Origin IGS: taaaaaaatttgacaagttatttatatctgtgttatactctaaaaaatttttaaaaaggagtgattaaaatgaaaaaattaaataatagtcattttgattacacatattattactactataaaaattagagagtcattaattaaattagatggctctatttgtatttgtaagagcctctaatttatttttataagatatgattatggacttcttacatttacatttgtaagaagtttttttattttaaattaatttataaatttttaggaggagagattttt .........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 aaaaatctctcctcctaaaaatttataaattaatttaaaataaaaaaacttcttacaaatgtaaatgtaagaagtccataatcatatcttataaaaataaattagaggctcttacaaatacaaatagagccatctaatttaattaatgactctctaatttttatagtagtaataatatgtgtaatcaaaatgactattatttaattttttcattttaatcactcctttttaaaaattttttagagtataacacagatataaataacttgtcaaattttttta Mask Tandem Repeat Region ================================================ taaaaaaatttgacaagttatttatatctgtgttatactctaaaaaatttttaaaaaggagtgattaaaatgaaaaaattaaataatagtcattttgattacacatattattactactataaaaattagagagtcattaattaaattagatggctctatttgtatttgtaagagcctctaatttatttttataagatatgattatggacttcttacatttacatttgtaagaagtttttttattttaaattaatttataaatttttaggaggagagattttt Find is-nt database================================================ Query_seq: FN0351:FN0352|FN0351:FN0352:hypothetical protein:NA+/H+ antiporter NHAC:->->:983399..983680 282 taaaaaaatttgacaagttatttatatctgtgttatactctaaaaaatttttaaaaaggagtgattaaaatgaaaaaattaaataatagtcattttgattacacatattattactactataaaaattagagagtcattaattaaattagatggctctatttgtatttgtaagagcctctaatttatttttataagatatgattatggacttcttacatttacatttgtaagaagtttttttattttaaattaatttataaatttttaggaggagagattttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0351:FN0352|FN0351:FN0352:hypothetical protein:NA+/H+ antiporter NHAC:->->:983399..983680 282 taaaaaaatttgacaagttatttatatctgtgttatactctaaaaaatttttaaaaaggagtgattaaaatgaaaaaattaaataatagtcattttgattacacatattattactactataaaaattagagagtcattaattaaattagatggctctatttgtatttgtaagagcctctaatttatttttataagatatgattatggacttcttacatttacatttgtaagaagtttttttattttaaattaatttataaatttttaggaggagagattttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0351:FN0352|FN0351:FN0352:hypothetical protein:NA+/H+ antiporter NHAC:->->:983399..983680 282 taaaaaaatttgacaagttatttatatctgtgttatactctaaaaaatttttaaaaaggagtgattaaaatgaaaaaattaaataatagtcattttgattacacatattattactactataaaaattagagagtcattaattaaattagatggctctatttgtatttgtaagagcctctaatttatttttataagatatgattatggacttcttacatttacatttgtaagaagtttttttattttaaattaatttataaatttttaggaggagagattttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaaaaaatttgacaagttatttatatctgtgttatactctaaaaaatttttaaaaaggagtgattaaaatgaaaaaattaaataatagtcattttgattacacatattattactactataaaaattagagagtcattaattaaattagatggctctatttgtatttgtaagagcctctaatttatttttataagatatgattatggacttcttacatttacatttgtaagaagtttttttattttaaattaatttataaatttttaggaggagagattttt Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 83 End: 178 .................................................................................. M I V I L I T H I I T T I K I R E S L I K L D G S I C I C K S L ........................................................................................................ taaaaaaatttgacaagttatttatatctgtgttatactctaaaaaatttttaaaaaggagtgattaaaatgaaaaaattaaataatagtcattttgattacacatattattactactataaaaattagagagtcattaattaaattagatggctctatttgtatttgtaagagcctctaatttatttttataagatatgattatggacttcttacatttacatttgtaagaagtttttttattttaaattaatttataaatttttaggaggagagattttt 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: 82 Start: 217 End: 246 ........................................................................................................................................................................................................................ATTTACATTTGTAAGAAGTTTTTTTATTTT.................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taaaaaaatttgacaagttatttatatctgtgttatactctaaaaaatttttaaaaaggagtgattaaaatgaaaaaattaaataatagtcattttgattacacatattattactactataaaaattagagagtcattaattaaattagatggctctatttgtatttgtaagagcctctaatttatttttataagatatgattatggacttcttacatttacatttgtaagaagtttttttattttaaattaatttataaatttttaggaggagagattttt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 60 HP_score: -3.5 Tail_Score: -4.8667 Start: 142 End: 185 Full_Region: TAGAGAGTCATTAAT TAAATTAGATGGCTCT ATTTGTATTTGTA AGAGCCTCTAATTTA TTTTTATAAGATATG .............................................................................................................................................TAAATTAGATGGCTCTATTTGTATTTGTAAGAGCCTCTAATTTA................................................................................................. TransTerm Strand: - Conf: 41 HP_score: -3.5 Tail_Score: -2.52491 Start: 142 End: 185 Full_Region: catatcttataaaaa taaattagaggctct tacaaatacaaat agagccatctaattta attaatgactctcta .............................................................................................................................................taaattagaggctcttacaaatacaaatagagccatctaattta................................................................................................. TransTerm Strand: + Conf: 95 HP_score: -6.3 Tail_Score: -6.09196 Start: 209 End: 234 Full_Region: AGATATGATTATGGA CTTCTTACA TTTACATT TGTAAGAAG TTTTTTTATTTTAAA ................................................................................................................................................................................................................CTTCTTACATTTACATTTGTAAGAAG................................................ Find igs database================================================ Query_seq: FN0351:FN0352|FN0351:FN0352:hypothetical protein:NA+/H+ antiporter NHAC:->->:983399..983680 282 taaaaaaatttgacaagttatttatatctgtgttatactctaaaaaatttttaaaaaggagtgattaaaatgaaaaaattaaataatagtcattttgattacacatattattactactataaaaattagagagtcattaattaaattagatggctctatttgtatttgtaagagcctctaatttatttttataagatatgattatggacttcttacatttacatttgtaagaagtttttttattttaaattaatttataaatttttaggaggagagattttt Intra-Species Hit: Count: 1 Min: 9 Max: 234 Len: 226 Subject: NC_003454_FN0351_FN0352|hypothetical protein:NA+/H+ antiporter NHAC|POSITIVE:POSITIVE|[983399,983680]|282 HSP 1 e-value: 7.0E-78 bit: 291.0 Len: 147 Query Start:88 Query End:234 Subject Strand: POSITIVE Subject Start: 88 Subject End: 234 .......................................................................................agtcattttgattacacatattattactactataaaaattagagagtcattaattaaattagatggctctatttgtatttgtaagagcctctaatttatttttataagatatgattatggacttcttacatttacatttgtaagaag................................................ .......................................................................................agtcattttgattacacatattattactactataaaaattagagagtcattaattaaattagatggctctatttgtatttgtaagagcctctaatttatttttataagatatgattatggacttcttacatttacatttgtaagaag................................................ HSP 2 e-value: 3.0E-9 bit: 63.9 Len: 32 Query Start:9 Query End:40 Subject Strand: POSITIVE Subject Start: 9 Subject End: 40 ........tttgacaagttatttatatctgtgttatactc.................................................................................................................................................................................................................................................. ........tttgacaagttatttatatctgtgttatactc.................................................................................................................................................................................................................................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUGACAAGUUAUUUAUAUCUGUGUUAUACUCUAAAAAAUUUUUAAAAAGGAGUGAUUAAAAUGAAAAAAUUAAAUAAUAGUCAUUUUGAUUACACAUAUUAUUACUACUAUAAAAAUUAGAGAGUCAUUAAUUAAAUUAGAUGGCUCUAUUUGUAUUUGUAAGAGCCUCUAAUUUAUUUUUAUAAGAUAUGAUUAUGGACUUCUUACAUUUACAUUUGUAAGAAG ..........((.((((((((.......(((((....((((((((.......(((((((((((((....(((....)))..)))))))))))))...((....))......))))))))..))))).......(((((((((.((((((((........)).)))))))))))))))........)))))))).))....(((((((((........))))))))) (-50.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUCUUACAAAUGUAAAUGUAAGAAGUCCAUAAUCAUAUCUUAUAAAAAUAAAUUAGAGGCUCUUACAAAUACAAAUAGAGCCAUCUAAUUUAAUUAAUGACUCUCUAAUUUUUAUAGUAGUAAUAAUAUGUGUAAUCAAAAUGACUAUUAUUUAAUUUUUUCAUUUUAAUCACUCCUUUUUAAAAAUUUUUUAGAGUAUAACACAGAUAUAAAUAACUUGUCAAA (((((((((........))))))))).........((((((........(((((((((((((((.............)))))).))))))))).......(((((..((((((((.((.(((..(((.(((........((((((...))))))........))).)))...))).))...))))))))....))))).......))))))............... (-41.61) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 297 170 128 202 162 NC_003454:FN1372|5end_Ribosomal_large_subunit_pseudouridine_synthase_D_2020981..2021211_NEGATIVE 254 171 132 208 169 NC_003454:FN1189|5end_hypothetical_protein_1851320..1851550_POSITIVE 244 200 151 193 133 NC_003454:FN1667|5end_dTDP-glucose_4,6-dehydratase_164472..164702_NEGATIVE 225 48 3 118 67 NC_003454:FN0532|5end_Hypothetical_membrane-spanning_protein_1187579..1187809_NEGATIVE 222 172 134 50 16 NC_003454:FN0048|5end_4-nitrophenylphosphatase_686043..686273_NEGATIVE 216 40 9 55 22 NC_003454:FN0598|5end_Phospholipid-lipopolysaccharide_ABC_transporter_1251881..1252111_POSITIVE 215 78 39 184 142 NC_003454:FN0042|5end_Rod_shape-determining_protein_rodA_682129..682359_NEGATIVE 210 208 163 140 100 NC_003454:FN0074|5end_Ethanolamine_utilization_protein_eutS_713328..713558_POSITIVE 207 187 142 175 113 NC_003454:FN1047|5end_Hypothetical_membrane-spanning_protein_1697175..1697405_POSITIVE 204 185 143 119 70 NC_003454:FN1152|5end_aspartate_aminotransferase_1806617..1806847_POSITIVE 200 206 169 84 47 NC_003454:FN0932|5end_hypothetical_protein_1584678..1584908_POSITIVE 196 190 143 188 137 NC_003454:FN0900|5end_Metal_dependent_hydrolase_1559180..1559410_POSITIVE 194 169 143 23 1 NC_003454:FN0773|5end_hypothetical_protein_1429274..1429504_POSITIVE 193 183 143 117 65 NC_003454:FN1365|5end_GTP-binding_protein_2016739..2016969_NEGATIVE 193 181 143 94 49 NC_003454:FN0930|5end_Glycerol-3-phosphate_cytidylyltransferase_1583964..1584194_NEGATIVE 187 33 1 39 5 NC_003454:FN1383|5end_DNA_polymerase_III_alpha_subunit_2037856..2038086_NEGATIVE 187 190 150 179 148 NC_003454:FN1507|5end_riboflavin_synthase_subunit_alpha_12073..12303_POSITIVE 186 170 121 176 116 NC_003454:FN1351|5end_15_kDa_lipoprotein_precursor_2003372..2003602_NEGATIVE 186 184 144 196 148 NC_003454:FN1257|5end_C4-dicarboxylate_transporter_small_subunit_1913664..1913894_NEGATIVE 186 174 133 92 43 NC_003454:FN1233|5end_Putative_NAD(P)H_oxidoreductase_1889389..1889619_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 270 190 146 100 57 NC_003454:FN1826|3end_Protease_314654..314804_NEGATIVE 245 187 144 95 55 NC_003454:FN0532|3end_Hypothetical_membrane-spanning_protein_1186524..1186674_NEGATIVE 225 48 3 96 45 NC_003454:FN0533|3end_Hypothetical_membrane-spanning_protein_1187601..1187751_NEGATIVE 216 40 9 58 25 NC_003454:FN0597|3end_Lipid-A-disaccharide_synthase_1251964..1252114_POSITIVE 208 159 112 91 44 NC_003454:FN1133|3end_N-acetylglucosamine-6-phosphate_deacetylase_1780269..1780419_NEGATIVE 207 187 142 108 46 NC_003454:FN1046|3end_hypothetical_protein_1697188..1697338_POSITIVE 204 168 123 81 27 NC_003454:FN0637|3end_Hypothetical_exported_24-amino_acid_repeat_protein_1295636..1295786_NEGATIVE 203 189 145 110 70 NC_003454:FN1009|3end_hypothetical_protein_1663606..1663756_NEGATIVE 193 183 143 93 41 NC_003454:FN1366|3end_Triosephosphate_isomerase_2016763..2016913_NEGATIVE 193 181 143 125 80 NC_003454:FN0931|3end_Phosphohydrolase_(MUTT/NUDIX_family_protein)_1583933..1584083_NEGATIVE 193 191 156 98 67 NC_003454:FN1907|3end_Thymidylate_synthase_400546..400696_POSITIVE 192 182 144 91 52 NC_003454:FN0405|3end_tryptophanyl-tRNA_synthetase_1042465..1042615_NEGATIVE 190 206 164 83 46 NC_003454:FN0799|3end_Isoamylase_1457889..1458039_NEGATIVE 190 170 144 58 30 NC_003454:FN1508|3end_3,4-dihydroxy-2-butanone-4-phosphate_synthase_14117..14267_POSITIVE 188 213 174 52 13 NC_003454:FN1314|3end_hypothetical_protein_1968500..1968650_NEGATIVE 187 190 150 86 55 NC_003454:FN1506|3end_5-amino-6-(5-phosphoribosylamino)uracil_reductase_12060..12210_POSITIVE 186 184 144 68 20 NC_003454:FN1258|3end_C4-dicarboxylate-binding_protein_1913792..1913942_NEGATIVE 186 173 136 63 32 NC_003454:FN2112|3end_hypothetical_protein_623169..623319_NEGATIVE 186 185 144 74 36 NC_003454:FN1985|3end_Inner_membrane_protein_487273..487423_NEGATIVE 185 206 161 84 45 NC_003454:FN1239|3end_hypothetical_protein_1896403..1896553_NEGATIVE