Origin IGS: cagagcgaagaccaggagcggagcgatggccttgaggccgacaacgaagatttggcccagaagtccgacggcttgtgcttgggggaagatgatagcagcaggacaccaatgccaataccgatggcaatccgcttgattagattggttttattccaaatagtgatgaagcgatggaccatgtatattcctttcttgtcttagatacttattttattatacgatagaaagagggcgaaagcaatgctaggtcgggttaaccattctatgtccgcgctgtgtggtctttgtggtataatggtagtaatctttttggaggtagcct .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 aggctacctccaaaaagattactaccattataccacaaagaccacacagcgcggacatagaatggttaacccgacctagcattgctttcgccctctttctatcgtataataaaataagtatctaagacaagaaaggaatatacatggtccatcgcttcatcactatttggaataaaaccaatctaatcaagcggattgccatcggtattggcattggtgtcctgctgctatcatcttcccccaagcacaagccgtcggacttctgggccaaatcttcgttgtcggcctcaaggccatcgctccgctcctggtcttcgctctg Mask Tandem Repeat Region ================================================ cagagcgaagaccaggagcggagcgatggccttgaggccgacaacgaagatttggcccagaagtccgacggcttgtgcttgggggaagatgatagcagcaggacaccaatgccaataccgatggcaatccgcttgattagattggttttattccaaatagtgatgaagcgatggaccatgtatattcctttcttgtcttagatacttattttattatacgatagaaagagggcgaaagcaatgctaggtcgggttaaccattctatgtccgcgctgtgtggtctttgtggtataatggtagtaatctttttggaggtagcct Find is-nt database================================================ Query_seq: SSA_0364:SSA_0365|SSA_0364:SSA_0365:Serine/threonine:Na+ symporter, putative:Small-conductance mechanosensitive efflux channel, putative:<-->:356439..356760 322 cagagcgaagaccaggagcggagcgatggccttgaggccgacaacgaagatttggcccagaagtccgacggcttgtgcttgggggaagatgatagcagcaggacaccaatgccaataccgatggcaatccgcttgattagattggttttattccaaatagtgatgaagcgatggaccatgtatattcctttcttgtcttagatacttattttattatacgatagaaagagggcgaaagcaatgctaggtcgggttaaccattctatgtccgcgctgtgtggtctttgtggtataatggtagtaatctttttggaggtagcct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0364:SSA_0365|SSA_0364:SSA_0365:Serine/threonine:Na+ symporter, putative:Small-conductance mechanosensitive efflux channel, putative:<-->:356439..356760 322 cagagcgaagaccaggagcggagcgatggccttgaggccgacaacgaagatttggcccagaagtccgacggcttgtgcttgggggaagatgatagcagcaggacaccaatgccaataccgatggcaatccgcttgattagattggttttattccaaatagtgatgaagcgatggaccatgtatattcctttcttgtcttagatacttattttattatacgatagaaagagggcgaaagcaatgctaggtcgggttaaccattctatgtccgcgctgtgtggtctttgtggtataatggtagtaatctttttggaggtagcct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0364:SSA_0365|SSA_0364:SSA_0365:Serine/threonine:Na+ symporter, putative:Small-conductance mechanosensitive efflux channel, putative:<-->:356439..356760 322 cagagcgaagaccaggagcggagcgatggccttgaggccgacaacgaagatttggcccagaagtccgacggcttgtgcttgggggaagatgatagcagcaggacaccaatgccaataccgatggcaatccgcttgattagattggttttattccaaatagtgatgaagcgatggaccatgtatattcctttcttgtcttagatacttattttattatacgatagaaagagggcgaaagcaatgctaggtcgggttaaccattctatgtccgcgctgtgtggtctttgtggtataatggtagtaatctttttggaggtagcct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 1 Min: 1 Max: 170 Len: 170 Subject: UniRef90_Q3D9A3 Cluster: Sodium:dicarboxylate symporter family protein; n=7; Streptococcus agalactiae|Rep: Sodium:dicarboxylate symporter family protein - Streptococcus agalactiae COH1 HSP 1 e-value: 2.0E-6 bit: 48.5 Len: 93 Query Start:1 Query End:93 Subject Strand: null Subject Start: 29 Subject End: 59 I I F P Q A Q A V G L L G Q I F V V G L K A I A P L L V F A L ..................................................................................................................................................................................................................................... I L V P K A S A I G L L G Q L F V G G L K A I A P L L V F T L ..................................................................................................................................................................................................................................... HSP 2 e-value: 2.0E-6 bit: 24.6 Len: 45 Query Start:126 Query End:170 Subject Strand: null Subject Start: 3 Subject End: 17 ............................................................................................................................. R F I T I W N K T N L I K R I ........................................................................................................................................................ ............................................................................................................................. R F L K A W R K T S L I K K I ........................................................................................................................................................ nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnagcagcaggacaccaatgccaataccgatggcnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnatggaccatgtatattcctttcttgtcttagatacttattttattatacgatagaaagagggcgaaagcaatgctaggtcgggttaaccattctatgtccgcgctgtgtggtctttgtggtataatggtagtaatctttttggaggtagcct Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 26 End: 133 ......................... M A L R P T T K I W P R S P T A C A W G K M I A A G H Q C Q Y R W Q S A ............................................................................................................................................................................................. Protein_Len: 49 Strand: + Start: 52 End: 198 ................................................... M A Q K S D G L C L G E D D S S R T P M P I P M A I R L I R L V L F Q I V M K R W T M Y I P F L S ............................................................................................................................ Protein_Len: 40 Strand: + Start: 202 End: 321 ......................................................................................................................................................................................................... M L I L L Y D R K R A K A M L G R V N H S M S A L C G L C G I M V V I F L E V A . Protein_Len: 35 Strand: - Start: 201 End: 305 ........................................................................................................................................................................................................ I S I K N Y S L F L A F A I S P R T L W E I D A S H P R Q P I I T T M ................. Protein_Len: 60 Strand: - Start: 3 End: 185 .. S S W S R L S P R S A S L S S K A W F D S P K H K P S S S L L L V G I G I G I A I R K I L N T K N W I T I F R H V M Y M ......................................................................................................................................... Protein_Len: 42 Strand: - Start: 2 End: 127 . S R L G P A S R H G Q P R C R L N P G S T R R S T S P P L H Y C C S V L A L V S P M ................................................................................................................................................................................................... Protein_Len: 31 Strand: - Start: 1 End: 93 L A F V L L P A I A K L G V V F I Q G L L G V A Q A Q P F I M ..................................................................................................................................................................................................................................... nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnagcagcaggacaccaatgccaataccgatggcnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnatggaccatgtatattcctttcttgtcttagatacttattttattatacgatagaaagagggcgaaagcaatgctaggtcgggttaaccattctatgtccgcgctgtgtggtctttgtggtataatggtagtaatctttttggaggtagcct 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: 213 End: 242 ....................................................................................................................................................................................................................ATTGCTTTCGCCCTCTTTCTATCGTATAAT................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnagcagcaggacaccaatgccaataccgatggcnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnatggaccatgtatattcctttcttgtcttagatacttattttattatacgatagaaagagggcgaaagcaatgctaggtcgggttaaccattctatgtccgcgctgtgtggtctttgtggtataatggtagtaatctttttggaggtagcct Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0364:SSA_0365|SSA_0364:SSA_0365:Serine/threonine:Na+ symporter, putative:Small-conductance mechanosensitive efflux channel, putative:<-->:356439..356760 322 nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnagcagcaggacaccaatgccaataccgatggcnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnatggaccatgtatattcctttcttgtcttagatacttattttattatacgatagaaagagggcgaaagcaatgctaggtcgggttaaccattctatgtccgcgctgtgtggtctttgtggtataatggtagtaatctttttggaggtagcct Intra-Species Hit: Count: 1 Min: 94 Max: 322 Len: 229 Subject: NC_009009_SSA_0364_SSA_0365|Serine/threonine:Na+ symporter, putative:Small-conductance mechanosensitive efflux channel, putative|NEGATIVE:POSITIVE|[356439,356760]|322 HSP 1 e-value: 8.0E-81 bit: 301.0 Len: 152 Query Start:171 Query End:322 Subject Strand: POSITIVE Subject Start: 171 Subject End: 322 ..........................................................................................................................................................................atggaccatgtatattcctttcttgtcttagatacttattttattatacgatagaaagagggcgaaagcaatgctaggtcgggttaaccattctatgtccgcgctgtgtggtctttgtggtataatggtagtaatctttttggaggtagcct ..........................................................................................................................................................................atggaccatgtatattcctttcttgtcttagatacttattttattatacgatagaaagagggcgaaagcaatgctaggtcgggttaaccattctatgtccgcgctgtgtggtctttgtggtataatggtagtaatctttttggaggtagcct HSP 2 e-value: 3.0E-9 bit: 63.9 Len: 32 Query Start:94 Query End:125 Subject Strand: POSITIVE Subject Start: 94 Subject End: 125 .............................................................................................agcagcaggacaccaatgccaataccgatggc..................................................................................................................................................................................................... .............................................................................................agcagcaggacaccaatgccaataccgatggc..................................................................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCAGCAGGACACCAAUGCCAAUACCGAUGGCAAUCCGCUUGAUUAGAUUGGUUUUAUUCCAAAUAGUGAUGAAGCGAUGGACCAUGUAUAUUCCUUUCUUGUCUUAGAUACUUAUUUUAUUAUACGAUAGAAAGAGGGCGAAAGCAAUGCUAGGUCGGGUUAACCAUUCUAUGUCCGCGCUGUGUGGUCUUUGUGGUAUAAUGGUAGUAAUCUUUUUGGAGGUAGCCU ......(((..(((..(((((.......))))).((((...(((((.....(((((((..(.....)..))))))).....(((((............((((.(((((...(((.(((((((....))))))).))).((....))....))))).))))...(((((.....(.((((.....)))).)...)))))...)))))..)))))....)))))))..))) (-57.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGGCUACCUCCAAAAAGAUUACUACCAUUAUACCACAAAGACCACACAGCGCGGACAUAGAAUGGUUAACCCGACCUAGCAUUGCUUUCGCCCUCUUUCUAUCGUAUAAUAAAAUAAGUAUCUAAGACAAGAAAGGAAUAUACAUGGUCCAUCGCUUCAUCACUAUUUGGAAUAAAACCAAUCUAAUCAAGCGGAUUGCCAUCGGUAUUGGCAUUGGUGUCCUGCUGCU .((......))...................................(((((.((((.((((.(((((.....((((....(((.(((((....((((.......(((......))).......))))...))))).)))......))))......((((........))))....))))).)))).....((.(((.((((.......))))))).))))))))))).. (-44.04) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 946 47 1 231 185 NC_009009:SSA_0364|5end_Serine/threonine:Na+_symporter,_putative_356348..356578_NEGATIVE 395 207 165 144 102 NC_009009:SSA_0140|5end_Copper-translocating_P-type_ATPase,_putative_134626..134856_POSITIVE 360 42 2 61 8 NC_009009:SSA_0319|5end_Branched-chain_amino_acid_permease_(L-methionine,_L-isoleucine,_leucine_and_valine),_putative_312721..312951_POSITIVE 353 196 151 204 166 NC_009009:SSA_1904|5end_ABC-type_multidrug_transport_system,_permease_component,_putative_1899279..1899509_NEGATIVE 335 42 3 82 29 NC_009009:SSA_1669|5end_hypothetical_protein_1668442..1668672_NEGATIVE 335 48 1 63 13 NC_009009:SSA_0588|5end_L-cystine_ABC_transporter,_substrate-binding_component,_putative_579800..580030_POSITIVE 325 180 137 210 161 NC_009009:SSA_0484|5end_Glutamyl-tRNA_reductase,_putative_484492..484722_POSITIVE 321 189 141 63 8 NC_009009:SSA_0603|5end_Cobalt_transporter,_putative_591596..591826_POSITIVE 320 183 143 95 56 NC_009009:SSA_0315|5end_Transcriptional_regulator,_MarR_family,_putative_310102..310332_POSITIVE 316 188 144 220 170 NC_009009:SSA_0931|5end_hypothetical_protein_940281..940511_POSITIVE 315 190 145 73 20 NC_009009:SSA_0049|5end_Dihydroxyacetone_kinase_(Dak1),_putative_53612..53842_POSITIVE 313 43 2 213 169 NC_009009:SSA_0653|5end_UDP-N-acetylglucosamine--N-acetylmuramyl-_(pentapeptide)_pyrophosphoryl-undecaprenol_N-acetylglucosamine_transferase,_putative_636390..636620_POSITIVE 311 218 175 104 56 NC_009009:SSA_0322|5end_Transcriptional_activator,_TipA_family,_putative_314717..314947_POSITIVE 310 197 151 202 149 NC_009009:SSA_2197|5end_hypothetical_protein_2197784..2198014_NEGATIVE 308 49 1 57 9 NC_009009:SSA_0341|5end_hypothetical_protein_334731..334961_NEGATIVE 307 179 133 200 138 NC_009009:SSA_1217|5end_Conserved_uncharacterized_protein_1238964..1239194_POSITIVE 304 219 172 106 57 NC_009009:SSA_0379|5end_PTS_system,_beta-glucoside-specific_EII_component,_putative_368822..369052_POSITIVE 303 206 161 85 36 NC_009009:SSA_1429|5end_hypothetical_protein_1437110..1437340_NEGATIVE 303 199 153 197 153 NC_009009:SSA_0251|5end_D-tyrosyl-tRNA(Tyr)_deacylase,_putative_244455..244685_POSITIVE 302 207 174 222 187 NC_009009:SSA_2046|5end_Uridine_phosphorylase,_putative_2049721..2049951_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 395 207 165 144 102 NC_009009:SSA_0139|3end_Copper_transport_operon_or_penicillinase_transcriptional_repressor,_putative_134706..134856_POSITIVE 339 42 5 51 1 NC_009009:SSA_0318|3end_Secreted_metalloendopeptidase_Gcp_312791..312941_POSITIVE 326 40 1 151 106 NC_009009:SSA_0599|3end_hypothetical_protein_589007..589157_POSITIVE 321 189 141 70 15 NC_009009:SSA_0602|3end_ABC-type_cobalt_transport_system,_ATPase_component,_putative_591683..591833_POSITIVE 316 188 144 122 72 NC_009009:SSA_0929|3end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_940263..940413_POSITIVE 315 180 132 96 42 NC_009009:SSA_0826|3end_hypothetical_protein_805516..805666_POSITIVE 310 197 151 144 91 NC_009009:SSA_2198|3end_hypothetical_protein_2197842..2197992_NEGATIVE 305 165 128 59 12 NC_009009:SSA_1012|3end_Phosphoenolpyruvate_synthase,_putative_1017314..1017464_POSITIVE 303 206 161 88 39 NC_009009:SSA_1430|3end_Ribonuclease_Z,_putative_1437107..1437257_NEGATIVE 303 199 153 128 84 NC_009009:SSA_0250|3end_GTP_pyrophosphokinase,_putative_244466..244616_POSITIVE 298 178 131 47 8 NC_009009:SSA_1784|3end_Glutamate_racemase,_putative_1769103..1769253_NEGATIVE 296 37 2 67 28 NC_009009:SSA_1982|3end_Transcriptional_regulator,_LytR/AlgR_family,_putative_1975427..1975577_NEGATIVE 291 90 41 132 77 NC_009009:SSA_1115|3end_Cytochrome_C-type_biogenesis_protein,_putative_1142404..1142554_POSITIVE 290 190 144 151 88 NC_009009:SSA_2336|3end_Transcriptional_regulator,_PadR_family,_putative_2338785..2338935_POSITIVE 282 180 138 133 97 NC_009009:SSA_0314|3end_Nucleoside-diphosphate-sugar_epimerase,_putative_308967..309117_NEGATIVE 279 188 155 151 101 NC_009009:SSA_0240|3end_Acetyltransferase,_GNAT_family,_putative_233960..234110_POSITIVE 274 44 2 52 9 NC_009009:SSA_1846|3end_Phosphoprotein_phosphatase,_putative_1840178..1840328_NEGATIVE 274 44 1 56 3 NC_009009:SSA_1602|3end_Exoribonuclease,_VacB/Rnb_family,_putative_1607022..1607172_NEGATIVE 273 47 1 83 42 NC_009009:SSA_1651|3end_hypothetical_protein_1649587..1649737_NEGATIVE 273 187 150 43 1 NC_009009:SSA_1365|3end_FmtA-like_protein,_putative_1381352..1381502_NEGATIVE