Origin IGS: ctagcgggtaagcccaaagtccgctttgcagactttgggcggcgagttttaggcttaccgcctaaaacatcgtacgcttaaaccaccgcacgtcctgtgcggcgtacattaggtc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gacctaatgtacgccgcacaggacgtgcggtggtttaagcgtacgatgttttaggcggtaagcctaaaactcgccgcccaaagtctgcaaagcggactttgggcttacccgctag Mask Tandem Repeat Region ================================================ ctagcgggtaagcccaaagtccgctttgcagactttgggcggcgagttttaggcttaccgcctaaaacatcgtacgcttaaaccaccgcacgtcctgtgcggcgtacattaggtc Find is-nt database================================================ Query_seq: TDE2735:TDE2736|TDE2735:TDE2736:surface antigen, putative:hypothetical protein:-><-:2791677..2791791 115 ctagcgggtaagcccaaagtccgctttgcagactttgggcggcgagttttaggcttaccgcctaaaacatcgtacgcttaaaccaccgcacgtcctgtgcggcgtacattaggtc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2735:TDE2736|TDE2735:TDE2736:surface antigen, putative:hypothetical protein:-><-:2791677..2791791 115 ctagcgggtaagcccaaagtccgctttgcagactttgggcggcgagttttaggcttaccgcctaaaacatcgtacgcttaaaccaccgcacgtcctgtgcggcgtacattaggtc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2735:TDE2736|TDE2735:TDE2736:surface antigen, putative:hypothetical protein:-><-:2791677..2791791 115 ctagcgggtaagcccaaagtccgctttgcagactttgggcggcgagttttaggcttaccgcctaaaacatcgtacgcttaaaccaccgcacgtcctgtgcggcgtacattaggtc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctagcgggtaagcccaaagtccgctttgcagactttgggcggcgagttttaggcttaccgcctaaaacatcgtacgcttaaaccaccgcacgtcctgtgcggcgtacattaggtc Predict ORF larger than 30AA ================================================ ctagcgggtaagcccaaagtccgctttgcagactttgggcggcgagttttaggcttaccgcctaaaacatcgtacgcttaaaccaccgcacgtcctgtgcggcgtacattaggtc 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================================================ ctagcgggtaagcccaaagtccgctttgcagactttgggcggcgagttttaggcttaccgcctaaaacatcgtacgcttaaaccaccgcacgtcctgtgcggcgtacattaggtc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2735:TDE2736|TDE2735:TDE2736:surface antigen, putative:hypothetical protein:-><-:2791677..2791791 115 ctagcgggtaagcccaaagtccgctttgcagactttgggcggcgagttttaggcttaccgcctaaaacatcgtacgcttaaaccaccgcacgtcctgtgcggcgtacattaggtc Intra-Species Hit: Count: 1 Min: 1 Max: 115 Len: 115 Subject: NC_002967_TDE2735_TDE2736|surface antigen, putative:hypothetical protein|POSITIVE:NEGATIVE|[2791677,2791791]|115 HSP 1 e-value: 3.0E-59 bit: 228.0 Len: 115 Query Start:1 Query End:115 Subject Strand: POSITIVE Subject Start: 1 Subject End: 115 ctagcgggtaagcccaaagtccgctttgcagactttgggcggcgagttttaggcttaccgcctaaaacatcgtacgcttaaaccaccgcacgtcctgtgcggcgtacattaggtc ctagcgggtaagcccaaagtccgctttgcagactttgggcggcgagttttaggcttaccgcctaaaacatcgtacgcttaaaccaccgcacgtcctgtgcggcgtacattaggtc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUAGCGGGUAAGCCCAAAGUCCGCUUUGCAGACUUUGGGCGGCGAGUUUUAGGCUUACCGCCUAAAACAUCGUACGCUUAAACCACCGCACGUCCUGUGCGGCGUACAUUAGGUC ..((((.....((((((((((.((...)).)))))))))).(((((((((((((.....))))))))).)))).)))).....(.((((((.....)))))).)........... (-51.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GACCUAAUGUACGCCGCACAGGACGUGCGGUGGUUUAAGCGUACGAUGUUUUAGGCGGUAAGCCUAAAACUCGCCGCCCAAAGUCUGCAAAGCGGACUUUGGGCUUACCCGCUAG ...........((((((((.....)))))))).....((((..(((.(((((((((.....))))))))))))..(((((((((((((...))))))))))))).....)))).. (-58.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 401 48 4 47 8 NC_002967:TDE2180|5end_tRNA_modification_GTPase_2212008..2212238_NEGATIVE 390 100 53 57 14 NC_002967:TDE2100|5end_hypothetical_protein_2125370..2125600_POSITIVE 372 100 51 82 21 NC_002967:TDE0740|5end_hypothetical_protein_775987..776217_POSITIVE 362 59 21 173 135 NC_002967:TDE2237|5end_hypothetical_protein_2276402..2276632_NEGATIVE 361 58 12 162 106 NC_002967:TDE2491|5end_DNA_polymerase_domain_protein_2515499..2515729_NEGATIVE 354 60 13 122 87 NC_002967:TDE1890|5end_hypothetical_protein_1911012..1911242_POSITIVE 349 80 34 228 191 NC_002967:TDE2143|5end_penicillin-binding_protein_2178107..2178337_POSITIVE 349 49 3 212 153 NC_002967:TDE2118|5end_DNA_topoisomerase_IV_subunit_A_2151265..2151495_NEGATIVE 339 96 52 117 68 NC_002967:TDE2751|5end_hypothetical_protein_2807570..2807800_POSITIVE 336 78 33 230 185 NC_002967:TDE0625|5end_ABC_transporter,_ATP-binding_protein_657253..657483_POSITIVE 334 50 5 219 170 NC_002967:TDE0873|5end_hypothetical_protein_896143..896373_POSITIVE 332 105 66 178 133 NC_002967:TDE0279|5end_hypothetical_protein_309782..310012_NEGATIVE 330 44 3 145 93 NC_002967:TDE2632|5end_peptide_ABC_transporter,_ATP-binding_protein,_putative_2672650..2672880_POSITIVE 328 100 51 172 128 NC_002967:TDE1335|5end_alginate_O-acetylation_protein,_putative_1370816..1371046_POSITIVE 326 60 23 225 182 NC_002967:TDE0043|5end_TPR_domain_protein_49688..49918_POSITIVE 325 51 12 57 17 NC_002967:TDE0239|5end_glycine_reductase_complex_protein_GrdD_272982..273212_NEGATIVE 323 67 22 109 68 NC_002967:TDE2129|5end_hypothetical_protein_2161463..2161693_POSITIVE 320 97 51 159 118 NC_002967:TDE0865|5end_hypothetical_protein_887127..887357_POSITIVE 319 54 12 179 126 NC_002967:TDE1884|5end_hypothetical_protein_1906857..1907087_NEGATIVE 319 44 5 49 19 NC_002967:TDE1856|5end_radical_SAM_domain_protein_1883133..1883363_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 491 110 70 52 12 NC_002967:TDE0471|3end_BNR_domain_protein_526657..526807_NEGATIVE 419 80 34 55 9 NC_002967:TDE2735|3end_surface_antigen,_putative_2791616..2791766_POSITIVE 409 78 36 112 57 NC_002967:TDE2714|3end_hypothetical_protein_2770627..2770777_NEGATIVE 408 100 53 51 9 NC_002967:TDE0833|3end_lipoprotein,_putative_854097..854247_POSITIVE 401 48 4 60 21 NC_002967:TDE2181|3end_PAP2_family_protein_2211995..2212145_NEGATIVE 387 103 71 49 12 NC_002967:TDE2493|3end_hypothetical_protein_2516745..2516895_NEGATIVE 374 45 4 47 1 NC_002967:TDE1277|3end_Fe-hydrogenase_large_subunit_family_protein_1312242..1312392_POSITIVE 371 66 23 65 19 NC_002967:TDE0617|3end_hypothetical_protein_650093..650243_NEGATIVE 361 63 21 68 34 NC_002967:TDE2100|3end_hypothetical_protein_2125572..2125722_POSITIVE 355 48 1 76 36 NC_002967:TDE1529|3end_hypothetical_protein_1575067..1575217_POSITIVE 349 49 3 79 20 NC_002967:TDE2119|3end_glycine_reductase_complex_selenoprotein_GrdB2_2151398..2151548_NEGATIVE 349 55 12 59 20 NC_002967:TDE1913|3end_hypothetical_protein_1930897..1931047_POSITIVE 348 47 4 54 14 NC_002967:TDE1982|3end_hypothetical_protein_1992511..1992661_NEGATIVE 337 62 22 72 32 NC_002967:TDE2312|3end_hypothetical_protein_2349049..2349199_POSITIVE 335 57 12 151 96 NC_002967:TDE2492|3end_hypothetical_protein_2515509..2515659_NEGATIVE 333 56 17 69 27 NC_002967:TDE2179|3end_voltage-gated_chloride_channel_2210614..2210764_POSITIVE 332 105 66 65 20 NC_002967:TDE0280|3end_PIN_domain_protein_309895..310045_NEGATIVE 331 100 52 60 22 NC_002967:TDE2269|3end_hypothetical_protein_2304931..2305081_NEGATIVE 330 44 3 148 96 NC_002967:TDE2631|3end_peptide_ABC_transporter,_permease_protein,_putative_2672733..2672883_POSITIVE 329 62 21 68 13 NC_002967:TDE0320|3end_CBS_domain_protein_352480..352630_NEGATIVE