Origin IGS: taattgatatttttcttgcaaagaacaggttgggtagatatactgcctagctcatttatttccttgacactctgtttgagtatcctgaaaacgggcttttcaagatcagagtgtcaactaatcaataaacaataggagtgcata .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tatgcactcctattgtttattgattagttgacactctgatcttgaaaagcccgttttcaggatactcaaacagagtgtcaaggaaataaatgagctaggcagtatatctacccaacctgttctttgcaagaaaaatatcaatta Mask Tandem Repeat Region ================================================ taattgatatttttcttgcaaagaacaggttgggtagatatactgcctagctcatttatttccttgacactctgtttgagtatcctgaaaacgggcttttcaagatcagagtgtcaactaatcaataaacaataggagtgcata Find is-nt database================================================ Query_seq: AA01238:AA01239|AA01238:AA01239:50S ribosomal protein L36:30S ribosomal protein S13:->->:844499..844642 144 taattgatatttttcttgcaaagaacaggttgggtagatatactgcctagctcatttatttccttgacactctgtttgagtatcctgaaaacgggcttttcaagatcagagtgtcaactaatcaataaacaataggagtgcata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA01238:AA01239|AA01238:AA01239:50S ribosomal protein L36:30S ribosomal protein S13:->->:844499..844642 144 taattgatatttttcttgcaaagaacaggttgggtagatatactgcctagctcatttatttccttgacactctgtttgagtatcctgaaaacgggcttttcaagatcagagtgtcaactaatcaataaacaataggagtgcata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA01238:AA01239|AA01238:AA01239:50S ribosomal protein L36:30S ribosomal protein S13:->->:844499..844642 144 taattgatatttttcttgcaaagaacaggttgggtagatatactgcctagctcatttatttccttgacactctgtttgagtatcctgaaaacgggcttttcaagatcagagtgtcaactaatcaataaacaataggagtgcata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taattgatatttttcttgcaaagaacaggttgggtagatatactgcctagctcatttatttccttgacactctgtttgagtatcctgaaaacgggcttttcaagatcagagtgtcaactaatcaataaacaataggagtgcata Predict ORF larger than 30AA ================================================ Protein_Len: 43 Strand: + Start: 4 End: 132 ... M I F F L Q R T G W V D I L P S S F I S L T L C L S I L K T G F S R S E C Q L I N K Q ............ taattgatatttttcttgcaaagaacaggttgggtagatatactgcctagctcatttatttccttgacactctgtttgagtatcctgaaaacgggcttttcaagatcagagtgtcaactaatcaataaacaataggagtgcata 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================================================ taattgatatttttcttgcaaagaacaggttgggtagatatactgcctagctcatttatttccttgacactctgtttgagtatcctgaaaacgggcttttcaagatcagagtgtcaactaatcaataaacaataggagtgcata Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: AA01238:AA01239|AA01238:AA01239:50S ribosomal protein L36:30S ribosomal protein S13:->->:844499..844642 144 taattgatatttttcttgcaaagaacaggttgggtagatatactgcctagctcatttatttccttgacactctgtttgagtatcctgaaaacgggcttttcaagatcagagtgtcaactaatcaataaacaataggagtgcata Intra-Species Hit: Count: 1 Min: 1 Max: 144 Len: 144 Subject: aact_AA01238_AA01239|50S ribosomal protein L36:30S ribosomal protein S13|POSITIVE:POSITIVE|[844499,844642]|144 HSP 1 e-value: 2.0E-76 bit: 285.0 Len: 144 Query Start:1 Query End:144 Subject Strand: POSITIVE Subject Start: 1 Subject End: 144 taattgatatttttcttgcaaagaacaggttgggtagatatactgcctagctcatttatttccttgacactctgtttgagtatcctgaaaacgggcttttcaagatcagagtgtcaactaatcaataaacaataggagtgcata taattgatatttttcttgcaaagaacaggttgggtagatatactgcctagctcatttatttccttgacactctgtttgagtatcctgaaaacgggcttttcaagatcagagtgtcaactaatcaataaacaataggagtgcata Inter-species Hit: Count: 5 Min: 5 Max: 119 Len: 115 Subject: NC_002663_PM1393_PM1394|30S ribosomal protein S13:50S ribosomal protein L36|NEGATIVE:NEGATIVE|[1587708,1587847]|140 HSP 1 e-value: 3.0E-32 bit: 139.0 Len: 110 Query Start:10 Query End:119 Subject Strand: NEGATIVE Subject Start: 24 Subject End: 133 .........tttttcttgcaaagaacaggttgggtagatatactgcctagctcatttatttccttgacactctgtttgagtatcctgaaaacgggcttttcaagatcagagtgtcaact......................... .........tttttcttgcaaagaaccagttgagcagttatactgctcagctcatttatgtccttgacactttgtttgagtatcctgaaaacgggcttttcaagatcaaagtgtcaact......................... Subject: NC_007146_NTHI0961_NTHI0962|preprotein translocase SecY:30S ribosomal protein S13|POSITIVE:POSITIVE|[914706,914986]|281 HSP 1 e-value: 4.0E-25 bit: 115.0 Len: 102 Query Start:9 Query End:110 Subject Strand: POSITIVE Subject Start: 148 Subject End: 249 ........atttttcttgcaaagaacaggttgggtagatatactgcctagctcatttatttccttgacactctgtttgagtatcctgaaaacgggcttttcaagatcaga.................................. ........atttttcttgccaagaaccagttgagtagttatactgctcaactcatttatgtccttgatattctgtttgagtatcctgaaaacgggcttttcaagatcaga.................................. Subject: NC_000907_HI0798.1_HI0799|50S ribosomal protein L36:30S ribosomal protein S13|POSITIVE:POSITIVE|[850503,850641]|139 HSP 1 e-value: 4.0E-25 bit: 115.0 Len: 102 Query Start:9 Query End:110 Subject Strand: POSITIVE Subject Start: 6 Subject End: 107 ........atttttcttgcaaagaacaggttgggtagatatactgcctagctcatttatttccttgacactctgtttgagtatcctgaaaacgggcttttcaagatcaga.................................. ........atttttcttgccaagaaccagttgagtagttatactgctcaactcatttatgtccttgatattctgtttgagtatcctgaaaacgggcttttcaagatcaga.................................. Subject: NC_008309_HS_0080a_HS_0081|50S ribosomal protein L36:30S ribosomal protein S13|POSITIVE:POSITIVE|[76617,76759]|143 HSP 1 e-value: 1.0E-19 bit: 97.6 Len: 105 Query Start:5 Query End:109 Subject Strand: POSITIVE Subject Start: 2 Subject End: 105 ....tgatatttttcttgcaaagaacaggttgggtagatatactgcctagctcatttatttccttgacactctgtttgagtatcctgaaaacgggcttttcaagatcag................................... ....tgatatttttcttgcaaagaaccagctgggtatatataatactcagctcatttatgtccttgatatactgtttgagtatcctg-aaacgggcttttcaagatcag................................... Subject: NC_006300_MS2026_MS2027|30S ribosomal protein S13:50S ribosomal protein L36|NEGATIVE:NEGATIVE|[1995645,1995783]|139 HSP 1 e-value: 4.0E-19 bit: 95.6 Len: 108 Query Start:10 Query End:117 Subject Strand: NEGATIVE Subject Start: 26 Subject End: 131 .........tttttcttgcaaagaacaggttgggtagatatactgcctagctcatttatttccttgacactctgtttgagtatcctgaaaacgggcttttcaagatcagagtgtcaa........................... .........tttttcttgcaa-gaaccagttgagcagttatactgctcaactcatttatgtccttg-cacactgtttgagtatcctgaaaacgggcttttcaagatcagtgtgtcaa........................... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUAUUUUUCUUGCAAAGAACAGGUUGGGUAGAUAUACUGCCUAGCUCAUUUAUUUCCUUGACACUCUGUUUGAGUAUCCUGAAAACGGGCUUUUCAAGAUCAGAGUGUCAACU ..................(((..((((((((((.....))))))))))..)))......(((((((((((((((((...((((....))))...))))))..))))))))))).. (-37.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUUGACACUCUGAUCUUGAAAAGCCCGUUUUCAGGAUACUCAAACAGAGUGUCAAGGAAAUAAAUGAGCUAGGCAGUAUAUCUACCCAACCUGUUCUUUGCAAGAAAAAUAUCA ..(((((((((((((((((((((.....)))))))))).......))))))))))).....((((.((((.(((..(((....)))....))))))))))).............. (-29.81) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 264 70 26 86 33 aact:AA01532|5end_hypothetical_protein_1028771..1029001_POSITIVE 264 89 41 45 9 aact:AA00075|5end_conserved_hypothetical_protein_54963..55193_POSITIVE 253 110 61 87 45 aact:AA02538|5end_conserved_hypothetical_protein_1765187..1765417_POSITIVE 251 109 66 81 37 aact:AA00980|5end_hypothetical_protein_684970..685200_POSITIVE 250 75 39 71 27 aact:AA01237|5end_preprotein_translocase_842897..843127_POSITIVE 250 110 67 189 135 aact:AA00141|5end_hypoxanthine_phosphoribosyl_transferase_(HPRT)_100814..101044_POSITIVE 245 70 23 157 108 aact:AA01146|5end_conserved_hypothetical_protein_784433..784663_POSITIVE 240 80 38 198 157 aact:AA01567|5end_conserved_hypothetical_protein_(possible_cell-wall-associated_hydrolase)_1054944..1055174_POSITIVE 240 80 38 199 158 aact:AA01262|5end_hydrolase_859576..859806_POSITIVE 236 46 8 231 191 aact:AA00863|5end_conserved_hypothetical_protein_596679..596909_POSITIVE 235 94 62 211 179 aact:AA01476|5end_hypothetical_protein_991402..991632_POSITIVE 230 99 60 65 30 aact:AA01573|5end_peptide_transport_periplasmic_protein_1059761..1059991_POSITIVE 229 74 31 58 1 aact:AA02374|5end_ribose_5-phosphate_isomerase_A_1625839..1626069_POSITIVE 226 109 66 80 24 aact:AA01780|5end_ABC-related_molybdenum_transport_system_permease_protein_1201084..1201314_POSITIVE 225 58 12 206 164 aact:AA01109|5end_oxidoreductase_(possible_short-chain_alcohol_dehydrogenase)_763899..764129_POSITIVE 223 64 23 101 60 aact:AA01338|5end_hypothetical_protein_904967..905197_POSITIVE 222 102 80 157 131 aact:AA02968|5end_hypothetical_protein_2075917..2076147_POSITIVE 222 66 21 103 59 aact:AA01477|5end_type_I_restriction_enzyme_R_protein_992249..992479_POSITIVE 222 50 17 219 179 aact:AA00931|5end_elongation_factor_Tu_(tufA)_641920..642150_POSITIVE 221 79 33 55 8 aact:AA00729|5end_possible_hemolysin_(TlyC-like)_500204..500434_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 264 70 26 112 59 aact:AA01531|3end_hypothetical_protein_1028877..1029027_POSITIVE 253 110 61 83 41 aact:AA02536|3end_conserved_hypothetical_protein_1765263..1765413_POSITIVE 251 109 66 85 41 aact:AA00979|3end_type_B_carboxylesterase;_p-nitrobenzyl_esterase_685054..685204_POSITIVE 250 75 39 64 20 aact:AA01236|3end_50S_ribosomal_protein_L15_842970..843120_POSITIVE 245 70 23 104 55 aact:AA01145|3end_glycyl-tRNA_synthetase_alpha_subunit_784460..784610_POSITIVE 238 67 25 104 56 aact:AA02420|3end_ISRSO11_related_transposase_1662668..1662818_POSITIVE 238 60 11 94 56 aact:AA00933|3end_ribose_ABC_transporter,_ATP-binding_protein_645197..645347_POSITIVE 233 100 51 56 2 aact:AA00213|3end_cold_shock_protein_(negative_regulator_of_cspA_transcription)_147357..147507_POSITIVE 230 99 60 62 27 aact:AA01572|3end_peptide_ABC_transporter,_permease_protein_1059838..1059988_POSITIVE 226 109 66 90 34 aact:AA01779|3end_molybdenum_ABC_transporter,_ATP-binding_protein_1201174..1201324_POSITIVE 223 64 23 85 44 aact:AA01337|3end_cell_division_protein_N_905031..905181_POSITIVE 222 102 80 74 48 aact:AA02967|3end_elongation_factor_P_(EF-P)_2075914..2076064_POSITIVE 219 91 54 58 17 aact:AA02205|3end_short_chain_dehydrogenase/reductase_1501984..1502134_POSITIVE 217 44 6 65 28 aact:AA02440|3end_ABC_transporter,_ATP-binding_protein_1685791..1685941_POSITIVE 217 90 44 133 80 aact:AA02439|3end_integral_membrane_protein;_possible_ABC_transporter_permease_1685118..1685268_POSITIVE 217 48 13 44 3 aact:AA02042|3end_tagatose_1,6-diphosphate_aldolase_1390277..1390427_POSITIVE 216 84 41 80 41 aact:AA01066|3end_conserved_hypothetical_protein_738900..739050_POSITIVE 215 79 40 102 58 aact:AA02021|3end_anaerobic_glycerol-3-phosphate_dehydrogenase_1376601..1376751_POSITIVE 214 49 1 115 53 aact:AA01487|3end_ATP_synthase_F1,_subunit_delta_1000739..1000889_POSITIVE 214 68 22 100 57 aact:AA01402|3end_beta_1-4_glucosyltransferase_948382..948532_POSITIVE