Origin IGS: aatttttaagatttatttttaacttggctgccttgttatgaattaataataacttattttctttgttattttcttttctatatggaccaatatacttctatggaatattttaaaaataatgttaaaaaaagctgttataaatctacaacagctctttctag .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ctagaaagagctgttgtagatttataacagctttttttaacattatttttaaaatattccatagaagtatattggtccatatagaaaagaaaataacaaagaaaataagttattattaattcataacaaggcagccaagttaaaaataaatcttaaaaatt Mask Tandem Repeat Region ================================================ aatttttaagatttatttttaacttggctgccttgttatgaattaataataacttattttctttgttattttcttttctatatggaccaatatacttctatggaatattttaaaaataatgttaaaaaaagctgttataaatctacaacagctctttctag Find is-nt database================================================ Query_seq: FN0038:FN0039|FN0038:FN0039:hypothetical protein:DNA primase (bacterial type) and small primase-like proteins:<-<-:678590..678750 161 aatttttaagatttatttttaacttggctgccttgttatgaattaataataacttattttctttgttattttcttttctatatggaccaatatacttctatggaatattttaaaaataatgttaaaaaaagctgttataaatctacaacagctctttctag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0038:FN0039|FN0038:FN0039:hypothetical protein:DNA primase (bacterial type) and small primase-like proteins:<-<-:678590..678750 161 aatttttaagatttatttttaacttggctgccttgttatgaattaataataacttattttctttgttattttcttttctatatggaccaatatacttctatggaatattttaaaaataatgttaaaaaaagctgttataaatctacaacagctctttctag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0038:FN0039|FN0038:FN0039:hypothetical protein:DNA primase (bacterial type) and small primase-like proteins:<-<-:678590..678750 161 aatttttaagatttatttttaacttggctgccttgttatgaattaataataacttattttctttgttattttcttttctatatggaccaatatacttctatggaatattttaaaaataatgttaaaaaaagctgttataaatctacaacagctctttctag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatttttaagatttatttttaacttggctgccttgttatgaattaataataacttattttctttgttattttcttttctatatggaccaatatacttctatggaatattttaaaaataatgttaaaaaaagctgttataaatctacaacagctctttctag Predict ORF larger than 30AA ================================================ Protein_Len: 44 Strand: + Start: 28 End: 159 ........................... M P C Y E L I I T Y F L C Y F L F Y M D Q Y T S M E Y F K N N V K K S C Y K S T T A L S .. Protein_Len: 35 Strand: + Start: 56 End: 160 ....................................................... M F F V I F F S I W T N I L L W N I L K I M L K K A V I N L Q Q L F L . Protein_Len: 31 Strand: - Start: 46 End: 138 ............................................. Y Y S I K K T I K K E I H V L I S R H F I K F I I N F F A T M ....................... Protein_Len: 30 Strand: - Start: 2 End: 91 . N K L N I K L K A A K N H I L L L K N E K N N E K R Y P G M ...................................................................... aatttttaagatttatttttaacttggctgccttgttatgaattaataataacttattttctttgttattttcttttctatatggaccaatatacttctatggaatattttaaaaataatgttaaaaaaagctgttataaatctacaacagctctttctag 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================================================ aatttttaagatttatttttaacttggctgccttgttatgaattaataataacttattttctttgttattttcttttctatatggaccaatatacttctatggaatattttaaaaataatgttaaaaaaagctgttataaatctacaacagctctttctag Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN0038:FN0039|FN0038:FN0039:hypothetical protein:DNA primase (bacterial type) and small primase-like proteins:<-<-:678590..678750 161 aatttttaagatttatttttaacttggctgccttgttatgaattaataataacttattttctttgttattttcttttctatatggaccaatatacttctatggaatattttaaaaataatgttaaaaaaagctgttataaatctacaacagctctttctag Intra-Species Hit: Count: 1 Min: 1 Max: 161 Len: 161 Subject: NC_003454_FN0038_FN0039|hypothetical protein:DNA primase (bacterial type) and small primase-like proteins|NEGATIVE:NEGATIVE|[678590,678750]|161 HSP 1 e-value: 5.0E-74 bit: 278.0 Len: 161 Query Start:1 Query End:161 Subject Strand: POSITIVE Subject Start: 1 Subject End: 161 aatttttaagatttatttttaacttggctgccttgttatgaattaataataacttattttctttgttattttcttttctatatggaccaatatacttctatggaatattttaaaaataatgttnnnnnnngctgttataaatctacaacagctctttctag aatttttaagatttatttttaacttggctgccttgttatgaattaataataacttattttctttgttattttcttttctatatggaccaatatacttctatggaatattttaaaaataatgttaaaaaaagctgttataaatctacaacagctctttctag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUUUUAAGAUUUAUUUUUAACUUGGCUGCCUUGUUAUGAAUUAAUAAUAACUUAUUUUCUUUGUUAUUUUCUUUUCUAUAUGGACCAAUAUACUUCUAUGGAAUAUUUUAAAAAUAAUGUUAAAAAAAGCUGUUAUAAAUCUACAACAGCUCUUUCUAG ..(((((((.(((.((((((((.((((...((.(((...(((.....((((((...........)))))).....))).))).)).)))).....(((....)))....))))))))))).))))))).(((((((.((....)).)))))))........ (-25.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUAGAAAGAGCUGUUGUAGAUUUAUAACAGCUUUUUUUAACAUUAUUUUUAAAAUAUUCCAUAGAAGUAUAUUGGUCCAUAUAGAAAAGAAAAUAACAAAGAAAAUAAGUUAUUAUUAAUUCAUAACAAGGCAGCCAAGUUAAAAAUAAAUCUUAAAAAUU .(((((((((((((((((....)))))))))))))))))...((((((((((....(((....))).....(((((((.(((.(((..((.((((((...........)))))).))..))))))....))..))))).))))))))))............ (-30.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 695 70 21 161 112 NC_003454:FN0038|5end_hypothetical_protein_678499..678729_NEGATIVE 321 158 122 139 95 NC_003454:FN1269|5end_Hypothetical_lipoprotein_1926242..1926472_NEGATIVE 288 100 51 183 134 NC_003454:FN0064|5end_Hypothetical_cytosolic_protein_699489..699719_POSITIVE 264 44 7 82 45 NC_003454:FN1939|5end_hypothetical_protein_439465..439695_NEGATIVE 213 63 22 97 59 NC_003454:FN1597|5end_peptidyl-tRNA_hydrolase_107810..108040_NEGATIVE 205 160 120 213 179 NC_003454:FN1482|5end_Guanosine-3',5'-bis(Diphosphate)_3'-pyrophosphohydrolase_2165992..2166222_NEGATIVE 203 99 51 127 68 NC_003454:FN0755|5end_Glutamyl-tRNA(Gln)_amidotransferase_subunit_C_1414953..1415183_NEGATIVE 203 151 129 78 52 NC_003454:FN0115|5end_hypothetical_protein_748511..748741_NEGATIVE 203 100 53 140 81 NC_003454:FN1875|5end_Peptidyl-prolyl_cis-trans_isomerase_364400..364630_NEGATIVE 201 160 119 143 93 NC_003454:FN0626|5end_Hypothetical_cytosolic_protein_1286092..1286322_NEGATIVE 200 70 23 117 60 NC_003454:FN1667|5end_dTDP-glucose_4,6-dehydratase_164472..164702_NEGATIVE 198 107 62 137 84 NC_003454:FN0818|5end_DNA-binding_protein_HU_1477034..1477264_NEGATIVE 197 66 29 162 116 NC_003454:FN0309|5end_Iron(III)-transport_system_permease_protein_sfuB_944099..944329_POSITIVE 195 156 129 68 37 NC_003454:FN1070|5end_glucose-inhibited_division_protein_A_1717121..1717351_POSITIVE 190 96 54 112 66 NC_003454:FN1545|5end_Ferredoxin_like_protein_59133..59363_POSITIVE 189 80 37 198 156 NC_003454:FN1170|5end_Pyruvate-flavodoxin_oxidoreductase_1832273..1832503_NEGATIVE 189 103 64 44 1 NC_003454:FN0545|5end_Lipopolysaccharide_core_biosynthesis_protein_rfaY_1198041..1198271_POSITIVE 187 160 131 160 133 NC_003454:FN0437|5end_Allophanate_hydrolase_1079642..1079872_NEGATIVE 186 78 31 100 55 NC_003454:FN1519|5end_23S_rRNA_methyltransferase_24792..25022_NEGATIVE 185 79 31 137 80 NC_003454:FN1253|5end_hypothetical_protein_1910405..1910635_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 321 158 122 55 11 NC_003454:FN1270|3end_Hypothetical_cytosolic_protein_1926326..1926476_NEGATIVE 225 155 130 79 50 NC_003454:FN1006|3end_Acetyltransferase_1660998..1661148_NEGATIVE 207 103 62 51 6 NC_003454:FN0544|3end_ADP-heptose:LPS_heptosyltransferase_II_1198128..1198278_POSITIVE 203 99 51 118 59 NC_003454:FN0756|3end_Ribosomal_large_subunit_pseudouridine_synthase_B_1414962..1415112_NEGATIVE 203 100 53 78 19 NC_003454:FN1876|3end_4-methyl-5(B-hydroxyethyl)-thiazole_monophosphate_biosynthesis_enzyme_364462..364612_NEGATIVE 201 160 119 80 30 NC_003454:FN0627|3end_Glucosamine--fructose-6-phosphate_aminotransferase_[isomerizing]_1286155..1286305_NEGATIVE 201 153 113 81 34 NC_003454:FN0212|3end_hypothetical_protein_837583..837733_NEGATIVE 197 66 29 143 97 NC_003454:FN0308|3end_Iron(III)-binding_protein_944160..944310_POSITIVE 194 100 56 76 17 NC_003454:FN0581|3end_Lipoprotein_releasing_system_transmembrane_protein_lolE_1238357..1238507_POSITIVE 193 160 131 87 55 NC_003454:FN1080|3end_Export_ABC_transporter_1727308..1727458_POSITIVE 193 157 112 83 31 NC_003454:FN1005|3end_hypothetical_protein_1660975..1661125_POSITIVE 190 157 127 90 51 NC_003454:FN1276|3end_hypothetical_protein_1935280..1935430_POSITIVE 190 96 54 109 63 NC_003454:FN1544|3end_Probable_electron_transfer_flavoprotein-quinone_oxidoreductase_ydiS_59210..59360_POSITIVE 189 80 37 106 64 NC_003454:FN1171|3end_Acetate_kinase_1832365..1832515_NEGATIVE 186 78 31 90 45 NC_003454:FN1520|3end_UDP-N-acetylglucosamine_1-carboxyvinyltransferase_24802..24952_NEGATIVE 184 101 69 144 107 NC_003454:FN0418|3end_pyrimidine_regulatory_protein_PyrR_1059731..1059881_POSITIVE 183 160 124 103 59 NC_003454:FN1497|3end_Multidrug_resistance_protein_2_1014..1164_NEGATIVE 182 99 63 87 48 NC_003454:FN0644|3end_UROPORPHYRINOGEN-III_SYNTHASE_1299887..1300037_NEGATIVE 182 105 61 142 103 NC_003454:FN0364|3end_ATP_synthase_A_chain,_sodium_ion_specific_993757..993907_NEGATIVE 181 142 101 80 41 NC_003454:FN1806|3end_Integral_membrane_protein_288667..288817_POSITIVE