Origin IGS: agaaaacgaggctggcacaattgtgtctaagcctcattttttatctttgaatatgtttcaagcagcagtcactttctttctatttatctcccttttcagaaaccgaatttctgaatacaatctttagaaaaattgtgataaaatagagacatcatttagaaaataggtatcagg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 cctgatacctattttctaaatgatgtctctattttatcacaatttttctaaagattgtattcagaaattcggtttctgaaaagggagataaatagaaagaaagtgactgctgcttgaaacatattcaaagataaaaaatgaggcttagacacaattgtgccagcctcgttttct Mask Tandem Repeat Region ================================================ agaaaacgaggctggcacaattgtgtctaagcctcattttttatctttgaatatgtttcaagcagcagtcactttctttctatttatctcccttttcagaaaccgaatttctgaatacaatctttagaaaaattgtgataaaatagagacatcatttagaaaataggtatcagg Find is-nt database================================================ Query_seq: SSA_1554:SSA_1555|SSA_1554:SSA_1555:hypothetical protein:Glucose-6-phosphate 1-dehydrogenase, putative:->->:1556908..1557081 174 agaaaacgaggctggcacaattgtgtctaagcctcattttttatctttgaatatgtttcaagcagcagtcactttctttctatttatctcccttttcagaaaccgaatttctgaatacaatctttagaaaaattgtgataaaatagagacatcatttagaaaataggtatcagg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1554:SSA_1555|SSA_1554:SSA_1555:hypothetical protein:Glucose-6-phosphate 1-dehydrogenase, putative:->->:1556908..1557081 174 agaaaacgaggctggcacaattgtgtctaagcctcattttttatctttgaatatgtttcaagcagcagtcactttctttctatttatctcccttttcagaaaccgaatttctgaatacaatctttagaaaaattgtgataaaatagagacatcatttagaaaataggtatcagg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1554:SSA_1555|SSA_1554:SSA_1555:hypothetical protein:Glucose-6-phosphate 1-dehydrogenase, putative:->->:1556908..1557081 174 agaaaacgaggctggcacaattgtgtctaagcctcattttttatctttgaatatgtttcaagcagcagtcactttctttctatttatctcccttttcagaaaccgaatttctgaatacaatctttagaaaaattgtgataaaatagagacatcatttagaaaataggtatcagg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agaaaacgaggctggcacaattgtgtctaagcctcattttttatctttgaatatgtttcaagcagcagtcactttctttctatttatctcccttttcagaaaccgaatttctgaatacaatctttagaaaaattgtgataaaatagagacatcatttagaaaataggtatcagg Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 20 End: 124 ................... M V S K P H F L S L N M F Q A A V T F F L F I S L F R N R I S E Y N L .................................................. Protein_Len: 31 Strand: + Start: 51 End: 143 .................................................. M C F K Q Q S L S F Y L S P F S E T E F L N T I F R K I V I K ............................... agaaaacgaggctggcacaattgtgtctaagcctcattttttatctttgaatatgtttcaagcagcagtcactttctttctatttatctcccttttcagaaaccgaatttctgaatacaatctttagaaaaattgtgataaaatagagacatcatttagaaaataggtatcagg 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: 82 Start: 92 End: 121 ...........................................................................................CTTTTCAGAAACCGAATTTCTGAATACAAT..................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agaaaacgaggctggcacaattgtgtctaagcctcattttttatctttgaatatgtttcaagcagcagtcactttctttctatttatctcccttttcagaaaccgaatttctgaatacaatctttagaaaaattgtgataaaatagagacatcatttagaaaataggtatcagg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1554:SSA_1555|SSA_1554:SSA_1555:hypothetical protein:Glucose-6-phosphate 1-dehydrogenase, putative:->->:1556908..1557081 174 agaaaacgaggctggcacaattgtgtctaagcctcattttttatctttgaatatgtttcaagcagcagtcactttctttctatttatctcccttttcagaaaccgaatttctgaatacaatctttagaaaaattgtgataaaatagagacatcatttagaaaataggtatcagg Intra-Species Hit: Count: 1 Min: 1 Max: 174 Len: 174 Subject: NC_009009_SSA_1554_SSA_1555|hypothetical protein:Glucose-6-phosphate 1-dehydrogenase, putative|POSITIVE:POSITIVE|[1556908,1557081]|174 HSP 1 e-value: 3.0E-94 bit: 345.0 Len: 174 Query Start:1 Query End:174 Subject Strand: POSITIVE Subject Start: 1 Subject End: 174 agaaaacgaggctggcacaattgtgtctaagcctcattttttatctttgaatatgtttcaagcagcagtcactttctttctatttatctcccttttcagaaaccgaatttctgaatacaatctttagaaaaattgtgataaaatagagacatcatttagaaaataggtatcagg agaaaacgaggctggcacaattgtgtctaagcctcattttttatctttgaatatgtttcaagcagcagtcactttctttctatttatctcccttttcagaaaccgaatttctgaatacaatctttagaaaaattgtgataaaatagagacatcatttagaaaataggtatcagg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAAAACGAGGCUGGCACAAUUGUGUCUAAGCCUCAUUUUUUAUCUUUGAAUAUGUUUCAAGCAGCAGUCACUUUCUUUCUAUUUAUCUCCCUUUUCAGAAACCGAAUUUCUGAAUACAAUCUUUAGAAAAAUUGUGAUAAAAUAGAGACAUCAUUUAGAAAAUAGGUAUCAGG ((((((.(((((((((((....)))))..)))))).))))))...((((((((((((((........(((((..(.((((((............((((((((.....)))))))).........)))))).)..)))))......))))))).))))))).............. (-42.74) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCUGAUACCUAUUUUCUAAAUGAUGUCUCUAUUUUAUCACAAUUUUUCUAAAGAUUGUAUUCAGAAAUUCGGUUUCUGAAAAGGGAGAUAAAUAGAAAGAAAGUGACUGCUGCUUGAAACAUAUUCAAAGAUAAAAAAUGAGGCUUAGACACAAUUGUGCCAGCCUCGUUUUCU .........((((((((......(((((((........((((((((....)))))))).(((((((((...)))))))))...))))))).......))))))))........(((((.....)))))......(((((((((((..(.(((....))).)))))))))))).. (-40.82) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 307 93 52 125 80 NC_009009:SSA_0929|5end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_938438..938668_POSITIVE 299 37 7 219 181 NC_009009:SSA_1928|5end_Acyl-CoA_dehydrogenase,_putative_1917010..1917240_NEGATIVE 297 67 25 41 5 NC_009009:SSA_0392|5end_hypothetical_protein_387876..388106_POSITIVE 290 120 72 174 133 NC_009009:SSA_0034|5end_hypothetical_protein_39547..39777_POSITIVE 286 49 1 224 180 NC_009009:SSA_2393|5end_Transcriptional_regulator,_XRE_family,_putative_204056..204286_POSITIVE 285 48 6 184 149 NC_009009:SSA_1771|5end_Conserved_DNA_methyltransferase_protein,_putative_1758799..1759029_NEGATIVE 285 62 32 154 121 NC_009009:SSA_0028|5end_Phosphoribosylaminoimidazole-succinocarboxamide_synthase,_putative_31883..32113_POSITIVE 271 47 8 111 68 NC_009009:SSA_1618|5end_hypothetical_protein_1621574..1621804_NEGATIVE 269 44 8 221 185 NC_009009:SSA_0854|5end_hypothetical_protein_841335..841565_POSITIVE 262 48 1 229 188 NC_009009:SSA_1997|5end_Membrane_spanning_protein,_putative_1994911..1995141_NEGATIVE 261 32 1 46 21 NC_009009:SSA_1430|5end_Ribonuclease_Z,_putative_1438036..1438266_NEGATIVE 258 34 6 65 36 NC_009009:SSA_1879|5end_Glycyl-tRNA_synthetase_beta_chain,_putative_1874262..1874492_NEGATIVE 256 49 8 45 3 NC_009009:SSA_0682|5end_Conserved_uncharacterized_protein_663438..663668_POSITIVE 253 47 1 185 141 NC_009009:SSA_1243|5end_Dihydroorotate_dehydrogenase_electron_transfer_subunit,_putative_1268204..1268434_NEGATIVE 253 94 61 78 33 NC_009009:SSA_0746|5end_Glucosamine-6-phosphate_deaminase,_putative_727078..727308_POSITIVE 251 88 54 117 84 NC_009009:SSA_0079|5end_ROK_family_protein,_putative_82855..83085_POSITIVE 250 68 30 199 162 NC_009009:SSA_2099|5end_ABC-type_arginine/histidine_transporter,_permease_protein,_putative_2104313..2104543_NEGATIVE 249 120 76 194 139 NC_009009:SSA_1758|5end_hypothetical_protein_1746619..1746849_NEGATIVE 248 110 61 144 83 NC_009009:SSA_1059|5end_hypothetical_protein_1076153..1076383_POSITIVE 245 100 54 130 80 NC_009009:SSA_1804|5end_NADPH-flavin_oxidoreductase,_putative_1788668..1788898_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 413 44 1 94 49 NC_009009:SSA_1554|3end_hypothetical_protein_1556847..1556997_POSITIVE 307 93 52 132 87 NC_009009:SSA_0928|3end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_938525..938675_POSITIVE 290 120 72 147 106 NC_009009:SSA_0033|3end_Phosphoribosylglycinamide_(GAR)_formyltransferase,_putative_39600..39750_POSITIVE 285 48 6 88 53 NC_009009:SSA_1772|3end_hypothetical_protein_1758895..1759045_NEGATIVE 263 100 58 121 68 NC_009009:SSA_0908|3end_ABC-type_uncharacterized_transport_system,_periplasmic_component,_putative_920787..920937_POSITIVE 262 48 1 92 51 NC_009009:SSA_1998|3end_Trigger_factor,_putative_1995048..1995198_NEGATIVE 261 32 1 35 10 NC_009009:SSA_1431|3end_hypothetical_protein_1438047..1438197_NEGATIVE 261 99 51 111 55 NC_009009:SSA_1087|3end_ABC-type_transporter_(antibiotic_resistance_protein),_ATPase_component,_putative_1106472..1106622_POSITIVE 258 34 6 62 33 NC_009009:SSA_1880|3end_Glycyl-tRNA_synthetase_alpha_chain,_putative_1874265..1874415_NEGATIVE 255 39 6 149 113 NC_009009:SSA_0093|3end_V-type_sodium_ATPase,_subunit_D,_putative_94989..95139_POSITIVE 251 88 54 83 50 NC_009009:SSA_0078|3end_N-acetylneuraminate_lyase,_putative_82901..83051_POSITIVE 249 50 1 127 67 NC_009009:SSA_1801|3end_hypothetical_protein_1782652..1782802_NEGATIVE 249 120 76 149 94 NC_009009:SSA_1759|3end_hypothetical_protein_1746664..1746814_NEGATIVE 248 110 61 122 61 NC_009009:SSA_1058|3end_Thiamine_biosynthesis_protein,_putative_1076211..1076361_POSITIVE 245 100 54 133 83 NC_009009:SSA_1805|3end_Primosomal_protein_DnaI,_putative_1788665..1788815_NEGATIVE 245 34 1 72 45 NC_009009:SSA_0564|3end_Potential_aminotransferase,_putative_556988..557138_POSITIVE 243 42 1 85 37 NC_009009:SSA_1808|3end_hypothetical_protein_1791394..1791544_NEGATIVE 243 34 3 61 30 NC_009009:SSA_1162|3end_Possible_fimbrial_assembly_protein_fimC,_putative_1188489..1188639_NEGATIVE 243 34 3 70 39 NC_009009:SSA_1161|3end_hypothetical_protein_1188443..1188593_POSITIVE 240 49 2 65 12 NC_009009:SSA_0732|3end_Transposase,_putative_715711..715861_NEGATIVE