Origin IGS: tttttagccgaagaattaaaagtatgttaatttatggattgtggttaagaggtaagaatgacaacagatattaaaactgaaattggtcatagagtaagacaggaacgtgaacgtcacaaattgacgagagaagagatctgtggacagaagctgacttaataatcaaacagctg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 cagctgtttgattattaagtcagcttctgtccacagatctcttctctcgtcaatttgtgacgttcacgttcctgtcttactctatgaccaatttcagttttaatatctgttgtcattcttacctcttaaccacaatccataaattaacatacttttaattcttcggctaaaaa Mask Tandem Repeat Region ================================================ tttttagccgaagaattaaaagtatgttaatttatggattgtggttaagaggtaagaatgacaacagatattaaaactgaaattggtcatagagtaagacaggaacgtgaacgtcacaaattgacgagagaagagatctgtggacagaagctgacttaataatcaaacagctg Find is-nt database================================================ Query_seq: SMT_437:SMT_438|SMT_437:SMT_438:transcriptional regulator, TetR family:hypothetical protein predicted by Glimmer/Critica:->->:379103..379275 173 tttttagccgaagaattaaaagtatgttaatttatggattgtggttaagaggtaagaatgacaacagatattaaaactgaaattggtcatagagtaagacaggaacgtgaacgtcacaaattgacgagagaagagatctgtggacagaagctgacttaataatcaaacagctg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_437:SMT_438|SMT_437:SMT_438:transcriptional regulator, TetR family:hypothetical protein predicted by Glimmer/Critica:->->:379103..379275 173 tttttagccgaagaattaaaagtatgttaatttatggattgtggttaagaggtaagaatgacaacagatattaaaactgaaattggtcatagagtaagacaggaacgtgaacgtcacaaattgacgagagaagagatctgtggacagaagctgacttaataatcaaacagctg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_437:SMT_438|SMT_437:SMT_438:transcriptional regulator, TetR family:hypothetical protein predicted by Glimmer/Critica:->->:379103..379275 173 tttttagccgaagaattaaaagtatgttaatttatggattgtggttaagaggtaagaatgacaacagatattaaaactgaaattggtcatagagtaagacaggaacgtgaacgtcacaaattgacgagagaagagatctgtggacagaagctgacttaataatcaaacagctg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttttagccgaagaattaaaagtatgttaatttatggattgtggttaagaggtaagaatgacaacagatattaaaactgaaattggtcatagagtaagacaggaacgtgaacgtcacaaattgacgagagaagagatctgtggacagaagctgacttaataatcaaacagctg Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 58 End: 156 ......................................................... M T T D I K T E I G H R V R Q E R E R H K L T R E E I C G Q K L T ................. Protein_Len: 31 Strand: - Start: 74 End: 166 ......................................................................... F Q F Q D Y L L V P V H V D C I S S L L S R H V S A S K I I M ....... Protein_Len: 43 Strand: - Start: 19 End: 147 .................. F Y T L K H I T T L L Y S H C C I N F S F N T M S Y S L F T F T V F Q R S F L D T S M .......................... tttttagccgaagaattaaaagtatgttaatttatggattgtggttaagaggtaagaatgacaacagatattaaaactgaaattggtcatagagtaagacaggaacgtgaacgtcacaaattgacgagagaagagatctgtggacagaagctgacttaataatcaaacagctg 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================================================ tttttagccgaagaattaaaagtatgttaatttatggattgtggttaagaggtaagaatgacaacagatattaaaactgaaattggtcatagagtaagacaggaacgtgaacgtcacaaattgacgagagaagagatctgtggacagaagctgacttaataatcaaacagctg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_437:SMT_438|SMT_437:SMT_438:transcriptional regulator, TetR family:hypothetical protein predicted by Glimmer/Critica:->->:379103..379275 173 tttttagccgaagaattaaaagtatgttaatttatggattgtggttaagaggtaagaatgacaacagatattaaaactgaaattggtcatagagtaagacaggaacgtgaacgtcacaaattgacgagagaagagatctgtggacagaagctgacttaataatcaaacagctg Intra-Species Hit: Count: 1 Min: 1 Max: 173 Len: 173 Subject: smit_SMT_437_SMT_438|transcriptional regulator, TetR family:hypothetical protein predicted by Glimmer/Critica|POSITIVE:POSITIVE|[379103,379275]|173 HSP 1 e-value: 1.0E-93 bit: 343.0 Len: 173 Query Start:1 Query End:173 Subject Strand: POSITIVE Subject Start: 1 Subject End: 173 tttttagccgaagaattaaaagtatgttaatttatggattgtggttaagaggtaagaatgacaacagatattaaaactgaaattggtcatagagtaagacaggaacgtgaacgtcacaaattgacgagagaagagatctgtggacagaagctgacttaataatcaaacagctg tttttagccgaagaattaaaagtatgttaatttatggattgtggttaagaggtaagaatgacaacagatattaaaactgaaattggtcatagagtaagacaggaacgtgaacgtcacaaattgacgagagaagagatctgtggacagaagctgacttaataatcaaacagctg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUUAGCCGAAGAAUUAAAAGUAUGUUAAUUUAUGGAUUGUGGUUAAGAGGUAAGAAUGACAACAGAUAUUAAAACUGAAAUUGGUCAUAGAGUAAGACAGGAACGUGAACGUCACAAAUUGACGAGAGAAGAGAUCUGUGGACAGAAGCUGACUUAAUAAUCAAACAGCUG ....((((.(..(((((((.......)))))))........((((((..((((.((..((...((((((.......(((...(((.((...)).)))..))).........(((((.....))))).........))))))...))....)).))))..))))))..).)))) (-28.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAGCUGUUUGAUUAUUAAGUCAGCUUCUGUCCACAGAUCUCUUCUCUCGUCAAUUUGUGACGUUCACGUUCCUGUCUUACUCUAUGACCAAUUUCAGUUUUAAUAUCUGUUGUCAUUCUUACCUCUUAACCACAAUCCAUAAAUUAACAUACUUUUAAUUCUUCGGCUAAAAA .(((((...(((((.((((.(((..((((....))))..........(((((.....))))).........))).))))....(((((......(((.........)))..))))).......................................)))))...)))))..... (-24.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 303 170 124 57 11 smit:SMT_2063|5end_hypothetical_protein_1971792..1972022_NEGATIVE 303 170 124 96 50 smit:SMT_1996|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1921078..1921308_NEGATIVE 279 169 125 95 46 smit:SMT_145|5end_hypothetical_protein_95873..96103_POSITIVE 271 117 78 162 126 smit:SMT_247|5end_K02996_small_subunit_ribosomal_protein_S9_183062..183292_POSITIVE 257 115 78 192 149 smit:SMT_1817|5end_exonuclease_RexB_1792113..1792343_NEGATIVE 254 152 112 56 5 smit:SMT_880|5end_beta-lactam_resistance_factor_828300..828530_NEGATIVE 247 112 77 145 109 smit:SMT_446|5end_ABC-type_cobalt_transport_system,_ATPase_component_384870..385100_POSITIVE 244 148 110 226 189 smit:SMT_626|5end_1,4-alpha-glucan_branching_enzyme_530804..531034_POSITIVE 234 130 88 112 67 smit:SMT_1872|5end_K03217_preprotein_translocase_YidC_subunit_1831764..1831994_NEGATIVE 234 137 91 64 8 smit:SMT_1856|5end_polypeptide_deformylase_1820650..1820880_POSITIVE 229 149 101 128 68 smit:SMT_146|5end_sugar_transport_system_permease_protein_96664..96894_POSITIVE 228 117 75 66 20 smit:SMT_345|5end_K01990_ABC-2_type_transport_system_ATP-binding_protein_283992..284222_POSITIVE 227 165 127 181 140 smit:SMT_90|5end_DNA_polymerase_III_beta_subunit_21377..21607_POSITIVE 226 100 64 101 63 smit:SMT_1206|5end_similar_to_sensor_histidine_kinase_(AgrC_from_Staphylococcus)_1167043..1167273_NEGATIVE 226 118 82 90 48 smit:SMT_1099|5end_protein_tyrosine_phosphatase_1042241..1042471_NEGATIVE 224 71 31 46 3 smit:SMT_459|5end_hypothetical_protein_397350..397580_POSITIVE 221 136 100 60 26 smit:SMT_879|5end_hypothetical_protein_826989..827219_NEGATIVE 220 150 101 107 61 smit:SMT_477|5end_K03308_neurotransmitter:Na+_symporter,_NSS_family_414651..414881_NEGATIVE 219 80 34 197 140 smit:SMT_2142|5end_hypothetical_protein_predicted_by_Glimmer/Critica_2019999..2020229_POSITIVE 218 110 67 212 155 smit:SMT_853|5end_ATP-dependent_endopeptidase_clp_ATP-binding_subunit_ClpX_799285..799515_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 303 170 124 51 5 smit:SMT_1997|3end_K03294_basic_amino_acid/polyamine_antiporter,_APA_family_1921123..1921273_NEGATIVE 266 110 62 115 65 smit:SMT_693|3end_hypothetical_protein_604078..604228_POSITIVE 263 127 91 51 5 smit:SMT_974|3end_DNA-binding_response_regulator_922170..922320_NEGATIVE 259 146 113 51 8 smit:SMT_1854|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1818952..1819102_POSITIVE 256 143 101 97 50 smit:SMT_433|3end_cell_division_protein_DivIB_375954..376104_POSITIVE 247 112 77 144 108 smit:SMT_445|3end_hypothetical_protein_384949..385099_POSITIVE 242 149 106 66 21 smit:SMT_342|3end_chaperone_protein_DnaJ_283016..283166_POSITIVE 241 155 120 55 11 smit:SMT_764|3end_alanyl-tRNA_synthetase_669495..669645_NEGATIVE 238 157 113 75 31 smit:SMT_763|3end_alpha-amylase_669280..669430_POSITIVE 229 156 116 85 48 smit:SMT_516|3end_hypothetical_protein_442527..442677_NEGATIVE 227 152 128 51 26 smit:SMT_881|3end_peptidoglycan_branched_peptide_synthesis_protein,_alanine_adding_enzyme_828305..828455_NEGATIVE 221 46 4 84 39 smit:SMT_847|3end_thioredoxin_reductase_793848..793998_POSITIVE 220 155 120 62 18 smit:SMT_913|3end_putative_sucrose-specific_PTS_permease,_enzyme_II_863923..864073_NEGATIVE 219 145 101 91 39 smit:SMT_1357|3end_endo-beta-N-acetylglucosaminidase_1334450..1334600_NEGATIVE 217 155 118 57 12 smit:SMT_124|3end_hypothetical_protein_75590..75740_NEGATIVE 214 127 99 78 46 smit:SMT_1182|3end_K02796_PTS_system,_mannose-specific_IID_component_1139821..1139971_NEGATIVE 207 87 43 71 29 smit:SMT_670|3end_aminotransferase_(class_V),_putative_580324..580474_POSITIVE 204 126 84 74 25 smit:SMT_2075|3end_phosphoribosylamine--glycine_ligase_1977769..1977919_NEGATIVE 204 148 108 55 6 smit:SMT_943|3end_hypothetical_protein_894136..894286_NEGATIVE 201 147 108 99 57 smit:SMT_2018|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1936956..1937106_POSITIVE