Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001608.1 Corchorus olitorius cultivar O-4 contig01608, 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, 805

Length: 1342
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.33


Found at i:716 original size:16 final size:16

Alignment explanation


    Indices: 680--802  Score: 144
    Period size: 16  Copynumber: 7.8  Consensus size: 16

        670 CGGGTTCGGG

                           *
        680 TTCGGGTTCGGGTA-C
          1 TTCGGGTTCGGGTATT

                            
        695 TTCGGGTTCGGGTATT
          1 TTCGGGTTCGGGTATT

                            
        711 TTCGGGTTCGGGTATT
          1 TTCGGGTTCGGGTATT

                  *         *
        727 TTCGGGCTCGGGT-TAA
          1 TTCGGGTTCGGGTAT-T

            *               
        743 GTCGGGTTCGGGTATT
          1 TTCGGGTTCGGGTATT

                  *          
        759 TTCGGGCTCGGGT-TAT
          1 TTCGGGTTCGGGTAT-T

            *               
        775 GTCGGGTTCGGGTATT
          1 TTCGGGTTCGGGTATT

               *        
        791 TTCAGGTTCGGG
          1 TTCGGGTTCGGG

        803 CTCGGGTCAG


Statistics
Matches: 91,  Mismatches: 12, Indels: 9
        0.81            0.11        0.08

Matches are distributed among these distances:
  15   16  0.18
  16   73  0.80
  17    2  0.02

ACGTcount: A:0.07, C:0.15, G:0.40, T:0.37


Consensus pattern (16 bp):   
TTCGGGTTCGGGTATT

Found at i:738 original size:32 final size:32

Alignment explanation


    Indices: 681--802  Score: 167
    Period size: 32  Copynumber: 3.8  Consensus size: 32

        671 GGGTTCGGGT

                          *      *          *
        681 TCGGGTTCGGGTA-CTTCGGGTTCGGG-TATTT
          1 TCGGGTTCGGGTATTTTCGGGCTCGGGTTA-TG

                                          * 
        712 TCGGGTTCGGGTATTTTCGGGCTCGGGTTAAG
          1 TCGGGTTCGGGTATTTTCGGGCTCGGGTTATG

                                            
        744 TCGGGTTCGGGTATTTTCGGGCTCGGGTTATG
          1 TCGGGTTCGGGTATTTTCGGGCTCGGGTTATG

                              *  *     
        776 TCGGGTTCGGGTATTTTCAGGTTCGGG
          1 TCGGGTTCGGGTATTTTCGGGCTCGGG

        803 CTCGGGTCAG


Statistics
Matches: 82,  Mismatches: 7, Indels: 3
        0.89            0.08        0.03

Matches are distributed among these distances:
  31   13  0.16
  32   67  0.82
  33    2  0.02

ACGTcount: A:0.07, C:0.16, G:0.40, T:0.37


Consensus pattern (32 bp):   
TCGGGTTCGGGTATTTTCGGGCTCGGGTTATG

Found at i:975 original size:13 final size:12

Alignment explanation


    Indices: 952--998  Score: 51
    Period size: 13  Copynumber: 3.8  Consensus size: 12

        942 AAGTTTATTG

                        
        952 ATAATATATAAT
          1 ATAATATATAAT

                         
        964 ATAATAATATAAT
          1 ATAAT-ATATAAT

                *     * 
        977 ATAACAT-TATT
          1 ATAATATATAAT

                       
        988 ATCAATATATA
          1 AT-AATATATA

        999 TAAAGATTGA


Statistics
Matches: 29,  Mismatches: 3, Indels: 5
        0.78            0.08        0.14

Matches are distributed among these distances:
  11    5  0.17
  12   11  0.38
  13   13  0.45

ACGTcount: A:0.55, C:0.04, G:0.00, T:0.40


Consensus pattern (12 bp):   
ATAATATATAAT

Found at i:1286 original size:31 final size:31

Alignment explanation


    Indices: 1242--1323  Score: 80
    Period size: 31  Copynumber: 2.6  Consensus size: 31

       1232 TAATCAATTC

                    *                 *       
       1242 TAAATTATTACAAATTAAAACAAAT-TAAG-CAT
          1 TAAATTA-AACAAATTAAAA-AAATGAAAGTC-T

                              *             
       1274 TAAATTAAACAAA-TAATTAAAATGAAAGTCT
          1 TAAATTAAACAAATTAA-AAAAATGAAAGTCT

                               
       1305 TAAATTAAACAAATTAAAA
          1 TAAATTAAACAAATTAAAA

       1324 GCTGATAGAC


Statistics
Matches: 42,  Mismatches: 4, Indels: 9
        0.76            0.07        0.16

Matches are distributed among these distances:
  30    7  0.17
  31   24  0.57
  32   11  0.26

ACGTcount: A:0.60, C:0.07, G:0.04, T:0.29


Consensus pattern (31 bp):   
TAAATTAAACAAATTAAAAAAATGAAAGTCT
Done.