Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012023.1 Corchorus olitorius cultivar O-4 contig12056, 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: 32897
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32


Found at i:14736 original size:21 final size:21

Alignment explanation


    Indices: 14712--14753  Score: 84
    Period size: 21  Copynumber: 2.0  Consensus size: 21

      14702 GCACCTTAAA

                                 
      14712 CAACTCCGATGAGCTTGAAAC
          1 CAACTCCGATGAGCTTGAAAC

                                 
      14733 CAACTCCGATGAGCTTGAAAC
          1 CAACTCCGATGAGCTTGAAAC

      14754 TTCTTTGTGA


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  21   21  1.00

ACGTcount: A:0.33, C:0.29, G:0.19, T:0.19


Consensus pattern (21 bp):   
CAACTCCGATGAGCTTGAAAC

Found at i:16152 original size:2 final size:2

Alignment explanation


    Indices: 16145--16189  Score: 72
    Period size: 2  Copynumber: 22.5  Consensus size: 2

      16135 GATGATTGTG

                                                *     *                   
      16145 TA TA TA TA TA TA TA TA TA TA TA TA AA TA AA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

                
      16187 TA T
          1 TA T

      16190 TTTACTTGTG


Statistics
Matches: 39,  Mismatches: 4, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
   2   39  1.00

ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47


Consensus pattern (2 bp):   
TA

Found at i:22814 original size:14 final size:15

Alignment explanation


    Indices: 22795--22824  Score: 53
    Period size: 15  Copynumber: 2.1  Consensus size: 15

      22785 AACTAGGAAA

                           
      22795 AATAAAT-AACAAGG
          1 AATAAATAAACAAGG

                           
      22809 AATAAATAAACAAGG
          1 AATAAATAAACAAGG

             
      22824 A
          1 A

      22825 TTGGACATAG


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  14    7  0.47
  15    8  0.53

ACGTcount: A:0.67, C:0.07, G:0.13, T:0.13


Consensus pattern (15 bp):   
AATAAATAAACAAGG

Found at i:22983 original size:26 final size:26

Alignment explanation


    Indices: 22947--23010  Score: 128
    Period size: 26  Copynumber: 2.5  Consensus size: 26

      22937 CATCTCTGGT

                                      
      22947 CCAACCCATGCATGGGGTACCTTCGA
          1 CCAACCCATGCATGGGGTACCTTCGA

                                      
      22973 CCAACCCATGCATGGGGTACCTTCGA
          1 CCAACCCATGCATGGGGTACCTTCGA

                        
      22999 CCAACCCATGCA
          1 CCAACCCATGCA

      23011 AGGGCTAGTG


Statistics
Matches: 38,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  26   38  1.00

ACGTcount: A:0.25, C:0.38, G:0.20, T:0.17


Consensus pattern (26 bp):   
CCAACCCATGCATGGGGTACCTTCGA

Found at i:31198 original size:33 final size:33

Alignment explanation


    Indices: 31112--31224  Score: 115
    Period size: 33  Copynumber: 3.4  Consensus size: 33

      31102 AAGAGTAATT

                    *      *                   
      31112 CTAAATCTCTTTTAGATGTTGTTTGTCGAT-AATA
          1 CTAAATCTGTTTTAGGTGTTGTTTGT-GATGAA-A

                 *  **                      * 
      31146 CTAAACCTAATTT-GAGTGTTGTTTGTGATGACA
          1 CTAAATCTGTTTTAG-GTGTTGTTTGTGATGAAA

                                             
      31179 CTAAATCTGTTTTAGGTGTTGTTTGTGATGAAA
          1 CTAAATCTGTTTTAGGTGTTGTTTGTGATGAAA

                          
      31212 C-AAATTCTGTTTT
          1 CTAAA-TCTGTTTT

      31225 GGATGCTAAT


Statistics
Matches: 66,  Mismatches: 9, Indels: 9
        0.79            0.11        0.11

Matches are distributed among these distances:
  32    3  0.05
  33   41  0.62
  34   22  0.33

ACGTcount: A:0.26, C:0.11, G:0.19, T:0.45


Consensus pattern (33 bp):   
CTAAATCTGTTTTAGGTGTTGTTTGTGATGAAA
Done.