Origin IGS: taattccggatttgttggccgaaccttgaaactctgaaagtccatactgataaaaagagagccgactcaaaatgagtcggctctcttttcagggaacttgatgcggttgctctgccgaaacgtgcaatgcgattccggcaaagtaactcactgtttattta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaataaacagtgagttactttgccggaatcgcattgcacgtttcggcagagcaaccgcatcaagttccctgaaaagagagccgactcattttgagtcggctctctttttatcagtatggactttcagagtttcaaggttcggccaacaaatccggaatta Mask Tandem Repeat Region ================================================ taattccggatttgttggccgaaccttgaaactctgaaagtccatactgataaaaagagagccgactcaaaatgagtcggctctcttttcagggaacttgatgcggttgctctgccgaaacgtgcaatgcgattccggcaaagtaactcactgtttattta Find is-nt database================================================ Query_seq: TF2924:TF2925|TF2924:TF2925:DNA-binding response regulator/sensor histidine kinase:beta-N-acetylglucosaminidase:->->:3125679..3125839 161 taattccggatttgttggccgaaccttgaaactctgaaagtccatactgataaaaagagagccgactcaaaatgagtcggctctcttttcagggaacttgatgcggttgctctgccgaaacgtgcaatgcgattccggcaaagtaactcactgtttattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2924:TF2925|TF2924:TF2925:DNA-binding response regulator/sensor histidine kinase:beta-N-acetylglucosaminidase:->->:3125679..3125839 161 taattccggatttgttggccgaaccttgaaactctgaaagtccatactgataaaaagagagccgactcaaaatgagtcggctctcttttcagggaacttgatgcggttgctctgccgaaacgtgcaatgcgattccggcaaagtaactcactgtttattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2924:TF2925|TF2924:TF2925:DNA-binding response regulator/sensor histidine kinase:beta-N-acetylglucosaminidase:->->:3125679..3125839 161 taattccggatttgttggccgaaccttgaaactctgaaagtccatactgataaaaagagagccgactcaaaatgagtcggctctcttttcagggaacttgatgcggttgctctgccgaaacgtgcaatgcgattccggcaaagtaactcactgtttattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taattccggatttgttggccgaaccttgaaactctgaaagtccatactgataaaaagagagccgactcaaaatgagtcggctctcttttcagggaacttgatgcggttgctctgccgaaacgtgcaatgcgattccggcaaagtaactcactgtttattta Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: + Start: 44 End: 160 ........................................... M L I K R E P T Q N E S A L F S G N L M R L L C R N V Q C D S G K V T H C L F . Protein_Len: 52 Strand: - Start: 3 End: 158 .. N R I Q Q G F R S V R F T W V S L F L A S E F H T P E R K L S S S A T A R G F R A I R N R C L L E S N M ... taattccggatttgttggccgaaccttgaaactctgaaagtccatactgataaaaagagagccgactcaaaatgagtcggctctcttttcagggaacttgatgcggttgctctgccgaaacgtgcaatgcgattccggcaaagtaactcactgtttattta 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================================================ taattccggatttgttggccgaaccttgaaactctgaaagtccatactgataaaaagagagccgactcaaaatgagtcggctctcttttcagggaacttgatgcggttgctctgccgaaacgtgcaatgcgattccggcaaagtaactcactgtttattta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -21.9 Tail_Score: -4.89852 Start: 57 End: 85 Full_Region: caagttccctgaaaa gagagccgactca ttt tgagtcggctctc tttttatcagtatgg ........................................................gagagccgactcattttgagtcggctctc............................................................................ Find igs database================================================ Query_seq: TF2924:TF2925|TF2924:TF2925:DNA-binding response regulator/sensor histidine kinase:beta-N-acetylglucosaminidase:->->:3125679..3125839 161 taattccggatttgttggccgaaccttgaaactctgaaagtccatactgataaaaagagagccgactcaaaatgagtcggctctcttttcagggaacttgatgcggttgctctgccgaaacgtgcaatgcgattccggcaaagtaactcactgtttattta Intra-Species Hit: Count: 1 Min: 1 Max: 161 Len: 161 Subject: tfor_TF2924_TF2925|DNA-binding response regulator/sensor histidine kinase:beta-N- acetylglucosaminidase|POSITIVE:POSITIVE|[3125679, 3125839]|161 HSP 1 e-value: 2.0E-86 bit: 319.0 Len: 161 Query Start:1 Query End:161 Subject Strand: POSITIVE Subject Start: 1 Subject End: 161 taattccggatttgttggccgaaccttgaaactctgaaagtccatactgataaaaagagagccgactcaaaatgagtcggctctcttttcagggaacttgatgcggttgctctgccgaaacgtgcaatgcgattccggcaaagtaactcactgtttattta taattccggatttgttggccgaaccttgaaactctgaaagtccatactgataaaaagagagccgactcaaaatgagtcggctctcttttcagggaacttgatgcggttgctctgccgaaacgtgcaatgcgattccggcaaagtaactcactgtttattta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUUCCGGAUUUGUUGGCCGAACCUUGAAACUCUGAAAGUCCAUACUGAUAAAAAGAGAGCCGACUCAAAAUGAGUCGGCUCUCUUUUCAGGGAACUUGAUGCGGUUGCUCUGCCGAAACGUGCAAUGCGAUUCCGGCAAAGUAACUCACUGUUUAUUUA .....(((((.((((..((((..(((((((.........(((......)))...((((((((((((((.....))))))))))))))))))))).........((((......))))...)).))...)))).)))))..(((((((.....).)))))). (-56.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAUAAACAGUGAGUUACUUUGCCGGAAUCGCAUUGCACGUUUCGGCAGAGCAACCGCAUCAAGUUCCCUGAAAAGAGAGCCGACUCAUUUUGAGUCGGCUCUCUUUUUAUCAGUAUGGACUUUCAGAGUUUCAAGGUUCGGCCAACAAAUCCGGAAUUA ..........(((.(((.((((((((((((.((...))..)))))))))))).))))))....((((((.((((((((((((((((((.....))))))))))))))))))...(..((((((((.........))))))))..).........)))))). (-63.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 485 139 92 59 13 tfor:TF2773|5end_S-adenosylmethionine_tRNA_ribosyltransferase_2958117..2958347_POSITIVE 437 140 91 56 1 tfor:TF0594|5end_conserved_hypothetical_protein;_possible_PAP2_superfamily_protein_626971..627201_POSITIVE 406 140 93 174 107 tfor:TF1198|5end_conserved_hypothetical_protein_1281464..1281694_POSITIVE 402 140 91 62 18 tfor:TF2008|5end_DNA_polymerase_I_2159302..2159532_POSITIVE 401 140 91 56 6 tfor:TF1475|5end_glucose-6-phosphate_1-dehydrogenase_1568034..1568264_POSITIVE 396 140 91 139 94 tfor:TF3108|5end_glutamine-hydrolyzing_carbamoyl-phosphate_synthase,_large_subunit_3338732..3338962_POSITIVE 394 140 102 198 148 tfor:TF2214|5end_peptidyl-prolyl_cis-trans_isomerase_2386897..2387127_POSITIVE 394 138 100 175 139 tfor:TF1923|5end_conserved_hypothetical_protein;_possible_phosphoserine_phosphatase_2072259..2072489_POSITIVE 393 140 91 134 81 tfor:TF1476|5end_outer_membrane_protein_P49_1569723..1569953_POSITIVE 387 118 76 222 163 tfor:TF0021|5end_outer_membrane_phospholipase_A_15949..16179_POSITIVE 383 117 77 187 134 tfor:TF2306|5end_hypothetical_protein_2466674..2466904_POSITIVE 378 119 71 82 29 tfor:TF1284|5end_glyceraldehyde_3-phosphate_dehydrogenase_1367939..1368169_POSITIVE 377 138 99 154 108 tfor:TF0002|5end_hypothetical_protein_316..546_POSITIVE 375 139 100 219 169 tfor:TF3139|5end_Na+-translocating_NADH-quinone_reductase,_subunit_C_3372581..3372811_POSITIVE 371 140 91 211 152 tfor:TF0881|5end_conserved_hypothetical_protein_934459..934689_POSITIVE 366 140 97 100 62 tfor:TF0600|5end_oxidoreductase/dehydrogenase_630083..630313_POSITIVE 363 138 92 84 36 tfor:TF2529|5end_nucleotidyl_transferase_family;_possible_mannose-1-phosphate_guanyltransferase_2710670..2710900_POSITIVE 363 141 101 51 5 tfor:TF1001|5end_penicillin-binding_protein_1A_1054097..1054327_POSITIVE 362 138 91 161 121 tfor:TF2775|5end_conserved_hypothetical_protein;_possible_mucoidy_inhibitor-related_protein_2959668..2959898_POSITIVE 362 137 91 56 4 tfor:TF0868|5end_isochorismate_synthase_919301..919531_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 633 99 53 53 2 tfor:TF2924|3end_DNA-binding_response_regulator/sensor_histidine_kinase_3125618..3125768_POSITIVE 437 140 91 56 1 tfor:TF0593|3end_membrane-associated_phospholipid_phosphatase_627051..627201_POSITIVE 408 99 53 76 29 tfor:TF2349|3end_conserved_hypothetical_protein_2514921..2515071_POSITIVE 403 140 92 65 5 tfor:TF1474|3end_6-phosphogluconolactonase_1568123..1568273_POSITIVE 396 140 91 63 18 tfor:TF3107|3end_hypothetical_protein_3338736..3338886_POSITIVE 386 139 102 41 3 tfor:TF2772|3end_tRNA_pseudouridine_synthase_B_2958179..2958329_POSITIVE 368 140 92 58 3 tfor:TF2836|3end_methyltransferase_3028028..3028178_POSITIVE 366 140 97 67 29 tfor:TF0599|3end_hypothetical_protein_630130..630280_POSITIVE 363 138 92 83 35 tfor:TF2527|3end_RNA_polymerase_ECF-type_sigma_factor_2710749..2710899_POSITIVE 362 138 91 132 92 tfor:TF2774|3end_2-amino-4-hydroxy-6-hydroxymethyldihydropteridine_pyrophosphokinase_2959719..2959869_POSITIVE 362 137 91 56 4 tfor:TF0867|3end_2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxy_late_synthase;_2-oxoglutarate_decarboxylase_919381..919531_POSITIVE 358 140 91 68 10 tfor:TF2488|3end_hypothetical_protein_2664478..2664628_POSITIVE 353 117 71 124 82 tfor:TF0350|3end_hypothetical_protein_371101..371251_POSITIVE 352 140 92 141 96 tfor:TF0012|3end_conserved_hypothetical_protein_6641..6791_POSITIVE 351 145 101 45 10 tfor:TF0026|3end_hypothetical_protein_22922..23072_POSITIVE 346 117 75 151 110 tfor:TF2143|3end_S-adenosylmethionine:tRNA_ribosyltransferase-isomerase_2319704..2319854_POSITIVE 344 135 91 145 114 tfor:TF0512|3end_2-oxoglutarate_oxidoreductase,_alpha_subunit_538264..538414_POSITIVE 343 149 102 84 37 tfor:TF1683|3end_conserved_hypothetical_protein_1796511..1796661_POSITIVE 339 141 102 43 5 tfor:TF1000|3end_sec-independent_protein_translocase_1054169..1054319_POSITIVE 337 117 74 110 51 tfor:TF2787|3end_30S_ribosomal_protein_S1_2972258..2972408_POSITIVE