Origin IGS: tctgactgtctctgtgtttaagttttaaaacttcatcacgagtaacgccaattactggtgatgaactgatcaaggttggcgtaccgtaacacggtgtaaacggcgatctttcgatccctcaaccagttcatcattgactacttttgaaaggggggtatcaaattgatgtacccctttaaagggtttgatttgctgattttcggctataaaaaaatcgccatttaggcgactataatttctaaccgccgtgttattcaggacgccaatcccgactttctgttgaaagtggggttagtttactgaattgagcggtgggtgtcaaataaaaaatcccacgttgtaaagtgggattttgaaaatttagtgttttgctgcttggttagcgaagtatgcccaacctatcattacagctgcaaatactgctaacccgaatgttaagcccatta .........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 taatgggcttaacattcgggttagcagtatttgcagctgtaatgataggttgggcatacttcgctaaccaagcagcaaaacactaaattttcaaaatcccactttacaacgtgggattttttatttgacacccaccgctcaattcagtaaactaaccccactttcaacagaaagtcgggattggcgtcctgaataacacggcggttagaaattatagtcgcctaaatggcgatttttttatagccgaaaatcagcaaatcaaaccctttaaaggggtacatcaatttgatacccccctttcaaaagtagtcaatgatgaactggttgagggatcgaaagatcgccgtttacaccgtgttacggtacgccaaccttgatcagttcatcaccagtaattggcgttactcgtgatgaagttttaaaacttaaacacagagacagtcaga Mask Tandem Repeat Region ================================================ tctgactgtctctgtgtttaagttttaaaacttcatcacgagtaacgccaattactggtgatgaactgatcaaggttggcgtaccgtaacacggtgtaaacggcgatctttcgatccctcaaccagttcatcattgactacttttgaaaggggggtatcaaattgatgtacccctttaaagggtttgatttgctgattttcggctataaaaaaatcgccatttaggcgactataatttctaaccgccgtgttattcaggacgccaatcccgactttctgttgaaagtggggttagtttactgaattgagcggtgggtgtcaaataaaaaatcccacgttgtaaagtgggattttgaaaatttagtgttttgctgcttggttagcgaagtatgcccaacctatcattacagctgcaaatactgctaacccgaatgttaagcccatta Find is-nt database================================================ Query_seq: AA01902:AA01903|AA01902:AA01903:conserved hypothetical protein:hypothetical protein:->->:1283677..1284122 446 tctgactgtctctgtgtttaagttttaaaacttcatcacgagtaacgccaattactggtgatgaactgatcaaggttggcgtaccgtaacacggtgtaaacggcgatctttcgatccctcaaccagttcatcattgactacttttgaaaggggggtatcaaattgatgtacccctttaaagggtttgatttgctgattttcggctataaaaaaatcgccatttaggcgactataatttctaaccgccgtgttattcaggacgccaatcccgactttctgttgaaagtggggttagtttactgaattgagcggtgggtgtcaaataaaaaatcccacgttgtaaagtgggattttgaaaatttagtgttttgctgcttggttagcgaagtatgcccaacctatcattacagctgcaaatactgctaacccgaatgttaagcccatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA01902:AA01903|AA01902:AA01903:conserved hypothetical protein:hypothetical protein:->->:1283677..1284122 446 tctgactgtctctgtgtttaagttttaaaacttcatcacgagtaacgccaattactggtgatgaactgatcaaggttggcgtaccgtaacacggtgtaaacggcgatctttcgatccctcaaccagttcatcattgactacttttgaaaggggggtatcaaattgatgtacccctttaaagggtttgatttgctgattttcggctataaaaaaatcgccatttaggcgactataatttctaaccgccgtgttattcaggacgccaatcccgactttctgttgaaagtggggttagtttactgaattgagcggtgggtgtcaaataaaaaatcccacgttgtaaagtgggattttgaaaatttagtgttttgctgcttggttagcgaagtatgcccaacctatcattacagctgcaaatactgctaacccgaatgttaagcccatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA01902:AA01903|AA01902:AA01903:conserved hypothetical protein:hypothetical protein:->->:1283677..1284122 446 tctgactgtctctgtgtttaagttttaaaacttcatcacgagtaacgccaattactggtgatgaactgatcaaggttggcgtaccgtaacacggtgtaaacggcgatctttcgatccctcaaccagttcatcattgactacttttgaaaggggggtatcaaattgatgtacccctttaaagggtttgatttgctgattttcggctataaaaaaatcgccatttaggcgactataatttctaaccgccgtgttattcaggacgccaatcccgactttctgttgaaagtggggttagtttactgaattgagcggtgggtgtcaaataaaaaatcccacgttgtaaagtgggattttgaaaatttagtgttttgctgcttggttagcgaagtatgcccaacctatcattacagctgcaaatactgctaacccgaatgttaagcccatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tctgactgtctctgtgtttaagttttaaaacttcatcacgagtaacgccaattactggtgatgaactgatcaaggttggcgtaccgtaacacggtgtaaacggcgatctttcgatccctcaaccagttcatcattgactacttttgaaaggggggtatcaaattgatgtacccctttaaagggtttgatttgctgattttcggctataaaaaaatcgccatttaggcgactataatttctaaccgccgtgttattcaggacgccaatcccgactttctgttgaaagtggggttagtttactgaattgagcggtgggtgtcaaataaaaaatcccacgttgtaaagtgggattttgaaaatttagtgttttgctgcttggttagcgaagtatgcccaacctatcattacagctgcaaatactgctaacccgaatgttaagcccatta Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: + Start: 304 End: 423 ............................................................................................................................................................................................................................................................................................................... M E R W V S N K K S H V V K W D F E N L V F C C L V S E V C P T Y H Y S C K Y C ....................... Protein_Len: 60 Strand: - Start: 73 End: 267 ........................................................................ V R H L R R D K S G E V L E D N V V K S L P T D F Q H V G K F P K I Q Q N E A I F F D G N L R S Y N R V A T N N L V G M ................................................................................................................................................................................... Protein_Len: 32 Strand: - Start: 39 End: 134 ...................................... S Y R W N S T I F Q D L N A Y R L V T Y V A I K R D R L W N M M ........................................................................................................................................................................................................................................................................................................................ Protein_Len: 38 Strand: - Start: 2 End: 115 . Q S D R H K L K L V E D R T V G I V P S S S I L T P T G Y C P T F P S R E M ........................................................................................................................................................................................................................................................................................................................................... tctgactgtctctgtgtttaagttttaaaacttcatcacgagtaacgccaattactggtgatgaactgatcaaggttggcgtaccgtaacacggtgtaaacggcgatctttcgatccctcaaccagttcatcattgactacttttgaaaggggggtatcaaattgatgtacccctttaaagggtttgatttgctgattttcggctataaaaaaatcgccatttaggcgactataatttctaaccgccgtgttattcaggacgccaatcccgactttctgttgaaagtggggttagtttactgaattgagcggtgggtgtcaaataaaaaatcccacgttgtaaagtgggattttgaaaatttagtgttttgctgcttggttagcgaagtatgcccaacctatcattacagctgcaaatactgctaacccgaatgttaagcccatta 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: 83 Start: 294 End: 323 .....................................................................................................................................................................................................................................................................................................TTTGACACCCACCGCTCAATTCAGTAAACT........................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tctgactgtctctgtgtttaagttttaaaacttcatcacgagtaacgccaattactggtgatgaactgatcaaggttggcgtaccgtaacacggtgtaaacggcgatctttcgatccctcaaccagttcatcattgactacttttgaaaggggggtatcaaattgatgtacccctttaaagggtttgatttgctgattttcggctataaaaaaatcgccatttaggcgactataatttctaaccgccgtgttattcaggacgccaatcccgactttctgttgaaagtggggttagtttactgaattgagcggtgggtgtcaaataaaaaatcccacgttgtaaagtgggattttgaaaatttagtgttttgctgcttggttagcgaagtatgcccaacctatcattacagctgcaaatactgctaacccgaatgttaagcccatta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 73 HP_score: -7.0 Tail_Score: -4.14392 Start: 31 End: 66 Full_Region: cgccaaccttgatca gttcatcaccagtaat tggc gttactcgtgatgaag ttttaaaacttaaac ..............................gttcatcaccagtaattggcgttactcgtgatgaag............................................................................................................................................................................................................................................................................................................................................................................................ TransTerm Strand: - Conf: 75 HP_score: -10.5 Tail_Score: -3.08314 Start: 32 End: 65 Full_Region: gccaaccttgatcag ttcatcaccagtaat tggc gttactcgtgatgaa gttttaaaacttaaa ...............................ttcatcaccagtaattggcgttactcgtgatgaa............................................................................................................................................................................................................................................................................................................................................................................................. TransTerm Strand: + Conf: 75 HP_score: -7.8 Tail_Score: -4.12225 Start: 141 End: 183 Full_Region: GTTCATCATTGACTA CTTTTGAAAGGGGGGTATCA AAT TGATGTACCCCTTTAAAGGG TTTGATTTGCTGATT ............................................................................................................................................CTTTTGAAAGGGGGGTATCAAATTGATGTACCCCTTTAAAGGG....................................................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 100 HP_score: -7.1 Tail_Score: -5.60993 Start: 215 End: 229 Full_Region: ggttagaaattatag tcgcc taaat ggcga tttttttatagccga ......................................................................................................................................................................................................................tcgcctaaatggcga......................................................................................................................................................................................................................... TransTerm Strand: + Conf: 77 HP_score: -9.6 Tail_Score: -3.5782 Start: 268 End: 291 Full_Region: ATTCAGGACGCCAAT CCCGACTTTC TGTT GAAAGTGGGG TTAGTTTACTGAATT ...........................................................................................................................................................................................................................................................................CCCGACTTTCTGTTGAAAGTGGGG........................................................................................................................................................... TransTerm Strand: - Conf: 95 HP_score: -6.4 Tail_Score: -5.63517 Start: 331 End: 350 Full_Region: actaaattttcaaaa tcccactt taca acgtggga ttttttatttgacac ..........................................................................................................................................................................................................................................................................................................................................tcccactttacaacgtggga................................................................................................ Find igs database================================================ Query_seq: AA01902:AA01903|AA01902:AA01903:conserved hypothetical protein:hypothetical protein:->->:1283677..1284122 446 tctgactgtctctgtgtttaagttttaaaacttcatcacgagtaacgccaattactggtgatgaactgatcaaggttggcgtaccgtaacacggtgtaaacggcgatctttcgatccctcaaccagttcatcattgactacttttgaaaggggggtatcaaattgatgtacccctttaaagggtttgatttgctgattttcggctataaaaaaatcgccatttaggcgactataatttctaaccgccgtgttattcaggacgccaatcccgactttctgttgaaagtggggttagtttactgaattgagcggtgggtgtcaaataaaaaatcccacgttgtaaagtgggattttgaaaatttagtgttttgctgcttggttagcgaagtatgcccaacctatcattacagctgcaaatactgctaacccgaatgttaagcccatta Intra-Species Hit: Count: 1 Min: 1 Max: 446 Len: 446 Subject: aact_AA01902_AA01903|conserved hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[1283677,1284122]|446 HSP 1 e-value: 0.0 bit: 842.0 Len: 446 Query Start:1 Query End:446 Subject Strand: POSITIVE Subject Start: 1 Subject End: 446 tctgactgtctctgtgtttaagttttaaaacttcatcacgagtaacgccaattactggtgatgaactgatcaaggttggcgtaccgtaacacggtgtaaacggcgatctttcgatccctcaaccagttcatcattgactacttttgaaaggggggtatcaaattgatgtacccctttaaagggtttgatttgctgattttcggctatnnnnnnntcgccatttaggcgactataatttctaaccgccgtgttattcaggacgccaatcccgactttctgttgaaagtggggttagtttactgaattgagcggtgggtgtcaaataaaaaatcccacgttgtaaagtgggattttgaaaatttagtgttttgctgcttggttagcgaagtatgcccaacctatcattacagctgcaaatactgctaacccgaatgttaagcccatta tctgactgtctctgtgtttaagttttaaaacttcatcacgagtaacgccaattactggtgatgaactgatcaaggttggcgtaccgtaacacggtgtaaacggcgatctttcgatccctcaaccagttcatcattgactacttttgaaaggggggtatcaaattgatgtacccctttaaagggtttgatttgctgattttcggctataaaaaaatcgccatttaggcgactataatttctaaccgccgtgttattcaggacgccaatcccgactttctgttgaaagtggggttagtttactgaattgagcggtgggtgtcaaataaaaaatcccacgttgtaaagtgggattttgaaaatttagtgttttgctgcttggttagcgaagtatgcccaacctatcattacagctgcaaatactgctaacccgaatgttaagcccatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUGACUGUCUCUGUGUUUAAGUUUUAAAACUUCAUCACGAGUAACGCCAAUUACUGGUGAUGAACUGAUCAAGGUUGGCGUACCGUAACACGGUGUAAACGGCGAUCUUUCGAUCCCUCAACCAGUUCAUCAUUGACUACUUUUGAAAGGGGGGUAUCAAAUUGAUGUACCCCUUUAAAGGGUUUGAUUUGCUGAUUUUCGGCUAUAAAAAAAUCGCCAUUUAGGCGACUAUAAUUUCUAACCGCCGUGUUAUUCAGGACGCCAAUCCCGACUUUCUGUUGAAAGUGGGGUUAGUUUACUGAAUUGAGCGGUGGGUGUCAAAUAAAAAAUCCCACGUUGUAAAGUGGGAUUUUGAAAAUUUAGUGUUUUGCUGCUUGGUUAGCGAAGUAUGCCCAACCUAUCAUUACAGCUGCAAAUACUGCUAACCCGAAUGUUAAGCCCAUUA .............((((((.((((.(((...((((((((.(((((......))))).))))))))..(((..((((((((((((...(((((.((.((((.((((((...((((.((((.....(((.((....))))).......(((((((..((((.....))))..)))))))..)))).))))...((((.....)))).........)))))).)))).))........((((...(((((((...((((((...((.((((((.((((((....)))))))))))).))...))))))...)))))))...........((((((((((........)))))))))))))).....)))))((((((......)))))).))))).)))))))))).))).))))..)))))).((((((......))).)))...... (-147.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUGGGCUUAACAUUCGGGUUAGCAGUAUUUGCAGCUGUAAUGAUAGGUUGGGCAUACUUCGCUAACCAAGCAGCAAAACACUAAAUUUUCAAAAUCCCACUUUACAACGUGGGAUUUUUUAUUUGACACCCACCGCUCAAUUCAGUAAACUAACCCCACUUUCAACAGAAAGUCGGGAUUGGCGUCCUGAAUAACACGGCGGUUAGAAAUUAUAGUCGCCUAAAUGGCGAUUUUUUUAUAGCCGAAAAUCAGCAAAUCAAACCCUUUAAAGGGGUACAUCAAUUUGAUACCCCCCUUUCAAAAGUAGUCAAUGAUGAACUGGUUGAGGGAUCGAAAGAUCGCCGUUUACACCGUGUUACGGUACGCCAACCUUGAUCAGUUCAUCACCAGUAAUUGGCGUUACUCGUGAUGAAGUUUUAAAACUUAAACACAGAGACAGUCAGA ...(((............((((((((((((.(.(((((.........))))).).)))))..))))))).......................((((((((((........))))))))))....(((((.......(((..((((((.(..(((((((.((((((....)))))).))).))))..).))))))....((((...((((((....(((((((.....)))))))))))))..))))......)))..........(((((((((((...(((.....)))...)))))))..))))..))))).(((((((((((..(((((((....))))..(((....((((.....)))))))....)))..))))))))))).)))....(((((....((((((...(((((....)))))...))).)))...))))). (-141.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 381 140 92 208 155 aact:AA02177|5end_conserved_hypothetical_protein_1488963..1489193_POSITIVE 378 290 244 128 87 aact:AA00551|5end_hypothetical_protein_377225..377455_POSITIVE 362 290 244 70 4 aact:AA00288|5end_conserved_hypothetical_protein_200485..200715_POSITIVE 361 208 167 92 48 aact:AA00902|5end_RNA_polymerase_sigma-E_factor_sigma-24_623829..624059_POSITIVE 354 400 364 169 138 aact:AA00480|5end_mannose-specific_phosphotransferase_system_IID_334286..334516_POSITIVE 348 87 41 219 179 aact:AA01747|5end_single-stranded-DNA-specific_exonuclease_1181359..1181589_POSITIVE 343 290 244 230 193 aact:AA00552|5end_periplasmic_nitrate_reductase_precursor_377331..377561_POSITIVE 342 260 216 132 85 aact:AA00596|5end_uridylate_kinase_407496..407726_POSITIVE 335 96 54 169 119 aact:AA01987|5end_hypothetical_protein_1350415..1350645_POSITIVE 333 146 101 60 8 aact:AA00993|5end_possible_D-tyrosyl-tRNA(Tyr)_deacylase_694488..694718_POSITIVE 333 80 31 138 86 aact:AA00595|5end_hypothetical_protein_407194..407424_POSITIVE 332 90 44 206 165 aact:AA02939|5end_phosphoserine_phosphatase_2056881..2057111_POSITIVE 332 250 201 201 151 aact:AA01421|5end_phosphoglycolate_phosphatase_955055..955285_POSITIVE 332 90 46 151 99 aact:AA01253|5end_hypothetical_protein_852189..852419_POSITIVE 329 318 277 70 21 aact:AA01017|5end_conserved_hypothetical_protein_710915..711145_POSITIVE 326 289 244 68 11 aact:AA02692|5end_hydrogenase_4_subunit;_hydrogenase_3_subunit_1876324..1876554_POSITIVE 324 116 77 231 183 aact:AA01825|5end_iron(III)_ABC_transporter,_permease_protein_1228475..1228705_POSITIVE 319 397 365 77 46 aact:AA01900|5end_hypothetical_protein_1282233..1282463_POSITIVE 318 255 214 92 53 aact:AA01515|5end_SlyX_family_protein_1020682..1020912_POSITIVE 316 107 69 52 8 aact:AA01744|5end_peptide_chain_release_factor_RF-2_1179373..1179603_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 381 140 92 131 78 aact:AA02175|3end_anthranilate_synthase_component_II_1488966..1489116_POSITIVE 335 399 364 151 121 aact:AA00479|3end_mannose-specific_phosphotransferase_system_IIC_334349..334499_POSITIVE 333 146 101 60 8 aact:AA00992|3end_ribonuclease_BN_694568..694718_POSITIVE 333 80 31 150 98 aact:AA00592|3end_conserved_hypothetical_protein_(membrane/transport_protein)_407286..407436_POSITIVE 316 120 71 64 8 aact:AA01117|3end_signal_recognition_particle_protein_54_(GTP-binding_export_factor)_769375..769525_POSITIVE 316 114 73 64 22 aact:AA00969|3end_conserved_hypothetical_protein_(possible_NADH_pyrophosphatase)_676206..676356_POSITIVE 314 290 243 141 99 aact:AA02821|3end_ribosomal-protein-alanine_acetyltransferase_1982775..1982925_POSITIVE 314 290 241 66 10 aact:AA00345|3end_transcription_antitermination_protein_232058..232208_POSITIVE 313 282 244 124 87 aact:AA00056|3end_cytochrome_c-type_biogenesis_protein_44520..44670_POSITIVE 311 418 373 132 89 aact:AA02315|3end_conserved_hypothetical_protein_1581752..1581902_POSITIVE 310 105 66 59 18 aact:AA01956|3end_3-deoxy-manno-octulosonate_cytidylyltransferase_1323286..1323436_POSITIVE 310 104 61 148 91 aact:AA01177|3end_beta-ketoacyl-ACP_synthase_IV_808053..808203_POSITIVE 307 118 76 142 99 aact:AA02035|3end_translation_initiation_factor_IF-3_1386905..1387055_POSITIVE 307 118 74 48 7 aact:AA00474|3end_cell_division_protein_Y_(GTP-binding_signal_recognition_particle)_331724..331874_POSITIVE 306 265 227 49 8 aact:AA01471|3end_type_I_restriction_enzyme_M_(modification_chain)_989002..989152_POSITIVE 305 228 181 131 91 aact:AA02532|3end_conserved_hypothetical_protein_1762009..1762159_POSITIVE 301 273 242 36 4 aact:AA01842|3end_conserved_hypothetical_protein_1238467..1238617_POSITIVE 301 119 74 44 2 aact:AA00361|3end_50S_ribosomal_protein_L16_244910..245060_POSITIVE 299 289 243 70 26 aact:AA01859|3end_hypothetical_protein_1251890..1252040_POSITIVE 298 290 242 117 74 aact:AA02108|3end_2-acylglycerophosphoethanolamine_acyltransferase;_acyl-acyl_carrier_protein_synthetase_1436643..1436793_POSITIVE