Origin IGS: ttctattaaacttcattcggtgttggtatttaattgattcttattttacaaaaaatgttggcttttgtcaatgtgtttattagtaaaacttaattcaacagtttttactgtataaagctcggaatactt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aagtattccgagctttatacagtaaaaactgttgaattaagttttactaataaacacattgacaaaagccaacattttttgtaaaataagaatcaattaaataccaacaccgaatgaagtttaatagaa Mask Tandem Repeat Region ================================================ ttctattaaacttcattcggtgttggtatttaattgattcttattttacaaaaaatgttggcttttgtcaatgtgtttattagtaaaacttaattcaacagtttttactgtataaagctcggaatactt Find is-nt database================================================ Query_seq: SMT_1529:SMT_1530|SMT_1529:SMT_1530:hypothetical protein predicted by Glimmer/Critica:K07456 DNA mismatch repair protein MutS2:<-<-:1512971..1513099 129 ttctattaaacttcattcggtgttggtatttaattgattcttattttacaaaaaatgttggcttttgtcaatgtgtttattagtaaaacttaattcaacagtttttactgtataaagctcggaatactt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1529:SMT_1530|SMT_1529:SMT_1530:hypothetical protein predicted by Glimmer/Critica:K07456 DNA mismatch repair protein MutS2:<-<-:1512971..1513099 129 ttctattaaacttcattcggtgttggtatttaattgattcttattttacaaaaaatgttggcttttgtcaatgtgtttattagtaaaacttaattcaacagtttttactgtataaagctcggaatactt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1529:SMT_1530|SMT_1529:SMT_1530:hypothetical protein predicted by Glimmer/Critica:K07456 DNA mismatch repair protein MutS2:<-<-:1512971..1513099 129 ttctattaaacttcattcggtgttggtatttaattgattcttattttacaaaaaatgttggcttttgtcaatgtgtttattagtaaaacttaattcaacagtttttactgtataaagctcggaatactt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttctattaaacttcattcggtgttggtatttaattgattcttattttacaaaaaatgttggcttttgtcaatgtgtttattagtaaaacttaattcaacagtttttactgtataaagctcggaatactt Predict ORF larger than 30AA ================================================ ttctattaaacttcattcggtgttggtatttaattgattcttattttacaaaaaatgttggcttttgtcaatgtgtttattagtaaaacttaattcaacagtttttactgtataaagctcggaatactt 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: 92 Start: 43 End: 72 ..........................................ATTGACAAAAGCCAACATTTTTTGTAAAAT......................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttctattaaacttcattcggtgttggtatttaattgattcttattttacaaaaaatgttggcttttgtcaatgtgtttattagtaaaacttaattcaacagtttttactgtataaagctcggaatactt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1529:SMT_1530|SMT_1529:SMT_1530:hypothetical protein predicted by Glimmer/Critica:K07456 DNA mismatch repair protein MutS2:<-<-:1512971..1513099 129 ttctattaaacttcattcggtgttggtatttaattgattcttattttacaaaaaatgttggcttttgtcaatgtgtttattagtaaaacttaattcaacagtttttactgtataaagctcggaatactt Intra-Species Hit: Count: 1 Min: 1 Max: 129 Len: 129 Subject: smit_SMT_1529_SMT_1530|hypothetical protein predicted by Glimmer/Critica:K07456 DNA mismatch repair protein MutS2|NEGATIVE:NEGATIVE|[1512971,1513099]|129 HSP 1 e-value: 2.0E-67 bit: 256.0 Len: 129 Query Start:1 Query End:129 Subject Strand: POSITIVE Subject Start: 1 Subject End: 129 ttctattaaacttcattcggtgttggtatttaattgattcttattttacaaaaaatgttggcttttgtcaatgtgtttattagtaaaacttaattcaacagtttttactgtataaagctcggaatactt ttctattaaacttcattcggtgttggtatttaattgattcttattttacaaaaaatgttggcttttgtcaatgtgtttattagtaaaacttaattcaacagtttttactgtataaagctcggaatactt Inter-species Hit: Count: 3 Min: 1 Max: 117 Len: 117 Subject: NC_008533_SPD_0371_SPD_0372|MutS2 family protein:sodium:alanine symporter family protein|POSITIVE:POSITIVE|[376277,376617]|341 HSP 1 e-value: 5.0E-46 bit: 184.0 Len: 117 Query Start:1 Query End:117 Subject Strand: NEGATIVE Subject Start: 13 Subject End: 128 ttctattaaacttcattcggtgttggtatttaattgattcttattttacaaaaaatgttggcttttgtcaatgtgtttattagtaaaacttaattcaacagtttttactgtataaag............ ttctattaaacttcattcggtgttggtatt-aattgattctaattttacaaaaaatgttggcttttgtcaatgtgtttattagtaaaaattagttcaacagtttttactttataaag............ Subject: NC_003098_spr0368_spr0369|DNA mismatch repair protein:D-alanine glycine permease|POSITIVE:POSITIVE|[368748,369088]|341 HSP 1 e-value: 5.0E-46 bit: 184.0 Len: 117 Query Start:1 Query End:117 Subject Strand: NEGATIVE Subject Start: 13 Subject End: 128 ttctattaaacttcattcggtgttggtatttaattgattcttattttacaaaaaatgttggcttttgtcaatgtgtttattagtaaaacttaattcaacagtttttactgtataaag............ ttctattaaacttcattcggtgttggtatt-aattgattctaattttacaaaaaatgttggcttttgtcaatgtgtttattagtaaaaattagttcaacagtttttactttataaag............ Subject: NC_003028_SP_0406_SP_0407|MutS2 family protein:hypothetical protein|POSITIVE:NEGATIVE|[387331,387450]|120 HSP 1 e-value: 2.0E-45 bit: 182.0 Len: 108 Query Start:10 Query End:117 Subject Strand: NEGATIVE Subject Start: 13 Subject End: 120 .........acttcattcggtgttggtatttaattgattcttattttacaaaaaatgttggcttttgtcaatgtgtttattagtaaaacttaattcaacagtttttactgtataaag............ .........acttcattcggtgttggtatttaattgattctaattttacaaaaaatgttggcttttgtcaatgtgtttattagtaaaaattagttcaacagtttttactttataaag............ Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCUAUUAAACUUCAUUCGGUGUUGGUAUUUAAUUGAUUCUUAUUUUACAAAAAAUGUUGGCUUUUGUCAAUGUGUUUAUUAGUAAAACUUAAUUCAACAGUUUUUACUGUAUAAAG .((.((((((..(((........)))..)))))).))......((((((.....((((((((....))))))))........)))))).........(((((....)))))...... (-17.22) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUUAUACAGUAAAAACUGUUGAAUUAAGUUUUACUAAUAAACACAUUGACAAAAGCCAACAUUUUUUGUAAAAUAAGAAUCAAUUAAAUACCAACACCGAAUGAAGUUUAAUAGAA ................((((((((((..((((.......))))......(((((((.......)))))))...................................)))))))))).. (-11.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 693 60 11 151 102 smit:SMT_1529|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1512880..1513110_NEGATIVE 219 42 1 69 29 smit:SMT_1336|5end_DNA_primase_1311964..1312194_NEGATIVE 213 110 73 158 120 smit:SMT_2012|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1930552..1930782_NEGATIVE 204 69 21 119 83 smit:SMT_2059|5end_hypothetical_protein_1967881..1968111_POSITIVE 203 28 8 119 97 smit:SMT_1685|5end_phenylalanyl-tRNA_synthetase_alpha_chain_1668845..1669075_NEGATIVE 202 70 49 36 14 smit:SMT_1350|5end_multidrug_resistance_efflux_pump_1329225..1329455_NEGATIVE 199 37 9 222 190 smit:SMT_372|5end_valyl-tRNA_synthetase_305819..306049_POSITIVE 197 42 13 87 52 smit:SMT_919|5end_hypothetical_protein_872499..872729_NEGATIVE 194 43 1 133 86 smit:SMT_1143|5end_K02025_multiple_sugar_transport_system_permease_protein_1086928..1087158_POSITIVE 190 45 18 92 61 smit:SMT_1831|5end_galactose-6-phosphate_isomerase_1799912..1800142_POSITIVE 188 82 53 68 33 smit:SMT_1526|5end_K07720_two-component_system,_response_regulator_YesN_1510554..1510784_NEGATIVE 187 69 21 123 69 smit:SMT_1294|5end_K02049_sulfonate/nitrate/taurine_transport_system_ATP-binding_protein_1255983..1256213_POSITIVE 178 60 14 104 57 smit:SMT_1245|5end_SOS_responce_UmuC_protein_1205120..1205350_POSITIVE 177 85 56 172 138 smit:SMT_1372|5end_hypothetical_protein_1351696..1351926_NEGATIVE 174 70 23 217 166 smit:SMT_1731|5end_K06442_putative_hemolysin_1715643..1715873_POSITIVE 172 70 22 65 2 smit:SMT_237|5end_aminopeptidase_C_175226..175456_POSITIVE 169 69 25 129 87 smit:SMT_1397|5end_mutator_MutT_protein_1372727..1372957_POSITIVE 167 78 60 24 5 smit:SMT_276|5end_exopolysaccharide_biosynthesis_protein_218821..219051_POSITIVE 167 41 1 76 37 smit:SMT_164|5end_hypothetical_membrane_spanning_protein_109095..109325_POSITIVE 166 66 21 65 15 smit:SMT_1766|5end_sucrose-6-phosphate_hydrolase_1741702..1741932_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 220 47 14 91 60 smit:SMT_501|3end_ABC_transporter,_ATP-binding_protein_434848..434998_POSITIVE 202 70 49 49 27 smit:SMT_1351|3end_dephospho-CoA_kinase_1329212..1329362_NEGATIVE 199 106 72 133 106 smit:SMT_1536|3end_trigger_factor_1520636..1520786_NEGATIVE 199 37 9 139 107 smit:SMT_380|3end_hypothetical_protein_316944..317094_POSITIVE 193 86 58 98 60 smit:SMT_959|3end_1-acyl-sn-glycerol-3-phosphate_acyltransferase_906112..906262_POSITIVE 188 82 53 56 21 smit:SMT_1527|3end_two-component_sensor_kinase_1510566..1510716_NEGATIVE 187 69 21 123 69 smit:SMT_1293|3end_K02051_sulfonate/nitrate/taurine_transport_system_substrate-binding_protein_1256063..1256213_POSITIVE 178 60 14 53 6 smit:SMT_1244|3end_putative_repressor_protein_1205149..1205299_POSITIVE 177 85 56 151 117 smit:SMT_1373|3end_K02838_ribosome_recycling_factor_1351717..1351867_NEGATIVE 172 50 12 73 33 smit:SMT_1254|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1220574..1220724_NEGATIVE 170 110 61 149 100 smit:SMT_1334|3end_hypothetical_protein_1308748..1308898_NEGATIVE 169 69 25 119 77 smit:SMT_1396|3end_uracil-DNA_glycosylase_1372797..1372947_POSITIVE 166 66 21 55 5 smit:SMT_1765|3end_ABC_transporter_sugar_permease_1741772..1741922_POSITIVE 165 105 61 111 66 smit:SMT_2007|3end_hypothetical_protein_1928147..1928297_POSITIVE 165 39 13 36 12 smit:SMT_827|3end_hypothetical_protein_751014..751164_POSITIVE 165 69 22 48 1 smit:SMT_232|3end_DNA_polymerase_III,_alpha_subunit,_Gram-positive_type_172717..172867_POSITIVE 164 47 1 149 86 smit:SMT_855|3end_dihydrofolate_reductase_799492..799642_NEGATIVE 164 89 41 125 71 smit:SMT_106|3end_hypothetical_protein_52336..52486_POSITIVE 163 70 40 54 17 smit:SMT_1431|3end_K08986_putative_membrane_protein_1416654..1416804_POSITIVE 161 47 1 107 59 smit:SMT_1612|3end_K06024_segregation_and_condensation_protein_B_1600701..1600851_POSITIVE