Origin IGS: acattacgtatatacattcattctccggaacgatccgaaatggagacaatcattggcgaacatattgttttgtgctcattgccaaatttttacatccccatacggctactttgattcatagaagtttcgactgagatcttcgtgccgtttcttctccaccgacaacttccgacaacgacccgttcacactcctcgaaaaggaagcgcagaatccccatttttggggagaattaatgtgtttttgggctactttgttagtcgggttagcaagatttgtgtatttttgccgcatcattagagttgtttgccttagacaatcaaacaaaaagacaaccacatttgcctaactatttaaa .........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 tttaaatagttaggcaaatgtggttgtctttttgtttgattgtctaaggcaaacaactctaatgatgcggcaaaaatacacaaatcttgctaacccgactaacaaagtagcccaaaaacacattaattctccccaaaaatggggattctgcgcttccttttcgaggagtgtgaacgggtcgttgtcggaagttgtcggtggagaagaaacggcacgaagatctcagtcgaaacttctatgaatcaaagtagccgtatggggatgtaaaaatttggcaatgagcacaaaacaatatgttcgccaatgattgtctccatttcggatcgttccggagaatgaatgtatatacgtaatgt Mask Tandem Repeat Region ================================================ acattacgtatatacattcattctccggaacgatccgaaatggagacaatcattggcgaacatattgttttgtgctcattgccaaatttttacatccccatacggctactttgattcatagaagtttcgactgagatcttcgtgccgtttcttctccaccgacaacttccgacaacgacccgttcacactcctcgaaaaggaagcgcagaatccccatttttggggagaattaatgtgtttttgggctactttgttagtcgggttagcaagatttgtgtatttttgccgcatcattagagttgtttgccttagacaatcaaacaaaaagacaaccacatttgcctaactatttaaa Find is-nt database================================================ Query_seq: PG0300:PG0302|PG0300:PG0302:TPR domain protein:hypothetical protein:->->:338003..338358 356 acattacgtatatacattcattctccggaacgatccgaaatggagacaatcattggcgaacatattgttttgtgctcattgccaaatttttacatccccatacggctactttgattcatagaagtttcgactgagatcttcgtgccgtttcttctccaccgacaacttccgacaacgacccgttcacactcctcgaaaaggaagcgcagaatccccatttttggggagaattaatgtgtttttgggctactttgttagtcgggttagcaagatttgtgtatttttgccgcatcattagagttgtttgccttagacaatcaaacaaaaagacaaccacatttgcctaactatttaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0300:PG0302|PG0300:PG0302:TPR domain protein:hypothetical protein:->->:338003..338358 356 acattacgtatatacattcattctccggaacgatccgaaatggagacaatcattggcgaacatattgttttgtgctcattgccaaatttttacatccccatacggctactttgattcatagaagtttcgactgagatcttcgtgccgtttcttctccaccgacaacttccgacaacgacccgttcacactcctcgaaaaggaagcgcagaatccccatttttggggagaattaatgtgtttttgggctactttgttagtcgggttagcaagatttgtgtatttttgccgcatcattagagttgtttgccttagacaatcaaacaaaaagacaaccacatttgcctaactatttaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0300:PG0302|PG0300:PG0302:TPR domain protein:hypothetical protein:->->:338003..338358 356 acattacgtatatacattcattctccggaacgatccgaaatggagacaatcattggcgaacatattgttttgtgctcattgccaaatttttacatccccatacggctactttgattcatagaagtttcgactgagatcttcgtgccgtttcttctccaccgacaacttccgacaacgacccgttcacactcctcgaaaaggaagcgcagaatccccatttttggggagaattaatgtgtttttgggctactttgttagtcgggttagcaagatttgtgtatttttgccgcatcattagagttgtttgccttagacaatcaaacaaaaagacaaccacatttgcctaactatttaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 acattacgtatatacattcattctccggaacgatccgaaatggagacaatcattggcgaacatattgttttgtgctcattgccaaatttttacatccccatacggctactttgattcatagaagtttcgactgagatcttcgtgccgtttcttctccaccgacaacttccgacaacgacccgttcacactcctcgaaaaggaagcgcagaatccccatttttggggagaattaatgtgtttttgggctactttgttagtcgggttagcaagatttgtgtatttttgccgcatcattagagttgtttgccttagacaatcaaacaaaaagacaaccacatttgcctaactatttaaa Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 10 End: 111 ......... M Y I H S P E R S E M E T I I G E H I V L C S L P N F Y I P I R L L ..................................................................................................................................................................................................................................................... Protein_Len: 33 Strand: + Start: 20 End: 118 ................... M L R N D P K W R Q S L A N I L F C A H C Q I F T S P Y G Y F D S .............................................................................................................................................................................................................................................. Protein_Len: 43 Strand: + Start: 3 End: 131 .. M T Y I H S F S G T I R N G D N H W R T Y C F V L I A K F L H P H T A T L I H R S F D ................................................................................................................................................................................................................................. Protein_Len: 38 Strand: + Start: 118 End: 231 ..................................................................................................................... M E V S T E I F V P F L L H R Q L P T T T R S H S S K R K R R I P I F G E N ............................................................................................................................. Protein_Len: 55 Strand: + Start: 131 End: 295 .................................................................................................................................. M R S S C R F F S T D N F R Q R P V H T P R K G S A E S P F L G R I N V F L G Y F V S R V S K I C V F L P H H ............................................................. Protein_Len: 37 Strand: + Start: 234 End: 344 ......................................................................................................................................................................................................................................... M C F W A T L L V G L A R F V Y F C R I I R V V C L R Q S N K K T T T F A ............ Protein_Len: 60 Strand: - Start: 119 End: 337 ...................................................................................................................... G V V E S L S G N V S R S F S A C F G W K Q P S N I H K Q A V K N T P N A L N T Y K Q R M M L T T Q R L C D F L F V V M ................... Protein_Len: 42 Strand: - Start: 93 End: 218 ............................................................................................ M G M R S S Q N M S T E V S I K T G N R R W R C S G V V V R E C E E F L F R L I G M .......................................................................................................................................... acattacgtatatacattcattctccggaacgatccgaaatggagacaatcattggcgaacatattgttttgtgctcattgccaaatttttacatccccatacggctactttgattcatagaagtttcgactgagatcttcgtgccgtttcttctccaccgacaacttccgacaacgacccgttcacactcctcgaaaaggaagcgcagaatccccatttttggggagaattaatgtgtttttgggctactttgttagtcgggttagcaagatttgtgtatttttgccgcatcattagagttgtttgccttagacaatcaaacaaaaagacaaccacatttgcctaactatttaaa 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================================================ acattacgtatatacattcattctccggaacgatccgaaatggagacaatcattggcgaacatattgttttgtgctcattgccaaatttttacatccccatacggctactttgattcatagaagtttcgactgagatcttcgtgccgtttcttctccaccgacaacttccgacaacgacccgttcacactcctcgaaaaggaagcgcagaatccccatttttggggagaattaatgtgtttttgggctactttgttagtcgggttagcaagatttgtgtatttttgccgcatcattagagttgtttgccttagacaatcaaacaaaaagacaaccacatttgcctaactatttaaa Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 71 HP_score: -9.0 Tail_Score: -3.3858 Start: 212 End: 227 Full_Region: aaaacacattaattc tcccca aaaa tgggga ttctgcgcttccttt ...................................................................................................................................................................................................................tccccaaaaatgggga................................................................................................................................. Find igs database================================================ Query_seq: PG0300:PG0302|PG0300:PG0302:TPR domain protein:hypothetical protein:->->:338003..338358 356 acattacgtatatacattcattctccggaacgatccgaaatggagacaatcattggcgaacatattgttttgtgctcattgccaaatttttacatccccatacggctactttgattcatagaagtttcgactgagatcttcgtgccgtttcttctccaccgacaacttccgacaacgacccgttcacactcctcgaaaaggaagcgcagaatccccatttttggggagaattaatgtgtttttgggctactttgttagtcgggttagcaagatttgtgtatttttgccgcatcattagagttgtttgccttagacaatcaaacaaaaagacaaccacatttgcctaactatttaaa Intra-Species Hit: Count: 1 Min: 1 Max: 356 Len: 356 Subject: NC_002950_PG0300_PG0302|TPR domain protein:hypothetical protein|POSITIVE:POSITIVE|[338003,338358]|356 HSP 1 e-value: 0.0 bit: 706.0 Len: 356 Query Start:1 Query End:356 Subject Strand: POSITIVE Subject Start: 1 Subject End: 356 acattacgtatatacattcattctccggaacgatccgaaatggagacaatcattggcgaacatattgttttgtgctcattgccaaatttttacatccccatacggctactttgattcatagaagtttcgactgagatcttcgtgccgtttcttctccaccgacaacttccgacaacgacccgttcacactcctcgaaaaggaagcgcagaatccccatttttggggagaattaatgtgtttttgggctactttgttagtcgggttagcaagatttgtgtatttttgccgcatcattagagttgtttgccttagacaatcaaacaaaaagacaaccacatttgcctaactatttaaa acattacgtatatacattcattctccggaacgatccgaaatggagacaatcattggcgaacatattgttttgtgctcattgccaaatttttacatccccatacggctactttgattcatagaagtttcgactgagatcttcgtgccgtttcttctccaccgacaacttccgacaacgacccgttcacactcctcgaaaaggaagcgcagaatccccatttttggggagaattaatgtgtttttgggctactttgttagtcgggttagcaagatttgtgtatttttgccgcatcattagagttgtttgccttagacaatcaaacaaaaagacaaccacatttgcctaactatttaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACAUUACGUAUAUACAUUCAUUCUCCGGAACGAUCCGAAAUGGAGACAAUCAUUGGCGAACAUAUUGUUUUGUGCUCAUUGCCAAAUUUUUACAUCCCCAUACGGCUACUUUGAUUCAUAGAAGUUUCGACUGAGAUCUUCGUGCCGUUUCUUCUCCACCGACAACUUCCGACAACGACCCGUUCACACUCCUCGAAAAGGAAGCGCAGAAUCCCCAUUUUUGGGGAGAAUUAAUGUGUUUUUGGGCUACUUUGUUAGUCGGGUUAGCAAGAUUUGUGUAUUUUUGCCGCAUCAUUAGAGUUGUUUGCCUUAGACAAUCAAACAAAAAGACAACCACAUUUGCCUAACUAUUUAAA .......(((.((((((....(((.((((....))))...((((((......(((((((.((((......))))....)))))))................(((((.((...((((((..((....))...))).)))...)))))))....)))))).........(((((((((((((((..((((.((((.....)))).........((((((....)))))).......))))....)))).....))))).))))))......)))...))))))...))).(((......(.(((((((.....................)))))))).....)))............. (-77.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUAAAUAGUUAGGCAAAUGUGGUUGUCUUUUUGUUUGAUUGUCUAAGGCAAACAACUCUAAUGAUGCGGCAAAAAUACACAAAUCUUGCUAACCCGACUAACAAAGUAGCCCAAAAACACAUUAAUUCUCCCCAAAAAUGGGGAUUCUGCGCUUCCUUUUCGAGGAGUGUGAACGGGUCGUUGUCGGAAGUUGUCGGUGGAGAAGAAACGGCACGAAGAUCUCAGUCGAAACUUCUAUGAAUCAAAGUAGCCGUAUGGGGAUGUAAAAAUUUGGCAAUGAGCACAAAACAAUAUGUUCGCCAAUGAUUGUCUCCAUUUCGGAUCGUUCCGGAGAAUGAAUGUAUAUACGUAAUGU .((((((((..((((((......))))))..))))))))((((.....))))....(((((.((((..(((((.............)))))...(((((.(((......((((................((((((....))))))....(((((.((((...)))))))))....)))).)))))))).....)))).))))).....(((((((...(((.(((...((....))..))))))...)).)))))..(((((((.......(((((...(((((..........))))))))))....))))))).(((((((....))))))).....((((....))))..... (-89.72) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 349 166 121 73 34 NC_002950:PG0665|5end_beta-galactosidase_711827..712057_POSITIVE 343 195 151 181 130 NC_002950:PG1923|5end_50S_ribosomal_protein_L6_2017941..2018171_NEGATIVE 342 195 154 215 161 NC_002950:PG0149|5end_hypothetical_protein_172203..172433_NEGATIVE 330 177 132 217 154 NC_002950:PG1803|5end_V-type_ATP_synthase_subunit_A_1896488..1896718_POSITIVE 324 177 138 65 28 NC_002950:PG2205|5end_2-dehydropantoate_2-reductase_2316121..2316351_POSITIVE 322 319 275 71 30 NC_002950:PG1825|5end_hypothetical_protein_1919671..1919901_NEGATIVE 320 277 235 169 122 NC_002950:PG1761|5end_acetyltransferase,_GNAT_family_1847084..1847314_POSITIVE 319 227 191 51 10 NC_002950:PG1988|5end_hypothetical_protein_2078867..2079097_NEGATIVE 319 148 103 84 37 NC_002950:PG0531|5end_NAD(+)_synthetase_581139..581369_NEGATIVE 314 248 203 218 173 NC_002950:PG0171|5end_5'-nucleotidase_family_protein_191724..191954_POSITIVE 313 316 272 208 165 NC_002950:PG0924|5end_5'-nucleotidase,_lipoprotein_e(P4)_family_983668..983898_NEGATIVE 313 187 141 73 14 NC_002950:PG0362|5end_hypothetical_protein_395301..395531_POSITIVE 311 290 242 189 138 NC_002950:PG0468|5end_mannose-6-phosphate_isomerase,_class_I_511384..511614_NEGATIVE 309 110 62 123 78 NC_002950:PG0148|5end_sigma-54-dependent_transcriptional_regulator_170907..171137_NEGATIVE 305 187 142 227 186 NC_002950:PG1874|5end_hypothetical_protein_1969660..1969890_NEGATIVE 302 226 188 155 111 NC_002950:PG0166|5end_peptidyl-tRNA_hydrolase_188370..188600_NEGATIVE 299 183 143 170 127 NC_002950:PG1676|5end_phosphoenolpyruvate_carboxykinase_1762096..1762326_NEGATIVE 298 187 141 61 6 NC_002950:PG2078|5end_hypothetical_protein_2178600..2178830_NEGATIVE 298 196 151 219 162 NC_002950:PG0888|5end_hypothetical_protein_949910..950140_POSITIVE 298 210 162 142 88 NC_002950:PG0438|5end_hypothetical_protein_476884..477114_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 355 207 161 75 39 NC_002950:PG1133|3end_hypothetical_protein_1214103..1214253_POSITIVE 329 196 152 134 94 NC_002950:PG0210|3end_precorrin-6x_reductase/cobalamin_biosynthetic_protein_CbiD_244161..244311_NEGATIVE 324 177 138 51 14 NC_002950:PG2204|3end_hypothetical_protein_2316187..2316337_POSITIVE 322 319 275 96 55 NC_002950:PG1826|3end_hypothetical_protein_1919646..1919796_NEGATIVE 322 174 131 66 5 NC_002950:PG0334|3end_glycosyl_transferase,_group_2_family_protein_368792..368942_NEGATIVE 318 290 242 136 84 NC_002950:PG0594|3end_RNA_polymerase_sigma-70_factor_652991..653141_POSITIVE 316 170 133 79 35 NC_002950:PG0322|3end_serine/threonine_transporter_356966..357116_POSITIVE 312 170 123 145 89 NC_002950:PG2050|3end_hypothetical_protein_2149159..2149309_NEGATIVE 311 148 101 71 17 NC_002950:PG0363|3end_hypothetical_protein_398377..398527_POSITIVE 309 110 62 95 50 NC_002950:PG0149|3end_hypothetical_protein_170935..171085_NEGATIVE 307 210 166 89 38 NC_002950:PG2040|3end_DNA-binding_protein,_histone-like_family_2138398..2138548_NEGATIVE 307 184 141 147 108 NC_002950:PG0443|3end_hemagglutinin-related_protein_483147..483297_POSITIVE 306 240 193 97 41 NC_002950:PG2044|3end_hypothetical_protein_2144165..2144315_POSITIVE 305 180 141 151 96 NC_002950:PG1980|3end_hypothetical_protein_2067760..2067910_NEGATIVE 303 195 156 65 30 NC_002950:PG1112|3end_hypothetical_protein_1185571..1185721_POSITIVE 300 217 171 58 11 NC_002950:PG0132|3end_hypothetical_protein_153054..153204_POSITIVE 297 170 125 140 95 NC_002950:PG1213|3end_ribonuclease_H_1293163..1293313_POSITIVE 296 279 235 62 27 NC_002950:PG0432|3end_NOL1/NOP2/sun_family_protein_469273..469423_NEGATIVE 295 278 234 67 21 NC_002950:PG2042|3end_thioredoxin_family_protein_2140099..2140249_NEGATIVE 294 156 112 58 1 NC_002950:PG0332|3end_transcription_termination_factor_Rho_367675..367825_POSITIVE