Similar regions between promoters of pycA

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub GTCGTTTATTAACCTTGGCGGTGTCAGCGGATTAATTCCGATTACAGGGGTTACGCTGCC hal ............................................................ ste ..CGTTCATTAACGTTGGTGGGGTCGTTGGCCTTATTCCGATTACAGGGGTGCCGCTGCC -300 -290 -280 -270 -260 -250 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub ATTTATCAGTTACGGGGGCTCTTCTTTGGTGCTGCTGCTGGGGAGTATGGGGATATTAGC hal .................GCTATTCTTTCGT.............................. ste GCTCGTCAGCTATGGGGGAACGTCGCTTGTCCTGACCATGGCTTCGCTCGGTCTTTTGGT -240 -230 -220 -210 -200 -190 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>>>> sub GAATATCAGCATGTTTGTGAAATATTCAGA---GAATAAGAAAAA-GAAAGAGCCCTTGG hal .............................A---TAATAAGAAAGA-TAGA.......... ste GAACATTTCTATGTTTGCAAAGTACGAACAACGGTATAAAAAAGCTGAAAAAACGATGGT -180 -170 -160 -150 -140 -130 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub CGCCGAAGGGAATGAAAAAGAAACAGCTCAAAAAAACTGTTTATCTGTAAAAAACAAGTG hal ...........................TCAAAAAAAGTTTT................... ste CAGCAAACAGAA........AAAAAGCTGAAAAAA......................... -120 -110 -100 -90 -80 -70 sub TGTACAGGGGAAGGATATTCCGCTATGATAGATTATATTCCATTCGGGTAAGGGGGAGAA hal ............................................................ ste ............................................................ -60 -50 -40 -30 -20 -10 sub AAGT hal .... ste .... -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...