Origin IGS: ttgtcagcacgtctctgtacacttttgagagaccaaaagtaaaaagtaccgtctatcattatagcacgacgatacttctctgtcaatacattttttctaattcaggcctatctctatttattagattgctgctaac .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gttagcagcaatctaataaatagagataggcctgaattagaaaaaatgtattgacagagaagtatcgtcgtgctataatgatagacggtactttttacttttggtctctcaaaagtgtacagagacgtgctgacaa Mask Tandem Repeat Region ================================================ ttgtcagcacgtctctgtacacttttgagagaccaaaagtaaaaagtaccgtctatcattatagcacgacgatacttctctgtcaatacattttttctaattcaggcctatctctatttattagattgctgctaac Find is-nt database================================================ Query_seq: SSA_2112:SSA_2113|SSA_2112:SSA_2113:hypothetical protein:hypothetical protein:<-<-:2116182..2116317 136 ttgtcagcacgtctctgtacacttttgagagaccaaaagtaaaaagtaccgtctatcattatagcacgacgatacttctctgtcaatacattttttctaattcaggcctatctctatttattagattgctgctaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2112:SSA_2113|SSA_2112:SSA_2113:hypothetical protein:hypothetical protein:<-<-:2116182..2116317 136 ttgtcagcacgtctctgtacacttttgagagaccaaaagtaaaaagtaccgtctatcattatagcacgacgatacttctctgtcaatacattttttctaattcaggcctatctctatttattagattgctgctaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2112:SSA_2113|SSA_2112:SSA_2113:hypothetical protein:hypothetical protein:<-<-:2116182..2116317 136 ttgtcagcacgtctctgtacacttttgagagaccaaaagtaaaaagtaccgtctatcattatagcacgacgatacttctctgtcaatacattttttctaattcaggcctatctctatttattagattgctgctaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttgtcagcacgtctctgtacacttttgagagaccaaaagtaaaaagtaccgtctatcattatagcacgacgatacttctctgtcaatacattttttctaattcaggcctatctctatttattagattgctgctaac Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: + Start: 15 End: 134 .............. M Y T F E R P K V K S T V Y H Y S T T I L L C Q Y I F S N S G L S L F I R L L L .. Protein_Len: 33 Strand: - Start: 3 End: 101 .. D A R R Q V S K L S W F Y F T G D I M I A R R Y K E T L V N K R M ................................... ttgtcagcacgtctctgtacacttttgagagaccaaaagtaaaaagtaccgtctatcattatagcacgacgatacttctctgtcaatacattttttctaattcaggcctatctctatttattagattgctgctaac 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: 58 End: 87 .........................................................ATTGACAGAGAAGTATCGTCGTGCTATAAT................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttgtcagcacgtctctgtacacttttgagagaccaaaagtaaaaagtaccgtctatcattatagcacgacgatacttctctgtcaatacattttttctaattcaggcctatctctatttattagattgctgctaac Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_2112:SSA_2113|SSA_2112:SSA_2113:hypothetical protein:hypothetical protein:<-<-:2116182..2116317 136 ttgtcagcacgtctctgtacacttttgagagaccaaaagtaaaaagtaccgtctatcattatagcacgacgatacttctctgtcaatacattttttctaattcaggcctatctctatttattagattgctgctaac Intra-Species Hit: Count: 1 Min: 1 Max: 136 Len: 136 Subject: NC_009009_SSA_2112_SSA_2113|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[2116182,2116317]|136 HSP 1 e-value: 1.0E-71 bit: 270.0 Len: 136 Query Start:1 Query End:136 Subject Strand: POSITIVE Subject Start: 1 Subject End: 136 ttgtcagcacgtctctgtacacttttgagagaccaaaagtaaaaagtaccgtctatcattatagcacgacgatacttctctgtcaatacattttttctaattcaggcctatctctatttattagattgctgctaac ttgtcagcacgtctctgtacacttttgagagaccaaaagtaaaaagtaccgtctatcattatagcacgacgatacttctctgtcaatacattttttctaattcaggcctatctctatttattagattgctgctaac Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGUCAGCACGUCUCUGUACACUUUUGAGAGACCAAAAGUAAAAAGUACCGUCUAUCAUUAUAGCACGACGAUACUUCUCUGUCAAUACAUUUUUUCUAAUUCAGGCCUAUCUCUAUUUAUUAGAUUGCUGCUAAC ..(.(((((......((((.(((((((......)))))))...(((((.((((..............)))).))))).........)))).....((((((..(((......)))....)))))).)))))).... (-22.44) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUAGCAGCAAUCUAAUAAAUAGAGAUAGGCCUGAAUUAGAAAAAAUGUAUUGACAGAGAAGUAUCGUCGUGCUAUAAUGAUAGACGGUACUUUUUACUUUUGGUCUCUCAAAAGUGUACAGAGACGUGCUGACAA (((((((....((((((...(((........))).)))))).....(((((.....(((((((((((((...(......)...)))))))))))))((((((((....)))))))))))))......))))))).. (-36.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 861 50 1 141 92 NC_009009:SSA_2112|5end_hypothetical_protein_2116091..2116321_NEGATIVE 861 50 1 220 171 NC_009009:SSA_2111|5end_30S_ribosomal_protein_S12,_putative_2116012..2116242_NEGATIVE 294 109 64 223 171 NC_009009:SSA_2191|5end_Conserved_uncharacterized_protein_2192049..2192279_POSITIVE 275 120 79 191 148 NC_009009:SSA_0520|5end_Ethanolamine_ammonia-lyase_light_chain,_putative_519462..519692_POSITIVE 267 91 56 49 15 NC_009009:SSA_0269|5end_Phosphotransferase_system_(PTS)_cellobiose-specific_component_IIA,_putative_262550..262780_POSITIVE 255 85 45 200 157 NC_009009:SSA_0835|5end_Accessory_secretory_protein_Asp3,_putative_821036..821266_POSITIVE 246 85 48 59 22 NC_009009:SSA_0457|5end_Fructokinase,_putative_460663..460893_POSITIVE 237 114 76 164 109 NC_009009:SSA_2257|5end_DNA_mismatch_repair_protein,_putative_2253184..2253414_NEGATIVE 237 81 49 65 36 NC_009009:SSA_0483|5end_Siroheme_synthase,_putative_484045..484275_POSITIVE 237 86 45 131 95 NC_009009:SSA_0018|5end_Cell-shape_determining_protein_MreD,_putative_23628..23858_POSITIVE 234 94 52 204 158 NC_009009:SSA_2156|5end_Conserved_uncharacterized_protein_2156932..2157162_NEGATIVE 232 60 11 168 115 NC_009009:SSA_1260|5end_Phosphopentomutase,_putative_1286963..1287193_NEGATIVE 231 30 3 211 178 NC_009009:SSA_0119|5end_50S_ribosomal_protein_L5,_putative_113692..113922_POSITIVE 229 53 11 160 116 NC_009009:SSA_2160|5end_Deoxyuridinetriphosphatase,_putative_2160066..2160296_NEGATIVE 228 69 24 61 19 NC_009009:SSA_2056|5end_Cinnamoyl_ester_hydrolase,_putative_2058587..2058817_POSITIVE 227 107 64 55 21 NC_009009:SSA_2141|5end_Argininosuccinate_lyase,_putative_2142201..2142431_NEGATIVE 227 113 74 59 16 NC_009009:SSA_0616|5end_YlbN-like_protein,_putative_609245..609475_POSITIVE 227 53 15 141 107 NC_009009:SSA_0320|5end_hypothetical_protein_313406..313636_POSITIVE 224 50 6 102 65 NC_009009:SSA_1264|5end_hypothetical_protein_1290042..1290272_NEGATIVE 224 104 63 105 64 NC_009009:SSA_0005|5end_GTP-binding_protein,_putative_3821..4051_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 267 91 56 40 6 NC_009009:SSA_0268|3end_Phosphotransferase_system_(PTS)_cellobiose-specific_component_IIB,_putative_262621..262771_POSITIVE 237 81 49 53 24 NC_009009:SSA_0482|3end_ATP:cobalamin_adenosyl_transferase,_putative_484113..484263_POSITIVE 237 86 45 129 93 NC_009009:SSA_0017|3end_Cell_shape_determining_protein_MreC,_putative_23706..23856_POSITIVE 234 94 52 88 42 NC_009009:SSA_2157|3end_ATP-dependent_serine_protease,_putative_2157048..2157198_NEGATIVE 229 53 11 75 31 NC_009009:SSA_2161|3end_NTP_pyrophosphohydrolases_including_oxidative_damage_repair_enzymes,_putative_2160151..2160301_NEGATIVE 227 107 64 40 6 NC_009009:SSA_2142|3end_Argininosuccinate_synthase,_putative_2142216..2142366_NEGATIVE 227 53 15 151 117 NC_009009:SSA_0319|3end_Branched-chain_amino_acid_permease_(L-methionine,_L-isoleucine,_leucine_and_valine),_putative_313496..313646_POSITIVE 223 80 36 104 56 NC_009009:SSA_1679|3end_ABC-type_multidrug_transport_system,_ATPase_component,_putative_1672183..1672333_NEGATIVE 222 85 44 51 9 NC_009009:SSA_2308|3end_hypothetical_protein_2309893..2310043_NEGATIVE 221 96 52 111 59 NC_009009:SSA_1406|3end_Histone_acetyltransferase_HPA2,_putative_1419455..1419605_NEGATIVE 219 109 75 131 103 NC_009009:SSA_1452|3end_Second_subunit_of_major_exonuclease,_putative_1456415..1456565_NEGATIVE 219 34 3 117 87 NC_009009:SSA_0244|3end_hypothetical_protein_239170..239320_POSITIVE 218 109 62 148 99 NC_009009:SSA_1124|3end_Oxidoreductase,_putative_1148547..1148697_NEGATIVE 215 112 75 147 102 NC_009009:SSA_2321|3end_Cation_(Co/Zn/Cd)_efflux_protein,_putative_2326050..2326200_NEGATIVE 212 108 67 64 20 NC_009009:SSA_0675|3end_Exodeoxyribonuclease_VII_small_subunit,_putative_658681..658831_POSITIVE 210 115 74 45 8 NC_009009:SSA_2030|3end_hypothetical_protein_2036514..2036664_NEGATIVE 209 99 57 93 44 NC_009009:SSA_0232|3end_hypothetical_protein_227277..227427_POSITIVE 208 89 42 66 11 NC_009009:SSA_2124|3end_Dehydrogenase,_eukaryotic-like,_putative_2128557..2128707_NEGATIVE 207 69 50 55 37 NC_009009:SSA_0355|3end_DNA_mismatch_repair_protein,_putative_349260..349410_POSITIVE 206 109 64 142 99 NC_009009:SSA_0515|3end_Propanediol_utilization_protein_PduU,_putative_514540..514690_POSITIVE