Origin IGS: acatttgaatttattttccctatgacaagcaccgagaatggtgcttgttttttcttgtttgtaaaagaaaatgattggtacagtttgcctgtttttaaaaaactgttattccatgttataaaacataacataaattactctttttttattgcataaattttcataataaagtataatataaaacaatttaaaataagtgaggggtagaaat .........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 atttctacccctcacttattttaaattgttttatattatactttattatgaaaatttatgcaataaaaaaagagtaatttatgttatgttttataacatggaataacagttttttaaaaacaggcaaactgtaccaatcattttcttttacaaacaagaaaaaacaagcaccattctcggtgcttgtcatagggaaaataaattcaaatgt Mask Tandem Repeat Region ================================================ acatttgaatttattttccctatgacaagcaccgagaatggtgcttgttttttcttgtttgtaaaagaaaatgattggtacagtttgcctgtttttaaaaaactgttattccatgttataaaacataacataaattactctttttttattgcataaattttcataataaagtataatataaaacaatttaaaataagtgaggggtagaaat Find is-nt database================================================ Query_seq: SSA_0701:SSA_0702|SSA_0701:SSA_0702:Cation transporter CorA family, putative:Aconitase A, putative:->->:685417..685627 211 acatttgaatttattttccctatgacaagcaccgagaatggtgcttgttttttcttgtttgtaaaagaaaatgattggtacagtttgcctgtttttaaaaaactgttattccatgttataaaacataacataaattactctttttttattgcataaattttcataataaagtataatataaaacaatttaaaataagtgaggggtagaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0701:SSA_0702|SSA_0701:SSA_0702:Cation transporter CorA family, putative:Aconitase A, putative:->->:685417..685627 211 acatttgaatttattttccctatgacaagcaccgagaatggtgcttgttttttcttgtttgtaaaagaaaatgattggtacagtttgcctgtttttaaaaaactgttattccatgttataaaacataacataaattactctttttttattgcataaattttcataataaagtataatataaaacaatttaaaataagtgaggggtagaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0701:SSA_0702|SSA_0701:SSA_0702:Cation transporter CorA family, putative:Aconitase A, putative:->->:685417..685627 211 acatttgaatttattttccctatgacaagcaccgagaatggtgcttgttttttcttgtttgtaaaagaaaatgattggtacagtttgcctgtttttaaaaaactgttattccatgttataaaacataacataaattactctttttttattgcataaattttcataataaagtataatataaaacaatttaaaataagtgaggggtagaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 acatttgaatttattttccctatgacaagcaccgagaatggtgcttgttttttcttgtttgtaaaagaaaatgattggtacagtttgcctgtttttaaaaaactgttattccatgttataaaacataacataaattactctttttttattgcataaattttcataataaagtataatataaaacaatttaaaataagtgaggggtagaaat Predict ORF larger than 30AA ================================================ Protein_Len: 47 Strand: + Start: 13 End: 153 ............ M F P M T S T E N G A C F F L F V K E N D W Y S L P V F K K L L F H V I K H N I N Y S F F I A .......................................................... Protein_Len: 43 Strand: - Start: 3 End: 131 .. N S N I K G I V L V S F P A Q K K K N T F S F S Q Y L K G T K L F S N N W T I F C L M ................................................................................ acatttgaatttattttccctatgacaagcaccgagaatggtgcttgttttttcttgtttgtaaaagaaaatgattggtacagtttgcctgtttttaaaaaactgttattccatgttataaaacataacataaattactctttttttattgcataaattttcataataaagtataatataaaacaatttaaaataagtgaggggtagaaat 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: 84 Start: 148 End: 177 ...................................................................................................................................................ATTGCATAAATTTTCATAATAAAGTATAAT.................................. PromScan Matrix: RpoD-17 Strand: + Score: 82 Start: 93 End: 122 ............................................................................................TTTTAAAAAACTGTTATTCCATGTTATAAA......................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ acatttgaatttattttccctatgacaagcaccgagaatggtgcttgttttttcttgtttgtaaaagaaaatgattggtacagtttgcctgtttttaaaaaactgttattccatgttataaaacataacataaattactctttttttattgcataaattttcataataaagtataatataaaacaatttaaaataagtgaggggtagaaat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0701:SSA_0702|SSA_0701:SSA_0702:Cation transporter CorA family, putative:Aconitase A, putative:->->:685417..685627 211 acatttgaatttattttccctatgacaagcaccgagaatggtgcttgttttttcttgtttgtaaaagaaaatgattggtacagtttgcctgtttttaaaaaactgttattccatgttataaaacataacataaattactctttttttattgcataaattttcataataaagtataatataaaacaatttaaaataagtgaggggtagaaat Intra-Species Hit: Count: 1 Min: 1 Max: 211 Len: 211 Subject: NC_009009_SSA_0701_SSA_0702|Cation transporter CorA family, putative:Aconitase A, putative|POSITIVE:POSITIVE|[685417,685627]|211 HSP 1 e-value: 1.0E-103 bit: 377.0 Len: 211 Query Start:1 Query End:211 Subject Strand: POSITIVE Subject Start: 1 Subject End: 211 acatttgaatttattttccctatgacaagcaccgagaatggtgcttgttttttcttgtttgtaaaagaaaatgattggtacagtttgcctgtttttaaaaaactgttattccatgttataaaacataacataaattactcnnnnnnnattgcataaattttcataataaagtataatataaaacaatttaaaataagtgaggggtagaaat acatttgaatttattttccctatgacaagcaccgagaatggtgcttgttttttcttgtttgtaaaagaaaatgattggtacagtttgcctgtttttaaaaaactgttattccatgttataaaacataacataaattactctttttttattgcataaattttcataataaagtataatataaaacaatttaaaataagtgaggggtagaaat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACAUUUGAAUUUAUUUUCCCUAUGACAAGCACCGAGAAUGGUGCUUGUUUUUUCUUGUUUGUAAAAGAAAAUGAUUGGUACAGUUUGCCUGUUUUUAAAAAACUGUUAUUCCAUGUUAUAAAACAUAACAUAAAUUACUCUUUUUUUAUUGCAUAAAUUUUCAUAAUAAAGUAUAAUAUAAAACAAUUUAAAAUAAGUGAGGGGUAGAAAU .(((((...(((((.........((((((((((......))))))))))...........)))))...)))))..(((.(((((((.............)))))))....))).(((((.....))))).....(((((((((.((((((...((((((.........................)))))).)))))).))))))))).... (-39.98) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUCUACCCCUCACUUAUUUUAAAUUGUUUUAUAUUAUACUUUAUUAUGAAAAUUUAUGCAAUAAAAAAAGAGUAAUUUAUGUUAUGUUUUAUAACAUGGAAUAACAGUUUUUUAAAAACAGGCAAACUGUACCAAUCAUUUUCUUUUACAAACAAGAAAAAACAAGCACCAUUCUCGGUGCUUGUCAUAGGGAAAAUAAAUUCAAAUGU ........((((.((((.((((..(((((((((((.((.....)).)))))).......)))))..)))).))))..(((((((((((...)))))))))))...((((((((((......))).)))))))........(((((((........))))))).(((((((((......)))))))))...))))................. (-39.01) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 279 69 33 224 189 NC_009009:SSA_2344|5end_hypothetical_protein_2346537..2346767_POSITIVE 279 55 18 39 1 NC_009009:SSA_0405|5end_Transcriptional_regulator,_XRE_family,_putative_401418..401648_POSITIVE 276 48 2 153 99 NC_009009:SSA_2269|5end_hypothetical_protein_2270327..2270557_NEGATIVE 257 50 6 176 127 NC_009009:SSA_0740|5end_C4-dicarboxylate_anaerobic_carrier,_possible_arginine_transporter,_putative_722240..722470_POSITIVE 250 48 2 154 105 NC_009009:SSA_1982|5end_Transcriptional_regulator,_LytR/AlgR_family,_putative_1975873..1976103_NEGATIVE 247 58 17 136 105 NC_009009:SSA_1712|5end_Arsenate_reductase_(ArsC),_glutaredoxin_family,_putative_1700084..1700314_NEGATIVE 244 55 13 197 146 NC_009009:SSA_2302|5end_Type_IV_fimbrial_biogenesis_protein,_prepilin_cysteine_protease_(C20)_PilD,_putative_2304044..2304274_NEGATIVE 243 78 32 72 26 NC_009009:SSA_2233|5end_hypothetical_protein_2233110..2233340_NEGATIVE 241 50 10 168 123 NC_009009:SSA_0469|5end_Precorrin-6B_methylase_2,putative_472310..472540_POSITIVE 240 60 17 136 99 NC_009009:SSA_1910|5end_hypothetical_protein_1902672..1902902_NEGATIVE 240 57 17 55 13 NC_009009:SSA_0606|5end_ABC-type_antimicrobial_peptide_transport_system,_ATPase_component,_putative_594532..594762_NEGATIVE 238 209 161 54 4 NC_009009:SSA_1244|5end_hypothetical_protein_1268704..1268934_NEGATIVE 238 60 19 70 30 NC_009009:SSA_0963|5end_Peptidoglycan_N-acetylglucosamine_deacetylase_A,_putative_971413..971643_POSITIVE 237 90 50 73 34 NC_009009:SSA_2340|5end_hypothetical_protein_2342843..2343073_NEGATIVE 236 61 23 68 31 NC_009009:SSA_2097|5end_Amino_acid_ABC_transporter,_ATP-binding_protein,_putative_2102918..2103148_NEGATIVE 235 60 18 193 149 NC_009009:SSA_0875|5end_Rod_shape_determining_protein_(cell-cycle_protein),_putative_868928..869158_POSITIVE 233 47 6 81 45 NC_009009:SSA_0362|5end_Thioredoxin,_putative_353290..353520_POSITIVE 233 44 1 220 184 NC_009009:SSA_0297|5end_Malolactic_enzyme,_putative_289706..289936_POSITIVE 232 57 13 182 139 NC_009009:SSA_2125|5end_Small_primase-like_protein_(Toprim_domain),_putative_2130019..2130249_NEGATIVE 231 48 17 141 108 NC_009009:SSA_1065|5end_Beta-hexosamidase_A,_putative_1081258..1081488_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 294 60 11 107 54 NC_009009:SSA_0966|3end_Uridine_kinase,_putative_975790..975940_POSITIVE 283 54 17 135 99 NC_009009:SSA_0826|3end_hypothetical_protein_805516..805666_POSITIVE 266 45 13 145 111 NC_009009:SSA_0303|3end_surface_protein_C_301051..301201_POSITIVE 255 89 41 113 73 NC_009009:SSA_0047|3end_NAD(P)H_dehydrogenase_(Quinone),_putative_52284..52434_NEGATIVE 254 68 27 100 69 NC_009009:SSA_1272|3end_50S_ribosomal_protein_L31_type_B,_putative_1295337..1295487_POSITIVE 244 55 13 128 77 NC_009009:SSA_2303|3end_hypothetical_protein_2304113..2304263_NEGATIVE 240 60 17 143 106 NC_009009:SSA_1911|3end_Conserved_uncharacterized_protein_1902665..1902815_NEGATIVE 238 67 22 88 47 NC_009009:SSA_0454|3end_Lactose_operon_transcriptional_repressor,_LacI_family,_putative_456050..456200_NEGATIVE 237 90 50 116 77 NC_009009:SSA_2342|3end_SPX_domain-like_protein,_putative_2342800..2342950_NEGATIVE 236 61 23 55 18 NC_009009:SSA_2098|3end_ABC-type_arginine/histidine_transporter,_permease_protein,_putative_2102931..2103081_NEGATIVE 233 43 14 151 116 NC_009009:SSA_2339|3end_Microcin_C7_resistance_protein,_putative_2341489..2341639_POSITIVE 230 54 11 92 46 NC_009009:SSA_2126|3end_hypothetical_protein_2129985..2130135_NEGATIVE 230 56 15 86 39 NC_009009:SSA_0483|3end_Siroheme_synthase,_putative_484556..484706_POSITIVE 229 57 11 138 91 NC_009009:SSA_0929|3end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_940263..940413_POSITIVE 227 47 17 35 3 NC_009009:SSA_1414|3end_hypothetical_protein_1424942..1425092_NEGATIVE 226 60 19 129 74 NC_009009:SSA_2206|3end_hypothetical_protein_2207275..2207425_POSITIVE 226 117 75 137 87 NC_009009:SSA_1179|3end_Carbamoylphosphate_synthase_large_subunit_/_biotin_carboxylase,_putative_1206640..1206790_NEGATIVE 222 67 32 103 59 NC_009009:SSA_1236|3end_Mutator_protein,_putative_1261240..1261390_NEGATIVE 217 53 13 82 45 NC_009009:SSA_0485|3end_Porphobilinogen_deaminase,_putative_486732..486882_POSITIVE 216 61 38 68 39 NC_009009:SSA_0925|3end_ABC-type_antimicrobial_peptide_transport_system,_ATPase_component,_putative_935494..935644_POSITIVE