Origin IGS: gttttctcctatttgcaatataaaagtttgacgtttttccttctcattttatagtaaataagccataaaatcaagcctagacagattgttttgacaattctaatcttttagattattaaagcaaaaagattgtcaaagagaaaaagcccacagatgtgagcccttttctaatataggttaggaaaaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tttttcctaacctatattagaaaagggctcacatctgtgggctttttctctttgacaatctttttgctttaataatctaaaagattagaattgtcaaaacaatctgtctaggcttgattttatggcttatttactataaaatgagaaggaaaaacgtcaaacttttatattgcaaataggagaaaac Mask Tandem Repeat Region ================================================ gttttctcctatttgcaatataaaagtttgacgtttttccttctcattttatagtaaataagccataaaatcaagcctagacagattgttttgacaattctaatcttttagattattaaagcaaaaagattgtcaaagagaaaaagcccacagatgtgagcccttttctaatataggttaggaaaaa Find is-nt database================================================ Query_seq: SMT_780:SMT_781|SMT_780:SMT_781:peptidase family U32:hypothetical protein:<-<-:689412..689598 187 gttttctcctatttgcaatataaaagtttgacgtttttccttctcattttatagtaaataagccataaaatcaagcctagacagattgttttgacaattctaatcttttagattattaaagcaaaaagattgtcaaagagaaaaagcccacagatgtgagcccttttctaatataggttaggaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_780:SMT_781|SMT_780:SMT_781:peptidase family U32:hypothetical protein:<-<-:689412..689598 187 gttttctcctatttgcaatataaaagtttgacgtttttccttctcattttatagtaaataagccataaaatcaagcctagacagattgttttgacaattctaatcttttagattattaaagcaaaaagattgtcaaagagaaaaagcccacagatgtgagcccttttctaatataggttaggaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_780:SMT_781|SMT_780:SMT_781:peptidase family U32:hypothetical protein:<-<-:689412..689598 187 gttttctcctatttgcaatataaaagtttgacgtttttccttctcattttatagtaaataagccataaaatcaagcctagacagattgttttgacaattctaatcttttagattattaaagcaaaaagattgtcaaagagaaaaagcccacagatgtgagcccttttctaatataggttaggaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gttttctcctatttgcaatataaaagtttgacgtttttccttctcattttatagtaaataagccataaaatcaagcctagacagattgttttgacaattctaatcttttagattattaaagcaaaaagattgtcaaagagaaaaagcccacagatgtgagcccttttctaatataggttaggaaaaa Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: - Start: 12 End: 104 ........... K C Y L L K V N K R R M K Y Y I L W L I L G L C I T K V I R M ................................................................................... gttttctcctatttgcaatataaaagtttgacgtttttccttctcattttatagtaaataagccataaaatcaagcctagacagattgttttgacaattctaatcttttagattattaaagcaaaaagattgtcaaagagaaaaagcccacagatgtgagcccttttctaatataggttaggaaaaa 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: 86 Start: 46 End: 75 .............................................CTTGATTTTATGGCTTATTTACTATAAAAT................................................................................................................ PromScan Matrix: RpoD-17 Strand: + Score: 84 Start: 90 End: 119 .........................................................................................TTTGACAATTCTAATCTTTTAGATTATTAA.................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gttttctcctatttgcaatataaaagtttgacgtttttccttctcattttatagtaaataagccataaaatcaagcctagacagattgttttgacaattctaatcttttagattattaaagcaaaaagattgtcaaagagaaaaagcccacagatgtgagcccttttctaatataggttaggaaaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_780:SMT_781|SMT_780:SMT_781:peptidase family U32:hypothetical protein:<-<-:689412..689598 187 gttttctcctatttgcaatataaaagtttgacgtttttccttctcattttatagtaaataagccataaaatcaagcctagacagattgttttgacaattctaatcttttagattattaaagcaaaaagattgtcaaagagaaaaagcccacagatgtgagcccttttctaatataggttaggaaaaa Intra-Species Hit: Count: 1 Min: 1 Max: 187 Len: 187 Subject: smit_SMT_780_SMT_781|peptidase family U32:hypothetical protein|NEGATIVE:NEGATIVE|[689412,689598]|187 HSP 1 e-value: 1.0E-102 bit: 371.0 Len: 187 Query Start:1 Query End:187 Subject Strand: POSITIVE Subject Start: 1 Subject End: 187 gttttctcctatttgcaatataaaagtttgacgtttttccttctcattttatagtaaataagccataaaatcaagcctagacagattgttttgacaattctaatcttttagattattaaagcaaaaagattgtcaaagagaaaaagcccacagatgtgagcccttttctaatataggttaggaaaaa gttttctcctatttgcaatataaaagtttgacgtttttccttctcattttatagtaaataagccataaaatcaagcctagacagattgttttgacaattctaatcttttagattattaaagcaaaaagattgtcaaagagaaaaagcccacagatgtgagcccttttctaatataggttaggaaaaa Inter-species Hit: Count: 2 Min: 3 Max: 112 Len: 110 Subject: NC_008533_SPD_1258_SPD_1260|peptidase, U32 family protein:type II DNA modification methyltransferase, putative|NEGATIVE:POSITIVE|[1286983,1288159]|1177 HSP 1 e-value: 4.0E-44 bit: 178.0 Len: 110 Query Start:3 Query End:112 Subject Strand: POSITIVE Subject Start: 3 Subject End: 112 ..tttctcctatttgcaatataaaagtttgacgtttttccttctcattttatagtaaataagccataaaatcaagcctagacagattgttttgacaattctaatcttttaga........................................................................... ..tttctcctatttgcaatataaaagtttgacatttttccttctcattttatagtaaataaaggataaaatcaagcctagacggattgttttgacaattctaatcttttaga........................................................................... Subject: NC_003028_SP_1429_SP_1431|peptidase, U32 family:type II DNA modification methyltransferase, putative|NEGATIVE:POSITIVE|[1348574,1349750]|1177 HSP 1 e-value: 4.0E-44 bit: 178.0 Len: 110 Query Start:3 Query End:112 Subject Strand: POSITIVE Subject Start: 3 Subject End: 112 ..tttctcctatttgcaatataaaagtttgacgtttttccttctcattttatagtaaataagccataaaatcaagcctagacagattgttttgacaattctaatcttttaga........................................................................... ..tttctcctatttgcaatataaaagtttgacatttttccttctcattttatagtaaataaaggataaaatcaagcctagacggattgttttgacaattctaatcttttaga........................................................................... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUCUCCUAUUUGCAAUAUAAAAGUUUGACGUUUUUCCUUCUCAUUUUAUAGUAAAUAAGCCAUAAAAUCAAGCCUAGACAGAUUGUUUUGACAAUUCUAAUCUUUUAGA .......(((((((..(((((((....((.(......).))...))))))))))))))................(((((.((((((............))))))))))). (-11.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUAAAAGAUUAGAAUUGUCAAAACAAUCUGUCUAGGCUUGAUUUUAUGGCUUAUUUACUAUAAAAUGAGAAGGAAAAACGUCAAACUUUUAUAUUGCAAAUAGGAGAAA (((...((((.(((.((((....)))))))))))...(((.(((((((((........))))))))))))..)))...........(((((((.......)))))))... (-15.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 768 100 51 193 144 smit:SMT_780|5end_peptidase_family_U32_689321..689551_NEGATIVE 324 65 30 92 51 smit:SMT_1179|5end_aldose_1-epimerase_1137854..1138084_NEGATIVE 291 63 24 138 103 smit:SMT_461|5end_mannose-6-phosphate_isomerase_399379..399609_POSITIVE 237 62 25 145 112 smit:SMT_536|5end_oxidoreductase,_aldo/keto_reductase_family_454451..454681_POSITIVE 232 90 45 151 100 smit:SMT_1062|5end_hypothetical_protein_1000281..1000511_POSITIVE 228 61 25 187 150 smit:SMT_1705|5end_UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-_diaminopimelate--D-alanyl-D-alanine_ligase_1688558..1688788_POSITIVE 224 92 58 63 22 smit:SMT_1540|5end_hypothetical_protein_1525005..1525235_NEGATIVE 223 107 61 103 47 smit:SMT_1668|5end_K+_transport_system,_NAD-binding_component_1658288..1658518_NEGATIVE 223 107 61 186 130 smit:SMT_1167|5end_aminopeptidase_N_1115076..1115306_NEGATIVE 208 61 23 63 21 smit:SMT_1283|5end_K02240_competence_protein_ComFA_1245667..1245897_POSITIVE 202 99 56 189 151 smit:SMT_348|5end_K07707_two-component_system,_AgrA_family,_response_regulator_AgrA_286456..286686_POSITIVE 201 73 32 147 109 smit:SMT_1075|5end_hypothetical_protein_1013473..1013703_POSITIVE 201 60 30 120 89 smit:SMT_920|5end_serine/threonine_protein_kinase_874501..874731_NEGATIVE 200 45 1 210 164 smit:SMT_1495|5end_hypothetical_protein_1480271..1480501_POSITIVE 200 86 41 185 131 smit:SMT_118|5end_K02026_multiple_sugar_transport_system_permease_protein_69430..69660_POSITIVE 199 80 31 141 92 smit:SMT_893|5end_leucine_rich_protein_841311..841541_NEGATIVE 198 44 3 112 66 smit:SMT_1734|5end_serine/threonine_protein_phosphatase_1718558..1718788_POSITIVE 197 65 21 140 93 smit:SMT_1245|5end_SOS_responce_UmuC_protein_1205120..1205350_POSITIVE 196 74 35 204 174 smit:SMT_329|5end_hypothetical_protein_265240..265470_POSITIVE 195 79 34 174 113 smit:SMT_129|5end_putative_glycosyltransferase_79973..80203_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 237 62 25 70 37 smit:SMT_535|3end_hypothetical_protein_454456..454606_POSITIVE 230 110 62 144 100 smit:SMT_468|3end_ABC-type_oligopeptide_transport_system,_periplasmic_component_404903..405053_POSITIVE 228 61 25 103 66 smit:SMT_1704|3end_D-alanine-D-alanine_ligase_1688554..1688704_POSITIVE 223 107 61 89 33 smit:SMT_1669|3end_potassium_uptake_protein_KtrB_1658302..1658452_NEGATIVE 223 107 61 89 33 smit:SMT_1168|3end_potassium_uptake_protein_KtrB_1115173..1115323_NEGATIVE 208 99 75 50 24 smit:SMT_541|3end_K03697_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpE_457120..457270_NEGATIVE 207 110 62 61 16 smit:SMT_1313|3end_extramembranal_protein_1278622..1278772_POSITIVE 201 60 30 123 92 smit:SMT_921|3end_putative_PP2C_protein_phosphatase_874498..874648_NEGATIVE 200 45 1 80 34 smit:SMT_1494|3end_nucleoside_diphosphate_kinase_1480221..1480371_POSITIVE 199 80 31 137 88 smit:SMT_894|3end_hypothetical_protein_841315..841465_NEGATIVE 198 44 3 110 64 smit:SMT_1733|3end_DNA_repair_protein_RecN_1718636..1718786_POSITIVE 197 65 21 89 42 smit:SMT_1244|3end_putative_repressor_protein_1205149..1205299_POSITIVE 196 76 31 139 94 smit:SMT_398|3end_hypothetical_protein_328279..328429_POSITIVE 194 42 2 79 24 smit:SMT_1268|3end_acetoin_reductase_1232655..1232805_NEGATIVE 194 87 47 45 1 smit:SMT_836|3end_cell_surface_protein_precursor_777664..777814_NEGATIVE 190 104 67 52 13 smit:SMT_1021|3end_K05846_osmoprotectant_transport_system_permease_protein_956479..956629_NEGATIVE 189 49 1 93 57 smit:SMT_364|3end_ribosome-binding_factor_A_301353..301503_POSITIVE 189 100 51 98 40 smit:SMT_226|3end_putative_L-glutamine-D-fructose-6-phosphate_amidotransferase_164000..164150_POSITIVE 189 100 51 98 40 smit:SMT_223|3end_D-fructose-6-phosphate_amidotransferase_158431..158581_POSITIVE 185 62 23 133 98 smit:SMT_1933|3end_K02006_cobalt_transport_system_ATP-binding_protein_1871986..1872136_NEGATIVE