Origin IGS: aaaatctttggaatatacgccagtttaatcaaaaagcagagacttcaatccaaaaagcatcgaagaatcatccataatcattgattgtcagccgattgaagtttagagcatccctatacgatttatcatttaaccgctgaaatggctttcagactccctttaaaaataaaaataaacgttcgacttaaactttttcatttatttttgcactcgcgtctctgataggaagtcacggatgaa .........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 ttcatccgtgacttcctatcagagacgcgagtgcaaaaataaatgaaaaagtttaagtcgaacgtttatttttatttttaaagggagtctgaaagccatttcagcggttaaatgataaatcgtatagggatgctctaaacttcaatcggctgacaatcaatgattatggatgattcttcgatgctttttggattgaagtctctgctttttgattaaactggcgtatattccaaagatttt Mask Tandem Repeat Region ================================================ aaaatctttggaatatacgccagtttaatcaaaaagcagagacttcaatccaaaaagcatcgaagaatcatccataatcattgattgtcagccgattgaagtttagagcatccctatacgatttatcatttaaccgctgaaatggctttcagactccctttaaaaataaaaataaacgttcgacttaaactttttcatttatttttgcactcgcgtctctgataggaagtcacggatgaa Find is-nt database================================================ Query_seq: TF1975:TF1976|TF1975:TF1976:uridylate kinase:RNA polymerase ECF-type sigma factor:->->:2122420..2122659 240 aaaatctttggaatatacgccagtttaatcaaaaagcagagacttcaatccaaaaagcatcgaagaatcatccataatcattgattgtcagccgattgaagtttagagcatccctatacgatttatcatttaaccgctgaaatggctttcagactccctttaaaaataaaaataaacgttcgacttaaactttttcatttatttttgcactcgcgtctctgataggaagtcacggatgaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1975:TF1976|TF1975:TF1976:uridylate kinase:RNA polymerase ECF-type sigma factor:->->:2122420..2122659 240 aaaatctttggaatatacgccagtttaatcaaaaagcagagacttcaatccaaaaagcatcgaagaatcatccataatcattgattgtcagccgattgaagtttagagcatccctatacgatttatcatttaaccgctgaaatggctttcagactccctttaaaaataaaaataaacgttcgacttaaactttttcatttatttttgcactcgcgtctctgataggaagtcacggatgaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1975:TF1976|TF1975:TF1976:uridylate kinase:RNA polymerase ECF-type sigma factor:->->:2122420..2122659 240 aaaatctttggaatatacgccagtttaatcaaaaagcagagacttcaatccaaaaagcatcgaagaatcatccataatcattgattgtcagccgattgaagtttagagcatccctatacgatttatcatttaaccgctgaaatggctttcagactccctttaaaaataaaaataaacgttcgacttaaactttttcatttatttttgcactcgcgtctctgataggaagtcacggatgaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaatctttggaatatacgccagtttaatcaaaaagcagagacttcaatccaaaaagcatcgaagaatcatccataatcattgattgtcagccgattgaagtttagagcatccctatacgatttatcatttaaccgctgaaatggctttcagactccctttaaaaataaaaataaacgttcgacttaaactttttcatttatttttgcactcgcgtctctgataggaagtcacggatgaa Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 121 End: 219 ........................................................................................................................ M Y H L T A E M A F R L P L K I K I N V R L K L F H L F L H S R L ..................... aaaatctttggaatatacgccagtttaatcaaaaagcagagacttcaatccaaaaagcatcgaagaatcatccataatcattgattgtcagccgattgaagtttagagcatccctatacgatttatcatttaaccgctgaaatggctttcagactccctttaaaaataaaaataaacgttcgacttaaactttttcatttatttttgcactcgcgtctctgataggaagtcacggatgaa 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================================================ aaaatctttggaatatacgccagtttaatcaaaaagcagagacttcaatccaaaaagcatcgaagaatcatccataatcattgattgtcagccgattgaagtttagagcatccctatacgatttatcatttaaccgctgaaatggctttcagactccctttaaaaataaaaataaacgttcgacttaaactttttcatttatttttgcactcgcgtctctgataggaagtcacggatgaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF1975:TF1976|TF1975:TF1976:uridylate kinase:RNA polymerase ECF-type sigma factor:->->:2122420..2122659 240 aaaatctttggaatatacgccagtttaatcaaaaagcagagacttcaatccaaaaagcatcgaagaatcatccataatcattgattgtcagccgattgaagtttagagcatccctatacgatttatcatttaaccgctgaaatggctttcagactccctttaaaaataaaaataaacgttcgacttaaactttttcatttatttttgcactcgcgtctctgataggaagtcacggatgaa Intra-Species Hit: Count: 1 Min: 1 Max: 240 Len: 240 Subject: tfor_TF1975_TF1976|uridylate kinase:RNA polymerase ECF-type sigma factor|POSITIVE:POSITIVE|[2122420,2122659]|240 HSP 1 e-value: 1.0E-133 bit: 476.0 Len: 240 Query Start:1 Query End:240 Subject Strand: POSITIVE Subject Start: 1 Subject End: 240 aaaatctttggaatatacgccagtttaatcaaaaagcagagacttcaatccaaaaagcatcgaagaatcatccataatcattgattgtcagccgattgaagtttagagcatccctatacgatttatcatttaaccgctgaaatggctttcagactccctttaaaaataaaaataaacgttcgacttaaactttttcatttatttttgcactcgcgtctctgataggaagtcacggatgaa aaaatctttggaatatacgccagtttaatcaaaaagcagagacttcaatccaaaaagcatcgaagaatcatccataatcattgattgtcagccgattgaagtttagagcatccctatacgatttatcatttaaccgctgaaatggctttcagactccctttaaaaataaaaataaacgttcgacttaaactttttcatttatttttgcactcgcgtctctgataggaagtcacggatgaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAUCUUUGGAAUAUACGCCAGUUUAAUCAAAAAGCAGAGACUUCAAUCCAAAAAGCAUCGAAGAAUCAUCCAUAAUCAUUGAUUGUCAGCCGAUUGAAGUUUAGAGCAUCCCUAUACGAUUUAUCAUUUAACCGCUGAAAUGGCUUUCAGACUCCCUUUAAAAAUAAAAAUAAACGUUCGACUUAAACUUUUUCAUUUAUUUUUGCACUCGCGUCUCUGAUAGGAAGUCACGGAUGAA .(((((.((((........))))............((..(((((((((((......(((((((.((...........)).)))).))).....)))))))))))...))..........))))).((((((....(((.....))).....((((.(((..(((((((((...(((.(((.......))).)))...)))))))))((....)).........))).))))..)))))). (-39.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCAUCCGUGACUUCCUAUCAGAGACGCGAGUGCAAAAAUAAAUGAAAAAGUUUAAGUCGAACGUUUAUUUUUAUUUUUAAAGGGAGUCUGAAAGCCAUUUCAGCGGUUAAAUGAUAAAUCGUAUAGGGAUGCUCUAAACUUCAAUCGGCUGACAAUCAAUGAUUAUGGAUGAUUCUUCGAUGCUUUUUGGAUUGAAGUCUCUGCUUUUUGAUUAAACUGGCGUAUAUUCCAAAGAUUUU .((((((((((((((((.......((....))..(((((((((((((...((((.....)))).)))))..))))))))..)))))))).(..((((......((((((........)))))).(((((...)))))..........))))..)...........))))))))..(((((((.(.....).))))))).....(((..((.....))..))).................. (-51.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 327 152 118 102 67 tfor:TF1790|5end_conserved_hypothetical_protein_1931227..1931457_POSITIVE 318 236 195 64 28 tfor:TF1659|5end_hypothetical_protein_1774854..1775084_POSITIVE 298 80 36 62 10 tfor:TF1543|5end_conserved_hypothetical_protein_1649429..1649659_POSITIVE 294 240 206 64 29 tfor:TF1501|5end_sugar_hydrolase_1600428..1600658_POSITIVE 292 236 196 59 17 tfor:TF1462|5end_erythronate-4-phosphate_dehydrogenase_1552184..1552414_POSITIVE 289 239 209 227 197 tfor:TF2022|5end_conserved_hypothetical_protein_2178524..2178754_POSITIVE 289 115 78 211 161 tfor:TF1451|5end_conserved_hypothetical_protein_1535876..1536106_POSITIVE 285 177 132 110 57 tfor:TF0218|5end_translation_initiation_factor_3_(IF-3)_243182..243412_POSITIVE 283 114 73 209 166 tfor:TF1716|5end_hypothetical_protein_1837442..1837672_POSITIVE 283 235 206 54 11 tfor:TF0464|5end_precorrin_methylase_480211..480441_POSITIVE 277 235 207 198 164 tfor:TF2689|5end_hypothetical_protein_2864824..2865054_POSITIVE 274 235 197 54 17 tfor:TF1580|5end_conserved_hypothetical_protein;_possible_fibronectin_domain_containing_protein_1687187..1687417_POSITIVE 269 158 135 126 96 tfor:TF2824|5end_nucleoside-transporting_protein_nupG_3014701..3014931_POSITIVE 269 238 194 173 131 tfor:TF0373|5end_conserved_hypothetical_protein,_yngK-related_391038..391268_POSITIVE 267 236 205 140 110 tfor:TF2465|5end_O-methyltransferase_2643737..2643967_POSITIVE 264 238 205 60 27 tfor:TF2879|5end_tRNA_(guanine-N-1)-methyltransferase_3068254..3068484_POSITIVE 263 136 91 101 60 tfor:TF1048|5end_permease_1109241..1109471_POSITIVE 260 161 136 113 85 tfor:TF2202|5end_hypothetical_protein_2378682..2378912_POSITIVE 260 236 194 178 135 tfor:TF2081|5end_phosphopantetheine_adenylyltransferase_2248475..2248705_POSITIVE 260 161 136 113 85 tfor:TF1516|5end_transposase_fragment_1626407..1626637_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 298 80 36 55 3 tfor:TF1542|3end_transcriptional_regulator_1649502..1649652_POSITIVE 292 236 196 48 6 tfor:TF1461|3end_DNA-damage-inducible_protein_F_1552253..1552403_POSITIVE 283 235 206 54 11 tfor:TF0463|3end_precorrin-6Y_C5,15-methyltransferase_480291..480441_POSITIVE 274 235 197 61 24 tfor:TF1579|3end_hypothetical_protein_1687274..1687424_POSITIVE 267 236 205 69 39 tfor:TF2464|3end_RNA_polymerase_ECF-type_sigma_factor_2643746..2643896_POSITIVE 263 136 91 98 57 tfor:TF1047|3end_tRNA_pseudouridylate_synthetase_A_(pseudouridylate_synthase_I)_1109318..1109468_POSITIVE 260 161 136 49 21 tfor:TF3003|3end_hypothetical_protein_3220629..3220779_POSITIVE 258 108 61 129 82 tfor:TF0995|3end_conserved_hypothetical_protein_1050962..1051112_POSITIVE 257 140 91 75 17 tfor:TF2089|3end_acyl_carrier_protein_2259749..2259899_POSITIVE 256 101 61 115 78 tfor:TF2694|3end_hypothetical_protein_2870863..2871013_POSITIVE 256 77 36 50 14 tfor:TF0501|3end_conserved_hypothetical_protein,_HicB-related_527361..527511_POSITIVE 255 160 112 96 36 tfor:TF2816|3end_hypothetical_protein_3007184..3007334_POSITIVE 255 218 177 49 3 tfor:TF0886|3end_conjugative_transposon_protein_fragment_938152..938302_POSITIVE 253 159 129 143 109 tfor:TF2511|3end_RNA_binding_protein_2690232..2690382_POSITIVE 253 239 209 116 82 tfor:TF1291|3end_response_regulator_(fimR__protein)_1372647..1372797_POSITIVE 252 214 171 81 46 tfor:TF2791|3end_GTP-binding_protein_TypA_2977219..2977369_POSITIVE 249 235 201 68 39 tfor:TF1815|3end_conserved_hypothetical_protein_1957442..1957592_POSITIVE 246 140 93 54 1 tfor:TF2015|3end_N6-adenine-specific_DNA_methylase_2173020..2173170_POSITIVE 246 107 67 44 5 tfor:TF0566|3end_hypothetical_protein_598858..599008_POSITIVE 245 161 133 52 19 tfor:TF0340|3end_hypothetical_protein_364257..364407_POSITIVE