Origin IGS: ctgtcattctcctttaaataaaatagtaaaccatcctgtcggaagctgcttgcagcttgtgtgacgaggatgtgtttaaatttttaaaacaggcatcttttagatgtcatattttattacatggaacattatagcagactttttttctcttgtaaagaaaaaagttgaattttctaaaaatttccacaatttattttctgaaacattccagaaaatagtcaagcgaacgggatgttttccgaacgttagtcaggaattgccggttaaaaaaacgaaaaagtggagtttggtgatataatagaggaaatgagctaaaggcactcgccttcaaaagaaaaaggagcgttttact .........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 agtaaaacgctcctttttcttttgaaggcgagtgcctttagctcatttcctctattatatcaccaaactccactttttcgtttttttaaccggcaattcctgactaacgttcggaaaacatcccgttcgcttgactattttctggaatgtttcagaaaataaattgtggaaatttttagaaaattcaacttttttctttacaagagaaaaaaagtctgctataatgttccatgtaataaaatatgacatctaaaagatgcctgttttaaaaatttaaacacatcctcgtcacacaagctgcaagcagcttccgacaggatggtttactattttatttaaaggagaatgacag Mask Tandem Repeat Region ================================================ ctgtcattctcctttaaataaaatagtaaaccatcctgtcggaagctgcttgcagcttgtgtgacgaggatgtgtttaaatttttaaaacaggcatcttttagatgtcatattttattacatggaacattatagcagactttttttctcttgtaaagaaaaaagttgaattttctaaaaatttccacaatttattttctgaaacattccagaaaatagtcaagcgaacgggatgttttccgaacgttagtcaggaattgccggttaaaaaaacgaaaaagtggagtttggtgatataatagaggaaatgagctaaaggcactcgccttcaaaagaaaaaggagcgttttact Find is-nt database================================================ Query_seq: SSA_0371:SSA_0373|SSA_0371:SSA_0373:NADP-specific glutamate dehydrogenase, putative:Dihydroorotate dehydrogenase, putative:<-->:361850..362201 352 ctgtcattctcctttaaataaaatagtaaaccatcctgtcggaagctgcttgcagcttgtgtgacgaggatgtgtttaaatttttaaaacaggcatcttttagatgtcatattttattacatggaacattatagcagactttttttctcttgtaaagaaaaaagttgaattttctaaaaatttccacaatttattttctgaaacattccagaaaatagtcaagcgaacgggatgttttccgaacgttagtcaggaattgccggttaaaaaaacgaaaaagtggagtttggtgatataatagaggaaatgagctaaaggcactcgccttcaaaagaaaaaggagcgttttact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0371:SSA_0373|SSA_0371:SSA_0373:NADP-specific glutamate dehydrogenase, putative:Dihydroorotate dehydrogenase, putative:<-->:361850..362201 352 ctgtcattctcctttaaataaaatagtaaaccatcctgtcggaagctgcttgcagcttgtgtgacgaggatgtgtttaaatttttaaaacaggcatcttttagatgtcatattttattacatggaacattatagcagactttttttctcttgtaaagaaaaaagttgaattttctaaaaatttccacaatttattttctgaaacattccagaaaatagtcaagcgaacgggatgttttccgaacgttagtcaggaattgccggttaaaaaaacgaaaaagtggagtttggtgatataatagaggaaatgagctaaaggcactcgccttcaaaagaaaaaggagcgttttact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0371:SSA_0373|SSA_0371:SSA_0373:NADP-specific glutamate dehydrogenase, putative:Dihydroorotate dehydrogenase, putative:<-->:361850..362201 352 ctgtcattctcctttaaataaaatagtaaaccatcctgtcggaagctgcttgcagcttgtgtgacgaggatgtgtttaaatttttaaaacaggcatcttttagatgtcatattttattacatggaacattatagcagactttttttctcttgtaaagaaaaaagttgaattttctaaaaatttccacaatttattttctgaaacattccagaaaatagtcaagcgaacgggatgttttccgaacgttagtcaggaattgccggttaaaaaaacgaaaaagtggagtttggtgatataatagaggaaatgagctaaaggcactcgccttcaaaagaaaaaggagcgttttact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctgtcattctcctttaaataaaatagtaaaccatcctgtcggaagctgcttgcagcttgtgtgacgaggatgtgtttaaatttttaaaacaggcatcttttagatgtcatattttattacatggaacattatagcagactttttttctcttgtaaagaaaaaagttgaattttctaaaaatttccacaatttattttctgaaacattccagaaaatagtcaagcgaacgggatgttttccgaacgttagtcaggaattgccggttaaaaaaacgaaaaagtggagtttggtgatataatagaggaaatgagctaaaggcactcgccttcaaaagaaaaaggagcgttttact Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 33 End: 131 ................................ M L S E A A C S L C D E D V F K F L K Q A S F R C H I L L H G T L ............................................................................................................................................................................................................................. Protein_Len: 60 Strand: + Start: 104 End: 295 ....................................................................................................... M S Y F I T W N I I A D F F S L V K K K V E F S K N F H N L F S E T F Q K I V K R T G C F P N V S Q E L P V K K T K K W ......................................................... Protein_Len: 46 Strand: - Start: 194 End: 331 ................................................................................................................................................................................................. K R F C E L F Y D L S R S T K R V N T L F Q R N F F R F L P T Q H Y L L P F S S F A S A K M ..................... Protein_Len: 40 Strand: - Start: 103 End: 222 ...................................................................................................... I D Y K I V H F M I A S K K E R T F F F T S N E L F K W L K N E S V N W F I T M .................................................................................................................................. ctgtcattctcctttaaataaaatagtaaaccatcctgtcggaagctgcttgcagcttgtgtgacgaggatgtgtttaaatttttaaaacaggcatcttttagatgtcatattttattacatggaacattatagcagactttttttctcttgtaaagaaaaaagttgaattttctaaaaatttccacaatttattttctgaaacattccagaaaatagtcaagcgaacgggatgttttccgaacgttagtcaggaattgccggttaaaaaaacgaaaaagtggagtttggtgatataatagaggaaatgagctaaaggcactcgccttcaaaagaaaaaggagcgttttact 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: 87 Start: 128 End: 157 ...............................................................................................................................CTTTACAAGAGAAAAAAAGTCTGCTATAAT................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ctgtcattctcctttaaataaaatagtaaaccatcctgtcggaagctgcttgcagcttgtgtgacgaggatgtgtttaaatttttaaaacaggcatcttttagatgtcatattttattacatggaacattatagcagactttttttctcttgtaaagaaaaaagttgaattttctaaaaatttccacaatttattttctgaaacattccagaaaatagtcaagcgaacgggatgttttccgaacgttagtcaggaattgccggttaaaaaaacgaaaaagtggagtttggtgatataatagaggaaatgagctaaaggcactcgccttcaaaagaaaaaggagcgttttact Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0371:SSA_0373|SSA_0371:SSA_0373:NADP-specific glutamate dehydrogenase, putative:Dihydroorotate dehydrogenase, putative:<-->:361850..362201 352 ctgtcattctcctttaaataaaatagtaaaccatcctgtcggaagctgcttgcagcttgtgtgacgaggatgtgtttaaatttttaaaacaggcatcttttagatgtcatattttattacatggaacattatagcagactttttttctcttgtaaagaaaaaagttgaattttctaaaaatttccacaatttattttctgaaacattccagaaaatagtcaagcgaacgggatgttttccgaacgttagtcaggaattgccggttaaaaaaacgaaaaagtggagtttggtgatataatagaggaaatgagctaaaggcactcgccttcaaaagaaaaaggagcgttttact Intra-Species Hit: Count: 1 Min: 1 Max: 352 Len: 352 Subject: NC_009009_SSA_0371_SSA_0373|NADP-specific glutamate dehydrogenase, putative:Dihydroorotate dehydrogenase, putative|NEGATIVE:POSITIVE|[361850,362201]|352 HSP 1 e-value: 1.0E-135 bit: 484.0 Len: 265 Query Start:1 Query End:265 Subject Strand: POSITIVE Subject Start: 1 Subject End: 265 ctgtcattctcctttaaataaaatagtaaaccatcctgtcggaagctgcttgcagcttgtgtgacgaggatgtgtttaaatttttaaaacaggcatcttttagatgtcatattttattacatggaacattatagcagacnnnnnnnctcttgtaaagaaaaaagttgaattttctaaaaatttccacaatttattttctgaaacattccagaaaatagtcaagcgaacgggatgttttccgaacgttagtcaggaattgccggtt....................................................................................... ctgtcattctcctttaaataaaatagtaaaccatcctgtcggaagctgcttgcagcttgtgtgacgaggatgtgtttaaatttttaaaacaggcatcttttagatgtcatattttattacatggaacattatagcagactttttttctcttgtaaagaaaaaagttgaattttctaaaaatttccacaatttattttctgaaacattccagaaaatagtcaagcgaacgggatgttttccgaacgttagtcaggaattgccggtt....................................................................................... HSP 2 e-value: 1.0E-33 bit: 145.0 Len: 73 Query Start:280 Query End:352 Subject Strand: POSITIVE Subject Start: 280 Subject End: 352 .......................................................................................................................................................................................................................................................................................gtggagtttggtgatataatagaggaaatgagctaaaggcactcgccttcaaaagaaaaaggagcgttttact .......................................................................................................................................................................................................................................................................................gtggagtttggtgatataatagaggaaatgagctaaaggcactcgccttcaaaagaaaaaggagcgttttact Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUGUCAUUCUCCUUUAAAUAAAAUAGUAAACCAUCCUGUCGGAAGCUGCUUGCAGCUUGUGUGACGAGGAUGUGUUUAAAUUUUUAAAACAGGCAUCUUUUAGAUGUCAUAUUUUAUUACAUGGAACAUUAUAGCAGACUUUUUUUCUCUUGUAAAGAAAAAAGUUGAAUUUUCUAAAAAUUUCCACAAUUUAUUUUCUGAAACAUUCCAGAAAAUAGUCAAGCGAACGGGAUGUUUUCCGAACGUUAGUCAGGAAUUGCCGGUUAAAAAAACGAAAAAGUGGAGUUUGGUGAUAUAAUAGAGGAAAUGAGCUAAAGGCACUCGCCUUCAAAAGAAAAAGGAGCGUUUUACU ...(((((.(((((((..(((((...(((((((((((((((.((((((....))))))...)))).)))))).)))))...))))).....((((((.....))))))......((((((.(((((.(((......((((((((((..........)))))))))).))).))))).....((((((...((((((((((........)))))))))).......(((.((.....((((..((....))..))))...)).)))..............))))))....))))))...))))))))))))(((.(((((....))))).............)))........ (-90.74) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUAAAACGCUCCUUUUUCUUUUGAAGGCGAGUGCCUUUAGCUCAUUUCCUCUAUUAUAUCACCAAACUCCACUUUUUCGUUUUUUUAACCGGCAAUUCCUGACUAACGUUCGGAAAACAUCCCGUUCGCUUGACUAUUUUCUGGAAUGUUUCAGAAAAUAAAUUGUGGAAAUUUUUAGAAAAUUCAACUUUUUUCUUUACAAGAGAAAAAAAGUCUGCUAUAAUGUUCCAUGUAAUAAAAUAUGACAUCUAAAAGAUGCCUGUUUUAAAAAUUUAAACACAUCCUCGUCACACAAGCUGCAAGCAGCUUCCGACAGGAUGGUUUACUAUUUUAUUUAAAGGAGAAUGACAG .((......(((((((.....((((((((....))))))))......................................((((((..(((.((((.((((.(((....))).)))).........(((((.....(((((((((((....)))))))))))....)))))..((((((((.........(((((((((.....))))))))).................(((((......)))))...)))))))).)))).)))..)))))).(((((.((((((.(((....((((((....))))))..))))))))))))))...........)))))))....)).. (-84.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 989 80 31 171 122 NC_009009:SSA_0371|5end_NADP-specific_glutamate_dehydrogenase,_putative_361759..361989_NEGATIVE 371 72 31 48 1 NC_009009:SSA_1879|5end_Glycyl-tRNA_synthetase_beta_chain,_putative_1874262..1874492_NEGATIVE 337 72 31 148 107 NC_009009:SSA_0620|5end_hypothetical_protein_612325..612555_NEGATIVE 337 330 286 106 68 NC_009009:SSA_0401|5end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_winged-helix_DNA-binding_domains),_putative_398462..398692_POSITIVE 314 258 216 171 126 NC_009009:SSA_1197|5end_DNA_alkylation_repair_enzyme,_putative_1222699..1222929_NEGATIVE 312 77 37 84 31 NC_009009:SSA_1581|5end_Metal-binding_ABC_transporter_(probably_hemin),_putative_1583662..1583892_POSITIVE 307 57 29 183 156 NC_009009:SSA_2277|5end_DNA_segregation_ATPase_FtsK/SpoIIIE_family_protein,_putative_2280407..2280637_NEGATIVE 302 75 31 197 154 NC_009009:SSA_0618|5end_hypothetical_protein_611973..612203_NEGATIVE 301 60 24 83 41 NC_009009:SSA_1750|5end_Extracellular_nuclease,_putative_1737922..1738152_NEGATIVE 298 73 36 188 141 NC_009009:SSA_2254|5end_Holliday_junction_DNA_helicase_ruvA,_putative_2250024..2250254_NEGATIVE 297 78 31 83 36 NC_009009:SSA_1994|5end_CTP_synthase,_putative_1992474..1992704_NEGATIVE 295 75 32 45 5 NC_009009:SSA_1027|5end_hypothetical_protein_1043527..1043757_POSITIVE 293 71 32 146 108 NC_009009:SSA_1744|5end_Iron_compound_ABC_transporter,_permease_protein,_putative_1730915..1731145_POSITIVE 293 63 34 35 1 NC_009009:SSA_0837|5end_Glucosyltransferase,_putative_823902..824132_POSITIVE 290 266 223 198 155 NC_009009:SSA_1076|5end_hypothetical_protein_1094227..1094457_POSITIVE 288 76 31 190 131 NC_009009:SSA_0637|5end_Tryptophan_synthase_beta_chain,_putative_625719..625949_POSITIVE 287 78 34 115 49 NC_009009:SSA_1353|5end_hypothetical_protein_1368519..1368749_NEGATIVE 285 77 33 86 44 NC_009009:SSA_2285|5end_hypothetical_protein_2287404..2287634_POSITIVE 284 74 33 224 171 NC_009009:SSA_0831|5end_Nucleotide_sugar_synthetase-like_protein,_putative_815671..815901_POSITIVE 283 69 31 32 3 NC_009009:SSA_2228|5end_Acetyltransferase_(GNAT)_family,_putative_2228768..2228998_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 337 72 31 151 110 NC_009009:SSA_0621|3end_SOS_responce_UmuC_protein,_putative_612322..612472_NEGATIVE 319 71 31 51 4 NC_009009:SSA_1551|3end_Transcriptional_accessory_ribonuclease_(YqgFc,_S1),_putative_1552652..1552802_NEGATIVE 310 263 222 150 112 NC_009009:SSA_1839|3end_Cysteine_synthase,_putative_1833985..1834135_POSITIVE 298 72 37 45 4 NC_009009:SSA_1880|3end_Glycyl-tRNA_synthetase_alpha_chain,_putative_1874265..1874415_NEGATIVE 295 75 32 55 15 NC_009009:SSA_1026|3end_ABC-type_multidrug_transporter,_ATPase_component,_putative_1043617..1043767_POSITIVE 293 62 21 84 35 NC_009009:SSA_1245|3end_Transcriptional_regulator,_LysR_family,_putative_1269710..1269860_POSITIVE 287 68 32 150 118 NC_009009:SSA_1743|3end_ABC-type_Fe3+-siderophore_transport_system,_permease_component,_putative_1731005..1731155_POSITIVE 287 78 34 79 13 NC_009009:SSA_1354|3end_hypothetical_protein_1368555..1368705_NEGATIVE 283 263 223 53 9 NC_009009:SSA_2135|3end_Transcriptional_repressor,_DeoR_family_(possibly_truncated),_putative_2137474..2137624_POSITIVE 281 69 23 49 4 NC_009009:SSA_1212|3end_Ribose-phosphate_pyrophosphokinase_2,_putative_1236437..1236587_POSITIVE 278 70 23 64 8 NC_009009:SSA_1463|3end_Shikimate_kinase,_putative_1469764..1469914_NEGATIVE 277 267 225 144 102 NC_009009:SSA_1186|3end_Acetyltransferase,_CysE/LacA/Lpx_A/NodL_family,_putative_1214656..1214806_NEGATIVE 273 324 282 88 48 NC_009009:SSA_2267|3end_Lactose_operon_transcriptional_repressor,_LacI_family,_putative_2267190..2267340_POSITIVE 273 69 29 87 41 NC_009009:SSA_1430|3end_Ribonuclease_Z,_putative_1437107..1437257_NEGATIVE 272 68 29 148 100 NC_009009:SSA_1442|3end_Imidazole_glycerol-phosphate_synthase_subunit_hisF,_putative_1445183..1445333_NEGATIVE 271 266 230 137 111 NC_009009:SSA_0350|3end_Helicase,_putative_341852..342002_NEGATIVE 270 266 234 119 77 NC_009009:SSA_0589|3end_Acetylornithine_deacetylase/succinyl-diaminopimelate_desuccinylase_(M20/M25/M40_family_peptidase),_putative_582207..582357_POSITIVE 268 344 305 50 9 NC_009009:SSA_1325|3end_Ketoacyl_reductase_hetN,_putative_1341573..1341723_NEGATIVE 266 342 309 72 38 NC_009009:SSA_0795|3end_hypothetical_protein_777065..777215_POSITIVE 266 74 34 140 98 NC_009009:SSA_0418|3end_AraC-type_DNA-binding_domain-containing_protein,_putative_416184..416334_POSITIVE