Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020049.1 Corchorus olitorius cultivar O-4 contig20082, 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: 2354
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30


Found at i:246 original size:29 final size:27

Alignment explanation


    Indices: 176--336  Score: 180
    Period size: 29  Copynumber: 5.7  Consensus size: 27

        166 AAATGAGCTT

                       *                
        176 AAAATGACCAAGATGCCCTTGAATGTGC
          1 AAAATGACCAAAATGCCC-TGAATGTGC

                                        
        204 AAAATGACCAAAATGCCCATGAATGTGC
          1 AAAATGACCAAAATGCCC-TGAATGTGC

                     *                    
        232 AAAAATGACTAAAATGCCCCT-AGATGTGC
          1 -AAAATGACCAAAATG-CCCTGA-ATGTGC

                                         
        261 AAAAATGACCAAAATGCTCCTGAATGTGC
          1 -AAAATGACCAAAATGC-CCTGAATGTGC

                                   * * **
        290 AAAATGACCAAAATGCCCCTAGATTTTTA
          1 AAAATGACCAAAATG-CCCT-GAATGTGC

                              
        319 AAAATGACCAAAATGCCC
          1 AAAATGACCAAAATGCCC

        337 CCTAGATTTT


Statistics
Matches: 118,  Mismatches: 8, Indels: 14
        0.84            0.06        0.10

Matches are distributed among these distances:
  28   49  0.42
  29   65  0.55
  30    4  0.03

ACGTcount: A:0.42, C:0.22, G:0.16, T:0.20


Consensus pattern (27 bp):   
AAAATGACCAAAATGCCCTGAATGTGC

Found at i:264 original size:57 final size:55

Alignment explanation


    Indices: 176--336  Score: 207
    Period size: 57  Copynumber: 2.8  Consensus size: 55

        166 AAATGAGCTT

                       *        *                                    
        176 AAAATGACCAAGATG-CCCTTGAATGTGCAAAATGACCAAAATGCCCATGAATGTGC
          1 AAAATGACCAAAATGCCCCTAG-ATGTGCAAAATGACCAAAATGCCC-TGAATGTGC

                     *                                                
        232 AAAAATGACTAAAATGCCCCTAGATGTGCAAAAATGACCAAAATGCTCCTGAATGTGC
          1 -AAAATGACCAAAATGCCCCTAGATGTGC-AAAATGACCAAAATGC-CCTGAATGTGC

                                     * **                  
        290 AAAATGACCAAAATGCCCCTAGATTTTTAAAAATGACCAAAATGCCC
          1 AAAATGACCAAAATGCCCCTAGA-TGTGCAAAATGACCAAAATGCCC

        337 CCTAGATTTT


Statistics
Matches: 93,  Mismatches: 7, Indels: 9
        0.85            0.06        0.08

Matches are distributed among these distances:
  56    2  0.02
  57   57  0.61
  58   32  0.34
  59    2  0.02

ACGTcount: A:0.42, C:0.22, G:0.16, T:0.20


Consensus pattern (55 bp):   
AAAATGACCAAAATGCCCCTAGATGTGCAAAATGACCAAAATGCCCTGAATGTGC

Found at i:289 original size:86 final size:87

Alignment explanation


    Indices: 176--343  Score: 243
    Period size: 86  Copynumber: 1.9  Consensus size: 87

        166 AAATGAGCTT

                       *                                                     
        176 AAAATGACCAAGATGCCCTTGAATGTGCAAAATGACCAAAATGCCCAT-GAATGTGCAAAAATGA
          1 AAAATGACCAAAATGCCCTTGAATGTGCAAAATGACCAAAATGCCCATAG-ATGTGCAAAAATGA

             *                     
        240 CTAAAATG-CCCCTAGATGTGCA
         65 CCAAAATGCCCCCTAGATGTGCA

                                                           *     * **        
        262 AAAATGACCAAAATGCTCC-TGAATGTGCAAAATGACCAAAATGCCCCTAGATTTTTAAAAATGA
          1 AAAATGACCAAAATGC-CCTTGAATGTGCAAAATGACCAAAATGCCCATAGATGTGCAAAAATGA

                              
        326 CCAAAATGCCCCCTAGAT
         65 CCAAAATGCCCCCTAGAT

        344 TTTTTTTTAA


Statistics
Matches: 73,  Mismatches: 6, Indels: 5
        0.87            0.07        0.06

Matches are distributed among these distances:
  86   61  0.84
  87   12  0.16

ACGTcount: A:0.41, C:0.22, G:0.16, T:0.21


Consensus pattern (87 bp):   
AAAATGACCAAAATGCCCTTGAATGTGCAAAATGACCAAAATGCCCATAGATGTGCAAAAATGAC
CAAAATGCCCCCTAGATGTGCA

Done.