Origin IGS: tctgctttcttttttattgccaattaagtcagaaaaaagcagagctgactagaccaatatgacaattgtcatatttttcctaacaaatgtcatctgggcaaaatgacatttgacaatatgaaaccgattacaaatcttgtacaataaaatcatcaataaatccttcgtcatctaaagcctgacttggctaagaagtcgaaggataaaggaggcaggaaag .........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 ctttcctgcctcctttatccttcgacttcttagccaagtcaggctttagatgacgaaggatttattgatgattttattgtacaagatttgtaatcggtttcatattgtcaaatgtcattttgcccagatgacatttgttaggaaaaatatgacaattgtcatattggtctagtcagctctgcttttttctgacttaattggcaataaaaaagaaagcaga Mask Tandem Repeat Region ================================================ tctgctttcttttttattgccaattaagtcagaaaaaagcagagctgactagaccaatatgacaattgtcatatttttcctaacaaatgtcatctgggcaaaatgacatttgacaatatgaaaccgattacaaatcttgtacaataaaatcatcaataaatccttcgtcatctaaagcctgacttggctaagaagtcgaaggataaaggaggcaggaaag Find is-nt database================================================ Query_seq: SSA_0218:SSA_0219|SSA_0218:SSA_0219:Sugar-binding periplasmic protein, putative:PTS system, sugar-specific enzyme IIA component, putative:->->:215287..215506 220 tctgctttcttttttattgccaattaagtcagaaaaaagcagagctgactagaccaatatgacaattgtcatatttttcctaacaaatgtcatctgggcaaaatgacatttgacaatatgaaaccgattacaaatcttgtacaataaaatcatcaataaatccttcgtcatctaaagcctgacttggctaagaagtcgaaggataaaggaggcaggaaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0218:SSA_0219|SSA_0218:SSA_0219:Sugar-binding periplasmic protein, putative:PTS system, sugar-specific enzyme IIA component, putative:->->:215287..215506 220 tctgctttcttttttattgccaattaagtcagaaaaaagcagagctgactagaccaatatgacaattgtcatatttttcctaacaaatgtcatctgggcaaaatgacatttgacaatatgaaaccgattacaaatcttgtacaataaaatcatcaataaatccttcgtcatctaaagcctgacttggctaagaagtcgaaggataaaggaggcaggaaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0218:SSA_0219|SSA_0218:SSA_0219:Sugar-binding periplasmic protein, putative:PTS system, sugar-specific enzyme IIA component, putative:->->:215287..215506 220 tctgctttcttttttattgccaattaagtcagaaaaaagcagagctgactagaccaatatgacaattgtcatatttttcctaacaaatgtcatctgggcaaaatgacatttgacaatatgaaaccgattacaaatcttgtacaataaaatcatcaataaatccttcgtcatctaaagcctgacttggctaagaagtcgaaggataaaggaggcaggaaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tctgctttcttttttattgccaattaagtcagaaaaaagcagagctgactagaccaatatgacaattgtcatatttttcctaacaaatgtcatctgggcaaaatgacatttgacaatatgaaaccgattacaaatcttgtacaataaaatcatcaataaatccttcgtcatctaaagcctgacttggctaagaagtcgaaggataaaggaggcaggaaag Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: - Start: 52 End: 171 ................................................... V L I V I T M N K R V F T M Q A F H C K V I H F R N C I K Y L L I M L L D K T M ................................................. tctgctttcttttttattgccaattaagtcagaaaaaagcagagctgactagaccaatatgacaattgtcatatttttcctaacaaatgtcatctgggcaaaatgacatttgacaatatgaaaccgattacaaatcttgtacaataaaatcatcaataaatccttcgtcatctaaagcctgacttggctaagaagtcgaaggataaaggaggcaggaaag 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================================================ tctgctttcttttttattgccaattaagtcagaaaaaagcagagctgactagaccaatatgacaattgtcatatttttcctaacaaatgtcatctgggcaaaatgacatttgacaatatgaaaccgattacaaatcttgtacaataaaatcatcaataaatccttcgtcatctaaagcctgacttggctaagaagtcgaaggataaaggaggcaggaaag Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 76 HP_score: -6.2 Tail_Score: -4.7254 Start: 58 End: 73 Full_Region: AGCTGACTAGACCAA TATGAC AATT GTCATA TTTTTCCTAACAAAT .........................................................TATGACAATTGTCATA................................................................................................................................................... TransTerm Strand: - Conf: 66 HP_score: -5.6 Tail_Score: -4.31737 Start: 161 End: 203 Full_Region: ttcctgcctccttta tccttcgacttcttagcc aagtca ggctttagatgacgaagga tttattgatgatttt ................................................................................................................................................................tccttcgacttcttagccaagtcaggctttagatgacgaagga................. Find igs database================================================ Query_seq: SSA_0218:SSA_0219|SSA_0218:SSA_0219:Sugar-binding periplasmic protein, putative:PTS system, sugar-specific enzyme IIA component, putative:->->:215287..215506 220 tctgctttcttttttattgccaattaagtcagaaaaaagcagagctgactagaccaatatgacaattgtcatatttttcctaacaaatgtcatctgggcaaaatgacatttgacaatatgaaaccgattacaaatcttgtacaataaaatcatcaataaatccttcgtcatctaaagcctgacttggctaagaagtcgaaggataaaggaggcaggaaag Intra-Species Hit: Count: 1 Min: 1 Max: 220 Len: 220 Subject: NC_009009_SSA_0218_SSA_0219|Sugar-binding periplasmic protein, putative:PTS system, sugar-specific enzyme IIA component, putative|POSITIVE:POSITIVE|[215287,215506]|220 HSP 1 e-value: 1.0E-121 bit: 436.0 Len: 220 Query Start:1 Query End:220 Subject Strand: POSITIVE Subject Start: 1 Subject End: 220 tctgctttcttttttattgccaattaagtcagaaaaaagcagagctgactagaccaatatgacaattgtcatatttttcctaacaaatgtcatctgggcaaaatgacatttgacaatatgaaaccgattacaaatcttgtacaataaaatcatcaataaatccttcgtcatctaaagcctgacttggctaagaagtcgaaggataaaggaggcaggaaag tctgctttcttttttattgccaattaagtcagaaaaaagcagagctgactagaccaatatgacaattgtcatatttttcctaacaaatgtcatctgggcaaaatgacatttgacaatatgaaaccgattacaaatcttgtacaataaaatcatcaataaatccttcgtcatctaaagcctgacttggctaagaagtcgaaggataaaggaggcaggaaag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUGCUUUCUUUUUUAUUGCCAAUUAAGUCAGAAAAAAGCAGAGCUGACUAGACCAAUAUGACAAUUGUCAUAUUUUUCCUAACAAAUGUCAUCUGGGCAAAAUGACAUUUGACAAUAUGAAACCGAUUACAAAUCUUGUACAAUAAAAUCAUCAAUAAAUCCUUCGUCAUCUAAAGCCUGACUUGGCUAAGAAGUCGAAGGAUAAAGGAGGCAGGAAAG (((((((((((((((((((.......((((((............)))))).((..((((((((....))))))))..))....((((((((((.(.....).)))))))))).............................))))))))..........((((((((.(.(((..((((......)))).))).).)))))))).))))))))))).... (-62.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUUCCUGCCUCCUUUAUCCUUCGACUUCUUAGCCAAGUCAGGCUUUAGAUGACGAAGGAUUUAUUGAUGAUUUUAUUGUACAAGAUUUGUAAUCGGUUUCAUAUUGUCAAAUGUCAUUUUGCCCAGAUGACAUUUGUUAGGAAAAAUAUGACAAUUGUCAUAUUGGUCUAGUCAGCUCUGCUUUUUUCUGACUUAAUUGGCAAUAAAAAAGAAAGCAGA .....((((.......((((((((.(.(((.((((......))))..))).).))))))))..........(((((((((.(((........................((((((((((((.....))))))))))))...(((..((((((((....))))))))..))).(((((............)))))....))))))))))))......)))). (-59.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 362 216 176 61 23 NC_009009:SSA_1673|5end_hypothetical_protein_1670353..1670583_POSITIVE 319 217 171 215 168 NC_009009:SSA_1986|5end_Acetyltransferase,_GNAT_family,_putative_1982531..1982761_NEGATIVE 315 209 161 175 127 NC_009009:SSA_1712|5end_Arsenate_reductase_(ArsC),_glutaredoxin_family,_putative_1700084..1700314_NEGATIVE 313 207 162 157 108 NC_009009:SSA_0978|5end_hypothetical_protein_983736..983966_POSITIVE 296 215 177 54 11 NC_009009:SSA_0590|5end_hypothetical_protein_582144..582374_POSITIVE 291 204 162 152 99 NC_009009:SSA_0051|5end_Dihydroxyacetone_kinase_phosphotransfer_protein,_putative_55190..55420_POSITIVE 280 217 177 167 124 NC_009009:SSA_2059|5end_16S_rRNA_uridine-516_pseudouridylate_synthase,_putative_2061222..2061452_NEGATIVE 279 207 162 49 6 NC_009009:SSA_1984|5end_Cell_surface_SD_repeat_antigen_precursor,_putative_1979035..1979265_NEGATIVE 278 197 161 52 2 NC_009009:SSA_1551|5end_Transcriptional_accessory_ribonuclease_(YqgFc,_S1),_putative_1554784..1555014_NEGATIVE 276 220 173 183 128 NC_009009:SSA_2334|5end_D-alanine--D-alanyl_carrier_protein_ligase,_putative_2338007..2338237_NEGATIVE 276 218 177 70 41 NC_009009:SSA_1315|5end_hypothetical_protein_1332052..1332282_NEGATIVE 272 219 173 213 162 NC_009009:SSA_1151|5end_Thymidine_kinase,_putative_1180150..1180380_POSITIVE 269 193 165 211 178 NC_009009:SSA_1506|5end_Lipopolysaccharide_biosynthesis_protein,_putative_1511222..1511452_NEGATIVE 268 208 164 209 168 NC_009009:SSA_0494|5end_ABC-type_dipeptide/oligopeptide/nickel_transport_system,_ATPase_component,_putative_494407..494637_POSITIVE 268 217 174 158 117 NC_009009:SSA_0319|5end_Branched-chain_amino_acid_permease_(L-methionine,_L-isoleucine,_leucine_and_valine),_putative_312721..312951_POSITIVE 267 217 177 63 6 NC_009009:SSA_2060|5end_Arabinose_efflux_permease,_putative_2062403..2062633_NEGATIVE 265 203 161 151 99 NC_009009:SSA_1990|5end_Zn-porter_lipoprotein,_putative_1986319..1986549_NEGATIVE 264 215 177 87 44 NC_009009:SSA_0157|5end_hypothetical_protein_153513..153743_POSITIVE 260 217 171 189 142 NC_009009:SSA_1550|5end_hypothetical_protein_1552665..1552895_NEGATIVE 258 210 161 226 170 NC_009009:SSA_1424|5end_Hydrolase,_putative_1434479..1434709_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 315 209 161 50 2 NC_009009:SSA_1713|3end_D-3-phosphoglycerate_dehydrogenase,_putative_1700209..1700359_NEGATIVE 315 220 175 57 13 NC_009009:SSA_1325|3end_Ketoacyl_reductase_hetN,_putative_1341573..1341723_NEGATIVE 282 199 151 65 3 NC_009009:SSA_1651|3end_hypothetical_protein_1649587..1649737_NEGATIVE 282 200 151 145 89 NC_009009:SSA_0050|3end_Dihydroxyacetone_kinase,_phosphatase_domain_(Dak2),_putative_55270..55420_POSITIVE 270 193 155 148 103 NC_009009:SSA_0977|3end_3-isopropylmalate_dehydrogenase,_putative_983819..983969_POSITIVE 268 217 174 148 107 NC_009009:SSA_0318|3end_Secreted_metalloendopeptidase_Gcp_312791..312941_POSITIVE 265 203 161 130 78 NC_009009:SSA_1991|3end_Pneumococcal_histidine_triad_protein_A,_putative_1986340..1986490_NEGATIVE 265 206 163 58 2 NC_009009:SSA_1153|3end_HemK_protein,_putative_1182748..1182898_POSITIVE 265 195 163 60 28 NC_009009:SSA_1130|3end_Iron-dependent_peroxidase,_putative_1157090..1157240_POSITIVE 261 50 1 142 87 NC_009009:SSA_1496|3end_hypothetical_protein_1502473..1502623_NEGATIVE 260 216 171 145 90 NC_009009:SSA_1314|3end_Fe-S-cluster_oxidoreductase,_putative_1330746..1330896_NEGATIVE 257 49 1 115 68 NC_009009:SSA_1368|3end_hypothetical_protein_1383748..1383898_NEGATIVE 256 202 161 124 79 NC_009009:SSA_1595|3end_Tellurite_resistance,_putative_1600951..1601101_NEGATIVE 255 208 163 136 86 NC_009009:SSA_0428|3end_Formimidoylglutamase,_putative_427665..427815_NEGATIVE 253 220 173 84 17 NC_009009:SSA_1685|3end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_winged-helix_DNA-binding_domains),_putative_1678390..1678540_NEGATIVE 253 96 56 51 16 NC_009009:SSA_0218|3end_Sugar-binding_periplasmic_protein,_putative_215226..215376_POSITIVE 253 216 178 35 4 NC_009009:SSA_0160|3end_hypothetical_protein_159519..159669_POSITIVE 251 187 160 137 109 NC_009009:SSA_2325|3end_3-methyladenine_DNA_glycosylase,_putative_2330113..2330263_NEGATIVE 251 215 176 59 28 NC_009009:SSA_1323|3end_hypothetical_protein_1339788..1339938_NEGATIVE 250 218 180 62 34 NC_009009:SSA_1533|3end_Glutathione_reductase,_putative_1542212..1542362_POSITIVE