Origin IGS: taagtaaatgtgtaatagtggtttagtatttgtgctttttagtatgttgtatcactgcgttatggtagagtgagacccttgatctatgcgcgcctctgtaaagaaaacgaccgataatataatagtgttgaataaaacaaaataaaatatattttaactaattatttgtgttttttaatacggtggatttgcataagatacttggcgggtgtacctttgcggccattaacttaaatatatttaatt .........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 aattaaatatatttaagttaatggccgcaaaggtacacccgccaagtatcttatgcaaatccaccgtattaaaaaacacaaataattagttaaaatatattttattttgttttattcaacactattatattatcggtcgttttctttacagaggcgcgcatagatcaagggtctcactctaccataacgcagtgatacaacatactaaaaagcacaaatactaaaccactattacacatttactta Mask Tandem Repeat Region ================================================ taagtaaatgtgtaatagtggtttagtatttgtgctttttagtatgttgtatcactgcgttatggtagagtgagacccttgatctatgcgcgcctctgtaaagaaaacgaccgataatataatagtgttgaataaaacaaaataaaatatattttaactaattatttgtgttttttaatacggtggatttgcataagatacttggcgggtgtacctttgcggccattaacttaaatatatttaatt Find is-nt database================================================ Query_seq: TF3079:TF3080|TF3079:TF3080:ribonucleoside-diphosphate reductase 1, beta subunit:conserved hypothetical protein:->->:3310374..3310619 246 taagtaaatgtgtaatagtggtttagtatttgtgctttttagtatgttgtatcactgcgttatggtagagtgagacccttgatctatgcgcgcctctgtaaagaaaacgaccgataatataatagtgttgaataaaacaaaataaaatatattttaactaattatttgtgttttttaatacggtggatttgcataagatacttggcgggtgtacctttgcggccattaacttaaatatatttaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF3079:TF3080|TF3079:TF3080:ribonucleoside-diphosphate reductase 1, beta subunit:conserved hypothetical protein:->->:3310374..3310619 246 taagtaaatgtgtaatagtggtttagtatttgtgctttttagtatgttgtatcactgcgttatggtagagtgagacccttgatctatgcgcgcctctgtaaagaaaacgaccgataatataatagtgttgaataaaacaaaataaaatatattttaactaattatttgtgttttttaatacggtggatttgcataagatacttggcgggtgtacctttgcggccattaacttaaatatatttaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF3079:TF3080|TF3079:TF3080:ribonucleoside-diphosphate reductase 1, beta subunit:conserved hypothetical protein:->->:3310374..3310619 246 taagtaaatgtgtaatagtggtttagtatttgtgctttttagtatgttgtatcactgcgttatggtagagtgagacccttgatctatgcgcgcctctgtaaagaaaacgaccgataatataatagtgttgaataaaacaaaataaaatatattttaactaattatttgtgttttttaatacggtggatttgcataagatacttggcgggtgtacctttgcggccattaacttaaatatatttaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taagtaaatgtgtaatagtggtttagtatttgtgctttttagtatgttgtatcactgcgttatggtagagtgagacccttgatctatgcgcgcctctgtaaagaaaacgaccgataatataatagtgttgaataaaacaaaataaaatatattttaactaattatttgtgttttttaatacggtggatttgcataagatacttggcgggtgtacctttgcggccattaacttaaatatatttaatt Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 142 End: 231 ............................................................................................................................................. M K Y I L T N Y L C F L I R W I C I R Y L A G V P L R P L T ............... Protein_Len: 32 Strand: - Start: 55 End: 150 ...................................................... Q T I T S H S G Q D I R A E T F F V V S L I I T N F L V F Y F M ................................................................................................ Protein_Len: 41 Strand: - Start: 26 End: 148 ......................... Y K H K K T H Q I V A N H Y L S V R S R H A G R Y L F R G I I Y Y H Q I F C F L M .................................................................................................. taagtaaatgtgtaatagtggtttagtatttgtgctttttagtatgttgtatcactgcgttatggtagagtgagacccttgatctatgcgcgcctctgtaaagaaaacgaccgataatataatagtgttgaataaaacaaaataaaatatattttaactaattatttgtgttttttaatacggtggatttgcataagatacttggcgggtgtacctttgcggccattaacttaaatatatttaatt 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================================================ taagtaaatgtgtaatagtggtttagtatttgtgctttttagtatgttgtatcactgcgttatggtagagtgagacccttgatctatgcgcgcctctgtaaagaaaacgaccgataatataatagtgttgaataaaacaaaataaaatatattttaactaattatttgtgttttttaatacggtggatttgcataagatacttggcgggtgtacctttgcggccattaacttaaatatatttaatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF3079:TF3080|TF3079:TF3080:ribonucleoside-diphosphate reductase 1, beta subunit:conserved hypothetical protein:->->:3310374..3310619 246 taagtaaatgtgtaatagtggtttagtatttgtgctttttagtatgttgtatcactgcgttatggtagagtgagacccttgatctatgcgcgcctctgtaaagaaaacgaccgataatataatagtgttgaataaaacaaaataaaatatattttaactaattatttgtgttttttaatacggtggatttgcataagatacttggcgggtgtacctttgcggccattaacttaaatatatttaatt Intra-Species Hit: Count: 1 Min: 1 Max: 246 Len: 246 Subject: tfor_TF3079_TF3080|ribonucleoside-diphosphate reductase 1, beta subunit:conserved hypothetical protein|POSITIVE:POSITIVE|[3310374,3310619]|246 HSP 1 e-value: 1.0E-137 bit: 488.0 Len: 246 Query Start:1 Query End:246 Subject Strand: POSITIVE Subject Start: 1 Subject End: 246 taagtaaatgtgtaatagtggtttagtatttgtgctttttagtatgttgtatcactgcgttatggtagagtgagacccttgatctatgcgcgcctctgtaaagaaaacgaccgataatataatagtgttgaataaaacaaaataaaatatattttaactaattatttgtgttttttaatacggtggatttgcataagatacttggcgggtgtacctttgcggccattaacttaaatatatttaatt taagtaaatgtgtaatagtggtttagtatttgtgctttttagtatgttgtatcactgcgttatggtagagtgagacccttgatctatgcgcgcctctgtaaagaaaacgaccgataatataatagtgttgaataaaacaaaataaaatatattttaactaattatttgtgttttttaatacggtggatttgcataagatacttggcgggtgtacctttgcggccattaacttaaatatatttaatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGUAAAUGUGUAAUAGUGGUUUAGUAUUUGUGCUUUUUAGUAUGUUGUAUCACUGCGUUAUGGUAGAGUGAGACCCUUGAUCUAUGCGCGCCUCUGUAAAGAAAACGACCGAUAAUAUAAUAGUGUUGAAUAAAACAAAAUAAAAUAUAUUUUAACUAAUUAUUUGUGUUUUUUAAUACGGUGGAUUUGCAUAAGAUACUUGGCGGGUGUACCUUUGCGGCCAUUAACUUAAAUAUAUUUAAUU (((((.((((.((..(((((((.(((....((((((....))))))))).))))))).......((((((..(.(((((..(((((((((..((.(((((.(((((((.((.((((((....((((...(((((...............)))))..)))))))))).)))))))))..))))).))...))))).)))...)..).)))).)..)))))).)))))).)))))............. (-52.86) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUAAAUAUAUUUAAGUUAAUGGCCGCAAAGGUACACCCGCCAAGUAUCUUAUGCAAAUCCACCGUAUUAAAAAACACAAAUAAUUAGUUAAAAUAUAUUUUAUUUUGUUUUAUUCAACACUAUUAUAUUAUCGGUCGUUUUCUUUACAGAGGCGCGCAUAGAUCAAGGGUCUCACUCUACCAUAACGCAGUGAUACAACAUACUAAAAAGCACAAAUACUAAACCACUAUUACACAUUUACUUA .............(((((.((((...((...(((......)))..(((((...(((.........(((....(((((((..((((((((((((((((..........)))))))......))))....)))))..)).)))))...))).(((((.(...........).))))).............)))..))))).............))...((((.........))))...)))).))))) (-34.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 408 99 53 118 75 tfor:TF2045|5end_aminoacyl-histidine_dipeptidase_2206114..2206344_POSITIVE 386 220 176 140 92 tfor:TF2031|5end_conserved_hypothetical_protein_2186605..2186835_POSITIVE 362 100 58 187 143 tfor:TF0754|5end_GDP-4-keto-6-deoxy-D-mannose-3,5-epimerase-4-redu_ctase_(GDP-L-fucose_synthetase)_801631..801861_POSITIVE 353 105 71 144 110 tfor:TF3061|5end_conserved_hypothetical_protein_3285022..3285252_POSITIVE 337 222 181 44 1 tfor:TF0910|5end_Tn5520-like_integrase_(transfer_factor)_952499..952729_POSITIVE 331 100 54 200 150 tfor:TF2611|5end_conserved_hypothetical_protein_2787204..2787434_POSITIVE 331 100 55 229 179 tfor:TF1909|5end_cobalamin_(5`-phosphate)_synthase_2063207..2063437_POSITIVE 324 230 181 190 137 tfor:TF2191|5end_hypothetical_protein_2365934..2366164_POSITIVE 321 225 182 163 111 tfor:TF1919|5end_hypothetical_protein_2070037..2070267_POSITIVE 321 225 182 123 71 tfor:TF1917|5end_hypothetical_protein_2069997..2070227_POSITIVE 321 227 181 206 163 tfor:TF0152|5end_RNA_polymerase_ECF-type_sigma_factor_162021..162251_POSITIVE 317 230 181 80 19 tfor:TF1963|5end_hypothetical_protein_2113359..2113589_POSITIVE 317 99 55 60 14 tfor:TF0414|5end_N-ethylammeline_chlorohydrolase_431789..432019_POSITIVE 314 98 53 214 165 tfor:TF3014|5end_oxidoreductase,_short-chain_dehydrogenase/reductase_family_3237623..3237853_POSITIVE 314 224 181 152 108 tfor:TF2849|5end_histidinol-phosphate_transaminase_3037288..3037518_POSITIVE 311 220 182 229 188 tfor:TF1863|5end_Fe-S_oxidoreductase_2018820..2019050_POSITIVE 311 226 181 228 189 tfor:TF1049|5end_cobyrinic_acid_a,c-diamide_synthase_1110140..1110370_POSITIVE 311 226 181 207 151 tfor:TF0425|5end_outer_membrane_protein_443069..443299_POSITIVE 310 99 52 137 81 tfor:TF2047|5end_hypothetical_protein_2210057..2210287_POSITIVE 310 93 56 158 107 tfor:TF1947|5end_conserved_hypothetical_protein_2095521..2095751_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 408 99 53 87 44 tfor:TF2044|3end_excinuclease_ABC,_subunit_A_2206163..2206313_POSITIVE 338 225 182 117 72 tfor:TF1862|3end_hypothetical_protein_2018784..2018934_POSITIVE 321 225 182 151 99 tfor:TF1918|3end_hypothetical_protein_2070105..2070255_POSITIVE 317 99 55 60 14 tfor:TF0413|3end_succinyl-diaminopimelate_desuccinylase_431869..432019_POSITIVE 314 98 53 50 1 tfor:TF3013|3end_conserved_hypothetical_protein_3237539..3237689_POSITIVE 313 94 52 108 61 tfor:TF1841|3end_hypothetical_protein_1992267..1992417_POSITIVE 303 225 181 149 105 tfor:TF1954|3end_long-chain-fatty-acid--CoA_ligase_2106940..2107090_POSITIVE 301 223 181 147 89 tfor:TF0961|3end_translation_initiation_inhibitor,_endoribonuclease_activity_1011673..1011823_POSITIVE 299 223 181 56 13 tfor:TF2150|3end_Na+/phosphate_symporter_2326655..2326805_POSITIVE 299 230 181 148 102 tfor:TF0528|3end_two-component_system_sensor_histidine_kinase_554779..554929_POSITIVE 298 224 181 49 3 tfor:TF2437|3end_elongation_factor_P_2615744..2615894_POSITIVE 297 223 181 69 24 tfor:TF1680|3end_peptide_chain_release_factor_3_1794969..1795119_POSITIVE 294 223 181 135 89 tfor:TF2373|3end_UDP-3-O-acyl-GlcNAc_deacetylase_2539806..2539956_POSITIVE 294 226 188 143 108 tfor:TF2271|3end_conserved_hypothetical_protein_2436187..2436337_POSITIVE 294 98 52 151 96 tfor:TF2046|3end_polyribonucleotide_nucleotidyltransferase_2210152..2210302_POSITIVE 294 223 181 135 89 tfor:TF1496|3end_tyrosyl-tRNA_synthetase_1596069..1596219_POSITIVE 292 224 181 61 8 tfor:TF0355|3end_transposase_element_373487..373637_POSITIVE 290 97 54 70 29 tfor:TF1729|3end_aspartokinase_1854718..1854868_POSITIVE 288 99 55 123 74 tfor:TF1832|3end_3-isopropylmalate_dehydratase,_small_subunit_1981502..1981652_POSITIVE 287 99 52 65 15 tfor:TF1756|3end_chromosome_partitioning_ATPase,_ParA_family_1893919..1894069_POSITIVE