From 46c1532c2e9ee940a28f7b4889131454c9d6b587 Mon Sep 17 00:00:00 2001
From: Sebastian Schmidt <61014855+sebschmi@users.noreply.github.com>
Date: Mon, 10 Aug 2026 11:58:03 +0300
Subject: [PATCH] Update README with detailed '-e' switch options

Clarify the usage of the '-e' switch for TSM uncertainties.
---
 README.md | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 1a3415a..dd63689 100644
--- a/README.md
+++ b/README.md
@@ -260,7 +260,8 @@ There are additional switches and parameters to influence the visualisation.
 
 * `-a` adds arrows for the jumps of the alignments
 * `-c` renders more of the complements of the input sequences
-* `-e` renders the heuristically computed uncertainties of a TSM with grey characters
+* `-e inner-only` renders the heuristically computed uncertainties of a TSM with blue characters in the TSM inner alignment
+* `-e full` or just `-e` renders the heuristically computed uncertainties of a TSM with blue characters in the TSM inner alignment and the source sequences
 * `-z X` renders only `X` bases of context around the TSMs
 
 ```bash