Origin IGS: ccgcgctgatcatctgcaaaataaaaatggctaacagaacatatcagcagttgaaaacggcgaatttacataaaaaacgcgatatttaagccaatggagataaaaaaacgaggagtgtagtttctccttagccaatgaaccatttacgacacccccagaggtggtacttcaaacgtaaggggtgattatgaccgaccgtcttaggtagaaatatgtatatctgtcacttaacgtgtgacatgaaactatttaggacaatattgcgtctctacgggtaaactgactgccggatgctgaaaatcgactgctgacgactatcccaaaggattttaaccatcccatacgacttttctcttcgtttttcgcttcttcatcgtttacgtatgacaaaaaa .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttttttgtcatacgtaaacgatgaagaagcgaaaaacgaagagaaaagtcgtatgggatggttaaaatcctttgggatagtcgtcagcagtcgattttcagcatccggcagtcagtttacccgtagagacgcaatattgtcctaaatagtttcatgtcacacgttaagtgacagatatacatatttctacctaagacggtcggtcataatcaccccttacgtttgaagtaccacctctgggggtgtcgtaaatggttcattggctaaggagaaactacactcctcgtttttttatctccattggcttaaatatcgcgttttttatgtaaattcgccgttttcaactgctgatatgttctgttagccatttttattttgcagatgatcagcgcgg Mask Tandem Repeat Region ================================================ ccgcgctgatcatctgcaaaataaaaatggctaacagaacatatcagcagttgaaaacggcgaatttacataaaaaacgcgatatttaagccaatggagataaaaaaacgaggagtgtagtttctccttagccaatgaaccatttacgacacccccagaggtggtacttcaaacgtaaggggtgattatgaccgaccgtcttaggtagaaatatgtatatctgtcacttaacgtgtgacatgaaactatttaggacaatattgcgtctctacgggtaaactgactgccggatgctgaaaatcgactgctgacgactatcccaaaggattttaaccatcccatacgacttttctcttcgtttttcgcttcttcatcgtttacgtatgacaaaaaa Find is-nt database================================================ Query_seq: TF2778:TF2779|TF2778:TF2779:outer membrane protein, TonB dependent receptor:fucose permease:->->:2964312..2964705 394 ccgcgctgatcatctgcaaaataaaaatggctaacagaacatatcagcagttgaaaacggcgaatttacataaaaaacgcgatatttaagccaatggagataaaaaaacgaggagtgtagtttctccttagccaatgaaccatttacgacacccccagaggtggtacttcaaacgtaaggggtgattatgaccgaccgtcttaggtagaaatatgtatatctgtcacttaacgtgtgacatgaaactatttaggacaatattgcgtctctacgggtaaactgactgccggatgctgaaaatcgactgctgacgactatcccaaaggattttaaccatcccatacgacttttctcttcgtttttcgcttcttcatcgtttacgtatgacaaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2778:TF2779|TF2778:TF2779:outer membrane protein, TonB dependent receptor:fucose permease:->->:2964312..2964705 394 ccgcgctgatcatctgcaaaataaaaatggctaacagaacatatcagcagttgaaaacggcgaatttacataaaaaacgcgatatttaagccaatggagataaaaaaacgaggagtgtagtttctccttagccaatgaaccatttacgacacccccagaggtggtacttcaaacgtaaggggtgattatgaccgaccgtcttaggtagaaatatgtatatctgtcacttaacgtgtgacatgaaactatttaggacaatattgcgtctctacgggtaaactgactgccggatgctgaaaatcgactgctgacgactatcccaaaggattttaaccatcccatacgacttttctcttcgtttttcgcttcttcatcgtttacgtatgacaaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2778:TF2779|TF2778:TF2779:outer membrane protein, TonB dependent receptor:fucose permease:->->:2964312..2964705 394 ccgcgctgatcatctgcaaaataaaaatggctaacagaacatatcagcagttgaaaacggcgaatttacataaaaaacgcgatatttaagccaatggagataaaaaaacgaggagtgtagtttctccttagccaatgaaccatttacgacacccccagaggtggtacttcaaacgtaaggggtgattatgaccgaccgtcttaggtagaaatatgtatatctgtcacttaacgtgtgacatgaaactatttaggacaatattgcgtctctacgggtaaactgactgccggatgctgaaaatcgactgctgacgactatcccaaaggattttaaccatcccatacgacttttctcttcgtttttcgcttcttcatcgtttacgtatgacaaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ccgcgctgatcatctgcaaaataaaaatggctaacagaacatatcagcagttgaaaacggcgaatttacataaaaaacgcgatatttaagccaatggagataaaaaaacgaggagtgtagtttctccttagccaatgaaccatttacgacacccccagaggtggtacttcaaacgtaaggggtgattatgaccgaccgtcttaggtagaaatatgtatatctgtcacttaacgtgtgacatgaaactatttaggacaatattgcgtctctacgggtaaactgactgccggatgctgaaaatcgactgctgacgactatcccaaaggattttaaccatcccatacgacttttctcttcgtttttcgcttcttcatcgtttacgtatgacaaaaaa Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: + Start: 284 End: 394 ........................................................................................................................................................................................................................................................................................... M P D A E N R L L T T I P K D F N H P I R L F S S F F A S S S F T Y D K K Protein_Len: 46 Strand: - Start: 253 End: 390 ............................................................................................................................................................................................................................................................ S L I A D R R T F Q S G S A S F R S S V V I G F S K L W G M R S K E E N K A E E D N V Y S M .... Protein_Len: 30 Strand: - Start: 131 End: 220 .................................................................................................................................. G I F W K R C G W L H Y K L R L P H N H G V T K P L F I Y M .............................................................................................................................................................................. Protein_Len: 34 Strand: - Start: 34 End: 135 ................................. C F M D A T S F P S N V Y F V R Y K L W H L Y F F S S H L K E K A M ................................................................................................................................................................................................................................................................... ccgcgctgatcatctgcaaaataaaaatggctaacagaacatatcagcagttgaaaacggcgaatttacataaaaaacgcgatatttaagccaatggagataaaaaaacgaggagtgtagtttctccttagccaatgaaccatttacgacacccccagaggtggtacttcaaacgtaaggggtgattatgaccgaccgtcttaggtagaaatatgtatatctgtcacttaacgtgtgacatgaaactatttaggacaatattgcgtctctacgggtaaactgactgccggatgctgaaaatcgactgctgacgactatcccaaaggattttaaccatcccatacgacttttctcttcgtttttcgcttcttcatcgtttacgtatgacaaaaaa 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================================================ ccgcgctgatcatctgcaaaataaaaatggctaacagaacatatcagcagttgaaaacggcgaatttacataaaaaacgcgatatttaagccaatggagataaaaaaacgaggagtgtagtttctccttagccaatgaaccatttacgacacccccagaggtggtacttcaaacgtaaggggtgattatgaccgaccgtcttaggtagaaatatgtatatctgtcacttaacgtgtgacatgaaactatttaggacaatattgcgtctctacgggtaaactgactgccggatgctgaaaatcgactgctgacgactatcccaaaggattttaaccatcccatacgacttttctcttcgtttttcgcttcttcatcgtttacgtatgacaaaaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF2778:TF2779|TF2778:TF2779:outer membrane protein, TonB dependent receptor:fucose permease:->->:2964312..2964705 394 ccgcgctgatcatctgcaaaataaaaatggctaacagaacatatcagcagttgaaaacggcgaatttacataaaaaacgcgatatttaagccaatggagataaaaaaacgaggagtgtagtttctccttagccaatgaaccatttacgacacccccagaggtggtacttcaaacgtaaggggtgattatgaccgaccgtcttaggtagaaatatgtatatctgtcacttaacgtgtgacatgaaactatttaggacaatattgcgtctctacgggtaaactgactgccggatgctgaaaatcgactgctgacgactatcccaaaggattttaaccatcccatacgacttttctcttcgtttttcgcttcttcatcgtttacgtatgacaaaaaa Intra-Species Hit: Count: 1 Min: 1 Max: 394 Len: 394 Subject: tfor_TF2778_TF2779|outer membrane protein, TonB dependent receptor:fucose permease|POSITIVE:POSITIVE|[2964312,2964705]|394 HSP 1 e-value: 0.0 bit: 739.0 Len: 394 Query Start:1 Query End:394 Subject Strand: POSITIVE Subject Start: 1 Subject End: 394 ccgcgctgatcatctgcaaaataaaaatggctaacagaacatatcagcagttgaaaacggcgaatttacataaaaaacgcgatatttaagccaatggagatnnnnnnncgaggagtgtagtttctccttagccaatgaaccatttacgacacccccagaggtggtacttcaaacgtaaggggtgattatgaccgaccgtcttaggtagaaatatgtatatctgtcacttaacgtgtgacatgaaactatttaggacaatattgcgtctctacgggtaaactgactgccggatgctgaaaatcgactgctgacgactatcccaaaggattttaaccatcccatacgacttttctcttcgtttttcgcttcttcatcgtttacgtatgacaaaaaa ccgcgctgatcatctgcaaaataaaaatggctaacagaacatatcagcagttgaaaacggcgaatttacataaaaaacgcgatatttaagccaatggagataaaaaaacgaggagtgtagtttctccttagccaatgaaccatttacgacacccccagaggtggtacttcaaacgtaaggggtgattatgaccgaccgtcttaggtagaaatatgtatatctgtcacttaacgtgtgacatgaaactatttaggacaatattgcgtctctacgggtaaactgactgccggatgctgaaaatcgactgctgacgactatcccaaaggattttaaccatcccatacgacttttctcttcgtttttcgcttcttcatcgtttacgtatgacaaaaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCGCGCUGAUCAUCUGCAAAAUAAAAAUGGCUAACAGAACAUAUCAGCAGUUGAAAACGGCGAAUUUACAUAAAAAACGCGAUAUUUAAGCCAAUGGAGAUAAAAAAACGAGGAGUGUAGUUUCUCCUUAGCCAAUGAACCAUUUACGACACCCCCAGAGGUGGUACUUCAAACGUAAGGGGUGAUUAUGACCGACCGUCUUAGGUAGAAAUAUGUAUAUCUGUCACUUAACGUGUGACAUGAAACUAUUUAGGACAAUAUUGCGUCUCUACGGGUAAACUGACUGCCGGAUGCUGAAAAUCGACUGCUGACGACUAUCCCAAAGGAUUUUAACCAUCCCAUACGACUUUUCUCUUCGUUUUUCGCUUCUUCAUCGUUUACGUAUGACAAAAAA ...(((((.(((.((((..........((.....))..........)))).)))...)))))................(..((((.(((((..(((((((...((((((((((((...((((..((.(((((.................((((((......(((....))).......))))))........(((..(((((((((((..((....)).((((((((.......)))))).))..)))))))))))......((((((.....((((.......))))))))))......)))...))))).))..((((....))))................))))...))))))))))))....))))))).))))).))))..)...... (-92.27) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUUUGUCAUACGUAAACGAUGAAGAAGCGAAAAACGAAGAGAAAAGUCGUAUGGGAUGGUUAAAAUCCUUUGGGAUAGUCGUCAGCAGUCGAUUUUCAGCAUCCGGCAGUCAGUUUACCCGUAGAGACGCAAUAUUGUCCUAAAUAGUUUCAUGUCACACGUUAAGUGACAGAUAUACAUAUUUCUACCUAAGACGGUCGGUCAUAAUCACCCCUUACGUUUGAAGUACCACCUCUGGGGGUGUCGUAAAUGGUUCAUUGGCUAAGGAGAAACUACACUCCUCGUUUUUUUAUCUCCAUUGGCUUAAAUAUCGCGUUUUUUAUGUAAAUUCGCCGUUUUCAACUGCUGAUAUGUUCUGUUAGCCAUUUUUAUUUUGCAGAUGAUCAGCGCGG ..........(((((((((((((...(((((((((((((.(((.(((((((..((.((((..((...(((....)))))..))))..))..))))))).....(((...(((((((..(((..(((.((((......))))))).......((.((((((.......))))))))..(((.((((((.((.((((..(((.(((....)))))).)))).))..)))))).(((((....)))))..)))...)))..)))))))..))).........))).)))))))))...........))))...))))).....))))))))......((((........((((((....(((((................)))))..)))))))))) (-94.79) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 437 320 272 164 114 tfor:TF2820|5end_argininosuccinate_synthetase_3009876..3010106_POSITIVE 410 387 346 221 180 tfor:TF2014|5end_dipeptidyl_aminopeptidase_IV_2169398..2169628_POSITIVE 373 327 282 57 12 tfor:TF2884|5end_conserved_hypothetical_protein_3075057..3075287_POSITIVE 370 296 251 55 2 tfor:TF2249|5end_transfer_region-related_protein,_TraC_2422988..2423218_POSITIVE 369 198 152 188 135 tfor:TF2307|5end_two-component_system_sensor_histidine_kinase/response_2462618..2462848_POSITIVE 349 200 151 63 1 tfor:TF1935|5end_ATP-dependent_RNA_helicase,_DEAD/DEAH-related_helicase_2082002..2082232_POSITIVE 345 319 272 106 61 tfor:TF1299|5end_conserved_hypothetical_protein_1380937..1381167_POSITIVE 344 310 263 71 22 tfor:TF1494|5end_cobinamide_kinase/cobinamide_phosphate_guanylyltransferase_1594016..1594246_POSITIVE 342 386 347 213 170 tfor:TF1877|5end_hypothetical_protein_2030412..2030642_POSITIVE 341 300 263 231 187 tfor:TF2949|5end_dihydroxynaphthoate_synthase_(naphthoate_synthase)_3156578..3156808_POSITIVE 341 308 264 199 148 tfor:TF0970|5end_2-keto-3-deoxygluconate_kinase_1020396..1020626_POSITIVE 340 320 274 222 175 tfor:TF2992|5end_hexapeptide_transferase_family_protein_3209042..3209272_POSITIVE 336 308 263 190 131 tfor:TF2332|5end_signal_peptidase_I_2491694..2491924_POSITIVE 335 294 264 231 197 tfor:TF2892|5end_seryl-tRNA_synthetase_3079309..3079539_POSITIVE 334 320 272 66 20 tfor:TF0777|5end_1,4-dihydroxy-2-naphthoate_octaprenyltransferase_826098..826328_POSITIVE 330 307 263 136 96 tfor:TF3108|5end_glutamine-hydrolyzing_carbamoyl-phosphate_synthase,_large_subunit_3338732..3338962_POSITIVE 330 305 263 65 12 tfor:TF2756|5end_conserved_hypothetical_protein_2940973..2941203_POSITIVE 330 293 252 91 55 tfor:TF2640|5end_hypothetical_protein_2809106..2809336_POSITIVE 330 309 261 219 167 tfor:TF0425|5end_outer_membrane_protein_443069..443299_POSITIVE 329 326 283 66 20 tfor:TF0307|5end_conserved_hypothetical_protein_332783..333013_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 410 387 346 84 43 tfor:TF2013|3end_polysaccharide_deacetylase_2169341..2169491_POSITIVE 396 308 261 144 91 tfor:TF2173|3end_hypothetical_protein_2346063..2346213_POSITIVE 396 308 261 144 91 tfor:TF0346|3end_hypothetical_protein_367316..367466_POSITIVE 373 327 282 49 4 tfor:TF2883|3end_peptidyl-prolyl_cis-trans_isomerase_3075129..3075279_POSITIVE 370 296 251 55 2 tfor:TF2248|3end_transfer_region-related_protein,_TraB_2423068..2423218_POSITIVE 352 310 261 68 8 tfor:TF1165|3end_conserved_hypothetical_protein_1245921..1246071_POSITIVE 346 310 263 146 94 tfor:TF2953|3end_possible_TonB-dependent_outer_membrane_receptor_3161501..3161651_POSITIVE 334 320 272 61 15 tfor:TF0776|3end_ABC_transporter,_permease_component_826173..826323_POSITIVE 330 307 263 60 20 tfor:TF3107|3end_hypothetical_protein_3338736..3338886_POSITIVE 330 305 263 65 12 tfor:TF2755|3end_hypothetical_protein_2941053..2941203_POSITIVE 328 305 261 66 19 tfor:TF0599|3end_hypothetical_protein_630130..630280_POSITIVE 328 318 271 129 95 tfor:TF0533|3end_hypothetical_protein_559519..559669_POSITIVE 324 198 151 65 10 tfor:TF0832|3end_conserved_hypothetical_protein_888788..888938_POSITIVE 324 297 253 48 8 tfor:TF0762|3end_chromate_transport_protein_809755..809905_POSITIVE 323 317 273 45 3 tfor:TF1474|3end_6-phosphogluconolactonase_1568123..1568273_POSITIVE 322 320 271 148 101 tfor:TF2125|3end_conserved_hypothetical_protein_2302465..2302615_POSITIVE 321 169 123 53 5 tfor:TF0054|3end_possible_flavodoxin_58460..58610_POSITIVE 319 313 272 121 73 tfor:TF1622|3end_conserved_hypothetical_protein_1736763..1736913_POSITIVE 318 308 264 151 108 tfor:TF2819|3end_N-acetyl-gamma-glutamylphosphate_reductase_3009956..3010106_POSITIVE 317 314 272 72 17 tfor:TF2836|3end_methyltransferase_3028028..3028178_POSITIVE