Origin IGS: aaatcaaagatcggtatcttccggtctttttttgtatcttggaaaggaaacgatttctttaactgggtatatggtatataaagtttatacggaatttcttgtaaaatatattcaaagatgataaaatgagggtataaaaccacgaaaggcgaatattaaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tttaatattcgcctttcgtggttttataccctcattttatcatctttgaatatattttacaagaaattccgtataaactttatataccatatacccagttaaagaaatcgtttcctttccaagatacaaaaaaagaccggaagataccgatctttgattt Mask Tandem Repeat Region ================================================ aaatcaaagatcggtatcttccggtctttttttgtatcttggaaaggaaacgatttctttaactgggtatatggtatataaagtttatacggaatttcttgtaaaatatattcaaagatgataaaatgagggtataaaaccacgaaaggcgaatattaaa Find is-nt database================================================ Query_seq: SSA_0027:SSA_0028|SSA_0027:SSA_0028:Acyl carrier protein, putative:Phosphoribosylaminoimidazole-succinocarboxamide synthase, putative:->->:31863..32022 160 aaatcaaagatcggtatcttccggtctttttttgtatcttggaaaggaaacgatttctttaactgggtatatggtatataaagtttatacggaatttcttgtaaaatatattcaaagatgataaaatgagggtataaaaccacgaaaggcgaatattaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0027:SSA_0028|SSA_0027:SSA_0028:Acyl carrier protein, putative:Phosphoribosylaminoimidazole-succinocarboxamide synthase, putative:->->:31863..32022 160 aaatcaaagatcggtatcttccggtctttttttgtatcttggaaaggaaacgatttctttaactgggtatatggtatataaagtttatacggaatttcttgtaaaatatattcaaagatgataaaatgagggtataaaaccacgaaaggcgaatattaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0027:SSA_0028|SSA_0027:SSA_0028:Acyl carrier protein, putative:Phosphoribosylaminoimidazole-succinocarboxamide synthase, putative:->->:31863..32022 160 aaatcaaagatcggtatcttccggtctttttttgtatcttggaaaggaaacgatttctttaactgggtatatggtatataaagtttatacggaatttcttgtaaaatatattcaaagatgataaaatgagggtataaaaccacgaaaggcgaatattaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaatcaaagatcggtatcttccggtctttttttgtatcttggaaaggaaacgatttctttaactgggtatatggtatataaagtttatacggaatttcttgtaaaatatattcaaagatgataaaatgagggtataaaaccacgaaaggcgaatattaaa Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: - Start: 62 End: 154 ............................................................. S P I H Y I F N I R F K K Y F I N L S S L I L T Y F W S L R M ...... Protein_Len: 47 Strand: - Start: 3 End: 143 .. D F I P I K R D K K T D Q F P F S K K L Q T Y P I Y L K Y P I E Q L I Y E F I I F H P Y L V M ................. aaatcaaagatcggtatcttccggtctttttttgtatcttggaaaggaaacgatttctttaactgggtatatggtatataaagtttatacggaatttcttgtaaaatatattcaaagatgataaaatgagggtataaaaccacgaaaggcgaatattaaa 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: 83 Start: 98 End: 127 .................................................................................................CTTGTAAAATATATTCAAAGATGATAAAAT................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaatcaaagatcggtatcttccggtctttttttgtatcttggaaaggaaacgatttctttaactgggtatatggtatataaagtttatacggaatttcttgtaaaatatattcaaagatgataaaatgagggtataaaaccacgaaaggcgaatattaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0027:SSA_0028|SSA_0027:SSA_0028:Acyl carrier protein, putative:Phosphoribosylaminoimidazole-succinocarboxamide synthase, putative:->->:31863..32022 160 aaatcaaagatcggtatcttccggtctttttttgtatcttggaaaggaaacgatttctttaactgggtatatggtatataaagtttatacggaatttcttgtaaaatatattcaaagatgataaaatgagggtataaaaccacgaaaggcgaatattaaa Intra-Species Hit: Count: 1 Min: 1 Max: 160 Len: 160 Subject: NC_009009_SSA_0027_SSA_0028|Acyl carrier protein, putative:Phosphoribosylaminoimidazole-succinocarboxamide synthase, putative|POSITIVE:POSITIVE|[31863,32022]|160 HSP 1 e-value: 2.0E-73 bit: 276.0 Len: 160 Query Start:1 Query End:160 Subject Strand: POSITIVE Subject Start: 1 Subject End: 160 aaatcaaagatcggtatcttccggtcnnnnnnngtatcttggaaaggaaacgatttctttaactgggtatatggtatataaagtttatacggaatttcttgtaaaatatattcaaagatgataaaatgagggtataaaaccacgaaaggcgaatattaaa aaatcaaagatcggtatcttccggtctttttttgtatcttggaaaggaaacgatttctttaactgggtatatggtatataaagtttatacggaatttcttgtaaaatatattcaaagatgataaaatgagggtataaaaccacgaaaggcgaatattaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUCAAAGAUCGGUAUCUUCCGGUCUUUUUUUGUAUCUUGGAAAGGAAACGAUUUCUUUAACUGGGUAUAUGGUAUAUAAAGUUUAUACGGAAUUUCUUGUAAAAUAUAUUCAAAGAUGAUAAAAUGAGGGUAUAAAACCACGAAAGGCGAAUAUUAAA .....(((((((((......)))))))))(((((((((((..(((((((....)))))))...(((((((((..((((..((((((.....))))))..))))..)))))))))..............)))))))))))...(....)............ (-35.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUAAUAUUCGCCUUUCGUGGUUUUAUACCCUCAUUUUAUCAUCUUUGAAUAUAUUUUACAAGAAAUUCCGUAUAAACUUUAUAUACCAUAUACCCAGUUAAAGAAAUCGUUUCCUUUCCAAGAUACAAAAAAAGACCGGAAGAUACCGAUCUUUGAUUU .................((((((((((((..........(((....)))....(((((....)))))...)))))))........)))))......(((((((((....((.((........)).))..........(((......))).))))))))). (-17.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 272 57 17 86 37 NC_009009:SSA_1431|5end_hypothetical_protein_1438730..1438960_NEGATIVE 270 66 21 217 163 NC_009009:SSA_0863|5end_Cof_family_protein,_putative_855015..855245_NEGATIVE 269 37 3 98 61 NC_009009:SSA_1600|5end_hypothetical_protein_1606595..1606825_NEGATIVE 269 42 4 160 119 NC_009009:SSA_0810|5end_P-loop_ATPase,_putative_791582..791812_POSITIVE 268 37 6 213 182 NC_009009:SSA_1596|5end_hypothetical_protein_1603034..1603264_NEGATIVE 264 37 6 183 152 NC_009009:SSA_1598|5end_hypothetical_protein_1605238..1605468_NEGATIVE 254 50 6 152 108 NC_009009:SSA_0392|5end_hypothetical_protein_387876..388106_POSITIVE 252 59 12 170 127 NC_009009:SSA_0939|5end_Inositol_monophosphatase_(Mg++_dependent),_putative_946810..947040_POSITIVE 249 53 11 200 154 NC_009009:SSA_2321|5end_Cation_(Co/Zn/Cd)_efflux_protein,_putative_2326925..2327155_NEGATIVE 247 69 21 128 75 NC_009009:SSA_0547|5end_Acyl_carrier_protein_synthase,_putative_541991..542221_POSITIVE 246 40 12 94 65 NC_009009:SSA_2176|5end_hypothetical_protein_2175159..2175389_NEGATIVE 245 40 4 60 18 NC_009009:SSA_0558|5end_Conserved_hypothetical_cytosolic_protein,_putative_552335..552565_POSITIVE 245 60 12 144 91 NC_009009:SSA_0110|5end_50S_ribosomal_protein_L2,_putative_109753..109983_POSITIVE 243 57 12 125 80 NC_009009:SSA_1842|5end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_HTH_DNA-binding_domains),_putative_1836494..1836724_NEGATIVE 237 40 7 94 56 NC_009009:SSA_1376|5end_Transport_protein,_putative_1396111..1396341_NEGATIVE 234 41 2 87 50 NC_009009:SSA_0676|5end_Farnesyl_diphosphate_synthase,_putative_658598..658828_POSITIVE 230 58 11 231 184 NC_009009:SSA_1531|5end_ABC-type_antimicrobial_peptide_transporter,_ATPase_component,_putative_1539476..1539706_NEGATIVE 230 65 22 229 178 NC_009009:SSA_1478|5end_Transposase_ORF1,_putative_1482889..1483119_POSITIVE 228 103 61 44 4 NC_009009:SSA_2189|5end_hypothetical_protein_2191097..2191327_NEGATIVE 228 68 21 221 175 NC_009009:SSA_2120|5end_GTPase,_putative_2121751..2121981_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 285 131 98 59 29 NC_009009:SSA_1554|3end_hypothetical_protein_1556847..1556997_POSITIVE 273 37 2 81 38 NC_009009:SSA_1909|3end_Transcriptional_attenuator_LytR,_putative_1900904..1901054_NEGATIVE 269 37 3 101 64 NC_009009:SSA_1601|3end_VacB-like_protein,_putative_1606592..1606742_NEGATIVE 269 42 4 104 63 NC_009009:SSA_0809|3end_Translation_initiation_inhibitor,_yjgF_family_/_endoribonuclease_L-PSP,_putative_791606..791756_POSITIVE 245 60 12 126 73 NC_009009:SSA_0109|3end_50S_ribosomal_protein_L23,_putative_109815..109965_POSITIVE 243 57 12 147 102 NC_009009:SSA_1843|3end_Histidine_kinase,_putative_1836472..1836622_NEGATIVE 237 55 17 151 104 NC_009009:SSA_1432|3end_HflX_GTPase,_putative_1438663..1438813_NEGATIVE 236 58 11 92 45 NC_009009:SSA_0153|3end_hypothetical_protein_149503..149653_POSITIVE 235 60 13 109 64 NC_009009:SSA_0214|3end_Single-strand_DNA-binding_protein_(conjugal_DNA-protein_transfer_system),_putative_210690..210840_POSITIVE 234 41 2 90 53 NC_009009:SSA_0675|3end_Exodeoxyribonuclease_VII_small_subunit,_putative_658681..658831_POSITIVE 233 59 11 130 75 NC_009009:SSA_2027|3end_P-type_ATPase-metal/cation_transport_(probably_copper),_putative_2033109..2033259_NEGATIVE 232 56 12 60 24 NC_009009:SSA_1590|3end_Transcriptional_regulator,_TetR/AcrR_family,_putative_1593342..1593492_POSITIVE 226 64 31 42 10 NC_009009:SSA_1166|3end_hypothetical_protein_1192350..1192500_POSITIVE 222 49 10 147 103 NC_009009:SSA_0945|3end_Phosphate_import_ATP-binding_protein_pstB_1,_putative_953458..953608_POSITIVE 221 43 3 95 48 NC_009009:SSA_1487|3end_Conserved_uncharacterized_protein_1493483..1493633_NEGATIVE 218 59 11 120 64 NC_009009:SSA_1585|3end_hypothetical_protein_1586975..1587125_NEGATIVE 218 54 11 111 67 NC_009009:SSA_1326|3end_Peptidase_T,_putative_1343735..1343885_POSITIVE 214 48 6 110 59 NC_009009:SSA_1664|3end_Phosphatidylethanolamine_N-methyltransferase,_putative_1664449..1664599_NEGATIVE 214 48 11 85 47 NC_009009:SSA_0932|3end_hypothetical_protein_942804..942954_POSITIVE 212 78 37 137 95 NC_009009:SSA_1215|3end_hypothetical_protein_1238247..1238397_POSITIVE