Origin IGS: aattgaaggggattgtctgtctagtcttgaatacgttaggtttcctctaacacattgattgagaagattagagtatatgcattttaatcagtaaggtagagaaataatttttccctgcctttatttttttataaatctgaaagcgcttcattgacaaagtcaatcagatagtttataatataataacagtatagaaaatggcaaggaagcctgatttgatcgcaatgaagcgagtgtttcagaatcaaaggggttttctatgccatttttttgcgcactattattttttatggaggattgtttct .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 agaaacaatcctccataaaaaataatagtgcgcaaaaaaatggcatagaaaacccctttgattctgaaacactcgcttcattgcgatcaaatcaggcttccttgccattttctatactgttattatattataaactatctgattgactttgtcaatgaagcgctttcagatttataaaaaaataaaggcagggaaaaattatttctctaccttactgattaaaatgcatatactctaatcttctcaatcaatgtgttagaggaaacctaacgtattcaagactagacagacaatccccttcaatt Mask Tandem Repeat Region ================================================ aattgaaggggattgtctgtctagtcttgaatacgttaggtttcctctaacacattgattgagaagattagagtatatgcattttaatcagtaaggtagagaaataatttttccctgcctttatttttttataaatctgaaagcgcttcattgacaaagtcaatcagatagtttataatataataacagtatagaaaatggcaaggaagcctgatttgatcgcaatgaagcgagtgtttcagaatcaaaggggttttctatgccatttttttgcgcactattattttttatggaggattgtttct Find is-nt database================================================ Query_seq: SSA_0507:SSA_0508|SSA_0507:SSA_0508:hypothetical protein:Conserved uncharacterized protein, possible phosphoserine phosphatase:->->:506503..506807 305 aattgaaggggattgtctgtctagtcttgaatacgttaggtttcctctaacacattgattgagaagattagagtatatgcattttaatcagtaaggtagagaaataatttttccctgcctttatttttttataaatctgaaagcgcttcattgacaaagtcaatcagatagtttataatataataacagtatagaaaatggcaaggaagcctgatttgatcgcaatgaagcgagtgtttcagaatcaaaggggttttctatgccatttttttgcgcactattattttttatggaggattgtttct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0507:SSA_0508|SSA_0507:SSA_0508:hypothetical protein:Conserved uncharacterized protein, possible phosphoserine phosphatase:->->:506503..506807 305 aattgaaggggattgtctgtctagtcttgaatacgttaggtttcctctaacacattgattgagaagattagagtatatgcattttaatcagtaaggtagagaaataatttttccctgcctttatttttttataaatctgaaagcgcttcattgacaaagtcaatcagatagtttataatataataacagtatagaaaatggcaaggaagcctgatttgatcgcaatgaagcgagtgtttcagaatcaaaggggttttctatgccatttttttgcgcactattattttttatggaggattgtttct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0507:SSA_0508|SSA_0507:SSA_0508:hypothetical protein:Conserved uncharacterized protein, possible phosphoserine phosphatase:->->:506503..506807 305 aattgaaggggattgtctgtctagtcttgaatacgttaggtttcctctaacacattgattgagaagattagagtatatgcattttaatcagtaaggtagagaaataatttttccctgcctttatttttttataaatctgaaagcgcttcattgacaaagtcaatcagatagtttataatataataacagtatagaaaatggcaaggaagcctgatttgatcgcaatgaagcgagtgtttcagaatcaaaggggttttctatgccatttttttgcgcactattattttttatggaggattgtttct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aattgaaggggattgtctgtctagtcttgaatacgttaggtttcctctaacacattgattgagaagattagagtatatgcattttaatcagtaaggtagagaaataatttttccctgcctttatttttttataaatctgaaagcgcttcattgacaaagtcaatcagatagtttataatataataacagtatagaaaatggcaaggaagcctgatttgatcgcaatgaagcgagtgtttcagaatcaaaggggttttctatgccatttttttgcgcactattattttttatggaggattgtttct Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 198 End: 305 ..................................................................................................................................................................................................... M A R K P D L I A M K R V F Q N Q R G F L C H F F A H Y Y F L W R I V S Protein_Len: 43 Strand: - Start: 163 End: 291 .................................................................................................................................................................. D S L K Y Y L L L I S F P L S A Q N S R L S A L T E S D F P N E I G N K Q A S N N K M .............. Protein_Len: 39 Strand: - Start: 132 End: 248 ................................................................................................................................... L D S L A E N V F D I L Y N I I Y Y C Y L F H C P L R I Q D C H L S H K L I M ......................................................... Protein_Len: 31 Strand: - Start: 71 End: 163 ...................................................................... L I H M K I L L T S F Y N K G A K I K K Y I Q F R K M S L T M .............................................................................................................................................. aattgaaggggattgtctgtctagtcttgaatacgttaggtttcctctaacacattgattgagaagattagagtatatgcattttaatcagtaaggtagagaaataatttttccctgcctttatttttttataaatctgaaagcgcttcattgacaaagtcaatcagatagtttataatataataacagtatagaaaatggcaaggaagcctgatttgatcgcaatgaagcgagtgtttcagaatcaaaggggttttctatgccatttttttgcgcactattattttttatggaggattgtttct 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: 92 Start: 150 End: 179 .....................................................................................................................................................ATTGACAAAGTCAATCAGATAGTTTATAAT.............................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aattgaaggggattgtctgtctagtcttgaatacgttaggtttcctctaacacattgattgagaagattagagtatatgcattttaatcagtaaggtagagaaataatttttccctgcctttatttttttataaatctgaaagcgcttcattgacaaagtcaatcagatagtttataatataataacagtatagaaaatggcaaggaagcctgatttgatcgcaatgaagcgagtgtttcagaatcaaaggggttttctatgccatttttttgcgcactattattttttatggaggattgtttct Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 80 HP_score: -5.0 Tail_Score: -5.27709 Start: 95 End: 119 Full_Region: CATTTTAATCAGTAA GGTAGAGAAA TAATT TTTCCCTGCC TTTATTTTTTTATAA ..............................................................................................GGTAGAGAAATAATTTTTCCCTGCC.......................................................................................................................................................................................... TransTerm Strand: - Conf: 54 HP_score: -5.0 Tail_Score: -3.27774 Start: 95 End: 119 Full_Region: ttataaaaaaataaa ggcagggaaa aatta tttctctacc ttactgattaaaatg ..............................................................................................ggcagggaaaaattatttctctacc.......................................................................................................................................................................................... Find igs database================================================ Query_seq: SSA_0507:SSA_0508|SSA_0507:SSA_0508:hypothetical protein:Conserved uncharacterized protein, possible phosphoserine phosphatase:->->:506503..506807 305 aattgaaggggattgtctgtctagtcttgaatacgttaggtttcctctaacacattgattgagaagattagagtatatgcattttaatcagtaaggtagagaaataatttttccctgcctttatttttttataaatctgaaagcgcttcattgacaaagtcaatcagatagtttataatataataacagtatagaaaatggcaaggaagcctgatttgatcgcaatgaagcgagtgtttcagaatcaaaggggttttctatgccatttttttgcgcactattattttttatggaggattgtttct Intra-Species Hit: Count: 1 Min: 1 Max: 305 Len: 305 Subject: NC_009009_SSA_0507_SSA_0508|hypothetical protein:Conserved uncharacterized protein, possible phosphoserine phosphatase|POSITIVE:POSITIVE|[506503,506807]|305 HSP 1 e-value: 1.0E-147 bit: 521.0 Len: 305 Query Start:1 Query End:305 Subject Strand: POSITIVE Subject Start: 1 Subject End: 305 aattgaaggggattgtctgtctagtcttgaatacgttaggtttcctctaacacattgattgagaagattagagtatatgcattttaatcagtaaggtagagaaataatttttccctgcctttannnnnnnataaatctgaaagcgcttcattgacaaagtcaatcagatagtttataatataataacagtatagaaaatggcaaggaagcctgatttgatcgcaatgaagcgagtgtttcagaatcaaaggggttttctatgccannnnnnngcgcactattattttttatggaggattgtttct aattgaaggggattgtctgtctagtcttgaatacgttaggtttcctctaacacattgattgagaagattagagtatatgcattttaatcagtaaggtagagaaataatttttccctgcctttatttttttataaatctgaaagcgcttcattgacaaagtcaatcagatagtttataatataataacagtatagaaaatggcaaggaagcctgatttgatcgcaatgaagcgagtgtttcagaatcaaaggggttttctatgccatttttttgcgcactattattttttatggaggattgtttct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUGAAGGGGAUUGUCUGUCUAGUCUUGAAUACGUUAGGUUUCCUCUAACACAUUGAUUGAGAAGAUUAGAGUAUAUGCAUUUUAAUCAGUAAGGUAGAGAAAUAAUUUUUCCCUGCCUUUAUUUUUUUAUAAAUCUGAAAGCGCUUCAUUGACAAAGUCAAUCAGAUAGUUUAUAAUAUAAUAACAGUAUAGAAAAUGGCAAGGAAGCCUGAUUUGAUCGCAAUGAAGCGAGUGUUUCAGAAUCAAAGGGGUUUUCUAUGCCAUUUUUUUGCGCACUAUUAUUUUUUAUGGAGGAUUGUUUCU ....((((..(((((.((.....(((.((((...((((((.....)))))).......((.(((.(((((((((......)))))))))...(((((((.((((.....)))).)))))))..............))).)).....))))..)))..)).))))).(((..(((((((.((((((...(((.((((((((((((((((((((..((((((.....((((((....))))))..)))))).))))))))).))))))))))))))....))))))...)))))))..))).)))). (-78.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAAACAAUCCUCCAUAAAAAAUAAUAGUGCGCAAAAAAAUGGCAUAGAAAACCCCUUUGAUUCUGAAACACUCGCUUCAUUGCGAUCAAAUCAGGCUUCCUUGCCAUUUUCUAUACUGUUAUUAUAUUAUAAACUAUCUGAUUGACUUUGUCAAUGAAGCGCUUUCAGAUUUAUAAAAAAAUAAAGGCAGGGAAAAAUUAUUUCUCUACCUUACUGAUUAAAAUGCAUAUACUCUAAUCUUCUCAAUCAAUGUGUUAGAGGAAACCUAACGUAUUCAAGACUAGACAGACAAUCCCCUUCAAUU .(((..((((..........((((((((((......(((((((((..(((...((...(((((.(((.....((((......)))))))))))))).)))..)))))))))...))))))))))...((((((...((((((..(.((((......))))..)..)))))))))))).......((((.(((((((.....))))))).))))...)))).............((((.((((.......((((((((((.(....))))))))))).)))).))))............))).... (-62.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 321 264 222 85 41 NC_009009:SSA_1118|5end_Peptide_methionine_sulfoxide_reductase,_putative_1143322..1143552_POSITIVE 305 49 4 158 114 NC_009009:SSA_0509|5end_Propanediol_utilization_protein,_putative_508024..508254_POSITIVE 301 170 137 197 166 NC_009009:SSA_2170|5end_hypothetical_protein_2170240..2170470_NEGATIVE 297 225 188 156 120 NC_009009:SSA_2366|5end_ABC-type_cobalt_transport_system,_ATPase_component,_putative_2368869..2369099_NEGATIVE 293 80 33 135 88 NC_009009:SSA_0363|5end_D-alanine/glycine/Na_permease,_putative_353858..354088_POSITIVE 286 176 134 79 34 NC_009009:SSA_0008|5end_Transcription-repair_coupling_factor,_putative_5571..5801_POSITIVE 276 240 192 212 158 NC_009009:SSA_0321|5end_Methylase,_putative_313867..314097_POSITIVE 274 265 222 182 141 NC_009009:SSA_0643|5end_hypothetical_protein_630194..630424_NEGATIVE 273 242 204 219 183 NC_009009:SSA_2000|5end_hypothetical_protein_1997469..1997699_NEGATIVE 273 240 199 89 49 NC_009009:SSA_1510|5end_Rhamnosyltransferase,_putative_1515336..1515566_NEGATIVE 265 265 221 149 101 NC_009009:SSA_2207|5end_hypothetical_protein_2207221..2207451_NEGATIVE 261 249 205 188 130 NC_009009:SSA_0452|5end_Nitrogen_utilization_substance_protein_B,_putative_451534..451764_POSITIVE 260 247 202 224 166 NC_009009:SSA_1446|5end_Histidinol_dehydrogenase,_putative_1449190..1449420_NEGATIVE 260 239 192 81 31 NC_009009:SSA_1443|5end_1-(5-phosphoribosyl)-5-[(5-_phosphoribosylamino)methylideneamino]_imidazole-4-carboxamide_isomerase,_putative_1446672..1446902_NEGATIVE 258 279 244 52 27 NC_009009:SSA_0088|5end_V-type_sodium_ATPase,_subunit_C,_putative_88930..89160_POSITIVE 257 130 91 79 34 NC_009009:SSA_0441|5end_hypothetical_protein_441481..441711_POSITIVE 255 249 207 71 22 NC_009009:SSA_1984|5end_Cell_surface_SD_repeat_antigen_precursor,_putative_1979035..1979265_NEGATIVE 255 266 221 76 32 NC_009009:SSA_0481|5end_Cobyric_acid_synthase,_putative_481962..482192_POSITIVE 252 159 111 156 96 NC_009009:SSA_1993|5end_Conserved_uncharacterized_protein_1990790..1991020_NEGATIVE 252 223 200 218 194 NC_009009:SSA_1571|5end_Threonyl-tRNA_synthetase,_putative_1575154..1575384_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 321 264 222 69 25 NC_009009:SSA_1117|3end_hypothetical_protein_1143386..1143536_POSITIVE 293 242 201 74 30 NC_009009:SSA_0683|3end_DNA-binding_protein_HU,_putative_664739..664889_POSITIVE 288 174 137 75 26 NC_009009:SSA_0327|3end_Glycosyltransferase,_putative_320436..320586_POSITIVE 286 176 134 86 41 NC_009009:SSA_0006|3end_Peptidyl-tRNA_hydrolase,_putative_5658..5808_POSITIVE 277 58 12 136 90 NC_009009:SSA_0377|3end_ABC-type_methionine_transporter,_permease_component,_putative_367218..367368_POSITIVE 276 240 192 89 35 NC_009009:SSA_0320|3end_hypothetical_protein_313824..313974_POSITIVE 266 238 193 62 7 NC_009009:SSA_1547|3end_HPr_kinase/phosphorylase,_putative_1550045..1550195_NEGATIVE 260 249 201 66 4 NC_009009:SSA_2171|3end_hypothetical_protein_2170224..2170374_NEGATIVE 260 239 192 109 59 NC_009009:SSA_1444|3end_Imidazole_glycerol-phosphate_synthase_subunit_hisH,_putative_1446644..1446794_NEGATIVE 259 235 192 68 17 NC_009009:SSA_2076|3end_Conserved_uncharacterized_protein_2079390..2079540_NEGATIVE 258 276 240 104 65 NC_009009:SSA_0385|3end_ABC_transporter,_glycine-betaine/proline_permease_protein,_putative_378526..378676_NEGATIVE 258 279 244 41 16 NC_009009:SSA_0087|3end_V-type_sodium_ATPase,_subunit_E,_putative_88999..89149_POSITIVE 255 266 221 91 47 NC_009009:SSA_0480|3end_Cobalt_ABC_transporter,_ATP-binding_protein,_putative_482057..482207_POSITIVE 254 240 198 69 24 NC_009009:SSA_1907|3end_hypothetical_protein_1900813..1900963_POSITIVE 254 243 201 150 99 NC_009009:SSA_0531|3end_Ethanolamine_utilization_protein_eutQ_(cobalamin-dependent_degradation_of_ethanolamine),_putative_527884..528034_POSITIVE 252 159 111 85 25 NC_009009:SSA_1994|3end_CTP_synthase,_putative_1990861..1991011_NEGATIVE 252 46 3 82 42 NC_009009:SSA_1194|3end_Aspartate-semialdehyde_dehydrogenase,_putative_1220113..1220263_NEGATIVE 251 125 88 111 70 NC_009009:SSA_1985|3end_hypothetical_protein_1979623..1979773_NEGATIVE 250 189 142 64 22 NC_009009:SSA_0440|3end_30S_ribosomal_protein_S18,_putative_441465..441615_POSITIVE 249 46 9 103 72 NC_009009:SSA_0267|3end_ROK_family_protein,_putative_260873..261023_NEGATIVE