Origin IGS: taatttgatttaaactccaaacgccattttcaaaggaaagtggcgttttgctttgttatatcttattgcgaagcctattttccttattggttaacacccgatataatagttccattatcgattcaaaggactaactgatgcttgaaatgcttcctttcaccttgcctgaagtaggagca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgctcctacttcaggcaaggtgaaaggaagcatttcaagcatcagttagtcctttgaatcgataatggaactattatatcgggtgttaaccaataaggaaaataggcttcgcaataagatataacaaagcaaaacgccactttcctttgaaaatggcgtttggagtttaaatcaaatta Mask Tandem Repeat Region ================================================ taatttgatttaaactccaaacgccattttcaaaggaaagtggcgttttgctttgttatatcttattgcgaagcctattttccttattggttaacacccgatataatagttccattatcgattcaaaggactaactgatgcttgaaatgcttcctttcaccttgcctgaagtaggagca Find is-nt database================================================ Query_seq: AA02351:AA02352|AA02351:AA02352:conserved hypothetical protein:glycine betaine/carnitine/choline ABC transporter:->->:1609529..1609707 179 taatttgatttaaactccaaacgccattttcaaaggaaagtggcgttttgctttgttatatcttattgcgaagcctattttccttattggttaacacccgatataatagttccattatcgattcaaaggactaactgatgcttgaaatgcttcctttcaccttgcctgaagtaggagca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA02351:AA02352|AA02351:AA02352:conserved hypothetical protein:glycine betaine/carnitine/choline ABC transporter:->->:1609529..1609707 179 taatttgatttaaactccaaacgccattttcaaaggaaagtggcgttttgctttgttatatcttattgcgaagcctattttccttattggttaacacccgatataatagttccattatcgattcaaaggactaactgatgcttgaaatgcttcctttcaccttgcctgaagtaggagca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA02351:AA02352|AA02351:AA02352:conserved hypothetical protein:glycine betaine/carnitine/choline ABC transporter:->->:1609529..1609707 179 taatttgatttaaactccaaacgccattttcaaaggaaagtggcgttttgctttgttatatcttattgcgaagcctattttccttattggttaacacccgatataatagttccattatcgattcaaaggactaactgatgcttgaaatgcttcctttcaccttgcctgaagtaggagca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taatttgatttaaactccaaacgccattttcaaaggaaagtggcgttttgctttgttatatcttattgcgaagcctattttccttattggttaacacccgatataatagttccattatcgattcaaaggactaactgatgcttgaaatgcttcctttcaccttgcctgaagtaggagca Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 40 End: 135 ....................................... M A F C F V I S Y C E A Y F P Y W L T P D I I V P L S I Q R T N ............................................ taatttgatttaaactccaaacgccattttcaaaggaaagtggcgttttgctttgttatatcttattgcgaagcctattttccttattggttaacacccgatataatagttccattatcgattcaaaggactaactgatgcttgaaatgcttcctttcaccttgcctgaagtaggagca Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: + Score: 86 Start: 78 End: 107 .............................................................................TTTTCCTTATTGGTTAACACCCGATATAAT........................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taatttgatttaaactccaaacgccattttcaaaggaaagtggcgttttgctttgttatatcttattgcgaagcctattttccttattggttaacacccgatataatagttccattatcgattcaaaggactaactgatgcttgaaatgcttcctttcaccttgcctgaagtaggagca Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 83 HP_score: -9.6 Tail_Score: -3.72363 Start: 22 End: 45 Full_Region: tataacaaagcaaaa cgccactttc cttt gaaaatggcg tttggagtttaaatc .....................cgccactttcctttgaaaatggcg...................................................................................................................................... Find igs database================================================ Query_seq: AA02351:AA02352|AA02351:AA02352:conserved hypothetical protein:glycine betaine/carnitine/choline ABC transporter:->->:1609529..1609707 179 taatttgatttaaactccaaacgccattttcaaaggaaagtggcgttttgctttgttatatcttattgcgaagcctattttccttattggttaacacccgatataatagttccattatcgattcaaaggactaactgatgcttgaaatgcttcctttcaccttgcctgaagtaggagca Intra-Species Hit: Count: 1 Min: 1 Max: 179 Len: 179 Subject: aact_AA02351_AA02352|conserved hypothetical protein:glycine betaine/carnitine/choline ABC transporter|POSITIVE:POSITIVE|[1609529,1609707]|179 HSP 1 e-value: 3.0E-97 bit: 355.0 Len: 179 Query Start:1 Query End:179 Subject Strand: POSITIVE Subject Start: 1 Subject End: 179 taatttgatttaaactccaaacgccattttcaaaggaaagtggcgttttgctttgttatatcttattgcgaagcctattttccttattggttaacacccgatataatagttccattatcgattcaaaggactaactgatgcttgaaatgcttcctttcaccttgcctgaagtaggagca taatttgatttaaactccaaacgccattttcaaaggaaagtggcgttttgctttgttatatcttattgcgaagcctattttccttattggttaacacccgatataatagttccattatcgattcaaaggactaactgatgcttgaaatgcttcctttcaccttgcctgaagtaggagca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUUUGAUUUAAACUCCAAACGCCAUUUUCAAAGGAAAGUGGCGUUUUGCUUUGUUAUAUCUUAUUGCGAAGCCUAUUUUCCUUAUUGGUUAACACCCGAUAUAAUAGUUCCAUUAUCGAUUCAAAGGACUAACUGAUGCUUGAAAUGCUUCCUUUCACCUUGCCUGAAGUAGGAGCA ..................(((((((((((((....))))))))))))).(((((((.(((...))).)))))))..........((((((.......)))))).....(((((....((((.....((......)).....))))..((((((..............))))))))))). (-40.24) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGCUCCUACUUCAGGCAAGGUGAAAGGAAGCAUUUCAAGCAUCAGUUAGUCCUUUGAAUCGAUAAUGGAACUAUUAUAUCGGGUGUUAACCAAUAAGGAAAAUAGGCUUCGCAAUAAGAUAUAACAAAGCAAAACGCCACUUUCCUUUGAAAAUGGCGUUUGGAGUUUAAAUCAAAUUA .(((((..(((...((.((((.....((.((.......)).))......(((((.......((((((....))))))....(((....)))...)))))......)))).))...))).............((((((((.((((....)))).)))))))))))))............. (-36.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 293 57 17 102 61 aact:AA00603|5end_undecaprenyl_pyrophosphate_synthetase_(UPPS)_410283..410513_POSITIVE 293 74 31 86 41 aact:AA00240|5end_hypothetical_protein_171390..171620_POSITIVE 283 70 22 55 11 aact:AA00387|5end_transcription_regulatory_protein_262305..262535_POSITIVE 278 104 68 60 6 aact:AA02787|5end_ribose_ABC_transporter,_sugar_binding_protein_1954386..1954616_POSITIVE 276 70 21 99 57 aact:AA00250|5end_lipoate_biosynthesis_protein_A_175496..175726_POSITIVE 273 51 16 209 168 aact:AA00887|5end_hypothetical_protein_616739..616969_POSITIVE 273 51 16 54 13 aact:AA00886|5end_hypothetical_protein_616584..616814_POSITIVE 270 51 12 223 189 aact:AA02472|5end_conserved_hypothetical_protein_1707631..1707861_POSITIVE 263 165 131 165 126 aact:AA01274|5end_hypothetical_protein_864519..864749_POSITIVE 263 69 25 89 37 aact:AA01028|5end_Na(+)-translocating_NADH-quinone_reductase_subunit_E_718923..719153_POSITIVE 262 100 51 60 11 aact:AA01755|5end_cobalt_membrane_transport_protein_1185825..1186055_POSITIVE 260 130 87 65 27 aact:AA01837|5end_transcriptional_regulatory_protein_1235450..1235680_POSITIVE 258 58 35 167 143 aact:AA02801|5end_myo-inositol_catabolism_protein_1968100..1968330_POSITIVE 256 57 14 73 26 aact:AA01340|5end_possible_lipoprotein;_possible_HlyD_family_secretion_domain_protein;_possible_membrane_fusion_protein_905746..905976_POSITIVE 256 170 121 173 112 aact:AA00784|5end_hypothetical_protein_539025..539255_POSITIVE 254 51 14 206 170 aact:AA01169|5end_hypothetical_protein_801985..802215_POSITIVE 253 158 112 69 22 aact:AA02293|5end_hypothetical_protein_1563531..1563761_POSITIVE 252 169 135 43 6 aact:AA00652|5end_arginyl-tRNA_synthetase_(arginine--tRNA_ligase)_445718..445948_POSITIVE 249 89 41 229 184 aact:AA01253|5end_hypothetical_protein_852189..852419_POSITIVE 249 89 41 63 18 aact:AA01252|5end_conserved_hypothetical_protein_(probable_SirA_homolog)_852023..852253_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 328 48 19 72 43 aact:AA02351|3end_conserved_hypothetical_protein_1609468..1609618_POSITIVE 273 51 16 49 8 aact:AA00885|3end_ribosomal_large_subunit_pseudouridine_synthase_c_616659..616809_POSITIVE 265 70 22 103 52 aact:AA01911|3end_hypothetical_protein_1288284..1288434_POSITIVE 263 69 25 74 22 aact:AA01027|3end_Na(+)-translocating_NADH-quinone_reductase_subunit_F_718988..719138_POSITIVE 262 100 51 57 8 aact:AA01753|3end_conserved_hypothetical_protein_1185902..1186052_POSITIVE 258 58 35 109 85 aact:AA02800|3end_probable_malonic_semialdehyde_oxidative_decarboxylase_1968122..1968272_POSITIVE 251 127 83 120 77 aact:AA00977|3end_transcriptional_regulator_(LysR_family)_683334..683484_POSITIVE 249 53 18 50 14 aact:AA00309|3end_3-hydroxyisobutyrate_dehydrogenase;_2-hydroxy-3-oxopropionate_reductase_210267..210417_POSITIVE 245 170 136 74 41 aact:AA01204|3end_hypothetical_protein_825196..825346_POSITIVE 244 90 42 85 40 aact:AA02707|3end_hypothetical_protein_1889931..1890081_POSITIVE 244 110 65 65 21 aact:AA02598|3end_long-chain-fatty-acid-CoA_ligase_1810117..1810267_POSITIVE 243 165 126 82 37 aact:AA02763|3end_DNA_polymerase_III,_epsilon_subunit_1934477..1934627_POSITIVE 237 167 131 151 115 aact:AA01273|3end_hypothetical_protein_864588..864738_POSITIVE 236 169 126 121 77 aact:AA02525|3end_conserved_hypothetical_protein_1755302..1755452_POSITIVE 233 57 17 138 101 aact:AA00442|3end_conserved_hypothetical_protein_(possible_zinc_finger_protein)_307681..307831_POSITIVE 232 57 21 46 11 aact:AA02490|3end_hypothetical_protein_1726896..1727046_POSITIVE 232 70 22 100 35 aact:AA02196|3end_oxaloacetate_decarboxylase_beta_chain_1497692..1497842_POSITIVE 232 166 121 144 86 aact:AA01519.1|3end_conserved_hypothetical_protein_1022920..1023070_POSITIVE 232 166 121 111 53 aact:AA01520|3end_hypothetical_protein_1022887..1023037_POSITIVE 230 69 22 151 94 aact:AA02103|3end_D-alanyl-D-alanine-endopeptidase;_penicillin-binding_protein_7_1431784..1431934_POSITIVE