Origin IGS: tagaacgattttcctcccttcctgtattttagtgctgcaattcttcaagatatcaccatcgataaagatgataaaagaaaaggccttttccgtatatggaaaaggcgcacaaataccacttttttcggtatgattcctacgctggcattacccagatcaggtgcggacgaagcttacacttcctctcagactgtacacagactcccatatataggactatgatagcgcaatcatcagcaaatgtcaaggttggagcttggactcactatttttcaacgataagtgaagcaaacaatcatcaa .........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 ttgatgattgtttgcttcacttatcgttgaaaaatagtgagtccaagctccaaccttgacatttgctgatgattgcgctatcatagtcctatatatgggagtctgtgtacagtctgagaggaagtgtaagcttcgtccgcacctgatctgggtaatgccagcgtaggaatcataccgaaaaaagtggtatttgtgcgccttttccatatacggaaaaggccttttcttttatcatctttatcgatggtgatatcttgaagaattgcagcactaaaatacaggaagggaggaaaatcgttcta Mask Tandem Repeat Region ================================================ tagaacgattttcctcccttcctgtattttagtgctgcaattcttcaagatatcaccatcgataaagatgataaaagaaaaggccttttccgtatatggaaaaggcgcacaaataccacttttttcggtatgattcctacgctggcattacccagatcaggtgcggacgaagcttacacttcctctcagactgtacacagactcccatatataggactatgatagcgcaatcatcagcaaatgtcaaggttggagcttggactcactatttttcaacgataagtgaagcaaacaatcatcaa Find is-nt database================================================ Query_seq: SSA_2353:SSA_2354|SSA_2353:SSA_2354:ABC-type nitrate/sulfonate/bicarbonate transport system, permease component, putative:hypothetical protein:<-<-:2355393..2355694 302 tagaacgattttcctcccttcctgtattttagtgctgcaattcttcaagatatcaccatcgataaagatgataaaagaaaaggccttttccgtatatggaaaaggcgcacaaataccacttttttcggtatgattcctacgctggcattacccagatcaggtgcggacgaagcttacacttcctctcagactgtacacagactcccatatataggactatgatagcgcaatcatcagcaaatgtcaaggttggagcttggactcactatttttcaacgataagtgaagcaaacaatcatcaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2353:SSA_2354|SSA_2353:SSA_2354:ABC-type nitrate/sulfonate/bicarbonate transport system, permease component, putative:hypothetical protein:<-<-:2355393..2355694 302 tagaacgattttcctcccttcctgtattttagtgctgcaattcttcaagatatcaccatcgataaagatgataaaagaaaaggccttttccgtatatggaaaaggcgcacaaataccacttttttcggtatgattcctacgctggcattacccagatcaggtgcggacgaagcttacacttcctctcagactgtacacagactcccatatataggactatgatagcgcaatcatcagcaaatgtcaaggttggagcttggactcactatttttcaacgataagtgaagcaaacaatcatcaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2353:SSA_2354|SSA_2353:SSA_2354:ABC-type nitrate/sulfonate/bicarbonate transport system, permease component, putative:hypothetical protein:<-<-:2355393..2355694 302 tagaacgattttcctcccttcctgtattttagtgctgcaattcttcaagatatcaccatcgataaagatgataaaagaaaaggccttttccgtatatggaaaaggcgcacaaataccacttttttcggtatgattcctacgctggcattacccagatcaggtgcggacgaagcttacacttcctctcagactgtacacagactcccatatataggactatgatagcgcaatcatcagcaaatgtcaaggttggagcttggactcactatttttcaacgataagtgaagcaaacaatcatcaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tagaacgattttcctcccttcctgtattttagtgctgcaattcttcaagatatcaccatcgataaagatgataaaagaaaaggccttttccgtatatggaaaaggcgcacaaataccacttttttcggtatgattcctacgctggcattacccagatcaggtgcggacgaagcttacacttcctctcagactgtacacagactcccatatataggactatgatagcgcaatcatcagcaaatgtcaaggttggagcttggactcactatttttcaacgataagtgaagcaaacaatcatcaa Predict ORF larger than 30AA ================================================ Protein_Len: 41 Strand: + Start: 8 End: 130 ....... M F L P S C I L V L Q F F K I S P S I K M I K E K A F S V Y G K G A Q I P L F S V ............................................................................................................................................................................ Protein_Len: 60 Strand: + Start: 22 End: 219 ..................... M Y F S A A I L Q D I T I D K D D K R K G L F R I W K R R T N T T F F G M I P T L A L P R S G A D E A Y T S S Q T V H R ................................................................................... Protein_Len: 60 Strand: + Start: 96 End: 302 ............................................................................................... M E K A H K Y H F F R Y D S Y A G I T Q I R C G R S L H F L S D C T Q T P I Y R T M I A Q S S A N V K V G A W T H Y F S Protein_Len: 36 Strand: - Start: 140 End: 247 ........................................................................................................................................... A P M V W I L H P R L K C K R E S Q V C V G M Y L V I I A C D D A F T M ....................................................... Protein_Len: 36 Strand: - Start: 48 End: 155 ............................................... S I V M S L S S L L F P R K R I H F L R V F V V K K P I I G V S A N G M ................................................................................................................................................... Protein_Len: 38 Strand: - Start: 1 End: 114 L V I K R G E Q I K T S C N K L I D G D I F I I F S F A K E T Y P F P A C M ............................................................................................................................................................................................ tagaacgattttcctcccttcctgtattttagtgctgcaattcttcaagatatcaccatcgataaagatgataaaagaaaaggccttttccgtatatggaaaaggcgcacaaataccacttttttcggtatgattcctacgctggcattacccagatcaggtgcggacgaagcttacacttcctctcagactgtacacagactcccatatataggactatgatagcgcaatcatcagcaaatgtcaaggttggagcttggactcactatttttcaacgataagtgaagcaaacaatcatcaa 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: 219 End: 248 ..........................................................................................................................................................................................................................CTTGACATTTGCTGATGATTGCGCTATCAT...................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tagaacgattttcctcccttcctgtattttagtgctgcaattcttcaagatatcaccatcgataaagatgataaaagaaaaggccttttccgtatatggaaaaggcgcacaaataccacttttttcggtatgattcctacgctggcattacccagatcaggtgcggacgaagcttacacttcctctcagactgtacacagactcccatatataggactatgatagcgcaatcatcagcaaatgtcaaggttggagcttggactcactatttttcaacgataagtgaagcaaacaatcatcaa Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 95 HP_score: -7.6 Tail_Score: -5.20781 Start: 82 End: 107 Full_Region: aaagtggtatttgtg cgccttttcc atatac ggaaaaggcc ttttcttttatcatc .................................................................................cgccttttccatatacggaaaaggcc................................................................................................................................................................................................... TransTerm Strand: - Conf: 84 HP_score: -11.1 Tail_Score: -3.70842 Start: 83 End: 106 Full_Region: aagtggtatttgtgc gccttttcc atatac ggaaaaggc cttttcttttatcat ..................................................................................gccttttccatatacggaaaaggc.................................................................................................................................................................................................... Find igs database================================================ Query_seq: SSA_2353:SSA_2354|SSA_2353:SSA_2354:ABC-type nitrate/sulfonate/bicarbonate transport system, permease component, putative:hypothetical protein:<-<-:2355393..2355694 302 tagaacgattttcctcccttcctgtattttagtgctgcaattcttcaagatatcaccatcgataaagatgataaaagaaaaggccttttccgtatatggaaaaggcgcacaaataccacttttttcggtatgattcctacgctggcattacccagatcaggtgcggacgaagcttacacttcctctcagactgtacacagactcccatatataggactatgatagcgcaatcatcagcaaatgtcaaggttggagcttggactcactatttttcaacgataagtgaagcaaacaatcatcaa Intra-Species Hit: Count: 1 Min: 1 Max: 302 Len: 302 Subject: NC_009009_SSA_2353_SSA_2354|ABC-type nitrate/sulfonate/bicarbonate transport system, permease component, putative:hypothetical protein|NEGATIVE:NEGATIVE|[2355393,2355694]|302 HSP 1 e-value: 1.0E-170 bit: 599.0 Len: 302 Query Start:1 Query End:302 Subject Strand: POSITIVE Subject Start: 1 Subject End: 302 tagaacgattttcctcccttcctgtattttagtgctgcaattcttcaagatatcaccatcgataaagatgataaaagaaaaggccttttccgtatatggaaaaggcgcacaaataccacttttttcggtatgattcctacgctggcattacccagatcaggtgcggacgaagcttacacttcctctcagactgtacacagactcccatatataggactatgatagcgcaatcatcagcaaatgtcaaggttggagcttggactcactatttttcaacgataagtgaagcaaacaatcatcaa tagaacgattttcctcccttcctgtattttagtgctgcaattcttcaagatatcaccatcgataaagatgataaaagaaaaggccttttccgtatatggaaaaggcgcacaaataccacttttttcggtatgattcctacgctggcattacccagatcaggtgcggacgaagcttacacttcctctcagactgtacacagactcccatatataggactatgatagcgcaatcatcagcaaatgtcaaggttggagcttggactcactatttttcaacgataagtgaagcaaacaatcatcaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGAACGAUUUUCCUCCCUUCCUGUAUUUUAGUGCUGCAAUUCUUCAAGAUAUCACCAUCGAUAAAGAUGAUAAAAGAAAAGGCCUUUUCCGUAUAUGGAAAAGGCGCACAAAUACCACUUUUUUCGGUAUGAUUCCUACGCUGGCAUUACCCAGAUCAGGUGCGGACGAAGCUUACACUUCCUCUCAGACUGUACACAGACUCCCAUAUAUAGGACUAUGAUAGCGCAAUCAUCAGCAAAUGUCAAGGUUGGAGCUUGGACUCACUAUUUUUCAACGAUAAGUGAAGCAAACAAUCAUCAA ......((((.((.(((...((((.(((((((((((((..................((((......))))......(((...((((((((((....))))))))))......(((((.........)))))..)))....)).)))))))...))))))))...))).)).((((.(((((.........(((....)))..(((........)))...(((((..((........))...)))))..(((((((..(((.....)))..)))))))...)))))))))....))))..... (-68.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGAUGAUUGUUUGCUUCACUUAUCGUUGAAAAAUAGUGAGUCCAAGCUCCAACCUUGACAUUUGCUGAUGAUUGCGCUAUCAUAGUCCUAUAUAUGGGAGUCUGUGUACAGUCUGAGAGGAAGUGUAAGCUUCGUCCGCACCUGAUCUGGGUAAUGCCAGCGUAGGAAUCAUACCGAAAAAAGUGGUAUUUGUGCGCCUUUUCCAUAUACGGAAAAGGCCUUUUCUUUUAUCAUCUUUAUCGAUGGUGAUAUCUUGAAGAAUUGCAGCACUAAAAUACAGGAAGGGAGGAAAAUCGUUCUA ..(((((((....((((.((((((..((....))..))))))..))))(((..((((..(((((((.((((((((((((..((((((((((....)))))..))))).....(((....))))))))))...))))).)).((((..((((......))))..))))..............)))))(((((((((((((((((((......))))))))).(((((...(((((((.........)))))))....)))))......))))..))))))...))))..))).)))))))... (-85.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 895 130 81 221 172 NC_009009:SSA_2353|5end_ABC-type_nitrate/sulfonate/bicarbonate_transport_system,_permease_component,_putative_2355302..2355532_NEGATIVE 390 169 127 193 150 NC_009009:SSA_0769|5end_hypothetical_protein_749216..749446_NEGATIVE 372 175 137 61 6 NC_009009:SSA_1304|5end_hypothetical_protein_1323449..1323679_NEGATIVE 339 200 152 212 158 NC_009009:SSA_0964|5end_DEAD_RNA_helicase,_putative_974114..974344_NEGATIVE 316 177 131 135 75 NC_009009:SSA_1412|5end_hypothetical_protein_1424095..1424325_NEGATIVE 315 190 152 39 9 NC_009009:SSA_0406|5end_hypothetical_protein_402918..403148_NEGATIVE 311 173 133 227 172 NC_009009:SSA_0319|5end_Branched-chain_amino_acid_permease_(L-methionine,_L-isoleucine,_leucine_and_valine),_putative_312721..312951_POSITIVE 309 178 141 71 25 NC_009009:SSA_0980|5end_3-isopropylmalate_dehydratase_large_subunit,_putative_984004..984234_POSITIVE 308 180 136 183 130 NC_009009:SSA_2159|5end_hypothetical_protein_2159621..2159851_NEGATIVE 307 130 83 177 116 NC_009009:SSA_1481|5end_FmtA-like_protein,_putative_1486622..1486852_NEGATIVE 305 207 162 170 112 NC_009009:SSA_1368|5end_hypothetical_protein_1384077..1384307_NEGATIVE 304 192 151 165 122 NC_009009:SSA_0133|5end_50S_ribosomal_protein_L17,_putative_122096..122326_POSITIVE 302 173 136 203 161 NC_009009:SSA_0620|5end_hypothetical_protein_612325..612555_NEGATIVE 300 175 134 96 43 NC_009009:SSA_0143|5end_Conserved_uncharacterized_protein_137465..137695_POSITIVE 299 186 141 106 57 NC_009009:SSA_0703|5end_Citrate_synthase,_putative_688154..688384_POSITIVE 298 169 125 53 12 NC_009009:SSA_2296|5end_Transcriptional_regulator,_XRE_family,_putative_2298773..2299003_NEGATIVE 298 169 121 166 113 NC_009009:SSA_0218|5end_Sugar-binding_periplasmic_protein,_putative_213863..214093_POSITIVE 298 263 221 68 20 NC_009009:SSA_0186|5end_Competence_protein_ComYC,_putative_190061..190291_POSITIVE 295 177 133 153 97 NC_009009:SSA_0057|5end_Phosphotransferase_system_sugar-specific_EII_component,_putative_60762..60992_POSITIVE 294 290 243 144 97 NC_009009:SSA_1644|5end_hypothetical_protein_1645617..1645847_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 321 190 141 46 4 NC_009009:SSA_0407|3end_ABC-type_multidrug_transport_system_(3-component_subtilin_immunity_exporter),_ATPase_component,_putative_402911..403061_NEGATIVE 316 177 131 135 75 NC_009009:SSA_1413|3end_GufA-like_protein,_putative_1424095..1424245_NEGATIVE 309 178 141 69 23 NC_009009:SSA_0978|3end_hypothetical_protein_984082..984232_POSITIVE 305 207 162 105 47 NC_009009:SSA_1369|3end_FmtA-like_protein,_putative_1384142..1384292_NEGATIVE 299 186 141 103 54 NC_009009:SSA_0702|3end_Aconitase_A,_putative_688231..688381_POSITIVE 298 169 125 50 9 NC_009009:SSA_2297|3end_hypothetical_protein_2298776..2298926_NEGATIVE 298 263 221 68 20 NC_009009:SSA_0185|3end_Competence_protein_ComYB,_putative_190141..190291_POSITIVE 295 177 133 141 85 NC_009009:SSA_0056|3end_Phosphotransferase_system_sugar-specific_EIID_component,_putative_60830..60980_POSITIVE 293 44 8 112 71 NC_009009:SSA_1929|3end_Macrophage_infectivity_potentiator_protein,_putative_1917029..1917179_NEGATIVE 293 207 162 138 96 NC_009009:SSA_1478|3end_Transposase_ORF1,_putative_1483124..1483274_POSITIVE 290 208 170 144 100 NC_009009:SSA_1245|3end_Transcriptional_regulator,_LysR_family,_putative_1269710..1269860_POSITIVE 289 187 141 150 99 NC_009009:SSA_1810|3end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_winged-helix_DNA-binding_domains),_putative_1794707..1794857_NEGATIVE 288 200 151 123 69 NC_009009:SSA_1459|3end_RNA_methyltransferase,_putative_1466111..1466261_NEGATIVE 285 266 221 140 76 NC_009009:SSA_2119|3end_Pentose-5-phosphate-3-epimerase,_putative_2120439..2120589_NEGATIVE 281 228 188 47 2 NC_009009:SSA_2214|3end_2-C-methyl-D-erythritol_4-phosphate_cytidylyltransferase_2,_putative_2215113..2215263_NEGATIVE 281 44 6 100 51 NC_009009:SSA_1328|3end_hypothetical_protein_1344342..1344492_NEGATIVE 280 198 152 125 78 NC_009009:SSA_1759|3end_hypothetical_protein_1746664..1746814_NEGATIVE 277 86 44 49 10 NC_009009:SSA_2055|3end_hypothetical_protein_2057936..2058086_NEGATIVE 276 173 134 128 84 NC_009009:SSA_2285|3end_hypothetical_protein_2287825..2287975_POSITIVE 276 249 202 128 88 NC_009009:SSA_0832|3end_SecY-like_protein,_putative_818011..818161_POSITIVE