Origin IGS: gtttacacctcttctctttttaaagtttttctgttctatttgaagattataatagtatatttgacttaaaaagtcaagtatttttatattttctttcttatttgaagaaatttttattgacaaaaattcttataacagctagaataaggtagtaaaataagttagcgatgactaaccgggttttttgaaatggagcatttt .........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 aaaatgctccatttcaaaaaacccggttagtcatcgctaacttattttactaccttattctagctgttataagaatttttgtcaataaaaatttcttcaaataagaaagaaaatataaaaatacttgactttttaagtcaaatatactattataatcttcaaatagaacagaaaaactttaaaaagagaagaggtgtaaac Mask Tandem Repeat Region ================================================ gtttacacctcttctctttttaaagtttttctgttctatttgaagattataatagtatatttgacttaaaaagtcaagtatttttatattttctttcttatttgaagaaatttttattgacaaaaattcttataacagctagaataaggtagtaaaataagttagcgatgactaaccgggttttttgaaatggagcatttt Find is-nt database================================================ Query_seq: TDE0895:TDE0896|TDE0895:TDE0896:transcriptional regulator, AraC family:ABC transporter, ATP-binding/permease protein:<-->:912265..912465 201 gtttacacctcttctctttttaaagtttttctgttctatttgaagattataatagtatatttgacttaaaaagtcaagtatttttatattttctttcttatttgaagaaatttttattgacaaaaattcttataacagctagaataaggtagtaaaataagttagcgatgactaaccgggttttttgaaatggagcatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0895:TDE0896|TDE0895:TDE0896:transcriptional regulator, AraC family:ABC transporter, ATP-binding/permease protein:<-->:912265..912465 201 gtttacacctcttctctttttaaagtttttctgttctatttgaagattataatagtatatttgacttaaaaagtcaagtatttttatattttctttcttatttgaagaaatttttattgacaaaaattcttataacagctagaataaggtagtaaaataagttagcgatgactaaccgggttttttgaaatggagcatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0895:TDE0896|TDE0895:TDE0896:transcriptional regulator, AraC family:ABC transporter, ATP-binding/permease protein:<-->:912265..912465 201 gtttacacctcttctctttttaaagtttttctgttctatttgaagattataatagtatatttgacttaaaaagtcaagtatttttatattttctttcttatttgaagaaatttttattgacaaaaattcttataacagctagaataaggtagtaaaataagttagcgatgactaaccgggttttttgaaatggagcatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtttacacctcttctctttttaaagtttttctgttctatttgaagattataatagtatatttgacttaaaaagtcaagtatttttatattttctttcttatttgaagaaatttttattgacaaaaattcttataacagctagaataaggtagtaaaataagttagcgatgactaaccgggttttttgaaatggagcatttt Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 57 End: 149 ........................................................ M F D L K S Q V F L Y F L S Y L K K F L L T K I L I T A R I R .................................................... Protein_Len: 41 Strand: - Start: 1 End: 123 N V G R R K K F N K Q E I Q L N Y Y Y I Q S L F D L I K I N E K K N S S I K I S M .............................................................................. gtttacacctcttctctttttaaagtttttctgttctatttgaagattataatagtatatttgacttaaaaagtcaagtatttttatattttctttcttatttgaagaaatttttattgacaaaaattcttataacagctagaataaggtagtaaaataagttagcgatgactaaccgggttttttgaaatggagcatttt 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: 91 Start: 116 End: 145 ...................................................................................................................ATTGACAAAAATTCTTATAACAGCTAGAAT........................................................ PromScan Matrix: RpoD-17 Strand: - Score: 86 Start: 49 End: 78 ................................................CTTGACTTTTTAAGTCAAATATACTATTAT........................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gtttacacctcttctctttttaaagtttttctgttctatttgaagattataatagtatatttgacttaaaaagtcaagtatttttatattttctttcttatttgaagaaatttttattgacaaaaattcttataacagctagaataaggtagtaaaataagttagcgatgactaaccgggttttttgaaatggagcatttt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -8.6 Tail_Score: -5.34632 Start: 58 End: 80 Full_Region: AAGATTATAATAGTA TATTTGACTT AAA AAGTCAAGTA TTTTTATATTTTCTT .........................................................TATTTGACTTAAAAAGTCAAGTA......................................................................................................................... Find igs database================================================ Query_seq: TDE0895:TDE0896|TDE0895:TDE0896:transcriptional regulator, AraC family:ABC transporter, ATP-binding/permease protein:<-->:912265..912465 201 gtttacacctcttctctttttaaagtttttctgttctatttgaagattataatagtatatttgacttaaaaagtcaagtatttttatattttctttcttatttgaagaaatttttattgacaaaaattcttataacagctagaataaggtagtaaaataagttagcgatgactaaccgggttttttgaaatggagcatttt Intra-Species Hit: Count: 1 Min: 1 Max: 201 Len: 201 Subject: NC_002967_TDE0895_TDE0896|transcriptional regulator, AraC family:ABC transporter, ATP-binding/permease protein|NEGATIVE:POSITIVE|[912265,912465]|201 HSP 1 e-value: 1.0E-110 bit: 398.0 Len: 201 Query Start:1 Query End:201 Subject Strand: POSITIVE Subject Start: 1 Subject End: 201 gtttacacctcttctctttttaaagtttttctgttctatttgaagattataatagtatatttgacttaaaaagtcaagtatttttatattttctttcttatttgaagaaatttttattgacaaaaattcttataacagctagaataaggtagtaaaataagttagcgatgactaaccgggttttttgaaatggagcatttt gtttacacctcttctctttttaaagtttttctgttctatttgaagattataatagtatatttgacttaaaaagtcaagtatttttatattttctttcttatttgaagaaatttttattgacaaaaattcttataacagctagaataaggtagtaaaataagttagcgatgactaaccgggttttttgaaatggagcatttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUUACACCUCUUCUCUUUUUAAAGUUUUUCUGUUCUAUUUGAAGAUUAUAAUAGUAUAUUUGACUUAAAAAGUCAAGUAUUUUUAUAUUUUCUUUCUUAUUUGAAGAAAUUUUUAUUGACAAAAAUUCUUAUAACAGCUAGAAUAAGGUAGUAAAAUAAGUUAGCGAUGACUAACCGGGUUUUUUGAAAUGGAGCAUUUU ...............................((((((((((.((((..........((((((((((.....)))))))))).....((((((((.((((((((.(((((.(((((......))))))))))..........)))))))).)).)))))).(((((......)))))......)))).)))))))))).... (-35.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAUGCUCCAUUUCAAAAAACCCGGUUAGUCAUCGCUAACUUAUUUUACUACCUUAUUCUAGCUGUUAUAAGAAUUUUUGUCAAUAAAAAUUUCUUCAAAUAAGAAAGAAAAUAUAAAAAUACUUGACUUUUUAAGUCAAAUAUACUAUUAUAAUCUUCAAAUAGAACAGAAAAACUUUAAAAAGAGAAGAGGUGUAAAC ........................(((((((....)))))))...(((((.(((((.((((.....(((.(((..((((((((........((((((.....)))))).....(((((..(((.((((((.....)))))).)))....)))))...........).)))))))..))))))....)))))))))))))). (-30.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 701 50 1 141 92 NC_002967:TDE0895|5end_transcriptional_regulator,_AraC_family_912174..912404_NEGATIVE 255 48 1 214 168 NC_002967:TDE1363|5end_nitroreductase_family_protein_1404635..1404865_NEGATIVE 240 171 135 81 42 NC_002967:TDE0343|5end_hydrolase,_alpha/beta_fold_family_385365..385595_NEGATIVE 236 200 161 210 170 NC_002967:TDE2715|5end_hypothetical_protein_2772668..2772898_POSITIVE 230 200 152 228 175 NC_002967:TDE1947|5end_ABC_transporter,_permease_protein_1963449..1963679_NEGATIVE 223 180 131 171 119 NC_002967:TDE2031|5end_hypothetical_protein_2059161..2059391_NEGATIVE 222 187 147 69 22 NC_002967:TDE2056|5end_outer_membrane_hemin-binding_protein_A_2085070..2085300_NEGATIVE 221 198 160 150 115 NC_002967:TDE2779|5end_hypothetical_protein_2830425..2830655_NEGATIVE 221 41 5 205 168 NC_002967:TDE1442|5end_histidyl-tRNA_synthetase_1487416..1487646_POSITIVE 221 110 65 125 80 NC_002967:TDE0285|5end_translation_elongation_factor_G_313622..313852_POSITIVE 219 180 131 72 29 NC_002967:TDE0705|5end_SPFH_domain/Band_7_family_protein_740268..740498_NEGATIVE 219 47 12 221 185 NC_002967:TDE0028|5end_ABC_transporter,_ATP-binding_protein,_HlyB_family_35930..36160_NEGATIVE 218 108 61 110 61 NC_002967:TDE0095|5end_hypothetical_protein_112399..112629_POSITIVE 216 48 11 186 142 NC_002967:TDE2593|5end_sigma-54-binding_protein_2627747..2627977_POSITIVE 211 179 131 45 1 NC_002967:TDE1360|5end_xanthine/uracil_permease_family_protein_1399297..1399527_POSITIVE 210 199 158 221 186 NC_002967:TDE0808|5end_acetyltransferase,_GNAT_family_829650..829880_NEGATIVE 209 48 1 140 93 NC_002967:TDE1554|5end_hypothetical_protein_1597005..1597235_POSITIVE 206 179 137 64 18 NC_002967:TDE2434|5end_polysaccharide_deacetylase_family_protein_2465657..2465887_NEGATIVE 204 50 1 190 135 NC_002967:TDE0565|5end_hypothetical_protein_597031..597261_POSITIVE 201 34 5 174 145 NC_002967:TDE0135|5end_pyridine_nucleotide-disulphide_oxidoreductase_family_protein_154927..155157_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 257 200 151 70 30 NC_002967:TDE0746|3end_iron_compound_ABC_transporter,_ATP-binding_protein,_putative_780931..781081_NEGATIVE 240 171 135 79 40 NC_002967:TDE0344|3end_transcriptional_regulator,_AbrB_family_385367..385517_NEGATIVE 221 198 160 67 32 NC_002967:TDE2780|3end_hypothetical_protein_2830508..2830658_NEGATIVE 221 41 5 124 87 NC_002967:TDE1441|3end_dTDP-glucose_4,6-dehydratase_1487415..1487565_POSITIVE 218 108 61 79 30 NC_002967:TDE0094|3end_hypothetical_protein_112448..112598_POSITIVE 216 48 11 91 47 NC_002967:TDE2592|3end_DbpA_RNA_binding_domain_protein_2627732..2627882_POSITIVE 204 50 1 94 39 NC_002967:TDE0564|3end_hypothetical_protein_597015..597165_POSITIVE 203 196 163 135 108 NC_002967:TDE1057|3end_hypothetical_protein_1086105..1086255_NEGATIVE 201 87 54 73 35 NC_002967:TDE0305|3end_GTP-binding_protein_YchF_335645..335795_NEGATIVE 198 195 158 74 33 NC_002967:TDE1913|3end_hypothetical_protein_1930897..1931047_POSITIVE 198 48 6 42 3 NC_002967:TDE1575|3end_lipoyl_synthase_1622855..1623005_POSITIVE 196 200 151 100 36 NC_002967:TDE0705|3end_SPFH_domain/Band_7_family_protein_739339..739489_NEGATIVE 195 186 141 76 22 NC_002967:TDE1243|3end_hemolysin_C_1275891..1276041_POSITIVE 194 193 160 49 6 NC_002967:TDE0497|3end_hypothetical_protein_551374..551524_NEGATIVE 192 200 159 51 7 NC_002967:TDE2431|3end_bacteriocin_ABC_transporter,_ATP-binding/permease_protein,_putative_2459170..2459320_NEGATIVE 191 44 1 150 106 NC_002967:TDE1553|3end_hypothetical_protein_1597098..1597248_POSITIVE 191 42 14 50 17 NC_002967:TDE1152|3end_head-to-tail_joining_protein,_putative_1188527..1188677_NEGATIVE 191 197 155 103 50 NC_002967:TDE0696|3end_hypothetical_protein_734210..734360_POSITIVE 191 119 71 42 4 NC_002967:TDE0126|3end_hypothetical_protein_143991..144141_NEGATIVE 190 181 166 51 35 NC_002967:TDE2612|3end_hypothetical_protein_2655459..2655609_POSITIVE