Origin IGS: agccactcctaaacttaggaaaaggcaggcgagaaacattgttagtctttttttcataaaatctctcactttaaaatttaattattaacagttattgtttcatttttgcttgggattttgtcccaatttctcatagcttagttaaaaacgaaagtgttttcatcttttaacgtaattgcaaagatagtatttcgtacgtaacggaacaaataaatttaatgaaatgacctctttttttacttttattaacaagaaagggattaaaccttaatgaaaggtggctgaaaccgctttgtaatgttagtttgcaaggcgttaaggcatcgtttgtctatggataagagcgcaaaaacgtaattgtgattagaaagaatggaaaaagatgtaaatataacaaacta .........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 tagtttgttatatttacatctttttccattctttctaatcacaattacgtttttgcgctcttatccatagacaaacgatgccttaacgccttgcaaactaacattacaaagcggtttcagccacctttcattaaggtttaatccctttcttgttaataaaagtaaaaaaagaggtcatttcattaaatttatttgttccgttacgtacgaaatactatctttgcaattacgttaaaagatgaaaacactttcgtttttaactaagctatgagaaattgggacaaaatcccaagcaaaaatgaaacaataactgttaataattaaattttaaagtgagagattttatgaaaaaaagactaacaatgtttctcgcctgccttttcctaagtttaggagtggct Mask Tandem Repeat Region ================================================ agccactcctaaacttaggaaaaggcaggcgagaaacattgttagtctttttttcataaaatctctcactttaaaatttaattattaacagttattgtttcatttttgcttgggattttgtcccaatttctcatagcttagttaaaaacgaaagtgttttcatcttttaacgtaattgcaaagatagtatttcgtacgtaacggaacaaataaatttaatgaaatgacctctttttttacttttattaacaagaaagggattaaaccttaatgaaaggtggctgaaaccgctttgtaatgttagtttgcaaggcgttaaggcatcgtttgtctatggataagagcgcaaaaacgtaattgtgattagaaagaatggaaaaagatgtaaatataacaaacta Find is-nt database================================================ Query_seq: PI1941:PI1942|PI1941:PI1942:outer membrane receptor; ragA protein:hypothetical protein:->->:1900680..1901080 401 agccactcctaaacttaggaaaaggcaggcgagaaacattgttagtctttttttcataaaatctctcactttaaaatttaattattaacagttattgtttcatttttgcttgggattttgtcccaatttctcatagcttagttaaaaacgaaagtgttttcatcttttaacgtaattgcaaagatagtatttcgtacgtaacggaacaaataaatttaatgaaatgacctctttttttacttttattaacaagaaagggattaaaccttaatgaaaggtggctgaaaccgctttgtaatgttagtttgcaaggcgttaaggcatcgtttgtctatggataagagcgcaaaaacgtaattgtgattagaaagaatggaaaaagatgtaaatataacaaacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1941:PI1942|PI1941:PI1942:outer membrane receptor; ragA protein:hypothetical protein:->->:1900680..1901080 401 agccactcctaaacttaggaaaaggcaggcgagaaacattgttagtctttttttcataaaatctctcactttaaaatttaattattaacagttattgtttcatttttgcttgggattttgtcccaatttctcatagcttagttaaaaacgaaagtgttttcatcttttaacgtaattgcaaagatagtatttcgtacgtaacggaacaaataaatttaatgaaatgacctctttttttacttttattaacaagaaagggattaaaccttaatgaaaggtggctgaaaccgctttgtaatgttagtttgcaaggcgttaaggcatcgtttgtctatggataagagcgcaaaaacgtaattgtgattagaaagaatggaaaaagatgtaaatataacaaacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1941:PI1942|PI1941:PI1942:outer membrane receptor; ragA protein:hypothetical protein:->->:1900680..1901080 401 agccactcctaaacttaggaaaaggcaggcgagaaacattgttagtctttttttcataaaatctctcactttaaaatttaattattaacagttattgtttcatttttgcttgggattttgtcccaatttctcatagcttagttaaaaacgaaagtgttttcatcttttaacgtaattgcaaagatagtatttcgtacgtaacggaacaaataaatttaatgaaatgacctctttttttacttttattaacaagaaagggattaaaccttaatgaaaggtggctgaaaccgctttgtaatgttagtttgcaaggcgttaaggcatcgtttgtctatggataagagcgcaaaaacgtaattgtgattagaaagaatggaaaaagatgtaaatataacaaacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agccactcctaaacttaggaaaaggcaggcgagaaacattgttagtctttttttcataaaatctctcactttaaaatttaattattaacagttattgtttcatttttgcttgggattttgtcccaatttctcatagcttagttaaaaacgaaagtgttttcatcttttaacgtaattgcaaagatagtatttcgtacgtaacggaacaaataaatttaatgaaatgacctctttttttacttttattaacaagaaagggattaaaccttaatgaaaggtggctgaaaccgctttgtaatgttagtttgcaaggcgttaaggcatcgtttgtctatggataagagcgcaaaaacgtaattgtgattagaaagaatggaaaaagatgtaaatataacaaacta Predict ORF larger than 30AA ================================================ Protein_Len: 43 Strand: - Start: 264 End: 392 ....................................................................................................................................................................................................................................................................... V K I F P P Q F R K T I N T Q L A N L C R K D I S L L A F V Y N H N S L I S F S T F M ......... Protein_Len: 33 Strand: - Start: 163 End: 261 .................................................................................................................................................................. R K V Y N C L Y Y K T R L P V F L N L S I V E K K V K I L L F P M ............................................................................................................................................ agccactcctaaacttaggaaaaggcaggcgagaaacattgttagtctttttttcataaaatctctcactttaaaatttaattattaacagttattgtttcatttttgcttgggattttgtcccaatttctcatagcttagttaaaaacgaaagtgttttcatcttttaacgtaattgcaaagatagtatttcgtacgtaacggaacaaataaatttaatgaaatgacctctttttttacttttattaacaagaaagggattaaaccttaatgaaaggtggctgaaaccgctttgtaatgttagtttgcaaggcgttaaggcatcgtttgtctatggataagagcgcaaaaacgtaattgtgattagaaagaatggaaaaagatgtaaatataacaaacta 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: 81 Start: 69 End: 98 ....................................................................CTTTAAAATTTAATTATTAACAGTTATTGT............................................................................................................................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agccactcctaaacttaggaaaaggcaggcgagaaacattgttagtctttttttcataaaatctctcactttaaaatttaattattaacagttattgtttcatttttgcttgggattttgtcccaatttctcatagcttagttaaaaacgaaagtgttttcatcttttaacgtaattgcaaagatagtatttcgtacgtaacggaacaaataaatttaatgaaatgacctctttttttacttttattaacaagaaagggattaaaccttaatgaaaggtggctgaaaccgctttgtaatgttagtttgcaaggcgttaaggcatcgtttgtctatggataagagcgcaaaaacgtaattgtgattagaaagaatggaaaaagatgtaaatataacaaacta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 74 HP_score: -7.3 Tail_Score: -3.99405 Start: 110 End: 126 Full_Region: TTGTTTCATTTTTGC TTGGGAT TTT GTCCCAA TTTCTCATAGCTTAG .............................................................................................................TTGGGATTTTGTCCCAA................................................................................................................................................................................................................................................................................... Find igs database================================================ Query_seq: PI1941:PI1942|PI1941:PI1942:outer membrane receptor; ragA protein:hypothetical protein:->->:1900680..1901080 401 agccactcctaaacttaggaaaaggcaggcgagaaacattgttagtctttttttcataaaatctctcactttaaaatttaattattaacagttattgtttcatttttgcttgggattttgtcccaatttctcatagcttagttaaaaacgaaagtgttttcatcttttaacgtaattgcaaagatagtatttcgtacgtaacggaacaaataaatttaatgaaatgacctctttttttacttttattaacaagaaagggattaaaccttaatgaaaggtggctgaaaccgctttgtaatgttagtttgcaaggcgttaaggcatcgtttgtctatggataagagcgcaaaaacgtaattgtgattagaaagaatggaaaaagatgtaaatataacaaacta Intra-Species Hit: Count: 1 Min: 1 Max: 401 Len: 401 Subject: pint_PI1941_PI1942|outer membrane receptor; ragA protein:hypothetical protein|POSITIVE:POSITIVE|[1900680,1901080]|401 HSP 1 e-value: 0.0 bit: 712.0 Len: 401 Query Start:1 Query End:401 Subject Strand: POSITIVE Subject Start: 1 Subject End: 401 agccactcctaaacttaggaaaaggcaggcgagaaacattgttagtcnnnnnnncataaaatctctcactttaaaatttaattattaacagttattgtttcatttttgcttgggattttgtcccaatttctcatagcttagttaaaaacgaaagtgttttcatcttttaacgtaattgcaaagatagtatttcgtacgtaacggaacaaataaatttaatgaaatgacctcnnnnnnnacttttattaacaagaaagggattaaaccttaatgaaaggtggctgaaaccgctttgtaatgttagtttgcaaggcgttaaggcatcgtttgtctatggataagagcgcaaaaacgtaattgtgattagaaagaatggaaaaagatgtaaatataacaaacta agccactcctaaacttaggaaaaggcaggcgagaaacattgttagtctttttttcataaaatctctcactttaaaatttaattattaacagttattgtttcatttttgcttgggattttgtcccaatttctcatagcttagttaaaaacgaaagtgttttcatcttttaacgtaattgcaaagatagtatttcgtacgtaacggaacaaataaatttaatgaaatgacctctttttttacttttattaacaagaaagggattaaaccttaatgaaaggtggctgaaaccgctttgtaatgttagtttgcaaggcgttaaggcatcgtttgtctatggataagagcgcaaaaacgtaattgtgattagaaagaatggaaaaagatgtaaatataacaaacta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCCACUCCUAAACUUAGGAAAAGGCAGGCGAGAAACAUUGUUAGUCUUUUUUUCAUAAAAUCUCUCACUUUAAAAUUUAAUUAUUAACAGUUAUUGUUUCAUUUUUGCUUGGGAUUUUGUCCCAAUUUCUCAUAGCUUAGUUAAAAACGAAAGUGUUUUCAUCUUUUAACGUAAUUGCAAAGAUAGUAUUUCGUACGUAACGGAACAAAUAAAUUUAAUGAAAUGACCUCUUUUUUUACUUUUAUUAACAAGAAAGGGAUUAAACCUUAAUGAAAGGUGGCUGAAACCGCUUUGUAAUGUUAGUUUGCAAGGCGUUAAGGCAUCGUUUGUCUAUGGAUAAGAGCGCAAAAACGUAAUUGUGAUUAGAAAGAAUGGAAAAAGAUGUAAAUAUAACAAACUA ((((((.((((....)))).((((((..((((......))))..)))))).((((((........................(((((((...((((((((((.(((((((.((((((...))))))...............(((((((((....)).........)))))))......)))))))..((((...)))).....))))).)))))..)))))))..(((.(((((((((.............))))))))).))).......)))))).)))))).....((((((((((.......)))))))))).....(((((.....(((((...(((...(((((........))))).)))......)))))....)))))............... (-83.12) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGUUUGUUAUAUUUACAUCUUUUUCCAUUCUUUCUAAUCACAAUUACGUUUUUGCGCUCUUAUCCAUAGACAAACGAUGCCUUAACGCCUUGCAAACUAACAUUACAAAGCGGUUUCAGCCACCUUUCAUUAAGGUUUAAUCCCUUUCUUGUUAAUAAAAGUAAAAAAAGAGGUCAUUUCAUUAAAUUUAUUUGUUCCGUUACGUACGAAAUACUAUCUUUGCAAUUACGUUAAAAGAUGAAAACACUUUCGUUUUUAACUAAGCUAUGAGAAAUUGGGACAAAAUCCCAAGCAAAAAUGAAACAAUAACUGUUAAUAAUUAAAUUUUAAAGUGAGAGAUUUUAUGAAAAAAAGACUAACAAUGUUUCUCGCCUGCCUUUUCCUAAGUUUAGGAGUGGCU ..((..(..(((((....(((((((.(((....(((..((((.....(((((((((.......(((((((.(..........((((((..(((((((............(((((...(((..(((((.....)))))......(((((.((.(((.......))).)).)))))..................)))..)))))..(((.....)))....)))))))...)))))).((.(((((((......))))))).))..)))))).))..((((((.....))))))))))))))).((((.....)))).................)))).)))....)))..))))))).....)))))..)..))..(((..((((((....)))))).))). (-74.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 362 315 279 224 191 pint:PI0929|5end_copper_homeostasis_protein_860294..860524_POSITIVE 357 318 275 182 139 pint:PI0088|5end_S-adenosylmethionine_synthetase_86663..86893_POSITIVE 351 348 308 57 18 pint:PI2134|5end_hypothetical_protein_2082269..2082499_POSITIVE 339 348 303 221 175 pint:PI1508|5end_undecaprenol_kinase_1427288..1427518_POSITIVE 338 348 303 112 44 pint:PI2118|5end_fumarate_reductase/succinate_dehydrogenase_flavoprotein_subunit,_N-terminal_2066466..2066696_POSITIVE 315 346 303 156 109 pint:PI1439|5end_hypothetical_protein_1360009..1360239_POSITIVE 312 320 272 70 22 pint:PI1086|5end_pyruvate:ferredoxin_oxidoreductase_1006602..1006832_POSITIVE 305 346 301 212 156 pint:PI1781|5end_membrane-associated_zinc_metalloprotease_1713074..1713304_POSITIVE 303 320 274 58 10 pint:PI2018|5end_50S_ribosomal_protein_L34_1975757..1975987_POSITIVE 303 320 277 78 25 pint:PI0351|5end_hypothetical_protein_324317..324547_POSITIVE 302 348 303 172 127 pint:PI0930|5end_alpha-L-fucosidase_precursor_860977..861207_POSITIVE 297 349 304 217 165 pint:PI0723|5end_conserved_hypothetical_protein_656043..656273_POSITIVE 293 328 281 216 157 pint:PI2155|5end_hypothetical_protein_2100664..2100894_POSITIVE 293 312 278 211 164 pint:PI1734|5end_possible_carboxyl-terminal_protease-related_protein_1652409..1652639_POSITIVE 291 347 303 191 146 pint:PI1620|5end__two-component_system_sensor_protein_1543956..1544186_POSITIVE 290 348 308 215 165 pint:PI0735|5end_ABC_transporter,_ATP-binding_/_permease_668793..669023_POSITIVE 289 316 277 206 159 pint:PI1295|5end_hypothetical_protein_1208636..1208866_POSITIVE 289 316 277 60 13 pint:PI1294|5end_hypothetical_protein_1208490..1208720_POSITIVE 288 330 282 202 155 pint:PI0203|5end_conserved_hypothetical_protein_195109..195339_POSITIVE 288 330 282 163 116 pint:PI0201|5end_hypothetical_protein_195070..195300_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 362 315 279 122 89 pint:PI0928|3end_hypothetical_protein_860272..860422_POSITIVE 300 339 291 135 86 pint:PI1366|3end_conserved_hypothetical_protein;_possible_hydrolase,_HAD_superfamily_1286647..1286797_POSITIVE 295 316 272 116 79 pint:PI1666|3end_conserved_hypothetical_protein_1579418..1579568_POSITIVE 290 348 308 102 52 pint:PI0734|3end_ABC_transporter,_ATP-binding_/_permease_668760..668910_POSITIVE 281 346 303 89 50 pint:PI1233|3end_conserved_hypothetical_protein;_possible__MazG_family_protein_1154247..1154397_POSITIVE 275 315 271 130 84 pint:PI2146|3end_prolipoprotein_diacylglyceryl_transferase_2093321..2093471_POSITIVE 275 347 307 137 92 pint:PI1741|3end_lipid-A-disaccharide_synthase_1663856..1664006_POSITIVE 275 360 311 60 2 pint:PI0953|3end_hypothetical_protein_885390..885540_POSITIVE 275 360 311 118 60 pint:PI0951|3end_hypothetical_protein_885448..885598_POSITIVE 274 326 281 118 66 pint:PI0037|3end_hypothetical_protein_39616..39766_POSITIVE 270 315 272 147 111 pint:PI0104|3end_hypothetical_protein_99346..99496_POSITIVE 269 346 305 141 99 pint:PI0654|3end_K+-dependent_Na+/Ca+_exchanger_related-protein_597223..597373_POSITIVE 268 361 321 47 1 pint:PI2133|3end_collagenase_2082319..2082469_POSITIVE 264 323 281 148 97 pint:PI0421|3end_hypothetical_protein_387774..387924_POSITIVE 264 209 170 54 18 pint:PI0328|3end_conserved_hypothetical_protein_309993..310143_POSITIVE 262 348 303 88 33 pint:PI0230|3end_hypothetical_protein_228906..229056_POSITIVE 261 50 1 113 59 pint:PI0494|3end_hypothetical_protein_455170..455320_POSITIVE 260 355 312 144 98 pint:PI0643|3end_hypothetical_protein_586660..586810_POSITIVE 260 355 312 53 7 pint:PI0644|3end_dnaJ_protein_586569..586719_POSITIVE 259 357 312 46 2 pint:PI1006|3end_conserved_hypothetical_protein_927049..927199_POSITIVE