Origin IGS: gtctagacaaattaacacactcaattcatttatacaaaaatcacggagaccgacagttgttttatcggtctctttttagatttattgaagaccagtatcaggttcaagtttcaaaaaagaagcaaatatgatatactaaagaacaagtattctattagaattggaacaaataat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 attatttgttccaattctaatagaatacttgttctttagtatatcatatttgcttcttttttgaaacttgaacctgatactggtcttcaataaatctaaaaagagaccgataaaacaactgtcggtctccgtgatttttgtataaatgaattgagtgtgttaatttgtctagac Mask Tandem Repeat Region ================================================ gtctagacaaattaacacactcaattcatttatacaaaaatcacggagaccgacagttgttttatcggtctctttttagatttattgaagaccagtatcaggttcaagtttcaaaaaagaagcaaatatgatatactaaagaacaagtattctattagaattggaacaaataat Find is-nt database================================================ Query_seq: SMT_1703:SMT_1704|SMT_1703:SMT_1704:recombination protein RecR:D-alanine-D-alanine ligase:->->:1687397..1687570 174 gtctagacaaattaacacactcaattcatttatacaaaaatcacggagaccgacagttgttttatcggtctctttttagatttattgaagaccagtatcaggttcaagtttcaaaaaagaagcaaatatgatatactaaagaacaagtattctattagaattggaacaaataat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1703:SMT_1704|SMT_1703:SMT_1704:recombination protein RecR:D-alanine-D-alanine ligase:->->:1687397..1687570 174 gtctagacaaattaacacactcaattcatttatacaaaaatcacggagaccgacagttgttttatcggtctctttttagatttattgaagaccagtatcaggttcaagtttcaaaaaagaagcaaatatgatatactaaagaacaagtattctattagaattggaacaaataat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1703:SMT_1704|SMT_1703:SMT_1704:recombination protein RecR:D-alanine-D-alanine ligase:->->:1687397..1687570 174 gtctagacaaattaacacactcaattcatttatacaaaaatcacggagaccgacagttgttttatcggtctctttttagatttattgaagaccagtatcaggttcaagtttcaaaaaagaagcaaatatgatatactaaagaacaagtattctattagaattggaacaaataat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtctagacaaattaacacactcaattcatttatacaaaaatcacggagaccgacagttgttttatcggtctctttttagatttattgaagaccagtatcaggttcaagtttcaaaaaagaagcaaatatgatatactaaagaacaagtattctattagaattggaacaaataat Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 24 End: 128 ....................... M H L Y K N H G D R Q L F Y R S L F R F I E D Q Y Q V Q V S K K K Q I .............................................. Protein_Len: 49 Strand: + Start: 28 End: 174 ........................... M Y T K I T E T D S C F I G L F L D L L K T S I R F K F Q K R S K Y D I L K N K Y S I R I G T N N gtctagacaaattaacacactcaattcatttatacaaaaatcacggagaccgacagttgttttatcggtctctttttagatttattgaagaccagtatcaggttcaagtttcaaaaaagaagcaaatatgatatactaaagaacaagtattctattagaattggaacaaataat 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================================================ gtctagacaaattaacacactcaattcatttatacaaaaatcacggagaccgacagttgttttatcggtctctttttagatttattgaagaccagtatcaggttcaagtttcaaaaaagaagcaaatatgatatactaaagaacaagtattctattagaattggaacaaataat Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 51 HP_score: -5.3 Tail_Score: -2.60854 Start: 45 End: 73 Full_Region: tcaataaatctaaaa agagaccgata aaacaac tgtcggtctcc gtgatttttgtataa ............................................agagaccgataaaacaactgtcggtctcc..................................................................................................... TransTerm Strand: + Conf: 85 HP_score: -7.3 Tail_Score: -4.86939 Start: 46 End: 72 Full_Region: TATACAAAAATCACG GAGACCGACAG TTGTT TTATCGGTCTC TTTTTAGATTTATTG .............................................GAGACCGACAGTTGTTTTATCGGTCTC...................................................................................................... Find igs database================================================ Query_seq: SMT_1703:SMT_1704|SMT_1703:SMT_1704:recombination protein RecR:D-alanine-D-alanine ligase:->->:1687397..1687570 174 gtctagacaaattaacacactcaattcatttatacaaaaatcacggagaccgacagttgttttatcggtctctttttagatttattgaagaccagtatcaggttcaagtttcaaaaaagaagcaaatatgatatactaaagaacaagtattctattagaattggaacaaataat Intra-Species Hit: Count: 1 Min: 1 Max: 174 Len: 174 Subject: smit_SMT_1703_SMT_1704|recombination protein RecR:D-alanine-D-alanine ligase|POSITIVE:POSITIVE|[1687397,1687570]|174 HSP 1 e-value: 3.0E-94 bit: 345.0 Len: 174 Query Start:1 Query End:174 Subject Strand: POSITIVE Subject Start: 1 Subject End: 174 gtctagacaaattaacacactcaattcatttatacaaaaatcacggagaccgacagttgttttatcggtctctttttagatttattgaagaccagtatcaggttcaagtttcaaaaaagaagcaaatatgatatactaaagaacaagtattctattagaattggaacaaataat gtctagacaaattaacacactcaattcatttatacaaaaatcacggagaccgacagttgttttatcggtctctttttagatttattgaagaccagtatcaggttcaagtttcaaaaaagaagcaaatatgatatactaaagaacaagtattctattagaattggaacaaataat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUCUAGACAAAUUAACACACUCAAUUCAUUUAUACAAAAAUCACGGAGACCGACAGUUGUUUUAUCGGUCUCUUUUUAGAUUUAUUGAAGACCAGUAUCAGGUUCAAGUUUCAAAAAAGAAGCAAAUAUGAUAUACUAAAGAACAAGUAUUCUAUUAGAAUUGGAACAAAUAAU ....................(((((((.......((((((((..(((((((((.((.....)).))))))))).....))))).))).......((((((.(((...(((((......))))).))).)))))).....((((......))))....))))))).......... (-31.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUAUUUGUUCCAAUUCUAAUAGAAUACUUGUUCUUUAGUAUAUCAUAUUUGCUUCUUUUUUGAAACUUGAACCUGAUACUGGUCUUCAAUAAAUCUAAAAAGAGACCGAUAAAACAACUGUCGGUCUCCGUGAUUUUUGUAUAAAUGAAUUGAGUGUGUUAAUUUGUCUAGAC ...............(((((((((((((((((((((((....(((((.......(((((((.((...(((((((.......)))..))))....)).)))))))((((((((.......))))))))...))))).......)))).))).))))))).....))))).)))). (-30.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 267 76 40 106 62 smit:SMT_1191|5end_phosphoribosylamine--glycine_ligase_1149737..1149967_NEGATIVE 250 82 45 113 73 smit:SMT_403|5end_two-component_sensor_kinase_YesM_331580..331810_POSITIVE 245 85 43 191 156 smit:SMT_1007|5end_radical_SAM_domain_protein_947035..947265_POSITIVE 241 68 39 157 125 smit:SMT_2130|5end_UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-_diaminopimelate--D-alanyl-D-alanine_ligase_2010717..2010947_POSITIVE 236 95 51 231 188 smit:SMT_1140|5end_glycogen_phosphorylase_1083574..1083804_NEGATIVE 234 87 42 78 37 smit:SMT_1328|5end_hypothetical_protein_1304468..1304698_NEGATIVE 234 110 63 180 127 smit:SMT_360|5end_K07742_hypothetical_protein_295628..295858_POSITIVE 228 90 41 212 162 smit:SMT_780|5end_peptidase_family_U32_689321..689551_NEGATIVE 227 58 19 210 174 smit:SMT_650|5end_pullulanase_559832..560062_NEGATIVE 225 92 52 126 73 smit:SMT_522|5end_K02003_446719..446949_POSITIVE 223 79 42 166 132 smit:SMT_192|5end_translation_initiation_factor_IF-1_126500..126730_POSITIVE 220 136 92 172 121 smit:SMT_596|5end_K03976_putative_transcription_regulator_513075..513305_NEGATIVE 218 79 32 107 54 smit:SMT_1606|5end_glutamate_racemase_1595857..1596087_POSITIVE 216 100 57 129 84 smit:SMT_643|5end_hypothetical_protein_548495..548725_NEGATIVE 216 108 61 56 14 smit:SMT_326|5end_K02029_polar_amino_acid_transport_system_permease_protein_263864..264094_NEGATIVE 216 107 69 145 103 smit:SMT_91|5end_hypothetical_protein_22578..22808_POSITIVE 215 95 64 145 111 smit:SMT_535|5end_hypothetical_protein_454215..454445_POSITIVE 215 110 65 154 117 smit:SMT_104|5end_DNA_repair_protein_49623..49853_POSITIVE 214 113 85 231 202 smit:SMT_1454|5end_cytidine_deaminase_1437886..1438116_NEGATIVE 213 90 43 190 137 smit:SMT_1898|5end_aminotransferase_(class_V),_putative_1849929..1850159_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 254 72 35 45 4 smit:SMT_1703|3end_recombination_protein_RecR_1687336..1687486_POSITIVE 252 104 64 121 74 smit:SMT_162|3end_hypothetical_protein_107134..107284_POSITIVE 250 82 45 116 76 smit:SMT_402|3end_two-component_response_regulator_YesN_331663..331813_POSITIVE 241 68 39 54 22 smit:SMT_2129|3end_cell_division_protein_FtsZ_2010694..2010844_POSITIVE 241 110 64 98 48 smit:SMT_742|3end_hypothetical_protein_645784..645934_NEGATIVE 234 87 42 68 27 smit:SMT_1329|3end_GTP-binding_protein_CgtA_1304478..1304628_NEGATIVE 227 58 19 56 20 smit:SMT_651|3end_DNA_ligase_559986..560136_NEGATIVE 225 92 52 142 89 smit:SMT_521|3end_K02005_HlyD_family_secretion_protein_446815..446965_POSITIVE 223 74 40 92 62 smit:SMT_724|3end_hypothetical_protein_629770..629920_NEGATIVE 223 79 42 49 15 smit:SMT_191|3end_adenylate_kinase_126463..126613_POSITIVE 221 55 37 146 125 smit:SMT_954|3end_cation-transporting_ATPase,_E1-E2_family_901677..901827_NEGATIVE 218 95 53 137 101 smit:SMT_359|3end_transcription_termination-antitermination_factor_295686..295836_POSITIVE 217 88 54 131 92 smit:SMT_2007|3end_hypothetical_protein_1928147..1928297_POSITIVE 217 89 43 100 60 smit:SMT_1149|3end_hypothetical_protein_1094040..1094190_NEGATIVE 216 107 69 80 38 smit:SMT_90|3end_DNA_polymerase_III_beta_subunit_22593..22743_POSITIVE 215 95 64 40 6 smit:SMT_534|3end_hypothetical_protein_predicted_by_Glimmer/Critica_454190..454340_POSITIVE 213 102 61 142 100 smit:SMT_128|3end_K03449_MFS_transporter,_CP_family,_cyanate_transporter_78702..78852_NEGATIVE 209 69 40 150 118 smit:SMT_324|3end_K02029_polar_amino_acid_transport_system_permease_protein_261912..262062_NEGATIVE 208 110 67 76 20 smit:SMT_715|3end_DHH_subfamily_1_protein_622394..622544_POSITIVE 205 107 69 141 104 smit:SMT_491|3end_K01998_branched-chain_amino_acid_transport_system_permease_protein_426453..426603_POSITIVE