Origin IGS: tattagctaaacgaatcatctcagctagctgagatgattttttcttgtctttgtcatcatctatccttgataatgtactgacggttaaatttataaactctaaagcaagcagtcattcaaatggatgtttttacggtggctaatatttgctaaacttgattttacagtcaatgaatacttgaaaataaaagtgaattcttgttttataaagaagatttgttacaataaaataagaaaaagtttctttgtttaaagggag .........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 ctccctttaaacaaagaaactttttcttattttattgtaacaaatcttctttataaaacaagaattcacttttattttcaagtattcattgactgtaaaatcaagtttagcaaatattagccaccgtaaaaacatccatttgaatgactgcttgctttagagtttataaatttaaccgtcagtacattatcaaggatagatgatgacaaagacaagaaaaaatcatctcagctagctgagatgattcgtttagctaata Mask Tandem Repeat Region ================================================ tattagctaaacgaatcatctcagctagctgagatgattttttcttgtctttgtcatcatctatccttgataatgtactgacggttaaatttataaactctaaagcaagcagtcattcaaatggatgtttttacggtggctaatatttgctaaacttgattttacagtcaatgaatacttgaaaataaaagtgaattcttgttttataaagaagatttgttacaataaaataagaaaaagtttctttgtttaaagggag Find is-nt database================================================ Query_seq: SSA_1019:SSA_1020|SSA_1019:SSA_1020:Collagen-binding surface protein, putative:hypothetical protein:->->:1035438..1035696 259 tattagctaaacgaatcatctcagctagctgagatgattttttcttgtctttgtcatcatctatccttgataatgtactgacggttaaatttataaactctaaagcaagcagtcattcaaatggatgtttttacggtggctaatatttgctaaacttgattttacagtcaatgaatacttgaaaataaaagtgaattcttgttttataaagaagatttgttacaataaaataagaaaaagtttctttgtttaaagggag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1019:SSA_1020|SSA_1019:SSA_1020:Collagen-binding surface protein, putative:hypothetical protein:->->:1035438..1035696 259 tattagctaaacgaatcatctcagctagctgagatgattttttcttgtctttgtcatcatctatccttgataatgtactgacggttaaatttataaactctaaagcaagcagtcattcaaatggatgtttttacggtggctaatatttgctaaacttgattttacagtcaatgaatacttgaaaataaaagtgaattcttgttttataaagaagatttgttacaataaaataagaaaaagtttctttgtttaaagggag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1019:SSA_1020|SSA_1019:SSA_1020:Collagen-binding surface protein, putative:hypothetical protein:->->:1035438..1035696 259 tattagctaaacgaatcatctcagctagctgagatgattttttcttgtctttgtcatcatctatccttgataatgtactgacggttaaatttataaactctaaagcaagcagtcattcaaatggatgtttttacggtggctaatatttgctaaacttgattttacagtcaatgaatacttgaaaataaaagtgaattcttgttttataaagaagatttgttacaataaaataagaaaaagtttctttgtttaaagggag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tattagctaaacgaatcatctcagctagctgagatgattttttcttgtctttgtcatcatctatccttgataatgtactgacggttaaatttataaactctaaagcaagcagtcattcaaatggatgtttttacggtggctaatatttgctaaacttgattttacagtcaatgaatacttgaaaataaaagtgaattcttgttttataaagaagatttgttacaataaaataagaaaaagtttctttgtttaaagggag Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 45 End: 140 ............................................ M S L S S S I L D N V L T V K F I N S K A S S H S N G C F Y G G ....................................................................................................................... Protein_Len: 42 Strand: + Start: 125 End: 250 ............................................................................................................................ M F L R W L I F A K L D F T V N E Y L K I K V N S C F I K K I C Y N K I R K S F F V ......... Protein_Len: 38 Strand: - Start: 103 End: 216 ...................................................................................................... L L C D N L H I N K R H S I N A L S S K V T L S Y K F I F T F E Q K I F F M ........................................... Protein_Len: 37 Strand: - Start: 2 End: 112 . N A L R I M E A L Q S S K K K D K D D D I R S L T S V T L N I F E L A L M ................................................................................................................................................... tattagctaaacgaatcatctcagctagctgagatgattttttcttgtctttgtcatcatctatccttgataatgtactgacggttaaatttataaactctaaagcaagcagtcattcaaatggatgtttttacggtggctaatatttgctaaacttgattttacagtcaatgaatacttgaaaataaaagtgaattcttgttttataaagaagatttgttacaataaaataagaaaaagtttctttgtttaaagggag 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: 202 End: 231 .........................................................................................................................................................................................................TTTTATAAAGAAGATTTGTTACAATAAAAT............................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tattagctaaacgaatcatctcagctagctgagatgattttttcttgtctttgtcatcatctatccttgataatgtactgacggttaaatttataaactctaaagcaagcagtcattcaaatggatgtttttacggtggctaatatttgctaaacttgattttacagtcaatgaatacttgaaaataaaagtgaattcttgttttataaagaagatttgttacaataaaataagaaaaagtttctttgtttaaagggag Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 84 HP_score: -10.8 Tail_Score: -2.72591 Start: 17 End: 36 Full_Region: aagacaagaaaaaat catctcag ctag ctgagatg attcgtttagctaat ................catctcagctagctgagatg............................................................................................................................................................................................................................... Find igs database================================================ Query_seq: SSA_1019:SSA_1020|SSA_1019:SSA_1020:Collagen-binding surface protein, putative:hypothetical protein:->->:1035438..1035696 259 tattagctaaacgaatcatctcagctagctgagatgattttttcttgtctttgtcatcatctatccttgataatgtactgacggttaaatttataaactctaaagcaagcagtcattcaaatggatgtttttacggtggctaatatttgctaaacttgattttacagtcaatgaatacttgaaaataaaagtgaattcttgttttataaagaagatttgttacaataaaataagaaaaagtttctttgtttaaagggag Intra-Species Hit: Count: 1 Min: 1 Max: 259 Len: 259 Subject: NC_009009_SSA_1019_SSA_1020|Collagen-binding surface protein, putative:hypothetical protein|POSITIVE:POSITIVE|[1035438,1035696]|259 HSP 1 e-value: 1.0E-145 bit: 513.0 Len: 259 Query Start:1 Query End:259 Subject Strand: POSITIVE Subject Start: 1 Subject End: 259 tattagctaaacgaatcatctcagctagctgagatgattttttcttgtctttgtcatcatctatccttgataatgtactgacggttaaatttataaactctaaagcaagcagtcattcaaatggatgtttttacggtggctaatatttgctaaacttgattttacagtcaatgaatacttgaaaataaaagtgaattcttgttttataaagaagatttgttacaataaaataagaaaaagtttctttgtttaaagggag tattagctaaacgaatcatctcagctagctgagatgattttttcttgtctttgtcatcatctatccttgataatgtactgacggttaaatttataaactctaaagcaagcagtcattcaaatggatgtttttacggtggctaatatttgctaaacttgattttacagtcaatgaatacttgaaaataaaagtgaattcttgttttataaagaagatttgttacaataaaataagaaaaagtttctttgtttaaagggag HSP 2 e-value: 1.0E-5 bit: 52.0 Len: 26 Query Start:14 Query End:39 Subject Strand: NEGATIVE Subject Start: 14 Subject End: 39 .............aatcatctcagctagctgagatgatt............................................................................................................................................................................................................................ .............aatcatctcagctagctgagatgatt............................................................................................................................................................................................................................ Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUUAGCUAAACGAAUCAUCUCAGCUAGCUGAGAUGAUUUUUUCUUGUCUUUGUCAUCAUCUAUCCUUGAUAAUGUACUGACGGUUAAAUUUAUAAACUCUAAAGCAAGCAGUCAUUCAAAUGGAUGUUUUUACGGUGGCUAAUAUUUGCUAAACUUGAUUUUACAGUCAAUGAAUACUUGAAAAUAAAAGUGAAUUCUUGUUUUAUAAAGAAGAUUUGUUACAAUAAAAUAAGAAAAAGUUUCUUUGUUUAAAGGGAG (((((((((...((((((((((((....)))))))))))).................(((((((..((((..(((.((((...(((.................)))...)))))))))))))))))).........)))))))))..........(((((......)))))....(((((........)))))..((((((((((((.................)))))))))))).....((((((.....)))))). (-54.46) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUCCCUUUAAACAAAGAAACUUUUUCUUAUUUUAUUGUAACAAAUCUUCUUUAUAAAACAAGAAUUCACUUUUAUUUUCAAGUAUUCAUUGACUGUAAAAUCAAGUUUAGCAAAUAUUAGCCACCGUAAAAACAUCCAUUUGAAUGACUGCUUGCUUUAGAGUUUAUAAAUUUAACCGUCAGUACAUUAUCAAGGAUAGAUGAUGACAAAGACAAGAAAAAAUCAUCUCAGCUAGCUGAGAUGAUUCGUUUAGCUAAUA ......((((((...........(((((.((((((.................)))))).))))).....((((((..((((.......))))..))))))....))))))....(((((((..................((((((....((((......))))......))))))..(((.((.(((((((.......)))))))))...)))..(((..(((((((((((....)))))))))))..))).))))))) (-47.43) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 314 69 21 198 154 NC_009009:SSA_0826|5end_hypothetical_protein_805098..805328_POSITIVE 310 70 24 116 62 NC_009009:SSA_1429|5end_hypothetical_protein_1437110..1437340_NEGATIVE 307 70 22 130 77 NC_009009:SSA_0964|5end_DEAD_RNA_helicase,_putative_974114..974344_NEGATIVE 306 65 21 203 160 NC_009009:SSA_1584|5end_Ring-cleavage_extradiol_dioxygenase,_putative_1587030..1587260_NEGATIVE 294 70 21 103 33 NC_009009:SSA_2228|5end_Acetyltransferase_(GNAT)_family,_putative_2228768..2228998_NEGATIVE 291 52 12 101 54 NC_009009:SSA_1661|5end_hypothetical_protein_1658004..1658234_NEGATIVE 288 140 105 167 124 NC_009009:SSA_0896|5end_Two-component_system_transcriptional_regulator_(CheY_domain_and_HTH-like_DNA-binding_domain),_putative_887705..887935_POSITIVE 284 44 6 172 135 NC_009009:SSA_2356|5end_Replicative_DNA_helicase,_putative_2357958..2358188_NEGATIVE 263 68 23 101 37 NC_009009:SSA_0861|5end_hypothetical_protein_852977..853207_NEGATIVE 261 70 23 81 30 NC_009009:SSA_0441|5end_hypothetical_protein_441481..441711_POSITIVE 259 56 16 39 3 NC_009009:SSA_2277|5end_DNA_segregation_ATPase_FtsK/SpoIIIE_family_protein,_putative_2280407..2280637_NEGATIVE 259 56 12 114 68 NC_009009:SSA_2157|5end_ATP-dependent_serine_protease,_putative_2158241..2158471_NEGATIVE 258 69 22 228 175 NC_009009:SSA_1322|5end_Glycosyl_transferase,_putative_1339819..1340049_NEGATIVE 256 68 24 103 55 NC_009009:SSA_2176|5end_hypothetical_protein_2175159..2175389_NEGATIVE 256 150 104 56 24 NC_009009:SSA_1529|5end_Lysyl-tRNA_synthetase,_putative_1535871..1536101_POSITIVE 255 57 16 104 61 NC_009009:SSA_1617|5end_hypothetical_protein_1620651..1620881_NEGATIVE 255 58 11 150 111 NC_009009:SSA_0547|5end_Acyl_carrier_protein_synthase,_putative_541991..542221_POSITIVE 254 33 3 182 155 NC_009009:SSA_0811|5end_hypothetical_protein_792469..792699_POSITIVE 252 68 28 109 66 NC_009009:SSA_2142|5end_Argininosuccinate_synthase,_putative_2143415..2143645_NEGATIVE 251 66 21 104 51 NC_009009:SSA_2221|5end_Cps9E,_putative_2223257..2223487_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 404 39 11 77 43 NC_009009:SSA_1019|3end_Collagen-binding_surface_protein,_putative_1035377..1035527_POSITIVE 314 69 21 76 32 NC_009009:SSA_0825|3end_DNA-directed_RNA_polymerase,_sigma_subunit_(sigma70/sigma32),_putative_805056..805206_POSITIVE 310 70 24 119 65 NC_009009:SSA_1430|3end_Ribonuclease_Z,_putative_1437107..1437257_NEGATIVE 288 140 105 145 102 NC_009009:SSA_0895|3end_ATP-binding_cassette_transporter-like_protein,_putative_887763..887913_POSITIVE 284 44 6 145 108 NC_009009:SSA_2357|3end_50S_ribosomal_protein_L9,_putative_2357985..2358135_NEGATIVE 279 59 13 100 57 NC_009009:SSA_2339|3end_Microcin_C7_resistance_protein,_putative_2341489..2341639_POSITIVE 274 58 15 144 101 NC_009009:SSA_1402|3end_ABC-type_multidrug_transport_system,_ATPase_and_permease_components,_putative_1414481..1414631_NEGATIVE 263 68 23 86 22 NC_009009:SSA_0862|3end_MurM,_putative_852992..853142_NEGATIVE 262 69 28 133 90 NC_009009:SSA_0436|3end_Imidazolonepropionase,_putative_440214..440364_POSITIVE 261 56 21 66 33 NC_009009:SSA_0907|3end_Fibronectin-binding_protein_A,_putative_917568..917718_NEGATIVE 255 58 11 42 3 NC_009009:SSA_0546|3end_Phospho-2-dehydro-3-deoxyheptonate_aldolase_(DAHP_synthatase),_possibly_tyr-sensitive,_putative_541963..542113_POSITIVE 251 66 21 62 9 NC_009009:SSA_2222|3end_Tyrosine-protein_kinase_Wze,_putative_2223299..2223449_NEGATIVE 245 56 19 36 4 NC_009009:SSA_2278|3end_Ukp_protein,_putative_2280410..2280560_NEGATIVE 244 48 10 86 56 NC_009009:SSA_1864|3end_Nicotinate_phosphoribosyltransferase_(NAPRTase),_subgroup_A,_putative_1859410..1859560_NEGATIVE 244 50 2 109 49 NC_009009:SSA_0713|3end_1-acyl-sn-glycerol-3-phosphate_acyltransferase,_putative_700028..700178_POSITIVE 243 66 23 110 65 NC_009009:SSA_1651|3end_hypothetical_protein_1649587..1649737_NEGATIVE 241 69 23 136 81 NC_009009:SSA_1679|3end_ABC-type_multidrug_transport_system,_ATPase_component,_putative_1672183..1672333_NEGATIVE 239 50 9 119 70 NC_009009:SSA_2373|3end_DNA_replication_and_repair_protein_recF,_putative_2375382..2375532_POSITIVE 239 55 11 139 100 NC_009009:SSA_0682|3end_Conserved_uncharacterized_protein_664351..664501_POSITIVE 237 67 29 67 25 NC_009009:SSA_2009|3end_Heat_shock_transcription_repressor_HrcA,_putative_2010098..2010248_NEGATIVE