Origin IGS: aagtgagaagattcgcgaacgaatcttctttattttgctctaaaaatggagtctttttttcaggtgtctatttttggacactatgcccctcaactacagtcatatccatggctaactaaatataaatgttgtataataccaattgctattaaatattaatataggagattct .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agaatctcctatattaatatttaatagcaattggtattatacaacatttatatttagttagccatggatatgactgtagttgaggggcatagtgtccaaaaatagacacctgaaaaaaagactccatttttagagcaaaataaagaagattcgttcgcgaatcttctcactt Mask Tandem Repeat Region ================================================ aagtgagaagattcgcgaacgaatcttctttattttgctctaaaaatggagtctttttttcaggtgtctatttttggacactatgcccctcaactacagtcatatccatggctaactaaatataaatgttgtataataccaattgctattaaatattaatataggagattct Find is-nt database================================================ Query_seq: SSA_0903:SSA_0904|SSA_0903:SSA_0904:NAD(P)H dehydrogenase (quinone), putative:CshA-like fibrillar surface protein A:->->:893874..894045 172 aagtgagaagattcgcgaacgaatcttctttattttgctctaaaaatggagtctttttttcaggtgtctatttttggacactatgcccctcaactacagtcatatccatggctaactaaatataaatgttgtataataccaattgctattaaatattaatataggagattct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0903:SSA_0904|SSA_0903:SSA_0904:NAD(P)H dehydrogenase (quinone), putative:CshA-like fibrillar surface protein A:->->:893874..894045 172 aagtgagaagattcgcgaacgaatcttctttattttgctctaaaaatggagtctttttttcaggtgtctatttttggacactatgcccctcaactacagtcatatccatggctaactaaatataaatgttgtataataccaattgctattaaatattaatataggagattct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0903:SSA_0904|SSA_0903:SSA_0904:NAD(P)H dehydrogenase (quinone), putative:CshA-like fibrillar surface protein A:->->:893874..894045 172 aagtgagaagattcgcgaacgaatcttctttattttgctctaaaaatggagtctttttttcaggtgtctatttttggacactatgcccctcaactacagtcatatccatggctaactaaatataaatgttgtataataccaattgctattaaatattaatataggagattct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aagtgagaagattcgcgaacgaatcttctttattttgctctaaaaatggagtctttttttcaggtgtctatttttggacactatgcccctcaactacagtcatatccatggctaactaaatataaatgttgtataataccaattgctattaaatattaatataggagattct Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 3 End: 116 .. M R R F A N E S S L F C S K N G V F F S G V Y F W T L C P S T T V I S M A N ........................................................ Protein_Len: 37 Strand: + Start: 46 End: 156 ............................................. M E S F F Q V S I F G H Y A P Q L Q S Y P W L T K Y K C C I I P I A I K Y ................ aagtgagaagattcgcgaacgaatcttctttattttgctctaaaaatggagtctttttttcaggtgtctatttttggacactatgcccctcaactacagtcatatccatggctaactaaatataaatgttgtataataccaattgctattaaatattaatataggagattct 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: 81 Start: 108 End: 137 ...........................................................................................................ATGGCTAACTAAATATAAATGTTGTATAAT................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aagtgagaagattcgcgaacgaatcttctttattttgctctaaaaatggagtctttttttcaggtgtctatttttggacactatgcccctcaactacagtcatatccatggctaactaaatataaatgttgtataataccaattgctattaaatattaatataggagattct Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0903:SSA_0904|SSA_0903:SSA_0904:NAD(P)H dehydrogenase (quinone), putative:CshA-like fibrillar surface protein A:->->:893874..894045 172 aagtgagaagattcgcgaacgaatcttctttattttgctctaaaaatggagtctttttttcaggtgtctatttttggacactatgcccctcaactacagtcatatccatggctaactaaatataaatgttgtataataccaattgctattaaatattaatataggagattct Intra-Species Hit: Count: 1 Min: 1 Max: 172 Len: 172 Subject: NC_009009_SSA_0903_SSA_0904|NAD(P)H dehydrogenase (quinone), putative:CshA-like fibrillar surface protein A|POSITIVE:POSITIVE|[893874,894045]|172 HSP 1 e-value: 2.0E-80 bit: 299.0 Len: 172 Query Start:1 Query End:172 Subject Strand: POSITIVE Subject Start: 1 Subject End: 172 aagtgagaagattcgcgaacgaatcttctttattttgctctaaaaatggagtcnnnnnnncaggtgtctatttttggacactatgcccctcaactacagtcatatccatggctaactaaatataaatgttgtataataccaattgctattaaatattaatataggagattct aagtgagaagattcgcgaacgaatcttctttattttgctctaaaaatggagtctttttttcaggtgtctatttttggacactatgcccctcaactacagtcatatccatggctaactaaatataaatgttgtataataccaattgctattaaatattaatataggagattct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGUGAGAAGAUUCGCGAACGAAUCUUCUUUAUUUUGCUCUAAAAAUGGAGUCUUUUUUUCAGGUGUCUAUUUUUGGACACUAUGCCCCUCAACUACAGUCAUAUCCAUGGCUAACUAAAUAUAAAUGUUGUAUAAUACCAAUUGCUAUUAAAUAUUAAUAUAGGAGAUUCU ....(((((((((((....)))))))))))......((((((....))))))..........((((((((....))))))))......(((......((((((....))))))......((((.((((((...(((((.(....).))))))))))).))))..)))..... (-38.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAAUCUCCUAUAUUAAUAUUUAAUAGCAAUUGGUAUUAUACAACAUUUAUAUUUAGUUAGCCAUGGAUAUGACUGUAGUUGAGGGGCAUAGUGUCCAAAAAUAGACACCUGAAAAAAAGACUCCAUUUUUAGAGCAAAAUAAAGAAGAUUCGUUCGCGAAUCUUCUCACUU .....(((((...........(((((.(....).))))).((.(((.(((((((((........))))))))).))).))..)))))....(((((........)))))..........(.(((........)))).......((((((((((....))))))))))..... (-34.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 313 42 5 215 168 NC_009009:SSA_0071|5end_N-acetylmannosamine-6-p_hosphate_2-epimerase_1,_putative_75210..75440_POSITIVE 293 109 64 91 49 NC_009009:SSA_1189|5end_GTP-binding_protein,_putative_1217657..1217887_NEGATIVE 289 113 74 65 29 NC_009009:SSA_1174|5end_Dihydrolipoamide_dehydrogenase,_putative_1202854..1203084_NEGATIVE 280 102 61 198 158 NC_009009:SSA_1076|5end_hypothetical_protein_1094227..1094457_POSITIVE 274 89 44 144 93 NC_009009:SSA_0452|5end_Nitrogen_utilization_substance_protein_B,_putative_451534..451764_POSITIVE 273 111 82 226 194 NC_009009:SSA_1878|5end_Conserved_uncharacterized_protein_1872200..1872430_NEGATIVE 266 110 62 130 73 NC_009009:SSA_0362|5end_Thioredoxin,_putative_353290..353520_POSITIVE 261 110 61 53 5 NC_009009:SSA_0483|5end_Siroheme_synthase,_putative_484045..484275_POSITIVE 260 80 37 86 43 NC_009009:SSA_2071|5end_hypothetical_protein_2074766..2074996_NEGATIVE 259 51 11 67 21 NC_009009:SSA_2279|5end_hypothetical_protein_2281910..2282140_NEGATIVE 257 99 55 188 146 NC_009009:SSA_0987|5end_ABC-type_choline_transporter,_membrane-spanning_permease,_putative_988994..989224_POSITIVE 255 118 76 75 35 NC_009009:SSA_0219|5end_PTS_system,_sugar-specific_enzyme_IIA_component,_putative_215367..215597_POSITIVE 254 102 61 100 42 NC_009009:SSA_1644|5end_hypothetical_protein_1645617..1645847_NEGATIVE 249 108 72 39 1 NC_009009:SSA_1828|5end_Glycerol_uptake_facilitator_protein,_putative_1818007..1818237_POSITIVE 249 120 80 102 57 NC_009009:SSA_0443|5end_Possible_ABC-type_efflux_pump_permease_component,_putative_442877..443107_POSITIVE 248 112 71 54 8 NC_009009:SSA_1454|5end_hypothetical_protein_1461100..1461330_NEGATIVE 247 102 63 223 180 NC_009009:SSA_1402|5end_ABC-type_multidrug_transport_system,_ATPase_and_permease_components,_putative_1416220..1416450_NEGATIVE 243 99 51 49 5 NC_009009:SSA_0458|5end_Formylmethionine_deformylase,_putative_461609..461839_POSITIVE 238 110 65 190 146 NC_009009:SSA_1940|5end_3-oxoacyl-[acyl-carrier-protein]_synthase_III,_putative_1927129..1927359_NEGATIVE 237 58 13 138 91 NC_009009:SSA_2230|5end_Ribonucleotide_reductase,_class_III,_anaerobic,_putative_2231158..2231388_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 281 36 1 91 56 NC_009009:SSA_0903|3end_NAD(P)H_dehydrogenase_(quinone),_putative_893813..893963_POSITIVE 274 122 86 146 109 NC_009009:SSA_0040|3end_Phosphoribosylaminoimidazole_carboxylase,_ATPase_subunit,_putative_47479..47629_POSITIVE 272 70 22 137 93 NC_009009:SSA_0146|3end_DNA_repair_ATPase,_putative_142159..142309_POSITIVE 260 80 37 52 9 NC_009009:SSA_2072|3end_Phosphatidate_cytidylyltransferase,_putative_2074800..2074950_NEGATIVE 259 51 11 65 19 NC_009009:SSA_2281|3end_hypothetical_protein_2281912..2282062_NEGATIVE 254 102 61 116 58 NC_009009:SSA_1645|3end_hypothetical_protein_1645601..1645751_NEGATIVE 253 57 11 105 70 NC_009009:SSA_2087|3end_Conserved_uncharacterized_protein_2091674..2091824_NEGATIVE 249 122 86 54 17 NC_009009:SSA_0042|3end_Amino_acid_recemase,_putative_48671..48821_POSITIVE 236 119 71 62 11 NC_009009:SSA_1593|3end_Dipeptidase,_putative_1596390..1596540_NEGATIVE 235 90 46 49 2 NC_009009:SSA_2317|3end_Tfp_pilus_assembly_protein,_pilus_retraction_ATPase_PilT,_putative_2318346..2318496_NEGATIVE 235 89 48 118 65 NC_009009:SSA_0268|3end_Phosphotransferase_system_(PTS)_cellobiose-specific_component_IIB,_putative_262621..262771_POSITIVE 230 68 24 137 98 NC_009009:SSA_1490|3end_Ribonuclease_BN,_putative_1495821..1495971_NEGATIVE 228 115 80 38 4 NC_009009:SSA_0478|3end_Cobalt_transport_protein_cbiN,_putative_480387..480537_POSITIVE 225 90 43 88 38 NC_009009:SSA_2228|3end_Acetyltransferase_(GNAT)_family,_putative_2228271..2228421_NEGATIVE 225 109 61 98 44 NC_009009:SSA_0488|3end_Glutamate-1-semialdehyde_2,1-aminotransferase,_putative_489742..489892_POSITIVE 224 95 62 135 97 NC_009009:SSA_2303|3end_hypothetical_protein_2304113..2304263_NEGATIVE 224 99 54 132 85 NC_009009:SSA_0674|3end_Exodeoxyribonuclease_VII_large_subunit,_putative_658491..658641_POSITIVE 224 69 24 145 101 NC_009009:SSA_0467|3end_Cobalt-precorrin-6A_synthase_[deacetylating],_putative_471795..471945_POSITIVE 223 89 48 106 59 NC_009009:SSA_1408|3end_hypothetical_protein_1420406..1420556_NEGATIVE 223 89 43 103 54 NC_009009:SSA_0046|3end_Adenylosuccinate_lyase,_putative_52269..52419_POSITIVE