Origin IGS: taattcaacataagcattacaatggcaataatgatggcgcgcgtctcccgaccacaagtgttcgaaagacgcgcactatctataaacaaccctaccaatcaatggattccga .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tcggaatccattgattggtagggttgtttatagatagtgcgcgtctttcgaacacttgtggtcgggagacgcgcgccatcattattgccattgtaatgcttatgttgaatta Mask Tandem Repeat Region ================================================ taattcaacataagcattacaatggcaataatgatggcgcgcgtctcccgaccacaagtgttcgaaagacgcgcactatctataaacaaccctaccaatcaatggattccga Find is-nt database================================================ Query_seq: AA00480:AA00482|AA00480:AA00482:mannose-specific phosphotransferase system IID:hydrolase (haloacid dehalogenase-like) (HAD superfamily):->->:335260..335371 112 taattcaacataagcattacaatggcaataatgatggcgcgcgtctcccgaccacaagtgttcgaaagacgcgcactatctataaacaaccctaccaatcaatggattccga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA00480:AA00482|AA00480:AA00482:mannose-specific phosphotransferase system IID:hydrolase (haloacid dehalogenase-like) (HAD superfamily):->->:335260..335371 112 taattcaacataagcattacaatggcaataatgatggcgcgcgtctcccgaccacaagtgttcgaaagacgcgcactatctataaacaaccctaccaatcaatggattccga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA00480:AA00482|AA00480:AA00482:mannose-specific phosphotransferase system IID:hydrolase (haloacid dehalogenase-like) (HAD superfamily):->->:335260..335371 112 taattcaacataagcattacaatggcaataatgatggcgcgcgtctcccgaccacaagtgttcgaaagacgcgcactatctataaacaaccctaccaatcaatggattccga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taattcaacataagcattacaatggcaataatgatggcgcgcgtctcccgaccacaagtgttcgaaagacgcgcactatctataaacaaccctaccaatcaatggattccga Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 3 End: 110 .. M Q H K H Y N G N N D G A R L P T T S V R K T R T I Y K Q P Y Q S M D S .. Protein_Len: 34 Strand: + Start: 10 End: 111 ......... M S I T M A I M M A R V S R P Q V F E R R A L S I N N P T N Q W I P . Protein_Len: 32 Strand: - Start: 3 End: 98 .. N L M L M V I A I I I A R T E R G C T N S L R A S D I F L G V M .............. taattcaacataagcattacaatggcaataatgatggcgcgcgtctcccgaccacaagtgttcgaaagacgcgcactatctataaacaaccctaccaatcaatggattccga 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================================================ taattcaacataagcattacaatggcaataatgatggcgcgcgtctcccgaccacaagtgttcgaaagacgcgcactatctataaacaaccctaccaatcaatggattccga Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -14.3 Tail_Score: -3.6968 Start: 32 End: 81 Full_Region: ggtagggttgtttat agatagtgcgcgtctttcgaaca cttg tggtcgggagacgcgcgccatca ttattgccattgtaa ...............................agatagtgcgcgtctttcgaacacttgtggtcgggagacgcgcgccatca............................... TransTerm Strand: - Conf: 100 HP_score: -17.8 Tail_Score: -2.81326 Start: 33 End: 80 Full_Region: gtagggttgtttata gatagtgcgcgtctttcgaaca cttg tggtcgggagacgcgcgccatc attattgccattgta ................................gatagtgcgcgtctttcgaacacttgtggtcgggagacgcgcgccatc................................ TransTerm Strand: - Conf: 89 HP_score: -14.6 Tail_Score: -2.94759 Start: 35 End: 78 Full_Region: agggttgtttataga tagtgcgcgtctttcgaaca cttg tggtcgggagacgcgcgcca tcattattgccattg ..................................tagtgcgcgtctttcgaacacttgtggtcgggagacgcgcgcca.................................. Find igs database================================================ Query_seq: AA00480:AA00482|AA00480:AA00482:mannose-specific phosphotransferase system IID:hydrolase (haloacid dehalogenase-like) (HAD superfamily):->->:335260..335371 112 taattcaacataagcattacaatggcaataatgatggcgcgcgtctcccgaccacaagtgttcgaaagacgcgcactatctataaacaaccctaccaatcaatggattccga Intra-Species Hit: Count: 1 Min: 1 Max: 112 Len: 112 Subject: aact_AA00480_AA00482|mannose-specific phosphotransferase system IID:hydrolase (haloacid dehalogenase-like) (HAD superfamily)|POSITIVE:POSITIVE|[335260,335371]|112 HSP 1 e-value: 2.0E-57 bit: 222.0 Len: 112 Query Start:1 Query End:112 Subject Strand: POSITIVE Subject Start: 1 Subject End: 112 taattcaacataagcattacaatggcaataatgatggcgcgcgtctcccgaccacaagtgttcgaaagacgcgcactatctataaacaaccctaccaatcaatggattccga taattcaacataagcattacaatggcaataatgatggcgcgcgtctcccgaccacaagtgttcgaaagacgcgcactatctataaacaaccctaccaatcaatggattccga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUUCAACAUAAGCAUUACAAUGGCAAUAAUGAUGGCGCGCGUCUCCCGACCACAAGUGUUCGAAAGACGCGCACUAUCUAUAAACAACCCUACCAAUCAAUGGAUUCCGA .((((((......((.........))......(((((.((((((((..(((.((....)).)))..)))))))).)))))......................)))))).... (-29.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCGGAAUCCAUUGAUUGGUAGGGUUGUUUAUAGAUAGUGCGCGUCUUUCGAACACUUGUGGUCGGGAGACGCGCGCCAUCAUUAUUGCCAUUGUAAUGCUUAUGUUGAAUUA ((((....(((((..((((((.((.....)).(((.((((((((((..(((.((....)).)))..)))))))))).)))....))))))...)))))......)))).... (-38.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 647 67 21 183 140 aact:AA00729|5end_possible_hemolysin_(TlyC-like)_500204..500434_POSITIVE 549 67 31 143 107 aact:AA02453|5end_conserved_hypothetical_protein_1688947..1689177_POSITIVE 474 79 32 68 10 aact:AA01270|5end_hydrolase_(possible_2-haloalkanoic_acid_dehalogenase_I)_863317..863547_POSITIVE 409 76 32 208 158 aact:AA01192|5end_conserved_hypothetical_protein_(possible_membrane_protein)_817358..817588_POSITIVE 409 68 23 71 3 aact:AA00384|5end_conserved_hypothetical_protein_(possible_nitrogen_fixation_protein)_260108..260338_POSITIVE 407 80 31 186 118 aact:AA00698|5end_iron(III)_ABC_transporter,_periplasmic_iron-compound-binding_protein_477191..477421_POSITIVE 385 68 21 54 11 aact:AA00544|5end_glutathionylspermidine_synthetase;amidase_372448..372678_POSITIVE 348 61 23 210 176 aact:AA00740|5end_citrate_lyase_related_biosynthesis_protein_(2-(5'-triphosphoribosyl)-3'-dephosphocoenzyme-A_synthase)_505260..505490_POSITIVE 348 61 23 37 3 aact:AA00738|5end_hypothetical_protein_505087..505317_POSITIVE 344 52 21 161 122 aact:AA01724|5end_valyl-tRNA_synthetase_1164446..1164676_POSITIVE 343 68 21 194 145 aact:AA00958|5end_adenylate_cyclase_662118..662348_POSITIVE 342 78 31 87 41 aact:AA01598|5end_conserved_hypothetical_protein_1078954..1079184_POSITIVE 339 80 32 174 125 aact:AA01982|5end_maltodextrin_phosphorylase_1339387..1339617_POSITIVE 337 54 16 60 6 aact:AA01996|5end_prephenate_dehydrogenase_1355314..1355544_POSITIVE 335 65 22 65 7 aact:AA01565|5end_conserved_hypothetical_protein_1050711..1050941_POSITIVE 335 72 35 147 110 aact:AA01544|5end_conserved_hypothetical_protein_1034265..1034495_POSITIVE 335 72 35 57 20 aact:AA01543|5end_hypothetical_protein_1034175..1034405_POSITIVE 334 50 14 44 11 aact:AA02124|5end_anaerobic_regulatory_protein;_transcription_regulator_Fnr_1448520..1448750_POSITIVE 333 78 31 191 134 aact:AA00799|5end_iron(III)_dicitrate_transport_ATP-binding_protein_547658..547888_POSITIVE 327 78 35 156 111 aact:AA01890|5end_cell-cycle_protein_1274544..1274774_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 549 67 31 42 6 aact:AA02451|3end_conserved_hypothetical_protein_1688926..1689076_POSITIVE 506 80 33 58 11 aact:AA00480|3end_mannose-specific_phosphotransferase_system_IID_335199..335349_POSITIVE 474 79 32 84 26 aact:AA01269|3end_hypothetical_protein_863413..863563_POSITIVE 408 68 21 65 4 aact:AA00383|3end_chloride_channel_protein_260182..260332_POSITIVE 407 80 31 89 21 aact:AA00697|3end_hypothetical_protein_477174..477324_POSITIVE 348 61 23 126 92 aact:AA00738|3end_hypothetical_protein_505256..505406_POSITIVE 339 80 32 61 12 aact:AA01981|3end_4-alpha-glucanotransferase_1339354..1339504_POSITIVE 337 54 16 60 6 aact:AA01995|3end_conserved_hypothetical_protein_(possible_chorismate_mutase)_1355394..1355544_POSITIVE 327 78 35 122 77 aact:AA01889|3end_conserved_hypothetical_protein_(possible_permease)_1274590..1274740_POSITIVE 325 77 31 70 26 aact:AA00209|3end_D-ribose_ABC_transporter,_periplasmic-binding_protein_146032..146182_POSITIVE 320 76 31 134 92 aact:AA00211|3end_hypothetical_protein_146163..146313_POSITIVE 317 74 31 136 91 aact:AA01732|3end_multidrug_resistance_protein_A_1171914..1172064_POSITIVE 316 90 42 117 63 aact:AA01651|3end_hypothetical_protein_1120004..1120154_POSITIVE 313 80 36 69 15 aact:AA00202|3end_conserved_hypothetical_protein_(possible_membrane_protein)_141420..141570_POSITIVE 308 60 13 138 84 aact:AA01543|3end_hypothetical_protein_1034350..1034500_POSITIVE 308 77 37 66 12 aact:AA01179|3end_beta-ketoacyl-ACP_reductase;_short-chain_alcohol_dehydrogenase_808801..808951_POSITIVE 300 80 32 102 36 aact:AA02740|3end_conserved_hypothetical_protein_1921394..1921544_POSITIVE 298 78 31 119 74 aact:AA00574|3end_regulatory_protein_392381..392531_POSITIVE 297 77 39 36 3 aact:AA02733|3end_cell_division_protein_K;_sporulation_protein_spoIIIE_1915029..1915179_POSITIVE 295 77 34 145 90 aact:AA02175|3end_anthranilate_synthase_component_II_1488966..1489116_POSITIVE