Origin IGS: aagatattacctcgtgatatcaataattttaatttataatatgaacttaataaagcagaacctcctcctgagctaggtctcacacctagctcaggtcggaagttgggggacaagtttttc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gaaaaacttgtcccccaacttccgacctgagctaggtgtgagacctagctcaggaggaggttctgctttattaagttcatattataaattaaaattattgatatcacgaggtaatatctt Mask Tandem Repeat Region ================================================ aagatattacctcgtgatatcaataattttaatttataatatgaacttaataaagcagaacctcctcctgagctaggtctcacacctagctcaggtcggaagttgggggacaagtttttc Find is-nt database================================================ Query_seq: SSA_0434:SSA_0435|SSA_0434:SSA_0435:Glutamate formiminotransferase, putative:Urocanate hydratase, putative:<-<-:436659..436778 120 aagatattacctcgtgatatcaataattttaatttataatatgaacttaataaagcagaacctcctcctgagctaggtctcacacctagctcaggtcggaagttgggggacaagtttttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0434:SSA_0435|SSA_0434:SSA_0435:Glutamate formiminotransferase, putative:Urocanate hydratase, putative:<-<-:436659..436778 120 aagatattacctcgtgatatcaataattttaatttataatatgaacttaataaagcagaacctcctcctgagctaggtctcacacctagctcaggtcggaagttgggggacaagtttttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0434:SSA_0435|SSA_0434:SSA_0435:Glutamate formiminotransferase, putative:Urocanate hydratase, putative:<-<-:436659..436778 120 aagatattacctcgtgatatcaataattttaatttataatatgaacttaataaagcagaacctcctcctgagctaggtctcacacctagctcaggtcggaagttgggggacaagtttttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aagatattacctcgtgatatcaataattttaatttataatatgaacttaataaagcagaacctcctcctgagctaggtctcacacctagctcaggtcggaagttgggggacaagtttttc Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: - Start: 3 End: 113 .. I N G R S I L L K L K Y Y S S L L A S G G G S S P R V G L E P R F N P S M ....... aagatattacctcgtgatatcaataattttaatttataatatgaacttaataaagcagaacctcctcctgagctaggtctcacacctagctcaggtcggaagttgggggacaagtttttc 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: 82 Start: 11 End: 40 ..........CTCGTGATATCAATAATTTTAATTTATAAT................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aagatattacctcgtgatatcaataattttaatttataatatgaacttaataaagcagaacctcctcctgagctaggtctcacacctagctcaggtcggaagttgggggacaagtttttc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 81 HP_score: -8.2 Tail_Score: -4.26351 Start: 55 End: 108 Full_Region: gaaaaacttgtc ccccaacttccgacctgagctaggt gtgag acctagctcaggaggaggttctgc tttattaagttcata ......................................................ccccaacttccgacctgagctaggtgtgagacctagctcaggaggaggttctgc............ TransTerm Strand: - Conf: 100 HP_score: -14.6 Tail_Score: -3.68962 Start: 61 End: 102 Full_Region: aaacttgtcccccaa cttccgacctgagctaggt gtgag acctagctcaggaggagg ttctgctttattaag ............................................................cttccgacctgagctaggtgtgagacctagctcaggaggagg.................. Find igs database================================================ Query_seq: SSA_0434:SSA_0435|SSA_0434:SSA_0435:Glutamate formiminotransferase, putative:Urocanate hydratase, putative:<-<-:436659..436778 120 aagatattacctcgtgatatcaataattttaatttataatatgaacttaataaagcagaacctcctcctgagctaggtctcacacctagctcaggtcggaagttgggggacaagtttttc Intra-Species Hit: Count: 1 Min: 1 Max: 120 Len: 120 Subject: NC_009009_SSA_0434_SSA_0435|Glutamate formiminotransferase, putative:Urocanate hydratase, putative|NEGATIVE:NEGATIVE|[436659,436778]|120 HSP 1 e-value: 3.0E-62 bit: 238.0 Len: 120 Query Start:1 Query End:120 Subject Strand: POSITIVE Subject Start: 1 Subject End: 120 aagatattacctcgtgatatcaataattttaatttataatatgaacttaataaagcagaacctcctcctgagctaggtctcacacctagctcaggtcggaagttgggggacaagtttttc aagatattacctcgtgatatcaataattttaatttataatatgaacttaataaagcagaacctcctcctgagctaggtctcacacctagctcaggtcggaagttgggggacaagtttttc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGAUAUUACCUCGUGAUAUCAAUAAUUUUAAUUUAUAAUAUGAACUUAAUAAAGCAGAACCUCCUCCUGAGCUAGGUCUCACACCUAGCUCAGGUCGGAAGUUGGGGGACAAGUUUUUC ..((((((((...))))))))..............................(((((..(((.(((.((((((((((((.....))))))))))))..))).))).(....)..))))).. (-37.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAAAACUUGUCCCCCAACUUCCGACCUGAGCUAGGUGUGAGACCUAGCUCAGGAGGAGGUUCUGCUUUAUUAAGUUCAUAUUAUAAAUUAAAAUUAUUGAUAUCACGAGGUAAUAUCUU ......(((((.....(((((((..((((((((((((.....)))))))))))).)))))))..((((....)))).............................))))).......... (-36.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1110 110 61 201 152 NC_009009:SSA_0434|5end_Glutamate_formiminotransferase,_putative_436568..436798_NEGATIVE 378 98 54 217 166 NC_009009:SSA_0098|5end_Hydrolase,_haloacid_dehalogenase-like_family,_putative_99422..99652_POSITIVE 371 108 61 159 102 NC_009009:SSA_1764|5end_hypothetical_protein_1750868..1751098_POSITIVE 365 99 56 142 95 NC_009009:SSA_0834|5end_Accessory_secretory_protein_Asp2,_putative_819510..819740_POSITIVE 350 92 54 69 33 NC_009009:SSA_1429|5end_hypothetical_protein_1437110..1437340_NEGATIVE 348 108 65 34 2 NC_009009:SSA_0355|5end_DNA_mismatch_repair_protein,_putative_346847..347077_POSITIVE 344 105 61 224 173 NC_009009:SSA_2317|5end_Tfp_pilus_assembly_protein,_pilus_retraction_ATPase_PilT,_putative_2319410..2319640_NEGATIVE 341 108 63 154 103 NC_009009:SSA_1045|5end_hypothetical_protein_1060841..1061071_POSITIVE 336 99 55 203 151 NC_009009:SSA_0759|5end_Acetylglutamate_kinase,_putative_741841..742071_POSITIVE 332 93 54 73 24 NC_009009:SSA_0069|5end_Hypothetical_protein,_possibly_membrane-associated_73037..73267_POSITIVE 330 108 61 51 10 NC_009009:SSA_0400|5end_hypothetical_protein_398251..398481_NEGATIVE 327 103 65 201 153 NC_009009:SSA_2275|5end_hypothetical_protein_2275590..2275820_NEGATIVE 323 110 69 222 179 NC_009009:SSA_1739|5end_UDP-N-acetylmuramoylalanyl-D-glutamate--2,_6-diaminopimelate_ligase,_putative_1725540..1725770_POSITIVE 322 106 65 80 37 NC_009009:SSA_0549|5end_ATP-dependent_DNA_helicase_recG,_transcription-repair_coupling_factor,_putative_543556..543786_POSITIVE 318 115 73 171 120 NC_009009:SSA_1527|5end_hypothetical_protein_1534587..1534817_POSITIVE 313 106 62 83 25 NC_009009:SSA_2071|5end_hypothetical_protein_2074766..2074996_NEGATIVE 313 100 55 61 12 NC_009009:SSA_0433|5end_Methenyl_tetrahydrofolate_cyclohydrolase,_putative_435654..435884_NEGATIVE 311 99 56 130 94 NC_009009:SSA_0402|5end_Histidine_kinase,_putative_399144..399374_POSITIVE 309 110 62 97 49 NC_009009:SSA_0767|5end_Diacylglycerol_kinase_catalytic_domain_protein,_putative_747087..747317_POSITIVE 307 97 54 70 21 NC_009009:SSA_0231|5end_Conserved_uncharacterized_protein_225713..225943_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 350 92 54 72 36 NC_009009:SSA_1430|3end_Ribonuclease_Z,_putative_1437107..1437257_NEGATIVE 334 99 56 146 102 NC_009009:SSA_2340|3end_hypothetical_protein_2341539..2341689_NEGATIVE 329 100 56 148 105 NC_009009:SSA_0833|3end_Accessory_secretory_protein_Asp1,_putative_819600..819750_POSITIVE 311 99 56 128 92 NC_009009:SSA_0401|3end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_winged-helix_DNA-binding_domains),_putative_399222..399372_POSITIVE 310 107 62 62 3 NC_009009:SSA_2086|3end_hypothetical_protein_2090397..2090547_NEGATIVE 310 99 52 82 33 NC_009009:SSA_1691|3end_Transcriptional_regulator,_XRE_family,_putative_1683570..1683720_POSITIVE 306 107 62 149 101 NC_009009:SSA_0500|3end_Peptide_ABC_transporter,_permease_protein,_putative_501524..501674_POSITIVE 305 120 73 133 86 NC_009009:SSA_1344|3end_Xanthine/uracil_permeases,_putative_1362069..1362219_NEGATIVE 305 110 61 151 95 NC_009009:SSA_0050|3end_Dihydroxyacetone_kinase,_phosphatase_domain_(Dak2),_putative_55270..55420_POSITIVE 299 105 64 86 46 NC_009009:SSA_0965|3end_Oxidoreductase,_putative_974035..974185_NEGATIVE 296 99 53 67 20 NC_009009:SSA_1248|3end_hypothetical_protein_1272355..1272505_NEGATIVE 293 110 63 60 4 NC_009009:SSA_1180|3end_hypothetical_protein_1207819..1207969_NEGATIVE 293 109 64 64 26 NC_009009:SSA_0484|3end_Glutamyl-tRNA_reductase,_putative_485825..485975_POSITIVE 290 109 62 118 72 NC_009009:SSA_0686|3end_Fe2+/Zn2+_uptake_regulation_protein,_putative_670079..670229_POSITIVE 289 108 61 125 72 NC_009009:SSA_1972|3end_Two-component_system_transcriptional_regulator_(CheY_domain_and_HTH-like_DNA-binding_domain),_putative_1967811..1967961_NEGATIVE 287 106 69 49 6 NC_009009:SSA_2072|3end_Phosphatidate_cytidylyltransferase,_putative_2074800..2074950_NEGATIVE 287 107 62 139 85 NC_009009:SSA_1380|3end_hypothetical_protein_1398538..1398688_NEGATIVE 285 111 72 85 55 NC_009009:SSA_0070|3end_Acetylxylan_esterase,_putative_74914..75064_POSITIVE 284 109 66 69 6 NC_009009:SSA_0217|3end_Two-component_system_transcriptional_regulator_(CheY_domain_and_HTH-like_DNA-binding_domain),_putative_213946..214096_POSITIVE 281 104 62 142 97 NC_009009:SSA_1799|3end_Acetyltransferase,_putative_1780513..1780663_NEGATIVE