Origin IGS: aggactagtataacacaaaggcgaaaaaatggcggcaggatttactcgggcgagacagaattctgctctgataaaaagcaatcagcagcccccaagattccccaccagtcgtgctataatagaaagaagtctaaaaaaggaaactcctactc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gagtaggagtttccttttttagacttctttctattatagcacgactggtggggaatcttgggggctgctgattgctttttatcagagcagaattctgtctcgcccgagtaaatcctgccgccattttttcgcctttgtgttatactagtcct Mask Tandem Repeat Region ================================================ aggactagtataacacaaaggcgaaaaaatggcggcaggatttactcgggcgagacagaattctgctctgataaaaagcaatcagcagcccccaagattccccaccagtcgtgctataatagaaagaagtctaaaaaaggaaactcctactc Find is-nt database================================================ Query_seq: SSA_2037:SSA_2038|SSA_2037:SSA_2038:tRNA (Guanosine-2'-O-)-methyltransferase, TrmH family, putative:hypothetical protein:<-->:2041615..2041766 152 aggactagtataacacaaaggcgaaaaaatggcggcaggatttactcgggcgagacagaattctgctctgataaaaagcaatcagcagcccccaagattccccaccagtcgtgctataatagaaagaagtctaaaaaaggaaactcctactc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2037:SSA_2038|SSA_2037:SSA_2038:tRNA (Guanosine-2'-O-)-methyltransferase, TrmH family, putative:hypothetical protein:<-->:2041615..2041766 152 aggactagtataacacaaaggcgaaaaaatggcggcaggatttactcgggcgagacagaattctgctctgataaaaagcaatcagcagcccccaagattccccaccagtcgtgctataatagaaagaagtctaaaaaaggaaactcctactc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2037:SSA_2038|SSA_2037:SSA_2038:tRNA (Guanosine-2'-O-)-methyltransferase, TrmH family, putative:hypothetical protein:<-->:2041615..2041766 152 aggactagtataacacaaaggcgaaaaaatggcggcaggatttactcgggcgagacagaattctgctctgataaaaagcaatcagcagcccccaagattccccaccagtcgtgctataatagaaagaagtctaaaaaaggaaactcctactc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aggactagtataacacaaaggcgaaaaaatggcggcaggatttactcgggcgagacagaattctgctctgataaaaagcaatcagcagcccccaagattccccaccagtcgtgctataatagaaagaagtctaaaaaaggaaactcctactc Predict ORF larger than 30AA ================================================ Protein_Len: 47 Strand: + Start: 10 End: 150 ......... M T Q R R K N G G R I Y S G E T E F C S D K K Q S A A P K I P H Q S C Y N R K K S K K G N S Y .. Protein_Len: 41 Strand: + Start: 29 End: 151 ............................ M A A G F T R A R Q N S A L I K S N Q Q P P R F P T S R A I I E R S L K K E T P T . aggactagtataacacaaaggcgaaaaaatggcggcaggatttactcgggcgagacagaattctgctctgataaaaagcaatcagcagcccccaagattccccaccagtcgtgctataatagaaagaagtctaaaaaaggaaactcctactc 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================================================ aggactagtataacacaaaggcgaaaaaatggcggcaggatttactcgggcgagacagaattctgctctgataaaaagcaatcagcagcccccaagattccccaccagtcgtgctataatagaaagaagtctaaaaaaggaaactcctactc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_2037:SSA_2038|SSA_2037:SSA_2038:tRNA (Guanosine-2'-O-)-methyltransferase, TrmH family, putative:hypothetical protein:<-->:2041615..2041766 152 aggactagtataacacaaaggcgaaaaaatggcggcaggatttactcgggcgagacagaattctgctctgataaaaagcaatcagcagcccccaagattccccaccagtcgtgctataatagaaagaagtctaaaaaaggaaactcctactc Intra-Species Hit: Count: 1 Min: 1 Max: 152 Len: 152 Subject: NC_009009_SSA_2037_SSA_2038|tRNA (Guanosine-2'-O-)-methyltransferase, TrmH family, putative:hypothetical protein|NEGATIVE:POSITIVE|[2041615,2041766]|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 aggactagtataacacaaaggcgaaaaaatggcggcaggatttactcgggcgagacagaattctgctctgataaaaagcaatcagcagcccccaagattccccaccagtcgtgctataatagaaagaagtctaaaaaaggaaactcctactc aggactagtataacacaaaggcgaaaaaatggcggcaggatttactcgggcgagacagaattctgctctgataaaaagcaatcagcagcccccaagattccccaccagtcgtgctataatagaaagaagtctaaaaaaggaaactcctactc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGGACUAGUAUAACACAAAGGCGAAAAAAUGGCGGCAGGAUUUACUCGGGCGAGACAGAAUUCUGCUCUGAUAAAAAGCAAUCAGCAGCCCCCAAGAUUCCCCACCAGUCGUGCUAUAAUAGAAAGAAGUCUAAAAAAGGAAACUCCUACUC .(((((.((.....))....((((.....(((.((..((((((....(((((((.(((....)))))).........((.....)).))))...)))))).)).))).))))...............))))).....(((.....))).... (-32.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAGUAGGAGUUUCCUUUUUUAGACUUCUUUCUAUUAUAGCACGACUGGUGGGGAAUCUUGGGGGCUGCUGAUUGCUUUUUAUCAGAGCAGAAUUCUGUCUCGCCCGAGUAAAUCCUGCCGCCAUUUUUUCGCCUUUGUGUUAUACUAGUCCU ....((((((((........))))))))..(((.((((((((((..((((..(((...(((.(((....((((((((.......((((((....))).)))....)))).))))..))).))).)))..)))).)))))))))).))).... (-49.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1008 70 21 161 112 NC_009009:SSA_2037|5end_tRNA_(Guanosine-2'-O-)-methyltransferase,_TrmH_family,_putative_2041524..2041754_NEGATIVE 416 80 31 216 168 NC_009009:SSA_0653|5end_UDP-N-acetylglucosamine--N-acetylmuramyl-_(pentapeptide)_pyrophosphoryl-undecaprenol_N-acetylglucosamine_transferase,_putative_636390..636620_POSITIVE 357 89 41 204 161 NC_009009:SSA_0116|5end_30S_ribosomal_protein_S17,_putative_112632..112862_POSITIVE 352 68 31 59 20 NC_009009:SSA_1465|5end_Conserved_uncharacterized_protein_1471986..1472216_NEGATIVE 345 90 44 59 11 NC_009009:SSA_1261|5end_Ribose-5-phosphate_isomerase_A,_putative_1287654..1287884_NEGATIVE 337 119 75 76 14 NC_009009:SSA_0069|5end_Hypothetical_protein,_possibly_membrane-associated_73037..73267_POSITIVE 332 130 85 56 1 NC_009009:SSA_0403|5end_CAAX_amino_terminal_protease_family,_putative_400475..400705_POSITIVE 325 89 41 165 110 NC_009009:SSA_1783|5end_Xanthosine_triphosphate_pyrophosphatase_(NTPase/HAM1_family),_putative_1769106..1769336_NEGATIVE 323 55 19 43 4 NC_009009:SSA_0942|5end_ABC_transporter_membrane-spanning_permease-phosphate_transport,_putative_949939..950169_POSITIVE 318 78 31 231 175 NC_009009:SSA_1579|5end_ABC-type_Fe3+-siderophore_transport_system,_ATPase_component,_putative_1582851..1583081_POSITIVE 317 117 78 119 77 NC_009009:SSA_1823|5end_hypothetical_protein_1812513..1812743_NEGATIVE 316 97 63 54 22 NC_009009:SSA_0210|5end_hypothetical_protein_207757..207987_POSITIVE 312 88 47 70 26 NC_009009:SSA_0502|5end_Peptide_ABC_transporter,_permease_protein,_putative_501554..501784_POSITIVE 311 114 77 201 160 NC_009009:SSA_0334|5end_Diphosphomevalonate_decarboxylase,_putative_327855..328085_POSITIVE 301 48 9 170 129 NC_009009:SSA_2109|5end_Elongation_factor_G,_putative_2114868..2115098_NEGATIVE 300 110 62 205 141 NC_009009:SSA_0239|5end_7,8-dihydro-8-oxoguanine-triphosphatase,_putative_232961..233191_POSITIVE 297 90 44 56 9 NC_009009:SSA_1957|5end_Glycosyl_transferase_N-acetylglucosaminyltransferase,_putative_1954670..1954900_NEGATIVE 297 90 50 219 169 NC_009009:SSA_0517|5end_Sensor_histidine_kinase,_putative_515060..515290_POSITIVE 292 80 33 74 16 NC_009009:SSA_0565|5end_hypothetical_protein_557230..557460_POSITIVE 291 90 49 227 184 NC_009009:SSA_2347|5end_Coenzyme_F390_synthetase,_putative_2349939..2350169_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 352 68 31 40 1 NC_009009:SSA_1466|3end_Prephenate_dehydrogenase,_putative_1472005..1472155_NEGATIVE 327 55 13 46 1 NC_009009:SSA_0941|3end_ABC-type_phosphate_transport_system,_periplasmic_component,_putative_950022..950172_POSITIVE 318 66 30 44 11 NC_009009:SSA_2168|3end_Glycerol-3-phosphate_dehydrogenase_[NAD(P)+],_putative_2168563..2168713_POSITIVE 317 117 78 116 74 NC_009009:SSA_1824|3end_hypothetical_protein_1812516..1812666_NEGATIVE 309 89 48 64 29 NC_009009:SSA_0243|3end_Cyclo-nucleotide_phosphodiesterase,_putative_235824..235974_NEGATIVE 297 90 44 65 18 NC_009009:SSA_1958|3end_Adapter_protein_mecA,_putative_1954661..1954811_NEGATIVE 297 118 76 151 114 NC_009009:SSA_1627|3end_hypothetical_protein_1629508..1629658_NEGATIVE 289 97 56 115 71 NC_009009:SSA_1013|3end_Phosphatidylserine_synthase,_putative_1017933..1018083_POSITIVE 285 70 25 75 29 NC_009009:SSA_0581|3end_Conserved_uncharacterized_protein_573774..573924_POSITIVE 281 123 81 150 104 NC_009009:SSA_0682|3end_Conserved_uncharacterized_protein_664351..664501_POSITIVE 279 109 64 55 5 NC_009009:SSA_0271|3end_Glycosylhydrolase,_family_35,_putative_266093..266243_POSITIVE 278 110 68 130 77 NC_009009:SSA_0401|3end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_winged-helix_DNA-binding_domains),_putative_399222..399372_POSITIVE 275 107 61 137 65 NC_009009:SSA_1413|3end_GufA-like_protein,_putative_1424095..1424245_NEGATIVE 274 71 32 150 105 NC_009009:SSA_1784|3end_Glutamate_racemase,_putative_1769103..1769253_NEGATIVE 273 67 21 140 94 NC_009009:SSA_2267|3end_Lactose_operon_transcriptional_repressor,_LacI_family,_putative_2267190..2267340_POSITIVE 272 115 76 141 98 NC_009009:SSA_0621|3end_SOS_responce_UmuC_protein,_putative_612322..612472_NEGATIVE 272 98 51 72 33 NC_009009:SSA_0242|3end_hypothetical_protein_235810..235960_POSITIVE 271 51 16 36 4 NC_009009:SSA_2309|3end_Fimbrial_assembly_protein,_putative_2310474..2310624_NEGATIVE 271 110 66 151 108 NC_009009:SSA_0679|3end_DNA_repair_and_genetic_recombination,_putative_662452..662602_POSITIVE 270 60 18 57 3 NC_009009:SSA_1982|3end_Transcriptional_regulator,_LytR/AlgR_family,_putative_1975427..1975577_NEGATIVE