Origin IGS: aacgataacaattgtttttgttttattctttttgaaattcagggtgcaaaattagcttttttatgggaataaacctcatgcacagactatattttttatttttgtcctgaaatctttgatgacatttatcgcatataaggattaacatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aatgttaatccttatatgcgataaatgtcatcaaagatttcaggacaaaaataaaaaatatagtctgtgcatgaggtttattcccataaaaaagctaattttgcaccctgaatttcaaaaagaataaaacaaaaacaattgttatcgtt Mask Tandem Repeat Region ================================================ aacgataacaattgtttttgttttattctttttgaaattcagggtgcaaaattagcttttttatgggaataaacctcatgcacagactatattttttatttttgtcctgaaatctttgatgacatttatcgcatataaggattaacatt Find is-nt database================================================ Query_seq: TF1620:TF1621|TF1620:TF1621:TPR domain protein:DNA replication and repair protein RecF:->->:1735284..1735432 149 aacgataacaattgtttttgttttattctttttgaaattcagggtgcaaaattagcttttttatgggaataaacctcatgcacagactatattttttatttttgtcctgaaatctttgatgacatttatcgcatataaggattaacatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1620:TF1621|TF1620:TF1621:TPR domain protein:DNA replication and repair protein RecF:->->:1735284..1735432 149 aacgataacaattgtttttgttttattctttttgaaattcagggtgcaaaattagcttttttatgggaataaacctcatgcacagactatattttttatttttgtcctgaaatctttgatgacatttatcgcatataaggattaacatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1620:TF1621|TF1620:TF1621:TPR domain protein:DNA replication and repair protein RecF:->->:1735284..1735432 149 aacgataacaattgtttttgttttattctttttgaaattcagggtgcaaaattagcttttttatgggaataaacctcatgcacagactatattttttatttttgtcctgaaatctttgatgacatttatcgcatataaggattaacatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aacgataacaattgtttttgttttattctttttgaaattcagggtgcaaaattagcttttttatgggaataaacctcatgcacagactatattttttatttttgtcctgaaatctttgatgacatttatcgcatataaggattaacatt Predict ORF larger than 30AA ================================================ Protein_Len: 41 Strand: - Start: 26 End: 148 ......................... E K Q F E P H L I L K K I P I F R M C L S Y K K N K D Q F R Q H C K D C I L I L M . aacgataacaattgtttttgttttattctttttgaaattcagggtgcaaaattagcttttttatgggaataaacctcatgcacagactatattttttatttttgtcctgaaatctttgatgacatttatcgcatataaggattaacatt 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================================================ aacgataacaattgtttttgttttattctttttgaaattcagggtgcaaaattagcttttttatgggaataaacctcatgcacagactatattttttatttttgtcctgaaatctttgatgacatttatcgcatataaggattaacatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF1620:TF1621|TF1620:TF1621:TPR domain protein:DNA replication and repair protein RecF:->->:1735284..1735432 149 aacgataacaattgtttttgttttattctttttgaaattcagggtgcaaaattagcttttttatgggaataaacctcatgcacagactatattttttatttttgtcctgaaatctttgatgacatttatcgcatataaggattaacatt Intra-Species Hit: Count: 1 Min: 1 Max: 149 Len: 149 Subject: tfor_TF1620_TF1621|TPR domain protein:DNA replication and repair protein RecF|POSITIVE:POSITIVE|[1735284,1735432]|149 HSP 1 e-value: 6.0E-58 bit: 224.0 Len: 149 Query Start:1 Query End:149 Subject Strand: POSITIVE Subject Start: 1 Subject End: 149 aacgataacaattgtttttgttttattctttttgaaattcagggtgcaaaattagcttttttatgggaataaacctcatgcacagactatannnnnnnnnnnngtcctgaaatctttgatgacatttatcgcatataaggattaacatt aacgataacaattgtttttgttttattctttttgaaattcagggtgcaaaattagcttttttatgggaataaacctcatgcacagactatattttttatttttgtcctgaaatctttgatgacatttatcgcatataaggattaacatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACGAUAACAAUUGUUUUUGUUUUAUUCUUUUUGAAAUUCAGGGUGCAAAAUUAGCUUUUUUAUGGGAAUAAACCUCAUGCACAGACUAUAUUUUUUAUUUUUGUCCUGAAAUCUUUGAUGACAUUUAUCGCAUAUAAGGAUUAACAUU ((((((....))))))..((((..((((((..((...((((((..((((((.(((((....((((((.......))))))...)).)))..........))))))))))))......(((((...))))).))...)))))).)))).. (-22.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUGUUAAUCCUUAUAUGCGAUAAAUGUCAUCAAAGAUUUCAGGACAAAAAUAAAAAAUAUAGUCUGUGCAUGAGGUUUAUUCCCAUAAAAAAGCUAAUUUUGCACCCUGAAUUUCAAAAAGAAUAAAACAAAAACAAUUGUUAUCGUU .................((((((............((.((((((..........................(((.((......)))))......((.......))..))))))..))............((((......)))))))))). (-18.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 275 60 13 160 111 tfor:TF0788|5end_protein-export_membrane_protein_840562..840792_POSITIVE 271 77 36 140 105 tfor:TF2824|5end_nucleoside-transporting_protein_nupG_3014701..3014931_POSITIVE 264 80 35 153 108 tfor:TF1885|5end_conserved_hypothetical_protein_2037307..2037537_POSITIVE 258 108 68 180 140 tfor:TF2850|5end_endoribonuclease_L-PSP_3038417..3038647_POSITIVE 242 137 97 166 127 tfor:TF2307|5end_two-component_system_sensor_histidine_kinase/response_2462618..2462848_POSITIVE 241 68 26 134 95 tfor:TF1946|5end_membrane_protein;_spore_maturation-like_protein_2094289..2094519_POSITIVE 240 118 72 60 14 tfor:TF0260|5end_conserved_hypothetical_protein_291116..291346_POSITIVE 230 106 62 141 84 tfor:TF2809|5end_conserved_hypothetical_protein;_possible_translation_factor_(SUA5)_2999832..3000062_POSITIVE 228 89 41 117 57 tfor:TF0310|5end_conserved_hypothetical_protein_334685..334915_POSITIVE 225 60 12 130 71 tfor:TF3034|5end_conserved_hypothetical_protein_3259113..3259343_POSITIVE 221 70 28 186 150 tfor:TF1553|5end_copper_homeostasis_protein_1658873..1659103_POSITIVE 220 90 44 73 32 tfor:TF1157|5end_glutamate_synthase,_small_subunit_1238012..1238242_POSITIVE 216 78 45 171 134 tfor:TF1294|5end_conserved_hypothetical_protein_1377142..1377372_POSITIVE 215 77 33 155 112 tfor:TF0137|5end_conserved_hypothetical_protein_146585..146815_POSITIVE 214 130 82 124 67 tfor:TF2740|5end_conserved_hypothetical_protein_2920657..2920887_POSITIVE 212 85 42 126 89 tfor:TF1983|5end_conserved_hypothetical_protein_2134684..2134914_POSITIVE 212 85 42 126 89 tfor:TF1905|5end_conserved_hypothetical_protein_2059932..2060162_POSITIVE 212 118 90 166 137 tfor:TF0123|5end_conserved_hypothetical_protein_133665..133895_POSITIVE 211 110 62 202 163 tfor:TF1141|5end_conserved_hypothetical_protein_1217972..1218202_POSITIVE 208 110 74 216 176 tfor:TF2561|5end_50S_ribosomal_protein_L16_2738693..2738923_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 258 108 68 97 57 tfor:TF2849|3end_histidinol-phosphate_transaminase_3038414..3038564_POSITIVE 241 68 26 42 3 tfor:TF1945|3end_glycerate_dehydrogenase_2094277..2094427_POSITIVE 230 106 62 138 81 tfor:TF2808|3end_bacterial_sugar_transferase_2999909..3000059_POSITIVE 228 89 41 127 67 tfor:TF0309|3end_conserved_hypothetical_protein_334775..334925_POSITIVE 222 62 26 72 35 tfor:TF0191|3end_conserved_hypothetical_protein,_possible_Iojap-related_protein_206528..206678_POSITIVE 221 70 28 59 23 tfor:TF1552|3end_conserved_hypothetical_protein_1658826..1658976_POSITIVE 220 90 44 73 32 tfor:TF1156|3end_oxidoreductase,_FAD-binding_1238092..1238242_POSITIVE 215 77 33 44 1 tfor:TF0135|3end_hypothetical_protein_146554..146704_POSITIVE 212 118 90 118 89 tfor:TF0122|3end_hypothetical_protein_133697..133847_POSITIVE 211 110 62 62 23 tfor:TF1140|3end_transcriptional_regulator,_AraC_family_1217912..1218062_POSITIVE 205 60 12 80 42 tfor:TF3098|3end_conserved_hypothetical_protein_3330535..3330685_POSITIVE 204 119 75 128 87 tfor:TF1489|3end_argininosuccinate_lyase_1590318..1590468_POSITIVE 202 51 12 131 85 tfor:TF2534|3end_conserved_hypothetical_protein_2717813..2717963_POSITIVE 202 133 97 78 35 tfor:TF0405|3end_conserved_hypothetical_protein_424308..424458_POSITIVE 200 112 77 51 12 tfor:TF1735|3end_dehydrogenase,_possible_NADH-dependent_dehydrogenase_1861460..1861610_POSITIVE 200 86 42 151 108 tfor:TF1159|3end_hypothetical_protein_1240342..1240492_POSITIVE 197 80 40 45 5 tfor:TF2224|3end_CTn_excision_protein_2394968..2395118_POSITIVE 196 132 94 94 45 tfor:TF0833|3end_conserved_hypothetical_protein_889052..889202_POSITIVE 196 88 43 120 82 tfor:TF0832|3end_conserved_hypothetical_protein_888788..888938_POSITIVE 194 132 101 108 76 tfor:TF0540|3end_conserved_hypothetical_protein;_possible_surface_protein_568496..568646_POSITIVE