Origin IGS: cttcctacctcactttccataaaaaagtccctgccatatccatgacagggacgaatcaatatccgcggtaccacccaatttcgggcaggcgcccgcaactctcgtctttgaagtaaatacaaagacacttttatttcatttttaaccatcagcaaccagtcttgacacatttgtggacttctcagcaccgccactttctgtaaaatgcttgactcaaaacacctctgatgaacttattctatcacctttccagccaaaaa .........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 tttttggctggaaaggtgatagaataagttcatcagaggtgttttgagtcaagcattttacagaaagtggcggtgctgagaagtccacaaatgtgtcaagactggttgctgatggttaaaaatgaaataaaagtgtctttgtatttacttcaaagacgagagttgcgggcgcctgcccgaaattgggtggtaccgcggatattgattcgtccctgtcatggatatggcagggacttttttatggaaagtgaggtaggaag Mask Tandem Repeat Region ================================================ cttcctacctcactttccataaaaaagtccctgccatatccatgacagggacgaatcaatatccgcggtaccacccaatttcgggcaggcgcccgcaactctcgtctttgaagtaaatacaaagacacttttatttcatttttaaccatcagcaaccagtcttgacacatttgtggacttctcagcaccgccactttctgtaaaatgcttgactcaaaacacctctgatgaacttattctatcacctttccagccaaaaa Find is-nt database================================================ Query_seq: SSA_1821:SSA_1822|SSA_1821:SSA_1822:Acetyltransferase (N-acetylase of ribosomal proteins), putative:hypothetical protein:<-<-:1810701..1810960 260 cttcctacctcactttccataaaaaagtccctgccatatccatgacagggacgaatcaatatccgcggtaccacccaatttcgggcaggcgcccgcaactctcgtctttgaagtaaatacaaagacacttttatttcatttttaaccatcagcaaccagtcttgacacatttgtggacttctcagcaccgccactttctgtaaaatgcttgactcaaaacacctctgatgaacttattctatcacctttccagccaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1821:SSA_1822|SSA_1821:SSA_1822:Acetyltransferase (N-acetylase of ribosomal proteins), putative:hypothetical protein:<-<-:1810701..1810960 260 cttcctacctcactttccataaaaaagtccctgccatatccatgacagggacgaatcaatatccgcggtaccacccaatttcgggcaggcgcccgcaactctcgtctttgaagtaaatacaaagacacttttatttcatttttaaccatcagcaaccagtcttgacacatttgtggacttctcagcaccgccactttctgtaaaatgcttgactcaaaacacctctgatgaacttattctatcacctttccagccaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1821:SSA_1822|SSA_1821:SSA_1822:Acetyltransferase (N-acetylase of ribosomal proteins), putative:hypothetical protein:<-<-:1810701..1810960 260 cttcctacctcactttccataaaaaagtccctgccatatccatgacagggacgaatcaatatccgcggtaccacccaatttcgggcaggcgcccgcaactctcgtctttgaagtaaatacaaagacacttttatttcatttttaaccatcagcaaccagtcttgacacatttgtggacttctcagcaccgccactttctgtaaaatgcttgactcaaaacacctctgatgaacttattctatcacctttccagccaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cttcctacctcactttccataaaaaagtccctgccatatccatgacagggacgaatcaatatccgcggtaccacccaatttcgggcaggcgcccgcaactctcgtctttgaagtaaatacaaagacacttttatttcatttttaaccatcagcaaccagtcttgacacatttgtggacttctcagcaccgccactttctgtaaaatgcttgactcaaaacacctctgatgaacttattctatcacctttccagccaaaaa Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 38 End: 142 ..................................... M H D R D E S I S A V P P N F G Q A P A T L V F E V N T K T L L F H F ...................................................................................................................... Protein_Len: 60 Strand: - Start: 3 End: 206 .. D R G Y G H C P R I L I R P V V W N R A P A R L E R R Q L L Y L S V K I E N K V M L L W D Q C M Q P S R L V A V K Q L M ...................................................... cttcctacctcactttccataaaaaagtccctgccatatccatgacagggacgaatcaatatccgcggtaccacccaatttcgggcaggcgcccgcaactctcgtctttgaagtaaatacaaagacacttttatttcatttttaaccatcagcaaccagtcttgacacatttgtggacttctcagcaccgccactttctgtaaaatgcttgactcaaaacacctctgatgaacttattctatcacctttccagccaaaaa 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================================================ cttcctacctcactttccataaaaaagtccctgccatatccatgacagggacgaatcaatatccgcggtaccacccaatttcgggcaggcgcccgcaactctcgtctttgaagtaaatacaaagacacttttatttcatttttaaccatcagcaaccagtcttgacacatttgtggacttctcagcaccgccactttctgtaaaatgcttgactcaaaacacctctgatgaacttattctatcacctttccagccaaaaa Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -14.1 Tail_Score: -5.24531 Start: 27 End: 52 Full_Region: cgcggatattgattc gtccctgtcat ggat atggcagggac ttttttatggaaagt ..........................gtccctgtcatggatatggcagggac................................................................................................................................................................................................................ Find igs database================================================ Query_seq: SSA_1821:SSA_1822|SSA_1821:SSA_1822:Acetyltransferase (N-acetylase of ribosomal proteins), putative:hypothetical protein:<-<-:1810701..1810960 260 cttcctacctcactttccataaaaaagtccctgccatatccatgacagggacgaatcaatatccgcggtaccacccaatttcgggcaggcgcccgcaactctcgtctttgaagtaaatacaaagacacttttatttcatttttaaccatcagcaaccagtcttgacacatttgtggacttctcagcaccgccactttctgtaaaatgcttgactcaaaacacctctgatgaacttattctatcacctttccagccaaaaa Intra-Species Hit: Count: 1 Min: 1 Max: 260 Len: 260 Subject: NC_009009_SSA_1821_SSA_1822|Acetyltransferase (N-acetylase of ribosomal proteins), putative:hypothetical protein|NEGATIVE:NEGATIVE|[1810701,1810960]|260 HSP 1 e-value: 1.0E-145 bit: 515.0 Len: 260 Query Start:1 Query End:260 Subject Strand: POSITIVE Subject Start: 1 Subject End: 260 cttcctacctcactttccataaaaaagtccctgccatatccatgacagggacgaatcaatatccgcggtaccacccaatttcgggcaggcgcccgcaactctcgtctttgaagtaaatacaaagacacttttatttcatttttaaccatcagcaaccagtcttgacacatttgtggacttctcagcaccgccactttctgtaaaatgcttgactcaaaacacctctgatgaacttattctatcacctttccagccaaaaa cttcctacctcactttccataaaaaagtccctgccatatccatgacagggacgaatcaatatccgcggtaccacccaatttcgggcaggcgcccgcaactctcgtctttgaagtaaatacaaagacacttttatttcatttttaaccatcagcaaccagtcttgacacatttgtggacttctcagcaccgccactttctgtaaaatgcttgactcaaaacacctctgatgaacttattctatcacctttccagccaaaaa Inter-species Hit: Count: 4 Min: 7 Max: 226 Len: 220 Subject: smit_SMT_369_SMT_370|hypothetical cytosolic protein:acetyltransferase, GNAT family|POSITIVE:POSITIVE|[304548,304827]|280 HSP 1 e-value: 4.0E-45 bit: 182.0 Len: 220 Query Start:7 Query End:226 Subject Strand: NEGATIVE Subject Start: 52 Subject End: 273 ......acctcactttccataaaaaa--gtccctgccatatccatgacagggacgaatcaat--atccgcggtaccacccaatttcgggcaggcgcccgcaactctcgtctttgaagtaaatacaaagacacttttatttcattttt--aaccatcagcaaccagtcttgacacatttgtggacttctcagcaccgccactttctgtaaaatgcttgactcaaaacacctct.................................. ......acctcactttctacaaaaaatcgcccctgccatctacatgacagggacgaatgtatttatccgcggtaccacccaatttcgggcagttgcccgcaactctcgtctttaaaacaaa----aagacacttttatttcaatttttcatccattagcaactagttttgacacatttgtggacttctcagctccgccactttctgtaaaatgcgggattcaaaacacctct.................................. Subject: NC_003028_SP_0564_SP_0565|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[530626,531037]|412 HSP 1 e-value: 2.0E-44 bit: 180.0 Len: 198 Query Start:29 Query End:226 Subject Strand: NEGATIVE Subject Start: 52 Subject End: 249 ............................ccctgccatatccatgacagggacgaatcaat--atccgcggtaccacccaatttcgggcaggcgcccgcaactctcgtctttgaagtaaatacaaagacacttttatttcattttt--aaccatcagcaaccagtcttgacacatttgtggacttctcagcaccgccactttctgtaaaatgcttgactcaaaacacctct.................................. ............................ccctgccatctacatgacagggacgaatgtgtttatccgcggtaccacccaatttcgggcagttgcccgcaactctcgtctttaaagcaaa----aagacacttttatttcaatttttcatccattagcaaccagttttgacacatttgtggacttctcagcgccgccactttctgtaaaatgtgggattcaaaacacctct.................................. Subject: NC_008533_SPD_0490_SPD_0491|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[496851,497261]|411 HSP 1 e-value: 3.0E-21 bit: 103.0 Len: 76 Query Start:151 Query End:226 Subject Strand: NEGATIVE Subject Start: 52 Subject End: 127 ......................................................................................................................................................agcaaccagtcttgacacatttgtggacttctcagcaccgccactttctgtaaaatgcttgactcaaaacacctct.................................. ......................................................................................................................................................agcaaccagttttgacacatttgtggacttctcagcgccgccactttctgtaaaatgtgggattcaaaacacctct.................................. HSP 2 e-value: 2.0E-7 bit: 58.0 Len: 58 Query Start:29 Query End:86 Subject Strand: NEGATIVE Subject Start: 189 Subject End: 248 ............................ccctgccatatccatgacagggacgaatcaat--atccgcggtaccacccaatttcgggc.............................................................................................................................................................................. ............................ccctgccatctacatgacagggacgaatgtgtttatccgcggtaccacccaatttcgggc.............................................................................................................................................................................. Subject: NC_003098_spr0488_spr0489|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[489321,489731]|411 HSP 1 e-value: 3.0E-21 bit: 103.0 Len: 76 Query Start:151 Query End:226 Subject Strand: NEGATIVE Subject Start: 52 Subject End: 127 ......................................................................................................................................................agcaaccagtcttgacacatttgtggacttctcagcaccgccactttctgtaaaatgcttgactcaaaacacctct.................................. ......................................................................................................................................................agcaaccagttttgacacatttgtggacttctcagcgccgccactttctgtaaaatgtgggattcaaaacacctct.................................. HSP 2 e-value: 2.0E-7 bit: 58.0 Len: 58 Query Start:29 Query End:86 Subject Strand: NEGATIVE Subject Start: 189 Subject End: 248 ............................ccctgccatatccatgacagggacgaatcaat--atccgcggtaccacccaatttcgggc.............................................................................................................................................................................. ............................ccctgccatctacatgacagggacgaatgtgtttatccgcggtaccacccaatttcgggc.............................................................................................................................................................................. Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACCUCACUUUCCAUAAAAAAGUCCCUGCCAUAUCCAUGACAGGGACGAAUCAAUAUCCGCGGUACCACCCAAUUUCGGGCAGGCGCCCGCAACUCUCGUCUUUGAAGUAAAUACAAAGACACUUUUAUUUCAUUUUUAACCAUCAGCAACCAGUCUUGACACAUUUGUGGACUUCUCAGCACCGCCACUUUCUGUAAAAUGCUUGACUCAAAACACCUCU .........((((((((...(((((((.(((....))).)))))))...((((.....((((..((.(((......)))..))..).))).......(((((((.........)))))))...................................))))....))))))))....((((((.....((.....))....))).))).............. (-47.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAGGUGUUUUGAGUCAAGCAUUUUACAGAAAGUGGCGGUGCUGAGAAGUCCACAAAUGUGUCAAGACUGGUUGCUGAUGGUUAAAAAUGAAAUAAAAGUGUCUUUGUAUUUACUUCAAAGACGAGAGUUGCGGGCGCCUGCCCGAAAUUGGGUGGUACCGCGGAUAUUGAUUCGUCCCUGUCAUGGAUAUGGCAGGGACUUUUUUAUGGAAAGUGAGGU (((((..((((........((((((.((...((..(((((..(((......(((....))))))..))).))..))..))....)))))).....))))..)))))......((((((....(((...((((((..(((.(((((....)))))))).))))))...)))....(((((((((((....)))))))))))..............)))))) (-64.52) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1127 90 41 187 138 NC_009009:SSA_1821|5end_Acetyltransferase_(N-acetylase_of_ribosomal_proteins),_putative_1810610..1810840_NEGATIVE 421 90 41 192 146 NC_009009:SSA_0661|5end_Isoleucyl-tRNA_synthetase,_putative_644876..645106_POSITIVE 392 84 42 190 145 NC_009009:SSA_2199|5end_ATP-dependent_Clp_protease,_ATP-binding_subunit,_putative_2201108..2201338_NEGATIVE 368 80 33 174 132 NC_009009:SSA_0755|5end_hypothetical_protein_736212..736442_POSITIVE 359 100 56 231 179 NC_009009:SSA_0632|5end_Anthranilate_synthase_component_I,_putative_621458..621688_POSITIVE 353 100 58 174 137 NC_009009:SSA_2203|5end_30S_ribosomal_protein_S2,_putative_2204205..2204435_NEGATIVE 349 90 41 71 26 NC_009009:SSA_0833|5end_Accessory_secretory_protein_Asp1,_putative_817940..818170_POSITIVE 326 90 41 57 1 NC_009009:SSA_1984|5end_Cell_surface_SD_repeat_antigen_precursor,_putative_1979035..1979265_NEGATIVE 324 45 1 207 149 NC_009009:SSA_1986|5end_Acetyltransferase,_GNAT_family,_putative_1982531..1982761_NEGATIVE 324 79 33 46 2 NC_009009:SSA_1410|5end_DTDP-4-keto-6-deoxyglucose-3,5-epimerase,_putative_1423086..1423316_NEGATIVE 324 99 73 57 25 NC_009009:SSA_0637|5end_Tryptophan_synthase_beta_chain,_putative_625719..625949_POSITIVE 324 100 58 222 169 NC_009009:SSA_0631|5end_Tryptophan_synthase_beta_chain,_putative_619872..620102_POSITIVE 317 70 21 190 147 NC_009009:SSA_1881|5end_hypothetical_protein_1875964..1876194_NEGATIVE 315 66 25 199 152 NC_009009:SSA_0812|5end_hypothetical_protein_793443..793673_POSITIVE 314 80 33 52 5 NC_009009:SSA_1936|5end_3-oxoacyl-[acyl-carrier_protein]_reductase,_putative_1923838..1924068_NEGATIVE 314 107 65 80 39 NC_009009:SSA_1510|5end_Rhamnosyltransferase,_putative_1515336..1515566_NEGATIVE 313 180 139 73 18 NC_009009:SSA_2270|5end_Aspartyl-tRNA_synthetase,_putative_2272068..2272298_NEGATIVE 313 103 66 83 50 NC_009009:SSA_0233|5end_Permease,_putative_227203..227433_POSITIVE 312 90 41 168 106 NC_009009:SSA_1736|5end_L-cysteine_desulfhydrase,_putative_1722619..1722849_NEGATIVE 312 119 78 215 177 NC_009009:SSA_0065|5end_Low_molecular_weight_phosphotyrosine_protein_phosphatase,_putative_67175..67405_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 357 89 56 126 83 NC_009009:SSA_0093|3end_V-type_sodium_ATPase,_subunit_D,_putative_94989..95139_POSITIVE 349 90 41 62 17 NC_009009:SSA_0832|3end_SecY-like_protein,_putative_818011..818161_POSITIVE 333 107 65 57 5 NC_009009:SSA_1710|3end_Transcriptional_regulator,_XRE_family,_putative_1699011..1699161_POSITIVE 332 188 143 127 85 NC_009009:SSA_0263|3end_Zinc_metalloproteinase_in_scaA_5'region,_putative_258246..258396_POSITIVE 324 99 73 67 35 NC_009009:SSA_0636|3end_N-(5'-phosphoribosyl)anthranilate_isomerase,_putative_625809..625959_POSITIVE 313 88 43 45 1 NC_009009:SSA_1937|3end_Malonyl-CoA:ACP_transacylase,_putative_1923851..1924001_NEGATIVE 313 103 66 77 44 NC_009009:SSA_0232|3end_hypothetical_protein_227277..227427_POSITIVE 305 220 177 58 5 NC_009009:SSA_0753|3end_Foldase_protein_prsA_precursor,_putative_736055..736205_POSITIVE 305 96 57 150 117 NC_009009:SSA_0576|3end_Conserved_GTPase,_putative_571225..571375_POSITIVE 304 67 24 104 49 NC_009009:SSA_0696|3end_hypothetical_protein_679920..680070_POSITIVE 303 205 162 135 80 NC_009009:SSA_0787|3end_Proton-translocating_ATPase,_F1_sector,_gamma_subunit,_putative_771078..771228_POSITIVE 297 187 143 149 105 NC_009009:SSA_0925|3end_ABC-type_antimicrobial_peptide_transport_system,_ATPase_component,_putative_935494..935644_POSITIVE 296 220 172 91 36 NC_009009:SSA_0488|3end_Glutamate-1-semialdehyde_2,1-aminotransferase,_putative_489742..489892_POSITIVE 296 88 45 150 95 NC_009009:SSA_0378|3end_TRZ/ATZ_family_hydrolase,_putative_368627..368777_POSITIVE 292 98 56 149 107 NC_009009:SSA_1784|3end_Glutamate_racemase,_putative_1769103..1769253_NEGATIVE 291 96 56 149 101 NC_009009:SSA_2052|3end_Thioredoxin,_putative_2057193..2057343_NEGATIVE 290 90 41 81 29 NC_009009:SSA_0319|3end_Branched-chain_amino_acid_permease_(L-methionine,_L-isoleucine,_leucine_and_valine),_putative_313496..313646_POSITIVE 286 90 41 48 3 NC_009009:SSA_0318|3end_Secreted_metalloendopeptidase_Gcp_312791..312941_POSITIVE 283 100 56 147 98 NC_009009:SSA_2047|3end_hypothetical_protein_2049735..2049885_NEGATIVE 283 205 163 138 104 NC_009009:SSA_1297|3end_Nuclease_subunit_of_the_excinuclease_complex,_subunit_C,_putative_1313141..1313291_NEGATIVE