Origin IGS: atcatagaaaagaatatatacaatcagggagtcctcagcggctcccttttttaataaaaattcccgtaatgccctaagattgctttacaggtcttggcctttgtgctatgatattctataaaatttatcataaggaggtccct .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agggacctccttatgataaattttatagaatatcatagcacaaaggccaagacctgtaaagcaatcttagggcattacgggaatttttattaaaaaagggagccgctgaggactccctgattgtatatattcttttctatgat Mask Tandem Repeat Region ================================================ atcatagaaaagaatatatacaatcagggagtcctcagcggctcccttttttaataaaaattcccgtaatgccctaagattgctttacaggtcttggcctttgtgctatgatattctataaaatttatcataaggaggtccct Find is-nt database================================================ Query_seq: SSA_2338:SSA_2339|SSA_2338:SSA_2339:Conserved uncharacterized protein:Microcin C7 resistance protein, putative:->->:2340453..2340595 143 atcatagaaaagaatatatacaatcagggagtcctcagcggctcccttttttaataaaaattcccgtaatgccctaagattgctttacaggtcttggcctttgtgctatgatattctataaaatttatcataaggaggtccct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2338:SSA_2339|SSA_2338:SSA_2339:Conserved uncharacterized protein:Microcin C7 resistance protein, putative:->->:2340453..2340595 143 atcatagaaaagaatatatacaatcagggagtcctcagcggctcccttttttaataaaaattcccgtaatgccctaagattgctttacaggtcttggcctttgtgctatgatattctataaaatttatcataaggaggtccct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2338:SSA_2339|SSA_2338:SSA_2339:Conserved uncharacterized protein:Microcin C7 resistance protein, putative:->->:2340453..2340595 143 atcatagaaaagaatatatacaatcagggagtcctcagcggctcccttttttaataaaaattcccgtaatgccctaagattgctttacaggtcttggcctttgtgctatgatattctataaaatttatcataaggaggtccct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atcatagaaaagaatatatacaatcagggagtcctcagcggctcccttttttaataaaaattcccgtaatgccctaagattgctttacaggtcttggcctttgtgctatgatattctataaaatttatcataaggaggtccct Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 14 End: 118 ............. M Y T I R E S S A A P F F N K N S R N A L R L L Y R S W P L C Y D I L ......................... atcatagaaaagaatatatacaatcagggagtcctcagcggctcccttttttaataaaaattcccgtaatgccctaagattgctttacaggtcttggcctttgtgctatgatattctataaaatttatcataaggaggtccct 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: 86 Start: 83 End: 112 ..................................................................................CTTTACAGGTCTTGGCCTTTGTGCTATGAT............................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atcatagaaaagaatatatacaatcagggagtcctcagcggctcccttttttaataaaaattcccgtaatgccctaagattgctttacaggtcttggcctttgtgctatgatattctataaaatttatcataaggaggtccct Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_2338:SSA_2339|SSA_2338:SSA_2339:Conserved uncharacterized protein:Microcin C7 resistance protein, putative:->->:2340453..2340595 143 atcatagaaaagaatatatacaatcagggagtcctcagcggctcccttttttaataaaaattcccgtaatgccctaagattgctttacaggtcttggcctttgtgctatgatattctataaaatttatcataaggaggtccct Intra-Species Hit: Count: 1 Min: 1 Max: 143 Len: 143 Subject: NC_009009_SSA_2338_SSA_2339|Conserved uncharacterized protein:Microcin C7 resistance protein, putative|POSITIVE:POSITIVE|[2340453,2340595]|143 HSP 1 e-value: 8.0E-76 bit: 283.0 Len: 143 Query Start:1 Query End:143 Subject Strand: POSITIVE Subject Start: 1 Subject End: 143 atcatagaaaagaatatatacaatcagggagtcctcagcggctcccttttttaataaaaattcccgtaatgccctaagattgctttacaggtcttggcctttgtgctatgatattctataaaatttatcataaggaggtccct atcatagaaaagaatatatacaatcagggagtcctcagcggctcccttttttaataaaaattcccgtaatgccctaagattgctttacaggtcttggcctttgtgctatgatattctataaaatttatcataaggaggtccct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCAUAGAAAAGAAUAUAUACAAUCAGGGAGUCCUCAGCGGCUCCCUUUUUUAAUAAAAAUUCCCGUAAUGCCCUAAGAUUGCUUUACAGGUCUUGGCCUUUGUGCUAUGAUAUUCUAUAAAAUUUAUCAUAAGGAGGUCCCU .........((((............((((((((......))))))))...............((.((((.((.........)).)))).))))))(((((((....(((((((............))))))).)))))))... (-29.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGGGACCUCCUUAUGAUAAAUUUUAUAGAAUAUCAUAGCACAAAGGCCAAGACCUGUAAAGCAAUCUUAGGGCAUUACGGGAAUUUUUAUUAAAAAAGGGAGCCGCUGAGGACUCCCUGAUUGUAUAUAUUCUUUUCUAUGAU ((((....))))..........((((((((....(((..((((.........(((((((.((.........)).)))))))...............((((((((.....)).))))))..))))...)))....)))))))). (-34.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 307 55 23 230 192 NC_009009:SSA_1910|5end_hypothetical_protein_1902672..1902902_NEGATIVE 306 67 23 60 20 NC_009009:SSA_1077|5end_N-acetyl-glucosamine_matabolism,_putative_1094979..1095209_POSITIVE 300 110 70 135 101 NC_009009:SSA_1769|5end_hypothetical_protein_1757490..1757720_NEGATIVE 296 49 21 170 124 NC_009009:SSA_2207|5end_hypothetical_protein_2207221..2207451_NEGATIVE 296 108 64 231 182 NC_009009:SSA_1720|5end_Initiation-control_protein,_putative_1707113..1707343_NEGATIVE 288 106 64 48 3 NC_009009:SSA_2214|5end_2-C-methyl-D-erythritol_4-phosphate_cytidylyltransferase_2,_putative_2215835..2216065_NEGATIVE 286 106 63 73 18 NC_009009:SSA_1866|5end_hypothetical_protein_1862182..1862412_NEGATIVE 286 63 26 130 93 NC_009009:SSA_0751|5end_Oligoendopeptidase_F,_putative_732367..732597_POSITIVE 283 106 63 171 133 NC_009009:SSA_1833|5end_hypothetical_protein_1822662..1822892_POSITIVE 282 46 25 70 52 NC_009009:SSA_1510|5end_Rhamnosyltransferase,_putative_1515336..1515566_NEGATIVE 277 110 61 208 159 NC_009009:SSA_0580|5end_Isochorismatase_family_protein,_putative_572816..573046_POSITIVE 276 104 62 195 156 NC_009009:SSA_2052|5end_Thioredoxin,_putative_2057507..2057737_NEGATIVE 272 47 25 55 32 NC_009009:SSA_1375|5end_Multidrug_ABC_transporter,_ATPase_and_permease_components,_putative_1394827..1395057_NEGATIVE 272 66 26 52 1 NC_009009:SSA_0659|5end_hypothetical_protein_643003..643233_POSITIVE 269 107 63 86 26 NC_009009:SSA_0378|5end_TRZ/ATZ_family_hydrolase,_putative_367276..367506_POSITIVE 266 119 72 198 148 NC_009009:SSA_1203|5end_hypothetical_protein_1226985..1227215_POSITIVE 266 51 24 223 190 NC_009009:SSA_1167|5end_SRP54,_signal_recognition_particle_GTPase_protein,_putative_1192517..1192747_POSITIVE 265 108 64 203 152 NC_009009:SSA_0486|5end_Uroporphyrinogen-III_synthase,_putative_486637..486867_POSITIVE 260 129 81 83 29 NC_009009:SSA_2131|5end_DNA-binding_protein,_putative_2133949..2134179_POSITIVE 260 116 71 214 151 NC_009009:SSA_2024|5end_hypothetical_protein_2029272..2029502_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 306 67 23 48 8 NC_009009:SSA_1076|3end_hypothetical_protein_1095047..1095197_POSITIVE 300 110 70 141 107 NC_009009:SSA_1770|3end_hypothetical_protein_1757484..1757634_NEGATIVE 288 106 64 51 6 NC_009009:SSA_2215|3end_Oligosaccharide_repeat_unit_polymerase_Wzy,_putative_2215832..2215982_NEGATIVE 283 106 63 43 5 NC_009009:SSA_1832|3end_hypothetical_protein_1822614..1822764_POSITIVE 269 107 62 38 3 NC_009009:SSA_1384|3end_hypothetical_protein_1401715..1401865_NEGATIVE 265 59 22 99 58 NC_009009:SSA_1027|3end_hypothetical_protein_1045244..1045394_POSITIVE 263 75 31 151 114 NC_009009:SSA_1984|3end_Cell_surface_SD_repeat_antigen_precursor,_putative_1976048..1976198_NEGATIVE 260 129 81 74 20 NC_009009:SSA_2130|3end_hypothetical_protein_2134020..2134170_POSITIVE 258 52 16 103 54 NC_009009:SSA_1443|3end_1-(5-phosphoribosyl)-5-[(5-_phosphoribosylamino)methylideneamino]_imidazole-4-carboxamide_isomerase,_putative_1445944..1446094_NEGATIVE 257 109 64 75 24 NC_009009:SSA_0163|3end_hypothetical_protein_162542..162692_POSITIVE 253 115 71 138 83 NC_009009:SSA_2194|3end_Nicotinamide_mononucleotide_transporter,_putative_2194848..2194998_NEGATIVE 250 138 91 136 81 NC_009009:SSA_0267|3end_ROK_family_protein,_putative_260873..261023_NEGATIVE 248 98 58 35 6 NC_009009:SSA_2348|3end_Metal_dependent_hydrolase,_putative_2349875..2350025_NEGATIVE 248 65 22 47 8 NC_009009:SSA_1039|3end_Sugar_ABC_transporter,_ATP-binding_protein,_putative_1055389..1055539_POSITIVE 247 114 82 40 3 NC_009009:SSA_0268|3end_Phosphotransferase_system_(PTS)_cellobiose-specific_component_IIB,_putative_262621..262771_POSITIVE 245 66 22 128 72 NC_009009:SSA_0939|3end_Inositol_monophosphatase_(Mg++_dependent),_putative_947705..947855_POSITIVE 244 108 65 136 95 NC_009009:SSA_2340|3end_hypothetical_protein_2341539..2341689_NEGATIVE 243 109 62 91 31 NC_009009:SSA_0480|3end_Cobalt_ABC_transporter,_ATP-binding_protein,_putative_482057..482207_POSITIVE 241 47 26 65 44 NC_009009:SSA_2338|3end_Conserved_uncharacterized_protein_2340392..2340542_POSITIVE 241 55 23 150 106 NC_009009:SSA_2223|3end_Capsular_polysaccharide_biosynthesis_protein_Wzd_(chain_length_regulator),_putative_2224008..2224158_NEGATIVE