Origin IGS: tgcagaacaacctatattactgattaaatgtgaaataaattgtatattcattttttactccattgattaaaatttaaaaataagactgctgcatgtccagtaatatttcatgagcatttttgagttcatgagatattgttggatgggaagcagcactttcttatagtataacaaattttactaactttataaatacttagggaaagtttttaacatttcaagtcattttttttacattttattccaaaaaatttaaatttgaataaaaaaattgtataataatattaaagaaattaaacaaaattaatgaagggggtataagtt .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 aacttatacccccttcattaattttgtttaatttctttaatattattatacaatttttttattcaaatttaaattttttggaataaaatgtaaaaaaaatgacttgaaatgttaaaaactttccctaagtatttataaagttagtaaaatttgttatactataagaaagtgctgcttcccatccaacaatatctcatgaactcaaaaatgctcatgaaatattactggacatgcagcagtcttatttttaaattttaatcaatggagtaaaaaatgaatatacaatttatttcacatttaatcagtaatataggttgttctgca Mask Tandem Repeat Region ================================================ tgcagaacaacctatattactgattaaatgtgaaataaattgtatattcattttttactccattgattaaaatttaaaaataagactgctgcatgtccagtaatatttcatgagcatttttgagttcatgagatattgttggatgggaagcagcactttcttatagtataacaaattttactaactttataaatacttagggaaagtttttaacatttcaagtcattttttttacattttattccaaaaaatttaaatttgaataaaaaaattgtataataatattaaagaaattaaacaaaattaatgaagggggtataagtt Find is-nt database================================================ Query_seq: FN0220:FN0221|FN0220:FN0221:Autolysin sensor kinase:Carbon starvation protein A:<-->:845025..845348 324 tgcagaacaacctatattactgattaaatgtgaaataaattgtatattcattttttactccattgattaaaatttaaaaataagactgctgcatgtccagtaatatttcatgagcatttttgagttcatgagatattgttggatgggaagcagcactttcttatagtataacaaattttactaactttataaatacttagggaaagtttttaacatttcaagtcattttttttacattttattccaaaaaatttaaatttgaataaaaaaattgtataataatattaaagaaattaaacaaaattaatgaagggggtataagtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0220:FN0221|FN0220:FN0221:Autolysin sensor kinase:Carbon starvation protein A:<-->:845025..845348 324 tgcagaacaacctatattactgattaaatgtgaaataaattgtatattcattttttactccattgattaaaatttaaaaataagactgctgcatgtccagtaatatttcatgagcatttttgagttcatgagatattgttggatgggaagcagcactttcttatagtataacaaattttactaactttataaatacttagggaaagtttttaacatttcaagtcattttttttacattttattccaaaaaatttaaatttgaataaaaaaattgtataataatattaaagaaattaaacaaaattaatgaagggggtataagtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0220:FN0221|FN0220:FN0221:Autolysin sensor kinase:Carbon starvation protein A:<-->:845025..845348 324 tgcagaacaacctatattactgattaaatgtgaaataaattgtatattcattttttactccattgattaaaatttaaaaataagactgctgcatgtccagtaatatttcatgagcatttttgagttcatgagatattgttggatgggaagcagcactttcttatagtataacaaattttactaactttataaatacttagggaaagtttttaacatttcaagtcattttttttacattttattccaaaaaatttaaatttgaataaaaaaattgtataataatattaaagaaattaaacaaaattaatgaagggggtataagtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgcagaacaacctatattactgattaaatgtgaaataaattgtatattcattttttactccattgattaaaatttaaaaataagactgctgcatgtccagtaatatttcatgagcatttttgagttcatgagatattgttggatgggaagcagcactttcttatagtataacaaattttactaactttataaatacttagggaaagtttttaacatttcaagtcattttttttacattttattccaaaaaatttaaatttgaataaaaaaattgtataataatattaaagaaattaaacaaaattaatgaagggggtataagtt Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: - Start: 70 End: 174 ..................................................................... F K F I L S S C T W Y Y K M L M K S N M L Y Q Q I P L L V K K Y Y L M ...................................................................................................................................................... tgcagaacaacctatattactgattaaatgtgaaataaattgtatattcattttttactccattgattaaaatttaaaaataagactgctgcatgtccagtaatatttcatgagcatttttgagttcatgagatattgttggatgggaagcagcactttcttatagtataacaaattttactaactttataaatacttagggaaagtttttaacatttcaagtcattttttttacattttattccaaaaaatttaaatttgaataaaaaaattgtataataatattaaagaaattaaacaaaattaatgaagggggtataagtt 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: 85 Start: 251 End: 280 ..........................................................................................................................................................................................................................................................ATTTAAATTTGAATAAAAAAATTGTATAAT............................................ PromScan Matrix: RpoD-17 Strand: + Score: 83 Start: 209 End: 238 ................................................................................................................................................................................................................TTTAACATTTCAAGTCATTTTTTTTACATT...................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 165 End: 194 ....................................................................................................................................................................ATTTATAAAGTTAGTAAAATTTGTTATACT.................................................................................................................................. PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 230 End: 259 .....................................................................................................................................................................................................................................TTTTACATTTTATTCCAAAAAATTTAAATT................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tgcagaacaacctatattactgattaaatgtgaaataaattgtatattcattttttactccattgattaaaatttaaaaataagactgctgcatgtccagtaatatttcatgagcatttttgagttcatgagatattgttggatgggaagcagcactttcttatagtataacaaattttactaactttataaatacttagggaaagtttttaacatttcaagtcattttttttacattttattccaaaaaatttaaatttgaataaaaaaattgtataataatattaaagaaattaaacaaaattaatgaagggggtataagtt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 53 HP_score: -5.1 Tail_Score: -3.05384 Start: 101 End: 138 Full_Region: CTGCTGCATGTCCAG TAATATTTCATGAGC ATTTTTGA GTTCATGAGATATTG TTGGATGGGAAGCAG ....................................................................................................TAATATTTCATGAGCATTTTTGAGTTCATGAGATATTG.......................................................................................................................................................................................... TransTerm Strand: + Conf: 55 HP_score: -4.6 Tail_Score: -3.67597 Start: 104 End: 135 Full_Region: CTGCATGTCCAGTAA TATTTCATGAGC ATTTTTGA GTTCATGAGATA TTGTTGGATGGGAAG .......................................................................................................TATTTCATGAGCATTTTTGAGTTCATGAGATA............................................................................................................................................................................................. TransTerm Strand: + Conf: 43 HP_score: -2.1 Tail_Score: -3.46602 Start: 146 End: 160 Full_Region: AGATATTGTTGGATG GGAAG CAGCA CTTTC TTATAGTATAACAAA .................................................................................................................................................GGAAGCAGCACTTTC.................................................................................................................................................................... Find igs database================================================ Query_seq: FN0220:FN0221|FN0220:FN0221:Autolysin sensor kinase:Carbon starvation protein A:<-->:845025..845348 324 tgcagaacaacctatattactgattaaatgtgaaataaattgtatattcattttttactccattgattaaaatttaaaaataagactgctgcatgtccagtaatatttcatgagcatttttgagttcatgagatattgttggatgggaagcagcactttcttatagtataacaaattttactaactttataaatacttagggaaagtttttaacatttcaagtcattttttttacattttattccaaaaaatttaaatttgaataaaaaaattgtataataatattaaagaaattaaacaaaattaatgaagggggtataagtt Intra-Species Hit: Count: 1 Min: 1 Max: 225 Len: 225 Subject: NC_003454_FN0220_FN0221|Autolysin sensor kinase:Carbon starvation protein A|NEGATIVE:POSITIVE|[845025,845348]|324 HSP 1 e-value: 1.0E-124 bit: 446.0 Len: 225 Query Start:1 Query End:225 Subject Strand: POSITIVE Subject Start: 1 Subject End: 225 tgcagaacaacctatattactgattaaatgtgaaataaattgtatattcattttttactccattgattaaaatttaaaaataagactgctgcatgtccagtaatatttcatgagcatttttgagttcatgagatattgttggatgggaagcagcactttcttatagtataacaaattttactaactttataaatacttagggaaagtttttaacatttcaagtca................................................................................................... tgcagaacaacctatattactgattaaatgtgaaataaattgtatattcattttttactccattgattaaaatttaaaaataagactgctgcatgtccagtaatatttcatgagcatttttgagttcatgagatattgttggatgggaagcagcactttcttatagtataacaaattttactaactttataaatacttagggaaagtttttaacatttcaagtca................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGCAGAACAACCUAUAUUACUGAUUAAAUGUGAAAUAAAUUGUAUAUUCAUUUUUUACUCCAUUGAUUAAAAUUUAAAAAUAAGACUGCUGCAUGUCCAGUAAUAUUUCAUGAGCAUUUUUGAGUUCAUGAGAUAUUGUUGGAUGGGAAGCAGCACUUUCUUAUAGUAUAACAAAUUUUACUAACUUUAUAAAUACUUAGGGAAAGUUUUUAACAUUUCAAGUCA ...(((((..((((((((..(((......(((((((...((((((.......(((((.((....)).))))).......((((((.((((((.((((((((((((((((((((((........))))))))))))))))))))))....))))))...)))))).))))))...))))))).....)))..))))..))))....)))))............... (-50.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGACUUGAAAUGUUAAAAACUUUCCCUAAGUAUUUAUAAAGUUAGUAAAAUUUGUUAUACUAUAAGAAAGUGCUGCUUCCCAUCCAACAAUAUCUCAUGAACUCAAAAAUGCUCAUGAAAUAUUACUGGACAUGCAGCAGUCUUAUUUUUAAAUUUUAAUCAAUGGAGUAAAAAAUGAAUAUACAAUUUAUUUCACAUUUAAUCAGUAAUAUAGGUUGUUCUGCA ((((((.......((((.((((.....)))).))))..)))))).(((((((((.......((((((...((((((......((((..(((((.((((((.(........).)))))).)))))..))))...)))))).))))))...))))))))).....(((((((((...((......)).)))))))))........(((.((((.....))))))).. (-42.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 836 130 81 221 172 NC_003454:FN0220|5end_Autolysin_sensor_kinase_844934..845164_NEGATIVE 425 130 81 188 138 NC_003454:FN1351|5end_15_kDa_lipoprotein_precursor_2003372..2003602_NEGATIVE 385 130 83 218 170 NC_003454:FN1581|5end_DNA_mismatch_repair_protein_mutS_93231..93461_NEGATIVE 353 130 81 216 165 NC_003454:FN0054|5end_tyrosyl-tRNA_synthetase_690836..691066_POSITIVE 342 137 93 222 178 NC_003454:FN1740|5end_ATP_synthase_subunit_K_238400..238630_NEGATIVE 322 127 86 206 164 NC_003454:FN1142|5end_Oxygen-independent_coproporphyrinogen_III_oxidase_1791529..1791759_POSITIVE 320 155 112 214 171 NC_003454:FN1439|5end_Transcriptional_regulator,_DeoR_family_2106428..2106658_POSITIVE 320 155 112 110 67 NC_003454:FN1438|5end_hypothetical_protein_2106324..2106554_POSITIVE 292 121 81 101 56 NC_003454:FN2105|5end_Integral_membrane_protein_614701..614931_POSITIVE 247 160 111 70 17 NC_003454:FN1468|5end_Flavoredoxin_2150385..2150615_NEGATIVE 242 158 113 181 133 NC_003454:FN0656|5end_hypothetical_protein_1313725..1313955_POSITIVE 235 157 113 68 14 NC_003454:FN0471|5end_Cell_surface_protein_1116525..1116755_POSITIVE 228 188 142 177 138 NC_003454:FN0104|5end_Acetyltransferase_739896..740126_NEGATIVE 227 127 83 222 176 NC_003454:FN1328|5end_Exodeoxyribonuclease_VII_small_subunit_1983129..1983359_NEGATIVE 225 127 95 167 134 NC_003454:FN1551|5end_hypothetical_protein_66187..66417_NEGATIVE 222 129 85 125 71 NC_003454:FN0068|5end_Lipoprotein_signal_peptidase_707308..707538_POSITIVE 220 187 142 138 99 NC_003454:FN1633|5end_LSU_ribosomal_protein_L24P_135939..136169_NEGATIVE 219 129 86 78 34 NC_003454:FN0182|5end_Sarcosine_oxidase_alpha_subunit_807066..807296_NEGATIVE 217 116 80 40 3 NC_003454:FN1430|5end_Branched-chain_amino_acid_transport_system_permease_protein_livM_2099202..2099432_NEGATIVE 217 125 82 63 19 NC_003454:FN1192|5end_hypothetical_protein_1854679..1854909_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 425 130 81 54 4 NC_003454:FN1352|3end_ABC_transporter_ATP-binding_protein_2003506..2003656_NEGATIVE 342 137 93 61 17 NC_003454:FN1741|3end_ATP_synthase_subunit_I_238561..238711_NEGATIVE 335 154 112 79 37 NC_003454:FN0828|3end_ABC_transporter_permease_protein_1489505..1489655_POSITIVE 331 153 111 65 22 NC_003454:FN1259|3end_Uracil-DNA_glycosylase_1915756..1915906_POSITIVE 292 121 81 80 35 NC_003454:FN2104|3end_hypothetical_protein_614760..614910_POSITIVE 274 155 111 133 92 NC_003454:FN0004|3end_Inner_membrane_protein_643834..643984_POSITIVE 247 160 111 68 15 NC_003454:FN1469|3end_Na+_driven_multidrug_efflux_pump_2150387..2150537_NEGATIVE 240 169 127 89 37 NC_003454:FN0100|3end_Flavodoxins/hemoproteins_735119..735269_NEGATIVE 219 129 86 66 22 NC_003454:FN0183|3end_Glycerol-3-phosphate_dehydrogenase_807078..807228_NEGATIVE 217 89 46 108 65 NC_003454:FN0781|3end_Integral_membrane_protein_1437511..1437661_NEGATIVE 213 116 75 106 64 NC_003454:FN0879|3end_ABC_transporter_integral_membrane_protein_1540161..1540311_NEGATIVE 207 173 140 39 3 NC_003454:FN1736|3end_V-type_sodium_ATP_synthase_subunit_A_235413..235563_NEGATIVE 203 184 141 143 107 NC_003454:FN0050|3end_Fumarate_reductase_flavoprotein_subunit_688799..688949_POSITIVE 200 74 46 73 46 NC_003454:FN0569|3end_Hypothetical_membrane-spanning_protein_1219476..1219626_NEGATIVE 199 49 1 75 26 NC_003454:FN0520|3end_hypothetical_protein_1171678..1171828_NEGATIVE 198 129 96 134 100 NC_003454:FN1746|3end_Cystathionine_beta-lyase_245680..245830_POSITIVE 195 96 57 126 78 NC_003454:FN1003|3end_Outer_membrane_protein_P1_precursor_1659723..1659873_POSITIVE 194 168 123 117 68 NC_003454:FN0473|3end_Regulatory_protein_betI_1118941..1119091_POSITIVE 191 139 93 56 9 NC_003454:FN0052|3end_Arsenate_reductase_689291..689441_POSITIVE 190 125 95 151 120 NC_003454:FN1552|3end_hypothetical_protein_66201..66351_NEGATIVE