Origin IGS: cttacccttcttcttcctcaaaacaaatctatattgatttacagcgtattgcaattatatggtacaaatctgatttcttaaatctattacaaacaatcggttatatcgtct .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agacgatataaccgattgtttgtaatagatttaagaaatcagatttgtaccatataattgcaatacgctgtaaatcaatatagatttgttttgaggaagaagaagggtaag Mask Tandem Repeat Region ================================================ cttacccttcttcttcctcaaaacaaatctatattgatttacagcgtattgcaattatatggtacaaatctgatttcttaaatctattacaaacaatcggttatatcgtct Find is-nt database================================================ Query_seq: PG1199:PG1200|PG1199:PG1200:hypothetical protein:hypothetical protein:-><-:1277459..1277569 111 cttacccttcttcttcctcaaaacaaatctatattgatttacagcgtattgcaattatatggtacaaatctgatttcttaaatctattacaaacaatcggttatatcgtct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1199:PG1200|PG1199:PG1200:hypothetical protein:hypothetical protein:-><-:1277459..1277569 111 cttacccttcttcttcctcaaaacaaatctatattgatttacagcgtattgcaattatatggtacaaatctgatttcttaaatctattacaaacaatcggttatatcgtct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1199:PG1200|PG1199:PG1200:hypothetical protein:hypothetical protein:-><-:1277459..1277569 111 cttacccttcttcttcctcaaaacaaatctatattgatttacagcgtattgcaattatatggtacaaatctgatttcttaaatctattacaaacaatcggttatatcgtct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cttacccttcttcttcctcaaaacaaatctatattgatttacagcgtattgcaattatatggtacaaatctgatttcttaaatctattacaaacaatcggttatatcgtct Predict ORF larger than 30AA ================================================ cttacccttcttcttcctcaaaacaaatctatattgatttacagcgtattgcaattatatggtacaaatctgatttcttaaatctattacaaacaatcggttatatcgtct 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: 54 End: 83 .....................................................ATTTAAGAAATCAGATTTGTACCATATAAT............................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ cttacccttcttcttcctcaaaacaaatctatattgatttacagcgtattgcaattatatggtacaaatctgatttcttaaatctattacaaacaatcggttatatcgtct Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG1199:PG1200|PG1199:PG1200:hypothetical protein:hypothetical protein:-><-:1277459..1277569 111 cttacccttcttcttcctcaaaacaaatctatattgatttacagcgtattgcaattatatggtacaaatctgatttcttaaatctattacaaacaatcggttatatcgtct Intra-Species Hit: Count: 1 Min: 1 Max: 111 Len: 111 Subject: NC_002950_PG1199_PG1200|hypothetical protein:hypothetical protein|POSITIVE:NEGATIVE|[1277459,1277569]|111 HSP 1 e-value: 7.0E-57 bit: 220.0 Len: 111 Query Start:1 Query End:111 Subject Strand: POSITIVE Subject Start: 1 Subject End: 111 cttacccttcttcttcctcaaaacaaatctatattgatttacagcgtattgcaattatatggtacaaatctgatttcttaaatctattacaaacaatcggttatatcgtct cttacccttcttcttcctcaaaacaaatctatattgatttacagcgtattgcaattatatggtacaaatctgatttcttaaatctattacaaacaatcggttatatcgtct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUACCCUUCUUCUUCCUCAAAACAAAUCUAUAUUGAUUUACAGCGUAUUGCAAUUAUAUGGUACAAAUCUGAUUUCUUAAAUCUAUUACAAACAAUCGGUUAUAUCGUCU ..((((..................(((((......)))))...((.....))........)))).....((((((...................))))))........... ( -7.91) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGACGAUAUAACCGAUUGUUUGUAAUAGAUUUAAGAAAUCAGAUUUGUACCAUAUAAUUGCAAUACGCUGUAAAUCAAUAUAGAUUUGUUUUGAGGAAGAAGAAGGGUAAG ............(((((((.((..((((((((.(....).))))))))..)).)))))))...(((.((.((((((......))))))((((.....))))..)).))).. (-14.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 227 84 43 166 134 NC_002950:PG1801|5end_v-type_ATPase,_subunit_E,_putative_1894946..1895176_POSITIVE 225 52 13 105 70 NC_002950:PG0876|5end_tRNA_modification_GTPase_940806..941036_NEGATIVE 222 79 44 227 195 NC_002950:PG0698|5end_lipoprotein,_putative_753356..753586_NEGATIVE 215 48 5 48 2 NC_002950:PG0882|5end_hypothetical_protein_944195..944425_POSITIVE 209 100 51 159 119 NC_002950:PG0532|5end_hypothetical_protein_582148..582378_NEGATIVE 208 47 4 220 180 NC_002950:PG0975|5end_PhoH_family_protein_1037284..1037514_POSITIVE 207 84 43 231 196 NC_002950:PG1350|5end_ISPg2,_transposase_1430866..1431096_POSITIVE 206 17 3 20 6 NC_002950:PG0889|5end_peptidase,_M24_family_950100..950330_POSITIVE 204 70 28 183 145 NC_002950:PG1876|5end_hypothetical_protein_1971460..1971690_NEGATIVE 202 110 61 152 85 NC_002950:PG0030|5end_cytidine_deaminase_35846..36076_POSITIVE 196 110 68 125 81 NC_002950:PG0114|5end_hypothetical_protein_136779..137009_POSITIVE 190 67 27 163 122 NC_002950:PG0028|5end_2C-methyl-D-erythritol_2,4-cyclodiphosphate_synthase_33863..34093_POSITIVE 188 65 42 180 154 NC_002950:PG2001|5end_signal_peptidase_I_2090855..2091085_NEGATIVE 188 110 61 202 155 NC_002950:PG1696|5end_type_II_DNA_modification_methyltransferase,_putative_1779973..1780203_POSITIVE 183 105 73 77 41 NC_002950:PG2190|5end_cell-division_ATP-binding_protein_2297909..2298139_NEGATIVE 183 47 4 85 41 NC_002950:PG2021|5end_hypothetical_protein_2114852..2115082_NEGATIVE 183 53 11 173 136 NC_002950:PG0599|5end_3,4-dihydroxy-2-butanone_4-phosphate_synthase/GTP_cyclohydrolase_II_656435..656665_POSITIVE 182 49 6 170 116 NC_002950:PG1394|5end_hypothetical_protein_1476782..1477012_NEGATIVE 182 106 65 69 30 NC_002950:PG1289|5end_GDP-fucose_synthetase_1367041..1367271_POSITIVE 181 65 29 39 1 NC_002950:PG1084|5end_thioredoxin_family_protein_1152958..1153188_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 225 52 13 73 38 NC_002950:PG0877|3end_hypothetical_protein_940838..940988_NEGATIVE 199 65 28 149 116 NC_002950:PG1877|3end_Na+/H+_antiporter_1971489..1971639_NEGATIVE 196 110 68 128 84 NC_002950:PG0113|3end_hypothetical_protein_136862..137012_POSITIVE 193 62 35 96 67 NC_002950:PG0053|3end_hypothetical_protein_64967..65117_NEGATIVE 186 53 27 143 115 NC_002950:PG0027|3end_hypothetical_protein_33936..34086_POSITIVE 184 88 42 138 92 NC_002950:PG1398|3end_hypothetical_protein_1480947..1481097_POSITIVE 183 47 4 81 37 NC_002950:PG2022|3end_hypothetical_protein_2114856..2115006_NEGATIVE 182 106 65 76 37 NC_002950:PG1288|3end_GDP-mannose_4,6-dehydratase_1367128..1367278_POSITIVE 178 62 30 143 109 NC_002950:PG0285|3end_hypothetical_protein_320044..320194_POSITIVE 177 44 2 116 71 NC_002950:PG1921|3end_ribosomal_protein_S5_2016503..2016653_NEGATIVE 177 45 5 148 102 NC_002950:PG0366|3end_hypothetical_protein_400255..400405_NEGATIVE 177 31 2 122 91 NC_002950:PG0173|3end_transcriptional_regulator,_putative_194388..194538_NEGATIVE 176 75 41 76 42 NC_002950:PG0715|3end_transporter_768676..768826_NEGATIVE 173 39 8 37 6 NC_002950:PG1136|3end_hypothetical_protein_1216699..1216849_NEGATIVE 172 48 1 137 90 NC_002950:PG2186|3end_transcriptional_regulator,_putative_2293284..2293434_NEGATIVE 172 48 1 133 90 NC_002950:PG0221|3end_hypothetical_protein_255613..255763_NEGATIVE 171 48 1 55 13 NC_002950:PG0445|3end_peptidase_T_486549..486699_POSITIVE 170 88 44 104 72 NC_002950:PG1620|3end_carboxyl-terminal_protease-related_protein_1699415..1699565_NEGATIVE 169 66 28 73 38 NC_002950:PG1459|3end_hypothetical_protein_1539632..1539782_NEGATIVE 168 107 69 132 82 NC_002950:PG2135|3end_lipoprotein,_putative_2243413..2243563_POSITIVE