Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016978.1 Corchorus olitorius cultivar O-4 contig17011, 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: 6198
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.29


Found at i:1883 original size:90 final size:91

Alignment explanation


    Indices: 1716--1886  Score: 249
    Period size: 90  Copynumber: 1.9  Consensus size: 91

       1706 ACGGTCCAGC

                                   *            *  *     *                *  
       1716 GCAATATTTCTCCAAAGATTGGAGTTCGGTGAGCTCGGTTCAGCATGTTTTCAGACAGATTATGG
          1 GCAATATTTCTCCAAAGATTGGAATTCGGTGAGCTCAGTGCAGCAGGTTTTCAGACAGATTAGGG

                                      
       1781 TGATTCGGTGAATCAATCTGGTACAG
         66 TGATTCGGTGAATCAATCTGGTACAG

                                                                    *        
       1807 GCAATATTTCGT-C-AAGATTGGAATTCGGTGAGCTCAGTGCAGCAGGTTTTCAGATA-ATTCAG
          1 GCAATATTTC-TCCAAAGATTGGAATTCGGTGAGCTCAGTGCAGCAGGTTTTCAGACAGATT-AG

                              
       1869 GGTGATTCGGTGAATCAA
         64 GGTGATTCGGTGAATCAA

       1887 GTTGATGGTG


Statistics
Matches: 72,  Mismatches: 6, Indels: 5
        0.87            0.07        0.06

Matches are distributed among these distances:
  89    3  0.04
  90   57  0.79
  91   11  0.15
  92    1  0.01

ACGTcount: A:0.26, C:0.16, G:0.27, T:0.31


Consensus pattern (91 bp):   
GCAATATTTCTCCAAAGATTGGAATTCGGTGAGCTCAGTGCAGCAGGTTTTCAGACAGATTAGGG
TGATTCGGTGAATCAATCTGGTACAG

Found at i:5355 original size:26 final size:26

Alignment explanation


    Indices: 5289--5359  Score: 72
    Period size: 26  Copynumber: 2.6  Consensus size: 26

       5279 AAAAATCCAG

                      *            * * 
       5289 GGGCATTTTGATCATTTTTCACATTCA
          1 GGGCA-TTTGGTCATTTTTCACACTAA

                                        
       5316 GTGGCATTATGGTCATTTTT-ACACTAA
          1 G-GGCATT-TGGTCATTTTTCACACTAA

                             
       5343 GGGCATTTCGGTCATTT
          1 GGGCATTT-GGTCATTT

       5360 GCATATTCAG


Statistics
Matches: 38,  Mismatches: 3, Indels: 7
        0.79            0.06        0.15

Matches are distributed among these distances:
  25    1  0.03
  26   14  0.37
  27    9  0.24
  28   14  0.37

ACGTcount: A:0.21, C:0.17, G:0.20, T:0.42


Consensus pattern (26 bp):   
GGGCATTTGGTCATTTTTCACACTAA

Found at i:5553 original size:25 final size:25

Alignment explanation


    Indices: 5524--5573  Score: 91
    Period size: 25  Copynumber: 2.0  Consensus size: 25

       5514 TAGTATTTTG

                                     
       5524 CATTCATGTAGCTCAAAGCTGATTT
          1 CATTCATGTAGCTCAAAGCTGATTT

                             *       
       5549 CATTCATGTAGCTCAAATCTGATTT
          1 CATTCATGTAGCTCAAAGCTGATTT

       5574 AATCGACTAA


Statistics
Matches: 24,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  25   24  1.00

ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38


Consensus pattern (25 bp):   
CATTCATGTAGCTCAAAGCTGATTT
Done.