Similar regions between promoters of yisS

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub AAGCAATAGAGGGAAAACGAAAGGCGAAACAAAAAATAGTGCTCCCGCCTGAGCTTGTAG ste .....ATTGATGAAATACGA.................AGTGCTACCGTCAGTGCAAGT.. -300 -290 -280 -270 -260 -250 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ]]]]]]]]]]]]]]]] sub TCAGACATTCTACATCACCGCTCAACACATGAGCCCGCTAATGAGCGGGTTTTTTCATTA ste ...............................................GGTGTGTGGATCA -240 -230 -220 -210 -200 -190 sub TGACAGTTGAAGCCAAAAAAACATATTGCGTGTAAACCAAAGGCGGTGTAAAATATAACC ste TGAC....................................AGGCGGTGGAA......... -180 -170 -160 -150 -140 -130 sub ATCTTTTGAGAAAGCGCTTGCGCAAAATGGCAGAGCGGATAGAACCGCTGTTTTTTTAGC ste .....TTTAGAAAGCGGTTAC....................................... -120 -110 -100 -90 -80 -70 sub TGTTAAGAGAAAACGCTTTCTCAAAGCGAGCCCGAAATGAGATAAAGGAGAGGATGGGAC ste .......AGAAAGCGGTTACATTAAGCGA..............AAACTGGGGGATGGG.. -60 -50 -40 -30 -20 -10 -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...