Origin IGS: tctcactgattggatttattgtaccaaaagaagcagaaaggcgcaatcgtttgcgtctttcactatcataaacacttaactcttttatattttgaaaaatctttttaaaattgaaaatgaaacatttttagctgagacaaaaagccacaaaaagagtatactaatctgtatagaaatcggtaaaggagctctctt .........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 aagagagctcctttaccgatttctatacagattagtatactctttttgtggctttttgtctcagctaaaaatgtttcattttcaattttaaaaagatttttcaaaatataaaagagttaagtgtttatgatagtgaaagacgcaaacgattgcgcctttctgcttcttttggtacaataaatccaatcagtgaga Mask Tandem Repeat Region ================================================ tctcactgattggatttattgtaccaaaagaagcagaaaggcgcaatcgtttgcgtctttcactatcataaacacttaactcttttatattttgaaaaatctttttaaaattgaaaatgaaacatttttagctgagacaaaaagccacaaaaagagtatactaatctgtatagaaatcggtaaaggagctctctt Find is-nt database================================================ Query_seq: SSA_1024:SSA_1026|SSA_1024:SSA_1026:Alpha-amylase, putative:ABC-type multidrug transporter, ATPase component, putative:<-->:1042739..1042933 195 tctcactgattggatttattgtaccaaaagaagcagaaaggcgcaatcgtttgcgtctttcactatcataaacacttaactcttttatattttgaaaaatctttttaaaattgaaaatgaaacatttttagctgagacaaaaagccacaaaaagagtatactaatctgtatagaaatcggtaaaggagctctctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1024:SSA_1026|SSA_1024:SSA_1026:Alpha-amylase, putative:ABC-type multidrug transporter, ATPase component, putative:<-->:1042739..1042933 195 tctcactgattggatttattgtaccaaaagaagcagaaaggcgcaatcgtttgcgtctttcactatcataaacacttaactcttttatattttgaaaaatctttttaaaattgaaaatgaaacatttttagctgagacaaaaagccacaaaaagagtatactaatctgtatagaaatcggtaaaggagctctctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1024:SSA_1026|SSA_1024:SSA_1026:Alpha-amylase, putative:ABC-type multidrug transporter, ATPase component, putative:<-->:1042739..1042933 195 tctcactgattggatttattgtaccaaaagaagcagaaaggcgcaatcgtttgcgtctttcactatcataaacacttaactcttttatattttgaaaaatctttttaaaattgaaaatgaaacatttttagctgagacaaaaagccacaaaaagagtatactaatctgtatagaaatcggtaaaggagctctctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tctcactgattggatttattgtaccaaaagaagcagaaaggcgcaatcgtttgcgtctttcactatcataaacacttaactcttttatattttgaaaaatctttttaaaattgaaaatgaaacatttttagctgagacaaaaagccacaaaaagagtatactaatctgtatagaaatcggtaaaggagctctctt Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 10 End: 105 ......... M D L L Y Q K K Q K G A I V C V F H Y H K H L T L L Y F E K S F .......................................................................................... Protein_Len: 35 Strand: + Start: 89 End: 193 ........................................................................................ M L K N L F K I E N E T F L A E T K S H K K S I L I C I E I G K G A L .. Protein_Len: 30 Strand: - Start: 88 End: 177 ....................................................................................... I K F F R K L I S F S V N K A S V F L W L F L I S I Q I S M .................. Protein_Len: 39 Strand: - Start: 2 End: 118 . E S I P N I T G F S A S L R L R K R R E S D Y V S L E K I N Q F I K K F N F M ............................................................................. tctcactgattggatttattgtaccaaaagaagcagaaaggcgcaatcgtttgcgtctttcactatcataaacacttaactcttttatattttgaaaaatctttttaaaattgaaaatgaaacatttttagctgagacaaaaagccacaaaaagagtatactaatctgtatagaaatcggtaaaggagctctctt 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: 18 End: 47 .................ATTGCGCCTTTCTGCTTCTTTTGGTACAAT.................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tctcactgattggatttattgtaccaaaagaagcagaaaggcgcaatcgtttgcgtctttcactatcataaacacttaactcttttatattttgaaaaatctttttaaaattgaaaatgaaacatttttagctgagacaaaaagccacaaaaagagtatactaatctgtatagaaatcggtaaaggagctctctt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 70 HP_score: -5.5 Tail_Score: -4.25658 Start: 33 End: 63 Full_Region: taagtgtttatgata gtgaaagacgcaa acga ttgcgcctttctgc ttcttttggtacaat ................................gtgaaagacgcaaacgattgcgcctttctgc.................................................................................................................................... TransTerm Strand: - Conf: 81 HP_score: -10.5 Tail_Score: -3.12766 Start: 36 End: 61 Full_Region: agtgtttatgatagt gaaagacgcaa acga ttgcgcctttc tgcttcttttggtac ...................................gaaagacgcaaacgattgcgcctttc...................................................................................................................................... Find igs database================================================ Query_seq: SSA_1024:SSA_1026|SSA_1024:SSA_1026:Alpha-amylase, putative:ABC-type multidrug transporter, ATPase component, putative:<-->:1042739..1042933 195 tctcactgattggatttattgtaccaaaagaagcagaaaggcgcaatcgtttgcgtctttcactatcataaacacttaactcttttatattttgaaaaatctttttaaaattgaaaatgaaacatttttagctgagacaaaaagccacaaaaagagtatactaatctgtatagaaatcggtaaaggagctctctt Intra-Species Hit: Count: 1 Min: 1 Max: 195 Len: 195 Subject: NC_009009_SSA_1024_SSA_1026|Alpha-amylase, putative:ABC-type multidrug transporter, ATPase component, putative|NEGATIVE:POSITIVE|[1042739,1042933]|195 HSP 1 e-value: 3.0E-39 bit: 163.0 Len: 82 Query Start:1 Query End:82 Subject Strand: POSITIVE Subject Start: 1 Subject End: 82 tctcactgattggatttattgtaccaaaagaagcagaaaggcgcaatcgtttgcgtctttcactatcataaacacttaactc................................................................................................................. tctcactgattggatttattgtaccaaaagaagcagaaaggcgcaatcgtttgcgtctttcactatcataaacacttaactc................................................................................................................. HSP 2 e-value: 2.0E-15 bit: 83.8 Len: 42 Query Start:154 Query End:195 Subject Strand: POSITIVE Subject Start: 154 Subject End: 195 .........................................................................................................................................................gagtatactaatctgtatagaaatcggtaaaggagctctctt .........................................................................................................................................................gagtatactaatctgtatagaaatcggtaaaggagctctctt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUCACUGAUUGGAUUUAUUGUACCAAAAGAAGCAGAAAGGCGCAAUCGUUUGCGUCUUUCACUAUCAUAAACACUUAACUCUUUUAUAUUUUGAAAAAUCUUUUUAAAAUUGAAAAUGAAACAUUUUUAGCUGAGACAAAAAGCCACAAAAAGAGUAUACUAAUCUGUAUAGAAAUCGGUAAAGGAGCUCUCUU .(((.((...(.(((((.((((((....(((....(((((((((((....))))))))))).................((((((((..(((((((((.....)))))))))((((((((...))))))))(((.........)))....)))))))).......)))))))))))))).)...)))))....... (-41.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGAGAGCUCCUUUACCGAUUUCUAUACAGAUUAGUAUACUCUUUUUGUGGCUUUUUGUCUCAGCUAAAAAUGUUUCAUUUUCAAUUUUAAAAAGAUUUUUCAAAAUAUAAAAGAGUUAAGUGUUUAUGAUAGUGAAAGACGCAAACGAUUGCGCCUUUCUGCUUCUUUUGGUACAAUAAAUCCAAUCAGUGAGA .(((((((..(......((....(((((......))))).)).....)..))))))).(((((.((.((((((...))))))............(((((.........(((((((................((((((((.(((((....))))).))))).)))))))))).......))))).....))))))) (-29.48) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 895 70 21 161 112 NC_009009:SSA_1024|5end_Alpha-amylase,_putative_1042648..1042878_NEGATIVE 301 90 41 72 22 NC_009009:SSA_0483|5end_Siroheme_synthase,_putative_484045..484275_POSITIVE 299 59 12 94 41 NC_009009:SSA_2166|5end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_2165642..2165872_NEGATIVE 289 54 19 34 3 NC_009009:SSA_2193|5end_ADP-ribose_pyrophosphatase,_putative_2194793..2195023_NEGATIVE 277 67 25 176 137 NC_009009:SSA_0858|5end_DTDP-L-rhamnose_synthase,_putative_845512..845742_POSITIVE 271 68 24 219 170 NC_009009:SSA_0040|5end_Phosphoribosylaminoimidazole_carboxylase,_ATPase_subunit,_putative_46308..46538_POSITIVE 267 80 33 58 17 NC_009009:SSA_0807|5end_GTP-binding_protein,_putative_789449..789679_POSITIVE 266 70 24 171 127 NC_009009:SSA_1459|5end_RNA_methyltransferase,_putative_1467481..1467711_NEGATIVE 265 66 28 199 160 NC_009009:SSA_1869|5end_ATP-dependent_RNA_helicase,_putative_1865495..1865725_NEGATIVE 264 58 15 153 112 NC_009009:SSA_0773|5end_PTS_enzyme_I,_putative_752603..752833_POSITIVE 256 60 11 202 144 NC_009009:SSA_1441|5end_Phosphoribosyl-AMP_cyclohydrolase,_putative_1445183..1445413_NEGATIVE 256 70 33 231 194 NC_009009:SSA_0055|5end_PTS_system,_IIC_component,_putative_59034..59264_POSITIVE 255 54 32 31 6 NC_009009:SSA_2303|5end_hypothetical_protein_2305177..2305407_NEGATIVE 254 50 1 67 4 NC_009009:SSA_0243|5end_Cyclo-nucleotide_phosphodiesterase,_putative_238235..238465_NEGATIVE 251 70 24 184 124 NC_009009:SSA_2359|5end_Glucose_inhibited_division_protein_A,_putative_2362520..2362750_NEGATIVE 251 68 35 68 34 NC_009009:SSA_1043|5end_Homoserine_dehydrogenase,_putative_1058565..1058795_POSITIVE 251 56 13 225 166 NC_009009:SSA_0924|5end_ABC-type_antimicrobial_peptide_transport_system,_permease_component,_putative_933738..933968_POSITIVE 248 60 14 172 119 NC_009009:SSA_2264|5end_hypothetical_protein_2261757..2261987_NEGATIVE 246 58 19 157 121 NC_009009:SSA_1280|5end_hypothetical_protein_1301596..1301826_NEGATIVE 245 69 24 91 52 NC_009009:SSA_1778|5end_Segregation_and_condensation_protein_B,_putative_1765711..1765941_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 301 90 41 60 10 NC_009009:SSA_0482|3end_ATP:cobalamin_adenosyl_transferase,_putative_484113..484263_POSITIVE 299 59 12 92 39 NC_009009:SSA_2167|3end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_2165644..2165794_NEGATIVE 277 67 25 66 27 NC_009009:SSA_0857|3end_hypothetical_protein_845482..845632_POSITIVE 270 68 31 85 39 NC_009009:SSA_0148|3end_Sugar_ABC_transporter,_ATP-binding_protein,_putative_143467..143617_POSITIVE 266 70 24 86 42 NC_009009:SSA_1460|3end_Transcriptional_attenuator_LytR,_putative_1467566..1467716_NEGATIVE 265 66 28 94 55 NC_009009:SSA_1870|3end_Phospho-N-acetylmuramoyl-pentapeptide-_transferase,_putative_1865600..1865750_NEGATIVE 264 58 15 151 110 NC_009009:SSA_0772|3end_Histidine-containing_phosphocarrier_protein_of_the_PTS,_putative_752681..752831_POSITIVE 263 60 13 112 46 NC_009009:SSA_0923|3end_Transcriptional_regulator,_TetR/AcrR_family,_putative_933698..933848_POSITIVE 256 62 31 87 53 NC_009009:SSA_0452|3end_Nitrogen_utilization_substance_protein_B,_putative_452060..452210_POSITIVE 248 77 32 110 52 NC_009009:SSA_0903|3end_NAD(P)H_dehydrogenase_(quinone),_putative_893813..893963_POSITIVE 248 59 13 60 15 NC_009009:SSA_0039|3end_Phosphoribosylaminoimidazole_carboxylase,_catalytic_subunit,_putative_46401..46551_POSITIVE 247 60 14 102 49 NC_009009:SSA_0583|3end_Nucleotidyltransferase,_putative_575679..575829_POSITIVE 246 58 19 145 109 NC_009009:SSA_1281|3end_Uracil-DNA_glycosylase,_putative_1301608..1301758_NEGATIVE 245 69 24 98 59 NC_009009:SSA_1779|3end_Segregation_and_condensation_protein_A,_putative_1765704..1765854_NEGATIVE 243 69 21 85 43 NC_009009:SSA_0232|3end_hypothetical_protein_227277..227427_POSITIVE 240 42 6 67 25 NC_009009:SSA_1957|3end_Glycosyl_transferase_N-acetylglucosaminyltransferase,_putative_1953504..1953654_NEGATIVE 237 63 32 140 106 NC_009009:SSA_1179|3end_Carbamoylphosphate_synthase_large_subunit_/_biotin_carboxylase,_putative_1206640..1206790_NEGATIVE 236 76 34 82 31 NC_009009:SSA_0520|3end_Ethanolamine_ammonia-lyase_light_chain,_putative_520462..520612_POSITIVE 231 54 15 78 43 NC_009009:SSA_1562|3end_hypothetical_protein_1566005..1566155_NEGATIVE 230 60 14 64 23 NC_009009:SSA_2116|3end_Cmp-binding-factor_1,_putative_2117622..2117772_NEGATIVE