Origin IGS: ttggttatttctcctattaatttattttacagtttattataacattatttagcaaaaacggataggcaggacctacccgttctcaatgtttatcttgttttgttggtttcaacttgtagataagttgaattgaactcgggctaaaagctcggaaaatagataagcttttctagaatctttgattctgcgtcaagcttcctaattttcagtcgcttttttaacgcccttagtatcttattc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gaataagatactaagggcgttaaaaaagcgactgaaaattaggaagcttgacgcagaatcaaagattctagaaaagcttatctattttccgagcttttagcccgagttcaattcaacttatctacaagttgaaaccaacaaaacaagataaacattgagaacgggtaggtcctgcctatccgtttttgctaaataatgttataataaactgtaaaataaattaataggagaaataaccaa Mask Tandem Repeat Region ================================================ ttggttatttctcctattaatttattttacagtttattataacattatttagcaaaaacggataggcaggacctacccgttctcaatgtttatcttgttttgttggtttcaacttgtagataagttgaattgaactcgggctaaaagctcggaaaatagataagcttttctagaatctttgattctgcgtcaagcttcctaattttcagtcgcttttttaacgcccttagtatcttattc Find is-nt database================================================ Query_seq: SSA_2109:SSA_2110|SSA_2109:SSA_2110:Elongation factor G, putative:30S ribosomal protein S7, putative:<-<-:2114959..2115198 240 ttggttatttctcctattaatttattttacagtttattataacattatttagcaaaaacggataggcaggacctacccgttctcaatgtttatcttgttttgttggtttcaacttgtagataagttgaattgaactcgggctaaaagctcggaaaatagataagcttttctagaatctttgattctgcgtcaagcttcctaattttcagtcgcttttttaacgcccttagtatcttattc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2109:SSA_2110|SSA_2109:SSA_2110:Elongation factor G, putative:30S ribosomal protein S7, putative:<-<-:2114959..2115198 240 ttggttatttctcctattaatttattttacagtttattataacattatttagcaaaaacggataggcaggacctacccgttctcaatgtttatcttgttttgttggtttcaacttgtagataagttgaattgaactcgggctaaaagctcggaaaatagataagcttttctagaatctttgattctgcgtcaagcttcctaattttcagtcgcttttttaacgcccttagtatcttattc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2109:SSA_2110|SSA_2109:SSA_2110:Elongation factor G, putative:30S ribosomal protein S7, putative:<-<-:2114959..2115198 240 ttggttatttctcctattaatttattttacagtttattataacattatttagcaaaaacggataggcaggacctacccgttctcaatgtttatcttgttttgttggtttcaacttgtagataagttgaattgaactcgggctaaaagctcggaaaatagataagcttttctagaatctttgattctgcgtcaagcttcctaattttcagtcgcttttttaacgcccttagtatcttattc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttggttatttctcctattaatttattttacagtttattataacattatttagcaaaaacggataggcaggacctacccgttctcaatgtttatcttgttttgttggtttcaacttgtagataagttgaattgaactcgggctaaaagctcggaaaatagataagcttttctagaatctttgattctgcgtcaagcttcctaattttcagtcgcttttttaacgcccttagtatcttattc Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: - Start: 144 End: 233 ............................................................................................................................................... F S P F Y I L K E L I K S E A D L K R I K L R K K L A R L M ....... ttggttatttctcctattaatttattttacagtttattataacattatttagcaaaaacggataggcaggacctacccgttctcaatgtttatcttgttttgttggtttcaacttgtagataagttgaattgaactcgggctaaaagctcggaaaatagataagcttttctagaatctttgattctgcgtcaagcttcctaattttcagtcgcttttttaacgcccttagtatcttattc 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: 81 Start: 36 End: 65 ...................................CTATCCGTTTTTGCTAAATAATGTTATAAT............................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttggttatttctcctattaatttattttacagtttattataacattatttagcaaaaacggataggcaggacctacccgttctcaatgtttatcttgttttgttggtttcaacttgtagataagttgaattgaactcgggctaaaagctcggaaaatagataagcttttctagaatctttgattctgcgtcaagcttcctaattttcagtcgcttttttaacgcccttagtatcttattc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -9.7 Tail_Score: -4.75372 Start: 59 End: 79 Full_Region: gataaacattgagaa cgggtaggt cct gcctatccg tttttgctaaataat ..........................................................cgggtaggtcctgcctatccg................................................................................................................................................................. Find igs database================================================ Query_seq: SSA_2109:SSA_2110|SSA_2109:SSA_2110:Elongation factor G, putative:30S ribosomal protein S7, putative:<-<-:2114959..2115198 240 ttggttatttctcctattaatttattttacagtttattataacattatttagcaaaaacggataggcaggacctacccgttctcaatgtttatcttgttttgttggtttcaacttgtagataagttgaattgaactcgggctaaaagctcggaaaatagataagcttttctagaatctttgattctgcgtcaagcttcctaattttcagtcgcttttttaacgcccttagtatcttattc Intra-Species Hit: Count: 1 Min: 1 Max: 240 Len: 240 Subject: NC_009009_SSA_2109_SSA_2110|Elongation factor G, putative:30S ribosomal protein S7, putative|NEGATIVE:NEGATIVE|[2114959,2115198]|240 HSP 1 e-value: 1.0E-133 bit: 476.0 Len: 240 Query Start:1 Query End:240 Subject Strand: POSITIVE Subject Start: 1 Subject End: 240 ttggttatttctcctattaatttattttacagtttattataacattatttagcaaaaacggataggcaggacctacccgttctcaatgtttatcttgttttgttggtttcaacttgtagataagttgaattgaactcgggctaaaagctcggaaaatagataagcttttctagaatctttgattctgcgtcaagcttcctaattttcagtcgcttttttaacgcccttagtatcttattc ttggttatttctcctattaatttattttacagtttattataacattatttagcaaaaacggataggcaggacctacccgttctcaatgtttatcttgttttgttggtttcaacttgtagataagttgaattgaactcgggctaaaagctcggaaaatagataagcttttctagaatctttgattctgcgtcaagcttcctaattttcagtcgcttttttaacgcccttagtatcttattc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGGUUAUUUCUCCUAUUAAUUUAUUUUACAGUUUAUUAUAACAUUAUUUAGCAAAAACGGAUAGGCAGGACCUACCCGUUCUCAAUGUUUAUCUUGUUUUGUUGGUUUCAACUUGUAGAUAAGUUGAAUUGAACUCGGGCUAAAAGCUCGGAAAAUAGAUAAGCUUUUCUAGAAUCUUUGAUUCUGCGUCAAGCUUCCUAAUUUUCAGUCGCUUUUUUAACGCCCUUAGUAUCUUAUUC ..((........)).............(((.(((((............(((((((((..(((((((((((((......))))....)))))))))..))))))))).(((((((((....))))))))).)))))..((((.((((((...((((((((..((((((..((((((((...))))))).)..)))))).)).))))))....)))))).....))))...)))........ (-54.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAUAAGAUACUAAGGGCGUUAAAAAAGCGACUGAAAAUUAGGAAGCUUGACGCAGAAUCAAAGAUUCUAGAAAAGCUUAUCUAUUUUCCGAGCUUUUAGCCCGAGUUCAAUUCAACUUAUCUACAAGUUGAAACCAACAAAACAAGAUAAACAUUGAGAACGGGUAGGUCCUGCCUAUCCGUUUUUGCUAAAUAAUGUUAUAAUAAACUGUAAAAUAAAUUAAUAGGAGAAAUAACCAA ......((.(((..((((.....((((((..(.((((((.(((((((((..(..((((((...)))))).)..)))))).))))))))).).)))))).)))).)))))..((((((((......)))))))).................(((((((((((((((((((.....))))))))))))).......))))))..........................((........)).. (-59.11) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 898 100 51 191 142 NC_009009:SSA_2109|5end_Elongation_factor_G,_putative_2114868..2115098_NEGATIVE 334 228 186 158 112 NC_009009:SSA_1560|5end_Structural_maintenance_of_chromosome_protein_(chromosome_segregation_ATPase),_putative_1565194..1565424_NEGATIVE 306 100 51 156 92 NC_009009:SSA_2322|5end_Transcriptional_regulator,_TetR/AcrR_family,_putative_2327044..2327274_POSITIVE 294 226 187 181 137 NC_009009:SSA_2222|5end_Tyrosine-protein_kinase_Wze,_putative_2223997..2224227_NEGATIVE 289 143 102 160 125 NC_009009:SSA_0121|5end_hypothetical_protein_115183..115413_POSITIVE 287 100 53 181 128 NC_009009:SSA_1459|5end_RNA_methyltransferase,_putative_1467481..1467711_NEGATIVE 285 225 181 192 155 NC_009009:SSA_1156|5end_hypothetical_protein_1184562..1184792_POSITIVE 278 219 185 222 191 NC_009009:SSA_1693|5end_Phosphotransferase_system_lactose-specific_component_IIBC,_putative_1686811..1687041_NEGATIVE 277 227 182 202 160 NC_009009:SSA_0978|5end_hypothetical_protein_983736..983966_POSITIVE 276 219 178 110 69 NC_009009:SSA_1296|5end_hypothetical_protein_1313013..1313243_NEGATIVE 271 225 181 69 21 NC_009009:SSA_0163|5end_hypothetical_protein_162127..162357_POSITIVE 270 207 164 116 68 NC_009009:SSA_1172|5end_hypothetical_protein_1199926..1200156_NEGATIVE 270 228 185 128 80 NC_009009:SSA_0964|5end_DEAD_RNA_helicase,_putative_974114..974344_NEGATIVE 268 206 164 117 57 NC_009009:SSA_1585|5end_hypothetical_protein_1587604..1587834_NEGATIVE 266 215 176 48 9 NC_009009:SSA_0199|5end_GTP_cyclohydrolase_I,_putative_198276..198506_POSITIVE 263 228 183 189 150 NC_009009:SSA_0778|5end_Glycogen_synthase,_putative_760566..760796_POSITIVE 262 114 71 160 112 NC_009009:SSA_0402|5end_Histidine_kinase,_putative_399144..399374_POSITIVE 262 203 163 105 63 NC_009009:SSA_0239|5end_7,8-dihydro-8-oxoguanine-triphosphatase,_putative_232961..233191_POSITIVE 261 239 191 85 34 NC_009009:SSA_0834|5end_Accessory_secretory_protein_Asp2,_putative_819510..819740_POSITIVE 258 240 192 186 133 NC_009009:SSA_1010|5end_UDP-glucose_4-epimerase,_putative_1012739..1012969_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 412 239 194 95 47 NC_009009:SSA_0093|3end_V-type_sodium_ATPase,_subunit_D,_putative_94989..95139_POSITIVE 325 234 196 86 49 NC_009009:SSA_2058|3end_30S_ribosomal_protein_S15,_putative_2060058..2060208_NEGATIVE 287 100 53 96 43 NC_009009:SSA_1460|3end_Transcriptional_attenuator_LytR,_putative_1467566..1467716_NEGATIVE 279 236 193 139 79 NC_009009:SSA_2287|3end_50S_ribosomal_protein_L32,_putative_2290083..2290233_POSITIVE 267 98 52 128 79 NC_009009:SSA_0272|3end_Oxidoreductase,_aldo/keto_reductase_family,_putative_267032..267182_POSITIVE 266 215 176 67 28 NC_009009:SSA_0198|3end_Dihydrofolate_synthetase,_putative_198375..198525_POSITIVE 262 203 163 95 53 NC_009009:SSA_0238|3end_hypothetical_protein_233031..233181_POSITIVE 261 239 191 95 44 NC_009009:SSA_0833|3end_Accessory_secretory_protein_Asp1,_putative_819600..819750_POSITIVE 257 226 181 62 18 NC_009009:SSA_1864|3end_Nicotinate_phosphoribosyltransferase_(NAPRTase),_subgroup_A,_putative_1859410..1859560_NEGATIVE 257 117 72 63 12 NC_009009:SSA_0676|3end_Farnesyl_diphosphate_synthase,_putative_659553..659703_POSITIVE 256 209 164 76 21 NC_009009:SSA_1451|3end_Exonuclease_RexA,_putative_1452744..1452894_NEGATIVE 255 106 61 150 103 NC_009009:SSA_0401|3end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_winged-helix_DNA-binding_domains),_putative_399222..399372_POSITIVE 254 210 164 52 7 NC_009009:SSA_0473|3end_Precorrin-6x_reductase,_putative_476331..476481_POSITIVE 253 224 189 126 76 NC_009009:SSA_1900|3end_N_utilization_substance_protein_A,_putative_1894750..1894900_NEGATIVE 253 214 174 145 99 NC_009009:SSA_1301|3end_Conserved_uncharacterized_protein,_possible_surface_protein_1319010..1319160_NEGATIVE 252 45 4 58 15 NC_009009:SSA_1999|3end_hypothetical_protein_1996411..1996561_NEGATIVE 252 152 116 67 34 NC_009009:SSA_1571|3end_Threonyl-tRNA_synthetase,_putative_1573211..1573361_NEGATIVE 252 228 184 55 3 NC_009009:SSA_0315|3end_Transcriptional_regulator,_MarR_family,_putative_310646..310796_POSITIVE 251 236 195 137 86 NC_009009:SSA_2228|3end_Acetyltransferase_(GNAT)_family,_putative_2228271..2228421_NEGATIVE 250 227 181 137 86 NC_009009:SSA_2261|3end_Transcriptional_repressor_(arginine_synthesis),_putative_2258229..2258379_NEGATIVE