Origin IGS: gttttagcgtgaataagttttttcttattttctttaactaaatagttatcatcctaacccagagtatactcaattaccttgagctttaacctaagataaagttgattttacttgtaatcagcttatttattttgcgaatatacttattttaagagaatgaagtccgctgattgattgtttatgagtcaaatctgaatctatacaaagagtgcgccggatctttcggatcgacgcactcctttcgttgtttagtcttgtggattgtctattggtctccggatcgtattcggg .........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 cccgaatacgatccggagaccaatagacaatccacaagactaaacaacgaaaggagtgcgtcgatccgaaagatccggcgcactctttgtatagattcagatttgactcataaacaatcaatcagcggacttcattctcttaaaataagtatattcgcaaaataaataagctgattacaagtaaaatcaactttatcttaggttaaagctcaaggtaattgagtatactctgggttaggatgataactatttagttaaagaaaataagaaaaaacttattcacgctaaaac Mask Tandem Repeat Region ================================================ gttttagcgtgaataagttttttcttattttctttaactaaatagttatcatcctaacccagagtatactcaattaccttgagctttaacctaagataaagttgattttacttgtaatcagcttatttattttgcgaatatacttattttaagagaatgaagtccgctgattgattgtttatgagtcaaatctgaatctatacaaagagtgcgccggatctttcggatcgacgcactcctttcgttgtttagtcttgtggattgtctattggtctccggatcgtattcggg Find is-nt database================================================ Query_seq: PG0565:PG0566|PG0565:PG0566:hypothetical protein:DNA-binding protein, histone-like family:<-<-:622734..623024 291 gttttagcgtgaataagttttttcttattttctttaactaaatagttatcatcctaacccagagtatactcaattaccttgagctttaacctaagataaagttgattttacttgtaatcagcttatttattttgcgaatatacttattttaagagaatgaagtccgctgattgattgtttatgagtcaaatctgaatctatacaaagagtgcgccggatctttcggatcgacgcactcctttcgttgtttagtcttgtggattgtctattggtctccggatcgtattcggg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0565:PG0566|PG0565:PG0566:hypothetical protein:DNA-binding protein, histone-like family:<-<-:622734..623024 291 gttttagcgtgaataagttttttcttattttctttaactaaatagttatcatcctaacccagagtatactcaattaccttgagctttaacctaagataaagttgattttacttgtaatcagcttatttattttgcgaatatacttattttaagagaatgaagtccgctgattgattgtttatgagtcaaatctgaatctatacaaagagtgcgccggatctttcggatcgacgcactcctttcgttgtttagtcttgtggattgtctattggtctccggatcgtattcggg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0565:PG0566|PG0565:PG0566:hypothetical protein:DNA-binding protein, histone-like family:<-<-:622734..623024 291 gttttagcgtgaataagttttttcttattttctttaactaaatagttatcatcctaacccagagtatactcaattaccttgagctttaacctaagataaagttgattttacttgtaatcagcttatttattttgcgaatatacttattttaagagaatgaagtccgctgattgattgtttatgagtcaaatctgaatctatacaaagagtgcgccggatctttcggatcgacgcactcctttcgttgtttagtcttgtggattgtctattggtctccggatcgtattcggg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gttttagcgtgaataagttttttcttattttctttaactaaatagttatcatcctaacccagagtatactcaattaccttgagctttaacctaagataaagttgattttacttgtaatcagcttatttattttgcgaatatacttattttaagagaatgaagtccgctgattgattgtttatgagtcaaatctgaatctatacaaagagtgcgccggatctttcggatcgacgcactcctttcgttgtttagtcttgtggattgtctattggtctccggatcgtattcggg Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 200 End: 289 ....................................................................................................................................................................................................... M Q R V R R I F R I D A L L S L F S L V D C L L V S G S Y S .. Protein_Len: 40 Strand: + Start: 171 End: 290 .......................................................................................................................................................................... M I V Y E S N L N L Y K E C A G S F G S T H S F R C L V L W I V Y W S P D R I R . Protein_Len: 33 Strand: - Start: 130 End: 228 ................................................................................................................................. K A F I S I K L S H L G S I S Q K H T L D S D I C L T R R I K R M ............................................................... gttttagcgtgaataagttttttcttattttctttaactaaatagttatcatcctaacccagagtatactcaattaccttgagctttaacctaagataaagttgattttacttgtaatcagcttatttattttgcgaatatacttattttaagagaatgaagtccgctgattgattgtttatgagtcaaatctgaatctatacaaagagtgcgccggatctttcggatcgacgcactcctttcgttgtttagtcttgtggattgtctattggtctccggatcgtattcggg 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================================================ gttttagcgtgaataagttttttcttattttctttaactaaatagttatcatcctaacccagagtatactcaattaccttgagctttaacctaagataaagttgattttacttgtaatcagcttatttattttgcgaatatacttattttaagagaatgaagtccgctgattgattgtttatgagtcaaatctgaatctatacaaagagtgcgccggatctttcggatcgacgcactcctttcgttgtttagtcttgtggattgtctattggtctccggatcgtattcggg Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 47 HP_score: -4.3 Tail_Score: -2.76162 Start: 69 End: 83 Full_Region: CTAACCCAGAGTATA CTCAA TTACC TTGAG CTTTAACCTAAGATA ....................................................................CTCAATTACCTTGAG................................................................................................................................................................................................................ TransTerm Strand: - Conf: 48 HP_score: -4.3 Tail_Score: -2.87522 Start: 69 End: 83 Full_Region: tatcttaggttaaag ctcaa ggtaa ttgag tatactctgggttag ....................................................................ctcaaggtaattgag................................................................................................................................................................................................................ TransTerm Strand: + Conf: 71 HP_score: -6.7 Tail_Score: -4.16371 Start: 206 End: 239 Full_Region: TCTGAATCTATACAA AGAGTGCGCCGGATCT TTC GGATCGACGCACTCC TTTCGTTGTTTAGTC .............................................................................................................................................................................................................AGAGTGCGCCGGATCTTTCGGATCGACGCACTCC.................................................... TransTerm Strand: - Conf: 100 HP_score: -11.7 Tail_Score: -4.09108 Start: 207 End: 238 Full_Region: actaaacaacgaaag gagtgcgtcgatc cgaaa gatccggcgcactc tttgtatagattcag ..............................................................................................................................................................................................................gagtgcgtcgatccgaaagatccggcgcactc..................................................... Find igs database================================================ Query_seq: PG0565:PG0566|PG0565:PG0566:hypothetical protein:DNA-binding protein, histone-like family:<-<-:622734..623024 291 gttttagcgtgaataagttttttcttattttctttaactaaatagttatcatcctaacccagagtatactcaattaccttgagctttaacctaagataaagttgattttacttgtaatcagcttatttattttgcgaatatacttattttaagagaatgaagtccgctgattgattgtttatgagtcaaatctgaatctatacaaagagtgcgccggatctttcggatcgacgcactcctttcgttgtttagtcttgtggattgtctattggtctccggatcgtattcggg Intra-Species Hit: Count: 1 Min: 1 Max: 291 Len: 291 Subject: NC_002950_PG0565_PG0566|hypothetical protein:DNA-binding protein, histone-like family|NEGATIVE:NEGATIVE|[622734,623024]|291 HSP 1 e-value: 1.0E-164 bit: 577.0 Len: 291 Query Start:1 Query End:291 Subject Strand: POSITIVE Subject Start: 1 Subject End: 291 gttttagcgtgaataagttttttcttattttctttaactaaatagttatcatcctaacccagagtatactcaattaccttgagctttaacctaagataaagttgattttacttgtaatcagcttatttattttgcgaatatacttattttaagagaatgaagtccgctgattgattgtttatgagtcaaatctgaatctatacaaagagtgcgccggatctttcggatcgacgcactcctttcgttgtttagtcttgtggattgtctattggtctccggatcgtattcggg gttttagcgtgaataagttttttcttattttctttaactaaatagttatcatcctaacccagagtatactcaattaccttgagctttaacctaagataaagttgattttacttgtaatcagcttatttattttgcgaatatacttattttaagagaatgaagtccgctgattgattgtttatgagtcaaatctgaatctatacaaagagtgcgccggatctttcggatcgacgcactcctttcgttgtttagtcttgtggattgtctattggtctccggatcgtattcggg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUUUAGCGUGAAUAAGUUUUUUCUUAUUUUCUUUAACUAAAUAGUUAUCAUCCUAACCCAGAGUAUACUCAAUUACCUUGAGCUUUAACCUAAGAUAAAGUUGAUUUUACUUGUAAUCAGCUUAUUUAUUUUGCGAAUAUACUUAUUUUAAGAGAAUGAAGUCCGCUGAUUGAUUGUUUAUGAGUCAAAUCUGAAUCUAUACAAAGAGUGCGCCGGAUCUUUCGGAUCGACGCACUCCUUUCGUUGUUUAGUCUUGUGGAUUGUCUAUUGGUCUCCGGAUCGUAUUCGGG (((..((...(((((((......))))))).))..)))...................(((.((((((((((((.....)))))......(.((((((((((((((((........))))))))...)))))))).)..))))))).........(((((..(((((..(((..((.(((((..((......((((((....((((((((((((.((.(((.....))))).)))))).)))).)).)))))).))..))))).....))..)))..)))))..)))))))) (-69.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCCGAAUACGAUCCGGAGACCAAUAGACAAUCCACAAGACUAAACAACGAAAGGAGUGCGUCGAUCCGAAAGAUCCGGCGCACUCUUUGUAUAGAUUCAGAUUUGACUCAUAAACAAUCAAUCAGCGGACUUCAUUCUCUUAAAAUAAGUAUAUUCGCAAAAUAAAUAAGCUGAUUACAAGUAAAAUCAACUUUAUCUUAGGUUAAAGCUCAAGGUAAUUGAGUAUACUCUGGGUUAGGAUGAUAACUAUUUAGUUAAAGAAAAUAAGAAAAAACUUAUUCACGCUAAAAC ..(((((..((...(((.............)))......(((.((((.....(((((((((((((.(....))).))))))))))))))).)))..))..)))))..................((((....((....((((((..(((((((((((...........(((.(((((........))))).)))((((((..((....))..))))))...))))))))).))..))))))...(((((....)))))..)).((((((......))))))..))))..... (-62.32) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 818 100 51 191 142 NC_002950:PG0565|5end_hypothetical_protein_622643..622873_NEGATIVE 414 280 232 55 7 NC_002950:PG0007|5end_hypothetical_protein_6913..7143_NEGATIVE 399 260 211 161 103 NC_002950:PG0526|5end_putative_inner_membrane_protein_translocase_component_YidC_570746..570976_POSITIVE 370 258 211 84 28 NC_002950:PG1318|5end_RNA_polymerase_sigma-70_factor,_ECF_subfamily_1397768..1397998_NEGATIVE 366 260 212 93 31 NC_002950:PG0430|5end_ferrodoxin_oxidoreductase_beta_subunit_467986..468216_POSITIVE 366 260 212 188 141 NC_002950:PG0191|5end_outer_membrane_protein,_putative_226858..227088_POSITIVE 360 259 211 219 176 NC_002950:PG0216|5end_hypothetical_protein_251956..252186_POSITIVE 357 245 207 91 55 NC_002950:PG1563|5end_glucose-1-phosphate_thymidylyltransferase_1642466..1642696_NEGATIVE 350 258 212 201 132 NC_002950:PG1978|5end_hypothetical_protein_2067337..2067567_NEGATIVE 344 290 243 200 140 NC_002950:PG2161|5end_transcriptional_regulator,_AraC_family_2267616..2267846_NEGATIVE 344 234 191 229 171 NC_002950:PG0074|5end_peptide_chain_release_factor_1_89172..89402_NEGATIVE 340 258 212 230 172 NC_002950:PG0150|5end_conserved_hypothetical_protein_TIGR01125_173544..173774_NEGATIVE 339 260 211 185 126 NC_002950:PG1635|5end_hypothetical_protein_1715861..1716091_NEGATIVE 339 260 211 213 161 NC_002950:PG1594|5end_ComEC/Rec2-related_protein_1673587..1673817_NEGATIVE 333 260 213 105 53 NC_002950:PG0242|5end_conserved_hypothetical_protein_TIGR00096_278960..279190_NEGATIVE 329 242 208 70 25 NC_002950:PG2062|5end_histidyl-tRNA_synthetase_2158971..2159201_POSITIVE 327 290 241 86 44 NC_002950:PG1561|5end_dTDP-4-dehydrorhamnose_reductase_1640995..1641225_NEGATIVE 325 280 232 127 86 NC_002950:PG0075|5end_phosphoribosylformylglycinamidine_cyclo-ligase,_putative_90438..90668_NEGATIVE 324 248 205 84 35 NC_002950:PG0472|5end_iron-sulfur_cluster_binding_protein,_putative_513339..513569_POSITIVE 323 260 213 179 135 NC_002950:PG1380|5end_ABC_transporter,_ATP-binding_protein_1459927..1460157_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 689 290 241 89 40 NC_002950:PG1276|3end_DNA-binding_protein,_histone-like_family_1353531..1353681_POSITIVE 366 260 212 66 4 NC_002950:PG0429|3end_pyruvate_synthase_468039..468189_POSITIVE 363 249 207 142 104 NC_002950:PG0800|3end_hypothetical_protein_854719..854869_NEGATIVE 351 239 202 59 18 NC_002950:PG0535|3end_hypothetical_protein_585956..586106_NEGATIVE 345 240 205 84 53 NC_002950:PG1283|3end_hypothetical_protein_1362795..1362945_POSITIVE 334 250 201 61 2 NC_002950:PG0537|3end_aminoacyl-histidine_dipeptidase_588394..588544_POSITIVE 333 260 213 89 37 NC_002950:PG0243|3end_hypothetical_protein_278976..279126_NEGATIVE 327 290 241 89 47 NC_002950:PG1562|3end_dTDP-4-dehydrorhamnose_3,5-epimerase_1640992..1641142_NEGATIVE 325 241 206 150 110 NC_002950:PG0190|3end_undecaprenyl_diphosphate_synthase_226920..227070_POSITIVE 325 258 211 128 80 NC_002950:PG0086|3end_ATP-dependent_RNA_helicase,_DEAD/DEAH_box_family_100545..100695_NEGATIVE 324 248 205 97 48 NC_002950:PG0471|3end_hypothetical_protein_513432..513582_POSITIVE 323 260 213 127 83 NC_002950:PG1379|3end_ABC_transporter,_periplasmic_substrate-binding_protein,_putative_1459955..1460105_POSITIVE 321 249 202 87 28 NC_002950:PG0758|3end_peptidyl-dipeptidase_Dcp_806467..806617_NEGATIVE 321 252 211 77 31 NC_002950:PG0572|3end_hypothetical_protein_627434..627584_NEGATIVE 320 289 243 64 10 NC_002950:PG1942|3end_30S_ribosomal_protein_S12_2027946..2028096_NEGATIVE 318 259 211 55 6 NC_002950:PG0144|3end_hypothetical_protein_166643..166793_NEGATIVE 317 245 204 61 14 NC_002950:PG0769|3end_fibronectin_type_III_domain_protein_822555..822705_NEGATIVE 317 257 211 124 72 NC_002950:PG0443|3end_hemagglutinin-related_protein_483147..483297_POSITIVE 315 260 211 78 19 NC_002950:PG2206|3end_ABC_transporter,_ATP-binding_protein_2317250..2317400_NEGATIVE 315 244 201 74 23 NC_002950:PG2031|3end_hypothetical_protein_2130871..2131021_POSITIVE