Origin IGS: cttgtcgtttatagtttctttctaatgtgagacaaaggtacaaaaagttattgaaaatttggtgttttggtaaacttaacgtacttttgcagtataaataataaaaacgtagcatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aatgctacgtttttattatttatactgcaaaagtacgttaagtttaccaaaacaccaaattttcaataactttttgtacctttgtctcacattagaaagaaactataaacgacaag Mask Tandem Repeat Region ================================================ cttgtcgtttatagtttctttctaatgtgagacaaaggtacaaaaagttattgaaaatttggtgttttggtaaacttaacgtacttttgcagtataaataataaaaacgtagcatt Find is-nt database================================================ Query_seq: PI1176:PI1177|PI1176:PI1177:endonuclease III:hypothtical protein:->->:1098880..1098995 116 cttgtcgtttatagtttctttctaatgtgagacaaaggtacaaaaagttattgaaaatttggtgttttggtaaacttaacgtacttttgcagtataaataataaaaacgtagcatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1176:PI1177|PI1176:PI1177:endonuclease III:hypothtical protein:->->:1098880..1098995 116 cttgtcgtttatagtttctttctaatgtgagacaaaggtacaaaaagttattgaaaatttggtgttttggtaaacttaacgtacttttgcagtataaataataaaaacgtagcatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1176:PI1177|PI1176:PI1177:endonuclease III:hypothtical protein:->->:1098880..1098995 116 cttgtcgtttatagtttctttctaatgtgagacaaaggtacaaaaagttattgaaaatttggtgttttggtaaacttaacgtacttttgcagtataaataataaaaacgtagcatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cttgtcgtttatagtttctttctaatgtgagacaaaggtacaaaaagttattgaaaatttggtgttttggtaaacttaacgtacttttgcagtataaataataaaaacgtagcatt Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: - Start: 2 End: 115 . Q R K Y N R E L T L C L Y L F N N F I Q H K P L S L T S K C Y L Y Y F R L M . cttgtcgtttatagtttctttctaatgtgagacaaaggtacaaaaagttattgaaaatttggtgttttggtaaacttaacgtacttttgcagtataaataataaaaacgtagcatt 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================================================ cttgtcgtttatagtttctttctaatgtgagacaaaggtacaaaaagttattgaaaatttggtgttttggtaaacttaacgtacttttgcagtataaataataaaaacgtagcatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1176:PI1177|PI1176:PI1177:endonuclease III:hypothtical protein:->->:1098880..1098995 116 cttgtcgtttatagtttctttctaatgtgagacaaaggtacaaaaagttattgaaaatttggtgttttggtaaacttaacgtacttttgcagtataaataataaaaacgtagcatt Intra-Species Hit: Count: 1 Min: 1 Max: 116 Len: 116 Subject: pint_PI1176_PI1177|endonuclease III:hypothtical protein|POSITIVE:POSITIVE|[1098880,1098995]|116 HSP 1 e-value: 8.0E-60 bit: 230.0 Len: 116 Query Start:1 Query End:116 Subject Strand: POSITIVE Subject Start: 1 Subject End: 116 cttgtcgtttatagtttctttctaatgtgagacaaaggtacaaaaagttattgaaaatttggtgttttggtaaacttaacgtacttttgcagtataaataataaaaacgtagcatt cttgtcgtttatagtttctttctaatgtgagacaaaggtacaaaaagttattgaaaatttggtgttttggtaaacttaacgtacttttgcagtataaataataaaaacgtagcatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUGUCGUUUAUAGUUUCUUUCUAAUGUGAGACAAAGGUACAAAAAGUUAUUGAAAAUUUGGUGUUUUGGUAAACUUAACGUACUUUUGCAGUAUAAAUAAUAAAAACGUAGCAUU .((((..((((((...((((.(....).))))(((((((((...(((((((..(((........)))..)).)))))...)))))))))...))))))..))))............ (-20.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUGCUACGUUUUUAUUAUUUAUACUGCAAAAGUACGUUAAGUUUACCAAAACACCAAAUUUUCAAUAACUUUUUGUACCUUUGUCUCACAUUAGAAAGAAACUAUAAACGACAAG ........((((((............(((((.(((((..(((((....((((.......))))....)))))..))))).)))))............))))))............. (-14.15) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 283 35 5 119 84 pint:PI1915|5end_conserved_hypothetical_protein_1858516..1858746_POSITIVE 250 90 50 228 188 pint:PI1197|5end_pseudouridylate_synthetase_1113558..1113788_POSITIVE 250 90 50 71 31 pint:PI1196|5end_hypothetical_protein_1113401..1113631_POSITIVE 244 91 56 190 155 pint:PI1859|5end_conserved_hypothetical_protein_1805394..1805624_POSITIVE 238 38 1 216 187 pint:PI0572|5end_tRNA_(5-methylaminomethyl-2-thiouridylate)-methyltransferase_516382..516612_POSITIVE 231 50 4 220 165 pint:PI1772|5end_pullulanase_1702257..1702487_POSITIVE 223 49 1 138 79 pint:PI0109|5end_hypothetical_protein_106717..106947_POSITIVE 220 50 1 189 134 pint:PI1496|5end_nucleoside_phosphorylase_1417116..1417346_POSITIVE 220 69 23 146 92 pint:PI0553|5end_recombination_protein_503344..503574_POSITIVE 210 110 61 184 134 pint:PI1320|5end_conserved_hypothetical_protein_1239031..1239261_POSITIVE 210 109 64 148 104 pint:PI0170|5end_hypothetical_protein_163305..163535_POSITIVE 206 100 59 171 127 pint:PI2168|5end_hypothetical_protein_2111286..2111516_POSITIVE 205 90 42 231 182 pint:PI0067|5end_hypothetical_protein_66273..66503_POSITIVE 203 90 44 106 71 pint:PI0410|5end_glutamyl-tRNA_synthetase_(glutamate--tRNA_ligase)_375947..376177_POSITIVE 201 64 30 41 1 pint:PI1344|5end_hypothetical_protein_1258551..1258781_POSITIVE 199 48 1 188 140 pint:PI0069|5end_hypothetical_protein_67072..67302_POSITIVE 197 95 52 152 108 pint:PI0066|5end_ABC_transport_system,_ATP-binding_component_65248..65478_POSITIVE 196 45 3 118 84 pint:PI1534|5end_ATPase/GTPase_1453679..1453909_POSITIVE 194 47 3 85 31 pint:PI2172|5end_hypothetical_protein_2113819..2114049_POSITIVE 194 47 3 61 7 pint:PI2173|5end_hypothetical_protein_2113795..2114025_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 283 35 5 119 84 pint:PI1914|3end_RNA_polymerase,_ECF-type_sigma_factor_1858596..1858746_POSITIVE 250 90 50 50 10 pint:PI1195|3end_hypothetical_protein_1113460..1113610_POSITIVE 244 91 56 71 36 pint:PI1858|3end_conserved_hypothetical_protein_1805355..1805505_POSITIVE 221 109 80 82 53 pint:PI0227|3end_ABC_transporter,_ATP-binding/permease_protein_225632..225782_POSITIVE 220 69 23 57 3 pint:PI0552|3end_hypothetical_protein_503335..503485_POSITIVE 210 110 61 65 15 pint:PI1319|3end_possible_OmpA_,_outer_membrane_protein-related_protein_1238992..1239142_POSITIVE 205 90 46 111 64 pint:PI0140|3end_conserved_hypothetical_protein_132106..132256_POSITIVE 203 40 6 56 23 pint:PI0976|3end_dihydrolipoamide_dehydrogenase_(dihydrolipoyl_dehydrogenanse)_903732..903882_POSITIVE 203 90 44 48 13 pint:PI0409|3end_3-deoxy-D-manno-octulosonic-acid_transferase_(kdotransferase)_375969..376119_POSITIVE 199 48 1 55 7 pint:PI0068|3end_arginine_repressor_67019..67169_POSITIVE 197 41 4 147 102 pint:PI1771|3end_alpha-glucosidase_1702274..1702424_POSITIVE 197 95 52 136 92 pint:PI0065|3end_conserved_hypothetical_protein_65312..65462_POSITIVE 194 47 3 150 96 pint:PI2173|3end_hypothetical_protein_2113964..2114114_POSITIVE 194 69 21 100 54 pint:PI0272|3end_conserved_hypothetical_protein_262943..263093_POSITIVE 193 64 25 130 98 pint:PI2015|3end_D-alanine--D-alanine_ligase_1973796..1973946_POSITIVE 187 70 25 140 91 pint:PI1473|3end_hypothetical_protein_1395830..1395980_POSITIVE 186 81 60 112 92 pint:PI1589|3end_conserved_hypothetical_protein_1517842..1517992_POSITIVE 186 92 56 138 104 pint:PI1153|3end_histidine_kinase_sensor_protein_1078638..1078788_POSITIVE 186 70 26 146 115 pint:PI0177|3end_2-oxoglutarate_synthase,_subunit_korB_169583..169733_POSITIVE 185 48 6 65 23 pint:PI1846|3end_hypothetical_protein_1791943..1792093_POSITIVE