Origin IGS: tacagccgatagcttaaagcgggattcaatagcttctgcgattcctccaggcttaaagtaagtatagagaaaggttccgccaatcagtacaaagcagacacagccgtaaatgataaaaaaatgaaccttcttcaaaattaatcctcctagaagccttctgtcattttatagcttatattataagcttttttagagctattt .........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 aaatagctctaaaaaagcttataatataagctataaaatgacagaaggcttctaggaggattaattttgaagaaggttcatttttttatcatttacggctgtgtctgctttgtactgattggcggaacctttctctatacttactttaagcctggaggaatcgcagaagctattgaatcccgctttaagctatcggctgta Mask Tandem Repeat Region ================================================ tacagccgatagcttaaagcgggattcaatagcttctgcgattcctccaggcttaaagtaagtatagagaaaggttccgccaatcagtacaaagcagacacagccgtaaatgataaaaaaatgaaccttcttcaaaattaatcctcctagaagccttctgtcattttatagcttatattataagcttttttagagctattt Find is-nt database================================================ Query_seq: SSA_1643:SSA_1644|SSA_1643:SSA_1644:hypothetical protein:hypothetical protein:<-<-:1645360..1645560 201 tacagccgatagcttaaagcgggattcaatagcttctgcgattcctccaggcttaaagtaagtatagagaaaggttccgccaatcagtacaaagcagacacagccgtaaatgataaaaaaatgaaccttcttcaaaattaatcctcctagaagccttctgtcattttatagcttatattataagcttttttagagctattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1643:SSA_1644|SSA_1643:SSA_1644:hypothetical protein:hypothetical protein:<-<-:1645360..1645560 201 tacagccgatagcttaaagcgggattcaatagcttctgcgattcctccaggcttaaagtaagtatagagaaaggttccgccaatcagtacaaagcagacacagccgtaaatgataaaaaaatgaaccttcttcaaaattaatcctcctagaagccttctgtcattttatagcttatattataagcttttttagagctattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1643:SSA_1644|SSA_1643:SSA_1644:hypothetical protein:hypothetical protein:<-<-:1645360..1645560 201 tacagccgatagcttaaagcgggattcaatagcttctgcgattcctccaggcttaaagtaagtatagagaaaggttccgccaatcagtacaaagcagacacagccgtaaatgataaaaaaatgaaccttcttcaaaattaatcctcctagaagccttctgtcattttatagcttatattataagcttttttagagctattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tacagccgatagcttaaagcgggattcaatagcttctgcgattcctccaggcttaaagtaagtatagagaaaggttccgccaatcagtacaaagcagacacagccgtaaatgataaaaaaatgaaccttcttcaaaattaatcctcctagaagccttctgtcattttatagcttatattataagcttttttagagctattt Predict ORF larger than 30AA ================================================ Protein_Len: 46 Strand: - Start: 1 End: 138 V A S L K F R S E I A E A I G G P K F Y T Y L F T G G I L V F C V C G Y I I F F H V K K L M ............................................................... tacagccgatagcttaaagcgggattcaatagcttctgcgattcctccaggcttaaagtaagtatagagaaaggttccgccaatcagtacaaagcagacacagccgtaaatgataaaaaaatgaaccttcttcaaaattaatcctcctagaagccttctgtcattttatagcttatattataagcttttttagagctattt 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================================================ tacagccgatagcttaaagcgggattcaatagcttctgcgattcctccaggcttaaagtaagtatagagaaaggttccgccaatcagtacaaagcagacacagccgtaaatgataaaaaaatgaaccttcttcaaaattaatcctcctagaagccttctgtcattttatagcttatattataagcttttttagagctattt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 85 HP_score: -7.2 Tail_Score: -5.04987 Start: 171 End: 185 Full_Region: TTCTGTCATTTTATA GCTTAT ATT ATAAGC TTTTTTAGAGCTATT ..........................................................................................................................................................................GCTTATATTATAAGC................ Find igs database================================================ Query_seq: SSA_1643:SSA_1644|SSA_1643:SSA_1644:hypothetical protein:hypothetical protein:<-<-:1645360..1645560 201 tacagccgatagcttaaagcgggattcaatagcttctgcgattcctccaggcttaaagtaagtatagagaaaggttccgccaatcagtacaaagcagacacagccgtaaatgataaaaaaatgaaccttcttcaaaattaatcctcctagaagccttctgtcattttatagcttatattataagcttttttagagctattt Intra-Species Hit: Count: 1 Min: 1 Max: 201 Len: 201 Subject: NC_009009_SSA_1643_SSA_1644|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[1645360,1645560]|201 HSP 1 e-value: 9.0E-98 bit: 357.0 Len: 201 Query Start:1 Query End:201 Subject Strand: POSITIVE Subject Start: 1 Subject End: 201 tacagccgatagcttaaagcgggattcaatagcttctgcgattcctccaggcttaaagtaagtatagagaaaggttccgccaatcagtacaaagcagacacagccgtaaatgatnnnnnnntgaaccttcttcaaaattaatcctcctagaagccttctgtcattttatagcttatattataagcttttttagagctattt tacagccgatagcttaaagcgggattcaatagcttctgcgattcctccaggcttaaagtaagtatagagaaaggttccgccaatcagtacaaagcagacacagccgtaaatgataaaaaaatgaaccttcttcaaaattaatcctcctagaagccttctgtcattttatagcttatattataagcttttttagagctattt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UACAGCCGAUAGCUUAAAGCGGGAUUCAAUAGCUUCUGCGAUUCCUCCAGGCUUAAAGUAAGUAUAGAGAAAGGUUCCGCCAAUCAGUACAAAGCAGACACAGCCGUAAAUGAUAAAAAAAUGAACCUUCUUCAAAAUUAAUCCUCCUAGAAGCCUUCUGUCAUUUUAUAGCUUAUAUUAUAAGCUUUUUUAGAGCUAUUU .......((((((((...((((((.......(((((((.((.........(((((...)))))...((..(((((((.....((((.(((...((.......)).)))..))))........)))))))..))...........)).))))))).))))))........(((((((...)))))))......)))))))). (-38.02) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUAGCUCUAAAAAAGCUUAUAAUAUAAGCUAUAAAAUGACAGAAGGCUUCUAGGAGGAUUAAUUUUGAAGAAGGUUCAUUUUUUUAUCAUUUACGGCUGUGUCUGCUUUGUACUGAUUGGCGGAACCUUUCUCUAUACUUACUUUAAGCCUGGAGGAAUCGCAGAAGCUAUUGAAUCCCGCUUUAAGCUAUCGGCUGUA ..(((((........(((((((...)))))))...........((.(((((..((..(((((.....((((((((.....))))))))........((((...(((((...((.(((.....))).)).((((((((..((((...))))..))))))))..)))))))))....)))))..))..))))).)).))))). (-46.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 981 50 1 141 92 NC_009009:SSA_1643|5end_hypothetical_protein_1645269..1645499_NEGATIVE 390 49 4 229 176 NC_009009:SSA_0990|5end_hypothetical_protein_991733..991963_POSITIVE 378 50 4 169 123 NC_009009:SSA_0179|5end_hypothetical_protein_183966..184196_POSITIVE 373 50 4 66 19 NC_009009:SSA_0089|5end_V-type_sodium_ATPase,_subunit_F,_putative_89930..90160_POSITIVE 371 58 11 48 5 NC_009009:SSA_1055|5end_Conserved_uncharacterized_protein_1070899..1071129_POSITIVE 334 80 31 64 7 NC_009009:SSA_2165|5end_ABC-type_oligopeptide_transporter,_periplasmic_component,_putative_2161734..2161964_POSITIVE 334 79 36 128 91 NC_009009:SSA_1222|5end_NTP_pyrophosphohydrolases_including_oxidative_damage_repair_enzymes,_putative_1245454..1245684_NEGATIVE 323 106 71 175 128 NC_009009:SSA_0334|5end_Diphosphomevalonate_decarboxylase,_putative_327855..328085_POSITIVE 318 49 1 59 10 NC_009009:SSA_2062|5end_hypothetical_protein_2063521..2063751_NEGATIVE 315 47 3 175 117 NC_009009:SSA_0596|5end_hypothetical_protein_586913..587143_POSITIVE 313 50 1 63 22 NC_009009:SSA_1066|5end_ABC-type_oligopeptide_transport_system,_putative_1084335..1084565_POSITIVE 306 107 70 154 107 NC_009009:SSA_0299|5end_hypothetical_protein_292759..292989_POSITIVE 305 49 4 45 1 NC_009009:SSA_1313|5end_hypothetical_protein_1330548..1330778_NEGATIVE 304 116 72 82 34 NC_009009:SSA_1117|5end_hypothetical_protein_1142743..1142973_POSITIVE 304 48 4 61 15 NC_009009:SSA_0474|5end_Uroporphyrin-III_C-methyltransferase/uroporphyrinogen-III_synthase,_putative_476270..476500_POSITIVE 303 49 4 195 149 NC_009009:SSA_0607|5end_ABC_transporter,_permease_component,_putative_596926..597156_NEGATIVE 302 59 18 168 117 NC_009009:SSA_0785|5end_Proton-translocating_ATPase,_F1_sector,_delta_subunit,_putative_768044..768274_POSITIVE 302 190 142 152 93 NC_009009:SSA_0343|5end_DNA-damage-inducible_protein_P,_putative_337525..337755_POSITIVE 297 118 71 63 21 NC_009009:SSA_2338|5end_Conserved_uncharacterized_protein_2339272..2339502_POSITIVE 297 50 2 147 105 NC_009009:SSA_1743|5end_ABC-type_Fe3+-siderophore_transport_system,_permease_component,_putative_1730170..1730400_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 373 50 4 79 32 NC_009009:SSA_0088|3end_V-type_sodium_ATPase,_subunit_C,_putative_90023..90173_POSITIVE 350 58 19 42 9 NC_009009:SSA_1054|3end_CBS_domain_protein,_putative_1070973..1071123_POSITIVE 339 99 51 65 28 NC_009009:SSA_0756|3end_Alanyl-tRNA_synthetase,_putative_739434..739584_POSITIVE 304 47 5 99 54 NC_009009:SSA_1309|3end_RNA-binding_protein_(KH_domain),_putative_1327079..1327229_NEGATIVE 297 118 71 70 28 NC_009009:SSA_2337|3end_hypothetical_protein_2339359..2339509_POSITIVE 291 80 31 57 3 NC_009009:SSA_0451|3end_Conserved_uncharacterized_protein_451636..451786_POSITIVE 287 55 14 136 96 NC_009009:SSA_2329|3end_hypothetical_protein_2333169..2333319_POSITIVE 287 45 4 132 93 NC_009009:SSA_1173|3end_Lipoate_protein_ligase_A,_putative_1200092..1200242_NEGATIVE 286 200 152 122 68 NC_009009:SSA_0833|3end_Accessory_secretory_protein_Asp1,_putative_819600..819750_POSITIVE 283 48 4 151 108 NC_009009:SSA_1810|3end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_winged-helix_DNA-binding_domains),_putative_1794707..1794857_NEGATIVE 283 55 18 80 41 NC_009009:SSA_1343|3end_Aspartate_carbamoyltransferase,_putative_1361042..1361192_NEGATIVE 282 80 32 63 3 NC_009009:SSA_0810|3end_P-loop_ATPase,_putative_792552..792702_POSITIVE 280 49 4 55 16 NC_009009:SSA_1784|3end_Glutamate_racemase,_putative_1769103..1769253_NEGATIVE 279 49 7 40 1 NC_009009:SSA_2073|3end_Undecaprenyl_pyrophosphate_synthetase,_putative_2075622..2075772_NEGATIVE 279 78 31 134 82 NC_009009:SSA_0203|3end_hypothetical_protein_202124..202274_POSITIVE 278 60 11 52 1 NC_009009:SSA_0733|3end_hypothetical_protein_716937..717087_POSITIVE 278 40 3 151 107 NC_009009:SSA_0595|3end_hypothetical_protein_586983..587133_POSITIVE 278 80 31 80 30 NC_009009:SSA_0407|3end_ABC-type_multidrug_transport_system_(3-component_subtilin_immunity_exporter),_ATPase_component,_putative_402911..403061_NEGATIVE 277 79 32 46 1 NC_009009:SSA_0350|3end_Helicase,_putative_341852..342002_NEGATIVE 276 52 11 71 21 NC_009009:SSA_1515|3end_hypothetical_protein_1521770..1521920_NEGATIVE