Origin IGS: ataaatgctgctacgtcggcagattattctggttaaaaagttatagatgcagctcttggttatagtgtcctaagatcgctatgcaacctgtaagaaacgattgtaggctgtttcttgcttcctgcacgaatgcaggagagcagaaacgcccgttgctgctcccgtcaatacactaattattatcgacttaaccccttaattcaaaaactaaa .........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 tttagtttttgaattaaggggttaagtcgataataattagtgtattgacgggagcagcaacgggcgtttctgctctcctgcattcgtgcaggaagcaagaaacagcctacaatcgtttcttacaggttgcatagcgatcttaggacactataaccaagagctgcatctataactttttaaccagaataatctgccgacgtagcagcatttat Mask Tandem Repeat Region ================================================ ataaatgctgctacgtcggcagattattctggttaaaaagttatagatgcagctcttggttatagtgtcctaagatcgctatgcaacctgtaagaaacgattgtaggctgtttcttgcttcctgcacgaatgcaggagagcagaaacgcccgttgctgctcccgtcaatacactaattattatcgacttaaccccttaattcaaaaactaaa Find is-nt database================================================ Query_seq: PG1974:PG1975|PG1974:PG1975:hypothetical protein:hemagglutinin protein HagC:<-->:2063146..2063357 212 ataaatgctgctacgtcggcagattattctggttaaaaagttatagatgcagctcttggttatagtgtcctaagatcgctatgcaacctgtaagaaacgattgtaggctgtttcttgcttcctgcacgaatgcaggagagcagaaacgcccgttgctgctcccgtcaatacactaattattatcgacttaaccccttaattcaaaaactaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1974:PG1975|PG1974:PG1975:hypothetical protein:hemagglutinin protein HagC:<-->:2063146..2063357 212 ataaatgctgctacgtcggcagattattctggttaaaaagttatagatgcagctcttggttatagtgtcctaagatcgctatgcaacctgtaagaaacgattgtaggctgtttcttgcttcctgcacgaatgcaggagagcagaaacgcccgttgctgctcccgtcaatacactaattattatcgacttaaccccttaattcaaaaactaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1974:PG1975|PG1974:PG1975:hypothetical protein:hemagglutinin protein HagC:<-->:2063146..2063357 212 ataaatgctgctacgtcggcagattattctggttaaaaagttatagatgcagctcttggttatagtgtcctaagatcgctatgcaacctgtaagaaacgattgtaggctgtttcttgcttcctgcacgaatgcaggagagcagaaacgcccgttgctgctcccgtcaatacactaattattatcgacttaaccccttaattcaaaaactaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ataaatgctgctacgtcggcagattattctggttaaaaagttatagatgcagctcttggttatagtgtcctaagatcgctatgcaacctgtaagaaacgattgtaggctgtttcttgcttcctgcacgaatgcaggagagcagaaacgcccgttgctgctcccgtcaatacactaattattatcgacttaaccccttaattcaaaaactaaa Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 75 End: 173 .......................................................................... M A M Q P V R N D C R L F L A S C T N A G E Q K R P L L L P S I H ....................................... Protein_Len: 37 Strand: + Start: 100 End: 210 ................................................................................................... M V G C F L L P A R M Q E S R N A R C C S R Q Y T N Y Y R L N P L I Q K L .. Protein_Len: 34 Strand: - Start: 82 End: 183 ................................................................................. A V Q L F R N Y A T E Q K R C S H L L A S V G T A A G T L V S I I M ............................. Protein_Len: 42 Strand: - Start: 44 End: 169 ........................................... L H L E Q N Y H G L I A I C G T L F S Q L S N R A E Q V F A P S C F R G N S S G D M ........................................... ataaatgctgctacgtcggcagattattctggttaaaaagttatagatgcagctcttggttatagtgtcctaagatcgctatgcaacctgtaagaaacgattgtaggctgtttcttgcttcctgcacgaatgcaggagagcagaaacgcccgttgctgctcccgtcaatacactaattattatcgacttaaccccttaattcaaaaactaaa 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: 81 Start: 176 End: 205 ...............................................................................................................................................................................TTTGAATTAAGGGGTTAAGTCGATAATAAT....... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ataaatgctgctacgtcggcagattattctggttaaaaagttatagatgcagctcttggttatagtgtcctaagatcgctatgcaacctgtaagaaacgattgtaggctgtttcttgcttcctgcacgaatgcaggagagcagaaacgcccgttgctgctcccgtcaatacactaattattatcgacttaaccccttaattcaaaaactaaa Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 77 HP_score: -11.4 Tail_Score: -2.52834 Start: 106 End: 151 Full_Region: TAAGAAACGATTGTA GGCTGTTTCTTGCTTCCTGCA CGAA TGCAGGAGAGCAGAAACGCCC GTTGCTGCTCCCGTC .........................................................................................................GGCTGTTTCTTGCTTCCTGCACGAATGCAGGAGAGCAGAAACGCCC............................................................. Find igs database================================================ Query_seq: PG1974:PG1975|PG1974:PG1975:hypothetical protein:hemagglutinin protein HagC:<-->:2063146..2063357 212 ataaatgctgctacgtcggcagattattctggttaaaaagttatagatgcagctcttggttatagtgtcctaagatcgctatgcaacctgtaagaaacgattgtaggctgtttcttgcttcctgcacgaatgcaggagagcagaaacgcccgttgctgctcccgtcaatacactaattattatcgacttaaccccttaattcaaaaactaaa Intra-Species Hit: Count: 1 Min: 1 Max: 212 Len: 212 Subject: NC_002950_PG1974_PG1975|hypothetical protein:hemagglutinin protein HagC|NEGATIVE:POSITIVE|[2063146,2063357]|212 HSP 1 e-value: 1.0E-117 bit: 420.0 Len: 212 Query Start:1 Query End:212 Subject Strand: POSITIVE Subject Start: 1 Subject End: 212 ataaatgctgctacgtcggcagattattctggttaaaaagttatagatgcagctcttggttatagtgtcctaagatcgctatgcaacctgtaagaaacgattgtaggctgtttcttgcttcctgcacgaatgcaggagagcagaaacgcccgttgctgctcccgtcaatacactaattattatcgacttaaccccttaattcaaaaactaaa ataaatgctgctacgtcggcagattattctggttaaaaagttatagatgcagctcttggttatagtgtcctaagatcgctatgcaacctgtaagaaacgattgtaggctgtttcttgcttcctgcacgaatgcaggagagcagaaacgcccgttgctgctcccgtcaatacactaattattatcgacttaaccccttaattcaaaaactaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAAAUGCUGCUACGUCGGCAGAUUAUUCUGGUUAAAAAGUUAUAGAUGCAGCUCUUGGUUAUAGUGUCCUAAGAUCGCUAUGCAACCUGUAAGAAACGAUUGUAGGCUGUUUCUUGCUUCCUGCACGAAUGCAGGAGAGCAGAAACGCCCGUUGCUGCUCCCGUCAAUACACUAAUUAUUAUCGACUUAACCCCUUAAUUCAAAAACUAAA .......(((((.....)))))........(((((..........((.(((((....((((((((((((....)).)))))))..))).................(((.((((((.((((((((((....))))))).))))))))))))....)))))))..(((.(((..........))).))).)))))................... (-54.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUAGUUUUUGAAUUAAGGGGUUAAGUCGAUAAUAAUUAGUGUAUUGACGGGAGCAGCAACGGGCGUUUCUGCUCUCCUGCAUUCGUGCAGGAAGCAAGAAACAGCCUACAAUCGUUUCUUACAGGUUGCAUAGCGAUCUUAGGACACUAUAACCAAGAGCUGCAUCUAUAACUUUUUAACCAGAAUAAUCUGCCGACGUAGCAGCAUUUAU ......(((((..(((((((((((.(((((((..........))))))).((((((((...(((((((((((((.(((((((....)))))))))).)))))).))))......((.(((((.(((((((...)))))))))))).))...........))))).))).))))))))))).)))))....((((.......))))....... (-67.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 946 140 91 231 182 NC_002950:PG1974|5end_hypothetical_protein_2063055..2063285_NEGATIVE 759 137 91 146 101 NC_002950:PG1970|5end_hypothetical_protein_2059783..2060013_NEGATIVE 676 174 131 94 51 NC_002950:PG2114|5end_hypothetical_protein_2224158..2224388_NEGATIVE 467 137 94 198 156 NC_002950:PG1972|5end_hemagglutinin_protein_HagB_2060002..2060232_POSITIVE 436 168 122 174 123 NC_002950:PG0504|5end_lipoyl_synthase_544234..544464_POSITIVE 389 167 127 219 179 NC_002950:PG1498|5end_hypothetical_protein_1574656..1574886_POSITIVE 383 167 121 51 2 NC_002950:PG1063|5end_transcriptional_regulator,_putative_1131056..1131286_POSITIVE 373 162 124 228 177 NC_002950:PG0319|5end_hypothetical_protein_352949..353179_POSITIVE 372 159 114 158 95 NC_002950:PG0268|5end_tRNA_(5-methylaminomethyl-2-thiouridylate)-methyltransferase_300898..301128_POSITIVE 369 159 115 206 166 NC_002950:PG2080|5end_adenosylmethionine--8-amino-7-oxononanoate_transaminase_2180679..2180909_NEGATIVE 366 160 118 208 159 NC_002950:PG0018|5end_hypothetical_protein_19648..19878_POSITIVE 363 150 101 230 187 NC_002950:PG1102|5end_hypothetical_protein_1173637..1173867_NEGATIVE 355 159 112 53 2 NC_002950:PG0441|5end_hypothetical_protein_478734..478964_POSITIVE 355 157 114 201 151 NC_002950:PG0047|5end_cell_division_protein_FtsH,_putative_59250..59480_NEGATIVE 353 158 116 69 11 NC_002950:PG1667|5end_outer_membrane_efflux_protein_1749545..1749775_POSITIVE 353 159 116 46 4 NC_002950:PG0147|5end_hypothetical_protein_169667..169897_NEGATIVE 352 166 122 193 133 NC_002950:PG0737|5end_hypothetical_protein_786188..786418_POSITIVE 351 59 14 43 9 NC_002950:PG0884|5end_hypothetical_protein_946479..946709_POSITIVE 349 167 121 60 10 NC_002950:PG1473|5end_conjugative_transposon_protein_TraQ_1550225..1550455_NEGATIVE 346 150 103 174 123 NC_002950:PG0544|5end_type_I_restriction-modification_system,_M_subunit,_putative_596052..596282_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 517 166 121 126 58 NC_002950:PG2040|3end_DNA-binding_protein,_histone-like_family_2138398..2138548_NEGATIVE 436 168 122 71 20 NC_002950:PG0503|3end_dipeptidyl_aminopeptidase_IV_544211..544361_POSITIVE 389 167 127 118 78 NC_002950:PG1497|3end_DNA-binding_protein,_histone-like_family_1574635..1574785_POSITIVE 367 166 122 129 63 NC_002950:PG0443|3end_hemagglutinin-related_protein_483147..483297_POSITIVE 361 164 124 64 14 NC_002950:PG0495|3end_hypothetical_protein_536936..537086_POSITIVE 354 139 91 106 55 NC_002950:PG1619|3end_biotin_synthesis_protein_BioC,_putative_1699415..1699565_POSITIVE 354 159 115 49 3 NC_002950:PG0439|3end_hypothetical_protein_478810..478960_POSITIVE 354 160 114 151 90 NC_002950:PG0267|3end_arginyl-tRNA_synthetase_300973..301123_POSITIVE 353 158 116 72 14 NC_002950:PG1666|3end_efflux_transporter,_MFP_component,_RND_family_1749628..1749778_POSITIVE 353 159 116 59 17 NC_002950:PG0148|3end_sigma-54-dependent_transcriptional_regulator_169654..169804_NEGATIVE 351 165 121 63 7 NC_002950:PG1055|3end_thiol_protease_1121202..1121352_NEGATIVE 351 59 14 46 12 NC_002950:PG0883|3end_hypothetical_protein_946562..946712_POSITIVE 349 167 123 151 100 NC_002950:PG1151|3end_alcohol_dehydrogenase,_iron-containing_1234378..1234528_POSITIVE 341 160 116 77 26 NC_002950:PG1352|3end_hypothetical_protein_1432737..1432887_NEGATIVE 338 150 103 132 80 NC_002950:PG1027|3end_hypothetical_protein_1089197..1089347_NEGATIVE 335 160 118 126 72 NC_002950:PG1675|3end_hypothetical_protein_1760360..1760510_POSITIVE 329 150 101 124 75 NC_002950:PG1078|3end_electron_transfer_flavoprotein,_alpha_subunit_1146525..1146675_POSITIVE 329 150 103 78 33 NC_002950:PG0483|3end_kinase,_putative_523236..523386_NEGATIVE 325 166 122 151 102 NC_002950:PG2062|3end_histidyl-tRNA_synthetase_2160415..2160565_POSITIVE 325 159 113 94 34 NC_002950:PG0334|3end_glycosyl_transferase,_group_2_family_protein_368792..368942_NEGATIVE