"%s" is being left adjusted to 7 places first - eg "%s ", and then you're substituting the '123456' for the %s... hence the result you get...

>>> '%s'.ljust(7)
'%s     '
>>> _ % '123456'
'123456     '

You could use:

>>> ('%s' % '123456').ljust(7)
'123456

Or specify appropriate width in the format string...

UPDATED ANSWER:

You can compose multiple format specifiers. Below, +.1f is used to keep the sign, and print to only 1 decimal place. and <10 is used to justify the string.

values = [-1.0, 2.2]

for value in values:
    print(f"someLjustedStrings{value:<+10.1f}someLjustedStrings")

OLD ANSWER:

You can try this:

values = [-1.0, 2.2]

for value in values:
    print(f"someLjustedStrings{['+', '-'][value<0]}{abs(value):<10}someLjustedStrings")

Output:

someLjustedStrings-1.0       someLjustedStrings
someLjustedStrings+2.2       someLjustedStrings

< followed by int for ljust

> followed by int for rjust

EDIT:

If you want to ljust by variable:

LJUST = {'value': 10}
values = [-1.0, 2.2]

for value in values:
    print(f"someLjustedStrings{['+', '-'][value<0]}{abs(value):<{LJUST['value']}}someLjustedStrings")

Output:

someLjustedStrings-1.0       someLjustedStrings
someLjustedStrings+2.2       someLjustedStrings

As Antti hints, justifying after encoding won't give very fruitful results. Try justifying first and then encoding:

with open(filename, "wt") as f:
    for pre, fill, node in anytree.RenderTree(root):
        prefix = (u"{pre_print}{node_print}".format(pre_print=pre, node_print=node.name)).ljust(40, '-').encode("utf-8")
        f.write("{pref}> {status}".format(pref=prefix, status="testing..."))
        f.write("\n")

Result:

root------------------------------------> testing...
├── child_1-----------------------------> testing...
│   └── grandchild_11-------------------> testing...
├── child_2-----------------------------> testing...
│   └── grandchild_21-------------------> testing...
└── child_3-----------------------------> testing...
    └── grandchild_31-------------------> testing...

Each line in your original text file ends with a newline character. You need to strip that off, then ljust, just append a newline. Otherwise, the padding gets added after the newline, which is what you are seeing.

padding = '*'
len = 16

with open("WordList.txt", "r") as input:
     with open("NewWordList.txt", "w") as output:
        for x in input:
            x = x.strip().ljust(len, padding)
            output.write(x + '\n')