Origin IGS: cggtctgaaattgattccgaccgtaaaggtagaggtttccccttgaagaggttataaggaatatacgaaaatgaggctgagcaggggcggtctcttttatgatgacgattttactgcaagacacttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaagtgtcttgcagtaaaatcgtcatcataaaagagaccgcccctgctcagcctcattttcgtatattccttataacctcttcaaggggaaacctctacctttacggtcggaatcaatttcagaccg Mask Tandem Repeat Region ================================================ cggtctgaaattgattccgaccgtaaaggtagaggtttccccttgaagaggttataaggaatatacgaaaatgaggctgagcaggggcggtctcttttatgatgacgattttactgcaagacacttt Find is-nt database================================================ Query_seq: PG0925:PG0926|PG0925:PG0926:thymidine kinase:hypothetical protein:<-<-:984370..984496 127 cggtctgaaattgattccgaccgtaaaggtagaggtttccccttgaagaggttataaggaatatacgaaaatgaggctgagcaggggcggtctcttttatgatgacgattttactgcaagacacttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0925:PG0926|PG0925:PG0926:thymidine kinase:hypothetical protein:<-<-:984370..984496 127 cggtctgaaattgattccgaccgtaaaggtagaggtttccccttgaagaggttataaggaatatacgaaaatgaggctgagcaggggcggtctcttttatgatgacgattttactgcaagacacttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0925:PG0926|PG0925:PG0926:thymidine kinase:hypothetical protein:<-<-:984370..984496 127 cggtctgaaattgattccgaccgtaaaggtagaggtttccccttgaagaggttataaggaatatacgaaaatgaggctgagcaggggcggtctcttttatgatgacgattttactgcaagacacttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cggtctgaaattgattccgaccgtaaaggtagaggtttccccttgaagaggttataaggaatatacgaaaatgaggctgagcaggggcggtctcttttatgatgacgattttactgcaagacacttt Predict ORF larger than 30AA ================================================ Protein_Len: 41 Strand: - Start: 2 End: 124 . T Q F Q N R G Y L Y L N G R S S T I L F I R F H P Q A P A T E K I I V I K S C S M ... cggtctgaaattgattccgaccgtaaaggtagaggtttccccttgaagaggttataaggaatatacgaaaatgaggctgagcaggggcggtctcttttatgatgacgattttactgcaagacacttt 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================================================ cggtctgaaattgattccgaccgtaaaggtagaggtttccccttgaagaggttataaggaatatacgaaaatgaggctgagcaggggcggtctcttttatgatgacgattttactgcaagacacttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG0925:PG0926|PG0925:PG0926:thymidine kinase:hypothetical protein:<-<-:984370..984496 127 cggtctgaaattgattccgaccgtaaaggtagaggtttccccttgaagaggttataaggaatatacgaaaatgaggctgagcaggggcggtctcttttatgatgacgattttactgcaagacacttt Intra-Species Hit: Count: 1 Min: 1 Max: 127 Len: 127 Subject: NC_002950_PG0925_PG0926|thymidine kinase:hypothetical protein|NEGATIVE:NEGATIVE|[984370,984496]|127 HSP 1 e-value: 2.0E-66 bit: 252.0 Len: 127 Query Start:1 Query End:127 Subject Strand: POSITIVE Subject Start: 1 Subject End: 127 cggtctgaaattgattccgaccgtaaaggtagaggtttccccttgaagaggttataaggaatatacgaaaatgaggctgagcaggggcggtctcttttatgatgacgattttactgcaagacacttt cggtctgaaattgattccgaccgtaaaggtagaggtttccccttgaagaggttataaggaatatacgaaaatgaggctgagcaggggcggtctcttttatgatgacgattttactgcaagacacttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGGUCUGAAAUUGAUUCCGACCGUAAAGGUAGAGGUUUCCCCUUGAAGAGGUUAUAAGGAAUAUACGAAAAUGAGGCUGAGCAGGGGCGGUCUCUUUUAUGAUGACGAUUUUACUGCAAGACACUUU (((((.(((.....))).)))))....(((((((.....((((((....((((.....................))))...))))))..(((((......)).)))..)))))))............ (-25.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAGUGUCUUGCAGUAAAAUCGUCAUCAUAAAAGAGACCGCCCCUGCUCAGCCUCAUUUUCGUAUAUUCCUUAUAACCUCUUCAAGGGGAAACCUCUACCUUUACGGUCGGAAUCAAUUUCAGACCG ((((((.((.((((.......(((.((......))))).....))))..))...))))))........................((((....)).)).......(((((.(((.....))).))))) (-22.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 975 120 71 211 162 NC_002950:PG0925|5end_thymidine_kinase_984279..984509_NEGATIVE 371 89 42 81 38 NC_002950:PG2098|5end_hypothetical_protein_2206635..2206865_NEGATIVE 341 44 1 84 29 NC_002950:PG1160|5end_L-threonine-O-3-phosphate_decarboxylase,_putative_1239988..1240218_NEGATIVE 325 107 75 68 22 NC_002950:PG2215|5end_mannose-1-phosphate_guanylyltransferase_2327695..2327925_NEGATIVE 325 117 71 204 153 NC_002950:PG2159|5end_protoporphyrinogen_oxidase_2264397..2264627_POSITIVE 324 120 71 85 30 NC_002950:PG2094|5end_hypothetical_protein_2197868..2198098_NEGATIVE 315 101 70 101 65 NC_002950:PG0300|5end_TPR_domain_protein_336570..336800_POSITIVE 313 107 72 62 22 NC_002950:PG2225|5end_hypothetical_protein_2339440..2339670_POSITIVE 308 117 71 194 138 NC_002950:PG0289|5end_hypothetical_protein_322860..323090_POSITIVE 305 98 53 201 158 NC_002950:PG1739|5end_hypothetical_protein_1825709..1825939_NEGATIVE 304 117 71 182 131 NC_002950:PG1760|5end_ABC_transporter,_ATP-binding_protein_1846507..1846737_POSITIVE 302 60 17 140 101 NC_002950:PG2219|5end_potassium_uptake_protein_TrkH_2332947..2333177_POSITIVE 302 94 57 149 109 NC_002950:PG1088|5end_acetyltransferase,_GNAT_family_1155426..1155656_NEGATIVE 298 68 21 222 170 NC_002950:PG0048|5end_conserved_hypothetical_protein_TIGR00092_60557..60787_NEGATIVE 297 48 4 64 17 NC_002950:PG0246|5end_hypothetical_protein_281241..281471_NEGATIVE 296 96 76 231 206 NC_002950:PG1006|5end_hypothetical_protein_1066478..1066708_NEGATIVE 296 90 41 54 13 NC_002950:PG0147|5end_hypothetical_protein_169667..169897_NEGATIVE 295 60 17 94 57 NC_002950:PG0333|5end_hypothetical_protein_367823..368053_POSITIVE 294 107 71 67 32 NC_002950:PG2187|5end_1,4-dihydroxy-2-naphthoate_octaprenyltransferase_2294643..2294873_NEGATIVE 294 104 67 203 162 NC_002950:PG1411|5end_potassium_uptake_protein_TrkA,_putative_1495166..1495396_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 393 92 57 150 117 NC_002950:PG0508|3end_HAD-superfamily_subfamily_IB_hydrolase,_TIGR01490_548136..548286_NEGATIVE 371 89 42 67 24 NC_002950:PG2099|3end_ATP-dependent_RNA_helicase,_DEAD/DEAH_box_family_2206649..2206799_NEGATIVE 315 41 1 134 89 NC_002950:PG1684|3end_hypothetical_protein_1771483..1771633_POSITIVE 315 78 31 49 5 NC_002950:PG1030|3end_hypothetical_protein_1092820..1092970_POSITIVE 313 107 72 42 2 NC_002950:PG2224|3end_hypothetical_protein_2339500..2339650_POSITIVE 305 98 53 54 11 NC_002950:PG1741|3end_aspartate_ammonia-lyase_1825856..1826006_NEGATIVE 304 108 75 142 100 NC_002950:PG2159|3end_protoporphyrinogen_oxidase_2265874..2266024_POSITIVE 302 60 17 113 74 NC_002950:PG2218|3end_potassium_uptake_protein_TrkA_2333000..2333150_POSITIVE 302 94 57 52 12 NC_002950:PG1089|3end_DNA-binding_response_regulator_RprY_1155523..1155673_NEGATIVE 296 107 75 73 34 NC_002950:PG2158|3end_hypothetical_protein_2264473..2264623_POSITIVE 296 60 15 86 44 NC_002950:PG0164|3end_hypothetical_protein_187081..187231_NEGATIVE 296 90 41 67 26 NC_002950:PG0148|3end_sigma-54-dependent_transcriptional_regulator_169654..169804_NEGATIVE 294 107 71 77 42 NC_002950:PG2188|3end_diaminopimelate_decarboxylase_2294633..2294783_NEGATIVE 292 111 74 55 9 NC_002950:PG0167|3end_ribosomal_protein_L25_188512..188662_NEGATIVE 291 96 66 63 24 NC_002950:PG0775|3end_acyl-CoA_dehydrogenase_family_protein_827432..827582_NEGATIVE 290 97 60 58 16 NC_002950:PG0933|3end_translation_elongation_factor_G,_putative_992236..992386_POSITIVE 286 119 71 137 93 NC_002950:PG1943|3end_hypothetical_protein_2028974..2029124_NEGATIVE 285 88 42 88 43 NC_002950:PG1118|3end_clpB_protein_1192083..1192233_NEGATIVE 282 110 74 67 31 NC_002950:PG1220|3end_erythronate-4-phosphate_dehydrogenase_1298199..1298349_POSITIVE 282 90 42 140 77 NC_002950:PG0321|3end_arginine/ornithine_transport_system_ATPase_355759..355909_POSITIVE