Origin IGS: taattaacagatccggcgaatccccgaagaagtgattagattgcactattcaccctctctgcaatcgcggctgcacgattccgggattccgaagaacgattaaaaataaagaataaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tttattctttatttttaatcgttcttcggaatcccggaatcgtgcagccgcgattgcagagagggtgaatagtgcaatctaatcacttcttcggggattcgccggatctgttaatta Mask Tandem Repeat Region ================================================ taattaacagatccggcgaatccccgaagaagtgattagattgcactattcaccctctctgcaatcgcggctgcacgattccgggattccgaagaacgattaaaaataaagaataaa Find is-nt database================================================ Query_seq: TF2578:TF2579|TF2578:TF2579:30S ribosomal protein S11:30S ribosomal protein S4:->->:2747225..2747341 117 taattaacagatccggcgaatccccgaagaagtgattagattgcactattcaccctctctgcaatcgcggctgcacgattccgggattccgaagaacgattaaaaataaagaataaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2578:TF2579|TF2578:TF2579:30S ribosomal protein S11:30S ribosomal protein S4:->->:2747225..2747341 117 taattaacagatccggcgaatccccgaagaagtgattagattgcactattcaccctctctgcaatcgcggctgcacgattccgggattccgaagaacgattaaaaataaagaataaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2578:TF2579|TF2578:TF2579:30S ribosomal protein S11:30S ribosomal protein S4:->->:2747225..2747341 117 taattaacagatccggcgaatccccgaagaagtgattagattgcactattcaccctctctgcaatcgcggctgcacgattccgggattccgaagaacgattaaaaataaagaataaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taattaacagatccggcgaatccccgaagaagtgattagattgcactattcaccctctctgcaatcgcggctgcacgattccgggattccgaagaacgattaaaaataaagaataaa Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 11 End: 100 .......... M R R I P E E V I R L H Y S P S L Q S R L H D S G I P K N D ................. taattaacagatccggcgaatccccgaagaagtgattagattgcactattcaccctctctgcaatcgcggctgcacgattccgggattccgaagaacgattaaaaataaagaataaa 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================================================ taattaacagatccggcgaatccccgaagaagtgattagattgcactattcaccctctctgcaatcgcggctgcacgattccgggattccgaagaacgattaaaaataaagaataaa Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 49 HP_score: -3.0 Tail_Score: -3.63569 Start: 32 End: 53 Full_Region: gcgattgcagagagg gtgaatag tgcaat ctaatcac ttcttcggggattcg ...............................gtgaatagtgcaatctaatcac................................................................ Find igs database================================================ Query_seq: TF2578:TF2579|TF2578:TF2579:30S ribosomal protein S11:30S ribosomal protein S4:->->:2747225..2747341 117 taattaacagatccggcgaatccccgaagaagtgattagattgcactattcaccctctctgcaatcgcggctgcacgattccgggattccgaagaacgattaaaaataaagaataaa Intra-Species Hit: Count: 1 Min: 1 Max: 117 Len: 117 Subject: tfor_TF2578_TF2579|30S ribosomal protein S11:30S ribosomal protein S4|POSITIVE:POSITIVE|[2747225,2747341]|117 HSP 1 e-value: 2.0E-60 bit: 232.0 Len: 117 Query Start:1 Query End:117 Subject Strand: POSITIVE Subject Start: 1 Subject End: 117 taattaacagatccggcgaatccccgaagaagtgattagattgcactattcaccctctctgcaatcgcggctgcacgattccgggattccgaagaacgattaaaaataaagaataaa taattaacagatccggcgaatccccgaagaagtgattagattgcactattcaccctctctgcaatcgcggctgcacgattccgggattccgaagaacgattaaaaataaagaataaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUUAACAGAUCCGGCGAAUCCCCGAAGAAGUGAUUAGAUUGCACUAUUCACCCUCUCUGCAAUCGCGGCUGCACGAUUCCGGGAUUCCGAAGAACGAUUAAAAAUAAAGAAUAAA ...((((..(.((....(((((((.(((...(((....(((((((..............))))))).......)))..))).)))))))....)).)..)))).............. (-25.14) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUAUUCUUUAUUUUUAAUCGUUCUUCGGAAUCCCGGAAUCGUGCAGCCGCGAUUGCAGAGAGGGUGAAUAGUGCAAUCUAAUCACUUCUUCGGGGAUUCGCCGGAUCUGUUAAUUA ..............(((((.(.(((...((((((((.(((((((....))))))).).(((..(((((.(((......))).)))))..))).)))))))...))).).)))))... (-33.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 429 100 52 215 169 tfor:TF3087|5end_conserved_hypothetical_protein_3319878..3320108_POSITIVE 421 91 54 71 29 tfor:TF2201|5end_hypothetical_protein_2377956..2378186_POSITIVE 403 99 53 227 181 tfor:TF1845|5end_hypothetical_protein_1996620..1996850_POSITIVE 385 98 51 139 89 tfor:TF1182|5end_hypothetical_protein_1268565..1268795_POSITIVE 379 99 51 211 140 tfor:TF0555|5end_Bacteroides_aerotolerance_protein,_BatB_587048..587278_POSITIVE 377 100 54 73 21 tfor:TF0722|5end_pyruvate_dehydrogenase_E3_component(dihydrolipoamide_dehydrogenase)_772873..773103_POSITIVE 376 91 54 216 178 tfor:TF0617|5end_alpha-1,2-mannosidase_650862..651092_POSITIVE 375 99 54 90 48 tfor:TF1289|5end_ribosomal_protein_L11_methyltransferase_1370302..1370532_POSITIVE 365 88 43 230 187 tfor:TF2993|5end_SAM-dependent_methyltransferase_3209636..3209866_POSITIVE 362 98 53 217 173 tfor:TF0265|5end_conserved_hypothetical_protein,_Rhs_family_293279..293509_POSITIVE 361 99 51 73 14 tfor:TF2274|5end_conserved_hypothetical_protein_2436652..2436882_POSITIVE 360 99 51 73 30 tfor:TF2893|5end_conserved_hypothetical_protein;_possible_phosphoesterase_3080766..3080996_POSITIVE 360 97 58 225 182 tfor:TF2693|5end_possible_aminotransferase_2868435..2868665_POSITIVE 357 98 54 65 16 tfor:TF1461|5end_DNA-damage-inducible_protein_F_1550845..1551075_POSITIVE 351 98 53 48 1 tfor:TF0538|5end_hypothetical_protein_566891..567121_POSITIVE 351 89 54 108 58 tfor:TF0145|5end_glutamine_synthetase_152446..152676_POSITIVE 345 100 54 64 8 tfor:TF0361|5end_hypothetical_protein_379458..379688_POSITIVE 342 98 53 74 26 tfor:TF2817|5end_hypothetical_protein_3007358..3007588_POSITIVE 342 99 57 53 5 tfor:TF2276|5end_conserved_hypothetical_protein_2438226..2438456_POSITIVE 340 100 54 61 16 tfor:TF2756|5end_conserved_hypothetical_protein_2940973..2941203_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 419 92 51 50 3 tfor:TF3043|3end_conserved_hypothetical_protein_3272409..3272559_POSITIVE 385 98 51 139 89 tfor:TF1186|3end_hypothetical_protein_1269815..1269965_POSITIVE 351 89 54 83 33 tfor:TF0143|3end_aspartate--ammonia_ligase_152501..152651_POSITIVE 347 91 55 85 50 tfor:TF1301|3end_hypothetical_protein_1383487..1383637_POSITIVE 345 100 54 64 8 tfor:TF0360|3end_hypothetical_protein_379538..379688_POSITIVE 340 100 54 61 16 tfor:TF2755|3end_hypothetical_protein_2941053..2941203_POSITIVE 330 91 58 146 117 tfor:TF2878|3end_conserved_hypothetical_protein;_possible_CAAX_amino_terminal_protease_family_3068283..3068433_POSITIVE 330 99 54 65 8 tfor:TF2164|3end_hypothetical_protein_2341708..2341858_POSITIVE 325 89 41 121 53 tfor:TF3069|3end_hypothetical_protein_3294413..3294563_POSITIVE 323 89 41 87 29 tfor:TF1326|3end_hypothetical_protein_1404100..1404250_POSITIVE 322 98 54 82 35 tfor:TF2107|3end_hypothetical_protein_2277436..2277586_POSITIVE 322 98 54 55 8 tfor:TF0368|3end_hypothetical_protein_385834..385984_POSITIVE 315 100 53 82 38 tfor:TF2671|3end_dipeptidyl_peptidase_IV_(DPP_IV)_N-terminal_region_2846163..2846313_POSITIVE 312 98 64 117 90 tfor:TF1443|3end_hypothetical_protein_1528203..1528353_POSITIVE 309 101 61 70 28 tfor:TF1199|3end_dephospho-CoA_kinase_1282797..1282947_POSITIVE 309 99 54 58 3 tfor:TF0358|3end_hypothetical_protein_376304..376454_POSITIVE 307 78 40 89 53 tfor:TF0351|3end_hypothetical_protein_371226..371376_POSITIVE 307 98 53 68 21 tfor:TF0238|3end_outer_membrane_protein_268957..269107_POSITIVE 305 98 54 54 7 tfor:TF2176|3end_hypothetical_protein_2349185..2349335_POSITIVE 305 85 43 62 5 tfor:TF1461|3end_DNA-damage-inducible_protein_F_1552253..1552403_POSITIVE