Origin IGS: ttaattaannnnngcgaaagctgatgcgaaagcaaaagccgacgcagcgaaaccagcgattgacaacgcgacaccaaatgatgcagtagaaaaagctaaaaatgatggagcaacatcggtagattcg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 cgaatctaccgatgttgctccatcatttttagctttttctactgcatcatttggtgtcgcgttgtcaatcgctggtttcgctgcgtcggcttttgctttcgcatcagctttcgcnnnnnttaattaa Mask Tandem Repeat Region ================================================ ttaattaannnnngcgaaagctgatgcgaaagcaaaagccgacgcagcgaaaccagcgattgacaacgcgacaccaaatgatgcagtagaaaaagctaaaaatgatggagcaacatcggtagattcg Find is-nt database================================================ Query_seq: SMT_1938:SMT_1939|SMT_1938:SMT_1939:zinc metalloprotease ZmpB, putative:hypothetical protein predicted by Glimmer/Critica:->->:1876291..1876417 127 ttaattaannnnngcgaaagctgatgcgaaagcaaaagccgacgcagcgaaaccagcgattgacaacgcgacaccaaatgatgcagtagaaaaagctaaaaatgatggagcaacatcggtagattcg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1938:SMT_1939|SMT_1938:SMT_1939:zinc metalloprotease ZmpB, putative:hypothetical protein predicted by Glimmer/Critica:->->:1876291..1876417 127 ttaattaannnnngcgaaagctgatgcgaaagcaaaagccgacgcagcgaaaccagcgattgacaacgcgacaccaaatgatgcagtagaaaaagctaaaaatgatggagcaacatcggtagattcg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1938:SMT_1939|SMT_1938:SMT_1939:zinc metalloprotease ZmpB, putative:hypothetical protein predicted by Glimmer/Critica:->->:1876291..1876417 127 ttaattaannnnngcgaaagctgatgcgaaagcaaaagccgacgcagcgaaaccagcgattgacaacgcgacaccaaatgatgcagtagaaaaagctaaaaatgatggagcaacatcggtagattcg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttaattaannnnngcgaaagctgatgcgaaagcaaaagccgacgcagcgaaaccagcgattgacaacgcgacaccaaatgatgcagtagaaaaagctaaaaatgatggagcaacatcggtagattcg Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: - Start: 8 End: 124 ....... X X R F S I R F C F G V C R F W R N V V R C W I I C Y F F S F I I S C C R Y M ... ttaattaannnnngcgaaagctgatgcgaaagcaaaagccgacgcagcgaaaccagcgattgacaacgcgacaccaaatgatgcagtagaaaaagctaaaaatgatggagcaacatcggtagattcg 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================================================ ttaattaannnnngcgaaagctgatgcgaaagcaaaagccgacgcagcgaaaccagcgattgacaacgcgacaccaaatgatgcagtagaaaaagctaaaaatgatggagcaacatcggtagattcg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1938:SMT_1939|SMT_1938:SMT_1939:zinc metalloprotease ZmpB, putative:hypothetical protein predicted by Glimmer/Critica:->->:1876291..1876417 127 ttaattaannnnngcgaaagctgatgcgaaagcaaaagccgacgcagcgaaaccagcgattgacaacgcgacaccaaatgatgcagtagaaaaagctaaaaatgatggagcaacatcggtagattcg Intra-Species Hit: Count: 1 Min: 14 Max: 127 Len: 114 Subject: smit_SMT_1938_SMT_1939|zinc metalloprotease ZmpB, putative:hypothetical protein predicted by Glimmer/Critica|POSITIVE:POSITIVE|[1876291,1876417]|127 HSP 1 e-value: 1.0E-58 bit: 226.0 Len: 114 Query Start:14 Query End:127 Subject Strand: POSITIVE Subject Start: 14 Subject End: 127 .............gcgaaagctgatgcgaaagcaaaagccgacgcagcgaaaccagcgattgacaacgcgacaccaaatgatgcagtagaaaaagctaaaaatgatggagcaacatcggtagattcg .............gcgaaagctgatgcgaaagcaaaagccgacgcagcgaaaccagcgattgacaacgcgacaccaaatgatgcagtagaaaaagctaaaaatgatggagcaacatcggtagattcg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCGAAAGCUGAUGCGAAAGCAAAAGCCGACGCAGCGAAACCAGCGAUUGACAACGCGACACCAAAUGAUGCAGUAGAAAAAGCUAAAAAUGAUGGAGCAACAUCGGUAGAUUCG (((...(((..(((....)))..)))...)))..((((....(((........)))..........................(((....(((((......))))).))).)))) (-25.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGAAUCUACCGAUGUUGCUCCAUCAUUUUUAGCUUUUUCUACUGCAUCAUUUGGUGUCGCGUUGUCAAUCGCUGGUUUCGCUGCGUCGGCUUUUGCUUUCGCAUCAGCUUUCGC ((((.(((.((((..(((..(((((......((..........))......)))))..)))......)))).))).))))..(((..((((..(((....)))..))))..))) (-28.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 360 46 6 200 159 smit:SMT_1982|5end_conserved_hypothetical_protein_1913036..1913266_POSITIVE 360 46 6 188 147 smit:SMT_1691|5end_putative_deoxyribonuclease_1674978..1675208_POSITIVE 360 46 6 213 172 smit:SMT_1156|5end_K07485_transposase_1099938..1100168_POSITIVE 352 63 23 90 42 smit:SMT_927|5end_KH_domain_protein_882677..882907_NEGATIVE 324 72 31 65 24 smit:SMT_147|5end_K02027_multiple_sugar_transport_system_substrate-binding_protein_97406..97636_POSITIVE 324 72 31 65 24 smit:SMT_119|5end_K02027_multiple_sugar_transport_system_substrate-binding_protein_70457..70687_POSITIVE 322 70 21 209 152 smit:SMT_414|5end_K03665_GTP-binding_protein_HflX_357554..357784_POSITIVE 320 65 26 139 94 smit:SMT_2074|5end_dTDP-glucose_4,6-dehydratase_1977021..1977251_POSITIVE 303 79 31 72 9 smit:SMT_980|5end_hypothetical_protein_927440..927670_POSITIVE 297 45 5 191 148 smit:SMT_1887|5end_LicC_protein_1841445..1841675_POSITIVE 297 59 17 185 136 smit:SMT_169|5end_30S_ribosomal_protein_S10_114515..114745_POSITIVE 296 60 11 178 125 smit:SMT_596|5end_K03976_putative_transcription_regulator_513075..513305_NEGATIVE 296 45 2 53 10 smit:SMT_555|5end_K09015_Fe-S_cluster_assembly_protein_SufD_472271..472501_POSITIVE 294 48 1 175 115 smit:SMT_1647|5end_3-isopropylmalate_dehydratase_small_subunit_1633403..1633633_POSITIVE 291 50 2 96 34 smit:SMT_1923|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1866021..1866251_POSITIVE 291 63 25 96 51 smit:SMT_1872|5end_K03217_preprotein_translocase_YidC_subunit_1831764..1831994_NEGATIVE 290 70 21 46 1 smit:SMT_1999|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1922792..1923022_NEGATIVE 290 70 21 46 1 smit:SMT_1665|5end_cell_wall_surface_anchor_family_protein_1656335..1656565_NEGATIVE 289 77 31 68 24 smit:SMT_412|5end_hypothetical_protein_predicted_by_Glimmer/Critica_356606..356836_NEGATIVE 286 63 22 129 82 smit:SMT_1685|5end_phenylalanyl-tRNA_synthetase_alpha_chain_1668845..1669075_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 468 86 43 48 5 smit:SMT_2092|3end_malolactic_enzyme_1987040..1987190_NEGATIVE 339 56 11 68 27 smit:SMT_2057|3end_cell_division_protein_FtsH_1966897..1967047_NEGATIVE 320 65 26 112 67 smit:SMT_2073|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1977074..1977224_POSITIVE 308 49 8 76 32 smit:SMT_1925|3end_K03697_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpE_1867458..1867608_POSITIVE 278 48 8 52 8 smit:SMT_1621|3end_K09134_hypothetical_protein_1607256..1607406_NEGATIVE 268 59 12 150 96 smit:SMT_1774|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1750151..1750301_NEGATIVE 266 63 27 40 7 smit:SMT_1914|3end_K03696_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpC_1860324..1860474_POSITIVE 261 70 25 57 12 smit:SMT_1941|3end_hypothetical_protein_1877663..1877813_POSITIVE 257 57 27 151 119 smit:SMT_1170|3end_acetyltransferase,_CysE/LacA/LpxA/NodL_family_1117569..1117719_NEGATIVE 255 73 39 140 103 smit:SMT_195|3end_30S_ribosomal_protein_S13_127322..127472_POSITIVE 254 69 27 63 22 smit:SMT_1258|3end_acetolactate_synthase_large_subunit_1223166..1223316_NEGATIVE 250 39 1 59 10 smit:SMT_1367|3end_K02237_competence_protein_ComEA_1346872..1347022_NEGATIVE 250 68 30 55 3 smit:SMT_1259|3end_hypothetical_protein_1225578..1225728_POSITIVE 249 45 1 148 103 smit:SMT_1778|3end_ATP-dependent_RNA_helicase_1753611..1753761_NEGATIVE 248 48 1 61 21 smit:SMT_173|3end_50S_ribosomal_protein_L2_117407..117557_POSITIVE 246 50 7 134 89 smit:SMT_1570|3end_hypothetical_protein_1563250..1563400_NEGATIVE 245 45 1 72 29 smit:SMT_1956|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1889537..1889687_NEGATIVE 244 35 1 150 105 smit:SMT_1646|3end_3-isopropylmalate_dehydratase_large_subunit_1633473..1633623_POSITIVE 241 58 17 73 33 smit:SMT_1865|3end_D-alanyl_carrier_protein_1827377..1827527_POSITIVE 241 58 17 73 33 smit:SMT_1312|3end_D-alanyl_carrier_protein_1277361..1277511_POSITIVE