Origin IGS: tgcagctgcgaataataacttcttcatacgatattgtttttttgaatagtggtgaattatttctaagcgcaaaagtaagtattttgatcttcatagacctgctatgccaaatcaaataaaacggattccatcccactgcactttgaaaatatccttcggaacatcaattaatgaaccatatactactgatattggttattgaaacgatagtgcaaattgtaatgataaactattcttttttgaaagaatttatttacttttgtgtaactaataattcatttagcaatttagatt .........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 aatctaaattgctaaatgaattattagttacacaaaagtaaataaattctttcaaaaaagaatagtttatcattacaatttgcactatcgtttcaataaccaatatcagtagtatatggttcattaattgatgttccgaaggatattttcaaagtgcagtgggatggaatccgttttatttgatttggcatagcaggtctatgaagatcaaaatacttacttttgcgcttagaaataattcaccactattcaaaaaaacaatatcgtatgaagaagttattattcgcagctgca Mask Tandem Repeat Region ================================================ tgcagctgcgaataataacttcttcatacgatattgtttttttgaatagtggtgaattatttctaagcgcaaaagtaagtattttgatcttcatagacctgctatgccaaatcaaataaaacggattccatcccactgcactttgaaaatatccttcggaacatcaattaatgaaccatatactactgatattggttattgaaacgatagtgcaaattgtaatgataaactattcttttttgaaagaatttatttacttttgtgtaactaataattcatttagcaatttagatt Find is-nt database================================================ Query_seq: PG1084:PG1085|PG1084:PG1085:thioredoxin family protein:hypothetical protein:<-->:1153049..1153342 294 tgcagctgcgaataataacttcttcatacgatattgtttttttgaatagtggtgaattatttctaagcgcaaaagtaagtattttgatcttcatagacctgctatgccaaatcaaataaaacggattccatcccactgcactttgaaaatatccttcggaacatcaattaatgaaccatatactactgatattggttattgaaacgatagtgcaaattgtaatgataaactattcttttttgaaagaatttatttacttttgtgtaactaataattcatttagcaatttagatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1084:PG1085|PG1084:PG1085:thioredoxin family protein:hypothetical protein:<-->:1153049..1153342 294 tgcagctgcgaataataacttcttcatacgatattgtttttttgaatagtggtgaattatttctaagcgcaaaagtaagtattttgatcttcatagacctgctatgccaaatcaaataaaacggattccatcccactgcactttgaaaatatccttcggaacatcaattaatgaaccatatactactgatattggttattgaaacgatagtgcaaattgtaatgataaactattcttttttgaaagaatttatttacttttgtgtaactaataattcatttagcaatttagatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1084:PG1085|PG1084:PG1085:thioredoxin family protein:hypothetical protein:<-->:1153049..1153342 294 tgcagctgcgaataataacttcttcatacgatattgtttttttgaatagtggtgaattatttctaagcgcaaaagtaagtattttgatcttcatagacctgctatgccaaatcaaataaaacggattccatcccactgcactttgaaaatatccttcggaacatcaattaatgaaccatatactactgatattggttattgaaacgatagtgcaaattgtaatgataaactattcttttttgaaagaatttatttacttttgtgtaactaataattcatttagcaatttagatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgcagctgcgaataataacttcttcatacgatattgtttttttgaatagtggtgaattatttctaagcgcaaaagtaagtattttgatcttcatagacctgctatgccaaatcaaataaaacggattccatcccactgcactttgaaaatatccttcggaacatcaattaatgaaccatatactactgatattggttattgaaacgatagtgcaaattgtaatgataaactattcttttttgaaagaatttatttacttttgtgtaactaataattcatttagcaatttagatt Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: + Start: 6 End: 116 ..... M R I I T S S Y D I V F L N S G E L F L S A K V S I L I F I D L L C Q I K .................................................................................................................................................................................. Protein_Len: 48 Strand: + Start: 56 End: 199 ....................................................... M I S K R K S K Y F D L H R P A M P N Q I K R I P S H C T L K I S F G T S I N E P Y T T D I G Y ............................................................................................... Protein_Len: 41 Strand: + Start: 171 End: 293 .......................................................................................................................................................................... M N H I L L I L V I E T I V Q I V M I N Y S F L K E F I Y F C V T N N S F S N L D . Protein_Len: 30 Strand: - Start: 186 End: 275 ......................................................................................................................................................................................... Q Y Q N N F R Y H L N Y H Y V I R K Q F F K N V K T Y S I M ................... Protein_Len: 45 Strand: - Start: 2 End: 136 . C S R I I V E E Y S I T K K F L P S N N R L A F T L I K I K M S R S H W I L Y F P N W G M .............................................................................................................................................................. tgcagctgcgaataataacttcttcatacgatattgtttttttgaatagtggtgaattatttctaagcgcaaaagtaagtattttgatcttcatagacctgctatgccaaatcaaataaaacggattccatcccactgcactttgaaaatatccttcggaacatcaattaatgaaccatatactactgatattggttattgaaacgatagtgcaaattgtaatgataaactattcttttttgaaagaatttatttacttttgtgtaactaataattcatttagcaatttagatt 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: 82 Start: 216 End: 245 .......................................................................................................................................................................................................................TTTCAAAAAAGAATAGTTTATCATTACAAT................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tgcagctgcgaataataacttcttcatacgatattgtttttttgaatagtggtgaattatttctaagcgcaaaagtaagtattttgatcttcatagacctgctatgccaaatcaaataaaacggattccatcccactgcactttgaaaatatccttcggaacatcaattaatgaaccatatactactgatattggttattgaaacgatagtgcaaattgtaatgataaactattcttttttgaaagaatttatttacttttgtgtaactaataattcatttagcaatttagatt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 71 HP_score: -4.8 Tail_Score: -4.69048 Start: 233 End: 248 Full_Region: TGTAATGATAAACTA TTCTTT TTTG AAAGAA TTTATTTACTTTTGT ........................................................................................................................................................................................................................................TTCTTTTTTGAAAGAA.............................................. Find igs database================================================ Query_seq: PG1084:PG1085|PG1084:PG1085:thioredoxin family protein:hypothetical protein:<-->:1153049..1153342 294 tgcagctgcgaataataacttcttcatacgatattgtttttttgaatagtggtgaattatttctaagcgcaaaagtaagtattttgatcttcatagacctgctatgccaaatcaaataaaacggattccatcccactgcactttgaaaatatccttcggaacatcaattaatgaaccatatactactgatattggttattgaaacgatagtgcaaattgtaatgataaactattcttttttgaaagaatttatttacttttgtgtaactaataattcatttagcaatttagatt Intra-Species Hit: Count: 1 Min: 1 Max: 294 Len: 294 Subject: NC_002950_PG1084_PG1085|thioredoxin family protein:hypothetical protein|NEGATIVE:POSITIVE|[1153049,1153342]|294 HSP 1 e-value: 1.0E-153 bit: 541.0 Len: 294 Query Start:1 Query End:294 Subject Strand: POSITIVE Subject Start: 1 Subject End: 294 tgcagctgcgaataataacttcttcatacgatattgnnnnnnngaatagtggtgaattatttctaagcgcaaaagtaagtattttgatcttcatagacctgctatgccaaatcaaataaaacggattccatcccactgcactttgaaaatatccttcggaacatcaattaatgaaccatatactactgatattggttattgaaacgatagtgcaaattgtaatgataaactattcttttttgaaagaatttatttacttttgtgtaactaataattcatttagcaatttagatt tgcagctgcgaataataacttcttcatacgatattgtttttttgaatagtggtgaattatttctaagcgcaaaagtaagtattttgatcttcatagacctgctatgccaaatcaaataaaacggattccatcccactgcactttgaaaatatccttcggaacatcaattaatgaaccatatactactgatattggttattgaaacgatagtgcaaattgtaatgataaactattcttttttgaaagaatttatttacttttgtgtaactaataattcatttagcaatttagatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGCAGCUGCGAAUAAUAACUUCUUCAUACGAUAUUGUUUUUUUGAAUAGUGGUGAAUUAUUUCUAAGCGCAAAAGUAAGUAUUUUGAUCUUCAUAGACCUGCUAUGCCAAAUCAAAUAAAACGGAUUCCAUCCCACUGCACUUUGAAAAUAUCCUUCGGAACAUCAAUUAAUGAACCAUAUACUACUGAUAUUGGUUAUUGAAACGAUAGUGCAAAUUGUAAUGAUAAACUAUUCUUUUUUGAAAGAAUUUAUUUACUUUUGUGUAACUAAUAAUUCAUUUAGCAAUUUAGAUU (((.((((((((.(((((..((.......))..)))))..))))..)))).((((((((((.....(((((((((((((((.((((((...(((((.....)))))....))))))............(((..((.(((((((((........(....)........(((((((.((((((.(....)))).))))))))))..))).))))))...))..))).......(((((((....))))))).)))))))))))))))....))))))))))...)))......... (-58.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUCUAAAUUGCUAAAUGAAUUAUUAGUUACACAAAAGUAAAUAAAUUCUUUCAAAAAAGAAUAGUUUAUCAUUACAAUUUGCACUAUCGUUUCAAUAACCAAUAUCAGUAGUAUAUGGUUCAUUAAUUGAUGUUCCGAAGGAUAUUUUCAAAGUGCAGUGGGAUGGAAUCCGUUUUAUUUGAUUUGGCAUAGCAGGUCUAUGAAGAUCAAAAUACUUACUUUUGCGCUUAGAAAUAAUUCACCACUAUUCAAAAAAACAAUAUCGUAUGAAGAAGUUAUUAUUCGCAGCUGCA .....((((((...(((((........((((......))))....(((((((....)))))))......))))).))))))(((((..((..(.((((((.......((((((...(((..((((....))))..)))..((((..((((.((((((((.(((((((...))))))).((((((((..(((((.....))))).))))))))..........)))))))).))))..))))...)))))).............((.......)).)))))))..)).)).))). (-51.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 908 140 91 231 182 NC_002950:PG1084|5end_thioredoxin_family_protein_1152958..1153188_NEGATIVE 318 164 122 199 158 NC_002950:PG0157|5end_regulatory_protein_RecX_179706..179936_POSITIVE 316 138 98 194 150 NC_002950:PG1125|5end_hypothetical_protein_1201727..1201957_NEGATIVE 290 130 88 52 11 NC_002950:PG0661|5end_hypothetical_protein_709853..710083_NEGATIVE 290 130 88 210 169 NC_002950:PG0660|5end_nitroreductase_family_protein_709695..709925_NEGATIVE 274 38 1 64 29 NC_002950:PG2144|5end_hypothetical_protein_2249911..2250141_POSITIVE 272 161 125 216 173 NC_002950:PG1288|5end_GDP-mannose_4,6-dehydratase_1365963..1366193_POSITIVE 270 175 135 216 177 NC_002950:PG1552|5end_TonB-dependent_receptor_HmuR_1628881..1629111_POSITIVE 256 139 92 213 169 NC_002950:PG1208|5end_molecular_chaperone_DnaK_1286915..1287145_NEGATIVE 254 165 124 46 7 NC_002950:PG1703|5end_MazG_family_protein_1790753..1790983_NEGATIVE 254 158 122 175 129 NC_002950:PG1687|5end_HIT_family_protein_1774201..1774431_NEGATIVE 250 140 94 81 33 NC_002950:PG2003|5end_deoxyguanosinetriphosphate_triphosphohydrolase_2092991..2093221_NEGATIVE 250 159 122 33 1 NC_002950:PG0493|5end_hypothetical_protein_534900..535130_NEGATIVE 250 159 122 33 1 NC_002950:PG0265|5end_hypothetical_protein_298551..298781_NEGATIVE 249 138 97 210 153 NC_002950:PG1853|5end_DNA_polymerase_III,_beta_subunit_1953119..1953349_NEGATIVE 249 160 122 216 175 NC_002950:PG0171|5end_5'-nucleotidase_family_protein_191724..191954_POSITIVE 246 212 176 228 184 NC_002950:PG1494|5end_hypothetical_protein_1569841..1570071_POSITIVE 245 109 82 166 140 NC_002950:PG0634|5end_ThiJ/PfpI_family_protein_686143..686373_POSITIVE 244 56 15 228 185 NC_002950:PG1726|5end_PDZ_domain_protein_1815281..1815511_POSITIVE 244 107 66 163 121 NC_002950:PG0589|5end_bifunctional_GMP_synthase/glutamine_amidotransferase_protein_647708..647938_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 249 166 122 110 63 NC_002950:PG2214|3end_hypothetical_protein_2325301..2325451_NEGATIVE 245 109 82 151 125 NC_002950:PG0633|3end_hypothetical_protein_686208..686358_POSITIVE 240 139 91 89 37 NC_002950:PG0171|3end_5'-nucleotidase_family_protein_193576..193726_POSITIVE 239 170 122 137 86 NC_002950:PG0210|3end_precorrin-6x_reductase/cobalamin_biosynthetic_protein_CbiD_244161..244311_NEGATIVE 235 164 121 108 43 NC_002950:PG0267|3end_arginyl-tRNA_synthetase_300973..301123_POSITIVE 234 163 139 35 14 NC_002950:PG0606|3end_hypothetical_protein_662451..662601_NEGATIVE 234 99 69 79 52 NC_002950:PG0371|3end_hypothetical_protein_404224..404374_POSITIVE 233 45 1 63 6 NC_002950:PG1392|3end_rod_shape-determining_protein_RodA,_putative_1472959..1473109_NEGATIVE 232 169 122 134 95 NC_002950:PG1408|3end_heavy_metal_efflux_pump,_CzcD_family_1492906..1493056_POSITIVE 230 160 124 136 99 NC_002950:PG0745|3end_lactoylglutathione_lyase,_putative_791982..792132_NEGATIVE 229 159 120 128 93 NC_002950:PG0806|3end_oxidoreductase,_Gfo/Idh/MocA_family_862687..862837_NEGATIVE 228 159 122 139 99 NC_002950:PG2037|3end_hypothetical_protein_2137591..2137741_NEGATIVE 227 164 122 99 63 NC_002950:PG1052|3end_transcriptional_regulator,_putative_1120126..1120276_POSITIVE 226 162 122 150 114 NC_002950:PG1688|3end_transcription_elongation_factor_GreA_1774216..1774366_NEGATIVE 226 80 33 86 38 NC_002950:PG1552|3end_TonB-dependent_receptor_HmuR_1630901..1631051_POSITIVE 225 108 66 144 101 NC_002950:PG0893|3end_hydroxylamine_reductase_954201..954351_NEGATIVE 225 43 2 86 45 NC_002950:PG0399|3end_lipoprotein,_putative_435707..435857_NEGATIVE 224 159 123 113 76 NC_002950:PG0280|3end_ABC_transporter,_permease_protein,_putative_313297..313447_NEGATIVE 222 138 91 98 52 NC_002950:PG1724|3end_O-sialoglycoprotein_endopeptidase_1814846..1814996_POSITIVE 220 134 93 77 27 NC_002950:PG0439|3end_hypothetical_protein_478810..478960_POSITIVE