Origin IGS: taaagaaaagcaggcagtaagaaaagtaatttctactgtctgctttttctaatggatttattgccactacctacttcatattctcttttttcagcgtataatggcaatctcaaaaggattctctttcatta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taatgaaagagaatccttttgagattgccattatacgctgaaaaaagagaatatgaagtaggtagtggcaataaatccattagaaaaagcagacagtagaaattacttttcttactgcctgcttttcttta Mask Tandem Repeat Region ================================================ taaagaaaagcaggcagtaagaaaagtaatttctactgtctgctttttctaatggatttattgccactacctacttcatattctcttttttcagcgtataatggcaatctcaaaaggattctctttcatta Find is-nt database================================================ Query_seq: PI0390:PI0391|PI0390:PI0391:conserved hypothetical protein:conserved hypothetical protein:->->:357816..357946 131 taaagaaaagcaggcagtaagaaaagtaatttctactgtctgctttttctaatggatttattgccactacctacttcatattctcttttttcagcgtataatggcaatctcaaaaggattctctttcatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0390:PI0391|PI0390:PI0391:conserved hypothetical protein:conserved hypothetical protein:->->:357816..357946 131 taaagaaaagcaggcagtaagaaaagtaatttctactgtctgctttttctaatggatttattgccactacctacttcatattctcttttttcagcgtataatggcaatctcaaaaggattctctttcatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0390:PI0391|PI0390:PI0391:conserved hypothetical protein:conserved hypothetical protein:->->:357816..357946 131 taaagaaaagcaggcagtaagaaaagtaatttctactgtctgctttttctaatggatttattgccactacctacttcatattctcttttttcagcgtataatggcaatctcaaaaggattctctttcatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaagaaaagcaggcagtaagaaaagtaatttctactgtctgctttttctaatggatttattgccactacctacttcatattctcttttttcagcgtataatggcaatctcaaaaggattctctttcatta Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 40 End: 129 ....................................... M L F L M D L L P L P T S Y S L F S A Y N G N L K R I L F H .. taaagaaaagcaggcagtaagaaaagtaatttctactgtctgctttttctaatggatttattgccactacctacttcatattctcttttttcagcgtataatggcaatctcaaaaggattctctttcatta 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================================================ taaagaaaagcaggcagtaagaaaagtaatttctactgtctgctttttctaatggatttattgccactacctacttcatattctcttttttcagcgtataatggcaatctcaaaaggattctctttcatta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI0390:PI0391|PI0390:PI0391:conserved hypothetical protein:conserved hypothetical protein:->->:357816..357946 131 taaagaaaagcaggcagtaagaaaagtaatttctactgtctgctttttctaatggatttattgccactacctacttcatattctcttttttcagcgtataatggcaatctcaaaaggattctctttcatta Intra-Species Hit: Count: 1 Min: 1 Max: 131 Len: 131 Subject: pint_PI0390_PI0391|conserved hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[357816,357946]|131 HSP 1 e-value: 1.0E-68 bit: 260.0 Len: 131 Query Start:1 Query End:131 Subject Strand: POSITIVE Subject Start: 1 Subject End: 131 taaagaaaagcaggcagtaagaaaagtaatttctactgtctgctttttctaatggatttattgccactacctacttcatattctcttttttcagcgtataatggcaatctcaaaaggattctctttcatta taaagaaaagcaggcagtaagaaaagtaatttctactgtctgctttttctaatggatttattgccactacctacttcatattctcttttttcagcgtataatggcaatctcaaaaggattctctttcatta Inter-species Hit: Count: 2 Min: 4 Max: 128 Len: 125 Subject: NC_002950_PG1451_PG1452|hypothetical protein:lipoprotein, putative|POSITIVE:NEGATIVE|[1535245,1535369]|125 HSP 1 e-value: 4.0E-65 bit: 248.0 Len: 125 Query Start:4 Query End:128 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 125 ...agaaaagcaggcagtaagaaaagtaatttctactgtctgctttttctaatggatttattgccactacctacttcatattctcttttttcagcgtataatggcaatctcaaaaggattctctttca... ...agaaaagcaggcagtaagaaaagtaatttctactgtctgctttttctaatggatttattgccactacctacttcatattctcttttttcagcgtataatggcaatctcaaaaggattctctttca... Subject: NC_002950_PG0821_PG0822|lipoprotein, putative:hypothetical protein|POSITIVE:NEGATIVE|[880293,880417]|125 HSP 1 e-value: 4.0E-65 bit: 248.0 Len: 125 Query Start:4 Query End:128 Subject Strand: POSITIVE Subject Start: 1 Subject End: 125 ...agaaaagcaggcagtaagaaaagtaatttctactgtctgctttttctaatggatttattgccactacctacttcatattctcttttttcagcgtataatggcaatctcaaaaggattctctttca... ...agaaaagcaggcagtaagaaaagtaatttctactgtctgctttttctaatggatttattgccactacctacttcatattctcttttttcagcgtataatggcaatctcaaaaggattctctttca... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAAAAGCAGGCAGUAAGAAAAGUAAUUUCUACUGUCUGCUUUUUCUAAUGGAUUUAUUGCCACUACCUACUUCAUAUUCUCUUUUUUCAGCGUAUAAUGGCAAUCUCAAAAGGAUUCUCUUUCA .(((((((((((((((.((((.....))))))))))))))))))).....(((((((((((((.(((((....................)).)))...))))))).......))))))....... (-30.76) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAAAGAGAAUCCUUUUGAGAUUGCCAUUAUACGCUGAAAAAAGAGAAUAUGAAGUAGGUAGUGGCAAUAAAUCCAUUAGAAAAAGCAGACAGUAGAAAUUACUUUUCUUACUGCCUGCUUUUCU .(((((......)))))...(((((((((((..(((.................)))..))))))))))).........((((((.((((.(((((((((.....)))).))))).)))))))))) (-35.23) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 412 46 1 139 98 pint:PI0218|5end_conserved_hypothetical_protein_210770..211000_POSITIVE 293 41 7 205 161 pint:PI0720|5end_conserved_hypothetical_protein_653949..654179_POSITIVE 258 48 8 180 144 pint:PI0659|5end_hypothetical_protein_603203..603433_POSITIVE 250 73 36 164 126 pint:PI0261|5end_conjugative_transposon_protein,_TraK_254065..254295_POSITIVE 248 47 1 160 123 pint:PI2011|5end_hypothetical_protein_1970429..1970659_POSITIVE 246 90 45 198 144 pint:PI2095|5end_hypothetical_protein_2049195..2049425_POSITIVE 246 90 45 193 139 pint:PI2093|5end_hypothetical_protein_2049190..2049420_POSITIVE 246 90 45 183 129 pint:PI2092|5end_hypothetical_protein_2049180..2049410_POSITIVE 240 47 1 127 76 pint:PI0272|5end_conserved_hypothetical_protein_262621..262851_POSITIVE 233 66 23 198 156 pint:PI0869|5end_possible_exodeoxyribonuclease_VII_(small_subunit)_805518..805748_POSITIVE 232 104 70 158 120 pint:PI0870|5end_branched-chain_amino_acid_aminotransferase_805933..806163_POSITIVE 231 43 7 195 166 pint:PI0831|5end_hypothetical_protein_768129..768359_POSITIVE 230 40 9 45 13 pint:PI0993|5end_probable_TPR-repeat-containing_protein_917175..917405_POSITIVE 228 75 50 26 6 pint:PI2051|5end_hypothetical_protein_2007567..2007797_POSITIVE 228 114 71 180 141 pint:PI0301|5end_probable_transposase_285672..285902_POSITIVE 226 120 84 89 57 pint:PI0258|5end_conjugative_transposon_protein,_TraG_249722..249952_POSITIVE 225 80 33 213 156 pint:PI0796|5end_competence_protein_733324..733554_POSITIVE 224 64 33 52 21 pint:PI0837|5end_conserved_hypothetical_protein_772308..772538_POSITIVE 220 63 22 223 174 pint:PI0479|5end_50S_ribosomal_protein_L15_441125..441355_POSITIVE 218 120 77 200 151 pint:PI1884|5end_conserved_hypothetical_protein_1826883..1827113_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 412 46 1 83 42 pint:PI0217|3end_conserved_hypothetical_protein;_possible_lipoprotein_210794..210944_POSITIVE 407 47 1 87 41 pint:PI0390|3end_conserved_hypothetical_protein_357755..357905_POSITIVE 263 76 32 122 75 pint:PI0492|3end_hypothetical_protein_452458..452608_POSITIVE 250 73 36 141 103 pint:PI0260|3end_conjugative_transposon_protein,_TraJ_254122..254272_POSITIVE 249 103 61 118 75 pint:PI0962|3end_phosphoglycerate_mutase_892702..892852_POSITIVE 246 90 45 149 95 pint:PI2091|3end_DNA_processing_protein_2049226..2049376_POSITIVE 240 71 33 45 3 pint:PI0881|3end_conserved_hypothetical_protein_815283..815433_POSITIVE 238 80 33 147 99 pint:PI1651|3end_hypothetical_protein_1564512..1564662_POSITIVE 235 43 5 69 35 pint:PI0410|3end_glutamyl-tRNA_synthetase_(glutamate--tRNA_ligase)_377490..377640_POSITIVE 232 47 6 140 90 pint:PI1631|3end_hypothetical_protein_1552797..1552947_POSITIVE 230 47 1 61 24 pint:PI0160|3end_conserved_hypothetical_protein_153268..153418_POSITIVE 226 120 84 89 57 pint:PI0257|3end_conjugative_transposon_protein,_TraF_249802..249952_POSITIVE 225 95 51 138 93 pint:PI0767|3end_possible_TonB-dependent_receptor_704025..704175_POSITIVE 224 64 33 37 6 pint:PI0836|3end_conserved_hypothetical_protein_772373..772523_POSITIVE 216 93 51 127 80 pint:PI1527|3end_immunoreactive_46_kDa_antigen_PG99_1449520..1449670_POSITIVE 215 47 7 126 86 pint:PI0309|3end_hypothetical_protein_291729..291879_POSITIVE 215 92 58 69 40 pint:PI0063|3end_transcriptional_regulator,_GntR_family_63620..63770_POSITIVE 214 107 65 136 89 pint:PI1659|3end_hypothetical_protein_1576472..1576622_POSITIVE 214 48 9 60 14 pint:PI1259|3end_ISPg4-related_transposase_(IS5_family)_1182089..1182239_POSITIVE 211 80 35 87 33 pint:PI0067|3end_hypothetical_protein_66586..66736_POSITIVE