Origin IGS: taccttggggctgtggcttgcgttaagcaaaagccagacagcccctttttatatttcttatctatcatgacctattggggttactacgacccccaataggtcaataatcaataatcacaaaaaattcaatttttttcaaaaaactttgcatctgacctgccatttctccttagtaatagagcccaaaagaaatgaggtaactgcct .........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 aggcagttacctcatttcttttgggctctattactaaggagaaatggcaggtcagatgcaaagttttttgaaaaaaattgaattttttgtgattattgattattgacctattgggggtcgtagtaaccccaataggtcatgatagataagaaatataaaaaggggctgtctggcttttgcttaacgcaagccacagccccaaggta Mask Tandem Repeat Region ================================================ taccttggggctgtggcttgcgttaagcaaaagccagacagcccctttttatatttcttatctatcatgacctattggggttactacgacccccaataggtcaataatcaataatcacaaaaaattcaatttttttcaaaaaactttgcatctgacctgccatttctccttagtaatagagcccaaaagaaatgaggtaactgcct Find is-nt database================================================ Query_seq: SSA_2293:SSA_2294|SSA_2293:SSA_2294:hypothetical protein:hypothetical protein:->->:2296016..2296221 206 taccttggggctgtggcttgcgttaagcaaaagccagacagcccctttttatatttcttatctatcatgacctattggggttactacgacccccaataggtcaataatcaataatcacaaaaaattcaatttttttcaaaaaactttgcatctgacctgccatttctccttagtaatagagcccaaaagaaatgaggtaactgcct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2293:SSA_2294|SSA_2293:SSA_2294:hypothetical protein:hypothetical protein:->->:2296016..2296221 206 taccttggggctgtggcttgcgttaagcaaaagccagacagcccctttttatatttcttatctatcatgacctattggggttactacgacccccaataggtcaataatcaataatcacaaaaaattcaatttttttcaaaaaactttgcatctgacctgccatttctccttagtaatagagcccaaaagaaatgaggtaactgcct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2293:SSA_2294|SSA_2293:SSA_2294:hypothetical protein:hypothetical protein:->->:2296016..2296221 206 taccttggggctgtggcttgcgttaagcaaaagccagacagcccctttttatatttcttatctatcatgacctattggggttactacgacccccaataggtcaataatcaataatcacaaaaaattcaatttttttcaaaaaactttgcatctgacctgccatttctccttagtaatagagcccaaaagaaatgaggtaactgcct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taccttggggctgtggcttgcgttaagcaaaagccagacagcccctttttatatttcttatctatcatgacctattggggttactacgacccccaataggtcaataatcaataatcacaaaaaattcaatttttttcaaaaaactttgcatctgacctgccatttctccttagtaatagagcccaaaagaaatgaggtaactgcct Predict ORF larger than 30AA ================================================ Protein_Len: 44 Strand: + Start: 74 End: 205 ......................................................................... M G V T T T P N R S I I N N H K K F N F F Q K T L H L T C H F S L V I E P K R N E V T A . taccttggggctgtggcttgcgttaagcaaaagccagacagcccctttttatatttcttatctatcatgacctattggggttactacgacccccaataggtcaataatcaataatcacaaaaaattcaatttttttcaaaaaactttgcatctgacctgccatttctccttagtaatagagcccaaaagaaatgaggtaactgcct 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: 85 Start: 111 End: 140 ..............................................................................................................TTTGAAAAAAATTGAATTTTTTGTGATTAT.................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ PromScan Matrix: RpoN Strand: - Score: 83 Start: 147 End: 163 ..................................................................................................................................................ATGGCAGGTCAGATGCA........................................... taccttggggctgtggcttgcgttaagcaaaagccagacagcccctttttatatttcttatctatcatgacctattggggttactacgacccccaataggtcaataatcaataatcacaaaaaattcaatttttttcaaaaaactttgcatctgacctgccatttctccttagtaatagagcccaaaagaaatgaggtaactgcct Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_2293:SSA_2294|SSA_2293:SSA_2294:hypothetical protein:hypothetical protein:->->:2296016..2296221 206 taccttggggctgtggcttgcgttaagcaaaagccagacagcccctttttatatttcttatctatcatgacctattggggttactacgacccccaataggtcaataatcaataatcacaaaaaattcaatttttttcaaaaaactttgcatctgacctgccatttctccttagtaatagagcccaaaagaaatgaggtaactgcct Intra-Species Hit: Count: 1 Min: 1 Max: 206 Len: 206 Subject: NC_009009_SSA_2293_SSA_2294|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[2296016,2296221]|206 HSP 1 e-value: 1.0E-100 bit: 367.0 Len: 206 Query Start:1 Query End:206 Subject Strand: POSITIVE Subject Start: 1 Subject End: 206 taccttggggctgtggcttgcgttaagcaaaagccagacagcccctttttatatttcttatctatcatgacctattggggttactacgacccccaataggtcaataatcaataatcacaaaaaattcaannnnnnncaaaaaactttgcatctgacctgccatttctccttagtaatagagcccaaaagaaatgaggtaactgcct taccttggggctgtggcttgcgttaagcaaaagccagacagcccctttttatatttcttatctatcatgacctattggggttactacgacccccaataggtcaataatcaataatcacaaaaaattcaatttttttcaaaaaactttgcatctgacctgccatttctccttagtaatagagcccaaaagaaatgaggtaactgcct Inter-species Hit: Count: 3 Min: 3 Max: 206 Len: 204 Subject: NC_007432_SAK_2057_SAK_2058|hypothetical protein:plasmid replication protein|POSITIVE:POSITIVE|[2049651,2049855]|205 HSP 1 e-value: 5.0E-78 bit: 291.0 Len: 204 Query Start:3 Query End:206 Subject Strand: POSITIVE Subject Start: 3 Subject End: 205 ..ccttggggctgtggcttgcgttaagcaaaagccagacagcccctttttatatttcttatctatcatgacctattggggttactacgacccccaataggtcaataatcaataatcacaaaaaattcaannnnnnncaaaaaactttgcatctgacctgccatttctccttagtaatagagcccaaaagaaatgaggtaactgcct ..ccttggggctgtggcttgcgttaagcaaaagccagacagcccctttttatatt-cttttctatcatgacctattggggtgactacgacccccaataggtcaataatcaataatcacaaaaaattcaattttttcaaaaaaactttgcatacgacctgtcatttctccttagtaatagaacccaaaagaaatgaggtaactgcct Subject: NC_004368_gbs2070_gbs2071|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[2143626,2143830]|205 HSP 1 e-value: 1.0E-75 bit: 283.0 Len: 204 Query Start:3 Query End:206 Subject Strand: POSITIVE Subject Start: 3 Subject End: 205 ..ccttggggctgtggcttgcgttaagcaaaagccagacagcccctttttatatttcttatctatcatgacctattggggttactacgacccccaataggtcaataatcaataatcacaaaaaattcaannnnnnncaaaaaactttgcatctgacctgccatttctccttagtaatagagcccaaaagaaatgaggtaactgcct ..ccttggggctgtggcttgcgttaagcaaaagccagacagcccctttttatatt-cttttctatcatgacatattggggtgactacgacccccaataggtcaataatcaataatcacaaaaaattcaattttttcaaaaaaactttgcatacgacctgtcatttctccttagtaatagaacccaaaagaaatgaggtaactgcct Subject: NC_008022_MGAS10270_Spy1915_MGAS10270_Spy1916|hypothetical protein:Replication protein|POSITIVE:POSITIVE|[1866825,1867022]|198 HSP 1 e-value: 1.0E-53 bit: 210.0 Len: 204 Query Start:3 Query End:206 Subject Strand: POSITIVE Subject Start: 3 Subject End: 198 ..ccttggggctgtggcttgcgttaagcaaaagccagacagcccc-tttttatatt-tcttatctatcatgacctattggggttactacgacccccaataggtcaataatcaataatcacaaaaaattcaannnnnnncaaaaaactttgcatctgacctgccatttctccttagtaatagagcccaaaagaaatgaggtaactgcct ..ccttggggctgtggcttgcgttaagcaaaagccaaacagccccctttttttatgctctattctatcatgacctattggggttactacgacccccaataggtcaataatcaacaatcacaaaattttca---------aaaaaactttgcatttgacctgtcatttctccttagtaataga-accaaaagaaatgaggtaactgcct Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCUUGGGGCUGUGGCUUGCGUUAAGCAAAAGCCAGACAGCCCCUUUUUAUAUUUCUUAUCUAUCAUGACCUAUUGGGGUUACUACGACCCCCAAUAGGUCAAUAAUCAAUAAUCACAAAAAAUUCAAUUUUUUUCAAAAAACUUUGCAUCUGACCUGCCAUUUCUCCUUAGUAAUAGAGCCCAAAAGAAAUGAGGUAACUGCCU ....(((((((((((((((.....)))..))))..))))))))......................(((((((((((((..........)))))))))))))...............((((((......))))))...........(((....((((..(((((((.....((......)).....)))))))))))...))).. (-58.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGGCAGUUACCUCAUUUCUUUUGGGCUCUAUUACUAAGGAGAAAUGGCAGGUCAGAUGCAAAGUUUUUUGAAAAAAAUUGAAUUUUUUGUGAUUAUUGAUUAUUGACCUAUUGGGGGUCGUAGUAACCCCAAUAGGUCAUGAUAGAUAAGAAAUAUAAAAAGGGGCUGUCUGGCUUUUGCUUAACGCAAGCCACAGCCCCAAGG ..(((...((((((((((((((.((........)).))))))))))..))))....)))..(((((((....)))))))....((((((((.(((((.(((((.((((((((((((..........))))))))))))))))).)))))....))))))))((((((((..((((..(((.....))))))))))))))).... (-71.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 355 182 143 229 183 NC_009009:SSA_1003|5end_ABC_transporter_substrate-binding_protein-multiple_sugars,_putative_1003875..1004105_POSITIVE 347 43 4 228 172 NC_009009:SSA_2060|5end_Arabinose_efflux_permease,_putative_2062403..2062633_NEGATIVE 345 43 2 49 7 NC_009009:SSA_0210|5end_hypothetical_protein_207757..207987_POSITIVE 337 42 5 65 30 NC_009009:SSA_0388|5end_Mismatch_repair_ATPase_(MutS_family),_putative_382474..382704_POSITIVE 333 50 2 168 113 NC_009009:SSA_2346|5end_3-oxoacyl-[acyl-carrier-protein]_synthase_III,_putative_2348546..2348776_NEGATIVE 320 45 1 200 155 NC_009009:SSA_1560|5end_Structural_maintenance_of_chromosome_protein_(chromosome_segregation_ATPase),_putative_1565194..1565424_NEGATIVE 305 44 4 71 24 NC_009009:SSA_1429|5end_hypothetical_protein_1437110..1437340_NEGATIVE 299 47 11 42 12 NC_009009:SSA_0087|5end_V-type_sodium_ATPase,_subunit_E,_putative_88329..88559_POSITIVE 297 44 1 225 178 NC_009009:SSA_2000|5end_hypothetical_protein_1997469..1997699_NEGATIVE 297 44 1 191 154 NC_009009:SSA_1483|5end_Sphingosine_kinase_(diacylglycerol_kinase),_putative_1490220..1490450_NEGATIVE 294 40 1 40 4 NC_009009:SSA_0218|5end_Sugar-binding_periplasmic_protein,_putative_213863..214093_POSITIVE 289 48 2 187 134 NC_009009:SSA_0504|5end_Peptide_ABC_transporter,_ATP-binding_protein,_putative_503009..503239_POSITIVE 288 177 144 199 156 NC_009009:SSA_0362|5end_Thioredoxin,_putative_353290..353520_POSITIVE 286 46 5 151 108 NC_009009:SSA_0500|5end_Peptide_ABC_transporter,_permease_protein,_putative_500503..500733_POSITIVE 285 189 146 223 179 NC_009009:SSA_0792|5end_hypothetical_protein_774618..774848_POSITIVE 282 50 1 158 99 NC_009009:SSA_0692|5end_D-Ala-D-Ala_adding_enzyme,_putative_676370..676600_POSITIVE 282 43 6 179 143 NC_009009:SSA_0179|5end_hypothetical_protein_183966..184196_POSITIVE 281 40 5 227 191 NC_009009:SSA_2281|5end_hypothetical_protein_2282370..2282600_NEGATIVE 281 42 1 214 168 NC_009009:SSA_1721|5end_DNA_polymerase_III,_delta'_subunit,_putative_1708028..1708258_NEGATIVE 281 41 3 46 2 NC_009009:SSA_1481|5end_FmtA-like_protein,_putative_1486622..1486852_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 481 43 5 84 46 NC_009009:SSA_2293|3end_hypothetical_protein_2295955..2296105_POSITIVE 370 60 13 102 37 NC_009009:SSA_1309|3end_RNA-binding_protein_(KH_domain),_putative_1327079..1327229_NEGATIVE 333 50 2 67 12 NC_009009:SSA_2347|3end_Coenzyme_F390_synthetase,_putative_2348647..2348797_NEGATIVE 305 44 4 74 27 NC_009009:SSA_1430|3end_Ribonuclease_Z,_putative_1437107..1437257_NEGATIVE 299 47 11 31 1 NC_009009:SSA_0086|3end_V-type_sodium_ATPase,_subunit_K,_putative_88398..88548_POSITIVE 294 40 1 43 7 NC_009009:SSA_0217|3end_Two-component_system_transcriptional_regulator_(CheY_domain_and_HTH-like_DNA-binding_domain),_putative_213946..214096_POSITIVE 286 46 5 59 16 NC_009009:SSA_0499|3end_ABC-type_dipeptide_transport_system,_periplasmic_component,_putative_500491..500641_POSITIVE 282 50 1 82 23 NC_009009:SSA_0691|3end_D-ala,D-ala_ligase,_putative_676374..676524_POSITIVE 282 46 1 66 21 NC_009009:SSA_0525|3end_Microcompartment_protein,_putative_523842..523992_POSITIVE 281 40 2 145 110 NC_009009:SSA_0592|3end_hypothetical_protein_584248..584398_POSITIVE 279 47 5 115 54 NC_009009:SSA_1743|3end_ABC-type_Fe3+-siderophore_transport_system,_permease_component,_putative_1731005..1731155_POSITIVE 279 58 14 93 38 NC_009009:SSA_0355|3end_DNA_mismatch_repair_protein,_putative_349260..349410_POSITIVE 278 42 2 140 90 NC_009009:SSA_0272|3end_Oxidoreductase,_aldo/keto_reductase_family,_putative_267032..267182_POSITIVE 277 43 1 53 1 NC_009009:SSA_2393|3end_Transcriptional_regulator,_XRE_family,_putative_204339..204489_POSITIVE 275 109 62 123 88 NC_009009:SSA_1013|3end_Phosphatidylserine_synthase,_putative_1017933..1018083_POSITIVE 274 43 12 25 2 NC_009009:SSA_1002|3end_Alpha-galactosidase,_putative_1003942..1004092_POSITIVE 273 48 2 79 28 NC_009009:SSA_2357|3end_50S_ribosomal_protein_L9,_putative_2357985..2358135_NEGATIVE 272 45 2 69 33 NC_009009:SSA_0733|3end_hypothetical_protein_716937..717087_POSITIVE 271 42 4 60 28 NC_009009:SSA_2217|3end_Cps9H,_putative_2218086..2218236_NEGATIVE 267 43 8 75 21 NC_009009:SSA_1130|3end_Iron-dependent_peroxidase,_putative_1157090..1157240_POSITIVE