Origin IGS: attgacaaattttctcaatttgctacaataataaaagcaatagaaatgatggtcaaagctcatggatgttgcaggcttttttgtcctgcacttctttggagttttgactgtttttgtgtcgtttaagggaaaggaaaaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tttttcctttcccttaaacgacacaaaaacagtcaaaactccaaagaagtgcaggacaaaaaagcctgcaacatccatgagctttgaccatcatttctattgcttttattattgtagcaaattgagaaaatttgtcaat Mask Tandem Repeat Region ================================================ attgacaaattttctcaatttgctacaataataaaagcaatagaaatgatggtcaaagctcatggatgttgcaggcttttttgtcctgcacttctttggagttttgactgtttttgtgtcgtttaagggaaaggaaaaa Find is-nt database================================================ Query_seq: SMT_138:SMT_139|SMT_138:SMT_139:tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase:hypothetical protein:->->:90524..90662 139 attgacaaattttctcaatttgctacaataataaaagcaatagaaatgatggtcaaagctcatggatgttgcaggcttttttgtcctgcacttctttggagttttgactgtttttgtgtcgtttaagggaaaggaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_138:SMT_139|SMT_138:SMT_139:tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase:hypothetical protein:->->:90524..90662 139 attgacaaattttctcaatttgctacaataataaaagcaatagaaatgatggtcaaagctcatggatgttgcaggcttttttgtcctgcacttctttggagttttgactgtttttgtgtcgtttaagggaaaggaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_138:SMT_139|SMT_138:SMT_139:tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase:hypothetical protein:->->:90524..90662 139 attgacaaattttctcaatttgctacaataataaaagcaatagaaatgatggtcaaagctcatggatgttgcaggcttttttgtcctgcacttctttggagttttgactgtttttgtgtcgtttaagggaaaggaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 attgacaaattttctcaatttgctacaataataaaagcaatagaaatgatggtcaaagctcatggatgttgcaggcttttttgtcctgcacttctttggagttttgactgtttttgtgtcgtttaagggaaaggaaaaa Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 9 End: 104 ........ M F S I C Y N N K S N R N D G Q S S W M L Q A F L S C T S L E F ................................... Protein_Len: 41 Strand: + Start: 1 End: 123 M D K F S Q F A T I I K A I E M M V K A H G C C R L F C P A L L W S F D C F C V V ................ attgacaaattttctcaatttgctacaataataaaagcaatagaaatgatggtcaaagctcatggatgttgcaggcttttttgtcctgcacttctttggagttttgactgtttttgtgtcgtttaagggaaaggaaaaa 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: 88 Start: 28 End: 57 ...........................TTTGACCATCATTTCTATTGCTTTTATTAT.................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ attgacaaattttctcaatttgctacaataataaaagcaatagaaatgatggtcaaagctcatggatgttgcaggcttttttgtcctgcacttctttggagttttgactgtttttgtgtcgtttaagggaaaggaaaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_138:SMT_139|SMT_138:SMT_139:tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase:hypothetical protein:->->:90524..90662 139 attgacaaattttctcaatttgctacaataataaaagcaatagaaatgatggtcaaagctcatggatgttgcaggcttttttgtcctgcacttctttggagttttgactgtttttgtgtcgtttaagggaaaggaaaaa Intra-Species Hit: Count: 1 Min: 1 Max: 139 Len: 139 Subject: smit_SMT_138_SMT_139|tRNA (5-methylaminomethyl-2-thiouridylate)- methyltransferase:hypothetical protein|POSITIVE:POSITIVE|[90524,90662]|139 HSP 1 e-value: 2.0E-73 bit: 276.0 Len: 139 Query Start:1 Query End:139 Subject Strand: POSITIVE Subject Start: 1 Subject End: 139 attgacaaattttctcaatttgctacaataataaaagcaatagaaatgatggtcaaagctcatggatgttgcaggcttttttgtcctgcacttctttggagttttgactgtttttgtgtcgtttaagggaaaggaaaaa attgacaaattttctcaatttgctacaataataaaagcaatagaaatgatggtcaaagctcatggatgttgcaggcttttttgtcctgcacttctttggagttttgactgtttttgtgtcgtttaagggaaaggaaaaa Inter-species Hit: Count: 3 Min: 1 Max: 135 Len: 135 Subject: NC_008533_SPD_0127_SPD_0128|tRNA (5-methylaminomethyl-2-thiouridylate)- methyltransferase:MutT/nudix family protein|POSITIVE:POSITIVE|[131738,131877]|140 HSP 1 e-value: 3.0E-66 bit: 252.0 Len: 135 Query Start:1 Query End:135 Subject Strand: POSITIVE Subject Start: 1 Subject End: 135 attgacaaattttctcaatttgctacaataataaaagcaatagaaatgatggtcaaagctcatggatgttgcaggcttttttgtcctgcacttctttggagttttgactgtttttgtgtcgtttaagggaaagga.... attgacaaattttctcaatttgctacaataataacagcaatagaaatgatggtcaaagctcatggatgttgcaggcttttttgtcctgcacttctttgtagttttgactgtttttgtgtcgtttaagggaaagga.... Subject: NC_003028_SP_0118_SP_0119|tRNA (5-methylaminomethyl-2-thiouridylate)- methyltransferase:MutT/nudix family protein|POSITIVE:POSITIVE|[122180,122319]|140 HSP 1 e-value: 3.0E-66 bit: 252.0 Len: 135 Query Start:1 Query End:135 Subject Strand: POSITIVE Subject Start: 1 Subject End: 135 attgacaaattttctcaatttgctacaataataaaagcaatagaaatgatggtcaaagctcatggatgttgcaggcttttttgtcctgcacttctttggagttttgactgtttttgtgtcgtttaagggaaagga.... attgacaaattttctcaatttgctacaataataacagcaatagaaatgatggtcaaagctcatggatgttgcaggcttttttgtcctgcacttctttgtagttttgactgtttttgtgtcgtttaagggaaagga.... Subject: NC_003098_spr0122_spr0123|tRNA (5-methylaminomethyl-2-thiouridylate)- methyltransferase:hypothetical protein|POSITIVE:POSITIVE|[131738,131850]|113 HSP 1 e-value: 4.0E-53 bit: 208.0 Len: 113 Query Start:1 Query End:113 Subject Strand: POSITIVE Subject Start: 1 Subject End: 113 attgacaaattttctcaatttgctacaataataaaagcaatagaaatgatggtcaaagctcatggatgttgcaggcttttttgtcctgcacttctttggagttttgactgttt.......................... attgacaaattttctcaatttgctacaataataacagcaatagaaatgatggtcaaagctcatggatgttgcaggcttttttgtcctgcacttctttgtagttttgactgttt.......................... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUGACAAAUUUUCUCAAUUUGCUACAAUAAUAAAAGCAAUAGAAAUGAUGGUCAAAGCUCAUGGAUGUUGCAGGCUUUUUUGUCCUGCACUUCUUUGGAGUUUUGACUGUUUUUGUGUCGUUUAAGGGAAAGGA .........(((((((...(((((...........)))))...((((((((((((((((((..(((.((.((((((......).))))))).)))...)))))))))))........)))))))..))))))).. (-40.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCCUUUCCCUUAAACGACACAAAAACAGUCAAAACUCCAAAGAAGUGCAGGACAAAAAAGCCUGCAACAUCCAUGAGCUUUGACCAUCAUUUCUAUUGCUUUUAUUAUUGUAGCAAAUUGAGAAAAUUUGUCAAU ...............((((........((((((.(((........((((((.(......)))))))........))).)))))).....(((((.(((((...........)))))....)))))...))))... (-29.29) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 360 120 71 119 63 smit:SMT_1694|5end_GTPase_1676674..1676904_POSITIVE 344 120 74 109 60 smit:SMT_2034|5end_hydrolase,_haloacid_dehalogenase-like_family_1946671..1946901_POSITIVE 316 101 64 39 2 smit:SMT_653|5end_positive_transcriptional_regulator_MutR_family_564155..564385_NEGATIVE 313 118 71 168 126 smit:SMT_1711|5end_Xaa-Pro_dipeptidase_1697494..1697724_NEGATIVE 306 118 72 211 160 smit:SMT_160|5end_folylpolyglutamate_synthase_104741..104971_POSITIVE 301 99 51 224 171 smit:SMT_640|5end_PTS_system,_lactose-specific_IIBC_component_546790..547020_NEGATIVE 284 94 55 149 101 smit:SMT_1911|5end_hypothetical_protein_1857614..1857844_POSITIVE 283 88 42 107 64 smit:SMT_155|5end_hypothetical_protein_102704..102934_NEGATIVE 280 97 51 218 168 smit:SMT_2143|5end_threonyl-tRNA_synthetase_2020255..2020485_POSITIVE 278 120 71 75 9 smit:SMT_1066|5end_holo-(acyl_carrier_protein)_synthase_1005411..1005641_POSITIVE 276 100 53 59 7 smit:SMT_1824|5end_hypothetical_protein_1796126..1796356_POSITIVE 274 78 34 223 167 smit:SMT_2122|5end_cell_surface_protein_precursor_2008116..2008346_NEGATIVE 274 76 37 87 48 smit:SMT_1759|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1735773..1736003_NEGATIVE 273 120 72 58 11 smit:SMT_2164|5end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_2037861..2038091_POSITIVE 272 119 71 204 163 smit:SMT_1418|5end_lysine_decarboxylase_1403147..1403377_NEGATIVE 272 117 74 169 127 smit:SMT_896|5end_hypothetical_protein_844003..844233_NEGATIVE 271 75 38 86 56 smit:SMT_1210|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1171051..1171281_NEGATIVE 271 75 38 165 135 smit:SMT_1209|5end_choline_binding_protein_PcpA_1170972..1171202_NEGATIVE 270 97 52 100 49 smit:SMT_2114|5end_x-prolyl-dipeptidyl_aminopeptidase_2001484..2001714_POSITIVE 270 110 62 62 14 smit:SMT_306|5end_3-oxoacyl-_248882..249112_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 360 120 71 117 61 smit:SMT_1693|3end_dimethyladenosine_transferase_1676752..1676902_POSITIVE 344 120 74 97 48 smit:SMT_2033|3end_hydrolase,_haloacid_dehalogenase-like_family_1946739..1946889_POSITIVE 289 101 64 37 1 smit:SMT_654|3end_K06158_ATP-binding_cassette,_sub-family_F,_member_3_564157..564307_NEGATIVE 284 94 55 109 61 smit:SMT_1910|3end_pyruvate-formate_lyase_activating_enzyme_1857654..1857804_POSITIVE 280 97 51 135 85 smit:SMT_2142|3end_hypothetical_protein_predicted_by_Glimmer/Critica_2020252..2020402_POSITIVE 274 76 37 117 78 smit:SMT_1760|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1735743..1735893_NEGATIVE 272 107 62 70 6 smit:SMT_1078|3end_folylpolyglutamate_synthase_1015391..1015541_NEGATIVE 267 110 67 143 89 smit:SMT_1544|3end_mevalonate_kinase_1528006..1528156_NEGATIVE 266 89 49 145 106 smit:SMT_629|3end_glycogen_synthase_535480..535630_POSITIVE 262 117 74 75 24 smit:SMT_1263|3end_hypothetical_protein_1228927..1229077_POSITIVE 258 98 51 49 6 smit:SMT_2149|3end_UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-_diaminopimelate--D-alanyl-D-alanine_ligase_2024734..2024884_POSITIVE 258 118 71 88 46 smit:SMT_1278|3end_30S_ribosomal_protein_S2_1242332..1242482_POSITIVE 257 101 61 112 62 smit:SMT_1934|3end_homoserine_dehydrogenase_1873150..1873300_POSITIVE 257 90 50 63 18 smit:SMT_1174|3end_acylneuraminate_cytidylyltransferase_1125617..1125767_NEGATIVE 256 105 63 54 15 smit:SMT_1920|3end_ABC_transporter,_ATP-binding_protein_1862736..1862886_NEGATIVE 254 100 57 122 73 smit:SMT_1618|3end_K02015_iron_complex_transport_system_permease_protein_1604490..1604640_NEGATIVE 252 85 42 65 7 smit:SMT_1807|3end_putative_mucus_binding_protein_1781740..1781890_NEGATIVE 249 116 74 67 18 smit:SMT_1946|3end_sucrose-6-phosphate_hydrolase_1881205..1881355_POSITIVE 249 68 21 87 43 smit:SMT_486|3end_hypothetical_protein_421460..421610_NEGATIVE 248 89 49 76 42 smit:SMT_1523|3end_ferrochelatase_1503390..1503540_NEGATIVE