Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013707.1 Corchorus olitorius cultivar O-4 contig13740, 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: 3978
ACGTcount: A:0.34, C:0.22, G:0.14, T:0.30


Found at i:284 original size:21 final size:21

Alignment explanation


    Indices: 260--330  Score: 117
    Period size: 21  Copynumber: 3.4  Consensus size: 21

        250 CTTAGACAAT

                         *       
        260 TCCAATGAGCTTGAAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                                 
        281 TCCAATGAGCTTGGAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                                  
        302 TCCAATGAGCTTGGAA-CTTGC
          1 TCCAATGAGCTTGGAACCTT-C

                    
        323 TCCAATGA
          1 TCCAATGA

        331 TCTCCTAGCA


Statistics
Matches: 48,  Mismatches: 1, Indels: 2
        0.94            0.02        0.04

Matches are distributed among these distances:
  20    3  0.06
  21   45  0.94

ACGTcount: A:0.27, C:0.27, G:0.18, T:0.28


Consensus pattern (21 bp):   
TCCAATGAGCTTGGAACCTTC

Found at i:2126 original size:33 final size:32

Alignment explanation


    Indices: 2089--2178  Score: 117
    Period size: 33  Copynumber: 2.7  Consensus size: 32

       2079 AGAATTTGTT

                                            *
       2089 TCATCACAAACAACACCTAAAACAGATTTAGTG
          1 TCATCACAAACAACA-CTAAAACAGATTTAGTA

                                 **  *       
       2122 TCATCACAAACAACACTCAAATTAGGTTTAGTA
          1 TCATCACAAACAACACT-AAAACAGATTTAGTA

                                    
       2155 TCATCACAAACAACATCTAAAACA
          1 TCATCACAAACAACA-CTAAAACA

       2179 CTCTTTGAAA


Statistics
Matches: 49,  Mismatches: 6, Indels: 4
        0.83            0.10        0.07

Matches are distributed among these distances:
  32    2  0.04
  33   45  0.92
  34    2  0.04

ACGTcount: A:0.47, C:0.24, G:0.07, T:0.22


Consensus pattern (32 bp):   
TCATCACAAACAACACTAAAACAGATTTAGTA
Done.