Origin IGS: tatacgtcttttttattttccactcctttacgctgtgataatatagtatgaagatgaatttttctacgtatatatacgtagaaaaatacagaggaacccgtagaaaatctctttaaatacttcttaactttgcgatagataaaaacagagatgctgttttaggaaaatatctttacttattcctcaatagtgtttttatttgtaatgggtgcgcgcgggattgcttatataagcaatcccgttttattaaggattttgtttatctgtgaagaacgccccatttcttatgttttgttcaggggataaa .........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 tttatcccctgaacaaaacataagaaatggggcgttcttcacagataaacaaaatccttaataaaacgggattgcttatataagcaatcccgcgcgcacccattacaaataaaaacactattgaggaataagtaaagatattttcctaaaacagcatctctgtttttatctatcgcaaagttaagaagtatttaaagagattttctacgggttcctctgtatttttctacgtatatatacgtagaaaaattcatcttcatactatattatcacagcgtaaaggagtggaaaataaaaaagacgtata Mask Tandem Repeat Region ================================================ tatacgtcttttttattttccactcctttacgctgtgataatatagtatgaagatgaatttttctacgtatatatacgtagaaaaatacagaggaacccgtagaaaatctctttaaatacttcttaactttgcgatagataaaaacagagatgctgttttaggaaaatatctttacttattcctcaatagtgtttttatttgtaatgggtgcgcgcgggattgcttatataagcaatcccgttttattaaggattttgtttatctgtgaagaacgccccatttcttatgttttgttcaggggataaa Find is-nt database================================================ Query_seq: PG1097:PG1098|PG1097:PG1098:Mur ligase domain protein/alanine racemase:hypothetical protein:-><-:1165569..1165875 307 tatacgtcttttttattttccactcctttacgctgtgataatatagtatgaagatgaatttttctacgtatatatacgtagaaaaatacagaggaacccgtagaaaatctctttaaatacttcttaactttgcgatagataaaaacagagatgctgttttaggaaaatatctttacttattcctcaatagtgtttttatttgtaatgggtgcgcgcgggattgcttatataagcaatcccgttttattaaggattttgtttatctgtgaagaacgccccatttcttatgttttgttcaggggataaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1097:PG1098|PG1097:PG1098:Mur ligase domain protein/alanine racemase:hypothetical protein:-><-:1165569..1165875 307 tatacgtcttttttattttccactcctttacgctgtgataatatagtatgaagatgaatttttctacgtatatatacgtagaaaaatacagaggaacccgtagaaaatctctttaaatacttcttaactttgcgatagataaaaacagagatgctgttttaggaaaatatctttacttattcctcaatagtgtttttatttgtaatgggtgcgcgcgggattgcttatataagcaatcccgttttattaaggattttgtttatctgtgaagaacgccccatttcttatgttttgttcaggggataaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1097:PG1098|PG1097:PG1098:Mur ligase domain protein/alanine racemase:hypothetical protein:-><-:1165569..1165875 307 tatacgtcttttttattttccactcctttacgctgtgataatatagtatgaagatgaatttttctacgtatatatacgtagaaaaatacagaggaacccgtagaaaatctctttaaatacttcttaactttgcgatagataaaaacagagatgctgttttaggaaaatatctttacttattcctcaatagtgtttttatttgtaatgggtgcgcgcgggattgcttatataagcaatcccgttttattaaggattttgtttatctgtgaagaacgccccatttcttatgttttgttcaggggataaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tatacgtcttttttattttccactcctttacgctgtgataatatagtatgaagatgaatttttctacgtatatatacgtagaaaaatacagaggaacccgtagaaaatctctttaaatacttcttaactttgcgatagataaaaacagagatgctgttttaggaaaatatctttacttattcctcaatagtgtttttatttgtaatgggtgcgcgcgggattgcttatataagcaatcccgttttattaaggattttgtttatctgtgaagaacgccccatttcttatgttttgttcaggggataaa Predict ORF larger than 30AA ================================================ Protein_Len: 50 Strand: + Start: 117 End: 266 .................................................................................................................... M L L N F A I D K N R D A V L G K Y L Y L F L N S V F I C N G C A R D C L Y K Q S R F I K D F V Y L ......................................... Protein_Len: 46 Strand: + Start: 169 End: 303 ........................................................................................................................................................................ M F T Y S S I V F L F V M G A R G I A Y I S N P V L L R I L F I C E E R P I S Y V L F R G * .... Protein_Len: 50 Strand: - Start: 3 End: 152 .. V D K K N E V G K R Q S L I T H L H I K R R I Y V Y F F V S S G T S F R K L Y K K V K R Y I F V S M ........................................................................................................................................................... Protein_Len: 30 Strand: - Start: 2 End: 91 . Y T K K I K W E K V S H Y Y L I F I F K E V Y I Y T S F Y M ........................................................................................................................................................................................................................ tatacgtcttttttattttccactcctttacgctgtgataatatagtatgaagatgaatttttctacgtatatatacgtagaaaaatacagaggaacccgtagaaaatctctttaaatacttcttaactttgcgatagataaaaacagagatgctgttttaggaaaatatctttacttattcctcaatagtgtttttatttgtaatgggtgcgcgcgggattgcttatataagcaatcccgttttattaaggattttgtttatctgtgaagaacgccccatttcttatgttttgttcaggggataaa 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: 38 End: 67 .....................................GTAGAAAAATTCATCTTCATACTATATTAT................................................................................................................................................................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tatacgtcttttttattttccactcctttacgctgtgataatatagtatgaagatgaatttttctacgtatatatacgtagaaaaatacagaggaacccgtagaaaatctctttaaatacttcttaactttgcgatagataaaaacagagatgctgttttaggaaaatatctttacttattcctcaatagtgtttttatttgtaatgggtgcgcgcgggattgcttatataagcaatcccgttttattaaggattttgtttatctgtgaagaacgccccatttcttatgttttgttcaggggataaa Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -13.6 Tail_Score: -3.19965 Start: 55 End: 90 Full_Region: ttctacgggttcctc tgtatttttctacgta tata tacgtagaaaaattca tcttcatactatatt ......................................................tgtatttttctacgtatatatacgtagaaaaattca......................................................................................................................................................................................................................... TransTerm Strand: - Conf: 100 HP_score: -13.0 Tail_Score: -3.40163 Start: 59 End: 86 Full_Region: acgggttcctctgta tttttctacgta tata tacgtagaaaaa ttcatcttcatacta ..........................................................tttttctacgtatatatacgtagaaaaa............................................................................................................................................................................................................................. TransTerm Strand: + Conf: 100 HP_score: -16.3 Tail_Score: -4.6635 Start: 216 End: 241 Full_Region: TGTAATGGGTGCGCG CGGGATTGCTT ATAT AAGCAATCCCG TTTTATTAAGGATTT .......................................................................................................................................................................................................................CGGGATTGCTTATATAAGCAATCCCG.................................................................. Find igs database================================================ Query_seq: PG1097:PG1098|PG1097:PG1098:Mur ligase domain protein/alanine racemase:hypothetical protein:-><-:1165569..1165875 307 tatacgtcttttttattttccactcctttacgctgtgataatatagtatgaagatgaatttttctacgtatatatacgtagaaaaatacagaggaacccgtagaaaatctctttaaatacttcttaactttgcgatagataaaaacagagatgctgttttaggaaaatatctttacttattcctcaatagtgtttttatttgtaatgggtgcgcgcgggattgcttatataagcaatcccgttttattaaggattttgtttatctgtgaagaacgccccatttcttatgttttgttcaggggataaa Intra-Species Hit: Count: 1 Min: 1 Max: 307 Len: 307 Subject: NC_002950_PG1097_PG1098|Mur ligase domain protein/alanine racemase:hypothetical protein|POSITIVE:NEGATIVE|[1165569,1165875]|307 HSP 1 e-value: 1.0E-173 bit: 609.0 Len: 307 Query Start:1 Query End:307 Subject Strand: POSITIVE Subject Start: 1 Subject End: 307 tatacgtcttttttattttccactcctttacgctgtgataatatagtatgaagatgaatttttctacgtatatatacgtagaaaaatacagaggaacccgtagaaaatctctttaaatacttcttaactttgcgatagataaaaacagagatgctgttttaggaaaatatctttacttattcctcaatagtgtttttatttgtaatgggtgcgcgcgggattgcttatataagcaatcccgttttattaaggattttgtttatctgtgaagaacgccccatttcttatgttttgttcaggggataaa tatacgtcttttttattttccactcctttacgctgtgataatatagtatgaagatgaatttttctacgtatatatacgtagaaaaatacagaggaacccgtagaaaatctctttaaatacttcttaactttgcgatagataaaaacagagatgctgttttaggaaaatatctttacttattcctcaatagtgtttttatttgtaatgggtgcgcgcgggattgcttatataagcaatcccgttttattaaggattttgtttatctgtgaagaacgccccatttcttatgttttgttcaggggataaa HSP 2 e-value: 5.0E-8 bit: 60.0 Len: 30 Query Start:58 Query End:87 Subject Strand: NEGATIVE Subject Start: 58 Subject End: 87 .........................................................atttttctacgtatatatacgtagaaaaat............................................................................................................................................................................................................................ .........................................................atttttctacgtatatatacgtagaaaaat............................................................................................................................................................................................................................ Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUACGUCUUUUUUAUUUUCCACUCCUUUACGCUGUGAUAAUAUAGUAUGAAGAUGAAUUUUUCUACGUAUAUAUACGUAGAAAAAUACAGAGGAACCCGUAGAAAAUCUCUUUAAAUACUUCUUAACUUUGCGAUAGAUAAAAACAGAGAUGCUGUUUUAGGAAAAUAUCUUUACUUAUUCCUCAAUAGUGUUUUUAUUUGUAAUGGGUGCGCGCGGGAUUGCUUAUAUAAGCAAUCCCGUUUUAUUAAGGAUUUUGUUUAUCUGUGAAGAACGCCCCAUUUCUUAUGUUUUGUUCAGGGGAUAAA ........((((((((.((((....(((((..(((((....)))))..))))).((.(((((((((((((....))))))))))))).))..))))...))))))))............(((((.(((...((.((((((((((((......((((((..(((((..............))))).))))))))))))))))))((((((.(((.((((((((((((....))))))))))))....(((.((((.......)))).)))....)))))))))......))...))).)))))..... (-83.04) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUAUCCCCUGAACAAAACAUAAGAAAUGGGGCGUUCUUCACAGAUAAACAAAAUCCUUAAUAAAACGGGAUUGCUUAUAUAAGCAAUCCCGCGCGCACCCAUUACAAAUAAAAACACUAUUGAGGAAUAAGUAAAGAUAUUUUCCUAAAACAGCAUCUCUGUUUUUAUCUAUCGCAAAGUUAAGAAGUAUUUAAAGAGAUUUUCUACGGGUUCCUCUGUAUUUUUCUACGUAUAUAUACGUAGAAAAAUUCAUCUUCAUACUAUAUUAUCACAGCGUAAAGGAGUGGAAAAUAAAAAAGACGUAUA ....((((((..((.........(.((((((((((........(((.......)))..........(((((((((((....))))))))))).)))).)))))).)................(((((((..((...((((..(....(((((((.....))))))).)..)))).........(((((.((((....)))))))))))..))))))).(.(((((((((((((....))))))))))))).)........................))..)))...))).................. (-69.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 330 247 201 215 163 NC_002950:PG1018|5end_hypothetical_protein_1078894..1079124_POSITIVE 308 242 206 218 186 NC_002950:PG1815|5end_3-deoxy-manno-octulosonate_cytidylyltransferase_1911433..1911663_NEGATIVE 294 241 206 49 22 NC_002950:PG1829|5end_long-chain-fatty-acid--CoA_ligase,_putative_1922980..1923210_NEGATIVE 293 247 207 222 176 NC_002950:PG1739|5end_hypothetical_protein_1825709..1825939_NEGATIVE 292 246 206 95 49 NC_002950:PG1735|5end_MutT/nudix_family_protein_1823082..1823312_NEGATIVE 284 242 207 151 113 NC_002950:PG2177|5end_Na(+)-translocating_NADH-quinone_reductase_subunit_F_2286504..2286734_NEGATIVE 280 220 181 123 68 NC_002950:PG2021|5end_hypothetical_protein_2114852..2115082_NEGATIVE 280 246 201 228 169 NC_002950:PG1959|5end_ribosomal_protein_L33_2048405..2048635_NEGATIVE 280 226 189 185 151 NC_002950:PG0639|5end_signal_peptide_peptidase_SppA,_67K_type_693000..693230_NEGATIVE 277 226 181 198 152 NC_002950:PG1221|5end_oxidoreductase,_short_chain_dehydrogenase/reductase_family_1298129..1298359_POSITIVE 276 227 181 194 156 NC_002950:PG1533|5end_Toprim_domain_protein_1613761..1613991_NEGATIVE 275 225 183 70 35 NC_002950:PG1857|5end_hypothetical_protein_1956373..1956603_NEGATIVE 275 246 201 170 115 NC_002950:PG0215|5end_hypothetical_protein_251460..251690_POSITIVE 274 249 202 197 160 NC_002950:PG1481|5end_conjugative_transposon_protein_TraG_1558447..1558677_NEGATIVE 272 224 185 44 4 NC_002950:PG2188|5end_diaminopimelate_decarboxylase_2295781..2296011_NEGATIVE 271 242 205 203 152 NC_002950:PG0489|5end_polysaccharide_biosynthesis-related_protein_529247..529477_POSITIVE 270 253 211 60 16 NC_002950:PG1625|5end_hypothetical_protein_1707436..1707666_POSITIVE 266 253 211 210 163 NC_002950:PG0704|5end_phosphoglycerate_mutase_family_protein_758928..759158_POSITIVE 265 219 176 164 121 NC_002950:PG1665|5end_ABC_transporter,_permease_protein,_putative_1747110..1747340_POSITIVE 264 241 210 53 18 NC_002950:PG2179|5end_NADH-ubiquinone_oxidoreductase_2287806..2288036_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 355 90 55 36 1 NC_002950:PG1097|3end_Mur_ligase_domain_protein/alanine_racemase_1165508..1165658_POSITIVE 338 224 181 143 103 NC_002950:PG2146|3end_hypothetical_protein_2254650..2254800_POSITIVE 315 245 201 91 45 NC_002950:PG0593|3end_htrA_protein_651938..652088_POSITIVE 301 239 192 99 51 NC_002950:PG0046|3end_phosphatidate_cytidylyltransferase_56346..56496_NEGATIVE 293 247 207 75 29 NC_002950:PG1741|3end_aspartate_ammonia-lyase_1825856..1826006_NEGATIVE 284 242 207 132 94 NC_002950:PG2178|3end_NADH:ubiquinone_oxidoreductase,_Na_translocating,_E_subunit_2286523..2286673_NEGATIVE 281 247 205 58 16 NC_002950:PG1742|3end_hypothetical_protein_1827506..1827656_POSITIVE 280 220 181 119 64 NC_002950:PG2022|3end_hypothetical_protein_2114856..2115006_NEGATIVE 277 226 183 58 12 NC_002950:PG0561|3end_peptidase,_M20/M25/M40_family_617700..617850_NEGATIVE 277 220 181 145 88 NC_002950:PG0195|3end_rubrerythrin_232704..232854_POSITIVE 265 219 176 141 98 NC_002950:PG1664|3end_ABC_transporter,_permease_protein,_putative_1747167..1747317_POSITIVE 264 241 210 47 12 NC_002950:PG2180|3end_Na(+)-translocating_NADH-quinone_reductase_subunit_C_2287812..2287962_NEGATIVE 263 227 198 98 61 NC_002950:PG1721|3end_ribonuclease_R_1812472..1812622_POSITIVE 262 220 177 125 71 NC_002950:PG0979|3end_hypothetical_protein_1040990..1041140_POSITIVE 260 245 205 54 21 NC_002950:PG0733|3end_riboflavin_synthase_subunit_alpha_783856..784006_POSITIVE 258 245 205 62 20 NC_002950:PG1089|3end_DNA-binding_response_regulator_RprY_1155523..1155673_NEGATIVE 255 238 195 139 90 NC_002950:PG1930|3end_50S_ribosomal_protein_L29_2020215..2020365_NEGATIVE 255 239 192 148 86 NC_002950:PG1594|3end_ComEC/Rec2-related_protein_1672052..1672202_NEGATIVE 255 235 193 137 88 NC_002950:PG1143|3end_sugar_dehydrogenase,_UDP-glucose/GDP-mannose_dehydrogenase_family_1225630..1225780_NEGATIVE 250 221 190 40 9 NC_002950:PG0513|3end_conserved_hypothetical_protein_TIGR00255_551947..552097_NEGATIVE