Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01000950.1 Corchorus capsularis cultivar CVL-1 contig00950, 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: 5728
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35


Found at i:1898 original size:28 final size:28

Alignment explanation


    Indices: 1844--1898  Score: 69
    Period size: 28  Copynumber: 2.0  Consensus size: 28

       1834 AACAATCAGC

                                  *     
       1844 AAAAAAAATAATTAAAGATTATTTATTT
          1 AAAAAAAATAATTAAAGATTATATATTT

                                         
       1872 AAAAAAACA-AATTAAAGATGTA-ATATT
          1 AAAAAAA-ATAATTAAAGAT-TATATATT

       1899 ATATATATAT


Statistics
Matches: 24,  Mismatches: 1, Indels: 4
        0.83            0.03        0.14

Matches are distributed among these distances:
  28   21  0.88
  29    3  0.12

ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33


Consensus pattern (28 bp):   
AAAAAAAATAATTAAAGATTATATATTT

Found at i:3417 original size:158 final size:151

Alignment explanation


    Indices: 3136--3444  Score: 546
    Period size: 158  Copynumber: 2.0  Consensus size: 151

       3126 TAACTCAAAA

                                                                             
       3136 TCATACCAAGTTACTTTGTCGTTCAAATACTATTTTAGGACTTTCCAATGACTTTTCAACATGTA
          1 TCATACCAAGTTACTTTGTCGTTCAAATACTATTTTAGGACTTTCCAATGACTTTTCAACATGTA

                                                                             
       3201 CTACACTTCTTATATAATCTACACACAGTATGATTATACCAATTACATAATAGTGATATATCTTT
         66 CTACACTTCTTATATAATCTACACACAGTATGATTATACCAATTACATAATAGTGATATATCTTT

                                 
       3266 TTTTATTTTGCTTAAGAAACC
        131 TTTTATTTTGCTTAAGAAACC

                                                                             
       3287 TCATACCAAGTTACTTTGTCGTTCAAATACTATTTTAGGACTTTCCAATGACTTTTCAACAATGA
          1 TCATACCAAGTTACTTTGTCGTTCAAATACTATTTTAGGACTTTCCAATGACTTTTCAAC-----

                              *                                              
       3352 AATTGTACTACACTTCTTGTATAATCTACACACAGTATGATTATACCAATTACATAATAGTGATA
         61 -A-TGTACTACACTTCTTATATAATCTACACACAGTATGATTATACCAATTACATAATAGTGATA

                                        
       3417 TATCTTTTTTTATTTTGCTTAAGAAACC
        124 TATCTTTTTTTATTTTGCTTAAGAAACC

       3445 AATACACCCC


Statistics
Matches: 150,  Mismatches: 1, Indels: 7
        0.95            0.01        0.04

Matches are distributed among these distances:
 151   60  0.40
 157    1  0.01
 158   89  0.59

ACGTcount: A:0.33, C:0.18, G:0.09, T:0.40


Consensus pattern (151 bp):   
TCATACCAAGTTACTTTGTCGTTCAAATACTATTTTAGGACTTTCCAATGACTTTTCAACATGTA
CTACACTTCTTATATAATCTACACACAGTATGATTATACCAATTACATAATAGTGATATATCTTT
TTTTATTTTGCTTAAGAAACC

Found at i:4812 original size:16 final size:16

Alignment explanation


    Indices: 4774--4805  Score: 64
    Period size: 16  Copynumber: 2.0  Consensus size: 16

       4764 AAAACGGTAG

                            
       4774 TCAAATAAATTAATTT
          1 TCAAATAAATTAATTT

                            
       4790 TCAAATAAATTAATTT
          1 TCAAATAAATTAATTT

       4806 CTAAATATGT


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  16   16  1.00

ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44


Consensus pattern (16 bp):   
TCAAATAAATTAATTT

Found at i:5119 original size:60 final size:60

Alignment explanation


    Indices: 5026--5145  Score: 231
    Period size: 60  Copynumber: 2.0  Consensus size: 60

       5016 TTGCAACTAT

                                                                        
       5026 TTGAGTAATTCAATCCATCAACGGGTTTCCAAATTAACTTCACAATTTTGAAACATCTAA
          1 TTGAGTAATTCAATCCATCAACGGGTTTCCAAATTAACTTCACAATTTTGAAACATCTAA

                                                                *       
       5086 TTGAGTAATTCAATCCATCAACGGGTTTCCAAATTAACTTCACAATTTTGAATCATCTAA
          1 TTGAGTAATTCAATCCATCAACGGGTTTCCAAATTAACTTCACAATTTTGAAACATCTAA

       5146 ATGGGTTTGC


Statistics
Matches: 59,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  60   59  1.00

ACGTcount: A:0.36, C:0.20, G:0.10, T:0.34


Consensus pattern (60 bp):   
TTGAGTAATTCAATCCATCAACGGGTTTCCAAATTAACTTCACAATTTTGAAACATCTAA
Done.