Origin IGS: ttttatttatttgtttatgattaatatcaatagttcgtttgtttagcccgcgatagccggcgaatcatgacttgcgcagtttgcgatcggcggaagggtttaccgcaaccggatgccgcgaaaggctcacttttcagcttgtaccgtcggggtagcaacttttttctcgatta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taatcgagaaaaaagttgctaccccgacggtacaagctgaaaagtgagcctttcgcggcatccggttgcggtaaacccttccgccgatcgcaaactgcgcaagtcatgattcgccggctatcgcgggctaaacaaacgaactattgatattaatcataaacaaataaataaaa Mask Tandem Repeat Region ================================================ ttttatttatttgtttatgattaatatcaatagttcgtttgtttagcccgcgatagccggcgaatcatgacttgcgcagtttgcgatcggcggaagggtttaccgcaaccggatgccgcgaaaggctcacttttcagcttgtaccgtcggggtagcaacttttttctcgatta Find is-nt database================================================ Query_seq: TF3140:TF3141|TF3140:TF3141:Na+-translocating NADH-quinone reductase, subunit B:NADH: ubiquinone oxidoreductase, subunit A:->->:3374634..3374806 173 ttttatttatttgtttatgattaatatcaatagttcgtttgtttagcccgcgatagccggcgaatcatgacttgcgcagtttgcgatcggcggaagggtttaccgcaaccggatgccgcgaaaggctcacttttcagcttgtaccgtcggggtagcaacttttttctcgatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF3140:TF3141|TF3140:TF3141:Na+-translocating NADH-quinone reductase, subunit B:NADH: ubiquinone oxidoreductase, subunit A:->->:3374634..3374806 173 ttttatttatttgtttatgattaatatcaatagttcgtttgtttagcccgcgatagccggcgaatcatgacttgcgcagtttgcgatcggcggaagggtttaccgcaaccggatgccgcgaaaggctcacttttcagcttgtaccgtcggggtagcaacttttttctcgatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF3140:TF3141|TF3140:TF3141:Na+-translocating NADH-quinone reductase, subunit B:NADH: ubiquinone oxidoreductase, subunit A:->->:3374634..3374806 173 ttttatttatttgtttatgattaatatcaatagttcgtttgtttagcccgcgatagccggcgaatcatgacttgcgcagtttgcgatcggcggaagggtttaccgcaaccggatgccgcgaaaggctcacttttcagcttgtaccgtcggggtagcaacttttttctcgatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttttatttatttgtttatgattaatatcaatagttcgtttgtttagcccgcgatagccggcgaatcatgacttgcgcagtttgcgatcggcggaagggtttaccgcaaccggatgccgcgaaaggctcacttttcagcttgtaccgtcggggtagcaacttttttctcgatta Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 64 End: 171 ............................................................... M M T C A V C D R R K G L P Q P D A A K G S L F S L Y R R G S N F F L D .. Protein_Len: 43 Strand: - Start: 30 End: 158 ............................. Y N T Q K A R S L R R I M V Q A T Q S R R F P K G C G S A A F P E S K L K Y R R P L M ............... ttttatttatttgtttatgattaatatcaatagttcgtttgtttagcccgcgatagccggcgaatcatgacttgcgcagtttgcgatcggcggaagggtttaccgcaaccggatgccgcgaaaggctcacttttcagcttgtaccgtcggggtagcaacttttttctcgatta 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================================================ ttttatttatttgtttatgattaatatcaatagttcgtttgtttagcccgcgatagccggcgaatcatgacttgcgcagtttgcgatcggcggaagggtttaccgcaaccggatgccgcgaaaggctcacttttcagcttgtaccgtcggggtagcaacttttttctcgatta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF3140:TF3141|TF3140:TF3141:Na+-translocating NADH-quinone reductase, subunit B:NADH: ubiquinone oxidoreductase, subunit A:->->:3374634..3374806 173 ttttatttatttgtttatgattaatatcaatagttcgtttgtttagcccgcgatagccggcgaatcatgacttgcgcagtttgcgatcggcggaagggtttaccgcaaccggatgccgcgaaaggctcacttttcagcttgtaccgtcggggtagcaacttttttctcgatta Intra-Species Hit: Count: 1 Min: 1 Max: 173 Len: 173 Subject: tfor_TF3140_TF3141|Na+-translocating NADH-quinone reductase, subunit B:NADH: ubiquinone oxidoreductase, subunit A|POSITIVE:POSITIVE|[3374634,3374806]|173 HSP 1 e-value: 1.0E-93 bit: 343.0 Len: 173 Query Start:1 Query End:173 Subject Strand: POSITIVE Subject Start: 1 Subject End: 173 ttttatttatttgtttatgattaatatcaatagttcgtttgtttagcccgcgatagccggcgaatcatgacttgcgcagtttgcgatcggcggaagggtttaccgcaaccggatgccgcgaaaggctcacttttcagcttgtaccgtcggggtagcaacttttttctcgatta ttttatttatttgtttatgattaatatcaatagttcgtttgtttagcccgcgatagccggcgaatcatgacttgcgcagtttgcgatcggcggaagggtttaccgcaaccggatgccgcgaaaggctcacttttcagcttgtaccgtcggggtagcaacttttttctcgatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUAUUUAUUUGUUUAUGAUUAAUAUCAAUAGUUCGUUUGUUUAGCCCGCGAUAGCCGGCGAAUCAUGACUUGCGCAGUUUGCGAUCGGCGGAAGGGUUUACCGCAACCGGAUGCCGCGAAAGGCUCACUUUUCAGCUUGUACCGUCGGGGUAGCAACUUUUUUCUCGAUUA ..............((((((((......(((((.....)))))..(((.((....)).))).))))))))....(((.....))).((((..((((((((((((.(...(((.(((.((((((((....)))))).))..))))))..).))))..))))))))..))))... (-42.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUCGAGAAAAAAGUUGCUACCCCGACGGUACAAGCUGAAAAGUGAGCCUUUCGCGGCAUCCGGUUGCGGUAAACCCUUCCGCCGAUCGCAAACUGCGCAAGUCAUGAUUCGCCGGCUAUCGCGGGCUAAACAAACGAACUAUUGAUAUUAAUCAUAAACAAAUAAAUAAAA ..(((((.......(((..((.((((.((((((..((.(((..((((..(((.(((((....(((((((((.........))).))))))....))))).)))))))..)))))..).))))))))).))....)))......)))))......................... (-41.82) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 453 118 71 228 179 tfor:TF2332|5end_signal_peptidase_I_2491694..2491924_POSITIVE 435 119 73 151 101 tfor:TF2229.1|5end_rteR_regulatory_ortholog_(with_internal_stop)_2399454..2399684_POSITIVE 431 114 71 229 183 tfor:TF2741|5end_ATP-dependent_DNA_helicase_RecQ_2921882..2922112_POSITIVE 431 119 71 116 60 tfor:TF0746|5end_possible_DNA_polymerase_III_792261..792491_POSITIVE 430 118 75 98 46 tfor:TF1304|5end_conserved_hypothetical_protein_1385008..1385238_POSITIVE 427 127 82 144 87 tfor:TF0280|5end_hypothetical_protein_308807..309037_POSITIVE 417 120 71 198 144 tfor:TF2044|5end_excinuclease_ABC,_subunit_A_2203228..2203458_POSITIVE 417 120 73 208 156 tfor:TF0147|5end_patatin-like_phospholipase_156798..157028_POSITIVE 414 156 111 61 8 tfor:TF2898|5end_conserved_hypothetical_protein_3087061..3087291_POSITIVE 414 130 86 159 109 tfor:TF2820|5end_argininosuccinate_synthetase_3009876..3010106_POSITIVE 414 120 74 178 124 tfor:TF2775|5end_conserved_hypothetical_protein;_possible_mucoidy_inhibitor-related_protein_2959668..2959898_POSITIVE 409 98 52 180 123 tfor:TF2410|5end_possible_endo-1,4-beta-xylanase_2584000..2584230_POSITIVE 406 120 72 65 17 tfor:TF1816|5end_hypothetical_protein_1957643..1957873_POSITIVE 402 119 71 55 2 tfor:TF0435|5end_DNA_mismatch_repair_protein_457182..457412_POSITIVE 399 85 49 228 184 tfor:TF1048|5end_permease_1109241..1109471_POSITIVE 398 128 88 201 170 tfor:TF2437|5end_elongation_factor_P_2615104..2615334_POSITIVE 396 119 74 90 53 tfor:TF3014|5end_oxidoreductase,_short-chain_dehydrogenase/reductase_family_3237623..3237853_POSITIVE 396 119 71 47 4 tfor:TF0684|5end_conserved_hypothetical_protein_728853..729083_POSITIVE 395 119 71 224 179 tfor:TF1889|5end_hypothetical_protein_2041479..2041709_POSITIVE 394 120 71 151 93 tfor:TF2158|5end_conserved_hypothetical_protein_2333857..2334087_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 431 119 71 83 27 tfor:TF0744|3end_DNA_polymerase_III_subunit,_gamma/tau_792308..792458_POSITIVE 414 120 74 149 95 tfor:TF2774|3end_2-amino-4-hydroxy-6-hydroxymethyldihydropteridine_pyrophosphokinase_2959719..2959869_POSITIVE 411 130 81 111 54 tfor:TF1322|3end_conserved_hypothetical_protein;_possible_surface_protein_1402567..1402717_POSITIVE 400 126 83 143 92 tfor:TF2746|3end_hypothetical_protein_2928246..2928396_POSITIVE 394 120 71 138 80 tfor:TF2157|3end_conserved_hypothetical_protein_2333924..2334074_POSITIVE 386 120 73 148 92 tfor:TF1918|3end_hypothetical_protein_2070105..2070255_POSITIVE 386 100 51 133 81 tfor:TF1553|3end_copper_homeostasis_protein_1659681..1659831_POSITIVE 384 129 88 90 48 tfor:TF1802|3end_conserved_hypothetical_protein_1946407..1946557_POSITIVE 383 140 92 67 18 tfor:TF2850|3end_endoribonuclease_L-PSP_3038871..3039021_POSITIVE 383 127 85 69 19 tfor:TF0300|3end_hypothetical_protein_325541..325691_POSITIVE 382 89 46 64 20 tfor:TF1934|3end_hypothetical_protein_2084079..2084229_POSITIVE 382 120 76 49 2 tfor:TF1436|3end_phosphoglycolate_phosphatase_1521867..1522017_POSITIVE 380 126 81 102 50 tfor:TF2593|3end_amino_acid_transport_protein_2764242..2764392_POSITIVE 380 100 51 77 13 tfor:TF1247|3end_alanyl-tRNA_synthetase_(alanine--tRNA_ligase)_1330928..1331078_POSITIVE 377 100 51 103 60 tfor:TF0880|3end_conserved_hypothetical_protein_934371..934521_POSITIVE 375 127 83 129 82 tfor:TF0419|3end_conserved_hypothetical_protein_435794..435944_POSITIVE 374 90 46 144 94 tfor:TF0538|3end_hypothetical_protein_567135..567285_POSITIVE 373 120 72 92 35 tfor:TF2726|3end_outer_membrane_protein,_possibly_involved_in_nutrient_binding_2903302..2903452_POSITIVE 373 118 74 149 101 tfor:TF0969|3end_oxidoreductase_1020439..1020589_POSITIVE 372 98 51 102 51 tfor:TF1400|3end_polysaccharide_biosynthesis_protein;_membrane_protein_1476573..1476723_POSITIVE