Origin IGS: ctggatagccctgtttggattgatcttcttttacaaatataacatggtaaaactgaatttttcctgaaatagcatgctctccctttgcagtcccgggatgtgcagatattttacgcctgtgttttggggacgaggtgcaaattcggtggcacttttttatatctttgtcccgagacgatttgctcgaatctcagcaaacgaagtctttcaatcacttaaaaacagatagtt .........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 aactatctgtttttaagtgattgaaagacttcgtttgctgagattcgagcaaatcgtctcgggacaaagatataaaaaagtgccaccgaatttgcacctcgtccccaaaacacaggcgtaaaatatctgcacatcccgggactgcaaagggagagcatgctatttcaggaaaaattcagttttaccatgttatatttgtaaaagaagatcaatccaaacagggctatccag Mask Tandem Repeat Region ================================================ ctggatagccctgtttggattgatcttcttttacaaatataacatggtaaaactgaatttttcctgaaatagcatgctctccctttgcagtcccgggatgtgcagatattttacgcctgtgttttggggacgaggtgcaaattcggtggcacttttttatatctttgtcccgagacgatttgctcgaatctcagcaaacgaagtctttcaatcacttaaaaacagatagtt Find is-nt database================================================ Query_seq: PG0720:PG0721|PG0720:PG0721:DNA-binding response regulator:NLP/P60 family protein:<-->:773756..773986 231 ctggatagccctgtttggattgatcttcttttacaaatataacatggtaaaactgaatttttcctgaaatagcatgctctccctttgcagtcccgggatgtgcagatattttacgcctgtgttttggggacgaggtgcaaattcggtggcacttttttatatctttgtcccgagacgatttgctcgaatctcagcaaacgaagtctttcaatcacttaaaaacagatagtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0720:PG0721|PG0720:PG0721:DNA-binding response regulator:NLP/P60 family protein:<-->:773756..773986 231 ctggatagccctgtttggattgatcttcttttacaaatataacatggtaaaactgaatttttcctgaaatagcatgctctccctttgcagtcccgggatgtgcagatattttacgcctgtgttttggggacgaggtgcaaattcggtggcacttttttatatctttgtcccgagacgatttgctcgaatctcagcaaacgaagtctttcaatcacttaaaaacagatagtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0720:PG0721|PG0720:PG0721:DNA-binding response regulator:NLP/P60 family protein:<-->:773756..773986 231 ctggatagccctgtttggattgatcttcttttacaaatataacatggtaaaactgaatttttcctgaaatagcatgctctccctttgcagtcccgggatgtgcagatattttacgcctgtgttttggggacgaggtgcaaattcggtggcacttttttatatctttgtcccgagacgatttgctcgaatctcagcaaacgaagtctttcaatcacttaaaaacagatagtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctggatagccctgtttggattgatcttcttttacaaatataacatggtaaaactgaatttttcctgaaatagcatgctctccctttgcagtcccgggatgtgcagatattttacgcctgtgttttggggacgaggtgcaaattcggtggcacttttttatatctttgtcccgagacgatttgctcgaatctcagcaaacgaagtctttcaatcacttaaaaacagatagtt Predict ORF larger than 30AA ================================================ Protein_Len: 44 Strand: + Start: 85 End: 216 .................................................................................... M Q S R D V Q I F Y A C V L G T R C K F G G T F L Y L C P E T I C S N L S K R S L S I T ............... Protein_Len: 52 Strand: + Start: 74 End: 226 ......................................................................... M L S L C S P G M C R Y F T P V F W G R G A N S V A L F Y I F V P R R F A R I S A N E V F Q S L K N R * ..... Protein_Len: 58 Strand: + Start: 57 End: 230 ........................................................ M F P E I A C S P F A V P G C A D I L R L C F G D E V Q I R W H F F I S L S R D D L L E S Q Q T K S F N H L K T D S . Protein_Len: 34 Strand: - Start: 114 End: 215 ................................................................................................................. A Q T K P V L H L N P P V K K Y R Q G S V I Q E F R L L R L R E I M ................ Protein_Len: 35 Strand: - Start: 3 End: 107 .. S L G T Q I S R R K C I Y C P L V S N K R F Y C A R G K C D R S T C M ............................................................................................................................ Protein_Len: 53 Strand: - Start: 2 End: 160 . P Y G Q K S Q D E K V F I V H Y F Q I K G S I A H E G K A T G P H A S I K R R H K P S S T C I R H C K K M ....................................................................... ctggatagccctgtttggattgatcttcttttacaaatataacatggtaaaactgaatttttcctgaaatagcatgctctccctttgcagtcccgggatgtgcagatattttacgcctgtgttttggggacgaggtgcaaattcggtggcacttttttatatctttgtcccgagacgatttgctcgaatctcagcaaacgaagtctttcaatcacttaaaaacagatagtt 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================================================ PromScan Matrix: RpoN Strand: - Score: 81 Start: 136 End: 152 .......................................................................................................................................GTGCCACCGAATTTGCA............................................................................... ctggatagccctgtttggattgatcttcttttacaaatataacatggtaaaactgaatttttcctgaaatagcatgctctccctttgcagtcccgggatgtgcagatattttacgcctgtgttttggggacgaggtgcaaattcggtggcacttttttatatctttgtcccgagacgatttgctcgaatctcagcaaacgaagtctttcaatcacttaaaaacagatagtt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG0720:PG0721|PG0720:PG0721:DNA-binding response regulator:NLP/P60 family protein:<-->:773756..773986 231 ctggatagccctgtttggattgatcttcttttacaaatataacatggtaaaactgaatttttcctgaaatagcatgctctccctttgcagtcccgggatgtgcagatattttacgcctgtgttttggggacgaggtgcaaattcggtggcacttttttatatctttgtcccgagacgatttgctcgaatctcagcaaacgaagtctttcaatcacttaaaaacagatagtt Intra-Species Hit: Count: 1 Min: 1 Max: 231 Len: 231 Subject: NC_002950_PG0720_PG0721|DNA-binding response regulator:NLP/P60 family protein|NEGATIVE:POSITIVE|[773756,773986]|231 HSP 1 e-value: 1.0E-128 bit: 458.0 Len: 231 Query Start:1 Query End:231 Subject Strand: POSITIVE Subject Start: 1 Subject End: 231 ctggatagccctgtttggattgatcttcttttacaaatataacatggtaaaactgaatttttcctgaaatagcatgctctccctttgcagtcccgggatgtgcagatattttacgcctgtgttttggggacgaggtgcaaattcggtggcacttttttatatctttgtcccgagacgatttgctcgaatctcagcaaacgaagtctttcaatcacttaaaaacagatagtt ctggatagccctgtttggattgatcttcttttacaaatataacatggtaaaactgaatttttcctgaaatagcatgctctccctttgcagtcccgggatgtgcagatattttacgcctgtgttttggggacgaggtgcaaattcggtggcacttttttatatctttgtcccgagacgatttgctcgaatctcagcaaacgaagtctttcaatcacttaaaaacagatagtt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUGGAUAGCCCUGUUUGGAUUGAUCUUCUUUUACAAAUAUAACAUGGUAAAACUGAAUUUUUCCUGAAAUAGCAUGCUCUCCCUUUGCAGUCCCGGGAUGUGCAGAUAUUUUACGCCUGUGUUUUGGGGACGAGGUGCAAAUUCGGUGGCACUUUUUUAUAUCUUUGUCCCGAGACGAUUUGCUCGAAUCUCAGCAAACGAAGUCUUUCAAUCACUUAAAAACAGAUAGUU ..........((((((.((((((.........((((((((((...(((...((((((((.....(((((((...(((.(((((...........)))).).)))..))))))).....(..(((((....)))))..).))))))))...)))...))))))..))))...(((((..((((((.(.....)))))))....)))))))))))......))))))...... (-54.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACUAUCUGUUUUUAAGUGAUUGAAAGACUUCGUUUGCUGAGAUUCGAGCAAAUCGUCUCGGGACAAAGAUAUAAAAAAGUGCCACCGAAUUUGCACCUCGUCCCCAAAACACAGGCGUAAAAUAUCUGCACAUCCCGGGACUGCAAAGGGAGAGCAUGCUAUUUCAGGAAAAAUUCAGUUUUACCAUGUUAUAUUUGUAAAAGAAGAUCAAUCCAAACAGGGCUAUCCAG .....(((((((....(.((((((....((((.(((((...((((......))))(((((((((...((((((......((((..........))))..((((...........))))....)))))).....))))))))).))))).)))).(((...(((..((((.(((((...))))).)).))..)))..))).........))))))))))))))......... (-51.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1029 120 71 211 162 NC_002950:PG0720|5end_DNA-binding_response_regulator_773665..773895_NEGATIVE 385 138 91 182 137 NC_002950:PG0684|5end_ABC_transporter,_permease_protein,_putative_737648..737878_POSITIVE 381 187 141 179 127 NC_002950:PG1961|5end_hypothetical_protein_2051153..2051383_NEGATIVE 368 129 81 53 11 NC_002950:PG1249|5end_1-acyl-sn-glycerol-3-phosphate_acetyltransferase,_putative_1327161..1327391_NEGATIVE 364 149 103 70 29 NC_002950:PG1852|5end_exonuclease_1951973..1952203_NEGATIVE 363 146 108 51 7 NC_002950:PG1305|5end_glycine_dehydrogenase_1386538..1386768_NEGATIVE 362 115 71 70 26 NC_002950:PG0671|5end_iron_compound_ABC_transporter,_permease_protein_721888..722118_POSITIVE 357 139 93 220 171 NC_002950:PG1968|5end_hypothetical_protein_2058564..2058794_NEGATIVE 356 138 93 126 82 NC_002950:PG0326|5end_hypothetical_protein_360974..361204_NEGATIVE 352 120 74 224 180 NC_002950:PG0657|5end_Maf-like_protein_707782..708012_NEGATIVE 351 153 114 197 157 NC_002950:PG0164|5end_hypothetical_protein_187395..187625_NEGATIVE 349 109 68 229 177 NC_002950:PG1312|5end_capA_protein,_putative_1390286..1390516_POSITIVE 348 129 87 113 64 NC_002950:PG0320|5end_hypothetical_protein_353409..353639_POSITIVE 345 115 71 62 22 NC_002950:PG0790|5end_GTP-binding_protein_Obg_842583..842813_NEGATIVE 343 190 145 223 173 NC_002950:PG1081|5end_acetate_kinase_1149627..1149857_NEGATIVE 339 150 102 229 182 NC_002950:PG1291|5end_hypothetical_protein_1371178..1371408_NEGATIVE 337 118 72 57 4 NC_002950:PG1255|5end_recombination_protein_RecR_1332751..1332981_NEGATIVE 335 138 94 219 163 NC_002950:PG0211|5end_cobalamin_biosynthesis_protein_CbiG/precorrin-4_C11-methyltransferase_247810..248040_NEGATIVE 334 128 82 170 120 NC_002950:PG1767|5end_lipoprotein,_putative_1853995..1854225_POSITIVE 334 121 87 198 165 NC_002950:PG0240|5end_hydrolase,_haloacid_dehalogenase-like_family_277093..277323_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 368 130 83 101 50 NC_002950:PG0323|3end_hypothetical_protein_357059..357209_NEGATIVE 364 149 103 57 16 NC_002950:PG1853|3end_DNA_polymerase_III,_beta_subunit_1951986..1952136_NEGATIVE 363 146 108 46 2 NC_002950:PG1306|3end_metallo-beta-lactamase_family_protein_1386543..1386693_NEGATIVE 362 115 71 73 29 NC_002950:PG0670|3end_lipoprotein,_putative_721971..722121_POSITIVE 348 129 87 81 32 NC_002950:PG0319|3end_hypothetical_protein_353457..353607_POSITIVE 345 115 71 52 12 NC_002950:PG0791|3end_adenylate_kinase_842593..842743_NEGATIVE 337 118 72 60 7 NC_002950:PG1256|3end_ribonuclease,_Rne/Rng_family_1332748..1332898_NEGATIVE 325 135 94 59 1 NC_002950:PG0052|3end_sensor_histidine_kinase_64686..64836_POSITIVE 324 158 114 109 53 NC_002950:PG2207|3end_hypothetical_protein_2319142..2319292_NEGATIVE 324 151 114 52 9 NC_002950:PG2028|3end_ebsC_protein_2126616..2126766_POSITIVE 324 170 124 130 82 NC_002950:PG1473|3end_conjugative_transposon_protein_TraQ_1549761..1549911_NEGATIVE 324 133 91 150 110 NC_002950:PG0683|3end_ABC_transporter,_permease_protein,_putative_737701..737851_POSITIVE 318 96 58 106 68 NC_002950:PG2214|3end_hypothetical_protein_2325301..2325451_NEGATIVE 316 104 72 119 85 NC_002950:PG1743|3end_2-dehydro-3-deoxyphosphooctonate_aldolase_1827530..1827680_NEGATIVE 316 118 74 88 29 NC_002950:PG0172|3end_exonuclease_194355..194505_POSITIVE 315 119 71 108 58 NC_002950:PG0296|3end_phosphoribosylformylglycinamidine_synthase_331293..331443_NEGATIVE 313 129 88 136 92 NC_002950:PG1093|3end_hypothetical_protein_1158779..1158929_POSITIVE 311 120 74 122 84 NC_002950:PG1563|3end_glucose-1-phosphate_thymidylyltransferase_1641597..1641747_NEGATIVE 310 107 61 70 13 NC_002950:PG0605|3end_hypothetical_protein_661165..661315_NEGATIVE 309 146 101 49 9 NC_002950:PG1852|3end_exonuclease_1951194..1951344_NEGATIVE