Origin IGS: aaagttacctttttcattcagattatagattttattataccaaaaaaaggtccatttccccaacgtatggcttgaaaaatcactctctttcgtttataattaagaatgattttatgaaagggagtgaaaataa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttattttcactccctttcataaaatcattcttaattataaacgaaagagagtgatttttcaagccatacgttggggaaatggacctttttttggtataataaaatctataatctgaatgaaaaaggtaacttt Mask Tandem Repeat Region ================================================ aaagttacctttttcattcagattatagattttattataccaaaaaaaggtccatttccccaacgtatggcttgaaaaatcactctctttcgtttataattaagaatgattttatgaaagggagtgaaaataa Find is-nt database================================================ Query_seq: SMT_1485:SMT_1486|SMT_1485:SMT_1486:exodeoxyribonuclease:hypothetical protein:<-->:1465916..1466048 133 aaagttacctttttcattcagattatagattttattataccaaaaaaaggtccatttccccaacgtatggcttgaaaaatcactctctttcgtttataattaagaatgattttatgaaagggagtgaaaataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1485:SMT_1486|SMT_1485:SMT_1486:exodeoxyribonuclease:hypothetical protein:<-->:1465916..1466048 133 aaagttacctttttcattcagattatagattttattataccaaaaaaaggtccatttccccaacgtatggcttgaaaaatcactctctttcgtttataattaagaatgattttatgaaagggagtgaaaataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1485:SMT_1486|SMT_1485:SMT_1486:exodeoxyribonuclease:hypothetical protein:<-->:1465916..1466048 133 aaagttacctttttcattcagattatagattttattataccaaaaaaaggtccatttccccaacgtatggcttgaaaaatcactctctttcgtttataattaagaatgattttatgaaagggagtgaaaataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaagttacctttttcattcagattatagattttattataccaaaaaaaggtccatttccccaacgtatggcttgaaaaatcactctctttcgtttataattaagaatgattttatgaaagggagtgaaaataa Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: - Start: 21 End: 131 .................... I I S K I I G F F P G N G W R I A Q F I V R K R K Y N L I I K H F P T F M .. aaagttacctttttcattcagattatagattttattataccaaaaaaaggtccatttccccaacgtatggcttgaaaaatcactctctttcgtttataattaagaatgattttatgaaagggagtgaaaataa 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: 93 Start: 71 End: 100 ......................................................................CTTGAAAAATCACTCTCTTTCGTTTATAAT................................. PromScan Matrix: RpoD-17 Strand: - Score: 83 Start: 34 End: 63 .................................TTGGGGAAATGGACCTTTTTTTGGTATAAT...................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaagttacctttttcattcagattatagattttattataccaaaaaaaggtccatttccccaacgtatggcttgaaaaatcactctctttcgtttataattaagaatgattttatgaaagggagtgaaaataa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1485:SMT_1486|SMT_1485:SMT_1486:exodeoxyribonuclease:hypothetical protein:<-->:1465916..1466048 133 aaagttacctttttcattcagattatagattttattataccaaaaaaaggtccatttccccaacgtatggcttgaaaaatcactctctttcgtttataattaagaatgattttatgaaagggagtgaaaataa Intra-Species Hit: Count: 1 Min: 1 Max: 133 Len: 133 Subject: smit_SMT_1485_SMT_1486|exodeoxyribonuclease:hypothetical protein|NEGATIVE:POSITIVE|[1465916,1466048]|133 HSP 1 e-value: 2.0E-57 bit: 222.0 Len: 133 Query Start:1 Query End:133 Subject Strand: POSITIVE Subject Start: 1 Subject End: 133 aaagttacctttttcattcagattatagattttattataccnnnnnnnggtccatttccccaacgtatggcttgaaaaatcactctctttcgtttataattaagaatgattttatgaaagggagtgaaaataa aaagttacctttttcattcagattatagattttattataccaaaaaaaggtccatttccccaacgtatggcttgaaaaatcactctctttcgtttataattaagaatgattttatgaaagggagtgaaaataa Inter-species Hit: Count: 3 Min: 1 Max: 132 Len: 132 Subject: NC_008533_SPD_1625_SPD_1626|hypothetical protein:exodeoxyribonuclease III|NEGATIVE:POSITIVE|[1640619,1640751]|133 HSP 1 e-value: 3.0E-47 bit: 188.0 Len: 132 Query Start:1 Query End:132 Subject Strand: NEGATIVE Subject Start: 2 Subject End: 133 aaagttacctttttcattcagattatagattttattataccnnnnnnnggtccatttccccaacgtatggcttgaaaaatcactctctttcgtttataattaagaatgattttatgaaagggagtgaaaata. aaagttacctttttcattcagattatagattttattataccaaaaaaagatctatttccccaacgtatggtttgaaaaattactctctttcgtttataattaagaatgattttatgaaagggagtgaaaata. Subject: NC_003098_spr1659_spr1660|hypothetical protein:Exodeoxyribonuclease|NEGATIVE:POSITIVE|[1632901, 1633220]|320 HSP 1 e-value: 3.0E-47 bit: 188.0 Len: 132 Query Start:1 Query End:132 Subject Strand: NEGATIVE Subject Start: 189 Subject End: 320 aaagttacctttttcattcagattatagattttattataccnnnnnnnggtccatttccccaacgtatggcttgaaaaatcactctctttcgtttataattaagaatgattttatgaaagggagtgaaaata. aaagttacctttttcattcagattatagattttattataccaaaaaaagatctatttccccaacgtatggtttgaaaaattactctctttcgtttataattaagaatgattttatgaaagggagtgaaaata. Subject: NC_003028_SP_1844_SP_1845|hypothetical protein:exodeoxyribonuclease|NEGATIVE:POSITIVE|[1753054, 1753186]|133 HSP 1 e-value: 3.0E-47 bit: 188.0 Len: 132 Query Start:1 Query End:132 Subject Strand: NEGATIVE Subject Start: 2 Subject End: 133 aaagttacctttttcattcagattatagattttattataccnnnnnnnggtccatttccccaacgtatggcttgaaaaatcactctctttcgtttataattaagaatgattttatgaaagggagtgaaaata. aaagttacctttttcattcagattatagattttattataccaaaaaaagatctatttccccaacgtatggtttgaaaaattactctctttcgtttataattaagaatgattttatgaaagggagtgaaaata. Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAGUUACCUUUUUCAUUCAGAUUAUAGAUUUUAUUAUACCAAAAAAAGGUCCAUUUCCCCAACGUAUGGCUUGAAAAAUCACUCUCUUUCGUUUAUAAUUAAGAAUGAUUUUAUGAAAGGGAGUGAAAAUA ......((((((((.........((.......)).........))))))))...((((.(((.....)))...))))..((((((((((((((....(((((....)))))..))))))))))))))..... (-26.37) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUUUUCACUCCCUUUCAUAAAAUCAUUCUUAAUUAUAAACGAAAGAGAGUGAUUUUUCAAGCCAUACGUUGGGGAAAUGGACCUUUUUUUGGUAUAAUAAAAUCUAUAAUCUGAAUGAAAAAGGUAACUUU .....((((((.(((((........................))))).))))))..((((...(((.....))).))))...(((((((((.((((((........))).))).....)))))))))...... (-22.86) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 835 90 41 181 132 smit:SMT_1485|5end_exodeoxyribonuclease_1465825..1466055_NEGATIVE 284 70 22 140 90 smit:SMT_1162|5end_ATP-dependent_DNA_helicase_1108895..1109125_NEGATIVE 241 72 32 94 49 smit:SMT_125|5end_hypothetical_protein_77664..77894_NEGATIVE 240 95 51 111 63 smit:SMT_1619|5end_K02006_cobalt_transport_system_ATP-binding_protein_1606526..1606756_NEGATIVE 234 68 28 229 183 smit:SMT_170|5end_50S_ribosomal_protein_L3_114906..115136_POSITIVE 234 87 48 196 166 smit:SMT_109|5end_beta-galactosidase_53925..54155_POSITIVE 229 95 52 93 46 smit:SMT_1124|5end_pyrrolidone-carboxylate_peptidase_1060869..1061099_NEGATIVE 224 71 48 34 8 smit:SMT_1967|5end_dicarboxylate/amino_acid:cation_(Na+_or_H+)_symporter_(DAACS)_family_protein_1899683..1899913_NEGATIVE 222 88 54 149 108 smit:SMT_1109|5end_hypothetical_protein_1050315..1050545_NEGATIVE 219 90 48 169 123 smit:SMT_1820|5end_cation_transporter_CorA_family_1793600..1793830_POSITIVE 219 83 54 54 18 smit:SMT_622|5end_methionine_aminopeptidase_528939..529169_POSITIVE 218 96 58 75 30 smit:SMT_1213|5end_fatty_acid/phospholipid_synthesis_protein_PlsX_1172655..1172885_NEGATIVE 216 92 51 211 177 smit:SMT_1623|5end_K03498_trk_system_potassium_uptake_protein_TrkH_1609596..1609826_POSITIVE 212 99 60 153 110 smit:SMT_2015|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1932655..1932885_POSITIVE 212 50 3 194 141 smit:SMT_1414|5end_hypothetical_protein_1398446..1398676_NEGATIVE 211 77 44 63 27 smit:SMT_1353|5end_GTP-binding_protein_1331589..1331819_NEGATIVE 211 88 48 42 15 smit:SMT_1266|5end_predicted_transcriptional_regulator_1231362..1231592_POSITIVE 210 95 70 96 72 smit:SMT_1512|5end_hypothetical_protein_1494747..1494977_NEGATIVE 203 89 51 56 22 smit:SMT_725|5end_hypothetical_protein_630415..630645_NEGATIVE 201 90 48 95 40 smit:SMT_817|5end_aminotransferase_728699..728929_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 241 72 32 101 56 smit:SMT_126|3end_hypothetical_membrane_associated_protein_77657..77807_NEGATIVE 234 68 28 146 100 smit:SMT_169|3end_30S_ribosomal_protein_S10_114903..115053_POSITIVE 234 87 48 64 34 smit:SMT_108|3end_hypothetical_protein_53873..54023_POSITIVE 230 92 55 72 42 smit:SMT_147|3end_K02027_multiple_sugar_transport_system_substrate-binding_protein_98016..98166_POSITIVE 226 98 58 46 10 smit:SMT_1946|3end_sucrose-6-phosphate_hydrolase_1881205..1881355_POSITIVE 222 88 54 88 47 smit:SMT_1110|3end_hypothetical_protein_1050376..1050526_NEGATIVE 219 83 54 94 58 smit:SMT_621|3end_K03346_replication_initiation_and_membrane_attachment_protein_529059..529209_POSITIVE 218 96 58 78 33 smit:SMT_1214|3end_K03584_DNA_repair_protein_RecO_(recombination_protein_O)_1172652..1172802_NEGATIVE 212 99 60 145 102 smit:SMT_2014|3end_tryptophan_synthase_beta_chain_1932727..1932877_POSITIVE 211 77 44 46 10 smit:SMT_1354|3end_diacylglycerol_kinase_1331606..1331756_NEGATIVE 210 95 70 82 58 smit:SMT_1513|3end_hypothetical_protein_1494761..1494911_NEGATIVE 208 74 38 83 38 smit:SMT_899|3end_5,10-methylenetetrahydrofolate_reductase_847397..847547_NEGATIVE 207 66 27 53 5 smit:SMT_1862|3end_K02027_multiple_sugar_transport_system_substrate-binding_protein_1825460..1825610_POSITIVE 206 41 7 31 1 smit:SMT_1361|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1338730..1338880_NEGATIVE 203 89 51 59 25 smit:SMT_726|3end_ImpB/MucB/SamB_family_protein_630412..630562_NEGATIVE 201 90 48 87 32 smit:SMT_818|3end_cystathionine_gamma-synthase_728707..728857_NEGATIVE 197 88 57 41 7 smit:SMT_801|3end_glycyl-tRNA_synthetase_alpha_chain_709892..710042_NEGATIVE 195 72 31 48 5 smit:SMT_702|3end_hypothetical_protein_611946..612096_NEGATIVE 194 90 48 145 109 smit:SMT_2051|3end_enoyl-CoA_hydratase_1960067..1960217_NEGATIVE 194 74 46 138 106 smit:SMT_1699|3end_purine_operon_repressor_1682045..1682195_POSITIVE