Origin IGS: tctttctttcctttcaagaatttattaatgagattatattatagcttatttatatgacatcctcaagatatttgcttgtcaaatattttacatttgcatcattttagtataaaatatagaatgatattct .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agaatatcattctatattttatactaaaatgatgcaaatgtaaaatatttgacaagcaaatatcttgaggatgtcatataaataagctataatataatctcattaataaattcttgaaaggaaagaaaga Mask Tandem Repeat Region ================================================ tctttctttcctttcaagaatttattaatgagattatattatagcttatttatatgacatcctcaagatatttgcttgtcaaatattttacatttgcatcattttagtataaaatatagaatgatattct Find is-nt database================================================ Query_seq: SSA_0822:SSA_0824|SSA_0822:SSA_0824:Large conductance mechano-sensitive ion channel, putative:DNA primase (bacterial type), putative:<-->:802063..802192 130 tctttctttcctttcaagaatttattaatgagattatattatagcttatttatatgacatcctcaagatatttgcttgtcaaatattttacatttgcatcattttagtataaaatatagaatgatattct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0822:SSA_0824|SSA_0822:SSA_0824:Large conductance mechano-sensitive ion channel, putative:DNA primase (bacterial type), putative:<-->:802063..802192 130 tctttctttcctttcaagaatttattaatgagattatattatagcttatttatatgacatcctcaagatatttgcttgtcaaatattttacatttgcatcattttagtataaaatatagaatgatattct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0822:SSA_0824|SSA_0822:SSA_0824:Large conductance mechano-sensitive ion channel, putative:DNA primase (bacterial type), putative:<-->:802063..802192 130 tctttctttcctttcaagaatttattaatgagattatattatagcttatttatatgacatcctcaagatatttgcttgtcaaatattttacatttgcatcattttagtataaaatatagaatgatattct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tctttctttcctttcaagaatttattaatgagattatattatagcttatttatatgacatcctcaagatatttgcttgtcaaatattttacatttgcatcattttagtataaaatatagaatgatattct Predict ORF larger than 30AA ================================================ tctttctttcctttcaagaatttattaatgagattatattatagcttatttatatgacatcctcaagatatttgcttgtcaaatattttacatttgcatcattttagtataaaatatagaatgatattct 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: 88 Start: 86 End: 115 .....................................................................................TTTTACATTTGCATCATTTTAGTATAAAAT............... PromScan Matrix: RpoD-17 Strand: - Score: 84 Start: 38 End: 67 .....................................CTTGAGGATGTCATATAAATAAGCTATAAT............................................................... PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 54 End: 83 .....................................................TTTGACAAGCAAATATCTTGAGGATGTCAT............................................... PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 93 End: 122 ............................................................................................TTTGCATCATTTTAGTATAAAATATAGAAT........ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tctttctttcctttcaagaatttattaatgagattatattatagcttatttatatgacatcctcaagatatttgcttgtcaaatattttacatttgcatcattttagtataaaatatagaatgatattct Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0822:SSA_0824|SSA_0822:SSA_0824:Large conductance mechano-sensitive ion channel, putative:DNA primase (bacterial type), putative:<-->:802063..802192 130 tctttctttcctttcaagaatttattaatgagattatattatagcttatttatatgacatcctcaagatatttgcttgtcaaatattttacatttgcatcattttagtataaaatatagaatgatattct Intra-Species Hit: Count: 1 Min: 1 Max: 130 Len: 130 Subject: NC_009009_SSA_0822_SSA_0824|Large conductance mechano-sensitive ion channel, putative:DNA primase (bacterial type), putative|NEGATIVE:POSITIVE|[802063,802192]|130 HSP 1 e-value: 4.0E-68 bit: 258.0 Len: 130 Query Start:1 Query End:130 Subject Strand: POSITIVE Subject Start: 1 Subject End: 130 tctttctttcctttcaagaatttattaatgagattatattatagcttatttatatgacatcctcaagatatttgcttgtcaaatattttacatttgcatcattttagtataaaatatagaatgatattct tctttctttcctttcaagaatttattaatgagattatattatagcttatttatatgacatcctcaagatatttgcttgtcaaatattttacatttgcatcattttagtataaaatatagaatgatattct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUUUCUUUCCUUUCAAGAAUUUAUUAAUGAGAUUAUAUUAUAGCUUAUUUAUAUGACAUCCUCAAGAUAUUUGCUUGUCAAAUAUUUUACAUUUGCAUCAUUUUAGUAUAAAAUAUAGAAUGAUAUUCU ...(((((.......)))))..(((.((((((.((((...)))))))))).)))..........((((((((((.....))))))))))........(((((((((..........)))))))))..... (-15.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAAUAUCAUUCUAUAUUUUAUACUAAAAUGAUGCAAAUGUAAAAUAUUUGACAAGCAAAUAUCUUGAGGAUGUCAUAUAAAUAAGCUAUAAUAUAAUCUCAUUAAUAAAUUCUUGAAAGGAAAGAAAGA ......((.((((.(((((((((...............))))))))).....((((....(((..(((((.(((..((((.......))))..))).)))))...)))....))))...)))).)).... (-12.36) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 744 100 51 191 142 NC_009009:SSA_0822|5end_Large_conductance_mechano-sensitive_ion_channel,_putative_801972..802202_NEGATIVE 246 106 61 95 52 NC_009009:SSA_1099|5end_Calcium_binding_hemolysin-like_protein,_putative_1115361..1115591_POSITIVE 229 101 65 204 169 NC_009009:SSA_1584|5end_Ring-cleavage_extradiol_dioxygenase,_putative_1587030..1587260_NEGATIVE 222 76 33 165 111 NC_009009:SSA_0714|5end_hypothetical_protein_700042..700272_POSITIVE 221 105 71 203 172 NC_009009:SSA_1660|5end_ABC-type_antimicrobial_peptide_transport_system,_ATPase_component,_putative_1657580..1657810_NEGATIVE 217 67 28 162 116 NC_009009:SSA_2381|5end_DegP_protein,_putative_2386298..2386528_POSITIVE 217 100 55 119 71 NC_009009:SSA_2118|5end_Thiamine_pyrophosphokinase,_putative_2120500..2120730_NEGATIVE 207 78 32 119 68 NC_009009:SSA_0475|5end_CbiK_protein,_putative_477723..477953_POSITIVE 206 45 2 145 94 NC_009009:SSA_1039|5end_Sugar_ABC_transporter,_ATP-binding_protein,_putative_1053774..1054004_POSITIVE 203 100 54 228 178 NC_009009:SSA_0185|5end_Competence_protein_ComYB,_putative_189057..189287_POSITIVE 198 50 3 142 93 NC_009009:SSA_1545|5end_Conserved_uncharacterized_protein_1549210..1549440_NEGATIVE 198 99 72 105 81 NC_009009:SSA_1296|5end_hypothetical_protein_1313013..1313243_NEGATIVE 194 76 43 118 84 NC_009009:SSA_0664|5end_Conserved_uncharacterized_protein_649086..649316_NEGATIVE 190 47 3 142 95 NC_009009:SSA_2082|5end_Carbohydrate_kinase,_FGGY_family,_putative_2086874..2087104_NEGATIVE 190 45 1 131 94 NC_009009:SSA_1679|5end_ABC-type_multidrug_transport_system,_ATPase_component,_putative_1673049..1673279_NEGATIVE 190 81 42 142 107 NC_009009:SSA_0433|5end_Methenyl_tetrahydrofolate_cyclohydrolase,_putative_435654..435884_NEGATIVE 188 90 54 53 18 NC_009009:SSA_2310|5end_hypothetical_protein_2313418..2313648_NEGATIVE 188 45 5 137 95 NC_009009:SSA_0858|5end_DTDP-L-rhamnose_synthase,_putative_845512..845742_POSITIVE 187 69 31 204 171 NC_009009:SSA_1948|5end_Oligopeptide-binding_lipoprotein_precursor,_putative_1942170..1942400_NEGATIVE 187 88 44 155 109 NC_009009:SSA_0263|5end_Zinc_metalloproteinase_in_scaA_5'region,_putative_256274..256504_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 222 76 33 71 17 NC_009009:SSA_0713|3end_1-acyl-sn-glycerol-3-phosphate_acyltransferase,_putative_700028..700178_POSITIVE 207 78 32 105 54 NC_009009:SSA_0474|3end_Uroporphyrin-III_C-methyltransferase/uroporphyrinogen-III_synthase,_putative_477789..477939_POSITIVE 198 50 3 85 36 NC_009009:SSA_1546|3end_Prolipoprotein_diacylglyceryl_transferase,_putative_1549267..1549417_NEGATIVE 196 81 43 103 64 NC_009009:SSA_0926|3end_Histone_acetyltransferase_HPA2,_putative_935961..936111_POSITIVE 194 76 43 50 16 NC_009009:SSA_0665|3end_NTP_pyrophosphohydrolases_including_oxidative_damage_repair_enzymes_(MutT/NUDIX_family)_649154..649304_NEGATIVE 190 76 41 33 5 NC_009009:SSA_2285|3end_hypothetical_protein_2287825..2287975_POSITIVE 190 47 3 66 19 NC_009009:SSA_2083|3end_hypothetical_protein_2086950..2087100_NEGATIVE 190 81 42 127 92 NC_009009:SSA_0434|3end_Glutamate_formiminotransferase,_putative_435669..435819_NEGATIVE 188 90 54 40 5 NC_009009:SSA_2311|3end_Nitric_oxide_reductase_NorD_/_Von_Willebrand_factor_type_A_(vWA)_domain_protein,_putative_2313431..2313581_NEGATIVE 186 78 31 126 79 NC_009009:SSA_0854|3end_hypothetical_protein_841813..841963_POSITIVE 183 81 43 109 69 NC_009009:SSA_0335|3end_Phosphomevalonate_kinase,_putative_329891..330041_POSITIVE 181 98 63 103 59 NC_009009:SSA_1614|3end_Acetyltransferase,_GNAT_family,_putative_1617476..1617626_NEGATIVE 181 78 45 116 90 NC_009009:SSA_0497|3end_Nickel_ABC_transporter,_putative_497997..498147_POSITIVE 177 46 7 98 55 NC_009009:SSA_2164|3end_Glutamine_amidotransferase,_putative_2160866..2161016_NEGATIVE 177 100 59 103 62 NC_009009:SSA_0239|3end_7,8-dihydro-8-oxoguanine-triphosphatase,_putative_233493..233643_POSITIVE 177 79 43 133 98 NC_009009:SSA_0039|3end_Phosphoribosylaminoimidazole_carboxylase,_catalytic_subunit,_putative_46401..46551_POSITIVE 175 97 53 135 92 NC_009009:SSA_1058|3end_Thiamine_biosynthesis_protein,_putative_1076211..1076361_POSITIVE 175 65 23 110 68 NC_009009:SSA_1026|3end_ABC-type_multidrug_transporter,_ATPase_component,_putative_1043617..1043767_POSITIVE 174 105 62 138 99 NC_009009:SSA_1735|3end_UreX,_putative_1720461..1720611_NEGATIVE 173 110 61 54 1 NC_009009:SSA_1395|3end_hypothetical_protein_1409045..1409195_NEGATIVE