Origin IGS: aattacacctctttatttaaatttaatttcgttttaaacaatacattaataatatcatatataagtttagttttcaatgaaattttaaaaagtagattaattaatttaataaaaataatatgaattatcaaaataataattaagatattttttaaatagaaaaatttacatagctctataatattgacaatatttatatatatagctataatgaaaaaaattataacttaattttaaggagttgacaa .........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 ttgtcaactccttaaaattaagttataatttttttcattatagctatatatataaatattgtcaatattatagagctatgtaaatttttctatttaaaaaatatcttaattattattttgataattcatattatttttattaaattaattaatctactttttaaaatttcattgaaaactaaacttatatatgatattattaatgtattgtttaaaacgaaattaaatttaaataaagaggtgtaatt Mask Tandem Repeat Region ================================================ aattacacctctttatttaaatttaatttcgttttaaacaatacattaataatatcatatataagtttagttttcaatgaaattttaaaaagtagattaattaatttaataaaaataatatgaattatcaaaataataattaagatattttttaaatagaaaaatttacatagctctataatattgacaatatttatatatatagctataatgaaaaaaattataacttaattttaaggagttgacaa Find is-nt database================================================ Query_seq: FN0760:FN0761|FN0760:FN0761:hypothetical protein:Bvg accessory factor:<-->:1418761..1419008 248 aattacacctctttatttaaatttaatttcgttttaaacaatacattaataatatcatatataagtttagttttcaatgaaattttaaaaagtagattaattaatttaataaaaataatatgaattatcaaaataataattaagatattttttaaatagaaaaatttacatagctctataatattgacaatatttatatatatagctataatgaaaaaaattataacttaattttaaggagttgacaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0760:FN0761|FN0760:FN0761:hypothetical protein:Bvg accessory factor:<-->:1418761..1419008 248 aattacacctctttatttaaatttaatttcgttttaaacaatacattaataatatcatatataagtttagttttcaatgaaattttaaaaagtagattaattaatttaataaaaataatatgaattatcaaaataataattaagatattttttaaatagaaaaatttacatagctctataatattgacaatatttatatatatagctataatgaaaaaaattataacttaattttaaggagttgacaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0760:FN0761|FN0760:FN0761:hypothetical protein:Bvg accessory factor:<-->:1418761..1419008 248 aattacacctctttatttaaatttaatttcgttttaaacaatacattaataatatcatatataagtttagttttcaatgaaattttaaaaagtagattaattaatttaataaaaataatatgaattatcaaaataataattaagatattttttaaatagaaaaatttacatagctctataatattgacaatatttatatatatagctataatgaaaaaaattataacttaattttaaggagttgacaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aattacacctctttatttaaatttaatttcgttttaaacaatacattaataatatcatatataagtttagttttcaatgaaattttaaaaagtagattaattaatttaataaaaataatatgaattatcaaaataataattaagatattttttaaatagaaaaatttacatagctctataatattgacaatatttatatatatagctataatgaaaaaaattataacttaattttaaggagttgacaa Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: - Start: 6 End: 224 ..... N I I D Y I L K T K L S I K F L L N I L K I F I I H I I L I I I L I N K L Y F F K C L E I I N V I N I Y I A I I F F I M ........................ aattacacctctttatttaaatttaatttcgttttaaacaatacattaataatatcatatataagtttagttttcaatgaaattttaaaaagtagattaattaatttaataaaaataatatgaattatcaaaataataattaagatattttttaaatagaaaaatttacatagctctataatattgacaatatttatatatatagctataatgaaaaaaattataacttaattttaaggagttgacaa 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: 92 Start: 183 End: 212 ......................................................................................................................................................................................ATTGACAATATTTATATATATAGCTATAAT.................................... PromScan Matrix: RpoD-17 Strand: - Score: 88 Start: 49 End: 78 ................................................ATTGAAAACTAAACTTATATATGATATTAT.......................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 84 Start: 103 End: 132 ......................................................................................................TTTGATAATTCATATTATTTTTATTAAATT.................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aattacacctctttatttaaatttaatttcgttttaaacaatacattaataatatcatatataagtttagttttcaatgaaattttaaaaagtagattaattaatttaataaaaataatatgaattatcaaaataataattaagatattttttaaatagaaaaatttacatagctctataatattgacaatatttatatatatagctataatgaaaaaaattataacttaattttaaggagttgacaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN0760:FN0761|FN0760:FN0761:hypothetical protein:Bvg accessory factor:<-->:1418761..1419008 248 aattacacctctttatttaaatttaatttcgttttaaacaatacattaataatatcatatataagtttagttttcaatgaaattttaaaaagtagattaattaatttaataaaaataatatgaattatcaaaataataattaagatattttttaaatagaaaaatttacatagctctataatattgacaatatttatatatatagctataatgaaaaaaattataacttaattttaaggagttgacaa Intra-Species Hit: Count: 1 Min: 1 Max: 248 Len: 248 Subject: NC_003454_FN0760_FN0761|hypothetical protein:Bvg accessory factor|NEGATIVE:POSITIVE|[1418761,1419008]|248 HSP 1 e-value: 5.0E-35 bit: 149.0 Len: 75 Query Start:1 Query End:75 Subject Strand: POSITIVE Subject Start: 1 Subject End: 75 aattacacctctttatttaaatttaatttcgttttaaacaatacattaataatatcatatataagtttagttttc............................................................................................................................................................................. aattacacctctttatttaaatttaatttcgttttaaacaatacattaataatatcatatataagtttagttttc............................................................................................................................................................................. HSP 2 e-value: 2.0E-25 bit: 117.0 Len: 80 Query Start:169 Query End:248 Subject Strand: POSITIVE Subject Start: 169 Subject End: 248 ........................................................................................................................................................................catagctctataatattgacaatatttatatatatagctataatgnnnnnnnttataacttaattttaaggagttgacaa ........................................................................................................................................................................catagctctataatattgacaatatttatatatatagctataatgaaaaaaattataacttaattttaaggagttgacaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUACACCUCUUUAUUUAAAUUUAAUUUCGUUUUAAACAAUACAUUAAUAAUAUCAUAUAUAAGUUUAGUUUUCAAUGAAAUUUUAAAAAGUAGAUUAAUUAAUUUAAUAAAAAUAAUAUGAAUUAUCAAAAUAAUAAUUAAGAUAUUUUUUAAAUAGAAAAAUUUACAUAGCUCUAUAAUAUUGACAAUAUUUAUAUAUAUAGCUAUAAUGAAAAAAAUUAUAACUUAAUUUUAAGGAGUUGACAA .....((.(((((((.((((...((((((.((.....))....(((((....(((.((((((((((...(((.((((((.....((((((((((..(((((((...........(((((....)))))........)))))))..))))))))))(((((..............)))))..)))))).))))))))))))))))....)))))....))))))....))))...))))))).)).... (-31.35) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGUCAACUCCUUAAAAUUAAGUUAUAAUUUUUUUCAUUAUAGCUAUAUAUAUAAAUAUUGUCAAUAUUAUAGAGCUAUGUAAAUUUUUCUAUUUAAAAAAUAUCUUAAUUAUUAUUUUGAUAAUUCAUAUUAUUUUUAUUAAAUUAAUUAAUCUACUUUUUAAAAUUUCAUUGAAAACUAAACUUAUAUAUGAUAUUAUUAAUGUAUUGUUUAAAACGAAAUUAAAUUUAAAUAAAGAGGUGUAAUU ......((.((((....(((((((.((((((((((((.(((((((.((((..................)))).)))))))............((((((((.((..(((((((....((((((((............)))))))).)))))))..)).)))))))).......)))))..(((((..((((((..........)))))).)))))....)))))))))))))).....)))).)).... (-33.57) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 599 80 31 171 122 NC_003454:FN0760|5end_hypothetical_protein_1418670..1418900_NEGATIVE 202 208 161 224 183 NC_003454:FN0473|5end_Regulatory_protein_betI_1118292..1118522_POSITIVE 186 209 167 163 126 NC_003454:FN2053|5end_Serine/threonine_sodium_symporter_562415..562645_NEGATIVE 185 43 6 131 89 NC_003454:FN1765|5end_pyruvate_kinase_259450..259680_NEGATIVE 177 199 165 51 20 NC_003454:FN1278|5end_Acetyltransferase_1937174..1937404_NEGATIVE 176 186 145 64 9 NC_003454:FN0281|5end_DNA_polymerase_III_alpha_subunit_912129..912359_NEGATIVE 175 183 148 133 97 NC_003454:FN0598|5end_Phospholipid-lipopolysaccharide_ABC_transporter_1251881..1252111_POSITIVE 174 35 2 129 94 NC_003454:FN1908|5end_Glycerophosphoryl_diester_phosphodiesterase_401669..401899_NEGATIVE 173 182 151 191 163 NC_003454:FN0895|5end_hypothetical_protein_1555373..1555603_NEGATIVE 170 37 5 162 126 NC_003454:FN1019|5end_3-hydroxybutyryl-CoA_dehydrogenase_1673784..1674014_NEGATIVE 167 207 173 83 45 NC_003454:FN0705|5end_DNA_polymerase_I_1362069..1362299_POSITIVE 165 130 81 229 181 NC_003454:FN0776|5end_asparagine_synthetase_AsnA_1431944..1432174_POSITIVE 162 34 3 128 88 NC_003454:FN1374|5end_Transcriptional_regulator_2022301..2022531_NEGATIVE 162 59 11 59 4 NC_003454:FN0187|5end_Thiol:disulfide_interchange_protein_tlpA_811590..811820_POSITIVE 161 180 146 50 14 NC_003454:FN1615|5end_Integral_membrane_protein_125125..125355_POSITIVE 157 74 45 37 6 NC_003454:FN1349|5end_ABC_transporter_permease_protein_2002355..2002585_NEGATIVE 157 203 170 44 18 NC_003454:FN0802|5end_Amino_acid_transport_system_permease_protein_1462136..1462366_NEGATIVE 157 96 61 219 186 NC_003454:FN0716|5end_Phophatidylinositol-4-phosphate_5-kinase_1373969..1374199_POSITIVE 157 89 52 68 27 NC_003454:FN0417|5end_Type_III_restriction-modification_system_restriction_subunit_1055887..1056117_POSITIVE 157 208 171 158 112 NC_003454:FN0157|5end_DNA_repair_protein_RadA_784898..785128_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 176 186 145 77 22 NC_003454:FN0282|3end_hypothetical_protein_912116..912266_NEGATIVE 175 183 148 136 100 NC_003454:FN0597|3end_Lipid-A-disaccharide_synthase_1251964..1252114_POSITIVE 174 35 2 86 51 NC_003454:FN1909|3end_UDP-3-O-[3-hydroxymyristoyl]_glucosamine_N-acyltransferase_401712..401862_NEGATIVE 174 48 8 56 14 NC_003454:FN1713|3end_tRNA_(Uracil-5-)_-methyltransferase_208968..209118_POSITIVE 172 98 54 119 70 NC_003454:FN1228|3end_hypothetical_protein_1885882..1886032_NEGATIVE 172 185 146 99 51 NC_003454:FN1185|3end_SIR2_family_protein_1847563..1847713_NEGATIVE 170 37 5 146 110 NC_003454:FN1020|3end_3-hydroxybutyryl-CoA_dehydratase_1673800..1673950_NEGATIVE 168 212 171 134 96 NC_003454:FN1279|3end_Zinc_metallohydrolase,_glyoxalase_II_family_1937290..1937440_NEGATIVE 165 130 81 142 94 NC_003454:FN0775|3end_putative_aminopeptidase_2_1431937..1432087_POSITIVE 162 149 110 141 102 NC_003454:FN1941|3end_ClpB_protein_443953..444103_POSITIVE 160 206 169 47 3 NC_003454:FN1260|3end_Sensory_Transduction_Protein_Kinase_1915863..1916013_NEGATIVE 160 86 43 79 32 NC_003454:FN1218|3end_hypothetical_protein_1877812..1877962_NEGATIVE 157 74 45 33 2 NC_003454:FN1350|3end_Integral_membrane_protein_2002359..2002509_NEGATIVE 157 89 52 58 17 NC_003454:FN0416|3end_Type_III_restriction-modification_system_methylation_subunit_1055957..1056107_POSITIVE 157 34 5 109 82 NC_003454:FN1837|3end_putative_nucleotide-binding_protein_326725..326875_NEGATIVE 154 221 181 62 25 NC_003454:FN2010|3end_Transcriptional_regulator,_MarR_family_509820..509970_NEGATIVE 151 203 170 110 80 NC_003454:FN0235|3end_ABC_transporter_ATP-binding_protein_859674..859824_NEGATIVE 150 42 10 138 102 NC_003454:FN1269|3end_Hypothetical_lipoprotein_1925613..1925763_NEGATIVE 150 99 55 47 4 NC_003454:FN1955|3end_hypothetical_protein_460210..460360_POSITIVE 147 27 3 106 81 NC_003454:FN1203|3end_GTP-binding_protein_1862311..1862461_NEGATIVE