Origin IGS: actgtccgtgtatacctttcatgccggcaaaggctgccttaagatattactctcggataaccgaaaaaaagcggatatcctcccgacatccgctttttcttggtgtagaatcttaaaattctaaaactccaatactatgaaaaaaactttattcaagcatgccgaaaaagaacggcacgtttctcttttta .........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 taaaaagagaaacgtgccgttctttttcggcatgcttgaataaagtttttttcatagtattggagttttagaattttaagattctacaccaagaaaaagcggatgtcgggaggatatccgctttttttcggttatccgagagtaatatcttaaggcagcctttgccggcatgaaaggtatacacggacagt Mask Tandem Repeat Region ================================================ actgtccgtgtatacctttcatgccggcaaaggctgccttaagatattactctcggataaccgaaaaaaagcggatatcctcccgacatccgctttttcttggtgtagaatcttaaaattctaaaactccaatactatgaaaaaaactttattcaagcatgccgaaaaagaacggcacgtttctcttttta Find is-nt database================================================ Query_seq: TF1740:TF1741|TF1740:TF1741:hypothetical protein:conserved hypothetical protein:->->:1869253..1869443 191 actgtccgtgtatacctttcatgccggcaaaggctgccttaagatattactctcggataaccgaaaaaaagcggatatcctcccgacatccgctttttcttggtgtagaatcttaaaattctaaaactccaatactatgaaaaaaactttattcaagcatgccgaaaaagaacggcacgtttctcttttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1740:TF1741|TF1740:TF1741:hypothetical protein:conserved hypothetical protein:->->:1869253..1869443 191 actgtccgtgtatacctttcatgccggcaaaggctgccttaagatattactctcggataaccgaaaaaaagcggatatcctcccgacatccgctttttcttggtgtagaatcttaaaattctaaaactccaatactatgaaaaaaactttattcaagcatgccgaaaaagaacggcacgtttctcttttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1740:TF1741|TF1740:TF1741:hypothetical protein:conserved hypothetical protein:->->:1869253..1869443 191 actgtccgtgtatacctttcatgccggcaaaggctgccttaagatattactctcggataaccgaaaaaaagcggatatcctcccgacatccgctttttcttggtgtagaatcttaaaattctaaaactccaatactatgaaaaaaactttattcaagcatgccgaaaaagaacggcacgtttctcttttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 actgtccgtgtatacctttcatgccggcaaaggctgccttaagatattactctcggataaccgaaaaaaagcggatatcctcccgacatccgctttttcttggtgtagaatcttaaaattctaaaactccaatactatgaaaaaaactttattcaagcatgccgaaaaagaacggcacgtttctcttttta Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 12 End: 113 ........... M P F M P A K A A L R Y Y S R I T E K K R I S S R H P L F L G V E S .............................................................................. Protein_Len: 40 Strand: + Start: 2 End: 121 . M S V Y T F H A G K G C L K I L L S D N R K K A D I L P T S A F S W C R I L K F ...................................................................... Protein_Len: 30 Strand: - Start: 22 End: 111 ..................... A P L P Q R L I N S E S L R F F A S I R G V D A K E Q H L M ................................................................................ actgtccgtgtatacctttcatgccggcaaaggctgccttaagatattactctcggataaccgaaaaaaagcggatatcctcccgacatccgctttttcttggtgtagaatcttaaaattctaaaactccaatactatgaaaaaaactttattcaagcatgccgaaaaagaacggcacgtttctcttttta 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================================================ actgtccgtgtatacctttcatgccggcaaaggctgccttaagatattactctcggataaccgaaaaaaagcggatatcctcccgacatccgctttttcttggtgtagaatcttaaaattctaaaactccaatactatgaaaaaaactttattcaagcatgccgaaaaagaacggcacgtttctcttttta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -15.1 Tail_Score: -3.2963 Start: 61 End: 103 Full_Region: ttttaagattctaca ccaagaaaaagcggatgtc gggag gatatccgctttttttcgg ttatccgagagtaat ............................................................ccaagaaaaagcggatgtcgggaggatatccgctttttttcgg........................................................................................ TransTerm Strand: - Conf: 100 HP_score: -9.9 Tail_Score: -5.55698 Start: 71 End: 93 Full_Region: ctacaccaagaaaaa gcggatgtc gggag gatatccgc tttttttcggttatc ......................................................................gcggatgtcgggaggatatccgc.................................................................................................. Find igs database================================================ Query_seq: TF1740:TF1741|TF1740:TF1741:hypothetical protein:conserved hypothetical protein:->->:1869253..1869443 191 actgtccgtgtatacctttcatgccggcaaaggctgccttaagatattactctcggataaccgaaaaaaagcggatatcctcccgacatccgctttttcttggtgtagaatcttaaaattctaaaactccaatactatgaaaaaaactttattcaagcatgccgaaaaagaacggcacgtttctcttttta Intra-Species Hit: Count: 1 Min: 1 Max: 191 Len: 191 Subject: tfor_TF1740_TF1741|hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[1869253,1869443]|191 HSP 1 e-value: 3.0E-79 bit: 295.0 Len: 191 Query Start:1 Query End:191 Subject Strand: POSITIVE Subject Start: 1 Subject End: 191 actgtccgtgtatacctttcatgccggcaaaggctgccttaagatattactctcggataaccgnnnnnnngcggatatcctcccgacatccgctttttcttggtgtagaatcttaaaattctaaaactccaatactatgnnnnnnnctttattcaagcatgccgaaaaagaacggcacgtttctcttttta actgtccgtgtatacctttcatgccggcaaaggctgccttaagatattactctcggataaccgaaaaaaagcggatatcctcccgacatccgctttttcttggtgtagaatcttaaaattctaaaactccaatactatgaaaaaaactttattcaagcatgccgaaaaagaacggcacgtttctcttttta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUGUCCGUGUAUACCUUUCAUGCCGGCAAAGGCUGCCUUAAGAUAUUACUCUCGGAUAACCGAAAAAAAGCGGAUAUCCUCCCGACAUCCGCUUUUUCUUGGUGUAGAAUCUUAAAAUUCUAAAACUCCAAUACUAUGAAAAAAACUUUAUUCAAGCAUGCCGAAAAAGAACGGCACGUUUCUCUUUUUA ..((((((.(((((.(((....(((......)))......))).)).)))...))))))(((((.(((((((((((.((.....)).))))))))))).))))).((((((......))))))...............................((((.(((((........))))).))))......... (-46.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAAGAGAAACGUGCCGUUCUUUUUCGGCAUGCUUGAAUAAAGUUUUUUUCAUAGUAUUGGAGUUUUAGAAUUUUAAGAUUCUACACCAAGAAAAAGCGGAUGUCGGGAGGAUAUCCGCUUUUUUUCGGUUAUCCGAGAGUAAUAUCUUAAGGCAGCCUUUGCCGGCAUGAAAGGUAUACACGGACAGU ......((((((.((((((........))))))((((.....)))).)))))).......(((((((((((....))))))))))).(((.((((((((((((((((.....)))))))))))))))).)))..((((...(((.((((((....(((((......))).)).))))))))).)))).... (-58.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 387 115 71 99 42 tfor:TF0816|5end_hypothetical_protein_874217..874447_POSITIVE 377 99 51 168 122 tfor:TF1740|5end_hypothetical_protein_1868645..1868875_POSITIVE 352 109 61 187 136 tfor:TF2789|5end_enoyl-[acyl-carrier-protein]_reductase_2972431..2972661_POSITIVE 340 78 31 207 141 tfor:TF1646|5end_hypothetical_protein_1756900..1757130_POSITIVE 339 112 71 207 155 tfor:TF1048|5end_permease_1109241..1109471_POSITIVE 337 110 62 96 34 tfor:TF1548|5end_thiophene_and_furan_oxidation_protein_1652501..1652731_POSITIVE 332 45 3 188 140 tfor:TF2829|5end_conserved_hypothetical_protein_3019562..3019792_POSITIVE 332 59 13 187 136 tfor:TF1586|5end_hypothetical_protein_1690971..1691201_POSITIVE 330 64 22 60 8 tfor:TF0441|5end_Na+-transporting_NADH:ubiquinone_oxidoreductase,_subunit_3_464614..464844_POSITIVE 326 44 3 208 160 tfor:TF1599|5end_ribonuclease_P_protein_component_1713564..1713794_POSITIVE 313 63 22 163 122 tfor:TF0992|5end_hypothetical_protein_1048251..1048481_POSITIVE 311 63 22 221 180 tfor:TF1322|5end_conserved_hypothetical_protein;_possible_surface_protein_1401864..1402094_POSITIVE 310 38 2 47 12 tfor:TF2014|5end_dipeptidyl_aminopeptidase_IV_2169398..2169628_POSITIVE 310 102 70 194 155 tfor:TF0669|5end_hypothetical_protein_713384..713614_POSITIVE 309 37 2 219 178 tfor:TF3143|5end_conserved_hypothetical_protein;_possible_membrane_protein_3377465..3377695_POSITIVE 308 59 14 224 183 tfor:TF1066|5end_hypothetical_protein_1136545..1136775_POSITIVE 308 45 2 162 112 tfor:TF0803|5end_hypothetical_protein_861045..861275_POSITIVE 307 99 53 158 109 tfor:TF1001|5end_penicillin-binding_protein_1A_1054097..1054327_POSITIVE 305 38 1 153 111 tfor:TF0809|5end_cation_efflux_protein_865358..865588_POSITIVE 303 105 68 47 6 tfor:TF2846|5end_cobyric_acid_synthase_3034896..3035126_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 432 56 18 143 110 tfor:TF2288|3end_hypothetical_protein_2442598..2442748_POSITIVE 377 99 51 47 1 tfor:TF1739|3end_possible_sulfatase_1868604..1868754_POSITIVE 339 105 61 56 8 tfor:TF2847|3end_hypothetical_protein_3034985..3035135_POSITIVE 330 64 22 54 2 tfor:TF0440|3end_Na+-transporting_NADH:ubiquinone_oxidoreductase,_subunit_2_464688..464838_POSITIVE 318 36 1 66 27 tfor:TF0655|3end_outer_membrane_protein_701907..702057_POSITIVE 308 45 2 119 69 tfor:TF0802|3end_glucose-1-phosphate_cytidylyltransferase_861082..861232_POSITIVE 307 99 53 150 101 tfor:TF1000|3end_sec-independent_protein_translocase_1054169..1054319_POSITIVE 306 56 19 128 88 tfor:TF2609|3end_dipeptidase,_pathogenicity_island-encoded_protein_D_2786264..2786414_POSITIVE 305 38 1 136 94 tfor:TF0808|3end_cation_efflux_system_protein_865421..865571_POSITIVE 304 37 1 117 78 tfor:TF0644|3end_pyruvate_phosphate_dikinase_688581..688731_POSITIVE 303 64 22 69 27 tfor:TF0178|3end_ferritin_188223..188373_POSITIVE 302 99 54 58 14 tfor:TF2651|3end_hypothetical_protein_2822014..2822164_POSITIVE 300 38 1 61 25 tfor:TF2343|3end_ribosome_recycling_factor_2507502..2507652_POSITIVE 298 107 72 151 115 tfor:TF1540|3end_possible_ATPase_1645987..1646137_POSITIVE 297 57 17 44 7 tfor:TF3052|3end_conserved_hypothetical_protein_3278654..3278804_POSITIVE 297 40 3 121 80 tfor:TF1621|3end_DNA_replication_and_repair_protein_RecF_1736473..1736623_POSITIVE 296 39 6 33 7 tfor:TF2874|3end_conserved_hypothetical_protein_3065224..3065374_POSITIVE 294 92 52 65 22 tfor:TF0564|3end_conserved_hypothetical_protein_597750..597900_POSITIVE 293 63 24 39 1 tfor:TF2911|3end_hypothetical_protein_3106640..3106790_POSITIVE 293 41 2 150 115 tfor:TF0688|3end_membrane-associated_protein,_possible_sulfatase_family_734360..734510_POSITIVE