Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014180.1 Corchorus olitorius cultivar O-4 contig14213, 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: 4702
ACGTcount: A:0.30, C:0.13, G:0.19, T:0.37


Found at i:314 original size:15 final size:14

Alignment explanation


    Indices: 294--323  Score: 51
    Period size: 15  Copynumber: 2.1  Consensus size: 14

        284 ATCTCTTTAA

                           
        294 TTTTCCTTGCATTAT
          1 TTTTCCTTG-ATTAT

                          
        309 TTTTCCTTGATTAT
          1 TTTTCCTTGATTAT

             
        323 T
          1 T

        324 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:1788 original size:11 final size:11

Alignment explanation


    Indices: 1772--1819  Score: 50
    Period size: 11  Copynumber: 4.7  Consensus size: 11

       1762 GAAGTTCGTG

                       
       1772 TTTGAAGACCA
          1 TTTGAAGACCA

                    ** 
       1783 TTTGAAGATAA
          1 TTTGAAGACCA

                       
       1794 TTTGAAGA-C-
          1 TTTGAAGACCA

                       
       1803 -TTGAAGACCA
          1 TTTGAAGACCA

                    
       1813 -TTGAAGA
          1 TTTGAAGA

       1820 TTTATTTCAA


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:3193 original size:15 final size:15

Alignment explanation


    Indices: 3163--3204  Score: 75
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       3153 TTACTTTGTT

                            
       3163 TTGTTTTCTAGTTTAA
          1 TTGTTTTCT-GTTTAA

                           
       3179 TTGTTTTCTGTTTAA
          1 TTGTTTTCTGTTTAA

                       
       3194 TTGTTTTCTGT
          1 TTGTTTTCTGT

       3205 CAACCTCTGT


Statistics
Matches: 26,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  15   17  0.65
  16    9  0.35

ACGTcount: A:0.12, C:0.07, G:0.14, T:0.67


Consensus pattern (15 bp):   
TTGTTTTCTGTTTAA
Done.