Origin IGS: aattataaatgtaaatgaatatccgtgtttgtacctaaaaactccattaaactatttaataacaataatttggatgcatggattggagtaagaaataaatttctgtagattagcaatatataattaattttaggcatatatacggacattcataatttattatctttgcatc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gatgcaaagataataaattatgaatgtccgtatatatgcctaaaattaattatatattgctaatctacagaaatttatttcttactccaatccatgcatccaaattattgttattaaatagtttaatggagtttttaggtacaaacacggatattcatttacatttataatt Mask Tandem Repeat Region ================================================ aattataaatgtaaatgaatatccgtgtttgtacctaaaaactccattaaactatttaataacaataatttggatgcatggattggagtaagaaataaatttctgtagattagcaatatataattaattttaggcatatatacggacattcataatttattatctttgcatc Find is-nt database================================================ Query_seq: TF2966:TF2967|TF2966:TF2967:hypothetical protein:hypothetical protein:->->:3177733..3177904 172 aattataaatgtaaatgaatatccgtgtttgtacctaaaaactccattaaactatttaataacaataatttggatgcatggattggagtaagaaataaatttctgtagattagcaatatataattaattttaggcatatatacggacattcataatttattatctttgcatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2966:TF2967|TF2966:TF2967:hypothetical protein:hypothetical protein:->->:3177733..3177904 172 aattataaatgtaaatgaatatccgtgtttgtacctaaaaactccattaaactatttaataacaataatttggatgcatggattggagtaagaaataaatttctgtagattagcaatatataattaattttaggcatatatacggacattcataatttattatctttgcatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2966:TF2967|TF2966:TF2967:hypothetical protein:hypothetical protein:->->:3177733..3177904 172 aattataaatgtaaatgaatatccgtgtttgtacctaaaaactccattaaactatttaataacaataatttggatgcatggattggagtaagaaataaatttctgtagattagcaatatataattaattttaggcatatatacggacattcataatttattatctttgcatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aattataaatgtaaatgaatatccgtgtttgtacctaaaaactccattaaactatttaataacaataatttggatgcatggattggagtaagaaataaatttctgtagattagcaatatataattaattttaggcatatatacggacattcataatttattatctttgcatc Predict ORF larger than 30AA ================================================ Protein_Len: 49 Strand: - Start: 6 End: 149 ..... * L H L H I D T N T G L F E M L S N L L L L K S A H I P T L F L N R Y I L L I Y N I K P M Y V S M ....................... aattataaatgtaaatgaatatccgtgtttgtacctaaaaactccattaaactatttaataacaataatttggatgcatggattggagtaagaaataaatttctgtagattagcaatatataattaattttaggcatatatacggacattcataatttattatctttgcatc Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aattataaatgtaaatgaatatccgtgtttgtacctaaaaactccattaaactatttaataacaataatttggatgcatggattggagtaagaaataaatttctgtagattagcaatatataattaattttaggcatatatacggacattcataatttattatctttgcatc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF2966:TF2967|TF2966:TF2967:hypothetical protein:hypothetical protein:->->:3177733..3177904 172 aattataaatgtaaatgaatatccgtgtttgtacctaaaaactccattaaactatttaataacaataatttggatgcatggattggagtaagaaataaatttctgtagattagcaatatataattaattttaggcatatatacggacattcataatttattatctttgcatc Intra-Species Hit: Count: 7 Min: 1 Max: 172 Len: 172 Subject: tfor_TF2966_TF2967|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[3177733,3177904]|172 HSP 1 e-value: 5.0E-93 bit: 341.0 Len: 172 Query Start:1 Query End:172 Subject Strand: POSITIVE Subject Start: 1 Subject End: 172 aattataaatgtaaatgaatatccgtgtttgtacctaaaaactccattaaactatttaataacaataatttggatgcatggattggagtaagaaataaatttctgtagattagcaatatataattaattttaggcatatatacggacattcataatttattatctttgcatc aattataaatgtaaatgaatatccgtgtttgtacctaaaaactccattaaactatttaataacaataatttggatgcatggattggagtaagaaataaatttctgtagattagcaatatataattaattttaggcatatatacggacattcataatttattatctttgcatc Subject: tfor_TF1890_TF1891|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[2043154,2043528]|375 HSP 1 e-value: 4.0E-75 bit: 281.0 Len: 142 Query Start:13 Query End:154 Subject Strand: POSITIVE Subject Start: 4 Subject End: 145 ............aaatgaatatccgtgtttgtacctaaaaactccattaaactatttaataacaataatttggatgcatggattggagtaagaaataaatttctgtagattagcaatatataattaattttaggcatatatacggacattcata.................. ............aaatgaatatccgtgtttgtacctaaaaactccattaaactatttaataacaataatttggatgcatggattggagtaagaaataaatttctgtagattagcaatatataattaattttaggcatatatacggacattcata.................. Subject: tfor_TF1369_TF1370|hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[1447647,1447991]|345 HSP 1 e-value: 4.0E-75 bit: 281.0 Len: 142 Query Start:14 Query End:155 Subject Strand: NEGATIVE Subject Start: 184 Subject End: 325 .............aatgaatatccgtgtttgtacctaaaaactccattaaactatttaataacaataatttggatgcatggattggagtaagaaataaatttctgtagattagcaatatataattaattttaggcatatatacggacattcataa................. .............aatgaatatccgtgtttgtacctaaaaactccattaaactatttaataacaataatttggatgcatggattggagtaagaaataaatttctgtagattagcaatatataattaattttaggcatatatacggacattcataa................. Subject: tfor_TF2175_TF2176|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[2348876,2349050]|175 HSP 1 e-value: 2.0E-73 bit: 276.0 Len: 139 Query Start:14 Query End:152 Subject Strand: POSITIVE Subject Start: 37 Subject End: 175 .............aatgaatatccgtgtttgtacctaaaaactccattaaactatttaataacaataatttggatgcatggattggagtaagaaataaatttctgtagattagcaatatataattaattttaggcatatatacggacattca.................... .............aatgaatatccgtgtttgtacctaaaaactccattaaactatttaataacaataatttggatgcatggattggagtaagaaataaatttctgtagattagcaatatataattaattttaggcatatatacggacattca.................... Subject: tfor_TF2478_TF2479|hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[2655674,2656131]|458 HSP 1 e-value: 2.0E-49 bit: 196.0 Len: 139 Query Start:12 Query End:150 Subject Strand: NEGATIVE Subject Start: 296 Subject End: 433 ...........taaatgaatatccgtgtttgtacctaaaaactccattaaactatttaataacaataatttggatgcatggattggagtaagaaataaatttctgtagattagcaatatataattaattttaggcatatatacggacatt...................... ...........taaataaatatccgtgtttgtacctaaaagctccattaaactatttaataacaataatttggatgtatggattgg-ggagggaataaatttctgtatatcagcaatatataattaattttaggcatatatacggacatt...................... Subject: tfor_TF2162_TF2163|thermolysin precursor:hypothetical protein|POSITIVE:POSITIVE|[2340774,2340941]|168 HSP 1 e-value: 1.0E-41 bit: 170.0 Len: 118 Query Start:36 Query End:153 Subject Strand: NEGATIVE Subject Start: 51 Subject End: 168 ...................................taaaaactccattaaactatttaataacaataatttggatgcatggattggagtaagaaataaatttctgtagattagcaatatataattaattttaggcatatatacggacattcat................... ...................................taaaagctccattaaactatttaataacaataatttggatgtatggattgaagcaagagataaatttctgtatatcagtaatatataattaattttaggcatatatacggacattcat................... Subject: tfor_TF0899_TF0901|hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[946220,946820]|601 HSP 1 e-value: 1.0E-40 bit: 167.0 Len: 140 Query Start:14 Query End:153 Subject Strand: POSITIVE Subject Start: 411 Subject End: 550 .............aatgaatatccgtgtttgtacctaaaaactccattaaactatttaataacaataatttggatgcatggattggagtaagaaataaatttctgtagattagcaatatataattaattttaggcatatatacggacattcat................... .............aatgaatatccgtttttgcacctaaaaactctattaaactatttaacaacaataatttagatgtataggtcggagagagaaatagatttctgtatatcagcaatatataattaattttaggcatatatacggacattcat................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUAUAAAUGUAAAUGAAUAUCCGUGUUUGUACCUAAAAACUCCAUUAAACUAUUUAAUAACAAUAAUUUGGAUGCAUGGAUUGGAGUAAGAAAUAAAUUUCUGUAGAUUAGCAAUAUAUAAUUAAUUUUAGGCAUAUAUACGGACAUUCAUAAUUUAUUAUCUUUGCAUC ....((((((....((((((.(((((((.(((.(((((((((((((......(((((((..........))))))).......)))))).(((((....)))))...(((((........)))))..))))))).))).))))))).)))))).))))))............ (-34.62) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUGCAAAGAUAAUAAAUUAUGAAUGUCCGUAUAUAUGCCUAAAAUUAAUUAUAUAUUGCUAAUCUACAGAAAUUUAUUUCUUACUCCAAUCCAUGCAUCCAAAUUAUUGUUAUUAAAUAGUUUAAUGGAGUUUUUAGGUACAAACACGGAUAUUCAUUUACAUUUAUAAUU ............((((((.((((((((((((.....(((((((((.......................(((((....)))))........(((((......((((((((.......)))))))).)))))..))))))))).....))))))))))))....)))))).... (-34.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 777 120 71 218 169 tfor:TF1370|5end_conserved_hypothetical_protein_1447852..1448082_POSITIVE 638 70 21 175 126 tfor:TF2479|5end_conserved_hypothetical_protein_2655992..2656222_POSITIVE 638 70 21 126 77 tfor:TF2163|5end_hypothetical_protein_2340802..2341032_POSITIVE 582 70 21 188 139 tfor:TF0845|5end_hypothetical_protein_896419..896649_POSITIVE 309 44 12 213 183 tfor:TF0671|5end_histidine_kinase_sensor_protein_715103..715333_POSITIVE 280 44 15 89 62 tfor:TF1377|5end_conserved_hypothetical_protein_1453767..1453997_POSITIVE 280 44 15 210 183 tfor:TF1265|5end_dihydroorotate_dehydrogenase_1352360..1352590_POSITIVE 265 44 4 225 187 tfor:TF1868|5end_conserved_hypothetical_protein;_possible_transposase_2022598..2022828_POSITIVE 265 44 4 89 51 tfor:TF1867|5end_transposase_2022462..2022692_POSITIVE 255 154 113 128 88 tfor:TF1865|5end_conserved_hypothetical_protein;_possible_transposase_2021532..2021762_POSITIVE 244 153 113 107 68 tfor:TF1264|5end_possible_transposase_1351290..1351520_POSITIVE 228 161 122 178 142 tfor:TF0220|5end_conserved_hypothetical_protein_246230..246460_POSITIVE 227 93 70 214 191 tfor:TF2583|5end_possible_ABC_transporter,__permease_component_2750206..2750436_POSITIVE 226 158 113 153 108 tfor:TF0670|5end_possible_transposase_714069..714299_POSITIVE 225 114 74 211 174 tfor:TF2768|5end_ferredoxin_oxidoreductase,_beta_subunit_2954076..2954306_POSITIVE 225 40 3 128 88 tfor:TF0199|5end_conserved_hypothetical_protein_222053..222283_POSITIVE 220 108 68 126 78 tfor:TF0751|5end_dipeptidyl_peptidase_IV_798663..798893_POSITIVE 217 114 73 211 174 tfor:TF1517|5end_hypothetical_protein_1626694..1626924_POSITIVE 216 85 42 53 19 tfor:TF3042|5end_ferrous_iron_transport_protein_B_3269362..3269592_POSITIVE 213 37 12 194 169 tfor:TF2304|5end_OmpA_family_protein_2459320..2459550_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 506 153 115 40 2 tfor:TF2162|3end_thermolysin_precursor_2340713..2340863_POSITIVE 309 44 12 111 81 tfor:TF0670|3end_possible_transposase_715081..715231_POSITIVE 301 44 1 111 63 tfor:TF2479|3end_conserved_hypothetical_protein_2657043..2657193_POSITIVE 280 44 15 111 84 tfor:TF1376|3end_possible_transposase_1453869..1454019_POSITIVE 280 44 15 111 84 tfor:TF1264|3end_possible_transposase_1352341..1352491_POSITIVE 265 44 4 111 73 tfor:TF1866|3end_conserved_hypothetical_protein;_possible_transposase_2022564..2022714_POSITIVE 255 154 113 48 8 tfor:TF1864|3end_conserved_hypothetical_protein_2021532..2021682_POSITIVE 250 55 14 119 83 tfor:TF1096|3end_conserved_hypothetical_protein_1165357..1165507_POSITIVE 244 153 113 72 33 tfor:TF1263|3end_DNA-mismatch_repair_protein_1351335..1351485_POSITIVE 226 158 113 55 10 tfor:TF0669|3end_hypothetical_protein_714051..714201_POSITIVE 225 40 3 61 21 tfor:TF0198|3end_transposase_related_sequence_222066..222216_POSITIVE 220 108 68 81 33 tfor:TF0750|3end_conserved_hypothetical_protein_798698..798848_POSITIVE 213 37 12 97 72 tfor:TF2303|3end_conserved_hypothetical_protein_2459303..2459453_POSITIVE 212 94 69 46 18 tfor:TF2417|3end_outer_membrane_protein,_TonB_dependent_receptor_2596960..2597110_POSITIVE 204 107 69 91 46 tfor:TF1428|3end_conserved_hypothetical_protein_1513996..1514146_POSITIVE 202 112 73 100 61 tfor:TF1936|3end_conserved_hypothetical_protein_2084549..2084699_POSITIVE 200 168 128 67 28 tfor:TF2175|3end_hypothetical_protein_2348815..2348965_POSITIVE 197 107 74 39 10 tfor:TF1007|3end_rod_shape-determining_protein_MreB_1063450..1063600_POSITIVE 196 169 132 63 28 tfor:TF0380|3end_conserved_hypothetical_protein_401633..401783_POSITIVE 195 55 15 119 84 tfor:TF0837|3end_possible_transposase_fragment_890058..890208_POSITIVE