Origin IGS: tgacggaataatcgaagtgctgcttcggtgaatttaaataccattgaaattaatataatgataattccaatcgtctggtctgctaaagcaaaatataaaatcacaccaattacagcccctaccataaagatgatattgagccattggcgcagtgctgaaacattgtttttattttctcttagtgggcgtctacgatggggtggacgtgccaagctatttccgttttcctctgtcataatacctgtatttatactattccttgccactaacttctgtcttgcttgttgtgcacgaagaaatgatagacgcaaagaatgtctatttaaaagagtacctatttaattgttataacaaataatttataaagcaaagttataaaaaaatacttgattgcagcttgcttataaaatatttaacgttcgttttgagtttca .........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 tgaaactcaaaacgaacgttaaatattttataagcaagctgcaatcaagtatttttttataactttgctttataaattatttgttataacaattaaataggtactcttttaaatagacattctttgcgtctatcatttcttcgtgcacaacaagcaagacagaagttagtggcaaggaatagtataaatacaggtattatgacagaggaaaacggaaatagcttggcacgtccaccccatcgtagacgcccactaagagaaaataaaaacaatgtttcagcactgcgccaatggctcaatatcatctttatggtaggggctgtaattggtgtgattttatattttgctttagcagaccagacgattggaattatcattatattaatttcaatggtatttaaattcaccgaagcagcacttcgattattccgtca Mask Tandem Repeat Region ================================================ tgacggaataatcgaagtgctgcttcggtgaatttaaataccattgaaattaatataatgataattccaatcgtctggtctgctaaagcaaaatataaaatcacaccaattacagcccctaccataaagatgatattgagccattggcgcagtgctgaaacattgtttttattttctcttagtgggcgtctacgatggggtggacgtgccaagctatttccgttttcctctgtcataatacctgtatttatactattccttgccactaacttctgtcttgcttgttgtgcacgaagaaatgatagacgcaaagaatgtctatttaaaagagtacctatttaattgttataacaaataatttataaagcaaagttataaaaaaatacttgattgcagcttgcttataaaatatttaacgttcgttttgagtttca Find is-nt database================================================ Query_seq: PI1050:PI1051|PI1050:PI1051:conserved hypothetical protein:hypothetical protein:->->:969759..970192 434 tgacggaataatcgaagtgctgcttcggtgaatttaaataccattgaaattaatataatgataattccaatcgtctggtctgctaaagcaaaatataaaatcacaccaattacagcccctaccataaagatgatattgagccattggcgcagtgctgaaacattgtttttattttctcttagtgggcgtctacgatggggtggacgtgccaagctatttccgttttcctctgtcataatacctgtatttatactattccttgccactaacttctgtcttgcttgttgtgcacgaagaaatgatagacgcaaagaatgtctatttaaaagagtacctatttaattgttataacaaataatttataaagcaaagttataaaaaaatacttgattgcagcttgcttataaaatatttaacgttcgttttgagtttca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1050:PI1051|PI1050:PI1051:conserved hypothetical protein:hypothetical protein:->->:969759..970192 434 tgacggaataatcgaagtgctgcttcggtgaatttaaataccattgaaattaatataatgataattccaatcgtctggtctgctaaagcaaaatataaaatcacaccaattacagcccctaccataaagatgatattgagccattggcgcagtgctgaaacattgtttttattttctcttagtgggcgtctacgatggggtggacgtgccaagctatttccgttttcctctgtcataatacctgtatttatactattccttgccactaacttctgtcttgcttgttgtgcacgaagaaatgatagacgcaaagaatgtctatttaaaagagtacctatttaattgttataacaaataatttataaagcaaagttataaaaaaatacttgattgcagcttgcttataaaatatttaacgttcgttttgagtttca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1050:PI1051|PI1050:PI1051:conserved hypothetical protein:hypothetical protein:->->:969759..970192 434 tgacggaataatcgaagtgctgcttcggtgaatttaaataccattgaaattaatataatgataattccaatcgtctggtctgctaaagcaaaatataaaatcacaccaattacagcccctaccataaagatgatattgagccattggcgcagtgctgaaacattgtttttattttctcttagtgggcgtctacgatggggtggacgtgccaagctatttccgttttcctctgtcataatacctgtatttatactattccttgccactaacttctgtcttgcttgttgtgcacgaagaaatgatagacgcaaagaatgtctatttaaaagagtacctatttaattgttataacaaataatttataaagcaaagttataaaaaaatacttgattgcagcttgcttataaaatatttaacgttcgttttgagtttca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgacggaataatcgaagtgctgcttcggtgaatttaaataccattgaaattaatataatgataattccaatcgtctggtctgctaaagcaaaatataaaatcacaccaattacagcccctaccataaagatgatattgagccattggcgcagtgctgaaacattgtttttattttctcttagtgggcgtctacgatggggtggacgtgccaagctatttccgttttcctctgtcataatacctgtatttatactattccttgccactaacttctgtcttgcttgttgtgcacgaagaaatgatagacgcaaagaatgtctatttaaaagagtacctatttaattgttataacaaataatttataaagcaaagttataaaaaaatacttgattgcagcttgcttataaaatatttaacgttcgttttgagtttca Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 143 End: 235 .............................................................................................................................................. M G A V L K H C F Y F L L V G V Y D G V D V P S Y F R F P L S ....................................................................................................................................................................................................... Protein_Len: 60 Strand: + Start: 28 End: 339 ........................... M N L N T I E I N I M I I P I V W S A K A K Y K I T P I T A P T I K M I L S H W R S A E T L F L F S L S G R L R W G G R ............................................................................................... Protein_Len: 38 Strand: + Start: 242 End: 355 ................................................................................................................................................................................................................................................. M Y L Y Y S L P L T S V L L V V H E E M I D A K N V Y L K E Y L F N C Y N K ............................................................................... Protein_Len: 36 Strand: - Start: 37 End: 144 .................................... I G N F N I Y H Y N W D D P R S F C F I F D C W N C G R G Y L H Y Q A M .................................................................................................................................................................................................................................................................................................. Protein_Len: 60 Strand: - Start: 3 End: 338 .. V N N K N E R L P R R R H P P R A L S N G N E E T M I G T N I S N R A V L K Q R A Q Q A R L F S L R L S H R N L L T G M ................................................................................................ tgacggaataatcgaagtgctgcttcggtgaatttaaataccattgaaattaatataatgataattccaatcgtctggtctgctaaagcaaaatataaaatcacaccaattacagcccctaccataaagatgatattgagccattggcgcagtgctgaaacattgtttttattttctcttagtgggcgtctacgatggggtggacgtgccaagctatttccgttttcctctgtcataatacctgtatttatactattccttgccactaacttctgtcttgcttgttgtgcacgaagaaatgatagacgcaaagaatgtctatttaaaagagtacctatttaattgttataacaaataatttataaagcaaagttataaaaaaatacttgattgcagcttgcttataaaatatttaacgttcgttttgagtttca 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: 299 End: 328 ..........................................................................................................................................................................................................................................................................................................TTTTAAATAGACATTCTTTGCGTCTATCAT.......................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tgacggaataatcgaagtgctgcttcggtgaatttaaataccattgaaattaatataatgataattccaatcgtctggtctgctaaagcaaaatataaaatcacaccaattacagcccctaccataaagatgatattgagccattggcgcagtgctgaaacattgtttttattttctcttagtgggcgtctacgatggggtggacgtgccaagctatttccgttttcctctgtcataatacctgtatttatactattccttgccactaacttctgtcttgcttgttgtgcacgaagaaatgatagacgcaaagaatgtctatttaaaagagtacctatttaattgttataacaaataatttataaagcaaagttataaaaaaatacttgattgcagcttgcttataaaatatttaacgttcgttttgagtttca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1050:PI1051|PI1050:PI1051:conserved hypothetical protein:hypothetical protein:->->:969759..970192 434 tgacggaataatcgaagtgctgcttcggtgaatttaaataccattgaaattaatataatgataattccaatcgtctggtctgctaaagcaaaatataaaatcacaccaattacagcccctaccataaagatgatattgagccattggcgcagtgctgaaacattgtttttattttctcttagtgggcgtctacgatggggtggacgtgccaagctatttccgttttcctctgtcataatacctgtatttatactattccttgccactaacttctgtcttgcttgttgtgcacgaagaaatgatagacgcaaagaatgtctatttaaaagagtacctatttaattgttataacaaataatttataaagcaaagttataaaaaaatacttgattgcagcttgcttataaaatatttaacgttcgttttgagtttca Intra-Species Hit: Count: 1 Min: 1 Max: 434 Len: 434 Subject: pint_PI1050_PI1051|conserved hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[969759,970192]|434 HSP 1 e-value: 0.0 bit: 819.0 Len: 434 Query Start:1 Query End:434 Subject Strand: POSITIVE Subject Start: 1 Subject End: 434 tgacggaataatcgaagtgctgcttcggtgaatttaaataccattgaaattaatataatgataattccaatcgtctggtctgctaaagcaaaatataaaatcacaccaattacagcccctaccataaagatgatattgagccattggcgcagtgctgaaacattgtttttattttctcttagtgggcgtctacgatggggtggacgtgccaagctatttccgttttcctctgtcataatacctgtatttatactattccttgccactaacttctgtcttgcttgttgtgcacgaagaaatgatagacgcaaagaatgtctatttaaaagagtacctatttaattgttataacaaataatttataaagcaaagttatnnnnnnntacttgattgcagcttgcttataaaatatttaacgttcgttttgagtttca tgacggaataatcgaagtgctgcttcggtgaatttaaataccattgaaattaatataatgataattccaatcgtctggtctgctaaagcaaaatataaaatcacaccaattacagcccctaccataaagatgatattgagccattggcgcagtgctgaaacattgtttttattttctcttagtgggcgtctacgatggggtggacgtgccaagctatttccgttttcctctgtcataatacctgtatttatactattccttgccactaacttctgtcttgcttgttgtgcacgaagaaatgatagacgcaaagaatgtctatttaaaagagtacctatttaattgttataacaaataatttataaagcaaagttataaaaaaatacttgattgcagcttgcttataaaatatttaacgttcgttttgagtttca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGACGGAAUAAUCGAAGUGCUGCUUCGGUGAAUUUAAAUACCAUUGAAAUUAAUAUAAUGAUAAUUCCAAUCGUCUGGUCUGCUAAAGCAAAAUAUAAAAUCACACCAAUUACAGCCCCUACCAUAAAGAUGAUAUUGAGCCAUUGGCGCAGUGCUGAAACAUUGUUUUUAUUUUCUCUUAGUGGGCGUCUACGAUGGGGUGGACGUGCCAAGCUAUUUCCGUUUUCCUCUGUCAUAAUACCUGUAUUUAUACUAUUCCUUGCCACUAACUUCUGUCUUGCUUGUUGUGCACGAAGAAAUGAUAGACGCAAAGAAUGUCUAUUUAAAAGAGUACCUAUUUAAUUGUUAUAACAAAUAAUUUAUAAAGCAAAGUUAUAAAAAAAUACUUGAUUGCAGCUUGCUUAUAAAAUAUUUAACGUUCGUUUUGAGUUUCA (((((((..(((.((((((..((((.((((..((((....((((((............((((....(((......)))..(((....))).........))))...........(((((((..(((((((..((.((.(((.((((...))))))).))..))..))))))).......))).)))).....))))))..))))..)))))))))))))).)))....)))))))........((((((.....................((((.((.(((.......))).))))))..((((((((.......)))))))).....))))))..((((((..........(((((.(((((((.((((.(((.(((..((....))..))).)))))))))))))).)))))..........)))))).... (-78.05) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAAACUCAAAACGAACGUUAAAUAUUUUAUAAGCAAGCUGCAAUCAAGUAUUUUUUUAUAACUUUGCUUUAUAAAUUAUUUGUUAUAACAAUUAAAUAGGUACUCUUUUAAAUAGACAUUCUUUGCGUCUAUCAUUUCUUCGUGCACAACAAGCAAGACAGAAGUUAGUGGCAAGGAAUAGUAUAAAUACAGGUAUUAUGACAGAGGAAAACGGAAAUAGCUUGGCACGUCCACCCCAUCGUAGACGCCCACUAAGAGAAAAUAAAAACAAUGUUUCAGCACUGCGCCAAUGGCUCAAUAUCAUCUUUAUGGUAGGGGCUGUAAUUGGUGUGAUUUUAUAUUUUGCUUUAGCAGACCAGACGAUUGGAAUUAUCAUUAUAUUAAUUUCAAUGGUAUUUAAAUUCACCGAAGCAGCACUUCGAUUAUUCCGUCA .....(((............(((((.((((((((((((((.......)))..............)))).))))))).)))))(((((((...........(((((.............(((((((((..(((..((((((((.(((.......))).)).)))))))))..))))))))))))))...........))))))).)))....((((((....(((((..((((.((......)).))))....)))))...............((((((......(((((((((((((..((((((....)))))).)))))...))))))))((.((((...(((((....)))))....((.((((((((((.........)))))))))).))...)))).))...))))))............)))))).. (-90.89) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 365 229 183 214 155 pint:PI0051|5end_hypothetical_protein_52607..52837_POSITIVE 363 222 181 127 90 pint:PI1381|5end_conserved_hypothetical_protein_1303060..1303290_POSITIVE 356 213 179 97 57 pint:PI0151|5end_ISPg4-related_transposase_(IS5_family)_143805..144035_POSITIVE 354 227 182 61 5 pint:PI0613|5end_glycerol-3-phosphate_dehydrogenase_(NAD(P)+)_562167..562397_POSITIVE 354 228 184 220 165 pint:PI0301|5end_probable_transposase_285672..285902_POSITIVE 348 220 180 174 126 pint:PI1539|5end_3-phosphoshikimate_1-carboxyvinyltransferase_1459804..1460034_POSITIVE 340 222 182 47 2 pint:PI1636|5end_hypothetical_protein_1554246..1554476_POSITIVE 339 167 128 103 58 pint:PI0858|5end_carbamyl_phosphate_synthase,_large_subunit_790093..790323_POSITIVE 339 222 183 93 43 pint:PI0715|5end_hypothetical_protein_652311..652541_POSITIVE 337 213 174 162 105 pint:PI0246|5end_conserved_hypothetical_protein_244166..244396_POSITIVE 335 214 178 209 175 pint:PI0596|5end_hypothetical_protein_546400..546630_POSITIVE 329 229 181 60 11 pint:PI0262|5end_conserved_hypothetical_protein_254685..254915_POSITIVE 327 229 181 110 46 pint:PI2006|5end_potassium_uptake_system_protein_1964480..1964710_POSITIVE 326 230 187 76 22 pint:PI0601|5end_hypothetical_protein_548758..548988_POSITIVE 323 210 164 197 137 pint:PI1227|5end_conserved_hypothetical_protein;_possible_DNA-binding_protein,_histone-like_family_1148448..1148678_POSITIVE 320 229 182 205 162 pint:PI1903|5end_hypothetical_protein_1845292..1845522_POSITIVE 320 229 182 81 38 pint:PI1904|5end_glutamine_synthetase_1845168..1845398_POSITIVE 320 225 182 129 78 pint:PI1707|5end_GTP-binding_protein_1623795..1624025_POSITIVE 320 225 186 65 24 pint:PI0093|5end_riboflavin_biosynthesis_protein_90489..90719_POSITIVE 315 237 192 217 168 pint:PI0341|5end_conserved_hypothetical_protein_317038..317268_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 356 213 179 45 5 pint:PI0150|3end_hypothetical_protein_143833..143983_POSITIVE 353 224 181 151 94 pint:PI1874|3end_hypothetical_protein_1818924..1819074_POSITIVE 341 290 242 137 83 pint:PI0798|3end_malonyl_CoA-acyl_carrier_protein_transacylase_736975..737125_POSITIVE 336 209 180 139 104 pint:PI1538|3end_conserved_hypothetical_protein_1459862..1460012_POSITIVE 335 214 178 135 101 pint:PI0595|3end_conserved_hypothetical_protein_546406..546556_POSITIVE 329 291 258 40 2 pint:PI0944|3end_hypothetical_protein_875249..875399_POSITIVE 329 229 181 60 11 pint:PI0261|3end_conjugative_transposon_protein,_TraK_254765..254915_POSITIVE 318 210 162 151 97 pint:PI2045|3end_hypothetical_protein_1998723..1998873_POSITIVE 318 229 186 39 3 pint:PI1729|3end_FKBP-type_peptidyl-prolyl_cis-trans_isomerase,_trigger_factor_1649935..1650085_POSITIVE 303 221 185 137 96 pint:PI0741|3end_conserved_hypothetical_protein_673997..674147_POSITIVE 298 227 182 145 93 pint:PI0043|3end_thiamine_phosphate_pyrophosphorylase_43156..43306_POSITIVE 295 230 182 138 85 pint:PI1726|3end_ATP-dependent_DNA_helicase_1645542..1645692_POSITIVE 292 224 183 51 14 pint:PI0315|3end_conserved_hypothetical_protein_298186..298336_POSITIVE 292 232 195 120 70 pint:PI0196|3end_hypothetical_protein_188643..188793_POSITIVE 291 215 176 88 44 pint:PI0103|3end_conserved_hypothetical_protein;_possible_permease_99100..99250_POSITIVE 290 229 183 136 77 pint:PI1638|3end_conserved_hypothetical_protein_1556613..1556763_POSITIVE 289 210 162 58 7 pint:PI0654|3end_K+-dependent_Na+/Ca+_exchanger_related-protein_597223..597373_POSITIVE 289 221 181 148 102 pint:PI0274|3end_conserved_hypothetical_protein_263187..263337_POSITIVE 289 229 181 56 8 pint:PI0221|3end_DNA_methylase,_site-specific_DNA-methyltransferase_(adenine-specific)_217796..217946_POSITIVE 285 207 164 140 92 pint:PI1179|3end_adenylosuccinate_synthetase_1101823..1101973_POSITIVE