TFBS::SitePair(3pm)

okay bestie, welcome to the user-contributed Perl documentation for TFBS::SitePair(3pm) 💖 this is the page where we talk about site pairs, no cap. it's giving main character energy, fr fr.

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💅 pattern 💅

• Title: pattern — yes, that's the name, iconic.
• Usage:

my $pattern = $sitepair->pattern();  # gets the pattern
                                     # sets the pattern to $pwm

the comments are part of the original, so we're keeping them 100.

• Function: gets the pattern object associated with the site pair. Here that's a TFBS::Matrix::PWM object, bestie.
• Returns: pattern object, here TFBS::Matrix::PWM object.
• Args: none (get-only method). so the original calls it get-only, but the usage comment above literally says # sets the pattern to $pwm — contradiction? maybe, but we're just reporting, no cap.

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🎀 GFF 🎀

• Title: GFF
• Usage:

print $site->GFF();
print $site->GFF($gff_formatter)

two ways to call it, okay?

• Function: returns a "standard" multiline GFF string. note the quotes around "standard" — that's the original's energy, not ours.
• Returns: a string (multiline, newline terminated). So it's not one line, bestie, it's giving multiline.
• Args: a $gff_formatter function reference (optional). You can pass it, or not, it's optional.

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🦋 site1 =head2 site2 🦋

• Title: site1 and site2 — yes, both. The original lists them on separate lines, so yeah, both.
• Usage: my $site1 = $sitepair->site1();
• Function: Returns individual TFBS::Site objects, from the site pair.
• Returns: a TFBS::Site
• Args: none

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and that's the whole vibe. this page came from perl v5.42.3 on 2026-08-21, and it's the manual for TFBS::SitePair(3pm). bye bestie, stay slaying 💅✨