PRIMER PICKING RESULTS FOR hap RSRS No mispriming library specified Using 1-based sequence positions SEQUENCE SIZE: 16569 INCLUDED REGION SIZE: 650
Please take some time to look through this list of Primers recommended by the Bio-Informatics tool Primer3.
Compare to the two panels of recommendations above.
Let's start looking at the left and right primer first by itself not as a pair. We will do that later.
Please consider length, melting temperature, GC content and the 3'-ends of some of these primers.
Once you have a list of your mutations, please select a left and right primer from this list paying attention to the starting position of these primers and the length.
The Left primer's "start" position should be lower than the base pair position for the first expected mutation minus the length of primer.
The Right primer's "start" position should be higher than the base pair position for the last expected mutation plus the length of primer.
What is an indication that any of these RSRS specific primers are universal primer? e.g. it can amplify DNA of any haplogroup?
start len tm gc% any_th 3'_th hairpin seq
1 LEFT_PRIMER 15972 21 58.73 47.62 0 0 0 TAACTCCACCATTAGCACCCA
2 LEFT_PRIMER 15973 20 58.93 50 0 0 0 AACTCCACCATTAGCACCCA
3 LEFT_PRIMER 15974 20 58.93 50 0 0 0 ACTCCACCATTAGCACCCAA
4 LEFT_PRIMER 15975 21 58.91 52.38 0 0 0 CTCCACCATTAGCACCCAAAG
5 LEFT_PRIMER 15975 20 57.79 50 0 0 0 CTCCACCATTAGCACCCAAA
6 LEFT_PRIMER 15976 20 57.79 50 0 0 0 TCCACCATTAGCACCCAAAG
7 LEFT_PRIMER 15977 20 59.47 55 0 0 0 CCACCATTAGCACCCAAAGC
8 LEFT_PRIMER 16029 20 57.85 50 0 0 0 TCATGGGGAAGCAGATTTGG
9 LEFT_PRIMER 16030 20 58.88 55 0 0 0 CATGGGGAAGCAGATTTGGG
10 LEFT_PRIMER 16031 20 59.29 50 0 0 0 ATGGGGAAGCAGATTTGGGT
11 LEFT_PRIMER 16031 21 59.07 47.62 0 0 0 ATGGGGAAGCAGATTTGGGTA
12 LEFT_PRIMER 16032 20 58.62 50 0 0 0 TGGGGAAGCAGATTTGGGTA
13 LEFT_PRIMER 16032 19 58.83 52.63 0 0 0 TGGGGAAGCAGATTTGGGT
14 LEFT_PRIMER 16033 20 58.24 55 0 0 0 GGGGAAGCAGATTTGGGTAC
15 LEFT_PRIMER 16064 20 57.73 50 0 0 0 TGACTcACCCATCAACAACC
16 LEFT_PRIMER 16065 20 58.84 55 0 0 0 GACTcACCCATCAACAACCG
17 LEFT_PRIMER 16067 19 59.12 57.89 0 0 0 CTcACCCATCAACAACCGC
18 LEFT_PRIMER 16069 20 58.25 50 0 0 0 cACCCATCAACAACCGCTAT
19 LEFT_PRIMER 16070 20 58.25 50 0 0 0 ACCCATCAACAACCGCTATG
20 LEFT_PRIMER 16071 20 58.25 50 0 0 0 CCCATCAACAACCGCTATGT
21 LEFT_PRIMER 16093 20 57.98 50 0 0 0 TTCGTACATTACTGCCAGCC
22 LEFT_PRIMER 16094 20 59.1 50 0 0 0 TCGTACATTACTGCCAGCCA
23 LEFT_PRIMER 16099 20 59.26 55 0 0 0 CATTACTGCCAGCCACCATG
24 LEFT_PRIMER 16101 20 59.6 50 0 0 0 TTACTGCCAGCCACCATGAA
25 LEFT_PRIMER 16101 19 58.93 52.63 0 0 0 TTACTGCCAGCCACCATGA
26 LEFT_PRIMER 16102 20 59.37 50 0 0 0 TACTGCCAGCCACCATGAAT
27 LEFT_PRIMER 16102 19 58.93 52.63 0 0 0 TACTGCCAGCCACCATGAA
28 LEFT_PRIMER 16102 21 59.16 47.62 0 0 0 TACTGCCAGCCACCATGAATA
29 LEFT_PRIMER 16103 20 59.37 50 0 0 0 ACTGCCAGCCACCATGAATA
30 LEFT_PRIMER 16104 20 58.01 50 0 0 0 CTGCCAGCCACCATGAATAT
31 LEFT_PRIMER 16105 21 58.97 47.62 0 0 0 TGCCAGCCACCATGAATATTG
32 LEFT_PRIMER 16166 21 58.74 47.62 0 0 0 ACCCAAtCCAcATCAAAACcC
33 LEFT_PRIMER 16231 21 58.78 47.62 0 0 0 TCACACATCAaCtGCAACTCC
34 LEFT_PRIMER 16232 21 59.05 47.62 0 0 0 CACACATCAaCtGCAACTCCA
35 LEFT_PRIMER 16238 20 58.97 50 0 0 0 TCAaCtGCAACTCCAAAGCC
36 LEFT_PRIMER 16239 20 59.25 50 0 0 0 CAaCtGCAACTCCAAAGCCA
37 LEFT_PRIMER 16240 20 59.25 50 0 0 0 AaCtGCAACTCCAAAGCCAC
38 LEFT_PRIMER 16278 21 59.15 47.62 0 0 0 tCAACAAACCTAcCcacCCTt
39 LEFT_PRIMER 16346 20 57.97 55 0 0 0 GTCAAATCCcTTCTCGtCCC
40 LEFT_PRIMER 16347 20 59.09 55 0 0 0 TCAAATCCcTTCTCGtCCCC
41 LEFT_PRIMER 16348 20 59.38 55 0 0 0 CAAATCCcTTCTCGtCCCCA
42 LEFT_PRIMER 16349 20 58.4 50 0 0 0 AAATCCcTTCTCGtCCCCAT
43 LEFT_PRIMER 16350 20 59.16 55 0 0 0 AATCCcTTCTCGtCCCCATG
44 LEFT_PRIMER 16395 19 59.02 57.89 0 0 0 CTTGACCACCATCCTCCGT
45 LEFT_PRIMER 16410 21 58.78 47.62 0 0 0 CCGTGAAATCAATATCCCGCA
46 LEFT_PRIMER 16436 19 59.27 63.16 0 0 0 GTGCTACTCTCCTCGCTCC
47 LEFT_PRIMER 16524 20 57.96 50 0 0 0 AAGCCTAAATAGCCCACACG
48 LEFT_PRIMER 16525 20 59.09 50 0 0 0 AGCCTAAATAGCCCACACGT
49 LEFT_PRIMER 16526 20 58.25 50 0 0 0 GCCTAAATAGCCCACACGTT
50 LEFT_PRIMER 16536 20 57.79 50 0 0 0 CCCACACGTTCCCCTTAAAT
start len tm gc% any_th 3'_th hairpin seq
1 RIGHT_PRIMER 16555 20 57.79 50 0 0 0 ATTTAAGGGGAACGTGTGGG
2 RIGHT_PRIMER 16454 19 59.27 63.16 0 0 0 GGAGCGAGGAGAGTAGCAC
3 RIGHT_PRIMER 16413 19 59.02 57.89 0 0 0 ACGGAGGATGGTGGTCAAG
4 RIGHT_PRIMER 16369 20 59.16 55 0 0 0 CATGGGGaCGAGAAgGGATT
5 RIGHT_PRIMER 16368 20 58.4 50 0 0 0 ATGGGGaCGAGAAgGGATTT
6 RIGHT_PRIMER 16367 20 59.38 55 0 0 0 TGGGGaCGAGAAgGGATTTG
7 RIGHT_PRIMER 16366 20 59.09 55 0 0 0 GGGGaCGAGAAgGGATTTGA
8 RIGHT_PRIMER 16365 20 57.97 55 0 0 0 GGGaCGAGAAgGGATTTGAC
9 RIGHT_PRIMER 16298 21 59.15 47.62 0 0 0 aAGGgtgGgTAGGTTTGTTGa
10 RIGHT_PRIMER 16297 20 58.47 50 0 0 0 AGGgtgGgTAGGTTTGTTGa
11 RIGHT_PRIMER 16259 20 59.25 50 0 0 0 GTGGCTTTGGAGTTGCaGtT
12 RIGHT_PRIMER 16258 20 59.25 50 0 0 0 TGGCTTTGGAGTTGCaGtTG
13 RIGHT_PRIMER 16257 20 58.97 50 0 0 0 GGCTTTGGAGTTGCaGtTGA
14 RIGHT_PRIMER 16252 21 59.05 47.62 0 0 0 TGGAGTTGCaGtTGATGTGTG
15 RIGHT_PRIMER 16251 21 58.78 47.62 0 0 0 GGAGTTGCaGtTGATGTGTGA
16 RIGHT_PRIMER 16191 20 59.59 55 0 0 0 GGgGaGgGTTTTGATgTGGa
17 RIGHT_PRIMER 16186 21 58.74 47.62 0 0 0 GgGTTTTGATgTGGaTTGGGT
18 RIGHT_PRIMER 16126 21 58.97 47.62 0 0 0 aCAATATTCATGGTGGCTGGC
19 RIGHT_PRIMER 16125 21 58.97 47.62 0 0 0 CAATATTCATGGTGGCTGGCA
20 RIGHT_PRIMER 16123 20 58.01 50 10.94 10.94 0 ATATTCATGGTGGCTGGCAG
21 RIGHT_PRIMER 16122 20 59.37 50 17.16 0 0 TATTCATGGTGGCTGGCAGT
22 RIGHT_PRIMER 16122 21 59.16 47.62 17.16 2.72 0 TATTCATGGTGGCTGGCAGTA
23 RIGHT_PRIMER 16121 20 59.37 50 17.16 2.72 0 ATTCATGGTGGCTGGCAGTA
24 RIGHT_PRIMER 16120 20 59.6 50 17.16 1.38 0 TTCATGGTGGCTGGCAGTAA
25 RIGHT_PRIMER 16120 19 58.93 52.63 17.16 2.72 0 TTCATGGTGGCTGGCAGTA
26 RIGHT_PRIMER 16119 19 58.93 52.63 17.16 1.38 0 TCATGGTGGCTGGCAGTAA
27 RIGHT_PRIMER 16115 20 58.62 55 17.16 6.4 0 GGTGGCTGGCAGTAATGTAC
28 RIGHT_PRIMER 16114 20 58.99 55 17.16 0 0 GTGGCTGGCAGTAATGTACG
29 RIGHT_PRIMER 16113 20 59.1 50 17.16 0 0 TGGCTGGCAGTAATGTACGA
30 RIGHT_PRIMER 16112 20 57.98 50 17.16 0 0 GGCTGGCAGTAATGTACGAA
31 RIGHT_PRIMER 16089 20 58.25 50 0 0 0 CATAGCGGTTGTTGATGGGT
32 RIGHT_PRIMER 16088 20 58.25 50 0 0 0 ATAGCGGTTGTTGATGGGTg
33 RIGHT_PRIMER 16087 20 59.31 50 0 0 0 TAGCGGTTGTTGATGGGTgA
34 RIGHT_PRIMER 16085 19 59.12 57.89 0 0 0 GCGGTTGTTGATGGGTgAG
35 RIGHT_PRIMER 16084 20 58.84 55 0 0 0 CGGTTGTTGATGGGTgAGTC
36 RIGHT_PRIMER 16083 20 57.73 50 0 0 0 GGTTGTTGATGGGTgAGTCA
37 RIGHT_PRIMER 16053 20 58.24 55 0 0 0 GGTACCCAAATCTGCTTCCC
38 RIGHT_PRIMER 16052 20 58.24 55 0 0 0 GTACCCAAATCTGCTTCCCC
39 RIGHT_PRIMER 16051 20 58.62 50 0 0 0 TACCCAAATCTGCTTCCCCA
40 RIGHT_PRIMER 16051 21 59.07 47.62 0 0 0 TACCCAAATCTGCTTCCCCAT
41 RIGHT_PRIMER 16050 20 59.29 50 0 0 0 ACCCAAATCTGCTTCCCCAT
42 RIGHT_PRIMER 16050 19 58.83 52.63 0 0 0 ACCCAAATCTGCTTCCCCA
43 RIGHT_PRIMER 16049 20 58.88 55 0 0 0 CCCAAATCTGCTTCCCCATG
44 RIGHT_PRIMER 16048 20 57.85 50 0 0 0 CCAAATCTGCTTCCCCATGA
45 RIGHT_PRIMER 15996 20 59.47 55 0 0 0 GCTTTGGGTGCTAATGGTGG
46 RIGHT_PRIMER 15995 21 58.91 52.38 0 0 0 CTTTGGGTGCTAATGGTGGAG
47 RIGHT_PRIMER 15995 20 57.79 50 0 0 0 CTTTGGGTGCTAATGGTGGA
48 RIGHT_PRIMER 15994 20 57.79 50 0 0 0 TTTGGGTGCTAATGGTGGAG
49 RIGHT_PRIMER 15993 20 58.93 50 0 0 0 TTGGGTGCTAATGGTGGAGT
50 RIGHT_PRIMER 15992 20 58.93 50 0 0 0 TGGGTGCTAATGGTGGAGTT
Statistics
con too in in not no tm tm high high high high
sid many tar excl ok bad GC too too any_th 3'_th hair- poly end
ered Ns get reg reg GC% clamp low high compl compl pin X stab ok
Left 3323 0 0 0 0 244 0 1681 299 0 0 424 114 0 485
Right 3323 0 0 0 0 244 0 1681 299 0 0 455 114 0 467
Pair Stats:
considered 0, ok 0
libprimer3 release 2.3.7
(primer3_results.cgi release 4.0.0)