$g is: >LG_I
This $g, >LG_I, has a set.
....We've hit a newline, which is: >LG_I
We are in the 'if buffer eq' loop.
..$g is: >LG_I, and $newline is >LG_I
Gathering sequence data from sequence >LG_I
....We've hit a newline, which is: >LG_II
......At FINISH, $num is: 73, and $i is: 68
in FINISH, $i is: 68, and $num is 73.  They should not be equal
$i is: 68, $HoA{>LG_I}[68][0] is: 22325699, $HoA{>LG_I}[68][1] is: 22326343, $position is: 33722650 and length($buffer) is: 1848919
The position of $highest is below that of $position!  How did this happen?!
substr outside of string at Test3 line 1483, <DNA> line 508168.
......At FINISH, $num is: 73, and $i is: 69
in FINISH, $i is: 69, and $num is 73.  They should not be equal
$i is: 69, $HoA{>LG_I}[69][0] is: 27156174, $HoA{>LG_I}[69][1] is: 27156931, $position is: 33722650 and length($buffer) is: 1848919
The position of $highest is below that of $position!  How did this happen?!
substr outside of string at Test3 line 1483, <DNA> line 508168.
......At FINISH, $num is: 73, and $i is: 70
in FINISH, $i is: 70, and $num is 73.  They should not be equal
$i is: 70, $HoA{>LG_I}[70][0] is: 10031764, $HoA{>LG_I}[70][1] is: 10032474, $position is: 33722650 and length($buffer) is: 1848919
The position of $highest is below that of $position!  How did this happen?!
substr outside of string at Test3 line 1483, <DNA> line 508168.
......At FINISH, $num is: 73, and $i is: 71
in FINISH, $i is: 71, and $num is 73.  They should not be equal
$i is: 71, $HoA{>LG_I}[71][0] is: 22783500, $HoA{>LG_I}[71][1] is: 22784101, $position is: 33722650 and length($buffer) is: 1848919
The position of $highest is below that of $position!  How did this happen?!
substr outside of string at Test3 line 1483, <DNA> line 508168.
......At FINISH, $num is: 73, and $i is: 72
in FINISH, $i is: 72, and $num is 73.  They should not be equal
$i is: 72, $HoA{>LG_I}[72][0] is: 28700514, $HoA{>LG_I}[72][1] is: 28701277, $position is: 33722650 and length($buffer) is: 1848919
The position of $highest is below that of $position!  How did this happen?!
substr outside of string at Test3 line 1483, <DNA> line 508168.
......At FINISH, $num is: 73, and $i is: 73
in FINISH, $i is: 73, and $num is 73.  They should be equal
$g is: >LG_II
This $g, >LG_II, has a set.
....We've hit a newline, which is: >LG_II
......At FINISH, $num is: 61, and $i is: 4
in FINISH, $i is: 4, and $num is 61.  They should not be equal
$i is: 4, $HoA{>LG_II}[4][0] is: 2635020, $HoA{>LG_II}[4][1] is: 2635237, $position is: 1822784 and length($buffer) is: 86
The position of $lowest is past the end of the buffer!  How did that happen?!
substr outside of string at Test3 line 1480, <DNA> line 534211.

...and so on.  it continues all the way up to $i is 61.