Origin IGS: tgatgtgcctatgagaaaaacggaagcataaaaaaaccggaaatgcggcaacatctccggttccgattcattaaataacattgttgacaagcaaaatattattcattaatcaattacaaatgt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 acatttgtaattgattaatgaataatattttgcttgtcaacaatgttatttaatgaatcggaaccggagatgttgccgcatttccggtttttttatgcttccgtttttctcataggcacatca Mask Tandem Repeat Region ================================================ tgatgtgcctatgagaaaaacggaagcataaaaaaaccggaaatgcggcaacatctccggttccgattcattaaataacattgttgacaagcaaaatattattcattaatcaattacaaatgt Find is-nt database================================================ Query_seq: TF1604:TF1605|TF1604:TF1605:possible anti-sigma factor:outer membrane protein, TonB dependent receptor:->->:1718977..1719099 123 tgatgtgcctatgagaaaaacggaagcataaaaaaaccggaaatgcggcaacatctccggttccgattcattaaataacattgttgacaagcaaaatattattcattaatcaattacaaatgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1604:TF1605|TF1604:TF1605:possible anti-sigma factor:outer membrane protein, TonB dependent receptor:->->:1718977..1719099 123 tgatgtgcctatgagaaaaacggaagcataaaaaaaccggaaatgcggcaacatctccggttccgattcattaaataacattgttgacaagcaaaatattattcattaatcaattacaaatgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1604:TF1605|TF1604:TF1605:possible anti-sigma factor:outer membrane protein, TonB dependent receptor:->->:1718977..1719099 123 tgatgtgcctatgagaaaaacggaagcataaaaaaaccggaaatgcggcaacatctccggttccgattcattaaataacattgttgacaagcaaaatattattcattaatcaattacaaatgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgatgtgcctatgagaaaaacggaagcataaaaaaaccggaaatgcggcaacatctccggttccgattcattaaataacattgttgacaagcaaaatattattcattaatcaattacaaatgt Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: - Start: 1 End: 102 S T G I L F V S A Y F F R F H P L M E P E S E N F L M T S L C F I M ..................... tgatgtgcctatgagaaaaacggaagcataaaaaaaccggaaatgcggcaacatctccggttccgattcattaaataacattgttgacaagcaaaatattattcattaatcaattacaaatgt 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================================================ tgatgtgcctatgagaaaaacggaagcataaaaaaaccggaaatgcggcaacatctccggttccgattcattaaataacattgttgacaagcaaaatattattcattaatcaattacaaatgt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -9.6 Tail_Score: -5.71983 Start: 37 End: 60 Full_Region: tttaatgaatcggaa ccggagatgt tgcc gcatttccgg tttttttatgcttcc ....................................ccggagatgttgccgcatttccgg............................................................... Find igs database================================================ Query_seq: TF1604:TF1605|TF1604:TF1605:possible anti-sigma factor:outer membrane protein, TonB dependent receptor:->->:1718977..1719099 123 tgatgtgcctatgagaaaaacggaagcataaaaaaaccggaaatgcggcaacatctccggttccgattcattaaataacattgttgacaagcaaaatattattcattaatcaattacaaatgt Intra-Species Hit: Count: 1 Min: 1 Max: 123 Len: 123 Subject: tfor_TF1604_TF1605|possible anti-sigma factor:outer membrane protein, TonB dependent receptor|POSITIVE:POSITIVE|[1718977,1719099]|123 HSP 1 e-value: 2.0E-51 bit: 202.0 Len: 123 Query Start:1 Query End:123 Subject Strand: POSITIVE Subject Start: 1 Subject End: 123 tgatgtgcctatgagaaaaacggaagcatnnnnnnnccggaaatgcggcaacatctccggttccgattcattaaataacattgttgacaagcaaaatattattcattaatcaattacaaatgt tgatgtgcctatgagaaaaacggaagcataaaaaaaccggaaatgcggcaacatctccggttccgattcattaaataacattgttgacaagcaaaatattattcattaatcaattacaaatgt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUGUGCCUAUGAGAAAAACGGAAGCAUAAAAAAACCGGAAAUGCGGCAACAUCUCCGGUUCCGAUUCAUUAAAUAACAUUGUUGACAAGCAAAAUAUUAUUCAUUAAUCAAUUACAAAUGU ((((......(((((.....((((...........((((((.(((......))).))))))))))...............(((((....))))).......)))))..))))........... (-21.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACAUUUGUAAUUGAUUAAUGAAUAAUAUUUUGCUUGUCAACAAUGUUAUUUAAUGAAUCGGAACCGGAGAUGUUGCCGCAUUUCCGGUUUUUUUAUGCUUCCGUUUUUCUCAUAGGCACAUCA ............((((..((((((((((((((.....))).)))))))))))...)))).(((((((((((((....))))))))))))).....(((((..(.......)..)))))..... (-28.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 374 68 21 190 143 tfor:TF0243|5end_conserved_hypothetical_protein_273728..273958_POSITIVE 348 80 35 224 168 tfor:TF2565|5end_50S_ribosomal_protein_L24_2739986..2740216_POSITIVE 341 65 21 154 107 tfor:TF0416|5end_possible_ATP-binding_protein_433134..433364_POSITIVE 329 69 21 150 97 tfor:TF2223|5end_CTn_excision__protein_2394247..2394477_POSITIVE 320 48 4 58 4 tfor:TF0349|5end_hypothetical_protein_370367..370597_POSITIVE 315 69 21 172 127 tfor:TF0819|5end_phosphoglycerate_mutase_878447..878677_POSITIVE 315 50 7 59 15 tfor:TF0452|5end_conserved_hypothetical_protein,_endonuclease/exonuclease/phosphatase_family_470972..471202_POSITIVE 313 70 22 178 120 tfor:TF0191|5end_conserved_hypothetical_protein,_possible_Iojap-related_protein_206053..206283_POSITIVE 312 48 2 114 55 tfor:TF2108|5end_hypothetical_protein_2277385..2277615_POSITIVE 310 46 1 231 176 tfor:TF2177|5end_hypothetical_protein_2349281..2349511_POSITIVE 308 48 1 215 157 tfor:TF0344|5end_hypothetical_protein_366722..366952_POSITIVE 300 69 39 225 183 tfor:TF2279|5end_hypothetical_protein_2438895..2439125_POSITIVE 298 70 21 60 12 tfor:TF0826|5end_primosomal_protein_N'_883751..883981_POSITIVE 292 40 1 100 63 tfor:TF1499|5end_3-oxyacyl-[acyl-carrier_protein]_synthase_1598394..1598624_POSITIVE 291 70 21 220 167 tfor:TF1168|5end_hypothetical_protein_1248755..1248985_POSITIVE 290 88 44 61 21 tfor:TF2255|5end_transfer_region-related_protein,_TraH_2427504..2427734_POSITIVE 289 89 44 148 97 tfor:TF3152|5end_hypothetical_protein_3386690..3386920_POSITIVE 288 65 21 209 168 tfor:TF2133|5end_aspartate-semialdehyde_dehydrogenase_2310275..2310505_POSITIVE 288 67 37 166 135 tfor:TF0974|5end_hypothetical_protein_1024189..1024419_POSITIVE 288 64 21 138 84 tfor:TF0381|5end_cell_cycle_protein_401632..401862_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 360 48 2 57 1 tfor:TF2176|3end_hypothetical_protein_2349185..2349335_POSITIVE 341 65 21 68 21 tfor:TF0414|3end_N-ethylammeline_chlorohydrolase_433128..433278_POSITIVE 324 48 2 57 1 tfor:TF2170|3end_hypothetical_protein_2345070..2345220_POSITIVE 320 48 4 58 4 tfor:TF0348|3end_hypothetical_protein_370447..370597_POSITIVE 315 50 7 53 9 tfor:TF0451|3end_rhomboid_family_membrane_protein_471046..471196_POSITIVE 313 70 22 151 93 tfor:TF0190|3end_cell_division_protein_FtsH_206106..206256_POSITIVE 312 48 2 85 26 tfor:TF2107|3end_hypothetical_protein_2277436..2277586_POSITIVE 308 48 3 56 1 tfor:TF0342|3end_hypothetical_protein_366643..366793_POSITIVE 298 70 21 79 31 tfor:TF0825|3end_hypothetical_protein_883850..884000_POSITIVE 292 40 1 116 79 tfor:TF1498|3end_GTP-binding_protein_1598490..1598640_POSITIVE 289 89 44 83 32 tfor:TF3151|3end_glyoxalase_family_protein_3386705..3386855_POSITIVE 288 64 21 59 5 tfor:TF0380|3end_conserved_hypothetical_protein_401633..401783_POSITIVE 284 48 3 61 1 tfor:TF0967|3end_alpha_glycan_phosphorylase_1018872..1019022_POSITIVE 282 73 37 60 20 tfor:TF2475|3end_GTP_pyrophosphokinase,_(p)ppGpp_synthetase_2654221..2654371_POSITIVE 281 70 35 137 103 tfor:TF2772|3end_tRNA_pseudouridine_synthase_B_2958179..2958329_POSITIVE 280 69 26 52 4 tfor:TF2221|3end_CTn_excision_protein_2394229..2394379_POSITIVE 280 61 21 46 3 tfor:TF1531|3end_potassium_uptake_protein_1637951..1638101_POSITIVE 275 64 36 117 90 tfor:TF2012|3end_conserved_hypothetical_protein_2168720..2168870_POSITIVE 270 69 22 113 66 tfor:TF3033|3end_S1_RNA_binding_domain_protein,_S1_ribosomal_protein_3258983..3259133_POSITIVE 270 67 37 146 113 tfor:TF0982|3end_conserved_hypothetical_protein_1039474..1039624_POSITIVE