Origin IGS: aacagaaacatggccaccgtaagtaccaacaggagataaaagactatcgtcagtatgccgttgactttcttgagatccattctcggactatattctctac .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gtagagaatatagtccgagaatggatctcaagaaagtcaacggcatactgacgatagtcttttatctcctgttggtacttacggtggccatgtttctgtt Mask Tandem Repeat Region ================================================ aacagaaacatggccaccgtaagtaccaacaggagataaaagactatcgtcagtatgccgttgactttcttgagatccattctcggactatattctctac Find is-nt database================================================ Query_seq: PG1811:PG1812|PG1811:PG1812:hypothetical protein:2-oxoglutarate ferredoxin oxidoreductase:-><-:1907036..1907135 100 aacagaaacatggccaccgtaagtaccaacaggagataaaagactatcgtcagtatgccgttgactttcttgagatccattctcggactatattctctac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1811:PG1812|PG1811:PG1812:hypothetical protein:2-oxoglutarate ferredoxin oxidoreductase:-><-:1907036..1907135 100 aacagaaacatggccaccgtaagtaccaacaggagataaaagactatcgtcagtatgccgttgactttcttgagatccattctcggactatattctctac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1811:PG1812|PG1811:PG1812:hypothetical protein:2-oxoglutarate ferredoxin oxidoreductase:-><-:1907036..1907135 100 aacagaaacatggccaccgtaagtaccaacaggagataaaagactatcgtcagtatgccgttgactttcttgagatccattctcggactatattctctac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aacagaaacatggccaccgtaagtaccaacaggagataaaagactatcgtcagtatgccgttgactttcttgagatccattctcggactatattctctac Predict ORF larger than 30AA ================================================ aacagaaacatggccaccgtaagtaccaacaggagataaaagactatcgtcagtatgccgttgactttcttgagatccattctcggactatattctctac 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================================================ aacagaaacatggccaccgtaagtaccaacaggagataaaagactatcgtcagtatgccgttgactttcttgagatccattctcggactatattctctac Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG1811:PG1812|PG1811:PG1812:hypothetical protein:2-oxoglutarate ferredoxin oxidoreductase:-><-:1907036..1907135 100 aacagaaacatggccaccgtaagtaccaacaggagataaaagactatcgtcagtatgccgttgactttcttgagatccattctcggactatattctctac Intra-Species Hit: Count: 1 Min: 1 Max: 100 Len: 100 Subject: NC_002950_PG1811_PG1812|hypothetical protein:2-oxoglutarate ferredoxin oxidoreductase|POSITIVE:NEGATIVE|[1907036,1907135]|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 aacagaaacatggccaccgtaagtaccaacaggagataaaagactatcgtcagtatgccgttgactttcttgagatccattctcggactatattctctac aacagaaacatggccaccgtaagtaccaacaggagataaaagactatcgtcagtatgccgttgactttcttgagatccattctcggactatattctctac Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACAGAAACAUGGCCACCGUAAGUACCAACAGGAGAUAAAAGACUAUCGUCAGUAUGCCGUUGACUUUCUUGAGAUCCAUUCUCGGACUAUAUUCUCUAC ...((((..((((((...(.((((..((((.((..(((...(((....)))..))).)))))))))).)..((((.....)))))).)))).)))).... (-16.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUAGAGAAUAUAGUCCGAGAAUGGAUCUCAAGAAAGUCAACGGCAUACUGACGAUAGUCUUUUAUCUCCUGUUGGUACUUACGGUGGCCAUGUUUCUGUU .((((((.........((((.....))))............(((.(((((..(((((....))))).((....))......))))))))...)))))).. (-20.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 376 60 11 59 4 NC_002950:PG1950|5end_hypothetical_protein_2039600..2039830_POSITIVE 332 86 41 193 153 NC_002950:PG1586|5end_batE_protein_1664054..1664284_POSITIVE 318 83 41 75 19 NC_002950:PG2147|5end_xanthine_phosphoribosyltransferase_2255400..2255630_NEGATIVE 305 89 42 69 7 NC_002950:PG1297|5end_ribosomal_protein_S1_1375831..1376061_POSITIVE 297 87 47 60 12 NC_002950:PG0738|5end_cytidine/deoxycytidylate_deaminase_family_protein_786463..786693_POSITIVE 296 59 13 70 12 NC_002950:PG0434|5end_hypothetical_protein_472513..472743_NEGATIVE 289 99 57 109 51 NC_002950:PG1814|5end_DNA_primase_1910627..1910857_NEGATIVE 283 87 42 61 1 NC_002950:PG0384|5end_MutS2_family_protein_416095..416325_POSITIVE 281 55 15 69 23 NC_002950:PG0719|5end_sensor_histidine_kinase_772979..773209_NEGATIVE 279 89 45 52 1 NC_002950:PG0160|5end_hypothetical_protein_184085..184315_NEGATIVE 278 91 52 102 59 NC_002950:PG2096|5end_hypothetical_protein_2205415..2205645_NEGATIVE 277 38 9 132 103 NC_002950:PG1541|5end_2-amino-4-hydroxy-6-_hydroxymethyldihydropteridine_pyrophosphokinase_1620326..1620556_POSITIVE 270 59 11 192 142 NC_002950:PG0333|5end_hypothetical_protein_367823..368053_POSITIVE 268 78 31 107 51 NC_002950:PG1977|5end_hypothetical_protein_2066693..2066923_NEGATIVE 266 60 25 56 26 NC_002950:PG0192|5end_cationic_outer_membrane_protein_OmpH_229590..229820_POSITIVE 265 87 43 158 107 NC_002950:PG1282|5end_hypothetical_protein_1360035..1360265_POSITIVE 264 89 47 231 178 NC_002950:PG0335|5end_tRNA_delta(2)-isopentenylpyrophosphate_transferase_370706..370936_NEGATIVE 260 84 42 192 132 NC_002950:PG0171|5end_5'-nucleotidase_family_protein_191724..191954_POSITIVE 258 87 46 98 43 NC_002950:PG2123|5end_hypothetical_protein_2229891..2230121_POSITIVE 258 59 13 71 13 NC_002950:PG0352|5end_sialidase,_putative_387187..387417_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 303 88 41 139 88 NC_002950:PG0443|3end_hemagglutinin-related_protein_483147..483297_POSITIVE 297 87 47 63 15 NC_002950:PG0737|3end_hypothetical_protein_786546..786696_POSITIVE 291 60 12 64 7 NC_002950:PG2076|3end_hypothetical_protein_2177073..2177223_POSITIVE 289 99 57 67 9 NC_002950:PG1815|3end_3-deoxy-manno-octulosonate_cytidylyltransferase_1910669..1910819_NEGATIVE 281 55 15 72 26 NC_002950:PG0720|3end_DNA-binding_response_regulator_772976..773126_NEGATIVE 277 38 9 135 106 NC_002950:PG1540|3end_S-adenosylmethionine:tRNA_ribosyltransferase-isomerase_1620409..1620559_POSITIVE 268 78 31 77 21 NC_002950:PG1978|3end_hypothetical_protein_2066723..2066873_NEGATIVE 265 87 43 134 83 NC_002950:PG1281|3end_hypothetical_protein_1360091..1360241_POSITIVE 260 49 2 60 4 NC_002950:PG1393|3end_penicillin-binding_protein_2,_putative_1474406..1474556_NEGATIVE 257 36 9 84 58 NC_002950:PG0211|3end_cobalamin_biosynthesis_protein_CbiG/precorrin-4_C11-methyltransferase_245966..246116_NEGATIVE 256 97 51 147 92 NC_002950:PG1353|3end_orotate_phosphoribosyltransferase_1433201..1433351_NEGATIVE 253 98 51 127 92 NC_002950:PG2000|3end_signal_peptidase-related_protein_2088842..2088992_NEGATIVE 251 60 11 122 78 NC_002950:PG1389|3end_DNA-binding_protein,_histone-like_family_1470870..1471020_NEGATIVE 250 49 1 68 11 NC_002950:PG1562|3end_dTDP-4-dehydrorhamnose_3,5-epimerase_1640992..1641142_NEGATIVE 250 60 11 54 3 NC_002950:PG1271|3end_acetylornithine_aminotransferase,_putative_1350214..1350364_NEGATIVE 249 64 31 116 81 NC_002950:PG0030|3end_cytidine_deaminase_36402..36552_POSITIVE 248 99 53 57 7 NC_002950:PG1171|3end_oxidoreductase,_putative_1251175..1251325_POSITIVE 248 49 9 67 41 NC_002950:PG0032|3end_beta-mannosidase,_putative_37627..37777_NEGATIVE 247 60 13 141 108 NC_002950:PG0143|3end_hydrolase,_carbon-nitrogen_family_165747..165897_NEGATIVE 245 89 49 41 2 NC_002950:PG1366|3end_UDP-N-acetylglucosamine_1-carboxyvinyltransferase_1446076..1446226_NEGATIVE