Origin IGS: actattccctctctacactctagttttgtttattataactcatttctctgtttttttccatattatttgtttgttttaaacaaaatatgatacaaaaatccgagaacagtaactgttgctgttctcggatttttaatatttc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gaaatattaaaaatccgagaacagcaacagttactgttctcggatttttgtatcatattttgtttaaaacaaacaaataatatggaaaaaaacagagaaatgagttataataaacaaaactagagtgtagagagggaatagt Mask Tandem Repeat Region ================================================ actattccctctctacactctagttttgtttattataactcatttctctgtttttttccatattatttgtttgttttaaacaaaatatgatacaaaaatccgagaacagtaactgttgctgttctcggatttttaatatttc Find is-nt database================================================ Query_seq: SSA_1701:SSA_1702|SSA_1701:SSA_1702:Transcriptional repressor of sugar metabolism, GlpR/DeoR family, putative:hypothetical protein:<-<-:1692145..1692286 142 actattccctctctacactctagttttgtttattataactcatttctctgtttttttccatattatttgtttgttttaaacaaaatatgatacaaaaatccgagaacagtaactgttgctgttctcggatttttaatatttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1701:SSA_1702|SSA_1701:SSA_1702:Transcriptional repressor of sugar metabolism, GlpR/DeoR family, putative:hypothetical protein:<-<-:1692145..1692286 142 actattccctctctacactctagttttgtttattataactcatttctctgtttttttccatattatttgtttgttttaaacaaaatatgatacaaaaatccgagaacagtaactgttgctgttctcggatttttaatatttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1701:SSA_1702|SSA_1701:SSA_1702:Transcriptional repressor of sugar metabolism, GlpR/DeoR family, putative:hypothetical protein:<-<-:1692145..1692286 142 actattccctctctacactctagttttgtttattataactcatttctctgtttttttccatattatttgtttgttttaaacaaaatatgatacaaaaatccgagaacagtaactgttgctgttctcggatttttaatatttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 actattccctctctacactctagttttgtttattataactcatttctctgtttttttccatattatttgtttgttttaaacaaaatatgatacaaaaatccgagaacagtaactgttgctgttctcggatttttaatatttc Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 42 End: 140 ......................................... M S L F F S I L F V C F K Q N M I Q K S E N S N C C C S R I F N I .. Protein_Len: 39 Strand: - Start: 23 End: 139 ...................... N Q K N Y S M E R N K E M N N T Q K L C F I I C F D S F L L Q Q Q E R I K L M ... actattccctctctacactctagttttgtttattataactcatttctctgtttttttccatattatttgtttgttttaaacaaaatatgatacaaaaatccgagaacagtaactgttgctgttctcggatttttaatatttc 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: 83 Start: 32 End: 61 ...............................ATGGAAAAAAACAGAGAAATGAGTTATAAT................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ actattccctctctacactctagttttgtttattataactcatttctctgtttttttccatattatttgtttgttttaaacaaaatatgatacaaaaatccgagaacagtaactgttgctgttctcggatttttaatatttc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1701:SSA_1702|SSA_1701:SSA_1702:Transcriptional repressor of sugar metabolism, GlpR/DeoR family, putative:hypothetical protein:<-<-:1692145..1692286 142 actattccctctctacactctagttttgtttattataactcatttctctgtttttttccatattatttgtttgttttaaacaaaatatgatacaaaaatccgagaacagtaactgttgctgttctcggatttttaatatttc Intra-Species Hit: Count: 1 Min: 1 Max: 142 Len: 142 Subject: NC_009009_SSA_1701_SSA_1702|Transcriptional repressor of sugar metabolism, GlpR/DeoR family, putative:hypothetical protein|NEGATIVE:NEGATIVE|[1692145,1692286]|142 HSP 1 e-value: 1.0E-62 bit: 240.0 Len: 142 Query Start:1 Query End:142 Subject Strand: POSITIVE Subject Start: 1 Subject End: 142 actattccctctctacactctagttttgtttattataactcatttctctgnnnnnnnccatattatttgtttgttttaaacaaaatatgatacaaaaatccgagaacagtaactgttgctgttctcggatttttaatatttc actattccctctctacactctagttttgtttattataactcatttctctgtttttttccatattatttgtttgttttaaacaaaatatgatacaaaaatccgagaacagtaactgttgctgttctcggatttttaatatttc HSP 2 e-value: 8.0E-8 bit: 58.0 Len: 41 Query Start:94 Query End:134 Subject Strand: NEGATIVE Subject Start: 94 Subject End: 134 .............................................................................................aaaaatccgagaacagtaactgttgctgttctcggattttt........ .............................................................................................aaaaatccgagaacagcaacagttactgttctcggattttt........ Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUAUUCCCUCUCUACACUCUAGUUUUGUUUAUUAUAACUCAUUUCUCUGUUUUUUUCCAUAUUAUUUGUUUGUUUUAAACAAAAUAUGAUACAAAAAUCCGAGAACAGUAACUGUUGCUGUUCUCGGAUUUUUAAUAUUUC ......................((((((((((..((((..((.........................)).))))..)))))))))).......((((((((((((((((((.....))))))))))))))))))........ (-33.81) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAAUAUUAAAAAUCCGAGAACAGCAACAGUUACUGUUCUCGGAUUUUUGUAUCAUAUUUUGUUUAAAACAAACAAAUAAUAUGGAAAAAAACAGAGAAAUGAGUUAUAAUAAACAAAACUAGAGUGUAGAGAGGGAAUAGU .......(((((((((((((((((.........)))))))))))))))))..(((((((((((((.....))))))..)))))))..................(((......)))........................... (-29.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 825 130 81 221 172 NC_009009:SSA_1701|5end_Transcriptional_repressor_of_sugar_metabolism,_GlpR/DeoR_family,_putative_1692054..1692284_NEGATIVE 276 109 66 175 134 NC_009009:SSA_0268|5end_Phosphotransferase_system_(PTS)_cellobiose-specific_component_IIB,_putative_262224..262454_POSITIVE 263 60 15 140 80 NC_009009:SSA_1835|5end_Late_competence_protein,_putative_1830941..1831171_NEGATIVE 259 134 101 34 1 NC_009009:SSA_0683|5end_DNA-binding_protein_HU,_putative_664384..664614_POSITIVE 245 59 11 160 98 NC_009009:SSA_1795|5end_Guanosine_3',5'-bis-pyrophosphate_(ppGpp)_synthetase,_putative_1777671..1777901_NEGATIVE 244 50 2 142 88 NC_009009:SSA_1958|5end_Adapter_protein_mecA,_putative_1955413..1955643_NEGATIVE 241 46 4 198 153 NC_009009:SSA_1758|5end_hypothetical_protein_1746619..1746849_NEGATIVE 232 51 14 146 114 NC_009009:SSA_1627|5end_hypothetical_protein_1629690..1629920_NEGATIVE 230 135 100 169 128 NC_009009:SSA_0133|5end_50S_ribosomal_protein_L17,_putative_122096..122326_POSITIVE 225 129 101 215 181 NC_009009:SSA_0477|5end_Cobalamin_biosynthesis_protein_CbiM_(ABC-type_cobalt_transporter),_putative_479223..479453_POSITIVE 225 69 24 117 82 NC_009009:SSA_0380|5end_Enzyme_of_poly-gamma-glutamate_biosynthesis_(capsule_formation),_putative_370916..371146_POSITIVE 223 140 98 51 2 NC_009009:SSA_2303|5end_hypothetical_protein_2305177..2305407_NEGATIVE 222 50 1 199 137 NC_009009:SSA_1453|5end_hypothetical_protein_1460208..1460438_NEGATIVE 221 49 5 130 96 NC_009009:SSA_1993|5end_Conserved_uncharacterized_protein_1990790..1991020_NEGATIVE 219 128 99 72 39 NC_009009:SSA_1794|5end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_winged-helix_DNA-binding_domains),_putative_1777049..1777279_NEGATIVE 219 128 87 162 126 NC_009009:SSA_0981|5end_3-isopropylmalate_dehydratase_small_subunit,_putative_985396..985626_POSITIVE 218 128 100 67 44 NC_009009:SSA_0487|5end_Delta-aminolevulinic_acid_dehydratase,_putative_487349..487579_POSITIVE 218 132 94 56 11 NC_009009:SSA_0481|5end_Cobyric_acid_synthase,_putative_481962..482192_POSITIVE 218 130 99 45 11 NC_009009:SSA_0101|5end_Conserved_uncharacterized_protein_103596..103826_POSITIVE 217 61 28 107 74 NC_009009:SSA_2259|5end_hypothetical_protein_2255422..2255652_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 263 60 15 143 83 NC_009009:SSA_1836|3end_Superfamily_II_ATP-dependent_DNA/RNA_helicase_required_for_DNA_uptake_(late_competence_protein),_putative_1830938..1831088_NEGATIVE 256 132 93 141 103 NC_009009:SSA_1713|3end_D-3-phosphoglycerate_dehydrogenase,_putative_1700209..1700359_NEGATIVE 224 129 89 38 1 NC_009009:SSA_0602|3end_ABC-type_cobalt_transport_system,_ATPase_component,_putative_591683..591833_POSITIVE 222 37 4 144 108 NC_009009:SSA_1759|3end_hypothetical_protein_1746664..1746814_NEGATIVE 221 49 5 59 25 NC_009009:SSA_1994|3end_CTP_synthase,_putative_1990861..1991011_NEGATIVE 219 128 99 70 37 NC_009009:SSA_1795|3end_Guanosine_3',5'-bis-pyrophosphate_(ppGpp)_synthetase,_putative_1777051..1777201_NEGATIVE 218 128 100 80 57 NC_009009:SSA_0486|3end_Uroporphyrinogen-III_synthase,_putative_487442..487592_POSITIVE 218 132 94 71 26 NC_009009:SSA_0480|3end_Cobalt_ABC_transporter,_ATP-binding_protein,_putative_482057..482207_POSITIVE 217 134 104 130 102 NC_009009:SSA_1038|3end_Lipoprotein,_putative_1053714..1053864_POSITIVE 214 131 101 145 106 NC_009009:SSA_2064|3end_hypothetical_protein_2064879..2065029_NEGATIVE 212 137 107 31 5 NC_009009:SSA_1675|3end_hypothetical_protein_1670847..1670997_POSITIVE 212 45 4 63 9 NC_009009:SSA_0040|3end_Phosphoribosylaminoimidazole_carboxylase,_ATPase_subunit,_putative_47479..47629_POSITIVE 209 128 82 69 19 NC_009009:SSA_1808|3end_hypothetical_protein_1791394..1791544_NEGATIVE 203 135 91 51 4 NC_009009:SSA_1530|3end_ABC-type_antimicrobial_peptide_transport_system,_permease_component,_putative_1537510..1537660_NEGATIVE 200 127 88 137 105 NC_009009:SSA_1181|3end_Hydrolase,_alpha/beta_superfamily,_putative_1208592..1208742_NEGATIVE 200 136 103 105 68 NC_009009:SSA_0826|3end_hypothetical_protein_805516..805666_POSITIVE 199 130 113 28 10 NC_009009:SSA_2230|3end_Ribonucleotide_reductase,_class_III,_anaerobic,_putative_2228963..2229113_NEGATIVE 199 50 6 108 61 NC_009009:SSA_0983|3end_Conserved_uncharacterized_protein_986945..987095_POSITIVE 199 130 101 144 115 NC_009009:SSA_0405|3end_Transcriptional_regulator,_XRE_family,_putative_402115..402265_POSITIVE 198 60 16 131 86 NC_009009:SSA_1478|3end_Transposase_ORF1,_putative_1483124..1483274_POSITIVE