Origin IGS: actgtgcctatcttatcataagtcgcttgctttgaaaaggcttgacgtgaaaagaaaagcacagtgaaaacatttacacttgcttgagttatgttatttacctgaaattatggtataatcgttcagttagaaaataaattttgaatattatagaggaaatc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gatttcctctataatattcaaaatttattttctaactgaacgattataccataatttcaggtaaataacataactcaagcaagtgtaaatgttttcactgtgcttttcttttcacgtcaagccttttcaaagcaagcgacttatgataagataggcacagt Mask Tandem Repeat Region ================================================ actgtgcctatcttatcataagtcgcttgctttgaaaaggcttgacgtgaaaagaaaagcacagtgaaaacatttacacttgcttgagttatgttatttacctgaaattatggtataatcgttcagttagaaaataaattttgaatattatagaggaaatc Find is-nt database================================================ Query_seq: SMT_428:SMT_429|SMT_428:SMT_429:ribosomal small subunit pseudouridine synthase A:K06207 GTP-binding protein:<-->:369948..370108 161 actgtgcctatcttatcataagtcgcttgctttgaaaaggcttgacgtgaaaagaaaagcacagtgaaaacatttacacttgcttgagttatgttatttacctgaaattatggtataatcgttcagttagaaaataaattttgaatattatagaggaaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_428:SMT_429|SMT_428:SMT_429:ribosomal small subunit pseudouridine synthase A:K06207 GTP-binding protein:<-->:369948..370108 161 actgtgcctatcttatcataagtcgcttgctttgaaaaggcttgacgtgaaaagaaaagcacagtgaaaacatttacacttgcttgagttatgttatttacctgaaattatggtataatcgttcagttagaaaataaattttgaatattatagaggaaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_428:SMT_429|SMT_428:SMT_429:ribosomal small subunit pseudouridine synthase A:K06207 GTP-binding protein:<-->:369948..370108 161 actgtgcctatcttatcataagtcgcttgctttgaaaaggcttgacgtgaaaagaaaagcacagtgaaaacatttacacttgcttgagttatgttatttacctgaaattatggtataatcgttcagttagaaaataaattttgaatattatagaggaaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 actgtgcctatcttatcataagtcgcttgctttgaaaaggcttgacgtgaaaagaaaagcacagtgaaaacatttacacttgcttgagttatgttatttacctgaaattatggtataatcgttcagttagaaaataaattttgaatattatagaggaaatc Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: - Start: 3 End: 92 .. T G I K D Y T A Q K S F A Q R S F F L V T F V N V S A Q T M ..................................................................... actgtgcctatcttatcataagtcgcttgctttgaaaaggcttgacgtgaaaagaaaagcacagtgaaaacatttacacttgcttgagttatgttatttacctgaaattatggtataatcgttcagttagaaaataaattttgaatattatagaggaaatc Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: + Score: 83 Start: 90 End: 119 .........................................................................................TATGTTATTTACCTGAAATTATGGTATAAT.......................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ actgtgcctatcttatcataagtcgcttgctttgaaaaggcttgacgtgaaaagaaaagcacagtgaaaacatttacacttgcttgagttatgttatttacctgaaattatggtataatcgttcagttagaaaataaattttgaatattatagaggaaatc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_428:SMT_429|SMT_428:SMT_429:ribosomal small subunit pseudouridine synthase A:K06207 GTP-binding protein:<-->:369948..370108 161 actgtgcctatcttatcataagtcgcttgctttgaaaaggcttgacgtgaaaagaaaagcacagtgaaaacatttacacttgcttgagttatgttatttacctgaaattatggtataatcgttcagttagaaaataaattttgaatattatagaggaaatc Intra-Species Hit: Count: 1 Min: 1 Max: 161 Len: 161 Subject: smit_SMT_428_SMT_429|ribosomal small subunit pseudouridine synthase A:K06207 GTP-binding protein|NEGATIVE:POSITIVE|[369948,370108]|161 HSP 1 e-value: 2.0E-86 bit: 319.0 Len: 161 Query Start:1 Query End:161 Subject Strand: POSITIVE Subject Start: 1 Subject End: 161 actgtgcctatcttatcataagtcgcttgctttgaaaaggcttgacgtgaaaagaaaagcacagtgaaaacatttacacttgcttgagttatgttatttacctgaaattatggtataatcgttcagttagaaaataaattttgaatattatagaggaaatc actgtgcctatcttatcataagtcgcttgctttgaaaaggcttgacgtgaaaagaaaagcacagtgaaaacatttacacttgcttgagttatgttatttacctgaaattatggtataatcgttcagttagaaaataaattttgaatattatagaggaaatc Inter-species Hit: Count: 3 Min: 1 Max: 161 Len: 161 Subject: NC_008533_SPD_0592_SPD_0593|ribosomal small subunit pseudouridine synthase A:elongation factor Tu family protein|NEGATIVE:POSITIVE|[617124,617284]|161 HSP 1 e-value: 6.0E-77 bit: 287.0 Len: 161 Query Start:1 Query End:161 Subject Strand: POSITIVE Subject Start: 1 Subject End: 161 actgtgcctatcttatcataagtcgcttgctttgaaaaggcttgacgtgaaaagaaaagcacagtgaaaacatttacacttgcttgagttatgttatttacctgaaattatggtataatcgttcagttagaaaataaattttgaatattatagaggaaatc actgtgcctatcttatcataagtcgcttgctttgaaaaggcttgacgtgaaaagaaaagcggagtgaaaacatttacacttgcttgagttatgttatttatttgaaattatggtataatcgttcagttagaaaataaattttgaatattatagaggaaatc Subject: NC_003028_SP_0680_SP_0681|ribosomal small subunit pseudouridine synthase A:elongation factor Tu family protein|NEGATIVE:POSITIVE|[653518,653678]|161 HSP 1 e-value: 6.0E-77 bit: 287.0 Len: 161 Query Start:1 Query End:161 Subject Strand: POSITIVE Subject Start: 1 Subject End: 161 actgtgcctatcttatcataagtcgcttgctttgaaaaggcttgacgtgaaaagaaaagcacagtgaaaacatttacacttgcttgagttatgttatttacctgaaattatggtataatcgttcagttagaaaataaattttgaatattatagaggaaatc actgtgcctatcttatcataagtcgctcgctttgaaaaggcttgacgtgaaaagaaaagcagagtgaaaacatttacacttgcttgagttatgttatttatttgaaattatggtataatcgttcagttagaaaataaattttgaatattatagaggaaatc Subject: NC_003098_spr0597_spr0598|Ribosomal small subunit pseudouridine synthase A:GTP-binding protein TypA/BipA (tyrosine phosphorylated protein A).|NEGATIVE:POSITIVE|[609593,609732]|140 HSP 1 e-value: 2.0E-64 bit: 246.0 Len: 140 Query Start:1 Query End:140 Subject Strand: POSITIVE Subject Start: 1 Subject End: 140 actgtgcctatcttatcataagtcgcttgctttgaaaaggcttgacgtgaaaagaaaagcacagtgaaaacatttacacttgcttgagttatgttatttacctgaaattatggtataatcgttcagttagaaaataaatt..................... actgtgcctatcttatcataagtcgcttgctttgaaaaggcttgacgtgaaaagaaaagcggagtgaaaacatttacacttgcttgagttatgttatttatttgaaattatggtataatcgttcagttagaaaataaatt..................... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUGUGCCUAUCUUAUCAUAAGUCGCUUGCUUUGAAAAGGCUUGACGUGAAAAGAAAAGCACAGUGAAAACAUUUACACUUGCUUGAGUUAUGUUAUUUACCUGAAAUUAUGGUAUAAUCGUUCAGUUAGAAAAUAAAUUUUGAAUAUUAUAGAGGAAAUC (((((((...((((.((((..((((...((((.....)))).)))))))).))))...)))))))...(((((....((((....)))).))))).....(((....(((((((((..(((.....(((.....)))....)))))))))))))))..... (-31.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUUUCCUCUAUAAUAUUCAAAAUUUAUUUUCUAACUGAACGAUUAUACCAUAAUUUCAGGUAAAUAACAUAACUCAAGCAAGUGUAAAUGUUUUCACUGUGCUUUUCUUUUCACGUCAAGCCUUUUCAAAGCAAGCGACUUAUGAUAAGAUAGGCACAGU ...................................((((..((((((...))))))))))......(((((.(((......)))....)))))...(((((((((.((((.(((.(((..(((((....)))...)))))...))).)))).))))))))) (-25.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 908 50 1 141 92 smit:SMT_428|5end_ribosomal_small_subunit_pseudouridine_synthase_A_369857..370087_NEGATIVE 299 49 5 60 6 smit:SMT_588|5end_hypothetical_protein_505477..505707_NEGATIVE 269 50 2 86 35 smit:SMT_1167|5end_aminopeptidase_N_1115076..1115306_NEGATIVE 268 47 3 230 194 smit:SMT_1570|5end_hypothetical_protein_1563504..1563734_NEGATIVE 266 67 22 96 45 smit:SMT_777|5end_hypothetical_protein_686770..687000_NEGATIVE 264 40 1 173 133 smit:SMT_1644|5end_3-isopropylmalate_dehydrogenase_1630704..1630934_POSITIVE 252 50 2 163 114 smit:SMT_1109|5end_hypothetical_protein_1050315..1050545_NEGATIVE 251 41 1 170 125 smit:SMT_2015|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1932655..1932885_POSITIVE 250 49 6 221 179 smit:SMT_1661|5end_K02986_small_subunit_ribosomal_protein_S4_1651110..1651340_NEGATIVE 238 43 9 74 43 smit:SMT_1890|5end_hypothetical_protein_1843407..1843637_POSITIVE 238 50 7 142 98 smit:SMT_1217|5end_hypothetical_protein_1176603..1176833_NEGATIVE 237 57 11 200 151 smit:SMT_1997|5end_K03294_basic_amino_acid/polyamine_antiporter,_APA_family_1921824..1922054_NEGATIVE 237 117 71 146 93 smit:SMT_320|5end_alcohol_dehydrogenase,_zinc-containing_259492..259722_NEGATIVE 232 123 83 128 83 smit:SMT_1073|5end_L-asparaginase_1011209..1011439_POSITIVE 231 60 11 205 147 smit:SMT_726|5end_ImpB/MucB/SamB_family_protein_631827..632057_NEGATIVE 229 47 2 196 153 smit:SMT_2022|5end_hypothetical_protein_1938257..1938487_POSITIVE 229 44 1 166 116 smit:SMT_1873|5end_K02006_cobalt_transport_system_ATP-binding_protein_1831936..1832166_POSITIVE 229 50 10 44 9 smit:SMT_369|5end_hypothetical_cytosolic_protein_304012..304242_POSITIVE 226 30 7 127 94 smit:SMT_266|5end_S-adenosyl-methyltransferase_204190..204420_POSITIVE 225 49 2 57 4 smit:SMT_1793|5end_inosine-5'-monophosphate_dehydrogenase_1767985..1768215_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 252 50 2 102 53 smit:SMT_1110|3end_hypothetical_protein_1050376..1050526_NEGATIVE 241 50 2 47 1 smit:SMT_1568|3end_putative_transketolase_C-terminal_section_1561134..1561284_POSITIVE 238 43 9 54 23 smit:SMT_1889|3end_hypothetical_protein_1843467..1843617_POSITIVE 238 50 7 57 13 smit:SMT_1218|3end_DNA_polymerase_I_1176688..1176838_NEGATIVE 229 52 11 46 2 smit:SMT_1148|3end_aspartyl-tRNA_synthetase_1092122..1092272_NEGATIVE 224 49 21 66 24 smit:SMT_834|3end_hypothetical_protein_775517..775667_NEGATIVE 224 49 21 65 23 smit:SMT_698|3end_uracil_permease_609769..609919_POSITIVE 224 66 36 44 13 smit:SMT_445|3end_hypothetical_protein_384949..385099_POSITIVE 223 49 2 132 71 smit:SMT_621|3end_K03346_replication_initiation_and_membrane_attachment_protein_529059..529209_POSITIVE 222 50 2 59 17 smit:SMT_2050|3end_K03712_MarR_family_transcriptional_regulator_1959539..1959689_NEGATIVE 220 47 4 72 45 smit:SMT_1784|3end_K06148_ATP-binding_cassette,_subfamily_C,_bacterial_1762364..1762514_POSITIVE 218 46 1 72 21 smit:SMT_2124|3end_hypothetical_protein_2008860..2009010_POSITIVE 218 50 1 66 21 smit:SMT_1794|3end_SOS_responce_UmuC_protein_1768442..1768592_NEGATIVE 218 46 1 72 21 smit:SMT_751|3end_hypothetical_protein_655339..655489_NEGATIVE 216 125 81 110 62 smit:SMT_1150|3end_hypothetical_protein_1094288..1094438_NEGATIVE 215 48 1 55 10 smit:SMT_1864|3end_integral_membrane_protein_1827172..1827322_POSITIVE 213 42 18 77 49 smit:SMT_1609|3end_hypothetical_protein_1598654..1598804_POSITIVE 213 85 46 79 31 smit:SMT_1275|3end_rod_shape-determining_protein_MreC_1239492..1239642_POSITIVE 213 49 21 67 34 smit:SMT_1216|3end_hypothetical_protein_1175969..1176119_POSITIVE 207 48 5 83 45 smit:SMT_589|3end_hypothetical_protein_506827..506977_POSITIVE