{"id":3524,"date":"2025-09-03T00:15:32","date_gmt":"2025-09-02T21:15:32","guid":{"rendered":"https:\/\/letgenbio.com\/advanced-primary-tm-calculator\/"},"modified":"2025-10-06T18:51:00","modified_gmt":"2025-10-06T15:51:00","slug":"advanced-primary-tm-calculator","status":"publish","type":"page","link":"https:\/\/letgenbio.com\/en\/advanced-primary-tm-calculator\/","title":{"rendered":"Advanced Primary Tm Calculator"},"content":{"rendered":"\t\t<div data-elementor-type=\"wp-page\" data-elementor-id=\"3524\" class=\"elementor elementor-3524 elementor-1550\">\n\t\t\t\t\t\t<section class=\"elementor-section elementor-top-section elementor-element elementor-element-932a4b9 ts-col-stretched-none ts-bg-color-over-image elementor-section-boxed elementor-section-height-default elementor-section-height-default\" data-id=\"932a4b9\" data-element_type=\"section\">\n\t\t\t\t\t\t<div class=\"elementor-container elementor-column-gap-default\">\n\t\t\t\t\t<div class=\"elementor-column elementor-col-100 elementor-top-column elementor-element elementor-element-f3da4a9 ts-bg-color-over-image\" data-id=\"f3da4a9\" data-element_type=\"column\">\n\t\t\t<div class=\"elementor-widget-wrap elementor-element-populated\">\n\t\t\t\t\t\t<div class=\"elementor-element elementor-element-852d57c elementor-widget elementor-widget-html\" data-id=\"852d57c\" data-element_type=\"widget\" data-widget_type=\"html.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<!-- LETGENBIO ADVANCED TM CALCULATOR START --><div id=\"letgenbio-tm-calculator\"><style>#letgenbio-tm-calculator {\n            background-color: #f5f3f7;\n            border-radius: 12px;\n            padding: 25px;\n            box-shadow: 0 4px 12px rgba(0, 0, 0, 0.08);\n            font-family: -apple-system, BlinkMacSystemFont, \"Segoe UI\", Roboto, Helvetica, Arial, sans-serif;\n            color: #333;\n            max-width: 500px;\n            margin: 20px auto;\n            border: 1px solid #e0dce4;\n        }\n        #letgenbio-tm-calculator h3 {\n            margin: 0 0 20px 0;\n            font-size: 22px;\n            color: #4a4e69;\n            text-align: center;\n            display: flex;\n            align-items: center;\n            justify-content: center;\n        }\n        #letgenbio-tm-calculator h3 svg {\n            margin-right: 10px;\n        }\n        #letgenbio-tm-calculator .calc-section {\n            margin-bottom: 20px;\n        }\n        #letgenbio-tm-calculator .calc-section-title {\n            font-weight: 600;\n            margin-bottom: 10px;\n            font-size: 16px;\n            color: #4a4e69;\n        }\n        #letgenbio-tm-calculator #primer-sequence {\n            width: 100%;\n            height: 100px;\n            padding: 10px;\n            border: 1px solid #c9c4d0;\n            border-radius: 8px;\n            font-family: 'Courier New', Courier, monospace;\n            font-size: 16px;\n            resize: vertical;\n            transition: border-color 0.2s, box-shadow 0.2s;\n        }\n        #letgenbio-tm-calculator #primer-sequence:focus {\n            outline: none;\n            border-color: #6a6e91;\n            box-shadow: 0 0 0 2px rgba(74, 78, 105, 0.2);\n        }\n        #letgenbio-tm-calculator .settings-grid {\n            display: grid;\n            grid-template-columns: 1fr 1fr;\n            gap: 20px;\n            margin-top: 15px;\n        }\n        #letgenbio-tm-calculator .input-group {\n            display: flex;\n            flex-direction: column;\n        }\n        #letgenbio-tm-calculator .input-group label {\n            font-weight: 500;\n            font-size: 14px;\n            margin-bottom: 5px;\n        }\n        #letgenbio-tm-calculator .input-field {\n            display: flex;\n        }\n        #letgenbio-tm-calculator .input-field input {\n            border: 1px solid #c9c4d0;\n            padding: 10px;\n            font-size: 16px;\n            width: 100%;\n            border-radius: 8px 0 0 8px;\n            border-right: none;\n            background-color: #fff;\n            -moz-appearance: textfield;\n        }\n        #letgenbio-tm-calculator .input-field input::-webkit-outer-spin-button,\n        #letgenbio-tm-calculator .input-field input::-webkit-inner-spin-button { -webkit-appearance: none; margin: 0; }\n        #letgenbio-tm-calculator .input-field span {\n            padding: 10px;\n            background-color: #e9ecef;\n            border: 1px solid #c9c4d0;\n            border-left: none;\n            border-radius: 0 8px 8px 0;\n            font-size: 14px;\n        }\n        #letgenbio-tm-calculator .results-grid {\n            display: grid;\n            grid-template-columns: repeat(2, 1fr);\n            gap: 15px;\n            margin-top: 20px;\n        }\n        #letgenbio-tm-calculator .result-section {\n            background-color: #e9e7ed;\n            border: 1px solid #d4d0da;\n            border-radius: 8px;\n            padding: 15px;\n            text-align: center;\n        }\n        #letgenbio-tm-calculator .result-title {\n            font-size: 14px;\n            color: #4a4e69;\n            margin: 0 0 8px 0;\n            font-weight: 600;\n        }\n        #letgenbio-tm-calculator .result-value {\n            font-size: 20px;\n            font-weight: 700;\n            color: #22223b;\n            word-wrap: break-word;\n        }\n        #letgenbio-tm-calculator .result-section.highlight {\n            background-color: #dcd9e3;\n            grid-column: span 2;\n            padding: 20px;\n        }\n        #letgenbio-tm-calculator .result-section.highlight .result-value {\n            font-size: 28px;\n        }\n        #letgenbio-tm-calculator .error-message {\n            color: #ae2012;\n            font-size: 14px;\n            text-align: center;\n            min-height: 20px;\n            margin-top: 15px;\n        }\n    <\/style><h3><svg xmlns=\"http:\/\/www.w3.org\/2000\/svg\" width=\"24\" height=\"24\" viewBox=\"0 0 24 24\" fill=\"none\" stroke=\"currentColor\" stroke-width=\"2\" stroke-linecap=\"round\" stroke-linejoin=\"round\"><path d=\"M14 4v10.54a4 4 0 1 1-4 0V4a2 2 0 0 1 4 0Z\"><\/path><\/svg>Advanced Primer Tm Calculator\n    <\/h3><div class=\"calc-section\"><div class=\"calc-section-title\">1. Enter Primer Sequence:<\/div><textarea id=\"primer-sequence\" placeholder=\"GATTACANATTACAGATTACA...\"><\/textarea><\/div><div class=\"calc-section\"><div class=\"calc-section-title\">2. PCR Conditions (for Salt-Adjusted Tm):<\/div><div class=\"settings-grid\"><div class=\"input-group\"><label for=\"salt-conc\">Salt Concentration<\/label><div class=\"input-field\"><input type=\"number\" id=\"salt-conc\" value=\"50\"><span>mM<\/span><\/div><\/div><div class=\"input-group\"><label for=\"primer-conc\">Primer Concentration<\/label><div class=\"input-field\"><input type=\"number\" id=\"primer-conc\" value=\"500\"><span>nM<\/span><\/div><\/div><\/div><\/div><div class=\"error-message\" id=\"error-message\"><\/div><div id=\"results-container\"><div class=\"results-grid\"><div class=\"result-section highlight\"><div class=\"result-title\">Salt-Adjusted Tm<\/div><div class=\"result-value\" id=\"tm-salt\">- \u00b0C<\/div><\/div><div class=\"result-section\"><div class=\"result-title\">Basic Tm<\/div><div class=\"result-value\" id=\"tm-basic\">- \u00b0C<\/div><\/div><div class=\"result-section\"><div class=\"result-title\">GC Content<\/div><div class=\"result-value\" id=\"gc-percent\">- %<\/div><\/div><div class=\"result-section\"><div class=\"result-title\">Length<\/div><div class=\"result-value\" id=\"length\">- bp<\/div><\/div><div class=\"result-section\"><div class=\"result-title\">Molecular Weight<\/div><div class=\"result-value\" id=\"mol-weight\">- g\/mol<\/div><\/div><\/div><\/div><script>(function() {\n            const calculator = document.getElementById('letgenbio-tm-calculator');\n            if (!calculator) return;\n\n            const sequenceInput = calculator.querySelector('#primer-sequence');\n            const saltInput = calculator.querySelector('#salt-conc');\n            const primerInput = calculator.querySelector('#primer-conc');\n            const resultsContainer = calculator.querySelector('#results-container');\n            \n            const tmBasicEl = calculator.querySelector('#tm-basic');\n            const tmSaltEl = calculator.querySelector('#tm-salt');\n            const gcPercentEl = calculator.querySelector('#gc-percent');\n            const lengthEl = calculator.querySelector('#length');\n            const molWeightEl = calculator.querySelector('#mol-weight');\n            const errorMessage = calculator.querySelector('#error-message');\n\n            function calculate() {\n                try {\n                    errorMessage.textContent = '';\n                    resultsContainer.style.display = 'block';\n\n                    const rawSeq = sequenceInput.value;\n                    const seq = rawSeq.toUpperCase().replace(\/[^ATGC]\/g, '');\n\n                    if (seq.length === 0) {\n                        clearResults();\n                        return;\n                    }\n\n                    const counts = { A: 0, T: 0, G: 0, C: 0 };\n                    for (const base of seq) {\n                        counts[base]++;\n                    }\n\n                    const length = seq.length;\n                    const gcCount = counts.G + counts.C;\n                    const gcPercent = (gcCount \/ length) * 100;\n\n                    \/\/ --- Calculations ---\n                    lengthEl.textContent = `${length} bp`;\n                    gcPercentEl.textContent = `${gcPercent.toFixed(1)} %`;\n                    \n                    const mw = counts.A * 313.21 + counts.T * 304.2 + counts.G * 329.21 + counts.C * 289.18 - 61.96;\n                    molWeightEl.textContent = `${mw.toFixed(2)} g\/mol`;\n\n                    let tmBasic = 0;\n                    if (length < 14) {\n                        tmBasic = (counts.A + counts.T) * 2 + gcCount * 4;\n                    } else {\n                        tmBasic = 64.9 + (41 * (gcCount - 16.4)) \/ length;\n                    }\n                    tmBasicEl.textContent = `${tmBasic.toFixed(1)} \u00b0C`;\n\n                    const saltConc = parseFloat(saltInput.value) \/ 1000;\n                    const primerConc = parseFloat(primerInput.value) \/ 1e9;\n                    \n                    if (isNaN(saltConc) || isNaN(primerConc) || saltConc <= 0 || primerConc <= 0) {\n                        throw new Error(\"PCR conditions must be positive values.\");\n                    }\n\n                    const dH_map = {\n                        'AA':-7.9, 'TT':-7.9, 'AT':-7.2, 'TA':-7.2, 'CA':-8.5, 'TG':-8.5, 'GT':-8.4, 'AC':-8.4,\n                        'CT':-7.8, 'AG':-7.8, 'GA':-8.2, 'TC':-8.2, 'CG':-10.6,'GC':-9.8, 'GG':-8.0, 'CC':-8.0\n                    };\n                    const dS_map = {\n                        'AA':-22.2,'TT':-22.2,'AT':-20.4,'TA':-21.3,'CA':-22.7,'TG':-22.7,'GT':-22.4,'AC':-22.4,\n                        'CT':-21.0,'AG':-21.0,'GA':-22.2,'TC':-22.2,'CG':-27.2,'GC':-24.4,'GG':-19.9,'CC':-19.9\n                    };\n                    const dH_init = {'A':2.3, 'T':2.3, 'G':0, 'C':0};\n                    const dS_init = {'A':4.1, 'T':4.1, 'G':-2.8, 'C':-2.8};\n\n                    let dH = dH_init[seq[0]] + dH_init[seq[seq.length - 1]];\n                    let dS = dS_init[seq[0]] + dS_init[seq[seq.length - 1]];\n                    \n                    for (let i = 0; i < seq.length - 1; i++) {\n                        const dinucleotide = seq.substring(i, i + 2);\n                        dH += dH_map[dinucleotide] || 0;\n                        dS += dS_map[dinucleotide] || 0;\n                    }\n\n                    const gasConstant = 1.987;\n                    let tmSaltK = (dH * 1000) \/ (dS + gasConstant * Math.log(primerConc \/ 4));\n                    tmSaltK += 16.6 * Math.log10(saltConc);\n\n                    const tmSaltC = tmSaltK - 273.15;\n                    tmSaltEl.textContent = `${tmSaltC.toFixed(1)} \u00b0C`;\n\n                } catch (error) {\n                    errorMessage.textContent = error.message;\n                    clearResults(true);\n                }\n            }\n            \n            function clearResults(error = false) {\n                 if (!error) errorMessage.textContent = '';\n                 resultsContainer.style.display = 'none';\n                 tmBasicEl.textContent = '- \u00b0C';\n                 tmSaltEl.textContent = '- \u00b0C';\n                 gcPercentEl.textContent = '- %';\n                 lengthEl.textContent = '- bp';\n                 molWeightEl.textContent = '- g\/mol';\n            }\n\n            [sequenceInput, saltInput, primerInput].forEach(el => el.addEventListener('input', calculate));\n            \n            clearResults();\n        })();\n    <\/script><\/div><!-- LETGENBIO ADVANCED TM CALCULATOR END -->\n\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t<\/div>\n\t\t","protected":false},"excerpt":{"rendered":"<p>Advanced Primer Tm Calculator 1. Enter Primer Sequence:2. PCR Conditions (for Salt-Adjusted Tm):Salt ConcentrationmMPrimer ConcentrationnMSalt-Adjusted Tm- \u00b0CBasic Tm- \u00b0CGC Content- %Length- bpMolecular Weight- g\/mol<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"inline_featured_image":false,"footnotes":""},"class_list":["post-3524","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/letgenbio.com\/en\/wp-json\/wp\/v2\/pages\/3524","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/letgenbio.com\/en\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/letgenbio.com\/en\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/letgenbio.com\/en\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/letgenbio.com\/en\/wp-json\/wp\/v2\/comments?post=3524"}],"version-history":[{"count":0,"href":"https:\/\/letgenbio.com\/en\/wp-json\/wp\/v2\/pages\/3524\/revisions"}],"wp:attachment":[{"href":"https:\/\/letgenbio.com\/en\/wp-json\/wp\/v2\/media?parent=3524"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}