Origin IGS: taaaaagtgaaaaggctgctggaagttgattttataaagaatttactagaacttttcataataaagcgcattatatcaagttttaagggttgatgtgatgcgtttttctgatttcaagattcttacgtcaatctcttgttctgtattacgatttcaaaaacaaaattcttctaaaatgctacacttcagcttaaaaaaacgacatttcagattttctggttcagaaatagctatcactatgatataattatttt .........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 aaaataattatatcatagtgatagctatttctgaaccagaaaatctgaaatgtcgtttttttaagctgaagtgtagcattttagaagaattttgtttttgaaatcgtaatacagaacaagagattgacgtaagaatcttgaaatcagaaaaacgcatcacatcaacccttaaaacttgatataatgcgctttattatgaaaagttctagtaaattctttataaaatcaacttccagcagccttttcacttttta Mask Tandem Repeat Region ================================================ taaaaagtgaaaaggctgctggaagttgattttataaagaatttactagaacttttcataataaagcgcattatatcaagttttaagggttgatgtgatgcgtttttctgatttcaagattcttacgtcaatctcttgttctgtattacgatttcaaaaacaaaattcttctaaaatgctacacttcagcttaaaaaaacgacatttcagattttctggttcagaaatagctatcactatgatataattatttt Find is-nt database================================================ Query_seq: SMT_618:SMT_619|SMT_618:SMT_619:methionine aminopeptidase:riboflavin kinase / FMN adenylyltransferase:->->:527698..527951 254 taaaaagtgaaaaggctgctggaagttgattttataaagaatttactagaacttttcataataaagcgcattatatcaagttttaagggttgatgtgatgcgtttttctgatttcaagattcttacgtcaatctcttgttctgtattacgatttcaaaaacaaaattcttctaaaatgctacacttcagcttaaaaaaacgacatttcagattttctggttcagaaatagctatcactatgatataattatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_618:SMT_619|SMT_618:SMT_619:methionine aminopeptidase:riboflavin kinase / FMN adenylyltransferase:->->:527698..527951 254 taaaaagtgaaaaggctgctggaagttgattttataaagaatttactagaacttttcataataaagcgcattatatcaagttttaagggttgatgtgatgcgtttttctgatttcaagattcttacgtcaatctcttgttctgtattacgatttcaaaaacaaaattcttctaaaatgctacacttcagcttaaaaaaacgacatttcagattttctggttcagaaatagctatcactatgatataattatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_618:SMT_619|SMT_618:SMT_619:methionine aminopeptidase:riboflavin kinase / FMN adenylyltransferase:->->:527698..527951 254 taaaaagtgaaaaggctgctggaagttgattttataaagaatttactagaacttttcataataaagcgcattatatcaagttttaagggttgatgtgatgcgtttttctgatttcaagattcttacgtcaatctcttgttctgtattacgatttcaaaaacaaaattcttctaaaatgctacacttcagcttaaaaaaacgacatttcagattttctggttcagaaatagctatcactatgatataattatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaaaagtgaaaaggctgctggaagttgattttataaagaatttactagaacttttcataataaagcgcattatatcaagttttaagggttgatgtgatgcgtttttctgatttcaagattcttacgtcaatctcttgttctgtattacgatttcaaaaacaaaattcttctaaaatgctacacttcagcttaaaaaaacgacatttcagattttctggttcagaaatagctatcactatgatataattatttt Predict ORF larger than 30AA ================================================ Protein_Len: 50 Strand: + Start: 95 End: 244 .............................................................................................. M M R F S D F K I L T S I S C S V L R F Q K Q N S S K M L H F S L K K R H F R F S G S E I A I T M I .......... taaaaagtgaaaaggctgctggaagttgattttataaagaatttactagaacttttcataataaagcgcattatatcaagttttaagggttgatgtgatgcgtttttctgatttcaagattcttacgtcaatctcttgttctgtattacgatttcaaaaacaaaattcttctaaaatgctacacttcagcttaaaaaaacgacatttcagattttctggttcagaaatagctatcactatgatataattatttt 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: 84 Start: 58 End: 87 .........................................................CTTAAAACTTGATATAATGCGCTTTATTAT....................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 84 Start: 219 End: 248 ..........................................................................................................................................................................................................................GTTCAGAAATAGCTATCACTATGATATAAT...... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taaaaagtgaaaaggctgctggaagttgattttataaagaatttactagaacttttcataataaagcgcattatatcaagttttaagggttgatgtgatgcgtttttctgatttcaagattcttacgtcaatctcttgttctgtattacgatttcaaaaacaaaattcttctaaaatgctacacttcagcttaaaaaaacgacatttcagattttctggttcagaaatagctatcactatgatataattatttt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 75 HP_score: -4.9 Tail_Score: -5.04325 Start: 67 End: 102 Full_Region: CTTTTCATAATAAAG CGCATTATATCAA GTTTTAAGGG TTGATGTGATGCG TTTTTCTGATTTCAA ..................................................................CGCATTATATCAAGTTTTAAGGGTTGATGTGATGCG........................................................................................................................................................ Find igs database================================================ Query_seq: SMT_618:SMT_619|SMT_618:SMT_619:methionine aminopeptidase:riboflavin kinase / FMN adenylyltransferase:->->:527698..527951 254 taaaaagtgaaaaggctgctggaagttgattttataaagaatttactagaacttttcataataaagcgcattatatcaagttttaagggttgatgtgatgcgtttttctgatttcaagattcttacgtcaatctcttgttctgtattacgatttcaaaaacaaaattcttctaaaatgctacacttcagcttaaaaaaacgacatttcagattttctggttcagaaatagctatcactatgatataattatttt Intra-Species Hit: Count: 1 Min: 1 Max: 254 Len: 254 Subject: smit_SMT_618_SMT_619|methionine aminopeptidase:riboflavin kinase / FMN adenylyltransferase|POSITIVE:POSITIVE|[527698, 527951]|254 HSP 1 e-value: 1.0E-129 bit: 462.0 Len: 254 Query Start:1 Query End:254 Subject Strand: POSITIVE Subject Start: 1 Subject End: 254 taaaaagtgaaaaggctgctggaagttgattttataaagaatttactagaacttttcataataaagcgcattatatcaagttttaagggttgatgtgatgcgtttttctgatttcaagattcttacgtcaatctcttgttctgtattacgatttcaaaaacaaaattcttctaaaatgctacacttcagcttnnnnnnncgacatttcagattttctggttcagaaatagctatcactatgatataattatttt taaaaagtgaaaaggctgctggaagttgattttataaagaatttactagaacttttcataataaagcgcattatatcaagttttaagggttgatgtgatgcgtttttctgatttcaagattcttacgtcaatctcttgttctgtattacgatttcaaaaacaaaattcttctaaaatgctacacttcagcttaaaaaaacgacatttcagattttctggttcagaaatagctatcactatgatataattatttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAAGUGAAAAGGCUGCUGGAAGUUGAUUUUAUAAAGAAUUUACUAGAACUUUUCAUAAUAAAGCGCAUUAUAUCAAGUUUUAAGGGUUGAUGUGAUGCGUUUUUCUGAUUUCAAGAUUCUUACGUCAAUCUCUUGUUCUGUAUUACGAUUUCAAAAACAAAAUUCUUCUAAAAUGCUACACUUCAGCUUAAAAAAACGACAUUUCAGAUUUUCUGGUUCAGAAAUAGCUAUCACUAUGAUAUAAUUAUUUU .....(((((...((((.((((((((((.((((...((((((((..((((((...(((....(((((((((((((((((.((....)).)))))))))))))))))..))).....(((((........)))))...))))))......(....).......)))))))).......(((.......)))....)))).)))).))))))..((((((...)))))).)))).)))))................ (-54.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAUAAUUAUAUCAUAGUGAUAGCUAUUUCUGAACCAGAAAAUCUGAAAUGUCGUUUUUUUAAGCUGAAGUGUAGCAUUUUAGAAGAAUUUUGUUUUUGAAAUCGUAAUACAGAACAAGAGAUUGACGUAAGAAUCUUGAAAUCAGAAAAACGCAUCACAUCAACCCUUAAAACUUGAUAUAAUGCGCUUUAUUAUGAAAAGUUCUAGUAAAUUCUUUAUAAAAUCAACUUCCAGCAGCCUUUUCACUUUUUA ................(((((..((..((((((...))))))......................((((((((...(.(((((((((((((((.......(((.((((((((.((..(((((..((......))..)))))............(((((.(.(((((..........))))).).))))))).))))))))....)))....))))))))).))))))).)))).)))).))....)))))..... (-44.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 296 127 87 71 21 smit:SMT_937|5end_dipeptidase_889579..889809_POSITIVE 270 180 135 112 67 smit:SMT_1636|5end_5-formyltetrahydrofolate_cyclo-ligase_family_protein_1622568..1622798_POSITIVE 268 127 90 71 30 smit:SMT_932|5end_tellurite_resistance_protein_885065..885295_POSITIVE 268 139 96 161 122 smit:SMT_307|5end_K02078_acyl_carrier_protein_249187..249417_POSITIVE 261 129 87 38 1 smit:SMT_348|5end_K07707_two-component_system,_AgrA_family,_response_regulator_AgrA_286456..286686_POSITIVE 260 130 87 175 133 smit:SMT_1531|5end_hypothetical_protein_1515997..1516227_NEGATIVE 253 138 91 220 167 smit:SMT_1839|5end_6-phosphogluconate_dehydrogenase,_decarboxylating_1805999..1806229_NEGATIVE 252 47 17 143 119 smit:SMT_296|5end_hypothetical_protein_predicted_by_Glimmer/Critica_238147..238377_POSITIVE 249 136 94 161 117 smit:SMT_609|5end_laminin-binding_surface_protein_521286..521516_POSITIVE 239 109 80 197 164 smit:SMT_1184|5end_phosphotransferase_system,_mannose/fructose/N-acetylgalactosamine-specific_component_IIB_1142037..1142267_NEGATIVE 239 141 103 143 97 smit:SMT_567|5end_conserved_hypothetical_protein_484845..485075_POSITIVE 235 239 192 157 110 smit:SMT_2106|5end_unknown,_predicted_membrane_protein_(TMS5)_1997163..1997393_POSITIVE 235 239 192 157 110 smit:SMT_1771|5end_unknown,_predicted_membrane_protein_(TMS5)_1747437..1747667_POSITIVE 235 153 111 142 92 smit:SMT_908|5end_hypothetical_protein_857230..857460_NEGATIVE 235 245 205 78 35 smit:SMT_312|5end_acetyl-CoA_carboxylase,_biotin_carboxyl_carrier_protein_253361..253591_POSITIVE 233 108 66 83 39 smit:SMT_1928|5end_O-methyltransferase_family_protein_1869652..1869882_NEGATIVE 229 29 5 52 29 smit:SMT_1284|5end_predicted_amidophosphoribosyltransferase_1246962..1247192_POSITIVE 226 145 106 56 1 smit:SMT_1916|5end_glutamine_amidotransferase_1860539..1860769_POSITIVE 225 46 4 100 47 smit:SMT_1390|5end_hypothetical_protein_1367321..1367551_NEGATIVE 225 130 84 209 152 smit:SMT_798|5end_hypothetical_protein_705788..706018_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 367 107 61 55 6 smit:SMT_638|3end_hypothetical_protein_543180..543330_NEGATIVE 336 99 52 57 2 smit:SMT_1308|3end_hypothetical_protein_1273854..1274004_POSITIVE 310 106 66 69 28 smit:SMT_637|3end_lactose_phosphotransferase_system_repressor_543105..543255_POSITIVE 308 109 61 62 13 smit:SMT_938|3end_hypothetical_protein_890813..890963_NEGATIVE 296 106 63 56 11 smit:SMT_1615|3end_K02016_iron_complex_transport_system_substrate-binding_protein_1601734..1601884_NEGATIVE 285 106 63 65 21 smit:SMT_937|3end_dipeptidase_890741..890891_POSITIVE 270 180 135 100 55 smit:SMT_1635|3end_putative_N-acetyldiaminopimelate_deacetylase_1622636..1622786_POSITIVE 269 107 61 74 25 smit:SMT_130|3end_capsular_polysaccharide_biosynthesis_protein_82925..83075_POSITIVE 267 120 76 132 86 smit:SMT_1932|3end_K02008_cobalt_transport_system_permease_protein_1871171..1871321_NEGATIVE 252 47 17 95 71 smit:SMT_295|3end_hypothetical_protein_predicted_by_Glimmer/Critica_238179..238329_POSITIVE 251 107 61 79 27 smit:SMT_778|3end_S-adenosylmethionine:tRNA_ribosyltransferase-isomerase_687834..687984_POSITIVE 247 129 81 49 2 smit:SMT_1053|3end_ABC_transporter_permease_protein_992907..993057_NEGATIVE 239 141 103 121 75 smit:SMT_566|3end_K07282_poly-gamma-glutamate_synthesis_protein_(capsule_biosynthesis_protein)_484903..485053_POSITIVE 235 153 111 149 99 smit:SMT_909|3end_type_I_restriction_enzyme_M_protein_857223..857373_NEGATIVE 235 245 205 75 32 smit:SMT_311|3end_3-oxoacyl-_253438..253588_POSITIVE 233 108 66 45 1 smit:SMT_1929|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1869690..1869840_NEGATIVE 229 29 5 55 32 smit:SMT_1283|3end_K02240_competence_protein_ComFA_1247045..1247195_POSITIVE 226 107 61 60 12 smit:SMT_1614|3end_K08998_hypothetical_protein_1601652..1601802_POSITIVE 224 57 13 105 52 smit:SMT_1188|3end_hypothetical_protein_1146426..1146576_NEGATIVE 219 105 63 71 33 smit:SMT_1673|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1660042..1660192_POSITIVE