Origin IGS: gttttcctccaatctaaaagttaaagtagcacgtcattgtttttttatcaagagggtatttatggttatgaaaatcgatttttaatatttttattaaaccgcctgtgatgtcaaaaagcgcaataagacactgtcaaccgacacggtaaggatttacatttttcattaatcttgctttccatgatatttggagcgcattttaattgacaggcaaaagacttatttatataatatcaaag .........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 ctttgatattatataaataagtcttttgcctgtcaattaaaatgcgctccaaatatcatggaaagcaagattaatgaaaaatgtaaatccttaccgtgtcggttgacagtgtcttattgcgctttttgacatcacaggcggtttaataaaaatattaaaaatcgattttcataaccataaataccctcttgataaaaaaacaatgacgtgctactttaacttttagattggaggaaaac Mask Tandem Repeat Region ================================================ gttttcctccaatctaaaagttaaagtagcacgtcattgtttttttatcaagagggtatttatggttatgaaaatcgatttttaatatttttattaaaccgcctgtgatgtcaaaaagcgcaataagacactgtcaaccgacacggtaaggatttacatttttcattaatcttgctttccatgatatttggagcgcattttaattgacaggcaaaagacttatttatataatatcaaag Find is-nt database================================================ Query_seq: TDE2178:TDE2179|TDE2178:TDE2179:hypothetical protein:voltage-gated chloride channel:<-->:2208849..2209087 239 gttttcctccaatctaaaagttaaagtagcacgtcattgtttttttatcaagagggtatttatggttatgaaaatcgatttttaatatttttattaaaccgcctgtgatgtcaaaaagcgcaataagacactgtcaaccgacacggtaaggatttacatttttcattaatcttgctttccatgatatttggagcgcattttaattgacaggcaaaagacttatttatataatatcaaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2178:TDE2179|TDE2178:TDE2179:hypothetical protein:voltage-gated chloride channel:<-->:2208849..2209087 239 gttttcctccaatctaaaagttaaagtagcacgtcattgtttttttatcaagagggtatttatggttatgaaaatcgatttttaatatttttattaaaccgcctgtgatgtcaaaaagcgcaataagacactgtcaaccgacacggtaaggatttacatttttcattaatcttgctttccatgatatttggagcgcattttaattgacaggcaaaagacttatttatataatatcaaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2178:TDE2179|TDE2178:TDE2179:hypothetical protein:voltage-gated chloride channel:<-->:2208849..2209087 239 gttttcctccaatctaaaagttaaagtagcacgtcattgtttttttatcaagagggtatttatggttatgaaaatcgatttttaatatttttattaaaccgcctgtgatgtcaaaaagcgcaataagacactgtcaaccgacacggtaaggatttacatttttcattaatcttgctttccatgatatttggagcgcattttaattgacaggcaaaagacttatttatataatatcaaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gttttcctccaatctaaaagttaaagtagcacgtcattgtttttttatcaagagggtatttatggttatgaaaatcgatttttaatatttttattaaaccgcctgtgatgtcaaaaagcgcaataagacactgtcaaccgacacggtaaggatttacatttttcattaatcttgctttccatgatatttggagcgcattttaattgacaggcaaaagacttatttatataatatcaaag Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: - Start: 114 End: 227 ................................................................................................................. F A C Y S V T L R C P L S K C K E N I K S E M I N P A C K L Q C A F S K N M ............ Protein_Len: 36 Strand: - Start: 17 End: 124 ................ F N F Y C T M T K K D L P Y K H N H F D I K L I K I L G G T I D F L A M ................................................................................................................... gttttcctccaatctaaaagttaaagtagcacgtcattgtttttttatcaagagggtatttatggttatgaaaatcgatttttaatatttttattaaaccgcctgtgatgtcaaaaagcgcaataagacactgtcaaccgacacggtaaggatttacatttttcattaatcttgctttccatgatatttggagcgcattttaattgacaggcaaaagacttatttatataatatcaaag 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: 90 Start: 203 End: 232 ..........................................................................................................................................................................................................ATTGACAGGCAAAAGACTTATTTATATAAT....... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gttttcctccaatctaaaagttaaagtagcacgtcattgtttttttatcaagagggtatttatggttatgaaaatcgatttttaatatttttattaaaccgcctgtgatgtcaaaaagcgcaataagacactgtcaaccgacacggtaaggatttacatttttcattaatcttgctttccatgatatttggagcgcattttaattgacaggcaaaagacttatttatataatatcaaag Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2178:TDE2179|TDE2178:TDE2179:hypothetical protein:voltage-gated chloride channel:<-->:2208849..2209087 239 gttttcctccaatctaaaagttaaagtagcacgtcattgtttttttatcaagagggtatttatggttatgaaaatcgatttttaatatttttattaaaccgcctgtgatgtcaaaaagcgcaataagacactgtcaaccgacacggtaaggatttacatttttcattaatcttgctttccatgatatttggagcgcattttaattgacaggcaaaagacttatttatataatatcaaag Intra-Species Hit: Count: 1 Min: 1 Max: 239 Len: 239 Subject: NC_002967_TDE2178_TDE2179|hypothetical protein:voltage-gated chloride channel|NEGATIVE:POSITIVE|[2208849,2209087]|239 HSP 1 e-value: 1.0E-120 bit: 432.0 Len: 239 Query Start:1 Query End:239 Subject Strand: POSITIVE Subject Start: 1 Subject End: 239 gttttcctccaatctaaaagttaaagtagcacgtcattgnnnnnnnatcaagagggtatttatggttatgaaaatcgatttttaatatttttattaaaccgcctgtgatgtcaaaaagcgcaataagacactgtcaaccgacacggtaaggatttacatttttcattaatcttgctttccatgatatttggagcgcattttaattgacaggcaaaagacttatttatataatatcaaag gttttcctccaatctaaaagttaaagtagcacgtcattgtttttttatcaagagggtatttatggttatgaaaatcgatttttaatatttttattaaaccgcctgtgatgtcaaaaagcgcaataagacactgtcaaccgacacggtaaggatttacatttttcattaatcttgctttccatgatatttggagcgcattttaattgacaggcaaaagacttatttatataatatcaaag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUUUCCUCCAAUCUAAAAGUUAAAGUAGCACGUCAUUGUUUUUUUAUCAAGAGGGUAUUUAUGGUUAUGAAAAUCGAUUUUUAAUAUUUUUAUUAAACCGCCUGUGAUGUCAAAAAGCGCAAUAAGACACUGUCAACCGACACGGUAAGGAUUUACAUUUUUCAUUAAUCUUGCUUUCCAUGAUAUUUGGAGCGCAUUUUAAUUGACAGGCAAAAGACUUAUUUAUAUAAUAUCAAAG .................(((((..........((((((((.(((((((((...((((.....(((((.....)))))...(((((((....)))))))..)))).)))))....)))).)))))..))).(((((.((((...)))).................(((((...(((.(((((.......))))).)))..))))).)))))......))))).................. (-39.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUUGAUAUUAUAUAAAUAAGUCUUUUGCCUGUCAAUUAAAAUGCGCUCCAAAUAUCAUGGAAAGCAAGAUUAAUGAAAAAUGUAAAUCCUUACCGUGUCGGUUGACAGUGUCUUAUUGCGCUUUUUGACAUCACAGGCGGUUUAAUAAAAAUAUUAAAAAUCGAUUUUCAUAACCAUAAAUACCCUCUUGAUAAAAAAACAAUGACGUGCUACUUUAACUUUUAGAUUGGAGGAAAAC (((..((...........((((.....((.(((((.......(((..((((.......))))..)))......(((((((.............(((((...((..(.(((((......)))))..)..))..))).))((((((((((....)))))..))))).)))))))...............................))))).)).))))..........))..)))...... (-38.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 890 140 91 231 182 NC_002967:TDE2178|5end_hypothetical_protein_2208758..2208988_NEGATIVE 296 177 132 208 152 NC_002967:TDE1127|5end_TPR_domain_protein_1158278..1158508_POSITIVE 283 166 121 91 35 NC_002967:TDE0108|5end_hypothetical_protein_128399..128629_POSITIVE 277 150 101 190 132 NC_002967:TDE0946|5end_hypothetical_protein_968212..968442_POSITIVE 272 150 101 118 70 NC_002967:TDE2103|5end_glycosyl_transferase,_group_2_family_protein_2128393..2128623_NEGATIVE 267 180 131 99 51 NC_002967:TDE0317|5end_hypothetical_protein_350656..350886_POSITIVE 266 146 101 228 176 NC_002967:TDE0819|5end_ABC_transporter,_ATP-binding/permease_protein_843385..843615_NEGATIVE 264 146 101 63 10 NC_002967:TDE0209|5end_arsenical_pump_membrane_protein,_putative_244195..244425_POSITIVE 262 127 97 46 16 NC_002967:TDE2369|5end_hypothetical_protein_2402292..2402522_POSITIVE 262 150 101 214 167 NC_002967:TDE0210|5end_cob(I)yrinic_acid_a,c-diamide_adenosyltransferase_245551..245781_POSITIVE 261 216 171 181 139 NC_002967:TDE2100|5end_hypothetical_protein_2125370..2125600_POSITIVE 259 146 103 163 123 NC_002967:TDE0773|5end_30S_ribosomal_protein_S3_809443..809673_POSITIVE 258 150 101 204 156 NC_002967:TDE0908|5end_ABC_transporter,_ATP-binding/permease_protein_925254..925484_POSITIVE 253 150 101 222 151 NC_002967:TDE0782|5end_50S_ribosomal_protein_L6_812970..813200_POSITIVE 249 146 101 193 142 NC_002967:TDE1313|5end_signal_peptidase_I_1350650..1350880_POSITIVE 249 159 117 58 17 NC_002967:TDE0364|5end_ABC_transporter,_ATP-binding_protein_411605..411835_NEGATIVE 248 147 101 193 143 NC_002967:TDE0079|5end_DNA-binding_protein_90670..90900_NEGATIVE 247 130 86 58 4 NC_002967:TDE1282|5end_hypothetical_protein_1316801..1317031_POSITIVE 246 148 118 60 27 NC_002967:TDE2631|5end_peptide_ABC_transporter,_permease_protein,_putative_2671829..2672059_POSITIVE 246 146 101 181 125 NC_002967:TDE1349|5end_rod_shape-determining_protein_MreB_1389286..1389516_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 262 150 101 144 97 NC_002967:TDE0209|3end_arsenical_pump_membrane_protein,_putative_245561..245711_POSITIVE 254 144 108 56 20 NC_002967:TDE1593|3end_Fe-hydrogenase_1641209..1641359_NEGATIVE 252 220 171 79 14 NC_002967:TDE2196|3end_hypothetical_protein_2231883..2232033_NEGATIVE 248 147 101 135 85 NC_002967:TDE0080|3end_betaine_aldehyde_dehydrogenase_90728..90878_NEGATIVE 246 148 118 63 30 NC_002967:TDE2630|3end_peptide_ABC_transporter,_permease_protein,_putative_2671912..2672062_POSITIVE 246 152 116 137 97 NC_002967:TDE0565|3end_hypothetical_protein_597230..597380_POSITIVE 243 140 91 137 91 NC_002967:TDE2237|3end_hypothetical_protein_2276298..2276448_NEGATIVE 238 156 118 56 7 NC_002967:TDE0964|3end_hypothetical_protein_990578..990728_POSITIVE 237 136 102 137 102 NC_002967:TDE2163|3end_hypothetical_protein_2195533..2195683_NEGATIVE 237 217 173 129 82 NC_002967:TDE1041|3end_polyribonucleotide_nucleotidyltransferase_1070500..1070650_POSITIVE 231 156 117 82 36 NC_002967:TDE2242|3end_antigen,_putative_2279569..2279719_NEGATIVE 228 194 158 128 96 NC_002967:TDE1660|3end_leucine_Rich_Repeat_domain_protein_1710710..1710860_NEGATIVE 227 148 101 90 56 NC_002967:TDE0745|3end_glycine_reductase_complex_selenoprotein_GrdA_780840..780990_POSITIVE 225 213 174 38 1 NC_002967:TDE2034|3end_glycosyl_transferase,_group_1_family_protein_2062823..2062973_POSITIVE 225 169 131 104 64 NC_002967:TDE1182|3end_hypothetical_protein_1210678..1210828_POSITIVE 224 125 100 29 4 NC_002967:TDE0847|3end_hypothetical_protein_871342..871492_POSITIVE 224 65 29 50 8 NC_002967:TDE0820|3end_transcriptional_regulator,_TetR_family_843714..843864_NEGATIVE 223 81 49 36 4 NC_002967:TDE1260|3end_cholinephosphate_cytidylyltransferase/choline_kinase_1295676..1295826_POSITIVE 221 140 100 39 3 NC_002967:TDE2573|3end_glucose-6-phosphate_isomerase_2600459..2600609_POSITIVE 221 128 95 131 100 NC_002967:TDE2160|3end_hypothetical_protein_2193873..2194023_NEGATIVE