Origin IGS: ttacatcaaaaattgaaagattgggagaattctcagtctttttttgcacaaaataaaaagcataatgtaaattatatattgcattatagagatttataaagtgaaaggagaatctataagataatggcagaaaaagcgctttgagaagtatttggaccaattggaagaagagagataagttgtccttctcatttaaactttccagctctgctatttttcaaacaaatattttgcccagttttttcaatcaggttataataaatagatgaattaaaaaattcagaaaattttatagagaaaagagagttgaaatctt .........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 aagatttcaactctcttttctctataaaattttctgaattttttaattcatctatttattataacctgattgaaaaaactgggcaaaatatttgtttgaaaaatagcagagctggaaagtttaaatgagaaggacaacttatctctcttcttccaattggtccaaatacttctcaaagcgctttttctgccattatcttatagattctcctttcactttataaatctctataatgcaatatataatttacattatgctttttattttgtgcaaaaaaagactgagaattctcccaatctttcaatttttgatgtaa Mask Tandem Repeat Region ================================================ ttacatcaaaaattgaaagattgggagaattctcagtctttttttgcacaaaataaaaagcataatgtaaattatatattgcattatagagatttataaagtgaaaggagaatctataagataatggcagaaaaagcgctttgagaagtatttggaccaattggaagaagagagataagttgtccttctcatttaaactttccagctctgctatttttcaaacaaatattttgcccagttttttcaatcaggttataataaatagatgaattaaaaaattcagaaaattttatagagaaaagagagttgaaatctt Find is-nt database================================================ Query_seq: SSA_0592:SSA_0593|SSA_0592:SSA_0593:hypothetical protein:Rhodanese-like sulfurtransferase, putative:->->:584309..584624 316 ttacatcaaaaattgaaagattgggagaattctcagtctttttttgcacaaaataaaaagcataatgtaaattatatattgcattatagagatttataaagtgaaaggagaatctataagataatggcagaaaaagcgctttgagaagtatttggaccaattggaagaagagagataagttgtccttctcatttaaactttccagctctgctatttttcaaacaaatattttgcccagttttttcaatcaggttataataaatagatgaattaaaaaattcagaaaattttatagagaaaagagagttgaaatctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0592:SSA_0593|SSA_0592:SSA_0593:hypothetical protein:Rhodanese-like sulfurtransferase, putative:->->:584309..584624 316 ttacatcaaaaattgaaagattgggagaattctcagtctttttttgcacaaaataaaaagcataatgtaaattatatattgcattatagagatttataaagtgaaaggagaatctataagataatggcagaaaaagcgctttgagaagtatttggaccaattggaagaagagagataagttgtccttctcatttaaactttccagctctgctatttttcaaacaaatattttgcccagttttttcaatcaggttataataaatagatgaattaaaaaattcagaaaattttatagagaaaagagagttgaaatctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0592:SSA_0593|SSA_0592:SSA_0593:hypothetical protein:Rhodanese-like sulfurtransferase, putative:->->:584309..584624 316 ttacatcaaaaattgaaagattgggagaattctcagtctttttttgcacaaaataaaaagcataatgtaaattatatattgcattatagagatttataaagtgaaaggagaatctataagataatggcagaaaaagcgctttgagaagtatttggaccaattggaagaagagagataagttgtccttctcatttaaactttccagctctgctatttttcaaacaaatattttgcccagttttttcaatcaggttataataaatagatgaattaaaaaattcagaaaattttatagagaaaagagagttgaaatctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttacatcaaaaattgaaagattgggagaattctcagtctttttttgcacaaaataaaaagcataatgtaaattatatattgcattatagagatttataaagtgaaaggagaatctataagataatggcagaaaaagcgctttgagaagtatttggaccaattggaagaagagagataagttgtccttctcatttaaactttccagctctgctatttttcaaacaaatattttgcccagttttttcaatcaggttataataaatagatgaattaaaaaattcagaaaattttatagagaaaagagagttgaaatctt Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 160 End: 255 ............................................................................................................................................................... M G R R E I S C P S H L N F P A L L F F K Q I F C P V F S I R L ............................................................. Protein_Len: 42 Strand: + Start: 141 End: 266 ............................................................................................................................................ M R S I W T N W K K R D K L S F S F K L S S S A I F Q T N I L P S F F N Q V I I N R .................................................. Protein_Len: 34 Strand: - Start: 192 End: 293 ............................................................................................................................................................................................... K F K G A R S N K L C I N Q G T K E I L N Y Y I S S N F F E S F K M ....................... Protein_Len: 32 Strand: - Start: 97 End: 192 ................................................................................................ L T F P S D I L Y H C F F R K S F Y K S W N S S S L Y T T R R M ............................................................................................................................ Protein_Len: 60 Strand: - Start: 2 End: 214 . T K K Q V F Y F A Y H L N Y I A N Y L N I F H F S F R Y S L P L F L A K L L I Q V L Q F F L S L N D K E N L S E L E A M ...................................................................................................... Protein_Len: 31 Strand: - Start: 4 End: 93 ... * M L F Q F I P L I R L R K K C L I F L M I Y I I Y Q M I S M ............................................................................................................................................................................................................................... ttacatcaaaaattgaaagattgggagaattctcagtctttttttgcacaaaataaaaagcataatgtaaattatatattgcattatagagatttataaagtgaaaggagaatctataagataatggcagaaaaagcgctttgagaagtatttggaccaattggaagaagagagataagttgtccttctcatttaaactttccagctctgctatttttcaaacaaatattttgcccagttttttcaatcaggttataataaatagatgaattaaaaaattcagaaaattttatagagaaaagagagttgaaatctt 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: 89 Start: 230 End: 259 .....................................................................................................................................................................................................................................TTTGCCCAGTTTTTTCAATCAGGTTATAAT......................................................... PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 71 End: 100 ......................................................................TTTATAAATCTCTATAATGCAATATATAAT........................................................................................................................................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttacatcaaaaattgaaagattgggagaattctcagtctttttttgcacaaaataaaaagcataatgtaaattatatattgcattatagagatttataaagtgaaaggagaatctataagataatggcagaaaaagcgctttgagaagtatttggaccaattggaagaagagagataagttgtccttctcatttaaactttccagctctgctatttttcaaacaaatattttgcccagttttttcaatcaggttataataaatagatgaattaaaaaattcagaaaattttatagagaaaagagagttgaaatctt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0592:SSA_0593|SSA_0592:SSA_0593:hypothetical protein:Rhodanese-like sulfurtransferase, putative:->->:584309..584624 316 ttacatcaaaaattgaaagattgggagaattctcagtctttttttgcacaaaataaaaagcataatgtaaattatatattgcattatagagatttataaagtgaaaggagaatctataagataatggcagaaaaagcgctttgagaagtatttggaccaattggaagaagagagataagttgtccttctcatttaaactttccagctctgctatttttcaaacaaatattttgcccagttttttcaatcaggttataataaatagatgaattaaaaaattcagaaaattttatagagaaaagagagttgaaatctt Intra-Species Hit: Count: 1 Min: 1 Max: 316 Len: 316 Subject: NC_009009_SSA_0592_SSA_0593|hypothetical protein:Rhodanese-like sulfurtransferase, putative|POSITIVE:POSITIVE|[584309,584624]|316 HSP 1 e-value: 1.0E-166 bit: 585.0 Len: 316 Query Start:1 Query End:316 Subject Strand: POSITIVE Subject Start: 1 Subject End: 316 ttacatcaaaaattgaaagattgggagaattctcagtcnnnnnnngcacaaaataaaaagcataatgtaaattatatattgcattatagagatttataaagtgaaaggagaatctataagataatggcagaaaaagcgctttgagaagtatttggaccaattggaagaagagagataagttgtccttctcatttaaactttccagctctgctatttttcaaacaaatattttgcccagttttttcaatcaggttataataaatagatgaattaaaaaattcagaaaattttatagagaaaagagagttgaaatctt ttacatcaaaaattgaaagattgggagaattctcagtctttttttgcacaaaataaaaagcataatgtaaattatatattgcattatagagatttataaagtgaaaggagaatctataagataatggcagaaaaagcgctttgagaagtatttggaccaattggaagaagagagataagttgtccttctcatttaaactttccagctctgctatttttcaaacaaatattttgcccagttttttcaatcaggttataataaatagatgaattaaaaaattcagaaaattttatagagaaaagagagttgaaatctt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUACAUCAAAAAUUGAAAGAUUGGGAGAAUUCUCAGUCUUUUUUUGCACAAAAUAAAAAGCAUAAUGUAAAUUAUAUAUUGCAUUAUAGAGAUUUAUAAAGUGAAAGGAGAAUCUAUAAGAUAAUGGCAGAAAAAGCGCUUUGAGAAGUAUUUGGACCAAUUGGAAGAAGAGAGAUAAGUUGUCCUUCUCAUUUAAACUUUCCAGCUCUGCUAUUUUUCAAACAAAUAUUUUGCCCAGUUUUUUCAAUCAGGUUAUAAUAAAUAGAUGAAUUAAAAAAUUCAGAAAAUUUUAUAGAGAAAAGAGAGUUGAAAUCUU ................((((((.....(((((((..((((((((..(.....(((((...((((((((((........))))))))).)...)))))...)..)))))))).((((((((((..(((..((((((((.......((((((((((......((((((((((((((..(((((..............))))).....)))).)).)))))))).)))))))))).....))))))))..)))................((((((....))))))....)))))))))).....)))))))..)))))) (-63.64) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGAUUUCAACUCUCUUUUCUCUAUAAAAUUUUCUGAAUUUUUUAAUUCAUCUAUUUAUUAUAACCUGAUUGAAAAAACUGGGCAAAAUAUUUGUUUGAAAAAUAGCAGAGCUGGAAAGUUUAAAUGAGAAGGACAACUUAUCUCUCUUCUUCCAAUUGGUCCAAAUACUUCUCAAAGCGCUUUUUCUGCCAUUAUCUUAUAGAUUCUCCUUUCACUUUAUAAAUCUCUAUAAUGCAAUAUAUAAUUUACAUUAUGCUUUUUAUUUUGUGCAAAAAAAGACUGAGAAUUCUCCCAAUCUUUCAAUUUUUGAUGUAA ......((((........................((((((....)))))).................((((((((....((((..................(((.((((((..((...((((...(((((((........(((...............))).......))))))))))).))..)))))).)))........((((((((((((((...(((((....(((((((.((........)).)))))))...)))))...))).....))))...)))))))..))))...)))))))).))))..... (-45.52) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 310 130 81 197 143 NC_009009:SSA_0013|5end_Cell_cycle_control_ATPase,_PP-loop_superfamily,_putative_11196..11426_POSITIVE 293 194 163 145 115 NC_009009:SSA_1299|5end_Maltose/maltodextrin_ABC_transport_system,_putative_1316629..1316859_POSITIVE 282 212 173 228 194 NC_009009:SSA_2212|5end_Possible_polysaccharide_transport_protein,_putative_2213928..2214158_NEGATIVE 279 222 182 160 125 NC_009009:SSA_0239|5end_7,8-dihydro-8-oxoguanine-triphosphatase,_putative_232961..233191_POSITIVE 277 163 127 62 27 NC_009009:SSA_0100|5end_DNA_polymerase_I_-_3'-5'_exonuclease_and_polymerase_domains,_putative_100680..100910_POSITIVE 271 48 1 165 113 NC_009009:SSA_0366|5end_hypothetical_protein_357506..357736_POSITIVE 269 219 178 227 176 NC_009009:SSA_0990|5end_hypothetical_protein_991733..991963_POSITIVE 267 190 143 99 46 NC_009009:SSA_1120|5end_Two-component_sensor_kinase_(with_C-terminal_ATPase_domain),_putative_1145222..1145452_POSITIVE 267 191 154 204 164 NC_009009:SSA_0474|5end_Uroporphyrin-III_C-methyltransferase/uroporphyrinogen-III_synthase,_putative_476270..476500_POSITIVE 265 223 181 178 135 NC_009009:SSA_0803|5end_hypothetical_protein_785145..785375_POSITIVE 260 154 111 123 85 NC_009009:SSA_1134|5end_Xanthine_phosphoribosyltransferase,_putative_1159628..1159858_POSITIVE 259 159 119 65 13 NC_009009:SSA_0491|5end_Alpha-ribazole-5'-phosphate_phosphatase,_putative_490961..491191_POSITIVE 259 61 32 189 160 NC_009009:SSA_0305|5end_hypothetical_protein_301985..302215_POSITIVE 257 170 122 219 172 NC_009009:SSA_1859|5end_Penicillin-binding_protein-like_factor_A/_recombinase,_putative_1853704..1853934_POSITIVE 255 51 18 231 188 NC_009009:SSA_1949|5end_AliA_protein,_putative_1944373..1944603_NEGATIVE 255 222 186 131 96 NC_009009:SSA_1459|5end_RNA_methyltransferase,_putative_1467481..1467711_NEGATIVE 255 208 169 225 182 NC_009009:SSA_0162|5end_hypothetical_protein_161391..161621_POSITIVE 254 219 171 217 170 NC_009009:SSA_1586|5end_hypothetical_protein_1588182..1588412_NEGATIVE 254 219 171 201 153 NC_009009:SSA_0226|5end_60_kDa_chaperonin_218947..219177_POSITIVE 253 177 137 167 120 NC_009009:SSA_1945|5end_Oligopeptide_transport_ATP-binding_protein,_putative_1937689..1937919_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 313 220 173 121 75 NC_009009:SSA_2213|3end_Nucleotide_sugar_dehydratase,_putative_2214047..2214197_NEGATIVE 293 194 163 63 33 NC_009009:SSA_1298|3end_Maltose/maltodextrin_ABC_transporter,_sugar-binding_protein_MalX,_putative_1316627..1316777_POSITIVE 284 48 4 95 55 NC_009009:SSA_0599|3end_hypothetical_protein_589007..589157_POSITIVE 283 47 6 34 1 NC_009009:SSA_0326|3end_Conserved_uncharacterized_BCR,_YbaB_family_319524..319674_NEGATIVE 279 222 182 150 115 NC_009009:SSA_0238|3end_hypothetical_protein_233031..233181_POSITIVE 274 216 176 96 48 NC_009009:SSA_0345|3end_hypothetical_protein_339209..339359_POSITIVE 271 48 1 143 91 NC_009009:SSA_0365|3end_Small-conductance_mechanosensitive_efflux_channel,_putative_357564..357714_POSITIVE 267 190 143 102 49 NC_009009:SSA_1119|3end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_AraC-type_DNA-binding_domains),_putative_1145305..1145455_POSITIVE 260 154 111 80 42 NC_009009:SSA_1133|3end_TatA,_sec-independent_protein_secretion_pathway_component,_putative_1159665..1159815_POSITIVE 259 159 119 68 16 NC_009009:SSA_0490|3end_Cobalamin_5'-phosphate_synthase,_putative_491044..491194_POSITIVE 256 147 101 47 4 NC_009009:SSA_0407|3end_ABC-type_multidrug_transport_system_(3-component_subtilin_immunity_exporter),_ATPase_component,_putative_402911..403061_NEGATIVE 255 222 186 46 11 NC_009009:SSA_1460|3end_Transcriptional_attenuator_LytR,_putative_1467566..1467716_NEGATIVE 254 168 128 36 3 NC_009009:SSA_2323|3end_Transporter,_putative_2328850..2329000_POSITIVE 248 207 178 125 95 NC_009009:SSA_0494|3end_ABC-type_dipeptide/oligopeptide/nickel_transport_system,_ATPase_component,_putative_495269..495419_POSITIVE 243 143 101 61 24 NC_009009:SSA_1442|3end_Imidazole_glycerol-phosphate_synthase_subunit_hisF,_putative_1445183..1445333_NEGATIVE 239 189 143 72 29 NC_009009:SSA_1915|3end_hypothetical_protein_1905276..1905426_NEGATIVE 237 213 175 118 73 NC_009009:SSA_0595|3end_hypothetical_protein_586983..587133_POSITIVE 236 218 180 119 79 NC_009009:SSA_0065|3end_Low_molecular_weight_phosphotyrosine_protein_phosphatase,_putative_67677..67827_POSITIVE 235 248 202 105 50 NC_009009:SSA_0703|3end_Citrate_synthase,_putative_689352..689502_POSITIVE 233 244 202 47 4 NC_009009:SSA_2308|3end_hypothetical_protein_2309893..2310043_NEGATIVE