Origin IGS: tttttacctccgaagctgggaaaaacagtcccagttcatactttgtgcccaagggcatactgtatgattttatcaaaaaaagctggaactgtcacgaactatggtgtataatgagaga .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tctctcattatacaccatagttcgtgacagttccagctttttttgataaaatcatacagtatgcccttgggcacaaagtatgaactgggactgtttttcccagcttcggaggtaaaaa Mask Tandem Repeat Region ================================================ tttttacctccgaagctgggaaaaacagtcccagttcatactttgtgcccaagggcatactgtatgattttatcaaaaaaagctggaactgtcacgaactatggtgtataatgagaga Find is-nt database================================================ Query_seq: SMT_1122:SMT_1123|SMT_1122:SMT_1123:queuine tRNA-ribosyltransferase:hypothetical protein:<-->:1059314..1059431 118 tttttacctccgaagctgggaaaaacagtcccagttcatactttgtgcccaagggcatactgtatgattttatcaaaaaaagctggaactgtcacgaactatggtgtataatgagaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1122:SMT_1123|SMT_1122:SMT_1123:queuine tRNA-ribosyltransferase:hypothetical protein:<-->:1059314..1059431 118 tttttacctccgaagctgggaaaaacagtcccagttcatactttgtgcccaagggcatactgtatgattttatcaaaaaaagctggaactgtcacgaactatggtgtataatgagaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1122:SMT_1123|SMT_1122:SMT_1123:queuine tRNA-ribosyltransferase:hypothetical protein:<-->:1059314..1059431 118 tttttacctccgaagctgggaaaaacagtcccagttcatactttgtgcccaagggcatactgtatgattttatcaaaaaaagctggaactgtcacgaactatggtgtataatgagaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttttacctccgaagctgggaaaaacagtcccagttcatactttgtgcccaagggcatactgtatgattttatcaaaaaaagctggaactgtcacgaactatggtgtataatgagaga Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 16 End: 108 ............... M G K T V P V H T L C P R A Y C M I L S K K A G T V T N Y G V .......... tttttacctccgaagctgggaaaaacagtcccagttcatactttgtgcccaagggcatactgtatgattttatcaaaaaaagctggaactgtcacgaactatggtgtataatgagaga 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: 85 Start: 67 End: 96 ..................................................................CGTGACAGTTCCAGCTTTTTTTGATAAAAT...................... PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 83 End: 112 ..................................................................................CTGGAACTGTCACGAACTATGGTGTATAAT...... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tttttacctccgaagctgggaaaaacagtcccagttcatactttgtgcccaagggcatactgtatgattttatcaaaaaaagctggaactgtcacgaactatggtgtataatgagaga Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 76 HP_score: -6.6 Tail_Score: -4.36914 Start: 36 End: 67 Full_Region: AAAAACAGTCCCAGT TCATACTTTGTGCC CAAG GGCATACTGTATGA TTTTATCAAAAAAAG ...................................TCATACTTTGTGCCCAAGGGCATACTGTATGA................................................... Find igs database================================================ Query_seq: SMT_1122:SMT_1123|SMT_1122:SMT_1123:queuine tRNA-ribosyltransferase:hypothetical protein:<-->:1059314..1059431 118 tttttacctccgaagctgggaaaaacagtcccagttcatactttgtgcccaagggcatactgtatgattttatcaaaaaaagctggaactgtcacgaactatggtgtataatgagaga Intra-Species Hit: Count: 1 Min: 1 Max: 118 Len: 118 Subject: smit_SMT_1122_SMT_1123|queuine tRNA-ribosyltransferase:hypothetical protein|NEGATIVE:POSITIVE|[1059314,1059431]|118 HSP 1 e-value: 2.0E-48 bit: 192.0 Len: 118 Query Start:1 Query End:118 Subject Strand: POSITIVE Subject Start: 1 Subject End: 118 tttttacctccgaagctgggaaaaacagtcccagttcatactttgtgcccaagggcatactgtatgattttatcnnnnnnngctggaactgtcacgaactatggtgtataatgagaga tttttacctccgaagctgggaaaaacagtcccagttcatactttgtgcccaagggcatactgtatgattttatcaaaaaaagctggaactgtcacgaactatggtgtataatgagaga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUUACCUCCGAAGCUGGGAAAAACAGUCCCAGUUCAUACUUUGUGCCCAAGGGCAUACUGUAUGAUUUUAUCAAAAAAAGCUGGAACUGUCACGAACUAUGGUGUAUAAUGAGAGA ........((((..(((((((.......)))))))((((((..((((((....))))))..))))))................)))).((.(((...((......))....))).)). (-32.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUCUCAUUAUACACCAUAGUUCGUGACAGUUCCAGCUUUUUUUGAUAAAAUCAUACAGUAUGCCCUUGGGCACAAAGUAUGAACUGGGACUGUUUUUCCCAGCUUCGGAGGUAAAAA ..........(((.((..((((.(.(((((((((((..(((......))).((((((..(.((((....)))).)..)))))).)))))))))))....).))))..))..))).... (-32.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 977 60 11 151 102 smit:SMT_1122|5end_queuine_tRNA-ribosyltransferase_1059223..1059453_NEGATIVE 378 57 11 80 24 smit:SMT_929|5end_hypothetical_protein_883342..883572_NEGATIVE 378 57 11 204 148 smit:SMT_928|5end_hypothetical_protein_883218..883448_NEGATIVE 289 47 7 70 31 smit:SMT_265|5end_DNA-binding_protein_204073..204303_NEGATIVE 284 54 11 75 40 smit:SMT_935|5end_UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-_diaminopimelate_ligase_887326..887556_POSITIVE 268 100 53 127 78 smit:SMT_1067|5end_alanine_racemase_1005769..1005999_POSITIVE 268 59 11 78 31 smit:SMT_382|5end_valyl-tRNA_synthetase_317706..317936_POSITIVE 257 110 67 160 121 smit:SMT_1672|5end_hypothetical_protein_1660051..1660281_NEGATIVE 256 88 41 66 16 smit:SMT_1169|5end_phosphorylase,_Pnp/UDP_family_1117350..1117580_NEGATIVE 254 77 31 226 181 smit:SMT_455|5end_cation_transport_ATPase_391670..391900_POSITIVE 253 55 15 62 27 smit:SMT_1638|5end_UTP-glucose-1-phosphate_uridylyltransferase_1624781..1625011_NEGATIVE 253 54 12 111 75 smit:SMT_1107|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1048081..1048311_NEGATIVE 253 54 12 220 184 smit:SMT_1106|5end_ribonuclease_P_protein_component_1047972..1048202_NEGATIVE 250 67 25 208 158 smit:SMT_1351|5end_dephospho-CoA_kinase_1329817..1330047_NEGATIVE 248 41 9 48 21 smit:SMT_2014|5end_tryptophan_synthase_beta_chain_1932471..1932701_POSITIVE 247 50 5 177 139 smit:SMT_1489|5end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_1468892..1469122_POSITIVE 246 63 33 39 8 smit:SMT_944|5end_PhnA_protein_895106..895336_NEGATIVE 246 53 11 166 120 smit:SMT_177|5end_K02878_large_subunit_ribosomal_protein_L16_118738..118968_POSITIVE 243 56 15 225 181 smit:SMT_1375|5end_putative_glucose-inhibited_division_protein_1354438..1354668_NEGATIVE 242 43 7 228 187 smit:SMT_948|5end_hypothetical_protein_predicted_by_Glimmer/Critica_896756..896986_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 330 57 12 84 33 smit:SMT_1774|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1750151..1750301_NEGATIVE 268 100 53 137 88 smit:SMT_1066|3end_holo-(acyl_carrier_protein)_synthase_1005859..1006009_POSITIVE 262 76 31 131 76 smit:SMT_1264|3end_oligoendopeptidase_F_1230734..1230884_POSITIVE 258 49 6 63 1 smit:SMT_1977|3end_endopeptidase_O_1908454..1908604_POSITIVE 253 55 15 40 5 smit:SMT_1639|3end_glycerol-3-phosphate_dehydrogenase_(NAD(P)+)_1624803..1624953_NEGATIVE 253 54 12 70 34 smit:SMT_1108|3end_acetate_kinase_1048122..1048272_NEGATIVE 242 64 31 148 114 smit:SMT_2011|3end_lysyl-tRNA_synthetase_1929759..1929909_NEGATIVE 242 68 26 122 82 smit:SMT_445|3end_hypothetical_protein_384949..385099_POSITIVE 239 61 25 146 98 smit:SMT_454|3end_hypothetical_protein_391740..391890_POSITIVE 238 56 11 106 57 smit:SMT_1273|3end_K02006_cobalt_transport_system_ATP-binding_protein_1237828..1237978_POSITIVE 237 56 15 57 14 smit:SMT_617|3end_hypothetical_protein_526761..526911_POSITIVE 236 57 13 55 11 smit:SMT_1477|3end_K02077_zinc/manganese_transport_system_substrate-binding_protein_1459447..1459597_NEGATIVE 236 57 13 54 10 smit:SMT_1140|3end_glycogen_phosphorylase_1081316..1081466_NEGATIVE 235 54 13 53 11 smit:SMT_834|3end_hypothetical_protein_775517..775667_NEGATIVE 235 54 13 52 10 smit:SMT_698|3end_uracil_permease_609769..609919_POSITIVE 234 51 15 151 111 smit:SMT_2040|3end_transcription-repair_coupling_factor_1950463..1950613_NEGATIVE 233 40 15 71 52 smit:SMT_1330|3end_hypothetical_protein_1305852..1306002_NEGATIVE 231 55 14 148 93 smit:SMT_1844|3end_hypothetical_protein_1809644..1809794_POSITIVE 231 55 14 148 93 smit:SMT_113|3end_hypothetical_protein_62785..62935_POSITIVE 230 65 26 125 92 smit:SMT_1894|3end_K02025_multiple_sugar_transport_system_permease_protein_1847187..1847337_POSITIVE