Origin IGS: tttcagaaaccatttgatcaattttagtaatgcagccttagggctgtatttttttgaaaaaacatttaaatttcacacttgaaaggtctaattcaaacaaagaagtcaattccattcagttctctagtacgatctttgactaactttctagtctctttttttatgttcgttggctatcaatctctaatatctaagcaaaaaaggtgacagatatatcaaagtttgttaaattgatttggtatattatgtaatcaaaaggagatgtt .........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 aacatctccttttgattacataatataccaaatcaatttaacaaactttgatatatctgtcaccttttttgcttagatattagagattgatagccaacgaacataaaaaaagagactagaaagttagtcaaagatcgtactagagaactgaatggaattgacttctttgtttgaattagacctttcaagtgtgaaatttaaatgttttttcaaaaaaatacagccctaaggctgcattactaaaattgatcaaatggtttctgaaa Mask Tandem Repeat Region ================================================ tttcagaaaccatttgatcaattttagtaatgcagccttagggctgtatttttttgaaaaaacatttaaatttcacacttgaaaggtctaattcaaacaaagaagtcaattccattcagttctctagtacgatctttgactaactttctagtctctttttttatgttcgttggctatcaatctctaatatctaagcaaaaaaggtgacagatatatcaaagtttgttaaattgatttggtatattatgtaatcaaaaggagatgtt Find is-nt database================================================ Query_seq: SSA_1101:SSA_1102|SSA_1101:SSA_1102:Multidrug resistance efflux pump/hemolysin secretion transmembrane protein, putative:hypothetical protein:->->:1123260..1123525 266 tttcagaaaccatttgatcaattttagtaatgcagccttagggctgtatttttttgaaaaaacatttaaatttcacacttgaaaggtctaattcaaacaaagaagtcaattccattcagttctctagtacgatctttgactaactttctagtctctttttttatgttcgttggctatcaatctctaatatctaagcaaaaaaggtgacagatatatcaaagtttgttaaattgatttggtatattatgtaatcaaaaggagatgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1101:SSA_1102|SSA_1101:SSA_1102:Multidrug resistance efflux pump/hemolysin secretion transmembrane protein, putative:hypothetical protein:->->:1123260..1123525 266 tttcagaaaccatttgatcaattttagtaatgcagccttagggctgtatttttttgaaaaaacatttaaatttcacacttgaaaggtctaattcaaacaaagaagtcaattccattcagttctctagtacgatctttgactaactttctagtctctttttttatgttcgttggctatcaatctctaatatctaagcaaaaaaggtgacagatatatcaaagtttgttaaattgatttggtatattatgtaatcaaaaggagatgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1101:SSA_1102|SSA_1101:SSA_1102:Multidrug resistance efflux pump/hemolysin secretion transmembrane protein, putative:hypothetical protein:->->:1123260..1123525 266 tttcagaaaccatttgatcaattttagtaatgcagccttagggctgtatttttttgaaaaaacatttaaatttcacacttgaaaggtctaattcaaacaaagaagtcaattccattcagttctctagtacgatctttgactaactttctagtctctttttttatgttcgttggctatcaatctctaatatctaagcaaaaaaggtgacagatatatcaaagtttgttaaattgatttggtatattatgtaatcaaaaggagatgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttcagaaaccatttgatcaattttagtaatgcagccttagggctgtatttttttgaaaaaacatttaaatttcacacttgaaaggtctaattcaaacaaagaagtcaattccattcagttctctagtacgatctttgactaactttctagtctctttttttatgttcgttggctatcaatctctaatatctaagcaaaaaaggtgacagatatatcaaagtttgttaaattgatttggtatattatgtaatcaaaaggagatgtt Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 48 End: 140 ............................................... M F L K K H L N F T L E R S N S N K E V N S I Q F S S T I F D .............................................................................................................................. Protein_Len: 45 Strand: + Start: 70 End: 204 ..................................................................... M S H L K G L I Q T K K S I P F S S L V R S L T N F L V S F F M F V G Y Q S L I S K Q K R .............................................................. tttcagaaaccatttgatcaattttagtaatgcagccttagggctgtatttttttgaaaaaacatttaaatttcacacttgaaaggtctaattcaaacaaagaagtcaattccattcagttctctagtacgatctttgactaactttctagtctctttttttatgttcgttggctatcaatctctaatatctaagcaaaaaaggtgacagatatatcaaagtttgttaaattgatttggtatattatgtaatcaaaaggagatgtt 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: 135 End: 164 ......................................................................................................................................TTTGACTAACTTTCTAGTCTCTTTTTTTAT...................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 203 End: 232 ..........................................................................................................................................................................................................GGTGACAGATATATCAAAGTTTGTTAAATT.................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tttcagaaaccatttgatcaattttagtaatgcagccttagggctgtatttttttgaaaaaacatttaaatttcacacttgaaaggtctaattcaaacaaagaagtcaattccattcagttctctagtacgatctttgactaactttctagtctctttttttatgttcgttggctatcaatctctaatatctaagcaaaaaaggtgacagatatatcaaagtttgttaaattgatttggtatattatgtaatcaaaaggagatgtt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 62 HP_score: -3.3 Tail_Score: -4.53737 Start: 138 End: 153 Full_Region: TCTAGTACGATCTTT GACTA ACTTTC TAGTC TCTTTTTTTATGTTC .........................................................................................................................................GACTAACTTTCTAGTC................................................................................................................. Find igs database================================================ Query_seq: SSA_1101:SSA_1102|SSA_1101:SSA_1102:Multidrug resistance efflux pump/hemolysin secretion transmembrane protein, putative:hypothetical protein:->->:1123260..1123525 266 tttcagaaaccatttgatcaattttagtaatgcagccttagggctgtatttttttgaaaaaacatttaaatttcacacttgaaaggtctaattcaaacaaagaagtcaattccattcagttctctagtacgatctttgactaactttctagtctctttttttatgttcgttggctatcaatctctaatatctaagcaaaaaaggtgacagatatatcaaagtttgttaaattgatttggtatattatgtaatcaaaaggagatgtt Intra-Species Hit: Count: 1 Min: 1 Max: 266 Len: 266 Subject: NC_009009_SSA_1101_SSA_1102|Multidrug resistance efflux pump/hemolysin secretion transmembrane protein, putative:hypothetical protein|POSITIVE:POSITIVE|[1123260,1123525]|266 HSP 1 e-value: 1.0E-124 bit: 444.0 Len: 266 Query Start:1 Query End:266 Subject Strand: POSITIVE Subject Start: 1 Subject End: 266 tttcagaaaccatttgatcaattttagtaatgcagccttagggctgtannnnnnngaaaaaacatttaaatttcacacttgaaaggtctaattcaaacaaagaagtcaattccattcagttctctagtacgatctttgactaactttctagtctcnnnnnnnatgttcgttggctatcaatctctaatatctaagcaaaaaaggtgacagatatatcaaagtttgttaaattgatttggtatattatgtaatcaaaaggagatgtt tttcagaaaccatttgatcaattttagtaatgcagccttagggctgtatttttttgaaaaaacatttaaatttcacacttgaaaggtctaattcaaacaaagaagtcaattccattcagttctctagtacgatctttgactaactttctagtctctttttttatgttcgttggctatcaatctctaatatctaagcaaaaaaggtgacagatatatcaaagtttgttaaattgatttggtatattatgtaatcaaaaggagatgtt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUCAGAAACCAUUUGAUCAAUUUUAGUAAUGCAGCCUUAGGGCUGUAUUUUUUUGAAAAAACAUUUAAAUUUCACACUUGAAAGGUCUAAUUCAAACAAAGAAGUCAAUUCCAUUCAGUUCUCUAGUACGAUCUUUGACUAACUUUCUAGUCUCUUUUUUUAUGUUCGUUGGCUAUCAAUCUCUAAUAUCUAAGCAAAAAAGGUGACAGAUAUAUCAAAGUUUGUUAAAUUGAUUUGGUAUAUUAUGUAAUCAAAAGGAGAUGUU .........((.((((((...((((((.(((((((((....)))))))))...))))))..((((....(((((....(((((........))))).....))))).....(((.((((((.......((((.((((((.......(((.(((.(((((((..(((...((((.(((.........))).)))))))))))))).))))))....)))))).))))..))))))..)))......)))).)))))).))....... (-47.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACAUCUCCUUUUGAUUACAUAAUAUACCAAAUCAAUUUAACAAACUUUGAUAUAUCUGUCACCUUUUUUGCUUAGAUAUUAGAGAUUGAUAGCCAACGAACAUAAAAAAAGAGACUAGAAAGUUAGUCAAAGAUCGUACUAGAGAACUGAAUGGAAUUGACUUCUUUGUUUGAAUUAGACCUUUCAAGUGUGAAAUUUAAAUGUUUUUUCAAAAAAAUACAGCCCUAAGGCUGCAUUACUAAAAUUGAUCAAAUGGUUUCUGAAA ..((...((.((((((((.......................(((.((((((((..((((.((.......))..)))))))))))).))).........((((((.........((((((....)))))).....(((((((.((((.((((.(.((((.(....)...)))).).))))...)))).))))))).......)))))).........(((.(((((....))))).)))........)))))))).))....))... (-42.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 290 163 128 109 76 NC_009009:SSA_0075|5end_ABC_sugar_transporter,_permease_protein,_putative_78963..79193_POSITIVE 283 47 17 36 5 NC_009009:SSA_0551|5end_L-asparaginase,_putative_547293..547523_NEGATIVE 275 179 133 208 160 NC_009009:SSA_1683|5end_NrdI_protein,_putative_1677405..1677635_NEGATIVE 264 46 1 197 163 NC_009009:SSA_1446|5end_Histidinol_dehydrogenase,_putative_1449190..1449420_NEGATIVE 263 207 169 195 161 NC_009009:SSA_0650|5end_GTP-binding_protein_TypA/BipA,_putative_632548..632778_POSITIVE 261 46 1 224 169 NC_009009:SSA_0409|5end_ABC-type_multidrug_transport_system,_ATPase_component,_putative_405605..405835_NEGATIVE 253 184 144 100 56 NC_009009:SSA_1243|5end_Dihydroorotate_dehydrogenase_electron_transfer_subunit,_putative_1268204..1268434_NEGATIVE 246 155 117 114 61 NC_009009:SSA_0481|5end_Cobyric_acid_synthase,_putative_481962..482192_POSITIVE 242 178 131 59 11 NC_009009:SSA_1777|5end_Ribosomal_large_subunit_pseudouridine_synthase_B,_putative_1765155..1765385_NEGATIVE 241 76 33 84 31 NC_009009:SSA_1912|5end_hypothetical_protein_1903220..1903450_NEGATIVE 241 76 33 199 146 NC_009009:SSA_1911|5end_Conserved_uncharacterized_protein_1903105..1903335_NEGATIVE 241 154 111 53 5 NC_009009:SSA_1373|5end_ATPase_components_of_ABC_transporters_with_duplicated_ATPase_domains,_multidrug_transport_system,_putative_1389707..1389937_POSITIVE 241 190 145 66 19 NC_009009:SSA_1218|5end_DNA_repair_protein_radC,_putative_1240459..1240689_NEGATIVE 240 60 11 183 133 NC_009009:SSA_2099|5end_ABC-type_arginine/histidine_transporter,_permease_protein,_putative_2104313..2104543_NEGATIVE 237 47 5 219 146 NC_009009:SSA_0474|5end_Uroporphyrin-III_C-methyltransferase/uroporphyrinogen-III_synthase,_putative_476270..476500_POSITIVE 235 140 93 58 3 NC_009009:SSA_2304|5end_Conserved_uncharacterized_protein_2306270..2306500_NEGATIVE 235 150 114 203 169 NC_009009:SSA_2160|5end_Deoxyuridinetriphosphatase,_putative_2160066..2160296_NEGATIVE 235 159 113 107 46 NC_009009:SSA_1066|5end_ABC-type_oligopeptide_transport_system,_putative_1084335..1084565_POSITIVE 234 47 1 185 135 NC_009009:SSA_0636|5end_N-(5'-phosphoribosyl)anthranilate_isomerase,_putative_625184..625414_POSITIVE 234 209 171 63 22 NC_009009:SSA_0165|5end_hypothetical_protein_163938..164168_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 347 166 122 91 48 NC_009009:SSA_1672|3end_hypothetical_protein_1670291..1670441_NEGATIVE 301 50 29 62 41 NC_009009:SSA_1101|3end_Multidrug_resistance_efflux_pump/hemolysin_secretion_transmembrane_protein,_putative_1123199..1123349_POSITIVE 290 163 128 41 8 NC_009009:SSA_0074|3end_ABC_transporter_substrate-binding_protein-sugar_transport,_putative_78975..79125_POSITIVE 281 185 144 145 101 NC_009009:SSA_0218|3end_Sugar-binding_periplasmic_protein,_putative_215226..215376_POSITIVE 262 111 72 151 110 NC_009009:SSA_0106|3end_30S_ribosomal_protein_S10,_putative_108160..108310_POSITIVE 261 46 1 79 24 NC_009009:SSA_0410|3end_hypothetical_protein_405750..405900_NEGATIVE 247 47 1 127 84 NC_009009:SSA_0568|3end_Aspartyl-tRNA_synthetase_1,_putative_563490..563640_POSITIVE 246 155 117 129 76 NC_009009:SSA_0480|3end_Cobalt_ABC_transporter,_ATP-binding_protein,_putative_482057..482207_POSITIVE 242 178 131 72 24 NC_009009:SSA_1778|3end_Segregation_and_condensation_protein_B,_putative_1765142..1765292_NEGATIVE 241 76 33 59 6 NC_009009:SSA_1913|3end_Xanthine/uracil_permease_family_protein,_putative_1903245..1903395_NEGATIVE 236 154 114 97 56 NC_009009:SSA_2242|3end_hypothetical_protein_2238121..2238271_NEGATIVE 235 150 114 118 84 NC_009009:SSA_2161|3end_NTP_pyrophosphohydrolases_including_oxidative_damage_repair_enzymes,_putative_2160151..2160301_NEGATIVE 234 209 171 42 1 NC_009009:SSA_0164|3end_hypothetical_protein_163997..164147_POSITIVE 233 59 33 29 3 NC_009009:SSA_2013|3end_hypothetical_protein_2013470..2013620_NEGATIVE 229 47 16 36 9 NC_009009:SSA_0318|3end_Secreted_metalloendopeptidase_Gcp_312791..312941_POSITIVE 228 198 156 130 86 NC_009009:SSA_1189|3end_GTP-binding_protein,_putative_1216806..1216956_NEGATIVE 226 50 18 132 98 NC_009009:SSA_0413|3end_Anthranilate/para-aminobenzoate_synthases_component_I/_Chorismate_binding_enzyme,_putative_408315..408465_NEGATIVE 223 58 18 48 4 NC_009009:SSA_0026|3end_Fatty_acid/phospholipid_synthesis_protein_plsX,_putative_31551..31701_POSITIVE 222 185 144 91 47 NC_009009:SSA_1449|3end_Histidinol-phosphate/aromatic_aminotransferase_and_cobyric_acid_decarboxylase,_putative_1450873..1451023_NEGATIVE 222 160 115 88 42 NC_009009:SSA_0178|3end_UDP-N-acetylglucosamine_2-epimerase,_putative_184053..184203_POSITIVE