Origin IGS: aatttgcacccctttaaaaaactttaacataataaaaaattttagtcaaactaattttaaagattggctgttaatataaaaaatagcacctactggcataggtgctattttagccatttataaactcatattacttatttaagtaattttagcataattatataaaaaaatcaagttttatgatataataaaatgccattttcccctctaacatccctttttaaaggaggtgaaagagtgaaaaaacttgtgttacttattgtgatagttgtaatatttttactactatctaaaaatacttactaattttaattagtaaaggttttatgtggggttactctggcaggtattccctgcttttttattt .........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 aaataaaaaagcagggaatacctgccagagtaaccccacataaaacctttactaattaaaattagtaagtatttttagatagtagtaaaaatattacaactatcacaataagtaacacaagttttttcactctttcacctcctttaaaaagggatgttagaggggaaaatggcattttattatatcataaaacttgatttttttatataattatgctaaaattacttaaataagtaatatgagtttataaatggctaaaatagcacctatgccagtaggtgctattttttatattaacagccaatctttaaaattagtttgactaaaattttttattatgttaaagttttttaaaggggtgcaaatt Mask Tandem Repeat Region ================================================ aatttgcacccctttaaaaaactttaacataataaaaaattttagtcaaactaattttaaagattggctgttaatataaaaaatagcacctactggcataggtgctattttagccatttataaactcatattacttatttaagtaattttagcataattatataaaaaaatcaagttttatgatataataaaatgccattttcccctctaacatccctttttaaaggaggtgaaagagtgaaaaaacttgtgttacttattgtgatagttgtaatatttttactactatctaaaaatacttactaattttaattagtaaaggttttatgtggggttactctggcaggtattccctgcttttttattt Find is-nt database================================================ Query_seq: FN0032:FN0033|FN0032:FN0033:hypothetical protein:hypothetical protein:<-<-:669869..670235 367 aatttgcacccctttaaaaaactttaacataataaaaaattttagtcaaactaattttaaagattggctgttaatataaaaaatagcacctactggcataggtgctattttagccatttataaactcatattacttatttaagtaattttagcataattatataaaaaaatcaagttttatgatataataaaatgccattttcccctctaacatccctttttaaaggaggtgaaagagtgaaaaaacttgtgttacttattgtgatagttgtaatatttttactactatctaaaaatacttactaattttaattagtaaaggttttatgtggggttactctggcaggtattccctgcttttttattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0032:FN0033|FN0032:FN0033:hypothetical protein:hypothetical protein:<-<-:669869..670235 367 aatttgcacccctttaaaaaactttaacataataaaaaattttagtcaaactaattttaaagattggctgttaatataaaaaatagcacctactggcataggtgctattttagccatttataaactcatattacttatttaagtaattttagcataattatataaaaaaatcaagttttatgatataataaaatgccattttcccctctaacatccctttttaaaggaggtgaaagagtgaaaaaacttgtgttacttattgtgatagttgtaatatttttactactatctaaaaatacttactaattttaattagtaaaggttttatgtggggttactctggcaggtattccctgcttttttattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0032:FN0033|FN0032:FN0033:hypothetical protein:hypothetical protein:<-<-:669869..670235 367 aatttgcacccctttaaaaaactttaacataataaaaaattttagtcaaactaattttaaagattggctgttaatataaaaaatagcacctactggcataggtgctattttagccatttataaactcatattacttatttaagtaattttagcataattatataaaaaaatcaagttttatgatataataaaatgccattttcccctctaacatccctttttaaaggaggtgaaagagtgaaaaaacttgtgttacttattgtgatagttgtaatatttttactactatctaaaaatacttactaattttaattagtaaaggttttatgtggggttactctggcaggtattccctgcttttttattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatttgcacccctttaaaaaactttaacataataaaaaattttagtcaaactaattttaaagattggctgttaatataaaaaatagcacctactggcataggtgctattttagccatttataaactcatattacttatttaagtaattttagcataattatataaaaaaatcaagttttatgatataataaaatgccattttcccctctaacatccctttttaaaggaggtgaaagagtgaaaaaacttgtgttacttattgtgatagttgtaatatttttactactatctaaaaatacttactaattttaattagtaaaggttttatgtggggttactctggcaggtattccctgcttttttattt Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: + Start: 193 End: 303 ................................................................................................................................................................................................ M P F S P L T S L F K G G E R V K K L V L L I V I V V I F L L L S K N T Y ................................................................ Protein_Len: 34 Strand: - Start: 174 End: 275 ............................................................................................................................................................................. T K H Y L L I G N E G R V D R K L P P S L T F F S T N S I T I T T M ............................................................................................ aatttgcacccctttaaaaaactttaacataataaaaaattttagtcaaactaattttaaagattggctgttaatataaaaaatagcacctactggcataggtgctattttagccatttataaactcatattacttatttaagtaattttagcataattatataaaaaaatcaagttttatgatataataaaatgccattttcccctctaacatccctttttaaaggaggtgaaagagtgaaaaaacttgtgttacttattgtgatagttgtaatatttttactactatctaaaaatacttactaattttaattagtaaaggttttatgtggggttactctggcaggtattccctgcttttttattt 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: 21 End: 50 ....................TTTGACTAAAATTTTTTATTATGTTAAAGT............................................................................................................................................................................................................................................................................................................................. PromScan Matrix: RpoD-17 Strand: - Score: 85 Start: 146 End: 175 .................................................................................................................................................CTTGATTTTTTTATATAATTATGCTAAAAT................................................................................................................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aatttgcacccctttaaaaaactttaacataataaaaaattttagtcaaactaattttaaagattggctgttaatataaaaaatagcacctactggcataggtgctattttagccatttataaactcatattacttatttaagtaattttagcataattatataaaaaaatcaagttttatgatataataaaatgccattttcccctctaacatccctttttaaaggaggtgaaagagtgaaaaaacttgtgttacttattgtgatagttgtaatatttttactactatctaaaaatacttactaattttaattagtaaaggttttatgtggggttactctggcaggtattccctgcttttttattt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 86 HP_score: -9.7 Tail_Score: -4.18161 Start: 84 End: 107 Full_Region: TGTTAATATAAAAAA TAGCACCTA CTGGCA TAGGTGCTA TTTTAGCCATTTATA ...................................................................................TAGCACCTACTGGCATAGGTGCTA.................................................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 100 HP_score: -10.4 Tail_Score: -5.47159 Start: 84 End: 107 Full_Region: tataaatggctaaaa tagcacctat gcca gtaggtgcta ttttttatattaaca ...................................................................................tagcacctatgccagtaggtgcta.................................................................................................................................................................................................................................................................... Find igs database================================================ Query_seq: FN0032:FN0033|FN0032:FN0033:hypothetical protein:hypothetical protein:<-<-:669869..670235 367 aatttgcacccctttaaaaaactttaacataataaaaaattttagtcaaactaattttaaagattggctgttaatataaaaaatagcacctactggcataggtgctattttagccatttataaactcatattacttatttaagtaattttagcataattatataaaaaaatcaagttttatgatataataaaatgccattttcccctctaacatccctttttaaaggaggtgaaagagtgaaaaaacttgtgttacttattgtgatagttgtaatatttttactactatctaaaaatacttactaattttaattagtaaaggttttatgtggggttactctggcaggtattccctgcttttttattt Intra-Species Hit: Count: 1 Min: 1 Max: 367 Len: 367 Subject: NC_003454_FN0032_FN0033|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[669869,670235]|367 HSP 1 e-value: 0.0 bit: 686.0 Len: 367 Query Start:1 Query End:367 Subject Strand: POSITIVE Subject Start: 1 Subject End: 367 aatttgcacccctttaaaaaactttaacataataaaaaattttagtcaaactaattttaaagattggctgttaatataaaaaatagcacctactggcataggtgctattttagccatttataaactcatattacttatttaagtaattttagcataattatatnnnnnnntcaagttttatgatataataaaatgccattttcccctctaacatccctttttaaaggaggtgaaagagtgaaaaaacttgtgttacttattgtgatagttgtaatatttttactactatctaaaaatacttactaattttaattagtaaaggttttatgtggggttactctggcaggtattccctgcttttttattt aatttgcacccctttaaaaaactttaacataataaaaaattttagtcaaactaattttaaagattggctgttaatataaaaaatagcacctactggcataggtgctattttagccatttataaactcatattacttatttaagtaattttagcataattatataaaaaaatcaagttttatgatataataaaatgccattttcccctctaacatccctttttaaaggaggtgaaagagtgaaaaaacttgtgttacttattgtgatagttgtaatatttttactactatctaaaaatacttactaattttaattagtaaaggttttatgtggggttactctggcaggtattccctgcttttttattt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUUGCACCCCUUUAAAAAACUUUAACAUAAUAAAAAAUUUUAGUCAAACUAAUUUUAAAGAUUGGCUGUUAAUAUAAAAAAUAGCACCUACUGGCAUAGGUGCUAUUUUAGCCAUUUAUAAACUCAUAUUACUUAUUUAAGUAAUUUUAGCAUAAUUAUAUAAAAAAAUCAAGUUUUAUGAUAUAAUAAAAUGCCAUUUUCCCCUCUAACAUCCCUUUUUAAAGGAGGUGAAAGAGUGAAAAAACUUGUGUUACUUAUUGUGAUAGUUGUAAUAUUUUUACUACUAUCUAAAAAUACUUACUAAUUUUAAUUAGUAAAGGUUUUAUGUGGGGUUACUCUGGCAGGUAUUCCCUGCUUUUUUAUUU .......(((((..((.((((((.((((((((..........(((((((.((........)).))))))).........(((((((((((((......))))))))))))).((..(((((....(((((..((((.((((.((((((.......)))))).))))......))))..)))))....)))))..))..(((((..((((..((((((((....)))).))))..)))).)))))...))))))))..((((..((((((.((((.....)))).))))))....)))).((((((((....)))))))).)))))).)).)))))......((((((.....))))))......... (-83.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUAAAAAAGCAGGGAAUACCUGCCAGAGUAACCCCACAUAAAACCUUUACUAAUUAAAAUUAGUAAGUAUUUUUAGAUAGUAGUAAAAAUAUUACAACUAUCACAAUAAGUAACACAAGUUUUUUCACUCUUUCACCUCCUUUAAAAAGGGAUGUUAGAGGGGAAAAUGGCAUUUUAUUAUAUCAUAAAACUUGAUUUUUUUAUAUAAUUAUGCUAAAAUUACUUAAAUAAGUAAUAUGAGUUUAUAAAUGGCUAAAAUAGCACCUAUGCCAGUAGGUGCUAUUUUUUAUAUUAACAGCCAAUCUUUAAAAUUAGUUUGACUAAAAUUUUUUAUUAUGUUAAAGUUUUUUAAAGGGGUGCAAAUU ..........(((((.....)))))....(((.((((....(((((.(((((((((....)))))))))........((((((.((((.....)))).))))))....(((((((........(((((.((((((.((.(((((.....))))).)).)))))))))))((((((...(((((((...((((......))))..))))))).))))))...)))))))......((((((((.........(((((((((((((((((((....))))))))))))))..........)))))..........((((.....)))).........))))))))..))))).....)))))))..... (-91.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 828 130 81 221 172 NC_003454:FN0032|5end_hypothetical_protein_669778..670008_NEGATIVE 288 107 61 185 129 NC_003454:FN0770|5end_Hemin_transport_system_ATP-binding_protein_hmuV_1426672..1426902_POSITIVE 253 110 68 159 119 NC_003454:FN2078|5end_Transcriptional_regulator,_DeoR_family_590266..590496_NEGATIVE 249 111 71 230 185 NC_003454:FN0034|5end_hypothetical_protein_676089..676319_NEGATIVE 245 106 65 62 22 NC_003454:FN1547|5end_PTS_permease_for_N-acetylglucosamine_and_glucose_63270..63500_NEGATIVE 243 234 193 196 159 NC_003454:FN1095|5end_hypothetical_protein_1740232..1740462_POSITIVE 243 112 79 190 158 NC_003454:FN0055|5end_Ribosomal-protein-alanine_acetyltransferase_692158..692388_POSITIVE 238 110 61 81 16 NC_003454:FN0226|5end_4-hydroxythreonine-4-phosphate_dehydrogenase_854089..854319_NEGATIVE 234 357 330 37 7 NC_003454:FN0435|5end_Purine_nucleoside_phosphorylase_1077016..1077246_POSITIVE 229 109 63 56 9 NC_003454:FN0699|5end_Protein_translocase_subunit_secD_1357051..1357281_POSITIVE 228 210 170 107 62 NC_003454:FN1029|5end_Zinc_protease_1683611..1683841_NEGATIVE 227 267 224 74 36 NC_003454:FN0570|5end_hypothetical_protein_1220912..1221142_POSITIVE 226 129 84 216 168 NC_003454:FN1068|5end_Smf_protein_1713811..1714041_POSITIVE 219 358 314 86 43 NC_003454:FN1253|5end_hypothetical_protein_1910405..1910635_NEGATIVE 218 289 247 73 30 NC_003454:FN1702|5end_undecaprenyl_pyrophosphate_phosphatase_197964..198194_NEGATIVE 217 209 172 150 102 NC_003454:FN0690|5end_hypothetical_protein_1345187..1345417_POSITIVE 217 119 89 163 137 NC_003454:FN1953|5end_Na(+)-linked_D-alanine_glycine_permease_459499..459729_NEGATIVE 216 249 206 47 1 NC_003454:FN0495|5end_Acetyl-CoA_acetyltransferase_1139567..1139797_POSITIVE 216 360 313 228 180 NC_003454:FN1706|5end_Transporter_201433..201663_POSITIVE 215 138 100 58 11 NC_003454:FN1838|5end_Glycerol_uptake_facilitator_protein_327489..327719_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 361 119 79 88 49 NC_003454:FN2099|3end_hypothetical_protein_608702..608852_POSITIVE 254 240 195 134 87 NC_003454:FN0769|3end_Hemin_transport_system_permease_protein_hmuU_1426752..1426902_POSITIVE 253 110 68 83 43 NC_003454:FN2079|3end_ABC_transporter_ATP-binding_protein_590342..590492_NEGATIVE 252 226 196 96 68 NC_003454:FN1342|3end_Holo-[acyl-carrier_protein]_synthase_1996091..1996241_NEGATIVE 250 112 79 80 47 NC_003454:FN0034|3end_hypothetical_protein_675439..675589_NEGATIVE 249 111 71 79 34 NC_003454:FN0035|3end_hypothetical_protein_676240..676390_NEGATIVE 243 112 79 88 56 NC_003454:FN0054|3end_tyrosyl-tRNA_synthetase_692136..692286_POSITIVE 232 128 81 100 59 NC_003454:FN0104|3end_Acetyltransferase_739618..739768_NEGATIVE 228 210 170 88 43 NC_003454:FN1030|3end_Hypothetical_membrane-spanning_protein_1683630..1683780_NEGATIVE 223 114 78 85 50 NC_003454:FN0103|3end_Ribonucleoside-diphosphate_reductase_beta_chain_739607..739757_POSITIVE 221 224 186 134 102 NC_003454:FN1009|3end_hypothetical_protein_1663606..1663756_NEGATIVE 217 209 172 82 34 NC_003454:FN0689|3end_hypothetical_protein_1345199..1345349_POSITIVE 214 228 203 117 85 NC_003454:FN0582|3end_Lipoprotein_releasing_system_ATP-binding_protein_lolD_1239027..1239177_POSITIVE 214 223 181 87 36 NC_003454:FN2084|3end_Permease_596507..596657_POSITIVE 214 127 81 72 28 NC_003454:FN1579|3end_Cysteinyl-tRNA_synthetase_88784..88934_NEGATIVE 211 357 320 42 3 NC_003454:FN0382|3end_hypothetical_protein_1014224..1014374_POSITIVE 204 255 214 43 1 NC_003454:FN2003|3end_bioY_protein_504373..504523_POSITIVE 202 117 89 76 45 NC_003454:FN1830|3end_DNA_polymerase_III_subunits_gamma_and_tau_318571..318721_NEGATIVE 200 144 112 35 4 NC_003454:FN1954|3end_Glycerophosphoryl_diester_phosphodiesterase_459777..459927_NEGATIVE 199 222 189 107 60 NC_003454:FN1645|3end_LSU_ribosomal_protein_L3P_140666..140816_NEGATIVE