Origin IGS: gtgtctcctccttgacattgtgtgctaaacagactctcttttcctcatcgtatcttttcacgacaaacaaaaagagacctgttaatcataacaagtctcgctgtttaagatagggccggaaaacatacttttcagtataaaattcggaatgacgacactatcacaggtttctgccagctactcccttgagtagtactattataccaaattttgaaaaattttcaaagagtaaaaaatgccttatttgaattttcccttgaaaaccagtataatggtagaatgctatgtgactagaaaggaagttga .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tcaacttcctttctagtcacatagcattctaccattatactggttttcaagggaaaattcaaataaggcattttttactctttgaaaatttttcaaaatttggtataatagtactactcaagggagtagctggcagaaacctgtgatagtgtcgtcattccgaattttatactgaaaagtatgttttccggccctatcttaaacagcgagacttgttatgattaacaggtctctttttgtttgtcgtgaaaagatacgatgaggaaaagagagtctgtttagcacacaatgtcaaggaggagacac Mask Tandem Repeat Region ================================================ gtgtctcctccttgacattgtgtgctaaacagactctcttttcctcatcgtatcttttcacgacaaacaaaaagagacctgttaatcataacaagtctcgctgtttaagatagggccggaaaacatacttttcagtataaaattcggaatgacgacactatcacaggtttctgccagctactcccttgagtagtactattataccaaattttgaaaaattttcaaagagtaaaaaatgccttatttgaattttcccttgaaaaccagtataatggtagaatgctatgtgactagaaaggaagttga Find is-nt database================================================ Query_seq: SMT_837:SMT_838|SMT_837:SMT_838:cation transport ATPase:cation efflux family protein:<-->:782758..783063 306 gtgtctcctccttgacattgtgtgctaaacagactctcttttcctcatcgtatcttttcacgacaaacaaaaagagacctgttaatcataacaagtctcgctgtttaagatagggccggaaaacatacttttcagtataaaattcggaatgacgacactatcacaggtttctgccagctactcccttgagtagtactattataccaaattttgaaaaattttcaaagagtaaaaaatgccttatttgaattttcccttgaaaaccagtataatggtagaatgctatgtgactagaaaggaagttga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_837:SMT_838|SMT_837:SMT_838:cation transport ATPase:cation efflux family protein:<-->:782758..783063 306 gtgtctcctccttgacattgtgtgctaaacagactctcttttcctcatcgtatcttttcacgacaaacaaaaagagacctgttaatcataacaagtctcgctgtttaagatagggccggaaaacatacttttcagtataaaattcggaatgacgacactatcacaggtttctgccagctactcccttgagtagtactattataccaaattttgaaaaattttcaaagagtaaaaaatgccttatttgaattttcccttgaaaaccagtataatggtagaatgctatgtgactagaaaggaagttga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_837:SMT_838|SMT_837:SMT_838:cation transport ATPase:cation efflux family protein:<-->:782758..783063 306 gtgtctcctccttgacattgtgtgctaaacagactctcttttcctcatcgtatcttttcacgacaaacaaaaagagacctgttaatcataacaagtctcgctgtttaagatagggccggaaaacatacttttcagtataaaattcggaatgacgacactatcacaggtttctgccagctactcccttgagtagtactattataccaaattttgaaaaattttcaaagagtaaaaaatgccttatttgaattttcccttgaaaaccagtataatggtagaatgctatgtgactagaaaggaagttga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtgtctcctccttgacattgtgtgctaaacagactctcttttcctcatcgtatcttttcacgacaaacaaaaagagacctgttaatcataacaagtctcgctgtttaagatagggccggaaaacatacttttcagtataaaattcggaatgacgacactatcacaggtttctgccagctactcccttgagtagtactattataccaaattttgaaaaattttcaaagagtaaaaaatgccttatttgaattttcccttgaaaaccagtataatggtagaatgctatgtgactagaaaggaagttga Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 12 End: 110 ........... M T L C A K Q T L F S S S Y L F T T N K K R P V N H N K S R C L R .................................................................................................................................................................................................... Protein_Len: 30 Strand: + Start: 101 End: 190 .................................................................................................... M F K I G P E N I L F S I K F G M T T L S Q V S A S Y S L E .................................................................................................................... Protein_Len: 41 Strand: - Start: 164 End: 286 ................................................................................................................................................................... L N R G A V G K L L V I I G F K S F N E F L L F H R I Q I K G Q F G T Y H Y F A M .................... Protein_Len: 31 Strand: - Start: 85 End: 177 .................................................................................... D Y C T E S N L I P G S F M S K L I F N P I V V S D C T E A M ................................................................................................................................. gtgtctcctccttgacattgtgtgctaaacagactctcttttcctcatcgtatcttttcacgacaaacaaaaagagacctgttaatcataacaagtctcgctgtttaagatagggccggaaaacatacttttcagtataaaattcggaatgacgacactatcacaggtttctgccagctactcccttgagtagtactattataccaaattttgaaaaattttcaaagagtaaaaaatgccttatttgaattttcccttgaaaaccagtataatggtagaatgctatgtgactagaaaggaagttga Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: + Score: 86 Start: 244 End: 273 ...................................................................................................................................................................................................................................................TTTGAATTTTCCCTTGAAAACCAGTATAAT................................. PromScan Matrix: RpoD-17 Strand: - Score: 85 Start: 198 End: 227 .....................................................................................................................................................................................................CTTTGAAAATTTTTCAAAATTTGGTATAAT............................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gtgtctcctccttgacattgtgtgctaaacagactctcttttcctcatcgtatcttttcacgacaaacaaaaagagacctgttaatcataacaagtctcgctgtttaagatagggccggaaaacatacttttcagtataaaattcggaatgacgacactatcacaggtttctgccagctactcccttgagtagtactattataccaaattttgaaaaattttcaaagagtaaaaaatgccttatttgaattttcccttgaaaaccagtataatggtagaatgctatgtgactagaaaggaagttga Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -11.3 Tail_Score: -5.40464 Start: 74 End: 99 Full_Region: cctatcttaaacagc gagacttgtta tgat taacaggtctc tttttgtttgtcgtg .........................................................................gagacttgttatgattaacaggtctc............................................................................................................................................................................................................... Find igs database================================================ Query_seq: SMT_837:SMT_838|SMT_837:SMT_838:cation transport ATPase:cation efflux family protein:<-->:782758..783063 306 gtgtctcctccttgacattgtgtgctaaacagactctcttttcctcatcgtatcttttcacgacaaacaaaaagagacctgttaatcataacaagtctcgctgtttaagatagggccggaaaacatacttttcagtataaaattcggaatgacgacactatcacaggtttctgccagctactcccttgagtagtactattataccaaattttgaaaaattttcaaagagtaaaaaatgccttatttgaattttcccttgaaaaccagtataatggtagaatgctatgtgactagaaaggaagttga Intra-Species Hit: Count: 1 Min: 1 Max: 306 Len: 306 Subject: smit_SMT_837_SMT_838|cation transport ATPase:cation efflux family protein|NEGATIVE:POSITIVE|[782758,783063]|306 HSP 1 e-value: 1.0E-173 bit: 607.0 Len: 306 Query Start:1 Query End:306 Subject Strand: POSITIVE Subject Start: 1 Subject End: 306 gtgtctcctccttgacattgtgtgctaaacagactctcttttcctcatcgtatcttttcacgacaaacaaaaagagacctgttaatcataacaagtctcgctgtttaagatagggccggaaaacatacttttcagtataaaattcggaatgacgacactatcacaggtttctgccagctactcccttgagtagtactattataccaaattttgaaaaattttcaaagagtaaaaaatgccttatttgaattttcccttgaaaaccagtataatggtagaatgctatgtgactagaaaggaagttga gtgtctcctccttgacattgtgtgctaaacagactctcttttcctcatcgtatcttttcacgacaaacaaaaagagacctgttaatcataacaagtctcgctgtttaagatagggccggaaaacatacttttcagtataaaattcggaatgacgacactatcacaggtttctgccagctactcccttgagtagtactattataccaaattttgaaaaattttcaaagagtaaaaaatgccttatttgaattttcccttgaaaaccagtataatggtagaatgctatgtgactagaaaggaagttga Inter-species Hit: Count: 3 Min: 1 Max: 306 Len: 306 Subject: NC_003098_spr1410_spr1411|P-type ATPase - calcium transporter:hypothetical protein|NEGATIVE:POSITIVE|[1396443,1396745]|303 HSP 1 e-value: 1.0E-133 bit: 476.0 Len: 306 Query Start:1 Query End:306 Subject Strand: POSITIVE Subject Start: 1 Subject End: 303 gtgtctcctccttgacattgtgtgctaaacagactctcttttcctcatcgtatcttttcacgacaaacaaaaagagacctgttaatcataacaagtctcgctgtttaagatagggccggaaaacatacttttcagtataaaattcggaatgacgacactatcacaggtttctgccagctactcccttgagtagtactattataccaaattttgaaaaattttcaaagagtaaaaaatgccttatttgaattttcccttgaaaaccagtataatggtagaatgctatgtgactagaaaggaagttga gtgtctcctccttgacattgtgtgcaaaacagactctctttctgtcat---atcttttcacgacaaacaaaaagagacctgttaatcataacaagtctcgctgtttaagatagggccggaaagcatacttttcagcataaaattcggaatgacgacactatcacaggtttctgccagctactcccttgagtagtaccattataccaaattttggggagttttcaaagagtaaaaactgccttatttgaatttttccttgaaaaccagtataatggtagaatgctatgtgactagaaaggaagttga Subject: NC_008533_SPD_1383_SPD_1384|cation-transporting ATPase, E1-E2 family protein:cation efflux family protein|NEGATIVE:POSITIVE|[1403974,1404276]|303 HSP 1 e-value: 1.0E-131 bit: 468.0 Len: 306 Query Start:1 Query End:306 Subject Strand: POSITIVE Subject Start: 1 Subject End: 303 gtgtctcctccttgacattgtgtgctaaacagactctcttttcctcatcgtatcttttcacgacaaacaaaaagagacctgttaatcataacaagtctcgctgtttaagatagggccggaaaacatacttttcagtataaaattcggaatgacgacactatcacaggtttctgccagctactcccttgagtagtactattataccaaattttgaaaaattttcaaagagtaaaaaatgccttatttgaattttcccttgaaaaccagtataatggtagaatgctatgtgactagaaaggaagttga gtgtctcctccttgacattgtgtgcaaaacagactctctttctgtcat---atcttttcacgacaaacaaaaagagacctgttaatcataacaagtctcgctgtttaagatagggccggaaagcatacttttcagcataaaattcggaatgacgacactatcacaggtttctgccagctactcccttgagtagtaccattataccaaattttggggtcttttcaaagagtaaaaactgccttatttgaatttttccttgaaaaccagtataatggtagaatgctatgtgactagaaaggaagttga Subject: NC_003028_SP_1551_SP_1552|cation-transporting ATPase, E1-E2 family:cation efflux family protein|NEGATIVE:POSITIVE|[1461050,1461304]|255 HSP 1 e-value: 1.0E-117 bit: 422.0 Len: 253 Query Start:54 Query End:306 Subject Strand: POSITIVE Subject Start: 3 Subject End: 255 .....................................................cttttcacgacaaacaaaaagagacctgttaatcataacaagtctcgctgtttaagatagggccggaaaacatacttttcagtataaaattcggaatgacgacactatcacaggtttctgccagctactcccttgagtagtactattataccaaattttgaaaaattttcaaagagtaaaaaatgccttatttgaattttcccttgaaaaccagtataatggtagaatgctatgtgactagaaaggaagttga .....................................................cttttcacgacaaacaaaaagaaacctgttaatcataacaagtctcgctgtttaagatagggccggaaagcatacttttcagcataaaattcggaatgacgacactatcacaggtttctgccagctactcccttgagtagtaccattataccaaattttggggagttttcaaagagtaaaaactgccttatttgaatttttccttgaaaaccagtataatggtagaatgctatgtgactagaaaggaagttga Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUGUCUCCUCCUUGACAUUGUGUGCUAAACAGACUCUCUUUUCCUCAUCGUAUCUUUUCACGACAAACAAAAAGAGACCUGUUAAUCAUAACAAGUCUCGCUGUUUAAGAUAGGGCCGGAAAACAUACUUUUCAGUAUAAAAUUCGGAAUGACGACACUAUCACAGGUUUCUGCCAGCUACUCCCUUGAGUAGUACUAUUAUACCAAAUUUUGAAAAAUUUUCAAAGAGUAAAAAAUGCCUUAUUUGAAUUUUCCCUUGAAAACCAGUAUAAUGGUAGAAUGCUAUGUGACUAGAAAGGAAGUUGA (((((........))))).............((((.(((((((.(((((.((((((........(((((....(((((.(((((....))))).)))))..))))))))))).).(((((....(((((....)))))....))))).))))........(((((((((((((((.(((((((....)))))))...(((((((....(((..(..((..((((((..(((.....)))....))))))..))...)..)))....)))))))))))))).))).)))))...))))))))))).. (-71.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCAACUUCCUUUCUAGUCACAUAGCAUUCUACCAUUAUACUGGUUUUCAAGGGAAAAUUCAAAUAAGGCAUUUUUUACUCUUUGAAAAUUUUUCAAAAUUUGGUAUAAUAGUACUACUCAAGGGAGUAGCUGGCAGAAACCUGUGAUAGUGUCGUCAUUCCGAAUUUUAUACUGAAAAGUAUGUUUUCCGGCCCUAUCUUAAACAGCGAGACUUGUUAUGAUUAACAGGUCUCUUUUUGUUUGUCGUGAAAAGAUACGAUGAGGAAAAGAGAGUCUGUUUAGCACACAAUGUCAAGGAGGAGACAC ....(((((((....((((((.....((((.((.((((((((((((((((((((((((((......)).))))))....)))))))))))...........))))))).....((((((....))))))..)).))))...)))))).((((.......(((.....((((((....)))))).....)))........(((((((.(((((((((((....))))))))))).((((.((..(((((......)))))..)).))))......)))))))..))))......)))))))...... (-79.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 934 50 1 141 92 smit:SMT_837|5end_cation_transport_ATPase_782667..782897_NEGATIVE 358 187 143 220 176 smit:SMT_1105|5end_K03217_preprotein_translocase_YidC_subunit_1047632..1047862_NEGATIVE 297 60 11 119 57 smit:SMT_1056|5end_K07738_ATP-cone_domain_protein_994842..995072_POSITIVE 292 49 1 161 106 smit:SMT_1675|5end_adenylosuccinate_synthetase_1661147..1661377_NEGATIVE 288 48 1 131 78 smit:SMT_378|5end_hypothetical_protein_predicted_by_Glimmer/Critica_315884..316114_POSITIVE 287 189 144 216 162 smit:SMT_220|5end_Hypothetical_zinc_metalloprotease_151747..151977_POSITIVE 285 200 154 85 48 smit:SMT_901|5end_hypothetical_protein_851434..851664_NEGATIVE 280 194 151 113 59 smit:SMT_1872|5end_K03217_preprotein_translocase_YidC_subunit_1831764..1831994_NEGATIVE 278 196 152 172 119 smit:SMT_2168|5end_threonyl-tRNA_synthetase_2040991..2041221_POSITIVE 278 290 250 127 95 smit:SMT_1907|5end_phosphate-binding_protein_1854105..1854335_POSITIVE 276 198 156 145 102 smit:SMT_894|5end_hypothetical_protein_841701..841931_NEGATIVE 274 50 2 76 29 smit:SMT_1106|5end_ribonuclease_P_protein_component_1047972..1048202_NEGATIVE 270 193 154 120 77 smit:SMT_1473|5end_hypothetical_protein_1454320..1454550_POSITIVE 269 62 32 152 118 smit:SMT_2017|5end_exonuclease_RexA_1936785..1937015_NEGATIVE 269 62 32 152 118 smit:SMT_1798|5end_exonuclease_RexA_1773441..1773671_NEGATIVE 267 137 95 183 137 smit:SMT_1214|5end_K03584_DNA_repair_protein_RecO_(recombination_protein_O)_1173422..1173652_NEGATIVE 266 206 165 50 3 smit:SMT_485|5end_hypothetical_protein_421401..421631_NEGATIVE 265 189 145 214 159 smit:SMT_877|5end_hypothetical_protein_824412..824642_NEGATIVE 264 195 152 225 189 smit:SMT_1541|5end_isopentenyl-diphosphate_delta-isomerase_1526093..1526323_NEGATIVE 261 208 161 170 110 smit:SMT_1766|5end_sucrose-6-phosphate_hydrolase_1741702..1741932_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 285 200 154 95 58 smit:SMT_902|3end_hypothetical_protein_851424..851574_NEGATIVE 274 50 2 59 12 smit:SMT_1107|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1047989..1048139_NEGATIVE 270 193 156 149 109 smit:SMT_895|3end_cysteinyl-tRNA_synthetase_841694..841844_NEGATIVE 269 62 32 53 19 smit:SMT_1800|3end_exonuclease_RexA_1773540..1773690_NEGATIVE 267 202 165 143 100 smit:SMT_1439|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1423262..1423412_NEGATIVE 257 189 143 89 30 smit:SMT_1484|3end_exonuclease_RexA_1464256..1464406_NEGATIVE 253 190 146 129 80 smit:SMT_1902|3end_proton-translocating_NADH-quinone_oxidoreductase,_chain_L_1852028..1852178_NEGATIVE 253 130 85 58 10 smit:SMT_652|3end_transporter,_putative_562037..562187_NEGATIVE 252 190 146 50 3 smit:SMT_295|3end_hypothetical_protein_predicted_by_Glimmer/Critica_238179..238329_POSITIVE 246 62 21 55 12 smit:SMT_301|3end_hypothetical_protein_244402..244552_POSITIVE 242 48 3 131 72 smit:SMT_1608|3end_hypothetical_protein_1598196..1598346_POSITIVE 242 46 6 97 58 smit:SMT_1443|3end_23S_rRNA_m(5)U_1939_methyltransferase_1426503..1426653_NEGATIVE 241 298 253 53 16 smit:SMT_402|3end_two-component_response_regulator_YesN_331663..331813_POSITIVE 239 215 172 111 66 smit:SMT_1889|3end_hypothetical_protein_1843467..1843617_POSITIVE 239 190 146 123 66 smit:SMT_1351|3end_dephospho-CoA_kinase_1329212..1329362_NEGATIVE 239 205 166 78 40 smit:SMT_230|3end_hypothetical_protein_predicted_by_Glimmer/Critica_165666..165816_NEGATIVE 237 200 154 115 66 smit:SMT_745|3end_glycosyl_transferase,_group_1_family_protein_649284..649434_NEGATIVE 236 200 161 137 100 smit:SMT_1765|3end_ABC_transporter_sugar_permease_1741772..1741922_POSITIVE 236 190 154 141 112 smit:SMT_671|3end_hypothetical_protein_580676..580826_POSITIVE 235 139 96 52 9 smit:SMT_1929|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1869690..1869840_NEGATIVE