Origin IGS: aattcttgtgttgtgataaatcgtcgttagttacatgctctgaaaacgtttcaaaattacaaaaacaatcaagtttttcatctatgctctaatagacagcatctataaaaacgtatttgcaatgcgatgcaattcgctatgataaagcgataaaatcaagtgggaggcctcttgtgagacagtaagccgccttacatattccctattgacggaccggtagtaaatgacgaagtgtttggcctcggacttcttcccgaaaccgatgcaccc .........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 gggtgcatcggtttcgggaagaagtccgaggccaaacacttcgtcatttactaccggtccgtcaatagggaatatgtaaggcggcttactgtctcacaagaggcctcccacttgattttatcgctttatcatagcgaattgcatcgcattgcaaatacgtttttatagatgctgtctattagagcatagatgaaaaacttgattgtttttgtaattttgaaacgttttcagagcatgtaactaacgacgatttatcacaacacaagaatt Mask Tandem Repeat Region ================================================ aattcttgtgttgtgataaatcgtcgttagttacatgctctgaaaacgtttcaaaattacaaaaacaatcaagtttttcatctatgctctaatagacagcatctataaaaacgtatttgcaatgcgatgcaattcgctatgataaagcgataaaatcaagtgggaggcctcttgtgagacagtaagccgccttacatattccctattgacggaccggtagtaaatgacgaagtgtttggcctcggacttcttcccgaaaccgatgcaccc Find is-nt database================================================ Query_seq: PG2213:PG2214|PG2213:PG2214:nitrite reductase-related protein:hypothetical protein:<-<-:2325121..2325390 270 aattcttgtgttgtgataaatcgtcgttagttacatgctctgaaaacgtttcaaaattacaaaaacaatcaagtttttcatctatgctctaatagacagcatctataaaaacgtatttgcaatgcgatgcaattcgctatgataaagcgataaaatcaagtgggaggcctcttgtgagacagtaagccgccttacatattccctattgacggaccggtagtaaatgacgaagtgtttggcctcggacttcttcccgaaaccgatgcaccc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG2213:PG2214|PG2213:PG2214:nitrite reductase-related protein:hypothetical protein:<-<-:2325121..2325390 270 aattcttgtgttgtgataaatcgtcgttagttacatgctctgaaaacgtttcaaaattacaaaaacaatcaagtttttcatctatgctctaatagacagcatctataaaaacgtatttgcaatgcgatgcaattcgctatgataaagcgataaaatcaagtgggaggcctcttgtgagacagtaagccgccttacatattccctattgacggaccggtagtaaatgacgaagtgtttggcctcggacttcttcccgaaaccgatgcaccc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG2213:PG2214|PG2213:PG2214:nitrite reductase-related protein:hypothetical protein:<-<-:2325121..2325390 270 aattcttgtgttgtgataaatcgtcgttagttacatgctctgaaaacgtttcaaaattacaaaaacaatcaagtttttcatctatgctctaatagacagcatctataaaaacgtatttgcaatgcgatgcaattcgctatgataaagcgataaaatcaagtgggaggcctcttgtgagacagtaagccgccttacatattccctattgacggaccggtagtaaatgacgaagtgtttggcctcggacttcttcccgaaaccgatgcaccc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aattcttgtgttgtgataaatcgtcgttagttacatgctctgaaaacgtttcaaaattacaaaaacaatcaagtttttcatctatgctctaatagacagcatctataaaaacgtatttgcaatgcgatgcaattcgctatgataaagcgataaaatcaagtgggaggcctcttgtgagacagtaagccgccttacatattccctattgacggaccggtagtaaatgacgaagtgtttggcctcggacttcttcccgaaaccgatgcaccc Predict ORF larger than 30AA ================================================ Protein_Len: 53 Strand: - Start: 106 End: 264 ......................................................................................................... L F T N A I R H L E S H Y L S L I L H S A E Q S V T L R R V Y E R N V S R Y Y I V F H K A E S K K G F G M ...... aattcttgtgttgtgataaatcgtcgttagttacatgctctgaaaacgtttcaaaattacaaaaacaatcaagtttttcatctatgctctaatagacagcatctataaaaacgtatttgcaatgcgatgcaattcgctatgataaagcgataaaatcaagtgggaggcctcttgtgagacagtaagccgccttacatattccctattgacggaccggtagtaaatgacgaagtgtttggcctcggacttcttcccgaaaccgatgcaccc 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================================================ aattcttgtgttgtgataaatcgtcgttagttacatgctctgaaaacgtttcaaaattacaaaaacaatcaagtttttcatctatgctctaatagacagcatctataaaaacgtatttgcaatgcgatgcaattcgctatgataaagcgataaaatcaagtgggaggcctcttgtgagacagtaagccgccttacatattccctattgacggaccggtagtaaatgacgaagtgtttggcctcggacttcttcccgaaaccgatgcaccc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG2213:PG2214|PG2213:PG2214:nitrite reductase-related protein:hypothetical protein:<-<-:2325121..2325390 270 aattcttgtgttgtgataaatcgtcgttagttacatgctctgaaaacgtttcaaaattacaaaaacaatcaagtttttcatctatgctctaatagacagcatctataaaaacgtatttgcaatgcgatgcaattcgctatgataaagcgataaaatcaagtgggaggcctcttgtgagacagtaagccgccttacatattccctattgacggaccggtagtaaatgacgaagtgtttggcctcggacttcttcccgaaaccgatgcaccc Intra-Species Hit: Count: 1 Min: 1 Max: 270 Len: 270 Subject: NC_002950_PG2213_PG2214|nitrite reductase-related protein:hypothetical protein|NEGATIVE:NEGATIVE|[2325121,2325390]|270 HSP 1 e-value: 1.0E-151 bit: 535.0 Len: 270 Query Start:1 Query End:270 Subject Strand: POSITIVE Subject Start: 1 Subject End: 270 aattcttgtgttgtgataaatcgtcgttagttacatgctctgaaaacgtttcaaaattacaaaaacaatcaagtttttcatctatgctctaatagacagcatctataaaaacgtatttgcaatgcgatgcaattcgctatgataaagcgataaaatcaagtgggaggcctcttgtgagacagtaagccgccttacatattccctattgacggaccggtagtaaatgacgaagtgtttggcctcggacttcttcccgaaaccgatgcaccc aattcttgtgttgtgataaatcgtcgttagttacatgctctgaaaacgtttcaaaattacaaaaacaatcaagtttttcatctatgctctaatagacagcatctataaaaacgtatttgcaatgcgatgcaattcgctatgataaagcgataaaatcaagtgggaggcctcttgtgagacagtaagccgccttacatattccctattgacggaccggtagtaaatgacgaagtgtttggcctcggacttcttcccgaaaccgatgcaccc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUCUUGUGUUGUGAUAAAUCGUCGUUAGUUACAUGCUCUGAAAACGUUUCAAAAUUACAAAAACAAUCAAGUUUUUCAUCUAUGCUCUAAUAGACAGCAUCUAUAAAAACGUAUUUGCAAUGCGAUGCAAUUCGCUAUGAUAAAGCGAUAAAAUCAAGUGGGAGGCCUCUUGUGAGACAGUAAGCCGCCUUACAUAUUCCCUAUUGACGGACCGGUAGUAAAUGACGAAGUGUUUGGCCUCGGACUUCUUCCCGAAACCGAUGCACCC ....................((((((((..((((.((.((((...((((((.........((((((......))))))..(((((......)))))............))))))..(((((......))))).(((((.......))))).....((((..(((((..(((....)))...(((((....)))))...)))))..)))))))).))))))..)))))))).((((((((..((((........))))..)))).)))).. (-62.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGGUGCAUCGGUUUCGGGAAGAAGUCCGAGGCCAAACACUUCGUCAUUUACUACCGGUCCGUCAAUAGGGAAUAUGUAAGGCGGCUUACUGUCUCACAAGAGGCCUCCCACUUGAUUUUAUCGCUUUAUCAUAGCGAAUUGCAUCGCAUUGCAAAUACGUUUUUAUAGAUGCUGUCUAUUAGAGCAUAGAUGAAAAACUUGAUUGUUUUUGUAAUUUUGAAACGUUUUCAGAGCAUGUAACUAACGACGAUUUAUCACAACACAAGAAUU ..(((....(((((((((......))))))))).......(((((...............(((((..((((....(((((....))))).(((((....))))).))))..)))))....(((((.......))))).((((((.((.(((((((.((((((((((..(((((.(.....).)))))..))))))).......))).))))))).((((((.....)))))))))))))).....)))))..........)))....... (-67.71) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 846 130 81 221 172 NC_002950:PG2213|5end_nitrite_reductase-related_protein_2325030..2325260_NEGATIVE 392 270 225 219 157 NC_002950:PG1588|5end_hypothetical_protein_1666532..1666762_NEGATIVE 388 270 228 187 142 NC_002950:PG0259|5end_hypothetical_protein_292278..292508_POSITIVE 386 247 210 64 20 NC_002950:PG0674|5end_indolepyruvate_ferredoxin_oxidoreductase,_beta_subunit_724802..725032_NEGATIVE 366 270 223 175 130 NC_002950:PG1964|5end_bacterial_sugar_transferase_2052910..2053140_POSITIVE 365 259 212 56 7 NC_002950:PG1297|5end_ribosomal_protein_S1_1375831..1376061_POSITIVE 356 269 235 46 3 NC_002950:PG0303|5end_ferredoxin_338651..338881_POSITIVE 351 206 162 74 21 NC_002950:PG1015|5end_hypothetical_protein_1076020..1076250_NEGATIVE 350 266 226 79 34 NC_002950:PG0268|5end_tRNA_(5-methylaminomethyl-2-thiouridylate)-methyltransferase_300898..301128_POSITIVE 345 220 174 70 20 NC_002950:PG1783|5end_glycosyl_transferase,_group_2_family_protein_1871868..1872098_POSITIVE 336 190 157 161 133 NC_002950:PG0521|5end_co-chaperonin_GroES_565777..566007_NEGATIVE 335 256 215 49 3 NC_002950:PG1997|5end_hypothetical_protein_2086831..2087061_POSITIVE 335 228 185 54 14 NC_002950:PG1566|5end_glutamyl-tRNA_synthetase_1647401..1647631_NEGATIVE 331 258 211 229 179 NC_002950:PG1992|5end_glucose-inhibited_division_protein_A_2081410..2081640_POSITIVE 329 230 186 179 129 NC_002950:PG1897|5end_thiamin_pyrophosphokinase_catalytic_domain_protein_1996730..1996960_NEGATIVE 329 263 224 223 177 NC_002950:PG0285|5end_hypothetical_protein_318459..318689_POSITIVE 324 246 208 53 6 NC_002950:PG0729|5end_D-alanylalanine_synthetase_780818..781048_NEGATIVE 323 249 202 147 101 NC_002950:PG1721|5end_ribonuclease_R_1810284..1810514_POSITIVE 320 248 210 73 26 NC_002950:PG1388|5end_hypothetical_protein_1470889..1471119_NEGATIVE 320 255 211 213 171 NC_002950:PG0333|5end_hypothetical_protein_367823..368053_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 398 255 213 63 22 NC_002950:PG2126|3end_conserved_hypothetical_protein_TIGR00044_2232438..2232588_NEGATIVE 380 269 225 120 83 NC_002950:PG2037|3end_hypothetical_protein_2137591..2137741_NEGATIVE 350 266 226 74 29 NC_002950:PG0267|3end_arginyl-tRNA_synthetase_300973..301123_POSITIVE 345 220 174 83 33 NC_002950:PG1782|3end_hypothetical_protein_1871961..1872111_POSITIVE 344 249 202 145 90 NC_002950:PG1954|3end_NAD_dependent_epimerase/reductase-related_protein_2045612..2045762_POSITIVE 330 191 160 66 28 NC_002950:PG1340|3end_L-lactate_permease_1420298..1420448_NEGATIVE 327 258 217 52 1 NC_002950:PG1751|3end_aminotransferase,_class_V_1838490..1838640_POSITIVE 320 248 210 92 45 NC_002950:PG1389|3end_DNA-binding_protein,_histone-like_family_1470870..1471020_NEGATIVE 317 267 224 85 24 NC_002950:PG1649|3end_hypothetical_protein_1730030..1730180_NEGATIVE 312 220 175 118 57 NC_002950:PG1542|3end_collagenase_1622112..1622262_POSITIVE 312 270 233 81 44 NC_002950:PG0400|3end_hypothetical_protein_436245..436395_NEGATIVE 310 247 201 85 39 NC_002950:PG2082|3end_POT_family_protein_2181843..2181993_NEGATIVE 306 267 228 72 22 NC_002950:PG1697|3end_type_II_restriction_endonuclease,_putative_1785074..1785224_POSITIVE 305 218 171 53 17 NC_002950:PG2127|3end_hypothetical_protein_2233109..2233259_NEGATIVE 305 270 225 149 108 NC_002950:PG0190|3end_undecaprenyl_diphosphate_synthase_226920..227070_POSITIVE 301 220 171 51 2 NC_002950:PG1739|3end_hypothetical_protein_1825128..1825278_NEGATIVE 300 243 210 59 20 NC_002950:PG1323|3end_PhoH_family_protein_1402844..1402994_POSITIVE 300 193 155 69 29 NC_002950:PG0425|3end_esterase,_putative_463219..463369_NEGATIVE 298 248 201 122 66 NC_002950:PG1745|3end_phosphoribulokinase_family_protein_1829435..1829585_NEGATIVE 298 215 171 150 107 NC_002950:PG0170|3end_methionyl-tRNA_synthetase_191774..191924_POSITIVE