Origin IGS: aatacccagcagaagagtagtaacatccctcctttcagagagtctgtggttgctgagaacaggcaggagaagttatgaaatgggctgttggagtcaacattttgtcctttagttgaacttttattattttgttagcttactttgctgtaaaatagtatgctgccttctgctaaaaggaatctaaatgactgtaaataagtaaatgagatgtggagcctaaaaactccataactgaggtggcaccgcgatgatacgccctcacaggatgaactgtgcgggcgtttttctgtagttttggagcaagttatgaccgtggacaggtgctatctgttcttgtgaaatgcagttatggcttgcagcttgctcctccttaaacgcttctgatttaaatagaaagaaacatt .........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 aatgtttctttctatttaaatcagaagcgtttaaggaggagcaagctgcaagccataactgcatttcacaagaacagatagcacctgtccacggtcataacttgctccaaaactacagaaaaacgcccgcacagttcatcctgtgagggcgtatcatcgcggtgccacctcagttatggagtttttaggctccacatctcatttacttatttacagtcatttagattccttttagcagaaggcagcatactattttacagcaaagtaagctaacaaaataataaaagttcaactaaaggacaaaatgttgactccaacagcccatttcataacttctcctgcctgttctcagcaaccacagactctctgaaaggagggatgttactactcttctgctgggtatt Mask Tandem Repeat Region ================================================ aatacccagcagaagagtagtaacatccctcctttcagagagtctgtggttgctgagaacaggcaggagaagttatgaaatgggctgttggagtcaacattttgtcctttagttgaacttttattattttgttagcttactttgctgtaaaatagtatgctgccttctgctaaaaggaatctaaatgactgtaaataagtaaatgagatgtggagcctaaaaactccataactgaggtggcaccgcgatgatacgccctcacaggatgaactgtgcgggcgtttttctgtagttttggagcaagttatgaccgtggacaggtgctatctgttcttgtgaaatgcagttatggcttgcagcttgctcctccttaaacgcttctgatttaaatagaaagaaacatt Find is-nt database================================================ Query_seq: SSA_0631:SSA_0632|SSA_0631:SSA_0632:Tryptophan synthase beta chain, putative:Anthranilate synthase component I, putative:->->:621194..621597 404 aatacccagcagaagagtagtaacatccctcctttcagagagtctgtggttgctgagaacaggcaggagaagttatgaaatgggctgttggagtcaacattttgtcctttagttgaacttttattattttgttagcttactttgctgtaaaatagtatgctgccttctgctaaaaggaatctaaatgactgtaaataagtaaatgagatgtggagcctaaaaactccataactgaggtggcaccgcgatgatacgccctcacaggatgaactgtgcgggcgtttttctgtagttttggagcaagttatgaccgtggacaggtgctatctgttcttgtgaaatgcagttatggcttgcagcttgctcctccttaaacgcttctgatttaaatagaaagaaacatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0631:SSA_0632|SSA_0631:SSA_0632:Tryptophan synthase beta chain, putative:Anthranilate synthase component I, putative:->->:621194..621597 404 aatacccagcagaagagtagtaacatccctcctttcagagagtctgtggttgctgagaacaggcaggagaagttatgaaatgggctgttggagtcaacattttgtcctttagttgaacttttattattttgttagcttactttgctgtaaaatagtatgctgccttctgctaaaaggaatctaaatgactgtaaataagtaaatgagatgtggagcctaaaaactccataactgaggtggcaccgcgatgatacgccctcacaggatgaactgtgcgggcgtttttctgtagttttggagcaagttatgaccgtggacaggtgctatctgttcttgtgaaatgcagttatggcttgcagcttgctcctccttaaacgcttctgatttaaatagaaagaaacatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0631:SSA_0632|SSA_0631:SSA_0632:Tryptophan synthase beta chain, putative:Anthranilate synthase component I, putative:->->:621194..621597 404 aatacccagcagaagagtagtaacatccctcctttcagagagtctgtggttgctgagaacaggcaggagaagttatgaaatgggctgttggagtcaacattttgtcctttagttgaacttttattattttgttagcttactttgctgtaaaatagtatgctgccttctgctaaaaggaatctaaatgactgtaaataagtaaatgagatgtggagcctaaaaactccataactgaggtggcaccgcgatgatacgccctcacaggatgaactgtgcgggcgtttttctgtagttttggagcaagttatgaccgtggacaggtgctatctgttcttgtgaaatgcagttatggcttgcagcttgctcctccttaaacgcttctgatttaaatagaaagaaacatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatacccagcagaagagtagtaacatccctcctttcagagagtctgtggttgctgagaacaggcaggagaagttatgaaatgggctgttggagtcaacattttgtcctttagttgaacttttattattttgttagcttactttgctgtaaaatagtatgctgccttctgctaaaaggaatctaaatgactgtaaataagtaaatgagatgtggagcctaaaaactccataactgaggtggcaccgcgatgatacgccctcacaggatgaactgtgcgggcgtttttctgtagttttggagcaagttatgaccgtggacaggtgctatctgttcttgtgaaatgcagttatggcttgcagcttgctcctccttaaacgcttctgatttaaatagaaagaaacatt Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 2 End: 109 . M P S R R V V T S L L S E S L W L L R T G R R S Y E M G C W S Q H F V L ....................................................................................................................................................................................................................................................................................................... Protein_Len: 35 Strand: + Start: 232 End: 336 ....................................................................................................................................................................................................................................... M R W H R D D T P S Q D E L C G R F S V V L E Q V M T V D R C Y L F L .................................................................... Protein_Len: 33 Strand: + Start: 273 End: 371 ................................................................................................................................................................................................................................................................................ M R A F F C S F G A S Y D R G Q V L S V L V K C S Y G L Q L A P P ................................. Protein_Len: 30 Strand: - Start: 173 End: 262 ............................................................................................................................................................................ F S D L H S Y I L L H S T S G L F E M V S T A G R H Y A R M .............................................................................................................................................. Protein_Len: 60 Strand: - Start: 135 End: 320 ...................................................................................................................................... K S Y F L I S G E A L L F R F S Q L Y T F S I H L R F V G Y S L H C R S S V G E C S S S H P R K E T T K S C T I V T S M .................................................................................... Protein_Len: 30 Strand: - Start: 38 End: 127 ..................................... L T Q P Q Q S C A P S T I F H A T P T L M K D K L Q V K I M ..................................................................................................................................................................................................................................................................................... aatacccagcagaagagtagtaacatccctcctttcagagagtctgtggttgctgagaacaggcaggagaagttatgaaatgggctgttggagtcaacattttgtcctttagttgaacttttattattttgttagcttactttgctgtaaaatagtatgctgccttctgctaaaaggaatctaaatgactgtaaataagtaaatgagatgtggagcctaaaaactccataactgaggtggcaccgcgatgatacgccctcacaggatgaactgtgcgggcgtttttctgtagttttggagcaagttatgaccgtggacaggtgctatctgttcttgtgaaatgcagttatggcttgcagcttgctcctccttaaacgcttctgatttaaatagaaagaaacatt 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: 81 Start: 101 End: 130 ....................................................................................................TTTGTCCTTTAGTTGAACTTTTATTATTTT.................................................................................................................................................................................................................................................................................. PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 123 End: 152 ..........................................................................................................................TTTTACAGCAAAGTAAGCTAACAAAATAAT............................................................................................................................................................................................................................................................ 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: 85 Start: 349 End: 365 ............................................................................................................................................................................................................................................................................................................................................................ATGGCTTGCAGCTTGCT....................................... aatacccagcagaagagtagtaacatccctcctttcagagagtctgtggttgctgagaacaggcaggagaagttatgaaatgggctgttggagtcaacattttgtcctttagttgaacttttattattttgttagcttactttgctgtaaaatagtatgctgccttctgctaaaaggaatctaaatgactgtaaataagtaaatgagatgtggagcctaaaaactccataactgaggtggcaccgcgatgatacgccctcacaggatgaactgtgcgggcgtttttctgtagttttggagcaagttatgaccgtggacaggtgctatctgttcttgtgaaatgcagttatggcttgcagcttgctcctccttaaacgcttctgatttaaatagaaagaaacatt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 73 HP_score: -5.3 Tail_Score: -4.64076 Start: 86 End: 99 Full_Region: AGTTATGAAATGGGC TGTTG GAGT CAACA TTTTGTCCTTTAGTT .....................................................................................TGTTGGAGTCAACA................................................................................................................................................................................................................................................................................................................. TransTerm Strand: + Conf: 100 HP_score: -12.7 Tail_Score: -5.07941 Start: 254 End: 281 Full_Region: GGCACCGCGATGATA CGCCCTCACAG GATGAA CTGTGCGGGCG TTTTTCTGTAGTTTT .............................................................................................................................................................................................................................................................CGCCCTCACAGGATGAACTGTGCGGGCG........................................................................................................................... TransTerm Strand: - Conf: 89 HP_score: -12.7 Tail_Score: -2.79183 Start: 254 End: 281 Full_Region: aaaactacagaaaaa cgcccgcacag ttcatc ctgtgagggcg tatcatcgcggtgcc .............................................................................................................................................................................................................................................................cgcccgcacagttcatcctgtgagggcg........................................................................................................................... Find igs database================================================ Query_seq: SSA_0631:SSA_0632|SSA_0631:SSA_0632:Tryptophan synthase beta chain, putative:Anthranilate synthase component I, putative:->->:621194..621597 404 aatacccagcagaagagtagtaacatccctcctttcagagagtctgtggttgctgagaacaggcaggagaagttatgaaatgggctgttggagtcaacattttgtcctttagttgaacttttattattttgttagcttactttgctgtaaaatagtatgctgccttctgctaaaaggaatctaaatgactgtaaataagtaaatgagatgtggagcctaaaaactccataactgaggtggcaccgcgatgatacgccctcacaggatgaactgtgcgggcgtttttctgtagttttggagcaagttatgaccgtggacaggtgctatctgttcttgtgaaatgcagttatggcttgcagcttgctcctccttaaacgcttctgatttaaatagaaagaaacatt Intra-Species Hit: Count: 1 Min: 1 Max: 404 Len: 404 Subject: NC_009009_SSA_0631_SSA_0632|Tryptophan synthase beta chain, putative:Anthranilate synthase component I, putative|POSITIVE:POSITIVE|[621194,621597]|404 HSP 1 e-value: 0.0 bit: 801.0 Len: 404 Query Start:1 Query End:404 Subject Strand: POSITIVE Subject Start: 1 Subject End: 404 aatacccagcagaagagtagtaacatccctcctttcagagagtctgtggttgctgagaacaggcaggagaagttatgaaatgggctgttggagtcaacattttgtcctttagttgaacttttattattttgttagcttactttgctgtaaaatagtatgctgccttctgctaaaaggaatctaaatgactgtaaataagtaaatgagatgtggagcctaaaaactccataactgaggtggcaccgcgatgatacgccctcacaggatgaactgtgcgggcgtttttctgtagttttggagcaagttatgaccgtggacaggtgctatctgttcttgtgaaatgcagttatggcttgcagcttgctcctccttaaacgcttctgatttaaatagaaagaaacatt aatacccagcagaagagtagtaacatccctcctttcagagagtctgtggttgctgagaacaggcaggagaagttatgaaatgggctgttggagtcaacattttgtcctttagttgaacttttattattttgttagcttactttgctgtaaaatagtatgctgccttctgctaaaaggaatctaaatgactgtaaataagtaaatgagatgtggagcctaaaaactccataactgaggtggcaccgcgatgatacgccctcacaggatgaactgtgcgggcgtttttctgtagttttggagcaagttatgaccgtggacaggtgctatctgttcttgtgaaatgcagttatggcttgcagcttgctcctccttaaacgcttctgatttaaatagaaagaaacatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUACCCAGCAGAAGAGUAGUAACAUCCCUCCUUUCAGAGAGUCUGUGGUUGCUGAGAACAGGCAGGAGAAGUUAUGAAAUGGGCUGUUGGAGUCAACAUUUUGUCCUUUAGUUGAACUUUUAUUAUUUUGUUAGCUUACUUUGCUGUAAAAUAGUAUGCUGCCUUCUGCUAAAAGGAAUCUAAAUGACUGUAAAUAAGUAAAUGAGAUGUGGAGCCUAAAAACUCCAUAACUGAGGUGGCACCGCGAUGAUACGCCCUCACAGGAUGAACUGUGCGGGCGUUUUUCUGUAGUUUUGGAGCAAGUUAUGACCGUGGACAGGUGCUAUCUGUUCUUGUGAAAUGCAGUUAUGGCUUGCAGCUUGCUCCUCCUUAAACGCUUCUGAUUUAAAUAGAAAGAAACAUU .......((((((((.((((((......(((((........((((((...........))))))))))).((((.......(((((((((....)))))....))))........))))..((((((((...((((.......))))..))))))))))))))))))))))..((((.((((.....(((.......))).....))))..(((((........((((.(((((..(((....)))...((.((((((.(((((......))))).))))))...))..))))).))))((((((((((((.(((.(((((.((.....)).)))))....))).)))))))))))).....))))).))))....(.((((.............)))).)... (-117.58) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUGUUUCUUUCUAUUUAAAUCAGAAGCGUUUAAGGAGGAGCAAGCUGCAAGCCAUAACUGCAUUUCACAAGAACAGAUAGCACCUGUCCACGGUCAUAACUUGCUCCAAAACUACAGAAAAACGCCCGCACAGUUCAUCCUGUGAGGGCGUAUCAUCGCGGUGCCACCUCAGUUAUGGAGUUUUUAGGCUCCACAUCUCAUUUACUUAUUUACAGUCAUUUAGAUUCCUUUUAGCAGAAGGCAGCAUACUAUUUUACAGCAAAGUAAGCUAACAAAAUAAUAAAAGUUCAACUAAAGGACAAAAUGUUGACUCCAACAGCCCAUUUCAUAACUUCUCCUGCCUGUUCUCAGCAACCACAGACUCUCUGAAAGGAGGGAUGUUACUACUCUUCUGCUGGGUAUU (((((((((.............)))))))))..((((((((.(((.......(((((((((...(((....)))......(((((.......((.((.....))..))..............((((((.(((((......))))).))))))........))))).....)))))))))........(((.........................(((.(((((...(((((.....))))).(((.((((............)))).))).....................))))).)))....(((((....))))))))..........)))))))).)))...(((((((........((((((....))))))..((....)).....))))))).... (-98.32) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 419 328 281 53 4 NC_009009:SSA_0268|5end_Phosphotransferase_system_(PTS)_cellobiose-specific_component_IIB,_putative_262224..262454_POSITIVE 366 258 214 203 152 NC_009009:SSA_1402|5end_ABC-type_multidrug_transport_system,_ATPase_and_permease_components,_putative_1416220..1416450_NEGATIVE 366 90 43 54 2 NC_009009:SSA_0227|5end_Collagen-binding_surface_protein,_putative_221037..221267_POSITIVE 362 70 22 141 87 NC_009009:SSA_2071|5end_hypothetical_protein_2074766..2074996_NEGATIVE 361 375 342 130 104 NC_009009:SSA_1404|5end_hypothetical_protein_1418723..1418953_NEGATIVE 355 74 35 231 192 NC_009009:SSA_1837|5end_hypothetical_protein_1832243..1832473_POSITIVE 354 390 348 166 114 NC_009009:SSA_0785|5end_Proton-translocating_ATPase,_F1_sector,_delta_subunit,_putative_768044..768274_POSITIVE 346 280 232 146 100 NC_009009:SSA_0512|5end_Nicotinate-nucleotide--dimethylbenzimidazole_phosphoribosyltransferase,_putative_510439..510669_POSITIVE 343 43 1 212 164 NC_009009:SSA_2089|5end_L-xylulose-5-phosphate_3-epimerase,_putative_2094339..2094569_NEGATIVE 337 267 221 73 13 NC_009009:SSA_1546|5end_Prolipoprotein_diacylglyceryl_transferase,_putative_1550052..1550282_NEGATIVE 334 95 51 225 176 NC_009009:SSA_2206|5end_hypothetical_protein_2206839..2207069_POSITIVE 331 70 27 145 100 NC_009009:SSA_0579|5end_Hydrolase,_HAD_superfamily,_putative_572220..572450_POSITIVE 330 315 271 202 149 NC_009009:SSA_1896|5end_Translation_initiation_factor_IF-2,_putative_1894134..1894364_NEGATIVE 330 360 311 229 176 NC_009009:SSA_1300|5end_Maltose_ABC_transporter,_permease_protein,_putative_1317987..1318217_POSITIVE 330 370 324 142 99 NC_009009:SSA_0486|5end_Uroporphyrinogen-III_synthase,_putative_486637..486867_POSITIVE 329 264 227 224 188 NC_009009:SSA_0489|5end_Adenosylcobinamide_kinase_/_adenosylcobinamide_phosphate_guanyltransferase,_putative_489655..489885_POSITIVE 329 370 322 197 145 NC_009009:SSA_0143|5end_Conserved_uncharacterized_protein_137465..137695_POSITIVE 328 383 343 189 145 NC_009009:SSA_0496|5end_Succinylglutamate_desuccinylase_/_Aspartoacylase_family,_putative_495946..496176_POSITIVE 326 287 243 61 19 NC_009009:SSA_1866|5end_hypothetical_protein_1862182..1862412_NEGATIVE 325 280 233 181 124 NC_009009:SSA_1530|5end_ABC-type_antimicrobial_peptide_transport_system,_permease_component,_putative_1538778..1539008_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 362 70 22 107 53 NC_009009:SSA_2072|3end_Phosphatidate_cytidylyltransferase,_putative_2074800..2074950_NEGATIVE 361 375 342 95 69 NC_009009:SSA_1405|3end_Copper_homeostasis_protein_CutC,_putative_1418758..1418908_NEGATIVE 353 279 236 47 1 NC_009009:SSA_2122|3end_hypothetical_protein_2127200..2127350_NEGATIVE 347 80 33 68 12 NC_009009:SSA_0184|3end_Competence_protein_ComYA,_putative_189177..189327_POSITIVE 337 267 221 80 20 NC_009009:SSA_1547|3end_HPr_kinase/phosphorylase,_putative_1550045..1550195_NEGATIVE 335 387 341 70 19 NC_009009:SSA_0468|3end_Precorrin-6y_C5,15-methyltransferase-like,_putative_472418..472568_POSITIVE 331 280 232 64 8 NC_009009:SSA_1417|3end_SAM-dependent_methyltransferase,_putative_1427304..1427454_NEGATIVE 331 70 27 148 103 NC_009009:SSA_0578|3end_Nicotinate-nucleotide_adenylyltransferase,_putative_572303..572453_POSITIVE 329 280 232 144 106 NC_009009:SSA_0576|3end_Conserved_GTPase,_putative_571225..571375_POSITIVE 329 370 322 141 89 NC_009009:SSA_0142|3end_hypothetical_protein_137489..137639_POSITIVE 328 56 15 148 106 NC_009009:SSA_1322|3end_Glycosyl_transferase,_putative_1338536..1338686_NEGATIVE 324 288 243 149 105 NC_009009:SSA_0413|3end_Anthranilate/para-aminobenzoate_synthases_component_I/_Chorismate_binding_enzyme,_putative_408315..408465_NEGATIVE 316 96 51 143 104 NC_009009:SSA_0967|3end_hypothetical_protein_976620..976770_POSITIVE 314 105 65 86 47 NC_009009:SSA_1765|3end_Conserved_uncharacterized_protein_1753880..1754030_POSITIVE 310 370 321 142 83 NC_009009:SSA_0463|3end_Cobyrinic_acid_A,C-diamide_synthase,_putative_468303..468453_POSITIVE 310 87 41 147 89 NC_009009:SSA_0306|3end_Transcription_regulator_(glutamine_synthetase_repressor),_putative_303035..303185_POSITIVE 307 280 232 53 6 NC_009009:SSA_1899|3end_hypothetical_protein_1894443..1894593_NEGATIVE 304 61 26 62 31 NC_009009:SSA_1054|3end_CBS_domain_protein,_putative_1070973..1071123_POSITIVE 302 250 203 49 2 NC_009009:SSA_1641|3end_MutT/nudix_family_protein,_putative_1642543..1642693_NEGATIVE 302 370 322 121 64 NC_009009:SSA_1522|3end_Cell_division_protein_FtsW,_putative_1530730..1530880_NEGATIVE