Origin IGS: tgtattctattatttaattctgtttaggataattctttacaaagataagaaatattttcaaaatagcaaaggaaaacaaacttttaaaacacaaaaatatactcgaaaaattcaaatagaggcagtcatacaatttatcgctgccaataaaaagaatattctatctgtta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taacagatagaatattctttttattggcagcgataaattgtatgactgcctctatttgaatttttcgagtatatttttgtgttttaaaagtttgttttcctttgctattttgaaaatatttcttatctttgtaaagaattatcctaaacagaattaaataatagaataca Mask Tandem Repeat Region ================================================ tgtattctattatttaattctgtttaggataattctttacaaagataagaaatattttcaaaatagcaaaggaaaacaaacttttaaaacacaaaaatatactcgaaaaattcaaatagaggcagtcatacaatttatcgctgccaataaaaagaatattctatctgtta Find is-nt database================================================ Query_seq: PI1280:PI1281|PI1280:PI1281:conserved hypothetical protein:hypothetical protein:->->:1196615..1196784 170 tgtattctattatttaattctgtttaggataattctttacaaagataagaaatattttcaaaatagcaaaggaaaacaaacttttaaaacacaaaaatatactcgaaaaattcaaatagaggcagtcatacaatttatcgctgccaataaaaagaatattctatctgtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1280:PI1281|PI1280:PI1281:conserved hypothetical protein:hypothetical protein:->->:1196615..1196784 170 tgtattctattatttaattctgtttaggataattctttacaaagataagaaatattttcaaaatagcaaaggaaaacaaacttttaaaacacaaaaatatactcgaaaaattcaaatagaggcagtcatacaatttatcgctgccaataaaaagaatattctatctgtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1280:PI1281|PI1280:PI1281:conserved hypothetical protein:hypothetical protein:->->:1196615..1196784 170 tgtattctattatttaattctgtttaggataattctttacaaagataagaaatattttcaaaatagcaaaggaaaacaaacttttaaaacacaaaaatatactcgaaaaattcaaatagaggcagtcatacaatttatcgctgccaataaaaagaatattctatctgtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgtattctattatttaattctgtttaggataattctttacaaagataagaaatattttcaaaatagcaaaggaaaacaaacttttaaaacacaaaaatatactcgaaaaattcaaatagaggcagtcatacaatttatcgctgccaataaaaagaatattctatctgtta Predict ORF larger than 30AA ================================================ Protein_Len: 51 Strand: + Start: 17 End: 169 ................ M L F R I I L Y K D K K Y F Q N S K G K Q T F K T Q K Y T R K I Q I E A V I Q F I A A N K K N I L S V . Protein_Len: 47 Strand: - Start: 17 End: 157 ................ N Q K P Y N K V F I L F I K L I A F S F L S K F C L F I S S F N L Y L C D Y L K D S G I F L M ............. tgtattctattatttaattctgtttaggataattctttacaaagataagaaatattttcaaaatagcaaaggaaaacaaacttttaaaacacaaaaatatactcgaaaaattcaaatagaggcagtcatacaatttatcgctgccaataaaaagaatattctatctgtta 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================================================ tgtattctattatttaattctgtttaggataattctttacaaagataagaaatattttcaaaatagcaaaggaaaacaaacttttaaaacacaaaaatatactcgaaaaattcaaatagaggcagtcatacaatttatcgctgccaataaaaagaatattctatctgtta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1280:PI1281|PI1280:PI1281:conserved hypothetical protein:hypothetical protein:->->:1196615..1196784 170 tgtattctattatttaattctgtttaggataattctttacaaagataagaaatattttcaaaatagcaaaggaaaacaaacttttaaaacacaaaaatatactcgaaaaattcaaatagaggcagtcatacaatttatcgctgccaataaaaagaatattctatctgtta Intra-Species Hit: Count: 1 Min: 1 Max: 170 Len: 170 Subject: pint_PI1280_PI1281|conserved hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[1196615,1196784]|170 HSP 1 e-value: 2.0E-21 bit: 103.0 Len: 52 Query Start:119 Query End:170 Subject Strand: POSITIVE Subject Start: 119 Subject End: 170 ......................................................................................................................gaggcagtcatacaatttatcgctgccaataaaaagaatattctatctgtta ......................................................................................................................gaggcagtcatacaatttatcgctgccaataaaaagaatattctatctgtta HSP 2 e-value: 4.0E-13 bit: 75.8 Len: 38 Query Start:1 Query End:38 Subject Strand: POSITIVE Subject Start: 1 Subject End: 38 tgtattctattatttaattctgtttaggataattcttt.................................................................................................................................... tgtattctattatttaattctgtttaggataattcttt.................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUAUUCUAUUAUUUAAUUCUGUUUAGGAUAAUUCUUUACAAAGAUAAGAAAUAUUUUCAAAAUAGCAAAGGAAAACAAACUUUUAAAACACAAAAAUAUACUCGAAAAAUUCAAAUAGAGGCAGUCAUACAAUUUAUCGCUGCCAAUAAAAAGAAUAUUCUAUCUGUUA .(((((((..........(((((((.((((...((((....))))...((.(((((((.........((((.........)))).........)))))))..)).....)))))))))))((((((.(((.....))).)))))).......)))))))........... (-24.37) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAACAGAUAGAAUAUUCUUUUUAUUGGCAGCGAUAAAUUGUAUGACUGCCUCUAUUUGAAUUUUUCGAGUAUAUUUUUGUGUUUUAAAAGUUUGUUUUCCUUUGCUAUUUUGAAAAUAUUUCUUAUCUUUGUAAAGAAUUAUCCUAAACAGAAUUAAAUAAUAGAAUACA ...((((((((..............(((((..(((.....)))..)))))))))))))...................(((((((((.(((..(((((((............)))))))...)))...(((((..((.......))..))))).........))))))))) (-24.73) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 245 157 120 172 133 pint:PI1500|5end_hypothetical_protein_1420626..1420856_POSITIVE 239 143 119 56 21 pint:PI1623|5end_hypothetical_protein_1547163..1547393_POSITIVE 239 143 119 56 21 pint:PI0330|5end_hypothetical_protein_310447..310677_POSITIVE 230 146 118 155 125 pint:PI0897|5end_ferredoxin,_4Fe-4S_828227..828457_POSITIVE 226 144 103 180 143 pint:PI1485|5end_hypothetical_protein_1405170..1405400_POSITIVE 222 167 122 67 27 pint:PI1701|5end_sensor_histidine_kinase_1619312..1619542_POSITIVE 220 167 124 186 138 pint:PI0005|5end_hypothetical_protein_6984..7214_POSITIVE 212 144 102 170 127 pint:PI0262|5end_conserved_hypothetical_protein_254685..254915_POSITIVE 209 146 103 221 173 pint:PI1260|5end_IS1001-related_transposase_1182053..1182283_POSITIVE 209 150 102 215 164 pint:PI0039|5end_conserved_hypothetical_protein;_possible_integral_membrane_protein_40503..40733_POSITIVE 207 141 101 230 205 pint:PI0044|5end_thiamine_biosynthetic_enzyme_42965..43195_POSITIVE 206 145 104 51 16 pint:PI1373|5end_purine_nucleoside_phosphorylase_(PNP)_1294031..1294261_POSITIVE 205 149 112 32 1 pint:PI1551|5end_HesA/MoeB/ThiF_family_protein_1467787..1468017_POSITIVE 198 146 123 139 119 pint:PI0285|5end_succinyltransferase_protein_270097..270327_POSITIVE 196 160 116 114 72 pint:PI0099|5end_hypothetical_protein_95530..95760_POSITIVE 195 106 70 154 118 pint:PI1008|5end_cytochrome_c_nitrite_reductase,_small_subunit_928784..929014_POSITIVE 192 145 104 154 109 pint:PI2011|5end_hypothetical_protein_1970429..1970659_POSITIVE 190 147 123 204 183 pint:PI0125|5end_undecaprenyl_pyrophosphate_synthase_117106..117336_POSITIVE 189 140 95 77 38 pint:PI0156|5end_conserved_hypothetical_protein_148716..148946_POSITIVE 187 144 119 170 143 pint:PI0841|5end_hypothetical_protein_775406..775636_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 239 143 119 43 8 pint:PI1622|3end_hypothetical_protein_1547230..1547380_POSITIVE 239 143 119 43 8 pint:PI0329|3end_hypothetical_protein_310514..310664_POSITIVE 235 145 103 52 12 pint:PI0618|3end_acyl-CoA_dehydrogenase_family_protein_569213..569363_POSITIVE 230 146 118 124 94 pint:PI0896|3end_2-oxoglutarate_oxidoreductase,_alpha_subunit_828276..828426_POSITIVE 198 146 123 119 99 pint:PI0284|3end_flavoprotein_A_270157..270307_POSITIVE 191 44 19 49 23 pint:PI0187|3end_hypothetical_protein_178211..178361_POSITIVE 189 143 118 148 123 pint:PI1749|3end_conserved_hypothetical_protein_1671637..1671787_POSITIVE 189 150 111 67 12 pint:PI1380|3end_conserved_hypothetical_protein_1303242..1303392_POSITIVE 188 146 105 61 22 pint:PI0145|3end_secDF_export_membrane_protein_139724..139874_POSITIVE 187 145 114 52 20 pint:PI0160|3end_conserved_hypothetical_protein_153268..153418_POSITIVE 186 145 118 71 40 pint:PI1054|3end_conserved_hypothetical_protein_974978..975128_POSITIVE 183 147 118 136 105 pint:PI1230|3end_probable_metallo-beta-lactamase_family_protein_1152729..1152879_POSITIVE 183 136 98 92 57 pint:PI0806|3end_heavy_metal_efflux_pump_744394..744544_POSITIVE 180 68 21 115 68 pint:PI1100|3end_conserved_hypothetical_protein;_possible_rhodanese-domain_protein_1024391..1024541_POSITIVE 180 39 12 90 64 pint:PI0488|3end_conserved_hypothetical_protein_447537..447687_POSITIVE 177 72 40 49 24 pint:PI1446|3end_conserved_hypothetical_protein_1369832..1369982_POSITIVE 177 146 105 110 65 pint:PI0875|3end_conserved_hypothetical_protein_811437..811587_POSITIVE 176 146 131 75 59 pint:PI1410|3end_conserved_hypothetical_protein_1331949..1332099_POSITIVE 176 145 102 51 17 pint:PI0162|3end_ADP-ribosylglycohydrolase_(ADP-ribosyl-[dinitrogen_reductase]_hydrolase)_157001..157151_POSITIVE 175 168 121 84 38 pint:PI0587|3end_conserved_hypothetical_protein_535347..535497_POSITIVE