Origin IGS: gaagggcgggacggatgtctcgctttttttgtgtggagaagtgtaaaatagcatccatcaagtaacagcataatcgggatttggaaggatttttgaagggggactggaaaaga .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tcttttccagtcccccttcaaaaatccttccaaatcccgattatgctgttacttgatggatgctattttacacttctccacacaaaaaaagcgagacatccgtcccgcccttc Mask Tandem Repeat Region ================================================ gaagggcgggacggatgtctcgctttttttgtgtggagaagtgtaaaatagcatccatcaagtaacagcataatcgggatttggaaggatttttgaagggggactggaaaaga Find is-nt database================================================ Query_seq: SMT_510:SMT_511|SMT_510:SMT_511:hypothetical protein:hypothetical protein predicted by Glimmer/Critica:->->:439418..439530 113 gaagggcgggacggatgtctcgctttttttgtgtggagaagtgtaaaatagcatccatcaagtaacagcataatcgggatttggaaggatttttgaagggggactggaaaaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_510:SMT_511|SMT_510:SMT_511:hypothetical protein:hypothetical protein predicted by Glimmer/Critica:->->:439418..439530 113 gaagggcgggacggatgtctcgctttttttgtgtggagaagtgtaaaatagcatccatcaagtaacagcataatcgggatttggaaggatttttgaagggggactggaaaaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_510:SMT_511|SMT_510:SMT_511:hypothetical protein:hypothetical protein predicted by Glimmer/Critica:->->:439418..439530 113 gaagggcgggacggatgtctcgctttttttgtgtggagaagtgtaaaatagcatccatcaagtaacagcataatcgggatttggaaggatttttgaagggggactggaaaaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gaagggcgggacggatgtctcgctttttttgtgtggagaagtgtaaaatagcatccatcaagtaacagcataatcgggatttggaaggatttttgaagggggactggaaaaga Predict ORF larger than 30AA ================================================ gaagggcgggacggatgtctcgctttttttgtgtggagaagtgtaaaatagcatccatcaagtaacagcataatcgggatttggaaggatttttgaagggggactggaaaaga 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================================================ gaagggcgggacggatgtctcgctttttttgtgtggagaagtgtaaaatagcatccatcaagtaacagcataatcgggatttggaaggatttttgaagggggactggaaaaga Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_510:SMT_511|SMT_510:SMT_511:hypothetical protein:hypothetical protein predicted by Glimmer/Critica:->->:439418..439530 113 gaagggcgggacggatgtctcgctttttttgtgtggagaagtgtaaaatagcatccatcaagtaacagcataatcgggatttggaaggatttttgaagggggactggaaaaga Intra-Species Hit: Count: 4 Min: 1 Max: 113 Len: 113 Subject: smit_SMT_533_SMT_534|RNA binding protein:hypothetical protein predicted by Glimmer/Critica|POSITIVE:POSITIVE|[453598,453710]|113 HSP 1 e-value: 2.0E-45 bit: 182.0 Len: 113 Query Start:1 Query End:113 Subject Strand: POSITIVE Subject Start: 1 Subject End: 113 gaagggcgggacggatgtctcgcnnnnnnngtgtggagaagtgtaaaatagcatccatcaagtaacagcataatcgggatttggaaggatttttgaagggggactggaaaaga gaagggcgggacggatgtctcgctttttttgtgtggagaagtgtaaaatagcatccatcaagtaacagcataatcgggatttggaaggatttttgaagggggactggaaaaga Subject: smit_SMT_530_SMT_531|RNA binding protein:hypothetical protein predicted by Glimmer/Critica|POSITIVE:POSITIVE|[452699,452811]|113 HSP 1 e-value: 2.0E-45 bit: 182.0 Len: 113 Query Start:1 Query End:113 Subject Strand: POSITIVE Subject Start: 1 Subject End: 113 gaagggcgggacggatgtctcgcnnnnnnngtgtggagaagtgtaaaatagcatccatcaagtaacagcataatcgggatttggaaggatttttgaagggggactggaaaaga gaagggcgggacggatgtctcgctttttttgtgtggagaagtgtaaaatagcatccatcaagtaacagcataatcgggatttggaaggatttttgaagggggactggaaaaga Subject: smit_SMT_526_SMT_527|RNA binding protein:hypothetical protein predicted by Glimmer/Critica|POSITIVE:POSITIVE|[451529,451641]|113 HSP 1 e-value: 2.0E-45 bit: 182.0 Len: 113 Query Start:1 Query End:113 Subject Strand: POSITIVE Subject Start: 1 Subject End: 113 gaagggcgggacggatgtctcgcnnnnnnngtgtggagaagtgtaaaatagcatccatcaagtaacagcataatcgggatttggaaggatttttgaagggggactggaaaaga gaagggcgggacggatgtctcgctttttttgtgtggagaagtgtaaaatagcatccatcaagtaacagcataatcgggatttggaaggatttttgaagggggactggaaaaga Subject: smit_SMT_510_SMT_511|hypothetical protein:hypothetical protein predicted by Glimmer/Critica|POSITIVE:POSITIVE|[439418,439530]|113 HSP 1 e-value: 2.0E-45 bit: 182.0 Len: 113 Query Start:1 Query End:113 Subject Strand: POSITIVE Subject Start: 1 Subject End: 113 gaagggcgggacggatgtctcgcnnnnnnngtgtggagaagtgtaaaatagcatccatcaagtaacagcataatcgggatttggaaggatttttgaagggggactggaaaaga gaagggcgggacggatgtctcgctttttttgtgtggagaagtgtaaaatagcatccatcaagtaacagcataatcgggatttggaaggatttttgaagggggactggaaaaga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAGGGCGGGACGGAUGUCUCGCUUUUUUUGUGUGGAGAAGUGUAAAAUAGCAUCCAUCAAGUAACAGCAUAAUCGGGAUUUGGAAGGAUUUUUGAAGGGGGACUGGAAAAGA ((((((((((((....))))))))))))....(((((...((........)).)))))(((((..(.........)..)))))......(((((...((....))...))))) (-25.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUUUUCCAGUCCCCCUUCAAAAAUCCUUCCAAAUCCCGAUUAUGCUGUUACUUGAUGGAUGCUAUUUUACACUUCUCCACACAAAAAAAGCGAGACAUCCGUCCCGCCCUUC .......((((......((...................))....))))......((((((((((.((((.................))))...)).))))))))......... (-10.94) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 787 110 67 130 87 smit:SMT_477|5end_K03308_neurotransmitter:Na+_symporter,_NSS_family_414651..414881_NEGATIVE 327 87 43 67 25 smit:SMT_2128|5end_cell_division_protein_FtsA_2009617..2009847_POSITIVE 292 42 8 214 177 smit:SMT_1161|5end_K05837_rod_shape_determining_protein_RodA_1106408..1106638_NEGATIVE 287 39 3 227 190 smit:SMT_853|5end_ATP-dependent_endopeptidase_clp_ATP-binding_subunit_ClpX_799285..799515_NEGATIVE 285 108 68 219 176 smit:SMT_1617|5end_K02015_iron_complex_transport_system_permease_protein_1604500..1604730_NEGATIVE 273 48 3 95 47 smit:SMT_1216|5end_hypothetical_protein_1174879..1175109_POSITIVE 269 37 1 99 57 smit:SMT_2033|5end_hydrolase,_haloacid_dehalogenase-like_family_1946492..1946722_POSITIVE 263 107 66 202 163 smit:SMT_1990|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1917565..1917795_POSITIVE 262 52 12 160 119 smit:SMT_1354|5end_diacylglycerol_kinase_1332001..1332231_NEGATIVE 260 32 2 208 175 smit:SMT_534|5end_hypothetical_protein_predicted_by_Glimmer/Critica_453571..453801_POSITIVE 260 32 2 208 175 smit:SMT_531|5end_hypothetical_protein_predicted_by_Glimmer/Critica_452672..452902_POSITIVE 260 32 2 208 175 smit:SMT_527|5end_hypothetical_protein_predicted_by_Glimmer/Critica_451502..451732_POSITIVE 260 100 55 75 33 smit:SMT_519|5end_glutathione_reductase_444884..445114_NEGATIVE 258 67 22 74 30 smit:SMT_1745|5end_UDP-glucose_4-epimerase_1725541..1725771_NEGATIVE 254 38 4 160 117 smit:SMT_1538|5end_two-component_response_regulator_YvqC_1523301..1523531_NEGATIVE 253 79 34 42 3 smit:SMT_2083|5end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_1982411..1982641_POSITIVE 252 43 5 56 10 smit:SMT_1678|5end_inorganic_pyrophosphatase_1662126..1662356_POSITIVE 251 110 66 207 162 smit:SMT_2051|5end_enoyl-CoA_hydratase_1960639..1960869_NEGATIVE 248 107 67 182 136 smit:SMT_413|5end_tRNA_delta(2)-isopentenylpyrophosphate_transferase_356677..356907_POSITIVE 247 39 3 69 29 smit:SMT_153|5end_sensor_histidine_kinase,_putative_101443..101673_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 302 84 41 46 3 smit:SMT_1071|3end_hypothetical_protein_1010386..1010536_POSITIVE 268 43 8 138 94 smit:SMT_1157|3end_septation_ring_formation_regulator_EzrA_1100202..1100352_NEGATIVE 261 40 1 58 18 smit:SMT_2016|3end_tyrosine_recombinase_1933021..1933171_NEGATIVE 261 40 1 68 28 smit:SMT_2001|3end_membrane_protease_protein_family_1923889..1924039_POSITIVE 261 40 1 68 28 smit:SMT_1985|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1914407..1914557_NEGATIVE 261 40 1 58 18 smit:SMT_1957|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1890829..1890979_POSITIVE 261 40 1 58 18 smit:SMT_1886|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1841198..1841348_POSITIVE 261 110 62 75 27 smit:SMT_1815|3end_K02035_peptide/nickel_transport_system_substrate-binding_protein_1788899..1789049_NEGATIVE 261 40 1 58 18 smit:SMT_1658|3end_hypothetical_protein_1648937..1649087_POSITIVE 261 40 1 58 18 smit:SMT_1558|3end_hypothetical_protein_1543855..1544005_NEGATIVE 261 40 1 58 18 smit:SMT_1155|3end_ABC-type_oligopeptide_transport_system,_periplasmic_component_1099183..1099333_NEGATIVE 260 32 2 94 61 smit:SMT_533|3end_RNA_binding_protein_453537..453687_POSITIVE 260 32 2 94 61 smit:SMT_530|3end_RNA_binding_protein_452638..452788_POSITIVE 260 32 2 94 61 smit:SMT_526|3end_RNA_binding_protein_451468..451618_POSITIVE 260 100 55 78 36 smit:SMT_520|3end_glutathione_reductase_444881..445031_NEGATIVE 260 32 2 94 61 smit:SMT_510|3end_hypothetical_protein_439357..439507_POSITIVE 254 40 1 58 18 smit:SMT_2006|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1926803..1926953_POSITIVE 254 38 4 146 103 smit:SMT_1539|3end_sensor_histidine_kinase,_putative_1523315..1523465_NEGATIVE 249 45 5 115 68 smit:SMT_2005|3end_pullulanase,_type_I_1925615..1925765_NEGATIVE 243 37 3 77 47 smit:SMT_2039|3end_malolactic_enzyme_1949681..1949831_NEGATIVE