Origin IGS: aatttacctccatttttcaaaaaagattgtatcacatctagtcagaaattgctgatttctgctacgctttttttcttcagtatttttagccttactttttatacagaatgtccatttttaagcaagattttcgcagttccagtcattctgtgttatactaagtttcgttatttattttaggagggcaaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tttgccctcctaaaataaataacgaaacttagtataacacagaatgactggaactgcgaaaatcttgcttaaaaatggacattctgtataaaaagtaaggctaaaaatactgaagaaaaaaagcgtagcagaaatcagcaatttctgactagatgtgatacaatcttttttgaaaaatggaggtaaatt Mask Tandem Repeat Region ================================================ aatttacctccatttttcaaaaaagattgtatcacatctagtcagaaattgctgatttctgctacgctttttttcttcagtatttttagccttactttttatacagaatgtccatttttaagcaagattttcgcagttccagtcattctgtgttatactaagtttcgttatttattttaggagggcaaa Find is-nt database================================================ Query_seq: SSA_0814:SSA_0815|SSA_0814:SSA_0815:Oxidoreductase, pyridine nucleotide-disulfide, class I, putative:hypothetical protein:<-->:796926..797114 189 aatttacctccatttttcaaaaaagattgtatcacatctagtcagaaattgctgatttctgctacgctttttttcttcagtatttttagccttactttttatacagaatgtccatttttaagcaagattttcgcagttccagtcattctgtgttatactaagtttcgttatttattttaggagggcaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0814:SSA_0815|SSA_0814:SSA_0815:Oxidoreductase, pyridine nucleotide-disulfide, class I, putative:hypothetical protein:<-->:796926..797114 189 aatttacctccatttttcaaaaaagattgtatcacatctagtcagaaattgctgatttctgctacgctttttttcttcagtatttttagccttactttttatacagaatgtccatttttaagcaagattttcgcagttccagtcattctgtgttatactaagtttcgttatttattttaggagggcaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0814:SSA_0815|SSA_0814:SSA_0815:Oxidoreductase, pyridine nucleotide-disulfide, class I, putative:hypothetical protein:<-->:796926..797114 189 aatttacctccatttttcaaaaaagattgtatcacatctagtcagaaattgctgatttctgctacgctttttttcttcagtatttttagccttactttttatacagaatgtccatttttaagcaagattttcgcagttccagtcattctgtgttatactaagtttcgttatttattttaggagggcaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatttacctccatttttcaaaaaagattgtatcacatctagtcagaaattgctgatttctgctacgctttttttcttcagtatttttagccttactttttatacagaatgtccatttttaagcaagattttcgcagttccagtcattctgtgttatactaagtttcgttatttattttaggagggcaaa Predict ORF larger than 30AA ================================================ Protein_Len: 49 Strand: + Start: 31 End: 177 .............................. M T S S Q K L L I S A T L F F F S I F S L T F Y T E C P F L S K I F A V P V I L C Y T K F R Y L F ............ Protein_Len: 32 Strand: - Start: 7 End: 102 ...... R W K E F F I T D C R T L F Q Q N R S R K K E E T N K A K S K M ....................................................................................... aatttacctccatttttcaaaaaagattgtatcacatctagtcagaaattgctgatttctgctacgctttttttcttcagtatttttagccttactttttatacagaatgtccatttttaagcaagattttcgcagttccagtcattctgtgttatactaagtttcgttatttattttaggagggcaaa 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================================================ aatttacctccatttttcaaaaaagattgtatcacatctagtcagaaattgctgatttctgctacgctttttttcttcagtatttttagccttactttttatacagaatgtccatttttaagcaagattttcgcagttccagtcattctgtgttatactaagtttcgttatttattttaggagggcaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0814:SSA_0815|SSA_0814:SSA_0815:Oxidoreductase, pyridine nucleotide-disulfide, class I, putative:hypothetical protein:<-->:796926..797114 189 aatttacctccatttttcaaaaaagattgtatcacatctagtcagaaattgctgatttctgctacgctttttttcttcagtatttttagccttactttttatacagaatgtccatttttaagcaagattttcgcagttccagtcattctgtgttatactaagtttcgttatttattttaggagggcaaa Intra-Species Hit: Count: 1 Min: 1 Max: 189 Len: 189 Subject: NC_009009_SSA_0814_SSA_0815|Oxidoreductase, pyridine nucleotide-disulfide, class I, putative:hypothetical protein|NEGATIVE:POSITIVE|[796926,797114]|189 HSP 1 e-value: 2.0E-30 bit: 133.0 Len: 67 Query Start:1 Query End:67 Subject Strand: POSITIVE Subject Start: 1 Subject End: 67 aatttacctccatttttcaaaaaagattgtatcacatctagtcagaaattgctgatttctgctacgc.......................................................................................................................... aatttacctccatttttcaaaaaagattgtatcacatctagtcagaaattgctgatttctgctacgc.......................................................................................................................... HSP 2 e-value: 5.0E-25 bit: 115.0 Len: 58 Query Start:132 Query End:189 Subject Strand: POSITIVE Subject Start: 132 Subject End: 189 ...................................................................................................................................cgcagttccagtcattctgtgttatactaagtttcgttatttattttaggagggcaaa ...................................................................................................................................cgcagttccagtcattctgtgttatactaagtttcgttatttattttaggagggcaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUUACCUCCAUUUUUCAAAAAAGAUUGUAUCACAUCUAGUCAGAAAUUGCUGAUUUCUGCUACGCUUUUUUUCUUCAGUAUUUUUAGCCUUACUUUUUAUACAGAAUGUCCAUUUUUAAGCAAGAUUUUCGCAGUUCCAGUCAUUCUGUGUUAUACUAAGUUUCGUUAUUUAUUUUAGGAGGGCAAA ......(((((........(((((((.((((.((.....((((((......))))))..)).)))).)))))))............((((...((((...((((((((((.(.........((.........)).......).))))))))))......))))...)))).........)))))..... (-34.39) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUGCCCUCCUAAAAUAAAUAACGAAACUUAGUAUAACACAGAAUGACUGGAACUGCGAAAAUCUUGCUUAAAAAUGGACAUUCUGUAUAAAAAGUAAGGCUAAAAAUACUGAAGAAAAAAAGCGUAGCAGAAAUCAGCAAUUUCUGACUAGAUGUGAUACAAUCUUUUUUGAAAAAUGGAGGUAAAUU ((((((.(((..................(((((((...((((((((.(((.....((((.....)))).......))).))))))))......((.....))....)))))))...(((((((..((((((((((.....))))))).)))..((.....))..))))))).......))))))))).. (-36.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 832 80 31 171 122 NC_009009:SSA_0814|5end_Oxidoreductase,_pyridine_nucleotide-disulfide,_class_I,_putative_796835..797065_NEGATIVE 297 170 121 84 35 NC_009009:SSA_1270|5end_Flavodoxin_1293916..1294146_NEGATIVE 297 100 56 104 65 NC_009009:SSA_0973|5end_hypothetical_protein_980296..980526_POSITIVE 289 80 37 67 32 NC_009009:SSA_0487|5end_Delta-aminolevulinic_acid_dehydratase,_putative_487349..487579_POSITIVE 275 150 111 95 57 NC_009009:SSA_1910|5end_hypothetical_protein_1902672..1902902_NEGATIVE 273 170 121 48 9 NC_009009:SSA_2045|5end_Reductase,_putative_2048948..2049178_NEGATIVE 272 90 48 88 56 NC_009009:SSA_0539|5end_PduO_protein,_putative_534233..534463_POSITIVE 271 97 52 72 19 NC_009009:SSA_2011|5end_ABC-type_multidrug_transport_system,_ATPase_component,_putative_2012856..2013086_NEGATIVE 266 99 51 208 151 NC_009009:SSA_2123|5end_Dimethyladenosine_transferase,_putative_2128536..2128766_NEGATIVE 264 167 121 57 7 NC_009009:SSA_0871|5end_Cell_division_protein_FtsX,_putative_863621..863851_POSITIVE 259 76 31 141 86 NC_009009:SSA_1131|5end_High-affinity_Fe_2+/Pb2+_permease,_putative_1157183..1157413_POSITIVE 258 90 48 158 121 NC_009009:SSA_0311|5end_hypothetical_protein_305877..306107_POSITIVE 257 99 60 125 79 NC_009009:SSA_2146|5end_Metallo-beta-lactamase,_putative_2148399..2148629_NEGATIVE 255 80 31 208 161 NC_009009:SSA_1649|5end_hypothetical_protein_1648886..1649116_NEGATIVE 254 78 32 106 45 NC_009009:SSA_2145|5end_Tributyrin_esterase,_putative_2146658..2146888_NEGATIVE 252 167 121 207 167 NC_009009:SSA_0570|5end_Glutamyl-tRNA(Gln)_amidotransferase_subunit_A,_putative_563915..564145_POSITIVE 248 96 51 128 88 NC_009009:SSA_0441|5end_hypothetical_protein_441481..441711_POSITIVE 248 74 31 66 27 NC_009009:SSA_0419|5end_Alpha-galactosidase,_putative_416213..416443_POSITIVE 248 68 24 69 18 NC_009009:SSA_0412|5end_ABC-type_multidrug_transport_system_(3-component_subtilin_immunity_exporter),_ATPase_component,_putative_408163..408393_NEGATIVE 247 149 104 103 47 NC_009009:SSA_1113|5end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_domain_and_a_winged-helix_DNA-binding_domains),_putative_1139742..1139972_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 311 170 128 139 102 NC_009009:SSA_0913|3end_Acetyltransferase,_putative_924784..924934_POSITIVE 297 100 56 92 53 NC_009009:SSA_0972|3end_hypothetical_protein_980364..980514_POSITIVE 289 90 41 129 80 NC_009009:SSA_1230|3end_Conserved_uncharacterized_protein_1252612..1252762_NEGATIVE 289 80 37 80 45 NC_009009:SSA_0486|3end_Uroporphyrinogen-III_synthase,_putative_487442..487592_POSITIVE 275 150 111 102 64 NC_009009:SSA_1911|3end_Conserved_uncharacterized_protein_1902665..1902815_NEGATIVE 264 167 121 64 14 NC_009009:SSA_0870|3end_Cell_division_protein_FtsE,_putative_863708..863858_POSITIVE 258 175 133 52 7 NC_009009:SSA_2046|3end_Uridine_phosphorylase,_putative_2048957..2049107_NEGATIVE 250 100 58 53 15 NC_009009:SSA_0568|3end_Aspartyl-tRNA_synthetase_1,_putative_563490..563640_POSITIVE 246 98 51 75 27 NC_009009:SSA_0567|3end_Isochorismitase_family_protein,_putative_561442..561592_POSITIVE 245 72 32 122 67 NC_009009:SSA_0628|3end_Fe-S-cluster_redox_enzyme/radical_SAM_enzyme,_Cfr_family,_putative_619060..619210_POSITIVE 245 99 51 125 72 NC_009009:SSA_0502|3end_Peptide_ABC_transporter,_permease_protein,_putative_502323..502473_POSITIVE 244 100 51 83 39 NC_009009:SSA_0834|3end_Accessory_secretory_protein_Asp2,_putative_821119..821269_POSITIVE 242 80 32 134 82 NC_009009:SSA_1148|3end_Beta-glucosides_PTS,_EIIC,_putative_1178473..1178623_POSITIVE 240 87 51 36 2 NC_009009:SSA_2203|3end_30S_ribosomal_protein_S2,_putative_2203423..2203573_NEGATIVE 240 169 131 50 11 NC_009009:SSA_1682|3end_hypothetical_protein_1676130..1676280_NEGATIVE 240 88 47 77 39 NC_009009:SSA_0205|3end_NisK_(sensor-receptor_histidine_kinase_domain),_putative_203839..203989_POSITIVE 238 79 41 115 69 NC_009009:SSA_1448|3end_ATP_phosphoribosyltransferase_regulatory_subunit,_putative_1449828..1449978_NEGATIVE 237 89 48 143 93 NC_009009:SSA_2113|3end_hypothetical_protein_2116228..2116378_NEGATIVE 237 79 36 133 89 NC_009009:SSA_1372|3end_hypothetical_protein_1388946..1389096_NEGATIVE 237 100 52 46 1 NC_009009:SSA_0538|3end_PduH_protein,_putative_534254..534404_POSITIVE