Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012134.1 Corchorus olitorius cultivar O-4 contig12167, 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: 12929
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30


Found at i:3431 original size:15 final size:14

Alignment explanation


    Indices: 3411--3440  Score: 51
    Period size: 15  Copynumber: 2.1  Consensus size: 14

       3401 GTCTCTTTAA

                           
       3411 TTTTCCTTGCATTAT
          1 TTTTCCTTG-ATTAT

                          
       3426 TTTTCCTTGATTAT
          1 TTTTCCTTGATTAT

             
       3440 T
          1 T

       3441 GCTTTAATTG


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  14    6  0.40
  15    9  0.60

ACGTcount: A:0.13, C:0.17, G:0.07, T:0.63


Consensus pattern (14 bp):   
TTTTCCTTGATTAT

Found at i:4895 original size:11 final size:11

Alignment explanation


    Indices: 4879--4926  Score: 50
    Period size: 11  Copynumber: 4.7  Consensus size: 11

       4869 GAAGTTCGTG

                       
       4879 TTTGAAGACCA
          1 TTTGAAGACCA

                    ** 
       4890 TTTGAAGATAA
          1 TTTGAAGACCA

                       
       4901 TTTGAAGA-C-
          1 TTTGAAGACCA

                       
       4910 -TTGAAGACCA
          1 TTTGAAGACCA

                    
       4920 -TTGAAGA
          1 TTTGAAGA

       4927 TTGTTGATGC


Statistics
Matches: 32,  Mismatches: 3, Indels: 5
        0.80            0.08        0.12

Matches are distributed among these distances:
   8    7  0.22
   9    1  0.03
  10    7  0.22
  11   17  0.53

ACGTcount: A:0.40, C:0.10, G:0.21, T:0.29


Consensus pattern (11 bp):   
TTTGAAGACCA

Found at i:6329 original size:15 final size:15

Alignment explanation


    Indices: 6295--6336  Score: 57
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       6285 TTACTTTTTT

                  *      *  
       6295 TTGTTTCCTAGTTTAA
          1 TTGTTTTCT-GTTCAA

                           
       6311 TTGTTTTCTGTTCAA
          1 TTGTTTTCTGTTCAA

                       
       6326 TTGTTTTCTGT
          1 TTGTTTTCTGT

       6337 CAACCTCTGT


Statistics
Matches: 24,  Mismatches: 2, Indels: 1
        0.89            0.07        0.04

Matches are distributed among these distances:
  15   16  0.67
  16    8  0.33

ACGTcount: A:0.12, C:0.12, G:0.14, T:0.62


Consensus pattern (15 bp):   
TTGTTTTCTGTTCAA

Found at i:9222 original size:106 final size:106

Alignment explanation


    Indices: 9051--9251  Score: 348
    Period size: 106  Copynumber: 1.9  Consensus size: 106

       9041 TACTTGGTTG

                           *          *                                      
       9051 CATAACTATTTATCATGGTTTCCAATCCCATCCGAAAAATCGAATCATTTATGCTTTATATCCAT
          1 CATAACTATTTATCAGGGTTTCCAATACCATCCGAAAAATCGAATCATTTATGCTTTATATCCAT

                                                     
       9116 AATATCCTCCACCTCATCAGGATCAAGTTGGTCGCATAACT
         66 AATATCCTCCACCTCATCAGGATCAAGTTGGTCGCATAACT

                       *                 *  *             *                  
       9157 CATAACTATTTGTCAGGGTTTCCAATACCGTCGGAAAAATCGAATCCTTTATGCTTTATATCCAT
          1 CATAACTATTTATCAGGGTTTCCAATACCATCCGAAAAATCGAATCATTTATGCTTTATATCCAT

                                          
       9222 AATATCCTCCACCTCATCAGGATCAAGTTG
         66 AATATCCTCCACCTCATCAGGATCAAGTTG

       9252 ACTAGTTGCC


Statistics
Matches: 89,  Mismatches: 6, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
 106   89  1.00

ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33


Consensus pattern (106 bp):   
CATAACTATTTATCAGGGTTTCCAATACCATCCGAAAAATCGAATCATTTATGCTTTATATCCAT
AATATCCTCCACCTCATCAGGATCAAGTTGGTCGCATAACT
Done.