Origin IGS: aaacctttttctgtgccaaagttatccgcttttacgttacacaacaaattttcgggctgatttttgcacaaaaaacccatttccgtgtatttttctattagtcagaggctgaaaaaacattcttacaactgctaaggaaaccttatgacagtgaagtaatgaaaaaggctgtgtcgtgagtttcctcatacacagccttttataagggtatttattcttctacaaggata .........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 tatccttgtagaagaataaatacccttataaaaggctgtgtatgaggaaactcacgacacagcctttttcattacttcactgtcataaggtttccttagcagttgtaagaatgttttttcagcctctgactaatagaaaaatacacggaaatgggttttttgtgcaaaaatcagcccgaaaatttgttgtgtaacgtaaaagcggataactttggcacagaaaaaggttt Mask Tandem Repeat Region ================================================ aaacctttttctgtgccaaagttatccgcttttacgttacacaacaaattttcgggctgatttttgcacaaaaaacccatttccgtgtatttttctattagtcagaggctgaaaaaacattcttacaactgctaaggaaaccttatgacagtgaagtaatgaaaaaggctgtgtcgtgagtttcctcatacacagccttttataagggtatttattcttctacaaggata Find is-nt database================================================ Query_seq: PG0778:PG0779|PG0778:PG0779:hypothetical protein:hypothetical protein:<-<-:831960..832189 230 aaacctttttctgtgccaaagttatccgcttttacgttacacaacaaattttcgggctgatttttgcacaaaaaacccatttccgtgtatttttctattagtcagaggctgaaaaaacattcttacaactgctaaggaaaccttatgacagtgaagtaatgaaaaaggctgtgtcgtgagtttcctcatacacagccttttataagggtatttattcttctacaaggata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0778:PG0779|PG0778:PG0779:hypothetical protein:hypothetical protein:<-<-:831960..832189 230 aaacctttttctgtgccaaagttatccgcttttacgttacacaacaaattttcgggctgatttttgcacaaaaaacccatttccgtgtatttttctattagtcagaggctgaaaaaacattcttacaactgctaaggaaaccttatgacagtgaagtaatgaaaaaggctgtgtcgtgagtttcctcatacacagccttttataagggtatttattcttctacaaggata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0778:PG0779|PG0778:PG0779:hypothetical protein:hypothetical protein:<-<-:831960..832189 230 aaacctttttctgtgccaaagttatccgcttttacgttacacaacaaattttcgggctgatttttgcacaaaaaacccatttccgtgtatttttctattagtcagaggctgaaaaaacattcttacaactgctaaggaaaccttatgacagtgaagtaatgaaaaaggctgtgtcgtgagtttcctcatacacagccttttataagggtatttattcttctacaaggata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaacctttttctgtgccaaagttatccgcttttacgttacacaacaaattttcgggctgatttttgcacaaaaaacccatttccgtgtatttttctattagtcagaggctgaaaaaacattcttacaactgctaaggaaaccttatgacagtgaagtaatgaaaaaggctgtgtcgtgagtttcctcatacacagccttttataagggtatttattcttctacaaggata Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 11 End: 109 .......... M C Q S Y P L L R Y T T N F R A D F C T K N P F P C I F L L V R G ......................................................................................................................... Protein_Len: 52 Strand: - Start: 40 End: 195 ....................................... V V F K R A S K Q V F F G N G H I K R N T L P Q F F M R V V A L S V K H C H L L S F P Q T T L K R M C M ................................... Protein_Len: 32 Strand: - Start: 3 End: 98 .. G K E T G F N D A K V N C L L N E P Q N K C L F G M E T Y K E M .................................................................................................................................... aaacctttttctgtgccaaagttatccgcttttacgttacacaacaaattttcgggctgatttttgcacaaaaaacccatttccgtgtatttttctattagtcagaggctgaaaaaacattcttacaactgctaaggaaaccttatgacagtgaagtaatgaaaaaggctgtgtcgtgagtttcctcatacacagccttttataagggtatttattcttctacaaggata 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================================================ aaacctttttctgtgccaaagttatccgcttttacgttacacaacaaattttcgggctgatttttgcacaaaaaacccatttccgtgtatttttctattagtcagaggctgaaaaaacattcttacaactgctaaggaaaccttatgacagtgaagtaatgaaaaaggctgtgtcgtgagtttcctcatacacagccttttataagggtatttattcttctacaaggata Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 95 HP_score: -11.3 Tail_Score: -4.39828 Start: 167 End: 197 Full_Region: TGAAGTAATGAAAAA GGCTGTGTCGTGAG TTTC CTCATACACAGCC TTTTATAAGGGTATT ......................................................................................................................................................................GGCTGTGTCGTGAGTTTCCTCATACACAGCC................................. TransTerm Strand: - Conf: 100 HP_score: -9.1 Tail_Score: -4.93547 Start: 167 End: 197 Full_Region: aatacccttataaaa ggctgtgtatgag gaaa ctcacgacacagcc tttttcattacttca ......................................................................................................................................................................ggctgtgtatgaggaaactcacgacacagcc................................. Find igs database================================================ Query_seq: PG0778:PG0779|PG0778:PG0779:hypothetical protein:hypothetical protein:<-<-:831960..832189 230 aaacctttttctgtgccaaagttatccgcttttacgttacacaacaaattttcgggctgatttttgcacaaaaaacccatttccgtgtatttttctattagtcagaggctgaaaaaacattcttacaactgctaaggaaaccttatgacagtgaagtaatgaaaaaggctgtgtcgtgagtttcctcatacacagccttttataagggtatttattcttctacaaggata Intra-Species Hit: Count: 1 Min: 1 Max: 230 Len: 230 Subject: NC_002950_PG0778_PG0779|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[831960,832189]|230 HSP 1 e-value: 1.0E-127 bit: 456.0 Len: 230 Query Start:1 Query End:230 Subject Strand: POSITIVE Subject Start: 1 Subject End: 230 aaacctttttctgtgccaaagttatccgcttttacgttacacaacaaattttcgggctgatttttgcacaaaaaacccatttccgtgtatttttctattagtcagaggctgaaaaaacattcttacaactgctaaggaaaccttatgacagtgaagtaatgaaaaaggctgtgtcgtgagtttcctcatacacagccttttataagggtatttattcttctacaaggata aaacctttttctgtgccaaagttatccgcttttacgttacacaacaaattttcgggctgatttttgcacaaaaaacccatttccgtgtatttttctattagtcagaggctgaaaaaacattcttacaactgctaaggaaaccttatgacagtgaagtaatgaaaaaggctgtgtcgtgagtttcctcatacacagccttttataagggtatttattcttctacaaggata Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAACCUUUUUCUGUGCCAAAGUUAUCCGCUUUUACGUUACACAACAAAUUUUCGGGCUGAUUUUUGCACAAAAAACCCAUUUCCGUGUAUUUUUCUAUUAGUCAGAGGCUGAAAAAACAUUCUUACAACUGCUAAGGAAACCUUAUGACAGUGAAGUAAUGAAAAAGGCUGUGUCGUGAGUUUCCUCAUACACAGCCUUUUAUAAGGGUAUUUAUUCUUCUACAAGGAUA ...((((....(((((.(((((((((((.......(((....))).......)))).))))))).)))))....((((...................(((((.....))))).....(((((((...((((((((((...))))).).)))).))).)))).((((((((((((.(((((....)))))))))))))))))....))))..............))))... (-62.54) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUCCUUGUAGAAGAAUAAAUACCCUUAUAAAAGGCUGUGUAUGAGGAAACUCACGACACAGCCUUUUUCAUUACUUCACUGUCAUAAGGUUUCCUUAGCAGUUGUAAGAAUGUUUUUUCAGCCUCUGACUAAUAGAAAAAUACACGGAAAUGGGUUUUUUGUGCAAAAAUCAGCCCGAAAAUUUGUUGUGUAACGUAAAAGCGGAUAACUUUGGCACAGAAAAAGGUUU ..(((.((((...(((.(((((..(((((((((((((((((.((((....))))..))))))))))))..........(((((..(((((...)))))))))).)))))..))))).)))....((((.....))))....)))).)))......((((((((((..........(((......((((....))))......))).........))))))))))...... (-61.41) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 885 60 11 151 102 NC_002950:PG0778|5end_hypothetical_protein_831869..832099_NEGATIVE 383 197 151 213 157 NC_002950:PG1739|5end_hypothetical_protein_1825709..1825939_NEGATIVE 370 200 160 100 62 NC_002950:PG1423|5end_hypothetical_protein_1509088..1509318_NEGATIVE 342 197 164 154 114 NC_002950:PG1759|5end_adhesion_protein,_putative_1845570..1845800_POSITIVE 336 45 7 181 134 NC_002950:PG1980|5end_hypothetical_protein_2067930..2068160_NEGATIVE 333 198 154 211 164 NC_002950:PG0898|5end_hypothetical_protein_963350..963580_NEGATIVE 304 210 167 56 21 NC_002950:PG1876|5end_hypothetical_protein_1971460..1971690_NEGATIVE 294 60 12 227 172 NC_002950:PG0680|5end_efflux_transporter,_MFP_component,_RND_family_730968..731198_POSITIVE 290 207 167 105 64 NC_002950:PG0158|5end_competence_protein_F-related_protein_180175..180405_POSITIVE 289 210 165 100 56 NC_002950:PG1233|5end_hypothetical_protein_1309885..1310115_POSITIVE 289 84 52 29 4 NC_002950:PG0062|5end_TPR_domain_protein_73688..73918_POSITIVE 286 198 153 180 134 NC_002950:PG1418|5end_DNA_polymerase_III,_gamma_and_tau_subunits_1503064..1503294_POSITIVE 282 197 158 224 184 NC_002950:PG0749|5end_hypothetical_protein_795654..795884_NEGATIVE 278 198 151 173 118 NC_002950:PG0757|5end_hypothetical_protein_806370..806600_NEGATIVE 274 188 142 136 87 NC_002950:PG1970|5end_hypothetical_protein_2059783..2060013_NEGATIVE 274 220 171 219 158 NC_002950:PG0203|5end_hypothetical_protein_240211..240441_NEGATIVE 272 208 167 69 29 NC_002950:PG1651|5end_TPR_domain_protein_1730326..1730556_POSITIVE 264 180 131 96 42 NC_002950:PG0671|5end_iron_compound_ABC_transporter,_permease_protein_721888..722118_POSITIVE 264 70 21 90 33 NC_002950:PG0302|5end_hypothetical_protein_338219..338449_POSITIVE 262 60 11 204 152 NC_002950:PG0283|5end_efflux_transporter,_MFP_component,_RND_family_318245..318475_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 417 200 151 69 17 NC_002950:PG0506|3end_arginine-specific_cysteine_proteinase_547625..547775_POSITIVE 390 209 167 62 16 NC_002950:PG1754|3end_hypothetical_protein_1842284..1842434_POSITIVE 383 197 151 66 10 NC_002950:PG1741|3end_aspartate_ammonia-lyase_1825856..1826006_NEGATIVE 373 197 153 63 18 NC_002950:PG0726|3end_lipoprotein,_putative_778003..778153_NEGATIVE 370 200 160 51 13 NC_002950:PG1424|3end_peptidylarginine_deiminase_1509137..1509287_NEGATIVE 345 200 161 64 20 NC_002950:PG1847|3end_endoribonuclease_L-PSP,_putative_1946227..1946377_NEGATIVE 344 208 161 55 9 NC_002950:PG0721|3end_NLP/P60_family_protein_774535..774685_POSITIVE 333 198 154 64 17 NC_002950:PG0899|3end_cytochrome_d_ubiquinol_oxidase,_subunit_II_963497..963647_NEGATIVE 328 208 166 79 22 NC_002950:PG0548|3end_pyruvate_ferredoxin/flavodoxin_oxidoreductase_family_protein_605759..605909_POSITIVE 320 207 166 49 8 NC_002950:PG1297|3end_ribosomal_protein_S1_1377710..1377860_POSITIVE 313 200 157 64 16 NC_002950:PG0159|3end_endopeptidase_PepO_181095..181245_NEGATIVE 312 200 167 58 19 NC_002950:PG2010|3end_phosphomannomutase,_putative_2100952..2101102_POSITIVE 305 197 167 38 1 NC_002950:PG1758|3end_ribosomal_protein_S15_1845534..1845684_POSITIVE 302 188 143 61 7 NC_002950:PG0694|3end_immunoreactive_42_kDa_antigen_PG33_749703..749853_NEGATIVE 302 218 171 84 25 NC_002950:PG0395|3end_DNA-directed_RNA_polymerase_beta'_subunit_433305..433455_POSITIVE 297 197 151 78 31 NC_002950:PG2076|3end_hypothetical_protein_2177073..2177223_POSITIVE 297 210 167 56 11 NC_002950:PG0619|3end_alkyl_hydroperoxide_reductase,_F_subunit_672731..672881_POSITIVE 290 207 167 121 80 NC_002950:PG0157|3end_regulatory_protein_RecX_180271..180421_POSITIVE 289 210 161 82 20 NC_002950:PG0350|3end_internalin-related_protein_385356..385506_NEGATIVE 286 198 153 57 11 NC_002950:PG1417|3end_fumarate_hydratase_class_I,_anaerobic_1503021..1503171_POSITIVE