Origin IGS: gagcaacaaagacaatctgctctttctgtttcacctgctgaagaaatgaagctggtggcatgctcatgtatgaggatgacgcttttggagactgggtgccagaaccagtttatggacttcnnnnn .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 nnnnngaagtccataaactggttctggcacccagtctccaaaagcgtcatcctcatacatgagcatgccaccagcttcatttcttcagcaggtgaaacagaaagagcagattgtctttgttgctc Mask Tandem Repeat Region ================================================ gagcaacaaagacaatctgctctttctgtttcacctgctgaagaaatgaagctggtggcatgctcatgtatgaggatgacgcttttggagactgggtgccagaaccagtttatggacttcnnnnn Find is-nt database================================================ Query_seq: SMT_1806:SMT_1807|SMT_1806:SMT_1807:aminoacylase/N-acyl-L-amino acid amidohydrolase/hippurate hydrolase:putative mucus binding protein:-><-:1781705..1781829 125 gagcaacaaagacaatctgctctttctgtttcacctgctgaagaaatgaagctggtggcatgctcatgtatgaggatgacgcttttggagactgggtgccagaaccagtttatggacttcnnnnn Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1806:SMT_1807|SMT_1806:SMT_1807:aminoacylase/N-acyl-L-amino acid amidohydrolase/hippurate hydrolase:putative mucus binding protein:-><-:1781705..1781829 125 gagcaacaaagacaatctgctctttctgtttcacctgctgaagaaatgaagctggtggcatgctcatgtatgaggatgacgcttttggagactgggtgccagaaccagtttatggacttcnnnnn Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1806:SMT_1807|SMT_1806:SMT_1807:aminoacylase/N-acyl-L-amino acid amidohydrolase/hippurate hydrolase:putative mucus binding protein:-><-:1781705..1781829 125 gagcaacaaagacaatctgctctttctgtttcacctgctgaagaaatgaagctggtggcatgctcatgtatgaggatgacgcttttggagactgggtgccagaaccagtttatggacttcnnnnn Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gagcaacaaagacaatctgctctttctgtttcacctgctgaagaaatgaagctggtggcatgctcatgtatgaggatgacgcttttggagactgggtgccagaaccagtttatggacttcnnnnn Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: - Start: 3 End: 113 .. C C L C D A R E T E G A S S I F S T A H E H I L I V S K S V P H W F W N M ............ gagcaacaaagacaatctgctctttctgtttcacctgctgaagaaatgaagctggtggcatgctcatgtatgaggatgacgcttttggagactgggtgccagaaccagtttatggacttcnnnnn 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================================================ gagcaacaaagacaatctgctctttctgtttcacctgctgaagaaatgaagctggtggcatgctcatgtatgaggatgacgcttttggagactgggtgccagaaccagtttatggacttcnnnnn Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1806:SMT_1807|SMT_1806:SMT_1807:aminoacylase/N-acyl-L-amino acid amidohydrolase/hippurate hydrolase:putative mucus binding protein:-><-:1781705..1781829 125 gagcaacaaagacaatctgctctttctgtttcacctgctgaagaaatgaagctggtggcatgctcatgtatgaggatgacgcttttggagactgggtgccagaaccagtttatggacttcnnnnn Intra-Species Hit: Count: 1 Min: 1 Max: 120 Len: 120 Subject: smit_SMT_1806_SMT_1807|aminoacylase/N-acyl-L-amino acid amidohydrolase/hippurate hydrolase:putative mucus binding protein|POSITIVE:NEGATIVE|[1781705,1781829]|125 HSP 1 e-value: 3.0E-62 bit: 238.0 Len: 120 Query Start:1 Query End:120 Subject Strand: POSITIVE Subject Start: 1 Subject End: 120 gagcaacaaagacaatctgctctttctgtttcacctgctgaagaaatgaagctggtggcatgctcatgtatgaggatgacgcttttggagactgggtgccagaaccagtttatggacttc..... gagcaacaaagacaatctgctctttctgtttcacctgctgaagaaatgaagctggtggcatgctcatgtatgaggatgacgcttttggagactgggtgccagaaccagtttatggacttc..... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAGCAACAAAGACAAUCUGCUCUUUCUGUUUCACCUGCUGAAGAAAUGAAGCUGGUGGCAUGCUCAUGUAUGAGGAUGACGCUUUUGGAGACUGGGUGCCAGAACCAGUUUAUGGACUUC (((((............)))))..((((...((((.(((..(....)..))).)))).(((.((((....)))).))).(((((..(....).))))).)))).(((.....)))..... (-31.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAGUCCAUAAACUGGUUCUGGCACCCAGUCUCCAAAAGCGUCAUCCUCAUACAUGAGCAUGCCACCAGCUUCAUUUCUUCAGCAGGUGAAACAGAAAGAGCAGAUUGUCUUUGUUGCUC .............(((..((((...))))...)))...((.((((........))))))....((((.(((..........))).)))).........((((((..........)))))) (-22.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 356 104 63 225 173 smit:SMT_1612|5end_K06024_segregation_and_condensation_protein_B_1600052..1600282_POSITIVE 333 60 16 68 6 smit:SMT_1342|5end_protease_maturation_protein,_putative_1320214..1320444_NEGATIVE 321 109 74 55 15 smit:SMT_761|5end_prephenate_dehydrogenase_667150..667380_NEGATIVE 321 109 74 55 15 smit:SMT_752|5end_prephenate_dehydrogenase_656791..657021_NEGATIVE 316 90 42 211 171 smit:SMT_1476|5end_thiol_peroxidase_1459219..1459449_NEGATIVE 315 99 52 128 69 smit:SMT_464|5end_ribonuclease_Z_402867..403097_POSITIVE 312 94 51 136 94 smit:SMT_448|5end_K03707_transcriptional_activator_TenA_386789..387019_POSITIVE 310 60 14 191 142 smit:SMT_1201|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1163920..1164150_NEGATIVE 310 98 51 124 81 smit:SMT_763|5end_alpha-amylase_667866..668096_POSITIVE 307 60 12 146 90 smit:SMT_2041|5end_transcription-repair_coupling_factor_1952518..1952748_NEGATIVE 306 100 52 116 65 smit:SMT_1914|5end_K03696_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpC_1859486..1859716_POSITIVE 304 88 42 118 73 smit:SMT_2088|5end_glucose-1-phosphate_thymidylyltransferase_1984624..1984854_POSITIVE 304 66 21 71 33 smit:SMT_1387|5end_hypothetical_protein_1364663..1364893_POSITIVE 298 88 42 152 105 smit:SMT_2121|5end_putative_mucus_binding_protein_2007145..2007375_NEGATIVE 298 88 42 152 105 smit:SMT_2068|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1974482..1974712_NEGATIVE 297 77 36 186 138 smit:SMT_1344|5end_oligoendopeptidase_F_1322798..1323028_NEGATIVE 296 77 33 181 137 smit:SMT_1642|5end_K03497_chromosome_partitioning_protein,_ParB_family_1628996..1629226_NEGATIVE 295 118 71 145 93 smit:SMT_1193|5end_phosphoribosylglycinamide_formyltransferase_1152152..1152382_NEGATIVE 295 100 51 164 105 smit:SMT_1011|5end_xanthine_phosphoribosyltransferase_948831..949061_POSITIVE 293 100 51 172 105 smit:SMT_2064|5end_amino_acid_ABC_transporter,_ATP-binding_protein_1972182..1972412_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 337 120 71 80 19 smit:SMT_1481|3end_endopeptidase_O_1463094..1463244_POSITIVE 321 109 74 45 5 smit:SMT_753|3end_chorismate_synthase_656801..656951_NEGATIVE 299 99 61 150 103 smit:SMT_1491|3end_capsular_polysaccharide_biosynthesis_protein,_putative_1471967..1472117_POSITIVE 298 95 53 146 99 smit:SMT_305|3end_seryl-tRNA_synthetase_247577..247727_NEGATIVE 295 118 71 148 96 smit:SMT_1194|3end_phosphoribosylformylglycinamidine_cyclo-ligase_1152149..1152299_NEGATIVE 292 88 48 59 10 smit:SMT_1766|3end_sucrose-6-phosphate_hydrolase_1743101..1743251_POSITIVE 291 98 52 67 14 smit:SMT_387|3end_hypothetical_protein_predicted_by_Glimmer/Critica_321118..321268_POSITIVE 288 79 36 146 99 smit:SMT_242|3end_PTS_system,_mannose-specific_IID_component_179163..179313_NEGATIVE 282 99 52 78 19 smit:SMT_1956|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1889537..1889687_NEGATIVE 276 89 50 72 25 smit:SMT_1037|3end_alpha-galactosidase_979022..979172_NEGATIVE 275 89 50 54 5 smit:SMT_1487|3end_hypothetical_protein_1467076..1467226_POSITIVE 274 88 48 62 13 smit:SMT_1964|3end_sodium/hydrogen_exchanger_family_protein_1896596..1896746_NEGATIVE 274 100 51 47 2 smit:SMT_1010|3end_hypothetical_protein_948761..948911_POSITIVE 274 88 48 67 18 smit:SMT_915|3end_sucrose_operon_repressor_868619..868769_POSITIVE 272 100 53 74 34 smit:SMT_2074|3end_dTDP-glucose_4,6-dehydratase_1977802..1977952_POSITIVE 268 100 54 69 4 smit:SMT_1379|3end_thymidylate_kinase_1356800..1356950_NEGATIVE 266 75 32 128 76 smit:SMT_1787|3end_phosphoribosylformylglycinamidine_synthase_1763668..1763818_NEGATIVE 264 57 13 141 92 smit:SMT_927|3end_KH_domain_protein_881046..881196_NEGATIVE 263 108 61 65 16 smit:SMT_1006|3end_6-pyruvoyl_tetrahydrobiopterin_synthase,_putative_947122..947272_POSITIVE 263 120 75 55 11 smit:SMT_757|3end_K06969_putative_SAM-dependent_methyltransferase_660581..660731_NEGATIVE