Origin IGS: tgatcttcctctgcatgcattttcggcaggtaactgacattttgtcgactggcactgtttttgcatcagagccggtgatgatatagtattaacttcaattgtagaaacg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 cgtttctacaattgaagttaatactatatcatcaccggctctgatgcaaaaacagtgccagtcgacaaaatgtcagttacctgccgaaaatgcatgcagaggaagatca Mask Tandem Repeat Region ================================================ tgatcttcctctgcatgcattttcggcaggtaactgacattttgtcgactggcactgtttttgcatcagagccggtgatgatatagtattaacttcaattgtagaaacg Find is-nt database================================================ Query_seq: TF2533:TF2534|TF2533:TF2534:adenylosuccinate synthetase:conserved hypothetical protein:->->:2717075..2717183 109 tgatcttcctctgcatgcattttcggcaggtaactgacattttgtcgactggcactgtttttgcatcagagccggtgatgatatagtattaacttcaattgtagaaacg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2533:TF2534|TF2533:TF2534:adenylosuccinate synthetase:conserved hypothetical protein:->->:2717075..2717183 109 tgatcttcctctgcatgcattttcggcaggtaactgacattttgtcgactggcactgtttttgcatcagagccggtgatgatatagtattaacttcaattgtagaaacg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2533:TF2534|TF2533:TF2534:adenylosuccinate synthetase:conserved hypothetical protein:->->:2717075..2717183 109 tgatcttcctctgcatgcattttcggcaggtaactgacattttgtcgactggcactgtttttgcatcagagccggtgatgatatagtattaacttcaattgtagaaacg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgatcttcctctgcatgcattttcggcaggtaactgacattttgtcgactggcactgtttttgcatcagagccggtgatgatatagtattaacttcaattgtagaaacg Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: - Start: 1 End: 99 S R G R C A N E A P L Q C K T S Q C Q K Q M L A P S S I T N V E M .......... tgatcttcctctgcatgcattttcggcaggtaactgacattttgtcgactggcactgtttttgcatcagagccggtgatgatatagtattaacttcaattgtagaaacg 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================================================ PromScan Matrix: RpoN Strand: + Score: 92 Start: 49 End: 65 ................................................CTGGCACTGTTTTTGCA............................................ tgatcttcctctgcatgcattttcggcaggtaactgacattttgtcgactggcactgtttttgcatcagagccggtgatgatatagtattaacttcaattgtagaaacg Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 39 HP_score: -2.4 Tail_Score: -2.70232 Start: 45 End: 78 Full_Region: GTAACTGACATTTTG TCGACTGGCACTGTT TTTGC ATCAGAGCCGGTGA TGATATAGTATTAAC ............................................TCGACTGGCACTGTTTTTGCATCAGAGCCGGTGA............................... Find igs database================================================ Query_seq: TF2533:TF2534|TF2533:TF2534:adenylosuccinate synthetase:conserved hypothetical protein:->->:2717075..2717183 109 tgatcttcctctgcatgcattttcggcaggtaactgacattttgtcgactggcactgtttttgcatcagagccggtgatgatatagtattaacttcaattgtagaaacg Intra-Species Hit: Count: 1 Min: 1 Max: 109 Len: 109 Subject: tfor_TF2533_TF2534|adenylosuccinate synthetase:conserved hypothetical protein|POSITIVE:POSITIVE|[2717075,2717183]|109 HSP 1 e-value: 1.0E-55 bit: 216.0 Len: 109 Query Start:1 Query End:109 Subject Strand: POSITIVE Subject Start: 1 Subject End: 109 tgatcttcctctgcatgcattttcggcaggtaactgacattttgtcgactggcactgtttttgcatcagagccggtgatgatatagtattaacttcaattgtagaaacg tgatcttcctctgcatgcattttcggcaggtaactgacattttgtcgactggcactgtttttgcatcagagccggtgatgatatagtattaacttcaattgtagaaacg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUCUUCCUCUGCAUGCAUUUUCGGCAGGUAACUGACAUUUUGUCGACUGGCACUGUUUUUGCAUCAGAGCCGGUGAUGAUAUAGUAUUAACUUCAAUUGUAGAAACG .........((((((.........(.(((....))).)...(..((.((((((.(((.........))).))))))))..)..................)))))).... (-23.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGUUUCUACAAUUGAAGUUAAUACUAUAUCAUCACCGGCUCUGAUGCAAAAACAGUGCCAGUCGACAAAAUGUCAGUUACCUGCCGAAAAUGCAUGCAGAGGAAGAUCA ....(((.....((((((....)))...))).......((((((((((.......((.(((..(((.........)))..))).))....))))).)))))..)))... (-16.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 446 60 11 103 53 tfor:TF1740|5end_hypothetical_protein_1868645..1868875_POSITIVE 387 55 11 130 95 tfor:TF1891|5end_hypothetical_protein_2043389..2043619_POSITIVE 345 58 12 46 1 tfor:TF2264|5end_transfer_region-related_protein,_TraO_2432890..2433120_POSITIVE 343 77 36 72 32 tfor:TF0122|5end_hypothetical_protein_133162..133392_POSITIVE 342 68 24 176 127 tfor:TF1489|5end_argininosuccinate_lyase_1588904..1589134_POSITIVE 336 60 11 220 178 tfor:TF0835|5end_conserved_hypothetical_protein_888933..889163_POSITIVE 336 60 11 44 2 tfor:TF0833|5end_conserved_hypothetical_protein_888757..888987_POSITIVE 329 75 33 193 158 tfor:TF2932|5end_capsule_biosynthesis_protein_3135514..3135744_POSITIVE 328 75 39 165 122 tfor:TF2572|5end_50S_ribosomal_protein_L30_2743081..2743311_POSITIVE 322 59 12 73 27 tfor:TF1922|5end_hypothetical_protein_2072018..2072248_POSITIVE 318 80 32 219 169 tfor:TF2884|5end_conserved_hypothetical_protein_3075057..3075287_POSITIVE 317 80 33 229 181 tfor:TF0982|5end_conserved_hypothetical_protein_1038633..1038863_POSITIVE 316 46 6 182 145 tfor:TF2616|5end_outer_membrane_protein,_TonB_dependent_receptor_2791470..2791700_POSITIVE 315 80 38 207 167 tfor:TF2208|5end_conserved_hypothetical_protein_2382349..2382579_POSITIVE 315 60 11 99 52 tfor:TF0953|5end_conserved_hypothetical_protein;_possible_DNA_binding_protein_997929..998159_POSITIVE 315 50 2 70 16 tfor:TF0932|5end_hypothitical_protein_972167..972397_POSITIVE 313 59 11 224 173 tfor:TF2160|5end_magnesium_chelatase,_subunit_I_2335974..2336204_POSITIVE 313 78 43 94 46 tfor:TF1421|5end_UDP-N-acetylmuramate--alanine_ligase_1503465..1503695_POSITIVE 311 48 5 54 8 tfor:TF0133|5end_transposase_element_145174..145404_POSITIVE 309 60 11 61 1 tfor:TF1241|5end_prolyl-tRNA_synthetase_1324711..1324941_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 343 77 36 47 7 tfor:TF0121|3end_hypothetical_protein_133217..133367_POSITIVE 328 75 39 144 101 tfor:TF2571|3end_30S_ribosomal_protein_S5_2743140..2743290_POSITIVE 315 60 11 99 52 tfor:TF0952|3end_conserved_hypothetical_protein_998009..998159_POSITIVE 315 50 2 60 6 tfor:TF0931|3end_superfamily_II_DNA/RNA_helicase,_SNF2_family_972237..972387_POSITIVE 313 78 43 94 46 tfor:TF1420|3end_cell_division_protein_1503545..1503695_POSITIVE 305 70 21 92 34 tfor:TF0096|3end_tRNA-guanine_transglycosylase_(queuine_tRNA-ribosyltransferase)_108178..108328_POSITIVE 304 60 12 146 84 tfor:TF1000|3end_sec-independent_protein_translocase_1054169..1054319_POSITIVE 303 58 17 40 1 tfor:TF2263|3end_transfer_region-related_protein,_TraN_2432964..2433114_POSITIVE 302 79 42 138 77 tfor:TF3039|3end_ABC_transporter,_ATP-binding_protein_3267697..3267847_POSITIVE 301 37 4 150 106 tfor:TF0568|3end_indolepyruvate_ferredoxin_oxidoreductase,_alpha_subunit_601798..601948_POSITIVE 296 60 13 77 27 tfor:TF0795|3end_hypothetical_protein_853199..853349_POSITIVE 296 79 34 138 73 tfor:TF0271|3end_oxidase/dehydrogenase_298530..298680_POSITIVE 295 47 5 98 40 tfor:TF0599|3end_hypothetical_protein_630130..630280_POSITIVE 294 77 34 46 2 tfor:TF1807|3end_thioesterase_family_protein_1949425..1949575_POSITIVE 293 60 17 62 7 tfor:TF2454|3end_D-alanyl-D-alanine_dipeptidase_2632025..2632175_POSITIVE 293 76 36 56 24 tfor:TF1498|3end_GTP-binding_protein_1598490..1598640_POSITIVE 292 77 32 145 101 tfor:TF1425|3end_phospho-N-acetylmuramoyl_pentapeptide_transferase_1509942..1510092_POSITIVE 292 67 23 88 35 tfor:TF0418|3end_possible_methyl-accepting_chemotaxis_protein_435326..435476_POSITIVE 291 46 5 141 97 tfor:TF3124|3end_dTDP-glucose_4,6-dehydratase_3359883..3360033_POSITIVE 286 51 11 108 60 tfor:TF2694|3end_hypothetical_protein_2870863..2871013_POSITIVE