Origin IGS: atgaagcttggtgtttaattttatagcttatatattgatgagagcaggagactaactgctctcttttctttgggagagtaagaaatttcactgacaaaaaaagcctgcctaaattaggcgggcttcataattttgagttgaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttcaactcaaaattatgaagcccgcctaatttaggcaggctttttttgtcagtgaaatttcttactctcccaaagaaaagagagcagttagtctcctgctctcatcaatatataagctataaaattaaacaccaagcttcat Mask Tandem Repeat Region ================================================ atgaagcttggtgtttaattttatagcttatatattgatgagagcaggagactaactgctctcttttctttgggagagtaagaaatttcactgacaaaaaaagcctgcctaaattaggcgggcttcataattttgagttgaa Find is-nt database================================================ Query_seq: SSA_0143:SSA_0144|SSA_0143:SSA_0144:Conserved uncharacterized protein:Transcriptional regulator, TetR family, putative:-><-:137941..138082 142 atgaagcttggtgtttaattttatagcttatatattgatgagagcaggagactaactgctctcttttctttgggagagtaagaaatttcactgacaaaaaaagcctgcctaaattaggcgggcttcataattttgagttgaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0143:SSA_0144|SSA_0143:SSA_0144:Conserved uncharacterized protein:Transcriptional regulator, TetR family, putative:-><-:137941..138082 142 atgaagcttggtgtttaattttatagcttatatattgatgagagcaggagactaactgctctcttttctttgggagagtaagaaatttcactgacaaaaaaagcctgcctaaattaggcgggcttcataattttgagttgaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0143:SSA_0144|SSA_0143:SSA_0144:Conserved uncharacterized protein:Transcriptional regulator, TetR family, putative:-><-:137941..138082 142 atgaagcttggtgtttaattttatagcttatatattgatgagagcaggagactaactgctctcttttctttgggagagtaagaaatttcactgacaaaaaaagcctgcctaaattaggcgggcttcataattttgagttgaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atgaagcttggtgtttaattttatagcttatatattgatgagagcaggagactaactgctctcttttctttgggagagtaagaaatttcactgacaaaaaaagcctgcctaaattaggcgggcttcataattttgagttgaa Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: - Start: 2 End: 97 . S A Q H K I K Y S I Y Q H S C S V L Q E R K K P L T L F K V S M ............................................. atgaagcttggtgtttaattttatagcttatatattgatgagagcaggagactaactgctctcttttctttgggagagtaagaaatttcactgacaaaaaaagcctgcctaaattaggcgggcttcataattttgagttgaa 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================================================ atgaagcttggtgtttaattttatagcttatatattgatgagagcaggagactaactgctctcttttctttgggagagtaagaaatttcactgacaaaaaaagcctgcctaaattaggcgggcttcataattttgagttgaa Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 90 HP_score: -8.2 Tail_Score: -4.86731 Start: 40 End: 63 Full_Region: AGCTTATATATTGAT GAGAGCAG GAGACTAA CTGCTCTC TTTTCTTTGGGAGAG .......................................GAGAGCAGGAGACTAACTGCTCTC............................................................................... TransTerm Strand: + Conf: 93 HP_score: -13.3 Tail_Score: -3.37935 Start: 103 End: 123 Full_Region: TCACTGACAAAAAAA GCCTGCCTA AAT TAGGCGGGC TTCATAATTTTGAGT ......................................................................................................GCCTGCCTAAATTAGGCGGGC................... Find igs database================================================ Query_seq: SSA_0143:SSA_0144|SSA_0143:SSA_0144:Conserved uncharacterized protein:Transcriptional regulator, TetR family, putative:-><-:137941..138082 142 atgaagcttggtgtttaattttatagcttatatattgatgagagcaggagactaactgctctcttttctttgggagagtaagaaatttcactgacaaaaaaagcctgcctaaattaggcgggcttcataattttgagttgaa Intra-Species Hit: Count: 1 Min: 1 Max: 142 Len: 142 Subject: NC_009009_SSA_0143_SSA_0144|Conserved uncharacterized protein:Transcriptional regulator, TetR family, putative|POSITIVE:NEGATIVE|[137941,138082]|142 HSP 1 e-value: 1.0E-62 bit: 240.0 Len: 142 Query Start:1 Query End:142 Subject Strand: POSITIVE Subject Start: 1 Subject End: 142 atgaagcttggtgtttaattttatagcttatatattgatgagagcaggagactaactgctctcttttctttgggagagtaagaaatttcactgacnnnnnnngcctgcctaaattaggcgggcttcataattttgagttgaa atgaagcttggtgtttaattttatagcttatatattgatgagagcaggagactaactgctctcttttctttgggagagtaagaaatttcactgacaaaaaaagcctgcctaaattaggcgggcttcataattttgagttgaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUGAAGCUUGGUGUUUAAUUUUAUAGCUUAUAUAUUGAUGAGAGCAGGAGACUAACUGCUCUCUUUUCUUUGGGAGAGUAAGAAAUUUCACUGACAAAAAAAGCCUGCCUAAAUUAGGCGGGCUUCAUAAUUUUGAGUUGAA ....(((((((((...((((((...((((...((..((.((((((((........))))))))...))..))...))))..)))))).))))........(((((((((((...))))))))))).........)))))... (-43.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCAACUCAAAAUUAUGAAGCCCGCCUAAUUUAGGCAGGCUUUUUUUGUCAGUGAAAUUUCUUACUCUCCCAAAGAAAAGAGAGCAGUUAGUCUCCUGCUCUCAUCAAUAUAUAAGCUAUAAAAUUAAACACCAAGCUUCAU ..............(((((((..(((((...))))).(((((((((((..(((((......)))))....)))))))..((((((((........))))))))...........)))).................))))))) (-35.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 370 128 91 151 122 NC_009009:SSA_2080|5end_hypothetical_protein_2085341..2085571_NEGATIVE 317 109 61 146 98 NC_009009:SSA_2338|5end_Conserved_uncharacterized_protein_2339272..2339502_POSITIVE 313 77 41 52 7 NC_009009:SSA_1994|5end_CTP_synthase,_putative_1992474..1992704_NEGATIVE 307 66 25 167 122 NC_009009:SSA_0273|5end_hypothetical_protein_267071..267301_POSITIVE 306 75 40 46 9 NC_009009:SSA_0511|5end_Propanediol_utilization_kinase,_putative_509610..509840_POSITIVE 298 136 101 164 124 NC_009009:SSA_2024|5end_hypothetical_protein_2029272..2029502_NEGATIVE 298 140 91 221 176 NC_009009:SSA_0051|5end_Dihydroxyacetone_kinase_phosphotransfer_protein,_putative_55190..55420_POSITIVE 283 90 42 147 102 NC_009009:SSA_2185|5end_Adenylosuccinate_synthetase,_putative_2185290..2185520_NEGATIVE 282 125 85 225 194 NC_009009:SSA_1189|5end_GTP-binding_protein,_putative_1217657..1217887_NEGATIVE 281 83 43 164 117 NC_009009:SSA_0790|5end_hypothetical_protein_773047..773277_POSITIVE 278 70 27 85 42 NC_009009:SSA_1901|5end_Conserved_uncharacterized_protein_1896599..1896829_NEGATIVE 277 140 102 211 177 NC_009009:SSA_1678|5end_ABC-type_multidrug_transport_system,_permease_component,_putative_1672181..1672411_NEGATIVE 274 72 34 154 108 NC_009009:SSA_1307|5end_Trk_transporter_membrane-spanning_protein-K+_transport,_putative_1326270..1326500_NEGATIVE 273 109 61 183 129 NC_009009:SSA_0072|5end_ABC_sugar_transporter,_MsmK-like_protein,_putative_75922..76152_POSITIVE 270 123 95 172 145 NC_009009:SSA_0244|5end_hypothetical_protein_238698..238928_POSITIVE 264 123 99 185 165 NC_009009:SSA_0250|5end_GTP_pyrophosphokinase,_putative_242167..242397_POSITIVE 263 66 22 127 91 NC_009009:SSA_1250|5end_Conserved_uncharacterized_protein,_putative_1274512..1274742_NEGATIVE 263 74 38 147 113 NC_009009:SSA_0509|5end_Propanediol_utilization_protein,_putative_508024..508254_POSITIVE 262 136 100 45 11 NC_009009:SSA_1783|5end_Xanthosine_triphosphate_pyrophosphatase_(NTPase/HAM1_family),_putative_1769106..1769336_NEGATIVE 259 82 41 172 108 NC_009009:SSA_2322|5end_Transcriptional_regulator,_TetR/AcrR_family,_putative_2327044..2327274_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 370 128 91 141 112 NC_009009:SSA_2082|3end_Carbohydrate_kinase,_FGGY_family,_putative_2085351..2085501_NEGATIVE 307 66 25 48 3 NC_009009:SSA_0272|3end_Oxidoreductase,_aldo/keto_reductase_family,_putative_267032..267182_POSITIVE 306 110 61 149 105 NC_009009:SSA_2337|3end_hypothetical_protein_2339359..2339509_POSITIVE 306 75 40 53 16 NC_009009:SSA_0510|3end_L-threonine-O-3-phosphate_decarboxylase,_putative_509697..509847_POSITIVE 282 125 85 83 52 NC_009009:SSA_1190|3end_Conserved_uncharacterized_protein_1217799..1217949_NEGATIVE 279 64 41 77 49 NC_009009:SSA_0669|3end_ATP_dependent_protease,_putative_651450..651600_NEGATIVE 264 78 46 96 52 NC_009009:SSA_0819|3end_hypothetical_protein_801181..801331_POSITIVE 264 123 99 53 33 NC_009009:SSA_0249|3end_hypothetical_protein_242115..242265_POSITIVE 263 66 22 146 110 NC_009009:SSA_1251|3end_Hydrolase,_HD_superfamily,_putative_1274493..1274643_NEGATIVE 263 137 98 89 55 NC_009009:SSA_1042|3end_Xylanase/chitin_deacetylase,_putative_1057509..1057659_NEGATIVE 263 84 43 61 13 NC_009009:SSA_0688|3end_2,3-bisphosphoglycerate-dependent_phosphoglycerate_mutase,_putative_672132..672282_POSITIVE 263 74 38 107 73 NC_009009:SSA_0508|3end_Conserved_uncharacterized_protein,_possible_phosphoserine_phosphatase_508064..508214_POSITIVE 263 89 41 63 23 NC_009009:SSA_0227|3end_Collagen-binding_surface_protein,_putative_222970..223120_POSITIVE 262 136 100 48 14 NC_009009:SSA_1784|3end_Glutamate_racemase,_putative_1769103..1769253_NEGATIVE 261 139 107 135 100 NC_009009:SSA_1557|3end_SRPR,_signal_recognition_particle-docking_protein,_putative_1558502..1558652_NEGATIVE 257 109 67 56 16 NC_009009:SSA_1567|3end_Polar_amino_acid_ABC_transporter,_amino_acid-binding_protein,_putative_1571267..1571417_POSITIVE 256 69 26 109 54 NC_009009:SSA_0939|3end_Inositol_monophosphatase_(Mg++_dependent),_putative_947705..947855_POSITIVE 255 124 91 56 23 NC_009009:SSA_0597|3end_hypothetical_protein_588563..588713_POSITIVE 251 70 34 151 111 NC_009009:SSA_1308|3end_hypothetical_protein_1326267..1326417_NEGATIVE 249 123 100 84 56 NC_009009:SSA_1364|3end_hypothetical_protein_1380482..1380632_NEGATIVE