Origin IGS: atatggatgatattataccctaaaacggcaaattaggcaagcattttgtgaaaagttatagggagcagtcaataactcaaataattcaatataaattgtggacaggtagaaaaaaataagttataattttgagtaactaataaaaaaaaggcttaaccatgttaagccttgatgctccacaatgagcggtcccaaaagggacgattttgatgaattcttatttgaactcgttgtgtaatttaagatggatcttaaattgtgtatgctgttattataatactttttaaaggaatggtcaaggt .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 accttgaccattcctttaaaaagtattataataacagcatacacaatttaagatccatcttaaattacacaacgagttcaaataagaattcatcaaaatcgtcccttttgggaccgctcattgtggagcatcaaggcttaacatggttaagccttttttttattagttactcaaaattataacttatttttttctacctgtccacaatttatattgaattatttgagttattgactgctccctataacttttcacaaaatgcttgcctaatttgccgttttagggtataatatcatccatat Mask Tandem Repeat Region ================================================ atatggatgatattataccctaaaacggcaaattaggcaagcattttgtgaaaagttatagggagcagtcaataactcaaataattcaatataaattgtggacaggtagaaaaaaataagttataattttgagtaactaataaaaaaaaggcttaaccatgttaagccttgatgctccacaatgagcggtcccaaaagggacgattttgatgaattcttatttgaactcgttgtgtaatttaagatggatcttaaattgtgtatgctgttattataatactttttaaaggaatggtcaaggt Find is-nt database================================================ Query_seq: TDE0326:TDE0327|TDE0326:TDE0327:ATP-dependent DNA helicase RecQ:CRISPR-associated SAG0894 family protein:<-->:360719..361020 302 atatggatgatattataccctaaaacggcaaattaggcaagcattttgtgaaaagttatagggagcagtcaataactcaaataattcaatataaattgtggacaggtagaaaaaaataagttataattttgagtaactaataaaaaaaaggcttaaccatgttaagccttgatgctccacaatgagcggtcccaaaagggacgattttgatgaattcttatttgaactcgttgtgtaatttaagatggatcttaaattgtgtatgctgttattataatactttttaaaggaatggtcaaggt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0326:TDE0327|TDE0326:TDE0327:ATP-dependent DNA helicase RecQ:CRISPR-associated SAG0894 family protein:<-->:360719..361020 302 atatggatgatattataccctaaaacggcaaattaggcaagcattttgtgaaaagttatagggagcagtcaataactcaaataattcaatataaattgtggacaggtagaaaaaaataagttataattttgagtaactaataaaaaaaaggcttaaccatgttaagccttgatgctccacaatgagcggtcccaaaagggacgattttgatgaattcttatttgaactcgttgtgtaatttaagatggatcttaaattgtgtatgctgttattataatactttttaaaggaatggtcaaggt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0326:TDE0327|TDE0326:TDE0327:ATP-dependent DNA helicase RecQ:CRISPR-associated SAG0894 family protein:<-->:360719..361020 302 atatggatgatattataccctaaaacggcaaattaggcaagcattttgtgaaaagttatagggagcagtcaataactcaaataattcaatataaattgtggacaggtagaaaaaaataagttataattttgagtaactaataaaaaaaaggcttaaccatgttaagccttgatgctccacaatgagcggtcccaaaagggacgattttgatgaattcttatttgaactcgttgtgtaatttaagatggatcttaaattgtgtatgctgttattataatactttttaaaggaatggtcaaggt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atatggatgatattataccctaaaacggcaaattaggcaagcattttgtgaaaagttatagggagcagtcaataactcaaataattcaatataaattgtggacaggtagaaaaaaataagttataattttgagtaactaataaaaaaaaggcttaaccatgttaagccttgatgctccacaatgagcggtcccaaaagggacgattttgatgaattcttatttgaactcgttgtgtaatttaagatggatcttaaattgtgtatgctgttattataatactttttaaaggaatggtcaaggt Predict ORF larger than 30AA ================================================ Protein_Len: 47 Strand: - Start: 124 End: 264 ........................................................................................................................... L K S Y S I F F L S L W T L G Q H E V I L P G L L S S K S S N K N S S T T Y N L I S R L N H M ...................................... Protein_Len: 34 Strand: - Start: 16 End: 117 ............... V R F R C I L C A N Q S F N Y P A T L L E F L E I Y I T S L Y F F M ......................................................................................................................................................................................... atatggatgatattataccctaaaacggcaaattaggcaagcattttgtgaaaagttatagggagcagtcaataactcaaataattcaatataaattgtggacaggtagaaaaaaataagttataattttgagtaactaataaaaaaaaggcttaaccatgttaagccttgatgctccacaatgagcggtcccaaaagggacgattttgatgaattcttatttgaactcgttgtgtaatttaagatggatcttaaattgtgtatgctgttattataatactttttaaaggaatggtcaaggt 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: 92 Start: 12 End: 41 ...........CTTGCCTAATTTGCCGTTTTAGGGTATAAT..................................................................................................................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 91 Start: 271 End: 300 ..............................................................................................................................................................................................................................................................................CTTGACCATTCCTTTAAAAAGTATTATAAT.. PromScan Matrix: RpoD-17 Strand: + Score: 85 Start: 98 End: 127 .................................................................................................GTGGACAGGTAGAAAAAAATAAGTTATAAT............................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atatggatgatattataccctaaaacggcaaattaggcaagcattttgtgaaaagttatagggagcagtcaataactcaaataattcaatataaattgtggacaggtagaaaaaaataagttataattttgagtaactaataaaaaaaaggcttaaccatgttaagccttgatgctccacaatgagcggtcccaaaagggacgattttgatgaattcttatttgaactcgttgtgtaatttaagatggatcttaaattgtgtatgctgttattataatactttttaaaggaatggtcaaggt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 93 HP_score: -11.8 Tail_Score: -3.21218 Start: 150 End: 168 Full_Region: AACTAATAAAAAAAA GGCTTAAC CAT GTTAAGCC TTGATGCTCCACAAT .....................................................................................................................................................GGCTTAACCATGTTAAGCC...................................................................................................................................... TransTerm Strand: - Conf: 100 HP_score: -11.8 Tail_Score: -6.15536 Start: 150 End: 168 Full_Region: attgtggagcatcaa ggcttaac atg gttaagcc ttttttttattagtt .....................................................................................................................................................ggcttaacatggttaagcc...................................................................................................................................... Find igs database================================================ Query_seq: TDE0326:TDE0327|TDE0326:TDE0327:ATP-dependent DNA helicase RecQ:CRISPR-associated SAG0894 family protein:<-->:360719..361020 302 atatggatgatattataccctaaaacggcaaattaggcaagcattttgtgaaaagttatagggagcagtcaataactcaaataattcaatataaattgtggacaggtagaaaaaaataagttataattttgagtaactaataaaaaaaaggcttaaccatgttaagccttgatgctccacaatgagcggtcccaaaagggacgattttgatgaattcttatttgaactcgttgtgtaatttaagatggatcttaaattgtgtatgctgttattataatactttttaaaggaatggtcaaggt Intra-Species Hit: Count: 1 Min: 1 Max: 302 Len: 302 Subject: NC_002967_TDE0326_TDE0327|ATP-dependent DNA helicase RecQ:CRISPR-associated SAG0894 family protein|NEGATIVE:POSITIVE|[360719,361020]|302 HSP 1 e-value: 1.0E-143 bit: 509.0 Len: 302 Query Start:1 Query End:302 Subject Strand: POSITIVE Subject Start: 1 Subject End: 302 atatggatgatattataccctaaaacggcaaattaggcaagcattttgtgaaaagttatagggagcagtcaataactcaaataattcaatataaattgtggacaggtagnnnnnnntaagttataattttgagtaactaatnnnnnnnnggcttaaccatgttaagccttgatgctccacaatgagcggtcccaaaagggacgattttgatgaattcttatttgaactcgttgtgtaatttaagatggatcttaaattgtgtatgctgttattataatactttttaaaggaatggtcaaggt atatggatgatattataccctaaaacggcaaattaggcaagcattttgtgaaaagttatagggagcagtcaataactcaaataattcaatataaattgtggacaggtagaaaaaaataagttataattttgagtaactaataaaaaaaaggcttaaccatgttaagccttgatgctccacaatgagcggtcccaaaagggacgattttgatgaattcttatttgaactcgttgtgtaatttaagatggatcttaaattgtgtatgctgttattataatactttttaaaggaatggtcaaggt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAUGGAUGAUAUUAUACCCUAAAACGGCAAAUUAGGCAAGCAUUUUGUGAAAAGUUAUAGGGAGCAGUCAAUAACUCAAAUAAUUCAAUAUAAAUUGUGGACAGGUAGAAAAAAAUAAGUUAUAAUUUUGAGUAACUAAUAAAAAAAAGGCUUAACCAUGUUAAGCCUUGAUGCUCCACAAUGAGCGGUCCCAAAAGGGACGAUUUUGAUGAAUUCUUAUUUGAACUCGUUGUGUAAUUUAAGAUGGAUCUUAAAUUGUGUAUGCUGUUAUUAUAAUACUUUUUAAAGGAAUGGUCAAGGU .......((((.......(((((.........)))))....(((((..(((((((((((((..((((((.......((((((((((((......((((((((((..............((((((........)))))).........((((((((((...))))))))))..)).)))))))).....(((((....)))))........)))))...)))))))......((..((((((((((....))))))))))..)).)))))).)))))..))))))))...))))))))).... (-72.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACCUUGACCAUUCCUUUAAAAAGUAUUAUAAUAACAGCAUACACAAUUUAAGAUCCAUCUUAAAUUACACAACGAGUUCAAAUAAGAAUUCAUCAAAAUCGUCCCUUUUGGGACCGCUCAUUGUGGAGCAUCAAGGCUUAACAUGGUUAAGCCUUUUUUUUAUUAGUUACUCAAAAUUAUAACUUAUUUUUUUCUACCUGUCCACAAUUUAUAUUGAAUUAUUUGAGUUAUUGACUGCUCCCUAUAACUUUUCACAAAAUGCUUGCCUAAUUUGCCGUUUUAGGGUAUAAUAUCAUCCAUAU (((((((........(((..(((((((........(((......(((((((((....))))))))).......((((((......)))))).........(((((....))))).)))......((((((..((((((((((...)))))))))).......(((((.(((((((..((.....))..................((((....)))).....))))))).))))).))))))................)))))))...))).........)))))))................ (-61.03) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 847 70 21 161 112 NC_002967:TDE0326|5end_ATP-dependent_DNA_helicase_RecQ_360628..360858_NEGATIVE 307 204 164 54 6 NC_002967:TDE0979|5end_penicillin_binding_protein_1003946..1004176_NEGATIVE 288 207 165 66 32 NC_002967:TDE2217|5end_galactose/glucose-binding_lipoprotein_2257975..2258205_NEGATIVE 270 191 156 140 97 NC_002967:TDE1048|5end_30S_ribosomal_protein_S7_1074482..1074712_POSITIVE 269 192 151 222 176 NC_002967:TDE0898|5end_hypothetical_protein_915878..916108_POSITIVE 265 67 26 229 180 NC_002967:TDE2475|5end_MATE_efflux_family_protein_2498521..2498751_NEGATIVE 263 189 151 216 174 NC_002967:TDE2603|5end_DNA_mismatch_repair_protein_2641476..2641706_POSITIVE 262 210 166 65 21 NC_002967:TDE0571|5end_hypothetical_protein_601135..601365_POSITIVE 254 210 166 212 168 NC_002967:TDE0957|5end_glycerophosphoryl_diester_phosphodiesterase_family_protein_980252..980482_POSITIVE 251 66 26 224 182 NC_002967:TDE2276|5end_hypothetical_protein_2312676..2312906_NEGATIVE 251 70 25 211 142 NC_002967:TDE0453|5end_hypothetical_protein_510364..510594_NEGATIVE 249 219 173 215 171 NC_002967:TDE0273|5end_ABC_transporter,_ATP-binding/permease_protein_304633..304863_NEGATIVE 249 203 173 50 21 NC_002967:TDE0084|5end_phosphoenolpyruvate-protein_phosphotransferase_97455..97685_NEGATIVE 246 193 151 148 103 NC_002967:TDE2660|5end_hypothetical_protein_2697517..2697747_NEGATIVE 243 219 175 177 103 NC_002967:TDE1284|5end_methyl-accepting_chemotaxis_protein,_putative_1318720..1318950_POSITIVE 243 196 152 160 123 NC_002967:TDE0601|5end_malonyl_CoA-acyl_carrier_protein_transacylase,_putative_639811..640041_NEGATIVE 241 45 3 229 195 NC_002967:TDE0960|5end_neuB_family_protein_982376..982606_POSITIVE 240 210 164 94 49 NC_002967:TDE2005|5end_hypothetical_protein_2023776..2024006_POSITIVE 239 200 151 198 153 NC_002967:TDE1796|5end_hypothetical_protein_1835515..1835745_NEGATIVE 239 199 157 199 145 NC_002967:TDE1394|5end_hypothetical_protein_1433084..1433314_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 370 267 221 51 8 NC_002967:TDE0331|3end_hypothetical_protein_370842..370992_NEGATIVE 284 169 121 79 28 NC_002967:TDE1494|3end_chemotaxis_protein_CheY_1539596..1539746_POSITIVE 270 191 156 129 86 NC_002967:TDE1047|3end_30S_ribosomal_protein_S12_1074551..1074701_POSITIVE 265 189 149 44 4 NC_002967:TDE1277|3end_Fe-hydrogenase_large_subunit_family_protein_1312242..1312392_POSITIVE 258 192 151 85 50 NC_002967:TDE1958|3end_surface_protein,_putative_1972309..1972459_NEGATIVE 252 58 11 148 89 NC_002967:TDE1959|3end_hypothetical_protein_1973805..1973955_NEGATIVE 252 189 144 113 74 NC_002967:TDE0793|3end_hypothetical_protein_819205..819355_POSITIVE 251 190 143 84 35 NC_002967:TDE1324|3end_hypothetical_protein_1360915..1361065_NEGATIVE 248 66 27 85 39 NC_002967:TDE1794|3end_hypothetical_protein_1831015..1831165_NEGATIVE 246 193 151 141 96 NC_002967:TDE2661|3end_hypothetical_protein_2697524..2697674_NEGATIVE 243 196 152 135 98 NC_002967:TDE0602|3end_3-oxoacyl-(acyl-carrier-protein)_synthase_III_639836..639986_NEGATIVE 241 45 3 138 104 NC_002967:TDE0959|3end_hypothetical_protein_982365..982515_POSITIVE 241 200 151 142 88 NC_002967:TDE0833|3end_lipoprotein,_putative_854097..854247_POSITIVE 240 210 164 83 38 NC_002967:TDE2004|3end_hypothetical_protein_2023845..2023995_POSITIVE 239 200 151 58 13 NC_002967:TDE1831|3end_hypothetical_protein_1864415..1864565_NEGATIVE 239 200 151 58 13 NC_002967:TDE1797|3end_hypothetical_protein_1835655..1835805_NEGATIVE 239 203 163 58 22 NC_002967:TDE0210|3end_cob(I)yrinic_acid_a,c-diamide_adenosyltransferase_246146..246296_POSITIVE 239 195 160 47 10 NC_002967:TDE0049|3end_hypothetical_protein_58199..58349_NEGATIVE 238 210 163 72 28 NC_002967:TDE2551|3end_hypothetical_protein_2576212..2576362_NEGATIVE 238 209 175 144 96 NC_002967:TDE1283|3end_extracellular_solute-binding_lipoprotein,_putative_1318793..1318943_POSITIVE