Origin IGS: cataaagaaaataagtaaaagaaaaactacatctataagtggtgttatttcaagaactaatgttccaccacttcttctttttattctttctaatttcatttactcacac .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gtgtgagtaaatgaaattagaaagaataaaaagaagaagtggtggaacattagttcttgaaataacaccacttatagatgtagtttttcttttacttattttctttatg Mask Tandem Repeat Region ================================================ cataaagaaaataagtaaaagaaaaactacatctataagtggtgttatttcaagaactaatgttccaccacttcttctttttattctttctaatttcatttactcacac Find is-nt database================================================ Query_seq: FN1833:FN1834|FN1833:FN1834:Biopolymer transport exbD protein:Biopolymer transport exbB protein:<-<-:322657..322765 109 cataaagaaaataagtaaaagaaaaactacatctataagtggtgttatttcaagaactaatgttccaccacttcttctttttattctttctaatttcatttactcacac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1833:FN1834|FN1833:FN1834:Biopolymer transport exbD protein:Biopolymer transport exbB protein:<-<-:322657..322765 109 cataaagaaaataagtaaaagaaaaactacatctataagtggtgttatttcaagaactaatgttccaccacttcttctttttattctttctaatttcatttactcacac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1833:FN1834|FN1833:FN1834:Biopolymer transport exbD protein:Biopolymer transport exbB protein:<-<-:322657..322765 109 cataaagaaaataagtaaaagaaaaactacatctataagtggtgttatttcaagaactaatgttccaccacttcttctttttattctttctaatttcatttactcacac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cataaagaaaataagtaaaagaaaaactacatctataagtggtgttatttcaagaactaatgttccaccacttcttctttttattctttctaatttcatttactcacac Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 2 End: 109 . M K K I S K R K T T S I S G V I S R T N V P P L L L F I L S N F I Y S H Protein_Len: 33 Strand: - Start: 1 End: 99 M F F I L L L F V V D I L P T I E L V L T G G S R R K I R E L K M .......... cataaagaaaataagtaaaagaaaaactacatctataagtggtgttatttcaagaactaatgttccaccacttcttctttttattctttctaatttcatttactcacac 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================================================ cataaagaaaataagtaaaagaaaaactacatctataagtggtgttatttcaagaactaatgttccaccacttcttctttttattctttctaatttcatttactcacac Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN1833:FN1834|FN1833:FN1834:Biopolymer transport exbD protein:Biopolymer transport exbB protein:<-<-:322657..322765 109 cataaagaaaataagtaaaagaaaaactacatctataagtggtgttatttcaagaactaatgttccaccacttcttctttttattctttctaatttcatttactcacac Intra-Species Hit: Count: 1 Min: 1 Max: 109 Len: 109 Subject: NC_003454_FN1833_FN1834|Biopolymer transport exbD protein:Biopolymer transport exbB protein|NEGATIVE:NEGATIVE|[322657,322765]|109 HSP 1 e-value: 1.0E-55 bit: 216.0 Len: 109 Query Start:1 Query End:109 Subject Strand: POSITIVE Subject Start: 1 Subject End: 109 cataaagaaaataagtaaaagaaaaactacatctataagtggtgttatttcaagaactaatgttccaccacttcttctttttattctttctaatttcatttactcacac cataaagaaaataagtaaaagaaaaactacatctataagtggtgttatttcaagaactaatgttccaccacttcttctttttattctttctaatttcatttactcacac Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAUAAAGAAAAUAAGUAAAAGAAAAACUACAUCUAUAAGUGGUGUUAUUUCAAGAACUAAUGUUCCACCACUUCUUCUUUUUAUUCUUUCUAAUUUCAUUUACUCACAC .....(((((......(((((((.............((((((((.........((((....)))))))))))).))))))).....))))).................. (-15.84) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUGUGAGUAAAUGAAAUUAGAAAGAAUAAAAAGAAGAAGUGGUGGAACAUUAGUUCUUGAAAUAACACCACUUAUAGAUGUAGUUUUUCUUUUACUUAUUUUCUUUAUG ..(((((((((.......(((((((...........((((((((((((....)))).........))))))))..........)))))))))))))))).......... (-22.01) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 784 80 31 171 122 NC_003454:FN1833|5end_Biopolymer_transport_exbD_protein_322566..322796_NEGATIVE 428 47 1 135 89 NC_003454:FN1311|5end_Biopolymer_transport_exbD_protein_1966250..1966480_NEGATIVE 263 79 38 209 174 NC_003454:FN1426|5end_Serine_protease_2095462..2095692_NEGATIVE 244 73 40 41 2 NC_003454:FN0606|5end_Translation_initiation_inhibitor_1261014..1261244_POSITIVE 237 77 40 216 178 NC_003454:FN1104|5end_Holliday_junction_DNA_helicase_ruvA_1749453..1749683_POSITIVE 227 96 55 116 64 NC_003454:FN0662|5end_Formiminoglutamase_1318152..1318382_POSITIVE 225 97 59 116 70 NC_003454:FN0211|5end_Plasmid_addiction_system_poison_protein_837224..837454_POSITIVE 218 70 39 98 67 NC_003454:FN1043|5end_hypothetical_protein_1694239..1694469_POSITIVE 217 66 30 157 123 NC_003454:FN0695|5end_ABC_transporter_ATP-binding_protein_1352886..1353116_POSITIVE 210 68 27 197 155 NC_003454:FN0890|5end_Thiamin_pyrophosphokinase_1552087..1552317_NEGATIVE 207 99 51 130 89 NC_003454:FN0677|5end_hypothetical_protein_1332641..1332871_POSITIVE 203 83 57 41 15 NC_003454:FN0465|5end_hypothetical_protein_1110046..1110276_POSITIVE 203 91 61 115 84 NC_003454:FN2087|5end_hypothetical_protein_599719..599949_NEGATIVE 203 78 33 122 64 NC_003454:FN1675|5end_Transposase_172478..172708_NEGATIVE 200 76 32 48 10 NC_003454:FN1483|5end_adenine_phosphoribosyltransferase_2166523..2166753_NEGATIVE 198 66 29 98 57 NC_003454:FN1422|5end_NA+/H+_antiporter_NHAC_2088426..2088656_NEGATIVE 198 96 53 108 53 NC_003454:FN0858|5end_4-alpha-glucanotransferase_1520507..1520737_NEGATIVE 197 70 31 53 11 NC_003454:FN0317|5end_tryptophan_synthase_subunit_beta_955006..955236_NEGATIVE 195 74 53 37 14 NC_003454:FN0490|5end_Integral_membrane_protein_1136234..1136464_NEGATIVE 193 98 64 47 11 NC_003454:FN0961|5end_hypothetical_protein_1616164..1616394_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 388 47 3 45 1 NC_003454:FN1312|3end_Biopolymer_transport_exbB_protein_1966340..1966490_NEGATIVE 244 73 40 44 5 NC_003454:FN0605|3end_aspartate_aminotransferase_1261097..1261247_POSITIVE 231 72 36 62 16 NC_003454:FN0014|3end_Transporter_652839..652989_POSITIVE 228 89 43 141 89 NC_003454:FN1351|3end_15_kDa_lipoprotein_precursor_2002950..2003100_NEGATIVE 227 96 55 97 45 NC_003454:FN0661|3end_hypothetical_protein_1318213..1318363_POSITIVE 225 97 59 108 62 NC_003454:FN0210|3end_Transcriptional_regulator,_COPG_family_837296..837446_POSITIVE 219 47 13 40 2 NC_003454:FN1624|3end_preprotein_translocase_SecY_131080..131230_NEGATIVE 217 66 30 55 21 NC_003454:FN0694|3end_S-layer_protein_1352864..1353014_POSITIVE 216 100 56 76 34 NC_003454:FN0415|3end_hypothetical_protein_1053996..1054146_POSITIVE 196 76 31 133 88 NC_003454:FN0016|3end_hypothetical_protein_654366..654516_POSITIVE 195 74 53 32 9 NC_003454:FN0491|3end_Alanine_racemase_1136239..1136389_NEGATIVE 192 89 63 102 71 NC_003454:FN1034|3end_Transcriptional_regulator,_TetR_family_1688345..1688495_POSITIVE 190 100 52 115 63 NC_003454:FN0854|3end_Glucose-1-phosphate_adenylyltransferase_1512324..1512474_NEGATIVE 190 100 52 97 42 NC_003454:FN1579|3end_Cysteinyl-tRNA_synthetase_88784..88934_NEGATIVE 189 97 63 144 103 NC_003454:FN1225|3end_UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--meso-_lanthionine_ligase_1883366..1883516_NEGATIVE 183 98 64 127 86 NC_003454:FN1431|3end_Branched-chain_amino_acid_transport_system_permease_protein_livH_2099326..2099476_NEGATIVE 183 80 33 77 28 NC_003454:FN0719|3end_Hypothetical_cytosolic_protein_1377056..1377206_POSITIVE 182 89 60 36 5 NC_003454:FN1180|3end_hypothetical_protein_1841857..1842007_NEGATIVE 182 97 53 151 104 NC_003454:FN0805|3end_hypothetical_protein_1464832..1464982_NEGATIVE 181 98 72 57 31 NC_003454:FN0410|3end_6-phosphofructokinase_1048299..1048449_POSITIVE