Origin IGS: aaaagacttgaaaaagcaaaataaggaaggctcagctctatcagctagcctcaaaatccgctcaaaaaacctcagctaatttttgaattggcggaggtttatttttagattaagtcgaagaaaggcatgataaagatgcctttttgttttgtgatttgaaaagcaagtcatatcaacgaggtcattttaccagtcaaagtgaaaaaacagccaattgctctaaccccttgatataactgacttgcaactgatagttgacaatgattccaagttcaatcactcaaaaagcaactagattttttctttattccaagtccagtcgctagaaaggcaactggcttttttgttaatctgaaagcagaagccaagtttttgatttcggaatgaacgagtcgctgtctttgaagatttggatcaaaaacttgagtttaattatactataaggaggtattctc .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gagaatacctccttatagtataattaaactcaagtttttgatccaaatcttcaaagacagcgactcgttcattccgaaatcaaaaacttggcttctgctttcagattaacaaaaaagccagttgcctttctagcgactggacttggaataaagaaaaaatctagttgctttttgagtgattgaacttggaatcattgtcaactatcagttgcaagtcagttatatcaaggggttagagcaattggctgttttttcactttgactggtaaaatgacctcgttgatatgacttgcttttcaaatcacaaaacaaaaaggcatctttatcatgcctttcttcgacttaatctaaaaataaacctccgccaattcaaaaattagctgaggttttttgagcggattttgaggctagctgatagagctgagccttccttattttgctttttcaagtctttt Mask Tandem Repeat Region ================================================ aaaagacttgaaaaagcaaaataaggaaggctcagctctatcagctagcctcaaaatccgctcaaaaaacctcagctaatttttgaattggcggaggtttatttttagattaagtcgaagaaaggcatgataaagatgcctttttgttttgtgatttgaaaagcaagtcatatcaacgaggtcattttaccagtcaaagtgaaaaaacagccaattgctctaaccccttgatataactgacttgcaactgatagttgacaatgattccaagttcaatcactcaaaaagcaactagattttttctttattccaagtccagtcgctagaaaggcaactggcttttttgttaatctgaaagcagaagccaagtttttgatttcggaatgaacgagtcgctgtctttgaagatttggatcaaaaacttgagtttaattatactataaggaggtattctc Find is-nt database================================================ Query_seq: SSA_0402:SSA_0403|SSA_0402:SSA_0403:Histidine kinase, putative:CAAX amino terminal protease family, putative:->->:400160..400614 455 aaaagacttgaaaaagcaaaataaggaaggctcagctctatcagctagcctcaaaatccgctcaaaaaacctcagctaatttttgaattggcggaggtttatttttagattaagtcgaagaaaggcatgataaagatgcctttttgttttgtgatttgaaaagcaagtcatatcaacgaggtcattttaccagtcaaagtgaaaaaacagccaattgctctaaccccttgatataactgacttgcaactgatagttgacaatgattccaagttcaatcactcaaaaagcaactagattttttctttattccaagtccagtcgctagaaaggcaactggcttttttgttaatctgaaagcagaagccaagtttttgatttcggaatgaacgagtcgctgtctttgaagatttggatcaaaaacttgagtttaattatactataaggaggtattctc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0402:SSA_0403|SSA_0402:SSA_0403:Histidine kinase, putative:CAAX amino terminal protease family, putative:->->:400160..400614 455 aaaagacttgaaaaagcaaaataaggaaggctcagctctatcagctagcctcaaaatccgctcaaaaaacctcagctaatttttgaattggcggaggtttatttttagattaagtcgaagaaaggcatgataaagatgcctttttgttttgtgatttgaaaagcaagtcatatcaacgaggtcattttaccagtcaaagtgaaaaaacagccaattgctctaaccccttgatataactgacttgcaactgatagttgacaatgattccaagttcaatcactcaaaaagcaactagattttttctttattccaagtccagtcgctagaaaggcaactggcttttttgttaatctgaaagcagaagccaagtttttgatttcggaatgaacgagtcgctgtctttgaagatttggatcaaaaacttgagtttaattatactataaggaggtattctc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0402:SSA_0403|SSA_0402:SSA_0403:Histidine kinase, putative:CAAX amino terminal protease family, putative:->->:400160..400614 455 aaaagacttgaaaaagcaaaataaggaaggctcagctctatcagctagcctcaaaatccgctcaaaaaacctcagctaatttttgaattggcggaggtttatttttagattaagtcgaagaaaggcatgataaagatgcctttttgttttgtgatttgaaaagcaagtcatatcaacgaggtcattttaccagtcaaagtgaaaaaacagccaattgctctaaccccttgatataactgacttgcaactgatagttgacaatgattccaagttcaatcactcaaaaagcaactagattttttctttattccaagtccagtcgctagaaaggcaactggcttttttgttaatctgaaagcagaagccaagtttttgatttcggaatgaacgagtcgctgtctttgaagatttggatcaaaaacttgagtttaattatactataaggaggtattctc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaagacttgaaaaagcaaaataaggaaggctcagctctatcagctagcctcaaaatccgctcaaaaaacctcagctaatttttgaattggcggaggtttatttttagattaagtcgaagaaaggcatgataaagatgcctttttgttttgtgatttgaaaagcaagtcatatcaacgaggtcattttaccagtcaaagtgaaaaaacagccaattgctctaaccccttgatataactgacttgcaactgatagttgacaatgattccaagttcaatcactcaaaaagcaactagattttttctttattccaagtccagtcgctagaaaggcaactggcttttttgttaatctgaaagcagaagccaagtttttgatttcggaatgaacgagtcgctgtctttgaagatttggatcaaaaacttgagtttaattatactataaggaggtattctc Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 144 End: 233 ............................................................................................................................................... M F C D L K S K S Y Q R G H F T S Q S E K T A N C S N P L I .............................................................................................................................................................................................................................. Protein_Len: 34 Strand: - Start: 350 End: 451 ............................................................................................................................................................................................................................................................................................................................................................. D S L L L W T K S K P I F S D S D K F I Q I L F K L K I I S Y P P M .... Protein_Len: 34 Strand: - Start: 276 End: 377 ................................................................................................................................................................................................................................................................................... D S L F C S S K K K I G L G T A L F A V P K K T L R F A S A L N K M .............................................................................. Protein_Len: 31 Strand: - Start: 79 End: 171 .............................................................................. N K F Q R L N I K L N L R L F A H Y L H R K T K H N S F C T M ............................................................................................................................................................................................................................................................................................ aaaagacttgaaaaagcaaaataaggaaggctcagctctatcagctagcctcaaaatccgctcaaaaaacctcagctaatttttgaattggcggaggtttatttttagattaagtcgaagaaaggcatgataaagatgcctttttgttttgtgatttgaaaagcaagtcatatcaacgaggtcattttaccagtcaaagtgaaaaaacagccaattgctctaaccccttgatataactgacttgcaactgatagttgacaatgattccaagttcaatcactcaaaaagcaactagattttttctttattccaagtccagtcgctagaaaggcaactggcttttttgttaatctgaaagcagaagccaagtttttgatttcggaatgaacgagtcgctgtctttgaagatttggatcaaaaacttgagtttaattatactataaggaggtattctc 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================================================ aaaagacttgaaaaagcaaaataaggaaggctcagctctatcagctagcctcaaaatccgctcaaaaaacctcagctaatttttgaattggcggaggtttatttttagattaagtcgaagaaaggcatgataaagatgcctttttgttttgtgatttgaaaagcaagtcatatcaacgaggtcattttaccagtcaaagtgaaaaaacagccaattgctctaaccccttgatataactgacttgcaactgatagttgacaatgattccaagttcaatcactcaaaaagcaactagattttttctttattccaagtccagtcgctagaaaggcaactggcttttttgttaatctgaaagcagaagccaagtttttgatttcggaatgaacgagtcgctgtctttgaagatttggatcaaaaacttgagtttaattatactataaggaggtattctc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -9.2 Tail_Score: -4.91473 Start: 70 End: 97 Full_Region: AATCCGCTCAAAAAA CCTCAGCTAATT TTTG AATTGGCGGAGG TTTATTTTTAGATTA .....................................................................CCTCAGCTAATTTTTGAATTGGCGGAGG...................................................................................................................................................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 85 HP_score: -7.0 Tail_Score: -5.01732 Start: 70 End: 97 Full_Region: taatctaaaaataaa cctccgccaatt caaa aattagctgagg ttttttgagcggatt .....................................................................cctccgccaattcaaaaattagctgagg...................................................................................................................................................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 81 HP_score: -3.7 Tail_Score: -5.56263 Start: 124 End: 140 Full_Region: ATTAAGTCGAAGAAA GGCAT GATAAAG ATGCC TTTTTGTTTTGTGAT ...........................................................................................................................GGCATGATAAAGATGCC........................................................................................................................................................................................................................................................................................................................... Find igs database================================================ Query_seq: SSA_0402:SSA_0403|SSA_0402:SSA_0403:Histidine kinase, putative:CAAX amino terminal protease family, putative:->->:400160..400614 455 aaaagacttgaaaaagcaaaataaggaaggctcagctctatcagctagcctcaaaatccgctcaaaaaacctcagctaatttttgaattggcggaggtttatttttagattaagtcgaagaaaggcatgataaagatgcctttttgttttgtgatttgaaaagcaagtcatatcaacgaggtcattttaccagtcaaagtgaaaaaacagccaattgctctaaccccttgatataactgacttgcaactgatagttgacaatgattccaagttcaatcactcaaaaagcaactagattttttctttattccaagtccagtcgctagaaaggcaactggcttttttgttaatctgaaagcagaagccaagtttttgatttcggaatgaacgagtcgctgtctttgaagatttggatcaaaaacttgagtttaattatactataaggaggtattctc Intra-Species Hit: Count: 1 Min: 1 Max: 455 Len: 455 Subject: NC_009009_SSA_0402_SSA_0403|Histidine kinase, putative:CAAX amino terminal protease family, putative|POSITIVE:POSITIVE|[400160,400614]|455 HSP 1 e-value: 0.0 bit: 902.0 Len: 455 Query Start:1 Query End:455 Subject Strand: POSITIVE Subject Start: 1 Subject End: 455 aaaagacttgaaaaagcaaaataaggaaggctcagctctatcagctagcctcaaaatccgctcaaaaaacctcagctaatttttgaattggcggaggtttatttttagattaagtcgaagaaaggcatgataaagatgcctttttgttttgtgatttgaaaagcaagtcatatcaacgaggtcattttaccagtcaaagtgaaaaaacagccaattgctctaaccccttgatataactgacttgcaactgatagttgacaatgattccaagttcaatcactcaaaaagcaactagattttttctttattccaagtccagtcgctagaaaggcaactggcttttttgttaatctgaaagcagaagccaagtttttgatttcggaatgaacgagtcgctgtctttgaagatttggatcaaaaacttgagtttaattatactataaggaggtattctc aaaagacttgaaaaagcaaaataaggaaggctcagctctatcagctagcctcaaaatccgctcaaaaaacctcagctaatttttgaattggcggaggtttatttttagattaagtcgaagaaaggcatgataaagatgcctttttgttttgtgatttgaaaagcaagtcatatcaacgaggtcattttaccagtcaaagtgaaaaaacagccaattgctctaaccccttgatataactgacttgcaactgatagttgacaatgattccaagttcaatcactcaaaaagcaactagattttttctttattccaagtccagtcgctagaaaggcaactggcttttttgttaatctgaaagcagaagccaagtttttgatttcggaatgaacgagtcgctgtctttgaagatttggatcaaaaacttgagtttaattatactataaggaggtattctc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAGACUUGAAAAAGCAAAAUAAGGAAGGCUCAGCUCUAUCAGCUAGCCUCAAAAUCCGCUCAAAAAACCUCAGCUAAUUUUUGAAUUGGCGGAGGUUUAUUUUUAGAUUAAGUCGAAGAAAGGCAUGAUAAAGAUGCCUUUUUGUUUUGUGAUUUGAAAAGCAAGUCAUAUCAACGAGGUCAUUUUACCAGUCAAAGUGAAAAAACAGCCAAUUGCUCUAACCCCUUGAUAUAACUGACUUGCAACUGAUAGUUGACAAUGAUUCCAAGUUCAAUCACUCAAAAAGCAACUAGAUUUUUUCUUUAUUCCAAGUCCAGUCGCUAGAAAGGCAACUGGCUUUUUUGUUAAUCUGAAAGCAGAAGCCAAGUUUUUGAUUUCGGAAUGAACGAGUCGCUGUCUUUGAAGAUUUGGAUCAAAAACUUGAGUUUAAUUAUACUAUAAGGAGGUAUUCUC ....(((((((.............((((((((.((((.....))))))))).....))).......(((((((.(((((((....))))))).))))))).........)))))))..((((((((((.......))))))))))(((((.(((((..((..((((((((((((((.(.(((..((((((........))))))....(((.....)))...)))).))))))....))))))))...........((((.((((((...(((((...........(((((..(((.....))).......(((.(((((.(((.....))).))))))))..)))))..(((((((.(((((((...))))))).))))))).))))))))))).))))........))..))))))))))..(((.......(((((.......))))).))) (-120.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAGAAUACCUCCUUAUAGUAUAAUUAAACUCAAGUUUUUGAUCCAAAUCUUCAAAGACAGCGACUCGUUCAUUCCGAAAUCAAAAACUUGGCUUCUGCUUUCAGAUUAACAAAAAAGCCAGUUGCCUUUCUAGCGACUGGACUUGGAAUAAAGAAAAAAUCUAGUUGCUUUUUGAGUGAUUGAACUUGGAAUCAUUGUCAACUAUCAGUUGCAAGUCAGUUAUAUCAAGGGGUUAGAGCAAUUGGCUGUUUUUUCACUUUGACUGGUAAAAUGACCUCGUUGAUAUGACUUGCUUUUCAAAUCACAAAACAAAAAGGCAUCUUUAUCAUGCCUUUCUUCGACUUAAUCUAAAAAUAAACCUCCGCCAAUUCAAAAAUUAGCUGAGGUUUUUUGAGCGGAUUUUGAGGCUAGCUGAUAGAGCUGAGCCUUCCUUAUUUUGCUUUUUCAAGUCUUUU ((((.....(((....(((.(((((..((((((((((((((.........)))))))).(((((......(((((((..........(((...((((....))))....))).....((((((((.......))))))))..)))))))..(((.....))).)))))...))))))))))).))).)))....(((.((((.....)))))))((.((((((((((((((((((.(((.....)))........(((......)))....))))))).))))))))))).)).))))..............((((((((.......))))))))....(((((...........(((((((.((.((((....)))).)).)))))))...(((((((....((((((((((.....)))).))))))......)))))))....))))).... (-118.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 360 64 24 65 24 NC_009009:SSA_1910|5end_hypothetical_protein_1902672..1902902_NEGATIVE 349 243 209 226 194 NC_009009:SSA_0140|5end_Copper-translocating_P-type_ATPase,_putative_134626..134856_POSITIVE 330 76 32 230 197 NC_009009:SSA_2060|5end_Arabinose_efflux_permease,_putative_2062403..2062633_NEGATIVE 325 78 31 42 4 NC_009009:SSA_1452|5end_Second_subunit_of_major_exonuclease,_putative_1459696..1459926_NEGATIVE 325 78 31 54 11 NC_009009:SSA_1417|5end_SAM-dependent_methyltransferase,_putative_1427993..1428223_NEGATIVE 321 249 208 55 19 NC_009009:SSA_0489|5end_Adenosylcobinamide_kinase_/_adenosylcobinamide_phosphate_guanyltransferase,_putative_489655..489885_POSITIVE 317 348 310 86 43 NC_009009:SSA_1070|5end_Ribosomal_large_subunit_pseudouridine_synthase_D,_putative_1088742..1088972_POSITIVE 317 49 5 202 165 NC_009009:SSA_0305|5end_hypothetical_protein_301985..302215_POSITIVE 315 50 23 222 193 NC_009009:SSA_1743|5end_ABC-type_Fe3+-siderophore_transport_system,_permease_component,_putative_1730170..1730400_POSITIVE 309 397 353 209 152 NC_009009:SSA_0309|5end_Glyoxalase/Bleomycin_resistance_protein/dioxygenase_domain,_putative_304894..305124_POSITIVE 308 412 375 176 138 NC_009009:SSA_1139|5end_Pyruvate_dehydrogenase_E1_component_beta_subunit,_putative_1166823..1167053_POSITIVE 306 332 301 230 202 NC_009009:SSA_0677|5end_rRNA_methylase,_putative_659466..659696_POSITIVE 298 260 211 117 71 NC_009009:SSA_2347|5end_Coenzyme_F390_synthetase,_putative_2349939..2350169_NEGATIVE 296 139 91 196 140 NC_009009:SSA_1712|5end_Arsenate_reductase_(ArsC),_glutaredoxin_family,_putative_1700084..1700314_NEGATIVE 295 340 292 49 5 NC_009009:SSA_2186|5end_Glutathione_biosynthesis_bifunctional_protein_gshAB_(Gamma-GCS-GS)_(GCS-GS),_putative_2185535..2185765_POSITIVE 295 75 32 62 18 NC_009009:SSA_0835|5end_Accessory_secretory_protein_Asp3,_putative_821036..821266_POSITIVE 294 77 32 84 28 NC_009009:SSA_1669|5end_hypothetical_protein_1668442..1668672_NEGATIVE 293 64 24 207 169 NC_009009:SSA_1586|5end_hypothetical_protein_1588182..1588412_NEGATIVE 292 359 311 231 172 NC_009009:SSA_1835|5end_Late_competence_protein,_putative_1830941..1831171_NEGATIVE 292 340 310 44 13 NC_009009:SSA_1462|5end_Prephenate_dehydratase,_putative_1469767..1469997_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 445 96 53 82 39 NC_009009:SSA_0406|3end_hypothetical_protein_402196..402346_NEGATIVE 360 64 24 72 31 NC_009009:SSA_1911|3end_Conserved_uncharacterized_protein_1902665..1902815_NEGATIVE 334 366 321 53 3 NC_009009:SSA_0585|3end_hypothetical_protein_577286..577436_POSITIVE 333 400 358 66 26 NC_009009:SSA_0470|3end_Precorrin-4_methylase,_putative_473732..473882_POSITIVE 321 249 208 62 26 NC_009009:SSA_0488|3end_Glutamate-1-semialdehyde_2,1-aminotransferase,_putative_489742..489892_POSITIVE 317 348 310 102 59 NC_009009:SSA_1069|3end_Lipoprotein_signal_peptidase,_putative_1088838..1088988_POSITIVE 309 397 353 119 62 NC_009009:SSA_0308|3end_hypothetical_protein_304884..305034_POSITIVE 308 385 341 99 43 NC_009009:SSA_0931|3end_hypothetical_protein_941335..941485_POSITIVE 305 140 91 67 29 NC_009009:SSA_1323|3end_hypothetical_protein_1339788..1339938_NEGATIVE 297 349 310 82 46 NC_009009:SSA_2286|3end_Dihydroxy-acid_dehydratase,_putative_2287878..2288028_NEGATIVE 297 53 15 50 2 NC_009009:SSA_2101|3end_Amino_acid_ABC_transporter,_periplasmic_amino_acid-binding_protein,_putative_2104509..2104659_NEGATIVE 296 139 91 71 15 NC_009009:SSA_1713|3end_D-3-phosphoglycerate_dehydrogenase,_putative_1700209..1700359_NEGATIVE 295 75 32 65 21 NC_009009:SSA_0834|3end_Accessory_secretory_protein_Asp2,_putative_821119..821269_POSITIVE 293 345 302 66 21 NC_009009:SSA_1661|3end_hypothetical_protein_1657759..1657909_NEGATIVE 293 64 24 151 113 NC_009009:SSA_1587|3end_hypothetical_protein_1588238..1588388_NEGATIVE 292 340 310 47 16 NC_009009:SSA_1463|3end_Shikimate_kinase,_putative_1469764..1469914_NEGATIVE 291 77 33 83 33 NC_009009:SSA_0486|3end_Uroporphyrinogen-III_synthase,_putative_487442..487592_POSITIVE 291 365 321 47 4 NC_009009:SSA_0089|3end_V-type_sodium_ATPase,_subunit_F,_putative_90330..90480_POSITIVE 288 50 3 72 11 NC_009009:SSA_1867|3end_ABC-type_polar_amino_acid_transport_system,_ATPase_component,_putative_1862353..1862503_NEGATIVE 284 340 300 139 86 NC_009009:SSA_0320|3end_hypothetical_protein_313824..313974_POSITIVE