Origin IGS: aagtacgttttcttttctgcaggaagttcaggcctttcagaaacgaatgttttgctaagtgcagactaggttgcctactttttatcataaactagaagaaggtagagttatgatatactgatgataccggcaagcaacaattcctttttttaacttttttctgattgggagcagtgttgatgactgctgtttgttggtatctcctaaataaggttttacgacaccttatttactttaaatctttttatttggaggagctggggaagccttattctcagctcttctagctttttattttgtaagatgaaacaaaaagtaacttgcttgaagaatagagacggtcagcttttgcggctgtctttttctttttatcataaacatttatcttgtttttttgggctataatacagac .........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 gtctgtattatagcccaaaaaaacaagataaatgtttatgataaaaagaaaaagacagccgcaaaagctgaccgtctctattcttcaagcaagttactttttgtttcatcttacaaaataaaaagctagaagagctgagaataaggcttccccagctcctccaaataaaaagatttaaagtaaataaggtgtcgtaaaaccttatttaggagataccaacaaacagcagtcatcaacactgctcccaatcagaaaaaagttaaaaaaaggaattgttgcttgccggtatcatcagtatatcataactctaccttcttctagtttatgataaaaagtaggcaacctagtctgcacttagcaaaacattcgtttctgaaaggcctgaacttcctgcagaaaagaaaacgtactt Mask Tandem Repeat Region ================================================ aagtacgttttcttttctgcaggaagttcaggcctttcagaaacgaatgttttgctaagtgcagactaggttgcctactttttatcataaactagaagaaggtagagttatgatatactgatgataccggcaagcaacaattcctttttttaacttttttctgattgggagcagtgttgatgactgctgtttgttggtatctcctaaataaggttttacgacaccttatttactttaaatctttttatttggaggagctggggaagccttattctcagctcttctagctttttattttgtaagatgaaacaaaaagtaacttgcttgaagaatagagacggtcagcttttgcggctgtctttttctttttatcataaacatttatcttgtttttttgggctataatacagac Find is-nt database================================================ Query_seq: SSA_0153:SSA_0154|SSA_0153:SSA_0154:hypothetical protein:hypothetical protein:->->:149564..149975 412 aagtacgttttcttttctgcaggaagttcaggcctttcagaaacgaatgttttgctaagtgcagactaggttgcctactttttatcataaactagaagaaggtagagttatgatatactgatgataccggcaagcaacaattcctttttttaacttttttctgattgggagcagtgttgatgactgctgtttgttggtatctcctaaataaggttttacgacaccttatttactttaaatctttttatttggaggagctggggaagccttattctcagctcttctagctttttattttgtaagatgaaacaaaaagtaacttgcttgaagaatagagacggtcagcttttgcggctgtctttttctttttatcataaacatttatcttgtttttttgggctataatacagac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0153:SSA_0154|SSA_0153:SSA_0154:hypothetical protein:hypothetical protein:->->:149564..149975 412 aagtacgttttcttttctgcaggaagttcaggcctttcagaaacgaatgttttgctaagtgcagactaggttgcctactttttatcataaactagaagaaggtagagttatgatatactgatgataccggcaagcaacaattcctttttttaacttttttctgattgggagcagtgttgatgactgctgtttgttggtatctcctaaataaggttttacgacaccttatttactttaaatctttttatttggaggagctggggaagccttattctcagctcttctagctttttattttgtaagatgaaacaaaaagtaacttgcttgaagaatagagacggtcagcttttgcggctgtctttttctttttatcataaacatttatcttgtttttttgggctataatacagac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0153:SSA_0154|SSA_0153:SSA_0154:hypothetical protein:hypothetical protein:->->:149564..149975 412 aagtacgttttcttttctgcaggaagttcaggcctttcagaaacgaatgttttgctaagtgcagactaggttgcctactttttatcataaactagaagaaggtagagttatgatatactgatgataccggcaagcaacaattcctttttttaacttttttctgattgggagcagtgttgatgactgctgtttgttggtatctcctaaataaggttttacgacaccttatttactttaaatctttttatttggaggagctggggaagccttattctcagctcttctagctttttattttgtaagatgaaacaaaaagtaacttgcttgaagaatagagacggtcagcttttgcggctgtctttttctttttatcataaacatttatcttgtttttttgggctataatacagac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aagtacgttttcttttctgcaggaagttcaggcctttcagaaacgaatgttttgctaagtgcagactaggttgcctactttttatcataaactagaagaaggtagagttatgatatactgatgataccggcaagcaacaattcctttttttaacttttttctgattgggagcagtgttgatgactgctgtttgttggtatctcctaaataaggttttacgacaccttatttactttaaatctttttatttggaggagctggggaagccttattctcagctcttctagctttttattttgtaagatgaaacaaaaagtaacttgcttgaagaatagagacggtcagcttttgcggctgtctttttctttttatcataaacatttatcttgtttttttgggctataatacagac Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: + Start: 165 End: 284 .................................................................................................................................................................... M G A V L M T A V C W Y L L N K V L R H L I Y F K S F Y L E E L G K P Y S Q L F ................................................................................................................................ Protein_Len: 60 Strand: + Start: 208 End: 402 ............................................................................................................................................................................................................... M R F Y D T L F T L N L F I W R S W G S L I L S S S S F L F C K M K Q K V T C L K N R D G Q L L R L S F S F Y H K H L S .......... Protein_Len: 40 Strand: - Start: 287 End: 406 .............................................................................................................................................................................................................................................................................................. S K I K Y S S V F L L K S S S Y L R D A K A A T K K K K D Y V N I K N K Q A I M ...... Protein_Len: 45 Strand: - Start: 95 End: 229 .............................................................................................. F F T S N H Y V S S V P L C C N R K K V K K Q N P A T N I V A T Q Q Y R R F L T K R C R M ....................................................................................................................................................................................... aagtacgttttcttttctgcaggaagttcaggcctttcagaaacgaatgttttgctaagtgcagactaggttgcctactttttatcataaactagaagaaggtagagttatgatatactgatgataccggcaagcaacaattcctttttttaacttttttctgattgggagcagtgttgatgactgctgtttgttggtatctcctaaataaggttttacgacaccttatttactttaaatctttttatttggaggagctggggaagccttattctcagctcttctagctttttattttgtaagatgaaacaaaaagtaacttgcttgaagaatagagacggtcagcttttgcggctgtctttttctttttatcataaacatttatcttgtttttttgggctataatacagac 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================================================ aagtacgttttcttttctgcaggaagttcaggcctttcagaaacgaatgttttgctaagtgcagactaggttgcctactttttatcataaactagaagaaggtagagttatgatatactgatgataccggcaagcaacaattcctttttttaacttttttctgattgggagcagtgttgatgactgctgtttgttggtatctcctaaataaggttttacgacaccttatttactttaaatctttttatttggaggagctggggaagccttattctcagctcttctagctttttattttgtaagatgaaacaaaaagtaacttgcttgaagaatagagacggtcagcttttgcggctgtctttttctttttatcataaacatttatcttgtttttttgggctataatacagac Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 79 HP_score: -3.3 Tail_Score: -5.54907 Start: 248 End: 288 Full_Region: CTTTAAATCTTTTTA TTTGGAGGAGCTGGGGA AGCCTTA TTCTCAGCTCTTCTAGC TTTTTATTTTGTAAG .......................................................................................................................................................................................................................................................TTTGGAGGAGCTGGGGAAGCCTTATTCTCAGCTCTTCTAGC............................................................................................................................ TransTerm Strand: + Conf: 68 HP_score: -6.8 Tail_Score: -3.91317 Start: 249 End: 287 Full_Region: TTTAAATCTTTTTAT TTGGAGGAGCTGGGGA AGCCTTA TTCTCAGCTCTTCTAG CTTTTTATTTTGTAA ........................................................................................................................................................................................................................................................TTGGAGGAGCTGGGGAAGCCTTATTCTCAGCTCTTCTAG............................................................................................................................. TransTerm Strand: + Conf: 67 HP_score: -8.5 Tail_Score: -2.98404 Start: 252 End: 284 Full_Region: AAATCTTTTTATTTG GAGGAGCTGGGGA AGCCTTA TTCTCAGCTCTTC TAGCTTTTTATTTTG ...........................................................................................................................................................................................................................................................GAGGAGCTGGGGAAGCCTTATTCTCAGCTCTTC................................................................................................................................ TransTerm Strand: + Conf: 85 HP_score: -4.1 Tail_Score: -5.69262 Start: 337 End: 359 Full_Region: TGCTTGAAGAATAGA GACGGTCAGC TTTT GCGGCTGTC TTTTTCTTTTTATCA ................................................................................................................................................................................................................................................................................................................................................GACGGTCAGCTTTTGCGGCTGTC..................................................... Find igs database================================================ Query_seq: SSA_0153:SSA_0154|SSA_0153:SSA_0154:hypothetical protein:hypothetical protein:->->:149564..149975 412 aagtacgttttcttttctgcaggaagttcaggcctttcagaaacgaatgttttgctaagtgcagactaggttgcctactttttatcataaactagaagaaggtagagttatgatatactgatgataccggcaagcaacaattcctttttttaacttttttctgattgggagcagtgttgatgactgctgtttgttggtatctcctaaataaggttttacgacaccttatttactttaaatctttttatttggaggagctggggaagccttattctcagctcttctagctttttattttgtaagatgaaacaaaaagtaacttgcttgaagaatagagacggtcagcttttgcggctgtctttttctttttatcataaacatttatcttgtttttttgggctataatacagac Intra-Species Hit: Count: 1 Min: 1 Max: 412 Len: 412 Subject: NC_009009_SSA_0153_SSA_0154|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[149564,149975]|412 HSP 1 e-value: 1.0E-128 bit: 458.0 Len: 252 Query Start:161 Query End:412 Subject Strand: POSITIVE Subject Start: 161 Subject End: 412 ................................................................................................................................................................ctgattgggagcagtgttgatgactgctgtttgttggtatctcctaaataaggttttacgacaccttatttactttaaatctttttatttggaggagctggggaagccttattctcagctcttctagctttttattttgtaagatgaaacaaaaagtaacttgcttgaagaatagagacggtcagcttttgcggctgtctttttctttttatcataaacatttatcttgnnnnnnngggctataatacagac ................................................................................................................................................................ctgattgggagcagtgttgatgactgctgtttgttggtatctcctaaataaggttttacgacaccttatttactttaaatctttttatttggaggagctggggaagccttattctcagctcttctagctttttattttgtaagatgaaacaaaaagtaacttgcttgaagaatagagacggtcagcttttgcggctgtctttttctttttatcataaacatttatcttgtttttttgggctataatacagac HSP 2 e-value: 6.0E-76 bit: 285.0 Len: 144 Query Start:1 Query End:144 Subject Strand: POSITIVE Subject Start: 1 Subject End: 144 aagtacgttttcttttctgcaggaagttcaggcctttcagaaacgaatgttttgctaagtgcagactaggttgcctactttttatcataaactagaagaaggtagagttatgatatactgatgataccggcaagcaacaattcc............................................................................................................................................................................................................................................................................ aagtacgttttcttttctgcaggaagttcaggcctttcagaaacgaatgttttgctaagtgcagactaggttgcctactttttatcataaactagaagaaggtagagttatgatatactgatgataccggcaagcaacaattcc............................................................................................................................................................................................................................................................................ Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGUACGUUUUCUUUUCUGCAGGAAGUUCAGGCCUUUCAGAAACGAAUGUUUUGCUAAGUGCAGACUAGGUUGCCUACUUUUUAUCAUAAACUAGAAGAAGGUAGAGUUAUGAUAUACUGAUGAUACCGGCAAGCAACAAUUCCUUUUUUUAACUUUUUUCUGAUUGGGAGCAGUGUUGAUGACUGCUGUUUGUUGGUAUCUCCUAAAUAAGGUUUUACGACACCUUAUUUACUUUAAAUCUUUUUAUUUGGAGGAGCUGGGGAAGCCUUAUUCUCAGCUCUUCUAGCUUUUUAUUUUGUAAGAUGAAACAAAAAGUAACUUGCUUGAAGAAUAGAGACGGUCAGCUUUUGCGGCUGUCUUUUUCUUUUUAUCAUAAACAUUUAUCUUGUUUUUUUGGGCUAUAAUACAGAC (((((.((..(((..((((((...(((..((((..(((......))).)))).)))...))))))..)))..)).)))))..(((.(((..(((((((((((((((.((((((((....((.(((((((((((((......((((..((.............))..))))(((((.......))))).))))))))))))))).((((((((((........))))))))))........((((((..((((((((((((((((.......))))))))))))))))..((((((((....)))))))).))))))..........((((((.((((((((((.((....)))))))))))))))))).))))))))...)))))))...))))))))..))).)))..... (-118.52) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUCUGUAUUAUAGCCCAAAAAAACAAGAUAAAUGUUUAUGAUAAAAAGAAAAAGACAGCCGCAAAAGCUGACCGUCUCUAUUCUUCAAGCAAGUUACUUUUUGUUUCAUCUUACAAAAUAAAAAGCUAGAAGAGCUGAGAAUAAGGCUUCCCCAGCUCCUCCAAAUAAAAAGAUUUAAAGUAAAUAAGGUGUCGUAAAACCUUAUUUAGGAGAUACCAACAAACAGCAGUCAUCAACACUGCUCCCAAUCAGAAAAAAGUUAAAAAAAGGAAUUGUUGCUUGCCGGUAUCAUCAGUAUAUCAUAACUCUACCUUCUUCUAGUUUAUGAUAAAAAGUAGGCAACCUAGUCUGCACUUAGCAAAACAUUCGUUUCUGAAAGGCCUGAACUUCCUGCAGAAAAGAAAACGUACUU .((((((....((((.....(((((.......)))))..................((((.......))))....((((..((((((.(((...(((..((((((........)))))))))...))).))))))..))))....))))....(((...((((...((((....))))...((((((((((........))))))))))))))...((.......((((((.......)))))).....(((((((..(((........(((...(((((((((.(((...)))....((((((((..(((........))).))))))))....)))))))))....)))((.....)).....)))..)))))))..)).))).......))))))............... (-84.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 395 380 340 158 118 NC_009009:SSA_0679|5end_DNA_repair_and_genetic_recombination,_putative_660714..660944_POSITIVE 366 367 324 178 138 NC_009009:SSA_0496|5end_Succinylglutamate_desuccinylase_/_Aspartoacylase_family,_putative_495946..496176_POSITIVE 336 297 253 185 139 NC_009009:SSA_1990|5end_Zn-porter_lipoprotein,_putative_1986319..1986549_NEGATIVE 335 368 336 35 1 NC_009009:SSA_2160|5end_Deoxyuridinetriphosphatase,_putative_2160066..2160296_NEGATIVE 332 359 314 216 171 NC_009009:SSA_2277|5end_DNA_segregation_ATPase_FtsK/SpoIIIE_family_protein,_putative_2280407..2280637_NEGATIVE 327 293 251 209 166 NC_009009:SSA_0337|5end_Hydroxymethylglutaryl-CoA_reductase,_putative_332163..332393_NEGATIVE 324 270 229 139 93 NC_009009:SSA_1444|5end_Imidazole_glycerol-phosphate_synthase_subunit_hisH,_putative_1447267..1447497_NEGATIVE 315 207 163 214 160 NC_009009:SSA_0076|5end_ABC_sugar_transporter,_permease_protein,_putative_79847..80077_POSITIVE 314 299 256 82 32 NC_009009:SSA_0835|5end_Accessory_secretory_protein_Asp3,_putative_821036..821266_POSITIVE 311 283 250 147 115 NC_009009:SSA_0589|5end_Acetylornithine_deacetylase/succinyl-diaminopimelate_desuccinylase_(M20/M25/M40_family_peptidase),_putative_580745..580975_POSITIVE 310 287 250 150 119 NC_009009:SSA_2202|5end_Elongation_factor_Ts,_putative_2203350..2203580_NEGATIVE 308 300 252 160 105 NC_009009:SSA_1632|5end_Surface_protein,_putative_1634045..1634275_NEGATIVE 308 359 327 89 54 NC_009009:SSA_1478|5end_Transposase_ORF1,_putative_1482889..1483119_POSITIVE 308 288 251 114 73 NC_009009:SSA_0620|5end_hypothetical_protein_612325..612555_NEGATIVE 304 210 161 114 41 NC_009009:SSA_2031|5end_Conserved_domain_uncharacterized_protein_2037153..2037383_POSITIVE 304 360 320 54 16 NC_009009:SSA_0900|5end_Tetratricopeptide_repeat_(TPR)_family_protein_891068..891298_POSITIVE 302 289 241 147 103 NC_009009:SSA_1805|5end_Primosomal_protein_DnaI,_putative_1789564..1789794_NEGATIVE 301 289 259 134 104 NC_009009:SSA_2345|5end_hypothetical_protein_2346919..2347149_POSITIVE 298 369 339 38 8 NC_009009:SSA_2171|5end_hypothetical_protein_2170760..2170990_NEGATIVE 298 360 320 208 156 NC_009009:SSA_0628|5end_Fe-S-cluster_redox_enzyme/radical_SAM_enzyme,_Cfr_family,_putative_617892..618122_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 395 380 340 149 109 NC_009009:SSA_0678|3end_Transcriptional_regulator,_ArgR_family,_putative_660785..660935_POSITIVE 334 76 32 151 97 NC_009009:SSA_0583|3end_Nucleotidyltransferase,_putative_575679..575829_POSITIVE 324 270 229 104 58 NC_009009:SSA_1445|3end_Imidazole_glycerol-phosphate_dehydratase,_putative_1447302..1447452_NEGATIVE 322 374 344 130 100 NC_009009:SSA_1686|3end_hypothetical_protein_1680470..1680620_POSITIVE 317 379 341 145 111 NC_009009:SSA_0929|3end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_940263..940413_POSITIVE 317 297 251 58 16 NC_009009:SSA_0375|3end_D-methionine-binding_lipoprotein_(ABC-type_transporter),_putative_365209..365359_POSITIVE 314 299 256 85 35 NC_009009:SSA_0834|3end_Accessory_secretory_protein_Asp2,_putative_821119..821269_POSITIVE 311 288 246 151 108 NC_009009:SSA_1991|3end_Pneumococcal_histidine_triad_protein_A,_putative_1986340..1986490_NEGATIVE 310 287 250 77 46 NC_009009:SSA_2203|3end_30S_ribosomal_protein_S2,_putative_2203423..2203573_NEGATIVE 308 300 252 99 44 NC_009009:SSA_1633|3end_FimA_fimbrial_subunit-like_protein,_putative_1634106..1634256_NEGATIVE 308 288 251 117 76 NC_009009:SSA_0621|3end_SOS_responce_UmuC_protein,_putative_612322..612472_NEGATIVE 308 290 241 144 99 NC_009009:SSA_0093|3end_V-type_sodium_ATPase,_subunit_D,_putative_94989..95139_POSITIVE 304 360 320 67 29 NC_009009:SSA_0899|3end_Conserved_permease,_putative_891161..891311_POSITIVE 302 289 241 146 102 NC_009009:SSA_1806|3end_Replication_initiation/membrane_attachment_protein_DnaB,_putative_1789565..1789715_NEGATIVE 302 285 250 100 57 NC_009009:SSA_0303|3end_surface_protein_C_301051..301201_POSITIVE 296 283 242 128 88 NC_009009:SSA_2258|3end_hypothetical_protein_2253389..2253539_NEGATIVE 293 80 39 131 83 NC_009009:SSA_2202|3end_Elongation_factor_Ts,_putative_2202307..2202457_NEGATIVE 293 58 17 82 32 NC_009009:SSA_1973|3end_Histidine_kinase,_putative_1968407..1968557_NEGATIVE 292 300 254 145 109 NC_009009:SSA_0515|3end_Propanediol_utilization_protein_PduU,_putative_514540..514690_POSITIVE 291 356 330 35 2 NC_009009:SSA_0314|3end_Nucleoside-diphosphate-sugar_epimerase,_putative_308967..309117_NEGATIVE