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Matrix families versus individual matrices

Searching transcription factor binding sites for NFkappaB in a HIV-1 long terminal repeat sequence (HIVTH475A) yields the following results:

- Using parameter settings "individual matrices"

Inspecting sequence hivth475a [L31963] (1 - 672):

   Family/matrix Opt. Position Str. Core sim. Matrix sim. Sequence
from - to anchor
  V$NFKB/NFKAPPAB.01 0.88 345 - 359 352 (+) 1.000 0.988 aaGGGActttccgct
  V$NFKB/NFKAPPAB65.01 0.87 345 - 359 352 (+) 1.000 0.984 aagggactTTCCgct 
  V$NFKB/NFKAPPAB.02 0.81 345 - 359 352 (+) 1.000 0.977 aaGGGActttccgct
  V$NFKB/NFKAPPAB.03 0.84 345 - 359 352 (+) 1.000 0.968 aaGGGActttccgct
  V$NFKB/NFKAPPAB.02 0.81 359 - 373 366 (+) 1.000 1.000 tgGGGActttccagg
  V$NFKB/NFKAPPAB.01 0.88 359 - 373 366 (+) 1.000 0.988 tgGGGActttccagg
  V$NFKB/NFKAPPAB65.01 0.87 359 - 373 366 (+) 1.000 0.984 tggggactTTCCagg
  V$NFKB/NFKAPPAB.03 0.84 359 - 373 366 (+) 1.000 0.994 tgGGGActttccagg
  V$NFKB/NFKAPPAB.03 0.84 385 - 399 392 (+) 1.000 0.845 tgGGGAactttccgc
  V$NFKB/NFKAPPAB.03 0.84 386 - 400 393 (+) 0.775 0.893 ggGGAActttccgct
  V$NFKB/NFKAPPAB.02 0.81 400 - 414 407 (+) 1.000 1.000 tgGGGActttccagg
  V$NFKB/NFKAPPAB.01 0.88 400 - 414 407 (+) 1.000 0.988 tgGGGActttccagg
  V$NFKB/NFKAPPAB65.01 0.87 400 - 414 407 (+) 1.000 0.984 tggggactTTCCagg
  V$NFKB/NFKAPPAB.03 0.84 400 - 414 407 (+) 1.000 0.994 tgGGGActttccagg

- With matrix families

Inspecting sequence hivth475a [L31963] (1 - 672):

   Family/matrix Opt. Position Str. Core sim. Matrix sim. Sequence
from - to anchor
  V$NFKB/NFKAPPAB.01 0.88 345 - 359 352 (+) 1.000 0.988 aaGGGActttccgct
  V$NFKB/NFKAPPAB.02 0.81 359 - 373 366 (+) 1.000 1.000 tgGGGActttccagg
  V$NFKB/NFKAPPAB.03 0.84 386 - 400 393 (+) 0.775 0.893 ggGGAActttccgct
  V$NFKB/NFKAPPAB.02 0.81 400 - 414 407 (+) 1.000 1.000 tgGGGActttccagg

This HIV-1 sequence (L31963) containing a 42 bp duplication (including the 2 NFkappaB sites) was published in: