Origin IGS: ctctaatattttttattaaaaaataacacataaaaaaaatgatgtcaaattttttgcttttaacgttaaatataatttttcttctaaaaaaatatgtgttatactattcataaaatagcactttaaatagtaattaacgtctataaaatagaaattttttcgttgatgttaaaatattttttaggaaaaggaggataaact .........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 agtttatcctccttttcctaaaaaatattttaacatcaacgaaaaaatttctattttatagacgttaattactatttaaagtgctattttatgaatagtataacacatatttttttagaagaaaaattatatttaacgttaaaagcaaaaaatttgacatcattttttttatgtgttattttttaataaaaaatattagag Mask Tandem Repeat Region ================================================ ctctaatattttttattaaaaaataacacataaaaaaaatgatgtcaaattttttgcttttaacgttaaatataatttttcttctaaaaaaatatgtgttatactattcataaaatagcactttaaatagtaattaacgtctataaaatagaaattttttcgttgatgttaaaatattttttaggaaaaggaggataaact Find is-nt database================================================ Query_seq: FN0632:FN0633|FN0632:FN0633:PTS system, IIA component:Replication protein:<-->:1290867..1291067 201 ctctaatattttttattaaaaaataacacataaaaaaaatgatgtcaaattttttgcttttaacgttaaatataatttttcttctaaaaaaatatgtgttatactattcataaaatagcactttaaatagtaattaacgtctataaaatagaaattttttcgttgatgttaaaatattttttaggaaaaggaggataaact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0632:FN0633|FN0632:FN0633:PTS system, IIA component:Replication protein:<-->:1290867..1291067 201 ctctaatattttttattaaaaaataacacataaaaaaaatgatgtcaaattttttgcttttaacgttaaatataatttttcttctaaaaaaatatgtgttatactattcataaaatagcactttaaatagtaattaacgtctataaaatagaaattttttcgttgatgttaaaatattttttaggaaaaggaggataaact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0632:FN0633|FN0632:FN0633:PTS system, IIA component:Replication protein:<-->:1290867..1291067 201 ctctaatattttttattaaaaaataacacataaaaaaaatgatgtcaaattttttgcttttaacgttaaatataatttttcttctaaaaaaatatgtgttatactattcataaaatagcactttaaatagtaattaacgtctataaaatagaaattttttcgttgatgttaaaatattttttaggaaaaggaggataaact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctctaatattttttattaaaaaataacacataaaaaaaatgatgtcaaattttttgcttttaacgttaaatataatttttcttctaaaaaaatatgtgttatactattcataaaatagcactttaaatagtaattaacgtctataaaatagaaattttttcgttgatgttaaaatattttttaggaaaaggaggataaact Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 23 End: 115 ...................... M T H K K N D V K F F A F N V K Y N F S S K K I C V I L F I K ...................................................................................... Protein_Len: 42 Strand: - Start: 19 End: 144 .................. F I V C L F F S T L N K A K L T L Y L K E E L F I H T I S N M F Y C K L Y Y N V D M ......................................................... ctctaatattttttattaaaaaataacacataaaaaaaatgatgtcaaattttttgcttttaacgttaaatataatttttcttctaaaaaaatatgtgttatactattcataaaatagcactttaaatagtaattaacgtctataaaatagaaattttttcgttgatgttaaaatattttttaggaaaaggaggataaact 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: 20 End: 49 ...................TTTGACATCATTTTTTTTATGTGTTATTTT........................................................................................................................................................ PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 76 End: 105 ...........................................................................TTTTTCTTCTAAAAAAATATGTGTTATACT................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ctctaatattttttattaaaaaataacacataaaaaaaatgatgtcaaattttttgcttttaacgttaaatataatttttcttctaaaaaaatatgtgttatactattcataaaatagcactttaaatagtaattaacgtctataaaatagaaattttttcgttgatgttaaaatattttttaggaaaaggaggataaact Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN0632:FN0633|FN0632:FN0633:PTS system, IIA component:Replication protein:<-->:1290867..1291067 201 ctctaatattttttattaaaaaataacacataaaaaaaatgatgtcaaattttttgcttttaacgttaaatataatttttcttctaaaaaaatatgtgttatactattcataaaatagcactttaaatagtaattaacgtctataaaatagaaattttttcgttgatgttaaaatattttttaggaaaaggaggataaact Intra-Species Hit: Count: 1 Min: 1 Max: 201 Len: 201 Subject: NC_003454_FN0632_FN0633|PTS system, IIA component:Replication protein|NEGATIVE:POSITIVE|[1290867,1291067]|201 HSP 1 e-value: 2.0E-83 bit: 309.0 Len: 201 Query Start:1 Query End:201 Subject Strand: POSITIVE Subject Start: 1 Subject End: 201 ctctaatattttttattaaaaaataacacatnnnnnnnntgatgtcaaattttttgcttttaacgttaaatataatttttcttctnnnnnnntatgtgttatactattcataaaatagcactttaaatagtaattaacgtctataaaatagaaattttttcgttgatgttaaaatattttttaggaaaaggaggataaact ctctaatattttttattaaaaaataacacataaaaaaaatgatgtcaaattttttgcttttaacgttaaatataatttttcttctaaaaaaatatgtgttatactattcataaaatagcactttaaatagtaattaacgtctataaaatagaaattttttcgttgatgttaaaatattttttaggaaaaggaggataaact Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUCUAAUAUUUUUUAUUAAAAAAUAACACAUAAAAAAAAUGAUGUCAAAUUUUUUGCUUUUAACGUUAAAUAUAAUUUUUCUUCUAAAAAAAUAUGUGUUAUACUAUUCAUAAAAUAGCACUUUAAAUAGUAAUUAACGUCUAUAAAAUAGAAAUUUUUUCGUUGAUGUUAAAAUAUUUUUUAGGAAAAGGAGGAUAAACU ((((.....(((((.((((((((((........(((((((........)))))))...(((((((((((....((..(((((.........(((..((((((((((((..((((.......)))))))))))..)))))..))).....)))))..))....))))))))))).)))))))))))))))))))........ (-28.04) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUUUAUCCUCCUUUUCCUAAAAAAUAUUUUAACAUCAACGAAAAAAUUUCUAUUUUAUAGACGUUAAUUACUAUUUAAAGUGCUAUUUUAUGAAUAGUAUAACACAUAUUUUUUUAGAAGAAAAAUUAUAUUUAACGUUAAAAGCAAAAAAUUUGACAUCAUUUUUUUUAUGUGUUAUUUUUUAAUAAAAAAUAUUAGAG .......................((((((((.............................((((((((............(((((((((...))))))))).....(((.((((((....)))))).)))..))))))))........((((..(((((.(((.......))))))))..)))).....)))))))).... (-24.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 659 140 91 231 182 NC_003454:FN0632|5end_PTS_system,_IIA_component_1290776..1291006_NEGATIVE 226 117 72 189 146 NC_003454:FN0688|5end_hypothetical_protein_1344068..1344298_POSITIVE 217 200 155 151 99 NC_003454:FN1700|5end_hypothetical_protein_195799..196029_NEGATIVE 200 108 69 131 87 NC_003454:FN2107|5end_galactokinase_618150..618380_POSITIVE 199 117 76 136 97 NC_003454:FN1029|5end_Zinc_protease_1683611..1683841_NEGATIVE 197 83 42 106 74 NC_003454:FN0334|5end_Aspartate/aromatic_aminotransferase_969066..969296_NEGATIVE 197 105 76 94 59 NC_003454:FN0169|5end_Coproporphyrinogen_III_oxidase_794741..794971_POSITIVE 192 137 105 200 168 NC_003454:FN0997|5end_hypothetical_protein_1652034..1652264_NEGATIVE 188 85 50 107 69 NC_003454:FN1428|5end_Branched-chain_amino_acid_transport_ATP-binding_protein_livF_2097573..2097803_NEGATIVE 188 86 43 231 183 NC_003454:FN1317|5end_RNA_polymerase_sigma_factor_1971085..1971315_NEGATIVE 186 121 81 197 158 NC_003454:FN1150|5end_hypothetical_protein_1805151..1805381_NEGATIVE 186 112 72 230 196 NC_003454:FN1019|5end_3-hydroxybutyryl-CoA_dehydrogenase_1673784..1674014_NEGATIVE 185 110 70 171 126 NC_003454:FN0663|5end_hypothetical_protein_1319286..1319516_POSITIVE 184 120 77 168 124 NC_003454:FN0742|5end_hypothetical_protein_1400121..1400351_POSITIVE 183 192 154 119 80 NC_003454:FN0033|5end_hypothetical_protein_674969..675199_NEGATIVE 178 176 134 195 146 NC_003454:FN0030|5end_5-nitroimidazole_antibiotic_resistance_protein_667120..667350_POSITIVE 177 84 44 188 153 NC_003454:FN1718|5end_translocase_215299..215529_POSITIVE 176 87 43 129 86 NC_003454:FN0707|5end_FMN_adenylyltransferase_1365737..1365967_POSITIVE 173 132 95 47 17 NC_003454:FN1116|5end_Peptidase_E_1759521..1759751_POSITIVE 172 120 76 206 167 NC_003454:FN1226|5end_uracil-DNA_glycosylase_1885503..1885733_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 226 117 72 87 44 NC_003454:FN0687|3end_hypothetical_protein_1344046..1344196_POSITIVE 220 176 138 100 61 NC_003454:FN0569|3end_Hypothetical_membrane-spanning_protein_1219476..1219626_NEGATIVE 202 200 171 32 3 NC_003454:FN0012|3end_DNA_topology_modulation_protein_FLAR-related_protein_651617..651767_NEGATIVE 199 117 76 117 78 NC_003454:FN1030|3end_Hypothetical_membrane-spanning_protein_1683630..1683780_NEGATIVE 197 105 76 78 43 NC_003454:FN0168|3end_hypothetical_protein_794805..794955_POSITIVE 188 85 50 107 69 NC_003454:FN1429|3end_Branched-chain_amino_acid_transport_ATP-binding_protein_livG_2097573..2097723_NEGATIVE 177 84 44 129 94 NC_003454:FN1717|3end_NAD-dependent_DNA_ligase_215320..215470_POSITIVE 176 87 43 114 71 NC_003454:FN0706|3end_Hypothetical_cytosolic_protein_1365802..1365952_POSITIVE 173 132 95 45 15 NC_003454:FN1115|3end_Hypothetical_membrane-spanning_protein_1759599..1759749_POSITIVE 167 85 47 142 107 NC_003454:FN0394|3end_Outer_membrane_protein_1033147..1033297_POSITIVE 165 85 46 86 52 NC_003454:FN1048|3end_Hypothetical_membrane-spanning_protein_1699094..1699244_POSITIVE 163 76 34 86 46 NC_003454:FN0734|3end_Fe-S_oxidoreductase_1392595..1392745_POSITIVE 159 86 43 146 102 NC_003454:FN1847|3end_DTDP-4-dehydrorhamnose_3,5-epimerase_337208..337358_POSITIVE 158 50 4 62 21 NC_003454:FN1383|3end_DNA_polymerase_III_alpha_subunit_2034455..2034605_NEGATIVE 158 119 82 80 39 NC_003454:FN1816|3end_hypothetical_protein_296139..296289_NEGATIVE 153 79 40 150 107 NC_003454:FN1140|3end_Activator_of_(R)-2-hydroxyglutaryl-CoA_dehydratase_1790473..1790623_POSITIVE 153 85 53 72 38 NC_003454:FN0188|3end_bifunctional_methionine_sulfoxide_reductase_A/B_protein_813252..813402_POSITIVE 153 82 45 127 91 NC_003454:FN1541|3end_Heptaprenyl_diphosphate_synthase_component_II_56275..56425_POSITIVE 151 86 44 140 89 NC_003454:FN0063|3end_hypothetical_protein_699394..699544_POSITIVE 150 147 104 126 88 NC_003454:FN1279|3end_Zinc_metallohydrolase,_glyoxalase_II_family_1937290..1937440_NEGATIVE