Origin IGS: aatgatattttaaagtttgcacaaaaataacgaatatttccctaatttccaaagttctttatattctatttggaacttaaataaatatccgttaactttgcaagtaaacttaattcaaaaaatgtaaaaactataaaacacaaaacacgaatatataattatcaaaacactatttattatggttaaactatttaaagctatggttatagctattttaatgatgctattgccagtagaacctatttccgctcaacaaggaaag .........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 ctttccttgttgagcggaaataggttctactggcaatagcatcattaaaatagctataaccatagctttaaatagtttaaccataataaatagtgttttgataattatatattcgtgttttgtgttttatagtttttacattttttgaattaagtttacttgcaaagttaacggatatttatttaagttccaaatagaatataaagaactttggaaattagggaaatattcgttatttttgtgcaaactttaaaatatcatt Mask Tandem Repeat Region ================================================ aatgatattttaaagtttgcacaaaaataacgaatatttccctaatttccaaagttctttatattctatttggaacttaaataaatatccgttaactttgcaagtaaacttaattcaaaaaatgtaaaaactataaaacacaaaacacgaatatataattatcaaaacactatttattatggttaaactatttaaagctatggttatagctattttaatgatgctattgccagtagaacctatttccgctcaacaaggaaag Find is-nt database================================================ Query_seq: PI1316:PI1317|PI1316:PI1317:conserved hypothetical protein:surface antigen BspA:->->:1232716..1232977 262 aatgatattttaaagtttgcacaaaaataacgaatatttccctaatttccaaagttctttatattctatttggaacttaaataaatatccgttaactttgcaagtaaacttaattcaaaaaatgtaaaaactataaaacacaaaacacgaatatataattatcaaaacactatttattatggttaaactatttaaagctatggttatagctattttaatgatgctattgccagtagaacctatttccgctcaacaaggaaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1316:PI1317|PI1316:PI1317:conserved hypothetical protein:surface antigen BspA:->->:1232716..1232977 262 aatgatattttaaagtttgcacaaaaataacgaatatttccctaatttccaaagttctttatattctatttggaacttaaataaatatccgttaactttgcaagtaaacttaattcaaaaaatgtaaaaactataaaacacaaaacacgaatatataattatcaaaacactatttattatggttaaactatttaaagctatggttatagctattttaatgatgctattgccagtagaacctatttccgctcaacaaggaaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1316:PI1317|PI1316:PI1317:conserved hypothetical protein:surface antigen BspA:->->:1232716..1232977 262 aatgatattttaaagtttgcacaaaaataacgaatatttccctaatttccaaagttctttatattctatttggaacttaaataaatatccgttaactttgcaagtaaacttaattcaaaaaatgtaaaaactataaaacacaaaacacgaatatataattatcaaaacactatttattatggttaaactatttaaagctatggttatagctattttaatgatgctattgccagtagaacctatttccgctcaacaaggaaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatgatattttaaagtttgcacaaaaataacgaatatttccctaatttccaaagttctttatattctatttggaacttaaataaatatccgttaactttgcaagtaaacttaattcaaaaaatgtaaaaactataaaacacaaaacacgaatatataattatcaaaacactatttattatggttaaactatttaaagctatggttatagctattttaatgatgctattgccagtagaacctatttccgctcaacaaggaaag Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 17 End: 124 ................ M H K N N E Y F P N F Q S S L Y S I W N L N K Y P L T L Q V N L I Q K M .......................................................................................................................................... Protein_Len: 33 Strand: + Start: 85 End: 183 .................................................................................... M S V N F A S K L N S K N V K T I K H K T R I Y N Y Q N T I Y Y G ............................................................................... Protein_Len: 36 Strand: + Start: 155 End: 262 .......................................................................................................................................................... M I I K T L F I M V K L F K A M V I A I L M M L L P V E P I S A Q Q G K Protein_Len: 42 Strand: - Start: 118 End: 243 ..................................................................................................................... F I Y F S Y F V F C S Y I I I L V S N I I T L S N L A I T I A I K I I S N G T S G M ................... Protein_Len: 34 Strand: - Start: 13 End: 114 ............ L K C L F L S Y K G L K W L E K Y E I Q F K F L Y G N V K C T F K M .................................................................................................................................................... aatgatattttaaagtttgcacaaaaataacgaatatttccctaatttccaaagttctttatattctatttggaacttaaataaatatccgttaactttgcaagtaaacttaattcaaaaaatgtaaaaactataaaacacaaaacacgaatatataattatcaaaacactatttattatggttaaactatttaaagctatggttatagctattttaatgatgctattgccagtagaacctatttccgctcaacaaggaaag 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: 24 End: 53 .......................TTTGGAAATTAGGGAAATATTCGTTATTTT................................................................................................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aatgatattttaaagtttgcacaaaaataacgaatatttccctaatttccaaagttctttatattctatttggaacttaaataaatatccgttaactttgcaagtaaacttaattcaaaaaatgtaaaaactataaaacacaaaacacgaatatataattatcaaaacactatttattatggttaaactatttaaagctatggttatagctattttaatgatgctattgccagtagaacctatttccgctcaacaaggaaag Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1316:PI1317|PI1316:PI1317:conserved hypothetical protein:surface antigen BspA:->->:1232716..1232977 262 aatgatattttaaagtttgcacaaaaataacgaatatttccctaatttccaaagttctttatattctatttggaacttaaataaatatccgttaactttgcaagtaaacttaattcaaaaaatgtaaaaactataaaacacaaaacacgaatatataattatcaaaacactatttattatggttaaactatttaaagctatggttatagctattttaatgatgctattgccagtagaacctatttccgctcaacaaggaaag Intra-Species Hit: Count: 1 Min: 1 Max: 262 Len: 262 Subject: pint_PI1316_PI1317|conserved hypothetical protein:surface antigen BspA|POSITIVE:POSITIVE|[1232716,1232977]|262 HSP 1 e-value: 3.0E-52 bit: 206.0 Len: 104 Query Start:1 Query End:104 Subject Strand: POSITIVE Subject Start: 1 Subject End: 104 aatgatattttaaagtttgcacaaaaataacgaatatttccctaatttccaaagttctttatattctatttggaacttaaataaatatccgttaactttgcaag.............................................................................................................................................................. aatgatattttaaagtttgcacaaaaataacgaatatttccctaatttccaaagttctttatattctatttggaacttaaataaatatccgttaactttgcaag.............................................................................................................................................................. HSP 2 e-value: 4.0E-39 bit: 163.0 Len: 82 Query Start:181 Query End:262 Subject Strand: POSITIVE Subject Start: 181 Subject End: 262 ....................................................................................................................................................................................ggttaaactatttaaagctatggttatagctattttaatgatgctattgccagtagaacctatttccgctcaacaaggaaag ....................................................................................................................................................................................ggttaaactatttaaagctatggttatagctattttaatgatgctattgccagtagaacctatttccgctcaacaaggaaag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUGAUAUUUUAAAGUUUGCACAAAAAUAACGAAUAUUUCCCUAAUUUCCAAAGUUCUUUAUAUUCUAUUUGGAACUUAAAUAAAUAUCCGUUAACUUUGCAAGUAAACUUAAUUCAAAAAAUGUAAAAACUAUAAAACACAAAACACGAAUAUAUAAUUAUCAAAACACUAUUUAUUAUGGUUAAACUAUUUAAAGCUAUGGUUAUAGCUAUUUUAAUGAUGCUAUUGCCAGUAGAACCUAUUUCCGCUCAACAAGGAAAG ..(((((.....((((((((.((((..(((((.((((((...(((.(((((((...............))))))).)))...)))))).)))))..))))...))))))))...........((((.....))))........................)))))....(((((.....)))))..............(((((((.(((((.(((.....)))))))).)))).)))......(((((.........))))). (-42.16) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUUCCUUGUUGAGCGGAAAUAGGUUCUACUGGCAAUAGCAUCAUUAAAAUAGCUAUAACCAUAGCUUUAAAUAGUUUAACCAUAAUAAAUAGUGUUUUGAUAAUUAUAUAUUCGUGUUUUGUGUUUUAUAGUUUUUACAUUUUUUGAAUUAAGUUUACUUGCAAAGUUAACGGAUAUUUAUUUAAGUUCCAAAUAGAAUAUAAAGAACUUUGGAAAUUAGGGAAAUAUUCGUUAUUUUUGUGCAAACUUUAAAAUAUCAUU .............(((((....((((..((((((....))...........((((((....)))))).....))))..)))).......(((((.........)))))...))))).....((((((((.(((((.((((..(((((...((((....))))))))).((((((((((((.(((((.(((((((...............))))))).))))).))))))))))))....)))).))))).)))))))).... (-48.46) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 287 258 217 74 40 pint:PI0672|5end_conserved_hypothetical_protein_611746..611976_POSITIVE 281 259 217 78 28 pint:PI0545|5end_sugar_kinase_496411..496641_POSITIVE 265 258 217 208 156 pint:PI0831|5end_hypothetical_protein_768129..768359_POSITIVE 254 251 216 186 158 pint:PI0661|5end_hypothetical_protein_603956..604186_POSITIVE 252 250 209 199 153 pint:PI1723|5end_conserved_hypothetical_protein_1641649..1641879_POSITIVE 248 257 220 47 7 pint:PI0224|5end_conserved_hypothetical_protein_220541..220771_POSITIVE 245 260 218 49 18 pint:PI1551|5end_HesA/MoeB/ThiF_family_protein_1467787..1468017_POSITIVE 243 260 219 194 151 pint:PI1885|5end_cell_division_protein_1826267..1826497_POSITIVE 237 250 201 200 149 pint:PI1722|5end_possible_peptidyl-prolyl_cis-trans_isomerase_1639536..1639766_POSITIVE 237 237 193 229 180 pint:PI1160|5end_possible_phosphatidylinositol-4-phosphate_5-kinase_1084756..1084986_POSITIVE 236 259 211 87 38 pint:PI1763|5end_two-component_system_sensor_histidine_kinase/response_regulator_1685877..1686107_POSITIVE 233 249 208 118 69 pint:PI1623|5end_hypothetical_protein_1547163..1547393_POSITIVE 230 249 201 94 52 pint:PI0206|5end_TPR-repeat-containing_protein_198112..198342_POSITIVE 224 253 222 123 86 pint:PI2162|5end_conserved_hypothetical_protein_2108796..2109026_POSITIVE 224 247 204 217 171 pint:PI1630|5end_hypothetical_protein_1552127..1552357_POSITIVE 224 249 223 169 144 pint:PI0086|5end_possible_uroporphyrinogen-III_synthase_84944..85174_POSITIVE 222 250 223 52 26 pint:PI1829|5end_hypothetical_protein_1769255..1769485_POSITIVE 222 240 195 83 32 pint:PI0175|5end_succinyl-CoA_synthetase_beta_subunit_167023..167253_POSITIVE 221 260 219 159 121 pint:PI0439|5end_conserved_hypothetical_protein;_possible_preprotein_translocase_subunit_SecE_410319..410549_POSITIVE 219 234 195 80 44 pint:PI1801|5end_30S_ribosomal_protein_S9_1733949..1734179_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 287 258 217 55 21 pint:PI0671|3end_hypothetical_protein_611807..611957_POSITIVE 278 237 194 128 85 pint:PI0591|3end_adenylosuccinate_lyase_540018..540168_POSITIVE 254 251 216 147 119 pint:PI0660|3end_conserved_hypothetical_protein_603997..604147_POSITIVE 237 237 193 150 101 pint:PI1159|3end_1,4-alpha-glucan_branching_enzyme,_N-terminal_region_1084757..1084907_POSITIVE 233 249 208 105 56 pint:PI1622|3end_hypothetical_protein_1547230..1547380_POSITIVE 233 256 217 45 1 pint:PI0027|3end_aminopeptidase_C_31756..31906_POSITIVE 224 249 223 105 80 pint:PI0085|3end_RNase_P_protein_component_84960..85110_POSITIVE 221 260 219 64 26 pint:PI0438|3end_elongation_factor_Tu_410304..410454_POSITIVE 219 259 218 83 36 pint:PI0731|3end_conserved_hypothetical_protein_663673..663823_POSITIVE 215 230 196 137 94 pint:PI1588|3end_DNA_polymerase_III,_epsilon_chain_1516930..1517080_POSITIVE 215 249 211 112 78 pint:PI0355|3end_probable__N-acetylmuramoyl-L-alanine_amidase_326698..326848_POSITIVE 212 240 198 50 4 pint:PI0174|3end_succinyl-CoA_synthetase_alpha_subunit_167070..167220_POSITIVE 211 249 201 133 88 pint:PI1988|3end_conserved_hypothetical_protein_1944068..1944218_POSITIVE 210 251 221 55 10 pint:PI2016|3end_ribosomal_large_subunit_pseudouridine_synthase_D_1974933..1975083_POSITIVE 208 244 203 104 63 pint:PI0820|3end_hypothetical_protein_759980..760130_POSITIVE 208 244 203 43 2 pint:PI0819|3end_hypothetical_protein_759919..760069_POSITIVE 208 250 201 95 28 pint:PI0026|3end_two-component_system_response_regulator_30537..30687_POSITIVE 207 258 223 41 8 pint:PI2030|3end_hypothetical_protein_1986127..1986277_POSITIVE 207 258 214 61 1 pint:PI1790|3end_hypothetical_protein_1722762..1722912_POSITIVE 206 248 201 146 102 pint:PI1957|3end_calcium-transporting_ATPase_1916574..1916724_POSITIVE