Origin IGS: aacgcaaaattaacctaatagccatagctgatttgttcttgcattataattaactccattataagcttaccaaagaagccgattctctatgagctgatcctaatc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gattaggatcagctcatagagaatcggcttctttggtaagcttataatggagttaattataatgcaagaacaaatcagctatggctattaggttaattttgcgtt Mask Tandem Repeat Region ================================================ aacgcaaaattaacctaatagccatagctgatttgttcttgcattataattaactccattataagcttaccaaagaagccgattctctatgagctgatcctaatc Find is-nt database================================================ Query_seq: TDE1957:TDE1958|TDE1957:TDE1958:hypothetical protein:surface protein, putative:-><-:1972294..1972398 105 aacgcaaaattaacctaatagccatagctgatttgttcttgcattataattaactccattataagcttaccaaagaagccgattctctatgagctgatcctaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1957:TDE1958|TDE1957:TDE1958:hypothetical protein:surface protein, putative:-><-:1972294..1972398 105 aacgcaaaattaacctaatagccatagctgatttgttcttgcattataattaactccattataagcttaccaaagaagccgattctctatgagctgatcctaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1957:TDE1958|TDE1957:TDE1958:hypothetical protein:surface protein, putative:-><-:1972294..1972398 105 aacgcaaaattaacctaatagccatagctgatttgttcttgcattataattaactccattataagcttaccaaagaagccgattctctatgagctgatcctaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aacgcaaaattaacctaatagccatagctgatttgttcttgcattataattaactccattataagcttaccaaagaagccgattctctatgagctgatcctaatc Predict ORF larger than 30AA ================================================ aacgcaaaattaacctaatagccatagctgatttgttcttgcattataattaactccattataagcttaccaaagaagccgattctctatgagctgatcctaatc 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================================================ aacgcaaaattaacctaatagccatagctgatttgttcttgcattataattaactccattataagcttaccaaagaagccgattctctatgagctgatcctaatc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1957:TDE1958|TDE1957:TDE1958:hypothetical protein:surface protein, putative:-><-:1972294..1972398 105 aacgcaaaattaacctaatagccatagctgatttgttcttgcattataattaactccattataagcttaccaaagaagccgattctctatgagctgatcctaatc Intra-Species Hit: Count: 1 Min: 1 Max: 105 Len: 105 Subject: NC_002967_TDE1957_TDE1958|hypothetical protein:surface protein, putative|POSITIVE:NEGATIVE|[1972294,1972398]|105 HSP 1 e-value: 3.0E-53 bit: 208.0 Len: 105 Query Start:1 Query End:105 Subject Strand: POSITIVE Subject Start: 1 Subject End: 105 aacgcaaaattaacctaatagccatagctgatttgttcttgcattataattaactccattataagcttaccaaagaagccgattctctatgagctgatcctaatc aacgcaaaattaacctaatagccatagctgatttgttcttgcattataattaactccattataagcttaccaaagaagccgattctctatgagctgatcctaatc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACGCAAAAUUAACCUAAUAGCCAUAGCUGAUUUGUUCUUGCAUUAUAAUUAACUCCAUUAUAAGCUUACCAAAGAAGCCGAUUCUCUAUGAGCUGAUCCUAAUC ..................(((((((((..((((.((((((((.(((((((.......)))))))))......))).))).))))..))))).))))......... (-16.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUUAGGAUCAGCUCAUAGAGAAUCGGCUUCUUUGGUAAGCUUAUAAUGGAGUUAAUUAUAAUGCAAGAACAAAUCAGCUAUGGCUAUUAGGUUAAUUUUGCGUU ..(((..((.((((..(((((((.....)))))))...)))).))..)))..........(((((((((...(((((((....)))....))))..))))))))) (-18.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 292 100 55 128 87 NC_002967:TDE1312|5end_hypothetical_protein_1349088..1349318_POSITIVE 275 100 54 200 162 NC_002967:TDE1261|5end_choline/carnitine/betaine_transporter_family_protein_1295593..1295823_POSITIVE 272 42 10 165 134 NC_002967:TDE0303|5end_hypothetical_protein_333498..333728_POSITIVE 270 58 15 97 46 NC_002967:TDE0392|5end_(R)-2-hydroxyglutaryl-CoA_dehydratase,_beta_subunit,_putative_443024..443254_NEGATIVE 266 100 54 211 164 NC_002967:TDE0772|5end_50S_ribosomal_protein_L22_809084..809314_POSITIVE 257 96 53 99 41 NC_002967:TDE2526|5end_hypothetical_protein_2555034..2555264_NEGATIVE 254 96 63 133 101 NC_002967:TDE0860|5end_ribosomal_small_subunit_pseudouridine_synthase_A_881023..881253_POSITIVE 245 45 1 73 21 NC_002967:TDE0021|5end_CDP-alcohol_phosphatidyltransferase_family_protein_26814..27044_POSITIVE 233 100 54 157 99 NC_002967:TDE0502|5end_ankyrin_repeat_protein_556558..556788_NEGATIVE 230 99 58 177 145 NC_002967:TDE2347|5end_30S_ribosomal_protein_S2_2384378..2384608_NEGATIVE 230 45 2 152 115 NC_002967:TDE0267|5end_HAM1_protein_299108..299338_NEGATIVE 229 100 54 148 99 NC_002967:TDE1961|5end_PIN_domain_protein_1974975..1975205_NEGATIVE 228 99 53 146 92 NC_002967:TDE2138|5end_ankyrin_repeat_protein_2171631..2171861_POSITIVE 228 99 74 70 44 NC_002967:TDE2047|5end_hypothetical_protein_2076351..2076581_NEGATIVE 225 99 51 186 125 NC_002967:TDE2754|5end_ornithine_cyclodeaminase_2811780..2812010_NEGATIVE 225 51 16 111 82 NC_002967:TDE0602|5end_3-oxoacyl-(acyl-carrier-protein)_synthase_III_640771..641001_NEGATIVE 224 100 55 224 189 NC_002967:TDE0791|5end_DNA-directed_RNA_polymerase_alpha_subunit_817342..817572_POSITIVE 223 100 65 67 33 NC_002967:TDE0693|5end_phosphomethylpyrimidine_kinase_729942..730172_POSITIVE 222 96 54 77 23 NC_002967:TDE0084|5end_phosphoenolpyruvate-protein_phosphotransferase_97455..97685_NEGATIVE 221 80 35 123 73 NC_002967:TDE1492|5end_chemotaxis_protein_CheW_1537231..1537461_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 254 96 63 136 104 NC_002967:TDE0859|3end_hypothetical_protein_881106..881256_POSITIVE 245 45 1 60 8 NC_002967:TDE0020|3end_glycyl-tRNA_synthetase_26881..27031_POSITIVE 235 96 63 38 2 NC_002967:TDE1093|3end_hypothetical_protein_1128158..1128308_POSITIVE 233 100 54 135 77 NC_002967:TDE0503|3end_hypothetical_protein_556580..556730_NEGATIVE 230 45 2 41 4 NC_002967:TDE0268|3end_hypothetical_protein_299219..299369_NEGATIVE 228 99 53 144 90 NC_002967:TDE2137|3end_hypothetical_protein_2171709..2171859_POSITIVE 228 98 56 149 88 NC_002967:TDE0813|3end_ABC_transporter,_ATP-binding_protein/permease_835707..835857_POSITIVE 225 99 51 68 7 NC_002967:TDE2756|3end_bacterial_extracellular_solute-binding_protein,_family_5_2811898..2812048_NEGATIVE 224 100 63 98 54 NC_002967:TDE2571|3end_hypothetical_protein_2597922..2598072_NEGATIVE 221 80 35 106 56 NC_002967:TDE1491|3end_chemotaxis_protein_CheA_1537294..1537444_POSITIVE 220 80 36 45 1 NC_002967:TDE2687|3end_L-threonine-O-3-phosphate_decarboxylase,_putative_2727196..2727346_NEGATIVE 220 48 13 129 89 NC_002967:TDE0271|3end_hypothetical_protein_302199..302349_POSITIVE 219 66 22 78 35 NC_002967:TDE1599|3end_ABC_transporter,_ATP-binding/permease_protein_1648920..1649070_NEGATIVE 218 100 64 129 96 NC_002967:TDE2527|3end_hypothetical_protein_2555449..2555599_NEGATIVE 216 100 65 136 101 NC_002967:TDE1403|3end_ABC_transporter,_ATP-binding_protein_1444500..1444650_NEGATIVE 212 91 65 55 31 NC_002967:TDE2339|3end_leucyl-tRNA_synthetase_2377501..2377651_POSITIVE 212 70 23 150 106 NC_002967:TDE1409|3end_flagellar_filament_outer_layer_protein_FlaA,_putative_1452381..1452531_POSITIVE 209 99 75 38 7 NC_002967:TDE1323|3end_hypothetical_protein_1360968..1361118_POSITIVE 209 57 18 50 18 NC_002967:TDE0986|3end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_1014121..1014271_POSITIVE 208 100 53 130 74 NC_002967:TDE1152|3end_head-to-tail_joining_protein,_putative_1188527..1188677_NEGATIVE