Origin IGS: actagcctcctctgctttttattttattatactatttttgctcttaaaatgcttcctaaccccaaaaaacaagcgcagcctcgcgcttgtttttctattttatgttaaaataaaaggt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 accttttattttaacataaaatagaaaaacaagcgcgaggctgcgcttgttttttggggttaggaagcattttaagagcaaaaatagtataataaaataaaaagcagaggaggctagt Mask Tandem Repeat Region ================================================ actagcctcctctgctttttattttattatactatttttgctcttaaaatgcttcctaaccccaaaaaacaagcgcagcctcgcgcttgtttttctattttatgttaaaataaaaggt Find is-nt database================================================ Query_seq: SSA_2189:SSA_2190|SSA_2189:SSA_2190:hypothetical protein:33 kDa chaperonin, putative:<-->:2191188..2191305 118 actagcctcctctgctttttattttattatactatttttgctcttaaaatgcttcctaaccccaaaaaacaagcgcagcctcgcgcttgtttttctattttatgttaaaataaaaggt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2189:SSA_2190|SSA_2189:SSA_2190:hypothetical protein:33 kDa chaperonin, putative:<-->:2191188..2191305 118 actagcctcctctgctttttattttattatactatttttgctcttaaaatgcttcctaaccccaaaaaacaagcgcagcctcgcgcttgtttttctattttatgttaaaataaaaggt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2189:SSA_2190|SSA_2189:SSA_2190:hypothetical protein:33 kDa chaperonin, putative:<-->:2191188..2191305 118 actagcctcctctgctttttattttattatactatttttgctcttaaaatgcttcctaaccccaaaaaacaagcgcagcctcgcgcttgtttttctattttatgttaaaataaaaggt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 actagcctcctctgctttttattttattatactatttttgctcttaaaatgcttcctaaccccaaaaaacaagcgcagcctcgcgcttgtttttctattttatgttaaaataaaaggt Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 26 End: 118 ......................... M I L F L L L K C F L T P K N K R S L A L V F L F Y V K I K G actagcctcctctgctttttattttattatactatttttgctcttaaaatgcttcctaaccccaaaaaacaagcgcagcctcgcgcttgtttttctattttatgttaaaataaaaggt 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================================================ actagcctcctctgctttttattttattatactatttttgctcttaaaatgcttcctaaccccaaaaaacaagcgcagcctcgcgcttgtttttctattttatgttaaaataaaaggt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 85 HP_score: -10.3 Tail_Score: -3.94773 Start: 64 End: 95 Full_Region: ATGCTTCCTAACCCC AAAAAACAAGCGC AGCCTC GCGCTTGTTTTTC TATTTTATGTTAAAA ...............................................................AAAAAACAAGCGCAGCCTCGCGCTTGTTTTTC....................... TransTerm Strand: + Conf: 100 HP_score: -9.3 Tail_Score: -5.32599 Start: 70 End: 89 Full_Region: CCTAACCCCAAAAAA CAAGCGC AGCCTC GCGCTTG TTTTTCTATTTTATG .....................................................................CAAGCGCAGCCTCGCGCTTG............................. Find igs database================================================ Query_seq: SSA_2189:SSA_2190|SSA_2189:SSA_2190:hypothetical protein:33 kDa chaperonin, putative:<-->:2191188..2191305 118 actagcctcctctgctttttattttattatactatttttgctcttaaaatgcttcctaaccccaaaaaacaagcgcagcctcgcgcttgtttttctattttatgttaaaataaaaggt Intra-Species Hit: Count: 1 Min: 1 Max: 118 Len: 118 Subject: NC_009009_SSA_2189_SSA_2190|hypothetical protein:33 kDa chaperonin, putative|NEGATIVE:POSITIVE|[2191188,2191305]|118 HSP 1 e-value: 5.0E-61 bit: 234.0 Len: 118 Query Start:1 Query End:118 Subject Strand: POSITIVE Subject Start: 1 Subject End: 118 actagcctcctctgctttttattttattatactatttttgctcttaaaatgcttcctaaccccaaaaaacaagcgcagcctcgcgcttgtttttctattttatgttaaaataaaaggt actagcctcctctgctttttattttattatactatttttgctcttaaaatgcttcctaaccccaaaaaacaagcgcagcctcgcgcttgtttttctattttatgttaaaataaaaggt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUAGCCUCCUCUGCUUUUUAUUUUAUUAUACUAUUUUUGCUCUUAAAAUGCUUCCUAACCCCAAAAAACAAGCGCAGCCUCGCGCUUGUUUUUCUAUUUUAUGUUAAAAUAAAAGGU .............(((((((((((((.((((........((.........))............((((((((((((......))))))))))))......)))).))))))))))))) (-27.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACCUUUUAUUUUAACAUAAAAUAGAAAAACAAGCGCGAGGCUGCGCUUGUUUUUUGGGGUUAGGAAGCAUUUUAAGAGCAAAAAUAGUAUAAUAAAAUAAAAAGCAGAGGAGGCUAGU .((((((.(((((((........((((((((((((((....))))))))))))))...))))))).((.(((((.......................))))).))..))))))..... (-26.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 964 90 41 181 132 NC_009009:SSA_2189|5end_hypothetical_protein_2191097..2191327_NEGATIVE 363 96 51 87 43 NC_009009:SSA_0554|5end_hypothetical_protein_549265..549495_POSITIVE 311 80 37 47 1 NC_009009:SSA_0210|5end_hypothetical_protein_207757..207987_POSITIVE 304 97 54 177 114 NC_009009:SSA_0596|5end_hypothetical_protein_586913..587143_POSITIVE 292 101 63 185 140 NC_009009:SSA_1243|5end_Dihydroorotate_dehydrogenase_electron_transfer_subunit,_putative_1268204..1268434_NEGATIVE 288 89 47 138 92 NC_009009:SSA_1196|5end_Acetyltransferase,_GNAT_family,_putative_1222052..1222282_NEGATIVE 285 85 52 231 192 NC_009009:SSA_0273|5end_hypothetical_protein_267071..267301_POSITIVE 283 100 51 142 93 NC_009009:SSA_1049|5end_ABC_transporter_membrane-spanning_permease-spermidine/putrescine_transport,_putative_1064085..1064315_POSITIVE 275 86 49 60 25 NC_009009:SSA_1454|5end_hypothetical_protein_1461100..1461330_NEGATIVE 274 63 21 79 45 NC_009009:SSA_1254|5end_hypothetical_protein_1281484..1281714_NEGATIVE 270 75 32 123 72 NC_009009:SSA_1294|5end_hypothetical_protein_1312581..1312811_NEGATIVE 264 91 63 201 175 NC_009009:SSA_1561|5end_Ribonuclease_III,_putative_1565883..1566113_NEGATIVE 257 106 62 80 31 NC_009009:SSA_2364|5end_Immunodominant_staphylococcal_antigen_A_precursor,_putative_2367032..2367262_NEGATIVE 256 98 51 136 94 NC_009009:SSA_1493|5end_hypothetical_protein_1499480..1499710_NEGATIVE 256 89 41 70 9 NC_009009:SSA_1417|5end_SAM-dependent_methyltransferase,_putative_1427993..1428223_NEGATIVE 252 106 61 55 5 NC_009009:SSA_1383|5end_Aspartate_aminotransferase,_putative_1401718..1401948_NEGATIVE 250 98 51 91 42 NC_009009:SSA_2168|5end_Glycerol-3-phosphate_dehydrogenase_[NAD(P)+],_putative_2167461..2167691_POSITIVE 250 86 51 48 11 NC_009009:SSA_0893|5end_ATP-binding_cassette_transporter-like_protein,_putative_884527..884757_POSITIVE 249 97 51 203 161 NC_009009:SSA_0226|5end_60_kDa_chaperonin_218947..219177_POSITIVE 248 100 71 203 176 NC_009009:SSA_0703|5end_Citrate_synthase,_putative_688154..688384_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 363 96 51 83 39 NC_009009:SSA_0553|3end_hypothetical_protein_549341..549491_POSITIVE 361 108 61 133 75 NC_009009:SSA_0272|3end_Oxidoreductase,_aldo/keto_reductase_family,_putative_267032..267182_POSITIVE 288 89 47 141 95 NC_009009:SSA_1197|3end_DNA_alkylation_repair_enzyme,_putative_1222049..1222199_NEGATIVE 274 63 21 107 73 NC_009009:SSA_1255|3end_hypothetical_protein_1281456..1281606_NEGATIVE 270 75 32 122 71 NC_009009:SSA_1296|3end_hypothetical_protein_1312582..1312732_NEGATIVE 267 94 58 92 53 NC_009009:SSA_1030|3end_Transcriptional_regulator,_TetR_family,_putative_1047749..1047899_POSITIVE 264 91 63 79 53 NC_009009:SSA_1562|3end_hypothetical_protein_1566005..1566155_NEGATIVE 256 98 51 102 60 NC_009009:SSA_1494|3end_Conserved_uncharacterized_protein_1499514..1499664_NEGATIVE 253 56 12 148 99 NC_009009:SSA_2321|3end_Cation_(Co/Zn/Cd)_efflux_protein,_putative_2326050..2326200_NEGATIVE 253 100 65 86 56 NC_009009:SSA_0571|3end_Aspartyl/glutamyl-tRNA(Asn/Gln)_amidotransferase_subunit_B,_putative_566894..567044_POSITIVE 252 106 61 58 8 NC_009009:SSA_1384|3end_hypothetical_protein_1401715..1401865_NEGATIVE 249 89 50 60 15 NC_009009:SSA_2239|3end_Conserved_uncharacterized_cytosolic_protein_2236922..2237072_NEGATIVE 244 95 62 99 55 NC_009009:SSA_1309|3end_RNA-binding_protein_(KH_domain),_putative_1327079..1327229_NEGATIVE 240 79 32 102 54 NC_009009:SSA_0049|3end_Dihydroxyacetone_kinase_(Dak1),_putative_54681..54831_POSITIVE 239 77 34 87 45 NC_009009:SSA_2119|3end_Pentose-5-phosphate-3-epimerase,_putative_2120439..2120589_NEGATIVE 239 84 59 70 35 NC_009009:SSA_1050|3end_ABC_transporter_membrane-spanning_permease-spermidine/putrescine_transport,_putative_1065741..1065891_POSITIVE 238 44 8 32 2 NC_009009:SSA_1796|3end_Transcription_elongation_factor_GreA,_putative_1777825..1777975_NEGATIVE 236 90 49 90 39 NC_009009:SSA_0679|3end_DNA_repair_and_genetic_recombination,_putative_662452..662602_POSITIVE 236 87 48 140 104 NC_009009:SSA_0593|3end_Rhodanese-like_sulfurtransferase,_putative_585551..585701_POSITIVE 236 84 42 151 112 NC_009009:SSA_0485|3end_Porphobilinogen_deaminase,_putative_486732..486882_POSITIVE