Origin IGS: agggaatccttagttaaaattaactgttcgtttatacaggatataatatactggcattttatccagtatgtcaagcgataaaaaagaaaagttttttctttgagaagtgagtgaaagtcagattttattgctaacgataaaatatactgtttccattgaatttttttatttcacacagaatatttttcggaattaaaaaattcccggcattcatattctgtttagtcaaaatttgagctatttttactaggtcttttaggggaatcaattttgattcgcaacgtgcattgaattaaaaaagatagtgagaatttttgatctgcacccaaaaagttagacgcctttaattcaaggactgagttctgtattccacagggcttagtccttttaattttac .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 gtaaaattaaaaggactaagccctgtggaatacagaactcagtccttgaattaaaggcgtctaactttttgggtgcagatcaaaaattctcactatcttttttaattcaatgcacgttgcgaatcaaaattgattcccctaaaagacctagtaaaaatagctcaaattttgactaaacagaatatgaatgccgggaattttttaattccgaaaaatattctgtgtgaaataaaaaaattcaatggaaacagtatattttatcgttagcaataaaatctgactttcactcacttctcaaagaaaaaacttttcttttttatcgcttgacatactggataaaatgccagtatattatatcctgtataaacgaacagttaattttaactaaggattccct Mask Tandem Repeat Region ================================================ agggaatccttagttaaaattaactgttcgtttatacaggatataatatactggcattttatccagtatgtcaagcgataaaaaagaaaagttttttctttgagaagtgagtgaaagtcagattttattgctaacgataaaatatactgtttccattgaatttttttatttcacacagaatatttttcggaattaaaaaattcccggcattcatattctgtttagtcaaaatttgagctatttttactaggtcttttaggggaatcaattttgattcgcaacgtgcattgaattaaaaaagatagtgagaatttttgatctgcacccaaaaagttagacgcctttaattcaaggactgagttctgtattccacagggcttagtccttttaattttac Find is-nt database================================================ Query_seq: AA00632:AA00633|AA00632:AA00633:inner membrane protein ImpA:hypothetical protein:->->:434714..435110 397 agggaatccttagttaaaattaactgttcgtttatacaggatataatatactggcattttatccagtatgtcaagcgataaaaaagaaaagttttttctttgagaagtgagtgaaagtcagattttattgctaacgataaaatatactgtttccattgaatttttttatttcacacagaatatttttcggaattaaaaaattcccggcattcatattctgtttagtcaaaatttgagctatttttactaggtcttttaggggaatcaattttgattcgcaacgtgcattgaattaaaaaagatagtgagaatttttgatctgcacccaaaaagttagacgcctttaattcaaggactgagttctgtattccacagggcttagtccttttaattttac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA00632:AA00633|AA00632:AA00633:inner membrane protein ImpA:hypothetical protein:->->:434714..435110 397 agggaatccttagttaaaattaactgttcgtttatacaggatataatatactggcattttatccagtatgtcaagcgataaaaaagaaaagttttttctttgagaagtgagtgaaagtcagattttattgctaacgataaaatatactgtttccattgaatttttttatttcacacagaatatttttcggaattaaaaaattcccggcattcatattctgtttagtcaaaatttgagctatttttactaggtcttttaggggaatcaattttgattcgcaacgtgcattgaattaaaaaagatagtgagaatttttgatctgcacccaaaaagttagacgcctttaattcaaggactgagttctgtattccacagggcttagtccttttaattttac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA00632:AA00633|AA00632:AA00633:inner membrane protein ImpA:hypothetical protein:->->:434714..435110 397 agggaatccttagttaaaattaactgttcgtttatacaggatataatatactggcattttatccagtatgtcaagcgataaaaaagaaaagttttttctttgagaagtgagtgaaagtcagattttattgctaacgataaaatatactgtttccattgaatttttttatttcacacagaatatttttcggaattaaaaaattcccggcattcatattctgtttagtcaaaatttgagctatttttactaggtcttttaggggaatcaattttgattcgcaacgtgcattgaattaaaaaagatagtgagaatttttgatctgcacccaaaaagttagacgcctttaattcaaggactgagttctgtattccacagggcttagtccttttaattttac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agggaatccttagttaaaattaactgttcgtttatacaggatataatatactggcattttatccagtatgtcaagcgataaaaaagaaaagttttttctttgagaagtgagtgaaagtcagattttattgctaacgataaaatatactgtttccattgaatttttttatttcacacagaatatttttcggaattaaaaaattcccggcattcatattctgtttagtcaaaatttgagctatttttactaggtcttttaggggaatcaattttgattcgcaacgtgcattgaattaaaaaagatagtgagaatttttgatctgcacccaaaaagttagacgcctttaattcaaggactgagttctgtattccacagggcttagtccttttaattttac Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 144 End: 233 ............................................................................................................................................... M L F P L N F F I S H R I F F G I K K F P A F I F C L V K I .................................................................................................................................................................... Protein_Len: 56 Strand: - Start: 225 End: 392 ................................................................................................................................................................................................................................ D F N S S N K S P R K P S D I K I R L T C Q I L F S L S F K Q D A G L F N S A K L E L V S N Q I G C P K T R K M ..... Protein_Len: 45 Strand: - Start: 134 End: 268 ..................................................................................................................................... R Y F I S N G N F K K I E C L I N K P I L F N G A N M N Q K T L I Q A I K V L D K L P I M ................................................................................................................................. Protein_Len: 53 Strand: - Start: 3 End: 161 .. S D K T L I L Q E N I C S I I Y Q C K I W Y T L R Y F L F T K E K L L S H F D S K I A L S L I Y Q K W Q M ............................................................................................................................................................................................................................................ agggaatccttagttaaaattaactgttcgtttatacaggatataatatactggcattttatccagtatgtcaagcgataaaaaagaaaagttttttctttgagaagtgagtgaaagtcagattttattgctaacgataaaatatactgtttccattgaatttttttatttcacacagaatatttttcggaattaaaaaattcccggcattcatattctgtttagtcaaaatttgagctatttttactaggtcttttaggggaatcaattttgattcgcaacgtgcattgaattaaaaaagatagtgagaatttttgatctgcacccaaaaagttagacgcctttaattcaaggactgagttctgtattccacagggcttagtccttttaattttac 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================================================ agggaatccttagttaaaattaactgttcgtttatacaggatataatatactggcattttatccagtatgtcaagcgataaaaaagaaaagttttttctttgagaagtgagtgaaagtcagattttattgctaacgataaaatatactgtttccattgaatttttttatttcacacagaatatttttcggaattaaaaaattcccggcattcatattctgtttagtcaaaatttgagctatttttactaggtcttttaggggaatcaattttgattcgcaacgtgcattgaattaaaaaagatagtgagaatttttgatctgcacccaaaaagttagacgcctttaattcaaggactgagttctgtattccacagggcttagtccttttaattttac Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 77 HP_score: -4.9 Tail_Score: -5.31456 Start: 86 End: 98 Full_Region: cactcacttctcaaa gaaaa aac ttttc ttttttatcgcttga .....................................................................................gaaaaaacttttc........................................................................................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 44 HP_score: -3.6 Tail_Score: -2.54272 Start: 357 End: 381 Full_Region: CTTTAATTCAAGGAC TGAGTTCTGT ATTCC ACAGGGCTTA GTCCTTTTAATTTTA ....................................................................................................................................................................................................................................................................................................................................................................TGAGTTCTGTATTCCACAGGGCTTA................ Find igs database================================================ Query_seq: AA00632:AA00633|AA00632:AA00633:inner membrane protein ImpA:hypothetical protein:->->:434714..435110 397 agggaatccttagttaaaattaactgttcgtttatacaggatataatatactggcattttatccagtatgtcaagcgataaaaaagaaaagttttttctttgagaagtgagtgaaagtcagattttattgctaacgataaaatatactgtttccattgaatttttttatttcacacagaatatttttcggaattaaaaaattcccggcattcatattctgtttagtcaaaatttgagctatttttactaggtcttttaggggaatcaattttgattcgcaacgtgcattgaattaaaaaagatagtgagaatttttgatctgcacccaaaaagttagacgcctttaattcaaggactgagttctgtattccacagggcttagtccttttaattttac Intra-Species Hit: Count: 1 Min: 1 Max: 397 Len: 397 Subject: aact_AA00632_AA00633|inner membrane protein ImpA:hypothetical protein|POSITIVE:POSITIVE|[434714,435110]|397 HSP 1 e-value: 0.0 bit: 745.0 Len: 397 Query Start:1 Query End:397 Subject Strand: POSITIVE Subject Start: 1 Subject End: 397 agggaatccttagttaaaattaactgttcgtttatacaggatataatatactggcattttatccagtatgtcaagcgataaaaaagaaaagttttttctttgagaagtgagtgaaagtcagattttattgctaacgataaaatatactgtttccattgaannnnnnnatttcacacagaatatttttcggaattaaaaaattcccggcattcatattctgtttagtcaaaatttgagctatttttactaggtcttttaggggaatcaattttgattcgcaacgtgcattgaattaaaaaagatagtgagaatttttgatctgcacccaaaaagttagacgcctttaattcaaggactgagttctgtattccacagggcttagtccttttaattttac agggaatccttagttaaaattaactgttcgtttatacaggatataatatactggcattttatccagtatgtcaagcgataaaaaagaaaagttttttctttgagaagtgagtgaaagtcagattttattgctaacgataaaatatactgtttccattgaatttttttatttcacacagaatatttttcggaattaaaaaattcccggcattcatattctgtttagtcaaaatttgagctatttttactaggtcttttaggggaatcaattttgattcgcaacgtgcattgaattaaaaaagatagtgagaatttttgatctgcacccaaaaagttagacgcctttaattcaaggactgagttctgtattccacagggcttagtccttttaattttac Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGGGAAUCCUUAGUUAAAAUUAACUGUUCGUUUAUACAGGAUAUAAUAUACUGGCAUUUUAUCCAGUAUGUCAAGCGAUAAAAAAGAAAAGUUUUUUCUUUGAGAAGUGAGUGAAAGUCAGAUUUUAUUGCUAACGAUAAAAUAUACUGUUUCCAUUGAAUUUUUUUAUUUCACACAGAAUAUUUUUCGGAAUUAAAAAAUUCCCGGCAUUCAUAUUCUGUUUAGUCAAAAUUUGAGCUAUUUUUACUAGGUCUUUUAGGGGAAUCAAUUUUGAUUCGCAACGUGCAUUGAAUUAAAAAAGAUAGUGAGAAUUUUUGAUCUGCACCCAAAAAGUUAGACGCCUUUAAUUCAAGGACUGAGUUCUGUAUUCCACAGGGCUUAGUCCUUUUAAUUUUAC .(((......((((((....)))))).........(((((((((.(((((((((........)))))))))...((.........(((((((...((((.((.((((((((.((((.(((((((((((((....)))))))))............)))).)))))))))))).)).)))).)))))))((((((....))))))..))....))))))))).((((((((((((..(((((((((..(((.((......(.((((((....)))))).)..........)).)))..)))))))))..))).)))))).)))..)))..(((((((((.............(((((((((((((((.....)))))))))))))))))))))))).. (-96.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUAAAAUUAAAAGGACUAAGCCCUGUGGAAUACAGAACUCAGUCCUUGAAUUAAAGGCGUCUAACUUUUUGGGUGCAGAUCAAAAAUUCUCACUAUCUUUUUUAAUUCAAUGCACGUUGCGAAUCAAAAUUGAUUCCCCUAAAAGACCUAGUAAAAAUAGCUCAAAUUUUGACUAAACAGAAUAUGAAUGCCGGGAAUUUUUUAAUUCCGAAAAAUAUUCUGUGUGAAAUAAAAAAAUUCAAUGGAAACAGUAUAUUUUAUCGUUAGCAAUAAAAUCUGACUUUCACUCACUUCUCAAAGAAAAAACUUUUCUUUUUUAUCGCUUGACAUACUGGAUAAAAUGCCAGUAUAUUAUAUCCUGUAUAAACGAACAGUUAAUUUUAACUAAGGAUUCCCU ..........(((((((.((..(((((...)))))..)).)))))))........((.((((..(((((.((((((((((.(((((............))))).)))...))))).....((((((....)))))).)).)))))...((((.(((((........((((((....(((((((((........((((((....)))))).....)))))))))(((((.....(((((....((....))....)))))...(((((.........))))).))))).......))))))....((((.(((.(((.(((.(..(((.(((((((........))))))).)))....).))).))).))).)))).))))).)))).)))).)).. (-77.72) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 356 390 357 169 136 aact:AA01269|5end_hypothetical_protein_863172..863402_POSITIVE 356 390 357 217 184 aact:AA01078|5end_transcriptional_regulator_(probable_MerR_family)_746873..747103_POSITIVE 299 385 357 231 203 aact:AA02343|5end_glutamine_synthetase_1600173..1600403_POSITIVE 295 342 304 142 98 aact:AA00674|5end_nicotinate-nucleotide-dimethylbenzimidazole_phosphoribosyltransferase_461810..462040_POSITIVE 293 378 331 102 61 aact:AA02351|5end_conserved_hypothetical_protein_1609233..1609463_POSITIVE 290 378 338 212 172 aact:AA00904|5end_sigma-E_factor_negative_regulatory_factor_624443..624673_POSITIVE 279 379 339 144 101 aact:AA02890|5end_hypothetical_protein_2025318..2025548_POSITIVE 277 390 344 230 184 aact:AA01407|5end_outer_membrane_antigenic_lipoprotein_b_precursor_949005..949235_POSITIVE 274 354 316 206 170 aact:AA01446|5end_conserved_hypothetical_protein_970151..970381_POSITIVE 268 380 337 126 87 aact:AA01556|5end_ABC_transporter_ATP-binding_protein_1044218..1044448_POSITIVE 266 366 321 165 119 aact:AA01022|5end_tRNA_(5-methylaminomethyl-2-thiouridylate)_methyltransferase_714689..714919_POSITIVE 266 389 344 231 186 aact:AA00632|5end_inner_membrane_protein_ImpA_434127..434357_POSITIVE 266 380 332 171 120 aact:AA00530|5end_hypothetical_protein_362373..362603_POSITIVE 258 127 89 157 115 aact:AA01838|5end_conserved_hypothetical_protein_1236396..1236626_POSITIVE 257 385 354 228 195 aact:AA00543|5end_ADP-heptose--LPS_heptosyltransferase_II_371287..371517_POSITIVE 257 390 344 191 145 aact:AA00536|5end_5'-nucleotidase_precursor_366151..366381_POSITIVE 255 354 311 157 117 aact:AA01291|5end_excinuclease_ABC_subunit_A_872829..873059_POSITIVE 252 342 303 200 161 aact:AA00585|5end_glycerol-3-phosphate_regulon_repressor_399195..399425_POSITIVE 249 290 245 204 153 aact:AA00357|5end_transposase_(probable_IS200-like_)_243334..243564_POSITIVE 249 286 247 163 122 aact:AA00244|5end_conserved_hypothetical_protein_(possible_deoxyribonuclease,_possible_hydrolase)_172043..172273_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 356 390 357 134 101 aact:AA02342|3end_ISRSO11/IS150_related_transposase,_orfB_1600151..1600301_POSITIVE 356 390 357 134 101 aact:AA01268|3end_transposase_863217..863367_POSITIVE 356 390 357 134 101 aact:AA01077|3end_transposase_746870..747020_POSITIVE 356 390 357 134 101 aact:AA00010|3end_transposase_orfB_fragment_6297..6447_POSITIVE 317 352 316 66 33 aact:AA01549|3end_hypothetical_protein_1037880..1038030_POSITIVE 274 354 316 82 46 aact:AA01445|3end_hypothetical_protein_970107..970257_POSITIVE 269 309 272 144 115 aact:AA02254|3end_2-oxoglutarate/malate_translocator_1536380..1536530_POSITIVE 268 380 337 151 112 aact:AA01555|3end_ABC_transporter,_ATP-binding_protein_1044323..1044473_POSITIVE 266 380 332 88 37 aact:AA00529|3end_outer_membrane_protein,_Omp_18/16_362370..362520_POSITIVE 262 360 314 49 1 aact:AA00535|3end_hypothetical_protein_366119..366269_POSITIVE 258 127 89 77 35 aact:AA01837|3end_transcriptional_regulatory_protein_1236396..1236546_POSITIVE 255 354 311 96 56 aact:AA01289|3end_hypothetical_protein_872848..872998_POSITIVE 252 342 303 135 96 aact:AA00583|3end_GlpG_protein_399210..399360_POSITIVE 249 290 245 72 21 aact:AA00356|3end_DNA-directed_RNA_polymerase,_beta'_chain_243282..243432_POSITIVE 249 286 247 130 89 aact:AA00241|3end_formate_acetyltransferase_activating_enzyme_(anaerobic_ribonucleoside-triphosphate_reductase_activating_protein)_172090..172240_POSITIVE 248 287 257 36 1 aact:AA01376|3end_hypothetical_protein_931410..931560_POSITIVE 247 285 259 151 118 aact:AA02242|3end_molybdenum_cofactor_biosynthesis_protein_A_1525088..1525238_POSITIVE 246 377 331 112 50 aact:AA02614|3end_conserved_hypothetical_protein_1823032..1823182_POSITIVE 246 377 331 45 4 aact:AA01913|3end_GMP_synthase_1290171..1290321_POSITIVE 241 288 244 114 66 aact:AA01524|3end_amino_acid_ABC_transporter,_ATP-binding_protein_1024344..1024494_POSITIVE