Origin IGS: ttccccagtccttttcctagtatagcaatagaaccattataccataaagcctctgaaaaatttcatcaagttggcagtcactcgaagtctgaaatacaaaaaagaagattggagatttccaatcttctttcaaatggtttgtaagtccttagtcgttta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaacgactaaggacttacaaaccatttgaaagaagattggaaatctccaatcttcttttttgtatttcagacttcgagtgactgccaacttgatgaaatttttcagaggctttatggtataatggttctattgctatactaggaaaaggactggggaa Mask Tandem Repeat Region ================================================ ttccccagtccttttcctagtatagcaatagaaccattataccataaagcctctgaaaaatttcatcaagttggcagtcactcgaagtctgaaatacaaaaaagaagattggagatttccaatcttctttcaaatggtttgtaagtccttagtcgttta Find is-nt database================================================ Query_seq: SSA_0341:SSA_0342|SSA_0341:SSA_0342:hypothetical protein:Pyruvate formate-lyase, putative:<-<-:334822..334980 159 ttccccagtccttttcctagtatagcaatagaaccattataccataaagcctctgaaaaatttcatcaagttggcagtcactcgaagtctgaaatacaaaaaagaagattggagatttccaatcttctttcaaatggtttgtaagtccttagtcgttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0341:SSA_0342|SSA_0341:SSA_0342:hypothetical protein:Pyruvate formate-lyase, putative:<-<-:334822..334980 159 ttccccagtccttttcctagtatagcaatagaaccattataccataaagcctctgaaaaatttcatcaagttggcagtcactcgaagtctgaaatacaaaaaagaagattggagatttccaatcttctttcaaatggtttgtaagtccttagtcgttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0341:SSA_0342|SSA_0341:SSA_0342:hypothetical protein:Pyruvate formate-lyase, putative:<-<-:334822..334980 159 ttccccagtccttttcctagtatagcaatagaaccattataccataaagcctctgaaaaatttcatcaagttggcagtcactcgaagtctgaaatacaaaaaagaagattggagatttccaatcttctttcaaatggtttgtaagtccttagtcgttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttccccagtccttttcctagtatagcaatagaaccattataccataaagcctctgaaaaatttcatcaagttggcagtcactcgaagtctgaaatacaaaaaagaagattggagatttccaatcttctttcaaatggtttgtaagtccttagtcgttta Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: + Start: 22 End: 141 ..................... M A I E P L Y H K A S E K F H Q V G S H S K S E I Q K R R L E I S N L L S N G L .................. Protein_Len: 38 Strand: + Start: 44 End: 157 ........................................... M K P L K N F I K L A V T R S L K Y K K E D W R F P I F F Q M V C K S L V V .. Protein_Len: 38 Strand: - Start: 20 End: 133 ................... Y L L L V M I G Y L R Q F I E D L Q C D S S T Q F V F F F I P S K W D E K M .......................... ttccccagtccttttcctagtatagcaatagaaccattataccataaagcctctgaaaaatttcatcaagttggcagtcactcgaagtctgaaatacaaaaaagaagattggagatttccaatcttctttcaaatggtttgtaagtccttagtcgttta 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================================================ ttccccagtccttttcctagtatagcaatagaaccattataccataaagcctctgaaaaatttcatcaagttggcagtcactcgaagtctgaaatacaaaaaagaagattggagatttccaatcttctttcaaatggtttgtaagtccttagtcgttta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 95 HP_score: -12.6 Tail_Score: -3.65754 Start: 104 End: 127 Full_Region: CTGAAATACAAAAAA GAAGATTGGA GATT TCCAATCTTC TTTCAAATGGTTTGT .......................................................................................................GAAGATTGGAGATTTCCAATCTTC................................ TransTerm Strand: + Conf: 77 HP_score: -8.5 Tail_Score: -3.95036 Start: 107 End: 124 Full_Region: AAATACAAAAAAGAA GATTGGA GATT TCCAATC TTCTTTCAAATGGTT ..........................................................................................................GATTGGAGATTTCCAATC................................... Find igs database================================================ Query_seq: SSA_0341:SSA_0342|SSA_0341:SSA_0342:hypothetical protein:Pyruvate formate-lyase, putative:<-<-:334822..334980 159 ttccccagtccttttcctagtatagcaatagaaccattataccataaagcctctgaaaaatttcatcaagttggcagtcactcgaagtctgaaatacaaaaaagaagattggagatttccaatcttctttcaaatggtttgtaagtccttagtcgttta Intra-Species Hit: Count: 1 Min: 1 Max: 159 Len: 159 Subject: NC_009009_SSA_0341_SSA_0342|hypothetical protein:Pyruvate formate-lyase, putative|NEGATIVE:NEGATIVE|[334822,334980]|159 HSP 1 e-value: 2.0E-85 bit: 315.0 Len: 159 Query Start:1 Query End:159 Subject Strand: POSITIVE Subject Start: 1 Subject End: 159 ttccccagtccttttcctagtatagcaatagaaccattataccataaagcctctgaaaaatttcatcaagttggcagtcactcgaagtctgaaatacaaaaaagaagattggagatttccaatcttctttcaaatggtttgtaagtccttagtcgttta ttccccagtccttttcctagtatagcaatagaaccattataccataaagcctctgaaaaatttcatcaagttggcagtcactcgaagtctgaaatacaaaaaagaagattggagatttccaatcttctttcaaatggtttgtaagtccttagtcgttta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCCCCAGUCCUUUUCCUAGUAUAGCAAUAGAACCAUUAUACCAUAAAGCCUCUGAAAAAUUUCAUCAAGUUGGCAGUCACUCGAAGUCUGAAAUACAAAAAAGAAGAUUGGAGAUUUCCAAUCUUCUUUCAAAUGGUUUGUAAGUCCUUAGUCGUUUA ................((((....((....((((((((..........(((.((((.........)).))..))).........................((((((((((((......))))))))))))..))))))))....))..))))....... (-28.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAACGACUAAGGACUUACAAACCAUUUGAAAGAAGAUUGGAAAUCUCCAAUCUUCUUUUUUGUAUUUCAGACUUCGAGUGACUGCCAACUUGAUGAAAUUUUUCAGAGGCUUUAUGGUAUAAUGGUUCUAUUGCUAUACUAGGAAAAGGACUGGGGAA ..........((((((.....(((((...(((((((((((((....)))))))))))))((((.((((((....((((((........))))))))))))....))))......))))).....)))))).........((((........)))).... (-40.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 877 90 41 181 132 NC_009009:SSA_0341|5end_hypothetical_protein_334731..334961_NEGATIVE 309 129 88 226 186 NC_009009:SSA_0139|5end_Copper_transport_operon_or_penicillinase_transcriptional_repressor,_putative_134183..134413_POSITIVE 293 80 34 166 120 NC_009009:SSA_2184|5end_hypothetical_protein_2183754..2183984_NEGATIVE 284 120 73 104 52 NC_009009:SSA_2054|5end_hypothetical_protein_2057899..2058129_NEGATIVE 277 150 111 52 13 NC_009009:SSA_1165|5end_Transcriptional_regulator,_GntR_family,_putative_1191087..1191317_POSITIVE 274 40 1 161 121 NC_009009:SSA_1835|5end_Late_competence_protein,_putative_1830941..1831171_NEGATIVE 274 78 33 59 12 NC_009009:SSA_0097|5end_Multi_antimicrobial_extrusion_(MATE)_family_transporter,_putative_98148..98378_POSITIVE 269 89 51 103 70 NC_009009:SSA_1412|5end_hypothetical_protein_1424095..1424325_NEGATIVE 266 49 2 212 159 NC_009009:SSA_2289|5end_Cadmium_efflux_system_transcriptional_regulator_(ArsR-like),_putative_2291087..2291317_POSITIVE 266 44 5 59 14 NC_009009:SSA_2124|5end_Dehydrogenase,_eukaryotic-like,_putative_2129411..2129641_NEGATIVE 266 49 2 212 159 NC_009009:SSA_2389|5end_Arsenical_resistance_operon_transcription_repressor,_putative_2032183..2032413_NEGATIVE 266 49 2 182 129 NC_009009:SSA_2387|5end_Arsenical_resistance_operon_transcription_repressor,_putative_2032213..2032443_NEGATIVE 266 91 53 73 29 NC_009009:SSA_1045|5end_hypothetical_protein_1060841..1061071_POSITIVE 265 120 74 172 121 NC_009009:SSA_1144|5end_Beta-N-acetylhexosaminidase,_putative_1175610..1175840_NEGATIVE 263 89 42 155 104 NC_009009:SSA_0583|5end_Nucleotidyltransferase,_putative_574505..574735_POSITIVE 262 149 102 124 69 NC_009009:SSA_1382|5end_hypothetical_protein_1400270..1400500_NEGATIVE 258 48 1 146 93 NC_009009:SSA_0135|5end_Multiple_antibiotic_resistance_operon_transcriptional_repressor_(MarR),_putative_130574..130804_POSITIVE 256 46 12 133 97 NC_009009:SSA_1083|5end_Conserved_uncharacterized_protein_1101298..1101528_POSITIVE 254 45 5 133 94 NC_009009:SSA_1452|5end_Second_subunit_of_major_exonuclease,_putative_1459696..1459926_NEGATIVE 253 57 11 152 98 NC_009009:SSA_0005|5end_GTP-binding_protein,_putative_3821..4051_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 309 129 88 78 38 NC_009009:SSA_0138|3end_Metal-binding_(Zn)_permease,_putative_134115..134265_POSITIVE 287 126 82 87 44 NC_009009:SSA_0680|3end_Serine/threonine_protein_phosphatase,_putative_663233..663383_POSITIVE 284 120 73 67 15 NC_009009:SSA_2055|3end_hypothetical_protein_2057936..2058086_NEGATIVE 281 130 81 83 43 NC_009009:SSA_0394|3end_hypothetical_protein_390931..391081_POSITIVE 273 63 24 54 11 NC_009009:SSA_2107|3end_Glucosamine--fructose-6-phosphate_aminotransferase_[isomerizing],_putative_2109295..2109445_NEGATIVE 269 89 51 103 70 NC_009009:SSA_1413|3end_GufA-like_protein,_putative_1424095..1424245_NEGATIVE 266 44 5 47 2 NC_009009:SSA_2125|3end_Small_primase-like_protein_(Toprim_domain),_putative_2129423..2129573_NEGATIVE 265 120 74 88 37 NC_009009:SSA_1145|3end_hypothetical_protein_1175694..1175844_NEGATIVE 257 90 46 151 109 NC_009009:SSA_2170|3end_hypothetical_protein_2169557..2169707_NEGATIVE 251 143 101 106 59 NC_009009:SSA_0599|3end_hypothetical_protein_589007..589157_POSITIVE 240 50 2 55 8 NC_009009:SSA_2069|3end_Prolyl-tRNA_synthetase,_putative_2071402..2071552_NEGATIVE 236 130 85 87 45 NC_009009:SSA_1223|3end_30S_ribosomal_protein_S1,_putative_1245667..1245817_NEGATIVE 233 45 1 144 98 NC_009009:SSA_1074|3end_Pyrroline-5-carboxylate_reductase,_putative_1093034..1093184_POSITIVE 232 115 71 56 16 NC_009009:SSA_1233|3end_Membrane_protein,_YqiH_family,_putative_1257626..1257776_POSITIVE 230 108 62 49 4 NC_009009:SSA_2244|3end_Arsenate_reductase,_putative_2239477..2239627_NEGATIVE 227 93 60 45 15 NC_009009:SSA_1726|3end_ABC_transporter_ATP-binding_protein-branched_chain_amino_acid_transport,_putative_1711703..1711853_NEGATIVE 225 89 43 105 61 NC_009009:SSA_1077|3end_N-acetyl-glucosamine_matabolism,_putative_1095829..1095979_POSITIVE 225 146 101 44 3 NC_009009:SSA_0326|3end_Conserved_uncharacterized_BCR,_YbaB_family_319524..319674_NEGATIVE 224 125 81 67 25 NC_009009:SSA_0380|3end_Enzyme_of_poly-gamma-glutamate_biosynthesis_(capsule_formation),_putative_372378..372528_POSITIVE 224 48 1 70 19 NC_009009:SSA_0376|3end_ABC-type_methionine_transporter,_ATPase_component,_putative_366526..366676_POSITIVE