Origin IGS: actgacaaaccagcttgaaaagctggttttttactttgaatcataaagctcttctttacaaatttttaaaagcattttataataaaaagaagattgattgacatattatttgcaatcttgtttagttgctactaactcttagtatgtcttgataaatcatggtagtcacagatgcaaggagaaataataatgtagaatagcgatttttttgcaccactatcagatgagacagatgttgacagtttgttgtgtaagggctttagagacttatgatataatgaattcataaaagtttgagaagtctcttaatcttttcaagctgattttcataaaaaagaataggaaataagt .........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 acttatttcctattcttttttatgaaaatcagcttgaaaagattaagagacttctcaaacttttatgaattcattatatcataagtctctaaagcccttacacaacaaactgtcaacatctgtctcatctgatagtggtgcaaaaaaatcgctattctacattattatttctccttgcatctgtgactaccatgatttatcaagacatactaagagttagtagcaactaaacaagattgcaaataatatgtcaatcaatcttctttttattataaaatgcttttaaaaatttgtaaagaagagctttatgattcaaagtaaaaaaccagcttttcaagctggtttgtcagt Mask Tandem Repeat Region ================================================ actgacaaaccagcttgaaaagctggttttttactttgaatcataaagctcttctttacaaatttttaaaagcattttataataaaaagaagattgattgacatattatttgcaatcttgtttagttgctactaactcttagtatgtcttgataaatcatggtagtcacagatgcaaggagaaataataatgtagaatagcgatttttttgcaccactatcagatgagacagatgttgacagtttgttgtgtaagggctttagagacttatgatataatgaattcataaaagtttgagaagtctcttaatcttttcaagctgattttcataaaaaagaataggaaataagt Find is-nt database================================================ Query_seq: SSA_1010:SSA_1011|SSA_1010:SSA_1011:UDP-glucose 4-epimerase, putative:hypothetical protein:->->:1013923..1014273 351 actgacaaaccagcttgaaaagctggttttttactttgaatcataaagctcttctttacaaatttttaaaagcattttataataaaaagaagattgattgacatattatttgcaatcttgtttagttgctactaactcttagtatgtcttgataaatcatggtagtcacagatgcaaggagaaataataatgtagaatagcgatttttttgcaccactatcagatgagacagatgttgacagtttgttgtgtaagggctttagagacttatgatataatgaattcataaaagtttgagaagtctcttaatcttttcaagctgattttcataaaaaagaataggaaataagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1010:SSA_1011|SSA_1010:SSA_1011:UDP-glucose 4-epimerase, putative:hypothetical protein:->->:1013923..1014273 351 actgacaaaccagcttgaaaagctggttttttactttgaatcataaagctcttctttacaaatttttaaaagcattttataataaaaagaagattgattgacatattatttgcaatcttgtttagttgctactaactcttagtatgtcttgataaatcatggtagtcacagatgcaaggagaaataataatgtagaatagcgatttttttgcaccactatcagatgagacagatgttgacagtttgttgtgtaagggctttagagacttatgatataatgaattcataaaagtttgagaagtctcttaatcttttcaagctgattttcataaaaaagaataggaaataagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1010:SSA_1011|SSA_1010:SSA_1011:UDP-glucose 4-epimerase, putative:hypothetical protein:->->:1013923..1014273 351 actgacaaaccagcttgaaaagctggttttttactttgaatcataaagctcttctttacaaatttttaaaagcattttataataaaaagaagattgattgacatattatttgcaatcttgtttagttgctactaactcttagtatgtcttgataaatcatggtagtcacagatgcaaggagaaataataatgtagaatagcgatttttttgcaccactatcagatgagacagatgttgacagtttgttgtgtaagggctttagagacttatgatataatgaattcataaaagtttgagaagtctcttaatcttttcaagctgattttcataaaaaagaataggaaataagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 actgacaaaccagcttgaaaagctggttttttactttgaatcataaagctcttctttacaaatttttaaaagcattttataataaaaagaagattgattgacatattatttgcaatcttgtttagttgctactaactcttagtatgtcttgataaatcatggtagtcacagatgcaaggagaaataataatgtagaatagcgatttttttgcaccactatcagatgagacagatgttgacagtttgttgtgtaagggctttagagacttatgatataatgaattcataaaagtttgagaagtctcttaatcttttcaagctgattttcataaaaaagaataggaaataagt Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 197 End: 286 .................................................................................................................................................................................................... M A I F L H H Y Q M R Q M L T V C C V R A L E T Y D I M N S ................................................................. Protein_Len: 51 Strand: - Start: 135 End: 287 ...................................................................................................................................... S K T H R S L D H Y D C I C P S I I I Y F L S K K A G S D S S V S T S L K N H L P K L S K H Y L S N M ................................................................ Protein_Len: 36 Strand: - Start: 125 End: 232 ............................................................................................................................ N S S V R L I D Q Y I M T T V S A L L F L L T S Y R N K Q V V I L H S M ....................................................................................................................... actgacaaaccagcttgaaaagctggttttttactttgaatcataaagctcttctttacaaatttttaaaagcattttataataaaaagaagattgattgacatattatttgcaatcttgtttagttgctactaactcttagtatgtcttgataaatcatggtagtcacagatgcaaggagaaataataatgtagaatagcgatttttttgcaccactatcagatgagacagatgttgacagtttgttgtgtaagggctttagagacttatgatataatgaattcataaaagtttgagaagtctcttaatcttttcaagctgattttcataaaaaagaataggaaataagt 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: 90 Start: 54 End: 83 .....................................................CTTTACAAATTTTTAAAAGCATTTTATAAT............................................................................................................................................................................................................................................................................ PromScan Matrix: RpoD-17 Strand: + Score: 82 Start: 97 End: 126 ................................................................................................ATTGACATATTATTTGCAATCTTGTTTAGT................................................................................................................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ actgacaaaccagcttgaaaagctggttttttactttgaatcataaagctcttctttacaaatttttaaaagcattttataataaaaagaagattgattgacatattatttgcaatcttgtttagttgctactaactcttagtatgtcttgataaatcatggtagtcacagatgcaaggagaaataataatgtagaatagcgatttttttgcaccactatcagatgagacagatgttgacagtttgttgtgtaagggctttagagacttatgatataatgaattcataaaagtttgagaagtctcttaatcttttcaagctgattttcataaaaaagaataggaaataagt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 40 HP_score: -2.9 Tail_Score: -2.72344 Start: 44 End: 58 Full_Region: gcttttaaaaatttg taaag aagag cttta tgattcaaagtaaaa ...........................................taaagaagagcttta..................................................................................................................................................................................................................................................................................................... Find igs database================================================ Query_seq: SSA_1010:SSA_1011|SSA_1010:SSA_1011:UDP-glucose 4-epimerase, putative:hypothetical protein:->->:1013923..1014273 351 actgacaaaccagcttgaaaagctggttttttactttgaatcataaagctcttctttacaaatttttaaaagcattttataataaaaagaagattgattgacatattatttgcaatcttgtttagttgctactaactcttagtatgtcttgataaatcatggtagtcacagatgcaaggagaaataataatgtagaatagcgatttttttgcaccactatcagatgagacagatgttgacagtttgttgtgtaagggctttagagacttatgatataatgaattcataaaagtttgagaagtctcttaatcttttcaagctgattttcataaaaaagaataggaaataagt Intra-Species Hit: Count: 1 Min: 1 Max: 351 Len: 351 Subject: NC_009009_SSA_1010_SSA_1011|UDP-glucose 4-epimerase, putative:hypothetical protein|POSITIVE:POSITIVE|[1013923,1014273]|351 HSP 1 e-value: 0.0 bit: 654.0 Len: 351 Query Start:1 Query End:351 Subject Strand: POSITIVE Subject Start: 1 Subject End: 351 actgacaaaccagcttgaaaagctggttttttactttgaatcataaagctcttctttacaaatttttaaaagcattttataataaaaagaagattgattgacatattatttgcaatcttgtttagttgctactaactcttagtatgtcttgataaatcatggtagtcacagatgcaaggagaaataataatgtagaatagcgannnnnnngcaccactatcagatgagacagatgttgacagtttgttgtgtaagggctttagagacttatgatataatgaattcataaaagtttgagaagtctcttaatcttttcaagctgattttcataaaaaagaataggaaataagt actgacaaaccagcttgaaaagctggttttttactttgaatcataaagctcttctttacaaatttttaaaagcattttataataaaaagaagattgattgacatattatttgcaatcttgtttagttgctactaactcttagtatgtcttgataaatcatggtagtcacagatgcaaggagaaataataatgtagaatagcgatttttttgcaccactatcagatgagacagatgttgacagtttgttgtgtaagggctttagagacttatgatataatgaattcataaaagtttgagaagtctcttaatcttttcaagctgattttcataaaaaagaataggaaataagt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUGACAAACCAGCUUGAAAAGCUGGUUUUUUACUUUGAAUCAUAAAGCUCUUCUUUACAAAUUUUUAAAAGCAUUUUAUAAUAAAAAGAAGAUUGAUUGACAUAUUAUUUGCAAUCUUGUUUAGUUGCUACUAACUCUUAGUAUGUCUUGAUAAAUCAUGGUAGUCACAGAUGCAAGGAGAAAUAAUAAUGUAGAAUAGCGAUUUUUUUGCACCACUAUCAGAUGAGACAGAUGUUGACAGUUUGUUGUGUAAGGGCUUUAGAGACUUAUGAUAUAAUGAAUUCAUAAAAGUUUGAGAAGUCUCUUAAUCUUUUCAAGCUGAUUUUCAUAAAAAAGAAUAGGAAAUAAGU .(((..(((((((((.....)))))))))....((((...((.(((((((((((...(((((((.(((...(((((.........(((.(((((((..(((....)))....))))))).)))......(((((.....))))).(((((.....(((.(((((((....(.((((((((((.....................)))))))))).)))))))))))))))).)))))))).)))))))...).))))))))))))...((((((....(((....)))...(((((((((((.........))))))))))).....)))))).))))..)))......... (-75.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUUAUUUCCUAUUCUUUUUUAUGAAAAUCAGCUUGAAAAGAUUAAGAGACUUCUCAAACUUUUAUGAAUUCAUUAUAUCAUAAGUCUCUAAAGCCCUUACACAACAAACUGUCAACAUCUGUCUCAUCUGAUAGUGGUGCAAAAAAAUCGCUAUUCUACAUUAUUAUUUCUCCUUGCAUCUGUGACUACCAUGAUUUAUCAAGACAUACUAAGAGUUAGUAGCAACUAAACAAGAUUGCAAAUAAUAUGUCAAUCAAUCUUCUUUUUAUUAUAAAAUGCUUUUAAAAAUUUGUAAAGAAGAGCUUUAUGAUUCAAAGUAAAAAACCAGCUUUUCAAGCUGGUUUGUCAGU ......................(((((((((((((((((((....((((((((...........(((....)))........)))))))).......((((.........((((.....(((((......))))).(((((((...............................)))))))......................))))......((((((..(((..........(((((((.......)).)))))..((((((((............................)))))))))))...))))))...))))........)))))))))))))))).))).. (-66.88) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 354 258 217 171 116 NC_009009:SSA_1530|5end_ABC-type_antimicrobial_peptide_transport_system,_permease_component,_putative_1538778..1539008_NEGATIVE 328 41 7 189 156 NC_009009:SSA_2143|5end_Conserved_uncharacterized_protein_2144225..2144455_NEGATIVE 300 266 221 54 7 NC_009009:SSA_2050|5end_Arabinose_efflux_permease,_putative_2053255..2053485_POSITIVE 298 240 194 168 116 NC_009009:SSA_0424|5end_Exopolysaccharide_biosynthesis_protein,_putative_422233..422463_NEGATIVE 288 166 127 61 23 NC_009009:SSA_2359|5end_Glucose_inhibited_division_protein_A,_putative_2362520..2362750_NEGATIVE 277 140 100 57 18 NC_009009:SSA_1153|5end_HemK_protein,_putative_1181838..1182068_POSITIVE 275 196 151 50 2 NC_009009:SSA_0838|5end_GtfB,_putative_825406..825636_POSITIVE 271 230 191 223 190 NC_009009:SSA_2245|5end_RecA_protein,_putative_2241109..2241339_NEGATIVE 271 232 193 140 102 NC_009009:SSA_1798|5end_hypothetical_protein_1780513..1780743_NEGATIVE 271 150 109 83 33 NC_009009:SSA_1070|5end_Ribosomal_large_subunit_pseudouridine_synthase_D,_putative_1088742..1088972_POSITIVE 257 266 223 54 16 NC_009009:SSA_0862|5end_MurM,_putative_854221..854451_NEGATIVE 255 330 293 143 102 NC_009009:SSA_2345|5end_hypothetical_protein_2346919..2347149_POSITIVE 255 37 7 149 120 NC_009009:SSA_1068|5end_Transcriptional_regulator,_LysR_family_(capsular_polysaccharide_biosynthesis_regulation),_putative_1087355..1087585_POSITIVE 254 266 224 181 140 NC_009009:SSA_2152|5end_ABC-type_transporter_(uncharacterized),_ATPase_component,_putative_2153801..2154031_NEGATIVE 254 260 213 63 3 NC_009009:SSA_0217|5end_Two-component_system_transcriptional_regulator_(CheY_domain_and_HTH-like_DNA-binding_domain),_putative_213183..213413_POSITIVE 254 330 291 178 138 NC_009009:SSA_0092|5end_V-type_sodium_ATPase,_subunit_B,_putative_92895..93125_POSITIVE 254 167 122 141 93 NC_009009:SSA_0018|5end_Cell-shape_determining_protein_MreD,_putative_23628..23858_POSITIVE 252 142 117 33 4 NC_009009:SSA_1452|5end_Second_subunit_of_major_exonuclease,_putative_1459696..1459926_NEGATIVE 251 260 211 56 15 NC_009009:SSA_2274|5end_hypothetical_protein_2275232..2275462_NEGATIVE 250 59 11 84 31 NC_009009:SSA_1912|5end_hypothetical_protein_1903220..1903450_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 328 41 7 99 66 NC_009009:SSA_2144|3end_Glutamyl-tRNA_synthetase,_putative_2144315..2144465_NEGATIVE 325 49 7 110 62 NC_009009:SSA_1010|3end_UDP-glucose_4-epimerase,_putative_1013862..1014012_POSITIVE 293 266 221 66 17 NC_009009:SSA_0173|3end_23S_rRNA_m1G745_methyltransferase,_putative_169696..169846_NEGATIVE 292 260 211 151 94 NC_009009:SSA_2307|3end_hypothetical_protein_2308323..2308473_NEGATIVE 283 259 214 48 2 NC_009009:SSA_0986|3end_Choline_transporter,_putative_989081..989231_POSITIVE 277 140 100 57 18 NC_009009:SSA_1152|3end_Protein_chain_release_factor_A,_putative_1181918..1182068_POSITIVE 275 58 11 118 68 NC_009009:SSA_2074|3end_Preprotein_translocase_subunit_YajC,_putative_2076600..2076750_NEGATIVE 275 196 151 66 18 NC_009009:SSA_0837|3end_Glucosyltransferase,_putative_825502..825652_POSITIVE 271 232 193 140 102 NC_009009:SSA_1799|3end_Acetyltransferase,_putative_1780513..1780663_NEGATIVE 271 150 109 99 49 NC_009009:SSA_1069|3end_Lipoprotein_signal_peptidase,_putative_1088838..1088988_POSITIVE 269 322 282 135 93 NC_009009:SSA_1206|3end_A/G-specific_adenine_glycosylase,_putative_1230071..1230221_NEGATIVE 257 266 223 69 31 NC_009009:SSA_0863|3end_Cof_family_protein,_putative_854206..854356_NEGATIVE 255 37 7 59 30 NC_009009:SSA_1067|3end_hypothetical_protein_1087345..1087495_POSITIVE 254 260 213 70 10 NC_009009:SSA_0216|3end_Histidine_kinase,_putative_213270..213420_POSITIVE 254 167 122 139 91 NC_009009:SSA_0017|3end_Cell_shape_determining_protein_MreC,_putative_23706..23856_POSITIVE 253 36 7 86 58 NC_009009:SSA_0571|3end_Aspartyl/glutamyl-tRNA(Asn/Gln)_amidotransferase_subunit_B,_putative_566894..567044_POSITIVE 251 260 211 63 22 NC_009009:SSA_2275|3end_hypothetical_protein_2275225..2275375_NEGATIVE 250 59 11 59 6 NC_009009:SSA_1913|3end_Xanthine/uracil_permease_family_protein,_putative_1903245..1903395_NEGATIVE 242 49 7 105 62 NC_009009:SSA_1226|3end_ParC,_putative_1248783..1248933_NEGATIVE 239 58 15 109 75 NC_009009:SSA_0995|3end_Antibiotic-resistance_protein,_alpha/beta_superfamily_hydrolase,_putative_996332..996482_POSITIVE