Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014391.1 Corchorus olitorius cultivar O-4 contig14424, 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: 2659
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.37


Found at i:1810 original size:5 final size:5

Alignment explanation


    Indices: 1802--1857  Score: 51
    Period size: 5  Copynumber: 10.4  Consensus size: 5

       1792 CTTTGCTTTA

                                                                *    
       1802 GTTTT GTTTT GTTTT GTATTTT GTTTTT GTTTTT GTTTT -TTTT TTTTT
          1 GTTTT GTTTT GTTTT G--TTTT G-TTTT G-TTTT GTTTT GTTTT GTTTT

                     
       1850 GCTTTT GT
          1 G-TTTT GT

       1858 GTTTTTGTTA


Statistics
Matches: 45,  Mismatches: 2, Indels: 8
        0.82            0.04        0.15

Matches are distributed among these distances:
   4    4  0.09
   5   20  0.44
   6   16  0.36
   7    5  0.11

ACGTcount: A:0.02, C:0.02, G:0.16, T:0.80


Consensus pattern (5 bp):   
GTTTT

Found at i:1813 original size:29 final size:29

Alignment explanation


    Indices: 1780--1845  Score: 80
    Period size: 29  Copynumber: 2.3  Consensus size: 29

       1770 GGGGAACTCA

                                          
       1780 TTTGTTTTGTTACTTTGCTTTAG-TTTTGT
          1 TTTGTTTTG-TACTTTGCTTTAGTTTTTGT

                       *    *   *        
       1809 TTTGTTTTGTATTTTGTTTTTGTTTTTGT
          1 TTTGTTTTGTACTTTGCTTTAGTTTTTGT

               *    
       1838 TTTTTTTT
          1 TTTGTTTT

       1846 TTTTGCTTTT


Statistics
Matches: 32,  Mismatches: 4, Indels: 2
        0.84            0.11        0.05

Matches are distributed among these distances:
  28   10  0.31
  29   22  0.69

ACGTcount: A:0.05, C:0.03, G:0.15, T:0.77


Consensus pattern (29 bp):   
TTTGTTTTGTACTTTGCTTTAGTTTTTGT

Found at i:1825 original size:12 final size:11

Alignment explanation


    Indices: 1802--1862  Score: 65
    Period size: 10  Copynumber: 5.5  Consensus size: 11

       1792 CTTTGCTTTA

                       
       1802 GTTTTG-TTTT
          1 GTTTTGTTTTT

                        
       1812 GTTTTGTATTTT
          1 GTTTTGT-TTTT

                        
       1824 GTTTTTGTTTTT
          1 G-TTTTGTTTTT

                       
       1836 GTTTT-TTTTT
          1 GTTTTGTTTTT

                         
       1846 -TTTTGCTTTTGT
          1 GTTTTG-TTTT-T

                 
       1858 GTTTT
          1 GTTTT

       1863 TGTTAATTTT


Statistics
Matches: 44,  Mismatches: 0, Indels: 11
        0.80            0.00        0.20

Matches are distributed among these distances:
   9    4  0.09
  10   11  0.25
  11    8  0.18
  12   11  0.25
  13   10  0.23

ACGTcount: A:0.02, C:0.02, G:0.16, T:0.80


Consensus pattern (11 bp):   
GTTTTGTTTTT

Found at i:1831 original size:6 final size:6

Alignment explanation


    Indices: 1803--1866  Score: 60
    Period size: 6  Copynumber: 10.2  Consensus size: 6

       1793 TTTGCTTTAG

                                                             *         
       1803 TTTTG- TTTTG- TTTTGT ATTTTGT TTTTGT TTTTGTTT TTTTTT TTTTGCT
          1 TTTTGT TTTTGT TTTTGT -TTTTGT TTTTGT TTTTG--T TTTTGT TTTTG-T

                            
       1853 TTTGTGT TTTTGT T
          1 TTT-TGT TTTTGT T

       1867 AATTTTGCAG


Statistics
Matches: 51,  Mismatches: 2, Indels: 11
        0.80            0.03        0.17

Matches are distributed among these distances:
   5   10  0.20
   6   20  0.39
   7   14  0.27
   8    7  0.14

ACGTcount: A:0.02, C:0.02, G:0.16, T:0.81


Consensus pattern (6 bp):   
TTTTGT

Found at i:1872 original size:28 final size:26

Alignment explanation


    Indices: 1820--1872  Score: 70
    Period size: 28  Copynumber: 2.0  Consensus size: 26

       1810 TTGTTTTGTA

                               **     
       1820 TTTTGTTTTTGTTTTTGTTTTTTTTT
          1 TTTTGTTTTTGTTTTTGTTAATTTTT

                                       
       1846 TTTTGCTTTTGTGTTTTTGTTAATTTT
          1 TTTTG-TTTT-TGTTTTTGTTAATTTT

       1873 GCAGGTTTAG


Statistics
Matches: 23,  Mismatches: 2, Indels: 2
        0.85            0.07        0.07

Matches are distributed among these distances:
  26    5  0.22
  27    4  0.17
  28   14  0.61

ACGTcount: A:0.04, C:0.02, G:0.13, T:0.81


Consensus pattern (26 bp):   
TTTTGTTTTTGTTTTTGTTAATTTTT
Done.