Origin IGS: accgatttccttcccttttggcgtgtaataggcacgtaaataaattcggggaattataaagaaaaaaatccgatttttatagagctactgtctagaattcagctgccttacagcaacatagataaacaaaatttctacaatcagaagctgaaacgataaattcactccataaaattattgtttttgtgagaattatcacattaattctgaaaaaatttcgttaatattcttcataacctaaaacaaaatgccaacgcaggttggcattaaatttttatatctcatggacaattaaagaggttattcgt .........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 acgaataacctctttaattgtccatgagatataaaaatttaatgccaacctgcgttggcattttgttttaggttatgaagaatattaacgaaattttttcagaattaatgtgataattctcacaaaaacaataattttatggagtgaatttatcgtttcagcttctgattgtagaaattttgtttatctatgttgctgtaaggcagctgaattctagacagtagctctataaaaatcggatttttttctttataattccccgaatttatttacgtgcctattacacgccaaaagggaaggaaatcggt Mask Tandem Repeat Region ================================================ accgatttccttcccttttggcgtgtaataggcacgtaaataaattcggggaattataaagaaaaaaatccgatttttatagagctactgtctagaattcagctgccttacagcaacatagataaacaaaatttctacaatcagaagctgaaacgataaattcactccataaaattattgtttttgtgagaattatcacattaattctgaaaaaatttcgttaatattcttcataacctaaaacaaaatgccaacgcaggttggcattaaatttttatatctcatggacaattaaagaggttattcgt Find is-nt database================================================ Query_seq: AA00695:AA00696|AA00695:AA00696:uridine kinase:iron(III) ABC transporter, periplasmic iron-compound-binding protein:->->:475821..476128 308 accgatttccttcccttttggcgtgtaataggcacgtaaataaattcggggaattataaagaaaaaaatccgatttttatagagctactgtctagaattcagctgccttacagcaacatagataaacaaaatttctacaatcagaagctgaaacgataaattcactccataaaattattgtttttgtgagaattatcacattaattctgaaaaaatttcgttaatattcttcataacctaaaacaaaatgccaacgcaggttggcattaaatttttatatctcatggacaattaaagaggttattcgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA00695:AA00696|AA00695:AA00696:uridine kinase:iron(III) ABC transporter, periplasmic iron-compound-binding protein:->->:475821..476128 308 accgatttccttcccttttggcgtgtaataggcacgtaaataaattcggggaattataaagaaaaaaatccgatttttatagagctactgtctagaattcagctgccttacagcaacatagataaacaaaatttctacaatcagaagctgaaacgataaattcactccataaaattattgtttttgtgagaattatcacattaattctgaaaaaatttcgttaatattcttcataacctaaaacaaaatgccaacgcaggttggcattaaatttttatatctcatggacaattaaagaggttattcgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA00695:AA00696|AA00695:AA00696:uridine kinase:iron(III) ABC transporter, periplasmic iron-compound-binding protein:->->:475821..476128 308 accgatttccttcccttttggcgtgtaataggcacgtaaataaattcggggaattataaagaaaaaaatccgatttttatagagctactgtctagaattcagctgccttacagcaacatagataaacaaaatttctacaatcagaagctgaaacgataaattcactccataaaattattgtttttgtgagaattatcacattaattctgaaaaaatttcgttaatattcttcataacctaaaacaaaatgccaacgcaggttggcattaaatttttatatctcatggacaattaaagaggttattcgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 accgatttccttcccttttggcgtgtaataggcacgtaaataaattcggggaattataaagaaaaaaatccgatttttatagagctactgtctagaattcagctgccttacagcaacatagataaacaaaatttctacaatcagaagctgaaacgataaattcactccataaaattattgtttttgtgagaattatcacattaattctgaaaaaatttcgttaatattcttcataacctaaaacaaaatgccaacgcaggttggcattaaatttttatatctcatggacaattaaagaggttattcgt Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: + Start: 40 End: 156 ....................................... M N S G N Y K E K N P I F I E L L S R I Q L P Y S N I D K Q N F Y N Q K L K R ........................................................................................................................................................ Protein_Len: 37 Strand: - Start: 95 End: 205 .............................................................................................. F E A A K C C C L Y V F N R C D S A S V I F E S W L I I T K T L I I V N M ....................................................................................................... accgatttccttcccttttggcgtgtaataggcacgtaaataaattcggggaattataaagaaaaaaatccgatttttatagagctactgtctagaattcagctgccttacagcaacatagataaacaaaatttctacaatcagaagctgaaacgataaattcactccataaaattattgtttttgtgagaattatcacattaattctgaaaaaatttcgttaatattcttcataacctaaaacaaaatgccaacgcaggttggcattaaatttttatatctcatggacaattaaagaggttattcgt 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: 83 Start: 53 End: 82 ....................................................CTATAAAAATCGGATTTTTTTCTTTATAAT.................................................................................................................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ accgatttccttcccttttggcgtgtaataggcacgtaaataaattcggggaattataaagaaaaaaatccgatttttatagagctactgtctagaattcagctgccttacagcaacatagataaacaaaatttctacaatcagaagctgaaacgataaattcactccataaaattattgtttttgtgagaattatcacattaattctgaaaaaatttcgttaatattcttcataacctaaaacaaaatgccaacgcaggttggcattaaatttttatatctcatggacaattaaagaggttattcgt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -9.9 Tail_Score: -5.13343 Start: 249 End: 266 Full_Region: gatataaaaatttaa tgccaac ctgc gttggca ttttgttttaggtta ........................................................................................................................................................................................................................................................tgccaacctgcgttggca.......................................... Find igs database================================================ Query_seq: AA00695:AA00696|AA00695:AA00696:uridine kinase:iron(III) ABC transporter, periplasmic iron-compound-binding protein:->->:475821..476128 308 accgatttccttcccttttggcgtgtaataggcacgtaaataaattcggggaattataaagaaaaaaatccgatttttatagagctactgtctagaattcagctgccttacagcaacatagataaacaaaatttctacaatcagaagctgaaacgataaattcactccataaaattattgtttttgtgagaattatcacattaattctgaaaaaatttcgttaatattcttcataacctaaaacaaaatgccaacgcaggttggcattaaatttttatatctcatggacaattaaagaggttattcgt Intra-Species Hit: Count: 1 Min: 1 Max: 308 Len: 308 Subject: aact_AA00695_AA00696|uridine kinase:iron(III) ABC transporter, periplasmic iron-compound-binding protein|POSITIVE:POSITIVE|[475821,476128]|308 HSP 1 e-value: 1.0E-161 bit: 569.0 Len: 308 Query Start:1 Query End:308 Subject Strand: POSITIVE Subject Start: 1 Subject End: 308 accgatttccttcccttttggcgtgtaataggcacgtaaataaattcggggaattataaagnnnnnnntccgatttttatagagctactgtctagaattcagctgccttacagcaacatagataaacaaaatttctacaatcagaagctgaaacgataaattcactccataaaattattgtttttgtgagaattatcacattaattctgaaaaaatttcgttaatattcttcataacctaaaacaaaatgccaacgcaggttggcattaaatttttatatctcatggacaattaaagaggttattcgt accgatttccttcccttttggcgtgtaataggcacgtaaataaattcggggaattataaagaaaaaaatccgatttttatagagctactgtctagaattcagctgccttacagcaacatagataaacaaaatttctacaatcagaagctgaaacgataaattcactccataaaattattgtttttgtgagaattatcacattaattctgaaaaaatttcgttaatattcttcataacctaaaacaaaatgccaacgcaggttggcattaaatttttatatctcatggacaattaaagaggttattcgt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACCGAUUUCCUUCCCUUUUGGCGUGUAAUAGGCACGUAAAUAAAUUCGGGGAAUUAUAAAGAAAAAAAUCCGAUUUUUAUAGAGCUACUGUCUAGAAUUCAGCUGCCUUACAGCAACAUAGAUAAACAAAAUUUCUACAAUCAGAAGCUGAAACGAUAAAUUCACUCCAUAAAAUUAUUGUUUUUGUGAGAAUUAUCACAUUAAUUCUGAAAAAAUUUCGUUAAUAUUCUUCAUAACCUAAAACAAAAUGCCAACGCAGGUUGGCAUUAAAUUUUUAUAUCUCAUGGACAAUUAAAGAGGUUAUUCGU ..(((...((((((((((((((((((.....))))))...))))...))))).(((((((((...........)))))))))......((((((.......((((.....)))).....(((((...(((((((......((((((...((((((((((...............))))))))))(((((......)))))....))))))....................................(((((((((....))))))))))))))))..)))))..)))))).......)))....))). (-60.56) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACGAAUAACCUCUUUAAUUGUCCAUGAGAUAUAAAAAUUUAAUGCCAACCUGCGUUGGCAUUUUGUUUUAGGUUAUGAAGAAUAUUAACGAAAUUUUUUCAGAAUUAAUGUGAUAAUUCUCACAAAAACAAUAAUUUUAUGGAGUGAAUUUAUCGUUUCAGCUUCUGAUUGUAGAAAUUUUGUUUAUCUAUGUUGCUGUAAGGCAGCUGAAUUCUAGACAGUAGCUCUAUAAAAAUCGGAUUUUUUUCUUUAUAAUUCCCCGAAUUUAUUUACGUGCCUAUUACACGCCAAAAGGGAAGGAAAUCGGU ....((((((........((((.....))))..(((((..(((((((((....)))))))))..))))).))))))((((((............))))))........(((((......)))))..........(((((((((((.........(((((.((........)).))))).(((((((((...((((((....)))))).))....)))))))..)))))))))))..(.(((((((((((((..(((((...)))))......((((.......)))).....))))))))))))).). (-67.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 290 113 71 216 171 aact:AA01089|5end_hypothetical_protein_753392..753622_POSITIVE 279 51 15 180 155 aact:AA00514|5end_hypothetical_protein_355609..355839_POSITIVE 272 265 227 153 98 aact:AA02687|5end_hydrogenase-4_component_D_1872521..1872751_POSITIVE 270 49 8 194 159 aact:AA00550|5end_ferredoxin-type_protein_376444..376674_POSITIVE 263 54 19 187 149 aact:AA00649|5end_peptide_chain_release_factor_1_(RF-1)_443277..443507_POSITIVE 261 121 84 210 171 aact:AA02025|5end_hypothetical_protein_1378667..1378897_POSITIVE 261 268 248 106 79 aact:AA01549|5end_hypothetical_protein_1037444..1037674_POSITIVE 260 36 1 41 9 aact:AA02872|5end_conserved_hypothetical_protein_2015539..2015769_POSITIVE 254 49 4 142 97 aact:AA01724|5end_valyl-tRNA_synthetase_1164446..1164676_POSITIVE 254 48 1 100 48 aact:AA01253|5end_hypothetical_protein_852189..852419_POSITIVE 250 50 1 71 15 aact:AA02253|5end_hypothetical_protein_1534605..1534835_POSITIVE 250 48 1 201 144 aact:AA01757|5end_cobalt_transport_ATP-binding_protein_1187137..1187367_POSITIVE 250 49 3 181 135 aact:AA00822|5end_conserved_hypothetical_protein_(possible_arsenate_reductase)_564596..564826_POSITIVE 249 58 12 92 45 aact:AA00810|5end_alcohol_dehydrogenase_555626..555856_POSITIVE 248 50 2 72 30 aact:AA02420|5end_ISRSO11_related_transposase_1662070..1662300_POSITIVE 248 118 83 51 16 aact:AA00342|5end_hypothetical_protein_229695..229925_POSITIVE 247 49 3 203 156 aact:AA00086|5end_2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxy_late_synthase_63437..63667_POSITIVE 246 111 81 226 186 aact:AA00198|5end_conserved_hypothetical_protein_(Cytosine_deaminase-related_enzyme)_138039..138269_POSITIVE 245 130 81 171 129 aact:AA02097|5end_DedA-family_integral_membrane_protein_1428823..1429053_POSITIVE 245 130 81 102 60 aact:AA02096|5end_hypothetical_protein_1428754..1428984_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 292 109 70 101 60 aact:AA02416|3end_conserved_hypothetical_protein_1659578..1659728_POSITIVE 272 265 227 137 82 aact:AA02686|3end_hydrogenase_4_component_C_1872585..1872735_POSITIVE 263 54 19 144 106 aact:AA00647|3end_protoporphyrinogen_oxidase_443314..443464_POSITIVE 254 48 1 113 61 aact:AA01252|3end_conserved_hypothetical_protein_(probable_SirA_homolog)_852282..852432_POSITIVE 250 50 1 82 26 aact:AA02252|3end_conserved_hypothetical_protein_1534696..1534846_POSITIVE 248 118 83 79 44 aact:AA00341|3end_hypothetical_protein_229803..229953_POSITIVE 246 111 81 122 82 aact:AA00196|3end_conserved_hypothetical_protein_138015..138165_POSITIVE 245 130 81 46 4 aact:AA02094|3end_glycogen_phosphorylase;_glycogen_synthase_1428778..1428928_POSITIVE 243 265 229 147 91 aact:AA00574|3end_regulatory_protein_392381..392531_POSITIVE 237 110 61 140 85 aact:AA00132|3end_conserved_hypothetical_protein_(possible_regulator_protein,_VirR_family)_95299..95449_POSITIVE 236 49 2 73 11 aact:AA00514|3end_hypothetical_protein_355838..355988_POSITIVE 235 287 248 106 62 aact:AA01930|3end_ribosome-binding_factor_A_1305175..1305325_POSITIVE 235 116 71 77 33 aact:AA01262|3end_hydrolase_860087..860237_POSITIVE 234 34 3 62 34 aact:AA02206|3end_tryptophan_synthase,_beta_chain_1503187..1503337_POSITIVE 232 48 7 129 91 aact:AA01325|3end_formamidopyrimidine-DNA_glycosylase_895639..895789_POSITIVE 231 115 71 95 38 aact:AA02697|3end_hydrogenase_3_maturation_protease_1880408..1880558_POSITIVE 228 36 2 48 1 aact:AA01765|3end_Mu-like_prophage_FluMu_transposase_A_1192636..1192786_POSITIVE 228 115 82 40 11 aact:AA00937|3end_L-xylulokinase_647525..647675_POSITIVE 227 128 82 57 10 aact:AA00525|3end_hypothetical_protein_359459..359609_POSITIVE 226 40 5 65 20 aact:AA02480|3end_excinuclease_ABC_subunit_B_1718442..1718592_POSITIVE