Origin IGS: tgagatcttgacattatcttgttaaaatccaccgcactttatgtgcaaacataaattgttcggacgaaggtagctggagagcggggaatcgaccccacgccgacgaggtaaaatctttcaggcgcgatggcagggactgttactggacgaacccttggagagatccaaggtacttttaaagcgtttactttcaaggtaacgactttttaagtgctaatggacgccgaaggcgcaaagaagcttgattccatcaggcttttcaaacgctcaggcaaaaggacaggggcaggagatattcggttagcgttaactcaaggcaattgggttaatttttcattttgttgatccgcaacattcttttcgcctccttgtaatttggttatttacgaggaacctcaa .........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 ttgaggttcctcgtaaataaccaaattacaaggaggcgaaaagaatgttgcggatcaacaaaatgaaaaattaacccaattgccttgagttaacgctaaccgaatatctcctgcccctgtccttttgcctgagcgtttgaaaagcctgatggaatcaagcttctttgcgccttcggcgtccattagcacttaaaaagtcgttaccttgaaagtaaacgctttaaaagtaccttggatctctccaagggttcgtccagtaacagtccctgccatcgcgcctgaaagattttacctcgtcggcgtggggtcgattccccgctctccagctaccttcgtccgaacaatttatgtttgcacataaagtgcggtggattttaacaagataatgtcaagatctca Mask Tandem Repeat Region ================================================ tgagatcttgacattatcttgttaaaatccaccgcactttatgtgcaaacataaattgttcggacgaaggtagctggagagcggggaatcgaccccacgccgacgaggtaaaatctttcaggcgcgatggcagggactgttactggacgaacccttggagagatccaaggtacttttaaagcgtttactttcaaggtaacgactttttaagtgctaatggacgccgaaggcgcaaagaagcttgattccatcaggcttttcaaacgctcaggcaaaaggacaggggcaggagatattcggttagcgttaactcaaggcaattgggttaatttttcattttgttgatccgcaacattcttttcgcctccttgtaatttggttatttacgaggaacctcaa Find is-nt database================================================ Query_seq: AA00166:AA00167|AA00166:AA00167:conserved hypothetical protein (possible acetyltransferase):possible amino-acid transporter (sodium-alanine symporters):->->:117980..118378 399 tgagatcttgacattatcttgttaaaatccaccgcactttatgtgcaaacataaattgttcggacgaaggtagctggagagcggggaatcgaccccacgccgacgaggtaaaatctttcaggcgcgatggcagggactgttactggacgaacccttggagagatccaaggtacttttaaagcgtttactttcaaggtaacgactttttaagtgctaatggacgccgaaggcgcaaagaagcttgattccatcaggcttttcaaacgctcaggcaaaaggacaggggcaggagatattcggttagcgttaactcaaggcaattgggttaatttttcattttgttgatccgcaacattcttttcgcctccttgtaatttggttatttacgaggaacctcaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA00166:AA00167|AA00166:AA00167:conserved hypothetical protein (possible acetyltransferase):possible amino-acid transporter (sodium-alanine symporters):->->:117980..118378 399 tgagatcttgacattatcttgttaaaatccaccgcactttatgtgcaaacataaattgttcggacgaaggtagctggagagcggggaatcgaccccacgccgacgaggtaaaatctttcaggcgcgatggcagggactgttactggacgaacccttggagagatccaaggtacttttaaagcgtttactttcaaggtaacgactttttaagtgctaatggacgccgaaggcgcaaagaagcttgattccatcaggcttttcaaacgctcaggcaaaaggacaggggcaggagatattcggttagcgttaactcaaggcaattgggttaatttttcattttgttgatccgcaacattcttttcgcctccttgtaatttggttatttacgaggaacctcaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA00166:AA00167|AA00166:AA00167:conserved hypothetical protein (possible acetyltransferase):possible amino-acid transporter (sodium-alanine symporters):->->:117980..118378 399 tgagatcttgacattatcttgttaaaatccaccgcactttatgtgcaaacataaattgttcggacgaaggtagctggagagcggggaatcgaccccacgccgacgaggtaaaatctttcaggcgcgatggcagggactgttactggacgaacccttggagagatccaaggtacttttaaagcgtttactttcaaggtaacgactttttaagtgctaatggacgccgaaggcgcaaagaagcttgattccatcaggcttttcaaacgctcaggcaaaaggacaggggcaggagatattcggttagcgttaactcaaggcaattgggttaatttttcattttgttgatccgcaacattcttttcgcctccttgtaatttggttatttacgaggaacctcaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgagatcttgacattatcttgttaaaatccaccgcactttatgtgcaaacataaattgttcggacgaaggtagctggagagcggggaatcgaccccacgccgacgaggtaaaatctttcaggcgcgatggcagggactgttactggacgaacccttggagagatccaaggtacttttaaagcgtttactttcaaggtaacgactttttaagtgctaatggacgccgaaggcgcaaagaagcttgattccatcaggcttttcaaacgctcaggcaaaaggacaggggcaggagatattcggttagcgttaactcaaggcaattgggttaatttttcattttgttgatccgcaacattcttttcgcctccttgtaatttggttatttacgaggaacctcaa Predict ORF larger than 30AA ================================================ Protein_Len: 50 Strand: + Start: 27 End: 176 .......................... M H R T L C A N I N C S D E G S W R A G N R P H A D E V K S F R R D G R D C Y W T N P W R D P R Y F ............................................................................................................................................................................................................................... Protein_Len: 41 Strand: + Start: 74 End: 196 ......................................................................... M E S G E S T P R R R G K I F Q A R W Q G L L L D E P L E R S K V L L K R L L S R ........................................................................................................................................................................................................... Protein_Len: 44 Strand: + Start: 211 End: 342 .................................................................................................................................................................................................................. M L M D A E G A K K L D S I R L F K R S G K R T G A G D I R L A L T Q G N W V N F S F C ......................................................... Protein_Len: 51 Strand: - Start: 42 End: 194 ......................................... T C V Y I T R V F T A P S R P I S G V G V L Y F R E P A I A P V T V P R V R P S I W P V K L A N V K M ............................................................................................................................................................................................................. Protein_Len: 30 Strand: - Start: 25 End: 114 ........................ F G G C K I H L C L N N P R L Y S S L P S D V G R R R P L M ............................................................................................................................................................................................................................................................................................. Protein_Len: 39 Strand: - Start: 17 End: 133 ................ R T L I W R V K H A F M F Q E S S P L Q L A P F R G W A S S T F D K L R S P M .......................................................................................................................................................................................................................................................................... tgagatcttgacattatcttgttaaaatccaccgcactttatgtgcaaacataaattgttcggacgaaggtagctggagagcggggaatcgaccccacgccgacgaggtaaaatctttcaggcgcgatggcagggactgttactggacgaacccttggagagatccaaggtacttttaaagcgtttactttcaaggtaacgactttttaagtgctaatggacgccgaaggcgcaaagaagcttgattccatcaggcttttcaaacgctcaggcaaaaggacaggggcaggagatattcggttagcgttaactcaaggcaattgggttaatttttcattttgttgatccgcaacattcttttcgcctccttgtaatttggttatttacgaggaacctcaa 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: 81 Start: -1 End: 28 ccTGAGATCTTGACATTATCTTGTTAAAAT................................................................................................................................................................................................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tgagatcttgacattatcttgttaaaatccaccgcactttatgtgcaaacataaattgttcggacgaaggtagctggagagcggggaatcgaccccacgccgacgaggtaaaatctttcaggcgcgatggcagggactgttactggacgaacccttggagagatccaaggtacttttaaagcgtttactttcaaggtaacgactttttaagtgctaatggacgccgaaggcgcaaagaagcttgattccatcaggcttttcaaacgctcaggcaaaaggacaggggcaggagatattcggttagcgttaactcaaggcaattgggttaatttttcattttgttgatccgcaacattcttttcgcctccttgtaatttggttatttacgaggaacctcaa Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 70 HP_score: -9.9 Tail_Score: -3.08776 Start: 153 End: 170 Full_Region: TGTTACTGGACGAAC CCTTGGA GAGA TCCAAGG TACTTTTAAAGCGTT ........................................................................................................................................................CCTTGGAGAGATCCAAGG..................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 71 HP_score: -7.3 Tail_Score: -4.08767 Start: 240 End: 256 Full_Region: CGAAGGCGCAAAGAA GCTTGAT TCC ATCAGGC TTTTCAAACGCTCAG ...............................................................................................................................................................................................................................................GCTTGATTCCATCAGGC............................................................................................................................................... TransTerm Strand: + Conf: 82 HP_score: -5.7 Tail_Score: -5.17786 Start: 307 End: 329 Full_Region: GATATTCGGTTAGCG TTAACTCAA GGCAA TTGGGTTAA TTTTTCATTTTGTTG ..................................................................................................................................................................................................................................................................................................................TTAACTCAAGGCAATTGGGTTAA...................................................................... Find igs database================================================ Query_seq: AA00166:AA00167|AA00166:AA00167:conserved hypothetical protein (possible acetyltransferase):possible amino-acid transporter (sodium-alanine symporters):->->:117980..118378 399 tgagatcttgacattatcttgttaaaatccaccgcactttatgtgcaaacataaattgttcggacgaaggtagctggagagcggggaatcgaccccacgccgacgaggtaaaatctttcaggcgcgatggcagggactgttactggacgaacccttggagagatccaaggtacttttaaagcgtttactttcaaggtaacgactttttaagtgctaatggacgccgaaggcgcaaagaagcttgattccatcaggcttttcaaacgctcaggcaaaaggacaggggcaggagatattcggttagcgttaactcaaggcaattgggttaatttttcattttgttgatccgcaacattcttttcgcctccttgtaatttggttatttacgaggaacctcaa Intra-Species Hit: Count: 1 Min: 1 Max: 399 Len: 399 Subject: aact_AA00166_AA00167|conserved hypothetical protein (possible acetyltransferase):possible amino-acid transporter (sodium-alanine symporters)|POSITIVE:POSITIVE|[117980,118378]|399 HSP 1 e-value: 0.0 bit: 791.0 Len: 399 Query Start:1 Query End:399 Subject Strand: POSITIVE Subject Start: 1 Subject End: 399 tgagatcttgacattatcttgttaaaatccaccgcactttatgtgcaaacataaattgttcggacgaaggtagctggagagcggggaatcgaccccacgccgacgaggtaaaatctttcaggcgcgatggcagggactgttactggacgaacccttggagagatccaaggtacttttaaagcgtttactttcaaggtaacgactttttaagtgctaatggacgccgaaggcgcaaagaagcttgattccatcaggcttttcaaacgctcaggcaaaaggacaggggcaggagatattcggttagcgttaactcaaggcaattgggttaatttttcattttgttgatccgcaacattcttttcgcctccttgtaatttggttatttacgaggaacctcaa tgagatcttgacattatcttgttaaaatccaccgcactttatgtgcaaacataaattgttcggacgaaggtagctggagagcggggaatcgaccccacgccgacgaggtaaaatctttcaggcgcgatggcagggactgttactggacgaacccttggagagatccaaggtacttttaaagcgtttactttcaaggtaacgactttttaagtgctaatggacgccgaaggcgcaaagaagcttgattccatcaggcttttcaaacgctcaggcaaaaggacaggggcaggagatattcggttagcgttaactcaaggcaattgggttaatttttcattttgttgatccgcaacattcttttcgcctccttgtaatttggttatttacgaggaacctcaa Inter-species Hit: Count: 3 Min: 58 Max: 288 Len: 231 Subject: NC_007146_NTHI1046_NTHI1047|predicted Na+/alanine symporter:aerobic respiration control protein ArcA|NEGATIVE:NEGATIVE|[992620,993018]|399 HSP 1 e-value: 1.0E-43 bit: 178.0 Len: 110 Query Start:58 Query End:167 Subject Strand: NEGATIVE Subject Start: 201 Subject End: 310 .........................................................gttcggacgaaggtagctggagagcggggaatcgaccccacgccgacgaggtaaaatctttcaggcgcgatggcagggactgttactggacgaacccttggagagatcca........................................................................................................................................................................................................................................ .........................................................gttcggatgaaggtagctggagagcggggaattgaccccacaccgacgatgtaaaatctttcaggtgcgatggcagggactgttactggacgaacccttggagagatcca........................................................................................................................................................................................................................................ HSP 2 e-value: 4.0E-9 bit: 63.9 Len: 32 Query Start:257 Query End:288 Subject Strand: NEGATIVE Subject Start: 118 Subject End: 149 ................................................................................................................................................................................................................................................................ttttcaaacgctcaggcaaaaggacaggggca............................................................................................................... ................................................................................................................................................................................................................................................................ttttcaaacgctcaggcaaaaggacaggggca............................................................................................................... Subject: NC_000907_HI0883_HI0884|amino acid carrier protein:aerobic respiration control protein ArcA|NEGATIVE:NEGATIVE|[936114,936510]|397 HSP 1 e-value: 2.0E-41 bit: 170.0 Len: 110 Query Start:58 Query End:167 Subject Strand: NEGATIVE Subject Start: 199 Subject End: 308 .........................................................gttcggacgaaggtagctggagagcggggaatcgaccccacgccgacgaggtaaaatctttcaggcgcgatggcagggactgttactggacgaacccttggagagatcca........................................................................................................................................................................................................................................ .........................................................gttcggatgaaggtagctggagagcgggaaattgaccccacaccgacgatgtaaaatctttcaggtgcgatggcagggactgttactggacgaacccttggagagatcca........................................................................................................................................................................................................................................ HSP 2 e-value: 4.0E-9 bit: 63.9 Len: 32 Query Start:257 Query End:288 Subject Strand: NEGATIVE Subject Start: 117 Subject End: 148 ................................................................................................................................................................................................................................................................ttttcaaacgctcaggcaaaaggacaggggca............................................................................................................... ................................................................................................................................................................................................................................................................ttttcaaacgctcaggcaaaaggacaggggca............................................................................................................... Subject: NC_002663_PM0090_PM0091|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[115840,116287]|448 HSP 1 e-value: 1.0E-24 bit: 115.0 Len: 106 Query Start:58 Query End:163 Subject Strand: POSITIVE Subject Start: 120 Subject End: 230 .........................................................gttcggacgaaggtagctggagagcggggaatcgaccccacgccgacgaggtaaaatctttcaggcgc-gat----ggcagggactgttactggacgaacccttggagaga............................................................................................................................................................................................................................................ .........................................................gttcggatgaaggtagctggagagtagggaattgaccctacgccgacgaggtaaactctttcaggcgctgattataagcagggactgttactggacgaacccttggagaga............................................................................................................................................................................................................................................ HSP 2 e-value: 4.0E-9 bit: 63.9 Len: 32 Query Start:257 Query End:288 Subject Strand: POSITIVE Subject Start: 297 Subject End: 328 ................................................................................................................................................................................................................................................................ttttcaaacgctcaggcaaaaggacaggggca............................................................................................................... ................................................................................................................................................................................................................................................................ttttcaaacgctcaggcaaaaggacaggggca............................................................................................................... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUCGGACGAAGGUAGCUGGAGAGCGGGGAAUCGACCCCACGCCGACGAGGUAAAAUCUUUCAGGCGCGAUGGCAGGGACUGUUACUGGACGAACCCUUGGAGAGAUCCAAGGUACUUUUAAAGCGUUUACUUUCAAGGUAACGACUUUUUAAGUGCUAAUGGACGCCGAAGGCGCAAAGAAGCUUGAUUCCAUCAGGCUUUUCAAACGCUCAGGCAAAAGGACAGGGGCA ((((((.....(((..(((......((((......)))).((((...(((((...)))))...))))......)))..)))....))))))...((((((......((((.(((((((..((((((((.(((.....))))))).))))..)))))))..)))).(((...((((...(((((((((((...)))))))))))....))))..))).......)))))).. (-78.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGCCCCUGUCCUUUUGCCUGAGCGUUUGAAAAGCCUGAUGGAAUCAAGCUUCUUUGCGCCUUCGGCGUCCAUUAGCACUUAAAAAGUCGUUACCUUGAAAGUAAACGCUUUAAAAGUACCUUGGAUCUCUCCAAGGGUUCGUCCAGUAACAGUCCCUGCCAUCGCGCCUGAAAGAUUUUACCUCGUCGGCGUGGGGUCGAUUCCCCGCUCUCCAGCUACCUUCGUCCGAAC ..........((((((...(((((((((....((.(((((((.....((......))(((...))).)))))))))..........(((......)))...)))))))))))))))..(((((((....)))))))(((((..(......((((...(((.(((((((.((.((.......))..)))))))))))).))))....(((....))).......)..))))) (-58.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 433 80 31 83 24 aact:AA02057|5end_phosphoglycerate_mutase_1401253..1401483_POSITIVE 401 80 33 209 156 aact:AA00507|5end_hypothetical_protein_352996..353226_POSITIVE 397 210 161 136 84 aact:AA01556|5end_ABC_transporter_ATP-binding_protein_1044218..1044448_POSITIVE 383 46 3 174 121 aact:AA01458|5end_aminotransferase_978820..979050_POSITIVE 378 48 8 51 1 aact:AA02973|5end_tyrosine-specific_transport_protein_2077707..2077937_POSITIVE 375 52 16 43 8 aact:AA02251|5end_biotin_sulfoxide_reductase;_Trimethylamine-N-oxide_reductase_precursor_1531286..1531516_POSITIVE 375 47 7 47 3 aact:AA01140|5end_anaerobic_dimethyl_sulfoxide_reductase,_chain_C_781610..781840_POSITIVE 375 50 4 225 167 aact:AA00866|5end_conserved_hypothetical_protein_599925..600155_POSITIVE 371 48 1 229 164 aact:AA00366|5end_50S_ribosomal_protein_L2_246215..246445_POSITIVE 371 49 1 190 123 aact:AA00290|5end_conserved_hypothetical_protein_201272..201502_POSITIVE 370 69 22 64 22 aact:AA02425|5end_glutamate-1-semialdehyde_aminotransferase_1670301..1670531_POSITIVE 367 110 61 61 13 aact:AA01526|5end_amino_acid_ABC_transporter,_periplasmic_amino_acid-binding_protein_1024983..1025213_POSITIVE 366 90 44 220 164 aact:AA02678|5end_formate_dehydrogenase,_gamma_subunit_1865021..1865251_POSITIVE 361 53 15 160 115 aact:AA00383|5end_chloride_channel_protein_258894..259124_POSITIVE 358 48 2 204 152 aact:AA00822|5end_conserved_hypothetical_protein_(possible_arsenate_reductase)_564596..564826_POSITIVE 357 54 16 74 21 aact:AA01306|5end_glutathione_reductase_886538..886768_POSITIVE 356 199 165 48 10 aact:AA01997|5end_probable_translation_factor_1356164..1356394_POSITIVE 356 48 1 191 130 aact:AA01323|5end_50S_ribosomal_protein_L28_894247..894477_POSITIVE 355 110 66 116 65 aact:AA02140|5end_ABC_transporter_ATP-binding_protein_1462144..1462374_POSITIVE 353 97 51 149 98 aact:AA02646|5end_D-glucose-1-phosphate_thymidylyltransferase_1842343..1842573_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 383 46 3 82 29 aact:AA01457|3end_D-xylose_ABC_transporter,_membrane_spanning_protein_978808..978958_POSITIVE 377 200 154 150 108 aact:AA01555|3end_ABC_transporter,_ATP-binding_protein_1044323..1044473_POSITIVE 376 84 41 62 21 aact:AA02393|3end_conserved_hypothetical_protein;_possible_sulfate_transporter_1644262..1644412_POSITIVE 374 52 15 47 2 aact:AA01138|3end_anaerobic_dimethyl_sulfoxide_reductase,_chain_B_781685..781835_POSITIVE 367 110 61 77 29 aact:AA01525|3end_amino_acid_ABC_transporter,_permease_component_1025079..1025229_POSITIVE 365 46 1 36 2 aact:AA02225|3end_ABC_transporter_ATP-binding_protein_1514592..1514742_POSITIVE 361 53 15 71 26 aact:AA00382|3end_hypothetical_protein_258885..259035_POSITIVE 358 48 2 64 12 aact:AA00820|3end_succinyl-diaminopimelate_desuccinylase_564536..564686_POSITIVE 355 110 66 110 59 aact:AA02139|3end_possible_membrane_protein_1462218..1462368_POSITIVE 355 56 16 54 3 aact:AA00525|3end_hypothetical_protein_359459..359609_POSITIVE 353 97 51 145 94 aact:AA02645|3end_dTDP-4-rhamnose_reductase_1842419..1842569_POSITIVE 346 70 21 81 6 aact:AA01187|3end_conserved_hypothetical_protein_813992..814142_POSITIVE 343 58 12 83 27 aact:AA00069|3end_conserved_hypothetical_protein_53333..53483_POSITIVE 338 59 12 50 2 aact:AA00926|3end_CyaY_protein_635891..636041_POSITIVE 335 59 15 151 100 aact:AA02874|3end_hypothetical_protein_2017899..2018049_POSITIVE 334 48 1 143 93 aact:AA01081|3end_hypothetical_protein_748189..748339_POSITIVE 333 45 1 57 6 aact:AA02609|3end_ABC_transporter,_ATP-binding_protein/permease_1820184..1820334_POSITIVE 330 210 162 48 1 aact:AA01829|3end_hypothetical_protein_1231662..1231812_POSITIVE 329 96 59 115 73 aact:AA01394|3end_transcriptional_regulator_(mtr_efflux_pump)_943211..943361_POSITIVE 324 65 24 54 9 aact:AA00713|3end_chaperone_protein_hscA,_heat_shock_cognate_66_490697..490847_POSITIVE