Similar regions between promoters of rocR

<<<<<<<<<<<<<<<<<<<< <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< sub GTTGGCTCCGTAATGAGACG-TCTGATCAATAATTTCTTTGGATTTAGATAAAGCTGTCA hal .TTTGCTCATTATTTTGGCGATATGAGCGAAAAACTTTTTGG.............TTTCA -300 -290 -280 -270 -260 -250 < sub TATTTGAATTCCCCCTTGTTTTCTGTTTCAACATGTTATCCTGCTTTCCCTTTATATAAA hal TGTTCAATCTCCCCCTT......................................ATCAA -240 -230 -220 -210 -200 -190 sub TGCAAGTTCTGTGCCAAATCAAGAATTCGTGTGTTTTCTACAATTTTCGAGGACAAGGTG hal TGCAAATCCTGTGCCAACTTTATAAACCACGATGTTTC...................... -180 -170 -160 -150 -140 -130 sub CAAAAACATTCTGATATTTCGAGCGAAAATTTCAGCAAGTGCAAAATTCTTTTGCATATC hal .............................................AGTCTTCGAAAAATT -120 -110 -100 -90 -80 -70 sub CTCTCCGTTTTTTTATAAAATAGAAGCAATATTAAGAAAATAATTGAGGGAGGTTCATAC hal ATTTTTCTTTATTTCTTAATCATAACCTATAAAACGAAAAAA.................. -60 -50 -40 -30 -20 -10 sub A hal . -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...