Origin IGS: tacatcaaatccctgtttgatattaaaaacagggatttttcgtgtcagagaatgctcgttggattctaagacctagataagatttgtcaaaaaatgtcctatttgactggttttttgatataataagcttagttatttcatggaggtggctc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gagccacctccatgaaataactaagcttattatatcaaaaaaccagtcaaataggacattttttgacaaatcttatctaggtcttagaatccaacgagcattctctgacacgaaaaatccctgtttttaatatcaaacagggatttgatgta Mask Tandem Repeat Region ================================================ tacatcaaatccctgtttgatattaaaaacagggatttttcgtgtcagagaatgctcgttggattctaagacctagataagatttgtcaaaaaatgtcctatttgactggttttttgatataataagcttagttatttcatggaggtggctc Find is-nt database================================================ Query_seq: SSA_0448:SSA_0449|SSA_0448:SSA_0449:Excinuclease ATPase subunit A, putative:Aminopeptidase P; XAA-pro aminopeptidase, putative:->->:449452..449603 152 tacatcaaatccctgtttgatattaaaaacagggatttttcgtgtcagagaatgctcgttggattctaagacctagataagatttgtcaaaaaatgtcctatttgactggttttttgatataataagcttagttatttcatggaggtggctc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0448:SSA_0449|SSA_0448:SSA_0449:Excinuclease ATPase subunit A, putative:Aminopeptidase P; XAA-pro aminopeptidase, putative:->->:449452..449603 152 tacatcaaatccctgtttgatattaaaaacagggatttttcgtgtcagagaatgctcgttggattctaagacctagataagatttgtcaaaaaatgtcctatttgactggttttttgatataataagcttagttatttcatggaggtggctc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0448:SSA_0449|SSA_0448:SSA_0449:Excinuclease ATPase subunit A, putative:Aminopeptidase P; XAA-pro aminopeptidase, putative:->->:449452..449603 152 tacatcaaatccctgtttgatattaaaaacagggatttttcgtgtcagagaatgctcgttggattctaagacctagataagatttgtcaaaaaatgtcctatttgactggttttttgatataataagcttagttatttcatggaggtggctc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tacatcaaatccctgtttgatattaaaaacagggatttttcgtgtcagagaatgctcgttggattctaagacctagataagatttgtcaaaaaatgtcctatttgactggttttttgatataataagcttagttatttcatggaggtggctc Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: - Start: 26 End: 136 ......................... F C P N K T D S F A R Q I R L G L Y S K D F F T R N S Q N K S I I L K T M ................ tacatcaaatccctgtttgatattaaaaacagggatttttcgtgtcagagaatgctcgttggattctaagacctagataagatttgtcaaaaaatgtcctatttgactggttttttgatataataagcttagttatttcatggaggtggctc 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================================================ tacatcaaatccctgtttgatattaaaaacagggatttttcgtgtcagagaatgctcgttggattctaagacctagataagatttgtcaaaaaatgtcctatttgactggttttttgatataataagcttagttatttcatggaggtggctc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0448:SSA_0449|SSA_0448:SSA_0449:Excinuclease ATPase subunit A, putative:Aminopeptidase P; XAA-pro aminopeptidase, putative:->->:449452..449603 152 tacatcaaatccctgtttgatattaaaaacagggatttttcgtgtcagagaatgctcgttggattctaagacctagataagatttgtcaaaaaatgtcctatttgactggttttttgatataataagcttagttatttcatggaggtggctc Intra-Species Hit: Count: 1 Min: 1 Max: 152 Len: 152 Subject: NC_009009_SSA_0448_SSA_0449|Excinuclease ATPase subunit A, putative:Aminopeptidase P; XAA-pro aminopeptidase, putative|POSITIVE:POSITIVE|[449452,449603]|152 HSP 1 e-value: 3.0E-81 bit: 301.0 Len: 152 Query Start:1 Query End:152 Subject Strand: POSITIVE Subject Start: 1 Subject End: 152 tacatcaaatccctgtttgatattaaaaacagggatttttcgtgtcagagaatgctcgttggattctaagacctagataagatttgtcaaaaaatgtcctatttgactggttttttgatataataagcttagttatttcatggaggtggctc tacatcaaatccctgtttgatattaaaaacagggatttttcgtgtcagagaatgctcgttggattctaagacctagataagatttgtcaaaaaatgtcctatttgactggttttttgatataataagcttagttatttcatggaggtggctc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UACAUCAAAUCCCUGUUUGAUAUUAAAAACAGGGAUUUUUCGUGUCAGAGAAUGCUCGUUGGAUUCUAAGACCUAGAUAAGAUUUGUCAAAAAAUGUCCUAUUUGACUGGUUUUUUGAUAUAAUAAGCUUAGUUAUUUCAUGGAGGUGGCUC ......((((((((((((........)))))))))))).((..(((..(((((.(.....).)))))..)))...)).......((((((((((((((......)))..)))))))))))..........(((((((((...))))))))). (-39.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAGCCACCUCCAUGAAAUAACUAAGCUUAUUAUAUCAAAAAACCAGUCAAAUAGGACAUUUUUUGACAAAUCUUAUCUAGGUCUUAGAAUCCAACGAGCAUUCUCUGACACGAAAAAUCCCUGUUUUUAAUAUCAAACAGGGAUUUGAUGUA ((((....................))))..((((((.........((((((..........)))))).............(((..(((((.(.....).)))))..))).....((((((((((((........)))))))))))))))))) (-30.45) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 291 149 102 99 44 NC_009009:SSA_1397|5end_hypothetical_protein_1410589..1410819_POSITIVE 275 89 41 90 34 NC_009009:SSA_0290|5end_hypothetical_protein_285229..285459_NEGATIVE 270 74 31 210 167 NC_009009:SSA_0621|5end_SOS_responce_UmuC_protein,_putative_613737..613967_NEGATIVE 269 76 31 46 5 NC_009009:SSA_2056|5end_Cinnamoyl_ester_hydrolase,_putative_2058587..2058817_POSITIVE 267 78 32 49 2 NC_009009:SSA_0781|5end_Mannose-6-phosphate_isomerase,_putative_765373..765603_POSITIVE 266 80 31 99 40 NC_009009:SSA_0729|5end_hypothetical_protein_714397..714627_POSITIVE 265 150 103 196 128 NC_009009:SSA_0043|5end_hypothetical_protein_48801..49031_POSITIVE 258 89 43 226 173 NC_009009:SSA_0546|5end_Phospho-2-dehydro-3-deoxyheptonate_aldolase_(DAHP_synthatase),_possibly_tyr-sensitive,_putative_540852..541082_POSITIVE 257 147 101 221 178 NC_009009:SSA_1550|5end_hypothetical_protein_1552665..1552895_NEGATIVE 255 89 48 224 185 NC_009009:SSA_1656|5end_Nisin_resistance_protein,_putative_1652890..1653120_NEGATIVE 253 78 31 210 171 NC_009009:SSA_1772|5end_hypothetical_protein_1759545..1759775_NEGATIVE 251 73 35 171 130 NC_009009:SSA_1930|5end_Acetyl-CoA_carboxylase_alpha_subunit,_putative_1918547..1918777_NEGATIVE 250 75 36 225 176 NC_009009:SSA_0957|5end_Dehydrogenase,_putative_966276..966506_POSITIVE 249 74 31 215 157 NC_009009:SSA_0332|5end_hypothetical_protein_325909..326139_POSITIVE 248 76 31 213 167 NC_009009:SSA_0540|5end_Glycerol_uptake_facilitator_protein,_putative_534955..535185_POSITIVE 248 88 41 169 121 NC_009009:SSA_0494|5end_ABC-type_dipeptide/oligopeptide/nickel_transport_system,_ATPase_component,_putative_494407..494637_POSITIVE 248 74 31 121 80 NC_009009:SSA_0070|5end_Acetylxylan_esterase,_putative_73833..74063_POSITIVE 247 90 41 75 39 NC_009009:SSA_1897|5end_Ribosomal_protein_HS6-type_(S12/L30/L7a),_putative_1894450..1894680_NEGATIVE 243 79 32 70 10 NC_009009:SSA_0065|5end_Low_molecular_weight_phosphotyrosine_protein_phosphatase,_putative_67175..67405_POSITIVE 241 74 31 104 62 NC_009009:SSA_1726|5end_ABC_transporter_ATP-binding_protein-branched_chain_amino_acid_transport,_putative_1712467..1712697_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 305 38 7 84 53 NC_009009:SSA_0448|3end_Excinuclease_ATPase_subunit_A,_putative_449391..449541_POSITIVE 300 68 30 130 92 NC_009009:SSA_0251|3end_D-tyrosyl-tRNA(Tyr)_deacylase,_putative_244978..245128_POSITIVE 281 80 31 149 102 NC_009009:SSA_0150|3end_hypothetical_protein_145227..145377_POSITIVE 273 148 107 107 56 NC_009009:SSA_1596|3end_hypothetical_protein_1602075..1602225_NEGATIVE 266 80 31 145 86 NC_009009:SSA_0728|3end_Protease,_putative_714523..714673_POSITIVE 251 145 101 124 71 NC_009009:SSA_1557|3end_SRPR,_signal_recognition_particle-docking_protein,_putative_1558502..1558652_NEGATIVE 247 90 41 82 46 NC_009009:SSA_1899|3end_hypothetical_protein_1894443..1894593_NEGATIVE 245 73 31 151 104 NC_009009:SSA_2005|3end_Chaperone_protein_dnaJ,_putative_2005251..2005401_NEGATIVE 241 74 31 104 62 NC_009009:SSA_1727|3end_ABC_transporter_membrane-spanning_permease-branched_chain_amino_acid_transport,_putative_1712467..1712617_NEGATIVE 238 88 48 151 113 NC_009009:SSA_1657|3end_hypothetical_protein_1652962..1653112_NEGATIVE 236 74 35 69 26 NC_009009:SSA_0451|3end_Conserved_uncharacterized_protein_451636..451786_POSITIVE 234 84 44 61 20 NC_009009:SSA_1467|3end_Chorismate_synthase,_putative_1473127..1473277_NEGATIVE 228 88 41 49 2 NC_009009:SSA_1720|3end_Initiation-control_protein,_putative_1706796..1706946_NEGATIVE 226 38 1 86 51 NC_009009:SSA_1680|3end_ABC-type_bacitracin_resistance_protein_A,_permease_component,_putative_1673200..1673350_NEGATIVE 226 61 33 148 116 NC_009009:SSA_1116|3end_hypothetical_protein_1142752..1142902_POSITIVE 226 88 47 144 109 NC_009009:SSA_0158|3end_hypothetical_protein_155074..155224_POSITIVE 225 89 41 93 22 NC_009009:SSA_0989|3end_Conserved_protein,_possible_transcriptional_regulator_(sigma-70,_region_4),_putative_991816..991966_POSITIVE 225 111 76 51 17 NC_009009:SSA_0854|3end_hypothetical_protein_841813..841963_POSITIVE 224 48 4 85 36 NC_009009:SSA_1443|3end_1-(5-phosphoribosyl)-5-[(5-_phosphoribosylamino)methylideneamino]_imidazole-4-carboxamide_isomerase,_putative_1445944..1446094_NEGATIVE 222 84 41 87 34 NC_009009:SSA_1238|3end_hypothetical_protein_1262402..1262552_NEGATIVE