Origin IGS: cttttacctccagtttttattattataccatacaggaattattaaaatcattttttattttccacgccgccttttctgtctttgtccgcctttcgtgttataataaacct .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aggtttattataacacgaaaggcggacaaagacagaaaaggcggcgtggaaaataaaaaatgattttaataattcctgtatggtataataataaaaactggaggtaaaag Mask Tandem Repeat Region ================================================ cttttacctccagtttttattattataccatacaggaattattaaaatcattttttattttccacgccgccttttctgtctttgtccgcctttcgtgttataataaacct Find is-nt database================================================ Query_seq: SSA_0099:SSA_0100|SSA_0099:SSA_0100:hypothetical protein:DNA polymerase I - 3'-5' exonuclease and polymerase domains, putative:<-->:100710..100819 110 cttttacctccagtttttattattataccatacaggaattattaaaatcattttttattttccacgccgccttttctgtctttgtccgcctttcgtgttataataaacct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0099:SSA_0100|SSA_0099:SSA_0100:hypothetical protein:DNA polymerase I - 3'-5' exonuclease and polymerase domains, putative:<-->:100710..100819 110 cttttacctccagtttttattattataccatacaggaattattaaaatcattttttattttccacgccgccttttctgtctttgtccgcctttcgtgttataataaacct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0099:SSA_0100|SSA_0099:SSA_0100:hypothetical protein:DNA polymerase I - 3'-5' exonuclease and polymerase domains, putative:<-->:100710..100819 110 cttttacctccagtttttattattataccatacaggaattattaaaatcattttttattttccacgccgccttttctgtctttgtccgcctttcgtgttataataaacct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cttttacctccagtttttattattataccatacaggaattattaaaatcattttttattttccacgccgccttttctgtctttgtccgcctttcgtgttataataaacct Predict ORF larger than 30AA ================================================ cttttacctccagtttttattattataccatacaggaattattaaaatcattttttattttccacgccgccttttctgtctttgtccgcctttcgtgttataataaacct 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: 75 End: 104 ..........................................................................TCTGTCTTTGTCCGCCTTTCGTGTTATAAT...... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ cttttacctccagtttttattattataccatacaggaattattaaaatcattttttattttccacgccgccttttctgtctttgtccgcctttcgtgttataataaacct Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0099:SSA_0100|SSA_0099:SSA_0100:hypothetical protein:DNA polymerase I - 3'-5' exonuclease and polymerase domains, putative:<-->:100710..100819 110 cttttacctccagtttttattattataccatacaggaattattaaaatcattttttattttccacgccgccttttctgtctttgtccgcctttcgtgttataataaacct Intra-Species Hit: Count: 1 Min: 1 Max: 110 Len: 110 Subject: NC_009009_SSA_0099_SSA_0100|hypothetical protein:DNA polymerase I - 3'-5' exonuclease and polymerase domains, putative|NEGATIVE:POSITIVE|[100710,100819]|110 HSP 1 e-value: 3.0E-56 bit: 218.0 Len: 110 Query Start:1 Query End:110 Subject Strand: POSITIVE Subject Start: 1 Subject End: 110 cttttacctccagtttttattattataccatacaggaattattaaaatcattttttattttccacgccgccttttctgtctttgtccgcctttcgtgttataataaacct cttttacctccagtttttattattataccatacaggaattattaaaatcattttttattttccacgccgccttttctgtctttgtccgcctttcgtgttataataaacct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUUUACCUCCAGUUUUUAUUAUUAUACCAUACAGGAAUUAUUAAAAUCAUUUUUUAUUUUCCACGCCGCCUUUUCUGUCUUUGUCCGCCUUUCGUGUUAUAAUAAACCU ...............((((((((.((((......((((....(((((.....)))))..))))..((.(.(............).).)).....)))).))))))))... (-11.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGGUUUAUUAUAACACGAAAGGCGGACAAAGACAGAAAAGGCGGCGUGGAAAAUAAAAAAUGAUUUUAAUAAUUCCUGUAUGGUAUAAUAAUAAAAACUGGAGGUAAAAG ...((((((....((((...(.(................).)..))))...))))))......(((((....((((.((....(((....)))...)).)))).))))). (-11.69) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 941 110 61 201 152 NC_009009:SSA_0099|5end_hypothetical_protein_100619..100849_NEGATIVE 351 91 62 66 30 NC_009009:SSA_0706|5end_RNA_helicase,_putative_691363..691593_POSITIVE 326 86 54 119 87 NC_009009:SSA_1154|5end_hypothetical_protein_1182661..1182891_POSITIVE 311 94 52 223 173 NC_009009:SSA_0226|5end_60_kDa_chaperonin_218947..219177_POSITIVE 308 107 63 123 83 NC_009009:SSA_0874|5end_hypothetical_protein_867935..868165_POSITIVE 297 110 62 172 138 NC_009009:SSA_0064|5end_hypothetical_protein_66330..66560_POSITIVE 295 96 51 148 97 NC_009009:SSA_1649|5end_hypothetical_protein_1648886..1649116_NEGATIVE 288 110 66 164 107 NC_009009:SSA_0978|5end_hypothetical_protein_983736..983966_POSITIVE 287 98 62 214 172 NC_009009:SSA_0030|5end_Phosphoribosylformylglycinamidine_synthase,_putative_32610..32840_POSITIVE 284 88 46 122 80 NC_009009:SSA_1447|5end_ATP_phosphoribosyltransferase,_putative_1449831..1450061_NEGATIVE 284 101 66 231 185 NC_009009:SSA_1152|5end_Protein_chain_release_factor_A,_putative_1180759..1180989_POSITIVE 282 80 45 109 77 NC_009009:SSA_1904|5end_ABC-type_multidrug_transport_system,_permease_component,_putative_1899279..1899509_NEGATIVE 272 97 59 53 13 NC_009009:SSA_1958|5end_Adapter_protein_mecA,_putative_1955413..1955643_NEGATIVE 271 98 62 203 162 NC_009009:SSA_0778|5end_Glycogen_synthase,_putative_760566..760796_POSITIVE 269 91 57 116 81 NC_009009:SSA_1844|5end_hypothetical_protein_1838183..1838413_NEGATIVE 269 42 7 133 98 NC_009009:SSA_1330|5end_hypothetical_protein_1346368..1346598_NEGATIVE 265 100 63 145 89 NC_009009:SSA_2042|5end_hypothetical_protein_2047073..2047303_NEGATIVE 265 110 62 166 114 NC_009009:SSA_0583|5end_Nucleotidyltransferase,_putative_574505..574735_POSITIVE 265 98 59 81 36 NC_009009:SSA_0482|5end_ATP:cobalamin_adenosyl_transferase,_putative_483458..483688_POSITIVE 264 89 41 164 108 NC_009009:SSA_2083|5end_hypothetical_protein_2087969..2088199_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 387 100 51 136 87 NC_009009:SSA_2340|3end_hypothetical_protein_2341539..2341689_NEGATIVE 346 90 61 126 100 NC_009009:SSA_1960|3end_hypothetical_protein_1956571..1956721_NEGATIVE 326 86 54 126 94 NC_009009:SSA_1153|3end_HemK_protein,_putative_1182748..1182898_POSITIVE 295 96 51 138 87 NC_009009:SSA_1650|3end_3-Ketoacyl-ACP_reductase,_putative_1648896..1649046_NEGATIVE 284 88 46 125 83 NC_009009:SSA_1448|3end_ATP_phosphoribosyltransferase_regulatory_subunit,_putative_1449828..1449978_NEGATIVE 283 94 62 137 102 NC_009009:SSA_0263|3end_Zinc_metalloproteinase_in_scaA_5'region,_putative_258246..258396_POSITIVE 282 80 45 112 80 NC_009009:SSA_1905|3end_ABC-type_multidrug_transport_system,_ATPase_component,_putative_1899276..1899426_NEGATIVE 265 98 59 84 39 NC_009009:SSA_0481|3end_Cobyric_acid_synthase,_putative_483541..483691_POSITIVE 263 93 52 145 88 NC_009009:SSA_0324|3end_Conserved_uncharacterized_protein_317593..317743_POSITIVE 260 110 63 85 12 NC_009009:SSA_0557|3end_hypothetical_protein_552393..552543_POSITIVE 259 99 60 110 62 NC_009009:SSA_1903|3end_hypothetical_protein_1897388..1897538_NEGATIVE 258 89 55 119 79 NC_009009:SSA_0686|3end_Fe2+/Zn2+_uptake_regulation_protein,_putative_670079..670229_POSITIVE 255 97 63 148 96 NC_009009:SSA_2044|3end_Cysteinyl-tRNA_synthetase,_putative_2047066..2047216_NEGATIVE 255 97 61 52 5 NC_009009:SSA_0580|3end_Isochorismatase_family_protein,_putative_573399..573549_POSITIVE 252 97 56 132 99 NC_009009:SSA_1350|3end_hypothetical_protein_1366945..1367095_NEGATIVE 251 100 56 118 69 NC_009009:SSA_0894|3end_ATP-binding_cassette_protein,_putative_886533..886683_POSITIVE 251 99 53 125 71 NC_009009:SSA_0150|3end_hypothetical_protein_145227..145377_POSITIVE 248 105 65 67 12 NC_009009:SSA_1224|3end_hypothetical_protein_1247251..1247401_NEGATIVE 248 93 62 61 25 NC_009009:SSA_0676|3end_Farnesyl_diphosphate_synthase,_putative_659553..659703_POSITIVE 247 97 66 123 83 NC_009009:SSA_2142|3end_Argininosuccinate_synthase,_putative_2142216..2142366_NEGATIVE