Origin IGS: atttgtaatccttttcttgagcaaaattagctaattcctatataaatctatgaatatgtgcagaatattcatttgcatttaagagatattaactttgtctgtggataaatatttaaagtttcggagaatttttattttctattgcttaaatcatttttttactgtatatttgcatgtatatgaaatcctcatcttgatgtattgggaatggtgaagtataacaatgcacctctcccctactgatttgaagaagaaaatagtataagaaacttataagtaacaagt .........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 acttgttacttataagtttcttatactattttcttcttcaaatcagtaggggagaggtgcattgttatacttcaccattcccaatacatcaagatgaggatttcatatacatgcaaatatacagtaaaaaaatgatttaagcaatagaaaataaaaattctccgaaactttaaatatttatccacagacaaagttaatatctcttaaatgcaaatgaatattctgcacatattcatagatttatataggaattagctaattttgctcaagaaaaggattacaaat Mask Tandem Repeat Region ================================================ atttgtaatccttttcttgagcaaaattagctaattcctatataaatctatgaatatgtgcagaatattcatttgcatttaagagatattaactttgtctgtggataaatatttaaagtttcggagaatttttattttctattgcttaaatcatttttttactgtatatttgcatgtatatgaaatcctcatcttgatgtattgggaatggtgaagtataacaatgcacctctcccctactgatttgaagaagaaaatagtataagaaacttataagtaacaagt Find is-nt database================================================ Query_seq: PI1100:PI1101|PI1100:PI1101:conserved hypothetical protein; possible rhodanese-domain protein:hypothetical protein:->->:1024452..1024736 285 atttgtaatccttttcttgagcaaaattagctaattcctatataaatctatgaatatgtgcagaatattcatttgcatttaagagatattaactttgtctgtggataaatatttaaagtttcggagaatttttattttctattgcttaaatcatttttttactgtatatttgcatgtatatgaaatcctcatcttgatgtattgggaatggtgaagtataacaatgcacctctcccctactgatttgaagaagaaaatagtataagaaacttataagtaacaagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1100:PI1101|PI1100:PI1101:conserved hypothetical protein; possible rhodanese-domain protein:hypothetical protein:->->:1024452..1024736 285 atttgtaatccttttcttgagcaaaattagctaattcctatataaatctatgaatatgtgcagaatattcatttgcatttaagagatattaactttgtctgtggataaatatttaaagtttcggagaatttttattttctattgcttaaatcatttttttactgtatatttgcatgtatatgaaatcctcatcttgatgtattgggaatggtgaagtataacaatgcacctctcccctactgatttgaagaagaaaatagtataagaaacttataagtaacaagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1100:PI1101|PI1100:PI1101:conserved hypothetical protein; possible rhodanese-domain protein:hypothetical protein:->->:1024452..1024736 285 atttgtaatccttttcttgagcaaaattagctaattcctatataaatctatgaatatgtgcagaatattcatttgcatttaagagatattaactttgtctgtggataaatatttaaagtttcggagaatttttattttctattgcttaaatcatttttttactgtatatttgcatgtatatgaaatcctcatcttgatgtattgggaatggtgaagtataacaatgcacctctcccctactgatttgaagaagaaaatagtataagaaacttataagtaacaagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atttgtaatccttttcttgagcaaaattagctaattcctatataaatctatgaatatgtgcagaatattcatttgcatttaagagatattaactttgtctgtggataaatatttaaagtttcggagaatttttattttctattgcttaaatcatttttttactgtatatttgcatgtatatgaaatcctcatcttgatgtattgggaatggtgaagtataacaatgcacctctcccctactgatttgaagaagaaaatagtataagaaacttataagtaacaagt Predict ORF larger than 30AA ================================================ Protein_Len: 42 Strand: + Start: 86 End: 211 ..................................................................................... M L T L S V D K Y L K F R R I F I F Y C L N H F F T V Y L H V Y E I L I L M Y W E W .......................................................................... Protein_Len: 35 Strand: - Start: 154 End: 258 ......................................................................................................................................................... K K V T Y K C T Y S I R M K I Y Q S H H L I V I C R E G V S K F F F M ........................... Protein_Len: 45 Strand: - Start: 149 End: 283 .................................................................................................................................................... I M K K S Y I Q M Y I F D E D Q H I P F P S T Y C H V E G R S I Q L L F Y Y L F S I L L M .. atttgtaatccttttcttgagcaaaattagctaattcctatataaatctatgaatatgtgcagaatattcatttgcatttaagagatattaactttgtctgtggataaatatttaaagtttcggagaatttttattttctattgcttaaatcatttttttactgtatatttgcatgtatatgaaatcctcatcttgatgtattgggaatggtgaagtataacaatgcacctctcccctactgatttgaagaagaaaatagtataagaaacttataagtaacaagt 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: 141 End: 170 ............................................................................................................................................ATTGCTTAAATCATTTTTTTACTGTATATT................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atttgtaatccttttcttgagcaaaattagctaattcctatataaatctatgaatatgtgcagaatattcatttgcatttaagagatattaactttgtctgtggataaatatttaaagtttcggagaatttttattttctattgcttaaatcatttttttactgtatatttgcatgtatatgaaatcctcatcttgatgtattgggaatggtgaagtataacaatgcacctctcccctactgatttgaagaagaaaatagtataagaaacttataagtaacaagt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 49 HP_score: -2.7 Tail_Score: -3.84451 Start: 51 End: 71 Full_Region: TCCTATATAAATCTA TGAATAT GTGCAGA ATATTCA TTTGCATTTAAGAGA ..................................................TGAATATGTGCAGAATATTCA...................................................................................................................................................................................................................... TransTerm Strand: - Conf: 40 HP_score: -2.7 Tail_Score: -2.73529 Start: 51 End: 71 Full_Region: tctcttaaatgcaaa tgaatat tctgcac atattca tagatttatatagga ..................................................tgaatattctgcacatattca...................................................................................................................................................................................................................... Find igs database================================================ Query_seq: PI1100:PI1101|PI1100:PI1101:conserved hypothetical protein; possible rhodanese-domain protein:hypothetical protein:->->:1024452..1024736 285 atttgtaatccttttcttgagcaaaattagctaattcctatataaatctatgaatatgtgcagaatattcatttgcatttaagagatattaactttgtctgtggataaatatttaaagtttcggagaatttttattttctattgcttaaatcatttttttactgtatatttgcatgtatatgaaatcctcatcttgatgtattgggaatggtgaagtataacaatgcacctctcccctactgatttgaagaagaaaatagtataagaaacttataagtaacaagt Intra-Species Hit: Count: 1 Min: 1 Max: 285 Len: 285 Subject: pint_PI1100_PI1101|conserved hypothetical protein; possible rhodanese-domain protein:hypothetical protein|POSITIVE:POSITIVE|[1024452,1024736]|285 HSP 1 e-value: 1.0E-147 bit: 523.0 Len: 285 Query Start:1 Query End:285 Subject Strand: POSITIVE Subject Start: 1 Subject End: 285 atttgtaatccttttcttgagcaaaattagctaattcctatataaatctatgaatatgtgcagaatattcatttgcatttaagagatattaactttgtctgtggataaatatttaaagtttcggagaatttttattttctattgcttaaatcannnnnnnactgtatatttgcatgtatatgaaatcctcatcttgatgtattgggaatggtgaagtataacaatgcacctctcccctactgatttgaagaagaaaatagtataagaaacttataagtaacaagt atttgtaatccttttcttgagcaaaattagctaattcctatataaatctatgaatatgtgcagaatattcatttgcatttaagagatattaactttgtctgtggataaatatttaaagtttcggagaatttttattttctattgcttaaatcatttttttactgtatatttgcatgtatatgaaatcctcatcttgatgtattgggaatggtgaagtataacaatgcacctctcccctactgatttgaagaagaaaatagtataagaaacttataagtaacaagt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUGUAAUCCUUUUCUUGAGCAAAAUUAGCUAAUUCCUAUAUAAAUCUAUGAAUAUGUGCAGAAUAUUCAUUUGCAUUUAAGAGAUAUUAACUUUGUCUGUGGAUAAAUAUUUAAAGUUUCGGAGAAUUUUUAUUUUCUAUUGCUUAAAUCAUUUUUUUACUGUAUAUUUGCAUGUAUAUGAAAUCCUCAUCUUGAUGUAUUGGGAAUGGUGAAGUAUAACAAUGCACCUCUCCCCUACUGAUUUGAAGAAGAAAAUAGUAUAAGAAACUUAUAAGUAACAAGU ((((((.....(((((((.(((.......)))..........((((((.((((((((.......)))))))).((((((.((((((((.......)))).(.((((.........((((...(((((((....)))))))...))))...((((.....(((((((....)))).))).)))).)))).).))))))))))..((((..((((.............))))..)))).....))))))...)))))))...((((((...))))))....)))))) (-52.12) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUUGUUACUUAUAAGUUUCUUAUACUAUUUUCUUCUUCAAAUCAGUAGGGGAGAGGUGCAUUGUUAUACUUCACCAUUCCCAAUACAUCAAGAUGAGGAUUUCAUAUACAUGCAAAUAUACAGUAAAAAAAUGAUUUAAGCAAUAGAAAAUAAAAAUUCUCCGAAACUUUAAAUAUUUAUCCACAGACAAAGUUAAUAUCUCUUAAAUGCAAAUGAAUAUUCUGCACAUAUUCAUAGAUUUAUAUAGGAAUUAGCUAAUUUUGCUCAAGAAAAGGAUUACAAAU ..((((..(((..(((((((......((((((((.(((.((((((....(((((.((((....(.....)..)))).)))))....(((....(((((...)))))....)))...................)))))))))....))))))))..........)))))))................((((((((((.((..(((((.(((...((((((((.......)))))))).....))).)))))..))..)))))))).)).....)))....)))).. (-44.39) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 300 235 194 104 65 pint:PI0041|5end_hypothetical_protein_41785..42015_POSITIVE 267 236 191 205 155 pint:PI0818|5end_alpha-amylase_758185..758415_POSITIVE 254 107 63 164 127 pint:PI1397|5end_histidine_ammonia-lyase_1317879..1318109_POSITIVE 252 250 208 231 186 pint:PI1605|5end_conserved_hypothetical_protein_1534244..1534474_POSITIVE 251 123 83 38 1 pint:PI0630|5end_peptidyl-tRNA_hydrolase_(aminoacyl-tRNA_hydrolase)_577045..577275_POSITIVE 250 205 161 78 27 pint:PI0560|5end_hypothetical_protein_508600..508830_POSITIVE 245 229 188 176 130 pint:PI1974|5end_hypothetical_protein_1931193..1931423_POSITIVE 244 230 188 188 136 pint:PI0250|5end_hypothetical_protein_246946..247176_POSITIVE 243 238 191 212 167 pint:PI2134|5end_hypothetical_protein_2082269..2082499_POSITIVE 241 242 222 228 206 pint:PI0514|5end_possible_cell_filamentation_protein_472408..472638_POSITIVE 241 233 192 47 3 pint:PI0039|5end_conserved_hypothetical_protein;_possible_integral_membrane_protein_40503..40733_POSITIVE 239 247 209 181 143 pint:PI1811|5end_conserved_hypothetical_protein_1749518..1749748_POSITIVE 236 256 223 53 22 pint:PI0431|5end_Xaa-Pro_aminopeptidase_403064..403294_POSITIVE 235 200 151 183 126 pint:PI0399|5end_conserved_hypothetical_protein_363585..363815_POSITIVE 231 216 171 230 186 pint:PI1743|5end_stationary-phase_survival_protein_1663948..1664178_POSITIVE 230 230 185 209 167 pint:PI1675|5end_TonB-dependent_outer_membrane_receptor_1588107..1588337_POSITIVE 226 230 191 64 12 pint:PI1576|5end_serine_protease_precursor_1502172..1502402_POSITIVE 226 133 96 62 20 pint:PI0749|5end_hypothetical_protein_677234..677464_POSITIVE 225 243 208 111 60 pint:PI2133|5end_collagenase_2081106..2081336_POSITIVE 225 218 172 77 23 pint:PI1223|5end_conserved_hypothetical_protein_1143537..1143767_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 300 235 194 111 72 pint:PI0040|3end_conserved_hypothetical_protein_(possible_integral_membrane_protein)_41872..42022_POSITIVE 267 236 191 149 99 pint:PI0817|3end_glycosyl_transferase,_group_1_family_protein_758209..758359_POSITIVE 266 270 226 121 75 pint:PI1604|3end_hypothetical_protein_1534195..1534345_POSITIVE 254 107 63 78 41 pint:PI1396|3end_urocanate_hydratase_1317873..1318023_POSITIVE 250 205 161 138 87 pint:PI0559|3end_conserved_hypothetical_protein_508740..508890_POSITIVE 245 229 188 74 28 pint:PI1973|3end_conserved_hypothetical_protein_1931171..1931321_POSITIVE 242 251 226 35 10 pint:PI0183|3end_hypothetical_protein_174810..174960_POSITIVE 241 242 222 111 89 pint:PI0513|3end_ion_transporter_472371..472521_POSITIVE 239 247 209 149 111 pint:PI1810|3end_outer_membrane_protein_1749566..1749716_POSITIVE 235 200 151 59 2 pint:PI0398|3end_hypothetical_protein_363541..363691_POSITIVE 233 190 147 77 31 pint:PI1056|3end_cell-division_ATP-binding_protein_977100..977250_POSITIVE 232 123 92 35 6 pint:PI0629|3end_heat_shock_protein_15_577122..577272_POSITIVE 231 216 171 58 14 pint:PI1741|3end_lipid-A-disaccharide_synthase_1663856..1664006_POSITIVE 225 243 208 64 13 pint:PI2132|3end_hypothetical_protein_2081139..2081289_POSITIVE 224 238 197 151 107 pint:PI1073|3end_hemogluttinin_A-related_protein_(HagA)_993693..993843_POSITIVE 224 240 197 47 10 pint:PI0042|3end_hypothetical_protein_43444..43594_POSITIVE 220 123 82 68 19 pint:PI1972|3end_hypothetical_protein_1930503..1930653_POSITIVE 219 239 193 63 7 pint:PI0302|3end_hypothetical_protein_287019..287169_POSITIVE 218 216 171 130 87 pint:PI1178|3end_histidyl-tRNA_synthetase_1100564..1100714_POSITIVE 217 244 203 141 101 pint:PI2124|3end_excinuclease_ABC,_subunit_C_2074496..2074646_POSITIVE