Origin IGS: atacgatactccttactaatgcgtttttttacatatcgcagaacaatctctactattccctatttcagatagtgcgatactcggacattgagtgcaataattgtaaatcacacaagtactgcagtttttactatcattcaaaataaaaagaaagctgcagttcttttaatcctgtatcaacgattcattctgaaatcgaataggagacatttcccaagtctacaattcacttcatctcaaattaatttctgtaattcacccttagtttatagattttatactcaacaaaagtataaagcatacaaaacttcactttgaaccagtatttatactatattccgtattaaaaattctattattggttttgaaaaaaacagtcttcaaatatcctgaaatatagcaaaaagagattgggtaaaaactcattgtctcttc .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 gaagagacaatgagtttttacccaatctctttttgctatatttcaggatatttgaagactgtttttttcaaaaccaataatagaatttttaatacggaatatagtataaatactggttcaaagtgaagttttgtatgctttatacttttgttgagtataaaatctataaactaagggtgaattacagaaattaatttgagatgaagtgaattgtagacttgggaaatgtctcctattcgatttcagaatgaatcgttgatacaggattaaaagaactgcagctttctttttattttgaatgatagtaaaaactgcagtacttgtgtgatttacaattattgcactcaatgtccgagtatcgcactatctgaaatagggaatagtagagattgttctgcgatatgtaaaaaaacgcattagtaaggagtatcgtat Mask Tandem Repeat Region ================================================ atacgatactccttactaatgcgtttttttacatatcgcagaacaatctctactattccctatttcagatagtgcgatactcggacattgagtgcaataattgtaaatcacacaagtactgcagtttttactatcattcaaaataaaaagaaagctgcagttcttttaatcctgtatcaacgattcattctgaaatcgaataggagacatttcccaagtctacaattcacttcatctcaaattaatttctgtaattcacccttagtttatagattttatactcaacaaaagtataaagcatacaaaacttcactttgaaccagtatttatactatattccgtattaaaaattctattattggttttgaaaaaaacagtcttcaaatatcctgaaatatagcaaaaagagattgggtaaaaactcattgtctcttc Find is-nt database================================================ Query_seq: SMT_972:SMT_973|SMT_972:SMT_973:ABC-type multidrug/protein/lipid transport system, ATPase component:signal transduction histidine kinase:<-<-:920858..921292 435 atacgatactccttactaatgcgtttttttacatatcgcagaacaatctctactattccctatttcagatagtgcgatactcggacattgagtgcaataattgtaaatcacacaagtactgcagtttttactatcattcaaaataaaaagaaagctgcagttcttttaatcctgtatcaacgattcattctgaaatcgaataggagacatttcccaagtctacaattcacttcatctcaaattaatttctgtaattcacccttagtttatagattttatactcaacaaaagtataaagcatacaaaacttcactttgaaccagtatttatactatattccgtattaaaaattctattattggttttgaaaaaaacagtcttcaaatatcctgaaatatagcaaaaagagattgggtaaaaactcattgtctcttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_972:SMT_973|SMT_972:SMT_973:ABC-type multidrug/protein/lipid transport system, ATPase component:signal transduction histidine kinase:<-<-:920858..921292 435 atacgatactccttactaatgcgtttttttacatatcgcagaacaatctctactattccctatttcagatagtgcgatactcggacattgagtgcaataattgtaaatcacacaagtactgcagtttttactatcattcaaaataaaaagaaagctgcagttcttttaatcctgtatcaacgattcattctgaaatcgaataggagacatttcccaagtctacaattcacttcatctcaaattaatttctgtaattcacccttagtttatagattttatactcaacaaaagtataaagcatacaaaacttcactttgaaccagtatttatactatattccgtattaaaaattctattattggttttgaaaaaaacagtcttcaaatatcctgaaatatagcaaaaagagattgggtaaaaactcattgtctcttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_972:SMT_973|SMT_972:SMT_973:ABC-type multidrug/protein/lipid transport system, ATPase component:signal transduction histidine kinase:<-<-:920858..921292 435 atacgatactccttactaatgcgtttttttacatatcgcagaacaatctctactattccctatttcagatagtgcgatactcggacattgagtgcaataattgtaaatcacacaagtactgcagtttttactatcattcaaaataaaaagaaagctgcagttcttttaatcctgtatcaacgattcattctgaaatcgaataggagacatttcccaagtctacaattcacttcatctcaaattaatttctgtaattcacccttagtttatagattttatactcaacaaaagtataaagcatacaaaacttcactttgaaccagtatttatactatattccgtattaaaaattctattattggttttgaaaaaaacagtcttcaaatatcctgaaatatagcaaaaagagattgggtaaaaactcattgtctcttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atacgatactccttactaatgcgtttttttacatatcgcagaacaatctctactattccctatttcagatagtgcgatactcggacattgagtgcaataattgtaaatcacacaagtactgcagtttttactatcattcaaaataaaaagaaagctgcagttcttttaatcctgtatcaacgattcattctgaaatcgaataggagacatttcccaagtctacaattcacttcatctcaaattaatttctgtaattcacccttagtttatagattttatactcaacaaaagtataaagcatacaaaacttcactttgaaccagtatttatactatattccgtattaaaaattctattattggttttgaaaaaaacagtcttcaaatatcctgaaatatagcaaaaagagattgggtaaaaactcattgtctcttc Predict ORF larger than 30AA ================================================ Protein_Len: 46 Strand: + Start: 6 End: 143 ..... M L L T N A F F Y I S Q N N L Y Y S L F Q I V R Y S D I E C N N C K S H K Y C S F Y Y H S K .................................................................................................................................................................................................................................................................................................... Protein_Len: 60 Strand: + Start: 88 End: 315 ....................................................................................... M S A I I V N H T S T A V F T I I Q N K K K A A V L L I L Y Q R F I L K S N R R H F P S L Q F T S S Q I N F C N S P L V ........................................................................................................................ Protein_Len: 43 Strand: + Start: 269 End: 397 ............................................................................................................................................................................................................................................................................ M D F I L N K S I K H T K L H F E P V F I L Y S V L K I L L L V L K K T V F K Y P E I ...................................... Protein_Len: 38 Strand: - Start: 313 End: 426 ........................................................................................................................................................................................................................................................................................................................ K S G T N I S Y E T N F I R N N T K F F V T K L Y G S I Y C F S I P Y F S M ......... Protein_Len: 42 Strand: - Start: 19 End: 144 .................. H T K K C I A S C D R S N G I E S L A I S P C Q T C Y N Y I V C T S C N K S D N L M ................................................................................................................................................................................................................................................................................................... atacgatactccttactaatgcgtttttttacatatcgcagaacaatctctactattccctatttcagatagtgcgatactcggacattgagtgcaataattgtaaatcacacaagtactgcagtttttactatcattcaaaataaaaagaaagctgcagttcttttaatcctgtatcaacgattcattctgaaatcgaataggagacatttcccaagtctacaattcacttcatctcaaattaatttctgtaattcacccttagtttatagattttatactcaacaaaagtataaagcatacaaaacttcactttgaaccagtatttatactatattccgtattaaaaattctattattggttttgaaaaaaacagtcttcaaatatcctgaaatatagcaaaaagagattgggtaaaaactcattgtctcttc 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: 82 Start: 27 End: 56 ..........................TTTTACATATCGCAGAACAATCTCTACTAT........................................................................................................................................................................................................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atacgatactccttactaatgcgtttttttacatatcgcagaacaatctctactattccctatttcagatagtgcgatactcggacattgagtgcaataattgtaaatcacacaagtactgcagtttttactatcattcaaaataaaaagaaagctgcagttcttttaatcctgtatcaacgattcattctgaaatcgaataggagacatttcccaagtctacaattcacttcatctcaaattaatttctgtaattcacccttagtttatagattttatactcaacaaaagtataaagcatacaaaacttcactttgaaccagtatttatactatattccgtattaaaaattctattattggttttgaaaaaaacagtcttcaaatatcctgaaatatagcaaaaagagattgggtaaaaactcattgtctcttc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_972:SMT_973|SMT_972:SMT_973:ABC-type multidrug/protein/lipid transport system, ATPase component:signal transduction histidine kinase:<-<-:920858..921292 435 atacgatactccttactaatgcgtttttttacatatcgcagaacaatctctactattccctatttcagatagtgcgatactcggacattgagtgcaataattgtaaatcacacaagtactgcagtttttactatcattcaaaataaaaagaaagctgcagttcttttaatcctgtatcaacgattcattctgaaatcgaataggagacatttcccaagtctacaattcacttcatctcaaattaatttctgtaattcacccttagtttatagattttatactcaacaaaagtataaagcatacaaaacttcactttgaaccagtatttatactatattccgtattaaaaattctattattggttttgaaaaaaacagtcttcaaatatcctgaaatatagcaaaaagagattgggtaaaaactcattgtctcttc Intra-Species Hit: Count: 1 Min: 1 Max: 435 Len: 435 Subject: smit_SMT_972_SMT_973|ABC-type multidrug/protein/lipid transport system, ATPase component:signal transduction histidine kinase|NEGATIVE:NEGATIVE|[920858,921292]|435 HSP 1 e-value: 0.0 bit: 779.0 Len: 435 Query Start:1 Query End:435 Subject Strand: POSITIVE Subject Start: 1 Subject End: 435 atacgatactccttactaatgcgnnnnnnnacatatcgcagaacaatctctactattccctatttcagatagtgcgatactcggacattgagtgcaataattgtaaatcacacaagtactgcagtttttactatcattcaaaataaaaagaaagctgcagttcttttaatcctgtatcaacgattcattctgaaatcgaataggagacatttcccaagtctacaattcacttcatctcaaattaatttctgtaattcacccttagtttatagattttatactcaacaaaagtataaagcatacaaaacttcactttgaaccagtatttatactatattccgtattaaaaattctattattggttttgnnnnnnncagtcttcaaatatcctgaaatatagcaaaaagagattgggtaaaaactcattgtctcttc atacgatactccttactaatgcgtttttttacatatcgcagaacaatctctactattccctatttcagatagtgcgatactcggacattgagtgcaataattgtaaatcacacaagtactgcagtttttactatcattcaaaataaaaagaaagctgcagttcttttaatcctgtatcaacgattcattctgaaatcgaataggagacatttcccaagtctacaattcacttcatctcaaattaatttctgtaattcacccttagtttatagattttatactcaacaaaagtataaagcatacaaaacttcactttgaaccagtatttatactatattccgtattaaaaattctattattggttttgaaaaaaacagtcttcaaatatcctgaaatatagcaaaaagagattgggtaaaaactcattgtctcttc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUACGAUACUCCUUACUAAUGCGUUUUUUUACAUAUCGCAGAACAAUCUCUACUAUUCCCUAUUUCAGAUAGUGCGAUACUCGGACAUUGAGUGCAAUAAUUGUAAAUCACACAAGUACUGCAGUUUUUACUAUCAUUCAAAAUAAAAAGAAAGCUGCAGUUCUUUUAAUCCUGUAUCAACGAUUCAUUCUGAAAUCGAAUAGGAGACAUUUCCCAAGUCUACAAUUCACUUCAUCUCAAAUUAAUUUCUGUAAUUCACCCUUAGUUUAUAGAUUUUAUACUCAACAAAAGUAUAAAGCAUACAAAACUUCACUUUGAACCAGUAUUUAUACUAUAUUCCGUAUUAAAAAUUCUAUUAUUGGUUUUGAAAAAAACAGUCUUCAAAUAUCCUGAAAUAUAGCAAAAAGAGAUUGGGUAAAAACUCAUUGUCUCUUC ...................(((((((((((.((....((((((.........((((((...((((((((..((..(((((..(((...(((.((((.....))))..)))...(((.((((((((((((....................)))))))))))).)))....))).))))).)).......)))))))).)))))).((((.........)))).........................))))))...........(((((.((..(((((((((.......)))))))))..))..))))).......(((((((((...((((........))))............)))))))))))))))))))....((((.......)))).....)))..((((((((((((....)))))..))))))). (-78.61) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAGAGACAAUGAGUUUUUACCCAAUCUCUUUUUGCUAUAUUUCAGGAUAUUUGAAGACUGUUUUUUUCAAAACCAAUAAUAGAAUUUUUAAUACGGAAUAUAGUAUAAAUACUGGUUCAAAGUGAAGUUUUGUAUGCUUUAUACUUUUGUUGAGUAUAAAAUCUAUAAACUAAGGGUGAAUUACAGAAAUUAAUUUGAGAUGAAGUGAAUUGUAGACUUGGGAAAUGUCUCCUAUUCGAUUUCAGAAUGAAUCGUUGAUACAGGAUUAAAAGAACUGCAGCUUUCUUUUUAUUUUGAAUGAUAGUAAAAACUGCAGUACUUGUGUGAUUUACAAUUAUUGCACUCAAUGUCCGAGUAUCGCACUAUCUGAAAUAGGGAAUAGUAGAGAUUGUUCUGCGAUAUGUAAAAAAACGCAUUAGUAAGGAGUAUCGUAU ..((((((.....)))))).(((((((((..((..((.(((((((((....((((...((((....((((...((....((((((((((.......((((.(((((....))))))))).....))))))))))....(((((((((.....))))))))).............)).))))..))))...))))))))))))).))..))..).))).))))).(((.(((.((((((.((((((((.......((((((((.((((...(((.(((((((.....((((((((.........))))))))))))))).)))(((..((........))..))).....))))..)))))).))..))))))))...)))))).))).)))....((((((((........((......)).....)))))))). (-101.12) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 878 90 41 181 132 smit:SMT_972|5end_ABC-type_multidrug/protein/lipid_transport_system,_ATPase_component_920767..920997_NEGATIVE 284 75 38 110 69 smit:SMT_885|5end_single-stranded-DNA-specific_exonuclease_RecJ_832660..832890_NEGATIVE 272 416 376 111 64 smit:SMT_211|5end_hypothetical_protein_predicted_by_Glimmer/Critica_144135..144365_POSITIVE 264 75 32 59 14 smit:SMT_1474|5end_K02003_1455170..1455400_POSITIVE 262 251 214 60 24 smit:SMT_1955|5end_carbamoyl-phosphate_synthase_small_chain_1889408..1889638_NEGATIVE 261 230 181 129 76 smit:SMT_1066|5end_holo-(acyl_carrier_protein)_synthase_1005411..1005641_POSITIVE 258 179 154 65 39 smit:SMT_191|5end_adenylate_kinase_125745..125975_POSITIVE 254 260 211 118 64 smit:SMT_1380|5end_pyrroline-5-carboxylate_reductase_1358464..1358694_NEGATIVE 254 236 203 218 191 smit:SMT_990|5end_hypothetical_protein_933947..934177_NEGATIVE 253 89 47 222 166 smit:SMT_1578|5end_K02057_simple_sugar_transport_system_permease_protein_1570854..1571084_POSITIVE 253 87 46 226 194 smit:SMT_540|5end_DNA_gyrase,_B_subunit_456358..456588_POSITIVE 245 200 158 119 65 smit:SMT_1870|5end_K07566_putative_translation_factor_1829819..1830049_NEGATIVE 242 209 162 142 82 smit:SMT_1750|5end_anthranilate_phosphoribosyltransferase_1728011..1728241_POSITIVE 241 208 169 116 80 smit:SMT_2109|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1999099..1999329_NEGATIVE 241 200 154 133 75 smit:SMT_848|5end_hypothetical_protein_795153..795383_NEGATIVE 241 198 153 99 56 smit:SMT_665|5end_NAD+_kinase_576745..576975_NEGATIVE 241 42 9 144 99 smit:SMT_566|5end_K07282_poly-gamma-glutamate_synthesis_protein_(capsule_biosynthesis_protein)_483498..483728_POSITIVE 236 224 181 170 134 smit:SMT_1521|5end_K02003_1501887..1502117_NEGATIVE 236 87 45 77 16 smit:SMT_595|5end_phosphoglycerate_mutase_512593..512823_NEGATIVE 232 98 57 216 176 smit:SMT_1526|5end_K07720_two-component_system,_response_regulator_YesN_1510554..1510784_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 261 230 181 90 37 smit:SMT_1065|3end_phospho-2-dehydro-3-deoxyheptonate_aldolase_1005452..1005602_POSITIVE 259 425 400 93 69 smit:SMT_593|3end_K02030_polar_amino_acid_transport_system_substrate-binding_protein_510317..510467_POSITIVE 254 260 211 114 60 smit:SMT_1381|3end_gamma-glutamyl_phosphate_reductase_1358468..1358618_NEGATIVE 254 236 203 132 105 smit:SMT_991|3end_hypothetical_protein_934033..934183_NEGATIVE 245 200 158 135 81 smit:SMT_1871|3end_modification_methylase,_HemK_family_1829803..1829953_NEGATIVE 245 95 53 150 102 smit:SMT_903|3end_hypothetical_protein_851945..852095_NEGATIVE 242 209 162 131 71 smit:SMT_1749|3end_anthranilate_synthase_component_II_1728080..1728230_POSITIVE 241 200 154 136 78 smit:SMT_849|3end_hypothetical_protein_795150..795300_NEGATIVE 241 198 153 115 72 smit:SMT_666|3end_GTP_pyrophosphokinase-like_protein_576729..576879_NEGATIVE 237 415 371 69 18 smit:SMT_1299|3end_MutT/NUDIX_family_protein_1262572..1262722_POSITIVE 236 216 171 79 34 smit:SMT_1864|3end_integral_membrane_protein_1827172..1827322_POSITIVE 236 87 45 80 19 smit:SMT_596|3end_K03976_putative_transcription_regulator_512590..512740_NEGATIVE 232 79 32 133 87 smit:SMT_963|3end_K02015_iron_complex_transport_system_permease_protein_908586..908736_NEGATIVE 231 115 72 85 41 smit:SMT_772|3end_spermidine/putrescine_ABC_transporter,_ATP-binding_protein_682143..682293_NEGATIVE 227 118 72 151 98 smit:SMT_1806|3end_aminoacylase/N-acyl-L-amino_acid_amidohydrolase/hippurate_hydrolase_1781644..1781794_POSITIVE 227 238 197 147 110 smit:SMT_1643|3end_2-isopropylmalate_synthase_1630772..1630922_POSITIVE 227 190 149 105 65 smit:SMT_1253|3end_beta-galactosidase_1212912..1213062_NEGATIVE 227 198 151 72 20 smit:SMT_541|3end_K03697_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpE_457120..457270_NEGATIVE 226 239 194 59 16 smit:SMT_877|3end_hypothetical_protein_823558..823708_NEGATIVE 225 205 169 51 21 smit:SMT_1614|3end_K08998_hypothetical_protein_1601652..1601802_POSITIVE