Origin IGS: gtatacgaacgaaatatggagccgaaccgatccttttccgccccggagtacggggctttgattttagagtatattatcgcacggattccggcagagagatcggtgaaattcccaccgtcgaggaactcctgcgtaacgacaagctcagagaatccaatcaagaaatgatcgctctgaacgaatagcagttgctcttaatatccgcatctcgcagtatgcgtcagttcgccgaggaagataatccgcctccctttgcactcgcaagtctgcatctgttgtgcataaatgatttacagcattattactacat .........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 atgtagtaataatgctgtaaatcatttatgcacaacagatgcagacttgcgagtgcaaagggaggcggattatcttcctcggcgaactgacgcatactgcgagatgcggatattaagagcaactgctattcgttcagagcgatcatttcttgattggattctctgagcttgtcgttacgcaggagttcctcgacggtgggaatttcaccgatctctctgccggaatccgtgcgataatatactctaaaatcaaagccccgtactccggggcggaaaaggatcggttcggctccatatttcgttcgtatac Mask Tandem Repeat Region ================================================ gtatacgaacgaaatatggagccgaaccgatccttttccgccccggagtacggggctttgattttagagtatattatcgcacggattccggcagagagatcggtgaaattcccaccgtcgaggaactcctgcgtaacgacaagctcagagaatccaatcaagaaatgatcgctctgaacgaatagcagttgctcttaatatccgcatctcgcagtatgcgtcagttcgccgaggaagataatccgcctccctttgcactcgcaagtctgcatctgttgtgcataaatgatttacagcattattactacat Find is-nt database================================================ Query_seq: PG0052:PG0053|PG0052:PG0053:sensor histidine kinase:hypothetical protein:-><-:64747..65056 310 gtatacgaacgaaatatggagccgaaccgatccttttccgccccggagtacggggctttgattttagagtatattatcgcacggattccggcagagagatcggtgaaattcccaccgtcgaggaactcctgcgtaacgacaagctcagagaatccaatcaagaaatgatcgctctgaacgaatagcagttgctcttaatatccgcatctcgcagtatgcgtcagttcgccgaggaagataatccgcctccctttgcactcgcaagtctgcatctgttgtgcataaatgatttacagcattattactacat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0052:PG0053|PG0052:PG0053:sensor histidine kinase:hypothetical protein:-><-:64747..65056 310 gtatacgaacgaaatatggagccgaaccgatccttttccgccccggagtacggggctttgattttagagtatattatcgcacggattccggcagagagatcggtgaaattcccaccgtcgaggaactcctgcgtaacgacaagctcagagaatccaatcaagaaatgatcgctctgaacgaatagcagttgctcttaatatccgcatctcgcagtatgcgtcagttcgccgaggaagataatccgcctccctttgcactcgcaagtctgcatctgttgtgcataaatgatttacagcattattactacat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0052:PG0053|PG0052:PG0053:sensor histidine kinase:hypothetical protein:-><-:64747..65056 310 gtatacgaacgaaatatggagccgaaccgatccttttccgccccggagtacggggctttgattttagagtatattatcgcacggattccggcagagagatcggtgaaattcccaccgtcgaggaactcctgcgtaacgacaagctcagagaatccaatcaagaaatgatcgctctgaacgaatagcagttgctcttaatatccgcatctcgcagtatgcgtcagttcgccgaggaagataatccgcctccctttgcactcgcaagtctgcatctgttgtgcataaatgatttacagcattattactacat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtatacgaacgaaatatggagccgaaccgatccttttccgccccggagtacggggctttgattttagagtatattatcgcacggattccggcagagagatcggtgaaattcccaccgtcgaggaactcctgcgtaacgacaagctcagagaatccaatcaagaaatgatcgctctgaacgaatagcagttgctcttaatatccgcatctcgcagtatgcgtcagttcgccgaggaagataatccgcctccctttgcactcgcaagtctgcatctgttgtgcataaatgatttacagcattattactacat Predict ORF larger than 30AA ================================================ Protein_Len: 50 Strand: + Start: 16 End: 165 ............... M E P N R S F S A P E Y G A L I L E Y I I A R I P A E R S V K F P P S R N S C V T T S S E N P I K K ................................................................................................................................................. Protein_Len: 60 Strand: + Start: 3 End: 182 .. M R T K Y G A E P I L F R P G V R G F D F R V Y Y R T D S G R E I G E I P T V E E L L R N D K L R E S N Q E M I A L N E ................................................................................................................................ Protein_Len: 40 Strand: + Start: 189 End: 308 ............................................................................................................................................................................................ M L L I S A S R S M R Q F A E E D N P P P F A L A S L H L L C I N D L Q H Y Y Y .. Protein_Len: 31 Strand: - Start: 198 End: 290 ..................................................................................................................................................................................................... Y G C R A T H T L E G L F I I R R G K C E C T Q M Q Q A Y I M .................... Protein_Len: 39 Strand: - Start: 148 End: 264 ................................................................................................................................................... L I W D L F S R E S R I A T A R L I R M E C Y A D T R R P L Y D A E R Q V R M .............................................. Protein_Len: 60 Strand: - Start: 3 End: 188 .. R F I S G F R D K E A G S Y P A K I K S Y I I A R I G A S L D T F N G G D L F E Q T V V L E S F G I L F H D S Q V F L M .......................................................................................................................... gtatacgaacgaaatatggagccgaaccgatccttttccgccccggagtacggggctttgattttagagtatattatcgcacggattccggcagagagatcggtgaaattcccaccgtcgaggaactcctgcgtaacgacaagctcagagaatccaatcaagaaatgatcgctctgaacgaatagcagttgctcttaatatccgcatctcgcagtatgcgtcagttcgccgaggaagataatccgcctccctttgcactcgcaagtctgcatctgttgtgcataaatgatttacagcattattactacat 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================================================ gtatacgaacgaaatatggagccgaaccgatccttttccgccccggagtacggggctttgattttagagtatattatcgcacggattccggcagagagatcggtgaaattcccaccgtcgaggaactcctgcgtaacgacaagctcagagaatccaatcaagaaatgatcgctctgaacgaatagcagttgctcttaatatccgcatctcgcagtatgcgtcagttcgccgaggaagataatccgcctccctttgcactcgcaagtctgcatctgttgtgcataaatgatttacagcattattactacat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG0052:PG0053|PG0052:PG0053:sensor histidine kinase:hypothetical protein:-><-:64747..65056 310 gtatacgaacgaaatatggagccgaaccgatccttttccgccccggagtacggggctttgattttagagtatattatcgcacggattccggcagagagatcggtgaaattcccaccgtcgaggaactcctgcgtaacgacaagctcagagaatccaatcaagaaatgatcgctctgaacgaatagcagttgctcttaatatccgcatctcgcagtatgcgtcagttcgccgaggaagataatccgcctccctttgcactcgcaagtctgcatctgttgtgcataaatgatttacagcattattactacat Intra-Species Hit: Count: 1 Min: 1 Max: 310 Len: 310 Subject: NC_002950_PG0052_PG0053|sensor histidine kinase:hypothetical protein|POSITIVE:NEGATIVE|[64747,65056]|310 HSP 1 e-value: 1.0E-175 bit: 615.0 Len: 310 Query Start:1 Query End:310 Subject Strand: POSITIVE Subject Start: 1 Subject End: 310 gtatacgaacgaaatatggagccgaaccgatccttttccgccccggagtacggggctttgattttagagtatattatcgcacggattccggcagagagatcggtgaaattcccaccgtcgaggaactcctgcgtaacgacaagctcagagaatccaatcaagaaatgatcgctctgaacgaatagcagttgctcttaatatccgcatctcgcagtatgcgtcagttcgccgaggaagataatccgcctccctttgcactcgcaagtctgcatctgttgtgcataaatgatttacagcattattactacat gtatacgaacgaaatatggagccgaaccgatccttttccgccccggagtacggggctttgattttagagtatattatcgcacggattccggcagagagatcggtgaaattcccaccgtcgaggaactcctgcgtaacgacaagctcagagaatccaatcaagaaatgatcgctctgaacgaatagcagttgctcttaatatccgcatctcgcagtatgcgtcagttcgccgaggaagataatccgcctccctttgcactcgcaagtctgcatctgttgtgcataaatgatttacagcattattactacat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUAUACGAACGAAAUAUGGAGCCGAACCGAUCCUUUUCCGCCCCGGAGUACGGGGCUUUGAUUUUAGAGUAUAUUAUCGCACGGAUUCCGGCAGAGAGAUCGGUGAAAUUCCCACCGUCGAGGAACUCCUGCGUAACGACAAGCUCAGAGAAUCCAAUCAAGAAAUGAUCGCUCUGAACGAAUAGCAGUUGCUCUUAAUAUCCGCAUCUCGCAGUAUGCGUCAGUUCGCCGAGGAAGAUAAUCCGCCUCCCUUUGCACUCGCAAGUCUGCAUCUGUUGUGCAUAAAUGAUUUACAGCAUUAUUACUACAU (((..............((((.((.((((((((((....((((((.....))))))......................((.(((...))))).))).)))))))..........((.(((..(((((..((((((.......(.((((((......((((.....))))..)))))).).....((((.(((...........))).)).))..))))))..)))))..))))).........)).))))...((((..(....)..))))..(((((((.((.....)).))))))).......))).. (-80.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUGUAGUAAUAAUGCUGUAAAUCAUUUAUGCACAACAGAUGCAGACUUGCGAGUGCAAAGGGAGGCGGAUUAUCUUCCUCGGCGAACUGACGCAUACUGCGAGAUGCGGAUAUUAAGAGCAACUGCUAUUCGUUCAGAGCGAUCAUUUCUUGAUUGGAUUCUCUGAGCUUGUCGUUACGCAGGAGUUCCUCGACGGUGGGAAUUUCACCGAUCUCUCUGCCGGAAUCCGUGCGAUAAUAUACUCUAAAAUCAAAGCCCCGUACUCCGGGGCGGAAAAGGAUCGGUUCGGCUCCAUAUUUCGUUCGUAUAC .((((.......(((.((((.....))))))).......))))....((((((((.(((.((((.(((....((((((((((.(((((..(((.....)))...((((.........(((....)))....((((((((((((((.....))))))....)))))))).........))))..))))).)))).)).)))).....((((((((...((((((...))).)))................((...((((((.....)))))).))...))))))))))).))))...)))))))))))... (-92.94) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 444 70 21 61 3 NC_002950:PG0959|5end_ATP-binding_protein,_Mrp/Nbp35_family_1021141..1021371_NEGATIVE 400 56 16 127 74 NC_002950:PG0499|5end_hypothetical_protein_538709..538939_POSITIVE 385 66 32 71 34 NC_002950:PG1831|5end_ATP-dependent_DNA_helicase_RecQ_1925422..1925652_NEGATIVE 385 60 18 228 188 NC_002950:PG1475|5end_conjugative_transposon_protein_TraN_1551835..1552065_NEGATIVE 379 250 201 50 3 NC_002950:PG2107|5end_thiamine_biosynthesis_protein_ThiH_2216658..2216888_NEGATIVE 378 56 16 72 25 NC_002950:PG0218|5end_hypothetical_protein_253295..253525_POSITIVE 378 89 41 189 142 NC_002950:PG0095|5end_DNA_mismatch_repair_protein_114763..114993_NEGATIVE 377 60 15 212 155 NC_002950:PG1125|5end_hypothetical_protein_1201727..1201957_NEGATIVE 375 129 82 231 170 NC_002950:PG1348|5end_conserved_hypothetical_protein_TIGR00147_1428608..1428838_POSITIVE 375 56 23 186 150 NC_002950:PG1017|5end_pyruvate_phosphate_dikinase_1076138..1076368_POSITIVE 369 59 21 113 69 NC_002950:PG1095|5end_RNA_methyltransferase,_TrmA_family_1160225..1160455_POSITIVE 369 56 16 127 74 NC_002950:PG1059|5end_hypothetical_protein_1126495..1126725_NEGATIVE 369 57 18 88 56 NC_002950:PG0145|5end_hypothetical_protein_167831..168061_POSITIVE 367 56 16 127 74 NC_002950:PG2220|5end_hypothetical_protein_2334935..2335165_POSITIVE 367 230 185 208 156 NC_002950:PG2032|5end_primosomal_protein_N'_2133381..2133611_NEGATIVE 363 130 81 182 132 NC_002950:PG1497|5end_DNA-binding_protein,_histone-like_family_1574085..1574315_POSITIVE 358 56 15 61 9 NC_002950:PG1566|5end_glutamyl-tRNA_synthetase_1647401..1647631_NEGATIVE 357 289 244 194 144 NC_002950:PG1311|5end_hypothetical_protein_1389709..1389939_POSITIVE 355 45 1 216 157 NC_002950:PG1739|5end_hypothetical_protein_1825709..1825939_NEGATIVE 355 247 202 174 123 NC_002950:PG1162|5end_ATP:cob(I)alamin_adenosyltransferase,_putative_1242039..1242269_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 418 90 45 119 75 NC_002950:PG0324|3end_histidine_ammonia-lyase_357589..357739_NEGATIVE 412 56 18 106 64 NC_002950:PG1391|3end_hypothetical_protein_1472961..1473111_POSITIVE 395 69 21 145 97 NC_002950:PG1497|3end_DNA-binding_protein,_histone-like_family_1574635..1574785_POSITIVE 389 55 18 72 22 NC_002950:PG1359|3end_hypothetical_protein_1437644..1437794_NEGATIVE 382 54 16 70 20 NC_002950:PG1723|3end_ribosomal_protein_S20_1813403..1813553_POSITIVE 375 129 82 118 74 NC_002950:PG0332|3end_transcription_termination_factor_Rho_367675..367825_POSITIVE 373 250 201 135 106 NC_002950:PG0443|3end_hemagglutinin-related_protein_483147..483297_POSITIVE 363 245 202 124 78 NC_002950:PG2126|3end_conserved_hypothetical_protein_TIGR00044_2232438..2232588_NEGATIVE 362 249 203 55 9 NC_002950:PG1112|3end_hypothetical_protein_1185571..1185721_POSITIVE 355 45 1 69 10 NC_002950:PG1741|3end_aspartate_ammonia-lyase_1825856..1826006_NEGATIVE 355 247 202 151 100 NC_002950:PG1163|3end_cobyrinic_acid_a,c-diamide_synthase_1242062..1242212_NEGATIVE 355 250 203 80 26 NC_002950:PG0213|3end_precorrin-3_methylase/precorrin-8X_methylmutase_249058..249208_NEGATIVE 351 57 16 92 45 NC_002950:PG0016|3end_sigma-54_dependent_DNA-binding_response_regulator_18376..18526_POSITIVE 350 251 211 68 25 NC_002950:PG0054|3end_single-stranded-DNA-specific_exonuclease_RecJ_66899..67049_POSITIVE 346 129 81 142 87 NC_002950:PG1854|3end_5-formyltetrahydrofolate_cyclo-ligase_family_protein_1953325..1953475_NEGATIVE 343 248 204 149 114 NC_002950:PG1057|3end_hypothetical_protein_1124092..1124242_POSITIVE 342 160 111 124 68 NC_002950:PG0340|3end_hypothetical_protein_376436..376586_POSITIVE 340 114 79 79 34 NC_002950:PG1338|3end_umuC_protein_1419624..1419774_POSITIVE 339 55 18 150 112 NC_002950:PG0127|3end_ferrochelatase_149667..149817_POSITIVE 338 63 27 96 48 NC_002950:PG0951|3end_phosphoribosylaminoimidazole_carboxylase,_PurE_protein_1010828..1010978_POSITIVE