Origin IGS: taaggagaaggctttatttttattcataatatcctctcaatatacttaaaaatatttataattttttaactataatgtctctcgagctccaaaatgctcttttaacattataggacgtcgcagtaatcttat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ataagattactgcgacgtcctataatgttaaaagagcattttggagctcgagagacattatagttaaaaaattataaatatttttaagtatattgagaggatattatgaataaaaataaagccttctcctta Mask Tandem Repeat Region ================================================ taaggagaaggctttatttttattcataatatcctctcaatatacttaaaaatatttataattttttaactataatgtctctcgagctccaaaatgctcttttaacattataggacgtcgcagtaatcttat Find is-nt database================================================ Query_seq: FN2091:FN2092|FN2091:FN2092:hypothetical protein:Integral membrane protein:<-<-:602572..602703 132 taaggagaaggctttatttttattcataatatcctctcaatatacttaaaaatatttataattttttaactataatgtctctcgagctccaaaatgctcttttaacattataggacgtcgcagtaatcttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN2091:FN2092|FN2091:FN2092:hypothetical protein:Integral membrane protein:<-<-:602572..602703 132 taaggagaaggctttatttttattcataatatcctctcaatatacttaaaaatatttataattttttaactataatgtctctcgagctccaaaatgctcttttaacattataggacgtcgcagtaatcttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN2091:FN2092|FN2091:FN2092:hypothetical protein:Integral membrane protein:<-<-:602572..602703 132 taaggagaaggctttatttttattcataatatcctctcaatatacttaaaaatatttataattttttaactataatgtctctcgagctccaaaatgctcttttaacattataggacgtcgcagtaatcttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaggagaaggctttatttttattcataatatcctctcaatatacttaaaaatatttataattttttaactataatgtctctcgagctccaaaatgctcttttaacattataggacgtcgcagtaatcttat Predict ORF larger than 30AA ================================================ taaggagaaggctttatttttattcataatatcctctcaatatacttaaaaatatttataattttttaactataatgtctctcgagctccaaaatgctcttttaacattataggacgtcgcagtaatcttat 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================================================ taaggagaaggctttatttttattcataatatcctctcaatatacttaaaaatatttataattttttaactataatgtctctcgagctccaaaatgctcttttaacattataggacgtcgcagtaatcttat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN2091:FN2092|FN2091:FN2092:hypothetical protein:Integral membrane protein:<-<-:602572..602703 132 taaggagaaggctttatttttattcataatatcctctcaatatacttaaaaatatttataattttttaactataatgtctctcgagctccaaaatgctcttttaacattataggacgtcgcagtaatcttat Intra-Species Hit: Count: 1 Min: 1 Max: 132 Len: 132 Subject: NC_003454_FN2091_FN2092|hypothetical protein:Integral membrane protein|NEGATIVE:NEGATIVE|[602572,602703]|132 HSP 1 e-value: 3.0E-69 bit: 262.0 Len: 132 Query Start:1 Query End:132 Subject Strand: POSITIVE Subject Start: 1 Subject End: 132 taaggagaaggctttatttttattcataatatcctctcaatatacttaaaaatatttataattttttaactataatgtctctcgagctccaaaatgctcttttaacattataggacgtcgcagtaatcttat taaggagaaggctttatttttattcataatatcctctcaatatacttaaaaatatttataattttttaactataatgtctctcgagctccaaaatgctcttttaacattataggacgtcgcagtaatcttat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGGAGAAGGCUUUAUUUUUAUUCAUAAUAUCCUCUCAAUAUACUUAAAAAUAUUUAUAAUUUUUUAACUAUAAUGUCUCUCGAGCUCCAAAAUGCUCUUUUAACAUUAUAGGACGUCGCAGUAAUCUUAU ....((((.((..((((........))))...))))))....((((((((((..........)))))).(((((((((.....((((........)))).....)))))))))........))))....... (-21.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAAGAUUACUGCGACGUCCUAUAAUGUUAAAAGAGCAUUUUGGAGCUCGAGAGACAUUAUAGUUAAAAAAUUAUAAAUAUUUUUAAGUAUAUUGAGAGGAUAUUAUGAAUAAAAAUAAAGCCUUCUCCUUA .......((((........((((((((((....((((........))))....))))))))))...((((((.......)))))).))))....((((((...((((........))))...)))))).... (-24.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 880 130 81 221 172 NC_003454:FN2091|5end_hypothetical_protein_602481..602711_NEGATIVE 384 129 82 187 137 NC_003454:FN0695|5end_ABC_transporter_ATP-binding_protein_1352886..1353116_POSITIVE 224 124 88 193 162 NC_003454:FN0751|5end_L-asparaginase_I_1410731..1410961_NEGATIVE 223 47 2 163 108 NC_003454:FN0549|5end_O-sialoglycoprotein_endopeptidase_1201326..1201556_POSITIVE 223 112 80 59 19 NC_003454:FN0187|5end_Thiol:disulfide_interchange_protein_tlpA_811590..811820_POSITIVE 221 103 61 160 113 NC_003454:FN1153|5end_hypothetical_protein_1807827..1808057_POSITIVE 206 43 2 62 14 NC_003454:FN0642|5end_hypothetical_protein_1299461..1299691_NEGATIVE 204 50 3 113 65 NC_003454:FN0670|5end_High-affinity_zinc_uptake_system_membrane_protein_znuB_1325702..1325932_POSITIVE 203 115 79 77 42 NC_003454:FN1694|5end_UDP-N-acetyl-D-quinovosamine_4-epimerase_190169..190399_NEGATIVE 201 42 3 133 81 NC_003454:FN1436|5end_Export_ABC_transporter_2105239..2105469_POSITIVE 201 115 76 101 68 NC_003454:FN0133|5end_hypothetical_protein_769121..769351_POSITIVE 201 38 6 60 26 NC_003454:FN0040|5end_asparaginyl-tRNA_synthetase_680609..680839_NEGATIVE 199 103 62 219 174 NC_003454:FN1073|5end_hypothetical_protein_1720403..1720633_POSITIVE 195 119 76 92 50 NC_003454:FN1298|5end_Adenylate_kinase_1955626..1955856_NEGATIVE 193 125 94 110 76 NC_003454:FN1154|5end_Ribonuclease_BN_1808232..1808462_POSITIVE 191 45 2 84 47 NC_003454:FN1177|5end_hypothetical_protein_1838805..1839035_NEGATIVE 191 36 3 176 142 NC_003454:FN1981|5end_Transposase_483299..483529_POSITIVE 191 130 87 155 100 NC_003454:FN1533|5end_Electron_transfer_flavoprotein_alpha-subunit_46321..46551_NEGATIVE 190 103 61 153 104 NC_003454:FN0772|5end_Flavodoxin_1428694..1428924_POSITIVE 189 119 79 215 179 NC_003454:FN1831|5end_Nitrogen_assimilation_regulatory_protein_321423..321653_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 626 125 84 66 25 NC_003454:FN0829|3end_hypothetical_protein_1489580..1489730_NEGATIVE 422 129 84 71 27 NC_003454:FN1076|3end_hypothetical_protein_1723677..1723827_POSITIVE 384 129 82 85 35 NC_003454:FN0694|3end_S-layer_protein_1352864..1353014_POSITIVE 376 125 81 48 1 NC_003454:FN1260|3end_Sensory_Transduction_Protein_Kinase_1915863..1916013_NEGATIVE 228 121 81 147 117 NC_003454:FN1253|3end_hypothetical_protein_1910229..1910379_NEGATIVE 221 103 61 140 93 NC_003454:FN1152|3end_aspartate_aminotransferase_1807887..1808037_POSITIVE 218 47 4 68 27 NC_003454:FN1901|3end_Transcription_regulator,_CRP_family_389364..389514_NEGATIVE 206 43 2 89 41 NC_003454:FN0643|3end_hypothetical_protein_1299434..1299584_NEGATIVE 203 115 79 77 42 NC_003454:FN1695|3end_Probable_quinovosaminephosphotransferae_190169..190319_NEGATIVE 201 115 71 68 24 NC_003454:FN0828|3end_ABC_transporter_permease_protein_1489505..1489655_POSITIVE 201 115 76 83 50 NC_003454:FN0132|3end_Hemolysin_769183..769333_POSITIVE 201 38 6 50 16 NC_003454:FN0041|3end_hypothetical_protein_680619..680769_NEGATIVE 193 60 14 42 2 NC_003454:FN2010|3end_Transcriptional_regulator,_MarR_family_509820..509970_NEGATIVE 192 124 88 135 95 NC_003454:FN1236|3end_Choline_transport_protein_1892512..1892662_NEGATIVE 191 45 2 96 59 NC_003454:FN1178|3end_Hypothetical_cytosolic_protein_1838793..1838943_NEGATIVE 191 36 3 49 15 NC_003454:FN1980|3end_Transporter_483252..483402_POSITIVE 191 130 87 143 88 NC_003454:FN1534|3end_Electron_transfer_flavoprotein_beta-subunit_46333..46483_NEGATIVE 189 45 2 85 57 NC_003454:FN1794|3end_Phosphocarrier_protein_HPr_275328..275478_NEGATIVE 188 104 78 122 95 NC_003454:FN0011|3end_Transcriptional_regulator_651620..651770_POSITIVE 186 118 71 116 74 NC_003454:FN1317|3end_RNA_polymerase_sigma_factor_1970273..1970423_NEGATIVE