I am not sure I can interpret the output of function "matchSeeds. I have run the on-line example myself:

> data(hsSeqs)
> data(s3utr)
> hSeedReg = seedRegions(hsSeqs)
> comphSeed = as.character(reverseComplement(RNAStringSet(hSeedReg)))
> comph = RNA2DNA(comphSeed)
> mx = matchSeeds(comph, s3utr)

mx is a vector of lists:

> is.vector(mx)
[1] TRUE
> length(mx)
[1] 676

I would appreciate some help at understanding the results.
For instance, I understand mx[1] is the list of matches for miRNA "hsa-let-7a".
Each element of list mx[[1]]  should be the list of target 3'utr sequances (??) to which
the current miRNA 5' region match ??? For instance:

> mx[1]
$`hsa-let-7a`
$`hsa-let-7a`$`1588`
[1]  125 1107

$`hsa-let-7a`$`599`
[1] 1240

$`hsa-let-7a`$`9180`
[1] 757

$`hsa-let-7a`$`9180`
[1] 757

I would like to understand what is the number apparing on the same line as the miRNA identifier, following the "$" sign.
($`1588`, $`599`, $`9180`;....) 
It must be an index into something ... But miRNA sequences are no more than 26 nucleotides long ... 
Does this coordinate mark the beginning of the matching region ?
What about the following list of numbers ? For instance:
[1]  125 1107
[1] 1240
[1] 757
Are these indices of 3'utr sequences ?

Thank you  in advance.
Maura






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