Origin IGS: gagcacccctcactttctccctctattataccatagttcggaacaatacgaggattaacggaataatatttgcggattaacggaatgatagtagctattaaataatgtaataccaacaattttctatcttgcagctagtttgtagtaaaaagagataacaaattgttatgctctctttcactgctatttcaaacataatttttccaagctagcttagaaaacc .........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 ggttttctaagctagcttggaaaaattatgtttgaaatagcagtgaaagagagcataacaatttgttatctctttttactacaaactagctgcaagatagaaaattgttggtattacattatttaatagctactatcattccgttaatccgcaaatattattccgttaatcctcgtattgttccgaactatggtataatagagggagaaagtgaggggtgctc Mask Tandem Repeat Region ================================================ gagcacccctcactttctccctctattataccatagttcggaacaatacgaggattaacggaataatatttgcggattaacggaatgatagtagctattaaataatgtaataccaacaattttctatcttgcagctagtttgtagtaaaaagagataacaaattgttatgctctctttcactgctatttcaaacataatttttccaagctagcttagaaaacc Find is-nt database================================================ Query_seq: SSA_1610:SSA_1611|SSA_1610:SSA_1611:hypothetical protein:Era-like GTP-binding protein, putative:<-<-:1615000..1615222 223 gagcacccctcactttctccctctattataccatagttcggaacaatacgaggattaacggaataatatttgcggattaacggaatgatagtagctattaaataatgtaataccaacaattttctatcttgcagctagtttgtagtaaaaagagataacaaattgttatgctctctttcactgctatttcaaacataatttttccaagctagcttagaaaacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1610:SSA_1611|SSA_1610:SSA_1611:hypothetical protein:Era-like GTP-binding protein, putative:<-<-:1615000..1615222 223 gagcacccctcactttctccctctattataccatagttcggaacaatacgaggattaacggaataatatttgcggattaacggaatgatagtagctattaaataatgtaataccaacaattttctatcttgcagctagtttgtagtaaaaagagataacaaattgttatgctctctttcactgctatttcaaacataatttttccaagctagcttagaaaacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1610:SSA_1611|SSA_1610:SSA_1611:hypothetical protein:Era-like GTP-binding protein, putative:<-<-:1615000..1615222 223 gagcacccctcactttctccctctattataccatagttcggaacaatacgaggattaacggaataatatttgcggattaacggaatgatagtagctattaaataatgtaataccaacaattttctatcttgcagctagtttgtagtaaaaagagataacaaattgttatgctctctttcactgctatttcaaacataatttttccaagctagcttagaaaacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gagcacccctcactttctccctctattataccatagttcggaacaatacgaggattaacggaataatatttgcggattaacggaatgatagtagctattaaataatgtaataccaacaattttctatcttgcagctagtttgtagtaaaaagagataacaaattgttatgctctctttcactgctatttcaaacataatttttccaagctagcttagaaaacc Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: - Start: 101 End: 199 .................................................................................................... I I Y Y W C N E I K C S T Q L L F L Y C I T I S E K V A I E F M M ........................ Protein_Len: 44 Strand: - Start: 3 End: 134 .. C G E S E G E I I G Y N P V I R P N V S Y Y K R I L P I I T A I L Y H L V L L K R D Q M ......................................................................................... gagcacccctcactttctccctctattataccatagttcggaacaatacgaggattaacggaataatatttgcggattaacggaatgatagtagctattaaataatgtaataccaacaattttctatcttgcagctagtttgtagtaaaaagagataacaaattgttatgctctctttcactgctatttcaaacataatttttccaagctagcttagaaaacc 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================================================ gagcacccctcactttctccctctattataccatagttcggaacaatacgaggattaacggaataatatttgcggattaacggaatgatagtagctattaaataatgtaataccaacaattttctatcttgcagctagtttgtagtaaaaagagataacaaattgttatgctctctttcactgctatttcaaacataatttttccaagctagcttagaaaacc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 74 HP_score: -5.3 Tail_Score: -4.7254 Start: 152 End: 173 Full_Region: aatagcagtgaaaga gagcataaca att tgttatctc tttttactacaaact .......................................................................................................................................................gagcataacaatttgttatctc.................................................. Find igs database================================================ Query_seq: SSA_1610:SSA_1611|SSA_1610:SSA_1611:hypothetical protein:Era-like GTP-binding protein, putative:<-<-:1615000..1615222 223 gagcacccctcactttctccctctattataccatagttcggaacaatacgaggattaacggaataatatttgcggattaacggaatgatagtagctattaaataatgtaataccaacaattttctatcttgcagctagtttgtagtaaaaagagataacaaattgttatgctctctttcactgctatttcaaacataatttttccaagctagcttagaaaacc Intra-Species Hit: Count: 1 Min: 1 Max: 223 Len: 223 Subject: NC_009009_SSA_1610_SSA_1611|hypothetical protein:Era-like GTP-binding protein, putative|NEGATIVE:NEGATIVE|[1615000,1615222]|223 HSP 1 e-value: 1.0E-123 bit: 442.0 Len: 223 Query Start:1 Query End:223 Subject Strand: POSITIVE Subject Start: 1 Subject End: 223 gagcacccctcactttctccctctattataccatagttcggaacaatacgaggattaacggaataatatttgcggattaacggaatgatagtagctattaaataatgtaataccaacaattttctatcttgcagctagtttgtagtaaaaagagataacaaattgttatgctctctttcactgctatttcaaacataatttttccaagctagcttagaaaacc gagcacccctcactttctccctctattataccatagttcggaacaatacgaggattaacggaataatatttgcggattaacggaatgatagtagctattaaataatgtaataccaacaattttctatcttgcagctagtttgtagtaaaaagagataacaaattgttatgctctctttcactgctatttcaaacataatttttccaagctagcttagaaaacc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAGCACCCCUCACUUUCUCCCUCUAUUAUACCAUAGUUCGGAACAAUACGAGGAUUAACGGAAUAAUAUUUGCGGAUUAACGGAAUGAUAGUAGCUAUUAAAUAAUGUAAUACCAACAAUUUUCUAUCUUGCAGCUAGUUUGUAGUAAAAAGAGAUAACAAAUUGUUAUGCUCUCUUUCACUGCUAUUUCAAACAUAAUUUUUCCAAGCUAGCUUAGAAAACC ((((...((((......(((..((((......))))...))).......))))......((((.(((..((((((((....((((.(((.((.(.(((((.......))))).).)).)))))))))).)))))...((((((((((.(((((((((((.....))))...)))))))...)))))...)))))...))).))))......))))........ (-39.52) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGUUUUCUAAGCUAGCUUGGAAAAAUUAUGUUUGAAAUAGCAGUGAAAGAGAGCAUAACAAUUUGUUAUCUCUUUUUACUACAAACUAGCUGCAAGAUAGAAAAUUGUUGGUAUUACAUUAUUUAAUAGCUACUAUCAUUCCGUUAAUCCGCAAAUAUUAUUCCGUUAAUCCUCGUAUUGUUCCGAACUAUGGUAUAAUAGAGGGAGAAAGUGAGGGGUGCUC ..(((((((((....)))))))))...(((((((.....(((((.((((((((.(((((.....)))))))))))))...........)))))..(((((....(((((((((......)).)))))))...)))))..............)))))))......((...((((((..((.((((...((((......)))).)))).))..))))))..)).. (-53.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 941 50 1 141 92 NC_009009:SSA_1610|5end_hypothetical_protein_1614909..1615139_NEGATIVE 292 36 3 129 93 NC_009009:SSA_0258|5end_hypothetical_protein_251845..252075_POSITIVE 289 40 1 161 109 NC_009009:SSA_0269|5end_Phosphotransferase_system_(PTS)_cellobiose-specific_component_IIA,_putative_262550..262780_POSITIVE 286 60 13 71 25 NC_009009:SSA_0468|5end_Precorrin-6y_C5,15-methyltransferase-like,_putative_471706..471936_POSITIVE 271 180 131 103 57 NC_009009:SSA_0339|5end_hypothetical_protein_333950..334180_NEGATIVE 261 56 11 175 130 NC_009009:SSA_0707|5end_Lactose_phosphotransferase_system_transcriptional_repressor,_putative_693215..693445_POSITIVE 259 48 7 138 93 NC_009009:SSA_2271|5end_hypothetical_protein_2272450..2272680_NEGATIVE 253 59 13 188 136 NC_009009:SSA_2205|5end_Transcription_antitermination_factor_NusG,_putative_2206100..2206330_NEGATIVE 252 38 1 125 86 NC_009009:SSA_0874|5end_hypothetical_protein_867935..868165_POSITIVE 249 33 10 118 98 NC_009009:SSA_1818|5end_Very_short_patch_repair_endonuclease,_putative_1806110..1806340_NEGATIVE 249 52 11 79 38 NC_009009:SSA_0591|5end_Conserved_uncharacterized_protein_582769..582999_POSITIVE 247 150 104 118 72 NC_009009:SSA_1246|5end_hypothetical_protein_1271225..1271455_NEGATIVE 244 52 11 200 145 NC_009009:SSA_0284|5end_Phosphotransferase_system_(PTS),_cellobiose-specific_IIC_component,_putative_274888..275118_POSITIVE 242 41 3 125 76 NC_009009:SSA_2161|5end_NTP_pyrophosphohydrolases_including_oxidative_damage_repair_enzymes,_putative_2160600..2160830_NEGATIVE 234 100 51 78 30 NC_009009:SSA_0217|5end_Two-component_system_transcriptional_regulator_(CheY_domain_and_HTH-like_DNA-binding_domain),_putative_213183..213413_POSITIVE 232 42 6 102 54 NC_009009:SSA_1254|5end_hypothetical_protein_1281484..1281714_NEGATIVE 230 91 51 230 173 NC_009009:SSA_2119|5end_Pentose-5-phosphate-3-epimerase,_putative_2121098..2121328_NEGATIVE 230 39 2 67 23 NC_009009:SSA_0749|5end_Competence_protein,_putative_730668..730898_POSITIVE 228 179 139 105 67 NC_009009:SSA_0597|5end_hypothetical_protein_587566..587796_POSITIVE 227 28 2 116 87 NC_009009:SSA_0343|5end_DNA-damage-inducible_protein_P,_putative_337525..337755_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 292 36 3 44 8 NC_009009:SSA_0257|3end_N-acetylmuramidase/lysin,_putative_251840..251990_POSITIVE 286 60 13 80 34 NC_009009:SSA_0467|3end_Cobalt-precorrin-6A_synthase_[deacetylating],_putative_471795..471945_POSITIVE 271 180 131 98 52 NC_009009:SSA_0341|3end_hypothetical_protein_333955..334105_NEGATIVE 261 47 2 74 9 NC_009009:SSA_1889|3end_Conserved_uncharacterized_protein_1886283..1886433_NEGATIVE 257 49 2 99 40 NC_009009:SSA_2092|3end_Phosphotransferase_system_sugar-specific_EII_component,_putative_2095697..2095847_NEGATIVE 255 39 1 151 100 NC_009009:SSA_0268|3end_Phosphotransferase_system_(PTS)_cellobiose-specific_component_IIB,_putative_262621..262771_POSITIVE 249 33 10 33 13 NC_009009:SSA_1819|3end_Valyl-tRNA_synthetase,_putative_1806195..1806345_NEGATIVE 249 52 11 47 6 NC_009009:SSA_0590|3end_hypothetical_protein_582817..582967_POSITIVE 247 150 104 121 75 NC_009009:SSA_1247|3end_hypothetical_protein_1271222..1271372_NEGATIVE 246 190 150 97 61 NC_009009:SSA_0829|3end_Platelet-binding_glycoprotein_812165..812315_POSITIVE 238 22 1 41 20 NC_009009:SSA_1745|3end_General_stress_response_protein_CsbD,_putative_1731997..1732147_NEGATIVE 236 43 5 120 85 NC_009009:SSA_0967|3end_hypothetical_protein_976620..976770_POSITIVE 234 100 51 85 37 NC_009009:SSA_0216|3end_Histidine_kinase,_putative_213270..213420_POSITIVE 232 42 6 130 82 NC_009009:SSA_1255|3end_hypothetical_protein_1281456..1281606_NEGATIVE 229 208 162 118 79 NC_009009:SSA_0405|3end_Transcriptional_regulator,_XRE_family,_putative_402115..402265_POSITIVE 226 137 93 134 97 NC_009009:SSA_0593|3end_Rhodanese-like_sulfurtransferase,_putative_585551..585701_POSITIVE 225 220 172 130 79 NC_009009:SSA_0507|3end_hypothetical_protein_506442..506592_POSITIVE 225 213 172 120 76 NC_009009:SSA_0150|3end_hypothetical_protein_145227..145377_POSITIVE 222 67 29 76 35 NC_009009:SSA_1689|3end_hypothetical_protein_1681945..1682095_NEGATIVE 220 24 1 144 122 NC_009009:SSA_1985|3end_hypothetical_protein_1979623..1979773_NEGATIVE