| blob | 2ab7aa6b816e68b9609dde57d7dca3274597ac1f |
1 ---
2 # indicator is the field that is used to test for form submission
3 indicator: submit
4 # Start listing the form elements
5 action: update
6 elements:
8 - type: Block
9 tag: p
10 elements:
11 - type: Block
12 tag: table
13 elements:
14 - type: Block
15 tag: tr
16 elements:
17 - type: Block
18 tag: td
19 elements:
20 - type: Select
21 label: "Paste source sequence below (5'->3', string of ACGTNacgtn -- other letters treated as N -- numbers and blanks ignored). FASTA format ok. Please N-out undesirable sequence (vector, ALUs, LINEs, etc.) or use a Mispriming Library (repeat library):"
22 name: PRIMER_MISPRIMING_LIBRARY
23 attributes:
24 title: "This selection indicates what mispriming library (if any) Primer3 should use to screen for interspersed repeats or for other sequence to avoid as a location for primers. The human and rodent libraries on the web page are adapted from Repbase (J. Jurka, A.F.A. Smit, C. Pethiyagoda, et al., 1995-1996) ftp://ftp.ncbi.nih.gov/repository/repbase). The human library is humrep.ref concatenated with simple.ref, translated to FASTA format. There are two rodent libraries. One is rodrep.ref translated to FASTA format, and the other is rodrep.ref concatenated with simple.ref, translated to FASTA format.
26 The Drosophila library is the concatenation of two libraries from the Berkeley Drosophila Genome Project:
28 1. A library of transposable elements The transposable elements of the Drosophila melanogaster euchromatin - a genomics perspective J.S. Kaminker, C.M. Bergman, B. Kronmiller, J. Carlson, R. Svirskas, S. Patel, E. Frise, D.A. Wheeler, S.E. Lewis, G.M. Rubin, M. Ashburner and S.E. Celniker Genome Biology (2002) 3(12):research0084.1-0084.20, http://www.fruitfly.org/p_disrupt/datasets/ASHBURNER/D_mel_transposon_sequence_set.fasta
30 2. A library of repetitive DNA sequences http://www.fruitfly.org/sequence/sequence_db/na_re.dros. "
31 options:
32 - [ '', 'NONE' ]
33 - [ 'static/documents/primer3-libraries/human.txt', 'HUMAN' ]
34 - [ 'static/documents/primer3-libraries/rodent_and_simple.txt', 'RODENT_AND_SIMPLE' ]
35 - [ 'static/documents/primer3-libraries/rodent.txt', 'RODENT' ]
36 - [ 'static/documents/primer3-libraries/drosophila.txt', 'DROSOPHILA' ]
38 - type: Block
39 tag: tr
40 elements:
41 - type: Block
42 tag: td
43 elements:
44 - type: Textarea
45 name: SEQUENCE_TEMPLATE
46 cols: 100
47 rows: 10
53 ##### Pick left primer, internal oligo, right primer #####
55 - type: Block
56 tag: p
57 elements:
58 - type: Block
59 tag: table border="1"
60 elements:
61 - type: Block
62 tag: tr
63 elements:
64 - type: Block
65 tag: td
66 elements:
67 - type: Checkbox
68 name: PRIMER_PICK_LEFT_PRIMER
69 label: "Pick left primer, or use left primer below:"
70 default: 1
71 - type: Block
72 tag: td
73 elements:
74 - type: Checkbox
75 name: PRIMER_PICK_INTERNAL_OLIGO
76 label: "Pick hybridization probe (internal oligo), or use oligo below:"
77 default: 0
78 - type: Block
79 tag: td
80 elements:
81 - type: Checkbox
82 name: PRIMER_PICK_RIGHT_PRIMER
83 label: "Pick right primer, or use right primer below (5' to 3' on opposite strand): "
84 default: 1
85 - type: Block
86 tag: tr
87 elements:
88 - type: Block
89 tag: td
90 elements:
91 - type: Text
92 name: SEQUENCE_PRIMER
93 attributes:
94 size: 30
95 - type: Block
96 tag: td
97 elements:
98 - type: Text
99 name: SEQUENCE_INTERNAL_OLIGO
100 attributes:
101 size: 30
102 - type: Block
103 tag: td
104 elements:
105 - type: Text
106 name: SEQUENCE_PRIMER_REVCOMP
107 attributes:
108 size: 30
111 ###### Sequence ID, Targets, Excluded Regions Table ######
113 - type: Block
114 tag: p
115 elements:
116 - type: Block
117 tag: table
118 elements:
119 - type: Block
120 tag: tr
121 elements:
122 - type: Block
123 tag: td style="color:blue;"
124 elements:
125 - type: Block
126 content: "Sequence Id:"
127 attributes:
128 title: An identifier that is reproduced in the output to enable you to identify the chosen primers.
129 - type: Block
130 tag: td
131 elements:
132 - type: Text
133 name: SEQUENCE_ID
134 - type: Block
135 tag: td
136 elements:
137 - type: Block
138 content: "A string to identify your output."
139 - type: Block
140 tag: tr
141 elements:
142 - type: Block
143 tag: td style="color:blue;"
144 elements:
145 - type: Block
146 content: "Targets:"
147 attributes:
148 title: "If one or more Targets is specified then a legal primer pair must flank at least one of them. A Target might be a simple sequence repeat site (for example a CA repeat) or a single-base-pair polymorphism. The value should be a space-separated list of
150 start,length
152 pairs where start is the index of the first base of a Target, and length is its length."
153 - type: Block
154 tag: td
155 elements:
156 - type: Text
157 name: SEQUENCE_TARGET
158 - type: Block
159 tag: td
160 elements:
161 - type: Block
162 content: "E.g. 50,2 requires primers to surround the 2 bases at positions 50 and 51."
163 - type: Block
164 tag: tr
165 elements:
166 - type: Block
167 tag: td style="color:blue;"
168 elements:
169 - type: Block
170 content: "Excluded Regions: "
171 attributes:
172 title: "Primer oligos may not overlap any region specified in this tag. The associated value must be a space-separated list of
174 start,length
176 pairs where start is the index of the first base of the excluded region, and length is its length. This tag is useful for tasks such as excluding regions of low sequence quality or for excluding regions containing repetitive elements such as ALUs or LINEs."
177 - type: Block
178 tag: td
179 elements:
180 - type: Text
181 name: SEQUENCE_EXCLUDED_REGION
182 - type: Block
183 tag: td
184 elements:
185 - type: Block
186 content: "E.g. 401,7 68,3 forbids selection of primers in the 7 bases starting at 401 and the 3 bases at 68."
188 - type: Block
189 tag: p
190 elements:
191 - type: Block
192 tag: table
193 elements:
194 - type: Block
195 tag: tr
196 elements:
197 - type: Block
198 tag: td style="color:blue;"
199 elements:
200 - type: Block
201 content: "Product Size Ranges:"
202 attributes:
203 title: "A list of product size ranges, for example
205 150-250 100-300 301-400
207 Primer3 first tries to pick primers in the first range. If that is not possible, it goes to the next range and tries again. It continues in this way until it has either picked all necessary primers or until there are no more ranges. For technical reasons this option makes much lighter computational demands than the Product Size option."
208 - type: Block
209 tag: td
210 elements:
211 - type: Text
212 name: PRIMER_PRODUCT_SIZE_RANGE
213 default: 100-300
214 attributes:
215 size: 70
219 ##### Number to Return, Max 3' Stability, ... #####
221 - type: Block
222 tag: p
223 elements:
224 - type: Block
225 tag: table
226 elements:
227 - type: Block
228 tag: tr
229 elements:
230 - type: Block
231 tag: td style="color:blue;"
232 elements:
233 - type: Block
234 content: "Number to Return (max 10):"
235 attributes:
236 title: "The maximum number of primer pairs to return. Primer pairs returned are sorted by their 'quality', in other words by the value of the objective function (where a lower number indicates a better primer pair). Caution: setting this parameter to a large value will increase running time."
237 - type: Block
238 tag: td
239 elements:
240 - type: Text
241 name: PRIMER_NUM_RETURN
242 default: 5
243 - type: Block
244 tag: td style="color:blue;"
245 elements:
246 - type: Block
247 content: "Max 3' Stability:"
248 attributes:
249 title: "The maximum stability for the last five 3' bases of a left or right primer. Bigger numbers mean more stable 3' ends. The value is the maximum delta G (kcal/mol) for duplex disruption for the five 3' bases as calculated using the Nearest-Neighbor parameter values specified by the option of 'Table of thermodynamic parameters'. For example if the table of thermodynamic parameters suggested by SantaLucia 1998, DOI:10.1073/pnas.95.4.1460 is used the deltaG values for the most stable and for the most labile 5mer duplex are 6.86 kcal/mol (GCGCG) and 0.86 kcal/mol (TATAT) respectively. If the table of thermodynamic parameters suggested by Breslauer et al. 1986, 10.1073/pnas.83.11.3746 is used the deltaG values for the most stable and for the most labile 5mer are 13.4 kcal/mol (GCGCG) and 4.6 kcal/mol (TATAC) respectively."
250 - type: Block
251 tag: td
252 elements:
253 - type: Text
254 name: PRIMER_MAX_END_STABILITY
255 default: 9.0
256 - type: Block
257 tag: tr
258 elements:
259 - type: Block
260 tag: td style="color:blue;"
261 elements:
262 - type: Block
263 content: "Max Repeat Mispriming:"
264 attributes:
265 title: "The maximum allowed weighted similarity with any sequence in Mispriming Library. Default is 12."
266 - type: Block
267 tag: td
268 elements:
269 - type: Text
270 name: PRIMER_MAX_LIBRARY_MISPRIMING
271 default: 12.00
272 - type: Block
273 tag: td style="color:blue;"
274 elements:
275 - type: Block
276 content: "Pair Max Repeat Mispriming:"
277 attributes:
278 title: "The maximum allowed sum of similarities of a primer pair (one similarity for each primer) with any single sequence in Mispriming Library. Library sequence weights are not used in computing the sum of similarities."
279 - type: Block
280 tag: td
281 elements:
282 - type: Text
283 name: PRIMER_PAIR_MAX_LIBRARY_MISPRIMING
284 default: 24.00
285 - type: Block
286 tag: tr
287 elements:
288 - type: Block
289 tag: td style="color:blue;"
290 elements:
291 - type: Block
292 content: "Max Template Mispriming: "
293 attributes:
294 title: "The maximum allowed similarity to ectopic sites in the sequence from which you are designing the primers. The scoring system is the same as used for Max Mispriming, except that an ambiguity code is never treated as a consensus."
295 - type: Block
296 tag: td
297 elements:
298 - type: Text
299 name: PRIMER_MAX_TEMPLATE_MISPRIMING
300 default: 12.00
301 - type: Block
302 tag: td style="color:blue;"
303 elements:
304 - type: Block
305 content: "Pair Max Template Mispriming: "
306 attributes:
307 title: "The maximum allowed summed similarity of both primers to ectopic sites in the sequence from which you are designing the primers. The scoring system is the same as used for Max Mispriming, except that an ambiguity code is never treated as a consensus."
308 - type: Block
309 tag: td
310 elements:
311 - type: Text
312 name: PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING
313 default: 24.00
315 - type: Submit
316 name: submit
317 value: Pick Primers
319 - type: Block
320 tag: h2
321 elements:
322 - type: Block
323 content: "General Primer Picking Conditions"
325 - type: Block
326 tag: p
327 elements:
328 - type: Block
329 tag: table
330 elements:
331 - type: Block
332 tag: tr
333 elements:
334 - type: Block
335 tag: td style="color:blue;"
336 elements:
337 - type: Block
338 content: "Primer Size"
339 attributes:
340 title: "Minimum, Optimum, and Maximum lengths (in bases) of a primer oligo. Primer3 will not pick primers shorter than Min or longer than Max, and with default arguments will attempt to pick primers close with size close to Opt. Min cannot be smaller than 1. Max cannot be larger than 36. (This limit is governed by maximum oligo size for which melting-temperature calculations are valid.) Min cannot be greater than Max."
341 - type: Block
342 tag: td
343 elements:
344 - type: Text
345 name: PRIMER_MIN_SIZE
346 label: Min
347 default: 18
348 attributes:
349 size: 10
350 - type: Block
351 tag: td
352 elements:
353 - type: Text
354 name: PRIMER_OPT_SIZE
355 label: Opt
356 default: 20
357 attributes:
358 size: 10
359 - type: Block
360 tag: td
361 elements:
362 - type: Text
363 name: PRIMER_MAX_SIZE
364 label: Max
365 default: 27
366 attributes:
367 size: 10
368 - type: Block
369 tag: tr
370 elements:
371 - type: Block
372 tag: td style="color:blue;"
373 elements:
374 - type: Block
375 content: "Primer Tm"
376 attributes:
377 title: "Minimum, Optimum, and Maximum melting temperatures (Celsius) for a primer oligo. Primer3 will not pick oligos with temperatures smaller than Min or larger than Max, and with default conditions will try to pick primers with melting temperatures close to Opt.
379 By default Primer3 uses the oligo melting temperature formula and the table of thermodynamic parameters given in Breslauer et al. 1986, DOI:10.1073/pnas.83.11.3746 For more information see caption Table of thermodynamic parameters"
380 - type: Block
381 tag: td
382 elements:
383 - type: Text
384 name: PRIMER_MIN_TM
385 label: Min
386 default: 57.0
387 attributes:
388 size: 10
389 - type: Block
390 tag: td
391 elements:
392 - type: Text
393 name: PRIMER_OPT_TM
394 label: Opt
395 default: 60.0
396 attributes:
397 size: 10
398 - type: Block
399 tag: td
400 elements:
401 - type: Text
402 name: PRIMER_MAX_TM
403 label: Max
404 default: 63.0
405 attributes:
406 size: 10
407 - type: Block
408 tag: td style="color:blue;"
409 elements:
410 - type: Block
411 content: "Max Tm Difference"
412 attributes:
413 title: "Maximum acceptable (unsigned) difference between the melting temperatures of the left and right primers."
414 - type: Block
415 tag: td
416 elements:
417 - type: Text
418 name: PRIMER_PAIR_MAX_DIFF_TM
419 default: 100.0
420 attributes:
421 size: 10
422 - type: Block
423 tag: tr
424 elements:
425 - type: Block
426 tag: td style="color:blue;"
427 elements:
428 - type: Block
429 content: "Product Tm"
430 attributes:
431 title: "The minimum, optimum, and maximum melting temperature of the amplicon. Primer3 will not pick a product with melting temperature less than min or greater than max. If Opt is supplied and the Penalty Weights for Product Size are non-0 Primer3 will attempt to pick an amplicon with melting temperature close to Opt.
433 The maximum allowed melting temperature of the amplicon. Primer3 calculates product Tm calculated using the formula from Bolton and McCarthy, PNAS 84:1390 (1962) as presented in Sambrook, Fritsch and Maniatis, Molecular Cloning, p 11.46 (1989, CSHL Press).
435 Tm = 81.5 + 16.6(log10([Na+])) + .41*(%GC) - 600/length,
437 where [Na+] is the molar sodium concentration, (%GC) is the percent of Gs and Cs in the sequence, and length is the length of the sequence.
439 A similar formula is used by the prime primer selection program in GCG (http://www.accelrys.com/products/gcg/), which instead uses 675.0 / length in the last term (after F. Baldino, Jr, M.-F. Chesselet, and M.E. Lewis, Methods in Enzymology 168:766 (1989) eqn (1) on page 766 without the mismatch and formamide terms). The formulas here and in Baldino et al. assume Na+ rather than K+. According to J.G. Wetmur, Critical Reviews in BioChem. and Mol. Bio. 26:227 (1991) 50 mM K+ should be equivalent in these formulae to .2 M Na+. Primer3 uses the same salt concentration value for calculating both the primer melting temperature and the oligo melting temperature. If you are planning to use the PCR product for hybridization later this behavior will not give you the Tm under hybridization conditions."
440 - type: Block
441 tag: td
442 elements:
443 - type: Text
444 name: PRIMER_PRODUCT_MIN_TM
445 label: Min
446 attributes:
447 size: 10
448 - type: Block
449 tag: td
450 elements:
451 - type: Text
452 name: PRIMER_PRODUCT_OPT_TM
453 label: Opt
454 attributes:
455 size: 10
456 - type: Block
457 tag: td
458 elements:
459 - type: Text
460 name: PRIMER_PRODUCT_MAX_TM
461 label: Max
462 attributes:
463 size: 10
464 - type: Block
465 tag: td style="color:blue;"
466 elements:
467 - type: Block
468 content: "Table of Thermodynamic Parameters"
469 attributes:
470 title: "Option for the table of Nearest-Neighbor thermodynamic parameters and for the method of melting temperature calculation. Two different tables of thermodynamic parameters are available:
472 Breslauer et al. 1986, DOI:10.1073/pnas.83.11.3746 In that case the formula for melting temperature calculation suggested by Rychlik et al. 1990 is used (this is used until Primer3 version 1.0.1). This is the default value of Primer3 (for backward compatibility).
473 SantaLucia 1998, DOI:10.1073/pnas.95.4.1460 This is the recommended value.
475 For specifying the salt correction method for melting temperature calculation see Salt correction formula."
476 - type: Block
477 tag: td
478 elements:
479 - type: Select
480 name: PRIMER_TM_FORMULA
481 options:
482 - ['0', 'Breslauer et al. 1986' ]
483 - ['1', 'SantaLucia' ]
484 - type: Block
485 tag: tr
486 elements:
487 - type: Block
488 tag: td style="color:blue;"
489 elements:
490 - type: Block
491 content: "Primer GC%"
492 attributes:
493 title: "Minimum, Optimum, and Maximum percentage of Gs and Cs in any primer or oligo."
494 - type: Block
495 tag: td
496 elements:
497 - type: Text
498 name: PRIMER_MIN_GC
499 label: Min
500 default: 20.0
501 attributes:
502 size: 10
503 - type: Block
504 tag: td
505 elements:
506 - type: Text
507 name: PRIMER_OPT_GC_PERCENT
508 label: Opt
509 attributes:
510 size: 10
511 - type: Block
512 tag: td
513 elements:
514 - type: Text
515 name: PRIMER_MAX_GC
516 label: Max
517 default: 80.0
518 attributes:
519 size: 10
521 ##### Max Self Complementarity, Max #Ns's, ... #####
523 - type: Block
524 tag: p
525 elements:
526 - type: Block
527 tag: table
528 elements:
529 - type: Block
530 tag: tr
531 elements:
532 - type: Block
533 tag: td style="color:blue;"
534 elements:
535 - type: Block
536 content: "Max Self Complementarity:"
537 attributes:
538 title: "The maximum allowable local alignment score when testing a single primer for (local) self-complementarity and the maximum allowable local alignment score when testing for complementarity between left and right primers. Local self-complementarity is taken to predict the tendency of primers to anneal to each other without necessarily causing self-priming in the PCR. The scoring system gives 1.00 for complementary bases, -0.25 for a match of any base (or N) with an N, -1.00 for a mismatch, and -2.00 for a gap. Only single-base-pair gaps are allowed. Scores are non-negative, and a score of 0.00 indicates that there is no reasonable local alignment between two oligos. "
539 - type: Block
540 tag: td
541 elements:
542 - type: Text
543 name: PRIMER_MAX_SELF_ANY
544 default: 8.00
545 - type: Block
546 tag: td style="color:blue;"
547 elements:
548 - type: Block
549 content: Max 3' Self Complementarity
550 attributes:
551 title: "The maximum allowable 3'-anchored global alignment score when testing a single primer for self-complementarity, and the maximum allowable 3'-anchored global alignment score when testing for complementarity between left and right primers. The 3'-anchored global alignment score is taken to predict the likelihood of PCR-priming primer-dimers."
552 - type: Block
553 tag: td
554 elements:
555 - type: Text
556 name: PRIMER_MAX_SELF_END
557 default: 3.00
558 - type: Block
559 tag: tr
560 elements:
561 - type: Block
562 tag: td style="color:blue;"
563 elements:
564 - type: Block
565 content: "Max #N's:"
566 attributes:
567 title: "Maximum number of unknown bases (N) allowable in any primer."
568 - type: Block
569 tag: td
570 elements:
571 - type: Text
572 name: PRIMER_MAX_NS_ACCEPTED
573 default: 0
574 - type: Block
575 tag: td style="color:blue;"
576 elements:
577 - type: Block
578 content: "Max Poly-X:"
579 attributes:
580 title: "The maximum allowable length of a mononucleotide repeat, for example AAAAAA."
581 - type: Block
582 tag: td
583 elements:
584 - type: Text
585 name: PRIMER_MAX_POLY_X
586 default: 5
587 - type: Block
588 tag: tr
589 elements:
590 - type: Block
591 tag: td style="color:blue;"
592 elements:
593 - type: Block
594 content: "Inside Target Penalty:"
595 attributes:
596 title: "Non-default values valid only for sequences with 0 or 1 target regions. If the primer is part of a pair that spans a target and overlaps the target, then multiply this value times the number of nucleotide positions by which the primer overlaps the (unique) target to get the 'position penalty'. The effect of this parameter is to allow Primer3 to include overlap with the target as a term in the objective function."
597 - type: Block
598 tag: td
599 elements:
600 - type: Text
601 name: PRIMER_INSIDE_PENALTY
602 - type: Block
603 tag: td style="color:blue;"
604 elements:
605 - type: Block
606 content: "Outside Target Penalty:"
607 attributes:
608 title: "Non-default values valid only for sequences with 0 or 1 target regions. If the primer is part of a pair that spans a target and does not overlap the target, then multiply this value times the number of nucleotide positions from the 3' end to the (unique) target to get the 'position penalty'. The effect of this parameter is to allow Primer3 to include nearness to the target as a term in the objective function."
609 - type: Block
610 tag: td
611 elements:
612 - type: Text
613 name: PRIMER_OUTSIDE_PENALTY
614 default: 0
615 - type: Block
616 tag: tr
617 elements:
618 - type: Block
619 tag: td style="color:blue;"
620 elements:
621 - type: Block
622 content: "First Base Index:"
623 attributes:
624 title: "The index of the first base in the input sequence. For input and output using 1-based indexing (such as that used in GenBank and to which many users are accustomed) set this parameter to 1. For input and output using 0-based indexing set this parameter to 0. (This parameter also affects the indexes in the contents of the files produced when the primer file flag is set.) In the WWW interface this parameter defaults to 1."
625 - type: Block
626 tag: td
627 elements:
628 - type: Text
629 name: PRIMER_FIRST_BASE_INDEX
630 default: 1
631 - type: Block
632 tag: td style="color:blue;"
633 elements:
634 - type: Block
635 content: "GC Clamp:"
636 attributes:
637 title: "Require the specified number of consecutive Gs and Cs at the 3' end of both the left and right primer. (This parameter has no effect on the hybridization oligo if one is requested.)"
638 - type: Block
639 tag: td
640 elements:
641 - type: Text
642 name: PRIMER_GC_CLAMP
643 default: 0
644 - type: Block
645 tag: tr
646 elements:
647 - type: Block
648 tag: td style="color:blue;"
649 elements:
650 - type: Block
651 content: "Concentration of monovalent cations:"
652 attributes:
653 title: "The millimolar concentration of salt (usually KCl) in the PCR. Primer3 uses this argument to calculate oligo melting temperatures."
654 - type: Block
655 tag: td
656 elements:
657 - type: Text
658 name: PRIMER_SALT_MONOVALENT
659 default: 50.0
660 - type: Block
661 tag: td style="color:blue;"
662 elements:
663 - type: Block
664 content: "Salt correction formula:"
665 attributes:
666 title: "Option for specifying the salt correction formula for the melting temperature calculation. There are three different options available: (1) Schildkraut and Lifson 1965, DOI:10.1002/bip.360030207 (this is used until the version 1.0.1 of Primer3).The default value of Primer3 version 1.1.0 (for backward compatibility) (2) SantaLucia 1998, DOI:10.1073/pnas.95.4.1460 This is the recommended value. (3) Owczarzy et al. 2004, DOI:10.1021/bi034621r"
667 - type: Block
668 tag: td
669 elements:
670 - type: Select
671 name: PRIMER_SALT_CORRECTIONS
672 options:
673 - ['0', 'Schildkraut and Lifson 1965' ]
674 - ['1', 'SantaLucia 1998' ]
675 - ['2', 'Owczarzy et. 2004' ]
676 - type: Block
677 tag: tr
678 elements:
679 - type: Block
680 tag: td style="color:blue;"
681 elements:
682 - type: Block
683 content: "Concentration of divalent cations:"
684 attributes:
685 title: "The millimolar concentration of divalent salt cations (usually MgCl2+ in the PCR). Primer3 converts concentration of divalent cations to concentration of monovalent cations using formula suggested in the paper Ahsen et al., 2001.
686 According to the formula concentration of desoxynucleotide triphosphate [dNTP] must be smaller than concentration of divalent cations. The concentration of dNTPs is included to the formula beacause of some magnesium is bound by the dNTP. Attained concentration of monovalent cations is used to calculate oligo/primer melting temperature. See Concentration of dNTPs to specify the concentration of dNTPs."
687 - type: Block
688 tag: td
689 elements:
690 - type: Text
691 name: PRIMER_SALT_DIVALENT
692 default: 0
693 - type: Block
694 tag: td style="color:blue;"
695 elements:
696 - type: Block
697 content: "Concentration of dNTPs:"
698 attributes:
699 title: "The millimolar concentration of deoxyribonucleotide triphosphate. This argument is considered only if Concentration of divalent cations is specified."
700 - type: Block
701 tag: td
702 elements:
703 - type: Text
704 name: PRIMER_DNTP_CONC
705 default: 0.0
707 - type: Block
708 tag: table
709 elements:
710 - type: Block
711 tag: tr
712 elements:
713 - type: Block
714 tag: td style="color:blue;"
715 elements:
716 - type: Block
717 content: "Annealing Oligo Concentration:"
718 attributes:
719 title: "The nanomolar concentration of annealing oligos in the PCR. Primer3 uses this argument to calculate oligo melting temperatures. The default (50nM) works well with the standard protocol used at the Whitehead/MIT Center for Genome Research--0.5 microliters of 20 micromolar concentration for each primer oligo in a 20 microliter reaction with 10 nanograms template, 0.025 units/microliter Taq polymerase in 0.1 mM each dNTP, 1.5mM MgCl2, 50mM KCl, 10mM Tris-HCL (pH 9.3) using 35 cycles with an annealing temperature of 56 degrees Celsius. This parameter corresponds to 'c' in Rychlik, Spencer and Rhoads' equation (ii) (Nucleic Acids Research, vol 18, num 21) where a suitable value (for a lower initial concentration of template) is 'empirically determined'. The value of this parameter is less than the actual concentration of oligos in the reaction because it is the concentration of annealing oligos, which in turn depends on the amount of template (including PCR product) in a given cycle. This concentration increases a great deal during a PCR; fortunately PCR seems quite robust for a variety of oligo melting temperatures."
720 - type: Block
721 tag: td
722 elements:
723 - type: Text
724 name: PRIMER_DNA_CONC
725 default: 50.0
726 - type: Block
727 tag: td
728 elements:
729 - type: Block
730 content: "(Not the concentration of oligos in the reaction mix but of those annealing to template.)"
732 - type: Block
733 tag: p
734 elements:
735 - type: Block
736 tag: table
737 elements:
738 - type: Block
739 tag: tr
740 elements:
741 - type: Block
742 tag: td
743 elements:
744 - type: Checkbox
745 name: PRIMER_LIBERAL_BASE
746 label: Liberal Base
747 default: 1
748 - type: Block
749 tag: td
750 elements:
751 - type: Checkbox
752 name: PRIMER_LIB_AMBIGUITY_CODES_CONSENSUS
753 label: Do not treat ambiguity codes in libraries as consensus
754 default: 1
755 - type: Block
756 tag: td
757 elements:
758 - type: Checkbox
759 name: PRIMER_LOWERCASE_MASKING
760 label: Lowercase masking
761 default: 0
763 - type: Submit
764 name: submit
765 value: Pick Primers
768 - type: Block
769 tag: h2
770 elements:
771 - type: Block
772 content: "Other Per-Sequence Inputs"
775 - type: Block
776 tag: p
777 elements:
778 - type: Block
779 tag: table
780 elements:
781 - type: Block
782 tag: tr
783 elements:
784 - type: Block
785 tag: td style="color:blue;"
786 elements:
787 - type: Block
788 content: "Included Region:"
789 attributes:
790 title: "A sub-region of the given sequence in which to pick primers. For example, often the first dozen or so bases of a sequence are vector, and should be excluded from consideration. The value for this parameter has the form
791 start,length
792 where start is the index of the first base to consider, and length is the number of subsequent bases in the primer-picking region."
793 - type: Block
794 tag: td
795 elements:
796 - type: Text
797 name: SEQUENCE_INCLUDED_REGION
798 - type: Block
799 tag: td
800 elements:
801 - type: Block
802 content: "E.g. 20,400: only pick primers in the 400 base region starting at position 20."
803 - type: Block
804 tag: tr
805 elements:
806 - type: Block
807 tag: td style="color:blue;"
808 elements:
809 - type: Block
810 content: "Start Codon Position:"
811 attributes:
812 title: "This parameter should be considered EXPERIMENTAL at this point. Please check the output carefully; some erroneous inputs might cause an error in Primer3. Index of the first base of a start codon. This parameter allows Primer3 to select primer pairs to create in-frame amplicons e.g. to create a template for a fusion protein. Primer3 will attempt to select an in-frame left primer, ideally starting at or to the left of the start codon, or to the right if necessary. Negative values of this parameter are legal if the actual start codon is to the left of available sequence. If this parameter is non-negative Primer3 signals an error if the codon at the position specified by this parameter is not an ATG. A value less than or equal to -10^6 indicates that Primer3 should ignore this parameter. Primer3 selects the position of the right primer by scanning right from the left primer for a stop codon. Ideally the right primer will end at or after the stop codon."
813 - type: Block
814 tag: td
815 elements:
816 - type: Text
817 name: SEQUENCE_START_CODON_POSITION
818 default: -1000000
819 - type: Block
820 tag: h3 style="color:blue;"
821 elements:
822 - type: Block
823 content: "Sequence Quality"
824 attributes:
825 title: "A list of space separated integers. There must be exactly one integer for each base in the Source Sequence if this argument is non-empty. High numbers indicate high confidence in the base call at that position and low numbers indicate low confidence in the base call at that position."
826 - type: Textarea
827 name: SEQUENCE_QUALITY
828 cols: 100
829 rows: 10
830 - type: Block
831 tag: table
832 elements:
833 - type: Block
834 tag: tr
835 elements:
836 - type: Block
837 tag: td style="color:blue;"
838 elements:
839 - type: Block
840 content: "Min Sequence Quality:"
841 attributes:
842 title: "The minimum sequence quality (as specified by Sequence Quality) allowed within a primer."
843 - type: Block
844 tag: td
845 elements:
846 - type: Text
847 name: PRIMER_MIN_QUALITY
848 default: 0
849 - type: Block
850 tag: td style="color:blue;"
851 elements:
852 - type: Block
853 content: "Min End Sequence Quality:"
854 attributes:
855 title: "The minimum sequence quality (as specified by Sequence Quality) allowed within the 3' pentamer of a primer."
856 - type: Block
857 tag: td
858 elements:
859 - type: Text
860 name: PRIMER_MIN_END_QUALITY
861 default: 0
862 - type: Block
863 tag: tr
864 elements:
865 - type: Block
866 tag: td style="color:blue;"
867 elements:
868 - type: Block
869 content: "Sequence Quality Range Min:"
870 attributes:
871 title: "The minimum legal sequence quality (used for interpreting Min Sequence Quality and Min 3' Sequence Quality)."
872 - type: Block
873 tag: td
874 elements:
875 - type: Text
876 name: PRIMER_QUALITY_RANGE_MIN
877 default: 0
878 - type: Block
879 tag: td style="color:blue;"
880 elements:
881 - type: Block
882 content: "Sequence Quality Range Max:"
883 attributes:
884 title: "The maximum legal sequence quality (used for interpreting Min Sequence Quality and Min 3' Sequence Quality)."
885 - type: Block
886 tag: td
887 elements:
888 - type: Text
889 name: PRIMER_QUALITY_RANGE_MAX
890 default: 100
892 - type: Block
893 tag: HR
894 elements:
895 - type: Block
897 - type: Block
898 tag: h1 style="color:blue;"
899 elements:
900 - type: Block
901 content: "Penalties"
902 attributes:
903 title: "This section describes 'penalty weights', which allow the user to modify the criteria that Primer3 uses to select the 'best' primers. There are two classes of weights:
905 (1) For some parameters there is a 'Lt' (less than) and a 'Gt' (greater than) weight. These are the weights that Primer3 uses when the value is less or greater than (respectively) the specified optimum.
907 (2) For the remaining parameters the optimum is understood and the actual value can only vary in one direction from the optimum.
909 The following weights are treated specially: Position Penalty Weight, Primer Weight, Hyb Oligo Weight.
911 The following govern the weight given to various parameters of primer pairs (or primer pairs plus hyb oligo): Tm Difference, Primer-Primer Complementarity, Primer-Primer 3' Complementarity, Primer Pair Mispriming Similarity."
913 - type: Block
914 tag: h2
915 elements:
916 - type: Block
917 content: "Objective Function Penalty Weights for Primers"
919 - type: Block
920 tag: p
921 elements:
922 - type: Block
923 tag: table
924 elements:
925 - type: Block
926 tag: tr
927 elements:
928 - type: Block
929 tag: td
930 elements:
931 - type: Block
932 content: "Tm"
933 - type: Block
934 tag: td
935 elements:
936 - type: Text
937 name: PRIMER_WT_TM_LT
938 default: 1.0
939 label: "LT:"
940 - type: Block
941 tag: td
942 elements:
943 - type: Text
944 name: PRIMER_WT_TM_GT
945 default: 1.0
946 label: "GT:"
947 - type: Block
948 tag: tr
949 elements:
950 - type: Block
951 tag: td
952 elements:
953 - type: Block
954 content: "Size"
955 - type: Block
956 tag: td
957 elements:
958 - type: Text
959 name: PRIMER_WT_SIZE_LT
960 default: 1.0
961 label: "LT:"
962 - type: Block
963 tag: td
964 elements:
965 - type: Text
966 name: PRIMER_WT_SIZE_GT
967 default: 1.0
968 label: "GT:"
969 - type: Block
970 tag: tr
971 elements:
972 - type: Block
973 tag: td
974 elements:
975 - type: Block
976 content: "GC%"
977 - type: Block
978 tag: td
979 elements:
980 - type: Text
981 name: PRIMER_WT_GC_PERCENT_LT
982 default: 0.0
983 label: "LT:"
984 - type: Block
985 tag: td
986 elements:
987 - type: Text
988 name: PRIMER_WT_GC_PERCENT_GT
989 default: 0.0
990 label: "GT:"
992 - type: Block
993 tag: p
994 elements:
995 - type: Block
996 tag: table
997 elements:
998 - type: Block
999 tag: tr
1000 elements:
1001 - type: Block
1002 tag: td
1003 elements:
1004 - type: Block
1005 content: "Self Complementarity:"
1006 - type: Block
1007 tag: td
1008 elements:
1009 - type: Text
1010 name: PRIMER_WT_SELF_ANY
1011 default: 0.0
1012 - type: Block
1013 tag: tr
1014 elements:
1015 - type: Block
1016 tag: td
1017 elements:
1018 - type: Block
1019 content: "3' Self Complementarity:"
1020 - type: Block
1021 tag: td
1022 elements:
1023 - type: Text
1024 name: PRIMER_WT_SELF_END
1025 default: 0.0
1026 - type: Block
1027 tag: tr
1028 elements:
1029 - type: Block
1030 tag: td
1031 elements:
1032 - type: Block
1033 content: "#N's:"
1034 - type: Block
1035 tag: td
1036 elements:
1037 - type: Text
1038 name: PRIMER_WT_NUM_NS
1039 default: 0.0
1040 - type: Block
1041 tag: tr
1042 elements:
1043 - type: Block
1044 tag: td
1045 elements:
1046 - type: Block
1047 content: "Mispriming:"
1048 - type: Block
1049 tag: td
1050 elements:
1051 - type: Text
1052 name: PRIMER_WT_LIBRARY_MISPRIMING
1053 default: 0.0
1054 - type: Block
1055 tag: tr
1056 elements:
1057 - type: Block
1058 tag: td
1059 elements:
1060 - type: Block
1061 content: "Sequence Quality:"
1062 - type: Block
1063 tag: td
1064 elements:
1065 - type: Text
1066 name: PRIMER_WT_SEQ_QUAL
1067 default: 0.0
1068 - type: Block
1069 tag: tr
1070 elements:
1071 - type: Block
1072 tag: td
1073 elements:
1074 - type: Block
1075 content: "End Sequence Quality:"
1076 - type: Block
1077 tag: td
1078 elements:
1079 - type: Text
1080 name: PRIMER_WT_END_QUAL
1081 default: 0.0
1082 - type: Block
1083 tag: tr
1084 elements:
1085 - type: Block
1086 tag: td style="color:blue;"
1087 elements:
1088 - type: Block
1089 content: "Position Penalty:"
1090 attributes:
1091 title: "Determines the overall weight of the position penalty in calculating the penalty for a primer."
1092 - type: Block
1093 tag: td
1094 elements:
1095 - type: Text
1096 name: PRIMER_WT_POS_PENALTY
1097 default: 0.0
1098 - type: Block
1099 tag: tr
1100 elements:
1101 - type: Block
1102 tag: td
1103 elements:
1104 - type: Block
1105 content: "End Stability:"
1106 - type: Block
1107 tag: td
1108 elements:
1109 - type: Text
1110 name: PRIMER_WT_END_STABILITY
1111 default: 0.0
1112 - type: Block
1113 tag: tr
1114 elements:
1115 - type: Block
1116 tag: td
1117 elements:
1118 - type: Block
1119 content: "Template Mispriming:"
1120 - type: Block
1121 tag: td
1122 elements:
1123 - type: Text
1124 name: PRIMER_WT_TEMPLATE_MISPRIMING
1125 default: 0.0
1127 ##### Objective Function Penalty Weights for Primer Pairs #####
1129 - type: Block
1130 tag: h2
1131 elements:
1132 - type: Block
1133 content: "Objective Function Penalty Weights for Primer Pairs"
1136 - type: Block
1137 tag: p
1138 elements:
1139 - type: Block
1140 tag: table
1141 elements:
1142 - type: Block
1143 tag: tr
1144 elements:
1145 - type: Block
1146 tag: td
1147 elements:
1148 - type: Block
1149 content: "Product Size"
1150 - type: Block
1151 tag: td
1152 elements:
1153 - type: Text
1154 name: PRIMER_PAIR_WT_PRODUCT_SIZE_LT
1155 default: 0.0
1156 label: "LT:"
1157 - type: Block
1158 tag: td
1159 elements:
1160 - type: Text
1161 name: PRIMER_PAIR_WT_PRODUCT_SIZE_GT
1162 default: 0.0
1163 label: "GT:"
1164 - type: Block
1165 tag: tr
1166 elements:
1167 - type: Block
1168 tag: td
1169 elements:
1170 - type: Block
1171 content: "Product Tm"
1172 - type: Block
1173 tag: td
1174 elements:
1175 - type: Text
1176 name: PRIMER_PAIR_WT_PRODUCT_TM_LT
1177 default: 0.0
1178 label: "LT:"
1179 - type: Block
1180 tag: td
1181 elements:
1182 - type: Text
1183 name: PRIMER_PAIR_WT_PRODUCT_TM_GT
1184 default: 0.0
1185 label: "GT:"
1187 - type: Block
1188 tag: p
1189 elements:
1190 - type: Block
1191 tag: table
1192 elements:
1193 - type: Block
1194 tag: tr
1195 elements:
1196 - type: Block
1197 tag: td
1198 elements:
1199 - type: Block
1200 content: "Tm Difference:"
1201 - type: Block
1202 tag: td
1203 elements:
1204 - type: Text
1205 name: PRIMER_PAIR_WT_DIFF_TM
1206 default: 0.0
1207 - type: Block
1208 tag: tr
1209 elements:
1210 - type: Block
1211 tag: td
1212 elements:
1213 - type: Block
1214 content: "Any Complementarity:"
1215 - type: Block
1216 tag: td
1217 elements:
1218 - type: Text
1219 name: PRIMER_PAIR_WT_COMPL_ANY
1220 default: 0.0
1221 - type: Block
1222 tag: tr
1223 elements:
1224 - type: Block
1225 tag: td
1226 elements:
1227 - type: Block
1228 content: "3' Complementarity:"
1229 - type: Block
1230 tag: td
1231 elements:
1232 - type: Text
1233 name: PRIMER_PAIR_WT_COMPL_END
1234 default: 0.0
1235 - type: Block
1236 tag: tr
1237 elements:
1238 - type: Block
1239 tag: td
1240 elements:
1241 - type: Block
1242 content: "Pair Mispriming:"
1243 - type: Block
1244 tag: td
1245 elements:
1246 - type: Text
1247 name: PRIMER_PAIR_WT_LIBRARY_MISPRIMING
1248 default: 0.0
1249 - type: Block
1250 tag: tr
1251 elements:
1252 - type: Block
1253 tag: td
1254 elements:
1255 - type: Block
1256 content: "Primer Penalty Weight:"
1257 - type: Block
1258 tag: td
1259 elements:
1260 - type: Text
1261 name: PRIMER_PAIR_WT_PR_PENALTY
1262 default: 1.0
1263 - type: Block
1264 tag: tr
1265 elements:
1266 - type: Block
1267 tag: td style="color:blue;"
1268 elements:
1269 - type: Block
1270 content: "Hyb Oligo Penalty Weight:"
1271 attributes:
1272 title: "Determines the weight of the hyb oligo penalty in calculating the penalty of a primer pair plus hyb oligo."
1273 - type: Block
1274 tag: td
1275 elements:
1276 - type: Text
1277 name: PRIMER_PAIR_WT_IO_PENALTY
1278 default: 0.0
1279 - type: Block
1280 tag: tr
1281 elements:
1282 - type: Block
1283 tag: td style="color:blue;"
1284 elements:
1285 - type: Block
1286 content: "Primer Pair Template Mispriming Weight:"
1287 attributes:
1288 title: Determines the weight of the 2 primer penalties in calculating the primer pair penalty.
1289 - type: Block
1290 tag: td
1291 elements:
1292 - type: Text
1293 name: PRIMER_PAIR_WT_TEMPLATE_MISPRIMING
1294 default: 0.0
1298 ######### Hyp Oligo Per-Sequence Inputs
1300 - type: Block
1301 tag: HR
1302 elements:
1303 - type: Block
1305 - type: Block
1306 tag: h1 style="color:blue;"
1307 elements:
1308 - type: Block
1309 content: "Hyb Oligos (Internal Oligos)"
1310 attributes:
1311 title: "Parameters governing choice of internal oligos are analogous to the parameters governing choice of primer pairs. The exception is Max 3' Complementarity which is meaningless when applied to internal oligos used for hybridization-based detection, since primer-dimer will not occur. We recommend that Max 3' Complementarity be set at least as high as Max Complementarity."
1313 - type: Block
1314 tag: h2
1315 elements:
1316 - type: Block
1317 content: "Hyb Oligo (Internal Oligo) Per-Sequence Inputs"
1319 - type: Block
1320 tag: p
1321 elements:
1322 - type: Block
1323 tag: table
1324 elements:
1325 - type: Block
1326 tag: tr
1327 elements:
1328 - type: Block
1329 tag: td
1330 elements:
1331 - type: Block
1332 content: "Hyb Oligo Excluded Region:"
1333 - type: Block
1334 tag: td
1335 elements:
1336 - type: Text
1337 name: SEQUENCE_INTERNAL_EXCLUDED_REGION
1340 ######## Hyb Oligo Gen Conditions
1342 - type: Block
1343 tag: h2
1344 elements:
1345 - type: Block
1346 content: "Hyb Oligo (Internal Oligo) General Conditions"
1348 - type: Block
1349 tag: p
1350 elements:
1351 - type: Block
1352 tag: table
1353 elements:
1354 - type: Block
1355 tag: tr
1356 elements:
1357 - type: Block
1358 tag: td
1359 elements:
1360 - type: Block
1361 content: "Hyb Oligo Size"
1362 - type: Block
1363 tag: td
1364 elements:
1365 - type: Text
1366 name: PRIMER_INTERNAL_MIN_SIZE
1367 default: 18
1368 label: "Min:"
1369 - type: Block
1370 tag: td
1371 elements:
1372 - type: Text
1373 name: PRIMER_INTERNAL_OPT_SIZE
1374 default: 20
1375 label: "Opt:"
1376 - type: Block
1377 tag: td
1378 elements:
1379 - type: Text
1380 name: PRIMER_INTERNAL_MAX_SIZE
1381 default: 27
1382 label: "Max:"
1383 - type: Block
1384 tag: tr
1385 elements:
1386 - type: Block
1387 tag: td
1388 elements:
1389 - type: Block
1390 content: "Hyb Oligo Tm"
1391 - type: Block
1392 tag: td
1393 elements:
1394 - type: Text
1395 name: PRIMER_INTERNAL_MIN_TM
1396 default: 57.0
1397 label: "Min:"
1398 - type: Block
1399 tag: td
1400 elements:
1401 - type: Text
1402 name: PRIMER_INTERNAL_OPT_TM
1403 default: 60.0
1404 label: "Opt:"
1405 - type: Block
1406 tag: td
1407 elements:
1408 - type: Text
1409 name: PRIMER_INTERNAL_MAX_TM
1410 default: 63.0
1411 label: "Max:"
1412 - type: Block
1413 tag: tr
1414 elements:
1415 - type: Block
1416 tag: td
1417 elements:
1418 - type: Block
1419 content: "Hyb Oligo GC%"
1420 - type: Block
1421 tag: td
1422 elements:
1423 - type: Text
1424 name: PRIMER_INTERNAL_MIN_GC
1425 default: 20.0
1426 label: "Min:"
1427 - type: Block
1428 tag: td
1429 elements:
1430 - type: Text
1431 name: PRIMER_INTERNAL_OPT_GC_PERCENT
1432 label: "Opt:"
1433 - type: Block
1434 tag: td
1435 elements:
1436 - type: Text
1437 name: PRIMER_INTERNAL_MAX_GC
1438 default: 80.0
1439 label: "Max:"
1444 - type: Block
1445 tag: p
1446 elements:
1447 - type: Block
1448 tag: table
1449 elements:
1450 - type: Block
1451 tag: tr
1452 elements:
1453 - type: Block
1454 tag: td
1455 elements:
1456 - type: Block
1457 content: "Hyb Oligo Self Complementarity:"
1458 - type: Block
1459 tag: td
1460 elements:
1461 - type: Text
1462 name: PRIMER_INTERNAL_MAX_SELF_ANY
1463 default: 12.00
1464 - type: Block
1465 tag: td
1466 elements:
1467 - type: Block
1468 content: "Hyb Oligo Max 3' Self Complementarity:"
1469 - type: Block
1470 tag: td
1471 elements:
1472 - type: Text
1473 name: PRIMER_INTERNAL_MAX_SELF_END
1474 default: 12.00
1475 - type: Block
1476 tag: tr
1477 elements:
1478 - type: Block
1479 tag: td
1480 elements:
1481 - type: Block
1482 content: "Max #N's:"
1483 attributes:
1484 title: "Maximum number of unknown bases (N) allowable in any primer."
1485 - type: Block
1486 tag: td
1487 elements:
1488 - type: Text
1489 name: PRIMER_INTERNAL_MAX_NS_ACCEPTED
1490 default: 0
1491 - type: Block
1492 tag: td
1493 elements:
1494 - type: Block
1495 content: "Hyb Oligo Max Poly-X:"
1496 - type: Block
1497 tag: td
1498 elements:
1499 - type: Text
1500 name: PRIMER_INTERNAL_MAX_POLY_X
1501 default: 5
1502 - type: Block
1503 tag: tr
1504 elements:
1505 - type: Block
1506 tag: td
1507 elements:
1508 - type: Block
1509 content: "Hyb Oligo Mishyb Library:"
1510 - type: Block
1511 tag: td
1512 elements:
1513 - type: Select
1514 name: PRIMER_INTERNAL_MISHYB_LIBRARY
1515 options:
1516 - [ '', 'NONE' ]
1517 - [ 'static/documents/primer3-libraries/human.txt', 'HUMAN' ]
1518 - [ 'static/documents/primer3-libraries/rodent_and_simple.txt', 'RODENT_AND_SIMPLE' ]
1519 - [ 'static/documents/primer3-libraries/rodent.txt', 'RODENT' ]
1520 - [ 'static/documents/primer3-libraries/drosophila.txt', 'DROSOPHILA' ]
1521 - type: Block
1522 tag: td
1523 elements:
1524 - type: Block
1525 content: "Hyb Oligo Max Mishyb:"
1526 - type: Block
1527 tag: td
1528 elements:
1529 - type: Text
1530 name: PRIMER_INTERNAL_MAX_LIBRARY_MISHYB
1531 default: 12.00
1532 - type: Block
1533 tag: tr
1534 elements:
1535 - type: Block
1536 tag: td
1537 elements:
1538 - type: Block
1539 content: "Hyb Oligo Min Sequence Quality:"
1540 - type: Block
1541 tag: td
1542 elements:
1543 - type: Text
1544 name: PRIMER_INTERNAL_MIN_QUALITY
1545 default: 0
1546 - type: Block
1547 tag: tr
1548 elements:
1549 - type: Block
1550 tag: td
1551 elements:
1552 - type: Block
1553 content: "Hyb Oligo Conc of Monovalent Cations:"
1554 - type: Block
1555 tag: td
1556 elements:
1557 - type: Text
1558 name: PRIMER_INTERNAL_SALT_MONOVALENT
1559 default: 50.0
1560 - type: Block
1561 tag: td
1562 elements:
1563 - type: Block
1564 content: "Hyb Oligo DNA Concentration:"
1565 - type: Block
1566 tag: td
1567 elements:
1568 - type: Text
1569 name: PRIMER_INTERNAL_DNA_CONC
1570 default: 50.0
1571 - type: Block
1572 tag: tr
1573 elements:
1574 - type: Block
1575 tag: td
1576 elements:
1577 - type: Block
1578 content: "Hyb Oligo Conc of Divalent Cations:"
1579 - type: Block
1580 tag: td
1581 elements:
1582 - type: Text
1583 name: PRIMER_INTERNAL_SALT_DIVALENT
1584 default: 0.0
1585 - type: Block
1586 tag: td
1587 elements:
1588 - type: Block
1589 content: "Hyb Oligo [dNTP]:"
1590 - type: Block
1591 tag: td
1592 elements:
1593 - type: Text
1594 name: PRIMER_INTERNAL_DNTP_CONC
1595 default: 0.0
1599 ##### Obj Function penalty wts for hyp oligos ######
1601 - type: Block
1602 tag: h2
1603 elements:
1604 - type: Block
1605 content: "Objective Function Penalty Weights for Hyb Oligos (Internal Oligos)"
1607 - type: Block
1608 tag: p
1609 elements:
1610 - type: Block
1611 tag: table
1612 elements:
1613 - type: Block
1614 tag: tr
1615 elements:
1616 - type: Block
1617 tag: td
1618 elements:
1619 - type: Block
1620 content: "Hyb Oligo Tm"
1621 - type: Block
1622 tag: td
1623 elements:
1624 - type: Text
1625 name: PRIMER_INTERNAL_WT_TM_LT
1626 default: 1.0
1627 label: "Lt:"
1628 - type: Block
1629 tag: td
1630 elements:
1631 - type: Text
1632 name: PRIMER_INTERNAL_WT_TM_GT
1633 default: 1.0
1634 label: "Gt:"
1635 - type: Block
1636 tag: tr
1637 elements:
1638 - type: Block
1639 tag: td
1640 elements:
1641 - type: Block
1642 content: "Hyb Oligo Size"
1643 - type: Block
1644 tag: td
1645 elements:
1646 - type: Text
1647 name: PRIMER_INTERNAL_WT_SIZE_LT
1648 default: 1.0
1649 label: "Lt:"
1650 - type: Block
1651 tag: td
1652 elements:
1653 - type: Text
1654 name: PRIMER_INTERNAL_WT_SIZE_GT
1655 default: 1.0
1656 label: "Gt:"
1657 - type: Block
1658 tag: tr
1659 elements:
1660 - type: Block
1661 tag: td
1662 elements:
1663 - type: Block
1664 content: "Hyb Oligo GC%"
1665 - type: Block
1666 tag: td
1667 elements:
1668 - type: Text
1669 name: PRIMER_INTERNAL_WT_GC_PERCENT_LT
1670 default: 0.0
1671 label: "Lt:"
1672 - type: Block
1673 tag: td
1674 elements:
1675 - type: Text
1676 name: PRIMER_INTERNAL_WT_GC_PERCENT_GT
1677 default: 0.0
1678 label: "Gt:"
1681 - type: Block
1682 tag: p
1683 elements:
1684 - type: Block
1685 tag: table
1686 elements:
1687 - type: Block
1688 tag: tr
1689 elements:
1690 - type: Block
1691 tag: td
1692 elements:
1693 - type: Block
1694 content: "Hyb Oligo Self Complementarity:"
1695 - type: Block
1696 tag: td
1697 elements:
1698 - type: Text
1699 name: PRIMER_INTERNAL_WT_SELF_ANY
1700 default: 0.0
1701 - type: Block
1702 tag: tr
1703 elements:
1704 - type: Block
1705 tag: td
1706 elements:
1707 - type: Block
1708 content: "Hyb Oligo #N's:"
1709 - type: Block
1710 tag: td
1711 elements:
1712 - type: Text
1713 name: PRIMER_INTERNAL_WT_NUM_NS
1714 default: 0.0
1715 - type: Block
1716 tag: tr
1717 elements:
1718 - type: Block
1719 tag: td
1720 elements:
1721 - type: Block
1722 content: "Hyb Oligo Mishybing:"
1723 - type: Block
1724 tag: td
1725 elements:
1726 - type: Text
1727 name: PRIMER_INTERNAL_WT_LIBRARY_MISHYB
1728 default: 0.0
1729 - type: Block
1730 tag: tr
1731 elements:
1732 - type: Block
1733 tag: td
1734 elements:
1735 - type: Block
1736 content: "Hyb Oligo Sequence Quality:"
1737 - type: Block
1738 tag: td
1739 elements:
1740 - type: Text
1741 name: PRIMER_INTERNAL_WT_SEQ_QUAL
1742 default: 0.0
1744 - type: Hidden
1745 name: PRIMER_EXPLAIN_FLAG
1746 value: 1
1748 - type: Hidden
1749 name: PRIMER_TASK
1750 value: 'pick_detection_primers'
1752 - type: Submit
1753 name: submit
1754 value: Pick Primers