Origin IGS: ttcacattcactcctttgttttgatataaaaaataaatcctaactaattataccataatatttttaataaagtaacaatattattttttatatttataatgaatataatgcttcctaagtaataaattactagttgttataaagttaagtttgtattaaaatgtaaaaaataactatgaaggaaaacttaatgtttattcattttaaatttattaaataaataactaaaagaaaataaaaaaattaatatttctataagttcacaatcaataaaaagtatgttaaaatacattaaatcaaatattaaattaagagaggtaagattaaaatgaaaaaaatttttaaaacaatattatttagtttactattgatatctgtatttgtatcttgttcaact .........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 agttgaacaagatacaaatacagatatcaatagtaaactaaataatattgttttaaaaatttttttcattttaatcttacctctcttaatttaatatttgatttaatgtattttaacatactttttattgattgtgaacttatagaaatattaatttttttattttcttttagttatttatttaataaatttaaaatgaataaacattaagttttccttcatagttattttttacattttaatacaaacttaactttataacaactagtaatttattacttaggaagcattatattcattataaatataaaaaataatattgttactttattaaaaatattatggtataattagttaggatttattttttatatcaaaacaaaggagtgaatgtgaa Mask Tandem Repeat Region ================================================ ttcacattcactcctttgttttgatataaaaaataaatcctaactaattataccataatatttttaataaagtaacaatattattttttatatttataatgaatataatgcttcctaagtaataaattactagttgttataaagttaagtttgtattaaaatgtaaaaaataactatgaaggaaaacttaatgtttattcattttaaatttattaaataaataactaaaagaaaataaaaaaattaatatttctataagttcacaatcaataaaaagtatgttaaaatacattaaatcaaatattaaattaagagaggtaagattaaaatgaaaaaaatttttaaaacaatattatttagtttactattgatatctgtatttgtatcttgttcaact Find is-nt database================================================ Query_seq: FN0557:FN0558|FN0557:FN0558:hypothetical protein:TraT complement resistance protein precursor:<-->:1210425..1210821 397 ttcacattcactcctttgttttgatataaaaaataaatcctaactaattataccataatatttttaataaagtaacaatattattttttatatttataatgaatataatgcttcctaagtaataaattactagttgttataaagttaagtttgtattaaaatgtaaaaaataactatgaaggaaaacttaatgtttattcattttaaatttattaaataaataactaaaagaaaataaaaaaattaatatttctataagttcacaatcaataaaaagtatgttaaaatacattaaatcaaatattaaattaagagaggtaagattaaaatgaaaaaaatttttaaaacaatattatttagtttactattgatatctgtatttgtatcttgttcaact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0557:FN0558|FN0557:FN0558:hypothetical protein:TraT complement resistance protein precursor:<-->:1210425..1210821 397 ttcacattcactcctttgttttgatataaaaaataaatcctaactaattataccataatatttttaataaagtaacaatattattttttatatttataatgaatataatgcttcctaagtaataaattactagttgttataaagttaagtttgtattaaaatgtaaaaaataactatgaaggaaaacttaatgtttattcattttaaatttattaaataaataactaaaagaaaataaaaaaattaatatttctataagttcacaatcaataaaaagtatgttaaaatacattaaatcaaatattaaattaagagaggtaagattaaaatgaaaaaaatttttaaaacaatattatttagtttactattgatatctgtatttgtatcttgttcaact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0557:FN0558|FN0557:FN0558:hypothetical protein:TraT complement resistance protein precursor:<-->:1210425..1210821 397 ttcacattcactcctttgttttgatataaaaaataaatcctaactaattataccataatatttttaataaagtaacaatattattttttatatttataatgaatataatgcttcctaagtaataaattactagttgttataaagttaagtttgtattaaaatgtaaaaaataactatgaaggaaaacttaatgtttattcattttaaatttattaaataaataactaaaagaaaataaaaaaattaatatttctataagttcacaatcaataaaaagtatgttaaaatacattaaatcaaatattaaattaagagaggtaagattaaaatgaaaaaaatttttaaaacaatattatttagtttactattgatatctgtatttgtatcttgttcaact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttcacattcactcctttgttttgatataaaaaataaatcctaactaattataccataatatttttaataaagtaacaatattattttttatatttataatgaatataatgcttcctaagtaataaattactagttgttataaagttaagtttgtattaaaatgtaaaaaataactatgaaggaaaacttaatgtttattcattttaaatttattaaataaataactaaaagaaaataaaaaaattaatatttctataagttcacaatcaataaaaagtatgttaaaatacattaaatcaaatattaaattaagagaggtaagattaaaatgaaaaaaatttttaaaacaatattatttagtttactattgatatctgtatttgtatcttgttcaact Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 308 End: 397 ................................................................................................................................................................................................................................................................................................................... M K R G K I K M K K I F K T I L F S L L L I S V F V S C S T Protein_Len: 38 Strand: - Start: 191 End: 304 .............................................................................................................................................................................................. H K N M K F K N F L Y S F S F L F I L I E I L E C D I F L I N F Y M L D F M ............................................................................................. ttcacattcactcctttgttttgatataaaaaataaatcctaactaattataccataatatttttaataaagtaacaatattattttttatatttataatgaatataatgcttcctaagtaataaattactagttgttataaagttaagtttgtattaaaatgtaaaaaataactatgaaggaaaacttaatgtttattcattttaaatttattaaataaataactaaaagaaaataaaaaaattaatatttctataagttcacaatcaataaaaagtatgttaaaatacattaaatcaaatattaaattaagagaggtaagattaaaatgaaaaaaatttttaaaacaatattatttagtttactattgatatctgtatttgtatcttgttcaact 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: 87 Start: 133 End: 162 ....................................................................................................................................GTTGTTATAAAGTTAAGTTTGTATTAAAAT........................................................................................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 86 Start: 259 End: 288 ..................................................................................................................................................................................................................................................................GTTCACAATCAATAAAAAGTATGTTAAAAT............................................................................................................. PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 47 End: 76 ..............................................GTTACTTTATTAAAAATATTATGGTATAAT................................................................................................................................................................................................................................................................................................................................. PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 279 End: 308 ......................................................................................................................................................................................................................................................................................TTTAATATTTGATTTAATGTATTTTAACAT......................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttcacattcactcctttgttttgatataaaaaataaatcctaactaattataccataatatttttaataaagtaacaatattattttttatatttataatgaatataatgcttcctaagtaataaattactagttgttataaagttaagtttgtattaaaatgtaaaaaataactatgaaggaaaacttaatgtttattcattttaaatttattaaataaataactaaaagaaaataaaaaaattaatatttctataagttcacaatcaataaaaagtatgttaaaatacattaaatcaaatattaaattaagagaggtaagattaaaatgaaaaaaatttttaaaacaatattatttagtttactattgatatctgtatttgtatcttgttcaact Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN0557:FN0558|FN0557:FN0558:hypothetical protein:TraT complement resistance protein precursor:<-->:1210425..1210821 397 ttcacattcactcctttgttttgatataaaaaataaatcctaactaattataccataatatttttaataaagtaacaatattattttttatatttataatgaatataatgcttcctaagtaataaattactagttgttataaagttaagtttgtattaaaatgtaaaaaataactatgaaggaaaacttaatgtttattcattttaaatttattaaataaataactaaaagaaaataaaaaaattaatatttctataagttcacaatcaataaaaagtatgttaaaatacattaaatcaaatattaaattaagagaggtaagattaaaatgaaaaaaatttttaaaacaatattatttagtttactattgatatctgtatttgtatcttgttcaact Intra-Species Hit: Count: 1 Min: 1 Max: 397 Len: 397 Subject: NC_003454_FN0557_FN0558|hypothetical protein:TraT complement resistance protein precursor|NEGATIVE:POSITIVE|[1210425,1210821]|397 HSP 1 e-value: 1.0E-49 bit: 198.0 Len: 121 Query Start:277 Query End:397 Subject Strand: POSITIVE Subject Start: 277 Subject End: 397 ....................................................................................................................................................................................................................................................................................gtatgttaaaatacattaaatcaaatattaaattaagagaggtaagattaaaatgnnnnnnntttttaaaacaatattatttagtttactattgatatctgtatttgtatcttgttcaact ....................................................................................................................................................................................................................................................................................gtatgttaaaatacattaaatcaaatattaaattaagagaggtaagattaaaatgaaaaaaatttttaaaacaatattatttagtttactattgatatctgtatttgtatcttgttcaact HSP 2 e-value: 1.0E-33 bit: 145.0 Len: 73 Query Start:110 Query End:182 Subject Strand: POSITIVE Subject Start: 110 Subject End: 182 .............................................................................................................gcttcctaagtaataaattactagttgttataaagttaagtttgtattaaaatgtaaaaaataactatgaagg....................................................................................................................................................................................................................... .............................................................................................................gcttcctaagtaataaattactagttgttataaagttaagtttgtattaaaatgtaaaaaataactatgaagg....................................................................................................................................................................................................................... HSP 3 e-value: 3.0E-16 bit: 87.7 Len: 44 Query Start:1 Query End:44 Subject Strand: POSITIVE Subject Start: 1 Subject End: 44 ttcacattcactcctttgttttgatataaaaaataaatcctaac................................................................................................................................................................................................................................................................................................................................................................. ttcacattcactcctttgttttgatataaaaaataaatcctaac................................................................................................................................................................................................................................................................................................................................................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCACAUUCACUCCUUUGUUUUGAUAUAAAAAAUAAAUCCUAACUAAUUAUACCAUAAUAUUUUUAAUAAAGUAACAAUAUUAUUUUUUAUAUUUAUAAUGAAUAUAAUGCUUCCUAAGUAAUAAAUUACUAGUUGUUAUAAAGUUAAGUUUGUAUUAAAAUGUAAAAAAUAACUAUGAAGGAAAACUUAAUGUUUAUUCAUUUUAAAUUUAUUAAAUAAAUAACUAAAAGAAAAUAAAAAAAUUAAUAUUUCUAUAAGUUCACAAUCAAUAAAAAGUAUGUUAAAAUACAUUAAAUCAAAUAUUAAAUUAAGAGAGGUAAGAUUAAAAUGAAAAAAAUUUUUAAAACAAUAUUAUUUAGUUUACUAUUGAUAUCUGUAUUUGUAUCUUGUUCAACU ...............(((....((((((((..............(((((.((((........(((((((..(((((....(((((((((((((((......(((((((.((((.((..(((((((........)))))))..))..))))))))))).))))))))))))))).......(((((..(((((.((((((..(((((.((((((...))))))...)))))...))))))...)))))..)))))....))).))............((((......))))...........)))))))........)))).)))))....................(((((((((..(((....))).)))))).))).)))))))).....))).. (-49.09) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUUGAACAAGAUACAAAUACAGAUAUCAAUAGUAAACUAAAUAAUAUUGUUUUAAAAAUUUUUUUCAUUUUAAUCUUACCUCUCUUAAUUUAAUAUUUGAUUUAAUGUAUUUUAACAUACUUUUUAUUGAUUGUGAACUUAUAGAAAUAUUAAUUUUUUUAUUUUCUUUUAGUUAUUUAUUUAAUAAAUUUAAAAUGAAUAAACAUUAAGUUUUCCUUCAUAGUUAUUUUUUACAUUUUAAUACAAACUUAACUUUAUAACAACUAGUAAUUUAUUACUUAGGAAGCAUUAUAUUCAUUAUAAAUAUAAAAAAUAAUAUUGUUACUUUAUUAAAAAUAUUAUGGUAUAAUUAGUUAGGAUUUAUUUUUUAUAUCAAAACAAAGGAGUGAAUGUGAA ............((((..(((.(((((...(((((((...((((((((((((((....((((.........(((((((.(((..............(((((((.((((((...((((......((((((((.((..((((...(((((...(((.....))).)))))...))))...)).))))))))......(((((.((((.....))))...))))).)))).....))))))..))).))))..................(((((....))))).)))))).))))..........))))....))))))))))))))..)))))))...))))).((((((((..(((........)))..))))))))..........)))..)))).. (-49.91) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 666 50 1 141 92 NC_003454:FN0557|5end_hypothetical_protein_1210334..1210564_NEGATIVE 194 80 39 188 142 NC_003454:FN1866|5end_Lysine_2,3-aminomutase_358440..358670_NEGATIVE 193 150 106 208 151 NC_003454:FN0983|5end_hypothetical_protein_1636447..1636677_NEGATIVE 190 113 77 129 92 NC_003454:FN1535|5end_Acyl-CoA_dehydrogenase,_short-chain_specific_48260..48490_NEGATIVE 189 26 3 53 26 NC_003454:FN0853|5end_Glycogen_synthase_1512307..1512537_NEGATIVE 188 337 296 220 182 NC_003454:FN1418|5end_AMINOTRANSFERASE_CLASS-I_2080500..2080730_NEGATIVE 186 160 111 139 99 NC_003454:FN1839|5end_glycerol_kinase_328272..328502_POSITIVE 182 45 1 191 136 NC_003454:FN1446|5end_Transposase_2116033..2116263_POSITIVE 181 100 51 156 107 NC_003454:FN1386|5end_SWF/SNF_family_helicase_2042866..2043096_NEGATIVE 180 117 71 84 47 NC_003454:FN1257|5end_C4-dicarboxylate_transporter_small_subunit_1913664..1913894_NEGATIVE 180 136 91 229 182 NC_003454:FN0625|5end_Aspartate_aminotransferase_1285515..1285745_NEGATIVE 177 335 305 84 51 NC_003454:FN0035|5end_hypothetical_protein_676902..677132_NEGATIVE 177 139 91 185 135 NC_003454:FN1592|5end_Na(+)-translocating_NADH-quinone_reductase_subunit_D_103746..103976_NEGATIVE 174 226 188 141 107 NC_003454:FN0422|5end_carbamoyl-phosphate_synthase_large_subunit_1063012..1063242_POSITIVE 174 80 32 211 164 NC_003454:FN0086|5end_hypothetical_protein_724037..724267_POSITIVE 173 348 301 145 90 NC_003454:FN1435|5end_Export_ABC_transporter_2105034..2105264_POSITIVE 171 41 6 132 99 NC_003454:FN1579|5end_Cysteinyl-tRNA_synthetase_90205..90435_NEGATIVE 169 43 4 178 136 NC_003454:FN1347|5end_Hypothetical_cytosolic_protein_2000300..2000530_NEGATIVE 168 285 241 175 132 NC_003454:FN2076|5end_MunI_regulatory_protein_587766..587996_NEGATIVE 167 148 111 100 57 NC_003454:FN1886|5end_hypothetical_protein_371399..371629_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 194 80 39 68 22 NC_003454:FN1867|3end_Zn-dependent_alcohol_dehydrogenase_and_related_dehydrogenase_358560..358710_NEGATIVE 190 113 77 98 61 NC_003454:FN1536|3end_(S)-2-hydroxy-acid_oxidase_chain_D_48291..48441_NEGATIVE 189 26 3 36 9 NC_003454:FN0854|3end_Glucose-1-phosphate_adenylyltransferase_1512324..1512474_NEGATIVE 186 160 111 120 80 NC_003454:FN1838|3end_Glycerol_uptake_facilitator_protein_328333..328483_POSITIVE 181 100 51 132 83 NC_003454:FN1387|3end_Metal_dependent_hydrolase_2042890..2043040_NEGATIVE 175 388 350 148 108 NC_003454:FN0291|3end_Hemolysin_919354..919504_NEGATIVE 174 120 90 59 31 NC_003454:FN1303|3end_Adenosylcobalamin-dependent_DIOL_dehydratase_gamma_subunit_1959706..1959856_NEGATIVE 174 226 188 141 107 NC_003454:FN0421|3end_carbamoyl-phosphate_synthase_small_subunit_1063092..1063242_POSITIVE 171 41 6 113 80 NC_003454:FN1580|3end_2-C-methyl-D-erythritol_4-phosphate_cytidylyltransferase_90224..90374_NEGATIVE 168 158 115 64 21 NC_003454:FN1266|3end_UTP--glucose-1-phosphate_uridylyltransferase_1922158..1922308_NEGATIVE 166 389 346 50 11 NC_003454:FN0597|3end_Lipid-A-disaccharide_synthase_1251964..1252114_POSITIVE 165 148 111 54 13 NC_003454:FN0418|3end_pyrimidine_regulatory_protein_PyrR_1059731..1059881_POSITIVE 164 299 257 67 28 NC_003454:FN0512|3end_Flavoprotein_1161386..1161536_NEGATIVE 160 333 291 60 13 NC_003454:FN1412|3end_5-methylthioribose_kinase_2072052..2072202_NEGATIVE 159 388 373 149 134 NC_003454:FN1249|3end_Transcriptional_regulator,_DeoR_family_1905297..1905447_NEGATIVE 159 388 348 47 2 NC_003454:FN0076|3end_Ethanolamine_two-component_response_regulator_714784..714934_POSITIVE 159 377 331 70 27 NC_003454:FN1668|3end_Cholinephosphate_cytidylyltransferase_164691..164841_NEGATIVE 158 160 111 95 50 NC_003454:FN0032|3end_hypothetical_protein_668789..668939_NEGATIVE 157 50 2 125 70 NC_003454:FN0541|3end_Hypothetical_cytosolic_protein_1195297..1195447_POSITIVE 155 369 334 60 10 NC_003454:FN0381|3end_hypothetical_protein_1013276..1013426_POSITIVE