Origin IGS: ttttcccccaattaaaaatctaattgacaatattttatcatagtgctaaaatattttcaattagagaataatatttatttttattatggaatatatttttttagaatagttttttcgttttaaagattaaaatattatttaaaatataaaagagtgctgtccgctaatcatttattgacaaccggggtactaaaattttaggaggtatatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aatatacctcctaaaattttagtaccccggttgtcaataaatgattagcggacagcactcttttatattttaaataatattttaatctttaaaacgaaaaaactattctaaaaaaatatattccataataaaaataaatattattctctaattgaaaatattttagcactatgataaaatattgtcaattagatttttaattgggggaaaa Mask Tandem Repeat Region ================================================ ttttcccccaattaaaaatctaattgacaatattttatcatagtgctaaaatattttcaattagagaataatatttatttttattatggaatatatttttttagaatagttttttcgttttaaagattaaaatattatttaaaatataaaagagtgctgtccgctaatcatttattgacaaccggggtactaaaattttaggaggtatatt Find is-nt database================================================ Query_seq: FN1942:FN1943|FN1942:FN1943:Hypothetical cytosolic protein:Tryptophanase:<-->:444780..444990 211 ttttcccccaattaaaaatctaattgacaatattttatcatagtgctaaaatattttcaattagagaataatatttatttttattatggaatatatttttttagaatagttttttcgttttaaagattaaaatattatttaaaatataaaagagtgctgtccgctaatcatttattgacaaccggggtactaaaattttaggaggtatatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1942:FN1943|FN1942:FN1943:Hypothetical cytosolic protein:Tryptophanase:<-->:444780..444990 211 ttttcccccaattaaaaatctaattgacaatattttatcatagtgctaaaatattttcaattagagaataatatttatttttattatggaatatatttttttagaatagttttttcgttttaaagattaaaatattatttaaaatataaaagagtgctgtccgctaatcatttattgacaaccggggtactaaaattttaggaggtatatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1942:FN1943|FN1942:FN1943:Hypothetical cytosolic protein:Tryptophanase:<-->:444780..444990 211 ttttcccccaattaaaaatctaattgacaatattttatcatagtgctaaaatattttcaattagagaataatatttatttttattatggaatatatttttttagaatagttttttcgttttaaagattaaaatattatttaaaatataaaagagtgctgtccgctaatcatttattgacaaccggggtactaaaattttaggaggtatatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttttcccccaattaaaaatctaattgacaatattttatcatagtgctaaaatattttcaattagagaataatatttatttttattatggaatatatttttttagaatagttttttcgttttaaagattaaaatattatttaaaatataaaagagtgctgtccgctaatcatttattgacaaccggggtactaaaattttaggaggtatatt Predict ORF larger than 30AA ================================================ ttttcccccaattaaaaatctaattgacaatattttatcatagtgctaaaatattttcaattagagaataatatttatttttattatggaatatatttttttagaatagttttttcgttttaaagattaaaatattatttaaaatataaaagagtgctgtccgctaatcatttattgacaaccggggtactaaaattttaggaggtatatt Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: + Score: 90 Start: 23 End: 52 ......................ATTGACAATATTTTATCATAGTGCTAAAAT............................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 86 Start: 32 End: 61 ...............................ATTGAAAATATTTTAGCACTATGATAAAAT...................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttttcccccaattaaaaatctaattgacaatattttatcatagtgctaaaatattttcaattagagaataatatttatttttattatggaatatatttttttagaatagttttttcgttttaaagattaaaatattatttaaaatataaaagagtgctgtccgctaatcatttattgacaaccggggtactaaaattttaggaggtatatt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -14.2 Tail_Score: -4.8622 Start: 19 End: 65 Full_Region: aaataaatattattc tctaattgaaaatattttagca cta tgataaaatattgtcaattaga tttttaattggggga ..................tctaattgaaaatattttagcactatgataaaatattgtcaattaga.................................................................................................................................................. Find igs database================================================ Query_seq: FN1942:FN1943|FN1942:FN1943:Hypothetical cytosolic protein:Tryptophanase:<-->:444780..444990 211 ttttcccccaattaaaaatctaattgacaatattttatcatagtgctaaaatattttcaattagagaataatatttatttttattatggaatatatttttttagaatagttttttcgttttaaagattaaaatattatttaaaatataaaagagtgctgtccgctaatcatttattgacaaccggggtactaaaattttaggaggtatatt Intra-Species Hit: Count: 1 Min: 1 Max: 211 Len: 211 Subject: NC_003454_FN1942_FN1943|Hypothetical cytosolic protein:Tryptophanase|NEGATIVE:POSITIVE|[444780, 444990]|211 HSP 1 e-value: 4.0E-32 bit: 139.0 Len: 70 Query Start:142 Query End:211 Subject Strand: POSITIVE Subject Start: 142 Subject End: 211 .............................................................................................................................................aaatataaaagagtgctgtccgctaatcatttattgacaaccggggtactaaaattttaggaggtatatt .............................................................................................................................................aaatataaaagagtgctgtccgctaatcatttattgacaaccggggtactaaaattttaggaggtatatt HSP 2 e-value: 1.0E-19 bit: 97.6 Len: 49 Query Start:1 Query End:49 Subject Strand: POSITIVE Subject Start: 1 Subject End: 49 ttttcccccaattaaaaatctaattgacaatattttatcatagtgctaa.................................................................................................................................................................. ttttcccccaattaaaaatctaattgacaatattttatcatagtgctaa.................................................................................................................................................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUCCCCCAAUUAAAAAUCUAAUUGACAAUAUUUUAUCAUAGUGCUAAAAUAUUUUCAAUUAGAGAAUAAUAUUUAUUUUUAUUAUGGAAUAUAUUUUUUUAGAAUAGUUUUUUCGUUUUAAAGAUUAAAAUAUUAUUUAAAAUAUAAAAGAGUGCUGUCCGCUAAUCAUUUAUUGACAACCGGGGUACUAAAAUUUUAGGAGGUAUAUU .....((((.........(((((((((.(((((((((.(.....).))))))))).)))))))))((((((((((((((((((..((((((..(((((.....)))))....))))))..)))))))..)))))))))))......(((((.((((((..(((....(((.....)))....)))))))))....))))))).))...... (-45.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUAUACCUCCUAAAAUUUUAGUACCCCGGUUGUCAAUAAAUGAUUAGCGGACAGCACUCUUUUAUAUUUUAAAUAAUAUUUUAAUCUUUAAAACGAAAAAACUAUUCUAAAAAAAUAUAUUCCAUAAUAAAAAUAAAUAUUAUUCUCUAAUUGAAAAUAUUUUAGCACUAUGAUAAAAUAUUGUCAAUUAGAUUUUUAAUUGGGGGAAAA ......(((((.....((((((.......((((((..(((....)))...))))))..(((((((....(((((......)))))....))))).))..........)))))).................................(((((((((.(((((((((.(.....).))))))))).))))))))).........))))).... (-36.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 692 50 1 141 92 NC_003454:FN1942|5end_Hypothetical_cytosolic_protein_444689..444919_NEGATIVE 216 63 23 222 188 NC_003454:FN1873|5end_Bis(5'-nucleosyl)-tetraphosphatase_363440..363670_NEGATIVE 210 208 162 72 31 NC_003454:FN0928|5end_O-sialoglycoprotein_endopeptidase_1583026..1583256_NEGATIVE 204 128 84 99 54 NC_003454:FN0232|5end_hypothetical_protein_858018..858248_NEGATIVE 202 69 34 74 35 NC_003454:FN0726|5end_hypothetical_protein_1385265..1385495_NEGATIVE 194 210 161 142 88 NC_003454:FN0395|5end_Transporter_1033106..1033336_POSITIVE 193 140 95 124 82 NC_003454:FN1366|5end_Triosephosphate_isomerase_2017518..2017748_NEGATIVE 192 209 162 58 7 NC_003454:FN0670|5end_High-affinity_zinc_uptake_system_membrane_protein_znuB_1325702..1325932_POSITIVE 188 181 157 91 66 NC_003454:FN0825|5end_Hypothetical_cytosolic_protein_1485124..1485354_POSITIVE 185 200 151 200 146 NC_003454:FN1124|5end_Outer_membrane_porin_F_1769005..1769235_NEGATIVE 184 189 153 227 192 NC_003454:FN0174|5end_Enoyl-[acyl-carrier-protein]_reductase_799427..799657_POSITIVE 183 208 162 228 175 NC_003454:FN1413|5end_translation_initiation_factor_IF-2B_subunit_alpha_2074270..2074500_NEGATIVE 181 59 19 78 41 NC_003454:FN1740|5end_ATP_synthase_subunit_K_238400..238630_NEGATIVE 180 121 84 198 154 NC_003454:FN1756|5end_ThiS_protein_251935..252165_NEGATIVE 179 126 87 71 26 NC_003454:FN0534|5end_hypothetical_protein_1188858..1189088_POSITIVE 178 201 161 81 39 NC_003454:FN0465|5end_hypothetical_protein_1110046..1110276_POSITIVE 178 192 151 208 170 NC_003454:FN0310|5end_Iron(III)-transport_ATP-binding_protein_sfuC_945796..946026_POSITIVE 176 65 40 37 12 NC_003454:FN1182|5end_hypothetical_protein_1845438..1845668_NEGATIVE 176 183 157 224 200 NC_003454:FN1816|5end_hypothetical_protein_296840..297070_NEGATIVE 175 187 158 157 132 NC_003454:FN1184|5end_hypothetical_protein_1847107..1847337_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 210 208 162 91 50 NC_003454:FN0929|3end_ATP/GTP_hydrolase_1583007..1583157_NEGATIVE 204 128 84 53 8 NC_003454:FN0233|3end_hypothetical_protein_858064..858214_NEGATIVE 194 210 161 103 49 NC_003454:FN0394|3end_Outer_membrane_protein_1033147..1033297_POSITIVE 193 140 95 104 62 NC_003454:FN1367|3end_Methyl-accepting_chemotaxis_protein_2017538..2017688_NEGATIVE 190 170 124 68 26 NC_003454:FN1589|3end_LexA_repressor_100531..100681_POSITIVE 181 162 123 54 21 NC_003454:FN1303|3end_Adenosylcobalamin-dependent_DIOL_dehydratase_gamma_subunit_1959706..1959856_NEGATIVE 180 47 1 150 104 NC_003454:FN1232|3end_Transcriptional_regulator,_MarR_family_1889000..1889150_NEGATIVE 176 65 40 47 22 NC_003454:FN1183|3end_Hypothetical_cytosolic_protein_1845428..1845578_NEGATIVE 175 188 141 56 7 NC_003454:FN1263|3end_Cobalt_chelatase_1919725..1919875_NEGATIVE 175 79 31 112 57 NC_003454:FN1083|3end_putative_surface_protein_1728639..1728789_POSITIVE 172 183 146 77 41 NC_003454:FN0514|3end_hypothetical_protein_1163912..1164062_POSITIVE 172 192 157 69 31 NC_003454:FN0182|3end_Sarcosine_oxidase_alpha_subunit_805801..805951_NEGATIVE 171 46 2 128 74 NC_003454:FN1147|3end_hypothetical_protein_1796594..1796744_NEGATIVE 170 120 74 133 90 NC_003454:FN1227|3end_hypothetical_protein_1885516..1885666_NEGATIVE 170 136 94 135 92 NC_003454:FN0966|3end_Precorrin-6Y_C5,15-methyltransferase_[decarboxylating]_1619280..1619430_NEGATIVE 168 178 136 46 5 NC_003454:FN1908|3end_Glycerophosphoryl_diester_phosphodiesterase_400596..400746_NEGATIVE 167 145 105 80 44 NC_003454:FN1270|3end_Hypothetical_cytosolic_protein_1926326..1926476_NEGATIVE 167 116 72 147 92 NC_003454:FN1054|3end_hypothetical_protein_1702052..1702202_POSITIVE 167 87 43 66 15 NC_003454:FN0154|3end_Ribonuclease_G_783196..783346_POSITIVE 166 206 161 148 107 NC_003454:FN1088|3end_NADH_oxidase_1733095..1733245_POSITIVE