Origin IGS: ttcaaaattagttcacgatatatataagatgccaaaaccatgccaaaacactcaaatcactaacatcaaaaaatttataaaatcattcaagaacagcctgtgtccaaaaattggacgtctgtgtccaatttttggacataaacagacgagccaacaataaaagacatgccccagacagttcattttttttcctaactttgcgaagcattatgtatatgcgttattattatatatgtattatatttctatattatcattaattttattttatacaat .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 attgtataaaataaaattaatgataatatagaaatataatacatatataataataacgcatatacataatgcttcgcaaagttaggaaaaaaaatgaactgtctggggcatgtcttttattgttggctcgtctgtttatgtccaaaaattggacacagacgtccaatttttggacacaggctgttcttgaatgattttataaattttttgatgttagtgatttgagtgttttggcatggttttggcatcttatatatatcgtgaactaattttgaa Mask Tandem Repeat Region ================================================ ttcaaaattagttcacgatatatataagatgccaaaaccatgccaaaacactcaaatcactaacatcaaaaaatttataaaatcattcaagaacagcctgtgtccaaaaattggacgtctgtgtccaatttttggacataaacagacgagccaacaataaaagacatgccccagacagttcattttttttcctaactttgcgaagcattatgtatatgcgttattattatatatgtattatatttctatattatcattaattttattttatacaat Find is-nt database================================================ Query_seq: TF1176:TF1177|TF1176:TF1177:outer membrane protein:conserved hypothetical protein; possible ribosomal protein S1:->->:1261039..1261314 276 ttcaaaattagttcacgatatatataagatgccaaaaccatgccaaaacactcaaatcactaacatcaaaaaatttataaaatcattcaagaacagcctgtgtccaaaaattggacgtctgtgtccaatttttggacataaacagacgagccaacaataaaagacatgccccagacagttcattttttttcctaactttgcgaagcattatgtatatgcgttattattatatatgtattatatttctatattatcattaattttattttatacaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1176:TF1177|TF1176:TF1177:outer membrane protein:conserved hypothetical protein; possible ribosomal protein S1:->->:1261039..1261314 276 ttcaaaattagttcacgatatatataagatgccaaaaccatgccaaaacactcaaatcactaacatcaaaaaatttataaaatcattcaagaacagcctgtgtccaaaaattggacgtctgtgtccaatttttggacataaacagacgagccaacaataaaagacatgccccagacagttcattttttttcctaactttgcgaagcattatgtatatgcgttattattatatatgtattatatttctatattatcattaattttattttatacaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1176:TF1177|TF1176:TF1177:outer membrane protein:conserved hypothetical protein; possible ribosomal protein S1:->->:1261039..1261314 276 ttcaaaattagttcacgatatatataagatgccaaaaccatgccaaaacactcaaatcactaacatcaaaaaatttataaaatcattcaagaacagcctgtgtccaaaaattggacgtctgtgtccaatttttggacataaacagacgagccaacaataaaagacatgccccagacagttcattttttttcctaactttgcgaagcattatgtatatgcgttattattatatatgtattatatttctatattatcattaattttattttatacaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttcaaaattagttcacgatatatataagatgccaaaaccatgccaaaacactcaaatcactaacatcaaaaaatttataaaatcattcaagaacagcctgtgtccaaaaattggacgtctgtgtccaatttttggacataaacagacgagccaacaataaaagacatgccccagacagttcattttttttcctaactttgcgaagcattatgtatatgcgttattattatatatgtattatatttctatattatcattaattttattttatacaat Predict ORF larger than 30AA ================================================ Protein_Len: 46 Strand: + Start: 20 End: 157 ................... M Y K M P K P C Q N T Q I T N I K K F I K S F K N S L C P K I G R L C P I F G H K Q T S Q Q ....................................................................................................................... Protein_Len: 49 Strand: + Start: 111 End: 257 .............................................................................................................. M D V C V Q F L D I N R R A N N K R H A P D S S F F F L T L R S I M Y M R Y Y Y I C I I F L Y Y H ................... Protein_Len: 31 Strand: + Start: 182 End: 274 ..................................................................................................................................................................................... M F F P N F A K H Y V Y A L L L Y M Y Y I S I L S L I L F Y T .. Protein_Len: 44 Strand: - Start: 86 End: 217 ..................................................................................... E L V A Q T W F N S T Q T W N K S M F L R A L L L L C A G S L E N K K R V K R L M I Y M ........................................................... Protein_Len: 43 Strand: - Start: 55 End: 183 ...................................................... I V L M L F N I F D N L F L R H G F I P R R H G I K P C L C V L W C Y F V H G L C N M ............................................................................................. ttcaaaattagttcacgatatatataagatgccaaaaccatgccaaaacactcaaatcactaacatcaaaaaatttataaaatcattcaagaacagcctgtgtccaaaaattggacgtctgtgtccaatttttggacataaacagacgagccaacaataaaagacatgccccagacagttcattttttttcctaactttgcgaagcattatgtatatgcgttattattatatatgtattatatttctatattatcattaattttattttatacaat 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================================================ PromScan Matrix: RpoN Strand: - Score: 85 Start: 30 End: 46 .............................TTGGCATGGTTTTGGCA...................................................................................................................................................................................................................................... ttcaaaattagttcacgatatatataagatgccaaaaccatgccaaaacactcaaatcactaacatcaaaaaatttataaaatcattcaagaacagcctgtgtccaaaaattggacgtctgtgtccaatttttggacataaacagacgagccaacaataaaagacatgccccagacagttcattttttttcctaactttgcgaagcattatgtatatgcgttattattatatatgtattatatttctatattatcattaattttattttatacaat Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -14.7 Tail_Score: -3.72527 Start: 94 End: 145 Full_Region: ttattgttggctcgt ctgtttatgtccaaaaattggac acagac gtccaatttttggacacaggctg ttcttgaatgatttt .............................................................................................ctgtttatgtccaaaaattggacacagacgtccaatttttggacacaggctg................................................................................................................................... TransTerm Strand: - Conf: 100 HP_score: -15.9 Tail_Score: -3.43104 Start: 96 End: 143 Full_Region: attgttggctcgtct gtttatgtccaaaaattggac acagac gtccaatttttggacacaggc tgttcttgaatgatt ...............................................................................................gtttatgtccaaaaattggacacagacgtccaatttttggacacaggc..................................................................................................................................... TransTerm Strand: + Conf: 76 HP_score: -6.3 Tail_Score: -4.59773 Start: 111 End: 128 Full_Region: GCCTGTGTCCAAAAA TTGGACG TCTG TGTCCAA TTTTTGGACATAAAC ..............................................................................................................TTGGACGTCTGTGTCCAA.................................................................................................................................................... TransTerm Strand: - Conf: 73 HP_score: -5.6 Tail_Score: -4.56597 Start: 111 End: 128 Full_Region: gtttatgtccaaaaa ttggac acagac gtccaa tttttggacacaggc ..............................................................................................................ttggacacagacgtccaa.................................................................................................................................................... Find igs database================================================ Query_seq: TF1176:TF1177|TF1176:TF1177:outer membrane protein:conserved hypothetical protein; possible ribosomal protein S1:->->:1261039..1261314 276 ttcaaaattagttcacgatatatataagatgccaaaaccatgccaaaacactcaaatcactaacatcaaaaaatttataaaatcattcaagaacagcctgtgtccaaaaattggacgtctgtgtccaatttttggacataaacagacgagccaacaataaaagacatgccccagacagttcattttttttcctaactttgcgaagcattatgtatatgcgttattattatatatgtattatatttctatattatcattaattttattttatacaat Intra-Species Hit: Count: 1 Min: 1 Max: 182 Len: 182 Subject: tfor_TF1176_TF1177|outer membrane protein:conserved hypothetical protein; possible ribosomal protein S1|POSITIVE:POSITIVE|[1261039,1261314]|276 HSP 1 e-value: 8.0E-99 bit: 361.0 Len: 182 Query Start:1 Query End:182 Subject Strand: POSITIVE Subject Start: 1 Subject End: 182 ttcaaaattagttcacgatatatataagatgccaaaaccatgccaaaacactcaaatcactaacatcaaaaaatttataaaatcattcaagaacagcctgtgtccaaaaattggacgtctgtgtccaatttttggacataaacagacgagccaacaataaaagacatgccccagacagttca.............................................................................................. ttcaaaattagttcacgatatatataagatgccaaaaccatgccaaaacactcaaatcactaacatcaaaaaatttataaaatcattcaagaacagcctgtgtccaaaaattggacgtctgtgtccaatttttggacataaacagacgagccaacaataaaagacatgccccagacagttca.............................................................................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCAAAAUUAGUUCACGAUAUAUAUAAGAUGCCAAAACCAUGCCAAAACACUCAAAUCACUAACAUCAAAAAAUUUAUAAAAUCAUUCAAGAACAGCCUGUGUCCAAAAAUUGGACGUCUGUGUCCAAUUUUUGGACAUAAACAGACGAGCCAACAAUAAAAGACAUGCCCCAGACAGUUCA ..........((((.............((((................................))))...............................(((((((((((((((((((....))))))))))))))))))).......))))............................... (-31.45) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAACUGUCUGGGGCAUGUCUUUUAUUGUUGGCUCGUCUGUUUAUGUCCAAAAAUUGGACACAGACGUCCAAUUUUUGGACACAGGCUGUUCUUGAAUGAUUUUAUAAAUUUUUUGAUGUUAGUGAUUUGAGUGUUUUGGCAUGGUUUUGGCAUCUUAUAUAUAUCGUGAACUAAUUUUGAA .((((.(((((.(((..(((..........)))..)))......((((((((((((((((......))))))))))))))))))))).))))....(((((..(((((.......((((((((.(((....((((....)))).))))))))))))))))...))))).............. (-49.71) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 301 159 113 62 2 tfor:TF1090|5end_hypothetical_protein_1159032..1159262_POSITIVE 296 156 115 199 151 tfor:TF1130|5end_ABC_transporter_ATP-binding_protein/permease_component_1205387..1205617_POSITIVE 284 157 113 179 121 tfor:TF0986|5end_50S_ribosomal_protein_L31_1041426..1041656_POSITIVE 280 133 91 212 168 tfor:TF2880|5end_phenylalanyl-tRNA_synthetase,_beta_subunit_3069052..3069282_POSITIVE 275 151 111 96 54 tfor:TF3139|5end_Na+-translocating_NADH-quinone_reductase,_subunit_C_3372581..3372811_POSITIVE 274 128 82 87 47 tfor:TF0893|5end_conserved_hypothetical_protein_941754..941984_POSITIVE 272 124 81 168 120 tfor:TF3147|5end_adenylate_kinase_3383049..3383279_POSITIVE 269 124 83 55 6 tfor:TF2504|5end_peptidyl-prolyl_cis-trans_isomerase_2680031..2680261_POSITIVE 267 156 113 170 113 tfor:TF2590|5end_transposase_2756056..2756286_POSITIVE 266 156 111 192 140 tfor:TF2902|5end_holliday_junction_DNA_helicase_3097813..3098043_POSITIVE 265 148 101 123 81 tfor:TF2239|5end_hypothetical_protein_2414537..2414767_POSITIVE 265 156 116 54 11 tfor:TF0496|5end_conserved_hypothetical_protein_522332..522562_POSITIVE 264 148 104 214 165 tfor:TF3134|5end_HD_superfamily_hydrolase_3367990..3368220_POSITIVE 257 178 137 177 118 tfor:TF2977|5end_candidate_b-glycosyltransferase,_Glycosyltransferase_Family_2_protein_3185228..3185458_POSITIVE 254 138 92 65 5 tfor:TF2469|5end_oxidoreductase,_possible_Gfo/Idh/MocA_family_2646505..2646735_POSITIVE 252 140 95 56 10 tfor:TF2629|5end_conserved_hypothetical_protein;_possible_lactoylglutathione_lyase_2801296..2801526_POSITIVE 252 125 92 58 27 tfor:TF1834|5end_3-isopropylmalate_dehydrogenase_1983161..1983391_POSITIVE 251 129 100 65 38 tfor:TF3093|5end_30S_ribosomal_protein_S2_3325244..3325474_POSITIVE 250 127 87 90 55 tfor:TF2446|5end_riboflavin-specific_deaminase_2622370..2622600_POSITIVE 245 179 133 51 12 tfor:TF2290|5end_ABC_transporter,_ATP-binding/permease_component_2443942..2444172_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 284 157 113 97 39 tfor:TF0984|3end_possible_mucin-desulfating_sulfatase_(MdsC_protein)_1041424..1041574_POSITIVE 280 133 91 88 44 tfor:TF2879|3end_tRNA_(guanine-N-1)-methyltransferase_3069008..3069158_POSITIVE 275 151 111 89 47 tfor:TF3138|3end_Na+-translocating_quinone_reductase,_subunit_D_3372654..3372804_POSITIVE 272 124 81 119 71 tfor:TF3146|3end_GTP-binding_protein_Obg_3383080..3383230_POSITIVE 272 139 94 108 68 tfor:TF2478|3end_hypothetical_protein_2655613..2655763_POSITIVE 269 124 83 55 6 tfor:TF2503|3end_conserved_hypothetical_protein_2680111..2680261_POSITIVE 265 160 112 62 1 tfor:TF2299|3end_hypothetical_protein_2450247..2450397_POSITIVE 265 148 101 94 52 tfor:TF2238|3end_conserved_hypothetical_protein_2414588..2414738_POSITIVE 255 126 84 106 61 tfor:TF2793|3end_possible_L-lysine_2,3-aminomutase_2979888..2980038_POSITIVE 254 138 92 62 2 tfor:TF2468|3end_hypothetical_protein_2646582..2646732_POSITIVE 252 140 95 56 10 tfor:TF2628|3end_conserved_hypothetical_protein_2801376..2801526_POSITIVE 247 159 115 59 2 tfor:TF1089|3end_ABC_transporter,_ATP-binding_fragment,_bacteriocin/lantibiotic_exporter_1159109..1159259_POSITIVE 242 126 93 120 77 tfor:TF0537|3end_conserved_hypothetical_protein_566836..566986_POSITIVE 240 149 111 150 110 tfor:TF3147|3end_adenylate_kinase_3383704..3383854_POSITIVE 239 135 97 43 13 tfor:TF1165|3end_conserved_hypothetical_protein_1245921..1246071_POSITIVE 237 149 101 119 68 tfor:TF0064|3end_conserved_hypothetical_protein_70412..70562_POSITIVE 235 179 142 33 2 tfor:TF2289|3end_secretion_protein,_possible_HlyD_family_2444004..2444154_POSITIVE 235 179 131 145 97 tfor:TF0444|3end_Na+-translocating_NADH-quinone_oxidoreductase,_subunit_5_466518..466668_POSITIVE 232 126 90 143 104 tfor:TF3065|3end_enolase_3292412..3292562_POSITIVE 232 179 132 64 10 tfor:TF1622|3end_conserved_hypothetical_protein_1736763..1736913_POSITIVE