Origin IGS: tccgtttttcaagtataagcacagcagtcattggcaagagaaaaagaattgactaattttgtcttccgaaaagcattgctccgaacagtgaatttccccgtgtattggaagtgagcaattaattgaaaaaagagagtattatattaatatgccacacatccataaactaccgactatgccccatcacctgacatcaagcccgaacaggctcctattcggatccttcagcacagcagcgacagtcctcgatccgatccgagattgtagagaggaatcgtgcagctacatcgaa .........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 ttcgatgtagctgcacgattcctctctacaatctcggatcggatcgaggactgtcgctgctgtgctgaaggatccgaataggagcctgttcgggcttgatgtcaggtgatggggcatagtcggtagtttatggatgtgtggcatattaatataatactctcttttttcaattaattgctcacttccaatacacggggaaattcactgttcggagcaatgcttttcggaagacaaaattagtcaattctttttctcttgccaatgactgctgtgcttatacttgaaaaacgga Mask Tandem Repeat Region ================================================ tccgtttttcaagtataagcacagcagtcattggcaagagaaaaagaattgactaattttgtcttccgaaaagcattgctccgaacagtgaatttccccgtgtattggaagtgagcaattaattgaaaaaagagagtattatattaatatgccacacatccataaactaccgactatgccccatcacctgacatcaagcccgaacaggctcctattcggatccttcagcacagcagcgacagtcctcgatccgatccgagattgtagagaggaatcgtgcagctacatcgaa Find is-nt database================================================ Query_seq: PG1573:PG1574|PG1573:PG1574:transcriptional regulator, Crp family:hypothetical protein:<-<-:1652259..1652550 292 tccgtttttcaagtataagcacagcagtcattggcaagagaaaaagaattgactaattttgtcttccgaaaagcattgctccgaacagtgaatttccccgtgtattggaagtgagcaattaattgaaaaaagagagtattatattaatatgccacacatccataaactaccgactatgccccatcacctgacatcaagcccgaacaggctcctattcggatccttcagcacagcagcgacagtcctcgatccgatccgagattgtagagaggaatcgtgcagctacatcgaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1573:PG1574|PG1573:PG1574:transcriptional regulator, Crp family:hypothetical protein:<-<-:1652259..1652550 292 tccgtttttcaagtataagcacagcagtcattggcaagagaaaaagaattgactaattttgtcttccgaaaagcattgctccgaacagtgaatttccccgtgtattggaagtgagcaattaattgaaaaaagagagtattatattaatatgccacacatccataaactaccgactatgccccatcacctgacatcaagcccgaacaggctcctattcggatccttcagcacagcagcgacagtcctcgatccgatccgagattgtagagaggaatcgtgcagctacatcgaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1573:PG1574|PG1573:PG1574:transcriptional regulator, Crp family:hypothetical protein:<-<-:1652259..1652550 292 tccgtttttcaagtataagcacagcagtcattggcaagagaaaaagaattgactaattttgtcttccgaaaagcattgctccgaacagtgaatttccccgtgtattggaagtgagcaattaattgaaaaaagagagtattatattaatatgccacacatccataaactaccgactatgccccatcacctgacatcaagcccgaacaggctcctattcggatccttcagcacagcagcgacagtcctcgatccgatccgagattgtagagaggaatcgtgcagctacatcgaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tccgtttttcaagtataagcacagcagtcattggcaagagaaaaagaattgactaattttgtcttccgaaaagcattgctccgaacagtgaatttccccgtgtattggaagtgagcaattaattgaaaaaagagagtattatattaatatgccacacatccataaactaccgactatgccccatcacctgacatcaagcccgaacaggctcctattcggatccttcagcacagcagcgacagtcctcgatccgatccgagattgtagagaggaatcgtgcagctacatcgaa Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 92 End: 292 ........................................................................................... M S P C I G S E Q L I E K R E Y Y I N M P H I H K L P T M P H H L T S S P N R L L F G S F S T A A T V L D P I R D C R E Protein_Len: 32 Strand: - Start: 187 End: 282 .......................................................................................................................................................................................... R V D L G F L S R N P D K L V A A V T R S G I R S Q L S S D H M .......... Protein_Len: 31 Strand: - Start: 31 End: 123 .............................. Q C S F F F Q S I K D E S F C Q E S C H I E G H I P L S C N M ......................................................................................................................................................................... Protein_Len: 36 Strand: - Start: 12 End: 119 ........... T Y A C C D N A L S F S N V L K T K R F A N S R V T F K G T Y Q F H A M ............................................................................................................................................................................. tccgtttttcaagtataagcacagcagtcattggcaagagaaaaagaattgactaattttgtcttccgaaaagcattgctccgaacagtgaatttccccgtgtattggaagtgagcaattaattgaaaaaagagagtattatattaatatgccacacatccataaactaccgactatgccccatcacctgacatcaagcccgaacaggctcctattcggatccttcagcacagcagcgacagtcctcgatccgatccgagattgtagagaggaatcgtgcagctacatcgaa 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: 138 End: 167 .........................................................................................................................................GTTTATGGATGTGTGGCATATTAATATAAT............................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tccgtttttcaagtataagcacagcagtcattggcaagagaaaaagaattgactaattttgtcttccgaaaagcattgctccgaacagtgaatttccccgtgtattggaagtgagcaattaattgaaaaaagagagtattatattaatatgccacacatccataaactaccgactatgccccatcacctgacatcaagcccgaacaggctcctattcggatccttcagcacagcagcgacagtcctcgatccgatccgagattgtagagaggaatcgtgcagctacatcgaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG1573:PG1574|PG1573:PG1574:transcriptional regulator, Crp family:hypothetical protein:<-<-:1652259..1652550 292 tccgtttttcaagtataagcacagcagtcattggcaagagaaaaagaattgactaattttgtcttccgaaaagcattgctccgaacagtgaatttccccgtgtattggaagtgagcaattaattgaaaaaagagagtattatattaatatgccacacatccataaactaccgactatgccccatcacctgacatcaagcccgaacaggctcctattcggatccttcagcacagcagcgacagtcctcgatccgatccgagattgtagagaggaatcgtgcagctacatcgaa Intra-Species Hit: Count: 2 Min: 1 Max: 292 Len: 292 Subject: NC_002950_PG1573_PG1574|transcriptional regulator, Crp family:hypothetical protein|NEGATIVE:NEGATIVE|[1652259,1652550]|292 HSP 1 e-value: 1.0E-164 bit: 579.0 Len: 292 Query Start:1 Query End:292 Subject Strand: POSITIVE Subject Start: 1 Subject End: 292 tccgtttttcaagtataagcacagcagtcattggcaagagaaaaagaattgactaattttgtcttccgaaaagcattgctccgaacagtgaatttccccgtgtattggaagtgagcaattaattgaaaaaagagagtattatattaatatgccacacatccataaactaccgactatgccccatcacctgacatcaagcccgaacaggctcctattcggatccttcagcacagcagcgacagtcctcgatccgatccgagattgtagagaggaatcgtgcagctacatcgaa tccgtttttcaagtataagcacagcagtcattggcaagagaaaaagaattgactaattttgtcttccgaaaagcattgctccgaacagtgaatttccccgtgtattggaagtgagcaattaattgaaaaaagagagtattatattaatatgccacacatccataaactaccgactatgccccatcacctgacatcaagcccgaacaggctcctattcggatccttcagcacagcagcgacagtcctcgatccgatccgagattgtagagaggaatcgtgcagctacatcgaa Subject: NC_002950_PG0371_PG0373|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[404285,404844]|560 HSP 1 e-value: 5.0E-91 bit: 335.0 Len: 291 Query Start:2 Query End:292 Subject Strand: NEGATIVE Subject Start: 46 Subject End: 338 .ccgtttttcaagtataagcacagcagtcattggcaagagaaaaa-gaattgactaattttgtcttccgaaaagcattgctccgaacagtgaatttcccc----gtgtattggaagtgagcaattaattgaaaaaagagagtattatattaatatgccacacatccataaactaccgactatgccccatcacctgacatcaagcccgaacaggctcctattcggatccttcagcacagcagcgacagtcctcgatccgatccgagattgtagagaggaatcgtgcagctacatcgaa .ccgtttttcaagtacaagcacaacagtcgttggcaggagaaaaaagatttggctaattttgtcttccgaaaagcattgctccgaacaatggatccccccccccgtgtattggaagcgagcaattaactgaaaaaagagagtattatattagtatgccacacatccataaactaccggctatgccccatcacctgacatcaagcccgaataggctcctattcggacacctcagca---caacgatagtcctcgatccggtccgagattgcagagaggaatcgtgcagctacatcgaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCCGUUUUUCAAGUAUAAGCACAGCAGUCAUUGGCAAGAGAAAAAGAAUUGACUAAUUUUGUCUUCCGAAAAGCAUUGCUCCGAACAGUGAAUUUCCCCGUGUAUUGGAAGUGAGCAAUUAAUUGAAAAAAGAGAGUAUUAUAUUAAUAUGCCACACAUCCAUAAACUACCGACUAUGCCCCAUCACCUGACAUCAAGCCCGAACAGGCUCCUAUUCGGAUCCUUCAGCACAGCAGCGACAGUCCUCGAUCCGAUCCGAGAUUGUAGAGAGGAAUCGUGCAGCUACAUCGAA .................(((...((.((((..((((.((((...((((((....)))))).))))..((((..(((((.......)))))..))))..((.(((.((((.(((.(((((((((...................)))))).)))..))).)))).....)))))....))))........)))).......(((((.((....)).)))))........))...(((.(((...(((((..(.(((((...))))).)..))))).)))))).)))........ (-59.21) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCGAUGUAGCUGCACGAUUCCUCUCUACAAUCUCGGAUCGGAUCGAGGACUGUCGCUGCUGUGCUGAAGGAUCCGAAUAGGAGCCUGUUCGGGCUUGAUGUCAGGUGAUGGGGCAUAGUCGGUAGUUUAUGGAUGUGUGGCAUAUUAAUAUAAUACUCUCUUUUUUCAAUUAAUUGCUCACUUCCAAUACACGGGGAAAUUCACUGUUCGGAGCAAUGCUUUUCGGAAGACAAAAUUAGUCAAUUCUUUUUCUCUUGCCAAUGACUGCUGUGCUUAUACUUGAAAAACGGA ((((...((((.((((((((((((....(.(((...))).)....)))))..)))).)))...)))).(((.(((((((((....))))))))))))....(((((((...((((((((.((((......((((.(((.((((.((((((...................))))))))))))).))))...((.(((((((....(((...(((((...))))).)))..(((.......)))......))))))).))......)))))))))))).)))))))....)))) (-79.21) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 931 110 61 201 152 NC_002950:PG1573|5end_transcriptional_regulator,_Crp_family_1652168..1652398_NEGATIVE 422 260 217 204 156 NC_002950:PG0934|5end_hypothetical_protein_994318..994548_NEGATIVE 418 279 231 205 143 NC_002950:PG0217|5end_hypothetical_protein_252490..252720_POSITIVE 392 290 241 83 20 NC_002950:PG1752|5end_hypothetical_protein_1838394..1838624_POSITIVE 389 258 213 196 136 NC_002950:PG0158|5end_competence_protein_F-related_protein_180175..180405_POSITIVE 382 279 233 92 42 NC_002950:PG0333|5end_hypothetical_protein_367823..368053_POSITIVE 377 239 197 221 172 NC_002950:PG1253|5end_DNA_ligase,_NAD-dependent_1331606..1331836_NEGATIVE 374 200 151 208 143 NC_002950:PG1945|5end_hypothetical_protein_2031697..2031927_POSITIVE 368 90 56 118 78 NC_002950:PG1735|5end_MutT/nudix_family_protein_1823082..1823312_NEGATIVE 366 280 235 54 8 NC_002950:PG1418|5end_DNA_polymerase_III,_gamma_and_tau_subunits_1503064..1503294_POSITIVE 363 249 201 212 150 NC_002950:PG2100|5end_immunoreactive_63_kDa_antigen_PG102_2210191..2210421_NEGATIVE 362 260 212 61 11 NC_002950:PG1059|5end_hypothetical_protein_1126495..1126725_NEGATIVE 352 258 211 57 7 NC_002950:PG1871|5end_hypothetical_protein_1966859..1967089_NEGATIVE 351 239 199 223 167 NC_002950:PG1719|5end_ABC_transporter,_ATP-binding_protein,_MsbA_family_1806749..1806979_POSITIVE 351 277 232 93 39 NC_002950:PG1388|5end_hypothetical_protein_1470889..1471119_NEGATIVE 347 257 212 117 61 NC_002950:PG0438|5end_hypothetical_protein_476884..477114_POSITIVE 346 219 171 229 179 NC_002950:PG0961|5end_hypothetical_protein_1022272..1022502_NEGATIVE 344 289 245 50 2 NC_002950:PG1063|5end_transcriptional_regulator,_putative_1131056..1131286_POSITIVE 344 267 221 56 8 NC_002950:PG0738|5end_cytidine/deoxycytidylate_deaminase_family_protein_786463..786693_POSITIVE 344 287 241 140 92 NC_002950:PG0133|5end_hypothetical_protein_155764..155994_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 793 290 248 43 1 NC_002950:PG0371|3end_hypothetical_protein_404224..404374_POSITIVE 428 290 245 87 37 NC_002950:PG1391|3end_hypothetical_protein_1472961..1473111_POSITIVE 392 290 241 99 36 NC_002950:PG1751|3end_aminotransferase,_class_V_1838490..1838640_POSITIVE 363 249 201 125 63 NC_002950:PG2101|3end_hypothetical_protein_2210278..2210428_NEGATIVE 362 249 205 85 28 NC_002950:PG0656|3end_50S_ribosomal_protein_L34_706945..707095_NEGATIVE 351 277 232 112 58 NC_002950:PG1389|3end_DNA-binding_protein,_histone-like_family_1470870..1471020_NEGATIVE 351 290 242 129 81 NC_002950:PG1364|3end_1-deoxy-D-xylulose_5-phosphate_reductoisomerase_1444388..1444538_NEGATIVE 344 217 171 60 22 NC_002950:PG1105|3end_RNA_polymerase_sigma-54_factor_1175716..1175866_NEGATIVE 344 267 221 59 11 NC_002950:PG0737|3end_hypothetical_protein_786546..786696_POSITIVE 344 287 241 121 73 NC_002950:PG0134|3end_magnesium_transporter_155783..155933_NEGATIVE 342 280 231 112 59 NC_002950:PG0199|3end_TatD_family_protein_237424..237574_NEGATIVE 341 247 201 96 42 NC_002950:PG2076|3end_hypothetical_protein_2177073..2177223_POSITIVE 337 229 183 64 12 NC_002950:PG0606|3end_hypothetical_protein_662451..662601_NEGATIVE 336 249 201 130 75 NC_002950:PG2214|3end_hypothetical_protein_2325301..2325451_NEGATIVE 334 245 208 35 1 NC_002950:PG0295|3end_DNA_processing_protein_DprA,_putative_330176..330326_NEGATIVE 332 220 176 49 12 NC_002950:PG0143|3end_hydrolase,_carbon-nitrogen_family_165747..165897_NEGATIVE 331 220 171 141 96 NC_002950:PG1980|3end_hypothetical_protein_2067760..2067910_NEGATIVE 328 218 191 58 26 NC_002950:PG1220|3end_erythronate-4-phosphate_dehydrogenase_1298199..1298349_POSITIVE 327 258 215 58 3 NC_002950:PG2031|3end_hypothetical_protein_2130871..2131021_POSITIVE 326 277 233 122 72 NC_002950:PG1600|3end_hypothetical_protein_1679959..1680109_NEGATIVE