Origin IGS: ctttacatagctgtcaatctagataagattgttccctttaaatctttatctacactatcattttctgcttataacaaaaaaccacagaaatctgtggttttttatttctatc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gatagaaataaaaaaccacagatttctgtggttttttgttataagcagaaaatgatagtgtagataaagatttaaagggaacaatcttatctagattgacagctatgtaaag Mask Tandem Repeat Region ================================================ ctttacatagctgtcaatctagataagattgttccctttaaatctttatctacactatcattttctgcttataacaaaaaaccacagaaatctgtggttttttatttctatc Find is-nt database================================================ Query_seq: SSA_2363:SSA_2364|SSA_2363:SSA_2364:Phosphoglycolate phosphatase, putative:Immunodominant staphylococcal antigen A precursor, putative:-><-:2366420..2366531 112 ctttacatagctgtcaatctagataagattgttccctttaaatctttatctacactatcattttctgcttataacaaaaaaccacagaaatctgtggttttttatttctatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2363:SSA_2364|SSA_2363:SSA_2364:Phosphoglycolate phosphatase, putative:Immunodominant staphylococcal antigen A precursor, putative:-><-:2366420..2366531 112 ctttacatagctgtcaatctagataagattgttccctttaaatctttatctacactatcattttctgcttataacaaaaaaccacagaaatctgtggttttttatttctatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2363:SSA_2364|SSA_2363:SSA_2364:Phosphoglycolate phosphatase, putative:Immunodominant staphylococcal antigen A precursor, putative:-><-:2366420..2366531 112 ctttacatagctgtcaatctagataagattgttccctttaaatctttatctacactatcattttctgcttataacaaaaaaccacagaaatctgtggttttttatttctatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctttacatagctgtcaatctagataagattgttccctttaaatctttatctacactatcattttctgcttataacaaaaaaccacagaaatctgtggttttttatttctatc Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 7 End: 111 ...... M A V N L D K I V P F K S L S T L S F S A Y N K K P Q K S V V F Y F Y . Protein_Len: 30 Strand: + Start: 23 End: 112 ...................... M R L F P L N L Y L H Y H F L L I T K N H R N L W F F I S I ctttacatagctgtcaatctagataagattgttccctttaaatctttatctacactatcattttctgcttataacaaaaaaccacagaaatctgtggttttttatttctatc 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================================================ ctttacatagctgtcaatctagataagattgttccctttaaatctttatctacactatcattttctgcttataacaaaaaaccacagaaatctgtggttttttatttctatc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 71 HP_score: -6.7 Tail_Score: -4.03302 Start: 83 End: 96 Full_Region: CTTATAACAAAAAAC CACAG AAAT CTGTG GTTTTTTATTTCTAT ..................................................................................CACAGAAATCTGTG................ Find igs database================================================ Query_seq: SSA_2363:SSA_2364|SSA_2363:SSA_2364:Phosphoglycolate phosphatase, putative:Immunodominant staphylococcal antigen A precursor, putative:-><-:2366420..2366531 112 ctttacatagctgtcaatctagataagattgttccctttaaatctttatctacactatcattttctgcttataacaaaaaaccacagaaatctgtggttttttatttctatc Intra-Species Hit: Count: 1 Min: 1 Max: 112 Len: 112 Subject: NC_009009_SSA_2363_SSA_2364|Phosphoglycolate phosphatase, putative:Immunodominant staphylococcal antigen A precursor, putative|POSITIVE:NEGATIVE|[2366420,2366531]|112 HSP 1 e-value: 2.0E-57 bit: 222.0 Len: 112 Query Start:1 Query End:112 Subject Strand: POSITIVE Subject Start: 1 Subject End: 112 ctttacatagctgtcaatctagataagattgttccctttaaatctttatctacactatcattttctgcttataacaaaaaaccacagaaatctgtggttttttatttctatc ctttacatagctgtcaatctagataagattgttccctttaaatctttatctacactatcattttctgcttataacaaaaaaccacagaaatctgtggttttttatttctatc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUUACAUAGCUGUCAAUCUAGAUAAGAUUGUUCCCUUUAAAUCUUUAUCUACACUAUCAUUUUCUGCUUAUAACAAAAAACCACAGAAAUCUGUGGUUUUUUAUUUCUAUC ......((((.(((......((((((((((..........)))).))))))))))))).................((((((((((((....))))))))))))......... (-22.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUAGAAAUAAAAAACCACAGAUUUCUGUGGUUUUUUGUUAUAAGCAGAAAAUGAUAGUGUAGAUAAAGAUUUAAAGGGAACAAUCUUAUCUAGAUUGACAGCUAUGUAAAG ......(((((((((((((((....)))))))))))))))....(((.....((.((((.(((((((.((((....(....)))))))))))).)))).))....))).... (-32.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 265 39 1 178 135 NC_009009:SSA_1635|5end_hypothetical_protein_1639221..1639451_NEGATIVE 249 68 21 184 128 NC_009009:SSA_1849|5end_Primosomal_protein_N',_putative_1845649..1845879_NEGATIVE 234 100 61 137 108 NC_009009:SSA_0113|5end_30S_ribosomal_protein_S3,_putative_111322..111552_POSITIVE 229 60 11 150 101 NC_009009:SSA_2159|5end_hypothetical_protein_2159621..2159851_NEGATIVE 224 69 24 164 111 NC_009009:SSA_0410|5end_hypothetical_protein_406442..406672_NEGATIVE 223 68 29 135 93 NC_009009:SSA_1523|5end_Glutathione_peroxidase,_putative_1532067..1532297_POSITIVE 215 60 12 68 7 NC_009009:SSA_1253|5end_hypothetical_protein_1281245..1281475_NEGATIVE 214 109 62 220 163 NC_009009:SSA_1561|5end_Ribonuclease_III,_putative_1565883..1566113_NEGATIVE 212 39 5 192 160 NC_009009:SSA_1687|5end_NADH-binding_ferric-oxidoreductase,_putative_1680547..1680777_POSITIVE 212 46 5 40 2 NC_009009:SSA_0749|5end_Competence_protein,_putative_730668..730898_POSITIVE 212 38 9 159 132 NC_009009:SSA_0514|5end_PduQ_protein,_putative_512877..513107_POSITIVE 210 50 1 114 61 NC_009009:SSA_1724|5end_CBS_domain_protein,_putative_1710553..1710783_NEGATIVE 209 97 54 136 92 NC_009009:SSA_0802|5end_hypothetical_protein_784300..784530_POSITIVE 208 74 32 143 98 NC_009009:SSA_2078|5end_hypothetical_protein_2083837..2084067_NEGATIVE 207 69 35 222 185 NC_009009:SSA_1374|5end_Multidrug_ABC_transporter,_ATPase_and_permease_components,_putative_1393095..1393325_NEGATIVE 206 78 32 126 77 NC_009009:SSA_2230|5end_Ribonucleotide_reductase,_class_III,_anaerobic,_putative_2231158..2231388_NEGATIVE 206 49 1 202 144 NC_009009:SSA_0547|5end_Acyl_carrier_protein_synthase,_putative_541991..542221_POSITIVE 205 50 7 47 8 NC_009009:SSA_0674|5end_Exodeoxyribonuclease_VII_large_subunit,_putative_657071..657301_POSITIVE 195 29 1 163 135 NC_009009:SSA_0780|5end_Acid_phosphatase_(PAP2_family),_putative_764748..764978_POSITIVE 195 44 10 151 109 NC_009009:SSA_0490|5end_Cobalamin_5'-phosphate_synthase,_putative_490236..490466_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 289 76 32 113 79 NC_009009:SSA_0419|3end_Alpha-galactosidase,_putative_418530..418680_POSITIVE 249 68 21 123 67 NC_009009:SSA_1850|3end_DNA-directed_RNA_polymerase,_subunit_K/omega,_putative_1845710..1845860_NEGATIVE 249 110 70 70 28 NC_009009:SSA_0422|3end_Phosphoglycerate_mutase_family_protein,_putative_420839..420989_POSITIVE 245 69 21 131 81 NC_009009:SSA_2321|3end_Cation_(Co/Zn/Cd)_efflux_protein,_putative_2326050..2326200_NEGATIVE 236 51 11 151 113 NC_009009:SSA_1893|3end_N-acetylglucosamine-6-phosphate_deacetylase,_putative_1889421..1889571_NEGATIVE 234 100 61 124 95 NC_009009:SSA_0112|3end_50S_ribosomal_protein_L22,_putative_111389..111539_POSITIVE 229 60 11 148 99 NC_009009:SSA_2160|3end_Deoxyuridinetriphosphatase,_putative_2159623..2159773_NEGATIVE 224 69 24 126 73 NC_009009:SSA_0411|3end_hypothetical_protein_406480..406630_NEGATIVE 218 69 25 134 66 NC_009009:SSA_0680|3end_Serine/threonine_protein_phosphatase,_putative_663233..663383_POSITIVE 215 60 12 71 10 NC_009009:SSA_1254|3end_hypothetical_protein_1281242..1281392_NEGATIVE 214 109 62 98 41 NC_009009:SSA_1562|3end_hypothetical_protein_1566005..1566155_NEGATIVE 212 39 5 35 3 NC_009009:SSA_1686|3end_hypothetical_protein_1680470..1680620_POSITIVE 211 45 17 151 121 NC_009009:SSA_2161|3end_NTP_pyrophosphohydrolases_including_oxidative_damage_repair_enzymes,_putative_2160151..2160301_NEGATIVE 210 49 7 73 36 NC_009009:SSA_1696|3end_Tagatose_1,6-diphosphate_aldolase_2,_putative_1688207..1688357_NEGATIVE 209 57 12 106 64 NC_009009:SSA_1610|3end_hypothetical_protein_1614004..1614154_NEGATIVE 206 49 1 94 36 NC_009009:SSA_0546|3end_Phospho-2-dehydro-3-deoxyheptonate_aldolase_(DAHP_synthatase),_possibly_tyr-sensitive,_putative_541963..542113_POSITIVE 202 110 84 42 11 NC_009009:SSA_2166|3end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_2163873..2164023_NEGATIVE 201 94 52 55 3 NC_009009:SSA_0631|3end_Tryptophan_synthase_beta_chain,_putative_621133..621283_POSITIVE 196 109 74 99 62 NC_009009:SSA_0861|3end_hypothetical_protein_851742..851892_NEGATIVE 193 70 29 140 91 NC_009009:SSA_0994|3end_Peptidase_E,_putative_995390..995540_POSITIVE