Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017534.1 Corchorus olitorius cultivar O-4 contig17567, 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: 21935
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33


Found at i:10912 original size:110 final size:112

Alignment explanation


    Indices: 10719--10949  Score: 430
    Period size: 110  Copynumber: 2.1  Consensus size: 112

      10709 GGTAGTTTTC

                                                                             
      10719 TTTATAATGGGTAGTTTTTATTTTGTTTTCGACTTTTAAAAACTGAGTTTGTGTCCAAGTCAACT
          1 TTTATAATGGGTAGTTTTTATTTTGTTTTCGACTTTTAAAAACTGAGTTTGTGTCCAAGTCAACT

                                                           
      10784 CGTGACACAAACTCGGGACTTGGTTTTATAATTAGTATAGAT-T-TA
         66 CGTGACACAAACTCGGGACTTGGTTTTATAATTAGTATAGATATATA

                                         *                                   
      10829 TTTATAATGGGTAGTTTTTATTTTGTTTTTGACTTTTAAAAACTGAGTTTGTGTCCAAGTCAACT
          1 TTTATAATGGGTAGTTTTTATTTTGTTTTCGACTTTTAAAAACTGAGTTTGTGTCCAAGTCAACT

                                                           
      10894 CGTGACACAAACTCGGGACTTGGTTTTATAATTAGTATAGATATATA
         66 CGTGACACAAACTCGGGACTTGGTTTTATAATTAGTATAGATATATA

             *       
      10941 TATATAATG
          1 TTTATAATG

      10950 CCAGATAAAT


Statistics
Matches: 117,  Mismatches: 2, Indels: 2
        0.97            0.02        0.02

Matches are distributed among these distances:
 110  106  0.91
 111    1  0.01
 112   10  0.09

ACGTcount: A:0.29, C:0.11, G:0.18, T:0.43


Consensus pattern (112 bp):   
TTTATAATGGGTAGTTTTTATTTTGTTTTCGACTTTTAAAAACTGAGTTTGTGTCCAAGTCAACT
CGTGACACAAACTCGGGACTTGGTTTTATAATTAGTATAGATATATA

Found at i:13935 original size:236 final size:233

Alignment explanation


    Indices: 13495--13959  Score: 849
    Period size: 236  Copynumber: 2.0  Consensus size: 233

      13485 AGGAAGAAGC

                                                 *                           
      13495 TTTTATTTCAGATTGAAAACTACTGTTTCCTAATTCATGCATTTTGGATGATAAACTGGAATATA
          1 TTTTATTTCAGATTGAAAACTACTGTTTCCTAATTCACGCATTTTGGATGATAAACTGGAATATA

                                                                             
      13560 ACTTTGGTGATACTTGGTGAAAATTACGGTTGGAGAAACTTGATGGTTCAATTGTTTAGCAAGCA
         66 ACTTTGGTGATACTTGGTGAAAATTACGGTTGGAGAAACTTGATGGTTCAATTGTTTAGCAAGCA

             *                                                    *          
      13625 TGTTCACCAATCCCACTATTGGAAGAGAGGATATTGGAGATTAAGGATCCTAAACGAGTATTTGG
        131 TCTTCACCAATCCCACTATTGGAAGAGAGGATATTGGAGATTAAGGATCCTAAAAGAGTATTTGG

                                                  
      13690 AGAAATGTTTGATGGTTTCCATTTAACTGATTAGATGG
        196 AGAAATGTTTGATGGTTTCCATTTAACTGATTAGATGG

                                                                             
      13728 TTTTATTTCAGATTGAAAACTACTGTTTCCTAATTCACGCATTTTGGATGATAAACTGGAATATA
          1 TTTTATTTCAGATTGAAAACTACTGTTTCCTAATTCACGCATTTTGGATGATAAACTGGAATATA

                                                   *                         
      13793 ACTTTGGTGATACTTGGTGAAAATTACGGTTGGTGGAGAGACTTGATGGTTCAATTGTTTAGCAA
         66 ACTTTGGTGATACTTGGTGAAAATTACGG-T--TGGAGAAACTTGATGGTTCAATTGTTTAGCAA

             *                                           *                   
      13858 GTATCTTCACCAATCCCACTATTGGAAGAGAGGATATTGGAGATTGAGGATCCTAAAAGAGTATT
        128 GCATCTTCACCAATCCCACTATTGGAAGAGAGGATATTGGAGATTAAGGATCCTAAAAGAGTATT

                                                 
      13923 TGGAGAAATGTTTGATGGTTTCCATTTAACTGATTAG
        193 TGGAGAAATGTTTGATGGTTTCCATTTAACTGATTAG

      13960 CAAAAATCAT


Statistics
Matches: 223,  Mismatches: 6, Indels: 3
        0.96            0.03        0.01

Matches are distributed among these distances:
 233   93  0.42
 234    1  0.00
 236  129  0.58

ACGTcount: A:0.31, C:0.12, G:0.22, T:0.35


Consensus pattern (233 bp):   
TTTTATTTCAGATTGAAAACTACTGTTTCCTAATTCACGCATTTTGGATGATAAACTGGAATATA
ACTTTGGTGATACTTGGTGAAAATTACGGTTGGAGAAACTTGATGGTTCAATTGTTTAGCAAGCA
TCTTCACCAATCCCACTATTGGAAGAGAGGATATTGGAGATTAAGGATCCTAAAAGAGTATTTGG
AGAAATGTTTGATGGTTTCCATTTAACTGATTAGATGG

Found at i:19328 original size:2 final size:2

Alignment explanation


    Indices: 19321--19352  Score: 64
    Period size: 2  Copynumber: 16.0  Consensus size: 2

      19311 TTTTCGATCC

                                                           
      19321 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

      19353 CTTGGGACTT


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   30  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Done.