Origin IGS: ttgaagtctattttcaaccaaggcagggcaagccttggttttttctttgaaaatcaactttaaagttacaagtaaacataaagatacttgtcctgatatggtatactaatatcaaaagaccgcaaaaaggaga .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tctcctttttgcggtcttttgatattagtataccatatcaggacaagtatctttatgtttacttgtaactttaaagttgattttcaaagaaaaaaccaaggcttgccctgccttggttgaaaatagacttcaa Mask Tandem Repeat Region ================================================ ttgaagtctattttcaaccaaggcagggcaagccttggttttttctttgaaaatcaactttaaagttacaagtaaacataaagatacttgtcctgatatggtatactaatatcaaaagaccgcaaaaaggaga Find is-nt database================================================ Query_seq: SSA_0849:SSA_0850|SSA_0849:SSA_0850:Signal peptidase I, putative:Ubiquitin C-terminal hydrolase, putative:->->:836825..836957 133 ttgaagtctattttcaaccaaggcagggcaagccttggttttttctttgaaaatcaactttaaagttacaagtaaacataaagatacttgtcctgatatggtatactaatatcaaaagaccgcaaaaaggaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0849:SSA_0850|SSA_0849:SSA_0850:Signal peptidase I, putative:Ubiquitin C-terminal hydrolase, putative:->->:836825..836957 133 ttgaagtctattttcaaccaaggcagggcaagccttggttttttctttgaaaatcaactttaaagttacaagtaaacataaagatacttgtcctgatatggtatactaatatcaaaagaccgcaaaaaggaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0849:SSA_0850|SSA_0849:SSA_0850:Signal peptidase I, putative:Ubiquitin C-terminal hydrolase, putative:->->:836825..836957 133 ttgaagtctattttcaaccaaggcagggcaagccttggttttttctttgaaaatcaactttaaagttacaagtaaacataaagatacttgtcctgatatggtatactaatatcaaaagaccgcaaaaaggaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttgaagtctattttcaaccaaggcagggcaagccttggttttttctttgaaaatcaactttaaagttacaagtaaacataaagatacttgtcctgatatggtatactaatatcaaaagaccgcaaaaaggaga Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: - Start: 17 End: 115 ................ G L C P L G Q N K R Q F D V K F N C T F M F I S T R I H Y V L I M .................. Protein_Len: 33 Strand: - Start: 1 End: 99 Q L R N E V L A P C A K T K E K F I L K L T V L L C L S V Q G S M .................................. ttgaagtctattttcaaccaaggcagggcaagccttggttttttctttgaaaatcaactttaaagttacaagtaaacataaagatacttgtcctgatatggtatactaatatcaaaagaccgcaaaaaggaga 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================================================ ttgaagtctattttcaaccaaggcagggcaagccttggttttttctttgaaaatcaactttaaagttacaagtaaacataaagatacttgtcctgatatggtatactaatatcaaaagaccgcaaaaaggaga Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0849:SSA_0850|SSA_0849:SSA_0850:Signal peptidase I, putative:Ubiquitin C-terminal hydrolase, putative:->->:836825..836957 133 ttgaagtctattttcaaccaaggcagggcaagccttggttttttctttgaaaatcaactttaaagttacaagtaaacataaagatacttgtcctgatatggtatactaatatcaaaagaccgcaaaaaggaga Intra-Species Hit: Count: 1 Min: 1 Max: 133 Len: 133 Subject: NC_009009_SSA_0849_SSA_0850|Signal peptidase I, putative:Ubiquitin C-terminal hydrolase, putative|POSITIVE:POSITIVE|[836825,836957]|133 HSP 1 e-value: 7.0E-70 bit: 264.0 Len: 133 Query Start:1 Query End:133 Subject Strand: POSITIVE Subject Start: 1 Subject End: 133 ttgaagtctattttcaaccaaggcagggcaagccttggttttttctttgaaaatcaactttaaagttacaagtaaacataaagatacttgtcctgatatggtatactaatatcaaaagaccgcaaaaaggaga ttgaagtctattttcaaccaaggcagggcaagccttggttttttctttgaaaatcaactttaaagttacaagtaaacataaagatacttgtcctgatatggtatactaatatcaaaagaccgcaaaaaggaga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGAAGUCUAUUUUCAACCAAGGCAGGGCAAGCCUUGGUUUUUUCUUUGAAAAUCAACUUUAAAGUUACAAGUAAACAUAAAGAUACUUGUCCUGAUAUGGUAUACUAAUAUCAAAAGACCGCAAAAAGGAGA (((((((..(((((((((((((((.......))))))))........)))))))..)))))))....(((((((..........)))))))..((((((((....)).)))))).....((.......))... (-31.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUCCUUUUUGCGGUCUUUUGAUAUUAGUAUACCAUAUCAGGACAAGUAUCUUUAUGUUUACUUGUAACUUUAAAGUUGAUUUUCAAAGAAAAAACCAAGGCUUGCCCUGCCUUGGUUGAAAAUAGACUUCAA ........(((.((((..(((((((.........))))))).(((((((..........))))))).............(((((((........((((((((.......))))))))))))))).)))).))) (-29.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 311 64 26 193 158 NC_009009:SSA_2099|5end_ABC-type_arginine/histidine_transporter,_permease_protein,_putative_2104313..2104543_NEGATIVE 300 50 18 32 7 NC_009009:SSA_1998|5end_Trigger_factor,_putative_1996331..1996561_NEGATIVE 280 49 6 199 156 NC_009009:SSA_0335|5end_Phosphomevalonate_kinase,_putative_328792..329022_POSITIVE 272 40 4 58 25 NC_009009:SSA_1340|5end_Zn/Mn_ABC-type_porter_lipoprotein,_putative_1356372..1356602_NEGATIVE 270 46 2 202 161 NC_009009:SSA_0481|5end_Cobyric_acid_synthase,_putative_481962..482192_POSITIVE 269 48 16 87 50 NC_009009:SSA_2312|5end_hypothetical_protein_2315281..2315511_NEGATIVE 267 45 4 222 191 NC_009009:SSA_0946|5end_Phosphate_transport_system_regulatory_protein,_putative_953393..953623_POSITIVE 266 43 2 178 119 NC_009009:SSA_1793|5end_Histidine_kinase_(sensor_protein),_putative_1776361..1776591_NEGATIVE 266 45 5 224 180 NC_009009:SSA_0940|5end_NOL1/NOP2/sun_family_protein,_putative_947626..947856_POSITIVE 265 69 21 220 172 NC_009009:SSA_0065|5end_Low_molecular_weight_phosphotyrosine_protein_phosphatase,_putative_67175..67405_POSITIVE 264 60 17 101 48 NC_009009:SSA_1671|5end_hypothetical_protein_1669304..1669534_POSITIVE 261 48 1 98 33 NC_009009:SSA_1778|5end_Segregation_and_condensation_protein_B,_putative_1765711..1765941_NEGATIVE 260 33 16 47 29 NC_009009:SSA_0415|5end_Permease,_putative_410568..410798_POSITIVE 257 37 1 167 131 NC_009009:SSA_0062|5end_Aldose_1-epimerase,_putative_63732..63962_POSITIVE 256 50 2 198 153 NC_009009:SSA_1955|5end_ABC-type_Fe-S_cluster_assembly_transporter,_permease_component,_putative_1952602..1952832_NEGATIVE 256 58 18 231 178 NC_009009:SSA_0350|5end_Helicase,_putative_344218..344448_NEGATIVE 250 46 1 187 135 NC_009009:SSA_2189|5end_hypothetical_protein_2191097..2191327_NEGATIVE 248 62 22 81 41 NC_009009:SSA_1441|5end_Phosphoribosyl-AMP_cyclohydrolase,_putative_1445183..1445413_NEGATIVE 247 40 5 213 171 NC_009009:SSA_0810|5end_P-loop_ATPase,_putative_791582..791812_POSITIVE 240 41 6 231 193 NC_009009:SSA_0596|5end_hypothetical_protein_586913..587143_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 332 35 1 146 110 NC_009009:SSA_0916|3end_2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate_hydrolase,_putative_928992..929142_POSITIVE 303 50 18 84 48 NC_009009:SSA_0539|3end_PduO_protein,_putative_534867..535017_POSITIVE 278 40 1 75 28 NC_009009:SSA_0849|3end_Signal_peptidase_I,_putative_836764..836914_POSITIVE 263 49 4 84 40 NC_009009:SSA_0288|3end_hypothetical_protein_280740..280890_NEGATIVE 261 48 1 105 40 NC_009009:SSA_1779|3end_Segregation_and_condensation_protein_A,_putative_1765704..1765854_NEGATIVE 257 37 1 142 106 NC_009009:SSA_0061|3end_Tagatose_1,6-diphosphate_aldolase,_putative_63787..63937_POSITIVE 248 62 22 81 41 NC_009009:SSA_1442|3end_Imidazole_glycerol-phosphate_synthase_subunit_hisF,_putative_1445183..1445333_NEGATIVE 246 51 16 104 69 NC_009009:SSA_0861|3end_hypothetical_protein_851742..851892_NEGATIVE 240 49 6 90 43 NC_009009:SSA_1731|3end_ATP-dependent_Clp_protease,_proteolytic_subunit,_putative_1716218..1716368_NEGATIVE 239 38 1 151 115 NC_009009:SSA_0492|3end_NADH-dependent_flavin_oxidoreductase,_putative_492771..492921_POSITIVE 236 48 4 150 104 NC_009009:SSA_2047|3end_hypothetical_protein_2049735..2049885_NEGATIVE 236 42 2 92 49 NC_009009:SSA_0664|3end_Conserved_uncharacterized_protein_648784..648934_NEGATIVE 236 44 6 82 40 NC_009009:SSA_0485|3end_Porphobilinogen_deaminase,_putative_486732..486882_POSITIVE 235 41 17 73 54 NC_009009:SSA_1203|3end_hypothetical_protein_1227628..1227778_POSITIVE 235 60 18 58 17 NC_009009:SSA_0160|3end_hypothetical_protein_159519..159669_POSITIVE 233 45 2 151 111 NC_009009:SSA_1956|3end_ABC-type_Fe-S_cluster_assembly_transporter,_ATPase_component,_putative_1952644..1952794_NEGATIVE 233 48 2 50 1 NC_009009:SSA_0143|3end_Conserved_uncharacterized_protein_137880..138030_POSITIVE 231 60 19 55 13 NC_009009:SSA_1576|3end_Catabolite_control_protein_A,_putative_1579177..1579327_NEGATIVE 231 40 5 125 86 NC_009009:SSA_0245|3end_hypothetical_protein_239608..239758_POSITIVE 230 55 18 38 8 NC_009009:SSA_0089|3end_V-type_sodium_ATPase,_subunit_F,_putative_90330..90480_POSITIVE