Origin IGS: ttaataagaaatccccatgctcaatatccgagcatggggatttcttattagagacggcacgataaagcatttgtttaatgattcatgatgatgctcatcaattttagcatacaaactctgataatattctaaaattttaatttttagactaataaatatctgaaatcgcttgcagttcctatttttttatgttattctatataaaatagatgcaatcatgtttctaaatctaaaaagataaggagaaatt .........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 aatttctccttatctttttagatttagaaacatgattgcatctattttatatagaataacataaaaaaataggaactgcaagcgatttcagatatttattagtctaaaaattaaaattttagaatattatcagagtttgtatgctaaaattgatgagcatcatcatgaatcattaaacaaatgctttatcgtgccgtctctaataagaaatccccatgctcggatattgagcatggggatttcttattaa Mask Tandem Repeat Region ================================================ ttaataagaaatccccatgctcaatatccgagcatggggatttcttattagagacggcacgataaagcatttgtttaatgattcatgatgatgctcatcaattttagcatacaaactctgataatattctaaaattttaatttttagactaataaatatctgaaatcgcttgcagttcctatttttttatgttattctatataaaatagatgcaatcatgtttctaaatctaaaaagataaggagaaatt Find is-nt database================================================ Query_seq: SSA_1062:SSA_1063|SSA_1062:SSA_1063:50S ribosomal protein L27, putative:Peptidoglycan-binding domain-containing protein, putative:->->:1078718..1078967 250 ttaataagaaatccccatgctcaatatccgagcatggggatttcttattagagacggcacgataaagcatttgtttaatgattcatgatgatgctcatcaattttagcatacaaactctgataatattctaaaattttaatttttagactaataaatatctgaaatcgcttgcagttcctatttttttatgttattctatataaaatagatgcaatcatgtttctaaatctaaaaagataaggagaaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1062:SSA_1063|SSA_1062:SSA_1063:50S ribosomal protein L27, putative:Peptidoglycan-binding domain-containing protein, putative:->->:1078718..1078967 250 ttaataagaaatccccatgctcaatatccgagcatggggatttcttattagagacggcacgataaagcatttgtttaatgattcatgatgatgctcatcaattttagcatacaaactctgataatattctaaaattttaatttttagactaataaatatctgaaatcgcttgcagttcctatttttttatgttattctatataaaatagatgcaatcatgtttctaaatctaaaaagataaggagaaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1062:SSA_1063|SSA_1062:SSA_1063:50S ribosomal protein L27, putative:Peptidoglycan-binding domain-containing protein, putative:->->:1078718..1078967 250 ttaataagaaatccccatgctcaatatccgagcatggggatttcttattagagacggcacgataaagcatttgtttaatgattcatgatgatgctcatcaattttagcatacaaactctgataatattctaaaattttaatttttagactaataaatatctgaaatcgcttgcagttcctatttttttatgttattctatataaaatagatgcaatcatgtttctaaatctaaaaagataaggagaaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttaataagaaatccccatgctcaatatccgagcatggggatttcttattagagacggcacgataaagcatttgtttaatgattcatgatgatgctcatcaattttagcatacaaactctgataatattctaaaattttaatttttagactaataaatatctgaaatcgcttgcagttcctatttttttatgttattctatataaaatagatgcaatcatgtttctaaatctaaaaagataaggagaaatt Predict ORF larger than 30AA ================================================ Protein_Len: 53 Strand: - Start: 4 End: 159 ... * Y S I G M S L I R A H P N R I L S P V I F C K N L S E H H H E D I K A Y L S Q Y Y E L I K I K L S I F M ........................................................................................... ttaataagaaatccccatgctcaatatccgagcatggggatttcttattagagacggcacgataaagcatttgtttaatgattcatgatgatgctcatcaattttagcatacaaactctgataatattctaaaattttaatttttagactaataaatatctgaaatcgcttgcagttcctatttttttatgttattctatataaaatagatgcaatcatgtttctaaatctaaaaagataaggagaaatt 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================================================ ttaataagaaatccccatgctcaatatccgagcatggggatttcttattagagacggcacgataaagcatttgtttaatgattcatgatgatgctcatcaattttagcatacaaactctgataatattctaaaattttaatttttagactaataaatatctgaaatcgcttgcagttcctatttttttatgttattctatataaaatagatgcaatcatgtttctaaatctaaaaagataaggagaaatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1062:SSA_1063|SSA_1062:SSA_1063:50S ribosomal protein L27, putative:Peptidoglycan-binding domain-containing protein, putative:->->:1078718..1078967 250 ttaataagaaatccccatgctcaatatccgagcatggggatttcttattagagacggcacgataaagcatttgtttaatgattcatgatgatgctcatcaattttagcatacaaactctgataatattctaaaattttaatttttagactaataaatatctgaaatcgcttgcagttcctatttttttatgttattctatataaaatagatgcaatcatgtttctaaatctaaaaagataaggagaaatt Intra-Species Hit: Count: 1 Min: 1 Max: 250 Len: 250 Subject: NC_009009_SSA_1062_SSA_1063|50S ribosomal protein L27, putative:Peptidoglycan-binding domain-containing protein, putative|POSITIVE:POSITIVE|[1078718,1078967]|250 HSP 1 e-value: 1.0E-127 bit: 454.0 Len: 250 Query Start:1 Query End:250 Subject Strand: POSITIVE Subject Start: 1 Subject End: 250 ttaataagaaatccccatgctcaatatccgagcatggggatttcttattagagacggcacgataaagcatttgtttaatgattcatgatgatgctcatcaattttagcatacaaactctgataatattctaaaattttaatttttagactaataaatatctgaaatcgcttgcagttcctannnnnnnatgttattctatataaaatagatgcaatcatgtttctaaatctaaaaagataaggagaaatt ttaataagaaatccccatgctcaatatccgagcatggggatttcttattagagacggcacgataaagcatttgtttaatgattcatgatgatgctcatcaattttagcatacaaactctgataatattctaaaattttaatttttagactaataaatatctgaaatcgcttgcagttcctatttttttatgttattctatataaaatagatgcaatcatgtttctaaatctaaaaagataaggagaaatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAAUAAGAAAUCCCCAUGCUCAAUAUCCGAGCAUGGGGAUUUCUUAUUAGAGACGGCACGAUAAAGCAUUUGUUUAAUGAUUCAUGAUGAUGCUCAUCAAUUUUAGCAUACAAACUCUGAUAAUAUUCUAAAAUUUUAAUUUUUAGACUAAUAAAUAUCUGAAAUCGCUUGCAGUUCCUAUUUUUUUAUGUUAUUCUAUAUAAAAUAGAUGCAAUCAUGUUUCUAAAUCUAAAAAGAUAAGGAGAAAUU ((((((((((((((((((((((.......)))))))))))))))))))))).....(((((((....((..((((((........(((((.....)))))...........................(((((((.......)))))))....))))))..))..))))..)))..((((((((((((((..((((.....))))..((((.(((....))).))))....))))))))).)))))..... (-65.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUUCUCCUUAUCUUUUUAGAUUUAGAAACAUGAUUGCAUCUAUUUUAUAUAGAAUAACAUAAAAAAAUAGGAACUGCAAGCGAUUUCAGAUAUUUAUUAGUCUAAAAAUUAAAAUUUUAGAAUAUUAUCAGAGUUUGUAUGCUAAAAUUGAUGAGCAUCAUCAUGAAUCAUUAAACAAAUGCUUUAUCGUGCCGUCUCUAAUAAGAAAUCCCCAUGCUCGGAUAUUGAGCAUGGGGAUUUCUUAUUAA ..(((((....((((....))))..)))))((((((.(((((((((((.................))))))).....(((.((((.(((.((((........(((((((.......)))))))....)))).))).)))).))).....(((((((...((.....)).)))))))....))))...)))))).......((((((((((((((((((((((.....)))))))))))))))))))))). (-66.73) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 298 58 15 137 88 NC_009009:SSA_0839|5end_hypothetical_protein_826751..826981_POSITIVE 297 55 11 143 90 NC_009009:SSA_1412|5end_hypothetical_protein_1424095..1424325_NEGATIVE 289 58 12 67 14 NC_009009:SSA_1610|5end_hypothetical_protein_1614909..1615139_NEGATIVE 285 60 11 180 121 NC_009009:SSA_2090|5end_Hexulose-6-phosphate_synthase,_putative_2095038..2095268_NEGATIVE 284 58 13 41 1 NC_009009:SSA_1356|5end_Helicase_subunit_of_the_DNA_excision_repair_complex,_subunit_B,_putative_1371915..1372145_NEGATIVE 282 198 152 120 71 NC_009009:SSA_1795|5end_Guanosine_3',5'-bis-pyrophosphate_(ppGpp)_synthetase,_putative_1777671..1777901_NEGATIVE 278 68 26 166 122 NC_009009:SSA_1199|5end_Phosphinothricin_acetyltransferase,_putative_1223958..1224188_NEGATIVE 274 60 14 67 31 NC_009009:SSA_1512|5end_hypothetical_protein_1517936..1518166_NEGATIVE 272 60 19 113 79 NC_009009:SSA_1793|5end_Histidine_kinase_(sensor_protein),_putative_1776361..1776591_NEGATIVE 272 59 14 62 17 NC_009009:SSA_1687|5end_NADH-binding_ferric-oxidoreductase,_putative_1680547..1680777_POSITIVE 267 59 15 142 79 NC_009009:SSA_2273|5end_hypothetical_protein_2273568..2273798_NEGATIVE 267 59 13 124 65 NC_009009:SSA_0518|5end_Ethanolamine_utilization_protein_EutA,_putative_516610..516840_POSITIVE 262 59 15 55 13 NC_009009:SSA_0496|5end_Succinylglutamate_desuccinylase_/_Aspartoacylase_family,_putative_495946..496176_POSITIVE 262 59 14 212 163 NC_009009:SSA_0162|5end_hypothetical_protein_161391..161621_POSITIVE 261 57 11 214 164 NC_009009:SSA_1829|5end_RNA_methyltransferase,_putative_1820329..1820559_NEGATIVE 261 99 52 64 5 NC_009009:SSA_0101|5end_Conserved_uncharacterized_protein_103596..103826_POSITIVE 261 57 12 199 159 NC_009009:SSA_0090|5end_Acetyltransferase,_GNAT_family,_putative_90258..90488_POSITIVE 260 109 70 154 111 NC_009009:SSA_2287|5end_50S_ribosomal_protein_L32,_putative_2289821..2290051_POSITIVE 257 59 17 184 139 NC_009009:SSA_0467|5end_Cobalt-precorrin-6A_synthase_[deacetylating],_putative_470588..470818_POSITIVE 256 40 14 221 193 NC_009009:SSA_0114|5end_50S_ribosomal_protein_L16,_putative_111979..112209_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 624 50 1 89 39 NC_009009:SSA_1062|3end_50S_ribosomal_protein_L27,_putative_1078657..1078807_POSITIVE 335 60 15 108 58 NC_009009:SSA_2242|3end_hypothetical_protein_2238121..2238271_NEGATIVE 298 58 15 135 86 NC_009009:SSA_0838|3end_GtfB,_putative_826829..826979_POSITIVE 297 55 11 143 90 NC_009009:SSA_1413|3end_GufA-like_protein,_putative_1424095..1424245_NEGATIVE 285 46 7 91 56 NC_009009:SSA_1890|3end_Acetyltransferase,_putative_1887693..1887843_NEGATIVE 272 60 19 129 95 NC_009009:SSA_1794|3end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_winged-helix_DNA-binding_domains),_putative_1776345..1776495_NEGATIVE 270 67 21 65 17 NC_009009:SSA_0156|3end_ATPase_with_chaperone_activity,_ATP-binding_subunit,_putative_153322..153472_POSITIVE 267 59 15 148 85 NC_009009:SSA_2274|3end_hypothetical_protein_2273562..2273712_NEGATIVE 262 59 15 65 23 NC_009009:SSA_0495|3end_ABC-type_oligopeptide/nickel_transport_system,_ATPase_component,_putative_496036..496186_POSITIVE 260 48 10 129 97 NC_009009:SSA_0826|3end_hypothetical_protein_805516..805666_POSITIVE 258 180 135 52 10 NC_009009:SSA_1532|3end_Membrane-fusion_protein_/_periplasmic_component_of_efflux_system,_putative_1539460..1539610_NEGATIVE 253 57 13 143 97 NC_009009:SSA_0380|3end_Enzyme_of_poly-gamma-glutamate_biosynthesis_(capsule_formation),_putative_372378..372528_POSITIVE 252 58 19 43 7 NC_009009:SSA_1561|3end_Ribonuclease_III,_putative_1565185..1565335_NEGATIVE 247 98 51 104 56 NC_009009:SSA_0091|3end_V-type_sodium_ATPase,_subunit_A,_putative_92988..93138_POSITIVE 244 68 29 44 12 NC_009009:SSA_1713|3end_D-3-phosphoglycerate_dehydrogenase,_putative_1700209..1700359_NEGATIVE 244 58 12 142 96 NC_009009:SSA_0017|3end_Cell_shape_determining_protein_MreC,_putative_23706..23856_POSITIVE 243 198 159 149 113 NC_009009:SSA_0190|3end_hypothetical_protein_191905..192055_POSITIVE 240 68 23 53 4 NC_009009:SSA_2220|3end_Galactosyltransferase,_putative_2220834..2220984_NEGATIVE 239 58 11 79 16 NC_009009:SSA_2366|3end_ABC-type_cobalt_transport_system,_ATPase_component,_putative_2368030..2368180_NEGATIVE 238 117 71 117 62 NC_009009:SSA_1937|3end_Malonyl-CoA:ACP_transacylase,_putative_1923851..1924001_NEGATIVE