Origin IGS: agaatcacctcgctttctacaaagtttagcattctaagcttagactttccaaaaaatcagtcagctactccagcaagatctaatagttctttgacaaaatcatcagccggctgttggagaatctcctgaggggaagcacgttgctggatatgtccttcatccaaaatcaagatagaggtacaaagacgctagcaaacgagtgatagcaatccgctaggtttaatcacccgaaagagcagctggatagtactactctatctcagcaaaacagttag .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 ctaactgttttgctgagatagagtagtactatccagctgctctttcgggtgattaaacctagcggattgctatcactcgtttgctagcgtctttgtacctctatcttgattttggatgaaggacatatccagcaacgtgcttcccctcaggagattctccaacagccggctgatgattttgtcaaagaactattagatcttgctggagtagctgactgattttttggaaagtctaagcttagaatgctaaactttgtagaaagcgaggtgattct Mask Tandem Repeat Region ================================================ agaatcacctcgctttctacaaagtttagcattctaagcttagactttccaaaaaatcagtcagctactccagcaagatctaatagttctttgacaaaatcatcagccggctgttggagaatctcctgaggggaagcacgttgctggatatgtccttcatccaaaatcaagatagaggtacaaagacgctagcaaacgagtgatagcaatccgctaggtttaatcacccgaaagagcagctggatagtactactctatctcagcaaaacagttag Find is-nt database================================================ Query_seq: SSA_1279:SSA_1280|SSA_1279:SSA_1280:Oxidoreductase, putative:hypothetical protein:<-<-:1300923..1301197 275 agaatcacctcgctttctacaaagtttagcattctaagcttagactttccaaaaaatcagtcagctactccagcaagatctaatagttctttgacaaaatcatcagccggctgttggagaatctcctgaggggaagcacgttgctggatatgtccttcatccaaaatcaagatagaggtacaaagacgctagcaaacgagtgatagcaatccgctaggtttaatcacccgaaagagcagctggatagtactactctatctcagcaaaacagttag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1279:SSA_1280|SSA_1279:SSA_1280:Oxidoreductase, putative:hypothetical protein:<-<-:1300923..1301197 275 agaatcacctcgctttctacaaagtttagcattctaagcttagactttccaaaaaatcagtcagctactccagcaagatctaatagttctttgacaaaatcatcagccggctgttggagaatctcctgaggggaagcacgttgctggatatgtccttcatccaaaatcaagatagaggtacaaagacgctagcaaacgagtgatagcaatccgctaggtttaatcacccgaaagagcagctggatagtactactctatctcagcaaaacagttag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1279:SSA_1280|SSA_1279:SSA_1280:Oxidoreductase, putative:hypothetical protein:<-<-:1300923..1301197 275 agaatcacctcgctttctacaaagtttagcattctaagcttagactttccaaaaaatcagtcagctactccagcaagatctaatagttctttgacaaaatcatcagccggctgttggagaatctcctgaggggaagcacgttgctggatatgtccttcatccaaaatcaagatagaggtacaaagacgctagcaaacgagtgatagcaatccgctaggtttaatcacccgaaagagcagctggatagtactactctatctcagcaaaacagttag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agaatcacctcgctttctacaaagtttagcattctaagcttagactttccaaaaaatcagtcagctactccagcaagatctaatagttctttgacaaaatcatcagccggctgttggagaatctcctgaggggaagcacgttgctggatatgtccttcatccaaaatcaagatagaggtacaaagacgctagcaaacgagtgatagcaatccgctaggtttaatcacccgaaagagcagctggatagtactactctatctcagcaaaacagttag Predict ORF larger than 30AA ================================================ Protein_Len: 41 Strand: + Start: 4 End: 126 ... M T S L S T K F S I L S L D F P K N Q S A T P A R S N S S L T K S S A G C W R I S ..................................................................................................................................................... Protein_Len: 34 Strand: + Start: 99 End: 200 .................................................................................................. M I S R L L E N L L R G S T L L D M S F I Q N Q D R G T K T L A N E ........................................................................... Protein_Len: 38 Strand: - Start: 60 End: 173 ........................................................... D A V G A L D L L E K V F D D A P Q Q L I E Q P S A R Q Q I H G E D L I L M ...................................................................................................... agaatcacctcgctttctacaaagtttagcattctaagcttagactttccaaaaaatcagtcagctactccagcaagatctaatagttctttgacaaaatcatcagccggctgttggagaatctcctgaggggaagcacgttgctggatatgtccttcatccaaaatcaagatagaggtacaaagacgctagcaaacgagtgatagcaatccgctaggtttaatcacccgaaagagcagctggatagtactactctatctcagcaaaacagttag 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================================================ agaatcacctcgctttctacaaagtttagcattctaagcttagactttccaaaaaatcagtcagctactccagcaagatctaatagttctttgacaaaatcatcagccggctgttggagaatctcctgaggggaagcacgttgctggatatgtccttcatccaaaatcaagatagaggtacaaagacgctagcaaacgagtgatagcaatccgctaggtttaatcacccgaaagagcagctggatagtactactctatctcagcaaaacagttag Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 40 HP_score: -2.1 Tail_Score: -2.73459 Start: 188 End: 207 Full_Region: taaacctagcggatt gctatca ctcgtt tgctagc gtctttgtacctcta ...........................................................................................................................................................................................gctatcactcgtttgctagc.................................................................... Find igs database================================================ Query_seq: SSA_1279:SSA_1280|SSA_1279:SSA_1280:Oxidoreductase, putative:hypothetical protein:<-<-:1300923..1301197 275 agaatcacctcgctttctacaaagtttagcattctaagcttagactttccaaaaaatcagtcagctactccagcaagatctaatagttctttgacaaaatcatcagccggctgttggagaatctcctgaggggaagcacgttgctggatatgtccttcatccaaaatcaagatagaggtacaaagacgctagcaaacgagtgatagcaatccgctaggtttaatcacccgaaagagcagctggatagtactactctatctcagcaaaacagttag Intra-Species Hit: Count: 1 Min: 1 Max: 275 Len: 275 Subject: NC_009009_SSA_1279_SSA_1280|Oxidoreductase, putative:hypothetical protein|NEGATIVE:NEGATIVE|[1300923,1301197]|275 HSP 1 e-value: 1.0E-154 bit: 545.0 Len: 275 Query Start:1 Query End:275 Subject Strand: POSITIVE Subject Start: 1 Subject End: 275 agaatcacctcgctttctacaaagtttagcattctaagcttagactttccaaaaaatcagtcagctactccagcaagatctaatagttctttgacaaaatcatcagccggctgttggagaatctcctgaggggaagcacgttgctggatatgtccttcatccaaaatcaagatagaggtacaaagacgctagcaaacgagtgatagcaatccgctaggtttaatcacccgaaagagcagctggatagtactactctatctcagcaaaacagttag agaatcacctcgctttctacaaagtttagcattctaagcttagactttccaaaaaatcagtcagctactccagcaagatctaatagttctttgacaaaatcatcagccggctgttggagaatctcctgaggggaagcacgttgctggatatgtccttcatccaaaatcaagatagaggtacaaagacgctagcaaacgagtgatagcaatccgctaggtttaatcacccgaaagagcagctggatagtactactctatctcagcaaaacagttag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAAUCACCUCGCUUUCUACAAAGUUUAGCAUUCUAAGCUUAGACUUUCCAAAAAAUCAGUCAGCUACUCCAGCAAGAUCUAAUAGUUCUUUGACAAAAUCAUCAGCCGGCUGUUGGAGAAUCUCCUGAGGGGAAGCACGUUGCUGGAUAUGUCCUUCAUCCAAAAUCAAGAUAGAGGUACAAAGACGCUAGCAAACGAGUGAUAGCAAUCCGCUAGGUUUAAUCACCCGAAAGAGCAGCUGGAUAGUACUACUCUAUCUCAGCAAAACAGUUAG ...........(((((....((((((((((.......)).))))))))...........(..(((...((((((((..((((((((((..((((........))))..))))))))))...(((((...)))))......))))))))..((((((..(((.........)))..))).))).....)))..)...((.(((((......((....))....))))).))..))))).(((((((((.......))))).))))........... (-70.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUAACUGUUUUGCUGAGAUAGAGUAGUACUAUCCAGCUGCUCUUUCGGGUGAUUAAACCUAGCGGAUUGCUAUCACUCGUUUGCUAGCGUCUUUGUACCUCUAUCUUGAUUUUGGAUGAAGGACAUAUCCAGCAACGUGCUUCCCCUCAGGAGAUUCUCCAACAGCCGGCUGAUGAUUUUGUCAAAGAACUAUUAGAUCUUGCUGGAGUAGCUGACUGAUUUUUUGGAAAGUCUAAGCUUAGAAUGCUAAACUUUGUAGAAAGCGAGGUGAUUCU .........((((.(((((((((..((((......(((((.....((((((((..((((....)).))...))))))))...)).)))......))))))))))))).....((((((.......))))))))))...(((((...((((.((...(((((.(((....((((((.((((.....)))).))))))...))).)))))...))..)))).((((((.(((((...(((.......)))..))))).))))))..)))))...... (-72.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1012 140 91 231 182 NC_009009:SSA_1279|5end_Oxidoreductase,_putative_1300832..1301062_NEGATIVE 399 147 105 66 9 NC_009009:SSA_1994|5end_CTP_synthase,_putative_1992474..1992704_NEGATIVE 384 149 106 79 32 NC_009009:SSA_0251|5end_D-tyrosyl-tRNA(Tyr)_deacylase,_putative_244455..244685_POSITIVE 378 145 103 132 78 NC_009009:SSA_2157|5end_ATP-dependent_serine_protease,_putative_2158241..2158471_NEGATIVE 375 179 131 226 179 NC_009009:SSA_1402|5end_ABC-type_multidrug_transport_system,_ATPase_and_permease_components,_putative_1416220..1416450_NEGATIVE 350 148 104 57 7 NC_009009:SSA_0227|5end_Collagen-binding_surface_protein,_putative_221037..221267_POSITIVE 347 50 3 194 134 NC_009009:SSA_0239|5end_7,8-dihydro-8-oxoguanine-triphosphatase,_putative_232961..233191_POSITIVE 341 260 212 188 132 NC_009009:SSA_0760|5end_Acetylornithine_aminotransferase,_putative_742581..742811_POSITIVE 332 79 35 200 160 NC_009009:SSA_0583|5end_Nucleotidyltransferase,_putative_574505..574735_POSITIVE 332 240 192 145 84 NC_009009:SSA_0479|5end_CbiQ_protein,_putative_480425..480655_POSITIVE 329 147 101 149 89 NC_009009:SSA_0051|5end_Dihydroxyacetone_kinase_phosphotransfer_protein,_putative_55190..55420_POSITIVE 325 145 105 167 129 NC_009009:SSA_2038|5end_hypothetical_protein_2041627..2041857_POSITIVE 322 157 114 129 86 NC_009009:SSA_2267|5end_Lactose_operon_transcriptional_repressor,_LacI_family,_putative_2266127..2266357_POSITIVE 321 137 101 70 28 NC_009009:SSA_2001|5end_Hydroxymethylpyrimidine/phosphomethylpyrimidine_kinase,_putative_1998220..1998450_NEGATIVE 321 148 105 201 153 NC_009009:SSA_0090|5end_Acetyltransferase,_GNAT_family,_putative_90258..90488_POSITIVE 319 243 205 199 156 NC_009009:SSA_0179|5end_hypothetical_protein_183966..184196_POSITIVE 318 166 122 204 146 NC_009009:SSA_1203|5end_hypothetical_protein_1226985..1227215_POSITIVE 314 150 103 78 27 NC_009009:SSA_1386|5end_NADPH-dependent_FMN_reductase,_putative_1402800..1403030_POSITIVE 313 149 106 44 2 NC_009009:SSA_2296|5end_Transcriptional_regulator,_XRE_family,_putative_2298773..2299003_NEGATIVE 313 130 85 159 116 NC_009009:SSA_2246|5end_Competence-damage_protein,_putative_2242496..2242726_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 358 139 101 79 38 NC_009009:SSA_2079|3end_Acetyltransferase,_putative_2084599..2084749_POSITIVE 329 147 101 149 89 NC_009009:SSA_0050|3end_Dihydroxyacetone_kinase,_phosphatase_domain_(Dak2),_putative_55270..55420_POSITIVE 328 145 101 71 3 NC_009009:SSA_1903|3end_hypothetical_protein_1897388..1897538_NEGATIVE 321 137 101 80 38 NC_009009:SSA_2002|3end_tRNA_pseudouridine_synthase_A,_putative_1998210..1998360_NEGATIVE 308 145 102 91 45 NC_009009:SSA_0899|3end_Conserved_permease,_putative_891161..891311_POSITIVE 304 170 121 149 106 NC_009009:SSA_1848|3end_Methionyl-tRNA_formyltransferase,_putative_1842243..1842393_NEGATIVE 302 147 106 144 104 NC_009009:SSA_2121|3end_Cell_wall_surface_anchor_family_protein,_putative_2122222..2122372_NEGATIVE 302 147 102 51 6 NC_009009:SSA_0484|3end_Glutamyl-tRNA_reductase,_putative_485825..485975_POSITIVE 302 150 102 106 46 NC_009009:SSA_0188|3end_hypothetical_protein_191111..191261_POSITIVE 295 230 187 111 71 NC_009009:SSA_2119|3end_Pentose-5-phosphate-3-epimerase,_putative_2120439..2120589_NEGATIVE 293 202 161 69 22 NC_009009:SSA_1788|3end_Integral_membrane_protein,_possible_receptor,_putative_1771656..1771806_NEGATIVE 289 78 31 74 25 NC_009009:SSA_2242|3end_hypothetical_protein_2238121..2238271_NEGATIVE 289 230 184 115 68 NC_009009:SSA_2077|3end_hypothetical_protein_2081352..2081502_NEGATIVE 286 145 105 49 2 NC_009009:SSA_2184|3end_hypothetical_protein_2183284..2183434_NEGATIVE 286 178 133 131 83 NC_009009:SSA_1454|3end_hypothetical_protein_1460255..1460405_NEGATIVE 286 112 71 143 111 NC_009009:SSA_0017|3end_Cell_shape_determining_protein_MreC,_putative_23706..23856_POSITIVE 285 149 101 86 23 NC_009009:SSA_1189|3end_GTP-binding_protein,_putative_1216806..1216956_NEGATIVE 284 168 122 64 6 NC_009009:SSA_1468|3end_3-dehydroquinate_synthase,_putative_1474385..1474535_NEGATIVE 284 66 23 143 88 NC_009009:SSA_0833|3end_Accessory_secretory_protein_Asp1,_putative_819600..819750_POSITIVE 284 150 103 103 47 NC_009009:SSA_0628|3end_Fe-S-cluster_redox_enzyme/radical_SAM_enzyme,_Cfr_family,_putative_619060..619210_POSITIVE