Origin IGS: gaatctcctttctttcgaacaatagactcagtacgcaaaagaaccacatccgacagtcctaggctattcacctaggggcgtcaagacgcggttccaccctaatttattacttcattacttttgaaattataaccgaaagcgccatctgcactgcttccctatccggctcacactatcccgaactcgctaaaaagtagacaatgagaattctttctaaaaaagattatagcagaaaatagggccaatgtaaaatacttatcgaaaaatccctcaagtttcaacttaagggattttaactgacttgaaaaccaa .........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 ttggttttcaagtcagttaaaatcccttaagttgaaacttgagggatttttcgataagtattttacattggccctattttctgctataatcttttttagaaagaattctcattgtctactttttagcgagttcgggatagtgtgagccggatagggaagcagtgcagatggcgctttcggttataatttcaaaagtaatgaagtaataaattagggtggaaccgcgtcttgacgcccctaggtgaatagcctaggactgtcggatgtggttcttttgcgtactgagtctattgttcgaaagaaaggagattc Mask Tandem Repeat Region ================================================ gaatctcctttctttcgaacaatagactcagtacgcaaaagaaccacatccgacagtcctaggctattcacctaggggcgtcaagacgcggttccaccctaatttattacttcattacttttgaaattataaccgaaagcgccatctgcactgcttccctatccggctcacactatcccgaactcgctaaaaagtagacaatgagaattctttctaaaaaagattatagcagaaaatagggccaatgtaaaatacttatcgaaaaatccctcaagtttcaacttaagggattttaactgacttgaaaaccaa Find is-nt database================================================ Query_seq: SSA_1881:SSA_1882|SSA_1881:SSA_1882:hypothetical protein:Subtilisin-like serine proteases, putative:<-<-:1876055..1876366 312 gaatctcctttctttcgaacaatagactcagtacgcaaaagaaccacatccgacagtcctaggctattcacctaggggcgtcaagacgcggttccaccctaatttattacttcattacttttgaaattataaccgaaagcgccatctgcactgcttccctatccggctcacactatcccgaactcgctaaaaagtagacaatgagaattctttctaaaaaagattatagcagaaaatagggccaatgtaaaatacttatcgaaaaatccctcaagtttcaacttaagggattttaactgacttgaaaaccaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1881:SSA_1882|SSA_1881:SSA_1882:hypothetical protein:Subtilisin-like serine proteases, putative:<-<-:1876055..1876366 312 gaatctcctttctttcgaacaatagactcagtacgcaaaagaaccacatccgacagtcctaggctattcacctaggggcgtcaagacgcggttccaccctaatttattacttcattacttttgaaattataaccgaaagcgccatctgcactgcttccctatccggctcacactatcccgaactcgctaaaaagtagacaatgagaattctttctaaaaaagattatagcagaaaatagggccaatgtaaaatacttatcgaaaaatccctcaagtttcaacttaagggattttaactgacttgaaaaccaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1881:SSA_1882|SSA_1881:SSA_1882:hypothetical protein:Subtilisin-like serine proteases, putative:<-<-:1876055..1876366 312 gaatctcctttctttcgaacaatagactcagtacgcaaaagaaccacatccgacagtcctaggctattcacctaggggcgtcaagacgcggttccaccctaatttattacttcattacttttgaaattataaccgaaagcgccatctgcactgcttccctatccggctcacactatcccgaactcgctaaaaagtagacaatgagaattctttctaaaaaagattatagcagaaaatagggccaatgtaaaatacttatcgaaaaatccctcaagtttcaacttaagggattttaactgacttgaaaaccaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gaatctcctttctttcgaacaatagactcagtacgcaaaagaaccacatccgacagtcctaggctattcacctaggggcgtcaagacgcggttccaccctaatttattacttcattacttttgaaattataaccgaaagcgccatctgcactgcttccctatccggctcacactatcccgaactcgctaaaaagtagacaatgagaattctttctaaaaaagattatagcagaaaatagggccaatgtaaaatacttatcgaaaaatccctcaagtttcaacttaagggattttaactgacttgaaaaccaa Predict ORF larger than 30AA ================================================ Protein_Len: 43 Strand: + Start: 66 End: 194 ................................................................. M H L G A S R R G S T L I Y Y F I T F E I I T E S A I C T A S L S G S H Y P E L A K K ...................................................................................................................... Protein_Len: 37 Strand: - Start: 171 End: 281 .......................................................................................................................................................................... V I G F E S F L L C H S N K R F F I I A S F L A L T F Y K D F F G E L K M ............................... gaatctcctttctttcgaacaatagactcagtacgcaaaagaaccacatccgacagtcctaggctattcacctaggggcgtcaagacgcggttccaccctaatttattacttcattacttttgaaattataaccgaaagcgccatctgcactgcttccctatccggctcacactatcccgaactcgctaaaaagtagacaatgagaattctttctaaaaaagattatagcagaaaatagggccaatgtaaaatacttatcgaaaaatccctcaagtttcaacttaagggattttaactgacttgaaaaccaa 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: 223 End: 252 ..............................................................................................................................................................................................................................TTTTACATTGGCCCTATTTTCTGCTATAAT............................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gaatctcctttctttcgaacaatagactcagtacgcaaaagaaccacatccgacagtcctaggctattcacctaggggcgtcaagacgcggttccaccctaatttattacttcattacttttgaaattataaccgaaagcgccatctgcactgcttccctatccggctcacactatcccgaactcgctaaaaagtagacaatgagaattctttctaaaaaagattatagcagaaaatagggccaatgtaaaatacttatcgaaaaatccctcaagtttcaacttaagggattttaactgacttgaaaaccaa Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 77 HP_score: -8.2 Tail_Score: -4.21462 Start: 41 End: 94 Full_Region: taataaattagggtg gaaccgcgtcttgacgcccctaggt gaata gcctaggactgtcggatgtggttc ttttgcgtactgagt ........................................gaaccgcgtcttgacgcccctaggtgaatagcctaggactgtcggatgtggttc.......................................................................................................................................................................................................................... TransTerm Strand: - Conf: 61 HP_score: -4.1 Tail_Score: -4.22883 Start: 44 End: 91 Full_Region: taaattagggtggaa ccgcgtcttgacgcccctaggt gaata gcctaggactgtcggatgtgg ttcttttgcgtactg ...........................................ccgcgtcttgacgcccctaggtgaatagcctaggactgtcggatgtgg............................................................................................................................................................................................................................. TransTerm Strand: + Conf: 77 HP_score: -8.2 Tail_Score: -4.21275 Start: 267 End: 290 Full_Region: ATACTTATCGAAAAA TCCCTCAAGT TTCA ACTTAAGGGA TTTTAACTGACTTGA ..........................................................................................................................................................................................................................................................................TCCCTCAAGTTTCAACTTAAGGGA...................... Find igs database================================================ Query_seq: SSA_1881:SSA_1882|SSA_1881:SSA_1882:hypothetical protein:Subtilisin-like serine proteases, putative:<-<-:1876055..1876366 312 gaatctcctttctttcgaacaatagactcagtacgcaaaagaaccacatccgacagtcctaggctattcacctaggggcgtcaagacgcggttccaccctaatttattacttcattacttttgaaattataaccgaaagcgccatctgcactgcttccctatccggctcacactatcccgaactcgctaaaaagtagacaatgagaattctttctaaaaaagattatagcagaaaatagggccaatgtaaaatacttatcgaaaaatccctcaagtttcaacttaagggattttaactgacttgaaaaccaa Intra-Species Hit: Count: 1 Min: 1 Max: 312 Len: 312 Subject: NC_009009_SSA_1881_SSA_1882|hypothetical protein:Subtilisin-like serine proteases, putative|NEGATIVE:NEGATIVE|[1876055,1876366]|312 HSP 1 e-value: 1.0E-176 bit: 618.0 Len: 312 Query Start:1 Query End:312 Subject Strand: POSITIVE Subject Start: 1 Subject End: 312 gaatctcctttctttcgaacaatagactcagtacgcaaaagaaccacatccgacagtcctaggctattcacctaggggcgtcaagacgcggttccaccctaatttattacttcattacttttgaaattataaccgaaagcgccatctgcactgcttccctatccggctcacactatcccgaactcgctaaaaagtagacaatgagaattctttctaaaaaagattatagcagaaaatagggccaatgtaaaatacttatcgaaaaatccctcaagtttcaacttaagggattttaactgacttgaaaaccaa gaatctcctttctttcgaacaatagactcagtacgcaaaagaaccacatccgacagtcctaggctattcacctaggggcgtcaagacgcggttccaccctaatttattacttcattacttttgaaattataaccgaaagcgccatctgcactgcttccctatccggctcacactatcccgaactcgctaaaaagtagacaatgagaattctttctaaaaaagattatagcagaaaatagggccaatgtaaaatacttatcgaaaaatccctcaagtttcaacttaagggattttaactgacttgaaaaccaa Inter-species Hit: Count: 3 Min: 4 Max: 144 Len: 141 Subject: NC_008533_SPD_1307_SPD_1308|hypothetical protein:oxidoreductase, aldo/keto reductase family protein|NEGATIVE:NEGATIVE|[1326033,1326304]|272 HSP 1 e-value: 4.0E-24 bit: 113.0 Len: 141 Query Start:4 Query End:144 Subject Strand: POSITIVE Subject Start: 4 Subject End: 147 ...tctcctttctttcgaacaatagactcagtacgcaaaagaaccacatccgacagtcctaggcta--ttcacctaggggcgtca-agacgcggttccaccctaatttattacttcattacttttgaaattataaccgaaagcgcca........................................................................................................................................................................ ...tctcctttctttcacacaatagactgaataagcaaaagaaccacatctgacaatcctaggttgatttaacctaggggcgtcagaaacgcggttccaccctaatttattacttcattgtttttgaaaatactacagaaagcgcca........................................................................................................................................................................ Subject: NC_003098_spr1331_spr1332|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[1318520,1318773]|254 HSP 1 e-value: 6.0E-20 bit: 99.6 Len: 126 Query Start:19 Query End:144 Subject Strand: POSITIVE Subject Start: 1 Subject End: 129 ..................acaatagactcagtacgcaaaagaaccacatccgacagtcctaggcta--ttcacctaggggcgtca-agacgcggttccaccctaatttattacttcattacttttgaaattataaccgaaagcgcca........................................................................................................................................................................ ..................acaatagactgaataagcaaaagaaccacatctgacaatcctaggttgatttaacctaggggcgtcagaaacgcggttccaccctaatttattacttcattgtttttgaaaatactacagaaagcgcca........................................................................................................................................................................ Subject: NC_003028_SP_1477_SP_1478|hypothetical protein:oxidoreductase, aldo/keto reductase family|NEGATIVE:NEGATIVE|[1390891,1391144]|254 HSP 1 e-value: 6.0E-20 bit: 99.6 Len: 126 Query Start:19 Query End:144 Subject Strand: POSITIVE Subject Start: 1 Subject End: 129 ..................acaatagactcagtacgcaaaagaaccacatccgacagtcctaggcta--ttcacctaggggcgtca-agacgcggttccaccctaatttattacttcattacttttgaaattataaccgaaagcgcca........................................................................................................................................................................ ..................acaatagactgaataagcaaaagaaccacatctgacaatcctaggttgatttaacctaggggcgtcagaaacgcggttccaccctaatttattacttcattgtttttgaaaatactacagaaagcgcca........................................................................................................................................................................ Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUCCUUUCUUUCGAACAAUAGACUCAGUACGCAAAAGAACCACAUCCGACAGUCCUAGGCUAUUCACCUAGGGGCGUCAAGACGCGGUUCCACCCUAAUUUAUUACUUCAUUACUUUUGAAAUUAUAACCGAAAGCGCCA ........((((((.......................(((((.(.((.(((..(((((((.......)))))))..)))..)).).))))).........((((...((((.......))))...)))).))))))..... (-28.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGGCGCUUUCGGUUAUAAUUUCAAAAGUAAUGAAGUAAUAAAUUAGGGUGGAACCGCGUCUUGACGCCCCUAGGUGAAUAGCCUAGGACUGUCGGAUGUGGUUCUUUUGCGUACUGAGUCUAUUGUUCGAAAGAAAGGAGA ..((((......((((.((((((.......)))))).))))........((((((((((((.((((..(((((((.....)))))))..))))))))))))))))...))))......(((....(((....)))...))) (-48.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1085 90 41 184 135 NC_009009:SSA_1881|5end_hypothetical_protein_1875964..1876194_NEGATIVE 432 96 52 167 117 NC_009009:SSA_1821|5end_Acetyltransferase_(N-acetylase_of_ribosomal_proteins),_putative_1810610..1810840_NEGATIVE 402 86 42 213 166 NC_009009:SSA_2197|5end_hypothetical_protein_2197784..2198014_NEGATIVE 354 97 53 196 145 NC_009009:SSA_1746|5end_hypothetical_protein_1732945..1733175_NEGATIVE 353 92 51 67 22 NC_009009:SSA_0747|5end_DD-carboxypeptidase,_putative_727936..728166_POSITIVE 341 88 41 229 169 NC_009009:SSA_2324|5end_hypothetical_protein_2330109..2330339_NEGATIVE 341 98 54 73 30 NC_009009:SSA_2141|5end_Argininosuccinate_lyase,_putative_2142201..2142431_NEGATIVE 336 120 71 191 136 NC_009009:SSA_0755|5end_hypothetical_protein_736212..736442_POSITIVE 333 90 41 219 160 NC_009009:SSA_1491|5end_Methionine_aminopeptidase_A,_putative_1497637..1497867_NEGATIVE 332 104 66 46 4 NC_009009:SSA_1572|5end_hypothetical_protein_1575908..1576138_NEGATIVE 329 115 72 60 25 NC_009009:SSA_0063|5end_Holliday_junction_DNA_helicase_ruvB,_putative_65335..65565_POSITIVE 327 100 51 59 12 NC_009009:SSA_0321|5end_Methylase,_putative_313867..314097_POSITIVE 324 107 72 163 130 NC_009009:SSA_1925|5end_Seryl-tRNA_synthetase,_putative_1913508..1913738_POSITIVE 324 90 41 165 96 NC_009009:SSA_1429|5end_hypothetical_protein_1437110..1437340_NEGATIVE 316 88 48 198 161 NC_009009:SSA_0043|5end_hypothetical_protein_48801..49031_POSITIVE 315 94 52 142 97 NC_009009:SSA_2316|5end_General_secretory_pathway_protein_F,_putative_2318342..2318572_NEGATIVE 315 93 54 132 92 NC_009009:SSA_1208|5end_23S_rRNA_pseudouridine_synthase,_putative_1233185..1233415_NEGATIVE 313 97 52 211 160 NC_009009:SSA_0863|5end_Cof_family_protein,_putative_855015..855245_NEGATIVE 310 90 42 71 22 NC_009009:SSA_1454|5end_hypothetical_protein_1461100..1461330_NEGATIVE 309 96 58 199 169 NC_009009:SSA_1306|5end_Trk_transporter_NAD+_binding_protein-K+_transport,_putative_1324910..1325140_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 371 80 32 151 99 NC_009009:SSA_2198|3end_hypothetical_protein_2197842..2197992_NEGATIVE 354 98 51 145 99 NC_009009:SSA_2074|3end_Preprotein_translocase_subunit_YajC,_putative_2076600..2076750_NEGATIVE 341 98 54 58 15 NC_009009:SSA_2142|3end_Argininosuccinate_synthase,_putative_2142216..2142366_NEGATIVE 315 94 52 138 93 NC_009009:SSA_2317|3end_Tfp_pilus_assembly_protein,_pilus_retraction_ATPase_PilT,_putative_2318346..2318496_NEGATIVE 315 93 54 135 95 NC_009009:SSA_1209|3end_Inorganic_polyphosphate/ATP-NAD_kinase,_putative_1233182..1233332_NEGATIVE 305 88 47 64 16 NC_009009:SSA_2337|3end_hypothetical_protein_2339359..2339509_POSITIVE 304 97 56 148 111 NC_009009:SSA_0593|3end_Rhodanese-like_sulfurtransferase,_putative_585551..585701_POSITIVE 301 95 51 49 2 NC_009009:SSA_2060|3end_Arabinose_efflux_permease,_putative_2061234..2061384_NEGATIVE 291 98 51 74 31 NC_009009:SSA_0297|3end_Malolactic_enzyme,_putative_291411..291561_POSITIVE 289 100 52 70 29 NC_009009:SSA_1066|3end_ABC-type_oligopeptide_transport_system,_putative_1086376..1086526_POSITIVE 288 86 41 134 86 NC_009009:SSA_1267|3end_crcB-like_protein_2,_putative_1290973..1291123_NEGATIVE 287 95 51 129 83 NC_009009:SSA_0221|3end_PTS_system,_mannose-specific_IIC_component,_putative_217295..217445_POSITIVE 284 95 51 56 8 NC_009009:SSA_2241|3end_Conserved_uncharacterized_protein_2237677..2237827_NEGATIVE 284 89 41 52 1 NC_009009:SSA_0463|3end_Cobyrinic_acid_A,C-diamide_synthase,_putative_468303..468453_POSITIVE 282 88 46 143 105 NC_009009:SSA_0576|3end_Conserved_GTPase,_putative_571225..571375_POSITIVE 281 90 43 67 19 NC_009009:SSA_0870|3end_Cell_division_protein_FtsE,_putative_863708..863858_POSITIVE 280 94 52 148 93 NC_009009:SSA_1651|3end_hypothetical_protein_1649587..1649737_NEGATIVE 274 97 51 59 7 NC_009009:SSA_0469|3end_Precorrin-6B_methylase_2,putative_472959..473109_POSITIVE 273 61 24 47 14 NC_009009:SSA_1467|3end_Chorismate_synthase,_putative_1473127..1473277_NEGATIVE 272 97 53 75 8 NC_009009:SSA_1903|3end_hypothetical_protein_1897388..1897538_NEGATIVE