Origin IGS: aaaaaacttactgattttgacccaagtcatgatataataagaatagcaaataaaacaaaaaccaaaagacataatcttggaaagttttattggaggaaagaaaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttttctttcctccaataaaactttccaagattatgtcttttggtttttgttttatttgctattcttattatatcatgacttgggtcaaaatcagtaagtttttt Mask Tandem Repeat Region ================================================ aaaaaacttactgattttgacccaagtcatgatataataagaatagcaaataaaacaaaaaccaaaagacataatcttggaaagttttattggaggaaagaaaa Find is-nt database================================================ Query_seq: SSA_0958:SSA_0959|SSA_0958:SSA_0959:hypothetical protein:Two-component response transcriptional regulator (CheY-like receiver domain and a winged-helix DNA-binding domains), putative:->->:967878..967981 104 aaaaaacttactgattttgacccaagtcatgatataataagaatagcaaataaaacaaaaaccaaaagacataatcttggaaagttttattggaggaaagaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0958:SSA_0959|SSA_0958:SSA_0959:hypothetical protein:Two-component response transcriptional regulator (CheY-like receiver domain and a winged-helix DNA-binding domains), putative:->->:967878..967981 104 aaaaaacttactgattttgacccaagtcatgatataataagaatagcaaataaaacaaaaaccaaaagacataatcttggaaagttttattggaggaaagaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0958:SSA_0959|SSA_0958:SSA_0959:hypothetical protein:Two-component response transcriptional regulator (CheY-like receiver domain and a winged-helix DNA-binding domains), putative:->->:967878..967981 104 aaaaaacttactgattttgacccaagtcatgatataataagaatagcaaataaaacaaaaaccaaaagacataatcttggaaagttttattggaggaaagaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaaaacttactgattttgacccaagtcatgatataataagaatagcaaataaaacaaaaaccaaaagacataatcttggaaagttttattggaggaaagaaaa Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: - Start: 1 End: 90 F F K S I K V W T M I Y Y S Y C I F C F G F S M I K S L K M .............. aaaaaacttactgattttgacccaagtcatgatataataagaatagcaaataaaacaaaaaccaaaagacataatcttggaaagttttattggaggaaagaaaa 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================================================ aaaaaacttactgattttgacccaagtcatgatataataagaatagcaaataaaacaaaaaccaaaagacataatcttggaaagttttattggaggaaagaaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0958:SSA_0959|SSA_0958:SSA_0959:hypothetical protein:Two-component response transcriptional regulator (CheY-like receiver domain and a winged-helix DNA-binding domains), putative:->->:967878..967981 104 aaaaaacttactgattttgacccaagtcatgatataataagaatagcaaataaaacaaaaaccaaaagacataatcttggaaagttttattggaggaaagaaaa Intra-Species Hit: Count: 1 Min: 1 Max: 104 Len: 104 Subject: NC_009009_SSA_0958_SSA_0959|hypothetical protein:Two-component response transcriptional regulator (CheY-like receiver domain and a winged-helix DNA-binding domains), putative|POSITIVE:POSITIVE|[967878,967981]|104 HSP 1 e-value: 1.0E-52 bit: 206.0 Len: 104 Query Start:1 Query End:104 Subject Strand: POSITIVE Subject Start: 1 Subject End: 104 aaaaaacttactgattttgacccaagtcatgatataataagaatagcaaataaaacaaaaaccaaaagacataatcttggaaagttttattggaggaaagaaaa aaaaaacttactgattttgacccaagtcatgatataataagaatagcaaataaaacaaaaaccaaaagacataatcttggaaagttttattggaggaaagaaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAAACUUACUGAUUUUGACCCAAGUCAUGAUAUAAUAAGAAUAGCAAAUAAAACAAAAACCAAAAGACAUAAUCUUGGAAAGUUUUAUUGGAGGAAAGAAAA ......((((...(((.((((....)))).)))....)))).......((((((((.....(((..(((.....))))))...))))))))............. (-11.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUCUUUCCUCCAAUAAAACUUUCCAAGAUUAUGUCUUUUGGUUUUUGUUUUAUUUGCUAUUCUUAUUAUAUCAUGACUUGGGUCAAAAUCAGUAAGUUUUUU .............((((((((...((((((.......)))))).....)))))))).......((((((......((((....)))).....))))))...... (-14.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 213 49 11 173 138 NC_009009:SSA_2334|5end_D-alanine--D-alanyl_carrier_protein_ligase,_putative_2338007..2338237_NEGATIVE 213 94 60 176 136 NC_009009:SSA_1352|5end_hypothetical_protein_1367941..1368171_NEGATIVE 207 59 13 213 168 NC_009009:SSA_0585|5end_hypothetical_protein_576937..577167_POSITIVE 195 46 15 231 200 NC_009009:SSA_2066|5end_DNA_polymerase_III_polC-type,_putative_2070137..2070367_NEGATIVE 187 35 7 175 140 NC_009009:SSA_0538|5end_PduH_protein,_putative_533794..534024_POSITIVE 185 31 5 58 18 NC_009009:SSA_0570|5end_Glutamyl-tRNA(Gln)_amidotransferase_subunit_A,_putative_563915..564145_POSITIVE 183 34 10 188 166 NC_009009:SSA_1746|5end_hypothetical_protein_1732945..1733175_NEGATIVE 182 30 7 70 41 NC_009009:SSA_1914|5end_hypothetical_protein_1905195..1905425_NEGATIVE 178 46 10 83 50 NC_009009:SSA_1705|5end_hypothetical_protein_1696853..1697083_NEGATIVE 178 41 10 183 146 NC_009009:SSA_1516|5end_Cell-wall_biogenesis_glycosyltransferase,_putative_1522833..1523063_NEGATIVE 177 62 21 56 15 NC_009009:SSA_0832|5end_SecY-like_protein,_putative_816708..816938_POSITIVE 174 28 1 137 107 NC_009009:SSA_0658|5end_Conserved_uncharacterized_protein_642126..642356_POSITIVE 172 47 11 228 194 NC_009009:SSA_2002|5end_tRNA_pseudouridine_synthase_A,_putative_1998959..1999189_NEGATIVE 172 49 6 163 121 NC_009009:SSA_0441|5end_hypothetical_protein_441481..441711_POSITIVE 170 37 10 148 112 NC_009009:SSA_1854|5end_Conserved_uncharacterized_protein_1850884..1851114_NEGATIVE 169 47 15 126 92 NC_009009:SSA_2124|5end_Dehydrogenase,_eukaryotic-like,_putative_2129411..2129641_NEGATIVE 168 32 11 56 38 NC_009009:SSA_0620|5end_hypothetical_protein_612325..612555_NEGATIVE 167 47 6 84 55 NC_009009:SSA_2054|5end_hypothetical_protein_2057899..2058129_NEGATIVE 167 30 2 147 122 NC_009009:SSA_0175|5end_Penicillin-binding_protein_1B,_putative_172152..172382_POSITIVE 162 24 4 223 201 NC_009009:SSA_1978|5end_Dihydroxyacetone_kinase_family_protein_(Dak2_domain),_putative_1973933..1974163_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 213 94 60 143 103 NC_009009:SSA_1353|3end_hypothetical_protein_1367974..1368124_NEGATIVE 189 97 55 75 27 NC_009009:SSA_2205|3end_Transcription_antitermination_factor_NusG,_putative_2205564..2205714_NEGATIVE 187 47 11 151 118 NC_009009:SSA_2335|3end_D-Ala-teichoic_acid_biosynthesis_protein,_putative_2338027..2338177_NEGATIVE 185 31 5 58 18 NC_009009:SSA_0569|3end_Aspartyl/glutamyl-tRNA(Asn/Gln)_amidotransferase_subunit_C,_putative_563995..564145_POSITIVE 174 28 1 127 97 NC_009009:SSA_0657|3end_PyridoxaL_5'-phosphate_Dependent_Enzymes_class_III,_putative_642196..642346_POSITIVE 172 49 6 67 25 NC_009009:SSA_0440|3end_30S_ribosomal_protein_S18,_putative_441465..441615_POSITIVE 171 43 21 36 12 NC_009009:SSA_2293|3end_hypothetical_protein_2295955..2296105_POSITIVE 170 37 10 135 99 NC_009009:SSA_1855|3end_hypothetical_protein_1850897..1851047_NEGATIVE 169 47 15 114 80 NC_009009:SSA_2125|3end_Small_primase-like_protein_(Toprim_domain),_putative_2129423..2129573_NEGATIVE 168 32 11 59 41 NC_009009:SSA_0621|3end_SOS_responce_UmuC_protein,_putative_612322..612472_NEGATIVE 167 47 6 47 18 NC_009009:SSA_2055|3end_hypothetical_protein_2057936..2058086_NEGATIVE 162 47 15 125 99 NC_009009:SSA_1986|3end_Acetyltransferase,_GNAT_family,_putative_1982073..1982223_NEGATIVE 161 96 65 82 56 NC_009009:SSA_0814|3end_Oxidoreductase,_pyridine_nucleotide-disulfide,_class_I,_putative_795519..795669_NEGATIVE 160 28 8 46 20 NC_009009:SSA_0313|3end_Conserved_uncharacterized_protein_308389..308539_NEGATIVE 159 55 16 88 42 NC_009009:SSA_1577|3end_Proline_dipeptidase,_putative_1581456..1581606_POSITIVE 159 92 52 76 38 NC_009009:SSA_1571|3end_Threonyl-tRNA_synthetase,_putative_1573211..1573361_NEGATIVE 158 35 12 142 123 NC_009009:SSA_1936|3end_3-oxoacyl-[acyl-carrier_protein]_reductase,_putative_1923104..1923254_NEGATIVE 158 29 11 32 11 NC_009009:SSA_1823|3end_hypothetical_protein_1811152..1811302_NEGATIVE 158 96 59 59 31 NC_009009:SSA_0422|3end_Phosphoglycerate_mutase_family_protein,_putative_420839..420989_POSITIVE 157 97 63 88 52 NC_009009:SSA_0935|3end_tRNA_pseudouridine_synthase_B,_putative_944973..945123_POSITIVE