Origin IGS: ttgctcaccagcttttgatgatataaaaaagcaggtatcgatcctccaggatcgatacctgcttcattcaaattaaatatcatcttatcccattattgaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttcaataatgggataagatgatatttaatttgaatgaagcaggtatcgatcctggaggatcgatacctgcttttttatatcatcaaaagctggtgagcaa Mask Tandem Repeat Region ================================================ ttgctcaccagcttttgatgatataaaaaagcaggtatcgatcctccaggatcgatacctgcttcattcaaattaaatatcatcttatcccattattgaa Find is-nt database================================================ Query_seq: PG0982:PG0984|PG0982:PG0984:TPR domain protein:hypothetical protein:-><-:1046703..1046802 100 ttgctcaccagcttttgatgatataaaaaagcaggtatcgatcctccaggatcgatacctgcttcattcaaattaaatatcatcttatcccattattgaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0982:PG0984|PG0982:PG0984:TPR domain protein:hypothetical protein:-><-:1046703..1046802 100 ttgctcaccagcttttgatgatataaaaaagcaggtatcgatcctccaggatcgatacctgcttcattcaaattaaatatcatcttatcccattattgaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0982:PG0984|PG0982:PG0984:TPR domain protein:hypothetical protein:-><-:1046703..1046802 100 ttgctcaccagcttttgatgatataaaaaagcaggtatcgatcctccaggatcgatacctgcttcattcaaattaaatatcatcttatcccattattgaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttgctcaccagcttttgatgatataaaaaagcaggtatcgatcctccaggatcgatacctgcttcattcaaattaaatatcatcttatcccattattgaa Predict ORF larger than 30AA ================================================ ttgctcaccagcttttgatgatataaaaaagcaggtatcgatcctccaggatcgatacctgcttcattcaaattaaatatcatcttatcccattattgaa 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================================================ ttgctcaccagcttttgatgatataaaaaagcaggtatcgatcctccaggatcgatacctgcttcattcaaattaaatatcatcttatcccattattgaa Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -21.8 Tail_Score: -5.39721 Start: 31 End: 62 Full_Region: tttaatttgaatgaa gcaggtatcgatcc tgga ggatcgatacctgc ttttttatatcatca ..............................gcaggtatcgatcctggaggatcgatacctgc...................................... Find igs database================================================ Query_seq: PG0982:PG0984|PG0982:PG0984:TPR domain protein:hypothetical protein:-><-:1046703..1046802 100 ttgctcaccagcttttgatgatataaaaaagcaggtatcgatcctccaggatcgatacctgcttcattcaaattaaatatcatcttatcccattattgaa Intra-Species Hit: Count: 1 Min: 1 Max: 100 Len: 100 Subject: NC_002950_PG0982_PG0984|TPR domain protein:hypothetical protein|POSITIVE:NEGATIVE|[1046703,1046802]|100 HSP 1 e-value: 2.0E-50 bit: 198.0 Len: 100 Query Start:1 Query End:100 Subject Strand: POSITIVE Subject Start: 1 Subject End: 100 ttgctcaccagcttttgatgatataaaaaagcaggtatcgatcctccaggatcgatacctgcttcattcaaattaaatatcatcttatcccattattgaa ttgctcaccagcttttgatgatataaaaaagcaggtatcgatcctccaggatcgatacctgcttcattcaaattaaatatcatcttatcccattattgaa HSP 2 e-value: 2.0E-7 bit: 56.0 Len: 36 Query Start:29 Query End:64 Subject Strand: NEGATIVE Subject Start: 29 Subject End: 64 ............................aagcaggtatcgatcctccaggatcgatacctgctt.................................... ............................aagcaggtatcgatcctggaggatcgatacctgctt.................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGCUCACCAGCUUUUGAUGAUAUAAAAAAGCAGGUAUCGAUCCUCCAGGAUCGAUACCUGCUUCAUUCAAAUUAAAUAUCAUCUUAUCCCAUUAUUGAA ..(((....)))....((((((((((..((((((((((((((((....))))))))))))))))..))........))))))))................ (-35.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCAAUAAUGGGAUAAGAUGAUAUUUAAUUUGAAUGAAGCAGGUAUCGAUCCUGGAGGAUCGAUACCUGCUUUUUUAUAUCAUCAAAAGCUGGUGAGCAA ................((((((((...........(((((((((((((((((....)))))))))))))))))...))))))))....(((....))).. (-39.94) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 333 63 31 68 27 NC_002950:PG0213|5end_precorrin-3_methylase/precorrin-8X_methylmutase_250464..250694_NEGATIVE 306 68 30 68 27 NC_002950:PG0397|5end_hypothetical_protein_434602..434832_NEGATIVE 295 64 31 147 107 NC_002950:PG0495|5end_hypothetical_protein_535447..535677_POSITIVE 293 67 28 150 112 NC_002950:PG1900|5end_ribosome-associated_GTPase_2000746..2000976_NEGATIVE 275 68 39 178 144 NC_002950:PG1494|5end_hypothetical_protein_1569841..1570071_POSITIVE 274 70 30 214 151 NC_002950:PG0660|5end_nitroreductase_family_protein_709695..709925_NEGATIVE 273 69 24 213 165 NC_002950:PG0138|5end_malonyl_CoA-acyl_carrier_protein_transacylase_160673..160903_POSITIVE 270 63 30 180 147 NC_002950:PG0217|5end_hypothetical_protein_252490..252720_POSITIVE 263 62 33 161 125 NC_002950:PG1338|5end_umuC_protein_1418246..1418476_POSITIVE 263 49 1 184 129 NC_002950:PG1184|5end_alginate_O-acetyltransferase,_putative_1266870..1267100_NEGATIVE 261 69 22 93 43 NC_002950:PG1850|5end_hypothetical_protein_1949957..1950187_NEGATIVE 261 69 31 102 55 NC_002950:PG0659|5end_hypothetical_protein_709148..709378_NEGATIVE 260 69 22 165 112 NC_002950:PG0094|5end_outer_membrane_efflux_protein,_putative_111193..111423_NEGATIVE 259 61 27 175 136 NC_002950:PG1817|5end_hypothetical_protein_1913035..1913265_NEGATIVE 258 50 8 39 4 NC_002950:PG1473|5end_conjugative_transposon_protein_TraQ_1550225..1550455_NEGATIVE 255 66 30 202 162 NC_002950:PG1921|5end_ribosomal_protein_S5_2017021..2017251_NEGATIVE 251 66 31 177 147 NC_002950:PG0188|5end_lipoprotein,_putative_223934..224164_POSITIVE 250 65 31 46 3 NC_002950:PG2224|5end_hypothetical_protein_2338863..2339093_POSITIVE 250 58 17 212 174 NC_002950:PG1599|5end_hypothetical_protein_1679087..1679317_POSITIVE 250 69 30 63 8 NC_002950:PG0268|5end_tRNA_(5-methylaminomethyl-2-thiouridylate)-methyltransferase_300898..301128_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 590 64 29 62 27 NC_002950:PG0982|3end_TPR_domain_protein_1046642..1046792_POSITIVE 325 59 11 107 53 NC_002950:PG1289|3end_GDP-fucose_synthetase_1368194..1368344_POSITIVE 306 68 30 54 13 NC_002950:PG0398|3end_recF_protein_434616..434766_NEGATIVE 293 67 28 65 27 NC_002950:PG1901|3end_ribosome_releasing_factor_2000831..2000981_NEGATIVE 286 68 31 142 96 NC_002950:PG1814|3end_DNA_primase_1908606..1908756_NEGATIVE 277 61 30 146 119 NC_002950:PG1731|3end_3-dehydroquinate_dehydratase_1819678..1819828_NEGATIVE 273 69 24 98 50 NC_002950:PG0137|3end_aminoacyl-histidine_dipeptidase_160638..160788_POSITIVE 270 63 30 146 113 NC_002950:PG0216|3end_hypothetical_protein_252536..252686_POSITIVE 267 66 31 95 50 NC_002950:PG0815|3end_hypothetical_protein_876447..876597_POSITIVE 264 65 23 42 1 NC_002950:PG0568|3end_elongation_factor_P_623999..624149_NEGATIVE 261 69 22 96 46 NC_002950:PG1851|3end_phosphopantothenoylcysteine_decarboxylase/phosphopantothenate--cysteine_ligase_1949954..1950104_NEGATIVE 261 69 31 109 62 NC_002950:PG0660|3end_nitroreductase_family_protein_709141..709291_NEGATIVE 256 68 30 89 55 NC_002950:PG2075|3end_hypothetical_protein_2176248..2176398_NEGATIVE 256 68 30 89 55 NC_002950:PG1671|3end_hypothetical_protein_1757440..1757590_NEGATIVE 256 68 30 89 55 NC_002950:PG1266|3end_hypothetical_protein_1346769..1346919_NEGATIVE 256 68 30 89 55 NC_002950:PG0101|3end_hypothetical_protein_119496..119646_POSITIVE 255 56 11 108 68 NC_002950:PG2091|3end_dihydroneopterin_aldolase_2191610..2191760_POSITIVE 250 69 30 58 3 NC_002950:PG0267|3end_arginyl-tRNA_synthetase_300973..301123_POSITIVE 249 69 33 80 36 NC_002950:PG2044|3end_hypothetical_protein_2144165..2144315_POSITIVE 248 69 31 96 47 NC_002950:PG2227|3end_hypothetical_protein_2342744..2342894_POSITIVE