Origin IGS: tgttgaaaaggatattactaagtagtgtgacgaatccccaaaagagaagtctcgaattggaaagaggtctcattttaggacttcaaagaaacaatttataagccaaaaaagcaagggagatttctccgagaaaagctgtttttccgtcctcttgaatagaagatagaccggaattgtatctatggcttgagattctgccgaggttctgctatatcggcatatgcaaatgcaataccatgatcttttacaatctatgcaggcaagcaat .........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 attgcttgcctgcatagattgtaaaagatcatggtattgcatttgcatatgccgatatagcagaacctcggcagaatctcaagccatagatacaattccggtctatcttctattcaagaggacggaaaaacagcttttctcggagaaatctcccttgcttttttggcttataaattgtttctttgaagtcctaaaatgagacctctttccaattcgagacttctcttttggggattcgtcacactacttagtaatatccttttcaaca Mask Tandem Repeat Region ================================================ tgttgaaaaggatattactaagtagtgtgacgaatccccaaaagagaagtctcgaattggaaagaggtctcattttaggacttcaaagaaacaatttataagccaaaaaagcaagggagatttctccgagaaaagctgtttttccgtcctcttgaatagaagatagaccggaattgtatctatggcttgagattctgccgaggttctgctatatcggcatatgcaaatgcaataccatgatcttttacaatctatgcaggcaagcaat Find is-nt database================================================ Query_seq: PG1816:PG1817|PG1816:PG1817:NAD(P)H dehydrogenase, quinone family, putative:hypothetical protein:<-<-:1912042..1912309 268 tgttgaaaaggatattactaagtagtgtgacgaatccccaaaagagaagtctcgaattggaaagaggtctcattttaggacttcaaagaaacaatttataagccaaaaaagcaagggagatttctccgagaaaagctgtttttccgtcctcttgaatagaagatagaccggaattgtatctatggcttgagattctgccgaggttctgctatatcggcatatgcaaatgcaataccatgatcttttacaatctatgcaggcaagcaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1816:PG1817|PG1816:PG1817:NAD(P)H dehydrogenase, quinone family, putative:hypothetical protein:<-<-:1912042..1912309 268 tgttgaaaaggatattactaagtagtgtgacgaatccccaaaagagaagtctcgaattggaaagaggtctcattttaggacttcaaagaaacaatttataagccaaaaaagcaagggagatttctccgagaaaagctgtttttccgtcctcttgaatagaagatagaccggaattgtatctatggcttgagattctgccgaggttctgctatatcggcatatgcaaatgcaataccatgatcttttacaatctatgcaggcaagcaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1816:PG1817|PG1816:PG1817:NAD(P)H dehydrogenase, quinone family, putative:hypothetical protein:<-<-:1912042..1912309 268 tgttgaaaaggatattactaagtagtgtgacgaatccccaaaagagaagtctcgaattggaaagaggtctcattttaggacttcaaagaaacaatttataagccaaaaaagcaagggagatttctccgagaaaagctgtttttccgtcctcttgaatagaagatagaccggaattgtatctatggcttgagattctgccgaggttctgctatatcggcatatgcaaatgcaataccatgatcttttacaatctatgcaggcaagcaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgttgaaaaggatattactaagtagtgtgacgaatccccaaaagagaagtctcgaattggaaagaggtctcattttaggacttcaaagaaacaatttataagccaaaaaagcaagggagatttctccgagaaaagctgtttttccgtcctcttgaatagaagatagaccggaattgtatctatggcttgagattctgccgaggttctgctatatcggcatatgcaaatgcaataccatgatcttttacaatctatgcaggcaagcaat Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 3 End: 98 .. M K R I L L S S V T N P Q K R S L E L E R G L I L G L Q R N N L .......................................................................................................................................................................... Protein_Len: 36 Strand: + Start: 56 End: 163 ....................................................... M G K R S H F R T S K K Q F I S Q K S K G D F S E K S C F S V L L N R R ......................................................................................................... Protein_Len: 37 Strand: + Start: 156 End: 266 ........................................................................................................................................................... M E D R P E L Y L W L E I L P R F C Y I G I C K C N T M I F Y N L C R Q A .. Protein_Len: 36 Strand: - Start: 86 End: 193 ..................................................................................... L F L K Y A L F A L S I E G L F A T K G D E Q I S S L G S N Y R H S S M ........................................................................... Protein_Len: 60 Strand: - Start: 73 End: 267 ........................................................................ F C N I L W F L L P S K E S F L Q K E T R K F L L Y V P I T D I A Q S E A S T R S Y R C I C I C Y W S R K C D I C A L M . tgttgaaaaggatattactaagtagtgtgacgaatccccaaaagagaagtctcgaattggaaagaggtctcattttaggacttcaaagaaacaatttataagccaaaaaagcaagggagatttctccgagaaaagctgtttttccgtcctcttgaatagaagatagaccggaattgtatctatggcttgagattctgccgaggttctgctatatcggcatatgcaaatgcaataccatgatcttttacaatctatgcaggcaagcaat 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================================================ PromScan Matrix: RpoN Strand: - Score: 81 Start: 222 End: 238 .............................................................................................................................................................................................................................ATGGTATTGCATTTGCA.............................. tgttgaaaaggatattactaagtagtgtgacgaatccccaaaagagaagtctcgaattggaaagaggtctcattttaggacttcaaagaaacaatttataagccaaaaaagcaagggagatttctccgagaaaagctgtttttccgtcctcttgaatagaagatagaccggaattgtatctatggcttgagattctgccgaggttctgctatatcggcatatgcaaatgcaataccatgatcttttacaatctatgcaggcaagcaat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG1816:PG1817|PG1816:PG1817:NAD(P)H dehydrogenase, quinone family, putative:hypothetical protein:<-<-:1912042..1912309 268 tgttgaaaaggatattactaagtagtgtgacgaatccccaaaagagaagtctcgaattggaaagaggtctcattttaggacttcaaagaaacaatttataagccaaaaaagcaagggagatttctccgagaaaagctgtttttccgtcctcttgaatagaagatagaccggaattgtatctatggcttgagattctgccgaggttctgctatatcggcatatgcaaatgcaataccatgatcttttacaatctatgcaggcaagcaat Intra-Species Hit: Count: 1 Min: 1 Max: 268 Len: 268 Subject: NC_002950_PG1816_PG1817|NAD(P)H dehydrogenase, quinone family, putative:hypothetical protein|NEGATIVE:NEGATIVE|[1912042,1912309]|268 HSP 1 e-value: 1.0E-150 bit: 531.0 Len: 268 Query Start:1 Query End:268 Subject Strand: POSITIVE Subject Start: 1 Subject End: 268 tgttgaaaaggatattactaagtagtgtgacgaatccccaaaagagaagtctcgaattggaaagaggtctcattttaggacttcaaagaaacaatttataagccaaaaaagcaagggagatttctccgagaaaagctgtttttccgtcctcttgaatagaagatagaccggaattgtatctatggcttgagattctgccgaggttctgctatatcggcatatgcaaatgcaataccatgatcttttacaatctatgcaggcaagcaat tgttgaaaaggatattactaagtagtgtgacgaatccccaaaagagaagtctcgaattggaaagaggtctcattttaggacttcaaagaaacaatttataagccaaaaaagcaagggagatttctccgagaaaagctgtttttccgtcctcttgaatagaagatagaccggaattgtatctatggcttgagattctgccgaggttctgctatatcggcatatgcaaatgcaataccatgatcttttacaatctatgcaggcaagcaat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUUGAAAAGGAUAUUACUAAGUAGUGUGACGAAUCCCCAAAAGAGAAGUCUCGAAUUGGAAAGAGGUCUCAUUUUAGGACUUCAAAGAAACAAUUUAUAAGCCAAAAAAGCAAGGGAGAUUUCUCCGAGAAAAGCUGUUUUUCCGUCCUCUUGAAUAGAAGAUAGACCGGAAUUGUAUCUAUGGCUUGAGAUUCUGCCGAGGUUCUGCUAUAUCGGCAUAUGCAAAUGCAAUACCAUGAUCUUUUACAAUCUAUGCAGGCAAGCAAU .((((.(((((((.((((........)))).(((((.((((..(((....)))...))))...(((((((.......)))))))..............(((((((.....((((.((((....))))..............(((((((.((((......))))..)).))))))))).....))))))).))))).(((((.((......)).)))))...(((....)))........))))))).))))...(((......))).. (-61.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUGCUUGCCUGCAUAGAUUGUAAAAGAUCAUGGUAUUGCAUUUGCAUAUGCCGAUAUAGCAGAACCUCGGCAGAAUCUCAAGCCAUAGAUACAAUUCCGGUCUAUCUUCUAUUCAAGAGGACGGAAAAACAGCUUUUCUCGGAGAAAUCUCCCUUGCUUUUUUGGCUUAUAAAUUGUUUCUUUGAAGUCCUAAAAUGAGACCUCUUUCCAAUUCGAGACUUCUCUUUUGGGGAUUCGUCACACUACUUAGUAAUAUCCUUUUCAACA ((((((...((((...((((......))))..((((((((....))).)))))......))))......(((.(((((..((((((.(((..((.(((((.....((((((.....)))))))))))..............((((....))))..))..))).))))))....................(((((((.((((..((((........))))..))))))))))))))))))).........))))))............. (-64.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 920 70 21 161 112 NC_002950:PG1816|5end_NAD(P)H_dehydrogenase,_quinone_family,_putative_1911951..1912181_NEGATIVE 385 224 181 147 103 NC_002950:PG0021|5end_TIM-barrel_protein,_putative,_NifR3_family_25123..25353_NEGATIVE 357 215 175 126 87 NC_002950:PG1546|5end_hypothetical_protein_1624087..1624317_POSITIVE 354 236 195 67 19 NC_002950:PG1807|5end_v-type_ATPase,_subunit_K_1902069..1902299_POSITIVE 349 220 178 227 181 NC_002950:PG1754|5end_hypothetical_protein_1839679..1839909_POSITIVE 336 228 183 56 1 NC_002950:PG0737|5end_hypothetical_protein_786188..786418_POSITIVE 336 224 183 61 21 NC_002950:PG0679|5end_outer_membrane_efflux_protein_729594..729824_POSITIVE 325 219 174 44 2 NC_002950:PG1154|5end_hypothetical_protein_1235825..1236055_NEGATIVE 325 219 174 180 138 NC_002950:PG1153|5end_hypothetical_protein_1235689..1235919_NEGATIVE 323 229 184 231 195 NC_002950:PG2204|5end_hypothetical_protein_2310381..2310611_POSITIVE 318 223 182 177 140 NC_002950:PG1018|5end_hypothetical_protein_1078894..1079124_POSITIVE 318 230 181 218 177 NC_002950:PG0091|5end_transporter,_putative_107400..107630_NEGATIVE 317 232 191 123 82 NC_002950:PG1605|5end_aminopeptidase_C_1685179..1685409_POSITIVE 316 237 191 55 4 NC_002950:PG1772|5end_endonuclease_III_1859079..1859309_POSITIVE 313 69 22 220 156 NC_002950:PG2061|5end_dihydrofolate_reductase_2158422..2158652_POSITIVE 307 70 25 69 24 NC_002950:PG0985|5end_RNA_polymerase_sigma-70_factor,_ECF_subfamily_1046930..1047160_POSITIVE 307 210 165 59 15 NC_002950:PG0485|5end_preprotein_translocase,_YajC_subunit_525324..525554_NEGATIVE 306 219 178 54 17 NC_002950:PG0953|5end_deoxyuridine_5'-triphosphate_nucleotidohydrolase_1012724..1012954_POSITIVE 306 153 111 225 186 NC_002950:PG0549|5end_ISPg1,_transposase_607072..607302_NEGATIVE 303 230 184 178 134 NC_002950:PG1274|5end_elongation_factor_P_1351843..1352073_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 397 218 185 141 114 NC_002950:PG0278|3end_hypothetical_protein_310477..310627_POSITIVE 385 224 181 150 106 NC_002950:PG0022|3end_sulfate_permease_family_protein_25120..25270_NEGATIVE 375 224 181 84 44 NC_002950:PG0555|3end_DNA-binding_protein,_histone-like_family_611716..611866_NEGATIVE 357 215 175 114 75 NC_002950:PG1545|3end_superoxide_dismutase,_Fe-Mn_1624155..1624305_POSITIVE 336 228 183 81 26 NC_002950:PG0736|3end_ribonuclease_HII_786293..786443_POSITIVE 335 237 195 143 101 NC_002950:PG2208|3end_hypothetical_protein_2320332..2320482_NEGATIVE 325 231 193 132 97 NC_002950:PG1229|3end_hypothetical_protein_1305559..1305709_NEGATIVE 318 223 182 147 110 NC_002950:PG1017|3end_pyruvate_phosphate_dikinase_1078944..1079094_POSITIVE 303 230 184 46 2 NC_002950:PG0569|3end_hypothetical_protein_624697..624847_NEGATIVE 302 237 196 140 102 NC_002950:PG2154|3end_hypothetical_protein_2260760..2260910_NEGATIVE 302 170 126 100 52 NC_002950:PG0016|3end_sigma-54_dependent_DNA-binding_response_regulator_18376..18526_POSITIVE 298 170 121 62 14 NC_002950:PG0139|3end_membrane-bound_lytic_murein_transglycosylase_D,_putative_161786..161936_NEGATIVE 298 219 175 146 98 NC_002950:PG0084|3end_L-serine_dehydratase,_iron-sulfur-dependent,_single_chain_form_99111..99261_POSITIVE 297 200 151 133 72 NC_002950:PG1389|3end_DNA-binding_protein,_histone-like_family_1470870..1471020_NEGATIVE 296 139 101 65 18 NC_002950:PG1102|3end_hypothetical_protein_1170860..1171010_NEGATIVE 294 219 173 118 76 NC_002950:PG2103|3end_hypothetical_protein_2213226..2213376_NEGATIVE 293 240 194 84 25 NC_002950:PG0351|3end_hypothetical_protein_387114..387264_POSITIVE 292 159 111 134 73 NC_002950:PG1213|3end_ribonuclease_H_1293163..1293313_POSITIVE 289 154 111 88 43 NC_002950:PG0963|3end_hypothetical_protein_1024087..1024237_NEGATIVE 288 149 101 130 75 NC_002950:PG2046|3end_hypothetical_protein_2145793..2145943_POSITIVE