Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013935.1 Corchorus olitorius cultivar O-4 contig13968, 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: 33107
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.32


Found at i:13220 original size:47 final size:47

Alignment explanation


    Indices: 13166--13259  Score: 170
    Period size: 47  Copynumber: 2.0  Consensus size: 47

      13156 TGAGCAGATA

                     *                           *         
      13166 TCAGGCATTTTTATTAATTTAGTAATCTAGAGAAATTTGTTACTATG
          1 TCAGGCATTGTTATTAATTTAGTAATCTAGAGAAATTCGTTACTATG

                                                           
      13213 TCAGGCATTGTTATTAATTTAGTAATCTAGAGAAATTCGTTACTATG
          1 TCAGGCATTGTTATTAATTTAGTAATCTAGAGAAATTCGTTACTATG

      13260 CTCCTATGAT


Statistics
Matches: 45,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  47   45  1.00

ACGTcount: A:0.32, C:0.10, G:0.16, T:0.43


Consensus pattern (47 bp):   
TCAGGCATTGTTATTAATTTAGTAATCTAGAGAAATTCGTTACTATG

Found at i:21728 original size:13 final size:13

Alignment explanation


    Indices: 21710--21735  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

      21700 GAGGTACATA

                         
      21710 AAGGGTGCTCTCT
          1 AAGGGTGCTCTCT

                         
      21723 AAGGGTGCTCTCT
          1 AAGGGTGCTCTCT

      21736 TCCCTAGTCT


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.15, C:0.23, G:0.31, T:0.31


Consensus pattern (13 bp):   
AAGGGTGCTCTCT

Found at i:22077 original size:4 final size:4

Alignment explanation


    Indices: 22070--22095  Score: 52
    Period size: 4  Copynumber: 6.5  Consensus size: 4

      22060 TTTTTTTTTT

                                            
      22070 ATTG ATTG ATTG ATTG ATTG ATTG AT
          1 ATTG ATTG ATTG ATTG ATTG ATTG AT

      22096 GGCCTGATAG


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:0.23, T:0.50


Consensus pattern (4 bp):   
ATTG

Found at i:22376 original size:79 final size:79

Alignment explanation


    Indices: 22267--22418  Score: 241
    Period size: 79  Copynumber: 1.9  Consensus size: 79

      22257 TGATTATACA

                   *         *       *                                     * 
      22267 GGGGCGCTATTTTAGGCGCTCAGCCGTTTCACGAGGGAAATGTCTCATAAGAGACGATCGTCCTC
          1 GGGGCGCCATTTTAGGCACTCAGCCATTTCACGAGGGAAATGTCTCATAAGAGACGATCGTCCGC

                          
      22332 TCGTTTAATTTCAC
         66 TCGTTTAATTTCAC

                                                            *     *   *      
      22346 GGGGCGCCATTTTAGGCACTCAGCCATTTCACGAGGGAAATGTCTCATGAGAGATGATTGTCCGC
          1 GGGGCGCCATTTTAGGCACTCAGCCATTTCACGAGGGAAATGTCTCATAAGAGACGATCGTCCGC

                    
      22411 TCGTTTAA
         66 TCGTTTAA

      22419 ATGAGTCATT


Statistics
Matches: 66,  Mismatches: 7, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  79   66  1.00

ACGTcount: A:0.22, C:0.23, G:0.26, T:0.28


Consensus pattern (79 bp):   
GGGGCGCCATTTTAGGCACTCAGCCATTTCACGAGGGAAATGTCTCATAAGAGACGATCGTCCGC
TCGTTTAATTTCAC
Done.