Origin IGS: tccatttcccacacaggctttcactaacggtttcactttggcgataccgtcaatcatggaaaaatcactgtgaacctgcaaatgaacgaaacgtggctgcgacataaaaatccttgggaaaaatcagacaaaagtgcggtgtattttagcggtattttacggggaattgtagggataatttgtcttgatgtcttgacgtaccgacacaataaatccctacaaaacgcagttttattgctagagttttgatcgttaatcggctatattagcgcacaactgttagctgattttggatttttaacc .........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 ggttaaaaatccaaaatcagctaacagttgtgcgctaatatagccgattaacgatcaaaactctagcaataaaactgcgttttgtagggatttattgtgtcggtacgtcaagacatcaagacaaattatccctacaattccccgtaaaataccgctaaaatacaccgcacttttgtctgatttttcccaaggatttttatgtcgcagccacgtttcgttcatttgcaggttcacagtgatttttccatgattgacggtatcgccaaagtgaaaccgttagtgaaagcctgtgtgggaaatgga Mask Tandem Repeat Region ================================================ tccatttcccacacaggctttcactaacggtttcactttggcgataccgtcaatcatggaaaaatcactgtgaacctgcaaatgaacgaaacgtggctgcgacataaaaatccttgggaaaaatcagacaaaagtgcggtgtattttagcggtattttacggggaattgtagggataatttgtcttgatgtcttgacgtaccgacacaataaatccctacaaaacgcagttttattgctagagttttgatcgttaatcggctatattagcgcacaactgttagctgattttggatttttaacc Find is-nt database================================================ Query_seq: AA00229:AA00231|AA00229:AA00231:DNA polymerase III, alpha subunit:long-chain-fatty-acid--CoA ligase:->->:160372..160674 303 tccatttcccacacaggctttcactaacggtttcactttggcgataccgtcaatcatggaaaaatcactgtgaacctgcaaatgaacgaaacgtggctgcgacataaaaatccttgggaaaaatcagacaaaagtgcggtgtattttagcggtattttacggggaattgtagggataatttgtcttgatgtcttgacgtaccgacacaataaatccctacaaaacgcagttttattgctagagttttgatcgttaatcggctatattagcgcacaactgttagctgattttggatttttaacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA00229:AA00231|AA00229:AA00231:DNA polymerase III, alpha subunit:long-chain-fatty-acid--CoA ligase:->->:160372..160674 303 tccatttcccacacaggctttcactaacggtttcactttggcgataccgtcaatcatggaaaaatcactgtgaacctgcaaatgaacgaaacgtggctgcgacataaaaatccttgggaaaaatcagacaaaagtgcggtgtattttagcggtattttacggggaattgtagggataatttgtcttgatgtcttgacgtaccgacacaataaatccctacaaaacgcagttttattgctagagttttgatcgttaatcggctatattagcgcacaactgttagctgattttggatttttaacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 1 Min: 1 Max: 105 Len: 105 Subject: gi|89107064|ref|AP_000844.1| DNA polymerase III alpha subunit [Escherichia coli W3110] HSP 1 e-value: 3.0E-8 bit: 53.9 Len: 105 Query Start:1 Query End:105 Subject Strand: null Subject Start: 1 Subject End: 35 M S Q P R F V H L Q V H S D F S M I D G I A K V K P L V K A C V G N G ...................................................................................................................................................................................................... M S E P R F V H L R V H S D Y S M I D G L A K T A P L V K K A A A L G ...................................................................................................................................................................................................... Find nr database================================================ Query_seq: AA00229:AA00231|AA00229:AA00231:DNA polymerase III, alpha subunit:long-chain-fatty-acid--CoA ligase:->->:160372..160674 303 nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnaaaaatccttgggaaaaatcagacaaaagtgcggtgtattttagcggtattttacggggaattgtagggataatttgtcttgatgtcttgacgtaccgacacaataaatccctacaaaacgcagttttattgctagagttttgatcgttaatcggctatattagcgcacaactgttagctgattttggatttttaacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnaaaaatccttgggaaaaatcagacaaaagtgcggtgtattttagcggtattttacggggaattgtagggataatttgtcttgatgtcttgacgtaccgacacaataaatccctacaaaacgcagttttattgctagagttttgatcgttaatcggctatattagcgcacaactgttagctgattttggatttttaacc Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 64 End: 246 ............................................................... M T V N L Q M N E T W L R H K N P W E K S D K S A V Y F S G I L R G I V G I I C L D V L T Y R H N K S L Q N A V L L L E ......................................................... Protein_Len: 34 Strand: - Start: 149 End: 250 .................................................................................................................................................... R Y K V P F Q L S L K D Q H R S T G V C Y I G V F R L K I A L T K M ..................................................... Protein_Len: 60 Strand: - Start: 57 End: 257 ........................................................ C I F S V H S R C L F G Q S F D S L L A T Y K L P I K R P I T P I I Q R S T K V Y R C L L D R C F A T K N S S N Q D N M .............................................. Protein_Len: 37 Strand: - Start: 1 End: 111 G N G V C A K V L P K V K A I G D I M S F D S H V Q L H V F R P Q S M F M ................................................................................................................................................................................................ nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnaaaaatccttgggaaaaatcagacaaaagtgcggtgtattttagcggtattttacggggaattgtagggataatttgtcttgatgtcttgacgtaccgacacaataaatccctacaaaacgcagttttattgctagagttttgatcgttaatcggctatattagcgcacaactgttagctgattttggatttttaacc 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================================================ nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnaaaaatccttgggaaaaatcagacaaaagtgcggtgtattttagcggtattttacggggaattgtagggataatttgtcttgatgtcttgacgtaccgacacaataaatccctacaaaacgcagttttattgctagagttttgatcgttaatcggctatattagcgcacaactgttagctgattttggatttttaacc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: AA00229:AA00231|AA00229:AA00231:DNA polymerase III, alpha subunit:long-chain-fatty-acid--CoA ligase:->->:160372..160674 303 nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnaaaaatccttgggaaaaatcagacaaaagtgcggtgtattttagcggtattttacggggaattgtagggataatttgtcttgatgtcttgacgtaccgacacaataaatccctacaaaacgcagttttattgctagagttttgatcgttaatcggctatattagcgcacaactgttagctgattttggatttttaacc Intra-Species Hit: Count: 1 Min: 106 Max: 303 Len: 198 Subject: aact_AA00229_AA00231|DNA polymerase III, alpha subunit:long-chain-fatty-acid--CoA ligase|POSITIVE:POSITIVE|[160372,160674]|303 HSP 1 e-value: 1.0E-108 bit: 392.0 Len: 198 Query Start:106 Query End:303 Subject Strand: POSITIVE Subject Start: 106 Subject End: 303 .........................................................................................................aaaaatccttgggaaaaatcagacaaaagtgcggtgtattttagcggtattttacggggaattgtagggataatttgtcttgatgtcttgacgtaccgacacaataaatccctacaaaacgcagttttattgctagagttttgatcgttaatcggctatattagcgcacaactgttagctgattttggatttttaacc .........................................................................................................aaaaatccttgggaaaaatcagacaaaagtgcggtgtattttagcggtattttacggggaattgtagggataatttgtcttgatgtcttgacgtaccgacacaataaatccctacaaaacgcagttttattgctagagttttgatcgttaatcggctatattagcgcacaactgttagctgattttggatttttaacc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAAUCCUUGGGAAAAAUCAGACAAAAGUGCGGUGUAUUUUAGCGGUAUUUUACGGGGAAUUGUAGGGAUAAUUUGUCUUGAUGUCUUGACGUACCGACACAAUAAAUCCCUACAAAACGCAGUUUUAUUGCUAGAGUUUUGAUCGUUAAUCGGCUAUAUUAGCGCACAACUGUUAGCUGAUUUUGGAUUUUUAACC ((((((((......(((((((((((...(((((.((.((((((((((((....((.(.(..((((((((((.(((((((...((((....))))...)))).)))..))))))))))..).).))..))))))))))))..((..((.....))..))...)).)))))...)))...)))))))))))))))).... (-55.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGUUAAAAAUCCAAAAUCAGCUAACAGUUGUGCGCUAAUAUAGCCGAUUAACGAUCAAAACUCUAGCAAUAAAACUGCGUUUUGUAGGGAUUUAUUGUGUCGGUACGUCAAGACAUCAAGACAAAUUAUCCCUACAAUUCCCCGUAAAAUACCGCUAAAAUACACCGCACUUUUGUCUGAUUUUUCCCAAGGAUUUUU ....((((((((((((((((...((((..(((((......((((.((((.(((............(((.......)))...((((((((((......((((.....((....)).....))))....)))))))))).....)))..))).).))))........)))))..))))))))))))......)))))))) (-47.74) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 385 66 21 172 116 aact:AA01564|5end_transaldolase_B_1049099..1049329_POSITIVE 379 59 12 231 185 aact:AA02195|5end_oxaloacetate_decarboxylase_alpha_chain_1494501..1494731_POSITIVE 361 59 17 136 93 aact:AA01453|5end_D-xylose_isomerase_973457..973687_POSITIVE 360 70 21 201 153 aact:AA00711|5end_conserved_hypothetical_protein_487893..488123_POSITIVE 360 61 22 153 107 aact:AA00174|5end_ribosomal_protein_L11_methyltransferase_123072..123302_POSITIVE 360 61 22 49 3 aact:AA00173|5end_hypothetical_protein_122968..123198_POSITIVE 349 70 25 151 93 aact:AA02231|5end_probable_dethiobiotin_synthetase_1_1517650..1517880_POSITIVE 346 167 121 231 183 aact:AA01572|5end_peptide_ABC_transporter,_permease_protein_1058796..1059026_POSITIVE 334 48 11 127 96 aact:AA00789|5end_DNA_topoisomerase_III_540486..540716_POSITIVE 331 66 21 169 111 aact:AA01666|5end_penicillin-binding_protein_4;_D-alanyl-D-alanine_carboxypeptidase;_D-alanyl-D-alanine-endopeptidase_1128231..1128461_POSITIVE 323 60 24 190 153 aact:AA00501|5end_hypothetical_protein_347293..347523_POSITIVE 323 60 24 48 11 aact:AA00500|5end_hypothetical_protein_347151..347381_POSITIVE 320 100 54 206 152 aact:AA02297|5end_conserved_hypothetical_protein_1569620..1569850_POSITIVE 320 100 54 206 152 aact:AA00621|5end_conserved_hypothetical_protein_428727..428957_POSITIVE 318 47 7 74 40 aact:AA00264|5end_hypothetical_protein_185052..185282_POSITIVE 317 56 19 176 138 aact:AA02509|5end_chorismate_synthase_1740952..1741182_POSITIVE 314 70 29 227 178 aact:AA01079|5end_conserved_hypothetical_protein_747404..747634_POSITIVE 314 58 11 163 118 aact:AA00145|5end_probable_degenerate_transposase_fragment_105046..105276_POSITIVE 313 70 25 144 101 aact:AA02418|5end_peptidyl-tRNA_hydrolase_1661090..1661320_POSITIVE 312 100 51 198 154 aact:AA00776|5end_conserved_hypothetical_protein_533496..533726_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 361 59 17 83 40 aact:AA01451|3end_D-xylulokinase_973484..973634_POSITIVE 360 70 21 66 18 aact:AA00709|3end_metallocluster_assembly_(NifU_protein)_487838..487988_POSITIVE 360 61 22 138 92 aact:AA00173|3end_hypothetical_protein_123137..123287_POSITIVE 341 60 13 110 61 aact:AA02253|3end_hypothetical_protein_1534786..1534936_POSITIVE 331 66 21 62 4 aact:AA01663|3end_GTP_cyclohydrolase_I_1128204..1128354_POSITIVE 329 48 9 72 35 aact:AA00221|3end_NADP-specific_glutamate_dehydrogenase_153865..154015_POSITIVE 323 60 24 96 59 aact:AA00499|3end_pyridoxamine-5'-phosphate_oxidase_347279..347429_POSITIVE 318 47 7 37 3 aact:AA00263|3end_ATP-dependent_RNA_helicase_185095..185245_POSITIVE 317 56 19 151 113 aact:AA02507|3end_penicillin-insensitive_murein_endopeptidase_A_1741007..1741157_POSITIVE 314 176 133 104 70 aact:AA01317|3end_probable_DNA_repair_protein_891739..891889_POSITIVE 311 61 24 86 47 aact:AA02616|3end_transcriptional_regulator_1824675..1824825_POSITIVE 308 167 126 94 51 aact:AA01351|3end_probable_sulfatase_916393..916543_POSITIVE 299 65 25 98 61 aact:AA00383|3end_chloride_channel_protein_260182..260332_POSITIVE 298 66 24 70 19 aact:AA02246|3end_peptidase_E_1528355..1528505_POSITIVE 297 58 18 81 43 aact:AA01957|3end_conserved_hypothetical_protein_1323467..1323617_POSITIVE 292 59 25 80 44 aact:AA00417|3end_outer_membrane_lipoprotein_precursor_(probable_D-methionine-binding_lipoprotein)_284308..284458_POSITIVE 291 48 6 94 52 aact:AA02063|3end_23S_rRNA_psedouridine_synthase,_Rlu_family_protein_1405217..1405367_POSITIVE 290 79 33 44 1 aact:AA02230|3end_sugar_kinase_1517617..1517767_POSITIVE 285 70 28 83 32 aact:AA02984|3end_formate_transporter_2088534..2088684_POSITIVE 285 57 26 83 51 aact:AA02409|3end_DNA_ligase_1655404..1655554_POSITIVE