Primer3 Output (primer3_results.cgi release 4.1.0) https://primer3.ut.ee/cgi-bin/primer3/primer3web_results.

cgi

Primer3 Output

PRIMER PICKING RESULTS FOR

Template masking not selected

Using mispriming library humrep_and_simple.txt
Using 1-based sequence positions
OLIGO start len tm gc% any_th 3'_th hairpin rep seq
LEFT PRIMER 159 20 58.79 55.00 0.00 0.00 0.00 12.00 AAAGCAGGAGGAGGGAGATG
RIGHT PRIMER 1142 20 58.39 50.00 22.86 0.00 0.00 10.00 CTTTGCAGTCCCGGGTTTTA
SEQUENCE SIZE: 1320
INCLUDED REGION SIZE: 1320

PRODUCT SIZE: 984, PAIR ANY_TH COMPL: 0.00, PAIR 3'_TH COMPL: 0.00
TARGETS (start len
EXCLUDED REGIONS (start len

1 CCCCACAGCGGCCCCAGAGCTAGGCAGGGCAAGGTCCCCGGGGCAGCGTGGCCGGGCTGC

61 CCGTCTGGTCCCCGCTTACAAGAACCTGCAAGCTTCCCTCCTTGCTTTCCTTCTTCCCCT

121 CGGTTCCTCCCCCGCCGACCTACCTGGAGGCCGATAATAAAGCAGGAGGAGGGAGATGGA
>>>>>>>>>>>>>>>>>>>>

181 TGGACGGGAGGGCGGGGCGCCGCGTGGTGCCATAAAGCCCAGCTGGAAGGGGCCTGTCTC

241 GGGAGTGTCCAGCCCCAGGAGCCGGGGACCGTCCGCGTCGCGAGCCGGGCCAAGGCAGTG
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

301 GGCAGAGGGCAGAGGGCAGAGGGCCGGGGCTGGGGCAGAGGGCGAGTGCCCGGGAAGGCC
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

361 ATGCTGCGGGGCGCGCCAGGACTAGGCCTCACGGCGCGGAAGGGGGCCGAGGACTCTGCG
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

421 GAGGACTTGGGGGGCCCCTGCCCCGAGCCCGGGGGCGATTCGGGGGTGCTGGGGGCGAAC
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

481 GGCGCTTCCTGCAGCCGGGGCGAGGCGGAGGAGCCGGCGGGCAGGAGGCGCGCGCGGCCG
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

541 GTGCGGTCCAAGGCGCGGCGCATGGCCGCCAACGTGCGGGAGCGCAAGCGCATCCTAGAC
************************************************************

601 TACAACGAGGCCTTCAACGCGCTGCGCCGGGCGCTGCGGCACGACCTGGGCGGCAAGAGG
************************************************************

661 CTCTCCAAGATCGCCACGCTGCGCAGGGCCATCCACCGCATCGCCGCGCTCTCCCTGGTC
************************************************************

721 CTGCGCGCCAGCCCCGCGCCCCGCGGGCCCTGCGGACACCTGGAGTGCCACGGCCCGGCC
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

781 GCGCGCGGGGACACCGGGGACACAGGCGCCAGCCCCCCGCCGCCTGCAGGGCCCAGCCTC
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

841 GCGCGCCCAGACGCCGCCCGCCCCTCGGTGCCGTCCGCGCCCCGCTGCGCCTCGTGCCCC
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

901 CCGCACGCGCCCCTGGCACGGCCCAGTGCGGTGGCCGAGGGGCCGGGCCTAGCACAGGCC
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

961 TCCGGGGGAAGCTGGCGCCGCTGTCCGGGGGCTTCCTCTGCCGGGCCGCCTCCCTGGCCG
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

1021 CGGGGCTACCTGCGATCCGCCCCCGGGATGGGCCATCCGCGCTCCTGACCGGCCTCGAGG
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

1081 CACCGGCTGGGCTGCAGGGAGGCCGGGCTGGCAGCTGGACTATAAAACCCGGGACTGCAA
<<<<<<<<<<<<<<<<<<

1141 AGGCGTCTTGGACAGAGCAGAACTGGACCGGCTGAGACCTGGCGTGGAAGAGAAGGAGCT
<<

1201 CGCCAGAGAGAAGGAGCTCCGGGACCCGGGGTTGCGCCCCCACATCCCAGCCTGGGGCAG

1261 AGAGAAGGAGCTCCGGGGCCTGGGGCTGCGCCCCCACATCCCAGCCTAGGGAGGCAGTTG

KEYS (in order of precedence):

XXXXXX excluded region
****** target
>>>>>> left primer
<<<<<< right primer

ADDITIONAL OLIGOS
start len tm gc% any_th 3'_th hairpin rep seq

1 LEFT PRIMER 166 20 58.65 60.00 0.00 0.00 0.00 10.00 GAGGAGGGAGATGGATGGAC
RIGHT PRIMER 1139 21 59.09 47.62 22.86 0.00 0.00 11.00 TGCAGTCCCGGGTTTTATAGT
PRODUCT SIZE: 974, PAIR ANY_TH COMPL: 0.00, PAIR 3'_TH COMPL: 0.00

2 LEFT PRIMER 172 19 58.95 63.16 0.00 0.00 0.00 11.00 GGAGATGGATGGACGGGAG
RIGHT PRIMER 1166 20 58.19 55.00 0.00 0.00 0.00 12.00 CCAGTTCTGCTCTGTCCAAG
PRODUCT SIZE: 995, PAIR ANY_TH COMPL: 4.71, PAIR 3'_TH COMPL: 9.98

3 LEFT PRIMER 223 18 59.01 66.67 0.84 0.00 0.00 10.00 CTGGAAGGGGCCTGTCTC
RIGHT PRIMER 1197 19 59.02 57.89 0.00 0.00 0.00 11.00 TCCTTCTCTTCCACGCCAG
PRODUCT SIZE: 975, PAIR ANY_TH COMPL: 0.00, PAIR 3'_TH COMPL: 0.00

4 LEFT PRIMER 203 18 58.80 61.11 0.00 0.00 0.00 11.00 CGTGGTGCCATAAAGCCC

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Primer3 Output (primer3_results.cgi release 4.1.0) https://primer3.ut.ee/cgi-bin/primer3/primer3web_results.cgi

RIGHT PRIMER 1169 20 60.04 60.00 0.00 0.00 0.00 12.00 GGTCCAGTTCTGCTCTGTCC
PRODUCT SIZE: 967, PAIR ANY_TH COMPL: 0.00, PAIR 3'_TH COMPL: 0.00

Statistics
con too in in not no tm tm high high high high high
sid many tar excl ok bad GC too too any_th 3'_th hair- lib poly end
ered Ns get reg reg GC% clamp low high compl compl pin sim X stab ok
Left 1612 0 0 300 0 529 0 140 317 0 0 9 0 6 0 311
Right 1658 0 0 360 0 493 0 73 424 0 0 28 14 8 0 258
Pair Stats:
considered 677195, unacceptable product size 677175, tm diff too large 11, high mispriming library similarity 3, primer in pair overlaps a primer in a better pair 1151, ok 6
libprimer3 release 2.4.0

(primer3_results.cgi release 4.1.0)

2 of 2 6/6/2023, 3:58 PM