Origin IGS: caaaacttatttttcttaagcaaagtttaaggctggtctagtattatatagtcattaaataaagacctcctaactttatttaatgaaatcctaaaaacttttttcatcataatctcctaatgaagtcacccaatcaggtggctttttttcttggataggtgatggtgatagaaattttttgcaaaatagcaaaatttgagaaaagttaagctatttttaagcttcgtcttgtatcatatagttattaagtaaagacctcctaactttatttaataaaatcctaaacttttctttttcataataatctcccttgactccacccaatcaggtggagtttt .........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 aaaactccacctgattgggtggagtcaagggagattattatgaaaaagaaaagtttaggattttattaaataaagttaggaggtctttacttaataactatatgatacaagacgaagcttaaaaatagcttaacttttctcaaattttgctattttgcaaaaaatttctatcaccatcacctatccaagaaaaaaagccacctgattgggtgacttcattaggagattatgatgaaaaaagtttttaggatttcattaaataaagttaggaggtctttatttaatgactatataatactagaccagccttaaactttgcttaagaaaaataagttttg Mask Tandem Repeat Region ================================================ caaaacttatttttcttaagcaaagtttaaggctggtctagtattatatagtcattaaataaagacctcctaactttatttaatgaaatcctaaaaacttttttcatcataatctcctaatgaagtcacccaatcaggtggctttttttcttggataggtgatggtgatagaaattttttgcaaaatagcaaaatttgagaaaagttaagctatttttaagcttcgtcttgtatcatatagttattaagtaaagacctcctaactttatttaataaaatcctaaacttttctttttcataataatctcccttgactccacccaatcaggtggagtttt Find is-nt database================================================ Query_seq: SMT_210:SMT_211|SMT_210:SMT_211:acetyltransferase, GNAT family:hypothetical protein predicted by Glimmer/Critica:->->:143937..144274 338 caaaacttatttttcttaagcaaagtttaaggctggtctagtattatatagtcattaaataaagacctcctaactttatttaatgaaatcctaaaaacttttttcatcataatctcctaatgaagtcacccaatcaggtggctttttttcttggataggtgatggtgatagaaattttttgcaaaatagcaaaatttgagaaaagttaagctatttttaagcttcgtcttgtatcatatagttattaagtaaagacctcctaactttatttaataaaatcctaaacttttctttttcataataatctcccttgactccacccaatcaggtggagtttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_210:SMT_211|SMT_210:SMT_211:acetyltransferase, GNAT family:hypothetical protein predicted by Glimmer/Critica:->->:143937..144274 338 caaaacttatttttcttaagcaaagtttaaggctggtctagtattatatagtcattaaataaagacctcctaactttatttaatgaaatcctaaaaacttttttcatcataatctcctaatgaagtcacccaatcaggtggctttttttcttggataggtgatggtgatagaaattttttgcaaaatagcaaaatttgagaaaagttaagctatttttaagcttcgtcttgtatcatatagttattaagtaaagacctcctaactttatttaataaaatcctaaacttttctttttcataataatctcccttgactccacccaatcaggtggagtttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_210:SMT_211|SMT_210:SMT_211:acetyltransferase, GNAT family:hypothetical protein predicted by Glimmer/Critica:->->:143937..144274 338 caaaacttatttttcttaagcaaagtttaaggctggtctagtattatatagtcattaaataaagacctcctaactttatttaatgaaatcctaaaaacttttttcatcataatctcctaatgaagtcacccaatcaggtggctttttttcttggataggtgatggtgatagaaattttttgcaaaatagcaaaatttgagaaaagttaagctatttttaagcttcgtcttgtatcatatagttattaagtaaagacctcctaactttatttaataaaatcctaaacttttctttttcataataatctcccttgactccacccaatcaggtggagtttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 caaaacttatttttcttaagcaaagtttaaggctggtctagtattatatagtcattaaataaagacctcctaactttatttaatgaaatcctaaaaacttttttcatcataatctcctaatgaagtcacccaatcaggtggctttttttcttggataggtgatggtgatagaaattttttgcaaaatagcaaaatttgagaaaagttaagctatttttaagcttcgtcttgtatcatatagttattaagtaaagacctcctaactttatttaataaaatcctaaacttttctttttcataataatctcccttgactccacccaatcaggtggagtttt Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: - Start: 220 End: 324 ........................................................................................................................................................................................................................... A E D Q I M Y N N L L S R R V K N L L I R F K E K E Y Y D G K V G G M .............. Protein_Len: 34 Strand: - Start: 94 End: 195 ............................................................................................. F S K E D Y D G L S T V W D P P K K E Q I P S P S L F K K C F L L M ............................................................................................................................................... caaaacttatttttcttaagcaaagtttaaggctggtctagtattatatagtcattaaataaagacctcctaactttatttaatgaaatcctaaaaacttttttcatcataatctcctaatgaagtcacccaatcaggtggctttttttcttggataggtgatggtgatagaaattttttgcaaaatagcaaaatttgagaaaagttaagctatttttaagcttcgtcttgtatcatatagttattaagtaaagacctcctaactttatttaataaaatcctaaacttttctttttcataataatctcccttgactccacccaatcaggtggagtttt 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================================================ caaaacttatttttcttaagcaaagtttaaggctggtctagtattatatagtcattaaataaagacctcctaactttatttaatgaaatcctaaaaacttttttcatcataatctcctaatgaagtcacccaatcaggtggctttttttcttggataggtgatggtgatagaaattttttgcaaaatagcaaaatttgagaaaagttaagctatttttaagcttcgtcttgtatcatatagttattaagtaaagacctcctaactttatttaataaaatcctaaacttttctttttcataataatctcccttgactccacccaatcaggtggagtttt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 48 HP_score: -4.0 Tail_Score: -2.96216 Start: 51 End: 87 Full_Region: aaaagtttttaggat ttcattaaataaag ttaggaggt ctttatttaatgac tatataatactagac ..................................................ttcattaaataaagttaggaggtctttatttaatgac........................................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 87 HP_score: -4.8 Tail_Score: -5.8187 Start: 125 End: 142 Full_Region: TAATCTCCTAATGAA GTCACC CAATCA GGTGGC TTTTTTTCTTGGATA ............................................................................................................................GTCACCCAATCAGGTGGC.................................................................................................................................................................................................... Find igs database================================================ Query_seq: SMT_210:SMT_211|SMT_210:SMT_211:acetyltransferase, GNAT family:hypothetical protein predicted by Glimmer/Critica:->->:143937..144274 338 caaaacttatttttcttaagcaaagtttaaggctggtctagtattatatagtcattaaataaagacctcctaactttatttaatgaaatcctaaaaacttttttcatcataatctcctaatgaagtcacccaatcaggtggctttttttcttggataggtgatggtgatagaaattttttgcaaaatagcaaaatttgagaaaagttaagctatttttaagcttcgtcttgtatcatatagttattaagtaaagacctcctaactttatttaataaaatcctaaacttttctttttcataataatctcccttgactccacccaatcaggtggagtttt Intra-Species Hit: Count: 1 Min: 1 Max: 338 Len: 338 Subject: smit_SMT_210_SMT_211|acetyltransferase, GNAT family:hypothetical protein predicted by Glimmer/Critica|POSITIVE:POSITIVE|[143937,144274]|338 HSP 1 e-value: 1.0E-179 bit: 628.0 Len: 338 Query Start:1 Query End:338 Subject Strand: POSITIVE Subject Start: 1 Subject End: 338 caaaacttatttttcttaagcaaagtttaaggctggtctagtattatatagtcattaaataaagacctcctaactttatttaatgaaatcctaaaaacttttttcatcataatctcctaatgaagtcacccaatcaggtggcnnnnnnncttggataggtgatggtgatagaaattttttgcaaaatagcaaaatttgagaaaagttaagctatttttaagcttcgtcttgtatcatatagttattaagtaaagacctcctaactttatttaataaaatcctaaacttttctttttcataataatctcccttgactccacccaatcaggtggagtttt caaaacttatttttcttaagcaaagtttaaggctggtctagtattatatagtcattaaataaagacctcctaactttatttaatgaaatcctaaaaacttttttcatcataatctcctaatgaagtcacccaatcaggtggctttttttcttggataggtgatggtgatagaaattttttgcaaaatagcaaaatttgagaaaagttaagctatttttaagcttcgtcttgtatcatatagttattaagtaaagacctcctaactttatttaataaaatcctaaacttttctttttcataataatctcccttgactccacccaatcaggtggagtttt Inter-species Hit: Count: 3 Min: 10 Max: 338 Len: 329 Subject: NC_008533_SPD_0240_SPD_0241|acetyltransferase, GNAT family protein:Holliday junction DNA helicase RuvB|POSITIVE:POSITIVE|[231089,232128]|1040 HSP 1 e-value: 1.0E-129 bit: 462.0 Len: 329 Query Start:10 Query End:338 Subject Strand: POSITIVE Subject Start: 11 Subject End: 337 .........tttttcttaagcaaagtttaaggctggtctagtattatatagtcattaaataaagacctcctaactttatttaatgaaatcctaaaaacttttttcatcataatctcctaatgaagtcacccaatcaggtggcnnnnnnncttggataggtgatggtgatagaaattttttgcaaaatagcaaaatttgagaaaagttaagctatttttaagcttcgtcttgtatcatatagttattaagtaaagacctcctaactttatttaataaaatcctaaacttttctttttcataataatctcccttgactccacccaatcaggtggagtttt .........tttttcttaagcaaaatttaaggatggtctagtattatatagtcattaaataaagacctcctaactttatttaataaaatcctaaa--cttttttcatcacaatctcctaatgaagccacccaatcaggtggcttttttgcgtggtgaggtgctggtgatagaaattttttgcaaaatagtaaaattttagaaaagttaagctagttttaagtttcgtcttgtatcatgtagttattaaataaagacctcctaactttatttaataaaatcctaaacttttctttttcataataatctcccttaactccacccaatcaggtggagtttt Subject: NC_003098_spr0237_spr0238|hypothetical protein:Holliday junction DNA helicase RuvB|POSITIVE:POSITIVE|[231088,232127]|1040 HSP 1 e-value: 1.0E-129 bit: 462.0 Len: 329 Query Start:10 Query End:338 Subject Strand: POSITIVE Subject Start: 11 Subject End: 337 .........tttttcttaagcaaagtttaaggctggtctagtattatatagtcattaaataaagacctcctaactttatttaatgaaatcctaaaaacttttttcatcataatctcctaatgaagtcacccaatcaggtggcnnnnnnncttggataggtgatggtgatagaaattttttgcaaaatagcaaaatttgagaaaagttaagctatttttaagcttcgtcttgtatcatatagttattaagtaaagacctcctaactttatttaataaaatcctaaacttttctttttcataataatctcccttgactccacccaatcaggtggagtttt .........tttttcttaagcaaaatttaaggatggtctagtattatatagtcattaaataaagacctcctaactttatttaataaaatcctaaa--cttttttcatcacaatctcctaatgaagccacccaatcaggtggcttttttgcgtggtgaggtgctggtgatagaaattttttgcaaaatagtaaaattttagaaaagttaagctagttttaagtttcgtcttgtatcatgtagttattaaataaagacctcctaactttatttaataaaatcctaaacttttctttttcataataatctcccttaactccacccaatcaggtggagtttt Subject: NC_003028_SP_0256_SP_0258|acetyltransferase, GNAT family:hypothetical protein|POSITIVE:NEGATIVE|[228572,231372]|2801 HSP 1 e-value: 3.0E-77 bit: 289.0 Len: 182 Query Start:157 Query End:338 Subject Strand: POSITIVE Subject Start: 2121 Subject End: 2302 ............................................................................................................................................................aggtgatggtgatagaaattttttgcaaaatagcaaaatttgagaaaagttaagctatttttaagcttcgtcttgtatcatatagttattaagtaaagacctcctaactttatttaataaaatcctaaacttttctttttcataataatctcccttgactccacccaatcaggtggagtttt ............................................................................................................................................................aggtgctggtgatagaaattttttgcaaaatagtaaaattttagaaaagttaagctagttttaagtttcgtcttgtatcatgtagttattaaataaagacctcctaactttatttaataaaatcctaaacttttctttttcataataatctcccttaactccaccgaatcaggtggagtttt HSP 2 e-value: 3.0E-49 bit: 196.0 Len: 130 Query Start:13 Query End:142 Subject Strand: POSITIVE Subject Start: 14 Subject End: 141 ............ttcttaagcaaagtttaaggctggtctagtattatatagtcattaaataaagacctcctaactttatttaatgaaatcctaaaaacttttttcatcataatctcctaatgaagtcacccaatcaggtggc.................................................................................................................................................................................................... ............ttcttaagcaaagtttaaggatggtctagtatcatatagtcattaaataaagacctcctaactttatttaataaaatcct--aaacttttttcatcacaatctcctaatgaagccacccaatcaggtggc.................................................................................................................................................................................................... HSP 3 e-value: 1.0E-21 bit: 105.0 Len: 65 Query Start:226 Query End:290 Subject Strand: POSITIVE Subject Start: 37 Subject End: 101 .................................................................................................................................................................................................................................gtcttgtatcatatagttattaagtaaagacctcctaactttatttaataaaatcctaaactttt................................................ .................................................................................................................................................................................................................................gtctagtatcatatagtcattaaataaagacctcctaactttatttaataaaatcctaaactttt................................................ HSP 4 e-value: 6.0E-14 bit: 79.8 Len: 60 Query Start:36 Query End:95 Subject Strand: POSITIVE Subject Start: 2190 Subject End: 2249 ...................................gtctagtattatatagtcattaaataaagacctcctaactttatttaatgaaatcctaaa................................................................................................................................................................................................................................................... ...................................gtcttgtatcatgtagttattaaataaagacctcctaactttatttaataaaatcctaaa................................................................................................................................................................................................................................................... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUUCUUAAGCAAAGUUUAAGGCUGGUCUAGUAUUAUAUAGUCAUUAAAUAAAGACCUCCUAACUUUAUUUAAUGAAAUCCUAAAAACUUUUUUCAUCAUAAUCUCCUAAUGAAGUCACCCAAUCAGGUGGCUUUUUUUCUUGGAUAGGUGAUGGUGAUAGAAAUUUUUUGCAAAAUAGCAAAAUUUGAGAAAAGUUAAGCUAUUUUUAAGCUUCGUCUUGUAUCAUAUAGUUAUUAAGUAAAGACCUCCUAACUUUAUUUAAUAAAAUCCUAAACUUUUCUUUUUCAUAAUAAUCUCCCUUGACUCCACCCAAUCAGGUGGAGUUUU ........(((.((((((((.((........((((.(((((.(((((((((((((.........))))))))))))).........(((((((((((((((.(((.((((..(((((((((......)))))))))..........)))).))).))))........((((((......))))))..)))))))))))(((((.......))))).....))))).))))..(((((((((((((.........)))))))))))))...)))))))))).)))...................(((((((((......))))))))).. (-81.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAACUCCACCUGAUUGGGUGGAGUCAAGGGAGAUUAUUAUGAAAAAGAAAAGUUUAGGAUUUUAUUAAAUAAAGUUAGGAGGUCUUUACUUAAUAACUAUAUGAUACAAGACGAAGCUUAAAAAUAGCUUAACUUUUCUCAAAUUUUGCUAUUUUGCAAAAAAUUUCUAUCACCAUCACCUAUCCAAGAAAAAAAGCCACCUGAUUGGGUGACUUCAUUAGGAGAUUAUGAUGAAAAAAGUUUUUAGGAUUUCAUUAAAUAAAGUUAGGAGGUCUUUAUUUAAUGACUAUAUAAUACUAGACCAGCCUUAAACUUUGCUUAAGAAAAA ...(((((((((....)))))))))....................(((.((((((((((.((((((...))))))......(((((...(((((.((((...(((.(.(((...(((((.......)))))..))).).)))..((((((......))))))..((((.((((..(((.((((...........(((.(((((....))))).)))...)))).)))..))))))))..)))).)))))...(((((((((((((.........)))))))))))))............)))))...)))))))))).)))........ (-76.94) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 298 150 105 52 1 smit:SMT_308|5end_trans-2-enoyl-ACP_reductase_II_249439..249669_POSITIVE 263 137 110 161 133 smit:SMT_2062|5end_phosphoglycerate_mutase_1971425..1971655_NEGATIVE 263 137 110 161 133 smit:SMT_1995|5end_phosphoglycerate_mutase_1920750..1920980_NEGATIVE 263 137 110 161 133 smit:SMT_201|5end_phosphoglycerate_mutase_131329..131559_POSITIVE 261 170 122 43 3 smit:SMT_2048|5end_competence-specific_global_transcription_modulator_1958278..1958508_NEGATIVE 259 158 120 44 7 smit:SMT_91|5end_hypothetical_protein_22578..22808_POSITIVE 258 150 104 112 51 smit:SMT_1609|5end_hypothetical_protein_1598113..1598343_POSITIVE 258 143 111 188 147 smit:SMT_1230|5end_hypothetical_protein_1191423..1191653_POSITIVE 257 170 127 197 140 smit:SMT_955|5end_acyltransferase_family_protein_904096..904326_POSITIVE 257 165 121 209 156 smit:SMT_120|5end_hypothetical_protein_72174..72404_POSITIVE 256 309 267 110 73 smit:SMT_1260|5end_hypothetical_protein_1225517..1225747_POSITIVE 252 159 113 141 84 smit:SMT_1835|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1803894..1804124_POSITIVE 251 146 106 113 65 smit:SMT_2063|5end_hypothetical_protein_1971792..1972022_NEGATIVE 251 150 104 57 3 smit:SMT_1294|5end_K02049_sulfonate/nitrate/taurine_transport_system_ATP-binding_protein_1255983..1256213_POSITIVE 250 179 131 82 29 smit:SMT_1263|5end_hypothetical_protein_1228104..1228334_POSITIVE 250 151 117 58 6 smit:SMT_1069|5end_acetyl_xylan_esterase,_putative_1009330..1009560_POSITIVE 249 164 121 229 184 smit:SMT_940|5end_tRNA_pseudouridine_synthase_A_892764..892994_NEGATIVE 249 155 113 212 174 smit:SMT_400|5end_hypothetical_protein_329090..329320_POSITIVE 249 150 106 159 118 smit:SMT_261|5end_ImpB/MucB/SamB_family_protein_200160..200390_POSITIVE 247 317 278 200 159 smit:SMT_1199|5end_lactococcin_A_ABC_transporter_permease_protein_1161063..1161293_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 300 147 113 96 58 smit:SMT_1742|3end_sodium-dependent_phosphate_transporter_1724991..1725141_POSITIVE 271 137 94 144 100 smit:SMT_261|3end_ImpB/MucB/SamB_family_protein_201655..201805_POSITIVE 258 150 104 115 54 smit:SMT_1608|3end_hypothetical_protein_1598196..1598346_POSITIVE 256 309 267 91 54 smit:SMT_1259|3end_hypothetical_protein_1225578..1225728_POSITIVE 252 227 182 58 4 smit:SMT_625|3end_50S_ribosomal_protein_L27_530400..530550_POSITIVE 251 150 104 57 3 smit:SMT_1293|3end_K02051_sulfonate/nitrate/taurine_transport_system_substrate-binding_protein_1256063..1256213_POSITIVE 250 179 131 80 27 smit:SMT_1262|3end_ribosomal_protein_L11_methyltransferase_1228182..1228332_POSITIVE 249 164 121 130 85 smit:SMT_941|3end_hypothetical_protein_892863..893013_NEGATIVE 248 144 106 142 97 smit:SMT_1625|3end_DNA_polymerase_IV_1615066..1615216_POSITIVE 245 110 65 86 36 smit:SMT_908|3end_hypothetical_protein_856073..856223_NEGATIVE 242 159 111 127 81 smit:SMT_840|3end_tRNA_nucleotidyltransferase_(CCA-adding_enzyme)_786062..786212_NEGATIVE 242 67 21 112 61 smit:SMT_379|3end_acetyltransferase,_GNAT_family_316456..316606_POSITIVE 242 67 21 112 61 smit:SMT_370|3end_acetyltransferase,_GNAT_family_305328..305478_POSITIVE 240 228 188 111 70 smit:SMT_2162|3end_hypothetical_protein_2037508..2037658_POSITIVE 240 228 188 111 70 smit:SMT_2157|3end_hypothetical_protein_2031399..2031549_POSITIVE 240 228 188 111 70 smit:SMT_1706|3end_hypothetical_protein_1690810..1690960_POSITIVE 240 228 188 111 70 smit:SMT_1546|3end_hypothetical_protein_1530852..1531002_POSITIVE 239 131 91 130 87 smit:SMT_771|3end_spermidine/putrescine_transport_system_permease_protein_PotB_681356..681506_NEGATIVE 239 160 113 91 53 smit:SMT_231|3end_translation_elongation_factor_G_168222..168372_POSITIVE 238 257 211 60 19 smit:SMT_1689|3end_PTS_enzyme,_maltose-and_glucose-specific,_factor_II_homologue_1673139..1673289_POSITIVE