Origin IGS: atcttttcacttagtctgttgaattgccaaatgcaatctactaattgcaaagataacgattatattttacattcacgtgccatttgctaactattttctacccattta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaatgggtagaaaatagttagcaaatggcacgtgaatgtaaaatataatcgttatctttgcaattagtagattgcatttggcaattcaacagactaagtgaaaagat Mask Tandem Repeat Region ================================================ atcttttcacttagtctgttgaattgccaaatgcaatctactaattgcaaagataacgattatattttacattcacgtgccatttgctaactattttctacccattta Find is-nt database================================================ Query_seq: PI0155:PI0156|PI0155:PI0156:conserved hypothetical protein:conserved hypothetical protein:->->:148748..148855 108 atcttttcacttagtctgttgaattgccaaatgcaatctactaattgcaaagataacgattatattttacattcacgtgccatttgctaactattttctacccattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0155:PI0156|PI0155:PI0156:conserved hypothetical protein:conserved hypothetical protein:->->:148748..148855 108 atcttttcacttagtctgttgaattgccaaatgcaatctactaattgcaaagataacgattatattttacattcacgtgccatttgctaactattttctacccattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0155:PI0156|PI0155:PI0156:conserved hypothetical protein:conserved hypothetical protein:->->:148748..148855 108 atcttttcacttagtctgttgaattgccaaatgcaatctactaattgcaaagataacgattatattttacattcacgtgccatttgctaactattttctacccattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atcttttcacttagtctgttgaattgccaaatgcaatctactaattgcaaagataacgattatattttacattcacgtgccatttgctaactattttctacccattta Predict ORF larger than 30AA ================================================ atcttttcacttagtctgttgaattgccaaatgcaatctactaattgcaaagataacgattatattttacattcacgtgccatttgctaactattttctacccattta 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================================================ atcttttcacttagtctgttgaattgccaaatgcaatctactaattgcaaagataacgattatattttacattcacgtgccatttgctaactattttctacccattta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI0155:PI0156|PI0155:PI0156:conserved hypothetical protein:conserved hypothetical protein:->->:148748..148855 108 atcttttcacttagtctgttgaattgccaaatgcaatctactaattgcaaagataacgattatattttacattcacgtgccatttgctaactattttctacccattta Intra-Species Hit: Count: 1 Min: 1 Max: 108 Len: 108 Subject: pint_PI0155_PI0156|conserved hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[148748,148855]|108 HSP 1 e-value: 4.0E-55 bit: 214.0 Len: 108 Query Start:1 Query End:108 Subject Strand: POSITIVE Subject Start: 1 Subject End: 108 atcttttcacttagtctgttgaattgccaaatgcaatctactaattgcaaagataacgattatattttacattcacgtgccatttgctaactattttctacccattta atcttttcacttagtctgttgaattgccaaatgcaatctactaattgcaaagataacgattatattttacattcacgtgccatttgctaactattttctacccattta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCUUUUCACUUAGUCUGUUGAAUUGCCAAAUGCAAUCUACUAAUUGCAAAGAUAACGAUUAUAUUUUACAUUCACGUGCCAUUUGCUAACUAUUUUCUACCCAUUUA ((((((.((.(((((..((((.(((....))).))))..))))).)).))))))...((..(((.((..((.............))..)).)))..)).......... (-12.42) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAUGGGUAGAAAAUAGUUAGCAAAUGGCACGUGAAUGUAAAAUAUAAUCGUUAUCUUUGCAAUUAGUAGAUUGCAUUUGGCAAUUCAACAGACUAAGUGAAAAGAU .................((((.....))))........................((((((.((.(((((.((((((.....))))))......))))).)).)))))) (-13.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 273 55 12 132 76 pint:PI1530|5end_conserved_hypothetical_protein_1450439..1450669_POSITIVE 259 49 2 219 172 pint:PI0929|5end_copper_homeostasis_protein_860294..860524_POSITIVE 252 42 4 185 149 pint:PI1023|5end_hypothetical_protein_939936..940166_POSITIVE 252 42 4 162 126 pint:PI1022|5end_hypothetical_protein_939913..940143_POSITIVE 244 86 45 48 1 pint:PI0633|5end_possible_preprotein_translocase,_YajC_subunit_579671..579901_POSITIVE 237 58 13 82 37 pint:PI0096|5end_glycerol-3-phosphate_cytidylyltransferase_91885..92115_POSITIVE 236 47 2 75 37 pint:PI0959|5end_uridine_kinase_890495..890725_POSITIVE 229 60 11 225 170 pint:PI1594|5end_MotA/TolQ/ExbB_proton_channel_1523528..1523758_POSITIVE 225 58 17 137 89 pint:PI0230|5end_hypothetical_protein_228590..228820_POSITIVE 224 58 26 78 43 pint:PI1139|5end_endopeptidase,_endothelin-converting_enzyme_1065216..1065446_POSITIVE 223 62 30 202 173 pint:PI0607|5end_2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxy_lic_acid_synthase/2-oxoglutarate_decarboxylase_553801..554031_POSITIVE 220 60 17 71 28 pint:PI0094|5end_protoporphyrinogen_oxidase_89571..89801_POSITIVE 218 41 14 81 58 pint:PI0316|5end_conserved_hypothetical_protein_298379..298609_POSITIVE 217 100 57 48 10 pint:PI2121|5end_glucose_inhibited_division_protein_A_2069889..2070119_POSITIVE 217 60 25 175 133 pint:PI0817|5end_glycosyl_transferase,_group_1_family_protein_756861..757091_POSITIVE 214 90 46 161 106 pint:PI0471|5end_50S_ribosomal_protein_L24_437736..437966_POSITIVE 213 58 14 99 60 pint:PI1745|5end_conserved_hypothetical_protein_1666615..1666845_POSITIVE 213 59 11 192 144 pint:PI1525|5end_CDP-diacylglycerol--serine_O-phosphatidyltransferase_1446758..1446988_POSITIVE 212 35 2 167 127 pint:PI1544|5end_hypothetical_protein_1463507..1463737_POSITIVE 210 58 17 187 144 pint:PI1032|5end_methylmalonyl-CoA_decarboxylase,_alpha_subunit_948463..948693_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 259 49 2 117 70 pint:PI0928|3end_hypothetical_protein_860272..860422_POSITIVE 237 59 13 74 29 pint:PI2014|3end_conserved_hypothetical_protein_1972603..1972753_POSITIVE 236 47 2 69 31 pint:PI0958|3end_G:T/U_mismatch-specific_DNA_glycosylase_890569..890719_POSITIVE 220 60 17 71 28 pint:PI0092|3end_regulatory_protein_RecX_89651..89801_POSITIVE 210 58 17 151 108 pint:PI1031|3end_hypothetical_protein_948507..948657_POSITIVE 203 88 45 78 35 pint:PI1861|3end_hypothetical_protein_1806114..1806264_POSITIVE 203 59 12 111 66 pint:PI0152|3end_DNA_mismatch_endonuclease_vsr_145984..146134_POSITIVE 202 88 46 87 41 pint:PI0452|3end_conserved_hypothetical_protein;_possible_surface_antigen_426791..426941_POSITIVE 201 39 16 124 95 pint:PI1686|3end_hypothetical_protein_1601898..1602048_POSITIVE 199 34 4 117 85 pint:PI2135|3end_conserved_hypothetical_protein_2083253..2083403_POSITIVE 198 39 3 146 111 pint:PI0024|3end_hypothetical_protein_28559..28709_POSITIVE 196 49 9 112 72 pint:PI0183|3end_hypothetical_protein_174810..174960_POSITIVE 195 69 24 64 21 pint:PI1831|3end_conserved_hypothetical_protein_1773167..1773317_POSITIVE 194 90 47 36 2 pint:PI2006|3end_potassium_uptake_system_protein_1965846..1965996_POSITIVE 194 56 14 91 45 pint:PI0917|3end_phosphoglycolate_phosphatase_847092..847242_POSITIVE 194 42 10 138 98 pint:PI0779|3end_predicted_TPR-repeat-containing_protein_715800..715950_POSITIVE 192 57 11 123 82 pint:PI1843|3end_hypothetical_protein_1788611..1788761_POSITIVE 192 22 2 128 108 pint:PI0248|3end_protein_associated_with_conjugate_transformation/chromosome_partioning_246647..246797_POSITIVE 191 95 56 88 57 pint:PI0827|3end_hypothetical_protein_764163..764313_POSITIVE 191 95 56 121 90 pint:PI0825|3end_hypothetical_protein_764196..764346_POSITIVE