Origin IGS: tgaatattttaagcgagtgaagggttttttccataaacagacccgttatttcggaataagttcctacttttgtacgatattacttttaaataaaattcgatctg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 cagatcgaattttatttaaaagtaatatcgtacaaaagtaggaacttattccgaaataacgggtctgtttatggaaaaaacccttcactcgcttaaaatattca Mask Tandem Repeat Region ================================================ tgaatattttaagcgagtgaagggttttttccataaacagacccgttatttcggaataagttcctacttttgtacgatattacttttaaataaaattcgatctg Find is-nt database================================================ Query_seq: TF2599:TF2600|TF2599:TF2600:alpha-amylase family protein:ribose-phosphate pyrophosphokinase:->->:2773724..2773827 104 tgaatattttaagcgagtgaagggttttttccataaacagacccgttatttcggaataagttcctacttttgtacgatattacttttaaataaaattcgatctg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2599:TF2600|TF2599:TF2600:alpha-amylase family protein:ribose-phosphate pyrophosphokinase:->->:2773724..2773827 104 tgaatattttaagcgagtgaagggttttttccataaacagacccgttatttcggaataagttcctacttttgtacgatattacttttaaataaaattcgatctg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2599:TF2600|TF2599:TF2600:alpha-amylase family protein:ribose-phosphate pyrophosphokinase:->->:2773724..2773827 104 tgaatattttaagcgagtgaagggttttttccataaacagacccgttatttcggaataagttcctacttttgtacgatattacttttaaataaaattcgatctg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgaatattttaagcgagtgaagggttttttccataaacagacccgttatttcggaataagttcctacttttgtacgatattacttttaaataaaattcgatctg Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: - Start: 12 End: 101 ........... A L S P N K G Y V S G N N R F L N R S K Y S I V K L Y F E M ... tgaatattttaagcgagtgaagggttttttccataaacagacccgttatttcggaataagttcctacttttgtacgatattacttttaaataaaattcgatctg 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================================================ tgaatattttaagcgagtgaagggttttttccataaacagacccgttatttcggaataagttcctacttttgtacgatattacttttaaataaaattcgatctg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF2599:TF2600|TF2599:TF2600:alpha-amylase family protein:ribose-phosphate pyrophosphokinase:->->:2773724..2773827 104 tgaatattttaagcgagtgaagggttttttccataaacagacccgttatttcggaataagttcctacttttgtacgatattacttttaaataaaattcgatctg Intra-Species Hit: Count: 1 Min: 1 Max: 104 Len: 104 Subject: tfor_TF2599_TF2600|alpha-amylase family protein:ribose-phosphate pyrophosphokinase|POSITIVE:POSITIVE|[2773724, 2773827]|104 HSP 1 e-value: 1.0E-52 bit: 206.0 Len: 104 Query Start:1 Query End:104 Subject Strand: POSITIVE Subject Start: 1 Subject End: 104 tgaatattttaagcgagtgaagggttttttccataaacagacccgttatttcggaataagttcctacttttgtacgatattacttttaaataaaattcgatctg tgaatattttaagcgagtgaagggttttttccataaacagacccgttatttcggaataagttcctacttttgtacgatattacttttaaataaaattcgatctg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAAUAUUUUAAGCGAGUGAAGGGUUUUUUCCAUAAACAGACCCGUUAUUUCGGAAUAAGUUCCUACUUUUGUACGAUAUUACUUUUAAAUAAAAUUCGAUCUG .((((..(((((..((((((.((((((.((.....)).))))))......(((....((((....)))).....)))..)))))))))))....))))...... (-16.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAGAUCGAAUUUUAUUUAAAAGUAAUAUCGUACAAAAGUAGGAACUUAUUCCGAAAUAACGGGUCUGUUUAUGGAAAAAACCCUUCACUCGCUUAAAAUAUUCA ......((((.((((((...(((((..((.(((....))).))..)))))...)))))).((((...(((....)))..))))................)))). (-12.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 300 55 12 67 26 tfor:TF2615|5end_conserved_hypothetical_protein_2790569..2790799_POSITIVE 293 57 12 103 47 tfor:TF2816|5end_hypothetical_protein_3006925..3007155_POSITIVE 292 68 21 57 3 tfor:TF0480|5end_ornithine_carbamoyltransferase_498550..498780_POSITIVE 286 57 12 187 130 tfor:TF1842|5end_hypothetical_protein_1992571..1992801_POSITIVE 280 60 12 199 135 tfor:TF2776|5end_hypothetical_protein_2961470..2961700_POSITIVE 279 57 12 165 109 tfor:TF2777|5end_hypothetical_protein_2961595..2961825_POSITIVE 278 60 13 71 15 tfor:TF2381|5end_muramidase/hemagglutinin_2545757..2545987_POSITIVE 270 54 11 185 134 tfor:TF2646|5end_conserved_hypothetical_protein_2814998..2815228_POSITIVE 264 55 11 67 24 tfor:TF2597|5end_outer_membrane_receptor_protein;_possible_TonB_dependent_receptor_2767916..2768146_POSITIVE 262 60 12 79 27 tfor:TF1739|5end_possible_sulfatase_1866983..1867213_POSITIVE 257 59 12 128 83 tfor:TF2378|5end_peptide_chain_release_factor_1_2542682..2542912_POSITIVE 257 50 12 228 192 tfor:TF0068|5end_arylsulfatase_regulator/oxidoreductase_73471..73701_POSITIVE 253 54 13 193 149 tfor:TF2558|5end_50S_ribosomal_protein_L22_2737459..2737689_POSITIVE 253 55 13 98 60 tfor:TF2392|5end_alpha-galactosidase_2563384..2563614_POSITIVE 252 55 12 154 111 tfor:TF2993|5end_SAM-dependent_methyltransferase_3209636..3209866_POSITIVE 252 58 13 46 2 tfor:TF0690|5end_preprotein_translocase_subunit_735243..735473_POSITIVE 247 57 13 176 121 tfor:TF0542|5end_hypothetical_protein_571918..572148_POSITIVE 242 56 12 188 140 tfor:TF1324|5end_conserved_hypothetical_protein_1403462..1403692_POSITIVE 242 55 14 169 121 tfor:TF0950|5end_ribosomal_large_subunit_pseudouridine_synthase_D_(pseudouridylate_synthase)_(uracil_hydrolyase)_994630..994860_POSITIVE 240 55 13 213 168 tfor:TF0414|5end_N-ethylammeline_chlorohydrolase_431789..432019_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 300 55 12 54 13 tfor:TF2614|3end_conserved_hypothetical_protein_2790636..2790786_POSITIVE 287 57 12 69 14 tfor:TF0369|3end_hypothetical_protein_386186..386336_POSITIVE 286 57 12 76 19 tfor:TF1841|3end_hypothetical_protein_1992267..1992417_POSITIVE 278 60 13 105 49 tfor:TF2380|3end_hemagglutinin_2545871..2546021_POSITIVE 273 68 22 54 1 tfor:TF0478|3end_conserved_hypothetical_protein_498627..498777_POSITIVE 270 54 11 113 62 tfor:TF2645|3end_conserved_hypothetical_protein_2815006..2815156_POSITIVE 264 55 11 50 7 tfor:TF2596|3end_conserved_hypothetical_protein;_possible_lipoprotein_2767979..2768129_POSITIVE 257 59 12 72 27 tfor:TF2377|3end_orotidine_5'_phosphate_decarboxylase_2542706..2542856_POSITIVE 253 55 13 98 60 tfor:TF2391|3end_conserved_hypothetical_protein_2563464..2563614_POSITIVE 252 55 12 129 86 tfor:TF2992|3end_hexapeptide_transferase_family_protein_3209691..3209841_POSITIVE 250 79 39 151 107 tfor:TF1305|3end_UDP-glucose_4-epimerase_1386812..1386962_POSITIVE 247 51 12 56 14 tfor:TF2385|3end_conserved_hypothetical_protein;_possible_MazG_family_protein_2551544..2551694_POSITIVE 244 45 12 131 102 tfor:TF1483|3end_glycosyltransferase_family_protein_1578825..1578975_POSITIVE 238 64 24 48 11 tfor:TF0893|3end_conserved_hypothetical_protein_942256..942406_POSITIVE 235 56 13 145 105 tfor:TF3115|3end_possible_sugar_kinase_3352025..3352175_POSITIVE 233 92 52 80 42 tfor:TF1968|3end_conserved_hypothetical_protein_2115959..2116109_POSITIVE 232 45 8 59 9 tfor:TF2791|3end_GTP-binding_protein_TypA_2977219..2977369_POSITIVE 230 53 11 119 69 tfor:TF1446|3end_hypothetical_protein_1531001..1531151_POSITIVE 223 91 51 60 21 tfor:TF0595|3end_hypothetical_protein_628073..628223_POSITIVE 221 84 42 89 48 tfor:TF2214|3end_peptidyl-prolyl_cis-trans_isomerase_2387564..2387714_POSITIVE