Origin IGS: ttctacccctaaaaattaataatttatattataacatattttatggttacatttctaaaaaaaaatgataaaataaaaaagataattaaataaaaaggtgagagggatagtctatgaaaattaaaagaatttttttatttttgttgttacttgtgtgttttgaattatttgcagtcagtaaa .........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 tttactgactgcaaataattcaaaacacacaagtaacaacaaaaataaaaaaattcttttaattttcatagactatccctctcacctttttatttaattatcttttttattttatcatttttttttagaaatgtaaccataaaatatgttataatataaattattaatttttaggggtagaa Mask Tandem Repeat Region ================================================ ttctacccctaaaaattaataatttatattataacatattttatggttacatttctannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnggtgagagggatagtctatgaaaattaaaagaatttttttatttttgttgttacttgtgtgttttgaattatttgcagtcagtaaa Find is-nt database================================================ Query_seq: FN0042:FN0043|FN0042:FN0043:Rod shape-determining protein rodA:Hypothetical exported 24-amino acid repeat protein:<-->:682220..682401 182 ttctacccctaaaaattaataatttatattataacatattttatggttacatttctaaaaaaaaatgataaaataaaaaagataattaaataaaaaggtgagagggatagtctatgaaaattaaaagaatttttttatttttgttgttacttgtgtgttttgaattatttgcagtcagtaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0042:FN0043|FN0042:FN0043:Rod shape-determining protein rodA:Hypothetical exported 24-amino acid repeat protein:<-->:682220..682401 182 ttctacccctaaaaattaataatttatattataacatattttatggttacatttctaaaaaaaaatgataaaataaaaaagataattaaataaaaaggtgagagggatagtctatgaaaattaaaagaatttttttatttttgttgttacttgtgtgttttgaattatttgcagtcagtaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0042:FN0043|FN0042:FN0043:Rod shape-determining protein rodA:Hypothetical exported 24-amino acid repeat protein:<-->:682220..682401 182 ttctacccctaaaaattaataatttatattataacatattttatggttacatttctaaaaaaaaatgataaaataaaaaagataattaaataaaaaggtgagagggatagtctatgaaaattaaaagaatttttttatttttgttgttacttgtgtgttttgaattatttgcagtcagtaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttctacccctaaaaattaataatttatattataacatattttatggttacatttctaaaaaaaaatgataaaataaaaaagataattaaataaaaaggtgagagggatagtctatgaaaattaaaagaatttttttatttttgttgttacttgtgtgttttgaattatttgcagtcagtaaa Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: - Start: 89 End: 178 ........................................................................................ I F L H S P Y D I F I L L I K K N K N N S T H K S N N A T M .... ttctacccctaaaaattaataatttatattataacatattttatggttacatttctaaaaaaaaatgataaaataaaaaagataattaaataaaaaggtgagagggatagtctatgaaaattaaaagaatttttttatttttgttgttacttgtgtgttttgaattatttgcagtcagtaaa Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttctacccctaaaaattaataatttatattataacatattttatggttacatttctaaaaaaaaatgataaaataaaaaagataattaaataaaaaggtgagagggatagtctatgaaaattaaaagaatttttttatttttgttgttacttgtgtgttttgaattatttgcagtcagtaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN0042:FN0043|FN0042:FN0043:Rod shape-determining protein rodA:Hypothetical exported 24-amino acid repeat protein:<-->:682220..682401 182 ttctacccctaaaaattaataatttatattataacatattttatggttacatttctaaaaaaaaatgataaaataaaaaagataattaaataaaaaggtgagagggatagtctatgaaaattaaaagaatttttttatttttgttgttacttgtgtgttttgaattatttgcagtcagtaaa Intra-Species Hit: Count: 1 Min: 1 Max: 182 Len: 182 Subject: NC_003454_FN0042_FN0043|Rod shape-determining protein rodA:Hypothetical exported 24-amino acid repeat protein|NEGATIVE:POSITIVE|[682220,682401]|182 HSP 1 e-value: 3.0E-23 bit: 109.0 Len: 55 Query Start:1 Query End:55 Subject Strand: POSITIVE Subject Start: 1 Subject End: 55 ttctacccctaaaaattaataatttatattataacatattttatggttacatttc............................................................................................................................... ttctacccctaaaaattaataatttatattataacatattttatggttacatttc............................................................................................................................... HSP 2 e-value: 3.0E-14 bit: 79.8 Len: 40 Query Start:143 Query End:182 Subject Strand: POSITIVE Subject Start: 143 Subject End: 182 ..............................................................................................................................................gttgttacttgtgtgttttgaattatttgcagtcagtaaa ..............................................................................................................................................gttgttacttgtgtgttttgaattatttgcagtcagtaaa HSP 3 e-value: 4.0E-10 bit: 65.9 Len: 33 Query Start:97 Query End:129 Subject Strand: POSITIVE Subject Start: 97 Subject End: 129 ................................................................................................ggtgagagggatagtctatgaaaattaaaagaa..................................................... ................................................................................................ggtgagagggatagtctatgaaaattaaaagaa..................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCUACCCCUAAAAAUUAAUAAUUUAUAUUAUAACAUAUUUUAUGGUUACAUUUCUAAAAAAAAAUGAUAAAAUAAAAAAGAUAAUUAAAUAAAAAGGUGAGAGGGAUAGUCUAUGAAAAUUAAAAGAAUUUUUUUAUUUUUGUUGUUACUUGUGUGUUUUGAAUUAUUUGCAGUCAGUAAA .................(((((((((......((((((((((((..((((((((........))))).))).)))))...((((((.((((((((((((......(((..((...))..)))......))))))))))))..))))))....))))))).)))))))))............. (-20.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUACUGACUGCAAAUAAUUCAAAACACACAAGUAACAACAAAAAUAAAAAAAUUCUUUUAAUUUUCAUAGACUAUCCCUCUCACCUUUUUAUUUAAUUAUCUUUUUUAUUUUAUCAUUUUUUUUUAGAAAUGUAACCAUAAAAUAUGUUAUAAUAUAAAUUAUUAAUUUUUAGGGGUAGAA .(((((.........................)))))....................................((((((((...........((((((((((..(...(((((((((((((((....))))))).....)))))))).)..))))).)))))...........)))))))).. (-19.86) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 690 130 81 221 172 NC_003454:FN0042|5end_Rod_shape-determining_protein_rodA_682129..682359_NEGATIVE 220 140 94 184 149 NC_003454:FN0781|5end_Integral_membrane_protein_1438281..1438511_NEGATIVE 218 179 131 214 165 NC_003454:FN1184|5end_hypothetical_protein_1847107..1847337_NEGATIVE 213 46 4 153 101 NC_003454:FN0871|5end_3-dehydroquinate_synthase_1531767..1531997_NEGATIVE 200 48 4 142 96 NC_003454:FN1254|5end_Dihydropteridine_reductase_1911014..1911244_NEGATIVE 195 177 139 54 20 NC_003454:FN1064|5end_hypothetical_protein_1710528..1710758_POSITIVE 195 146 101 66 15 NC_003454:FN0963|5end_hypothetical_protein_1617591..1617821_NEGATIVE 192 68 34 205 171 NC_003454:FN1288|5end_hypothetical_protein_1944580..1944810_POSITIVE 190 120 94 206 178 NC_003454:FN0407|5end_hypothetical_protein_1045178..1045408_NEGATIVE 189 48 5 148 100 NC_003454:FN0187|5end_Thiol:disulfide_interchange_protein_tlpA_811590..811820_POSITIVE 188 145 101 98 50 NC_003454:FN0264|5end_hypothetical_protein_890862..891092_POSITIVE 187 139 93 67 30 NC_003454:FN1920|5end_tRNA_(5-methylaminomethyl-2-thiouridylate)_-methyltransferase_416910..417140_NEGATIVE 186 49 2 147 91 NC_003454:FN1259|5end_Uracil-DNA_glycosylase_1915083..1915313_POSITIVE 184 160 127 118 79 NC_003454:FN1270|5end_Hypothetical_cytosolic_protein_1926592..1926822_NEGATIVE 183 150 105 208 157 NC_003454:FN0303|5end_Nitrogenase_iron_protein_937526..937756_POSITIVE 181 117 72 149 96 NC_003454:FN1654|5end_hypothetical_protein_150878..151108_NEGATIVE 178 136 95 130 90 NC_003454:FN1258|5end_C4-dicarboxylate-binding_protein_1914793..1915023_NEGATIVE 178 179 131 136 91 NC_003454:FN0903|5end_Polysialic_acid_capsule_expression_protein_kpsF_1561116..1561346_POSITIVE 178 176 133 125 86 NC_003454:FN0734|5end_Fe-S_oxidoreductase_1390809..1391039_POSITIVE 176 176 149 82 57 NC_003454:FN1867|5end_Zn-dependent_alcohol_dehydrogenase_and_related_dehydrogenase_359597..359827_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 200 48 4 91 45 NC_003454:FN1255|3end_NagD_protein_1911065..1911215_NEGATIVE 195 177 139 35 1 NC_003454:FN1063|3end_N-acyl-L-amino_acid_amidohydrolase_1710589..1710739_POSITIVE 193 135 93 53 10 NC_003454:FN0219|3end_Autolysin_response_regulator_842594..842744_NEGATIVE 189 48 5 64 16 NC_003454:FN0186|3end_Cytochrome_c-type_biogenesis_protein_ccdA_811586..811736_POSITIVE 188 178 139 128 80 NC_003454:FN1335|3end_Protein_translocase_subunit_YajC_1988727..1988877_NEGATIVE 187 139 93 67 30 NC_003454:FN1921|3end_Biotin_operon_repressor_416910..417060_NEGATIVE 180 108 64 66 13 NC_003454:FN0926|3end_GTP_pyrophosphokinase_1581671..1581821_POSITIVE 178 179 131 114 69 NC_003454:FN0902|3end_5-formyltetrahydrofolate_cyclo-ligase_1561174..1561324_POSITIVE 178 130 92 58 14 NC_003454:FN0844|3end_hypothetical_protein_1503774..1503924_POSITIVE 178 176 133 118 79 NC_003454:FN0733|3end_peptidase_T_1390882..1391032_POSITIVE 176 176 149 64 39 NC_003454:FN1868|3end_Hypothetical_cytosolic_protein_359615..359765_NEGATIVE 175 147 107 101 64 NC_003454:FN1345|3end_2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate_hydrolase_1998130..1998280_NEGATIVE 175 159 114 84 32 NC_003454:FN0274|3end_Transposase_900285..900435_NEGATIVE 173 172 135 113 73 NC_003454:FN0843|3end_hypothetical_protein_1503186..1503336_NEGATIVE 173 162 121 78 36 NC_003454:FN0507|3end_hypothetical_protein_1157710..1157860_POSITIVE 173 104 67 76 40 NC_003454:FN2000|3end_HIPA_protein_501303..501453_POSITIVE 172 180 139 131 94 NC_003454:FN0785|3end_Electron_transfer_flavoprotein_alpha-subunit_1442401..1442551_POSITIVE 171 172 133 132 83 NC_003454:FN0250|3end_hypothetical_protein_873815..873965_POSITIVE 171 172 133 132 83 NC_003454:FN2062|3end_hypothetical_protein_574107..574257_NEGATIVE 171 172 133 132 83 NC_003454:FN2051|3end_hypothetical_protein_560031..560181_NEGATIVE