Origin IGS: aacaaaaagagccgttgggctcttttttgtttatagattttttaagactttccttaagtaatgacggacggtagcgaccttcttcgaagttccatacctaaactttgagcctaggtctcaaagtttccgaacatctgaaagcaagctgtttcagatgttttcattccgtcggaaagtcttggatttagttgtgaaatggtgaatgagttgcctaaattatgatgtataattaatgggatataacttgtttaccttttaaaaaagagccgtcgggctcttt .........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 aaagagcccgacggctcttttttaaaaggtaaacaagttatatcccattaattatacatcataatttaggcaactcattcaccatttcacaactaaatccaagactttccgacggaatgaaaacatctgaaacagcttgctttcagatgttcggaaactttgagacctaggctcaaagtttaggtatggaacttcgaagaaggtcgctaccgtccgtcattacttaaggaaagtcttaaaaaatctataaacaaaaaagagcccaacggctctttttgtt Mask Tandem Repeat Region ================================================ aacaaaaagagccgttgggctcttttttgtttatagattttttaagactttccttaagtaatgacggacggtagcgaccttcttcgaagttccatacctaaactttgagcctaggtctcaaagtttccgaacatctgaaagcaagctgtttcagatgttttcattccgtcggaaagtcttggatttagttgtgaaatggtgaatgagttgcctaaattatgatgtataattaatgggatataacttgtttaccttttaaaaaagagccgtcgggctcttt Find is-nt database================================================ Query_seq: SMT_342:SMT_343|SMT_342:SMT_343:chaperone protein DnaJ:hypothetical protein:-><-:283077..283356 280 aacaaaaagagccgttgggctcttttttgtttatagattttttaagactttccttaagtaatgacggacggtagcgaccttcttcgaagttccatacctaaactttgagcctaggtctcaaagtttccgaacatctgaaagcaagctgtttcagatgttttcattccgtcggaaagtcttggatttagttgtgaaatggtgaatgagttgcctaaattatgatgtataattaatgggatataacttgtttaccttttaaaaaagagccgtcgggctcttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_342:SMT_343|SMT_342:SMT_343:chaperone protein DnaJ:hypothetical protein:-><-:283077..283356 280 aacaaaaagagccgttgggctcttttttgtttatagattttttaagactttccttaagtaatgacggacggtagcgaccttcttcgaagttccatacctaaactttgagcctaggtctcaaagtttccgaacatctgaaagcaagctgtttcagatgttttcattccgtcggaaagtcttggatttagttgtgaaatggtgaatgagttgcctaaattatgatgtataattaatgggatataacttgtttaccttttaaaaaagagccgtcgggctcttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_342:SMT_343|SMT_342:SMT_343:chaperone protein DnaJ:hypothetical protein:-><-:283077..283356 280 aacaaaaagagccgttgggctcttttttgtttatagattttttaagactttccttaagtaatgacggacggtagcgaccttcttcgaagttccatacctaaactttgagcctaggtctcaaagtttccgaacatctgaaagcaagctgtttcagatgttttcattccgtcggaaagtcttggatttagttgtgaaatggtgaatgagttgcctaaattatgatgtataattaatgggatataacttgtttaccttttaaaaaagagccgtcgggctcttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aacaaaaagagccgttgggctcttttttgtttatagattttttaagactttccttaagtaatgacggacggtagcgaccttcttcgaagttccatacctaaactttgagcctaggtctcaaagtttccgaacatctgaaagcaagctgtttcagatgttttcattccgtcggaaagtcttggatttagttgtgaaatggtgaatgagttgcctaaattatgatgtataattaatgggatataacttgtttaccttttaaaaaagagccgtcgggctcttt Predict ORF larger than 30AA ================================================ Protein_Len: 42 Strand: - Start: 114 End: 239 ................................................................................................................. T E F N G F M Q F C A T E S T K M G D S L R P N L Q S I T F S N G L N H H I I L P M ......................................... aacaaaaagagccgttgggctcttttttgtttatagattttttaagactttccttaagtaatgacggacggtagcgaccttcttcgaagttccatacctaaactttgagcctaggtctcaaagtttccgaacatctgaaagcaagctgtttcagatgttttcattccgtcggaaagtcttggatttagttgtgaaatggtgaatgagttgcctaaattatgatgtataattaatgggatataacttgtttaccttttaaaaaagagccgtcgggctcttt 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================================================ aacaaaaagagccgttgggctcttttttgtttatagattttttaagactttccttaagtaatgacggacggtagcgaccttcttcgaagttccatacctaaactttgagcctaggtctcaaagtttccgaacatctgaaagcaagctgtttcagatgttttcattccgtcggaaagtcttggatttagttgtgaaatggtgaatgagttgcctaaattatgatgtataattaatgggatataacttgtttaccttttaaaaaagagccgtcgggctcttt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 72 HP_score: -8.3 Tail_Score: -3.55071 Start: 103 End: 123 Full_Region: AGTTCCATACCTAAA CTTTGAGCC TAG GTCTCAAAG TTTCCGAACATCTGA ......................................................................................................CTTTGAGCCTAGGTCTCAAAG............................................................................................................................................................. TransTerm Strand: - Conf: 74 HP_score: -8.3 Tail_Score: -3.7108 Start: 103 End: 123 Full_Region: tcagatgttcggaaa ctttgagac cta ggctcaaag tttaggtatggaact ......................................................................................................ctttgagacctaggctcaaag............................................................................................................................................................. TransTerm Strand: + Conf: 86 HP_score: -8.5 Tail_Score: -4.43477 Start: 132 End: 157 Full_Region: CTCAAAGTTTCCGAA CATCTGAAAGCA AGC TGTTTCAGATG TTTTCATTCCGTCGG ...................................................................................................................................CATCTGAAAGCAAGCTGTTTCAGATG........................................................................................................................... Find igs database================================================ Query_seq: SMT_342:SMT_343|SMT_342:SMT_343:chaperone protein DnaJ:hypothetical protein:-><-:283077..283356 280 aacaaaaagagccgttgggctcttttttgtttatagattttttaagactttccttaagtaatgacggacggtagcgaccttcttcgaagttccatacctaaactttgagcctaggtctcaaagtttccgaacatctgaaagcaagctgtttcagatgttttcattccgtcggaaagtcttggatttagttgtgaaatggtgaatgagttgcctaaattatgatgtataattaatgggatataacttgtttaccttttaaaaaagagccgtcgggctcttt Intra-Species Hit: Count: 1 Min: 1 Max: 280 Len: 280 Subject: smit_SMT_342_SMT_343|chaperone protein DnaJ:hypothetical protein|POSITIVE:NEGATIVE|[283077,283356]|280 HSP 1 e-value: 1.0E-157 bit: 555.0 Len: 280 Query Start:1 Query End:280 Subject Strand: POSITIVE Subject Start: 1 Subject End: 280 aacaaaaagagccgttgggctcttttttgtttatagattttttaagactttccttaagtaatgacggacggtagcgaccttcttcgaagttccatacctaaactttgagcctaggtctcaaagtttccgaacatctgaaagcaagctgtttcagatgttttcattccgtcggaaagtcttggatttagttgtgaaatggtgaatgagttgcctaaattatgatgtataattaatgggatataacttgtttaccttttaaaaaagagccgtcgggctcttt aacaaaaagagccgttgggctcttttttgtttatagattttttaagactttccttaagtaatgacggacggtagcgaccttcttcgaagttccatacctaaactttgagcctaggtctcaaagtttccgaacatctgaaagcaagctgtttcagatgttttcattccgtcggaaagtcttggatttagttgtgaaatggtgaatgagttgcctaaattatgatgtataattaatgggatataacttgtttaccttttaaaaaagagccgtcgggctcttt Inter-species Hit: Count: 4 Min: 30 Max: 280 Len: 251 Subject: NC_003028_SP_0519_SP_0520|dnaJ protein:hypothetical protein|POSITIVE:NEGATIVE|[501204,501892]|689 HSP 1 e-value: 1.0E-57 bit: 224.0 Len: 177 Query Start:30 Query End:206 Subject Strand: POSITIVE Subject Start: 136 Subject End: 311 .............................tttatagattttttaagactttccttaagtaatgacggacggtagcgaccttcttcgaagttccatacctaaactttgagcctaggtctcaaagtttccgaacatctgaaagcaagctgtttcagatgttttcattccgtcggaaagtcttggatttagttgtgaaatggtgaatga.......................................................................... .............................tttatagattttttaagactttcct-aagtaatgacggacggtagtgacctccttcgaagttccatacctaaactttgaacctaagttttaaagtttccggacagctgaaaccaagctgtttcaggtgttttcattacggcagaaagtcttcgatttagttgtgaaatggtgaatga.......................................................................... HSP 2 e-value: 7.0E-13 bit: 75.8 Len: 42 Query Start:239 Query End:280 Subject Strand: POSITIVE Subject Start: 648 Subject End: 689 ..............................................................................................................................................................................................................................................tataacttgtttaccttttaaaaaagagccgtcgggctcttt ..............................................................................................................................................................................................................................................tataacttgtttacgttttaaaaaagagccgtcgggctcttt Subject: NC_008533_SPD_1530_SPD_1531|hypothetical protein:fructokinase|POSITIVE:NEGATIVE|[1552680, 1552998]|319 HSP 1 e-value: 9.0E-28 bit: 125.0 Len: 102 Query Start:39 Query End:140 Subject Strand: NEGATIVE Subject Start: 166 Subject End: 268 ......................................tttttaagactttccttaagtaatgacggacggtagcgaccttcttcgaagttccatacctaaactttgagcctag-gtctcaaagtttccgaacatctgaaa............................................................................................................................................ ......................................tttttgagcctttccttaagtgattacggacggtagcgactttcttcgaaattccatacctaaactttgagcctagtgtctcaaagtttccgaatacctgaaa............................................................................................................................................ Subject: NC_003098_spr1564_spr1565|hypothetical protein:Fructokinase|POSITIVE:NEGATIVE|[1545149, 1545467]|319 HSP 1 e-value: 9.0E-28 bit: 125.0 Len: 102 Query Start:39 Query End:140 Subject Strand: NEGATIVE Subject Start: 166 Subject End: 268 ......................................tttttaagactttccttaagtaatgacggacggtagcgaccttcttcgaagttccatacctaaactttgagcctag-gtctcaaagtttccgaacatctgaaa............................................................................................................................................ ......................................tttttgagcctttccttaagtgattacggacggtagcgactttcttcgaaattccatacctaaactttgagcctagtgtctcaaagtttccgaatacctgaaa............................................................................................................................................ Subject: NC_003028_SP_1720_SP_1721|hypothetical protein:fructokinase|POSITIVE:NEGATIVE|[1623748, 1624066]|319 HSP 1 e-value: 5.0E-17 bit: 89.7 Len: 102 Query Start:39 Query End:140 Subject Strand: NEGATIVE Subject Start: 166 Subject End: 268 ......................................tttttaagactttccttaagtaatgacggacggtagcgaccttcttcgaagttccatacctaaactttgag--cctaggtctcaaagtttccgaacatctgaaa............................................................................................................................................ ......................................tttttgagcctttccttaagtgattacggacggtagcgactttcttcaaaattccatacctaaactttgagacactagg-ctcaaagtttccgaatacctgaaa............................................................................................................................................ Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUAUAGAUUUUUUAAGACUUUCCUUAAGUAAUGACGGACGGUAGCGACCUUCUUCGAAGUUCCAUACCUAAACUUUGAGCCUAGGUCUCAAAGUUUCCGAACAUCUGAAAGCAAGCUGUUUCAGAUGUUUUCAUUCCGUCGGAAAGUCUUGGAUUUAGUUGUGAAAUGGUGAAUGAGUUGCCUAAAUUAUGAUGUAUAAUUAAUGGGAUAUAACUUGUUUACCUUUUAAAAAAGAGCCGUCGGGCUCUUU (((((((....(((((((((((((.........((((((.((((..((.((((...)))).))..)))).(((((((((((....).))))))))))..((((((((((((........))))))))))))....))))))))))))))))))).....)))))))..((((((..((((((((((((((((...)))))))..))))...)))))..)))))).......((((((((....)))))))) (-86.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAGAGCCCGACGGCUCUUUUUUAAAAGGUAAACAAGUUAUAUCCCAUUAAUUAUACAUCAUAAUUUAGGCAACUCAUUCACCAUUUCACAACUAAAUCCAAGACUUUCCGACGGAAUGAAAACAUCUGAAACAGCUUGCUUUCAGAUGUUCGGAAACUUUGAGACCUAGGCUCAAAGUUUAGGUAUGGAACUUCGAAGAAGGUCGCUACCGUCCGUCAUUACUUAAGGAAAGUCUUAAAAAAUCUAUAAA ((((((((....)))))))).......(((.((..((((....((....((((((.....))))))..)).))))..)).))).................((((((((((((((((.....(((((((((((........)))))))))))...((((((((((.(....))))))))))).((((..((.((((...)))).))..)))).)))))).........)))))))))).............. (-67.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 431 100 51 202 152 smit:SMT_995|5end_K07574_putative_RNA-binding_protein_containing_KH_domain_936468..936698_NEGATIVE 333 150 103 219 165 smit:SMT_975|5end_hypothetical_protein_922953..923183_POSITIVE 332 90 44 165 122 smit:SMT_1076|5end_2-amino-4-hydroxy-6-_hydroxymethyldihydropteridine_pyrophosphokinase_/_dihydroneopterin_aldolase_1014813..1015043_NEGATIVE 309 123 84 231 197 smit:SMT_1728|5end_exodeoxyribonuclease_VII_large_subunit_1713248..1713478_POSITIVE 308 70 25 101 39 smit:SMT_318|5end_hypothetical_protein_258282..258512_NEGATIVE 306 89 41 193 144 smit:SMT_1190|5end_phosphoribosylaminoimidazole_carboxylase,_catalytic_subunit_1148232..1148462_NEGATIVE 296 148 103 53 1 smit:SMT_1833|5end_tagatose_1,6-diphosphate_aldolase_1801369..1801599_POSITIVE 296 72 34 176 135 smit:SMT_625|5end_50S_ribosomal_protein_L27_530027..530257_POSITIVE 295 118 75 228 169 smit:SMT_1981|5end_K03696_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpC_1912261..1912491_POSITIVE 291 105 61 67 24 smit:SMT_1118|5end_hypothetical_protein_1055150..1055380_NEGATIVE 289 250 205 215 161 smit:SMT_1452|5end_ABC-type_uncharacterized_transport_system,_ATPase_component_1436211..1436441_NEGATIVE 288 108 61 192 135 smit:SMT_1925|5end_K03697_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpE_1867262..1867492_POSITIVE 288 57 20 169 133 smit:SMT_340|5end_chaperone_protein_278663..278893_POSITIVE 286 79 32 84 32 smit:SMT_1096|5end_glyceraldehyde-3-phosphate_dehydrogenase_1038376..1038606_NEGATIVE 285 96 52 54 3 smit:SMT_1729|5end_exodeoxyribonuclease_VII_small_subunit_1714566..1714796_POSITIVE 285 152 112 230 191 smit:SMT_1644|5end_3-isopropylmalate_dehydrogenase_1630704..1630934_POSITIVE 285 123 84 205 167 smit:SMT_1508|5end_hypothetical_protein_1491568..1491798_NEGATIVE 284 90 41 204 161 smit:SMT_451|5end_thiamine-phosphate_pyrophosphorylase_388935..389165_POSITIVE 283 130 81 190 137 smit:SMT_1586|5end_K07177_PDZ_domain-containing_protein_1575714..1575944_POSITIVE 282 99 53 69 10 smit:SMT_2086|5end_hypothetical_protein_1983696..1983926_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 367 90 41 71 12 smit:SMT_1728|3end_exodeoxyribonuclease_VII_large_subunit_1714668..1714818_POSITIVE 332 90 44 122 79 smit:SMT_1077|3end_GTP_cyclohydrolase_I_1014856..1015006_NEGATIVE 318 130 84 109 70 smit:SMT_1727|3end_uridine_kinase_1713201..1713351_POSITIVE 308 70 25 79 17 smit:SMT_319|3end_K02356_elongation_factor_EF-P_258304..258454_NEGATIVE 297 67 21 67 27 smit:SMT_621|3end_K03346_replication_initiation_and_membrane_attachment_protein_529059..529209_POSITIVE 291 148 112 51 16 smit:SMT_1832|3end_tagatose-6-phosphate_kinase_1801447..1801597_POSITIVE 290 88 41 87 29 smit:SMT_2006|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1926803..1926953_POSITIVE 289 120 74 56 10 smit:SMT_1946|3end_sucrose-6-phosphate_hydrolase_1881205..1881355_POSITIVE 289 250 205 71 17 smit:SMT_1453|3end_K07335_basic_membrane_protein_A_and_related_proteins_1436355..1436505_NEGATIVE 283 99 53 62 3 smit:SMT_951|3end_oxidoreductase,_DadA_family_protein/D-amino_acid_oxidase_898995..899145_NEGATIVE 280 90 41 69 12 smit:SMT_360|3end_K07742_hypothetical_protein_296001..296151_POSITIVE 279 77 32 53 7 smit:SMT_1353|3end_GTP-binding_protein_1330690..1330840_NEGATIVE 275 90 44 131 79 smit:SMT_1124|3end_pyrrolidone-carboxylate_peptidase_1060225..1060375_NEGATIVE 274 89 41 145 89 smit:SMT_260|3end_phage_transcriptional_repressor_200236..200386_POSITIVE 269 107 63 66 13 smit:SMT_1733|3end_DNA_repair_protein_RecN_1718636..1718786_POSITIVE 266 64 21 66 27 smit:SMT_1078|3end_folylpolyglutamate_synthase_1015391..1015541_NEGATIVE 264 67 23 66 20 smit:SMT_929|3end_hypothetical_protein_883202..883352_NEGATIVE 264 66 24 58 16 smit:SMT_545|3end_hypothetical_protein_predicted_by_Glimmer/Critica_461424..461574_POSITIVE 261 180 131 128 80 smit:SMT_445|3end_hypothetical_protein_384949..385099_POSITIVE 258 106 61 120 69 smit:SMT_750|3end_3-phosphoshikimate_1-carboxyvinyltransferase_653964..654114_NEGATIVE