Origin IGS: aaagcacgtcgttgctttttatttttaccctttttatcttgttttgaaaaagatttagtaggtctgaaaattttaccactagctgccaatgaatcctcgtcttataaccttgtataagaaaaagttataggctgggcacagatttttttggtataatgaaaaagataatgaaaaagaaatgagaatgac .........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 gtcattctcatttctttttcattatctttttcattataccaaaaaaatctgtgcccagcctataactttttcttatacaaggttataagacgaggattcattggcagctagtggtaaaattttcagacctactaaatctttttcaaaacaagataaaaagggtaaaaataaaaagcaacgacgtgcttt Mask Tandem Repeat Region ================================================ aaagcacgtcgttgctttttatttttaccctttttatcttgttttgaaaaagatttagtaggtctgaaaattttaccactagctgccaatgaatcctcgtcttataaccttgtataagaaaaagttataggctgggcacagatttttttggtnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngaatgac Find is-nt database================================================ Query_seq: SSA_0670:SSA_0671|SSA_0670:SSA_0671:Conserved uncharacterized protein:Methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase, putative:->->:654291..654479 189 aaagcacgtcgttgctttttatttttaccctttttatcttgttttgaaaaagatttagtaggtctgaaaattttaccactagctgccaatgaatcctcgtcttataaccttgtataagaaaaagttataggctgggcacagatttttttggtataatgaaaaagataatgaaaaagaaatgagaatgac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0670:SSA_0671|SSA_0670:SSA_0671:Conserved uncharacterized protein:Methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase, putative:->->:654291..654479 189 aaagcacgtcgttgctttttatttttaccctttttatcttgttttgaaaaagatttagtaggtctgaaaattttaccactagctgccaatgaatcctcgtcttataaccttgtataagaaaaagttataggctgggcacagatttttttggtataatgaaaaagataatgaaaaagaaatgagaatgac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0670:SSA_0671|SSA_0670:SSA_0671:Conserved uncharacterized protein:Methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase, putative:->->:654291..654479 189 aaagcacgtcgttgctttttatttttaccctttttatcttgttttgaaaaagatttagtaggtctgaaaattttaccactagctgccaatgaatcctcgtcttataaccttgtataagaaaaagttataggctgggcacagatttttttggtataatgaaaaagataatgaaaaagaaatgagaatgac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaagcacgtcgttgctttttatttttaccctttttatcttgttttgaaaaagatttagtaggtctgaaaattttaccactagctgccaatgaatcctcgtcttataaccttgtataagaaaaagttataggctgggcacagatttttttggtataatgaaaaagataatgaaaaagaaatgagaatgac Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: - Start: 82 End: 186 ................................................................................. S G I F G R R I V K Y L F F N Y A P C L N K Q Y L S F S L S F S I L M ... Protein_Len: 38 Strand: - Start: 2 End: 115 . L V D N S K I K V R K I K N Q F L N L L D S F K V V L Q W H I R T K Y G Q M .......................................................................... aaagcacgtcgttgctttttatttttaccctttttatcttgttttgaaaaagatttagtaggtctgaaaattttaccactagctgccaatgaatcctcgtcttataaccttgtataagaaaaagttataggctgggcacagatttttttggtataatgaaaaagataatgaaaaagaaatgagaatgac 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================================================ aaagcacgtcgttgctttttatttttaccctttttatcttgttttgaaaaagatttagtaggtctgaaaattttaccactagctgccaatgaatcctcgtcttataaccttgtataagaaaaagttataggctgggcacagatttttttggtataatgaaaaagataatgaaaaagaaatgagaatgac Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0670:SSA_0671|SSA_0670:SSA_0671:Conserved uncharacterized protein:Methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase, putative:->->:654291..654479 189 aaagcacgtcgttgctttttatttttaccctttttatcttgttttgaaaaagatttagtaggtctgaaaattttaccactagctgccaatgaatcctcgtcttataaccttgtataagaaaaagttataggctgggcacagatttttttggtataatgaaaaagataatgaaaaagaaatgagaatgac Intra-Species Hit: Count: 1 Min: 46 Max: 189 Len: 144 Subject: NC_009009_SSA_0670_SSA_0671|Conserved uncharacterized protein:Methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase, putative|POSITIVE:POSITIVE|[654291,654479]|189 HSP 1 e-value: 9.0E-64 bit: 244.0 Len: 144 Query Start:46 Query End:189 Subject Strand: POSITIVE Subject Start: 46 Subject End: 189 .............................................gaaaaagatttagtaggtctgaaaattttaccactagctgccaatgaatcctcgtcttataaccttgtataagaaaaagttataggctgggcacagannnnnnnggtataatgaaaaagataatgaaaaagaaatgagaatgac .............................................gaaaaagatttagtaggtctgaaaattttaccactagctgccaatgaatcctcgtcttataaccttgtataagaaaaagttataggctgggcacagatttttttggtataatgaaaaagataatgaaaaagaaatgagaatgac Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAAAAGAUUUAGUAGGUCUGAAAAUUUUACCACUAGCUGCCAAUGAAUCCUCGUCUUAUAACCUUGUAUAAGAAAAAGUUAUAGGCUGGGCACAGAUUUUUUUGGUAUAAUGAAAAAGAUAAUGAAAAAGAAAUGAGAAUGAC .........(((((.(((..((...))..)))))))).((((((.(((((((((.((((((((.((.........)).)))))))).))))....)))))..)))))).................................... (-21.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUCAUUCUCAUUUCUUUUUCAUUAUCUUUUUCAUUAUACCAAAAAAAUCUGUGCCCAGCCUAUAACUUUUUCUUAUACAAGGUUAUAAGACGAGGAUUCAUUGGCAGCUAGUGGUAAAAUUUUCAGACCUACUAAAUCUUUUUC ........................(((.....(((.(((((.......(((.((...(((.....((((.(((((((......))))))).)))).......))).)))))))))).)))....)))................. (-16.61) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 288 58 33 186 156 NC_009009:SSA_2103|5end_hypothetical_protein_2106700..2106930_NEGATIVE 286 90 43 119 79 NC_009009:SSA_2330|5end_Acetyltransferase,_putative_2333655..2333885_NEGATIVE 276 59 15 51 15 NC_009009:SSA_0835|5end_Accessory_secretory_protein_Asp3,_putative_821036..821266_POSITIVE 260 49 9 141 92 NC_009009:SSA_0689|5end_Penicillin-binding_protein_2B,_putative_672262..672492_POSITIVE 253 110 63 193 144 NC_009009:SSA_2233|5end_hypothetical_protein_2233110..2233340_NEGATIVE 251 75 33 62 11 NC_009009:SSA_1452|5end_Second_subunit_of_major_exonuclease,_putative_1459696..1459926_NEGATIVE 251 56 12 156 112 NC_009009:SSA_1132|5end_TatC,_sec-independent_protein_translocase,_putative_1158645..1158875_POSITIVE 250 60 18 148 104 NC_009009:SSA_1040|5end_Sugar_ABC_transporter,_permease_protein,_putative_1055302..1055532_POSITIVE 248 43 6 90 49 NC_009009:SSA_2024|5end_hypothetical_protein_2029272..2029502_NEGATIVE 245 79 37 114 66 NC_009009:SSA_1493|5end_hypothetical_protein_1499480..1499710_NEGATIVE 243 74 35 71 37 NC_009009:SSA_1679|5end_ABC-type_multidrug_transport_system,_ATPase_component,_putative_1673049..1673279_NEGATIVE 239 52 15 177 140 NC_009009:SSA_1395|5end_hypothetical_protein_1409773..1410003_NEGATIVE 238 95 52 218 179 NC_009009:SSA_1953|5end_NifU_family_protein,_putative_1950079..1950309_NEGATIVE 237 118 76 198 155 NC_009009:SSA_0751|5end_Oligoendopeptidase_F,_putative_732367..732597_POSITIVE 235 100 51 154 101 NC_009009:SSA_2241|5end_Conserved_uncharacterized_protein_2237943..2238173_NEGATIVE 235 55 11 91 46 NC_009009:SSA_1661|5end_hypothetical_protein_1658004..1658234_NEGATIVE 234 50 16 227 191 NC_009009:SSA_0883|5end_Glycerate_kinase,_putative_877560..877790_POSITIVE 233 58 13 210 173 NC_009009:SSA_2091|5end_Phosphotransferase_system_sugar-specific_EII_component,_putative_2095562..2095792_NEGATIVE 230 107 61 74 24 NC_009009:SSA_1649|5end_hypothetical_protein_1648886..1649116_NEGATIVE 230 68 34 221 182 NC_009009:SSA_0854|5end_hypothetical_protein_841335..841565_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 294 130 83 61 10 NC_009009:SSA_0889|3end_Isoleucyl-tRNA_synthetase,_putative_882763..882913_NEGATIVE 288 58 33 130 100 NC_009009:SSA_2105|3end_hypothetical_protein_2106756..2106906_NEGATIVE 286 90 43 78 38 NC_009009:SSA_2331|3end_D-alanine_transfer_protein,_putative_2333696..2333846_NEGATIVE 285 43 9 102 56 NC_009009:SSA_0531|3end_Ethanolamine_utilization_protein_eutQ_(cobalamin-dependent_degradation_of_ethanolamine),_putative_527884..528034_POSITIVE 276 59 15 54 18 NC_009009:SSA_0834|3end_Accessory_secretory_protein_Asp2,_putative_821119..821269_POSITIVE 266 60 15 125 79 NC_009009:SSA_1495|3end_S-adenosylmethionine_synthetase,_putative_1501019..1501169_NEGATIVE 253 110 63 62 13 NC_009009:SSA_2234|3end_Phosphatidylserine/phosphatidylglycerophosphate/_cardiolipin_synthase,_phospholipase_D_family,_putative_2233241..2233391_NEGATIVE 245 79 37 80 32 NC_009009:SSA_1494|3end_Conserved_uncharacterized_protein_1499514..1499664_NEGATIVE 241 89 48 134 87 NC_009009:SSA_0967|3end_hypothetical_protein_976620..976770_POSITIVE 234 48 5 119 77 NC_009009:SSA_1120|3end_Two-component_sensor_kinase_(with_C-terminal_ATPase_domain),_putative_1147005..1147155_POSITIVE 233 58 13 75 38 NC_009009:SSA_2092|3end_Phosphotransferase_system_sugar-specific_EII_component,_putative_2095697..2095847_NEGATIVE 232 58 18 149 111 NC_009009:SSA_1039|3end_Sugar_ABC_transporter,_ATP-binding_protein,_putative_1055389..1055539_POSITIVE 232 90 50 54 14 NC_009009:SSA_0638|3end_Tryptophan_synthase_alpha_chain,_putative_627794..627944_POSITIVE 230 107 61 64 14 NC_009009:SSA_1650|3end_3-Ketoacyl-ACP_reductase,_putative_1648896..1649046_NEGATIVE 226 107 66 83 39 NC_009009:SSA_0098|3end_Hydrolase,_haloacid_dehalogenase-like_family,_putative_100116..100266_POSITIVE 225 68 29 91 43 NC_009009:SSA_2125|3end_Small_primase-like_protein_(Toprim_domain),_putative_2129423..2129573_NEGATIVE 225 69 32 37 7 NC_009009:SSA_1076|3end_hypothetical_protein_1095047..1095197_POSITIVE 223 74 36 81 46 NC_009009:SSA_1836|3end_Superfamily_II_ATP-dependent_DNA/RNA_helicase_required_for_DNA_uptake_(late_competence_protein),_putative_1830938..1831088_NEGATIVE 220 127 82 75 34 NC_009009:SSA_0050|3end_Dihydroxyacetone_kinase,_phosphatase_domain_(Dak2),_putative_55270..55420_POSITIVE 219 64 35 114 82 NC_009009:SSA_1824|3end_hypothetical_protein_1812516..1812666_NEGATIVE