Origin IGS: gcaataagttgttttccgtatatatttaaaaatgcctagactgtaaaaagtctaggtattttttctgctatttatttctaataaaacaataataatccatccgagtttgattaaaaaaataatttgtaacttttttgtaacgaaagtagacaaagaatagaaaaatgctaataaaaattatagtttacagaacgtaaattataatattttatgttataattgatatgtatatgtcatatttgcttatcatatacaaacacattcatttttagtttggtaataaatcttgatttagatcgactgaaaatgagggggtagacagatgatggtgtgcctgccagcatttgtcaaaaataaaatttaaaaagaaggaggaccgcattcaag .........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 cttgaatgcggtcctccttctttttaaattttatttttgacaaatgctggcaggcacaccatcatctgtctaccccctcattttcagtcgatctaaatcaagatttattaccaaactaaaaatgaatgtgtttgtatatgataagcaaatatgacatatacatatcaattataacataaaatattataatttacgttctgtaaactataatttttattagcatttttctattctttgtctactttcgttacaaaaaagttacaaattatttttttaatcaaactcggatggattattattgttttattagaaataaatagcagaaaaaatacctagactttttacagtctaggcatttttaaatatatacggaaaacaacttattgc Mask Tandem Repeat Region ================================================ gcaataagttgttttccgtatatatttaaaaatgcctagactgtaaaaagtctaggtattttttctgctatttatttctaataaaacaataataatccatccgagtttgattaaaaaaataatttgtaacttttttgtaacgaaagtagacaaagaatagaaaaatgctaataaaaattatagtttacagaacgtaaattataatattttatgttataattgatatgtatatgtcatatttgcttatcatatacaaacacattcatttttagtttggtaataaatcttgatttagatcgactgaaaatgagggggtagacagatgatggtgtgcctgccagcatttgtcaaaaataaaatttaaaaagaaggaggaccgcattcaag Find is-nt database================================================ Query_seq: SSA_1018:SSA_1019|SSA_1018:SSA_1019:Zinc metalloprotease zmpC precursor, putative:Collagen-binding surface protein, putative:->->:1032630..1033016 387 gcaataagttgttttccgtatatatttaaaaatgcctagactgtaaaaagtctaggtattttttctgctatttatttctaataaaacaataataatccatccgagtttgattaaaaaaataatttgtaacttttttgtaacgaaagtagacaaagaatagaaaaatgctaataaaaattatagtttacagaacgtaaattataatattttatgttataattgatatgtatatgtcatatttgcttatcatatacaaacacattcatttttagtttggtaataaatcttgatttagatcgactgaaaatgagggggtagacagatgatggtgtgcctgccagcatttgtcaaaaataaaatttaaaaagaaggaggaccgcattcaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1018:SSA_1019|SSA_1018:SSA_1019:Zinc metalloprotease zmpC precursor, putative:Collagen-binding surface protein, putative:->->:1032630..1033016 387 gcaataagttgttttccgtatatatttaaaaatgcctagactgtaaaaagtctaggtattttttctgctatttatttctaataaaacaataataatccatccgagtttgattaaaaaaataatttgtaacttttttgtaacgaaagtagacaaagaatagaaaaatgctaataaaaattatagtttacagaacgtaaattataatattttatgttataattgatatgtatatgtcatatttgcttatcatatacaaacacattcatttttagtttggtaataaatcttgatttagatcgactgaaaatgagggggtagacagatgatggtgtgcctgccagcatttgtcaaaaataaaatttaaaaagaaggaggaccgcattcaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1018:SSA_1019|SSA_1018:SSA_1019:Zinc metalloprotease zmpC precursor, putative:Collagen-binding surface protein, putative:->->:1032630..1033016 387 gcaataagttgttttccgtatatatttaaaaatgcctagactgtaaaaagtctaggtattttttctgctatttatttctaataaaacaataataatccatccgagtttgattaaaaaaataatttgtaacttttttgtaacgaaagtagacaaagaatagaaaaatgctaataaaaattatagtttacagaacgtaaattataatattttatgttataattgatatgtatatgtcatatttgcttatcatatacaaacacattcatttttagtttggtaataaatcttgatttagatcgactgaaaatgagggggtagacagatgatggtgtgcctgccagcatttgtcaaaaataaaatttaaaaagaaggaggaccgcattcaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gcaataagttgttttccgtatatatttaaaaatgcctagactgtaaaaagtctaggtattttttctgctatttatttctaataaaacaataataatccatccgagtttgattaaaaaaataatttgtaacttttttgtaacgaaagtagacaaagaatagaaaaatgctaataaaaattatagtttacagaacgtaaattataatattttatgttataattgatatgtatatgtcatatttgcttatcatatacaaacacattcatttttagtttggtaataaatcttgatttagatcgactgaaaatgagggggtagacagatgatggtgtgcctgccagcatttgtcaaaaataaaatttaaaaagaaggaggaccgcattcaag Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 65 End: 157 ................................................................ M L F I S N K T I I I H P S L I K K I I C N F F V T K V D K E ...................................................................................................................................................................................................................................... Protein_Len: 32 Strand: + Start: 220 End: 315 ........................................................................................................................................................................................................................... M I C I C H I C L S Y T N T F I F S L V I N L D L D R L K M R G ........................................................................ Protein_Len: 37 Strand: - Start: 272 End: 382 ............................................................................................................................................................................................................................................................................... N P L L D Q N L D V S F S P T S L H H H A Q W C K D F I F N L F F S S R M ..... Protein_Len: 36 Strand: - Start: 237 End: 344 ............................................................................................................................................................................................................................................ I Q K D Y V F V N M K L K T I F R S K S R S F I L P Y V S S P T G A L M ........................................... Protein_Len: 37 Strand: - Start: 71 End: 181 ...................................................................... K N R I F C Y Y D M R T Q N F F Y N T V K K Y R F Y V F F L F I S I F I M .............................................................................................................................................................................................................. Protein_Len: 33 Strand: - Start: 55 End: 153 ...................................................... T N K R S N I E L L V I I I W G L K I L F I I Q L K K T V F T S M .......................................................................................................................................................................................................................................... gcaataagttgttttccgtatatatttaaaaatgcctagactgtaaaaagtctaggtattttttctgctatttatttctaataaaacaataataatccatccgagtttgattaaaaaaataatttgtaacttttttgtaacgaaagtagacaaagaatagaaaaatgctaataaaaattatagtttacagaacgtaaattataatattttatgttataattgatatgtatatgtcatatttgcttatcatatacaaacacattcatttttagtttggtaataaatcttgatttagatcgactgaaaatgagggggtagacagatgatggtgtgcctgccagcatttgtcaaaaataaaatttaaaaagaaggaggaccgcattcaag 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: 85 Start: 323 End: 352 ..................................................................................................................................................................................................................................................................................................................................TTTGACAAATGCTGGCAGGCACACCATCAT................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gcaataagttgttttccgtatatatttaaaaatgcctagactgtaaaaagtctaggtattttttctgctatttatttctaataaaacaataataatccatccgagtttgattaaaaaaataatttgtaacttttttgtaacgaaagtagacaaagaatagaaaaatgctaataaaaattatagtttacagaacgtaaattataatattttatgttataattgatatgtatatgtcatatttgcttatcatatacaaacacattcatttttagtttggtaataaatcttgatttagatcgactgaaaatgagggggtagacagatgatggtgtgcctgccagcatttgtcaaaaataaaatttaaaaagaaggaggaccgcattcaag Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 57 HP_score: -5.9 Tail_Score: -3.00214 Start: 26 End: 65 Full_Region: GTTTTCCGTATATAT TTAAAAATGCCTAGACT GTAAAA AGTCTAGGTATTTTTTC TGCTATTTATTTCTA .........................TTAAAAATGCCTAGACTGTAAAAAGTCTAGGTATTTTTTC.................................................................................................................................................................................................................................................................................................................................. TransTerm Strand: - Conf: 76 HP_score: -6.2 Tail_Score: -4.72846 Start: 33 End: 58 Full_Region: aaatagcagaaaaaa tacctagact ttttac agtctaggca tttttaaatatatac ................................tacctagactttttacagtctaggca......................................................................................................................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 72 HP_score: -8.8 Tail_Score: -2.65068 Start: 35 End: 56 Full_Region: atagcagaaaaaata cctagact ttttac agtctagg catttttaaatatat ..................................cctagactttttacagtctagg........................................................................................................................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 65 HP_score: -3.5 Tail_Score: -4.76193 Start: 176 End: 206 Full_Region: AAAAATGCTAATAAA AATTATAGTTTAC AGAAC GTAAATTATAATA TTTTATGTTATAATT ...............................................................................................................................................................................AATTATAGTTTACAGAACGTAAATTATAATA..................................................................................................................................................................................... TransTerm Strand: + Conf: 66 HP_score: -6.1 Tail_Score: -3.98053 Start: 178 End: 204 Full_Region: AAATGCTAATAAAAA TTATAGTTTAC AGAAC GTAAATTATAA TATTTTATGTTATAA .................................................................................................................................................................................TTATAGTTTACAGAACGTAAATTATAA....................................................................................................................................................................................... TransTerm Strand: - Conf: 77 HP_score: -4.6 Tail_Score: -5.11112 Start: 178 End: 204 Full_Region: ttataacataaaata ttataatttacg ttc tgtaaactataa tttttattagcattt .................................................................................................................................................................................ttataatttacgttctgtaaactataa....................................................................................................................................................................................... Find igs database================================================ Query_seq: SSA_1018:SSA_1019|SSA_1018:SSA_1019:Zinc metalloprotease zmpC precursor, putative:Collagen-binding surface protein, putative:->->:1032630..1033016 387 gcaataagttgttttccgtatatatttaaaaatgcctagactgtaaaaagtctaggtattttttctgctatttatttctaataaaacaataataatccatccgagtttgattaaaaaaataatttgtaacttttttgtaacgaaagtagacaaagaatagaaaaatgctaataaaaattatagtttacagaacgtaaattataatattttatgttataattgatatgtatatgtcatatttgcttatcatatacaaacacattcatttttagtttggtaataaatcttgatttagatcgactgaaaatgagggggtagacagatgatggtgtgcctgccagcatttgtcaaaaataaaatttaaaaagaaggaggaccgcattcaag Intra-Species Hit: Count: 1 Min: 1 Max: 387 Len: 387 Subject: NC_009009_SSA_1018_SSA_1019|Zinc metalloprotease zmpC precursor, putative:Collagen-binding surface protein, putative|POSITIVE:POSITIVE|[1032630,1033016]|387 HSP 1 e-value: 0.0 bit: 726.0 Len: 387 Query Start:1 Query End:387 Subject Strand: POSITIVE Subject Start: 1 Subject End: 387 gcaataagttgttttccgtatatatttaaaaatgcctagactgtaaaaagtctaggtattttttctgctatttatttctaataaaacaataataatccatccgagtttgattnnnnnnntaatttgtaacttttttgtaacgaaagtagacaaagaatagaaaaatgctaataaaaattatagtttacagaacgtaaattataatattttatgttataattgatatgtatatgtcatatttgcttatcatatacaaacacattcatttttagtttggtaataaatcttgatttagatcgactgaaaatgagggggtagacagatgatggtgtgcctgccagcatttgtcaaaaataaaatttaaaaagaaggaggaccgcattcaag gcaataagttgttttccgtatatatttaaaaatgcctagactgtaaaaagtctaggtattttttctgctatttatttctaataaaacaataataatccatccgagtttgattaaaaaaataatttgtaacttttttgtaacgaaagtagacaaagaatagaaaaatgctaataaaaattatagtttacagaacgtaaattataatattttatgttataattgatatgtatatgtcatatttgcttatcatatacaaacacattcatttttagtttggtaataaatcttgatttagatcgactgaaaatgagggggtagacagatgatggtgtgcctgccagcatttgtcaaaaataaaatttaaaaagaaggaggaccgcattcaag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCAAUAAGUUGUUUUCCGUAUAUAUUUAAAAAUGCCUAGACUGUAAAAAGUCUAGGUAUUUUUUCUGCUAUUUAUUUCUAAUAAAACAAUAAUAAUCCAUCCGAGUUUGAUUAAAAAAAUAAUUUGUAACUUUUUUGUAACGAAAGUAGACAAAGAAUAGAAAAAUGCUAAUAAAAAUUAUAGUUUACAGAACGUAAAUUAUAAUAUUUUAUGUUAUAAUUGAUAUGUAUAUGUCAUAUUUGCUUAUCAUAUACAAACACAUUCAUUUUUAGUUUGGUAAUAAAUCUUGAUUUAGAUCGACUGAAAAUGAGGGGGUAGACAGAUGAUGGUGUGCCUGCCAGCAUUUGUCAAAAAUAAAAUUUAAAAAGAAGGAGGACCGCAUUCAAG .......((.(((((((..........(((((((((((((((......))))))))))))))).......(((((((.....................((((..(((((..............(((((((.(((((((.((....))..)))))))..............((((((((((((((((((.....)))))))))))).))))))))))))).(((((.(((...........))).)))))....)))))...(((((((((((((.(((..(((((....))))).)))))))))))))))).)))).((((((((.((((......)))).))))))))..)))))))............))))))).))....... (-97.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUGAAUGCGGUCCUCCUUCUUUUUAAAUUUUAUUUUUGACAAAUGCUGGCAGGCACACCAUCAUCUGUCUACCCCCUCAUUUUCAGUCGAUCUAAAUCAAGAUUUAUUACCAAACUAAAAAUGAAUGUGUUUGUAUAUGAUAAGCAAAUAUGACAUAUACAUAUCAAUUAUAACAUAAAAUAUUAUAAUUUACGUUCUGUAAACUAUAAUUUUUAUUAGCAUUUUUCUAUUCUUUGUCUACUUUCGUUACAAAAAAGUUACAAAUUAUUUUUUUAAUCAAACUCGGAUGGAUUAUUAUUGUUUUAUUAGAAAUAAAUAGCAGAAAAAAUACCUAGACUUUUUACAGUCUAGGCAUUUUUAAAUAUAUACGGAAAACAACUUAUUGC .........((((((((.....................((.(((((((((.(((((..........))))).))...(((((((.(((.(((((......))))).........))).)))))))...((..((((((((.((........)).))))))))...))........((((((.((((((.(((((.....))))).)))))))))))).))))))).)).....(((((..(((((.........))))).)))))....................))).)))))....(((((((.(((....)))........((((((.((((((((......)))))))).))))))............)))))))........ (-62.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 338 339 297 153 115 NC_009009:SSA_2005|5end_Chaperone_protein_dnaJ,_putative_2006384..2006614_NEGATIVE 320 350 310 168 114 NC_009009:SSA_2320|5end_hypothetical_protein_2325796..2326026_NEGATIVE 319 340 297 74 33 NC_009009:SSA_2339|5end_Microcin_C7_resistance_protein,_putative_2340456..2340686_POSITIVE 311 350 307 56 1 NC_009009:SSA_0987|5end_ABC-type_choline_transporter,_membrane-spanning_permease,_putative_988994..989224_POSITIVE 310 343 306 141 105 NC_009009:SSA_0339|5end_hypothetical_protein_333950..334180_NEGATIVE 302 342 302 144 107 NC_009009:SSA_1828|5end_Glycerol_uptake_facilitator_protein,_putative_1818007..1818237_POSITIVE 301 342 315 56 20 NC_009009:SSA_0865|5end_hypothetical_protein_856378..856608_POSITIVE 296 350 320 199 166 NC_009009:SSA_0535|5end_Propanediol_utilization:_dehydratase,_medium_subunit,_putative_530643..530873_POSITIVE 292 349 301 76 21 NC_009009:SSA_1133|5end_TatA,_sec-independent_protein_secretion_pathway_component,_putative_1159397..1159627_POSITIVE 288 349 301 211 157 NC_009009:SSA_0486|5end_Uroporphyrinogen-III_synthase,_putative_486637..486867_POSITIVE 286 305 262 164 118 NC_009009:SSA_2357|5end_50S_ribosomal_protein_L9,_putative_2358437..2358667_NEGATIVE 286 347 313 79 50 NC_009009:SSA_0085|5end_V-type_sodium_ATPase,_subunit_I,_putative_85750..85980_POSITIVE 282 350 309 63 21 NC_009009:SSA_0498|5end_ABC-type_dipeptide/oligopeptide/nickel_transport_systems,_permease_components,_putative_497910..498140_POSITIVE 274 340 293 66 15 NC_009009:SSA_0725|5end_hypothetical_protein_710247..710477_POSITIVE 270 349 310 100 53 NC_009009:SSA_0185|5end_Competence_protein_ComYB,_putative_189057..189287_POSITIVE 268 337 295 75 32 NC_009009:SSA_2206|5end_hypothetical_protein_2206839..2207069_POSITIVE 267 334 292 162 111 NC_009009:SSA_0914|5end_Phenylalanyl-tRNA_synthetase_beta_chain,_putative_924952..925182_POSITIVE 266 346 302 144 108 NC_009009:SSA_0877|5end_Phosphoglycolate_phosphatase,_putative_871008..871238_POSITIVE 265 347 303 231 177 NC_009009:SSA_1237|5end_Uracil-DNA_glycosylase,_putative_1262366..1262596_NEGATIVE 263 349 324 123 96 NC_009009:SSA_0862|5end_MurM,_putative_854221..854451_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 324 63 28 63 28 NC_009009:SSA_1018|3end_Zinc_metalloprotease_zmpC_precursor,_putative_1032569..1032719_POSITIVE 320 350 306 63 7 NC_009009:SSA_0986|3end_Choline_transporter,_putative_989081..989231_POSITIVE 310 343 306 136 100 NC_009009:SSA_0341|3end_hypothetical_protein_333955..334105_NEGATIVE 302 342 302 75 38 NC_009009:SSA_1827|3end_Alpha-glycerophosphate_oxidase,_putative_1818018..1818168_POSITIVE 292 349 301 76 21 NC_009009:SSA_1132|3end_TatC,_sec-independent_protein_translocase,_putative_1159477..1159627_POSITIVE 291 349 301 69 17 NC_009009:SSA_0492|3end_NADH-dependent_flavin_oxidoreductase,_putative_492771..492921_POSITIVE 286 347 313 89 60 NC_009009:SSA_0083|3end_hypothetical_protein_85840..85990_POSITIVE 282 350 309 70 28 NC_009009:SSA_0497|3end_Nickel_ABC_transporter,_putative_497997..498147_POSITIVE 281 333 297 72 34 NC_009009:SSA_0293|3end_hypothetical_protein_287356..287506_NEGATIVE 270 322 283 44 5 NC_009009:SSA_1911|3end_Conserved_uncharacterized_protein_1902665..1902815_NEGATIVE 270 349 310 140 93 NC_009009:SSA_0184|3end_Competence_protein_ComYA,_putative_189177..189327_POSITIVE 267 341 309 150 109 NC_009009:SSA_1839|3end_Cysteine_synthase,_putative_1833985..1834135_POSITIVE 263 349 324 138 111 NC_009009:SSA_0863|3end_Cof_family_protein,_putative_854206..854356_NEGATIVE 263 340 294 51 1 NC_009009:SSA_0724|3end_ABC-type_multidrug/protein/lipid_transport_system_(pediocin_PA-1_exporter),_ATPase_and_permease_components,_putative_710312..710462_POSITIVE 257 337 302 64 27 NC_009009:SSA_0209|3end_Glutamyl_aminopeptidase,_putative_206572..206722_NEGATIVE 256 351 321 139 101 NC_009009:SSA_0064|3end_hypothetical_protein_66979..67129_POSITIVE 252 342 301 142 103 NC_009009:SSA_1607|3end_Formamidopyrimidine-DNA_glycosylase,_putative_1612431..1612581_NEGATIVE 252 348 301 150 98 NC_009009:SSA_0142|3end_hypothetical_protein_137489..137639_POSITIVE 250 333 296 151 121 NC_009009:SSA_1920|3end_Phosphotransferase_system,_mannose-specific_EIID,_putative_1910884..1911034_POSITIVE 248 340 294 64 12 NC_009009:SSA_0187|3end_Competence_protein_ComYD,_putative_190852..191002_POSITIVE