Origin IGS: acaaacaaaaacctaatatccagatgcaacatgaggtagaattgaatagtataaaccaatgtaagtaaaggcatttacttttttagtgtgattttatcaagtaaaacaaaataataattaattgat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atcaattaattattattttgttttacttgataaaatcacactaaaaaagtaaatgcctttacttacattggtttatactattcaattctacctcatgttgcatctggatattaggtttttgtttgt Mask Tandem Repeat Region ================================================ acaaacaaaaacctaatatccagatgcaacatgaggtagaattgaatagtataaaccaatgtaagtaaaggcatttacttttttagtgtgattttatcaagtaaaacaaaataataattaattgat Find is-nt database================================================ Query_seq: PG1528:PG1529|PG1528:PG1529:hypothetical protein:hypothetical protein:->->:1607249..1607374 126 acaaacaaaaacctaatatccagatgcaacatgaggtagaattgaatagtataaaccaatgtaagtaaaggcatttacttttttagtgtgattttatcaagtaaaacaaaataataattaattgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1528:PG1529|PG1528:PG1529:hypothetical protein:hypothetical protein:->->:1607249..1607374 126 acaaacaaaaacctaatatccagatgcaacatgaggtagaattgaatagtataaaccaatgtaagtaaaggcatttacttttttagtgtgattttatcaagtaaaacaaaataataattaattgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1528:PG1529|PG1528:PG1529:hypothetical protein:hypothetical protein:->->:1607249..1607374 126 acaaacaaaaacctaatatccagatgcaacatgaggtagaattgaatagtataaaccaatgtaagtaaaggcatttacttttttagtgtgattttatcaagtaaaacaaaataataattaattgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 acaaacaaaaacctaatatccagatgcaacatgaggtagaattgaatagtataaaccaatgtaagtaaaggcatttacttttttagtgtgattttatcaagtaaaacaaaataataattaattgat Predict ORF larger than 30AA ================================================ acaaacaaaaacctaatatccagatgcaacatgaggtagaattgaatagtataaaccaatgtaagtaaaggcatttacttttttagtgtgattttatcaagtaaaacaaaataataattaattgat Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ acaaacaaaaacctaatatccagatgcaacatgaggtagaattgaatagtataaaccaatgtaagtaaaggcatttacttttttagtgtgattttatcaagtaaaacaaaataataattaattgat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 74 HP_score: -3.9 Tail_Score: -5.2422 Start: 65 End: 78 Full_Region: TATAAACCAATGTAA GTAAA GGCA TTTAC TTTTTTAGTGTGATT ................................................................GTAAAGGCATTTAC................................................ Find igs database================================================ Query_seq: PG1528:PG1529|PG1528:PG1529:hypothetical protein:hypothetical protein:->->:1607249..1607374 126 acaaacaaaaacctaatatccagatgcaacatgaggtagaattgaatagtataaaccaatgtaagtaaaggcatttacttttttagtgtgattttatcaagtaaaacaaaataataattaattgat Intra-Species Hit: Count: 1 Min: 1 Max: 126 Len: 126 Subject: NC_002950_PG1528_PG1529|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[1607249,1607374]|126 HSP 1 e-value: 9.0E-66 bit: 250.0 Len: 126 Query Start:1 Query End:126 Subject Strand: POSITIVE Subject Start: 1 Subject End: 126 acaaacaaaaacctaatatccagatgcaacatgaggtagaattgaatagtataaaccaatgtaagtaaaggcatttacttttttagtgtgattttatcaagtaaaacaaaataataattaattgat acaaacaaaaacctaatatccagatgcaacatgaggtagaattgaatagtataaaccaatgtaagtaaaggcatttacttttttagtgtgattttatcaagtaaaacaaaataataattaattgat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACAAACAAAAACCUAAUAUCCAGAUGCAACAUGAGGUAGAAUUGAAUAGUAUAAACCAAUGUAAGUAAAGGCAUUUACUUUUUUAGUGUGAUUUUAUCAAGUAAAACAAAAUAAUAAUUAAUUGAU ........................(((...(((((((...((((((.((((......(((((........)))))))))..))))))...)))))))...)))....................... (-10.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCAAUUAAUUAUUAUUUUGUUUUACUUGAUAAAAUCACACUAAAAAAGUAAAUGCCUUUACUUACAUUGGUUUAUACUAUUCAAUUCUACCUCAUGUUGCAUCUGGAUAUUAGGUUUUUGUUUGU ..............((((((((......))))))))...(((((..(((((((....)))))))...)))))......((..(((....((((.(((((.......))))).))))..)))..)). (-14.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 252 56 12 70 32 NC_002950:PG1977|5end_hypothetical_protein_2066693..2066923_NEGATIVE 240 58 20 145 102 NC_002950:PG1326|5end_hemagglutinin,_putative_1404033..1404263_POSITIVE 238 45 2 179 136 NC_002950:PG1337|5end_umuD_protein_1417813..1418043_POSITIVE 222 90 49 213 165 NC_002950:PG0172|5end_exonuclease_193493..193723_POSITIVE 207 73 35 78 36 NC_002950:PG1817|5end_hypothetical_protein_1913035..1913265_NEGATIVE 204 69 21 222 161 NC_002950:PG2217|5end_1-deoxy-D-xylulose-5-phosphate_synthase_2329623..2329853_POSITIVE 202 59 13 157 112 NC_002950:PG0363|5end_hypothetical_protein_397470..397700_POSITIVE 199 41 11 201 167 NC_002950:PG0671|5end_iron_compound_ABC_transporter,_permease_protein_721888..722118_POSITIVE 198 73 31 105 57 NC_002950:PG1383|5end_amino_acid_exporter,_putative_1462669..1462899_POSITIVE 196 51 12 225 190 NC_002950:PG2165|5end_glycyl-tRNA_synthetase_2271669..2271899_NEGATIVE 195 41 1 208 159 NC_002950:PG0184|5end_ISPg1,_transposase_216402..216632_POSITIVE 193 58 12 90 35 NC_002950:PG1340|5end_L-lactate_permease_1421848..1422078_NEGATIVE 191 60 20 56 10 NC_002950:PG0703|5end_cobalamin_(5'-phosphate)_synthase,_putative_758144..758374_POSITIVE 190 40 7 163 129 NC_002950:PG1273|5end_hypothetical_protein_1351837..1352067_NEGATIVE 188 72 31 104 54 NC_002950:PG1251|5end_hypothetical_protein_1327779..1328009_POSITIVE 186 98 59 100 66 NC_002950:PG1020|5end_hypothetical_protein_1080568..1080798_POSITIVE 186 40 11 37 11 NC_002950:PG0030|5end_cytidine_deaminase_35846..36076_POSITIVE 184 37 16 27 3 NC_002950:PG0647|5end_iron_compound_ABC_transporter,_permease_protein_700113..700343_NEGATIVE 181 74 33 135 96 NC_002950:PG1630|5end_hypothetical_protein_1711772..1712002_POSITIVE 181 45 6 48 16 NC_002950:PG0779|5end_hypothetical_protein_832573..832803_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 252 56 12 40 2 NC_002950:PG1978|3end_hypothetical_protein_2066723..2066873_NEGATIVE 240 70 23 66 19 NC_002950:PG2223|3end_glycosyl_transferase,_group_2_family_protein_2338761..2338911_POSITIVE 207 73 35 85 43 NC_002950:PG1818|3end_hypothetical_protein_1913028..1913178_NEGATIVE 203 58 12 101 56 NC_002950:PG1795|3end_hypothetical_protein_1888955..1889105_NEGATIVE 194 90 42 113 58 NC_002950:PG0106|3end_glycosyl_transferase,_group_4_family_protein_129934..130084_POSITIVE 193 92 56 68 39 NC_002950:PG2177|3end_Na(+)-translocating_NADH-quinone_reductase_subunit_F_2285266..2285416_NEGATIVE 191 60 20 49 3 NC_002950:PG0702|3end_nicotinate-nucleotide--dimethylbenzimidazole_phosphoribosyltransferase,_putative_758217..758367_POSITIVE 184 37 16 30 6 NC_002950:PG0648|3end_iron_compound_ABC_transporter,_periplasmic_iron_compound-binding_protein,_putative_700110..700260_NEGATIVE 181 71 31 139 99 NC_002950:PG1143|3end_sugar_dehydrogenase,_UDP-glucose/GDP-mannose_dehydrogenase_family_1225630..1225780_NEGATIVE 179 59 12 54 22 NC_002950:PG1863|3end_hypothetical_protein_1960364..1960514_NEGATIVE 179 39 5 75 37 NC_002950:PG1273|3end_hypothetical_protein_1351682..1351832_NEGATIVE 177 46 31 51 36 NC_002950:PG1901|3end_ribosome_releasing_factor_2000831..2000981_NEGATIVE 176 66 31 91 57 NC_002950:PG0888|3end_hypothetical_protein_950121..950271_POSITIVE 175 45 12 46 8 NC_002950:PG1625|3end_hypothetical_protein_1708718..1708868_POSITIVE 175 58 18 81 48 NC_002950:PG0564|3end_hypothetical_protein_621416..621566_NEGATIVE 172 45 20 55 31 NC_002950:PG2127|3end_hypothetical_protein_2233109..2233259_NEGATIVE 172 60 11 58 1 NC_002950:PG0580|3end_N-acetylglucosaminyl_transferase_638316..638466_POSITIVE 172 36 13 135 111 NC_002950:PG0362|3end_hypothetical_protein_397549..397699_POSITIVE 171 52 20 67 33 NC_002950:PG0140|3end_hypothetical_protein_163151..163301_NEGATIVE 165 57 12 150 116 NC_002950:PG1404|3end_rhomboid_family_protein_1487071..1487221_NEGATIVE