Origin IGS: taagaactccttgcttcaaattataaaattacttcttgtatatattatattcttttatttccttatatgcaaaccctttcgatacataatatattgtttataagatttgttatatttttgtaaaaataatttactaatccagaaaattactaaattcattttattatcaaaaaatgagcaacttttatattaagttactcatttttataaactctattttatttagattatactatcctactagttaaatcagtattaacactttatat .........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 atataaagtgttaatactgatttaactagtaggatagtataatctaaataaaatagagtttataaaaatgagtaacttaatataaaagttgctcattttttgataataaaatgaatttagtaattttctggattagtaaattatttttacaaaaatataacaaatcttataaacaatatattatgtatcgaaagggtttgcatataaggaaataaaagaatataatatatacaagaagtaattttataatttgaagcaaggagttctta Mask Tandem Repeat Region ================================================ taagaactccttgcttcaaattataaaattacttcttgtatatattatattcttttatttccttatatgcaaaccctttcgatacataatatattgtttataagatttgttatatttttgtaaaaataatttactaatccagaaaattactaaattcattttattatcaaaaaatgagcaacttttatattaagttactcatttttataaactctattttatttagattatactatcctactagttaaatcagtattaacactttatat Find is-nt database================================================ Query_seq: SMT_828:SMT_829|SMT_828:SMT_829:surface protein Rib:putative mucus binding protein:<-<-:760858..761126 269 taagaactccttgcttcaaattataaaattacttcttgtatatattatattcttttatttccttatatgcaaaccctttcgatacataatatattgtttataagatttgttatatttttgtaaaaataatttactaatccagaaaattactaaattcattttattatcaaaaaatgagcaacttttatattaagttactcatttttataaactctattttatttagattatactatcctactagttaaatcagtattaacactttatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_828:SMT_829|SMT_828:SMT_829:surface protein Rib:putative mucus binding protein:<-<-:760858..761126 269 taagaactccttgcttcaaattataaaattacttcttgtatatattatattcttttatttccttatatgcaaaccctttcgatacataatatattgtttataagatttgttatatttttgtaaaaataatttactaatccagaaaattactaaattcattttattatcaaaaaatgagcaacttttatattaagttactcatttttataaactctattttatttagattatactatcctactagttaaatcagtattaacactttatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_828:SMT_829|SMT_828:SMT_829:surface protein Rib:putative mucus binding protein:<-<-:760858..761126 269 taagaactccttgcttcaaattataaaattacttcttgtatatattatattcttttatttccttatatgcaaaccctttcgatacataatatattgtttataagatttgttatatttttgtaaaaataatttactaatccagaaaattactaaattcattttattatcaaaaaatgagcaacttttatattaagttactcatttttataaactctattttatttagattatactatcctactagttaaatcagtattaacactttatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taagaactccttgcttcaaattataaaattacttcttgtatatattatattcttttatttccttatatgcaaaccctttcgatacataatatattgtttataagatttgttatatttttgtaaaaataatttactaatccagaaaattactaaattcattttattatcaaaaaatgagcaacttttatattaagttactcatttttataaactctattttatttagattatactatcctactagttaaatcagtattaacactttatat Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 11 End: 100 .......... M L Q I I K L L L V Y I I F F Y F L I C K P F R Y I I Y C L ......................................................................................................................................................................... Protein_Len: 31 Strand: + Start: 28 End: 120 ........................... M T S C I Y Y I L L F P Y M Q T L S I H N I L F I R F V I F L ..................................................................................................................................................... Protein_Len: 34 Strand: - Start: 58 End: 159 ......................................................... K R I H L G K R Y M I Y Q K Y S K N Y K Q L F L K S I W F I V L N M .............................................................................................................. taagaactccttgcttcaaattataaaattacttcttgtatatattatattcttttatttccttatatgcaaaccctttcgatacataatatattgtttataagatttgttatatttttgtaaaaataatttactaatccagaaaattactaaattcattttattatcaaaaaatgagcaacttttatattaagttactcatttttataaactctattttatttagattatactatcctactagttaaatcagtattaacactttatat 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: 82 Start: 44 End: 73 ...........................................TTTGCATATAAGGAAATAAAAGAATATAAT.................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taagaactccttgcttcaaattataaaattacttcttgtatatattatattcttttatttccttatatgcaaaccctttcgatacataatatattgtttataagatttgttatatttttgtaaaaataatttactaatccagaaaattactaaattcattttattatcaaaaaatgagcaacttttatattaagttactcatttttataaactctattttatttagattatactatcctactagttaaatcagtattaacactttatat Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 78 HP_score: -6.0 Tail_Score: -5.1861 Start: 175 End: 201 Full_Region: tagagtttataaaaa tgagtaactt aatataa aagttgctca ttttttgataataaa ..............................................................................................................................................................................tgagtaacttaatataaaagttgctca.................................................................... Find igs database================================================ Query_seq: SMT_828:SMT_829|SMT_828:SMT_829:surface protein Rib:putative mucus binding protein:<-<-:760858..761126 269 taagaactccttgcttcaaattataaaattacttcttgtatatattatattcttttatttccttatatgcaaaccctttcgatacataatatattgtttataagatttgttatatttttgtaaaaataatttactaatccagaaaattactaaattcattttattatcaaaaaatgagcaacttttatattaagttactcatttttataaactctattttatttagattatactatcctactagttaaatcagtattaacactttatat Intra-Species Hit: Count: 1 Min: 1 Max: 269 Len: 269 Subject: smit_SMT_828_SMT_829|surface protein Rib:putative mucus binding protein|NEGATIVE:NEGATIVE|[760858,761126]|269 HSP 1 e-value: 1.0E-150 bit: 533.0 Len: 269 Query Start:1 Query End:269 Subject Strand: POSITIVE Subject Start: 1 Subject End: 269 taagaactccttgcttcaaattataaaattacttcttgtatatattatattcttttatttccttatatgcaaaccctttcgatacataatatattgtttataagatttgttatatttttgtaaaaataatttactaatccagaaaattactaaattcattttattatcaaaaaatgagcaacttttatattaagttactcatttttataaactctattttatttagattatactatcctactagttaaatcagtattaacactttatat taagaactccttgcttcaaattataaaattacttcttgtatatattatattcttttatttccttatatgcaaaccctttcgatacataatatattgtttataagatttgttatatttttgtaaaaataatttactaatccagaaaattactaaattcattttattatcaaaaaatgagcaacttttatattaagttactcatttttataaactctattttatttagattatactatcctactagttaaatcagtattaacactttatat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGAACUCCUUGCUUCAAAUUAUAAAAUUACUUCUUGUAUAUAUUAUAUUCUUUUAUUUCCUUAUAUGCAAACCCUUUCGAUACAUAAUAUAUUGUUUAUAAGAUUUGUUAUAUUUUUGUAAAAAUAAUUUACUAAUCCAGAAAAUUACUAAAUUCAUUUUAUUAUCAAAAAAUGAGCAACUUUUAUAUUAAGUUACUCAUUUUUAUAAACUCUAUUUUAUUUAGAUUAUACUAUCCUACUAGUUAAAUCAGUAUUAACACUUUAUAU .....................((((((........(((((((((..(((......))).....)))))))))........(((((.(((.(((..((((((((((.........((((((..(((((((((((.((((.......)))).)))))).))))).....)))))).((((.(((((.......))))).)))).))))))))))..))).)))....((((..((((......))))..)))).))))).....)))))). (-34.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAUAAAGUGUUAAUACUGAUUUAACUAGUAGGAUAGUAUAAUCUAAAUAAAAUAGAGUUUAUAAAAAUGAGUAACUUAAUAUAAAAGUUGCUCAUUUUUUGAUAAUAAAAUGAAUUUAGUAAUUUUCUGGAUUAGUAAAUUAUUUUUACAAAAAUAUAACAAAUCUUAUAAACAAUAUAUUAUGUAUCGAAAGGGUUUGCAUAUAAGGAAAUAAAAGAAUAUAAUAUAUACAAGAAGUAAUUUUAUAAUUUGAAGCAAGGAGUUCUUA .((((((((....((((((.((((.....)))).))))))..(((............((((((((..(((((((((((.......)))))))))))((((((.....(((((((.((((.(((((.....))))).)))))))))))..))))))...........)))))))).(((((((((((.((......((((.(......).))))....)))))))))))))...)))....))))))))..................... (-44.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 722 110 61 201 152 smit:SMT_828|5end_surface_protein_Rib_760767..760997_NEGATIVE 221 60 11 129 79 smit:SMT_319|5end_K02356_elongation_factor_EF-P_258864..259094_NEGATIVE 208 85 50 222 194 smit:SMT_1153|5end_alpha-mannosidase_1098117..1098347_NEGATIVE 203 180 131 109 64 smit:SMT_2075|5end_phosphoribosylamine--glycine_ligase_1978485..1978715_NEGATIVE 202 75 33 119 61 smit:SMT_1811|5end_hypothetical_protein_1785654..1785884_POSITIVE 202 50 7 135 97 smit:SMT_953|5end_hypothetical_protein_901576..901806_NEGATIVE 200 74 31 115 71 smit:SMT_1064|5end_phospho-2-dehydro-3-deoxyheptonate_aldolase_1003308..1003538_POSITIVE 198 260 213 213 158 smit:SMT_719|5end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_625647..625877_NEGATIVE 194 227 195 189 163 smit:SMT_1336|5end_DNA_primase_1311964..1312194_NEGATIVE 193 260 212 213 162 smit:SMT_1553|5end_K04074_cell_division_initiation_protein_1535913..1536143_POSITIVE 193 38 8 150 111 smit:SMT_1109|5end_hypothetical_protein_1050315..1050545_NEGATIVE 189 220 173 107 65 smit:SMT_1413|5end_putative_carbon-nitrogen_hydrolase_1397351..1397581_NEGATIVE 186 84 51 123 84 smit:SMT_1750|5end_anthranilate_phosphoribosyltransferase_1728011..1728241_POSITIVE 182 37 7 30 5 smit:SMT_642|5end_beta-glucoside_operon_antiterminator_547979..548209_NEGATIVE 181 217 176 104 62 smit:SMT_1612|5end_K06024_segregation_and_condensation_protein_B_1600052..1600282_POSITIVE 180 92 52 83 40 smit:SMT_931|5end_cobyric_acid_synthase_884491..884721_POSITIVE 179 41 7 55 28 smit:SMT_498|5end_hypothetical_protein_431751..431981_POSITIVE 178 219 174 128 67 smit:SMT_2020|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1937595..1937825_POSITIVE 178 219 174 128 67 smit:SMT_1317|5end_glycosyltransferase_1281921..1282151_POSITIVE 178 244 201 229 182 smit:SMT_240|5end_glutamate_synthase_small_subunit,_putative_177875..178105_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 204 206 163 49 4 smit:SMT_699|3end_K03106_signal_recognition_particle,_subunit_SRP54_609941..610091_NEGATIVE 203 180 131 112 67 smit:SMT_2076|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1978482..1978632_NEGATIVE 194 227 195 99 73 smit:SMT_1337|3end_K05833_putative_ABC_transport_system_ATP-binding_protein_1312054..1312204_NEGATIVE 193 38 8 89 50 smit:SMT_1110|3end_hypothetical_protein_1050376..1050526_NEGATIVE 189 220 173 97 55 smit:SMT_1414|3end_hypothetical_protein_1397361..1397511_NEGATIVE 186 84 51 112 73 smit:SMT_1749|3end_anthranilate_synthase_component_II_1728080..1728230_POSITIVE 186 118 74 136 90 smit:SMT_769|3end_spermidine/putrescine-binding_periplasmic_protein_679519..679669_NEGATIVE 182 70 28 132 87 smit:SMT_1242|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1203027..1203177_NEGATIVE 181 217 176 85 43 smit:SMT_1611|3end_K05896_segregation_and_condensation_protein_A_1600113..1600263_POSITIVE 179 85 42 40 4 smit:SMT_1063|3end_preprotein_translocase_SecA_subunit_1003307..1003457_POSITIVE 179 41 7 34 7 smit:SMT_497|3end_hypothetical_protein_431810..431960_POSITIVE 178 219 174 96 35 smit:SMT_2019|3end_dTDP-glucose_4,6-dehydratase_1937643..1937793_POSITIVE 178 219 174 96 35 smit:SMT_1316|3end_dTDP-glucose_4,6-dehydratase_1281969..1282119_POSITIVE 178 244 201 62 15 smit:SMT_239|3end_hypothetical_protein_177788..177938_POSITIVE 176 83 49 144 105 smit:SMT_2086|3end_hypothetical_protein_1983331..1983481_NEGATIVE 175 104 64 96 54 smit:SMT_1162|3end_ATP-dependent_DNA_helicase_1106445..1106595_NEGATIVE 175 51 15 35 3 smit:SMT_954|3end_cation-transporting_ATPase,_E1-E2_family_901677..901827_NEGATIVE 174 252 233 133 114 smit:SMT_1827|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1797722..1797872_POSITIVE 174 252 233 33 14 smit:SMT_1826|3end_ATP_synthase_beta_chain_1797622..1797772_POSITIVE 174 239 197 98 57 smit:SMT_1566|3end_K03475_PTS_system,_unknown_pentitol_phosphotransferase_enzyme_IIC_component_1559344..1559494_POSITIVE