Origin IGS: tctttccccttgctagtactttgaccttcaaataattttatattatcttaccatcttttctgctatttgtcagttctcggctttgttacaaaaaataggacagataaatccagcatctagcctgatcttctgtcctagttttatttc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gaaataaaactaggacagaagatcaggctagatgctggatttatctgtcctattttttgtaacaaagccgagaactgacaaatagcagaaaagatggtaagataatataaaattatttgaaggtcaaagtactagcaaggggaaaga Mask Tandem Repeat Region ================================================ tctttccccttgctagtactttgaccttcaaataattttatattatcttaccatcttttctgctatttgtcagttctcggctttgttacaaaaaataggacagataaatccagcatctagcctgatcttctgtcctagttttatttc Find is-nt database================================================ Query_seq: SSA_2154:SSA_2155|SSA_2154:SSA_2155:Conserved uncharacterized protein:hypothetical protein:<-<-:2155350..2155496 147 tctttccccttgctagtactttgaccttcaaataattttatattatcttaccatcttttctgctatttgtcagttctcggctttgttacaaaaaataggacagataaatccagcatctagcctgatcttctgtcctagttttatttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2154:SSA_2155|SSA_2154:SSA_2155:Conserved uncharacterized protein:hypothetical protein:<-<-:2155350..2155496 147 tctttccccttgctagtactttgaccttcaaataattttatattatcttaccatcttttctgctatttgtcagttctcggctttgttacaaaaaataggacagataaatccagcatctagcctgatcttctgtcctagttttatttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2154:SSA_2155|SSA_2154:SSA_2155:Conserved uncharacterized protein:hypothetical protein:<-<-:2155350..2155496 147 tctttccccttgctagtactttgaccttcaaataattttatattatcttaccatcttttctgctatttgtcagttctcggctttgttacaaaaaataggacagataaatccagcatctagcctgatcttctgtcctagttttatttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tctttccccttgctagtactttgaccttcaaataattttatattatcttaccatcttttctgctatttgtcagttctcggctttgttacaaaaaataggacagataaatccagcatctagcctgatcttctgtcctagttttatttc Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 32 End: 145 ............................... M I L Y Y L T I F S A I C Q F S A L L Q K I G Q I N P A S S L I F C P S F I .. tctttccccttgctagtactttgaccttcaaataattttatattatcttaccatcttttctgctatttgtcagttctcggctttgttacaaaaaataggacagataaatccagcatctagcctgatcttctgtcctagttttatttc 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: 84 Start: 20 End: 49 ...................TTTGACCTTCAAATAATTTTATATTATCTT.................................................................................................. PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 45 End: 74 ............................................ACTGACAAATAGCAGAAAAGATGGTAAGAT......................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tctttccccttgctagtactttgaccttcaaataattttatattatcttaccatcttttctgctatttgtcagttctcggctttgttacaaaaaataggacagataaatccagcatctagcctgatcttctgtcctagttttatttc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_2154:SSA_2155|SSA_2154:SSA_2155:Conserved uncharacterized protein:hypothetical protein:<-<-:2155350..2155496 147 tctttccccttgctagtactttgaccttcaaataattttatattatcttaccatcttttctgctatttgtcagttctcggctttgttacaaaaaataggacagataaatccagcatctagcctgatcttctgtcctagttttatttc Intra-Species Hit: Count: 1 Min: 1 Max: 147 Len: 147 Subject: NC_009009_SSA_2154_SSA_2155|Conserved uncharacterized protein:hypothetical protein|NEGATIVE:NEGATIVE|[2155350,2155496]|147 HSP 1 e-value: 3.0E-78 bit: 291.0 Len: 147 Query Start:1 Query End:147 Subject Strand: POSITIVE Subject Start: 1 Subject End: 147 tctttccccttgctagtactttgaccttcaaataattttatattatcttaccatcttttctgctatttgtcagttctcggctttgttacaaaaaataggacagataaatccagcatctagcctgatcttctgtcctagttttatttc tctttccccttgctagtactttgaccttcaaataattttatattatcttaccatcttttctgctatttgtcagttctcggctttgttacaaaaaataggacagataaatccagcatctagcctgatcttctgtcctagttttatttc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUUUCCCCUUGCUAGUACUUUGACCUUCAAAUAAUUUUAUAUUAUCUUACCAUCUUUUCUGCUAUUUGUCAGUUCUCGGCUUUGUUACAAAAAAUAGGACAGAUAAAUCCAGCAUCUAGCCUGAUCUUCUGUCCUAGUUUUAUUUC ...........(((.....((((.....))))...........................((((.....).))).....))).........((((.(((((((((...(((..((.....))..)))..))))))))).))))..... (-22.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAAUAAAACUAGGACAGAAGAUCAGGCUAGAUGCUGGAUUUAUCUGUCCUAUUUUUUGUAACAAAGCCGAGAACUGACAAAUAGCAGAAAAGAUGGUAAGAUAAUAUAAAAUUAUUUGAAGGUCAAAGUACUAGCAAGGGGAAAGA ...((((((.((((((((((((((.(((.....))).))))).)))))))))..)))))).......((.....(((........)))....(((..(.(((((((.....))))))).)..))).............))....... (-31.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 870 140 91 231 182 NC_009009:SSA_2154|5end_Conserved_uncharacterized_protein_2155259..2155489_NEGATIVE 303 139 108 114 83 NC_009009:SSA_0973|5end_hypothetical_protein_980296..980526_POSITIVE 287 87 46 135 96 NC_009009:SSA_0894|5end_ATP-binding_cassette_protein,_putative_885779..886009_POSITIVE 276 139 97 184 138 NC_009009:SSA_1660|5end_ABC-type_antimicrobial_peptide_transport_system,_ATPase_component,_putative_1657580..1657810_NEGATIVE 273 134 101 125 96 NC_009009:SSA_2226|5end_Organic_radical_activating_chaperone,_putative_2227756..2227986_NEGATIVE 273 134 96 226 190 NC_009009:SSA_1903|5end_hypothetical_protein_1898182..1898412_NEGATIVE 271 80 34 129 79 NC_009009:SSA_0800|5end_Glutamine_amidotransferase,_putative_782774..783004_NEGATIVE 270 138 91 156 104 NC_009009:SSA_0582|5end_Methylase,_putative_573769..573999_POSITIVE 269 135 95 178 139 NC_009009:SSA_0759|5end_Acetylglutamate_kinase,_putative_741841..742071_POSITIVE 267 140 98 48 5 NC_009009:SSA_2171|5end_hypothetical_protein_2170760..2170990_NEGATIVE 267 138 98 111 62 NC_009009:SSA_0051|5end_Dihydroxyacetone_kinase_phosphotransfer_protein,_putative_55190..55420_POSITIVE 265 99 51 149 98 NC_009009:SSA_1442|5end_Imidazole_glycerol-phosphate_synthase_subunit_hisF,_putative_1445941..1446171_NEGATIVE 265 83 43 125 88 NC_009009:SSA_0279|5end_Sugar-binding_transcriptional_repressor_(DeoR),_putative_272319..272549_POSITIVE 263 136 94 214 176 NC_009009:SSA_0925|5end_ABC-type_antimicrobial_peptide_transport_system,_ATPase_component,_putative_934749..934979_POSITIVE 260 138 92 49 3 NC_009009:SSA_0389|5end_hypothetical_protein_384172..384402_POSITIVE 257 135 93 231 184 NC_009009:SSA_1793|5end_Histidine_kinase_(sensor_protein),_putative_1776361..1776591_NEGATIVE 257 132 91 55 6 NC_009009:SSA_0146|5end_DNA_repair_ATPase,_putative_139686..139916_POSITIVE 256 119 87 90 56 NC_009009:SSA_1672|5end_hypothetical_protein_1670389..1670619_NEGATIVE 255 120 77 152 112 NC_009009:SSA_1866|5end_hypothetical_protein_1862182..1862412_NEGATIVE 254 135 93 205 164 NC_009009:SSA_1770|5end_hypothetical_protein_1758431..1758661_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 303 139 108 102 71 NC_009009:SSA_0972|3end_hypothetical_protein_980364..980514_POSITIVE 287 87 46 148 109 NC_009009:SSA_0893|3end_ATP-binding_cassette_transporter-like_protein,_putative_885872..886022_POSITIVE 284 140 97 92 41 NC_009009:SSA_0767|3end_Diacylglycerol_kinase_catalytic_domain_protein,_putative_748054..748204_POSITIVE 274 139 102 78 38 NC_009009:SSA_0099|3end_hypothetical_protein_100134..100284_NEGATIVE 271 80 34 129 79 NC_009009:SSA_0801|3end_Mur_ligase_family_protein,_putative_782774..782924_NEGATIVE 270 138 91 81 29 NC_009009:SSA_0581|3end_Conserved_uncharacterized_protein_573774..573924_POSITIVE 267 138 98 111 62 NC_009009:SSA_0050|3end_Dihydroxyacetone_kinase,_phosphatase_domain_(Dak2),_putative_55270..55420_POSITIVE 265 99 51 146 95 NC_009009:SSA_1443|3end_1-(5-phosphoribosyl)-5-[(5-_phosphoribosylamino)methylideneamino]_imidazole-4-carboxamide_isomerase,_putative_1445944..1446094_NEGATIVE 265 83 43 108 71 NC_009009:SSA_0278|3end_Transcriptional_repressor_of_sugar_metabolism,_GlpR/DeoR_family,_putative_272382..272532_POSITIVE 262 119 71 68 20 NC_009009:SSA_0690|3end_Recombinational_DNA_repair_protein_(RecF_pathway),_putative_675108..675258_POSITIVE 257 119 73 47 1 NC_009009:SSA_2094|3end_Conserved_uncharacterized_protein_2097990..2098140_NEGATIVE 254 135 93 145 104 NC_009009:SSA_1771|3end_Conserved_DNA_methyltransferase_protein,_putative_1758491..1758641_NEGATIVE 254 139 101 52 19 NC_009009:SSA_0473|3end_Precorrin-6x_reductase,_putative_476331..476481_POSITIVE 253 90 43 128 80 NC_009009:SSA_0263|3end_Zinc_metalloproteinase_in_scaA_5'region,_putative_258246..258396_POSITIVE 250 90 50 106 64 NC_009009:SSA_1010|3end_UDP-glucose_4-epimerase,_putative_1013862..1014012_POSITIVE 249 136 94 64 30 NC_009009:SSA_2214|3end_2-C-methyl-D-erythritol_4-phosphate_cytidylyltransferase_2,_putative_2215113..2215263_NEGATIVE 249 139 96 142 92 NC_009009:SSA_2198|3end_hypothetical_protein_2197842..2197992_NEGATIVE 247 140 93 78 37 NC_009009:SSA_0899|3end_Conserved_permease,_putative_891161..891311_POSITIVE 247 84 52 87 54 NC_009009:SSA_0405|3end_Transcriptional_regulator,_XRE_family,_putative_402115..402265_POSITIVE 246 87 50 52 9 NC_009009:SSA_1230|3end_Conserved_uncharacterized_protein_1252612..1252762_NEGATIVE