Origin IGS: ccgaaagagtggtagagtgttcaaggagtgcaggaataactttctatattaataagaaaaaaccagtttatccttgtgttgtttagactcgaaaagacagagcaagacctctgccttttcttttttatcctcgaatctcctgccatctcccagttctgtaagcacagtctaatggagcttttttgcttttttcattcttgaaagatataggaaaacatgctataatgaaaagaacattctaaaaatcagaaagattattatatagtaaggaaaaaa .........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 ttttttccttactatataataatctttctgatttttagaatgttcttttcattatagcatgttttcctatatctttcaagaatgaaaaaagcaaaaaagctccattagactgtgcttacagaactgggagatggcaggagattcgaggataaaaaagaaaaggcagaggtcttgctctgtcttttcgagtctaaacaacacaaggataaactggttttttcttattaatatagaaagttattcctgcactccttgaacactctaccactctttcgg Mask Tandem Repeat Region ================================================ ccgaaagagtggtagagtgttcaaggagtgcaggaataactttctatattaataagaaaaaaccagtttatccttgtgttgtttagactcgaaaagacagagcaagacctctgccttttcttttttatcctcgaatctcctgccatctcccagttctgtaagcacagtctaatggagcttttttgcttttttcattcttgaaagatataggaaaacatgctataatgaaaagaacattctaaaaatcagaaagattattatatagtaaggaaaaaa Find is-nt database================================================ Query_seq: SSA_0541:SSA_0543|SSA_0541:SSA_0543:Acetate kinase, putative:SecA, putative:->->:537143..537418 276 ccgaaagagtggtagagtgttcaaggagtgcaggaataactttctatattaataagaaaaaaccagtttatccttgtgttgtttagactcgaaaagacagagcaagacctctgccttttcttttttatcctcgaatctcctgccatctcccagttctgtaagcacagtctaatggagcttttttgcttttttcattcttgaaagatataggaaaacatgctataatgaaaagaacattctaaaaatcagaaagattattatatagtaaggaaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0541:SSA_0543|SSA_0541:SSA_0543:Acetate kinase, putative:SecA, putative:->->:537143..537418 276 ccgaaagagtggtagagtgttcaaggagtgcaggaataactttctatattaataagaaaaaaccagtttatccttgtgttgtttagactcgaaaagacagagcaagacctctgccttttcttttttatcctcgaatctcctgccatctcccagttctgtaagcacagtctaatggagcttttttgcttttttcattcttgaaagatataggaaaacatgctataatgaaaagaacattctaaaaatcagaaagattattatatagtaaggaaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0541:SSA_0543|SSA_0541:SSA_0543:Acetate kinase, putative:SecA, putative:->->:537143..537418 276 ccgaaagagtggtagagtgttcaaggagtgcaggaataactttctatattaataagaaaaaaccagtttatccttgtgttgtttagactcgaaaagacagagcaagacctctgccttttcttttttatcctcgaatctcctgccatctcccagttctgtaagcacagtctaatggagcttttttgcttttttcattcttgaaagatataggaaaacatgctataatgaaaagaacattctaaaaatcagaaagattattatatagtaaggaaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ccgaaagagtggtagagtgttcaaggagtgcaggaataactttctatattaataagaaaaaaccagtttatccttgtgttgtttagactcgaaaagacagagcaagacctctgccttttcttttttatcctcgaatctcctgccatctcccagttctgtaagcacagtctaatggagcttttttgcttttttcattcttgaaagatataggaaaacatgctataatgaaaagaacattctaaaaatcagaaagattattatatagtaaggaaaaaa Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 74 End: 169 ......................................................................... M C C L D S K R Q S K T S A F S F L S S N L L P S P S S V S T V ........................................................................................................... Protein_Len: 51 Strand: + Start: 46 End: 198 ............................................. M L I R K N Q F I L V L F R L E K T E Q D L C L F F F I L E S P A I S Q F C K H S L M E L F C F F H S .............................................................................. Protein_Len: 33 Strand: - Start: 128 End: 226 ............................................................................................................................... G R I E Q W R G T R Y A C D L P A K K S K E N K F S I P F C A I M .................................................. Protein_Len: 38 Strand: - Start: 52 End: 165 ................................................... Y S F V L K D K H Q K S E F L C L L V E A K E K K D E F R R G D G L E T L M ............................................................................................................... Protein_Len: 50 Strand: - Start: 24 End: 173 ....................... P T C S Y S E I N I L F F W N I R T N N L S S F V S C S R Q R K K K I R S D G A M E W N Q L C L R M ....................................................................................................... ccgaaagagtggtagagtgttcaaggagtgcaggaataactttctatattaataagaaaaaaccagtttatccttgtgttgtttagactcgaaaagacagagcaagacctctgccttttcttttttatcctcgaatctcctgccatctcccagttctgtaagcacagtctaatggagcttttttgcttttttcattcttgaaagatataggaaaacatgctataatgaaaagaacattctaaaaatcagaaagattattatatagtaaggaaaaaa 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: 90 Start: 197 End: 226 ....................................................................................................................................................................................................CTTGAAAGATATAGGAAAACATGCTATAAT.................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ PromScan Matrix: RpoN Strand: - Score: 83 Start: 101 End: 117 ....................................................................................................AAGGCAGAGGTCTTGCT............................................................................................................................................................... ccgaaagagtggtagagtgttcaaggagtgcaggaataactttctatattaataagaaaaaaccagtttatccttgtgttgtttagactcgaaaagacagagcaagacctctgccttttcttttttatcctcgaatctcctgccatctcccagttctgtaagcacagtctaatggagcttttttgcttttttcattcttgaaagatataggaaaacatgctataatgaaaagaacattctaaaaatcagaaagattattatatagtaaggaaaaaa Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -9.4 Tail_Score: -5.31275 Start: 91 End: 120 Full_Region: GTGTTGTTTAGACTC GAAAAGACAGAG CAAGAC CTCTGCCTTTTC TTTTTTATCCTCGAA ..........................................................................................GAAAAGACAGAGCAAGACCTCTGCCTTTTC............................................................................................................................................................ TransTerm Strand: + Conf: 79 HP_score: -3.5 Tail_Score: -5.49579 Start: 96 End: 115 Full_Region: GTTTAGACTCGAAAA GACAGAG CAAGAC CTCTGCC TTTTCTTTTTTATCC ...............................................................................................GACAGAGCAAGACCTCTGCC................................................................................................................................................................. TransTerm Strand: - Conf: 65 HP_score: -5.7 Tail_Score: -4.16943 Start: 96 End: 115 Full_Region: ggataaaaaagaaaa ggcagag gtcttg ctctgtc ttttcgagtctaaac ...............................................................................................ggcagaggtcttgctctgtc................................................................................................................................................................. Find igs database================================================ Query_seq: SSA_0541:SSA_0543|SSA_0541:SSA_0543:Acetate kinase, putative:SecA, putative:->->:537143..537418 276 ccgaaagagtggtagagtgttcaaggagtgcaggaataactttctatattaataagaaaaaaccagtttatccttgtgttgtttagactcgaaaagacagagcaagacctctgccttttcttttttatcctcgaatctcctgccatctcccagttctgtaagcacagtctaatggagcttttttgcttttttcattcttgaaagatataggaaaacatgctataatgaaaagaacattctaaaaatcagaaagattattatatagtaaggaaaaaa Intra-Species Hit: Count: 1 Min: 1 Max: 276 Len: 276 Subject: NC_009009_SSA_0541_SSA_0543|Acetate kinase, putative:SecA, putative|POSITIVE:POSITIVE|[537143,537418]|276 HSP 1 e-value: 2.0E-96 bit: 353.0 Len: 178 Query Start:1 Query End:178 Subject Strand: POSITIVE Subject Start: 1 Subject End: 178 ccgaaagagtggtagagtgttcaaggagtgcaggaataactttctatattaataagaaaaaaccagtttatccttgtgttgtttagactcgaaaagacagagcaagacctctgccttttcttttttatcctcgaatctcctgccatctcccagttctgtaagcacagtctaatggagc.................................................................................................. ccgaaagagtggtagagtgttcaaggagtgcaggaataactttctatattaataagaaaaaaccagtttatccttgtgttgtttagactcgaaaagacagagcaagacctctgccttttcttttttatcctcgaatctcctgccatctcccagttctgtaagcacagtctaatggagc.................................................................................................. HSP 2 e-value: 3.0E-40 bit: 167.0 Len: 84 Query Start:193 Query End:276 Subject Strand: POSITIVE Subject Start: 193 Subject End: 276 ................................................................................................................................................................................................cattcttgaaagatataggaaaacatgctataatgaaaagaacattctaaaaatcagaaagattattatatagtaaggaaaaaa ................................................................................................................................................................................................cattcttgaaagatataggaaaacatgctataatgaaaagaacattctaaaaatcagaaagattattatatagtaaggaaaaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCGAAAGAGUGGUAGAGUGUUCAAGGAGUGCAGGAAUAACUUUCUAUAUUAAUAAGAAAAAACCAGUUUAUCCUUGUGUUGUUUAGACUCGAAAAGACAGAGCAAGACCUCUGCCUUUUCUUUUUUAUCCUCGAAUCUCCUGCCAUCUCCCAGUUCUGUAAGCACAGUCUAAUGGAGCUUUUUUGCUUUUUUCAUUCUUGAAAGAUAUAGGAAAACAUGCUAUAAUGAAAAGAACAUUCUAAAAAUCAGAAAGAUUAUUAUAUAGUAAGGAAAAAA ((....((....((((((((((..((((.((((((.......((((.((..(((((...(((....)))...)))))...)).))))...((((((.(((((......))))).)))))).................))))))...)))).((((((((.((......)).))))))))((((((..(((((((....)))))))..))))))..(((......)))....))))))))))....))......(((((...)))))..))...... (-61.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUUUCCUUACUAUAUAAUAAUCUUUCUGAUUUUUAGAAUGUUCUUUUCAUUAUAGCAUGUUUUCCUAUAUCUUUCAAGAAUGAAAAAAGCAAAAAAGCUCCAUUAGACUGUGCUUACAGAACUGGGAGAUGGCAGGAGAUUCGAGGAUAAAAAAGAAAAGGCAGAGGUCUUGCUCUGUCUUUUCGAGUCUAAACAACACAAGGAUAAACUGGUUUUUUCUUAUUAAUAUAGAAAGUUAUUCCUGCACUCCUUGAACACUCUACCACUCUUUCGG .........................(((((..........((((.((((((((..((.((((......))))))......)))))))).))))...((((..((......)).)))).)))))(((..((((((..((((.((((((((.......((((((((((((......))))))))))))................((((..((((......((((.........))))))))..))))....))))))))..)))).))).)))..))) (-62.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 392 169 128 144 96 NC_009009:SSA_0343|5end_DNA-damage-inducible_protein_P,_putative_337525..337755_POSITIVE 351 183 141 73 17 NC_009009:SSA_0538|5end_PduH_protein,_putative_533794..534024_POSITIVE 342 179 136 53 4 NC_009009:SSA_1592|5end_hypothetical_protein_1596397..1596627_NEGATIVE 342 218 173 199 151 NC_009009:SSA_1320|5end_hypothetical_protein_1337194..1337424_NEGATIVE 331 157 111 185 140 NC_009009:SSA_1010|5end_UDP-glucose_4-epimerase,_putative_1012739..1012969_POSITIVE 325 172 140 198 155 NC_009009:SSA_2221|5end_Cps9E,_putative_2223257..2223487_NEGATIVE 324 168 129 197 144 NC_009009:SSA_1414|5end_hypothetical_protein_1425412..1425642_NEGATIVE 317 176 133 68 15 NC_009009:SSA_0375|5end_D-methionine-binding_lipoprotein_(ABC-type_transporter),_putative_364257..364487_POSITIVE 315 189 144 45 1 NC_009009:SSA_1896|5end_Translation_initiation_factor_IF-2,_putative_1894134..1894364_NEGATIVE 312 164 121 142 84 NC_009009:SSA_1323|5end_hypothetical_protein_1340450..1340680_NEGATIVE 301 157 111 111 53 NC_009009:SSA_1453|5end_hypothetical_protein_1460208..1460438_NEGATIVE 300 31 1 172 133 NC_009009:SSA_0339|5end_hypothetical_protein_333950..334180_NEGATIVE 297 160 111 177 114 NC_009009:SSA_1481|5end_FmtA-like_protein,_putative_1486622..1486852_NEGATIVE 296 148 101 175 118 NC_009009:SSA_1307|5end_Trk_transporter_membrane-spanning_protein-K+_transport,_putative_1326270..1326500_NEGATIVE 296 199 151 197 157 NC_009009:SSA_0818|5end_SPX_domain-like_protein,_putative_799675..799905_POSITIVE 295 170 121 134 80 NC_009009:SSA_0486|5end_Uroporphyrinogen-III_synthase,_putative_486637..486867_POSITIVE 293 189 141 196 149 NC_009009:SSA_0102|5end_Kinase,_putative_104035..104265_POSITIVE 292 213 171 118 71 NC_009009:SSA_0080|5end_Superfamily_I_DNA_and_RNA_helicases,_putative_83785..84015_POSITIVE 291 158 116 225 175 NC_009009:SSA_0216|5end_Histidine_kinase,_putative_211877..212107_POSITIVE 290 43 1 230 170 NC_009009:SSA_1259|5end_Purine_nucleoside_phosphorylase,_putative_1285722..1285952_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 396 175 132 151 110 NC_009009:SSA_1732|3end_Uracil_phosphoribosyltransferase,_putative_1716916..1717066_NEGATIVE 351 183 141 92 36 NC_009009:SSA_0537|3end_Propanediol_utilization:dioldehydratase_reactivation,_putative_533893..534043_POSITIVE 342 179 136 60 11 NC_009009:SSA_1593|3end_Dipeptidase,_putative_1596390..1596540_NEGATIVE 342 218 173 147 99 NC_009009:SSA_1321|3end_Ferrochelatase,_putative_1337246..1337396_NEGATIVE 318 199 152 70 3 NC_009009:SSA_1501|3end_Cytidylate_kinase,_putative_1505095..1505245_NEGATIVE 312 140 95 119 75 NC_009009:SSA_0911|3end_hypothetical_protein_922898..923048_POSITIVE 309 165 140 143 113 NC_009009:SSA_2222|3end_Tyrosine-protein_kinase_Wze,_putative_2223299..2223449_NEGATIVE 309 178 142 151 118 NC_009009:SSA_0273|3end_hypothetical_protein_268566..268716_POSITIVE 304 149 101 55 3 NC_009009:SSA_1292|3end_hypothetical_protein_1311099..1311249_NEGATIVE 301 157 111 64 6 NC_009009:SSA_1454|3end_hypothetical_protein_1460255..1460405_NEGATIVE 295 170 121 149 95 NC_009009:SSA_0485|3end_Porphobilinogen_deaminase,_putative_486732..486882_POSITIVE 295 115 75 145 98 NC_009009:SSA_0428|3end_Formimidoylglutamase,_putative_427665..427815_NEGATIVE 292 157 116 121 82 NC_009009:SSA_0796|3end_ABC-NBD_transporters_with_duplicated_ATPase_domains,_putative_779060..779210_POSITIVE 292 213 171 72 25 NC_009009:SSA_0079|3end_ROK_family_protein,_putative_83819..83969_POSITIVE 289 164 128 59 20 NC_009009:SSA_0376|3end_ABC-type_methionine_transporter,_ATPase_component,_putative_366526..366676_POSITIVE 285 170 128 49 8 NC_009009:SSA_0657|3end_PyridoxaL_5'-phosphate_Dependent_Enzymes_class_III,_putative_642196..642346_POSITIVE 285 115 71 50 7 NC_009009:SSA_0470|3end_Precorrin-4_methylase,_putative_473732..473882_POSITIVE 285 167 121 137 84 NC_009009:SSA_0323|3end_Flavoprotein,_putative_315624..315774_NEGATIVE 277 102 65 69 30 NC_009009:SSA_2210|3end_Ribosomal_large_subunit_pseudouridine_synthase_D,_putative_2211454..2211604_POSITIVE 275 150 101 135 80 NC_009009:SSA_1256|3end_NAD-dependent_deacetylase,_putative_1282357..1282507_NEGATIVE