Origin IGS: tttatctccttttgtacaaaataatcttcatccctttattacttaagcaaaaagaccatgaggaacacaccgcaagtcaatagaatgcagggctagacctaatggacttcttttattatacaccgaaacaccatcgtcttcaactaaatactcctcaaatttttaagtcgtctggtgatttctatcagaaagttacttctactaagttaatctgccattgatagctgctat .........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 atagcagctatcaatggcagattaacttagtagaagtaactttctgatagaaatcaccagacgacttaaaaatttgaggagtatttagttgaagacgatggtgtttcggtgtataataaaagaagtccattaggtctagccctgcattctattgacttgcggtgtgttcctcatggtctttttgcttaagtaataaagggatgaagattattttgtacaaaaggagataaa Mask Tandem Repeat Region ================================================ tttatctccttttgtacaaaataatcttcatccctttattacttaagcaaaaagaccatgaggaacacaccgcaagtcaatagaatgcagggctagacctaatggacttcttttattatacaccgaaacaccatcgtcttcaactaaatactcctcaaatttttaagtcgtctggtgatttctatcagaaagttacttctactaagttaatctgccattgatagctgctat Find is-nt database================================================ Query_seq: SSA_1381:SSA_1382|SSA_1381:SSA_1382:hypothetical protein:hypothetical protein:<-<-:1399656..1399886 231 tttatctccttttgtacaaaataatcttcatccctttattacttaagcaaaaagaccatgaggaacacaccgcaagtcaatagaatgcagggctagacctaatggacttcttttattatacaccgaaacaccatcgtcttcaactaaatactcctcaaatttttaagtcgtctggtgatttctatcagaaagttacttctactaagttaatctgccattgatagctgctat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1381:SSA_1382|SSA_1381:SSA_1382:hypothetical protein:hypothetical protein:<-<-:1399656..1399886 231 tttatctccttttgtacaaaataatcttcatccctttattacttaagcaaaaagaccatgaggaacacaccgcaagtcaatagaatgcagggctagacctaatggacttcttttattatacaccgaaacaccatcgtcttcaactaaatactcctcaaatttttaagtcgtctggtgatttctatcagaaagttacttctactaagttaatctgccattgatagctgctat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1381:SSA_1382|SSA_1381:SSA_1382:hypothetical protein:hypothetical protein:<-<-:1399656..1399886 231 tttatctccttttgtacaaaataatcttcatccctttattacttaagcaaaaagaccatgaggaacacaccgcaagtcaatagaatgcagggctagacctaatggacttcttttattatacaccgaaacaccatcgtcttcaactaaatactcctcaaatttttaagtcgtctggtgatttctatcagaaagttacttctactaagttaatctgccattgatagctgctat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttatctccttttgtacaaaataatcttcatccctttattacttaagcaaaaagaccatgaggaacacaccgcaagtcaatagaatgcagggctagacctaatggacttcttttattatacaccgaaacaccatcgtcttcaactaaatactcctcaaatttttaagtcgtctggtgatttctatcagaaagttacttctactaagttaatctgccattgatagctgctat Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: + Start: 102 End: 218 ..................................................................................................... M D F F Y Y T P K H H R L Q L N T P Q I F K S S G D F Y Q K V T S T K L I C H ............. tttatctccttttgtacaaaataatcttcatccctttattacttaagcaaaaagaccatgaggaacacaccgcaagtcaatagaatgcagggctagacctaatggacttcttttattatacaccgaaacaccatcgtcttcaactaaatactcctcaaatttttaagtcgtctggtgatttctatcagaaagttacttctactaagttaatctgccattgatagctgctat 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: 87 Start: 115 End: 144 ..................................................................................................................GTTGAAGACGATGGTGTTTCGGTGTATAAT....................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tttatctccttttgtacaaaataatcttcatccctttattacttaagcaaaaagaccatgaggaacacaccgcaagtcaatagaatgcagggctagacctaatggacttcttttattatacaccgaaacaccatcgtcttcaactaaatactcctcaaatttttaagtcgtctggtgatttctatcagaaagttacttctactaagttaatctgccattgatagctgctat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1381:SSA_1382|SSA_1381:SSA_1382:hypothetical protein:hypothetical protein:<-<-:1399656..1399886 231 tttatctccttttgtacaaaataatcttcatccctttattacttaagcaaaaagaccatgaggaacacaccgcaagtcaatagaatgcagggctagacctaatggacttcttttattatacaccgaaacaccatcgtcttcaactaaatactcctcaaatttttaagtcgtctggtgatttctatcagaaagttacttctactaagttaatctgccattgatagctgctat Intra-Species Hit: Count: 1 Min: 1 Max: 231 Len: 231 Subject: NC_009009_SSA_1381_SSA_1382|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[1399656,1399886]|231 HSP 1 e-value: 1.0E-128 bit: 458.0 Len: 231 Query Start:1 Query End:231 Subject Strand: POSITIVE Subject Start: 1 Subject End: 231 tttatctccttttgtacaaaataatcttcatccctttattacttaagcaaaaagaccatgaggaacacaccgcaagtcaatagaatgcagggctagacctaatggacttcttttattatacaccgaaacaccatcgtcttcaactaaatactcctcaaatttttaagtcgtctggtgatttctatcagaaagttacttctactaagttaatctgccattgatagctgctat tttatctccttttgtacaaaataatcttcatccctttattacttaagcaaaaagaccatgaggaacacaccgcaagtcaatagaatgcagggctagacctaatggacttcttttattatacaccgaaacaccatcgtcttcaactaaatactcctcaaatttttaagtcgtctggtgatttctatcagaaagttacttctactaagttaatctgccattgatagctgctat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUAUCUCCUUUUGUACAAAAUAAUCUUCAUCCCUUUAUUACUUAAGCAAAAAGACCAUGAGGAACACACCGCAAGUCAAUAGAAUGCAGGGCUAGACCUAAUGGACUUCUUUUAUUAUACACCGAAACACCAUCGUCUUCAACUAAAUACUCCUCAAAUUUUUAAGUCGUCUGGUGAUUUCUAUCAGAAAGUUACUUCUACUAAGUUAAUCUGCCAUUGAUAGCUGCUAU ........................(((((((..((((.............))))...))))))).......(((..((....)).)))..(((((....((((((...................(((((((((.((.(((.....((((.........))))..))).))..))))).))))...((((.....((((.....))))...)))))))))).)))))..... (-31.72) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAGCAGCUAUCAAUGGCAGAUUAACUUAGUAGAAGUAACUUUCUGAUAGAAAUCACCAGACGACUUAAAAAUUUGAGGAGUAUUUAGUUGAAGACGAUGGUGUUUCGGUGUAUAAUAAAAGAAGUCCAUUAGGUCUAGCCCUGCAUUCUAUUGACUUGCGGUGUGUUCCUCAUGGUCUUUUUGCUUAAGUAAUAAAGGGAUGAAGAUUAUUUUGUACAAAAGGAGAUAAA ....((((((....(((..((((..((...((((((....))))))..)).)))).))).((..(((((....)))))..))...))))))..........((((((..(((((((...((((((.((((.(((....((.(((((.((....))..))))).))...))).)))).)))))).(((.(....).)))..............)))))))....)))))).. (-48.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 977 100 51 191 142 NC_009009:SSA_1381|5end_hypothetical_protein_1399565..1399795_NEGATIVE 304 170 128 181 147 NC_009009:SSA_1019|5end_Collagen-binding_surface_protein,_putative_1032877..1033107_POSITIVE 303 110 61 52 6 NC_009009:SSA_0189|5end_Competence_protein_ComGF,_putative_191015..191245_POSITIVE 290 108 69 200 158 NC_009009:SSA_0197|5end_Dihydropteroate_synthase,_putative_195946..196176_POSITIVE 284 110 73 72 26 NC_009009:SSA_1890|5end_Acetyltransferase,_putative_1888145..1888375_NEGATIVE 284 97 53 68 28 NC_009009:SSA_1118|5end_Peptide_methionine_sulfoxide_reductase,_putative_1143322..1143552_POSITIVE 280 63 25 193 155 NC_009009:SSA_1940|5end_3-oxoacyl-[acyl-carrier-protein]_synthase_III,_putative_1927129..1927359_NEGATIVE 279 100 54 59 16 NC_009009:SSA_2352|5end_ABC-type_nitrate/sulfonate/bicarbonate_transporter,_periplasmic_component,_putative_2354508..2354738_NEGATIVE 275 175 131 50 4 NC_009009:SSA_1443|5end_1-(5-phosphoribosyl)-5-[(5-_phosphoribosylamino)methylideneamino]_imidazole-4-carboxamide_isomerase,_putative_1446672..1446902_NEGATIVE 275 99 53 124 86 NC_009009:SSA_0299|5end_hypothetical_protein_292759..292989_POSITIVE 274 99 55 69 27 NC_009009:SSA_2312|5end_hypothetical_protein_2315281..2315511_NEGATIVE 273 107 61 52 5 NC_009009:SSA_2153|5end_ABC-type_transporter_(uncharacterized),_permease_component,_putative_2154664..2154894_NEGATIVE 272 109 71 202 161 NC_009009:SSA_0043|5end_hypothetical_protein_48801..49031_POSITIVE 270 158 124 167 140 NC_009009:SSA_1231|5end_hypothetical_protein_1254758..1254988_NEGATIVE 266 91 57 58 23 NC_009009:SSA_1474|5end_Lipoprotein,_putative_1479741..1479971_NEGATIVE 266 229 181 54 6 NC_009009:SSA_0458|5end_Formylmethionine_deformylase,_putative_461609..461839_POSITIVE 265 99 61 157 121 NC_009009:SSA_0563|5end_Universal_stress_protein_family,_putative_555399..555629_NEGATIVE 264 229 181 187 135 NC_009009:SSA_1808|5end_hypothetical_protein_1792209..1792439_NEGATIVE 264 106 61 68 13 NC_009009:SSA_0375|5end_D-methionine-binding_lipoprotein_(ABC-type_transporter),_putative_364257..364487_POSITIVE 263 100 55 168 123 NC_009009:SSA_0365|5end_Small-conductance_mechanosensitive_efflux_channel,_putative_356621..356851_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 303 110 61 68 22 NC_009009:SSA_0188|3end_hypothetical_protein_191111..191261_POSITIVE 292 98 51 57 1 NC_009009:SSA_0842|3end_Effector_of_murein_hydrolase_LrgA/holin-like_protein,_putative_827790..827940_POSITIVE 288 124 82 47 8 NC_009009:SSA_1495|3end_S-adenosylmethionine_synthetase,_putative_1501019..1501169_NEGATIVE 284 110 73 71 25 NC_009009:SSA_1891|3end_Oxidoreductase,_aldo/keto_reductase_family,_putative_1888146..1888296_NEGATIVE 284 97 53 52 12 NC_009009:SSA_1117|3end_hypothetical_protein_1143386..1143536_POSITIVE 282 220 171 63 16 NC_009009:SSA_0287|3end_Glycerol_dehydrogenase,_NAD+_dependent,_putative_280702..280852_POSITIVE 275 175 131 78 32 NC_009009:SSA_1444|3end_Imidazole_glycerol-phosphate_synthase_subunit_hisH,_putative_1446644..1446794_NEGATIVE 270 158 124 119 92 NC_009009:SSA_1232|3end_Topoisomerase_IV_subunit_B,_putative_1254806..1254956_NEGATIVE 268 70 21 76 24 NC_009009:SSA_0563|3end_Universal_stress_protein_family,_putative_554947..555097_NEGATIVE 260 112 75 60 14 NC_009009:SSA_1650|3end_3-Ketoacyl-ACP_reductase,_putative_1648896..1649046_NEGATIVE 260 99 55 139 87 NC_009009:SSA_0203|3end_hypothetical_protein_202124..202274_POSITIVE 257 180 137 130 79 NC_009009:SSA_2279|3end_hypothetical_protein_2281671..2281821_NEGATIVE 256 216 174 123 75 NC_009009:SSA_1960|3end_hypothetical_protein_1956571..1956721_NEGATIVE 256 97 54 54 7 NC_009009:SSA_1016|3end_Phosphoenolpyruvate_synthase,_putative_1022165..1022315_POSITIVE 256 105 70 108 65 NC_009009:SSA_0897|3end_Two_component_system_histidine_kinase,_putative_889811..889961_POSITIVE 256 126 81 75 22 NC_009009:SSA_0133|3end_50S_ribosomal_protein_L17,_putative_122562..122712_POSITIVE 253 91 58 87 52 NC_009009:SSA_0929|3end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_940263..940413_POSITIVE 252 97 51 42 9 NC_009009:SSA_1131|3end_High-affinity_Fe_2+/Pb2+_permease,_putative_1158768..1158918_POSITIVE 250 132 91 62 27 NC_009009:SSA_0672|3end_hypothetical_protein_656044..656194_POSITIVE 249 225 181 133 90 NC_009009:SSA_0270|3end_Phosphotransferase_system_(PTS)_cellobiose-specific,_IIC_component,_putative_264314..264464_POSITIVE