Origin IGS: tgtccctgtcgtttattttatctaccgaaacacaaaaatatgaaacatggtaagatttgccaaatcccggtacggcaaatcggtttgcccatattggcatgtcctgccgctctttgcaggacgaaacacgatacagtcaaatgcgaaataccgtattttttctaccttcgttgtagcaaatcgccctttgcctcgttatagggatgaacagtcaaacga .........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 tcgtttgactgttcatccctataacgaggcaaagggcgatttgctacaacgaaggtagaaaaaatacggtatttcgcatttgactgtatcgtgtttcgtcctgcaaagagcggcaggacatgccaatatgggcaaaccgatttgccgtaccgggatttggcaaatcttaccatgtttcatatttttgtgtttcggtagataaaataaacgacagggaca Mask Tandem Repeat Region ================================================ tgtccctgtcgtttattttatctaccgaaacacaaaaatatgaaacatggtaagatttgccaaatcccggtacggcaaatcggtttgcccatattggcatgtcctgccgctctttgcaggacgaaacacgatacagtcaaatgcgaaataccgtattttttctaccttcgttgtagcaaatcgccctttgcctcgttatagggatgaacagtcaaacga Find is-nt database================================================ Query_seq: TF1887:TF1888|TF1887:TF1888:hypothetical protein:RNA polymerase ECF-type sigma factor:->->:2040861..2041079 219 tgtccctgtcgtttattttatctaccgaaacacaaaaatatgaaacatggtaagatttgccaaatcccggtacggcaaatcggtttgcccatattggcatgtcctgccgctctttgcaggacgaaacacgatacagtcaaatgcgaaataccgtattttttctaccttcgttgtagcaaatcgccctttgcctcgttatagggatgaacagtcaaacga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1887:TF1888|TF1887:TF1888:hypothetical protein:RNA polymerase ECF-type sigma factor:->->:2040861..2041079 219 tgtccctgtcgtttattttatctaccgaaacacaaaaatatgaaacatggtaagatttgccaaatcccggtacggcaaatcggtttgcccatattggcatgtcctgccgctctttgcaggacgaaacacgatacagtcaaatgcgaaataccgtattttttctaccttcgttgtagcaaatcgccctttgcctcgttatagggatgaacagtcaaacga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1887:TF1888|TF1887:TF1888:hypothetical protein:RNA polymerase ECF-type sigma factor:->->:2040861..2041079 219 tgtccctgtcgtttattttatctaccgaaacacaaaaatatgaaacatggtaagatttgccaaatcccggtacggcaaatcggtttgcccatattggcatgtcctgccgctctttgcaggacgaaacacgatacagtcaaatgcgaaataccgtattttttctaccttcgttgtagcaaatcgccctttgcctcgttatagggatgaacagtcaaacga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgtccctgtcgtttattttatctaccgaaacacaaaaatatgaaacatggtaagatttgccaaatcccggtacggcaaatcggtttgcccatattggcatgtcctgccgctctttgcaggacgaaacacgatacagtcaaatgcgaaataccgtattttttctaccttcgttgtagcaaatcgccctttgcctcgttatagggatgaacagtcaaacga Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: + Start: 57 End: 173 ........................................................ M P N P G T A N R F A H I G M S C R S L Q D E T R Y S Q M R N T V F F L P S L .............................................. Protein_Len: 53 Strand: + Start: 40 End: 198 ....................................... M K H G K I C Q I P V R Q I G L P I L A C P A A L C R T K H D T V K C E I P Y F F Y L R C S K S P F A S L ..................... Protein_Len: 57 Strand: + Start: 47 End: 217 .............................................. M V R F A K S R Y G K S V C P Y W H V L P L F A G R N T I Q S N A K Y R I F S T F V V A N R P L P R Y R D E Q S N .. Protein_Len: 44 Strand: - Start: 25 End: 156 ........................ R F V F I H F M T L N A L D R Y P L D T Q G Y Q C T R G S K A P R F V I C D F A F Y R M ............................................................... Protein_Len: 43 Strand: - Start: 21 End: 149 .................... R G F C L F I F C P L I Q W I G T R C I P K G M N A H G A A R Q L V F C S V T L H S M ...................................................................... Protein_Len: 45 Strand: - Start: 2 End: 136 . D R D N I K D V S V C F Y S V H Y S K G F G P V A F R N A W I P M D Q R E K C S S V R Y M ................................................................................... tgtccctgtcgtttattttatctaccgaaacacaaaaatatgaaacatggtaagatttgccaaatcccggtacggcaaatcggtttgcccatattggcatgtcctgccgctctttgcaggacgaaacacgatacagtcaaatgcgaaataccgtattttttctaccttcgttgtagcaaatcgccctttgcctcgttatagggatgaacagtcaaacga 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: 35 End: 64 ..................................TTTGGCAAATCTTACCATGTTTCATATTTT........................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tgtccctgtcgtttattttatctaccgaaacacaaaaatatgaaacatggtaagatttgccaaatcccggtacggcaaatcggtttgcccatattggcatgtcctgccgctctttgcaggacgaaacacgatacagtcaaatgcgaaataccgtattttttctaccttcgttgtagcaaatcgccctttgcctcgttatagggatgaacagtcaaacga Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF1887:TF1888|TF1887:TF1888:hypothetical protein:RNA polymerase ECF-type sigma factor:->->:2040861..2041079 219 tgtccctgtcgtttattttatctaccgaaacacaaaaatatgaaacatggtaagatttgccaaatcccggtacggcaaatcggtttgcccatattggcatgtcctgccgctctttgcaggacgaaacacgatacagtcaaatgcgaaataccgtattttttctaccttcgttgtagcaaatcgccctttgcctcgttatagggatgaacagtcaaacga Intra-Species Hit: Count: 1 Min: 1 Max: 219 Len: 219 Subject: tfor_TF1887_TF1888|hypothetical protein:RNA polymerase ECF-type sigma factor|POSITIVE:POSITIVE|[2040861,2041079]|219 HSP 1 e-value: 1.0E-121 bit: 434.0 Len: 219 Query Start:1 Query End:219 Subject Strand: POSITIVE Subject Start: 1 Subject End: 219 tgtccctgtcgtttattttatctaccgaaacacaaaaatatgaaacatggtaagatttgccaaatcccggtacggcaaatcggtttgcccatattggcatgtcctgccgctctttgcaggacgaaacacgatacagtcaaatgcgaaataccgtattttttctaccttcgttgtagcaaatcgccctttgcctcgttatagggatgaacagtcaaacga tgtccctgtcgtttattttatctaccgaaacacaaaaatatgaaacatggtaagatttgccaaatcccggtacggcaaatcggtttgcccatattggcatgtcctgccgctctttgcaggacgaaacacgatacagtcaaatgcgaaataccgtattttttctaccttcgttgtagcaaatcgccctttgcctcgttatagggatgaacagtcaaacga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUCCCUGUCGUUUAUUUUAUCUACCGAAACACAAAAAUAUGAAACAUGGUAAGAUUUGCCAAAUCCCGGUACGGCAAAUCGGUUUGCCCAUAUUGGCAUGUCCUGCCGCUCUUUGCAGGACGAAACACGAUACAGUCAAAUGCGAAAUACCGUAUUUUUUCUACCUUCGUUGUAGCAAAUCGCCCUUUGCCUCGUUAUAGGGAUGAACAGUCAAACGA .((((((((.............(((((.....((......)).....(((((.....))))).....))))).((((((.((((((((...........((((((((........))))))))..((((((...((..(((((((......)))))))...))....))).))).))))))))...)))))).....)))))))).............. (-58.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCGUUUGACUGUUCAUCCCUAUAACGAGGCAAAGGGCGAUUUGCUACAACGAAGGUAGAAAAAAUACGGUAUUUCGCAUUUGACUGUAUCGUGUUUCGUCCUGCAAAGAGCGGCAGGACAUGCCAAUAUGGGCAAACCGAUUUGCCGUACCGGGAUUUGGCAAAUCUUACCAUGUUUCAUAUUUUUGUGUUUCGGUAGAUAAAAUAAACGACAGGGACA (((((((..((((.(((((..((....((((((...((.((((((........((((....(((((((((((.(((....)))..))))))))))).(((((((........))))))).))))......)))))).)).)))))).))..)))))..)))).((((.(((......((((....))))....)))))))....)))))))........ (-63.64) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 435 115 73 77 29 tfor:TF0816|5end_hypothetical_protein_874217..874447_POSITIVE 427 108 68 200 156 tfor:TF2770|5end_conserved_hypothetical_protein_2956308..2956538_POSITIVE 404 110 65 179 137 tfor:TF2259|5end_transfer_region-related_protein,_TraK_2429577..2429807_POSITIVE 399 109 66 185 141 tfor:TF2022|5end_conserved_hypothetical_protein_2178524..2178754_POSITIVE 397 209 166 230 195 tfor:TF0543|5end_glycine_cleavage_system_p-protein_572251..572481_POSITIVE 385 130 95 229 191 tfor:TF3065|5end_enolase_3291055..3291285_POSITIVE 383 209 166 229 193 tfor:TF1845|5end_hypothetical_protein_1996620..1996850_POSITIVE 379 130 81 72 13 tfor:TF2014|5end_dipeptidyl_aminopeptidase_IV_2169398..2169628_POSITIVE 377 109 61 211 158 tfor:TF1833|5end_2-isopropylmalate_synthase_1981511..1981741_POSITIVE 376 119 73 82 28 tfor:TF2439|5end_conserved_hypothetical_protein_2616380..2616610_POSITIVE 375 124 81 223 172 tfor:TF2904|5end_ATP-dependent__helicase,_possible_UvrD/REP_helicase_domain_protein_3098903..3099133_POSITIVE 375 209 166 73 38 tfor:TF2817|5end_hypothetical_protein_3007358..3007588_POSITIVE 375 209 166 138 103 tfor:TF1182|5end_hypothetical_protein_1268565..1268795_POSITIVE 370 120 73 75 18 tfor:TF0301|5end_outer_membrane_protein,_TonB_dependent_receptor_325457..325687_POSITIVE 366 109 64 209 149 tfor:TF1194|5end_glycogen_debranching_enzyme_1276627..1276857_POSITIVE 365 110 65 225 190 tfor:TF2307|5end_two-component_system_sensor_histidine_kinase/response_2462618..2462848_POSITIVE 365 120 72 225 167 tfor:TF2157|5end_conserved_hypothetical_protein_2332915..2333145_POSITIVE 364 110 64 40 2 tfor:TF2893|5end_conserved_hypothetical_protein;_possible_phosphoesterase_3080766..3080996_POSITIVE 364 124 87 57 1 tfor:TF0969|5end_oxidoreductase_1019550..1019780_POSITIVE 364 120 73 197 157 tfor:TF0265|5end_conserved_hypothetical_protein,_Rhs_family_293279..293509_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 406 120 71 149 89 tfor:TF1097|3end_hypothetical_protein_1165893..1166043_POSITIVE 404 110 65 144 102 tfor:TF2257|3end_transfer_region-related_protein,_TraJ_2429622..2429772_POSITIVE 390 138 95 87 40 tfor:TF3064|3end_oxidoreductase,_aldo/keto_reductase_family_3290984..3291134_POSITIVE 387 120 73 151 100 tfor:TF1815|3end_conserved_hypothetical_protein_1957442..1957592_POSITIVE 377 109 61 122 69 tfor:TF1832|3end_3-isopropylmalate_dehydratase,_small_subunit_1981502..1981652_POSITIVE 375 209 166 138 103 tfor:TF1186|3end_hypothetical_protein_1269815..1269965_POSITIVE 370 109 61 112 67 tfor:TF1848|3end_conserved_hypothetical_protein_1997944..1998094_POSITIVE 370 120 73 79 22 tfor:TF0300|3end_hypothetical_protein_325541..325691_POSITIVE 354 129 83 111 45 tfor:TF2245|3end_conserved_hypothetical_protein_2421291..2421441_POSITIVE 353 109 68 60 20 tfor:TF2260|3end_transfer_region-related_protein,_TraL_2430592..2430742_POSITIVE 345 119 74 118 74 tfor:TF3021|3end_FKBP-type_peptidyl-prolyl_cis-trans_isomerase_3246194..3246344_POSITIVE 344 109 66 54 11 tfor:TF0214|3end_DNA_recombination_and_repair_protein,_RecN_241571..241721_POSITIVE 341 109 61 105 55 tfor:TF0567|3end_conserved_hypothetical_protein;_possible_periplasmic_solute-binding_protein_600134..600284_POSITIVE 337 110 65 151 96 tfor:TF2548|3end_30S_ribosomal_protein_S12_2731704..2731854_POSITIVE 336 130 82 45 1 tfor:TF1872|3end_ABC_transporter,_ATP-binding/permease_component_2026811..2026961_POSITIVE 336 130 82 45 1 tfor:TF1130|3end_ABC_transporter_ATP-binding_protein/permease_component_1207677..1207827_POSITIVE 336 123 82 107 63 tfor:TF1042|3end_possible_surface_antigen_with_leucine-rich_repeat_1105295..1105445_POSITIVE 336 98 58 60 15 tfor:TF0818|3end_bifunctional_protein:__aspartokinase_I;_homoserine_dehydrogenase_878517..878667_POSITIVE 334 119 73 151 89 tfor:TF2221|3end_CTn_excision_protein_2394229..2394379_POSITIVE 329 110 67 86 37 tfor:TF2000|3end_conserved_hypothetical_protein_2155483..2155633_POSITIVE