December 1, 2023
13 min

15 Best Ecommerce Accounting Softwares in 2024 (Must-Try Solutions)

Streamline your ecommerce accounting with the 9 best software options in 2023. Automate tasks, gain insights, and choose the best-fit solution for your business
15 Best Ecommerce Accounting Softwares in 2024 (Must-Try Solutions)
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Ecommerce accounting can be very complex but the correct software provides a powerful solution to streamline accounting processes, automate tasks, and gain valuable insights into the financial health of your ecommerce venture. In this article, we will explore the top ecommerce accounting software options available in 2023, their features and benefits, and help you choose the best-fit solution for your business.

Key Takeaways from this Post

Explore the top ecommerce accounting software options available in 2024 and their features and benefits.
Simplify your ecommerce accounting processes, automate tasks, and gain valuable insights into your financial health.
Consider criteria like ease of use, integration capabilities, pricing, and reporting features to choose the best software for your business.
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Best Ecommerce Accounting Software

When it comes to choosing the right ecommerce accounting software, there are several options available in the market. Here are the top ecommerce accounting software solutions that you must consider:

1. Xero

2. QuickBooks

3. Zoho Books

4. FreshBooks

5. Sage Business Cloud Accounting

6. NetSuite

7. Wave

8. KashFlow

9. FreeAgent

10. Bench

11. Multiview ERP

12. Kashoo

13. Acumatica

14. FinancialForce

15. Blackline

Now, let's dive deeper into each of the accounting software for bookkeepers to understand their unique features and how they can benefit your ecommerce business.

1. Xero: Simplify Ecommerce Accounting with Flexible Automation

Xero is a cloud-based accounting software platform that caters to the needs of small and medium-sized businesses. With its intuitive interface and robust features, Xero simplifies ecommerce accounting processes and allows you to focus on growing your online business. Let's explore some of the key features that make Xero a popular choice among ecommerce entrepreneurs:


Invoicing: Create professional invoices and send them to customers directly from the software.

Bank Reconciliation: Automatically import and categorize bank transactions to save time and reduce errors.

Inventory Tracking: Keep track of your inventory levels, set reorder points, and manage purchase orders.

Expense Management: Capture and categorize expenses, and easily reconcile them with your bank accounts.

Integration with Ecommerce Platforms: Seamlessly connect Xero with popular ecommerce platforms like Shopify and WooCommerce for a complete accounting and financial management solution.


Real-Time Visibility: Monitor your cash flow, sales, and expenses in real-time to make informed business decisions.

Simplified Tax Compliance: Automate tax calculations and easily generate tax reports for hassle-free tax filing.

Efficient Financial Reporting: Generate customized financial reports and gain insights into the financial performance of your ecommerce business.

Scalability: Xero grows with your business, allowing you to add advanced features and users as needed.

2. QuickBooks: Streamline Ecommerce Accounting and Financial Management

QuickBooks, developed by Intuit, is a versatile accounting software package that offers both on-premises and cloud-based solutions for businesses of all sizes. It is widely recognized for its user-friendly interface and comprehensive suite of accounting tools. Let's explore how QuickBooks can simplify your ecommerce accounting tasks:


Business Payments: Accept online payments and easily manage invoices, sales receipts, and purchase orders.

Bill Management: Effectively track and pay bills, manage vendor information, and stay on top of your payables.

Payroll Functions: Streamline payroll processing, calculate employee wages, and generate pay stubs and taxation forms.

Inventory Management: Track inventory levels, manage stock items, and receive alerts for low inventory.


Advanced Reporting: Generate customized reports to analyze financial performance, identify trends, and make data-driven decisions.

Time Savings: Automate repetitive accounting tasks, such as transaction categorization and bank reconciliation, saving you valuable time.

Robust Security: Protect your financial data with industry-standard security measures, ensuring the privacy and integrity of sensitive information.

Integration Capabilities: QuickBooks seamlessly integrates with popular ecommerce platforms, payment gateways, and shipping providers for efficient data synchronization.

3. Zoho Books: Streamline Ecommerce Finances and Simplify Accounting Processes

Zoho Books Logo

Zoho Books is an online accounting software designed for small businesses. Its user-friendly interface and robust features make it a valuable tool for ecommerce entrepreneurs looking to streamline their financial management processes. Let's explore the key features and benefits of Zoho Books:


Financials and Banking: Manage your financials, track income and expenses, and reconcile bank statements effortlessly.

Sales and Purchases Automation: Streamline sales processes, create professional invoices, and track purchase orders.

Inventory Management: Keep track of inventory levels, set reorder points, and generate stock reports.

Time Tracking and Project Profitability: Track time spent on projects, accurately bill clients, and evaluate project profitability.

Integration with Payment Gateways: Seamlessly integrate Zoho Books with payment gateways to facilitate online payments.


Time Savings: Automate recurring tasks such as invoice generation, payment reminders, and bank reconciliation.

Mobility: Access your financial data on the go through Zoho Books' mobile apps for iOS and Android.

Collaboration: Collaborate with your team members, accountants, or bookkeepers in real-time.

Financial Insights: Generate financial reports to gain deeper insights into your business's performance and make informed decisions.

4. FreshBooks: Simplify Ecommerce Invoicing and Accounting for Service-Based Businesses

FreshBooks Logo

FreshBooks is a cloud-based accounting software service designed specifically for service-based businesses. Whether you're a freelancer or run a small client-service business, FreshBooks offers a range of features to streamline invoicing, expense tracking, and time management. Let's explore the key features and benefits of FreshBooks:


Invoicing: Create professional-looking invoices and send them to clients directly from the software.

Expense Tracking: Easily track business expenses and categorize them for hassle-free record-keeping.

Time Tracking: Keep track of billable hours, assign them to clients, and generate accurate timesheets.

Project Management: Organize projects, set milestones, and collaborate with team members on project-related tasks.

Reporting and Insights: Generate financial reports that provide a clear overview of your business's performance.


Simplified Invoicing: Create and send professional invoices quickly, allowing you to get paid faster.

Expense Management: Track and categorize expenses effortlessly, ensuring accurate financial reporting.

Time Monitoring: Accurately track billable hours and ensure fair pricing for your services.

Seamless Payment Collection: Integrate FreshBooks with payment gateways to easily collect payments online.

5. Sage Business Cloud Accounting: Comprehensive Accounting Solution for Small Businesses

Sage Logo

Sage Business Cloud Accounting is a cloud-based accounting and invoice management solution designed specifically for small businesses. Its user-friendly interface and powerful features make it a valuable tool for ecommerce entrepreneurs looking to manage their finances efficiently. Let's explore the key features and benefits of Sage Business Cloud Accounting:


Core Accounting: Manage your financials, track expenses, and reconcile bank statements seamlessly.

Project Accounting: Track project income and expenses, analyze profitability, and manage project budgets.

Expense Management: Capture and categorize expenses, and easily monitor spending with real-time insights.

Compliance Management: Stay compliant with tax regulations and generate accurate tax reports.

Integration Capabilities: Easily integrate Sage Business Cloud Accounting with other business applications and ecommerce platforms.


Streamlined Financial Management: Automate accounting processes, reduce manual errors, and save time on bookkeeping tasks.

Real-Time Insights: Access real-time reports to gain visibility into your financial health and make informed business decisions.

Efficient Invoicing: Create professional invoices, send reminders, and manage payments directly from the software.

Scalability: Sage Business Cloud Accounting grows with your business, adapting to your evolving needs.

6. NetSuite: Integrated Business Management Software for Ecommerce Enterprises

Oracle NetSuite Logo

NetSuite is a comprehensive business management software suite offered as a service. With its scalable and adaptable features, NetSuite is a popular choice for medium to large ecommerce enterprises. Let's explore the key features and benefits of NetSuite:


Enterprise Resource Planning (ERP): Automate processes such as financial management, supply chain management, and order fulfillment.

Customer Relationship Management (CRM): Manage customer interactions, improve sales processes, and enhance customer satisfaction.

Ecommerce Integration: Seamlessly integrate your ecommerce platform with NetSuite for a unified view of your business operations.

Financial Planning: Streamline budgeting, forecasting, and financial planning processes for better decision-making.

Reporting and Analytics: Generate insightful reports and gain a deeper understanding of your business performance.


End-to-End Business Management: NetSuite provides a comprehensive suite of applications to manage various aspects of your ecommerce enterprise.

Scalability and Adaptability: NetSuite grows with your business and can be customized to meet your evolving needs.

Integration Capabilities: NetSuite seamlessly integrates with other business applications, providing a unified view of your data.

Data Security: Protect your sensitive business data with robust security measures and compliance standards.

7. Wave: Free Accounting Software for Small Ecommerce Businesses

Wave Logo

Wave is a free, cloud-based accounting software that offers a range of features for small ecommerce businesses. With its user-friendly interface and intuitive tools, Wave simplifies the accounting process and helps you stay on top of your financials. Let's explore the key features and benefits of Wave:


Accounting: Track income and expenses, generate financial reports, and manage your business transactions.

Invoicing: Create professional invoices, send them to clients, and monitor payment status.

Credit Card Processing: Accept credit card payments directly through Wave for seamless transactions.

Receipt Scanning: Scan and upload receipts for easy expense tracking and record-keeping.


Cost-Effective Solution: Wave offers a range of features for free, making it an excellent choice for small ecommerce businesses.

User-Friendly Interface: Wave's intuitive interface allows users to navigate through its features effortlessly.

Secure Data Management: Wave prioritizes the security of your financial data, ensuring privacy and compliance.

Integration Possibilities: Although Wave is known for its standalone functionality, it can integrate with select applications to enhance its capabilities.

8. KashFlow: Cloud-Based Accounting Solution for Streamlining Ecommerce Finances

KashFlow Logo

KashFlow is a cloud-based accounting solution designed to simplify financial management for businesses of all sizes. With its user-friendly interface and powerful features, KashFlow helps ecommerce entrepreneurs streamline their accounting processes. Let's explore the key features and benefits of KashFlow:


Invoicing: Create professional invoices and send them to clients directly from the software.

Expenses and Purchases: Track and manage business expenses, purchase orders, and supplier information.

Credit Control: Automate credit control processes and manage customer credit limits and payment terms.

Payroll: Process employee payroll with built-in calculations for tax, National Insurance, and pension contributions.

Reporting and Analytics: Generate financial reports to gain insights into your business performance.


Time Savings: KashFlow automates repetitive accounting tasks, reducing manual effort and saving time.

Financial Visibility: Access real-time financial data and reports, allowing you to make informed business decisions.

Seamless Integration: KashFlow integrates with popular ecommerce platforms and payment gateways for smoother data synchronization.

Collaboration: Collaborate with your team members, your ecommerce accountant, or bookkeepers within the software, improving communication and productivity.

9. FreeAgent: Streamline Ecommerce Accounting for Freelancers and Small Business Owners

FreeAgent Logo

FreeAgent is a cloud-based accounting solution designed specifically for freelancers, accountants, and small business owners. With its powerful features and user-friendly interface, FreeAgent simplifies accounting processes and provides valuable insights into your business's finances.

Invoicing and Estimates: Create professional invoices, send estimates, and track project profitability.

Expense Tracking: Categorize expenses, upload receipts, and easily track business expenses.

Time Tracking: Track billable hours, assign them to clients, and generate accurate timesheets.

Tax and VAT Management: Automate tax calculations, generate tax reports, and stay compliant with tax regulations.

Payroll Integration: Seamlessly integrate FreeAgent with your payroll provider for efficient payroll management.


Effortless Invoicing: Create and send professional invoices to clients, allowing you to get paid faster.

Financial Insights: Access real-time reports on your business's financial health, empowering informed decision-making.

Tax Compliance: Automate tax calculations and generate accurate tax reports, simplifying the tax filing process.

Time Savings: FreeAgent automates repetitive tasks, reducing manual effort and freeing up time for other important business activities.

10. Bench: Hands-Off Bookkeeping for Growing Ecommerce Stores

Bench Logo

Bench is a unique combination of software and professional bookkeeping services, designed for businesses that require hands-off financial management. It's particularly beneficial for ecommerce stores experiencing rapid growth and needing expert financial oversight.


  • Expert Bookkeeping: Access to professional bookkeepers for managing your financials.
  • Financial Reporting: Comprehensive reports providing insights into your business's financial health.
  • Tax-Ready Financials: Ensures your financial records are tax-compliant and ready for filing.


  • Time-Saving: Delegates essential accounting tasks, freeing up time for business owners.
  • Expert Advice: Offers professional advice for better understanding and managing financial reports.
  • Seamless Integrations: Works with major ecommerce platforms for streamlined financial tracking.

11. Multiview ERP: In-Depth Financial Data Analysis for Ecommerce

multiview logo

Multiview ERP is a robust enterprise resource planning tool, offering deep financial visibility and data analysis. It is especially suitable for businesses needing comprehensive and data-centric financial tools.


  • General Ledger Capabilities: Advanced features for detailed financial tracking and reporting.
  • Business Intelligence Tools: In-depth analysis tools for extracting actionable insights from financial data.
  • Fully Integrated Budgeting: Comprehensive suite for budget management and forecasting.


  • Financial Visibility: Provides a single source of truth for all financial data, enhancing transparency.
  • Scalable Reporting: Offers customizable and extensive reporting options for various business sizes.
  • Data-Driven Decisions: Aids in making informed decisions based on accurate financial data.

12. Kashoo: Simplifying Ecommerce Accounting for Small Businesses

Kashoo Logo

Kashoo is designed for simplicity and ease of use, offering essential accounting features to manage financials effectively. It's an ideal choice for small businesses aiming to automate much of their administrative accounting work.


  • Basic Accounting Features: Includes recurring invoicing and automatic bank reconciliation.
  • Machine Learning Algorithms: Automates transaction categorization for efficiency.
  • Smart Inbox Feature: Prioritizes emails from regular vendors for streamlined communication.


  • Ease of Use: Simplifies accounting tasks for non-accountants and small business owners.
  • Time Efficiency: Automates routine tasks, saving time and reducing manual errors.
  • Business Insights: Machine learning provides insights tailored to your business operations.

13. Acumatica Cloud ERP: Customizable Accounting for Scalable Ecommerce

Acumatica Logo

Acumatica Cloud ERP provides a customizable and scalable accounting solution, ideal for businesses of any size. It is tailored to align with your ecommerce store's accounting needs and supports growth.


  • Customization Capabilities: Extensive customization options to tailor the tool to your business.
  • Integrated Workflow Capabilities: Offers visibility into financial, project accounting, and inventory data.
  • Document Linking: Links documents to financial transactions for simplified information sharing.


  • Scalability: Ready to scale with your business, adapting to changing needs.
  • Access Anytime, Anywhere: Provides financial data access across devices, enhancing flexibility.
  • Audit-Ready: Simplifies auditing processes, reducing expenses and complexity.

14. FinancialForce: Agile Financial Management Integrated with Salesforce

Salesforce Logo

FinancialForce, from SalesForce, offers a straightforward and trouble-free accounting solution, integrating seamlessly with Salesforce. It's designed for real-time business intelligence and is particularly effective for agile financial operations.


  • Real-Time Reporting: Access to up-to-date financial reports and analytics.
  • Single Ledger Design: Streamlines financial management with a unified ledger system.
  • Revenue Recognition and Forecasting: Automates complex revenue management processes.


  • Decision-Making: Provides data-driven insights for informed decision-making.
  • Operational Efficiency: Shortens accounting cycles and enhances overall efficiency.
  • Salesforce Integration: Links financial data with Salesforce CRM for a comprehensive view.

15. BlackLine: Streamlined Accounting Processes with Automation

Blackline Logo

BlackLine specializes in automating and enhancing accounting processes. It focuses on reconciliations, automation, and transaction matching, making it a key tool for high-quality financial statements.


  • Automated Reconciliations: Standardizes and automates reconciliation processes.
  • Transaction Matching: Automatically matches millions of transactions from different systems.
  • Automated Journal Entries: Streamlines journal entry creation and approvals.


  • Efficiency in Reconciliation: Saves time and improves accuracy in financial reporting.
  • Reduced Manual Effort: Minimizes the time spent on manual transaction matching.
  • Enhanced Financial Accuracy: Automates complex processes, reducing errors and improving compliance.

Criteria for Choosing the Best Ecommerce Accounting Software

When selecting the best ecommerce accounting software for your business, consider the following criteria:

1. Ease of Use: Choose a software solution with a user-friendly interface and intuitive navigation.

2. Integration with Ecommerce Platforms: Ensure the software integrates seamlessly with your ecommerce platform for efficient data synchronization.

3. Pricing: Consider the cost of the software, including any subscription fees or additional charges for add-ons.

4. Customer Support: Look for software providers that offer reliable customer support and assistance when needed.

5. Scalability: Select a software solution that can accommodate the growing needs of your ecommerce business.

6. Reporting Capabilities: Opt for software that provides robust reporting features to gain valuable insights into your financial performance.

7. Tax Compliance Features: Choose software that simplifies tax compliance by automating tax calculations and generating accurate tax reports.

Which Software is Right for you?

| **Software** | **Ease of Use** | **Integration** | **Scalability** | **Cost-Effectiveness** | **Compliance & Reporting** | **Overall** | |---|---|---|---|---|---|---| | **Xero** | 4.9 | 4.8 | 4.9 | 4.8 | 4.9 | 4.9 | | **QuickBooks** | 4.8 | 4.7 | 4.8 | 4.7 | 4.8 | 4.8 | | **Zoho Books** | 4.3 | 4.2 | 4.6 | 4.1 | 4.4 | 4.3 | | **FreshBooks** | 4.5 | 4.4 | 4.2 | 4.5 | 4.5 | 4.5 | | **Sage Business Cloud Accounting** | 4.4 | 4.3 | 4.5 | 4.4 | 4.6 | 4.5 | | **NetSuite** | 4.2 | 4.4 | 4.6 | 4.1 | 4.5 | 4.4 | | **Wave** | 4.6 | 4.5 | 4.3 | 4.6 | 4.7 | 4.6 | | **KashFlow** | 4.3 | 4.2 | 4.4 | 4.2 | 4.4 | 4.3 | | **FreeAgent** | 4.5 | 4.4 | 4.3 | 4.5 | 4.6 | 4.5 |

Using Spreadsheets for Ecommerce Accounting

While spreadsheets can be used for basic accounting needs, they have limitations when it comes to managing the complexities of ecommerce accounting. Spreadsheets lack automation capabilities and can become error-prone and time-consuming as your ecommerce business grows. Dedicated ecommerce accounting software offers advanced features, integration possibilities, and more comprehensive financial management solutions.

Introduction to Link My Books

Link My Books Happy Accountant

Link My Books is an accounting automation solution that simplifies the accounting process for ecommerce sellers.

By integrating with Xero and QuickBooks, Link My Books automates the import and categorization of sales data from popular ecommerce platforms like Amazon, eBay, and Shopify. Let's explore the key features and benefits of Link My Books:


Streamlined Accounting: Automate the reconciliation of sales data, reducing manual effort and saving time.

VAT and Sales Tax Calculations: Automatically calculate VAT and sales tax, ensuring accurate tax compliance.

Integration with Xero and QuickBooks: Seamlessly connect with your chosen accounting software for streamlined financial management.

Order Matching: Match sales orders to invoices for accurate accounting and financial reporting.


Time Savings: Link My Books automates time-consuming manual tasks, allowing you to focus on growing your ecommerce business.

Accurate Accounting: Ensure accurate recording, tracking, and categorization of sales transactions, reducing the risk of errors.

VAT and Sales Tax Compliance: Simplify VAT and sales tax calculations, ensuring compliance with tax regulations.

Seamless Integration: Link My Books seamlessly integrates with Xero and QuickBooks, allowing for efficient data synchronization and financial reporting.

Frequently Asked Questions

1. How to simplify ecommerce accounting?

Simplify ecommerce accounting by using dedicated ecommerce accounting software that offers automation, integration capabilities, and robust reporting features. Consider solutions like Xero, QuickBooks, or specialized ecommerce accounting tools tailored to your business needs.

2. Is QuickBooks good for ecommerce?

Yes, QuickBooks is a popular choice for ecommerce businesses due to its comprehensive features, integration capabilities, and scalability. It offers a range of tools to manage finances, inventory, and sales, making it suitable for growing ecommerce enterprises.

3. How do I set up sales tax for ecommerce?

Setting up sales tax for ecommerce involves understanding the tax laws and regulations in your jurisdiction, configuring your ecommerce platform to calculate and collect sales tax, and periodically remitting the collected taxes to the taxing authority. Ecommerce accounting software often provides built-in tools for sales tax calculation and compliance.

4. Can ecommerce accounting software integrate with my ecommerce platform?

Yes, many ecommerce accounting software solutions offer integrations with popular ecommerce platforms such as Link My Books, Shopify, WooCommerce, Amazon, eBay, and more. These integrations enable seamless data synchronization between your ecommerce platform and accounting software, providing you with accurate financial records.

5) What is the best accounting software for bookkeepers?

When it comes to selecting the best accounting software for bookkeepers, a combination of Link My Books with either Xero or QuickBooks emerges as a top choice. Both Xero and QuickBooks are renowned for their robust features, user-friendly interfaces, and extensive integrations, making them ideal for a range of bookkeeping needs. The integration with Link My Books further enhances their capabilities, particularly for those managing ecommerce accounting.

Link My Books

Link My Books is an ecommerce accounting automation tool specifically designed to streamline and simplify the accounting process for online sellers. It integrates seamlessly with major ecommerce platforms like Amazon, eBay, and Shopify, making it an essential tool for bookkeepers managing ecommerce accounts.

Key Features:

  • Ecommerce Platform Integration: Automatically imports sales data from ecommerce platforms.
  • Automatic Calculation of COGS: Calculates the cost of goods sold, crucial for accurate profit reporting.
  • VAT Compliance: Assists in managing VAT for international sales, a critical feature for ecommerce.

Xero + Link My Books

Xero is known for its intuitive design and comprehensive features that cater to both small and medium-sized businesses. It offers real-time financial reporting, easy bank reconciliation, and efficient invoice management.

Integration with Link My Books: When combined with Link My Books, Xero becomes even more powerful for ecommerce businesses. Link My Books seamlessly integrates with Xero, automating the accounting for sales, fees, and taxes from online marketplaces like Amazon and Shopify. This integration simplifies the process of reconciling ecommerce sales and expenses, ensuring accuracy and saving time for bookkeepers.

QuickBooks + Link My Books

QuickBooks, developed by Intuit, is another excellent choice, especially known for its flexibility and scalability. It offers a range of features including, but not limited to, invoice management, payroll processing, and advanced reporting capabilities.

Integration with Link My Books: Integrating QuickBooks with Link My Books offers a streamlined solution for managing ecommerce finances. This combination automates the entry of sales and expenses from various online platforms into QuickBooks, ensuring that all financial data is accurately captured and categorized. It's particularly useful for bookkeepers handling multiple ecommerce clients, as it simplifies the tracking of sales, expenses, and VAT/GST.

QuickBooks or Xero?

Both Xero and QuickBooks, when paired with Link My Books, provide a comprehensive solution for bookkeepers, particularly those working with ecommerce businesses.

The choice between Xero and QuickBooks can be guided by the specific needs and preferences of the business or the bookkeeper, such as the size of the business, the complexity of the financial transactions, and the preferred user interface.

Both combinations are equipped to handle a wide array of bookkeeping tasks efficiently, ensuring accuracy and compliance in financial management.

Software Choices Summarised

Choosing the right ecommerce accounting software is essential for effectively managing your online business's finances. Xero, QuickBooks, Zoho Books, FreshBooks, Sage Business Cloud Accounting, NetSuite, Wave, KashFlow, and FreeAgent are all excellent options to consider. Each software solution offers unique features and benefits tailored to different business needs.

To make an informed decision, consider criteria such as ease of use, integration capabilities, pricing, customer support, scalability, reporting features, and tax compliance functionalities. It's also important to evaluate the limitations of using spreadsheets for ecommerce accounting and the advantages offered by dedicated software solutions.

Simplify eCommerce Accounting with Link My Books

To simplify ecommerce accounting and streamline your financial management processes, consider utilizing Link My Books. Our accounting automation solution integrates seamlessly with Xero and QuickBooks, automating the import and categorization of sales data from major ecommerce platforms. With features like efficient accounting, VAT and sales tax calculations, integration capabilities, and order matching, Link My Books ensures accurate and time-saving ecommerce accounting.

With the right ecommerce accounting software and tools at your disposal, you can confidently manage your finances, gain valuable insights into your business's performance, and focus on driving the success of your ecommerce venture.

Ready to simplify your ecommerce accounting? Try Link My Books today and experience seamless accounting automation for your ecommerce business. Start your 14 day free trial here! 

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