATAG
          1 AATTAAACTAGAAAACAAGAAAATAG

                        * **          
      16293 AATTAAACTAGAGATTAAGAAAATAG
          1 AATTAAACTAGAAAACAAGAAAATAG

      16319 TTTGAGAAAA


Statistics
Matches: 22,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  26   22  1.00

ACGTcount: A:0.62, C:0.06, G:0.12, T:0.21


Consensus pattern (26 bp):   
AATTAAACTAGAAAACAAGAAAATAG

Found at i:17746 original size:76 final size:76

Alignment explanation


    Indices: 17596--17739  Score: 177
    Period size: 76  Copynumber: 1.9  Consensus size: 76

      17586 ACAAGGACCC

                                                               *           * 
      17596 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCTTGAGAACCCAGGT
          1 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT

                       
      17661 GGGCAGTGTCA
         66 GGGCAGTGTCA

                    *     *              *                            **     
      17672 CGACTCCAGCTGGGTGCCCACATGGTTTGTC-TGAAG-ACCCATGT-GTTTCGCCTGATCACCCA
          1 CGACTCCACCTGGGCGCCCACATGG-TTGCCTTG-AGCACCCATGTGGTTT-GCCTGAGAACCCA

                  
      17734 GATGGG
         63 GATGGG

      17740 TTGTGTCTTA


Statistics
Matches: 58,  Mismatches: 7, Indels: 6
        0.82            0.10        0.08

Matches are distributed among these distances:
  75    4  0.07
  76   48  0.83
  77    6  0.10

ACGTcount: A:0.17, C:0.30, G:0.29, T:0.24


Consensus pattern (76 bp):   
CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
GGGCAGTGTCA
Done.