Origin IGS: taaaaagtgatccctccctcattcttcgtttatcactctgtcttctcggatatttacgagcagaaacgatacgttcatgtattataatggatattcggaccctgaatttccgaatatatcggaatacgattcgtaacgtataataacgtaaaaaatggggctgtctcataacgattcggcctctttttttgttta .........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 taaacaaaaaaagaggccgaatcgttatgagacagccccattttttacgttattatacgttacgaatcgtattccgatatattcggaaattcagggtccgaatatccattataatacatgaacgtatcgtttctgctcgtaaatatccgagaagacagagtgataaacgaagaatgagggagggatcacttttta Mask Tandem Repeat Region ================================================ taaaaagtgatccctccctcattcttcgtttatcactctgtcttctcggatatttacgagcagaaacgatacgttcatgtattataatggatattcggaccctgaatttccgaatatatcggaatacgattcgtaacgtataataacgtaaaaaatggggctgtctcataacgattcggcctctttttttgttta Find is-nt database================================================ Query_seq: TF1985:TF1986|TF1985:TF1986:surface antigen BspA:hypothetical protein:->->:2136966..2137160 195 taaaaagtgatccctccctcattcttcgtttatcactctgtcttctcggatatttacgagcagaaacgatacgttcatgtattataatggatattcggaccctgaatttccgaatatatcggaatacgattcgtaacgtataataacgtaaaaaatggggctgtctcataacgattcggcctctttttttgttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1985:TF1986|TF1985:TF1986:surface antigen BspA:hypothetical protein:->->:2136966..2137160 195 taaaaagtgatccctccctcattcttcgtttatcactctgtcttctcggatatttacgagcagaaacgatacgttcatgtattataatggatattcggaccctgaatttccgaatatatcggaatacgattcgtaacgtataataacgtaaaaaatggggctgtctcataacgattcggcctctttttttgttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1985:TF1986|TF1985:TF1986:surface antigen BspA:hypothetical protein:->->:2136966..2137160 195 taaaaagtgatccctccctcattcttcgtttatcactctgtcttctcggatatttacgagcagaaacgatacgttcatgtattataatggatattcggaccctgaatttccgaatatatcggaatacgattcgtaacgtataataacgtaaaaaatggggctgtctcataacgattcggcctctttttttgttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaaaagtgatccctccctcattcttcgtttatcactctgtcttctcggatatttacgagcagaaacgatacgttcatgtattataatggatattcggaccctgaatttccgaatatatcggaatacgattcgtaacgtataataacgtaaaaaatggggctgtctcataacgattcggcctctttttttgttta Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 32 End: 133 ............................... M T L S S R I F T S R N D T F M Y Y N G Y S D P E F P N I S E Y D S .............................................................. Protein_Len: 40 Strand: + Start: 21 End: 140 .................... M L R L S L C L L G Y L R A E T I R S C I I M D I R T L N F R I Y R N T I R N V ....................................................... Protein_Len: 58 Strand: - Start: 2 End: 175 . F L S G E R M R R K D S Q R R P Y K R A S V I R E H I I I S I R V R F K R I Y R F V I R L T Y Y R L F H P Q R M V M .................... taaaaagtgatccctccctcattcttcgtttatcactctgtcttctcggatatttacgagcagaaacgatacgttcatgtattataatggatattcggaccctgaatttccgaatatatcggaatacgattcgtaacgtataataacgtaaaaaatggggctgtctcataacgattcggcctctttttttgttta 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================================================ taaaaagtgatccctccctcattcttcgtttatcactctgtcttctcggatatttacgagcagaaacgatacgttcatgtattataatggatattcggaccctgaatttccgaatatatcggaatacgattcgtaacgtataataacgtaaaaaatggggctgtctcataacgattcggcctctttttttgttta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 47 HP_score: -4.4 Tail_Score: -2.61727 Start: 92 End: 116 Full_Region: aatcgtattccgata tattcgga aattcaggg tccgaata tccattataatacat ...........................................................................................tattcggaaattcagggtccgaata............................................................................... Find igs database================================================ Query_seq: TF1985:TF1986|TF1985:TF1986:surface antigen BspA:hypothetical protein:->->:2136966..2137160 195 taaaaagtgatccctccctcattcttcgtttatcactctgtcttctcggatatttacgagcagaaacgatacgttcatgtattataatggatattcggaccctgaatttccgaatatatcggaatacgattcgtaacgtataataacgtaaaaaatggggctgtctcataacgattcggcctctttttttgttta Intra-Species Hit: Count: 1 Min: 1 Max: 183 Len: 183 Subject: tfor_TF1985_TF1986|surface antigen BspA:hypothetical protein|POSITIVE:POSITIVE|[2136966,2137160]|195 HSP 1 e-value: 1.0E-99 bit: 363.0 Len: 183 Query Start:1 Query End:183 Subject Strand: POSITIVE Subject Start: 1 Subject End: 183 taaaaagtgatccctccctcattcttcgtttatcactctgtcttctcggatatttacgagcagaaacgatacgttcatgtattataatggatattcggaccctgaatttccgaatatatcggaatacgattcgtaacgtataataacgtaaaaaatggggctgtctcataacgattcggcctc............ taaaaagtgatccctccctcattcttcgtttatcactctgtcttctcggatatttacgagcagaaacgatacgttcatgtattataatggatattcggaccctgaatttccgaatatatcggaatacgattcgtaacgtataataacgtaaaaaatggggctgtctcataacgattcggcctc............ Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAAGUGAUCCCUCCCUCAUUCUUCGUUUAUCACUCUGUCUUCUCGGAUAUUUACGAGCAGAAACGAUACGUUCAUGUAUUAUAAUGGAUAUUCGGACCCUGAAUUUCCGAAUAUAUCGGAAUACGAUUCGUAACGUAUAAUAACGUAAAAAAUGGGGCUGUCUCAUAACGAUUCGGCCUC .....((((((....................))))))...(((.((((........)))).))).(((.((((....((((((....((((((((((((.........))))))))).))).))))))...)))).))).................(((((((..((.....))..))))))) (-41.85) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAGGCCGAAUCGUUAUGAGACAGCCCCAUUUUUUACGUUAUUAUACGUUACGAAUCGUAUUCCGAUAUAUUCGGAAAUUCAGGGUCCGAAUAUCCAUUAUAAUACAUGAACGUAUCGUUUCUGCUCGUAAAUAUCCGAGAAGACAGAGUGAUAAACGAAGAAUGAGGGAGGGAUCACUUUUUA ...............(((..(..(((((((((((...((((((((((.((((..((((.((((((.....)))))).....((((......))))..........)))).)))).))).(((.((((........)))).)))....)))))))..)))))))).)))..)..)))....... (-43.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 358 60 12 151 95 tfor:TF2951|5end_O-succinylbenzoic_acid--CoA_ligase_3158496..3158726_POSITIVE 332 62 22 79 41 tfor:TF0659|5end_RNA_polymerase,_ECF-type_sigma_factor_705428..705658_POSITIVE 305 160 111 125 79 tfor:TF2008|5end_DNA_polymerase_I_2159302..2159532_POSITIVE 304 68 22 230 173 tfor:TF2101|5end_hypothetical_protein_2273702..2273932_POSITIVE 301 64 22 221 188 tfor:TF2014|5end_dipeptidyl_aminopeptidase_IV_2169398..2169628_POSITIVE 291 81 42 216 175 tfor:TF2265|5end_transfer_region-related_protein,_TraP;_DNA_primase_involved_in_conjugation_2433474..2433704_POSITIVE 291 70 23 207 157 tfor:TF0440|5end_Na+-transporting_NADH:ubiquinone_oxidoreductase,_subunit_2_463655..463885_POSITIVE 290 49 7 227 182 tfor:TF2729|5end_possible_outer_membrane_protein_2908216..2908446_POSITIVE 289 50 7 79 24 tfor:TF0239|5end_conserved_hypothetical_protein_268894..269124_POSITIVE 288 150 101 99 48 tfor:TF2665|5end_hypothetical_protein_2841973..2842203_POSITIVE 283 50 6 88 44 tfor:TF1548|5end_thiophene_and_furan_oxidation_protein_1652501..1652731_POSITIVE 281 43 4 213 159 tfor:TF2584|5end_hypothetical_protein_2751180..2751410_POSITIVE 280 139 95 91 46 tfor:TF2771|5end_undecaprenol_kinase,_bacitracin_resistance_protein_2956559..2956789_POSITIVE 279 130 88 213 170 tfor:TF1721|5end_2,3-bisphosphoglycerate-independent_phosphoglycerate_mutase_1844374..1844604_POSITIVE 275 63 21 180 131 tfor:TF1968|5end_conserved_hypothetical_protein_2115415..2115645_POSITIVE 274 130 90 142 102 tfor:TF1744|5end_phenylacetate-CoA_ligase_1877822..1878052_POSITIVE 273 77 52 52 26 tfor:TF0257|5end_hypothetical_protein_287610..287840_POSITIVE 272 79 36 68 8 tfor:TF2375|5end_conserved_hypothetical_protein_2540953..2541183_POSITIVE 272 50 6 194 148 tfor:TF1583|5end_conserved_hypothetical_protein;_possible_endonuclease_1689445..1689675_POSITIVE 271 49 5 75 31 tfor:TF2878|5end_conserved_hypothetical_protein;_possible_CAAX_amino_terminal_protease_family_3067304..3067534_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 358 60 12 124 68 tfor:TF2950|3end_chloromuconate_cycloisomerase_3158549..3158699_POSITIVE 329 60 13 65 19 tfor:TF1259|3end_hypothetical_protein_1345204..1345354_POSITIVE 317 50 4 121 65 tfor:TF1697|3end_mobilizable_transposon,_excision_protein_1819293..1819443_POSITIVE 305 160 111 70 24 tfor:TF2007|3end_uracil_phosphoribosyltransferase_2159327..2159477_POSITIVE 304 68 22 134 77 tfor:TF2100|3end_hypothetical_protein_2273686..2273836_POSITIVE 301 64 22 84 51 tfor:TF2013|3end_polysaccharide_deacetylase_2169341..2169491_POSITIVE 297 140 91 142 90 tfor:TF1962|3end_TatD-related_deoxyribonuclease,_Mg-dependent_DNase_2113297..2113447_POSITIVE 296 59 13 70 18 tfor:TF2744|3end_methionyl-tRNA_formyltransferase_2927378..2927528_POSITIVE 289 50 7 62 7 tfor:TF0238|3end_outer_membrane_protein_268957..269107_POSITIVE 285 59 11 93 38 tfor:TF1204|3end_possible_metal-dependent_membrane_protease_1287461..1287611_POSITIVE 280 139 95 91 46 tfor:TF2770|3end_conserved_hypothetical_protein_2956639..2956789_POSITIVE 279 130 88 135 92 tfor:TF1720|3end_conserved_hypothetical_protein_1844376..1844526_POSITIVE 275 46 5 104 56 tfor:TF2757|3end_hypothetical_protein_2942335..2942485_POSITIVE 274 130 90 149 109 tfor:TF1743|3end_conserved_hypothetical_protein_1877909..1878059_POSITIVE 272 50 6 136 90 tfor:TF1581|3end_hypothetical_protein_1689467..1689617_POSITIVE 271 43 1 59 14 tfor:TF2647|3end_transcriptional_regulator,_possible_arylsulfatase_regulator_2818135..2818285_POSITIVE 271 51 14 123 91 tfor:TF2158|3end_conserved_hypothetical_protein_2334584..2334734_POSITIVE 269 138 94 100 55 tfor:TF2789|3end_enoyl-[acyl-carrier-protein]_reductase_2973365..2973515_POSITIVE 268 133 93 69 18 tfor:TF1900|3end_conserved_hypothetical_protein_2056532..2056682_POSITIVE 266 52 14 147 103 tfor:TF1966|3end_conserved_hypothetical_protein_2115476..2115626_POSITIVE