Origin IGS: atttgcttattaaaaaagtagagaaaaatgttagccttagtttacccccccattttctctattaactataatatctctaacgaataactttttacattattgtttttcttataaaaataattttatttataaaattagatctcaaaaaggaaggattaaaatgaaacaaaaaagatcgatttcgatggtttgtgcattaattttaataattggtgcaatggtaggaggtatgatat .........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 atatcatacctcctaccattgcaccaattattaaaattaatgcacaaaccatcgaaatcgatcttttttgtttcattttaatccttcctttttgagatctaattttataaataaaattatttttataagaaaaacaataatgtaaaaagttattcgttagagatattatagttaatagagaaaatgggggggtaaactaaggctaacatttttctctacttttttaataagcaaat Mask Tandem Repeat Region ================================================ atttgcttattaaaaaagtagagaaaaatgttagccttagtttacccccccattttctctattaactataatatctctaacgaataactttttacattattgtttttcttataaaaataattttatttataaaattagatctcaaaaaggaaggattaaaatgaaacaaaaaagatcgatttcgatggtttgtgcattaattttaataattggtgcaatggtaggaggtatgatat Find is-nt database================================================ Query_seq: TDE0377:TDE0378|TDE0377:TDE0378:hypothetical protein:hypothetical protein:<-->:432068..432303 236 atttgcttattaaaaaagtagagaaaaatgttagccttagtttacccccccattttctctattaactataatatctctaacgaataactttttacattattgtttttcttataaaaataattttatttataaaattagatctcaaaaaggaaggattaaaatgaaacaaaaaagatcgatttcgatggtttgtgcattaattttaataattggtgcaatggtaggaggtatgatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0377:TDE0378|TDE0377:TDE0378:hypothetical protein:hypothetical protein:<-->:432068..432303 236 atttgcttattaaaaaagtagagaaaaatgttagccttagtttacccccccattttctctattaactataatatctctaacgaataactttttacattattgtttttcttataaaaataattttatttataaaattagatctcaaaaaggaaggattaaaatgaaacaaaaaagatcgatttcgatggtttgtgcattaattttaataattggtgcaatggtaggaggtatgatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0377:TDE0378|TDE0377:TDE0378:hypothetical protein:hypothetical protein:<-->:432068..432303 236 atttgcttattaaaaaagtagagaaaaatgttagccttagtttacccccccattttctctattaactataatatctctaacgaataactttttacattattgtttttcttataaaaataattttatttataaaattagatctcaaaaaggaaggattaaaatgaaacaaaaaagatcgatttcgatggtttgtgcattaattttaataattggtgcaatggtaggaggtatgatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atttgcttattaaaaaagtagagaaaaatgttagccttagtttacccccccattttctctattaactataatatctctaacgaataactttttacattattgtttttcttataaaaataattttatttataaaattagatctcaaaaaggaaggattaaaatgaaacaaaaaagatcgatttcgatggtttgtgcattaattttaataattggtgcaatggtaggaggtatgatat Predict ORF larger than 30AA ================================================ Protein_Len: 56 Strand: + Start: 68 End: 235 ................................................................... M I S L T N N F L H Y C F S Y K N N F I Y K I R S Q K G R I K M K Q K R S I S M V C A L I L I I G A M V G G M I . Protein_Len: 30 Strand: - Start: 145 End: 234 ................................................................................................................................................ F P L I L I F C F L D I E I T Q A N I K I I P A I T P P I M .. atttgcttattaaaaaagtagagaaaaatgttagccttagtttacccccccattttctctattaactataatatctctaacgaataactttttacattattgtttttcttataaaaataattttatttataaaattagatctcaaaaaggaaggattaaaatgaaacaaaaaagatcgatttcgatggtttgtgcattaattttaataattggtgcaatggtaggaggtatgatat 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================================================ atttgcttattaaaaaagtagagaaaaatgttagccttagtttacccccccattttctctattaactataatatctctaacgaataactttttacattattgtttttcttataaaaataattttatttataaaattagatctcaaaaaggaaggattaaaatgaaacaaaaaagatcgatttcgatggtttgtgcattaattttaataattggtgcaatggtaggaggtatgatat Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 70 HP_score: -5.2 Tail_Score: -4.82901 Start: 118 End: 137 Full_Region: ttcctttttgagatc taatttta taaa taaaatta tttttataagaaaaa .....................................................................................................................taattttataaataaaatta................................................................................................... Find igs database================================================ Query_seq: TDE0377:TDE0378|TDE0377:TDE0378:hypothetical protein:hypothetical protein:<-->:432068..432303 236 atttgcttattaaaaaagtagagaaaaatgttagccttagtttacccccccattttctctattaactataatatctctaacgaataactttttacattattgtttttcttataaaaataattttatttataaaattagatctcaaaaaggaaggattaaaatgaaacaaaaaagatcgatttcgatggtttgtgcattaattttaataattggtgcaatggtaggaggtatgatat Intra-Species Hit: Count: 1 Min: 1 Max: 236 Len: 236 Subject: NC_002967_TDE0377_TDE0378|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[432068,432303]|236 HSP 1 e-value: 3.0E-42 bit: 172.0 Len: 108 Query Start:1 Query End:108 Subject Strand: POSITIVE Subject Start: 1 Subject End: 108 atttgcttattaaaaaagtagagaaaaatgttagccttagtttannnnnnnattttctctattaactataatatctctaacgaataactttttacattattgtttttc................................................................................................................................ atttgcttattaaaaaagtagagaaaaatgttagccttagtttacccccccattttctctattaactataatatctctaacgaataactttttacattattgtttttc................................................................................................................................ HSP 2 e-value: 7.0E-28 bit: 125.0 Len: 63 Query Start:174 Query End:236 Subject Strand: POSITIVE Subject Start: 174 Subject End: 236 .............................................................................................................................................................................gatcgatttcgatggtttgtgcattaattttaataattggtgcaatggtaggaggtatgatat .............................................................................................................................................................................gatcgatttcgatggtttgtgcattaattttaataattggtgcaatggtaggaggtatgatat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUGCUUAUUAAAAAAGUAGAGAAAAAUGUUAGCCUUAGUUUACCCCCCCAUUUUCUCUAUUAACUAUAAUAUCUCUAACGAAUAACUUUUUACAUUAUUGUUUUUCUUAUAAAAAUAAUUUUAUUUAUAAAAUUAGAUCUCAAAAAGGAAGGAUUAAAAUGAAACAAAAAAGAUCGAUUUCGAUGGUUUGUGCAUUAAUUUUAAUAAUUGGUGCAAUGGUAGGAGGUAUGAUAU ................(((((((((((..((.(((....))).)).......)))))))))))...(((.((((((((.((.............((((...(((((((((.......((((((((....))))))))..........)))))))))...))))..(((((....((((....))))..)))))(((((((((.....)))))))))....)).)))))))).))). (-41.93) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAUCAUACCUCCUACCAUUGCACCAAUUAUUAAAAUUAAUGCACAAACCAUCGAAAUCGAUCUUUUUUGUUUCAUUUUAAUCCUUCCUUUUUGAGAUCUAAUUUUAUAAAUAAAAUUAUUUUUAUAAGAAAAACAAUAAUGUAAAAAGUUAUUCGUUAGAGAUAUUAUAGUUAAUAGAGAAAAUGGGGGGGUAAACUAAGGCUAACAUUUUUCUCUACUUUUUUAAUAAGCAAAU ..................((((.......((((((((....(((.(((..((((....))))..))).)))...))))))))..........(((.((((..(((((((((..........)))))))))..(((((((((.......)))))).)))..)))).))).......(((((((((...(..(((........)))..)..)))))))))............)))).. (-33.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 804 70 21 161 112 NC_002967:TDE0377|5end_hypothetical_protein_431977..432207_NEGATIVE 274 55 31 230 205 NC_002967:TDE1199|5end_cell_division_protein_FtsL,_putative_1231341..1231571_POSITIVE 249 48 1 57 12 NC_002967:TDE1147|5end_hypothetical_protein_1185960..1186190_NEGATIVE 244 216 173 49 1 NC_002967:TDE0519|5end_hypothetical_protein_565989..566219_NEGATIVE 237 227 181 227 174 NC_002967:TDE2714|5end_hypothetical_protein_2772618..2772848_NEGATIVE 234 128 96 212 181 NC_002967:TDE0612|5end_hypothetical_protein_647471..647701_NEGATIVE 232 220 172 223 174 NC_002967:TDE0238|5end_thioredoxin,_selenocysteine-containing_271380..271610_POSITIVE 229 66 41 212 183 NC_002967:TDE0016|5end_ATPase,_AAA_family_20457..20687_POSITIVE 226 195 158 100 67 NC_002967:TDE2616|5end_cyclic_nucleotide-binding_protein_2658339..2658569_NEGATIVE 224 61 28 182 142 NC_002967:TDE0565|5end_hypothetical_protein_597031..597261_POSITIVE 220 223 186 182 147 NC_002967:TDE2059|5end_hypothetical_protein_2086509..2086739_NEGATIVE 214 199 180 214 194 NC_002967:TDE1882|5end_glycosyl_hydrolase,_family_1_1903544..1903774_POSITIVE 210 70 34 132 93 NC_002967:TDE1209|5end_site-specific_recombinase,_phage_integrase_family_1242345..1242575_POSITIVE 209 227 183 195 148 NC_002967:TDE0678|5end_hypothetical_protein_716014..716244_POSITIVE 206 59 37 175 150 NC_002967:TDE2051|5end_hypothetical_protein_2080298..2080528_NEGATIVE 205 214 171 109 65 NC_002967:TDE2554|5end_chaperonin,_33_kDa_family_2580745..2580975_POSITIVE 205 202 161 182 147 NC_002967:TDE0993|5end_lipoprotein,_putative_1020415..1020645_NEGATIVE 203 186 143 82 43 NC_002967:TDE1848|5end_hypothetical_protein_1877354..1877584_NEGATIVE 203 96 55 214 170 NC_002967:TDE1263|5end_hypothetical_protein_1297304..1297534_POSITIVE 202 230 199 190 160 NC_002967:TDE2477|5end_selenocysteine_synthase_2499523..2499753_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 248 69 22 39 2 NC_002967:TDE2196|3end_hypothetical_protein_2231883..2232033_NEGATIVE 241 200 151 119 79 NC_002967:TDE2713|3end_RNA_methyltransferase,_TrmH_family_2769557..2769707_NEGATIVE 234 128 96 109 78 NC_002967:TDE0613|3end_hypothetical_protein_647574..647724_NEGATIVE 233 204 166 91 50 NC_002967:TDE0648|3end_protein-glutamate_methylesterase_683998..684148_POSITIVE 226 195 158 96 63 NC_002967:TDE2617|3end_cyclic_nucleotide-binding_protein_2658343..2658493_NEGATIVE 224 61 28 86 46 NC_002967:TDE0564|3end_hypothetical_protein_597015..597165_POSITIVE 222 58 18 149 104 NC_002967:TDE1983|3end_hypothetical_protein_1993376..1993526_NEGATIVE 217 48 4 43 1 NC_002967:TDE1148|3end_hypothetical_protein_1185974..1186124_NEGATIVE 210 70 34 139 100 NC_002967:TDE1208|3end_DNA_topoisomerase_I_1242432..1242582_POSITIVE 208 67 37 88 64 NC_002967:TDE0210|3end_cob(I)yrinic_acid_a,c-diamide_adenosyltransferase_246146..246296_POSITIVE 206 229 181 88 44 NC_002967:TDE0165|3end_hypothetical_protein_195056..195206_POSITIVE 205 50 16 75 40 NC_002967:TDE1907|3end_holo-(acyl-carrier-protein)_synthase_1924726..1924876_NEGATIVE 203 186 143 80 41 NC_002967:TDE1849|3end_hypothetical_protein_1877356..1877506_NEGATIVE 203 96 55 71 27 NC_002967:TDE1261|3end_choline/carnitine/betaine_transporter_family_protein_1297241..1297391_POSITIVE 202 230 190 87 53 NC_002967:TDE2162|3end_NOL1/NOP2/sun_family_protein_2195560..2195710_POSITIVE 202 220 176 149 101 NC_002967:TDE1891|3end_hypothetical_protein_1912050..1912200_POSITIVE 200 187 142 44 3 NC_002967:TDE2514|3end_serine/threonine_protein_phosphatase_family_protein_2539855..2540005_NEGATIVE 199 47 14 74 46 NC_002967:TDE1715|3end_phosphoglycerate_kinase_1769503..1769653_NEGATIVE 198 84 41 129 90 NC_002967:TDE0230|3end_DNA_replication_and_repair_protein_RecF_262799..262949_NEGATIVE 196 59 15 48 15 NC_002967:TDE2548|3end_hypothetical_protein_2573064..2573214_NEGATIVE