Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014478.1 Corchorus olitorius cultivar O-4 contig14511, 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: 10896
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34


Found at i:366 original size:4 final size:4

Alignment explanation


    Indices: 357--416  Score: 120
    Period size: 4  Copynumber: 15.0  Consensus size: 4

        347 ACCGCTTTGT

                                                                       
        357 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
          1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC

                          
        405 TTTC TTTC TTTC
          1 TTTC TTTC TTTC

        417 CCTCTATTCC


Statistics
Matches: 56,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   4   56  1.00

ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75


Consensus pattern (4 bp):   
TTTC

Found at i:1938 original size:2 final size:2

Alignment explanation


    Indices: 1933--1966  Score: 68
    Period size: 2  Copynumber: 17.0  Consensus size: 2

       1923 ATATATTGTG

                                                              
       1933 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

       1967 GTTAATGAAT


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   32  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:4301 original size:1 final size:1

Alignment explanation


    Indices: 4295--4330  Score: 72
    Period size: 1  Copynumber: 36.0  Consensus size: 1

       4285 TCGTGGAAGC

                                                
       4295 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

       4331 TTGTTATTGT


Statistics
Matches: 35,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   35  1.00

ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00


Consensus pattern (1 bp):   
A

Found at i:4902 original size:19 final size:18

Alignment explanation


    Indices: 4873--4914  Score: 57
    Period size: 19  Copynumber: 2.3  Consensus size: 18

       4863 GCAGTTATTT

                *         *   
       4873 TTAAGTAAAAATATGATA
          1 TTAAATAAAAATATAATA

                               
       4891 TATAAATAAAAATATAATA
          1 T-TAAATAAAAATATAATA

                 
       4910 TTAAA
          1 TTAAA

       4915 ATAATTAATT


Statistics
Matches: 21,  Mismatches: 2, Indels: 2
        0.84            0.08        0.08

Matches are distributed among these distances:
  18    5  0.24
  19   16  0.76

ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33


Consensus pattern (18 bp):   
TTAAATAAAAATATAATA

Found at i:4918 original size:19 final size:19

Alignment explanation


    Indices: 4878--4914  Score: 58
    Period size: 19  Copynumber: 2.0  Consensus size: 19

       4868 TATTTTTAAG

                     *         
       4878 TAAAAATATGATATATAAA
          1 TAAAAATATAATATATAAA

                               
       4897 TAAAAATATAATAT-TAAA
          1 TAAAAATATAATATATAAA

       4915 ATAATTAATT


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  18    4  0.24
  19   13  0.76

ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32


Consensus pattern (19 bp):   
TAAAAATATAATATATAAA

Found at i:5628 original size:17 final size:17

Alignment explanation


    Indices: 5600--5633  Score: 52
    Period size: 16  Copynumber: 2.0  Consensus size: 17

       5590 ATGTCACGTG

                             
       5600 GAAAATAAAATT-TTAA
          1 GAAAATAAAATTATTAA

                              
       5616 GAAAATAAAAATTATTAA
          1 GAAAAT-AAAATTATTAA

       5634 AATAAAGAAC


Statistics
Matches: 16,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  16    6  0.38
  17    6  0.38
  18    4  0.25

ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29


Consensus pattern (17 bp):   
GAAAATAAAATTATTAA

Found at i:8853 original size:107 final size:107

Alignment explanation


    Indices: 8729--8993  Score: 415
    Period size: 107  Copynumber: 2.5  Consensus size: 107

       8719 TTTTTATTCT

                                           *         **                      
       8729 TTTTAGAAATT-AAATATAAAATTAATGTCATTAAGTTTAGTTCCAAATTAAAATTTTAATTTAA
          1 TTTTAG-AATTAAAATATAAAATTAATGTCACTAAGTTTAGCCCCAAATTAAAATTTTAATTTAA

                  *                                    
       8793 TTTTAAGGGTAAATTCCAAAATTAATAATTTATTCTTATAGGG
         65 TTTTAAAGGTAAATTCCAAAATTAATAATTTATTCTTATAGGG

                                            *                                
       8836 TTTTAGAATTAAAATATAAAATTAATGTCACTCAGTTTAGCCCCAAATTAAAATTTTAATTTAAT
          1 TTTTAGAATTAAAATATAAAATTAATGTCACTAAGTTTAGCCCCAAATTAAAATTTTAATTTAAT

                                             *        
       8901 TTTAAAGGTAAATTCCAAAATTAATAATTTATTGTTATAGGG
         66 TTTAAAGGTAAATTCCAAAATTAATAATTTATTCTTATAGGG

                 *            *  *   *        *                
       8943 TTTTAAAATTAAAATATAGAACTAAAGTCACTAAATTTAGCCCCAAATTAA
          1 TTTTAGAATTAAAATATAAAATTAATGTCACTAAGTTTAGCCCCAAATTAA

       8994 TATATTTTTA


Statistics
Matches: 145,  Mismatches: 12, Indels: 2
        0.91            0.08        0.01

Matches are distributed among these distances:
 106    4  0.03
 107  141  0.97

ACGTcount: A:0.43, C:0.08, G:0.09, T:0.40


Consensus pattern (107 bp):   
TTTTAGAATTAAAATATAAAATTAATGTCACTAAGTTTAGCCCCAAATTAAAATTTTAATTTAAT
TTTAAAGGTAAATTCCAAAATTAATAATTTATTCTTATAGGG
Done.