Origin IGS: atagttcctttctatttacaggtcagcttattccaaacttttagcataaatttgcttaatttcattccattttgtgtctagattgaccttgattcgttacaattatttcaattataccacaaaatgaaaaattagtaaaagacggaaacgagaaagtcacaggacgatttctttagtaaacgtttgcaaaaataaagaaaatatgttattttgataatggaaatgagttttattgtttgtcataattccatatagattttaagtcaaggaggttgccct .........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 agggcaacctccttgacttaaaatctatatggaattatgacaaacaataaaactcatttccattatcaaaataacatattttctttatttttgcaaacgtttactaaagaaatcgtcctgtgactttctcgtttccgtcttttactaatttttcattttgtggtataattgaaataattgtaacgaatcaaggtcaatctagacacaaaatggaatgaaattaagcaaatttatgctaaaagtttggaataagctgacctgtaaatagaaaggaactat Mask Tandem Repeat Region ================================================ atagttcctttctatttacaggtcagcttattccaaacttttagcataaatttgcttaatttcattccattttgtgtctagattgaccttgattcgttacaattatttcaattataccacaaaatgaaaaattagtaaaagacggaaacgagaaagtcacaggacgatttctttagtaaacgtttgcaaaaataaagaaaatatgttattttgataatggaaatgagttttattgtttgtcataattccatatagattttaagtcaaggaggttgccct Find is-nt database================================================ Query_seq: SMT_143:SMT_144|SMT_143:SMT_144:hypothetical protein:hypothetical protein predicted by Glimmer/Critica:<-->:95414..95692 279 atagttcctttctatttacaggtcagcttattccaaacttttagcataaatttgcttaatttcattccattttgtgtctagattgaccttgattcgttacaattatttcaattataccacaaaatgaaaaattagtaaaagacggaaacgagaaagtcacaggacgatttctttagtaaacgtttgcaaaaataaagaaaatatgttattttgataatggaaatgagttttattgtttgtcataattccatatagattttaagtcaaggaggttgccct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_143:SMT_144|SMT_143:SMT_144:hypothetical protein:hypothetical protein predicted by Glimmer/Critica:<-->:95414..95692 279 atagttcctttctatttacaggtcagcttattccaaacttttagcataaatttgcttaatttcattccattttgtgtctagattgaccttgattcgttacaattatttcaattataccacaaaatgaaaaattagtaaaagacggaaacgagaaagtcacaggacgatttctttagtaaacgtttgcaaaaataaagaaaatatgttattttgataatggaaatgagttttattgtttgtcataattccatatagattttaagtcaaggaggttgccct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_143:SMT_144|SMT_143:SMT_144:hypothetical protein:hypothetical protein predicted by Glimmer/Critica:<-->:95414..95692 279 atagttcctttctatttacaggtcagcttattccaaacttttagcataaatttgcttaatttcattccattttgtgtctagattgaccttgattcgttacaattatttcaattataccacaaaatgaaaaattagtaaaagacggaaacgagaaagtcacaggacgatttctttagtaaacgtttgcaaaaataaagaaaatatgttattttgataatggaaatgagttttattgtttgtcataattccatatagattttaagtcaaggaggttgccct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atagttcctttctatttacaggtcagcttattccaaacttttagcataaatttgcttaatttcattccattttgtgtctagattgaccttgattcgttacaattatttcaattataccacaaaatgaaaaattagtaaaagacggaaacgagaaagtcacaggacgatttctttagtaaacgtttgcaaaaataaagaaaatatgttattttgataatggaaatgagttttattgtttgtcataattccatatagattttaagtcaaggaggttgccct Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: - Start: 135 End: 233 ...................................................................................................................................... Y F V S V L F D C S S K K L L R K C F Y L F Y T I K I I S I L K M .............................................. Protein_Len: 32 Strand: - Start: 65 End: 160 ................................................................ E M K H R S Q G Q N T V I I E I I G C F S F N T F S P F S F T M ....................................................................................................................... atagttcctttctatttacaggtcagcttattccaaacttttagcataaatttgcttaatttcattccattttgtgtctagattgaccttgattcgttacaattatttcaattataccacaaaatgaaaaattagtaaaagacggaaacgagaaagtcacaggacgatttctttagtaaacgtttgcaaaaataaagaaaatatgttattttgataatggaaatgagttttattgtttgtcataattccatatagattttaagtcaaggaggttgccct 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: 91 Start: 111 End: 140 ..............................................................................................................TTTTACTAATTTTTCATTTTGTGGTATAAT........................................................................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 102 End: 131 .....................................................................................................TTTTTCATTTTGTGGTATAATTGAAATAAT.................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 183 End: 212 ......................................................................................................................................................................................TTTGCAAAAATAAAGAAAATATGTTATTTT................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atagttcctttctatttacaggtcagcttattccaaacttttagcataaatttgcttaatttcattccattttgtgtctagattgaccttgattcgttacaattatttcaattataccacaaaatgaaaaattagtaaaagacggaaacgagaaagtcacaggacgatttctttagtaaacgtttgcaaaaataaagaaaatatgttattttgataatggaaatgagttttattgtttgtcataattccatatagattttaagtcaaggaggttgccct Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_143:SMT_144|SMT_143:SMT_144:hypothetical protein:hypothetical protein predicted by Glimmer/Critica:<-->:95414..95692 279 atagttcctttctatttacaggtcagcttattccaaacttttagcataaatttgcttaatttcattccattttgtgtctagattgaccttgattcgttacaattatttcaattataccacaaaatgaaaaattagtaaaagacggaaacgagaaagtcacaggacgatttctttagtaaacgtttgcaaaaataaagaaaatatgttattttgataatggaaatgagttttattgtttgtcataattccatatagattttaagtcaaggaggttgccct Intra-Species Hit: Count: 1 Min: 1 Max: 279 Len: 279 Subject: smit_SMT_143_SMT_144|hypothetical protein:hypothetical protein predicted by Glimmer/Critica|NEGATIVE:POSITIVE|[95414,95692]|279 HSP 1 e-value: 1.0E-156 bit: 553.0 Len: 279 Query Start:1 Query End:279 Subject Strand: POSITIVE Subject Start: 1 Subject End: 279 atagttcctttctatttacaggtcagcttattccaaacttttagcataaatttgcttaatttcattccattttgtgtctagattgaccttgattcgttacaattatttcaattataccacaaaatgaaaaattagtaaaagacggaaacgagaaagtcacaggacgatttctttagtaaacgtttgcaaaaataaagaaaatatgttattttgataatggaaatgagttttattgtttgtcataattccatatagattttaagtcaaggaggttgccct atagttcctttctatttacaggtcagcttattccaaacttttagcataaatttgcttaatttcattccattttgtgtctagattgaccttgattcgttacaattatttcaattataccacaaaatgaaaaattagtaaaagacggaaacgagaaagtcacaggacgatttctttagtaaacgtttgcaaaaataaagaaaatatgttattttgataatggaaatgagttttattgtttgtcataattccatatagattttaagtcaaggaggttgccct Inter-species Hit: Count: 3 Min: 1 Max: 279 Len: 279 Subject: NC_008533_SPD_0131_SPD_0132|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[136551,137367]|817 HSP 1 e-value: 1.0E-116 bit: 418.0 Len: 279 Query Start:1 Query End:279 Subject Strand: POSITIVE Subject Start: 1 Subject End: 279 atagttcctttctatttacaggtcagcttattccaaacttttagcataaatttgcttaatttcattccattttgtgtctagattgaccttgattcgttacaattatttcaattataccacaaaatgaaaaattagtaaaagacggaaacgagaaagtcacaggacgatttctttagtaaacgtttgcaaaaataaagaaaatatgttattttgataatggaaatgagttttattgtttgtcataattccatatagattttaagtcaaggaggttgccct atagttcctttctatttacaggtcagcttattccaaacttttagcagatatttgcttgatttcattccattttgtgtctagattgaccttgattcgttacaattatttcaattataccacaaaatgaaaaattagtaaaagacggaaacgagaaagttaggggacgatttctttggtaagcgtttgcaagaataaagaaaatgtattatgttgataacggaagtgaaatttattgcttgtcataattccatatagattttaagtcaaggaggttgccct Subject: NC_003098_spr0126_spr0127|hypothetical protein:orf51|NEGATIVE:NEGATIVE|[136551,137367]|817 HSP 1 e-value: 1.0E-116 bit: 418.0 Len: 279 Query Start:1 Query End:279 Subject Strand: POSITIVE Subject Start: 1 Subject End: 279 atagttcctttctatttacaggtcagcttattccaaacttttagcataaatttgcttaatttcattccattttgtgtctagattgaccttgattcgttacaattatttcaattataccacaaaatgaaaaattagtaaaagacggaaacgagaaagtcacaggacgatttctttagtaaacgtttgcaaaaataaagaaaatatgttattttgataatggaaatgagttttattgtttgtcataattccatatagattttaagtcaaggaggttgccct atagttcctttctatttacaggtcagcttattccaaacttttagcagatatttgcttgatttcattccattttgtgtctagattgaccttgattcgttacaattatttcaattataccacaaaatgaaaaattagtaaaagacggaaacgagaaagttaggggacgatttctttggtaagcgtttgcaagaataaagaaaatgtattatgttgataacggaagtgaaatttattgcttgtcataattccatatagattttaagtcaaggaggttgccct Subject: NC_003028_SP_0122_SP_0123|hypothetical protein:competence-induced protein Ccs1|NEGATIVE:NEGATIVE|[126966,127290]|325 HSP 1 e-value: 1.0E-116 bit: 418.0 Len: 279 Query Start:1 Query End:279 Subject Strand: POSITIVE Subject Start: 1 Subject End: 279 atagttcctttctatttacaggtcagcttattccaaacttttagcataaatttgcttaatttcattccattttgtgtctagattgaccttgattcgttacaattatttcaattataccacaaaatgaaaaattagtaaaagacggaaacgagaaagtcacaggacgatttctttagtaaacgtttgcaaaaataaagaaaatatgttattttgataatggaaatgagttttattgtttgtcataattccatatagattttaagtcaaggaggttgccct atagttcctttctatttacaggtcagcttattccaaacttttagcagatatttgcttgatttcattccattttgtgtctagattgaccttgattcgttacaattatttcaattataccacaaaatgaaaaattagtaaaagacggaaacgagaaagttaggggacgatttctttggtaagcgttttcaaaaataaagaaaatgtattatgttgataacggaagtgaaatttattgcttgtcataattccatatagattttaagtcaaggaggttgccct Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAGUUCCUUUCUAUUUACAGGUCAGCUUAUUCCAAACUUUUAGCAUAAAUUUGCUUAAUUUCAUUCCAUUUUGUGUCUAGAUUGACCUUGAUUCGUUACAAUUAUUUCAAUUAUACCACAAAAUGAAAAAUUAGUAAAAGACGGAAACGAGAAAGUCACAGGACGAUUUCUUUAGUAAACGUUUGCAAAAAUAAAGAAAAUAUGUUAUUUUGAUAAUGGAAAUGAGUUUUAUUGUUUGUCAUAAUUCCAUAUAGAUUUUAAGUCAAGGAGGUUGCCCU ...((..(((((..(((((.......................((((......))))...........(((((((((....((((((...(((((......)))))..))))))....)))))))))........)))))...((....)).)))))..)).((.((((((((((.((((....)))).....(((((...(((((..(((.((((((....(((((...)))))..)))))).)))..)))))...)))))....)))))))))).)). (-53.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGGGCAACCUCCUUGACUUAAAAUCUAUAUGGAAUUAUGACAAACAAUAAAACUCAUUUCCAUUAUCAAAAUAACAUAUUUUCUUUAUUUUUGCAAACGUUUACUAAAGAAAUCGUCCUGUGACUUUCUCGUUUCCGUCUUUUACUAAUUUUUCAUUUUGUGGUAUAAUUGAAAUAAUUGUAACGAAUCAAGGUCAAUCUAGACACAAAAUGGAAUGAAAUUAAGCAAAUUUAUGCUAAAAGUUUGGAAUAAGCUGACCUGUAAAUAGAAAGGAACUAU (((....)))....(((...........((((((..((((.............))))))))))................((((((((.....((....))....))))))))..)))..((..((((((...(((((.(((((.......((((((((((((.....(((((.....(((........)))..))))).....))))))))))))........((((......)))))))))..)))))...((......))....))))))..))... (-49.12) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 773 100 51 191 142 smit:SMT_143|5end_hypothetical_protein_95323..95553_NEGATIVE 312 95 59 133 98 smit:SMT_894|5end_hypothetical_protein_841701..841931_NEGATIVE 304 190 141 92 26 smit:SMT_1660|5end_serine_protease_1650634..1650864_NEGATIVE 278 99 56 93 51 smit:SMT_2080|5end_glycosyl_transferase_CpsE_1980452..1980682_POSITIVE 269 187 141 45 2 smit:SMT_1488|5end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_1467157..1467387_POSITIVE 263 186 142 50 14 smit:SMT_1364|5end_50S_ribosomal_protein_L35_1343865..1344095_NEGATIVE 249 48 3 161 100 smit:SMT_1944|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1879494..1879724_NEGATIVE 246 97 51 72 31 smit:SMT_408|5end_hypothetical_protein_353087..353317_POSITIVE 237 99 51 139 81 smit:SMT_1019|5end_K03295_cation_efflux_system_protein,_CDF_family_955672..955902_NEGATIVE 236 68 23 55 9 smit:SMT_1427|5end_S1_RNA_binding_domain_protein_1413429..1413659_NEGATIVE 236 189 143 164 116 smit:SMT_188|5end_LSU_ribosomal_protein_L30P_123505..123735_POSITIVE 235 40 5 126 94 smit:SMT_1612|5end_K06024_segregation_and_condensation_protein_B_1600052..1600282_POSITIVE 230 45 2 145 97 smit:SMT_1378|5end_DNA_polymerase_III,_delta'_subunit_1356803..1357033_NEGATIVE 229 48 3 126 65 smit:SMT_1961|5end_K07485_transposase_1894206..1894436_POSITIVE 228 99 58 182 139 smit:SMT_1509|5end_phosphopentomutase_1492781..1493011_NEGATIVE 228 93 52 52 11 smit:SMT_1295|5end_transcriptional_regulator_CtsR_1256830..1257060_POSITIVE 228 69 22 56 5 smit:SMT_161|5end_putative_folyl-polyglutamate_synthetase_105358..105588_POSITIVE 224 47 8 43 3 smit:SMT_1687|5end_K02027_multiple_sugar_transport_system_substrate-binding_protein_1670400..1670630_POSITIVE 223 45 3 225 186 smit:SMT_593|5end_K02030_polar_amino_acid_transport_system_substrate-binding_protein_509398..509628_POSITIVE 223 187 148 220 192 smit:SMT_548|5end_K02035_peptide/nickel_transport_system_substrate-binding_protein_464992..465222_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 312 95 59 140 105 smit:SMT_895|3end_cysteinyl-tRNA_synthetase_841694..841844_NEGATIVE 278 99 56 60 18 smit:SMT_2079|3end_single_strand_binding_protein_1980499..1980649_POSITIVE 246 97 51 71 30 smit:SMT_407|3end_para-aminobenzoate_synthetase_component_I_/_4-amino-4-deoxychorismate_lyase_353166..353316_POSITIVE 236 189 143 150 102 smit:SMT_187|3end_30S_ribosomal_protein_S5_123571..123721_POSITIVE 235 40 5 107 75 smit:SMT_1611|3end_K05896_segregation_and_condensation_protein_A_1600113..1600263_POSITIVE 231 173 132 66 17 smit:SMT_1073|3end_L-asparaginase_1012251..1012401_POSITIVE 230 45 2 148 100 smit:SMT_1379|3end_thymidylate_kinase_1356800..1356950_NEGATIVE 224 190 160 144 118 smit:SMT_562|3end_ATP-dependent_RNA_helicase,_DEAD/DEAH_box_family_480809..480959_NEGATIVE 223 50 7 111 60 smit:SMT_1895|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1847402..1847552_POSITIVE 220 183 143 47 2 smit:SMT_627|3end_glucose-1-phosphate_adenylyltransferase_532921..533071_POSITIVE 219 78 38 149 108 smit:SMT_543|3end_topoisomerase_IV_subunit_B_460344..460494_POSITIVE 218 46 5 100 60 smit:SMT_1492|3end_DNA-directed_RNA_polymerase_beta_chain_1475778..1475928_POSITIVE 216 60 16 151 102 smit:SMT_972|3end_ABC-type_multidrug/protein/lipid_transport_system,_ATPase_component_919256..919406_NEGATIVE 216 197 154 50 1 smit:SMT_185|3end_50S_ribosomal_protein_L6_122619..122769_POSITIVE 213 110 74 89 53 smit:SMT_463|3end_para-aminobenzoate_synthetase_component_I_/_4-amino-4-deoxychorismate_lyase_402839..402989_POSITIVE 212 97 64 128 94 smit:SMT_434|3end_orotidine_5'-phosphate_decarboxylase_376888..377038_POSITIVE 209 174 133 100 55 smit:SMT_377|3end_hypothetical_protein_315848..315998_POSITIVE 209 55 19 117 80 smit:SMT_154|3end_K03647_protein_involved_in_ribonucleotide_reduction_102474..102624_POSITIVE 205 98 51 95 37 smit:SMT_1750|3end_anthranilate_phosphoribosyltransferase_1729095..1729245_POSITIVE 205 60 20 73 29 smit:SMT_1543|3end_diphosphomevalonate_decarboxylase_1527071..1527221_NEGATIVE