Origin IGS: ttctagtcaaggctgctaaattcccataccagccatctatatatgattaagctcttctttcatttttcaagtccagcagaacactaattgatgtgacggtcaactaaatcctaaaaatctagttttctcctatttccacacctttctagtataagctatttttagcattttgacaaatctcttttaggaattccaacatgtcttgacctttctgcaaaaacagtatactatactagtgtatatacagataaaaaggagtcact .........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 agtgactcctttttatctgtatatacactagtatagtatactgtttttgcagaaaggtcaagacatgttggaattcctaaaagagatttgtcaaaatgctaaaaatagcttatactagaaaggtgtggaaataggagaaaactagatttttaggatttagttgaccgtcacatcaattagtgttctgctggacttgaaaaatgaaagaagagcttaatcatatatagatggctggtatgggaatttagcagccttgactagaa Mask Tandem Repeat Region ================================================ ttctagtcaaggctgctaaattcccataccagccatctatatatgattaagctcttctttcatttttcaagtccagcagaacactaattgatgtgacggtcaactaaatcctaaaaatctagttttctcctatttccacacctttctagtataagctatttttagcattttgacaaatctcttttaggaattccaacatgtcttgacctttctgcaaaaacagtatactatactagtgtatatacagataaaaaggagtcact Find is-nt database================================================ Query_seq: SSA_1347:SSA_1348|SSA_1347:SSA_1348:PhnA protein, putative:hypothetical protein:<-->:1365232..1365494 263 ttctagtcaaggctgctaaattcccataccagccatctatatatgattaagctcttctttcatttttcaagtccagcagaacactaattgatgtgacggtcaactaaatcctaaaaatctagttttctcctatttccacacctttctagtataagctatttttagcattttgacaaatctcttttaggaattccaacatgtcttgacctttctgcaaaaacagtatactatactagtgtatatacagataaaaaggagtcact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1347:SSA_1348|SSA_1347:SSA_1348:PhnA protein, putative:hypothetical protein:<-->:1365232..1365494 263 ttctagtcaaggctgctaaattcccataccagccatctatatatgattaagctcttctttcatttttcaagtccagcagaacactaattgatgtgacggtcaactaaatcctaaaaatctagttttctcctatttccacacctttctagtataagctatttttagcattttgacaaatctcttttaggaattccaacatgtcttgacctttctgcaaaaacagtatactatactagtgtatatacagataaaaaggagtcact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1347:SSA_1348|SSA_1347:SSA_1348:PhnA protein, putative:hypothetical protein:<-->:1365232..1365494 263 ttctagtcaaggctgctaaattcccataccagccatctatatatgattaagctcttctttcatttttcaagtccagcagaacactaattgatgtgacggtcaactaaatcctaaaaatctagttttctcctatttccacacctttctagtataagctatttttagcattttgacaaatctcttttaggaattccaacatgtcttgacctttctgcaaaaacagtatactatactagtgtatatacagataaaaaggagtcact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttctagtcaaggctgctaaattcccataccagccatctatatatgattaagctcttctttcatttttcaagtccagcagaacactaattgatgtgacggtcaactaaatcctaaaaatctagttttctcctatttccacacctttctagtataagctatttttagcattttgacaaatctcttttaggaattccaacatgtcttgacctttctgcaaaaacagtatactatactagtgtatatacagataaaaaggagtcact Predict ORF larger than 30AA ================================================ ttctagtcaaggctgctaaattcccataccagccatctatatatgattaagctcttctttcatttttcaagtccagcagaacactaattgatgtgacggtcaactaaatcctaaaaatctagttttctcctatttccacacctttctagtataagctatttttagcattttgacaaatctcttttaggaattccaacatgtcttgacctttctgcaaaaacagtatactatactagtgtatatacagataaaaaggagtcact 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: 86 Start: 148 End: 177 ...................................................................................................................................................TTTGTCAAAATGCTAAAAATAGCTTATACT...................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 83 Start: 202 End: 231 .........................................................................................................................................................................................................CTTGACCTTTCTGCAAAAACAGTATACTAT................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttctagtcaaggctgctaaattcccataccagccatctatatatgattaagctcttctttcatttttcaagtccagcagaacactaattgatgtgacggtcaactaaatcctaaaaatctagttttctcctatttccacacctttctagtataagctatttttagcattttgacaaatctcttttaggaattccaacatgtcttgacctttctgcaaaaacagtatactatactagtgtatatacagataaaaaggagtcact Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1347:SSA_1348|SSA_1347:SSA_1348:PhnA protein, putative:hypothetical protein:<-->:1365232..1365494 263 ttctagtcaaggctgctaaattcccataccagccatctatatatgattaagctcttctttcatttttcaagtccagcagaacactaattgatgtgacggtcaactaaatcctaaaaatctagttttctcctatttccacacctttctagtataagctatttttagcattttgacaaatctcttttaggaattccaacatgtcttgacctttctgcaaaaacagtatactatactagtgtatatacagataaaaaggagtcact Intra-Species Hit: Count: 1 Min: 1 Max: 263 Len: 263 Subject: NC_009009_SSA_1347_SSA_1348|PhnA protein, putative:hypothetical protein|NEGATIVE:POSITIVE|[1365232,1365494]|263 HSP 1 e-value: 1.0E-147 bit: 521.0 Len: 263 Query Start:1 Query End:263 Subject Strand: POSITIVE Subject Start: 1 Subject End: 263 ttctagtcaaggctgctaaattcccataccagccatctatatatgattaagctcttctttcatttttcaagtccagcagaacactaattgatgtgacggtcaactaaatcctaaaaatctagttttctcctatttccacacctttctagtataagctatttttagcattttgacaaatctcttttaggaattccaacatgtcttgacctttctgcaaaaacagtatactatactagtgtatatacagataaaaaggagtcact ttctagtcaaggctgctaaattcccataccagccatctatatatgattaagctcttctttcatttttcaagtccagcagaacactaattgatgtgacggtcaactaaatcctaaaaatctagttttctcctatttccacacctttctagtataagctatttttagcattttgacaaatctcttttaggaattccaacatgtcttgacctttctgcaaaaacagtatactatactagtgtatatacagataaaaaggagtcact Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCUAGUCAAGGCUGCUAAAUUCCCAUACCAGCCAUCUAUAUAUGAUUAAGCUCUUCUUUCAUUUUUCAAGUCCAGCAGAACACUAAUUGAUGUGACGGUCAACUAAAUCCUAAAAAUCUAGUUUUCUCCUAUUUCCACACCUUUCUAGUAUAAGCUAUUUUUAGCAUUUUGACAAAUCUCUUUUAGGAAUUCCAACAUGUCUUGACCUUUCUGCAAAAACAGUAUACUAUACUAGUGUAUAUACAGAUAAAAAGGAGUCACU ..........(((((.((........)).)))))................((((((.(((.((((..........(((((.(((........)))..((((((.....((((((((..((((.......................)))).....((((....))))...............))))))))....(.....)..))))))..))))).......((((((((...))))))))....))))))).)))))).... (-45.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUGACUCCUUUUUAUCUGUAUAUACACUAGUAUAGUAUACUGUUUUUGCAGAAAGGUCAAGACAUGUUGGAAUUCCUAAAAGAGAUUUGUCAAAAUGCUAAAAAUAGCUUAUACUAGAAAGGUGUGGAAAUAGGAGAAAACUAGAUUUUUAGGAUUUAGUUGACCGUCACAUCAAUUAGUGUUCUGCUGGACUUGAAAAAUGAAAGAAGAGCUUAAUCAUAUAUAGAUGGCUGGUAUGGGAAUUUAGCAGCCUUGACUAGAA (((...........((((((((((...(((((((((....(((((((((((.....(.((((.(...((((.....))))....).)))).)....))).)))))))).)))))))))...(((((((.....((....(((((((((.....)))))))))..)).))))))).(((((.(((((.((....((....))....)).)))))))))).))))))))))(((((.((........)).)))))...))).... (-61.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 871 60 11 151 102 NC_009009:SSA_1347|5end_PhnA_protein,_putative_1365141..1365371_NEGATIVE 287 79 32 129 72 NC_009009:SSA_0240|5end_Acetyltransferase,_GNAT_family,_putative_233410..233640_POSITIVE 276 80 32 109 61 NC_009009:SSA_0580|5end_Isochorismatase_family_protein,_putative_572816..573046_POSITIVE 271 35 4 49 13 NC_009009:SSA_0396|5end_hypothetical_protein_393595..393825_NEGATIVE 266 37 2 231 193 NC_009009:SSA_1087|5end_ABC-type_transporter_(antibiotic_resistance_protein),_ATPase_component,_putative_1104524..1104754_POSITIVE 260 147 102 167 113 NC_009009:SSA_1168|5end_hypothetical_protein_1194151..1194381_POSITIVE 260 63 24 91 46 NC_009009:SSA_0786|5end_Proton-translocating_ATPase,_F1_sector,_alpha_subunit,_putative_768737..768967_POSITIVE 259 75 31 231 179 NC_009009:SSA_2265|5end_Maltodextrin_phosphorylase,_putative_2264197..2264427_NEGATIVE 259 70 22 138 84 NC_009009:SSA_1483|5end_Sphingosine_kinase_(diacylglycerol_kinase),_putative_1490220..1490450_NEGATIVE 258 135 98 122 86 NC_009009:SSA_1771|5end_Conserved_DNA_methyltransferase_protein,_putative_1758799..1759029_NEGATIVE 257 99 60 204 163 NC_009009:SSA_0934|5end_HydD,_putative_943208..943438_POSITIVE 257 32 1 209 181 NC_009009:SSA_0582|5end_Methylase,_putative_573769..573999_POSITIVE 256 70 22 49 3 NC_009009:SSA_2017|5end_Hypothetical_protein_(possibly_membrane-associated)_2017331..2017561_NEGATIVE 256 39 3 42 1 NC_009009:SSA_0680|5end_Serine/threonine_protein_phosphatase,_putative_662425..662655_POSITIVE 255 45 3 222 179 NC_009009:SSA_0854|5end_hypothetical_protein_841335..841565_POSITIVE 254 130 88 99 61 NC_009009:SSA_0254|5end_hypothetical_protein_247492..247722_NEGATIVE 253 94 68 85 55 NC_009009:SSA_1949|5end_AliA_protein,_putative_1944373..1944603_NEGATIVE 252 229 185 188 140 NC_009009:SSA_1091|5end_Thymidylate_synthase,_putative_1108635..1108865_POSITIVE 250 47 5 79 45 NC_009009:SSA_2143|5end_Conserved_uncharacterized_protein_2144225..2144455_NEGATIVE 249 65 21 65 16 NC_009009:SSA_1602|5end_Exoribonuclease,_VacB/Rnb_family,_putative_1609370..1609600_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 336 103 61 138 102 NC_009009:SSA_0242|3end_hypothetical_protein_235810..235960_POSITIVE 287 79 32 132 75 NC_009009:SSA_0239|3end_7,8-dihydro-8-oxoguanine-triphosphatase,_putative_233493..233643_POSITIVE 284 37 2 121 90 NC_009009:SSA_1372|3end_hypothetical_protein_1388946..1389096_NEGATIVE 283 58 11 115 71 NC_009009:SSA_0325|3end_Membrane-anchored_glycerophosphoryl_diester_phosphodiesterase,_putative_319437..319587_POSITIVE 276 80 32 112 64 NC_009009:SSA_0579|3end_Hydrolase,_HAD_superfamily,_putative_572899..573049_POSITIVE 268 55 11 63 23 NC_009009:SSA_1495|3end_S-adenosylmethionine_synthetase,_putative_1501019..1501169_NEGATIVE 262 215 180 148 108 NC_009009:SSA_0716|3end_Competence_protein,_putative_703710..703860_POSITIVE 260 236 191 141 94 NC_009009:SSA_1959|3end_Undecaprenyl-diphosphatase,_putative_1955589..1955739_NEGATIVE 260 147 102 107 53 NC_009009:SSA_1167|3end_SRP54,_signal_recognition_particle_GTPase_protein,_putative_1194171..1194321_POSITIVE 259 70 22 128 74 NC_009009:SSA_1484|3end_DNA_ligase,_putative_1490230..1490380_NEGATIVE 257 32 1 134 106 NC_009009:SSA_0581|3end_Conserved_uncharacterized_protein_573774..573924_POSITIVE 254 130 88 106 68 NC_009009:SSA_0255|3end_Multiple_antibiotic_resistance_operon_transcription_repressor_(MarR),_putative_247485..247635_NEGATIVE 252 229 185 83 35 NC_009009:SSA_1090|3end_Glucokinase,_putative_1108610..1108760_POSITIVE 250 80 31 124 80 NC_009009:SSA_0343|3end_DNA-damage-inducible_protein_P,_putative_338669..338819_POSITIVE 249 58 15 52 15 NC_009009:SSA_0376|3end_ABC-type_methionine_transporter,_ATPase_component,_putative_366526..366676_POSITIVE 248 54 31 98 71 NC_009009:SSA_1541|3end_Peptidase,_U32_family,_putative_1545311..1545461_NEGATIVE 247 34 1 140 101 NC_009009:SSA_0273|3end_hypothetical_protein_268566..268716_POSITIVE 247 100 51 140 96 NC_009009:SSA_0139|3end_Copper_transport_operon_or_penicillinase_transcriptional_repressor,_putative_134706..134856_POSITIVE 246 99 51 57 9 NC_009009:SSA_0829|3end_Platelet-binding_glycoprotein_812165..812315_POSITIVE 246 78 31 136 93 NC_009009:SSA_0551|3end_L-asparaginase,_putative_546331..546481_NEGATIVE