Origin IGS: actcttctaattttaaaaaaacaacatacattcattcctctcaattcatacatccgattccactgcatccggacaaatcatttttttattttcatggcctctattcgtactttcaaataaattttcatacaccattggatgctttctcttaataagcatcgactgcaaaaatagcgaaaatttgttattcgcaaatattttctgataaaaaaaactttttattccaaataaggctttccgattgcgtcaattataaaaaatttgcactacatacggctttgcattatctttgtactttcatcataaaataaaatcgtatcaat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 attgatacgattttattttatgatgaaagtacaaagataatgcaaagccgtatgtagtgcaaattttttataattgacgcaatcggaaagccttatttggaataaaaagttttttttatcagaaaatatttgcgaataacaaattttcgctatttttgcagtcgatgcttattaagagaaagcatccaatggtgtatgaaaatttatttgaaagtacgaatagaggccatgaaaataaaaaaatgatttgtccggatgcagtggaatcggatgtatgaattgagaggaatgaatgtatgttgtttttttaaaattagaagagt Mask Tandem Repeat Region ================================================ actcttctaattttaaaaaaacaacatacattcattcctctcaattcatacatccgattccactgcatccggacaaatcatttttttattttcatggcctctattcgtactttcaaataaattttcatacaccattggatgctttctcttaataagcatcgactgcaaaaatagcgaaaatttgttattcgcaaatattttctgataaaaaaaactttttattccaaataaggctttccgattgcgtcaattataaaaaatttgcactacatacggctttgcattatctttgtactttcatcataaaataaaatcgtatcaat Find is-nt database================================================ Query_seq: TF2417:TF2418|TF2417:TF2418:outer membrane protein, TonB dependent receptor:GTP-binding protein:->->:2597021..2597343 323 actcttctaattttaaaaaaacaacatacattcattcctctcaattcatacatccgattccactgcatccggacaaatcatttttttattttcatggcctctattcgtactttcaaataaattttcatacaccattggatgctttctcttaataagcatcgactgcaaaaatagcgaaaatttgttattcgcaaatattttctgataaaaaaaactttttattccaaataaggctttccgattgcgtcaattataaaaaatttgcactacatacggctttgcattatctttgtactttcatcataaaataaaatcgtatcaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2417:TF2418|TF2417:TF2418:outer membrane protein, TonB dependent receptor:GTP-binding protein:->->:2597021..2597343 323 actcttctaattttaaaaaaacaacatacattcattcctctcaattcatacatccgattccactgcatccggacaaatcatttttttattttcatggcctctattcgtactttcaaataaattttcatacaccattggatgctttctcttaataagcatcgactgcaaaaatagcgaaaatttgttattcgcaaatattttctgataaaaaaaactttttattccaaataaggctttccgattgcgtcaattataaaaaatttgcactacatacggctttgcattatctttgtactttcatcataaaataaaatcgtatcaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2417:TF2418|TF2417:TF2418:outer membrane protein, TonB dependent receptor:GTP-binding protein:->->:2597021..2597343 323 actcttctaattttaaaaaaacaacatacattcattcctctcaattcatacatccgattccactgcatccggacaaatcatttttttattttcatggcctctattcgtactttcaaataaattttcatacaccattggatgctttctcttaataagcatcgactgcaaaaatagcgaaaatttgttattcgcaaatattttctgataaaaaaaactttttattccaaataaggctttccgattgcgtcaattataaaaaatttgcactacatacggctttgcattatctttgtactttcatcataaaataaaatcgtatcaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 actcttctaattttaaaaaaacaacatacattcattcctctcaattcatacatccgattccactgcatccggacaaatcatttttttattttcatggcctctattcgtactttcaaataaattttcatacaccattggatgctttctcttaataagcatcgactgcaaaaatagcgaaaatttgttattcgcaaatattttctgataaaaaaaactttttattccaaataaggctttccgattgcgtcaattataaaaaatttgcactacatacggctttgcattatctttgtactttcatcataaaataaaatcgtatcaat Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 10 End: 117 ......... M L K K Q H T F I P L N S Y I R F H C I R T N H F F I F M A S I R T F K .............................................................................................................................................................................................................. Protein_Len: 40 Strand: + Start: 30 End: 149 ............................. M H S S Q F I H P I P L H P D K S F F Y F H G L Y S Y F Q I N F H T P L D A F S .............................................................................................................................................................................. Protein_Len: 59 Strand: + Start: 26 End: 202 ......................... M H S F L S I H T S D S T A S G Q I I F L F S W P L F V L S N K F S Y T I G C F L L I S I D C K N S E N L L F A N I F ......................................................................................................................... Protein_Len: 46 Strand: + Start: 171 End: 308 .......................................................................................................................................................................... M A K I C Y S Q I F S D K K N F L F Q I R L S D C V N Y K K F A L H T A L H Y L C T F I I K ............... Protein_Len: 42 Strand: - Start: 81 End: 206 ................................................................................ K K I K M A E I R V K L Y I K M C W Q I S E R L L C R S C F Y R F N T I R L Y K R M ..................................................................................................................... Protein_Len: 58 Strand: - Start: 49 End: 222 ................................................ V D S E V A D P C I M K K N E H G R N T S E F L N E Y V M P H K R K I L M S Q L F L S F K N N A F I K Q Y F F S K M ..................................................................................................... actcttctaattttaaaaaaacaacatacattcattcctctcaattcatacatccgattccactgcatccggacaaatcatttttttattttcatggcctctattcgtactttcaaataaattttcatacaccattggatgctttctcttaataagcatcgactgcaaaaatagcgaaaatttgttattcgcaaatattttctgataaaaaaaactttttattccaaataaggctttccgattgcgtcaattataaaaaatttgcactacatacggctttgcattatctttgtactttcatcataaaataaaatcgtatcaat 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================================================ actcttctaattttaaaaaaacaacatacattcattcctctcaattcatacatccgattccactgcatccggacaaatcatttttttattttcatggcctctattcgtactttcaaataaattttcatacaccattggatgctttctcttaataagcatcgactgcaaaaatagcgaaaatttgttattcgcaaatattttctgataaaaaaaactttttattccaaataaggctttccgattgcgtcaattataaaaaatttgcactacatacggctttgcattatctttgtactttcatcataaaataaaatcgtatcaat Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 54 HP_score: -3.1 Tail_Score: -3.92746 Start: 174 End: 192 Full_Region: tatcagaaaatattt gcgaata acaaa ttttcgc tatttttgcagtcga .............................................................................................................................................................................gcgaataacaaattttcgc................................................................................................................................... Find igs database================================================ Query_seq: TF2417:TF2418|TF2417:TF2418:outer membrane protein, TonB dependent receptor:GTP-binding protein:->->:2597021..2597343 323 actcttctaattttaaaaaaacaacatacattcattcctctcaattcatacatccgattccactgcatccggacaaatcatttttttattttcatggcctctattcgtactttcaaataaattttcatacaccattggatgctttctcttaataagcatcgactgcaaaaatagcgaaaatttgttattcgcaaatattttctgataaaaaaaactttttattccaaataaggctttccgattgcgtcaattataaaaaatttgcactacatacggctttgcattatctttgtactttcatcataaaataaaatcgtatcaat Intra-Species Hit: Count: 1 Min: 22 Max: 323 Len: 302 Subject: tfor_TF2417_TF2418|outer membrane protein, TonB dependent receptor:GTP-binding protein|POSITIVE:POSITIVE|[2597021,2597343]|323 HSP 1 e-value: 1.0E-143 bit: 509.0 Len: 302 Query Start:22 Query End:323 Subject Strand: POSITIVE Subject Start: 22 Subject End: 323 .....................caacatacattcattcctctcaattcatacatccgattccactgcatccggacaaatcannnnnnnattttcatggcctctattcgtactttcaaataaattttcatacaccattggatgctttctcttaataagcatcgactgcaaaaatagcgaaaatttgttattcgcaaatattttctgatnnnnnnnnctttttattccaaataaggctttccgattgcgtcaattataaaaaatttgcactacatacggctttgcattatctttgtactttcatcataaaataaaatcgtatcaat .....................caacatacattcattcctctcaattcatacatccgattccactgcatccggacaaatcatttttttattttcatggcctctattcgtactttcaaataaattttcatacaccattggatgctttctcttaataagcatcgactgcaaaaatagcgaaaatttgttattcgcaaatattttctgataaaaaaaactttttattccaaataaggctttccgattgcgtcaattataaaaaatttgcactacatacggctttgcattatctttgtactttcatcataaaataaaatcgtatcaat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAACAUACAUUCAUUCCUCUCAAUUCAUACAUCCGAUUCCACUGCAUCCGGACAAAUCAUUUUUUUAUUUUCAUGGCCUCUAUUCGUACUUUCAAAUAAAUUUUCAUACACCAUUGGAUGCUUUCUCUUAAUAAGCAUCGACUGCAAAAAUAGCGAAAAUUUGUUAUUCGCAAAUAUUUUCUGAUAAAAAAAACUUUUUAUUCCAAAUAAGGCUUUCCGAUUGCGUCAAUUAUAAAAAAUUUGCACUACAUACGGCUUUGCAUUAUCUUUGUACUUUCAUCAUAAAAUAAAAUCGUAUCAAU ....((((.......................((((.............))))..........(((((((((.((((.......(((((......(((((((((((...........(((((((.........)))))))....((.......)))))))))))))....((((((.((((..((((((((....)))))))).........((.........)).........)))).))))))......)))))...((((.......))))......)))))))))))))..)))).... (-40.62) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUGAUACGAUUUUAUUUUAUGAUGAAAGUACAAAGAUAAUGCAAAGCCGUAUGUAGUGCAAAUUUUUUAUAAUUGACGCAAUCGGAAAGCCUUAUUUGGAAUAAAAAGUUUUUUUUAUCAGAAAAUAUUUGCGAAUAACAAAUUUUCGCUAUUUUUGCAGUCGAUGCUUAUUAAGAGAAAGCAUCCAAUGGUGUAUGAAAAUUUAUUUGAAAGUACGAAUAGAGGCCAUGAAAAUAAAAAAAUGAUUUGUCCGGAUGCAGUGGAAUCGGAUGUAUGAAUUGAGAGGAAUGAAUGUAUGUUG .(((.(((...((((((....)))))).)))))).....((((......))))...(((((.(((((((.(((((.(..((.((.((...((.((((((((.((((..((((((((.....(((((((...(((((.........))))))))))))......(((((((.........)))))))..(((((.........((((((((......)))))))).)))))......))))))))..))))))))))))....))..)).))))..).))))).)))))))...))))).... (-55.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 327 49 3 206 148 tfor:TF0187|5end_ferredoxin_202151..202381_POSITIVE 298 52 11 120 73 tfor:TF2553|5end_50S_ribosomal_protein_L4_2735365..2735595_POSITIVE 293 58 11 93 31 tfor:TF2883|5end_peptidyl-prolyl_cis-trans_isomerase_3074321..3074551_POSITIVE 291 154 115 105 73 tfor:TF2700|5end_possible_nifS-like_aminotransferase_2872855..2873085_POSITIVE 289 80 42 40 1 tfor:TF0836|5end_possible_transposase_889335..889565_POSITIVE 286 55 13 39 3 tfor:TF2671|5end_dipeptidyl_peptidase_IV_(DPP_IV)_N-terminal_region_2843918..2844148_POSITIVE 283 59 11 127 76 tfor:TF0328|5end_conserved_hypothetical_protein_354182..354412_POSITIVE 282 80 31 175 117 tfor:TF2887|5end_phosphomannomutase/phosphoglucomutase_3076327..3076557_POSITIVE 278 157 111 115 70 tfor:TF3068|5end_flavodoxin_A_3292812..3293042_POSITIVE 278 50 4 133 76 tfor:TF2951|5end_O-succinylbenzoic_acid--CoA_ligase_3158496..3158726_POSITIVE 277 80 34 193 154 tfor:TF2181|5end_conserved_hypothetical_protein_2353870..2354100_POSITIVE 275 279 240 184 145 tfor:TF3123|5end_dTDP-4-dehydrorhamnose_3,5-epimerase_3357775..3358005_POSITIVE 271 44 1 172 128 tfor:TF2131|5end_conserved_hypothetical_protein_2306867..2307097_POSITIVE 270 259 214 139 97 tfor:TF0162|5end_possible_CRISPR-associated_protein,_TM1793_family_172183..172413_POSITIVE 269 58 16 201 153 tfor:TF2307|5end_two-component_system_sensor_histidine_kinase/response_2462618..2462848_POSITIVE 267 50 17 186 147 tfor:TF0154|5end_conserved_hypothetical_protein_163564..163794_POSITIVE 266 53 17 124 67 tfor:TF1573|5end_ATP_synthase,_subunit_E_1680955..1681185_POSITIVE 266 76 41 37 6 tfor:TF0320|5end_dihydroorotase_346062..346292_POSITIVE 265 156 113 100 53 tfor:TF2908|5end_transcriptional_regulator,_AraC_family_3103696..3103926_POSITIVE 258 297 253 177 136 tfor:TF1199|5end_dephospho-CoA_kinase_1282136..1282366_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 298 52 11 127 80 tfor:TF2552|3end_50S_ribosomal_protein_L3_2735452..2735602_POSITIVE 293 58 11 93 31 tfor:TF2882|3end_conserved_hypothetical_protein_3074401..3074551_POSITIVE 278 157 111 100 55 tfor:TF3067|3end_conserved_hypothetical_protein_3292877..3293027_POSITIVE 278 50 4 106 49 tfor:TF2950|3end_chloromuconate_cycloisomerase_3158549..3158699_POSITIVE 275 279 240 72 33 tfor:TF3122|3end_ABC_transporter,_ATP-binding_protein_3357743..3357893_POSITIVE 271 44 1 141 97 tfor:TF2130|3end_conserved_hypothetical_protein;_possible_permease_2306916..2307066_POSITIVE 270 259 214 89 47 tfor:TF0161|3end_conserved_hypothetical_protein;_possible_CRISPR-associated_protein_Cas4_172213..172363_POSITIVE 266 53 17 121 64 tfor:TF1571|3end_conserved_hypothetical_protein_1681032..1681182_POSITIVE 264 150 108 80 43 tfor:TF2657|3end_conserved_hypothetical_protein_2830873..2831023_POSITIVE 258 60 16 140 91 tfor:TF1540|3end_possible_ATPase_1645987..1646137_POSITIVE 258 297 253 77 36 tfor:TF1198|3end_conserved_hypothetical_protein_1282116..1282266_POSITIVE 257 52 16 67 21 tfor:TF2931|3end_3-deoxy-D-manno-2-octulosonic_acid_(Kdo_transferase)_3135584..3135734_POSITIVE 257 78 31 127 62 tfor:TF2483|3end_hypothetical_protein_2660022..2660172_POSITIVE 256 54 19 50 4 tfor:TF2340|3end_hypothetical_protein_2500915..2501065_POSITIVE 250 232 196 119 86 tfor:TF1779|3end_conserved_hypothetical_protein_1921048..1921198_POSITIVE 250 59 16 78 29 tfor:TF0022|3end_two-component_system_sensor_histidine_kinase_19522..19672_POSITIVE 248 260 211 142 86 tfor:TF0960|3end_beta-galactosidase_1010506..1010656_POSITIVE 246 287 253 68 26 tfor:TF1447|3end_D-ribulose-phosphate-3_epimerase_1531764..1531914_POSITIVE 245 119 71 104 60 tfor:TF3133|3end_conserved_hypothetical_protein_3369913..3370063_POSITIVE 242 50 14 149 115 tfor:TF0058|3end_conserved_hypothetical_protein_60614..60764_POSITIVE