Origin IGS: ctaatttaaaagattaaactacagaaaggattgtttggttccttaaggtaactgaacatgggactaattcccgtaaaatatcttttactgcataaaaacctactctacattctttgaaaggagttgaacacgccctaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttagggcgtgttcaactcctttcaaagaatgtagagtaggtttttatgcagtaaaagatattttacgggaattagtcccatgttcagttaccttaaggaaccaaacaatcctttctgtagtttaatcttttaaattag Mask Tandem Repeat Region ================================================ ctaatttaaaagattaaactacagaaaggattgtttggttccttaaggtaactgaacatgggactaattcccgtaaaatatcttttactgcataaaaacctactctacattctttgaaaggagttgaacacgccctaa Find is-nt database================================================ Query_seq: SMT_544:SMT_545|SMT_544:SMT_545:aminoglycoside 6-adenylyltransferase:hypothetical protein predicted by Glimmer/Critica:->->:461251..461388 138 ctaatttaaaagattaaactacagaaaggattgtttggttccttaaggtaactgaacatgggactaattcccgtaaaatatcttttactgcataaaaacctactctacattctttgaaaggagttgaacacgccctaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_544:SMT_545|SMT_544:SMT_545:aminoglycoside 6-adenylyltransferase:hypothetical protein predicted by Glimmer/Critica:->->:461251..461388 138 ctaatttaaaagattaaactacagaaaggattgtttggttccttaaggtaactgaacatgggactaattcccgtaaaatatcttttactgcataaaaacctactctacattctttgaaaggagttgaacacgccctaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_544:SMT_545|SMT_544:SMT_545:aminoglycoside 6-adenylyltransferase:hypothetical protein predicted by Glimmer/Critica:->->:461251..461388 138 ctaatttaaaagattaaactacagaaaggattgtttggttccttaaggtaactgaacatgggactaattcccgtaaaatatcttttactgcataaaaacctactctacattctttgaaaggagttgaacacgccctaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctaatttaaaagattaaactacagaaaggattgtttggttccttaaggtaactgaacatgggactaattcccgtaaaatatcttttactgcataaaaacctactctacattctttgaaaggagttgaacacgccctaa Predict ORF larger than 30AA ================================================ ctaatttaaaagattaaactacagaaaggattgtttggttccttaaggtaactgaacatgggactaattcccgtaaaatatcttttactgcataaaaacctactctacattctttgaaaggagttgaacacgccctaa 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================================================ ctaatttaaaagattaaactacagaaaggattgtttggttccttaaggtaactgaacatgggactaattcccgtaaaatatcttttactgcataaaaacctactctacattctttgaaaggagttgaacacgccctaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_544:SMT_545|SMT_544:SMT_545:aminoglycoside 6-adenylyltransferase:hypothetical protein predicted by Glimmer/Critica:->->:461251..461388 138 ctaatttaaaagattaaactacagaaaggattgtttggttccttaaggtaactgaacatgggactaattcccgtaaaatatcttttactgcataaaaacctactctacattctttgaaaggagttgaacacgccctaa Intra-Species Hit: Count: 1 Min: 1 Max: 138 Len: 138 Subject: smit_SMT_544_SMT_545|aminoglycoside 6-adenylyltransferase:hypothetical protein predicted by Glimmer/Critica|POSITIVE:POSITIVE|[461251,461388]|138 HSP 1 e-value: 7.0E-73 bit: 274.0 Len: 138 Query Start:1 Query End:138 Subject Strand: POSITIVE Subject Start: 1 Subject End: 138 ctaatttaaaagattaaactacagaaaggattgtttggttccttaaggtaactgaacatgggactaattcccgtaaaatatcttttactgcataaaaacctactctacattctttgaaaggagttgaacacgccctaa ctaatttaaaagattaaactacagaaaggattgtttggttccttaaggtaactgaacatgggactaattcccgtaaaatatcttttactgcataaaaacctactctacattctttgaaaggagttgaacacgccctaa Inter-species Hit: Count: 5 Min: 2 Max: 138 Len: 137 Subject: NC_003098_spr0756_spr0757|DNA topoisomerase IV subunit B:DNA topoisomerase IV subunit A|POSITIVE:POSITIVE|[751831,752240]|410 HSP 1 e-value: 2.0E-42 bit: 172.0 Len: 111 Query Start:27 Query End:137 Subject Strand: POSITIVE Subject Start: 218 Subject End: 328 ..........................aggattgtttggttccttaaggtaactgaacatgggactaattcccgtaaaatatcttttactgcataaaaacctactctacattctttgaaaggagttgaacacgcccta. ..........................aggatagtttggttacttatcgtaactgaacacgggacgaattcccgtaaaatatcttttactgcataaaaacctactctacattctttgaaaggagttgaacacgcccta. Subject: NC_009009_SSA_1226_SSA_1227|ParC, putative:Aminoglycoside adenylyltransferase, putative|NEGATIVE:NEGATIVE|[1251324,1251568]|245 HSP 1 e-value: 1.0E-34 bit: 147.0 Len: 137 Query Start:2 Query End:138 Subject Strand: NEGATIVE Subject Start: 94 Subject End: 231 .taatttaaaagattaaa-ctacagaaaggattgtttggttccttaaggtaactgaacatgggactaattcccgtaaaatatcttttactgcataaaaacctactctacattctttgaaaggagttgaacacgccctaa .taatttaaaacattaaaactacagaaaggatagtttggttacttatagtaattgaacacgggactaattttcgtaaaatatcctttattttataaaaaactactctacattctttgaaaggagttgaacacgccctaa Subject: NC_008532_STER_0633_STER_0634|DNA topoisomerase IV subunit B:DNA topoisomerase IV subunit A|POSITIVE:POSITIVE|[576342,577013]|672 HSP 1 e-value: 3.0E-10 bit: 65.9 Len: 37 Query Start:102 Query End:138 Subject Strand: POSITIVE Subject Start: 396 Subject End: 432 .....................................................................................................actctacattctttgaaaggagttgaacacgccctaa .....................................................................................................actcaacattctttgaaaggagttgaacacgccctaa HSP 2 e-value: 5.0E-6 bit: 52.0 Len: 50 Query Start:20 Query End:69 Subject Strand: POSITIVE Subject Start: 483 Subject End: 532 ...................tacagaaaggattgtttggttccttaaggtaactgaacatgggactaatt..................................................................... ...................tacagaaagggtcgtttggttactgaatgtaactgaacacgggactaatt..................................................................... Subject: NC_006449_str0588_str0589|DNA topoisomerase IV subunit B:DNA topoisomerase IV subunit A|POSITIVE:POSITIVE|[553699,554271]|573 HSP 1 e-value: 3.0E-10 bit: 65.9 Len: 37 Query Start:102 Query End:138 Subject Strand: POSITIVE Subject Start: 396 Subject End: 432 .....................................................................................................actctacattctttgaaaggagttgaacacgccctaa .....................................................................................................actcaacattctttgaaaggagttgaacacgccctaa HSP 2 e-value: 2.0E-8 bit: 60.0 Len: 50 Query Start:20 Query End:69 Subject Strand: POSITIVE Subject Start: 483 Subject End: 532 ...................tacagaaaggattgtttggttccttaaggtaactgaacatgggactaatt..................................................................... ...................tacagaaaggatcgtttggttactgaatgtaactgaacacgggactaatt..................................................................... Subject: NC_006448_stu0588_stu0589|DNA topoisomerase IV subunit B:DNA topoisomerase IV subunit A|POSITIVE:POSITIVE|[558515,559087]|573 HSP 1 e-value: 3.0E-10 bit: 65.9 Len: 37 Query Start:102 Query End:138 Subject Strand: POSITIVE Subject Start: 396 Subject End: 432 .....................................................................................................actctacattctttgaaaggagttgaacacgccctaa .....................................................................................................actcaacattctttgaaaggagttgaacacgccctaa HSP 2 e-value: 5.0E-6 bit: 52.0 Len: 50 Query Start:20 Query End:69 Subject Strand: POSITIVE Subject Start: 483 Subject End: 532 ...................tacagaaaggattgtttggttccttaaggtaactgaacatgggactaatt..................................................................... ...................tacagaaagggtcgtttggttactgaatgtaactgaacacgggactaatt..................................................................... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUUUAAAAGAUUAAACUACAGAAAGGAUUGUUUGGUUCCUUAAGGUAACUGAACAUGGGACUAAUUCCCGUAAAAUAUCUUUUACUGCAUAAAAACCUACUCUACAUUCUUUGAAAGGAGUUGAACACGCCCUAA ....................((((((((((((((..(((((....)).)))..)))).((((.....)))).......))))))).))).........(.(((((.((.....))...))))).)............ (-25.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAGGGCGUGUUCAACUCCUUUCAAAGAAUGUAGAGUAGGUUUUUAUGCAGUAAAAGAUAUUUUACGGGAAUUAGUCCCAUGUUCAGUUACCUUAAGGAACCAAACAAUCCUUUCUGUAGUUUAAUCUUUUAAAUUA .....(((((.....((.((((((.....)).)))).)).....)))))..(((((((((..((((((((.....)))).((((..(((.((....)))))..)))).........))))..).))))))))..... (-24.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 253 74 32 92 45 smit:SMT_236|5end_ribosomal_small_subunit_pseudouridine_synthase_A_174625..174855_POSITIVE 244 78 31 55 18 smit:SMT_1668|5end_K+_transport_system,_NAD-binding_component_1658288..1658518_NEGATIVE 238 75 35 42 1 smit:SMT_335|5end_glutamine_synthetase_273753..273983_POSITIVE 234 70 28 205 161 smit:SMT_1840|5end_6-phosphogluconate_dehydrogenase,_decarboxylating_1806285..1806515_NEGATIVE 234 79 35 151 91 smit:SMT_546|5end_DNA_topoisomerase_IV_subunit_A_461377..461607_POSITIVE 231 118 80 153 117 smit:SMT_1348|5end_exoribonuclease_II_1327502..1327732_NEGATIVE 227 71 35 47 1 smit:SMT_310|5end_3-oxoacyl-_251370..251600_POSITIVE 223 64 21 193 146 smit:SMT_185|5end_50S_ribosomal_protein_L6_122003..122233_POSITIVE 216 73 32 113 70 smit:SMT_1834|5end_cell_division_protein_1803695..1803925_NEGATIVE 215 75 31 184 144 smit:SMT_1214|5end_K03584_DNA_repair_protein_RecO_(recombination_protein_O)_1173422..1173652_NEGATIVE 214 70 27 80 33 smit:SMT_158|5end_putative_Holliday_junction_resolvase_103795..104025_POSITIVE 213 72 31 215 175 smit:SMT_1938|5end_zinc_metalloprotease_ZmpB,_putative_1875374..1875604_POSITIVE 213 68 22 147 110 smit:SMT_1162|5end_ATP-dependent_DNA_helicase_1108895..1109125_NEGATIVE 212 64 22 227 167 smit:SMT_1971|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1903282..1903512_POSITIVE 211 73 31 161 114 smit:SMT_923|5end_methionyl-tRNA_formyltransferase_877494..877724_NEGATIVE 209 110 61 189 144 smit:SMT_129|5end_putative_glycosyltransferase_79973..80203_POSITIVE 208 97 58 187 137 smit:SMT_102|5end_competence-specific_global_transcription_modulator_34108..34338_POSITIVE 206 74 32 174 131 smit:SMT_387|5end_hypothetical_protein_predicted_by_Glimmer/Critica_320937..321167_POSITIVE 205 73 33 50 12 smit:SMT_2000|5end_hypothetical_protein_1923108..1923338_NEGATIVE 205 89 46 52 13 smit:SMT_309|5end_acyl-carrier-protein_S-malonyltransferase_250406..250636_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 249 67 23 147 100 smit:SMT_1419|3end_hypothetical_protein_1404582..1404732_POSITIVE 244 78 31 41 4 smit:SMT_1669|3end_potassium_uptake_protein_KtrB_1658302..1658452_NEGATIVE 237 75 31 151 97 smit:SMT_763|3end_alpha-amylase_669280..669430_POSITIVE 234 70 28 129 85 smit:SMT_1841|3end_hypothetical_protein_1806361..1806511_NEGATIVE 234 70 28 129 85 smit:SMT_303|3end_hypothetical_protein_245758..245908_POSITIVE 231 118 80 51 15 smit:SMT_1349|3end_K03075_preprotein_translocase_SecG_subunit_1327604..1327754_NEGATIVE 219 62 21 146 103 smit:SMT_1716|3end_hypothetical_protein_1703657..1703807_POSITIVE 214 70 27 76 29 smit:SMT_157|3end_hypothetical_protein_103871..104021_POSITIVE 211 122 87 39 5 smit:SMT_1475|3end_K02004_1458661..1458811_POSITIVE 211 73 31 148 101 smit:SMT_924|3end_primosomal_protein_N'_877507..877657_NEGATIVE 211 62 24 137 105 smit:SMT_774|3end_hypothetical_protein_684479..684629_NEGATIVE 208 97 58 66 16 smit:SMT_101|3end_cell_division_protein_34067..34217_POSITIVE 206 62 22 147 98 smit:SMT_2089|3end_dTDP-4-dehydrorhamnose_3,5-epimerase_related_enzyme_1985270..1985420_POSITIVE 205 89 46 59 20 smit:SMT_308|3end_trans-2-enoyl-ACP_reductase_II_250493..250643_POSITIVE 196 80 34 75 27 smit:SMT_2040|3end_transcription-repair_coupling_factor_1950463..1950613_NEGATIVE 196 47 20 96 62 smit:SMT_1806|3end_aminoacylase/N-acyl-L-amino_acid_amidohydrolase/hippurate_hydrolase_1781644..1781794_POSITIVE 195 90 56 128 96 smit:SMT_1258|3end_acetolactate_synthase_large_subunit_1223166..1223316_NEGATIVE 195 127 85 87 39 smit:SMT_676|3end_DNA_helicase_II_583020..583170_NEGATIVE 194 100 63 146 118 smit:SMT_660|3end_two-component_sensor_histidine_kinase_570538..570688_NEGATIVE 193 100 61 139 105 smit:SMT_1203|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1164221..1164371_NEGATIVE