Origin IGS: taaaataaggaatatgcaaacaaagttgcacatattctgacccacaaaagtcaaatcgcagccagtgtaaaaatagaatattattatctctcattatatatattatcaataaattaaaaatacttaatcaacttgttaaataaatattaatccttacatttgcaagaaaaagaaaacaaatattaatcaatgcaaagagaaaataaataaagtagaaagagtttctgttcatatccgagacagaagtaatcgaaagccattgaagatatagaaacattttgaatgtaaa .........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 tttacattcaaaatgtttctatatcttcaatggctttcgattacttctgtctcggatatgaacagaaactctttctactttatttattttctctttgcattgattaatatttgttttctttttcttgcaaatgtaaggattaatatttatttaacaagttgattaagtatttttaatttattgataatatatataatgagagataataatattctatttttacactggctgcgatttgacttttgtgggtcagaatatgtgcaactttgtttgcatattccttatttta Mask Tandem Repeat Region ================================================ taaaataaggaatatgcaaacaaagttgcacatattctgacccacaaaagtcaaatcgcagccagtgtaaaaatagaatattattatctctcattatatatattatcaataaattaaaaatacttaatcaacttgttaaataaatattaatccttacatttgcaagaaaaagaaaacaaatattaatcaatgcaaagagaaaataaataaagtagaaagagtttctgttcatatccgagacagaagtaatcgaaagccattgaagatatagaaacattttgaatgtaaa Find is-nt database================================================ Query_seq: PI1926:PI1927|PI1926:PI1927:conserved hypothetical protein:hypothetical protein:->->:1871038..1871326 289 taaaataaggaatatgcaaacaaagttgcacatattctgacccacaaaagtcaaatcgcagccagtgtaaaaatagaatattattatctctcattatatatattatcaataaattaaaaatacttaatcaacttgttaaataaatattaatccttacatttgcaagaaaaagaaaacaaatattaatcaatgcaaagagaaaataaataaagtagaaagagtttctgttcatatccgagacagaagtaatcgaaagccattgaagatatagaaacattttgaatgtaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1926:PI1927|PI1926:PI1927:conserved hypothetical protein:hypothetical protein:->->:1871038..1871326 289 taaaataaggaatatgcaaacaaagttgcacatattctgacccacaaaagtcaaatcgcagccagtgtaaaaatagaatattattatctctcattatatatattatcaataaattaaaaatacttaatcaacttgttaaataaatattaatccttacatttgcaagaaaaagaaaacaaatattaatcaatgcaaagagaaaataaataaagtagaaagagtttctgttcatatccgagacagaagtaatcgaaagccattgaagatatagaaacattttgaatgtaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1926:PI1927|PI1926:PI1927:conserved hypothetical protein:hypothetical protein:->->:1871038..1871326 289 taaaataaggaatatgcaaacaaagttgcacatattctgacccacaaaagtcaaatcgcagccagtgtaaaaatagaatattattatctctcattatatatattatcaataaattaaaaatacttaatcaacttgttaaataaatattaatccttacatttgcaagaaaaagaaaacaaatattaatcaatgcaaagagaaaataaataaagtagaaagagtttctgttcatatccgagacagaagtaatcgaaagccattgaagatatagaaacattttgaatgtaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaaataaggaatatgcaaacaaagttgcacatattctgacccacaaaagtcaaatcgcagccagtgtaaaaatagaatattattatctctcattatatatattatcaataaattaaaaatacttaatcaacttgttaaataaatattaatccttacatttgcaagaaaaagaaaacaaatattaatcaatgcaaagagaaaataaataaagtagaaagagtttctgttcatatccgagacagaagtaatcgaaagccattgaagatatagaaacattttgaatgtaaa Predict ORF larger than 30AA ================================================ Protein_Len: 43 Strand: + Start: 12 End: 140 ........... M C K Q S C T Y S D P Q K S N R S Q C K N R I L L S L I I Y I I N K L K I L N Q L V K ..................................................................................................................................................... Protein_Len: 43 Strand: + Start: 140 End: 268 ........................................................................................................................................... M N I N P Y I C K K K K T N I N Q C K E K I N K V E R V S V H I R D R S N R K P L K I ..................... Protein_Len: 33 Strand: - Start: 186 End: 284 ......................................................................................................................................................................................... D I C L S F L Y L L F L K Q E Y G L C F Y D F A M S S I S V N Q M ..... Protein_Len: 49 Strand: - Start: 131 End: 277 .................................................................................................................................. S T L Y I N I R V N A L F L F C I N I L A F L F Y I F Y F S N R N M D S V S T I S L W Q L Y L F M ............ Protein_Len: 40 Strand: - Start: 2 End: 121 . F Y P I H L C L Q V Y E S G C F D F R L W H L F L I N N D R M I Y I I L L N F M ........................................................................................................................................................................ taaaataaggaatatgcaaacaaagttgcacatattctgacccacaaaagtcaaatcgcagccagtgtaaaaatagaatattattatctctcattatatatattatcaataaattaaaaatacttaatcaacttgttaaataaatattaatccttacatttgcaagaaaaagaaaacaaatattaatcaatgcaaagagaaaataaataaagtagaaagagtttctgttcatatccgagacagaagtaatcgaaagccattgaagatatagaaacattttgaatgtaaa Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taaaataaggaatatgcaaacaaagttgcacatattctgacccacaaaagtcaaatcgcagccagtgtaaaaatagaatattattatctctcattatatatattatcaataaattaaaaatacttaatcaacttgttaaataaatattaatccttacatttgcaagaaaaagaaaacaaatattaatcaatgcaaagagaaaataaataaagtagaaagagtttctgttcatatccgagacagaagtaatcgaaagccattgaagatatagaaacattttgaatgtaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1926:PI1927|PI1926:PI1927:conserved hypothetical protein:hypothetical protein:->->:1871038..1871326 289 taaaataaggaatatgcaaacaaagttgcacatattctgacccacaaaagtcaaatcgcagccagtgtaaaaatagaatattattatctctcattatatatattatcaataaattaaaaatacttaatcaacttgttaaataaatattaatccttacatttgcaagaaaaagaaaacaaatattaatcaatgcaaagagaaaataaataaagtagaaagagtttctgttcatatccgagacagaagtaatcgaaagccattgaagatatagaaacattttgaatgtaaa Intra-Species Hit: Count: 1 Min: 1 Max: 289 Len: 289 Subject: pint_PI1926_PI1927|conserved hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[1871038,1871326]|289 HSP 1 e-value: 2.0E-31 bit: 137.0 Len: 69 Query Start:221 Query End:289 Subject Strand: POSITIVE Subject Start: 221 Subject End: 289 ............................................................................................................................................................................................................................gtttctgttcatatccgagacagaagtaatcgaaagccattgaagatatagaaacattttgaatgtaaa ............................................................................................................................................................................................................................gtttctgttcatatccgagacagaagtaatcgaaagccattgaagatatagaaacattttgaatgtaaa HSP 2 e-value: 4.0E-30 bit: 133.0 Len: 67 Query Start:1 Query End:67 Subject Strand: POSITIVE Subject Start: 1 Subject End: 67 taaaataaggaatatgcaaacaaagttgcacatattctgacccacaaaagtcaaatcgcagccagtg.............................................................................................................................................................................................................................. taaaataaggaatatgcaaacaaagttgcacatattctgacccacaaaagtcaaatcgcagccagtg.............................................................................................................................................................................................................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAUAAGGAAUAUGCAAACAAAGUUGCACAUAUUCUGACCCACAAAAGUCAAAUCGCAGCCAGUGUAAAAAUAGAAUAUUAUUAUCUCUCAUUAUAUAUAUUAUCAAUAAAUUAAAAAUACUUAAUCAACUUGUUAAAUAAAUAUUAAUCCUUACAUUUGCAAGAAAAAGAAAACAAAUAUUAAUCAAUGCAAAGAGAAAAUAAAUAAAGUAGAAAGAGUUUCUGUUCAUAUCCGAGACAGAAGUAAUCGAAAGCCAUUGAAGAUAUAGAAACAUUUUGAAUGUAAA ........(((((((((((......)))))..))))))......(((((.((..(((.....(((((.............(((((.(((((((((....(((((........(((((......)))))...(((((.((((................)))))))))............))))).....))))...))))).)))))............((.(((((((((......)).)))))))...))......)))))..)))...))....)))))........ (-32.79) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUACAUUCAAAAUGUUUCUAUAUCUUCAAUGGCUUUCGAUUACUUCUGUCUCGGAUAUGAACAGAAACUCUUUCUACUUUAUUUAUUUUCUCUUUGCAUUGAUUAAUAUUUGUUUUCUUUUUCUUGCAAAUGUAAGGAUUAAUAUUUAUUUAACAAGUUGAUUAAGUAUUUUUAAUUUAUUGAUAAUAUAUAUAAUGAGAGAUAAUAAUAUUCUAUUUUUACACUGGCUGCGAUUUGACUUUUGUGGGUCAGAAUAUGUGCAACUUUGUUUGCAUAUUCCUUAUUUUA .........((((((..((((((...(((((.((..(((.....((((((.(((....)))))))))................(((((.((((((.......(((((((............(((((((....)))))))..((((((((.((((....)))).)))))))).......)))))))............)))))).)))))................)))..)).).))))....))))))...(((((((((((....)))..))))))))..)))))). (-45.41) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 307 44 5 121 82 pint:PI0853|5end_glycosyl_transferase,_group_2_family_protein_785515..785745_POSITIVE 290 258 211 106 57 pint:PI1431|5end_conserved_hypothetical_protein_1352079..1352309_POSITIVE 289 50 2 137 98 pint:PI0774|5end_phosphoserine_aminotransferase_(phosphoserine_transaminase)_709497..709727_POSITIVE 265 68 24 208 166 pint:PI0496|5end_heat_shock_protein_hsp70_(chaperone_protein_dnaK)_456632..456862_POSITIVE 259 258 217 227 181 pint:PI1641|5end_hypothetical_protein_1558495..1558725_POSITIVE 259 258 217 227 181 pint:PI0347|5end_hypothetical_protein_321267..321497_POSITIVE 250 260 214 104 64 pint:PI0720|5end_conserved_hypothetical_protein_653949..654179_POSITIVE 246 64 23 41 3 pint:PI1551|5end_HesA/MoeB/ThiF_family_protein_1467787..1468017_POSITIVE 241 258 211 229 170 pint:PI0238|5end_two-component_system_response_regulator_237054..237284_POSITIVE 239 280 236 122 69 pint:PI2146|5end_prolipoprotein_diacylglyceryl_transferase_2092402..2092632_POSITIVE 239 261 222 92 50 pint:PI0011|5end_conserved_hypothetical_protein_12142..12372_POSITIVE 238 257 211 114 71 pint:PI1081|5end_probable_endonuclease/resolvase_1000806..1001036_POSITIVE 236 50 8 155 118 pint:PI0198|5end_hypothetical_protein_190719..190949_POSITIVE 234 269 225 198 159 pint:PI1364|5end_dipeptidyl_peptidase_IV_1281862..1282092_POSITIVE 233 67 38 34 3 pint:PI2015|5end_D-alanine--D-alanine_ligase_1972724..1972954_POSITIVE 232 67 21 180 129 pint:PI1423|5end_hypothetical_protein_1341888..1342118_POSITIVE 232 67 21 93 42 pint:PI1421|5end_hypothetical_protein_1341801..1342031_POSITIVE 232 268 237 214 180 pint:PI1319|5end_possible_OmpA_,_outer_membrane_protein-related_protein_1235655..1235885_POSITIVE 231 266 221 73 23 pint:PI1693|5end_possible_RmuC_domain_protein_1608183..1608413_POSITIVE 229 50 2 202 158 pint:PI1201|5end_peptidyl-arginine_deiminase_1116598..1116828_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 289 50 2 52 13 pint:PI0773|3end_D-3-phosphoglycerate_dehydrogenase_709492..709642_POSITIVE 250 260 214 85 45 pint:PI0719|3end_conserved_hypothetical_protein_654010..654160_POSITIVE 239 69 23 111 63 pint:PI1265|3end_hypothetical_protein_1185512..1185662_POSITIVE 239 273 237 87 43 pint:PI0401|3end_conserved_hypothetical_protein_367107..367257_POSITIVE 238 257 211 111 68 pint:PI1080|3end_conserved_hypothetical_protein;_possible_outer_membrane_lipoprotein_1000883..1001033_POSITIVE 236 89 43 117 75 pint:PI1553|3end_hypothetical_protein_1470170..1470320_POSITIVE 234 269 225 69 30 pint:PI1362|3end_60Kd_inner_membrane_protein_1281813..1281963_POSITIVE 234 257 211 49 4 pint:PI0267|3end_conjugative_transposon_protein,_TraQ_259291..259441_POSITIVE 231 266 221 58 8 pint:PI1692|3end_alanine_racemase_1608248..1608398_POSITIVE 231 47 8 129 86 pint:PI1284|3end_ATP_synthase,_delta_subunit_1200323..1200473_POSITIVE 229 50 2 126 82 pint:PI1200|3end_carbon-nitrogen_hydrolase/beta-alanine_synthase_1116602..1116752_POSITIVE 227 280 236 44 1 pint:PI0270|3end_conserved_hypothetical_protein_262493..262643_POSITIVE 220 260 211 132 81 pint:PI0914|3end_ATPase,_AAA_family_844992..845142_POSITIVE 218 77 38 80 31 pint:PI1801|3end_30S_ribosomal_protein_S9_1734412..1734562_POSITIVE 218 71 37 113 74 pint:PI1641|3end_hypothetical_protein_1558883..1559033_POSITIVE 218 240 195 115 68 pint:PI1456|3end_conserved_hypothetical_protein_1379921..1380071_POSITIVE 216 268 242 34 4 pint:PI1318|3end_hypothetical_protein_1235555..1235705_POSITIVE 216 42 9 69 27 pint:PI0669|3end_hypothetical_protein_611147..611297_POSITIVE 215 276 235 147 108 pint:PI2167|3end_hypothetical_protein_2111891..2112041_POSITIVE 213 67 27 48 10 pint:PI0913|3end_glycerate_dehydrogenase_843733..843883_POSITIVE