Hi everyone!

I have a large file of maf alignments for multiple non-coding RNA. I want to use the RNAz server (http://rna.tbi.univie.ac.at/cgi-bin/RNAz.cgi) with the standard analysis. Here is an example of two maf alignments:

Alignment 1

##maf version=1
# maf_parse -s 1000 -e 1100 chromosome_1_nine_species.maf
a score=3095.0
s AT.scaffold1      999 72 + 30427671 TGGTTATAAATTATTAGAAGTTTTCCACTTATGACTTAAGAACTTGTGAAGCAGAAAGTGGCAACANNNNNN
s CR.scaffold1 19180319 67 - 19624517 TGTTGAAAATCAATAAAAAGTTTTCCACATATGACTT-----TGTGAGAGGGAGAAGGAGGCAACAAACCCC
a score=1449.0
s AT.scaffold1     1097 3 + 30427671 AAA
s CR.scaffold1 19180393 3 - 19624517 AAA
#eof

Alignment 2

##maf version=1
# maf_parse -s 1200 -e 1300 chromosome_1_nine_species.maf
a score=1449.0
s AT.scaffold1     1199 101 + 30427671 AAAAAGTTGTAATTATTAATGATAGTTCTGTGATTCCTCCATGAATCACATCTGCTTGATTTTTCTTTCATAAATTTATAAGTAATACATTCTTATAAAAT
s CR.scaffold1 19180510  26 - 19624517 AGAAAGGTGTAAAT-------------TTGTAATTC--------------------------------------------------------------AAT
#eof

I am trying to put them into a file so, I can send the file to the server that will parse the maf alignments. My problem is that the server recognizes everything as 1 maf. Could someone please tell how to add multiple mafs together so a parser can read them? Thank you!