Origin IGS: gatacaatttgtttttcaagtttatgtcctgtaaaaaagtctttatttgttttttgtctttaatttttaagaatgttcctttttttaagatcgagatgttcggaataaccgacgttctacacatcaatatatcgaacatctctaaataatgtttttgttatttctattcctgcttcatattcatattttgcatttttgtacaagcaaagatatattataattttcacattaagaacttttattctgtttttttatatattaggtttaaattttaacaattatatctttacaaaccaacgacaaaaggcggaaaaaagagataaaaaaatcagaaaatca .........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 tgattttctgatttttttatctcttttttccgccttttgtcgttggtttgtaaagatataattgttaaaatttaaacctaatatataaaaaaacagaataaaagttcttaatgtgaaaattataatatatctttgcttgtacaaaaatgcaaaatatgaatatgaagcaggaatagaaataacaaaaacattatttagagatgttcgatatattgatgtgtagaacgtcggttattccgaacatctcgatcttaaaaaaaggaacattcttaaaaattaaagacaaaaaacaaataaagacttttttacaggacataaacttgaaaaacaaattgtatc Mask Tandem Repeat Region ================================================ gatacaatttgtttttcaagtttatgtcctgtaaaaaagtctttatttgttttttgtctttaatttttaagaatgttcctttttttaagatcgagatgttcggaataaccgacgttctacacatcaatatatcgaacatctctaaataatgtttttgttatttctattcctgcttcatattcatattttgcatttttgtacaagcaaagatatattataattttcacattaagaacttttattctgtttttttatatattaggtttaaattttaacaattatatctttacaaaccaacgacaaaaggcggaaaaaagagataaaaaaatcagaaaatca Find is-nt database================================================ Query_seq: TF1057:TF1058|TF1057:TF1058:possible outer membrane receptor, TonB-linked:N-acetylglucosamine kinase:->->:1125664..1126002 339 gatacaatttgtttttcaagtttatgtcctgtaaaaaagtctttatttgttttttgtctttaatttttaagaatgttcctttttttaagatcgagatgttcggaataaccgacgttctacacatcaatatatcgaacatctctaaataatgtttttgttatttctattcctgcttcatattcatattttgcatttttgtacaagcaaagatatattataattttcacattaagaacttttattctgtttttttatatattaggtttaaattttaacaattatatctttacaaaccaacgacaaaaggcggaaaaaagagataaaaaaatcagaaaatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1057:TF1058|TF1057:TF1058:possible outer membrane receptor, TonB-linked:N-acetylglucosamine kinase:->->:1125664..1126002 339 gatacaatttgtttttcaagtttatgtcctgtaaaaaagtctttatttgttttttgtctttaatttttaagaatgttcctttttttaagatcgagatgttcggaataaccgacgttctacacatcaatatatcgaacatctctaaataatgtttttgttatttctattcctgcttcatattcatattttgcatttttgtacaagcaaagatatattataattttcacattaagaacttttattctgtttttttatatattaggtttaaattttaacaattatatctttacaaaccaacgacaaaaggcggaaaaaagagataaaaaaatcagaaaatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1057:TF1058|TF1057:TF1058:possible outer membrane receptor, TonB-linked:N-acetylglucosamine kinase:->->:1125664..1126002 339 gatacaatttgtttttcaagtttatgtcctgtaaaaaagtctttatttgttttttgtctttaatttttaagaatgttcctttttttaagatcgagatgttcggaataaccgacgttctacacatcaatatatcgaacatctctaaataatgtttttgttatttctattcctgcttcatattcatattttgcatttttgtacaagcaaagatatattataattttcacattaagaacttttattctgtttttttatatattaggtttaaattttaacaattatatctttacaaaccaacgacaaaaggcggaaaaaagagataaaaaaatcagaaaatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gatacaatttgtttttcaagtttatgtcctgtaaaaaagtctttatttgttttttgtctttaatttttaagaatgttcctttttttaagatcgagatgttcggaataaccgacgttctacacatcaatatatcgaacatctctaaataatgtttttgttatttctattcctgcttcatattcatattttgcatttttgtacaagcaaagatatattataattttcacattaagaacttttattctgtttttttatatattaggtttaaattttaacaattatatctttacaaaccaacgacaaaaggcggaaaaaagagataaaaaaatcagaaaatca Predict ORF larger than 30AA ================================================ Protein_Len: 46 Strand: + Start: 9 End: 146 ........ M F F K F M S C K K V F I C F L S L I F K N V P F F K I E M F G I T D V L H I N I S N I S K ................................................................................................................................................................................................. Protein_Len: 32 Strand: + Start: 177 End: 272 ................................................................................................................................................................................ M F I F C I F V Q A K I Y Y N F H I K N F Y S V F L Y I R F K F ................................................................... Protein_Len: 60 Strand: + Start: 127 End: 339 .............................................................................................................................. M Y R T S L N N V F V I S I P A S Y S Y F A F L Y K Q R Y I I I F T L R T F I L F F Y I L G L N F N N Y I F T N Q R Q K Protein_Len: 41 Strand: - Start: 120 End: 242 ....................................................................................................................... V D I Y R V D R F L T K T I E I G A E Y E Y K A N K Y L C L Y I I I K V N L V K M ................................................................................................. Protein_Len: 46 Strand: - Start: 2 End: 139 . Y L K N K L N I D Q L F T K I Q K K D K I K L F T G K K L I S I N P I V S T R C M L I D F M ........................................................................................................................................................................................................ gatacaatttgtttttcaagtttatgtcctgtaaaaaagtctttatttgttttttgtctttaatttttaagaatgttcctttttttaagatcgagatgttcggaataaccgacgttctacacatcaatatatcgaacatctctaaataatgtttttgttatttctattcctgcttcatattcatattttgcatttttgtacaagcaaagatatattataattttcacattaagaacttttattctgtttttttatatattaggtttaaattttaacaattatatctttacaaaccaacgacaaaaggcggaaaaaagagataaaaaaatcagaaaatca 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: 82 Start: 269 End: 298 ............................................................................................................................................................................................................................................................................GTTGGTTTGTAAAGATATAATTGTTAAAAT......................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gatacaatttgtttttcaagtttatgtcctgtaaaaaagtctttatttgttttttgtctttaatttttaagaatgttcctttttttaagatcgagatgttcggaataaccgacgttctacacatcaatatatcgaacatctctaaataatgtttttgttatttctattcctgcttcatattcatattttgcatttttgtacaagcaaagatatattataattttcacattaagaacttttattctgtttttttatatattaggtttaaattttaacaattatatctttacaaaccaacgacaaaaggcggaaaaaagagataaaaaaatcagaaaatca Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 41 HP_score: -2.6 Tail_Score: -3.01712 Start: 91 End: 144 Full_Region: aacaaaaacattatt tagagatgttcgatatattgatgt gtaga acgtcggttattccgaacatctcga tcttaaaaaaaggaa ..........................................................................................tagagatgttcgatatattgatgtgtagaacgtcggttattccgaacatctcga................................................................................................................................................................................................... Find igs database================================================ Query_seq: TF1057:TF1058|TF1057:TF1058:possible outer membrane receptor, TonB-linked:N-acetylglucosamine kinase:->->:1125664..1126002 339 gatacaatttgtttttcaagtttatgtcctgtaaaaaagtctttatttgttttttgtctttaatttttaagaatgttcctttttttaagatcgagatgttcggaataaccgacgttctacacatcaatatatcgaacatctctaaataatgtttttgttatttctattcctgcttcatattcatattttgcatttttgtacaagcaaagatatattataattttcacattaagaacttttattctgtttttttatatattaggtttaaattttaacaattatatctttacaaaccaacgacaaaaggcggaaaaaagagataaaaaaatcagaaaatca Intra-Species Hit: Count: 1 Min: 88 Max: 301 Len: 214 Subject: tfor_TF1057_TF1058|possible outer membrane receptor, TonB-linked:N-acetylglucosamine kinase|POSITIVE:POSITIVE|[1125664,1126002]|339 HSP 1 e-value: 1.0E-105 bit: 383.0 Len: 214 Query Start:88 Query End:301 Subject Strand: POSITIVE Subject Start: 88 Subject End: 301 .......................................................................................agatcgagatgttcggaataaccgacgttctacacatcaatatatcgaacatctctaaataatgtttttgttatttctattcctgcttcatattcatattttgcatttttgtacaagcaaagatatattataattttcacattaagaacttttattctgnnnnnnnatatattaggtttaaattttaacaattatatctttacaaaccaacgac...................................... .......................................................................................agatcgagatgttcggaataaccgacgttctacacatcaatatatcgaacatctctaaataatgtttttgttatttctattcctgcttcatattcatattttgcatttttgtacaagcaaagatatattataattttcacattaagaacttttattctgtttttttatatattaggtttaaattttaacaattatatctttacaaaccaacgac...................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAUCGAGAUGUUCGGAAUAACCGACGUUCUACACAUCAAUAUAUCGAACAUCUCUAAAUAAUGUUUUUGUUAUUUCUAUUCCUGCUUCAUAUUCAUAUUUUGCAUUUUUGUACAAGCAAAGAUAUAUUAUAAUUUUCACAUUAAGAACUUUUAUUCUGUUUUUUUAUAUAUUAGGUUUAAAUUUUAACAAUUAUAUCUUUACAAACCAACGAC .....(((((((((((.(((...((.((.....)).))..))).)))))))))))..((..((((..((((((....((..((((...........(((..((.((((((((....)))))))).))..)))...........((((((.........))))))........))))..)).....))))))..))))..))............. (-33.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUCGUUGGUUUGUAAAGAUAUAAUUGUUAAAAUUUAAACCUAAUAUAUAAAAAAACAGAAUAAAAGUUCUUAAUGUGAAAAUUAUAAUAUAUCUUUGCUUGUACAAAAAUGCAAAAUAUGAAUAUGAAGCAGGAAUAGAAAUAACAAAAACAUUAUUUAGAGAUGUUCGAUAUAUUGAUGUGUAGAACGUCGGUUAUUCCGAACAUCUCGAUCU ((..(((....(((((((((((..................................(((((....)))))((((......))))...)))))))))))...........(((...(((....)))...))).............)))..))........((((((((((..((((((((((.....))))))).)))..))))))))))..... (-41.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 288 48 5 66 14 tfor:TF0012|5end_conserved_hypothetical_protein_5512..5742_POSITIVE 270 39 2 180 144 tfor:TF0234|5end_5,10-methylenetetrahydrofolate_reductase_260482..260712_POSITIVE 269 47 1 217 173 tfor:TF2372|5end_acyl-(acyl-carrier-protein)-UDP-N-acetylglucosami_ne_acyltransferase_2537558..2537788_POSITIVE 263 33 8 126 99 tfor:TF2842|5end_methyltransferase_3032094..3032324_POSITIVE 260 33 4 140 115 tfor:TF2016|5end_hypothetical_protein_2172948..2173178_POSITIVE 260 96 51 90 42 tfor:TF1538|5end_conserved_hypothetical_protein_1643531..1643761_POSITIVE 252 48 3 87 44 tfor:TF1469|5end_2-methylthioadenine_synthetase_1561293..1561523_POSITIVE 251 47 8 26 1 tfor:TF0227|5end_transcriptional_regulator,_Crp/Fnr_family_252820..253050_POSITIVE 249 28 3 43 17 tfor:TF0317|5end_conserved_hypothetical_protein_341586..341816_POSITIVE 248 47 1 64 15 tfor:TF0426|5end_conserved_hypothetical_protein_444728..444958_POSITIVE 245 48 1 69 27 tfor:TF2772|5end_tRNA_pseudouridine_synthase_B_2957383..2957613_POSITIVE 244 47 1 159 107 tfor:TF1898|5end_RNA_polymerase_ECF-type_sigma_factor_2052115..2052345_POSITIVE 243 39 4 219 183 tfor:TF0651|5end_hypothetical_protein_693338..693568_POSITIVE 242 54 13 231 187 tfor:TF2517|5end_hypothetical_protein_2695089..2695319_POSITIVE 241 41 5 174 135 tfor:TF2177|5end_hypothetical_protein_2349281..2349511_POSITIVE 237 124 82 226 178 tfor:TF2305|5end_S-adenosylmethionine:tRNA_ribosyltransferase-isomerase_2461348..2461578_POSITIVE 236 101 63 59 13 tfor:TF2958|5end_type_I_restriction-modification_system_R_subunit_3166573..3166803_POSITIVE 236 53 12 84 38 tfor:TF0690|5end_preprotein_translocase_subunit_735243..735473_POSITIVE 235 50 1 64 13 tfor:TF0628|5end_conserved_hypothetical_protein_664305..664535_POSITIVE 231 35 1 88 48 tfor:TF1975|5end_uridylate_kinase_2121536..2121766_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 263 33 8 108 81 tfor:TF2841|3end_conserved_hypothetical_protein_3032156..3032306_POSITIVE 260 33 4 132 107 tfor:TF2015|3end_N6-adenine-specific_DNA_methylase_2173020..2173170_POSITIVE 245 48 1 54 12 tfor:TF2771|3end_undecaprenol_kinase,_bacitracin_resistance_protein_2957448..2957598_POSITIVE 245 31 2 128 93 tfor:TF2477|3end_phosphatase_2654965..2655115_POSITIVE 244 47 1 71 19 tfor:TF1897|3end_conserved_hypothetical_protein;_possible_aminopeptidase_2052107..2052257_POSITIVE 231 30 1 40 2 tfor:TF0013|3end_conserved_hypothetical_protein;_possible_TPR-repeat-containing_protein_7285..7435_POSITIVE 225 86 42 117 58 tfor:TF2457|3end_ABC_transporter,_permease_component,_zinc-binding_protein_2635302..2635452_POSITIVE 224 90 41 79 26 tfor:TF1333|3end_probable_acylaminoacyl_peptidase;_alanyl_dipeptidyl_peptidase_1416014..1416164_POSITIVE 224 128 81 123 68 tfor:TF0809|3end_cation_efflux_protein_868518..868668_POSITIVE 222 48 1 126 78 tfor:TF2676|3end_conserved_hypothetical_protein_2850831..2850981_POSITIVE 222 31 3 71 38 tfor:TF2384|3end_thiol:disulfide_interchange_protein_2550756..2550906_POSITIVE 219 39 2 107 68 tfor:TF0961|3end_translation_initiation_inhibitor,_endoribonuclease_activity_1011673..1011823_POSITIVE 218 34 1 131 97 tfor:TF0002|3end_hypothetical_protein_647..797_POSITIVE 210 36 4 38 1 tfor:TF2883|3end_peptidyl-prolyl_cis-trans_isomerase_3075129..3075279_POSITIVE 210 130 82 141 84 tfor:TF1720|3end_conserved_hypothetical_protein_1844376..1844526_POSITIVE 210 53 13 52 10 tfor:TF1622|3end_conserved_hypothetical_protein_1736763..1736913_POSITIVE 208 24 1 54 27 tfor:TF1262|3end_PDZ_domain_protein_1348831..1348981_POSITIVE 207 35 3 83 38 tfor:TF2848|3end_cobalamin_biosynthesis_protein_3037389..3037539_POSITIVE 207 48 1 91 25 tfor:TF2099|3end_D-tyrosyl-tRNA(Tyr)_deacylase_2273419..2273569_POSITIVE 207 129 85 53 20 tfor:TF0763|3end_chromate_transport_protein_810285..810435_POSITIVE