Origin IGS: taagcggatgctacaaaaaggctggacaaagttccggcctttttcttatctatcttacatattttttatttcaactactgtctttgaattgcaaaaataaaaaaatcaagatgctctggaacccgaatttgaggtcgattggtaaaaattataggcgactttaccgacattttttaggattttgtccaacattttttatgcatctgtccaaaaatgcttaaaaaaatgtgttagcgtcttccttccagaagataaacatgatagaatgtgtttgtcaatgtttttaacaatgatgaaaaagtggaggagattatattgaca .........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 tgtcaatataatctcctccactttttcatcattgttaaaaacattgacaaacacattctatcatgtttatcttctggaaggaagacgctaacacatttttttaagcatttttggacagatgcataaaaaatgttggacaaaatcctaaaaaatgtcggtaaagtcgcctataatttttaccaatcgacctcaaattcgggttccagagcatcttgatttttttatttttgcaattcaaagacagtagttgaaataaaaaatatgtaagatagataagaaaaaggccggaactttgtccagcctttttgtagcatccgctta Mask Tandem Repeat Region ================================================ taagcggatgctacaaaaaggctggacaaagttccggcctttttcttatctatcttacatattttttatttcaactactgtctttgaattgcaaaaataaaaaaatcaagatgctctggaacccgaatttgaggtcgattggtaaaaattataggcgactttaccgacattttttaggattttgtccaacattttttatgcatctgtccaaaaatgcttaaaaaaatgtgttagcgtcttccttccagaagataaacatgatagaatgtgtttgtcaatgtttttaacaatgatgaaaaagtggaggagattatattgaca Find is-nt database================================================ Query_seq: SSA_0564:SSA_0565|SSA_0564:SSA_0565:Potential aminotransferase, putative:hypothetical protein:->->:557049..557369 321 taagcggatgctacaaaaaggctggacaaagttccggcctttttcttatctatcttacatattttttatttcaactactgtctttgaattgcaaaaataaaaaaatcaagatgctctggaacccgaatttgaggtcgattggtaaaaattataggcgactttaccgacattttttaggattttgtccaacattttttatgcatctgtccaaaaatgcttaaaaaaatgtgttagcgtcttccttccagaagataaacatgatagaatgtgtttgtcaatgtttttaacaatgatgaaaaagtggaggagattatattgaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0564:SSA_0565|SSA_0564:SSA_0565:Potential aminotransferase, putative:hypothetical protein:->->:557049..557369 321 taagcggatgctacaaaaaggctggacaaagttccggcctttttcttatctatcttacatattttttatttcaactactgtctttgaattgcaaaaataaaaaaatcaagatgctctggaacccgaatttgaggtcgattggtaaaaattataggcgactttaccgacattttttaggattttgtccaacattttttatgcatctgtccaaaaatgcttaaaaaaatgtgttagcgtcttccttccagaagataaacatgatagaatgtgtttgtcaatgtttttaacaatgatgaaaaagtggaggagattatattgaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0564:SSA_0565|SSA_0564:SSA_0565:Potential aminotransferase, putative:hypothetical protein:->->:557049..557369 321 taagcggatgctacaaaaaggctggacaaagttccggcctttttcttatctatcttacatattttttatttcaactactgtctttgaattgcaaaaataaaaaaatcaagatgctctggaacccgaatttgaggtcgattggtaaaaattataggcgactttaccgacattttttaggattttgtccaacattttttatgcatctgtccaaaaatgcttaaaaaaatgtgttagcgtcttccttccagaagataaacatgatagaatgtgtttgtcaatgtttttaacaatgatgaaaaagtggaggagattatattgaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taagcggatgctacaaaaaggctggacaaagttccggcctttttcttatctatcttacatattttttatttcaactactgtctttgaattgcaaaaataaaaaaatcaagatgctctggaacccgaatttgaggtcgattggtaaaaattataggcgactttaccgacattttttaggattttgtccaacattttttatgcatctgtccaaaaatgcttaaaaaaatgtgttagcgtcttccttccagaagataaacatgatagaatgtgtttgtcaatgtttttaacaatgatgaaaaagtggaggagattatattgaca Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 8 End: 97 ....... M L Q K G W T K F R P F S Y L S Y I F F I S T T V F E L Q K ................................................................................................................................................................................................................................ Protein_Len: 57 Strand: + Start: 48 End: 218 ............................................... M Y L T Y F L F Q L L S L N C K N K K I K M L W N P N L R S I G K N Y R R L Y R H F L G F C P T F F M H L S K N A ....................................................................................................... Protein_Len: 47 Strand: + Start: 179 End: 316 .................................................................................................................................................................................. M L S N I F Y A S V Q K C L K K C V S V F L P E D K H D R M C L S M F L T M M K K W R R L Y * ..... Protein_Len: 32 Strand: - Start: 199 End: 294 ...................................................................................................................................................................................................... A D T W F H K F F H T L T K R G S S L C S L I H K D I N K V I M ........................... Protein_Len: 31 Strand: - Start: 78 End: 170 ............................................................................. Q R Q I A F I F F D L H E P V R I Q P R N T F I I P S K V S M ....................................................................................................................................................... taagcggatgctacaaaaaggctggacaaagttccggcctttttcttatctatcttacatattttttatttcaactactgtctttgaattgcaaaaataaaaaaatcaagatgctctggaacccgaatttgaggtcgattggtaaaaattataggcgactttaccgacattttttaggattttgtccaacattttttatgcatctgtccaaaaatgcttaaaaaaatgtgttagcgtcttccttccagaagataaacatgatagaatgtgtttgtcaatgtttttaacaatgatgaaaaagtggaggagattatattgaca 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================================================ taagcggatgctacaaaaaggctggacaaagttccggcctttttcttatctatcttacatattttttatttcaactactgtctttgaattgcaaaaataaaaaaatcaagatgctctggaacccgaatttgaggtcgattggtaaaaattataggcgactttaccgacattttttaggattttgtccaacattttttatgcatctgtccaaaaatgcttaaaaaaatgtgttagcgtcttccttccagaagataaacatgatagaatgtgtttgtcaatgtttttaacaatgatgaaaaagtggaggagattatattgaca Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 72 HP_score: -4.9 Tail_Score: -4.85599 Start: 20 End: 39 Full_Region: gatagataagaaaaa ggccgga actttg tccagcc tttttgtagcatccg ...................ggccggaactttgtccagcc.......................................................................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 85 HP_score: -2.8 Tail_Score: -6.20267 Start: 106 End: 120 Full_Region: acctcaaattcgggt tccaga gca tcttga tttttttatttttgc .........................................................................................................tccagagcatcttga......................................................................................................................................................................................................... TransTerm Strand: - Conf: 52 HP_score: -4.8 Tail_Score: -3.02144 Start: 192 End: 225 Full_Region: aagacgctaacacat ttttttaagcattt ttggac agatgcataaaaaa tgttggacaaaatcc ...............................................................................................................................................................................................ttttttaagcatttttggacagatgcataaaaaa................................................................................................ Find igs database================================================ Query_seq: SSA_0564:SSA_0565|SSA_0564:SSA_0565:Potential aminotransferase, putative:hypothetical protein:->->:557049..557369 321 taagcggatgctacaaaaaggctggacaaagttccggcctttttcttatctatcttacatattttttatttcaactactgtctttgaattgcaaaaataaaaaaatcaagatgctctggaacccgaatttgaggtcgattggtaaaaattataggcgactttaccgacattttttaggattttgtccaacattttttatgcatctgtccaaaaatgcttaaaaaaatgtgttagcgtcttccttccagaagataaacatgatagaatgtgtttgtcaatgtttttaacaatgatgaaaaagtggaggagattatattgaca Intra-Species Hit: Count: 1 Min: 1 Max: 321 Len: 321 Subject: NC_009009_SSA_0564_SSA_0565|Potential aminotransferase, putative:hypothetical protein|POSITIVE:POSITIVE|[557049,557369]|321 HSP 1 e-value: 1.0E-106 bit: 387.0 Len: 216 Query Start:106 Query End:321 Subject Strand: POSITIVE Subject Start: 106 Subject End: 321 .........................................................................................................tcaagatgctctggaacccgaatttgaggtcgattggtaaaaattataggcgactttaccgacattttttaggattttgtccaacattttttatgcatctgtccaaaaatgcttnnnnnnntgtgttagcgtcttccttccagaagataaacatgatagaatgtgtttgtcaatgtttttaacaatgatgaaaaagtggaggagattatattgaca .........................................................................................................tcaagatgctctggaacccgaatttgaggtcgattggtaaaaattataggcgactttaccgacattttttaggattttgtccaacattttttatgcatctgtccaaaaatgcttaaaaaaatgtgttagcgtcttccttccagaagataaacatgatagaatgtgtttgtcaatgtttttaacaatgatgaaaaagtggaggagattatattgaca HSP 2 e-value: 5.0E-45 bit: 182.0 Len: 92 Query Start:1 Query End:92 Subject Strand: POSITIVE Subject Start: 1 Subject End: 92 taagcggatgctacaaaaaggctggacaaagttccggcctttttcttatctatcttacatattttttatttcaactactgtctttgaattgc..................................................................................................................................................................................................................................... taagcggatgctacaaaaaggctggacaaagttccggcctttttcttatctatcttacatattttttatttcaactactgtctttgaattgc..................................................................................................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGCGGAUGCUACAAAAAGGCUGGACAAAGUUCCGGCCUUUUUCUUAUCUAUCUUACAUAUUUUUUAUUUCAACUACUGUCUUUGAAUUGCAAAAAUAAAAAAAUCAAGAUGCUCUGGAACCCGAAUUUGAGGUCGAUUGGUAAAAAUUAUAGGCGACUUUACCGACAUUUUUUAGGAUUUUGUCCAACAUUUUUUAUGCAUCUGUCCAAAAAUGCUUAAAAAAAUGUGUUAGCGUCUUCCUUCCAGAAGAUAAACAUGAUAGAAUGUGUUUGUCAAUGUUUUUAACAAUGAUGAAAAAGUGGAGGAGAUUAUAUUGACA ((((.(((((....((((((((((((......))))))))))))..)))))..))))..........(((((..(((((.((.....((((.(((((((...............(((((((........((((((((....(((.....)))...))))))))..(((........((((...)))).(((((((((..((((.(......).))))...)))))))))......)))....))))))).(((((((((........)))))))))..)))))))..))))...))...)))))..))))).......... (-75.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUCAAUAUAAUCUCCUCCACUUUUUCAUCAUUGUUAAAAACAUUGACAAACACAUUCUAUCAUGUUUAUCUUCUGGAAGGAAGACGCUAACACAUUUUUUUAAGCAUUUUUGGACAGAUGCAUAAAAAAUGUUGGACAAAAUCCUAAAAAAUGUCGGUAAAGUCGCCUAUAAUUUUUACCAAUCGACCUCAAAUUCGGGUUCCAGAGCAUCUUGAUUUUUUUAUUUUUGCAAUUCAAAGACAGUAGUUGAAAUAAAAAAUAUGUAAGAUAGAUAAGAAAAAGGCCGGAACUUUGUCCAGCCUUUUUGUAGCAUCCGCUUA ...............................(((((((.....)))))))........((((..........(((((.((((.....((((((...(((((((.((((((......)))))).)))))))))))))......))))..........(((((((...........)))))))....(((((.......))))))))))..((((((..(((((((((((.((.(((.......))).)).)))))))))))....)))))).))))..((((((((.(((......))).))))))))..(((....))).. (-64.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 452 51 13 182 149 NC_009009:SSA_1771|5end_Conserved_DNA_methyltransferase_protein,_putative_1758799..1759029_NEGATIVE 397 46 3 182 139 NC_009009:SSA_1861|5end_Aminopeptidase_C,_putative_1857902..1858132_NEGATIVE 345 42 2 212 172 NC_009009:SSA_2393|5end_Transcriptional_regulator,_XRE_family,_putative_204056..204286_POSITIVE 322 55 19 42 4 NC_009009:SSA_0749|5end_Competence_protein,_putative_730668..730898_POSITIVE 315 48 6 59 20 NC_009009:SSA_0814|5end_Oxidoreductase,_pyridine_nucleotide-disulfide,_class_I,_putative_796835..797065_NEGATIVE 312 209 161 101 60 NC_009009:SSA_0963|5end_Peptidoglycan_N-acetylglucosamine_deacetylase_A,_putative_971413..971643_POSITIVE 304 55 18 147 112 NC_009009:SSA_2330|5end_Acetyltransferase,_putative_2333655..2333885_NEGATIVE 294 71 32 192 155 NC_009009:SSA_1795|5end_Guanosine_3',5'-bis-pyrophosphate_(ppGpp)_synthetase,_putative_1777671..1777901_NEGATIVE 292 53 18 180 150 NC_009009:SSA_0794|5end_Zn-dependent_protease,_putative_775896..776126_POSITIVE 288 49 5 158 109 NC_009009:SSA_0692|5end_D-Ala-D-Ala_adding_enzyme,_putative_676370..676600_POSITIVE 288 170 121 182 130 NC_009009:SSA_0051|5end_Dihydroxyacetone_kinase_phosphotransfer_protein,_putative_55190..55420_POSITIVE 287 61 22 186 145 NC_009009:SSA_0997|5end_DNA-directed_DNA_polymerase_III_chain,_putative_996779..997009_POSITIVE 284 57 19 197 144 NC_009009:SSA_0155|5end_hypothetical_protein_150961..151191_POSITIVE 283 219 173 47 2 NC_009009:SSA_0555|5end_Conserved_hypothetical_cytosolic_protein_549615..549845_POSITIVE 281 248 201 204 153 NC_009009:SSA_0486|5end_Uroporphyrinogen-III_synthase,_putative_486637..486867_POSITIVE 280 58 20 226 180 NC_009009:SSA_0406|5end_hypothetical_protein_402918..403148_NEGATIVE 278 42 2 207 165 NC_009009:SSA_0398|5end_hypothetical_protein_396452..396682_NEGATIVE 277 69 21 106 50 NC_009009:SSA_1256|5end_NAD-dependent_deacetylase,_putative_1283094..1283324_NEGATIVE 276 54 20 217 169 NC_009009:SSA_0251|5end_D-tyrosyl-tRNA(Tyr)_deacylase,_putative_244455..244685_POSITIVE 273 44 13 190 157 NC_009009:SSA_0464|5end_Cobalamin_biosynthesis_protein_cobD,_putative_468225..468455_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 452 51 13 86 53 NC_009009:SSA_1772|3end_hypothetical_protein_1758895..1759045_NEGATIVE 397 46 3 103 60 NC_009009:SSA_1862|3end_hypothetical_protein_1857981..1858131_NEGATIVE 364 49 1 79 21 NC_009009:SSA_1909|3end_Transcriptional_attenuator_LytR,_putative_1900904..1901054_NEGATIVE 340 47 3 87 46 NC_009009:SSA_0718|3end_Conserved_uncharacterized_protein_704935..705085_POSITIVE 327 60 15 101 62 NC_009009:SSA_0774|3end_NADP-dependent_glyceraldehyde-3-phosphate_dehydrogenase,_putative_756075..756225_POSITIVE 327 59 15 100 56 NC_009009:SSA_0395|3end_6-phospho-beta-glucosidase,_putative_392580..392730_POSITIVE 326 50 6 102 52 NC_009009:SSA_1309|3end_RNA-binding_protein_(KH_domain),_putative_1327079..1327229_NEGATIVE 319 60 16 51 13 NC_009009:SSA_1409|3end_DTDP-glucose-4,6-dehydratase,_putative_1421209..1421359_NEGATIVE 312 47 13 73 31 NC_009009:SSA_1962|3end_Amino_acid_ABC_transporter,_ATP-binding_protein,_putative_1960930..1961080_POSITIVE 304 55 18 106 71 NC_009009:SSA_2331|3end_D-alanine_transfer_protein,_putative_2333696..2333846_NEGATIVE 301 49 2 84 31 NC_009009:SSA_1591|3end_Dipeptidase,_putative_1593403..1593553_NEGATIVE 298 48 12 82 33 NC_009009:SSA_1278|3end_Rhodanese-like_domain_protein,_putative_1299563..1299713_NEGATIVE 296 41 4 92 59 NC_009009:SSA_0583|3end_Nucleotidyltransferase,_putative_575679..575829_POSITIVE 296 44 15 76 47 NC_009009:SSA_0564|3end_Potential_aminotransferase,_putative_556988..557138_POSITIVE 294 71 32 38 1 NC_009009:SSA_1796|3end_Transcription_elongation_factor_GreA,_putative_1777825..1777975_NEGATIVE 294 46 2 100 52 NC_009009:SSA_0799|3end_hypothetical_protein_781713..781863_NEGATIVE 291 57 19 110 68 NC_009009:SSA_1318|3end_GTP-binding_protein_lepA,_putative_1333989..1334139_NEGATIVE 290 44 3 45 6 NC_009009:SSA_0375|3end_D-methionine-binding_lipoprotein_(ABC-type_transporter),_putative_365209..365359_POSITIVE 288 49 5 82 33 NC_009009:SSA_0691|3end_D-ala,D-ala_ligase,_putative_676374..676524_POSITIVE 284 57 19 106 53 NC_009009:SSA_0154|3end_hypothetical_protein_150950..151100_POSITIVE