Origin IGS: ggattgatactcaaaagagggaaatataaattttcatatttgcttcttagctaagatgctttttcattcatcctgtacgcatttcttgcttcttaaatttgacagtattttatcccttatccaagtgaaattaaaccccaaacaacagagctattctcccccaaatagacaacaatcccccaaaatgctatattccgagcccattttatttcactgaatttccgttcatgtcatttgcccgaattgcgcttcctgtgccgttacatcgctattttgattatatcctgccggcgtcgctgaatgctgtcgtgggggcgagggtgtgggtgccgtttggggcgcagaagcgtgttggcatggtggttgaggtggcggagcagtcggat .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 atccgactgctccgccacctcaaccaccatgccaacacgcttctgcgccccaaacggcacccacaccctcgcccccacgacagcattcagcgacgccggcaggatataatcaaaatagcgatgtaacggcacaggaagcgcaattcgggcaaatgacatgaacggaaattcagtgaaataaaatgggctcggaatatagcattttgggggattgttgtctatttgggggagaatagctctgttgtttggggtttaatttcacttggataagggataaaatactgtcaaatttaagaagcaagaaatgcgtacaggatgaatgaaaaagcatcttagctaagaagcaaatatgaaaatttatatttccctcttttgagtatcaatcc Mask Tandem Repeat Region ================================================ ggattgatactcaaaagagggaaatataaattttcatatttgcttcttagctaagatgctttttcattcatcctgtacgcatttcttgcttcttaaatttgacagtattttatcccttatccaagtgaaattaaaccccaaacaacagagctattctcccccaaatagacaacaatcccccaaaatgctatattccgagcccattttatttcactgaatttccgttcatgtcatttgcccgaattgcgcttcctgtgccgttacatcgctattttgattatatcctgccggcgtcgctgaatgctgtcgtgggggcgagggtgtgggtgccgtttggggcgcagaagcgtgttggcatggtggttgaggtggcggagcagtcggat Find is-nt database================================================ Query_seq: AA01334:AA01335|AA01334:AA01335:HtrL protein involved in lipopolysaccharide biosynthesis (ADP-L-glycero-D-mannoheptose-6-epimerase):primosomal protein N':->->:901747..902132 386 ggattgatactcaaaagagggaaatataaattttcatatttgcttcttagctaagatgctttttcattcatcctgtacgcatttcttgcttcttaaatttgacagtattttatcccttatccaagtgaaattaaaccccaaacaacagagctattctcccccaaatagacaacaatcccccaaaatgctatattccgagcccattttatttcactgaatttccgttcatgtcatttgcccgaattgcgcttcctgtgccgttacatcgctattttgattatatcctgccggcgtcgctgaatgctgtcgtgggggcgagggtgtgggtgccgtttggggcgcagaagcgtgttggcatggtggttgaggtggcggagcagtcggat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA01334:AA01335|AA01334:AA01335:HtrL protein involved in lipopolysaccharide biosynthesis (ADP-L-glycero-D-mannoheptose-6-epimerase):primosomal protein N':->->:901747..902132 386 ggattgatactcaaaagagggaaatataaattttcatatttgcttcttagctaagatgctttttcattcatcctgtacgcatttcttgcttcttaaatttgacagtattttatcccttatccaagtgaaattaaaccccaaacaacagagctattctcccccaaatagacaacaatcccccaaaatgctatattccgagcccattttatttcactgaatttccgttcatgtcatttgcccgaattgcgcttcctgtgccgttacatcgctattttgattatatcctgccggcgtcgctgaatgctgtcgtgggggcgagggtgtgggtgccgtttggggcgcagaagcgtgttggcatggtggttgaggtggcggagcagtcggat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 1 Min: 228 Max: 386 Len: 159 Subject: gi|89110094|ref|AP_003874.1| primosome factor n' [Escherichia coli W3110] HSP 1 e-value: 4.0E-9 bit: 56.6 Len: 159 Query Start:228 Query End:386 Subject Strand: null Subject Start: 1 Subject End: 54 ................................................................................................................................................................................................................................... M S F A R I A L P V P L H R Y F D Y I L P A S L N A V V G A R V W V P F G - A Q K R V G M V V E V A E Q S D ................................................................................................................................................................................................................................... M P V A H V A L P V P L P R T F D Y L L P E G M T V K A G C R V R V P F G K Q Q E R I G I V V S V S D A S E Find nr database================================================ Query_seq: AA01334:AA01335|AA01334:AA01335:HtrL protein involved in lipopolysaccharide biosynthesis (ADP-L-glycero-D-mannoheptose-6-epimerase):primosomal protein N':->->:901747..902132 386 ggattgatactcaaaagagggaaatataaattttcatatttgcttcttagctaagatgctttttcattcatcctgtacgcatttcttgcttcttaaatttgacagtattttatcccttatccaagtgaaattaaaccccaaacaacagagctattctcccccaaatagacaacaatcccccaaaatgctatattccgagcccattttatttcactgaatttccgttcnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ggattgatactcaaaagagggaaatataaattttcatatttgcttcttagctaagatgctttttcattcatcctgtacgcatttcttgcttcttaaatttgacagtattttatcccttatccaagtgaaattaaaccccaaacaacagagctattctcccccaaatagacaacaatcccccaaaatgctatattccgagcccattttatttcactgaatttccgttcnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 26 End: 214 ......................... M N F H I C F L A K M L F H S S C T H F L L L K F D S I L S L I Q V K L N P K Q Q S Y S P P N R Q Q S P K M L Y S E P I ............................................................................................................................................................................ Protein_Len: 41 Strand: + Start: 175 End: 297 .............................................................................................................................................................................. M P Q N A I F R A H F I S L N F R S C H L P E L R F L C R Y I A I L I I S C R R R ......................................................................................... Protein_Len: 60 Strand: + Start: 153 End: 386 ........................................................................................................................................................ M L P Q I D N N P P K C Y I P S P F Y F T E F P F M S F A R I A L P V P L H R Y F D Y I L P A S L N A V V G A R V W V P Protein_Len: 41 Strand: - Start: 264 End: 386 ....................................................................................................................................................................................................................................................................... M A I K I I D Q R R R Q I S D H P R P H P H R K P R L L T N A H H N L H R L L R M Protein_Len: 30 Strand: - Start: 120 End: 209 ....................................................................................................................... G L S I L G W V V S S N E G L Y V V I G W F A I N R A W K M ................................................................................................................................................................................. ggattgatactcaaaagagggaaatataaattttcatatttgcttcttagctaagatgctttttcattcatcctgtacgcatttcttgcttcttaaatttgacagtattttatcccttatccaagtgaaattaaaccccaaacaacagagctattctcccccaaatagacaacaatcccccaaaatgctatattccgagcccattttatttcactgaatttccgttcnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn 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================================================ ggattgatactcaaaagagggaaatataaattttcatatttgcttcttagctaagatgctttttcattcatcctgtacgcatttcttgcttcttaaatttgacagtattttatcccttatccaagtgaaattaaaccccaaacaacagagctattctcccccaaatagacaacaatcccccaaaatgctatattccgagcccattttatttcactgaatttccgttcnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: AA01334:AA01335|AA01334:AA01335:HtrL protein involved in lipopolysaccharide biosynthesis (ADP-L-glycero-D-mannoheptose-6-epimerase):primosomal protein N':->->:901747..902132 386 ggattgatactcaaaagagggaaatataaattttcatatttgcttcttagctaagatgctttttcattcatcctgtacgcatttcttgcttcttaaatttgacagtattttatcccttatccaagtgaaattaaaccccaaacaacagagctattctcccccaaatagacaacaatcccccaaaatgctatattccgagcccattttatttcactgaatttccgttcnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn Intra-Species Hit: Count: 1 Min: 1 Max: 227 Len: 227 Subject: aact_AA01334_AA01335|HtrL protein involved in lipopolysaccharide biosynthesis (ADP-L-glycero-D-mannoheptose-6-epimerase):primosomal protein N'|POSITIVE:POSITIVE|[901747,902132]|386 HSP 1 e-value: 1.0E-125 bit: 450.0 Len: 227 Query Start:1 Query End:227 Subject Strand: POSITIVE Subject Start: 1 Subject End: 227 ggattgatactcaaaagagggaaatataaattttcatatttgcttcttagctaagatgctttttcattcatcctgtacgcatttcttgcttcttaaatttgacagtattttatcccttatccaagtgaaattaaaccccaaacaacagagctattctcccccaaatagacaacaatcccccaaaatgctatattccgagcccattttatttcactgaatttccgttc............................................................................................................................................................... ggattgatactcaaaagagggaaatataaattttcatatttgcttcttagctaagatgctttttcattcatcctgtacgcatttcttgcttcttaaatttgacagtattttatcccttatccaagtgaaattaaaccccaaacaacagagctattctcccccaaatagacaacaatcccccaaaatgctatattccgagcccattttatttcactgaatttccgttc............................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGAUUGAUACUCAAAAGAGGGAAAUAUAAAUUUUCAUAUUUGCUUCUUAGCUAAGAUGCUUUUUCAUUCAUCCUGUACGCAUUUCUUGCUUCUUAAAUUUGACAGUAUUUUAUCCCUUAUCCAAGUGAAAUUAAACCCCAAACAACAGAGCUAUUCUCCCCCAAAUAGACAACAAUCCCCCAAAAUGCUAUAUUCCGAGCCCAUUUUAUUUCACUGAAUUUCCGUUC ((((.((((((...((((((.((((((........)))))).)))))).((..((((((...................))))))...))..............))))))..))))........((((((((.(((..............((((((........))))).)................(((........)))...))).))))))))............ (-33.51) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAACGGAAAUUCAGUGAAAUAAAAUGGGCUCGGAAUAUAGCAUUUUGGGGGAUUGUUGUCUAUUUGGGGGAGAAUAGCUCUGUUGUUUGGGGUUUAAUUUCACUUGGAUAAGGGAUAAAAUACUGUCAAAUUUAAGAAGCAAGAAAUGCGUACAGGAUGAAUGAAAAAGCAUCUUAGCUAAGAAGCAAAUAUGAAAAUUUAUAUUUCCCUCUUUUGAGUAUCAAUCC ............................((((((((.....))))))))((((((.((..((...((((((((...(((((...(((((((((......((.(((.....)))))......))).))))))...)).)))...((((.((((.((((((..(....)..)))))).(((....)))...))))...))))...))))))))...))..)).)))))) (-44.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 326 218 174 167 122 aact:AA01568|5end_dipeptide_transport_system_ATP-binding_protein_1056037..1056267_POSITIVE 316 109 66 137 93 aact:AA02663|5end_DNA_ligase_1853564..1853794_POSITIVE 307 99 51 164 121 aact:AA02070|5end_hypothetical_protein_1406508..1406738_POSITIVE 292 80 40 42 1 aact:AA01069|5end_translation_elongation_factor_(EF-Ts)_739775..740005_POSITIVE 289 200 160 124 81 aact:AA01586|5end_DNA_mismatch_repair_protein_1066966..1067196_POSITIVE 282 213 175 230 181 aact:AA01730|5end_conserved_hypothetical_protein_(possible_transcriptional_regulator)_1168725..1168955_POSITIVE 282 213 175 90 41 aact:AA01729|5end_hypothetical_protein_1168585..1168815_POSITIVE 270 87 43 114 70 aact:AA01598|5end_conserved_hypothetical_protein_1078954..1079184_POSITIVE 269 159 117 88 52 aact:AA00825|5end_P-protein_(chorismate_mutase/prephenate_dehydratase)_567020..567250_POSITIVE 268 174 134 63 20 aact:AA02940|5end_conserved_hypothetical_protein_2057922..2058152_POSITIVE 263 217 171 48 9 aact:AA00993|5end_possible_D-tyrosyl-tRNA(Tyr)_deacylase_694488..694718_POSITIVE 259 200 158 189 151 aact:AA00782|5end_conserved_hypothetical_protein_538723..538953_POSITIVE 251 178 147 192 148 aact:AA01779|5end_molybdenum_ABC_transporter,_ATP-binding_protein_1200036..1200266_POSITIVE 251 115 72 128 79 aact:AA00596|5end_uridylate_kinase_407496..407726_POSITIVE 250 74 34 99 55 aact:AA01894|5end_conserved_hypothetical_protein_(possible_transthyretin-like_periplasmic_protein)_1278967..1279197_POSITIVE 247 151 114 222 184 aact:AA00814|5end_conserved_hypothetical_protein_559125..559355_POSITIVE 246 195 158 111 72 aact:AA00574|5end_regulatory_protein_392113..392343_POSITIVE 245 209 169 129 85 aact:AA01928|5end_ATP-dependent_RNA_helicase_1301986..1302216_POSITIVE 242 187 143 75 12 aact:AA00989|5end_hypothetical_protein_692319..692549_POSITIVE 241 202 161 224 182 aact:AA02545|5end_conserved_hypothetical_protein_1773965..1774195_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 316 109 66 89 45 aact:AA02662|3end_hypothetical_protein_1853596..1853746_POSITIVE 307 99 51 107 64 aact:AA02069|3end_alkylphosphonate_uptake_protein_1406531..1406681_POSITIVE 300 217 173 136 84 aact:AA02190|3end_hydrogenase-2_component_protein_1493271..1493421_POSITIVE 289 200 160 151 108 aact:AA01585|3end_tRNA_delta(2)-isopentenylpyrophosphate_1067073..1067223_POSITIVE 282 213 175 90 41 aact:AA01728|3end_conserved_hypothetical_protein(related_to_HipA_protein)_1168665..1168815_POSITIVE 269 159 117 113 77 aact:AA00824|3end_hypothetical_protein_567125..567275_POSITIVE 263 217 171 48 9 aact:AA00992|3end_ribonuclease_BN_694568..694718_POSITIVE 250 205 172 66 27 aact:AA01873|3end_mannose-6-phosphate_isomerase_1261940..1262090_POSITIVE 245 209 169 54 10 aact:AA01927|3end_conserved_hypothetical_protein_1301991..1302141_POSITIVE 245 218 178 68 20 aact:AA01705|3end_beta-galactosidase_1157980..1158130_POSITIVE 241 202 161 124 82 aact:AA02544|3end_ATP-dependent_RNA_helicase_1773945..1774095_POSITIVE 240 219 175 64 21 aact:AA02568|3end_sugar_phosphotransferase_component_II_B_1788725..1788875_POSITIVE 240 201 161 144 107 aact:AA01651|3end_hypothetical_protein_1120004..1120154_POSITIVE 239 178 151 41 5 aact:AA01778|3end_aminopeptidase_A/I;_cytosol_aminopeptidase;_leucyl_aminopeptidase_1199965..1200115_POSITIVE 237 165 121 148 93 aact:AA01590|3end_hypothetical_protein_1070971..1071121_POSITIVE 234 190 145 57 17 aact:AA01857|3end_glutamate-ammonia-ligase_adenylyltransferase_1250357..1250507_POSITIVE 233 60 12 95 36 aact:AA00249|3end_cysteinyl-tRNA_synthetase_(cysteine--tRNA_ligase)_175422..175572_POSITIVE 232 84 47 136 101 aact:AA00931|3end_elongation_factor_Tu_(tufA)_643181..643331_POSITIVE 231 200 151 56 11 aact:AA00613|3end_lipid-A-disaccharide_synthase_419974..420124_POSITIVE 226 90 50 124 85 aact:AA01262|3end_hydrolase_860087..860237_POSITIVE