Origin IGS: aattccctattgactaattctcttctttatagtattatgcgttcttactcgtattttcattgaaacacgggttttatattgaaattttgggttaatcccgggaggtttac .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gtaaacctcccgggattaacccaaaatttcaatataaaacccgtgtttcaatgaaaatacgagtaagaacgcataatactataaagaagagaattagtcaatagggaatt Mask Tandem Repeat Region ================================================ aattccctattgactaattctcttctttatagtattatgcgttcttactcgtattttcattgaaacacgggttttatattgaaattttgggttaatcccgggaggtttac Find is-nt database================================================ Query_seq: TDE0880:TDE0881|TDE0880:TDE0881:nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase:ribosomal protein S16:->->:901197..901306 110 aattccctattgactaattctcttctttatagtattatgcgttcttactcgtattttcattgaaacacgggttttatattgaaattttgggttaatcccgggaggtttac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0880:TDE0881|TDE0880:TDE0881:nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase:ribosomal protein S16:->->:901197..901306 110 aattccctattgactaattctcttctttatagtattatgcgttcttactcgtattttcattgaaacacgggttttatattgaaattttgggttaatcccgggaggtttac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0880:TDE0881|TDE0880:TDE0881:nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase:ribosomal protein S16:->->:901197..901306 110 aattccctattgactaattctcttctttatagtattatgcgttcttactcgtattttcattgaaacacgggttttatattgaaattttgggttaatcccgggaggtttac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aattccctattgactaattctcttctttatagtattatgcgttcttactcgtattttcattgaaacacgggttttatattgaaattttgggttaatcccgggaggtttac Predict ORF larger than 30AA ================================================ aattccctattgactaattctcttctttatagtattatgcgttcttactcgtattttcattgaaacacgggttttatattgaaattttgggttaatcccgggaggtttac 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: 9 End: 38 ........ATTGACTAATTCTCTTCTTTATAGTATTAT........................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aattccctattgactaattctcttctttatagtattatgcgttcttactcgtattttcattgaaacacgggttttatattgaaattttgggttaatcccgggaggtttac Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0880:TDE0881|TDE0880:TDE0881:nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase:ribosomal protein S16:->->:901197..901306 110 aattccctattgactaattctcttctttatagtattatgcgttcttactcgtattttcattgaaacacgggttttatattgaaattttgggttaatcccgggaggtttac Intra-Species Hit: Count: 1 Min: 1 Max: 110 Len: 110 Subject: NC_002967_TDE0880_TDE0881|nicotinate-nucleotide- dimethylbenzimidazole phosphoribosyltransferase:ribosomal protein S16|POSITIVE:POSITIVE|[901197,901306]|110 HSP 1 e-value: 3.0E-56 bit: 218.0 Len: 110 Query Start:1 Query End:110 Subject Strand: POSITIVE Subject Start: 1 Subject End: 110 aattccctattgactaattctcttctttatagtattatgcgttcttactcgtattttcattgaaacacgggttttatattgaaattttgggttaatcccgggaggtttac aattccctattgactaattctcttctttatagtattatgcgttcttactcgtattttcattgaaacacgggttttatattgaaattttgggttaatcccgggaggtttac Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUCCCUAUUGACUAAUUCUCUUCUUUAUAGUAUUAUGCGUUCUUACUCGUAUUUUCAUUGAAACACGGGUUUUAUAUUGAAAUUUUGGGUUAAUCCCGGGAGGUUUAC ..(((((.(((((((.....................(((((........)))))(((((.((((((....))))))...))))).....)))))))...)))))...... (-19.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUAAACCUCCCGGGAUUAACCCAAAAUUUCAAUAUAAAACCCGUGUUUCAAUGAAAAUACGAGUAAGAACGCAUAAUACUAUAAAGAAGAGAAUUAGUCAAUAGGGAAUU .......(((((((.....)))....((((........((.(((((((......))))))).))..............((....))..))))...........))))... (-15.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 293 110 80 126 98 NC_002967:TDE2149|5end_transglycosylase,_SLT_family_2187293..2187523_NEGATIVE 253 105 66 73 32 NC_002967:TDE0142|5end_hypothetical_protein_164074..164304_NEGATIVE 253 52 18 225 183 NC_002967:TDE0027|5end_DHH_superfamily_protein,_subfamily_1_33986..34216_NEGATIVE 234 108 61 59 14 NC_002967:TDE0743|5end_thioredoxin_reductase_778718..778948_POSITIVE 229 52 18 218 176 NC_002967:TDE0029|5end_ABC_transporter,_ATP-binding_protein,_HlyB_family_37722..37952_NEGATIVE 223 74 33 159 118 NC_002967:TDE0687|5end_phosphoribosylaminoimidazole_carboxylase,_PurE_protein_723674..723904_POSITIVE 222 70 22 121 70 NC_002967:TDE1878|5end_hydrolase,_haloacid_dehalogenase-like_family_1900745..1900975_NEGATIVE 221 61 26 57 24 NC_002967:TDE2051|5end_hypothetical_protein_2080298..2080528_NEGATIVE 221 67 21 146 96 NC_002967:TDE1804|5end_hypothetical_protein_1842022..1842252_NEGATIVE 220 77 32 182 137 NC_002967:TDE1803|5end_hypothetical_protein_1839270..1839500_NEGATIVE 220 70 22 217 177 NC_002967:TDE1216|5end_flagellar_motor_protein_1248441..1248671_POSITIVE 215 109 69 59 4 NC_002967:TDE1242|5end_hypothetical_protein_1274565..1274795_POSITIVE 213 110 75 85 52 NC_002967:TDE2276|5end_hypothetical_protein_2312676..2312906_NEGATIVE 213 59 17 136 97 NC_002967:TDE0622|5end_radical_SAM_domain_protein_655718..655948_NEGATIVE 211 56 11 202 151 NC_002967:TDE0783|5end_ribosomal_protein_L18_813520..813750_POSITIVE 208 104 68 198 162 NC_002967:TDE0771|5end_ribosomal_protein_S19_808795..809025_POSITIVE 207 72 39 84 54 NC_002967:TDE1033|5end_polyA_polymerase_family_protein_1061069..1061299_POSITIVE 207 106 68 49 4 NC_002967:TDE0971|5end_arginyl-tRNA_synthetase_995179..995409_POSITIVE 207 105 67 227 199 NC_002967:TDE0144|5end_thiamine_ABC_transporter,_permease_protein_165007..165237_POSITIVE 205 49 1 165 104 NC_002967:TDE0594|5end_cysteine_protease_domain,_YopT-type_634805..635035_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 236 105 67 67 26 NC_002967:TDE1087|3end_cytidylate_kinase_1119313..1119463_POSITIVE 227 72 31 84 45 NC_002967:TDE1811|3end_hypothetical_protein_1846773..1846923_NEGATIVE 221 67 21 133 83 NC_002967:TDE1805|3end_radical_SAM_domain_protein_1842035..1842185_NEGATIVE 218 104 68 119 85 NC_002967:TDE1533|3end_hypothetical_protein_1578657..1578807_POSITIVE 215 109 69 66 11 NC_002967:TDE1241|3end_HD_domain_protein_1274652..1274802_POSITIVE 209 74 34 134 94 NC_002967:TDE2103|3end_glycosyl_transferase,_group_2_family_protein_2127527..2127677_NEGATIVE 207 72 39 32 2 NC_002967:TDE1032|3end_hypothetical_protein_1061097..1061247_POSITIVE 207 53 18 149 113 NC_002967:TDE0028|3end_ABC_transporter,_ATP-binding_protein,_HlyB_family_34056..34206_NEGATIVE 205 49 1 132 71 NC_002967:TDE0595|3end_hypothetical_protein_634838..634988_NEGATIVE 205 107 65 109 62 NC_002967:TDE0490|3end_hypothetical_protein_546272..546422_NEGATIVE 205 48 1 132 85 NC_002967:TDE0422|3end_bacteriocin-type_signal_domain_protein_476610..476760_POSITIVE 202 72 31 127 93 NC_002967:TDE1468|3end_glycoprotease_family_protein_1516680..1516830_NEGATIVE 202 107 68 148 108 NC_002967:TDE1401|3end_DedA_family_protein_1443068..1443218_POSITIVE 201 106 63 67 22 NC_002967:TDE1692|3end_hypothetical_protein_1748471..1748621_POSITIVE 199 58 23 149 116 NC_002967:TDE0686|3end_phosphoribosylaminoimidazole-succinocarboxamide_synthase_723757..723907_POSITIVE 198 103 61 123 76 NC_002967:TDE2547|3end_hypothetical_protein_2573184..2573334_POSITIVE 198 72 41 53 19 NC_002967:TDE2516|3end_hypothetical_protein_2542193..2542343_POSITIVE 197 108 70 86 46 NC_002967:TDE2610|3end_hypothetical_protein_2651854..2652004_NEGATIVE 197 106 62 101 48 NC_002967:TDE2136|3end_hypothetical_protein_2165390..2165540_NEGATIVE 196 108 69 135 95 NC_002967:TDE2667|3end_hypothetical_protein_2704579..2704729_POSITIVE