Alternative spellings

Alternative spellings are the different ways to spell a sound.For example, the English sound /k/ can be written  with the graphemes ck, the diagraph ck and very few times with ch. 
If we are not sure how to spell a word, best guesses become very interesting.

Short vowels
(they don't have alternative spellings)
Sound
Spelling
Example
/æ/
a
cat
/e/
e
pen
/i/
i
chin
/o/
o
top
/ʌ/
u
cup

Long vowels
Sound
Spelling*
Example
/eɪ/
ai, ay, a, a-e, ae, ey, eigh, ea
aim, clay, angel, cake, sundae, grey, eight, great
/i:/
ee, y, ea, e-e, e, ey, ie, ine
bee, funny, beach, compete, be, donkey, belief, sardine
/ /
ie, igh, y, i, i-e
bright, dry, pie, child, drive
/əʊ /
oa, ow, o, o-e, oe, ough, eau
boat, blow, fold, hope, toe, although, beau
/ju/
ue, ew, u, u-e, eu
rescue, few, music, cube, neutral
/u:/
oo, ue, ew, u-e, u, o, ou, ough, ui
broom, blue, chew, flute, super, move, group, through, fruit

Other important sounds
Sound
Spelling*
Example
/ʃ/
sh, ch, ti, ci, sci, ssi
shape, chef, celebration, delicious, conscious, expression
/tʃ/
ch, tch, ture
chair, pitch, future
/θ/ /ð/
th
thumb, this
/kw/
qu
queen
/ŋ/
ng, nk
king, monkey
/ɑ:/
ar, al
arm, half
/ɔ:/
or, aw, au, al, augh, our, oar, oor, ore, ough, ar, a
born, draw, saucer, talk, caugh, door, four, aboard, more, bought, warm
/ɜ:/
er, ur, ir, or, ear
perfect, curl, girl, learn, worm
/aʊ/
ou, ow, ough
found, flower, plough
/ɔɪ/
oi, oy
soil, boy
/eə/
air, are, ear, ere
chair, hare, bear, there

Rest of the English sounds
Sound
Spelling*
Example
/b/
 b, bb
cab, rubber
/k/
c, k, ck, ch
cap, kick, character
/d/
d, dd, ed
dog, addition, loved
/f/
f,ff, ph, gh, lf
fit, cuff, philosophy, laugh, half
/g/
g, gg, gu, gh
grapes, agglomerate, guitar, ghost
/h/
h, wh
hot, who
/dʒ/
j, g, dge
jam, gym, judge
/l/
l, ll, le, al, el, il
lip, doll, cuddle, animal, camel, pencil
/m/
m, mm, mb, mn
mum, mummy, lamb, autumn
/n/
n, nn, kn, gn
can, sunny, knot, gnome
/ŋ/
ng, nk
sing, monkey
/p/
p, pp
pin, puppet
/r/
r, rr, wr
red, carrot, write
/s/
s, ss, ce, ci, cy, -ce, -se, sc, ps, st
sand, class, central, circus, cycle, dance, horse, science, listen, psychologist
/t/
t, tt, ed
top, letter, jumped
/v/
v, ve
van, give
/w/
w, wh, gu
wig, whale, penguin
/x/
x
box
/j/
y
yacht
/z/
z, zz, -ze
zip, buzz, freeze

*Depending on the percentage of usage of each alternative spelling, we can decide if we teach the alternative spelling or we teach those few words as non-decodable words (tricky words). Find in grey the ones that I consider tricky words.

And what if we have to spell a word that has a sound with different spellings? Knowing the best guesses will help you.