Output files for usage example File: paamir.sixpack PAAMIR Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regulation G T A G R A S A R S P P A G R R E L H D F1 V P L A E H L L D H H Q P G D G N C T I F2 Y R W P S I C S I T T S R A T G T A R S F3 1 ggtaccgctggccgagcatctgctcgatcaccaccagccgggcgacgggaactgcacgat 60 ----:----|----:----|----:----|----:----|----:----|----:----| 1 ccatggcgaccggctcgtagacgagctagtggtggtcggcccgctgcccttgacgtgcta 60 P V A P R A D A R D G G A P R R S S C S F6 X Y R Q G L M Q E I V V L R A V P V A R F5 T G S A S C R S S * W W G P S P F Q V I F4 L P G E P G A R A G S L R T A L S D S H F1 Y L A S L E H E R V R F V R R * A T V T F2 T W R A W S T S G F A S Y G A E R Q S Q F3 61 ctacctggcgagcctggagcacgagcgggttcgcttcgtacggcgctgagcgacagtcac 120 ----:----|----:----|----:----|----:----|----:----|----:----| 61 gatggaccgctcggacctcgtgctcgcccaagcgaagcatgccgcgactcgctgtcagtg 120 R G P S G P A R A P E S R V A S L S L * F6 D V Q R A Q L V L P N A E Y P A S R C D F5 * R A L R S C S R T R K T R R Q A V T V F4 R R G N G W D R T R S G R * S A C C S P F1 G E E T D G I A P G A A A D R P A V L R F2 E R K R M G S H Q E R P L I G L L F S E F3 121 aggagaggaaacggatgggatcgcaccaggagcggccgctgatcggcctgctgttctccg 180 ----:----|----:----|----:----|----:----|----:----|----:----| 121 tcctctcctttgcctaccctagcgtggtcctcgccggcgactagccggacgacaagaggc 180 L L P F P H S R V L L P R Q D A Q Q E G F6 C S L F R I P D C W S R G S I P R S N E F5 P S S V S P I A G P A A A S R G A T R R F4 K P A S P P I S S A R T R M A H C S R S F1 N R R H R R Y R A L A R V W R I A R G R F2 T G V T A D I E R S H A Y G A L L A V E F3 181 aaaccggcgtcaccgccgatatcgagcgctcgcacgcgtatggcgcattgctcgcggtcg 240 ----:----|----:----|----:----|----:----|----:----|----:----| 181 tttggccgcagtggcggctatagctcgcgagcgtgcgcataccgcgtaacgagcgccagc 240 F G A D G G I D L A R V R I A C Q E R D F6 S V P T V A S I S R E C A Y P A N S A T F5 F R R * R R Y R A S A R T H R M A R P R F4 S N * T A R A A S A V A R S K R C P R T F1 [Part of this file has been deleted for brevity] 1981 caacgacccgttctagtcgccagccctccaccgccactagttgaaggaccagccgcacga 2040 T A P C S * R D P P P P S * S G P R R A F6 P Q Q A L D A T P L H R H D V E Q D A H F5 N S P L I L P R S T A T I L K R T P T S F4 E R L R R V L P D L F R S S R A G L A E F1 S A C V A F Y L I F S A A A G Q G S L K F2 A P A S R S T * S F P Q Q P G R A R * R F3 2041 gagcgcctgcgtcgcgttctacctgatcttttccgcagcagccgggcagggctcgctgaa 2100 ----:----|----:----|----:----|----:----|----:----|----:----| 2041 ctcgcggacgcagcgcaagatggactagaaaaggcgtcgtcggcccgtcccgagcgactt 2100 S R R R R T R G S R K R L L R A P S A S F6 Q A G A D R E V Q D K G C C G P L A R Q F5 L A Q T A N * R I K E A A A P C P E S F F4 G R S A D P A I R F Y L S V G G R Q P V F1 A G A L T L L F A F T Y L W V A A N Q F F2 P E R * P C Y S L L P I C G W P P T S S F3 2101 ggccggagcgctgaccctgctattcgcttttacctatctgtgggtggccgccaaccagtt 2160 ----:----|----:----|----:----|----:----|----:----|----:----| 2101 ccggcctcgcgactgggacgataagcgaaaatggatagacacccaccggcggttggtcaa 2160 P R L A S G A I R K * R D T P P R W G T F6 L G S R Q G Q * E S K G I Q P H G G V L F5 A P A S V R S N A K V * R H T A A L W N F4 P R X F1 L E F2 S X F3 2161 cctcgag 2167 ----:-- 2161 ggagctc 2220 G R F6 E E L F5 R S F4 ############################## Minimum size of ORFs : 1 Total ORFs in frame 1 : 8 Total ORFs in frame 2 : 5 Total ORFs in frame 3 : 13 Total ORFs in frame 4 : 10 Total ORFs in frame 5 : 16 Total ORFs in frame 6 : 15 Total ORFs : 67 ############################## File: paamir.fasta >PAAMIR_1_ORF1 Translation of PAAMIR in frame 1, ORF 1, threshold 1, 53aa GTAGRASARSPPAGRRELHDLPGEPGARAGSLRTALSDSHRRGNGWDRTRSGR >PAAMIR_1_ORF2 Translation of PAAMIR in frame 1, ORF 2, threshold 1, 28aa SACCSPKPASPPISSARTRMAHCSRSSN >PAAMIR_1_ORF3 Translation of PAAMIR in frame 1, ORF 3, threshold 1, 52aa TARAASAVARSKRCPRTPAATRTAIGCAPRTSFATGGYGSSWAATCRTRARR >PAAMIR_1_ORF4 Translation of PAAMIR in frame 1, ORF 4, threshold 1, 43aa CRWSSAPTRCSATRPPTRASSIRRTSSTAVRRRTRTVRRWRRT >PAAMIR_1_ORF5 Translation of PAAMIR in frame 1, ORF 5, threshold 1, 23aa FATTASGWCSSARTTSIRGKATM >PAAMIR_1_ORF6 Translation of PAAMIR in frame 1, ORF 6, threshold 1, 72aa CATCIASTAARCSRKSTFRCIPPTTTCSAPSSASTRRAPTWSSPPWWAPAPPSCIAPSPV ATATAGGRRSPA >PAAMIR_1_ORF7 Translation of PAAMIR in frame 1, ORF 7, threshold 1, 357aa PPARRRWRRWRVTWQRGRWWSRLTSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTGR PCCSAAPRRPQATGGWKTCSGTCTTSTSTRHRGRSGWSARTTTAACLRASRKSMRAACSR SAGSRPNRFAPTLMSSCITSTTGPPAWAGDRSHERQLAARQPARVAGAGPQPAGGGQRRP GLAADPHRLFGAPVLAAAGSLRRAGGRGLHQHFPEWPPRRDRCAARRRDSAHYPGGAGGV RKPRGALADHRAGVPRRDHPAARCPPGAACAGIGAAHQRGNGEAEAEDRAAPGPHRRPGP DQPGQGVADAAPWLGRARGAPAPVAGSDEAARADPEDRSGVAGKRAVRLSDPGRPEQ >PAAMIR_1_ORF8 Translation of PAAMIR in frame 1, ORF 8, threshold 1, 88aa QEGYRHHAGTGSAVRWRGAVSQCRLVAGQDQRSGGGGDQLPGRRAERLRRVLPDLFRSSR AGLAEGRSADPAIRFYLSVGGRQPVPRX >PAAMIR_2_ORF1 Translation of PAAMIR in frame 2, ORF 1, threshold 1, 35aa VPLAEHLLDHHQPGDGNCTIYLASLEHERVRFVRR >PAAMIR_2_ORF2 Translation of PAAMIR in frame 2, ORF 2, threshold 1, 252aa ATVTGEETDGIAPGAAADRPAVLRNRRHRRYRALARVWRIARGRATEPRGRRRRSPDRNA VPGPRRRPGPLSAVRRGLHSQPGGTVPRGLLHVAHAQGGDAGGRARRRAALLPDPLRGLR VFAEHRLRRSGAEPEQCAAGGVPDSPLRRAGGVHRLGLHLSAGKQPCDAPPVSPARRHGA RGNLHSAVSLRRRLAARRRAHLPGARRRGLLHRGGHRHRRAVSRHRPSLRRRQAAADRQP DHQRGGGGEDGE >PAAMIR_2_ORF3 Translation of PAAMIR in frame 2, ORF 3, threshold 1, 125aa RGRGAGGGRALLLQHRYARQPGLRPGLPWFLPGERDHHRLGRGGLLADLVARPRRAGRRQ LAGGRRAAAPVRHRHRRATGAGPGGAPEQPQPPVFAHRGNRCARRVPGPLAVARTDSPRP LCRRA >PAAMIR_2_ORF4 Translation of PAAMIR in frame 2, ORF 4, threshold 1, 210aa PRRLVRQHGRGTAPMSANSLLGSLRELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPP EAFDVPVDVVFTSIFQNGHHDEIAALLAAGTPRTTLVALVEYESPAVLSQIIELECHGVI TQPLDAHRVLPVLVSARRISEEMAKLKQKTEQLQDRIAGQARINQAKVLLMQRHGWDERE AHQHLSREAMKRREPILKIAQELLGNEPSA >PAAMIR_2_ORF5 Translation of PAAMIR in frame 2, ORF 5, threshold 1, 96aa AIRADQNNNKRGIVIMLGLVLLYVGAVLFLNAVWLLGKISGREVAVINFLVGVLSACVAF YLIFSAAAGQGSLKAGALTLLFAFTYLWVAANQFLE >PAAMIR_3_ORF1 Translation of PAAMIR in frame 3, ORF 1, threshold 1, 429aa YRWPSICSITTSRATGTARSTWRAWSTSGFASYGAERQSQERKRMGSHQERPLIGLLFSE TGVTADIERSHAYGALLAVEQLNREGGVGGRPIETLSQDPGGDPDRYRLCAEDFIRNRGV RFLVGCYMSHTRKAVMPVVERADALLCYPTPYEGFEYSPNIVYGGPAPNQNSAPLAAYLI RHYGERVVFIGSDYIYPRESNHVMRHLYRQHGGTVLEEIYIPLYPSDDDLQRAVERIYQA RADVVFSTVVGTGTAELYRAIARRYGDGRRPPIASLTTSEAEVAKMESDVAEGQVVVAPY FSSIDTPASRAFVQACHGFFPENATITAWAEAAYWQTLLLGRAAQAAGNWRVEDVQRHLY [Part of this file has been deleted for brevity] SEPMNTTRSP >PAAMIR_5_ORF11 Translation of PAAMIR in frame 5, ORF 11, threshold 1, 19aa WRIRYAASGALFWFGAGPP >PAAMIR_5_ORF12 Translation of PAAMIR in frame 5, ORF 12, threshold 1, 10aa TMFGEYSKPS >PAAMIR_5_ORF13 Translation of PAAMIR in frame 5, ORF 13, threshold 1, 3aa GVG >PAAMIR_5_ORF14 Translation of PAAMIR in frame 5, ORF 14, threshold 1, 20aa QSSASARSTTGITALRVCDM >PAAMIR_5_ORF15 Translation of PAAMIR in frame 5, ORF 15, threshold 1, 19aa QPTRNRTPRLRMKSSAHSR >PAAMIR_5_ORF16 Translation of PAAMIR in frame 5, ORF 16, threshold 1, 107aa RSGSPPGSWDSVSIGRPPTPPSRFSCSTASNAPYACERSISAVTPVSENSRPISGRSWCD PIRFLSCDCRSAPYEANPLVLQARQVDRAVPVARLVVIEQMLGQRYX >PAAMIR_6_ORF1 Translation of PAAMIR in frame 6, ORF 1, threshold 1, 11aa RGTGWRPPTDR >PAAMIR_6_ORF2 Translation of PAAMIR in frame 6, ORF 2, threshold 1, 36aa KRIAGSALRPSASPARLLRKRSGRTRRRRSARRPGS >PAAMIR_6_ORF3 Translation of PAAMIR in frame 6, ORF 3, threshold 1, 7aa SPPPPDR >PAAMIR_6_ORF4 Translation of PAAMIR in frame 6, ORF 4, threshold 1, 8aa SCPATRRH >PAAMIR_6_ORF5 Translation of PAAMIR in frame 6, ORF 5, threshold 1, 14aa ETAPRQRTAEPVPA >PAAMIR_6_ORF6 Translation of PAAMIR in frame 6, ORF 6, threshold 1, 61aa RYPSCYCSGRPGSLRRTARFPATPERSSGSARAASSLPATGAGAPRARPSHGAASATPWP G >PAAMIR_6_ORF7 Translation of PAAMIR in frame 6, ORF 7, threshold 1, 23aa SGPGRRCGPGAARSSASASPFPR >PAAMIR_6_ORF8 Translation of PAAMIR in frame 6, ORF 8, threshold 1, 18aa CAAPIPAQAAPGGHRAAG >PAAMIR_6_ORF9 Translation of PAAMIR in frame 6, ORF 9, threshold 1, 8aa SRRGTPAR >PAAMIR_6_ORF10 Translation of PAAMIR in frame 6, ORF 10, threshold 1, 16aa SARAPRGFRTPPAPPG >PAAMIR_6_ORF11 Translation of PAAMIR in frame 6, ORF 11, threshold 1, 22aa CAESRRRAAQRSRRGGHSGKCW >PAAMIR_6_ORF12 Translation of PAAMIR in frame 6, ORF 12, threshold 1, 32aa RPRPPARRRLPAAASTGAPNNRCGSAARPGRR >PAAMIR_6_ORF13 Translation of PAAMIR in frame 6, ORF 13, threshold 1, 5aa PPPAG >PAAMIR_6_ORF14 Translation of PAAMIR in frame 6, ORF 14, threshold 1, 407aa GPAPATRAGCRAASWRSWERSPAHAGGPVVEVMHDDIRVGANRFGRLPADLEHAARIDFR DARRQAAVVVLALHPDRPLWRVDVDVVQVPLHVFHPPVACGLRGAAEQQGLPVGRLGPGG DGRVLREETMAGLDEGPAGGRIDAGEVRRDHHLPLCHVTLHLRHLRLAGGQAGDRRPPAV AVATGDGAIQLGGAGAHHGGEDHVGARLVDALDGALQVVVGGIQRNVDFLEHRAAVLAIQ VAHHMVAFPRIDVVRADEHHPLAVVANQVRRQRRTVLVRRRTAVDDVRRILEALVGGRVA EQRVGALDHRHHRLARVRHVAAHEEPYPPVANEVLGAQPIAVRVAAGVLGQRFDRATADA ALAVQLLDREQCAIRVRALDIGGDAGFGEQQADQRPLLVRSHPFPLL >PAAMIR_6_ORF15 Translation of PAAMIR in frame 6, ORF 15, threshold 1, 39aa LSLSAVRSEPARAPGSPGRSCSSRRPAGGDRADARPAVP
