Origin IGS: cagagcgacctcctaatttgatttttaggttaataaaattgatattttaataacttataattgattgtaacttgttttgtaagatttgtctatagttttaacatgatgaatttgcttatatcaatttttttctatcttcttgtaagtttcttatctttatagtagtatgagctttctttagtttaaggaagcattaaatct .........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 agatttaatgcttccttaaactaaagaaagctcatactactataaagataagaaacttacaagaagatagaaaaaaattgatataagcaaattcatcatgttaaaactatagacaaatcttacaaaacaagttacaatcaattataagttattaaaatatcaattttattaacctaaaaatcaaattaggaggtcgctctg Mask Tandem Repeat Region ================================================ cagagcgacctcctaatttgatttttaggttaataaaattgatattttaataacttataattgattgtaacttgttttgtaagatttgtctatagttttaacatgatgaatttgcttatatcaatttttttctatcttcttgtaagtttcttatctttatagtagtatgagctttctttagtttaaggaagcattaaatct Find is-nt database================================================ Query_seq: TDE0705:TDE0706|TDE0705:TDE0706:SPFH domain/Band 7 family protein:adenine-specific DNA modification methyltransferase:<-->:740359..740559 201 cagagcgacctcctaatttgatttttaggttaataaaattgatattttaataacttataattgattgtaacttgttttgtaagatttgtctatagttttaacatgatgaatttgcttatatcaatttttttctatcttcttgtaagtttcttatctttatagtagtatgagctttctttagtttaaggaagcattaaatct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0705:TDE0706|TDE0705:TDE0706:SPFH domain/Band 7 family protein:adenine-specific DNA modification methyltransferase:<-->:740359..740559 201 cagagcgacctcctaatttgatttttaggttaataaaattgatattttaataacttataattgattgtaacttgttttgtaagatttgtctatagttttaacatgatgaatttgcttatatcaatttttttctatcttcttgtaagtttcttatctttatagtagtatgagctttctttagtttaaggaagcattaaatct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0705:TDE0706|TDE0705:TDE0706:SPFH domain/Band 7 family protein:adenine-specific DNA modification methyltransferase:<-->:740359..740559 201 cagagcgacctcctaatttgatttttaggttaataaaattgatattttaataacttataattgattgtaacttgttttgtaagatttgtctatagttttaacatgatgaatttgcttatatcaatttttttctatcttcttgtaagtttcttatctttatagtagtatgagctttctttagtttaaggaagcattaaatct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cagagcgacctcctaatttgatttttaggttaataaaattgatattttaataacttataattgattgtaacttgttttgtaagatttgtctatagttttaacatgatgaatttgcttatatcaatttttttctatcttcttgtaagtttcttatctttatagtagtatgagctttctttagtttaaggaagcattaaatct Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 61 End: 159 ............................................................ M I V T C F V R F V Y S F N M M N L L I S I F F Y L L V S F L S L .......................................... cagagcgacctcctaatttgatttttaggttaataaaattgatattttaataacttataattgattgtaacttgttttgtaagatttgtctatagttttaacatgatgaatttgcttatatcaatttttttctatcttcttgtaagtttcttatctttatagtagtatgagctttctttagtttaaggaagcattaaatct 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: 85 Start: 64 End: 93 ...............................................................ATAGACAAATCTTACAAAACAAGTTACAAT............................................................................................................ PromScan Matrix: RpoD-17 Strand: + Score: 82 Start: 139 End: 168 ..........................................................................................................................................CTTGTAAGTTTCTTATCTTTATAGTAGTAT................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ cagagcgacctcctaatttgatttttaggttaataaaattgatattttaataacttataattgattgtaacttgttttgtaagatttgtctatagttttaacatgatgaatttgcttatatcaatttttttctatcttcttgtaagtttcttatctttatagtagtatgagctttctttagtttaaggaagcattaaatct Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0705:TDE0706|TDE0705:TDE0706:SPFH domain/Band 7 family protein:adenine-specific DNA modification methyltransferase:<-->:740359..740559 201 cagagcgacctcctaatttgatttttaggttaataaaattgatattttaataacttataattgattgtaacttgttttgtaagatttgtctatagttttaacatgatgaatttgcttatatcaatttttttctatcttcttgtaagtttcttatctttatagtagtatgagctttctttagtttaaggaagcattaaatct Intra-Species Hit: Count: 1 Min: 1 Max: 201 Len: 201 Subject: NC_002967_TDE0705_TDE0706|SPFH domain/Band 7 family protein:adenine-specific DNA modification methyltransferase|NEGATIVE:POSITIVE|[740359,740559]|201 HSP 1 e-value: 9.0E-98 bit: 357.0 Len: 201 Query Start:1 Query End:201 Subject Strand: POSITIVE Subject Start: 1 Subject End: 201 cagagcgacctcctaatttgatttttaggttaataaaattgatattttaataacttataattgattgtaacttgttttgtaagatttgtctatagttttaacatgatgaatttgcttatatcaannnnnnnctatcttcttgtaagtttcttatctttatagtagtatgagctttctttagtttaaggaagcattaaatct cagagcgacctcctaatttgatttttaggttaataaaattgatattttaataacttataattgattgtaacttgttttgtaagatttgtctatagttttaacatgatgaatttgcttatatcaatttttttctatcttcttgtaagtttcttatctttatagtagtatgagctttctttagtttaaggaagcattaaatct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAGAGCGACCUCCUAAUUUGAUUUUUAGGUUAAUAAAAUUGAUAUUUUAAUAACUUAUAAUUGAUUGUAACUUGUUUUGUAAGAUUUGUCUAUAGUUUUAACAUGAUGAAUUUGCUUAUAUCAAUUUUUUUCUAUCUUCUUGUAAGUUUCUUAUCUUUAUAGUAGUAUGAGCUUUCUUUAGUUUAAGGAAGCAUUAAAUCU ((((((((.........(..(((..(((((((.((((((....)))))).))))))).)))..).......))))))))..(((((((.((((((.........(((((....(((((((....................)))))))...))))).))))))........((((((((......))))))))..))))))) (-35.94) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAUUUAAUGCUUCCUUAAACUAAAGAAAGCUCAUACUACUAUAAAGAUAAGAAACUUACAAGAAGAUAGAAAAAAAUUGAUAUAAGCAAAUUCAUCAUGUUAAAACUAUAGACAAAUCUUACAAAACAAGUUACAAUCAAUUAUAAGUUAUUAAAAUAUCAAUUUUAUUAACCUAAAAAUCAAAUUAGGAGGUCGCUCUG .........((((.(((......))).))))..............................(((.(((.....(((((((((((.((((.........))))..((((((((.........((.......)).........)))).))))......))))))))))).....(((((........)))))..)))..))). (-20.47) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 710 50 1 141 92 NC_002967:TDE0705|5end_SPFH_domain/Band_7_family_protein_740268..740498_NEGATIVE 254 192 156 228 188 NC_002967:TDE1440|5end_glucose-1-phosphate_thymidylyltransferase_1485353..1485583_POSITIVE 243 175 136 136 97 NC_002967:TDE0902|5end_hypothetical_protein_920132..920362_NEGATIVE 241 110 64 206 160 NC_002967:TDE0041|5end_birA_bifunctional_protein_47497..47727_POSITIVE 237 160 113 124 72 NC_002967:TDE0138|5end_alkyldihydroxyacetonephosphate_synthase,_putative_158221..158451_POSITIVE 236 149 104 108 65 NC_002967:TDE2778|5end_PspC_domain_protein_2829604..2829834_NEGATIVE 231 158 111 120 84 NC_002967:TDE0502|5end_ankyrin_repeat_protein_556558..556788_NEGATIVE 229 184 142 50 7 NC_002967:TDE1569|5end_hypothetical_protein_1619785..1620015_POSITIVE 229 150 111 195 156 NC_002967:TDE0090|5end_hypothetical_protein_109206..109436_NEGATIVE 228 47 1 179 140 NC_002967:TDE1273|5end_oligopeptide/dipeptide_ABC_transporter,_peptide-binding_protein_1308624..1308854_NEGATIVE 222 178 135 51 5 NC_002967:TDE0493|5end_hypothetical_protein_549342..549572_NEGATIVE 218 123 83 107 72 NC_002967:TDE1742|5end_AMP-binding_enzyme_family_protein_1797578..1797808_NEGATIVE 216 48 7 133 96 NC_002967:TDE2120|5end_glycine_reductase_complex_proprotein_GrdE2_2153994..2154224_NEGATIVE 216 149 104 111 49 NC_002967:TDE1956|5end_hypothetical_protein_1971114..1971344_POSITIVE 213 195 154 92 51 NC_002967:TDE1291|5end_HD_domain_protein_1329213..1329443_NEGATIVE 211 160 123 72 29 NC_002967:TDE2781|5end_ABC_transporter,_ATP-binding/permease_protein_2832468..2832698_NEGATIVE 210 177 131 132 69 NC_002967:TDE0817|5end_histidine_kinase-related_ATPase,_putative_838800..839030_POSITIVE 208 168 135 169 137 NC_002967:TDE1911|5end_hypothetical_protein_1929098..1929328_NEGATIVE 208 41 1 126 91 NC_002967:TDE0969|5end_hypothetical_protein_993260..993490_POSITIVE 207 180 136 62 19 NC_002967:TDE1860|5end_hypothetical_protein_1886152..1886382_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 237 160 113 102 50 NC_002967:TDE0137|3end_carbohydrate_kinase,_FGGY_family_158279..158429_POSITIVE 236 149 104 84 41 NC_002967:TDE2779|3end_hypothetical_protein_2829628..2829778_NEGATIVE 235 158 111 126 86 NC_002967:TDE0060|3end_hypothetical_protein_67527..67677_NEGATIVE 231 158 111 98 62 NC_002967:TDE0503|3end_hypothetical_protein_556580..556730_NEGATIVE 226 179 140 147 107 NC_002967:TDE1713|3end_hypothetical_protein_1768010..1768160_NEGATIVE 221 192 151 53 15 NC_002967:TDE2570|3end_ribonuclease_HI_2597937..2598087_POSITIVE 211 160 123 54 11 NC_002967:TDE2782|3end_ABC_transporter,_ATP-binding/permease_protein_2832486..2832636_NEGATIVE 209 132 91 141 102 NC_002967:TDE2395|3end_Jag_protein,_putative_2422744..2422894_NEGATIVE 207 180 136 60 17 NC_002967:TDE1859|3end_hypothetical_protein_1886230..1886380_POSITIVE 206 159 113 59 9 NC_002967:TDE1784|3end_transcriptional_activator,_AraC_family_1823581..1823731_NEGATIVE 205 150 109 112 66 NC_002967:TDE1820|3end_hypothetical_protein_1854297..1854447_NEGATIVE 204 177 133 137 99 NC_002967:TDE1264|3end_hypothetical_protein_1298152..1298302_NEGATIVE 201 164 123 98 53 NC_002967:TDE0702|3end_ABC_transporter,_ATP-binding_protein_737244..737394_NEGATIVE 200 90 43 133 87 NC_002967:TDE1212|3end_flagellar_basal-body_rod_protein_FlgB_1245873..1246023_POSITIVE 200 178 135 82 27 NC_002967:TDE1045|3end_hypothetical_protein_1073739..1073889_POSITIVE 199 100 61 66 28 NC_002967:TDE0193|3end_hypothetical_protein_228613..228763_NEGATIVE 198 31 2 91 67 NC_002967:TDE2762|3end_flagellar_motor_switch_protein_FliY_2816563..2816713_NEGATIVE 197 31 5 148 120 NC_002967:TDE0696|3end_hypothetical_protein_734210..734360_POSITIVE 197 192 156 103 69 NC_002967:TDE0616|3end_hypothetical_protein_650079..650229_POSITIVE 194 176 131 132 90 NC_002967:TDE1206|3end_TPR_domain_protein_1239312..1239462_POSITIVE