Origin IGS: tgaatctgcctccttcttattatgacttgattataacattttcctacattttgaacaaaggaaaactgaagcatcaaaaaagaagagactgcctgagtctctcctagaaattt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaatttctaggagagactcaggcagtctcttcttttttgatgcttcagttttcctttgttcaaaatgtaggaaaatgttataatcaagtcataataagaaggaggcagattca Mask Tandem Repeat Region ================================================ tgaatctgcctccttcttattatgacttgattataacattttcctacattttgaacaaaggaaaactgaagcatcaaaaaagaagagactgcctgagtctctcctagaaattt Find is-nt database================================================ Query_seq: SSA_2155:SSA_2156|SSA_2155:SSA_2156:hypothetical protein:Conserved uncharacterized protein:<-<-:2156193..2156305 113 tgaatctgcctccttcttattatgacttgattataacattttcctacattttgaacaaaggaaaactgaagcatcaaaaaagaagagactgcctgagtctctcctagaaattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2155:SSA_2156|SSA_2155:SSA_2156:hypothetical protein:Conserved uncharacterized protein:<-<-:2156193..2156305 113 tgaatctgcctccttcttattatgacttgattataacattttcctacattttgaacaaaggaaaactgaagcatcaaaaaagaagagactgcctgagtctctcctagaaattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2155:SSA_2156|SSA_2155:SSA_2156:hypothetical protein:Conserved uncharacterized protein:<-<-:2156193..2156305 113 tgaatctgcctccttcttattatgacttgattataacattttcctacattttgaacaaaggaaaactgaagcatcaaaaaagaagagactgcctgagtctctcctagaaattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgaatctgcctccttcttattatgacttgattataacattttcctacattttgaacaaaggaaaactgaagcatcaaaaaagaagagactgcctgagtctctcctagaaattt Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 6 End: 104 ..... M P P S Y Y D L I I T F S Y I L N K G K L K H Q K R R D C L S L S ......... tgaatctgcctccttcttattatgacttgattataacattttcctacattttgaacaaaggaaaactgaagcatcaaaaaagaagagactgcctgagtctctcctagaaattt 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: 84 Start: 30 End: 59 .............................TTTGTTCAAAATGTAGGAAAATGTTATAAT...................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tgaatctgcctccttcttattatgacttgattataacattttcctacattttgaacaaaggaaaactgaagcatcaaaaaagaagagactgcctgagtctctcctagaaattt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_2155:SSA_2156|SSA_2155:SSA_2156:hypothetical protein:Conserved uncharacterized protein:<-<-:2156193..2156305 113 tgaatctgcctccttcttattatgacttgattataacattttcctacattttgaacaaaggaaaactgaagcatcaaaaaagaagagactgcctgagtctctcctagaaattt Intra-Species Hit: Count: 1 Min: 1 Max: 113 Len: 113 Subject: NC_009009_SSA_2155_SSA_2156|hypothetical protein:Conserved uncharacterized protein|NEGATIVE:NEGATIVE|[2156193,2156305]|113 HSP 1 e-value: 5.0E-58 bit: 224.0 Len: 113 Query Start:1 Query End:113 Subject Strand: POSITIVE Subject Start: 1 Subject End: 113 tgaatctgcctccttcttattatgacttgattataacattttcctacattttgaacaaaggaaaactgaagcatcaaaaaagaagagactgcctgagtctctcctagaaattt tgaatctgcctccttcttattatgacttgattataacattttcctacattttgaacaaaggaaaactgaagcatcaaaaaagaagagactgcctgagtctctcctagaaattt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAAUCUGCCUCCUUCUUAUUAUGACUUGAUUAUAACAUUUUCCUACAUUUUGAACAAAGGAAAACUGAAGCAUCAAAAAAGAAGAGACUGCCUGAGUCUCUCCUAGAAAUUU (((...(((.((.......((((((.....))))))..(((((((.............)))))))..)).))))))....((.(((((((.....))))))).))........ (-18.42) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUUUCUAGGAGAGACUCAGGCAGUCUCUUCUUUUUUGAUGCUUCAGUUUUCCUUUGUUCAAAAUGUAGGAAAAUGUUAUAAUCAAGUCAUAAUAAGAAGGAGGCAGAUUCA ...(((((.(((((((((.....)))))))))...((((((......((((((((.(((.....))).))))))))......))))))........)))))............ (-25.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 871 110 61 201 152 NC_009009:SSA_2155|5end_hypothetical_protein_2156102..2156332_NEGATIVE 278 108 81 38 12 NC_009009:SSA_0086|5end_V-type_sodium_ATPase,_subunit_K,_putative_87839..88069_POSITIVE 276 107 66 207 164 NC_009009:SSA_0209|5end_Glutamyl_aminopeptidase,_putative_207636..207866_NEGATIVE 275 48 5 129 83 NC_009009:SSA_2176|5end_hypothetical_protein_2175159..2175389_NEGATIVE 257 48 2 221 180 NC_009009:SSA_2220|5end_Galactosyltransferase,_putative_2221439..2221669_NEGATIVE 245 108 65 47 1 NC_009009:SSA_1055|5end_Conserved_uncharacterized_protein_1070899..1071129_POSITIVE 240 107 65 179 127 NC_009009:SSA_2160|5end_Deoxyuridinetriphosphatase,_putative_2160066..2160296_NEGATIVE 240 100 57 178 133 NC_009009:SSA_1711|5end_Endonuclease_III,_putative_1699636..1699866_NEGATIVE 234 28 5 47 24 NC_009009:SSA_0163|5end_hypothetical_protein_162127..162357_POSITIVE 232 105 71 136 110 NC_009009:SSA_1793|5end_Histidine_kinase_(sensor_protein),_putative_1776361..1776591_NEGATIVE 232 100 52 223 168 NC_009009:SSA_0150|5end_hypothetical_protein_143936..144166_POSITIVE 231 74 38 185 145 NC_009009:SSA_1091|5end_Thymidylate_synthase,_putative_1108635..1108865_POSITIVE 230 100 51 170 121 NC_009009:SSA_1057|5end_Aminotransferase,_class-V,_putative_1073771..1074001_POSITIVE 228 106 66 65 18 NC_009009:SSA_0219|5end_PTS_system,_sugar-specific_enzyme_IIA_component,_putative_215367..215597_POSITIVE 227 109 65 169 123 NC_009009:SSA_0293|5end_hypothetical_protein_287613..287843_NEGATIVE 224 107 66 197 137 NC_009009:SSA_1144|5end_Beta-N-acetylhexosaminidase,_putative_1175610..1175840_NEGATIVE 223 106 79 223 195 NC_009009:SSA_1666|5end_Collagen-binding_surface_protein,_putative_1667312..1667542_NEGATIVE 222 100 52 57 12 NC_009009:SSA_1486|5end_hypothetical_protein_1492922..1493152_POSITIVE 221 55 13 76 32 NC_009009:SSA_1964|5end_conserved_uncharacterized_protein_1961211..1961441_NEGATIVE 219 101 64 56 11 NC_009009:SSA_1575|5end_Glycosyl_transferase,_putative_1579110..1579340_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 275 48 5 56 10 NC_009009:SSA_2177|3end_hypothetical_protein_2175232..2175382_NEGATIVE 240 107 65 94 42 NC_009009:SSA_2161|3end_NTP_pyrophosphohydrolases_including_oxidative_damage_repair_enzymes,_putative_2160151..2160301_NEGATIVE 240 100 57 83 38 NC_009009:SSA_1712|3end_Arsenate_reductase_(ArsC),_glutaredoxin_family,_putative_1699731..1699881_NEGATIVE 231 74 38 80 40 NC_009009:SSA_1090|3end_Glucokinase,_putative_1108610..1108760_POSITIVE 230 100 51 69 20 NC_009009:SSA_1056|3end_Firmicute_fructose-1,6-bisphosphatase,_putative_1073750..1073900_POSITIVE 228 107 65 55 6 NC_009009:SSA_1051|3end_Spermidine/putrescine_ABC_transporter,_spermidine/putrescine-binding_protein,_putative_1066808..1066958_POSITIVE 225 102 62 74 37 NC_009009:SSA_2108|3end_Glyceraldehyde_3-phosphate_dehydrogenase,_putative_2111457..2111607_NEGATIVE 224 107 66 113 53 NC_009009:SSA_1145|3end_hypothetical_protein_1175694..1175844_NEGATIVE 222 108 64 60 22 NC_009009:SSA_0683|3end_DNA-binding_protein_HU,_putative_664739..664889_POSITIVE 220 110 71 49 7 NC_009009:SSA_0149|3end_hypothetical_protein_143833..143983_POSITIVE 219 109 84 140 115 NC_009009:SSA_0108|3end_50S_ribosomal_protein_L4,_putative_109519..109669_POSITIVE 218 97 56 71 28 NC_009009:SSA_0506|3end_Iron-sulfur_cluster-binding_protein,_putative_504430..504580_NEGATIVE 214 28 6 45 24 NC_009009:SSA_0482|3end_ATP:cobalamin_adenosyl_transferase,_putative_484113..484263_POSITIVE 214 107 66 79 30 NC_009009:SSA_0154|3end_hypothetical_protein_150950..151100_POSITIVE 213 104 71 151 126 NC_009009:SSA_1794|3end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_winged-helix_DNA-binding_domains),_putative_1776345..1776495_NEGATIVE 211 107 67 41 2 NC_009009:SSA_0628|3end_Fe-S-cluster_redox_enzyme/radical_SAM_enzyme,_Cfr_family,_putative_619060..619210_POSITIVE 210 44 5 130 98 NC_009009:SSA_1841|3end_Cof_family_protein/peptidyl-prolyl_cis-trans_isomerase,_cyclophilin_type,_putative_1834422..1834572_NEGATIVE 209 104 64 65 31 NC_009009:SSA_2244|3end_Arsenate_reductase,_putative_2239477..2239627_NEGATIVE 209 103 70 79 40 NC_009009:SSA_0403|3end_CAAX_amino_terminal_protease_family,_putative_401388..401538_POSITIVE 204 25 7 28 9 NC_009009:SSA_2254|3end_Holliday_junction_DNA_helicase_ruvA,_putative_2249434..2249584_NEGATIVE