Origin IGS: gatcttttctcctcttctttacttctgagactatgatagcaagtcttttttgaaaaatctcagctttttggacaagcggtaaaatgagggagatgagaggtaaaaatccatacaccaaaaaatccccgaccagaggtcagggatttgctc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gagcaaatccctgacctctggtcggggattttttggtgtatggatttttacctctcatctccctcattttaccgcttgtccaaaaagctgagatttttcaaaaaagacttgctatcatagtctcagaagtaaagaagaggagaaaagatc Mask Tandem Repeat Region ================================================ gatcttttctcctcttctttacttctgagactatgatagcaagtcttttttgaaaaatctcagctttttggacaagcggtaaaatgagggagatgagaggtaaaaatccatacaccaaaaaatccccgaccagaggtcagggatttgctc Find is-nt database================================================ Query_seq: SSA_1679:SSA_1680|SSA_1679:SSA_1680:ABC-type multidrug transport system, ATPase component, putative:ABC-type bacitracin resistance protein A, permease component, putative:<-<-:1673140..1673289 150 gatcttttctcctcttctttacttctgagactatgatagcaagtcttttttgaaaaatctcagctttttggacaagcggtaaaatgagggagatgagaggtaaaaatccatacaccaaaaaatccccgaccagaggtcagggatttgctc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1679:SSA_1680|SSA_1679:SSA_1680:ABC-type multidrug transport system, ATPase component, putative:ABC-type bacitracin resistance protein A, permease component, putative:<-<-:1673140..1673289 150 gatcttttctcctcttctttacttctgagactatgatagcaagtcttttttgaaaaatctcagctttttggacaagcggtaaaatgagggagatgagaggtaaaaatccatacaccaaaaaatccccgaccagaggtcagggatttgctc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1679:SSA_1680|SSA_1679:SSA_1680:ABC-type multidrug transport system, ATPase component, putative:ABC-type bacitracin resistance protein A, permease component, putative:<-<-:1673140..1673289 150 gatcttttctcctcttctttacttctgagactatgatagcaagtcttttttgaaaaatctcagctttttggacaagcggtaaaatgagggagatgagaggtaaaaatccatacaccaaaaaatccccgaccagaggtcagggatttgctc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gatcttttctcctcttctttacttctgagactatgatagcaagtcttttttgaaaaatctcagctttttggacaagcggtaaaatgagggagatgagaggtaaaaatccatacaccaaaaaatccccgaccagaggtcagggatttgctc Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 57 End: 149 ........................................................ M S A F W T S G K M R E M R G K N P Y T K K S P T R G Q G F A . Protein_Len: 37 Strand: - Start: 34 End: 144 ................................. S L L D K K F F R L K K S L R Y F S P S S L Y F D M C W F I G S W L D P M ...... Protein_Len: 44 Strand: - Start: 2 End: 133 . D K R R K K V E S V I I A L R K Q F I E A K Q V L P L I L S I L P L F G Y V L F D G V M ................. gatcttttctcctcttctttacttctgagactatgatagcaagtcttttttgaaaaatctcagctttttggacaagcggtaaaatgagggagatgagaggtaaaaatccatacaccaaaaaatccccgaccagaggtcagggatttgctc 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================================================ gatcttttctcctcttctttacttctgagactatgatagcaagtcttttttgaaaaatctcagctttttggacaagcggtaaaatgagggagatgagaggtaaaaatccatacaccaaaaaatccccgaccagaggtcagggatttgctc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1679:SSA_1680|SSA_1679:SSA_1680:ABC-type multidrug transport system, ATPase component, putative:ABC-type bacitracin resistance protein A, permease component, putative:<-<-:1673140..1673289 150 gatcttttctcctcttctttacttctgagactatgatagcaagtcttttttgaaaaatctcagctttttggacaagcggtaaaatgagggagatgagaggtaaaaatccatacaccaaaaaatccccgaccagaggtcagggatttgctc Intra-Species Hit: Count: 1 Min: 1 Max: 150 Len: 150 Subject: NC_009009_SSA_1679_SSA_1680|ABC-type multidrug transport system, ATPase component, putative:ABC-type bacitracin resistance protein A, permease component, putative|NEGATIVE:NEGATIVE|[1673140,1673289]|150 HSP 1 e-value: 5.0E-80 bit: 297.0 Len: 150 Query Start:1 Query End:150 Subject Strand: POSITIVE Subject Start: 1 Subject End: 150 gatcttttctcctcttctttacttctgagactatgatagcaagtcttttttgaaaaatctcagctttttggacaagcggtaaaatgagggagatgagaggtaaaaatccatacaccaaaaaatccccgaccagaggtcagggatttgctc gatcttttctcctcttctttacttctgagactatgatagcaagtcttttttgaaaaatctcagctttttggacaagcggtaaaatgagggagatgagaggtaaaaatccatacaccaaaaaatccccgaccagaggtcagggatttgctc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUCUUUUCUCCUCUUCUUUACUUCUGAGACUAUGAUAGCAAGUCUUUUUUGAAAAAUCUCAGCUUUUUGGACAAGCGGUAAAAUGAGGGAGAUGAGAGGUAAAAAUCCAUACACCAAAAAAUCCCCGACCAGAGGUCAGGGAUUUGCUC ..((((.(((((.(((.((((((.((((((((.((....)))))))).((..((((........))))..))..)).))))))..)))))))).)))).....................(((((((.((((...)))).))))))).... (-38.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAGCAAAUCCCUGACCUCUGGUCGGGGAUUUUUUGGUGUAUGGAUUUUUACCUCUCAUCUCCCUCAUUUUACCGCUUGUCCAAAAAGCUGAGAUUUUUCAAAAAAGACUUGCUAUCAUAGUCUCAGAAGUAAAGAAGAGGAGAAAAGAUC (((.((((((((((((...))))))))))))...((((..........)))).))).(((((((..((((((.((((.......)))).((((((.......................))))))....)))))).)).)))))....... (-39.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 915 140 91 231 182 NC_009009:SSA_1679|5end_ABC-type_multidrug_transport_system,_ATPase_component,_putative_1673049..1673279_NEGATIVE 316 97 57 131 99 NC_009009:SSA_1606|5end_Dephospho-CoA_kinase,_putative_1612425..1612655_NEGATIVE 301 110 64 57 2 NC_009009:SSA_0622|5end_Transcriptional_regulator_(XRE_family),_SOS-response_transcriptional_repressors_(RecA-mediated_autopeptidases),_putative_614419..614649_NEGATIVE 297 102 62 213 167 NC_009009:SSA_2235|5end_Conserved_uncharacterized_protein_2235450..2235680_NEGATIVE 296 66 22 57 7 NC_009009:SSA_0852|5end_ATP-dependent_DNA_helicase,_putative_839050..839280_POSITIVE 286 128 81 164 108 NC_009009:SSA_0063|5end_Holliday_junction_DNA_helicase_ruvB,_putative_65335..65565_POSITIVE 284 47 3 129 92 NC_009009:SSA_1657|5end_hypothetical_protein_1653231..1653461_NEGATIVE 281 100 52 190 136 NC_009009:SSA_0899|5end_Conserved_permease,_putative_889903..890133_POSITIVE 277 100 52 86 37 NC_009009:SSA_1553|5end_Permease,_putative_1555047..1555277_POSITIVE 277 45 2 131 90 NC_009009:SSA_0219|5end_PTS_system,_sugar-specific_enzyme_IIA_component,_putative_215367..215597_POSITIVE 274 99 52 148 93 NC_009009:SSA_0741|5end_Acetylornithine_deacetylase/Succinyl-diaminopimelate_desuccinylase,_putative_723773..724003_POSITIVE 273 47 2 152 90 NC_009009:SSA_2278|5end_Ukp_protein,_putative_2281669..2281899_NEGATIVE 273 119 77 178 139 NC_009009:SSA_0379|5end_PTS_system,_beta-glucoside-specific_EII_component,_putative_368822..369052_POSITIVE 272 109 65 214 160 NC_009009:SSA_0326|5end_Conserved_uncharacterized_BCR,_YbaB_family_319823..320053_NEGATIVE 271 148 113 79 47 NC_009009:SSA_1050|5end_ABC_transporter_membrane-spanning_permease-spermidine/putrescine_transport,_putative_1064888..1065118_POSITIVE 270 149 115 55 13 NC_009009:SSA_0720|5end_hypothetical_protein_705106..705336_POSITIVE 269 110 63 215 162 NC_009009:SSA_2073|5end_Undecaprenyl_pyrophosphate_synthetase,_putative_2076371..2076601_NEGATIVE 269 150 114 49 1 NC_009009:SSA_2039|5end_Aminoacid_specific_permease,_putative_2044455..2044685_NEGATIVE 266 138 91 67 18 NC_009009:SSA_1562|5end_hypothetical_protein_1566364..1566594_NEGATIVE 265 103 63 213 179 NC_009009:SSA_1920|5end_Phosphotransferase_system,_mannose-specific_EIID,_putative_1909863..1910093_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 340 142 110 45 13 NC_009009:SSA_0068|3end_Alcohol-acetaldehyde_dehydrogenase,_putative_72848..72998_POSITIVE 316 97 57 125 93 NC_009009:SSA_1607|3end_Formamidopyrimidine-DNA_glycosylase,_putative_1612431..1612581_NEGATIVE 284 47 3 86 49 NC_009009:SSA_1658|3end_Cationic_amino_acid_transporter,_putative_1653274..1653424_NEGATIVE 277 100 52 89 40 NC_009009:SSA_1552|3end_hypothetical_protein_1555130..1555280_POSITIVE 276 102 61 151 105 NC_009009:SSA_2050|3end_Arabinose_efflux_permease,_putative_2054696..2054846_POSITIVE 274 99 52 126 71 NC_009009:SSA_0740|3end_C4-dicarboxylate_anaerobic_carrier,_possible_arginine_transporter,_putative_723831..723981_POSITIVE 273 47 2 150 88 NC_009009:SSA_2279|3end_hypothetical_protein_2281671..2281821_NEGATIVE 271 148 113 82 50 NC_009009:SSA_1049|3end_ABC_transporter_membrane-spanning_permease-spermidine/putrescine_transport,_putative_1064971..1065121_POSITIVE 264 80 31 124 70 NC_009009:SSA_1459|3end_RNA_methyltransferase,_putative_1466111..1466261_NEGATIVE 262 79 34 120 60 NC_009009:SSA_1782|3end_hypothetical_protein_1767602..1767752_NEGATIVE 262 139 95 56 9 NC_009009:SSA_0621|3end_SOS_responce_UmuC_protein,_putative_612322..612472_NEGATIVE 261 149 106 122 87 NC_009009:SSA_1618|3end_hypothetical_protein_1620720..1620870_NEGATIVE 261 119 75 138 88 NC_009009:SSA_0642|3end_Type_4_prepilin_peptidase,_putative_629391..629541_NEGATIVE 256 100 59 35 1 NC_009009:SSA_1961|3end_Amino_acid_ABC_transporter,_amino_acid-binding_protein/permease_protein,_putative_1960193..1960343_POSITIVE 251 79 33 50 3 NC_009009:SSA_1805|3end_Primosomal_protein_DnaI,_putative_1788665..1788815_NEGATIVE 249 110 61 46 2 NC_009009:SSA_2332|3end_D-alanyl_carrier_protein,_putative_2334957..2335107_NEGATIVE 248 150 107 52 1 NC_009009:SSA_1651|3end_hypothetical_protein_1649587..1649737_NEGATIVE 248 72 35 145 108 NC_009009:SSA_1118|3end_Peptide_methionine_sulfoxide_reductase,_putative_1144511..1144661_POSITIVE 247 108 62 62 1 NC_009009:SSA_0779|3end_Glycogen_phosphorylase,_putative_764685..764835_POSITIVE 246 128 85 108 57 NC_009009:SSA_0263|3end_Zinc_metalloproteinase_in_scaA_5'region,_putative_258246..258396_POSITIVE