Origin IGS: tgacctcattcaagccccgtccaagaccgtaggggagcaatcttaattatcctacgtagatggtgaacagaataagaattttcttgcttctgtgcaccgagttcgtcctaatagcagttttattaggtatctaaattccgagcaatcggagtgtattcaggagctaacagcca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tggctgttagctcctgaatacactccgattgctcggaatttagatacctaataaaactgctattaggacgaactcggtgcacagaagcaagaaaattcttattctgttcaccatctacgtaggataattaagattgctcccctacggtcttggacggggcttgaatgaggtca Mask Tandem Repeat Region ================================================ tgacctcattcaagccccgtccaagaccgtaggggagcaatcttaattatcctacgtagatggtgaacagaataagaattttcttgcttctgtgcaccgagttcgtcctaatagcagttttattaggtatctaaattccgagcaatcggagtgtattcaggagctaacagcca Find is-nt database================================================ Query_seq: AA00349:AA00350|AA00349:AA00350:hypothetical protein:50S ribosomal protein L10:->->:233588..233760 173 tgacctcattcaagccccgtccaagaccgtaggggagcaatcttaattatcctacgtagatggtgaacagaataagaattttcttgcttctgtgcaccgagttcgtcctaatagcagttttattaggtatctaaattccgagcaatcggagtgtattcaggagctaacagcca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA00349:AA00350|AA00349:AA00350:hypothetical protein:50S ribosomal protein L10:->->:233588..233760 173 tgacctcattcaagccccgtccaagaccgtaggggagcaatcttaattatcctacgtagatggtgaacagaataagaattttcttgcttctgtgcaccgagttcgtcctaatagcagttttattaggtatctaaattccgagcaatcggagtgtattcaggagctaacagcca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA00349:AA00350|AA00349:AA00350:hypothetical protein:50S ribosomal protein L10:->->:233588..233760 173 tgacctcattcaagccccgtccaagaccgtaggggagcaatcttaattatcctacgtagatggtgaacagaataagaattttcttgcttctgtgcaccgagttcgtcctaatagcagttttattaggtatctaaattccgagcaatcggagtgtattcaggagctaacagcca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgacctcattcaagccccgtccaagaccgtaggggagcaatcttaattatcctacgtagatggtgaacagaataagaattttcttgcttctgtgcaccgagttcgtcctaatagcagttttattaggtatctaaattccgagcaatcggagtgtattcaggagctaacagcca Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: - Start: 55 End: 156 ...................................................... T S P S C F L F K R A E T C R T R G L L L K I L Y R F E S C D S H M ................. tgacctcattcaagccccgtccaagaccgtaggggagcaatcttaattatcctacgtagatggtgaacagaataagaattttcttgcttctgtgcaccgagttcgtcctaatagcagttttattaggtatctaaattccgagcaatcggagtgtattcaggagctaacagcca 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================================================ tgacctcattcaagccccgtccaagaccgtaggggagcaatcttaattatcctacgtagatggtgaacagaataagaattttcttgcttctgtgcaccgagttcgtcctaatagcagttttattaggtatctaaattccgagcaatcggagtgtattcaggagctaacagcca Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 50 HP_score: -4.8 Tail_Score: -2.94912 Start: 107 End: 127 Full_Region: GTGCACCGAGTTCGT CCTAATAG CAGTT TTATTAGG TATCTAAATTCCGAG ..........................................................................................................CCTAATAGCAGTTTTATTAGG.............................................. Find igs database================================================ Query_seq: AA00349:AA00350|AA00349:AA00350:hypothetical protein:50S ribosomal protein L10:->->:233588..233760 173 tgacctcattcaagccccgtccaagaccgtaggggagcaatcttaattatcctacgtagatggtgaacagaataagaattttcttgcttctgtgcaccgagttcgtcctaatagcagttttattaggtatctaaattccgagcaatcggagtgtattcaggagctaacagcca Intra-Species Hit: Count: 1 Min: 1 Max: 173 Len: 173 Subject: aact_AA00349_AA00350|hypothetical protein:50S ribosomal protein L10|POSITIVE:POSITIVE|[233588,233760]|173 HSP 1 e-value: 1.0E-93 bit: 343.0 Len: 173 Query Start:1 Query End:173 Subject Strand: POSITIVE Subject Start: 1 Subject End: 173 tgacctcattcaagccccgtccaagaccgtaggggagcaatcttaattatcctacgtagatggtgaacagaataagaattttcttgcttctgtgcaccgagttcgtcctaatagcagttttattaggtatctaaattccgagcaatcggagtgtattcaggagctaacagcca tgacctcattcaagccccgtccaagaccgtaggggagcaatcttaattatcctacgtagatggtgaacagaataagaattttcttgcttctgtgcaccgagttcgtcctaatagcagttttattaggtatctaaattccgagcaatcggagtgtattcaggagctaacagcca Inter-species Hit: Count: 4 Min: 8 Max: 173 Len: 166 Subject: NC_007146_NTHI0758_NTHI0759|adenylosuccinate lyase:50S ribosomal protein L10|POSITIVE:POSITIVE|[715164,715434]|271 HSP 1 e-value: 9.0E-39 bit: 161.0 Len: 166 Query Start:8 Query End:173 Subject Strand: POSITIVE Subject Start: 108 Subject End: 271 .......attcaagccccgtccaagaccgtaggggagcaatcttaattatcctacgtagatggtgaacagaataagaa-ttttcttgcttctgtgcaccgagttcgtcctaatagcagttttattaggtatctaaattccgagcaatcggagtgtattcaggagctaacagcca .......attcaagccccatccaagaccgtaggggagtaatcttaattatcctacgtagatggtgaacagaataagaatttttcttgcttctgggcgccgaagtcatcctaatcttag---gattaggtaaattaattccgagtaatcggagtgtattcaggagctaaaagcca Subject: NC_000907_HI0639_HI0640|adenylosuccinate lyase:50S ribosomal protein L10|POSITIVE:POSITIVE|[681695,681965]|271 HSP 1 e-value: 2.0E-36 bit: 153.0 Len: 166 Query Start:8 Query End:173 Subject Strand: POSITIVE Subject Start: 108 Subject End: 271 .......attcaagccccgtccaagaccgtaggggagcaatcttaattatcctacgtagatggtgaacagaataagaa-ttttcttgcttctgtgcaccgagttcgtcctaatagcagttttattaggtatctaaattccgagcaatcggagtgtattcaggagctaacagcca .......attcaagccccatccaagaccgtaggggagtaatcttaattatcctacgtagatggtgaacagaataagaatttttcttgcttctgggcgccgaagtcatcctagtcttag---gattaggtaaattaattccgagtaatcggagtgtattcaggagctaaaagcca Subject: NC_006300_MS0208_MS0209|50S ribosomal protein L1:50S ribosomal protein L10|POSITIVE:POSITIVE|[181089,181385]|297 HSP 1 e-value: 5.0E-28 bit: 125.0 Len: 126 Query Start:48 Query End:173 Subject Strand: POSITIVE Subject Start: 172 Subject End: 297 ...............................................tatcctacgtagatggtgaacagaataagaattttcttgcttctgtgcaccgagttcgtcctaatagcagttt-tattaggtatctaaattccgagcaatcggagtgtattcaggagctaacagcca ...............................................tatcctacgtagatggtgaacagagtacgaatttttctgcttctgtacaccgaagtcgtcctaat-gcggtttgtattaggtaatttaattccgagcaatcggagtgtattcaggagctaaaagcca HSP 2 e-value: 4.0E-7 bit: 56.0 Len: 28 Query Start:9 Query End:36 Subject Strand: POSITIVE Subject Start: 99 Subject End: 126 ........ttcaagccccgtccaagaccgtagggga......................................................................................................................................... ........ttcaagccccgtccaagaccgtagggga......................................................................................................................................... Subject: NC_008309_HS_0170_HS_0171|50S ribosomal protein L1:50S ribosomal protein L10|POSITIVE:POSITIVE|[151609,151891]|283 HSP 1 e-value: 1.0E-16 bit: 87.7 Len: 89 Query Start:10 Query End:98 Subject Strand: POSITIVE Subject Start: 97 Subject End: 192 .........tcaagccccgtccaagaccgtaggggagcaa-----tcttaattatcctacgtagatggtga-acagaataagaa-ttttcttgcttctgtgcacc........................................................................... .........tcaagccccgtccaagaccgtaggggaaagaatatttcttaataatcctacgtagatggtgatacagaataagaatttttcttgcttctgtgcacc........................................................................... HSP 2 e-value: 2.0E-9 bit: 63.9 Len: 40 Query Start:134 Query End:173 Subject Strand: POSITIVE Subject Start: 244 Subject End: 283 .....................................................................................................................................aattccgagcaatcggagtgtattcaggagctaacagcca .....................................................................................................................................aattccgatcaatcggagtgtattcaggagctaaaagcca Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUCAAGCCCCGUCCAAGACCGUAGGGGAGCAAUCUUAAUUAUCCUACGUAGAUGGUGAACAGAAUAAGAAUUUUCUUGCUUCUGUGCACCGAGUUCGUCCUAAUAGCAGUUUUAUUAGGUAUCUAAAUUCCGAGCAAUCGGAGUGUAUUCAGGAGCUAACAGCCA .....(((.((.........(((((((((....))).......))))))(((((((((.(((((((((((....))))).)))))).))))........((((((((.....)))))))).))))).(((((((....))))))).......)).)))........ (-48.21) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGGCUGUUAGCUCCUGAAUACACUCCGAUUGCUCGGAAUUUAGAUACCUAAUAAAACUGCUAUUAGGACGAACUCGGUGCACAGAAGCAAGAAAAUUCUUAUUCUGUUCACCAUCUACGUAGGAUAAUUAAGAUUGCUCCCCUACGGUCUUGGACGGGGCUUGAAU ........((((((....(((..(((((....)))))...((((..(((((((.......)))))))........((((.((((((..((((....)))).)))))).)))).)))).)))......(((((((((........)))))))))..))))))..... (-46.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 315 50 4 216 175 aact:AA01188|5end_conserved_hypothetical_protein_813912..814142_POSITIVE 303 63 24 58 16 aact:AA02659|5end_conserved_hypothetical_protein_1852527..1852757_POSITIVE 301 51 11 198 148 aact:AA02297|5end_conserved_hypothetical_protein_1569620..1569850_POSITIVE 301 51 11 198 148 aact:AA00621|5end_conserved_hypothetical_protein_428727..428957_POSITIVE 289 47 4 182 138 aact:AA01890|5end_cell-cycle_protein_1274544..1274774_POSITIVE 288 51 11 198 148 aact:AA00412|5end_conserved_hypothetical_protein_279174..279404_POSITIVE 286 108 66 185 132 aact:AA01715|5end_conserved_hypothetical_protein_1160480..1160710_POSITIVE 281 46 1 157 113 aact:AA01565|5end_conserved_hypothetical_protein_1050711..1050941_POSITIVE 281 69 21 49 7 aact:AA01098|5end_bis(5'-nucleosyl)-tetraphosphatase_757699..757929_POSITIVE 273 87 41 205 163 aact:AA02696|5end_formate_hydrogenlyase_maturation_protein_1879476..1879706_POSITIVE 273 50 3 134 88 aact:AA01449|5end_prophage_CP4-57_integrase_970569..970799_POSITIVE 270 57 14 99 37 aact:AA02561|5end_conserved_hypothetical_protein_1783553..1783783_POSITIVE 270 29 1 179 139 aact:AA02524|5end_orotidine_5'-phosphate_decarboxylase_1753313..1753543_POSITIVE 269 34 5 196 160 aact:AA00531|5end_DNA_polymerase_I_362621..362851_POSITIVE 267 48 11 204 170 aact:AA02142|5end_outer_membrane_protein_OprM_precursor_1466037..1466267_POSITIVE 265 112 72 185 142 aact:AA01995|5end_conserved_hypothetical_protein_(possible_chorismate_mutase)_1355120..1355350_POSITIVE 264 49 3 157 106 aact:AA01355|5end_large_subunit_pseudouridylate_synthase_D_917228..917458_POSITIVE 264 99 53 222 182 aact:AA00803|5end_hypothetical_protein_549526..549756_POSITIVE 262 59 11 156 116 aact:AA00702|5end_conserved_hypothetical_protein_481660..481890_POSITIVE 262 129 85 49 4 aact:AA00092|5end_serine_transporter_68398..68628_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 335 31 4 145 115 aact:AA00396|3end_conserved_hypothetical_protein_265952..266102_POSITIVE 292 35 7 105 69 aact:AA02014|3end_probable_hemolysin_1370977..1371127_POSITIVE 289 47 4 148 104 aact:AA01889|3end_conserved_hypothetical_protein_(possible_permease)_1274590..1274740_POSITIVE 286 108 66 127 74 aact:AA01711|3end_conserved_hypothetical_protein_1160502..1160652_POSITIVE 284 63 25 42 1 aact:AA02658|3end_conserved_hypothetical_protein_1852591..1852741_POSITIVE 273 87 41 67 25 aact:AA02695|3end_hydrogenase-3_component_G_1879418..1879568_POSITIVE 272 49 2 92 55 aact:AA02947|3end_riboflavin_biosynthesis_protein_2061874..2062024_POSITIVE 270 57 14 96 34 aact:AA02560|3end_integral_membrane_protein_1783630..1783780_POSITIVE 262 49 5 69 24 aact:AA00980|3end_hypothetical_protein_685409..685559_POSITIVE 259 110 77 150 110 aact:AA01146|3end_conserved_hypothetical_protein_784770..784920_POSITIVE 259 100 78 34 11 aact:AA00140|3end_hypothetical_protein_100872..101022_POSITIVE 253 99 51 116 68 aact:AA01609|3end_p-aminobenzoate_synthase_component_I_homolog_1088822..1088972_POSITIVE 251 30 6 63 33 aact:AA02420|3end_ISRSO11_related_transposase_1662668..1662818_POSITIVE 251 111 76 96 50 aact:AA01555|3end_ABC_transporter,_ATP-binding_protein_1044323..1044473_POSITIVE 251 69 24 82 34 aact:AA00174|3end_ribosomal_protein_L11_methyltransferase_124033..124183_POSITIVE 249 37 4 95 52 aact:AA02990|3end_beta_hexosaminadase_2090596..2090746_POSITIVE 249 50 7 73 30 aact:AA02723|3end_hypothetical_protein_1906453..1906603_POSITIVE 249 99 55 77 38 aact:AA00549|3end_ferredoxin-type_protein_376521..376671_POSITIVE 246 32 6 124 93 aact:AA00426|3end_conserved_hypothetical_protein_288205..288355_POSITIVE 245 103 83 37 15 aact:AA00448|3end_C-terminal_region_of_competence_protein_M_313058..313208_POSITIVE