Origin IGS: ctttccctcctaatttcttgctagttacattataccaaaaaagtcgcatgcttgtttatcatcctcagtctgaggtaggatttttctggaaaagataaaatctcttagaaaaatatgctatactaactagtagaaattggagacgaaat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atttcgtctccaatttctactagttagtatagcatatttttctaagagattttatcttttccagaaaaatcctacctcagactgaggatgataaacaagcatgcgacttttttggtataatgtaactagcaagaaattaggagggaaag Mask Tandem Repeat Region ================================================ ctttccctcctaatttcttgctagttacattataccaaaaaagtcgcatgcttgtttatcatcctcagtctgaggtaggatttttctggaaaagataaaatctcttagaaaaatatgctatactaactagtagaaattggagacgaaat Find is-nt database================================================ Query_seq: SSA_1685:SSA_1686|SSA_1685:SSA_1686:Two-component response transcriptional regulator (CheY-like receiver and winged-helix DNA-binding domains), putative:hypothetical protein:<-->:1679167..1679315 149 ctttccctcctaatttcttgctagttacattataccaaaaaagtcgcatgcttgtttatcatcctcagtctgaggtaggatttttctggaaaagataaaatctcttagaaaaatatgctatactaactagtagaaattggagacgaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1685:SSA_1686|SSA_1685:SSA_1686:Two-component response transcriptional regulator (CheY-like receiver and winged-helix DNA-binding domains), putative:hypothetical protein:<-->:1679167..1679315 149 ctttccctcctaatttcttgctagttacattataccaaaaaagtcgcatgcttgtttatcatcctcagtctgaggtaggatttttctggaaaagataaaatctcttagaaaaatatgctatactaactagtagaaattggagacgaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1685:SSA_1686|SSA_1685:SSA_1686:Two-component response transcriptional regulator (CheY-like receiver and winged-helix DNA-binding domains), putative:hypothetical protein:<-->:1679167..1679315 149 ctttccctcctaatttcttgctagttacattataccaaaaaagtcgcatgcttgtttatcatcctcagtctgaggtaggatttttctggaaaagataaaatctcttagaaaaatatgctatactaactagtagaaattggagacgaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctttccctcctaatttcttgctagttacattataccaaaaaagtcgcatgcttgtttatcatcctcagtctgaggtaggatttttctggaaaagataaaatctcttagaaaaatatgctatactaactagtagaaattggagacgaaat Predict ORF larger than 30AA ================================================ ctttccctcctaatttcttgctagttacattataccaaaaaagtcgcatgcttgtttatcatcctcagtctgaggtaggatttttctggaaaagataaaatctcttagaaaaatatgctatactaactagtagaaattggagacgaaat 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================================================ ctttccctcctaatttcttgctagttacattataccaaaaaagtcgcatgcttgtttatcatcctcagtctgaggtaggatttttctggaaaagataaaatctcttagaaaaatatgctatactaactagtagaaattggagacgaaat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1685:SSA_1686|SSA_1685:SSA_1686:Two-component response transcriptional regulator (CheY-like receiver and winged-helix DNA-binding domains), putative:hypothetical protein:<-->:1679167..1679315 149 ctttccctcctaatttcttgctagttacattataccaaaaaagtcgcatgcttgtttatcatcctcagtctgaggtaggatttttctggaaaagataaaatctcttagaaaaatatgctatactaactagtagaaattggagacgaaat Intra-Species Hit: Count: 1 Min: 1 Max: 149 Len: 149 Subject: NC_009009_SSA_1685_SSA_1686|Two-component response transcriptional regulator (CheY-like receiver and winged-helix DNA-binding domains), putative:hypothetical protein|NEGATIVE:POSITIVE|[1679167,1679315]|149 HSP 1 e-value: 2.0E-79 bit: 295.0 Len: 149 Query Start:1 Query End:149 Subject Strand: POSITIVE Subject Start: 1 Subject End: 149 ctttccctcctaatttcttgctagttacattataccaaaaaagtcgcatgcttgtttatcatcctcagtctgaggtaggatttttctggaaaagataaaatctcttagaaaaatatgctatactaactagtagaaattggagacgaaat ctttccctcctaatttcttgctagttacattataccaaaaaagtcgcatgcttgtttatcatcctcagtctgaggtaggatttttctggaaaagataaaatctcttagaaaaatatgctatactaactagtagaaattggagacgaaat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUUCCCUCCUAAUUUCUUGCUAGUUACAUUAUACCAAAAAAGUCGCAUGCUUGUUUAUCAUCCUCAGUCUGAGGUAGGAUUUUUCUGGAAAAGAUAAAAUCUCUUAGAAAAAUAUGCUAUACUAACUAGUAGAAAUUGGAGACGAAAU .((((.((((.(((((((.((((((((......((.......)).....((.(((((.((..((((.....))))..((((((((((.....))).)))))))....)).))))).)).....)))))))))))))))))))..)))). (-34.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUCGUCUCCAAUUUCUACUAGUUAGUAUAGCAUAUUUUUCUAAGAGAUUUUAUCUUUUCCAGAAAAAUCCUACCUCAGACUGAGGAUGAUAAACAAGCAUGCGACUUUUUUGGUAUAAUGUAACUAGCAAGAAAUUAGGAGGGAAAG .((((.((((((((((((.(((((((((((.((..(((((((((((((((...)))))))..))))))))....((((.....))))...........)))))).(((.....)))......)))))))..))))))).))))))))). (-39.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 907 90 41 181 132 NC_009009:SSA_1685|5end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_winged-helix_DNA-binding_domains),_putative_1679076..1679306_NEGATIVE 340 80 31 170 121 NC_009009:SSA_1869|5end_ATP-dependent_RNA_helicase,_putative_1865495..1865725_NEGATIVE 335 90 43 71 22 NC_009009:SSA_2257|5end_DNA_mismatch_repair_protein,_putative_2253184..2253414_NEGATIVE 309 88 43 70 30 NC_009009:SSA_0481|5end_Cobyric_acid_synthase,_putative_481962..482192_POSITIVE 294 86 42 148 97 NC_009009:SSA_0990|5end_hypothetical_protein_991733..991963_POSITIVE 288 76 34 75 36 NC_009009:SSA_0487|5end_Delta-aminolevulinic_acid_dehydratase,_putative_487349..487579_POSITIVE 287 88 42 45 3 NC_009009:SSA_2317|5end_Tfp_pilus_assembly_protein,_pilus_retraction_ATPase_PilT,_putative_2319410..2319640_NEGATIVE 271 78 36 45 1 NC_009009:SSA_0537|5end_Propanediol_utilization:dioldehydratase_reactivation,_putative_531957..532187_POSITIVE 269 80 42 162 124 NC_009009:SSA_1563|5end_Metal-dependent_hydrolase,_beta-lactamase_superfamily_I,_putative_1567256..1567486_NEGATIVE 269 89 41 43 1 NC_009009:SSA_0631|5end_Tryptophan_synthase_beta_chain,_putative_619872..620102_POSITIVE 268 81 44 43 3 NC_009009:SSA_2200|5end_Firmicutes_transcriptional_repressor_of_class_III_stress_genes_(CtsR),_putative_2201573..2201803_NEGATIVE 267 110 62 106 57 NC_009009:SSA_0465|5end_Precorrin-8X_methylmutase_/_precorrin_isomerase,_putative_469185..469415_POSITIVE 267 45 2 142 92 NC_009009:SSA_0341|5end_hypothetical_protein_334731..334961_NEGATIVE 262 90 42 197 149 NC_009009:SSA_1479|5end_Transposase,_putative_1483180..1483410_POSITIVE 260 74 43 63 16 NC_009009:SSA_1092|5end_Dihydrofolate_reductase,_putative_1109599..1109829_POSITIVE 258 89 46 179 141 NC_009009:SSA_0512|5end_Nicotinate-nucleotide--dimethylbenzimidazole_phosphoribosyltransferase,_putative_510439..510669_POSITIVE 258 80 46 56 25 NC_009009:SSA_0282|5end_Phosphotransferase_system_(PTS),_cellobiose-specific_IIA_component,_putative_274215..274445_POSITIVE 254 90 41 203 139 NC_009009:SSA_1197|5end_DNA_alkylation_repair_enzyme,_putative_1222699..1222929_NEGATIVE 250 79 42 118 81 NC_009009:SSA_0093|5end_V-type_sodium_ATPase,_subunit_D,_putative_94286..94516_POSITIVE 249 90 44 226 181 NC_009009:SSA_1574|5end_Glycosyl_transferase,_family_1,_putative_1577930..1578160_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 340 80 31 65 16 NC_009009:SSA_1870|3end_Phospho-N-acetylmuramoyl-pentapeptide-_transferase,_putative_1865600..1865750_NEGATIVE 316 89 43 121 69 NC_009009:SSA_0917|3end_Cobalamin-independent_methionine_synthase_II,_putative_929087..929237_NEGATIVE 309 88 43 85 45 NC_009009:SSA_0480|3end_Cobalt_ABC_transporter,_ATP-binding_protein,_putative_482057..482207_POSITIVE 294 86 42 151 100 NC_009009:SSA_0989|3end_Conserved_protein,_possible_transcriptional_regulator_(sigma-70,_region_4),_putative_991816..991966_POSITIVE 288 76 34 88 49 NC_009009:SSA_0486|3end_Uroporphyrinogen-III_synthase,_putative_487442..487592_POSITIVE 287 88 42 43 1 NC_009009:SSA_2318|3end_PilB-like_pili_biogenesis_ATPase,_putative_2319412..2319562_NEGATIVE 269 90 44 85 41 NC_009009:SSA_1269|3end_hypothetical_protein_1291970..1292120_NEGATIVE 267 110 62 96 47 NC_009009:SSA_0464|3end_Cobalamin_biosynthesis_protein_cobD,_putative_469255..469405_POSITIVE 264 88 48 149 104 NC_009009:SSA_0931|3end_hypothetical_protein_941335..941485_POSITIVE 262 90 42 61 13 NC_009009:SSA_1478|3end_Transposase_ORF1,_putative_1483124..1483274_POSITIVE 253 79 42 151 114 NC_009009:SSA_1564|3end_Histidine_kinase,_putative_1567266..1567416_NEGATIVE 251 87 41 88 24 NC_009009:SSA_2126|3end_hypothetical_protein_2129985..2130135_NEGATIVE 250 79 42 121 84 NC_009009:SSA_0092|3end_V-type_sodium_ATPase,_subunit_B,_putative_94369..94519_POSITIVE 248 60 14 127 76 NC_009009:SSA_0325|3end_Membrane-anchored_glycerophosphoryl_diester_phosphodiesterase,_putative_319437..319587_POSITIVE 246 91 52 137 91 NC_009009:SSA_1318|3end_GTP-binding_protein_lepA,_putative_1333989..1334139_NEGATIVE 246 80 50 46 11 NC_009009:SSA_1234|3end_5'-nucleotidase,_putative_1257636..1257786_NEGATIVE 246 90 42 81 35 NC_009009:SSA_0885|3end_hypothetical_protein_879065..879215_NEGATIVE 245 90 62 134 99 NC_009009:SSA_2257|3end_DNA_mismatch_repair_protein,_putative_2251241..2251391_NEGATIVE 240 46 2 63 20 NC_009009:SSA_0348|3end_CAAX_amino_terminal_protease_family,_putative_341114..341264_POSITIVE 238 89 44 135 100 NC_009009:SSA_1150|3end_Tautomerase,_putative_1179894..1180044_NEGATIVE