for ( $linesFromFile ) {
    if ( /^StartTr1/gm .. /^oflTr1/gm ) {
        print;
    }
}

##</code><code>##

StartTr1
sample 1
sample 1
sample 1
sample 1
SAMPLE 1
oflTr1
nothing
nothing
nothing
StartTr1
sample 2
sample 2
sample 2
sample 2
sample 2
last line before sample 2
oflTr1
junk
junk
junk

##</code><code>##

sample 1
sample 1
sample 1
sample 1
SAMPLE 1

sample 2
sample 2
sample 2
sample 2
sample 2
last line before sample 2