Origin IGS: agaaaagcaggcagtaagaaaagtaatttctactgtctgctttttctaatggatttattgccactacctacttcatattctcttttttcagcgtataatggcaatctcaaaaggattctctttca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgaaagagaatccttttgagattgccattatacgctgaaaaaagagaatatgaagtaggtagtggcaataaatccattagaaaaagcagacagtagaaattacttttcttactgcctgcttttct Mask Tandem Repeat Region ================================================ agaaaagcaggcagtaagaaaagtaatttctactgtctgctttttctaatggatttattgccactacctacttcatattctcttttttcagcgtataatggcaatctcaaaaggattctctttca Find is-nt database================================================ Query_seq: PG0821:PG0822|PG0821:PG0822:lipoprotein, putative:hypothetical protein:-><-:880293..880417 125 agaaaagcaggcagtaagaaaagtaatttctactgtctgctttttctaatggatttattgccactacctacttcatattctcttttttcagcgtataatggcaatctcaaaaggattctctttca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0821:PG0822|PG0821:PG0822:lipoprotein, putative:hypothetical protein:-><-:880293..880417 125 agaaaagcaggcagtaagaaaagtaatttctactgtctgctttttctaatggatttattgccactacctacttcatattctcttttttcagcgtataatggcaatctcaaaaggattctctttca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0821:PG0822|PG0821:PG0822:lipoprotein, putative:hypothetical protein:-><-:880293..880417 125 agaaaagcaggcagtaagaaaagtaatttctactgtctgctttttctaatggatttattgccactacctacttcatattctcttttttcagcgtataatggcaatctcaaaaggattctctttca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agaaaagcaggcagtaagaaaagtaatttctactgtctgctttttctaatggatttattgccactacctacttcatattctcttttttcagcgtataatggcaatctcaaaaggattctctttca Predict ORF larger than 30AA ================================================ agaaaagcaggcagtaagaaaagtaatttctactgtctgctttttctaatggatttattgccactacctacttcatattctcttttttcagcgtataatggcaatctcaaaaggattctctttca 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================================================ agaaaagcaggcagtaagaaaagtaatttctactgtctgctttttctaatggatttattgccactacctacttcatattctcttttttcagcgtataatggcaatctcaaaaggattctctttca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG0821:PG0822|PG0821:PG0822:lipoprotein, putative:hypothetical protein:-><-:880293..880417 125 agaaaagcaggcagtaagaaaagtaatttctactgtctgctttttctaatggatttattgccactacctacttcatattctcttttttcagcgtataatggcaatctcaaaaggattctctttca Intra-Species Hit: Count: 2 Min: 1 Max: 125 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:1 Query End:125 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:1 Query End:125 Subject Strand: POSITIVE Subject Start: 1 Subject End: 125 agaaaagcaggcagtaagaaaagtaatttctactgtctgctttttctaatggatttattgccactacctacttcatattctcttttttcagcgtataatggcaatctcaaaaggattctctttca agaaaagcaggcagtaagaaaagtaatttctactgtctgctttttctaatggatttattgccactacctacttcatattctcttttttcagcgtataatggcaatctcaaaaggattctctttca Inter-species Hit: Count: 1 Min: 1 Max: 125 Len: 125 Subject: pint_PI0390_PI0391|conserved hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[357816,357946]|131 HSP 1 e-value: 4.0E-65 bit: 248.0 Len: 125 Query Start:1 Query End:125 Subject Strand: POSITIVE Subject Start: 4 Subject End: 128 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 299 106 61 177 129 NC_002950:PG1999|5end_hypothetical_protein_2088821..2089051_NEGATIVE 272 94 57 91 50 NC_002950:PG1369|5end_glycerol-3-phosphate_dehydrogenase_(NAD(P)+)_1450407..1450637_NEGATIVE 270 117 79 74 34 NC_002950:PG2207|5end_hypothetical_protein_2320161..2320391_NEGATIVE 258 75 33 100 54 NC_002950:PG1781|5end_uridine_kinase_1870023..1870253_POSITIVE 256 119 71 217 168 NC_002950:PG1479|5end_conjugative_transposon_protein_TraJ_1555234..1555464_NEGATIVE 253 49 5 116 53 NC_002950:PG0171|5end_5'-nucleotidase_family_protein_191724..191954_POSITIVE 249 74 31 223 188 NC_002950:PG0647|5end_iron_compound_ABC_transporter,_permease_protein_700113..700343_NEGATIVE 247 94 60 201 165 NC_002950:PG0399|5end_lipoprotein,_putative_436237..436467_NEGATIVE 247 75 34 118 80 NC_002950:PG0114|5end_hypothetical_protein_136779..137009_POSITIVE 237 90 48 211 165 NC_002950:PG0576|5end_UDP-N-acetylmuramoylalanyl-D-glutamate--2,_6-diaminopimelate_ligase_631719..631949_POSITIVE 237 40 1 52 1 NC_002950:PG0462|5end_transporter,_putative_506279..506509_NEGATIVE 234 85 57 207 175 NC_002950:PG2089|5end_hypothetical_protein_2188640..2188870_POSITIVE 230 54 11 142 82 NC_002950:PG2147|5end_xanthine_phosphoribosyltransferase_2255400..2255630_NEGATIVE 230 46 1 106 69 NC_002950:PG1029|5end_hypothetical_protein_1091080..1091310_POSITIVE 228 79 37 94 59 NC_002950:PG1901|5end_ribosome_releasing_factor_2001352..2001582_NEGATIVE 227 74 33 159 108 NC_002950:PG2222|5end_acyltransferase,_HtrB/MsbB_family_2336757..2336987_POSITIVE 226 68 31 227 191 NC_002950:PG0513|5end_conserved_hypothetical_protein_TIGR00255_552837..553067_NEGATIVE 225 92 59 106 71 NC_002950:PG0065|5end_efflux_transporter,_RND_family,_MFP_subunit_81187..81417_NEGATIVE 223 44 1 212 157 NC_002950:PG1583|5end_batB_protein_1660315..1660545_POSITIVE 223 67 23 91 36 NC_002950:PG1511|5end_hypothetical_protein_1587609..1587839_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 834 110 61 75 26 NC_002950:PG1451|3end_hypothetical_protein_1535184..1535334_POSITIVE 407 47 1 90 44 NC_002950:PG1452|3end_lipoprotein,_putative_1535280..1535430_NEGATIVE 407 47 1 90 44 NC_002950:PG0821|3end_lipoprotein,_putative_880232..880382_POSITIVE 287 102 61 149 108 NC_002950:PG2000|3end_signal_peptidase-related_protein_2088842..2088992_NEGATIVE 259 80 33 145 88 NC_002950:PG1162|3end_ATP:cob(I)alamin_adenosyltransferase,_putative_1241473..1241623_NEGATIVE 258 75 33 50 4 NC_002950:PG1780|3end_8-amino-7-oxononanoate_synthase_1870053..1870203_POSITIVE 257 103 66 125 86 NC_002950:PG1013|3end_acetyl-CoA_hydrolase/transferase_family_protein_1073310..1073460_POSITIVE 253 49 5 86 23 NC_002950:PG0170|3end_methionyl-tRNA_synthetase_191774..191924_POSITIVE 247 75 34 121 83 NC_002950:PG0113|3end_hypothetical_protein_136862..137012_POSITIVE 245 93 51 119 79 NC_002950:PG1761|3end_acetyltransferase,_GNAT_family_1847739..1847889_POSITIVE 240 47 8 127 92 NC_002950:PG0799|3end_hypothetical_protein_854599..854749_POSITIVE 234 85 57 150 118 NC_002950:PG2088|3end_bifunctional_methionine_sulfoxide_reductase_A/B_protein_2188663..2188813_POSITIVE 233 89 47 49 13 NC_002950:PG2037|3end_hypothetical_protein_2137591..2137741_NEGATIVE 230 54 11 105 45 NC_002950:PG2148|3end_xanthine/uracil_permease_family_protein_2255437..2255587_NEGATIVE 230 46 1 42 5 NC_002950:PG1028|3end_TPR_domain_protein_1091096..1091246_POSITIVE 226 68 31 135 99 NC_002950:PG0514|3end_translocase_552929..553079_NEGATIVE 224 94 51 105 62 NC_002950:PG0893|3end_hydroxylamine_reductase_954201..954351_NEGATIVE 221 86 45 92 58 NC_002950:PG0166|3end_peptidyl-tRNA_hydrolase_187813..187963_NEGATIVE 218 103 61 107 59 NC_002950:PG0058|3end_nicotinic_acid_mononucleotide_adenyltransferase_71592..71742_POSITIVE 217 63 28 149 119 NC_002950:PG1166|3end_hypothetical_protein_1248300..1248450_NEGATIVE