Origin IGS: taaaacaaccataacgccagaacctccgacacgacgttgctccgaaaggagttccaacagggaggctacttaactatatgtacagaatacgagcaaaacaacgacttccaccgtccaacttgacagacaaaacacccctttcaataccccactcgtggggtacgaatacaccccactcgtggggtatgagagcacctcactcgtggggtacaaaagacatcattatataacaattatcatgaatcgaataaacaaaaaacaaca .........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 tgttgttttttgtttattcgattcatgataattgttatataatgatgtcttttgtaccccacgagtgaggtgctctcataccccacgagtggggtgtattcgtaccccacgagtggggtattgaaaggggtgttttgtctgtcaagttggacggtggaagtcgttgttttgctcgtattctgtacatatagttaagtagcctccctgttggaactcctttcggagcaacgtcgtgtcggaggttctggcgttatggttgtttta Mask Tandem Repeat Region ================================================ taaaacaaccataacgccagaacctccgacacgacgttgctccgaaaggagttccaacagggaggctacttaactatatgtacagaatacgagcaaaacaacgacttccaccgtccaacttgacagacaaaacacccctttcaatnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnaaaagacatcattatataacaattatcatgaatcgaataaacaaaaaacaaca Find is-nt database================================================ Query_seq: PI1226:PI1227|PI1226:PI1227:hypothetical protein:conserved hypothetical protein; possible DNA-binding protein, histone-like family:->->:1148324..1148587 264 taaaacaaccataacgccagaacctccgacacgacgttgctccgaaaggagttccaacagggaggctacttaactatatgtacagaatacgagcaaaacaacgacttccaccgtccaacttgacagacaaaacacccctttcaataccccactcgtggggtacgaatacaccccactcgtggggtatgagagcacctcactcgtggggtacaaaagacatcattatataacaattatcatgaatcgaataaacaaaaaacaaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1226:PI1227|PI1226:PI1227:hypothetical protein:conserved hypothetical protein; possible DNA-binding protein, histone-like family:->->:1148324..1148587 264 taaaacaaccataacgccagaacctccgacacgacgttgctccgaaaggagttccaacagggaggctacttaactatatgtacagaatacgagcaaaacaacgacttccaccgtccaacttgacagacaaaacacccctttcaataccccactcgtggggtacgaatacaccccactcgtggggtatgagagcacctcactcgtggggtacaaaagacatcattatataacaattatcatgaatcgaataaacaaaaaacaaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1226:PI1227|PI1226:PI1227:hypothetical protein:conserved hypothetical protein; possible DNA-binding protein, histone-like family:->->:1148324..1148587 264 taaaacaaccataacgccagaacctccgacacgacgttgctccgaaaggagttccaacagggaggctacttaactatatgtacagaatacgagcaaaacaacgacttccaccgtccaacttgacagacaaaacacccctttcaataccccactcgtggggtacgaatacaccccactcgtggggtatgagagcacctcactcgtggggtacaaaagacatcattatataacaattatcatgaatcgaataaacaaaaaacaaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaaacaaccataacgccagaacctccgacacgacgttgctccgaaaggagttccaacagggaggctacttaactatatgtacagaatacgagcaaaacaacgacttccaccgtccaacttgacagacaaaacacccctttcaataccccactcgtggggtacgaatacaccccactcgtggggtatgagagcacctcactcgtggggtacaaaagacatcattatataacaattatcatgaatcgaataaacaaaaaacaaca Predict ORF larger than 30AA ================================================ Protein_Len: 50 Strand: + Start: 78 End: 227 ............................................................................. M Y R I R A K Q R L P P S N L T D K T P L S I P H S W G T N T P H S W G M R A P H S W G T K D I I I ..................................... Protein_Len: 36 Strand: + Start: 155 End: 262 .......................................................................................................................................................... M G Y E Y T P L V G Y E S T S L V G Y K R H H Y I T I I M N R I N K K Q .. Protein_Len: 30 Strand: - Start: 144 End: 233 ............................................................................................................................................... Y G V R P T R I C G V R P T H S C R V R P T C F V D N Y L M ............................... Protein_Len: 37 Strand: - Start: 77 End: 187 ............................................................................ I Y L I R A F C R S G G D L K V S L V G R E I G W E H P V F V G W E H P M ............................................................................. Protein_Len: 47 Strand: - Start: 73 End: 213 ........................................................................ S Y T C F V L L V V V E V T W S S L C F V G K L V G S T P Y S Y V G S T P Y S L V E S T P Y M ................................................... taaaacaaccataacgccagaacctccgacacgacgttgctccgaaaggagttccaacagggaggctacttaactatatgtacagaatacgagcaaaacaacgacttccaccgtccaacttgacagacaaaacacccctttcaataccccactcgtggggtacgaatacaccccactcgtggggtatgagagcacctcactcgtggggtacaaaagacatcattatataacaattatcatgaatcgaataaacaaaaaacaaca 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================================================ taaaacaaccataacgccagaacctccgacacgacgttgctccgaaaggagttccaacagggaggctacttaactatatgtacagaatacgagcaaaacaacgacttccaccgtccaacttgacagacaaaacacccctttcaataccccactcgtggggtacgaatacaccccactcgtggggtatgagagcacctcactcgtggggtacaaaagacatcattatataacaattatcatgaatcgaataaacaaaaaacaaca Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 85 HP_score: -14.1 Tail_Score: -3.02263 Start: 147 End: 184 Full_Region: tgaggtgctctcata ccccacgagtggggtgt attc gtaccccacgagtgggg tattgaaaggggtgt ..................................................................................................................................................ccccacgagtggggtgtattcgtaccccacgagtgggg................................................................................ TransTerm Strand: - Conf: 59 HP_score: -6.8 Tail_Score: -3.14132 Start: 167 End: 212 Full_Region: tataatgatgtcttt tgtaccccacgagtgaggtg ctctca taccccacgagtggggtgta ttcgtaccccacgag ......................................................................................................................................................................tgtaccccacgagtgaggtgctctcataccccacgagtggggtgta.................................................... Find igs database================================================ Query_seq: PI1226:PI1227|PI1226:PI1227:hypothetical protein:conserved hypothetical protein; possible DNA-binding protein, histone-like family:->->:1148324..1148587 264 taaaacaaccataacgccagaacctccgacacgacgttgctccgaaaggagttccaacagggaggctacttaactatatgtacagaatacgagcaaaacaacgacttccaccgtccaacttgacagacaaaacacccctttcaataccccactcgtggggtacgaatacaccccactcgtggggtatgagagcacctcactcgtggggtacaaaagacatcattatataacaattatcatgaatcgaataaacaaaaaacaaca Intra-Species Hit: Count: 1 Min: 1 Max: 264 Len: 264 Subject: pint_PI1226_PI1227|hypothetical protein:conserved hypothetical protein; possible DNA-binding protein, histone-like family|POSITIVE:POSITIVE|[1148324,1148587]|264 HSP 1 e-value: 1.0E-148 bit: 523.0 Len: 264 Query Start:1 Query End:264 Subject Strand: POSITIVE Subject Start: 1 Subject End: 264 taaaacaaccataacgccagaacctccgacacgacgttgctccgaaaggagttccaacagggaggctacttaactatatgtacagaatacgagcaaaacaacgacttccaccgtccaacttgacagacaaaacacccctttcaataccccactcgtggggtacgaatacaccccactcgtggggtatgagagcacctcactcgtggggtacaaaagacatcattatataacaattatcatgaatcgaataaacaaaaaacaaca taaaacaaccataacgccagaacctccgacacgacgttgctccgaaaggagttccaacagggaggctacttaactatatgtacagaatacgagcaaaacaacgacttccaccgtccaacttgacagacaaaacacccctttcaataccccactcgtggggtacgaatacaccccactcgtggggtatgagagcacctcactcgtggggtacaaaagacatcattatataacaattatcatgaatcgaataaacaaaaaacaaca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAACAACCAUAACGCCAGAACCUCCGACACGACGUUGCUCCGAAAGGAGUUCCAACAGGGAGGCUACUUAACUAUAUGUACAGAAUACGAGCAAAACAACGACUUCCACCGUCCAACUUGACAGACAAAACACCCCUUUCAAUACCCCACUCGUGGGGUACGAAUACACCCCACUCGUGGGGUAUGAGAGCACCUCACUCGUGGGGUACAAAAGACAUCAUUAUAUAACAAUUAUCAUGAAUCGAAUAAACAAAAAACAACA ......................(((((........(..(((((....)))))..).....))))).............(((((....((((((...................(((......))).............((((((.((((((((..(((((((........)))))))..)))))))))))))).......))))))..)))))...((..((((.(((.......))).)))).))................... (-69.02) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUUGUUUUUUGUUUAUUCGAUUCAUGAUAAUUGUUAUAUAAUGAUGUCUUUUGUACCCCACGAGUGAGGUGCUCUCAUACCCCACGAGUGGGGUGUAUUCGUACCCCACGAGUGGGGUAUUGAAAGGGGUGUUUUGUCUGUCAAGUUGGACGGUGGAAGUCGUUGUUUUGCUCGUAUUCUGUACAUAUAGUUAAGUAGCCUCCCUGUUGGAACUCCUUUCGGAGCAACGUCGUGUCGGAGGUUCUGGCGUUAUGGUUGUUUUA .......................((.((((...((...((((((((.(((....((((((..((((.....))))..(((((((((..((((((((......))))))))..))))))))).....))))))......(((((......))))).))).))))))))...))...)))).))..((((..((((.(.(((((((.(((((...((((....))))))))).......))))))))))))..))))......... (-83.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 476 200 151 230 181 pint:PI2053|5end_conserved_hypothetical_protein;_possible_outer_membrane_receptor_protein_2010673..2010903_POSITIVE 370 63 27 50 10 pint:PI0644|5end_dnaJ_protein_585704..585934_POSITIVE 362 65 23 215 161 pint:PI0889|5end_pyruvate_kinase_818758..818988_POSITIVE 358 44 6 127 89 pint:PI1575|5end_LemA_protein_1501143..1501373_POSITIVE 344 179 131 55 2 pint:PI1120|5end_conserved_hypothetical_protein_1044870..1045100_POSITIVE 336 68 22 63 11 pint:PI1925|5end_conserved_hypothetical_protein_1866387..1866617_POSITIVE 335 197 153 66 6 pint:PI2086|5end_signal_peptidase_I_2041835..2042065_POSITIVE 321 200 152 106 48 pint:PI0098|5end_conserved_hypothetical_protein_(possible_glycosyl/glycerophosphate_transferase)_94622..94852_POSITIVE 320 46 4 124 74 pint:PI1727|5end__ATP-dependent_Clp_protease,_ATP-binding_subunit_1645680..1645910_POSITIVE 320 69 21 183 127 pint:PI0683|5end_hypothetical_protein_619292..619522_POSITIVE 312 219 171 69 7 pint:PI1640|5end_hypothetical_protein_1558062..1558292_POSITIVE 309 59 16 230 180 pint:PI1072|5end_hypothetical_protein_990220..990450_POSITIVE 303 203 162 129 84 pint:PI2166|5end_hypothetical_protein_2111394..2111624_POSITIVE 302 58 16 231 189 pint:PI0684|5end_coproporphyrinogen_III_oxidase_619357..619587_POSITIVE 301 57 16 74 36 pint:PI1724|5end_inosine-5'-monophosphate_dehydrogenase_1641075..1641305_POSITIVE 300 54 14 44 8 pint:PI0189|5end_integrase_179623..179853_POSITIVE 299 208 167 174 135 pint:PI1223|5end_conserved_hypothetical_protein_1143537..1143767_POSITIVE 297 65 22 58 14 pint:PI0810|5end_hypothetical_protein_746743..746973_POSITIVE 297 65 22 53 9 pint:PI0811|5end_protease/hemagglutinin_PrtT,_streptopain_family_746738..746968_POSITIVE 296 60 16 208 157 pint:PI1980|5end_conserved_hypothetical_protein_1937470..1937700_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 441 210 161 66 19 pint:PI1223|3end_conserved_hypothetical_protein_1144459..1144609_POSITIVE 372 197 151 66 20 pint:PI0756|3end_50S_ribosomal_protein_L7/L12_688980..689130_POSITIVE 358 44 6 130 92 pint:PI1574|3end_conserved_hypothetical_protein_1501226..1501376_POSITIVE 348 211 171 136 84 pint:PI1546|3end_mobilizable_transposon,_excision_protein_1465099..1465249_POSITIVE 343 70 26 77 30 pint:PI1490|3end_GTP_cyclohydrolase_I_1409127..1409277_POSITIVE 339 210 162 58 3 pint:PI0042|3end_hypothetical_protein_43444..43594_POSITIVE 336 68 22 91 39 pint:PI1924|3end_cytidine_deaminase_1866495..1866645_POSITIVE 321 200 152 86 28 pint:PI0097|3end_aspartate_aminotransferase_94682..94832_POSITIVE 320 69 21 67 11 pint:PI0681|3end_hypothetical_protein_619256..619406_POSITIVE 310 195 152 151 94 pint:PI1343|3end_conserved_hypothetical_protein_1258539..1258689_POSITIVE 303 68 35 121 87 pint:PI2076|3end_hypothetical_protein_2035758..2035908_POSITIVE 298 68 27 60 25 pint:PI1639|3end_conserved_hypothetical_protein_1558133..1558283_POSITIVE 293 129 89 45 6 pint:PI0929|3end_copper_homeostasis_protein_861048..861198_POSITIVE 291 50 5 149 97 pint:PI0094|3end_protoporphyrinogen_oxidase_90511..90661_POSITIVE 288 56 22 59 15 pint:PI2036|3end_hypothetical_protein_1989516..1989666_POSITIVE 288 210 169 99 59 pint:PI1794|3end_conserved_hypothetical_protein_1726696..1726846_POSITIVE 288 208 163 58 1 pint:PI1135|3end_hypothetical_protein_1062203..1062353_POSITIVE 288 207 164 140 89 pint:PI0914|3end_ATPase,_AAA_family_844992..845142_POSITIVE 287 197 152 149 112 pint:PI1652|3end_hypothetical_protein_1565235..1565385_POSITIVE 287 178 131 151 96 pint:PI0087|3end_conserved_hypothetical_protein_86733..86883_POSITIVE