Origin IGS: gaaaatgtgttattagtttttacagttgcaaatatatatgttatacgatttgtaggtcactctaatcaaaagatagtatggtcttccttcgtattattcagccgttgcga .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tcgcaacggctgaataatacgaaggaagaccatactatcttttgattagagtgacctacaaatcgtataacatatatatttgcaactgtaaaaactaataacacattttc Mask Tandem Repeat Region ================================================ gaaaatgtgttattagtttttacagttgcaaatatatatgttatacgatttgtaggtcactctaatcaaaagatagtatggtcttccttcgtattattcagccgttgcga Find is-nt database================================================ Query_seq: PG1139:PG1140|PG1139:PG1140:hypothetical protein:glycosyl transferase, group 2 family protein:<-<-:1222155..1222264 110 gaaaatgtgttattagtttttacagttgcaaatatatatgttatacgatttgtaggtcactctaatcaaaagatagtatggtcttccttcgtattattcagccgttgcga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1139:PG1140|PG1139:PG1140:hypothetical protein:glycosyl transferase, group 2 family protein:<-<-:1222155..1222264 110 gaaaatgtgttattagtttttacagttgcaaatatatatgttatacgatttgtaggtcactctaatcaaaagatagtatggtcttccttcgtattattcagccgttgcga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1139:PG1140|PG1139:PG1140:hypothetical protein:glycosyl transferase, group 2 family protein:<-<-:1222155..1222264 110 gaaaatgtgttattagtttttacagttgcaaatatatatgttatacgatttgtaggtcactctaatcaaaagatagtatggtcttccttcgtattattcagccgttgcga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gaaaatgtgttattagtttttacagttgcaaatatatatgttatacgatttgtaggtcactctaatcaaaagatagtatggtcttccttcgtattattcagccgttgcga Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 7 End: 108 ...... M L L V F T V A N I Y V I R F V G H S N Q K I V W S S F V L F S R C .. gaaaatgtgttattagtttttacagttgcaaatatatatgttatacgatttgtaggtcactctaatcaaaagatagtatggtcttccttcgtattattcagccgttgcga 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================================================ gaaaatgtgttattagtttttacagttgcaaatatatatgttatacgatttgtaggtcactctaatcaaaagatagtatggtcttccttcgtattattcagccgttgcga Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG1139:PG1140|PG1139:PG1140:hypothetical protein:glycosyl transferase, group 2 family protein:<-<-:1222155..1222264 110 gaaaatgtgttattagtttttacagttgcaaatatatatgttatacgatttgtaggtcactctaatcaaaagatagtatggtcttccttcgtattattcagccgttgcga Intra-Species Hit: Count: 1 Min: 1 Max: 110 Len: 110 Subject: NC_002950_PG1139_PG1140|hypothetical protein:glycosyl transferase, group 2 family protein|NEGATIVE:NEGATIVE|[1222155,1222264]|110 HSP 1 e-value: 3.0E-56 bit: 218.0 Len: 110 Query Start:1 Query End:110 Subject Strand: POSITIVE Subject Start: 1 Subject End: 110 gaaaatgtgttattagtttttacagttgcaaatatatatgttatacgatttgtaggtcactctaatcaaaagatagtatggtcttccttcgtattattcagccgttgcga gaaaatgtgttattagtttttacagttgcaaatatatatgttatacgatttgtaggtcactctaatcaaaagatagtatggtcttccttcgtattattcagccgttgcga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAAAUGUGUUAUUAGUUUUUACAGUUGCAAAUAUAUAUGUUAUACGAUUUGUAGGUCACUCUAAUCAAAAGAUAGUAUGGUCUUCCUUCGUAUUAUUCAGCCGUUGCGA .....((((..(.....)..)))).((((((...........((((((.....((..((..(((.((....)))))..))..))....))))))..........)))))) (-18.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCGCAACGGCUGAAUAAUACGAAGGAAGACCAUACUAUCUUUUGAUUAGAGUGACCUACAAAUCGUAUAACAUAUAUAUUUGCAACUGUAAAAACUAAUAACACAUUUUC ..(((...((.(((((((((((..(.((..(((.(((((....)).))).)))..)).)...))))))........)))))))...)))..................... (-12.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 862 110 61 201 152 NC_002950:PG1139|5end_hypothetical_protein_1222064..1222294_NEGATIVE 311 106 70 183 143 NC_002950:PG1735|5end_MutT/nudix_family_protein_1823082..1823312_NEGATIVE 287 109 71 188 155 NC_002950:PG1814|5end_DNA_primase_1910627..1910857_NEGATIVE 273 109 61 134 83 NC_002950:PG1620|5end_carboxyl-terminal_protease-related_protein_1700491..1700721_NEGATIVE 267 110 82 221 198 NC_002950:PG0987|5end_hypothetical_protein_1048002..1048232_POSITIVE 264 110 73 204 165 NC_002950:PG1225|5end_ABC_transporter,_ATP-binding_protein_1301385..1301615_POSITIVE 261 109 78 53 19 NC_002950:PG0210|5end_precorrin-6x_reductase/cobalamin_biosynthetic_protein_CbiD_245969..246199_NEGATIVE 257 110 75 217 172 NC_002950:PG1403|5end_rhomboid_family_protein_1487039..1487269_NEGATIVE 251 108 81 103 81 NC_002950:PG1901|5end_ribosome_releasing_factor_2001352..2001582_NEGATIVE 249 109 72 213 183 NC_002950:PG0672|5end_iron_compound_ABC_transporter,_ATP-binding_protein_723002..723232_POSITIVE 247 110 79 192 160 NC_002950:PG0899|5end_cytochrome_d_ubiquinol_oxidase,_subunit_II_964660..964890_NEGATIVE 247 110 70 71 30 NC_002950:PG0568|5end_elongation_factor_P_624565..624795_NEGATIVE 246 109 73 182 143 NC_002950:PG0324|5end_histidine_ammonia-lyase_359082..359312_NEGATIVE 245 106 72 101 71 NC_002950:PG1391|5end_hypothetical_protein_1471670..1471900_POSITIVE 241 106 78 142 113 NC_002950:PG2101|5end_hypothetical_protein_2211273..2211503_NEGATIVE 235 110 69 190 158 NC_002950:PG1758|5end_ribosomal_protein_S15_1845185..1845415_POSITIVE 235 80 39 137 100 NC_002950:PG1718|5end_hypothetical_protein_1806807..1807037_NEGATIVE 234 110 76 39 2 NC_002950:PG2066|5end_lipoprotein,_putative_2162116..2162346_POSITIVE 234 110 67 176 120 NC_002950:PG0937|5end_hypothetical_protein_997194..997424_NEGATIVE 232 109 66 153 106 NC_002950:PG0665|5end_beta-galactosidase_711827..712057_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 287 109 71 146 113 NC_002950:PG1815|3end_3-deoxy-manno-octulosonate_cytidylyltransferase_1910669..1910819_NEGATIVE 273 109 61 141 90 NC_002950:PG1621|3end_hypothetical_protein_1700484..1700634_NEGATIVE 261 109 78 56 22 NC_002950:PG0211|3end_cobalamin_biosynthesis_protein_CbiG/precorrin-4_C11-methyltransferase_245966..246116_NEGATIVE 251 108 81 27 5 NC_002950:PG1902|3end_uridylate_kinase_2001428..2001578_NEGATIVE 247 110 79 146 114 NC_002950:PG0900|3end_cytochrome_d_ubiquinol_oxidase,_subunit_I_964706..964856_NEGATIVE 246 106 79 137 105 NC_002950:PG0933|3end_translation_elongation_factor_G,_putative_992236..992386_POSITIVE 238 83 44 127 92 NC_002950:PG0046|3end_phosphatidate_cytidylyltransferase_56346..56496_NEGATIVE 233 109 80 31 3 NC_002950:PG0737|3end_hypothetical_protein_786546..786696_POSITIVE 233 110 72 106 67 NC_002950:PG0619|3end_alkyl_hydroperoxide_reductase,_F_subunit_672731..672881_POSITIVE 232 109 66 106 59 NC_002950:PG0664|3end_oxidoreductase,_Gfo/Idh/MocA_family_711860..712010_POSITIVE 231 110 62 127 63 NC_002950:PG0268|3end_tRNA_(5-methylaminomethyl-2-thiouridylate)-methyltransferase_302063..302213_POSITIVE 226 108 61 141 85 NC_002950:PG2086|3end_hypothetical_protein_2187070..2187220_POSITIVE 216 110 79 133 99 NC_002950:PG0675|3end_indolepyruvate_ferredoxin_oxidoreductase,_alpha_subunit_724829..724979_NEGATIVE 212 89 45 71 4 NC_002950:PG0815|3end_hypothetical_protein_876447..876597_POSITIVE 210 103 74 69 40 NC_002950:PG0544|3end_type_I_restriction-modification_system,_M_subunit,_putative_598078..598228_POSITIVE 209 107 68 120 78 NC_002950:PG2091|3end_dihydroneopterin_aldolase_2191610..2191760_POSITIVE 208 109 63 104 36 NC_002950:PG1166|3end_hypothetical_protein_1248300..1248450_NEGATIVE 207 110 62 72 8 NC_002950:PG2021|3end_hypothetical_protein_2112921..2113071_NEGATIVE 206 106 70 142 107 NC_002950:PG0788|3end_hypothetical_protein_838043..838193_NEGATIVE 206 110 61 58 3 NC_002950:PG0333|3end_hypothetical_protein_368811..368961_POSITIVE