Origin IGS: gtcgatgaaaaatgtacatccgtgtacatttttcatcttagagttttagacttgtgtctaaaactcttggaagtttggaaccaccgccgtccatggcggtgttgtattaactatttaatttgttgtagttggaaatgatcagttttcaccaaaataagagatgatagttaatatttagaattttttatttgaatctttagttttacccaaatccttctgttcacaatctcaattaaaga .........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 tctttaattgagattgtgaacagaaggatttgggtaaaactaaagattcaaataaaaaattctaaatattaactatcatctcttattttggtgaaaactgatcatttccaactacaacaaattaaatagttaatacaacaccgccatggacggcggtggttccaaacttccaagagttttagacacaagtctaaaactctaagatgaaaaatgtacacggatgtacatttttcatcgac Mask Tandem Repeat Region ================================================ gtcgatgaaaaatgtacatccgtgtacatttttcatcttagagttttagacttgtgtctaaaactcttggaagtttggaaccaccgccgtccatggcggtgttgtattaactatttaatttgttgtagttggaaatgatcagttttcaccaaaataagagatgatagttaatatttagaattttttatttgaatctttagttttacccaaatccttctgttcacaatctcaattaaaga Find is-nt database================================================ Query_seq: TDE1056:TDE1057|TDE1056:TDE1057:hypothetical protein:hypothetical protein:-><-:1085956..1086194 239 gtcgatgaaaaatgtacatccgtgtacatttttcatcttagagttttagacttgtgtctaaaactcttggaagtttggaaccaccgccgtccatggcggtgttgtattaactatttaatttgttgtagttggaaatgatcagttttcaccaaaataagagatgatagttaatatttagaattttttatttgaatctttagttttacccaaatccttctgttcacaatctcaattaaaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1056:TDE1057|TDE1056:TDE1057:hypothetical protein:hypothetical protein:-><-:1085956..1086194 239 gtcgatgaaaaatgtacatccgtgtacatttttcatcttagagttttagacttgtgtctaaaactcttggaagtttggaaccaccgccgtccatggcggtgttgtattaactatttaatttgttgtagttggaaatgatcagttttcaccaaaataagagatgatagttaatatttagaattttttatttgaatctttagttttacccaaatccttctgttcacaatctcaattaaaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1056:TDE1057|TDE1056:TDE1057:hypothetical protein:hypothetical protein:-><-:1085956..1086194 239 gtcgatgaaaaatgtacatccgtgtacatttttcatcttagagttttagacttgtgtctaaaactcttggaagtttggaaccaccgccgtccatggcggtgttgtattaactatttaatttgttgtagttggaaatgatcagttttcaccaaaataagagatgatagttaatatttagaattttttatttgaatctttagttttacccaaatccttctgttcacaatctcaattaaaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtcgatgaaaaatgtacatccgtgtacatttttcatcttagagttttagacttgtgtctaaaactcttggaagtttggaaccaccgccgtccatggcggtgttgtattaactatttaatttgttgtagttggaaatgatcagttttcaccaaaataagagatgatagttaatatttagaattttttatttgaatctttagttttacccaaatccttctgttcacaatctcaattaaaga Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 22 End: 135 ..................... M Y I F H L R V L D L C L K L L E V W N H R R P W R C C I N Y L I C C S W K ........................................................................................................ gtcgatgaaaaatgtacatccgtgtacatttttcatcttagagttttagacttgtgtctaaaactcttggaagtttggaaccaccgccgtccatggcggtgttgtattaactatttaatttgttgtagttggaaatgatcagttttcaccaaaataagagatgatagttaatatttagaattttttatttgaatctttagttttacccaaatccttctgttcacaatctcaattaaaga 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================================================ gtcgatgaaaaatgtacatccgtgtacatttttcatcttagagttttagacttgtgtctaaaactcttggaagtttggaaccaccgccgtccatggcggtgttgtattaactatttaatttgttgtagttggaaatgatcagttttcaccaaaataagagatgatagttaatatttagaattttttatttgaatctttagttttacccaaatccttctgttcacaatctcaattaaaga Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 90 HP_score: -11.6 Tail_Score: -3.53012 Start: 34 End: 73 Full_Region: TCCGTGTACATTTTT CATCTTAGAGTTTTAGAC TTGT GTCTAAAACTCTTGGAAG TTTGGAACCACCGCC .................................CATCTTAGAGTTTTAGACTTGTGTCTAAAACTCTTGGAAG...................................................................................................................................................................... TransTerm Strand: + Conf: 93 HP_score: -11.4 Tail_Score: -3.7212 Start: 82 End: 101 Full_Region: TTGGAAGTTTGGAAC CACCGCCG TCCA TGGCGGTG TTGTATTAACTATTT .................................................................................CACCGCCGTCCATGGCGGTG.......................................................................................................................................... Find igs database================================================ Query_seq: TDE1056:TDE1057|TDE1056:TDE1057:hypothetical protein:hypothetical protein:-><-:1085956..1086194 239 gtcgatgaaaaatgtacatccgtgtacatttttcatcttagagttttagacttgtgtctaaaactcttggaagtttggaaccaccgccgtccatggcggtgttgtattaactatttaatttgttgtagttggaaatgatcagttttcaccaaaataagagatgatagttaatatttagaattttttatttgaatctttagttttacccaaatccttctgttcacaatctcaattaaaga Intra-Species Hit: Count: 1 Min: 1 Max: 239 Len: 239 Subject: NC_002967_TDE1056_TDE1057|hypothetical protein:hypothetical protein|POSITIVE:NEGATIVE|[1085956,1086194]|239 HSP 1 e-value: 1.0E-133 bit: 474.0 Len: 239 Query Start:1 Query End:239 Subject Strand: POSITIVE Subject Start: 1 Subject End: 239 gtcgatgaaaaatgtacatccgtgtacatttttcatcttagagttttagacttgtgtctaaaactcttggaagtttggaaccaccgccgtccatggcggtgttgtattaactatttaatttgttgtagttggaaatgatcagttttcaccaaaataagagatgatagttaatatttagaattttttatttgaatctttagttttacccaaatccttctgttcacaatctcaattaaaga gtcgatgaaaaatgtacatccgtgtacatttttcatcttagagttttagacttgtgtctaaaactcttggaagtttggaaccaccgccgtccatggcggtgttgtattaactatttaatttgttgtagttggaaatgatcagttttcaccaaaataagagatgatagttaatatttagaattttttatttgaatctttagttttacccaaatccttctgttcacaatctcaattaaaga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUCGAUGAAAAAUGUACAUCCGUGUACAUUUUUCAUCUUAGAGUUUUAGACUUGUGUCUAAAACUCUUGGAAGUUUGGAACCACCGCCGUCCAUGGCGGUGUUGUAUUAACUAUUUAAUUUGUUGUAGUUGGAAAUGAUCAGUUUUCACCAAAAUAAGAGAUGAUAGUUAAUAUUUAGAAUUUUUUAUUUGAAUCUUUAGUUUUACCCAAAUCCUUCUGUUCACAAUCUCAAUUAAAGA ...(((((((((((((((....)))))))))))))))..((((((((((((....)))))))))))).((((((((((...((((((((....))))))))..((((((((((((..((((.((((..((((...(((.......))))))).)))).))))))))))))))))................................)))))..)))))..................... (-73.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUUUAAUUGAGAUUGUGAACAGAAGGAUUUGGGUAAAACUAAAGAUUCAAAUAAAAAAUUCUAAAUAUUAACUAUCAUCUCUUAUUUUGGUGAAAACUGAUCAUUUCCAACUACAACAAAUUAAAUAGUUAAUACAACACCGCCAUGGACGGCGGUGGUUCCAAACUUCCAAGAGUUUUAGACACAAGUCUAAAACUCUAAGAUGAAAAAUGUACACGGAUGUACAUUUUUCAUCGAC .........(((.(((.((((.(((...(((((......)))))..))).................((((((((((((((.........))))).....((.....))..................)))))))))...(((((((......)))))))))))))).)))...((((((((((((....))))))))))))..(((((((((((((((....)))))))))))))))... (-69.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 910 100 51 155 106 NC_002967:TDE2100|5end_hypothetical_protein_2125370..2125600_POSITIVE 757 90 41 167 114 NC_002967:TDE2133|5end_cobalt_transport_protein,_putative_2164323..2164553_NEGATIVE 705 60 11 229 180 NC_002967:TDE2339|5end_leucyl-tRNA_synthetase_2374845..2375075_POSITIVE 691 78 31 231 184 NC_002967:TDE2549|5end_methyl-accepting_chemotaxis_protein_2573285..2573515_POSITIVE 653 47 1 174 127 NC_002967:TDE1095|5end_alanine_racemase_1129826..1130056_POSITIVE 545 100 76 25 1 NC_002967:TDE2238|5end_hypothetical_protein_2276337..2276567_POSITIVE 527 46 1 179 133 NC_002967:TDE2492|5end_hypothetical_protein_2516414..2516644_NEGATIVE 517 46 2 231 187 NC_002967:TDE1933|5end_hypothetical_protein_1952611..1952841_NEGATIVE 386 50 6 230 186 NC_002967:TDE0970|5end_hypothetical_protein_994769..994999_POSITIVE 359 46 4 215 173 NC_002967:TDE1889|5end_branched-chain_amino_acid_transport_system_II_carrier_protein_1910888..1911118_NEGATIVE 350 118 73 175 124 NC_002967:TDE2237|5end_hypothetical_protein_2276402..2276632_NEGATIVE 339 80 31 171 111 NC_002967:TDE2338|5end_hypothetical_protein_2374719..2374949_NEGATIVE 336 120 81 181 145 NC_002967:TDE0594|5end_cysteine_protease_domain,_YopT-type_634805..635035_NEGATIVE 334 100 52 108 39 NC_002967:TDE1890|5end_hypothetical_protein_1911012..1911242_POSITIVE 333 46 2 196 152 NC_002967:TDE1612|5end_phosphoribosyl_transferase_domain_protein_1660549..1660779_POSITIVE 327 44 2 50 8 NC_002967:TDE1934|5end_hypothetical_protein_1952614..1952844_POSITIVE 325 80 31 135 86 NC_002967:TDE2548|5end_hypothetical_protein_2573198..2573428_NEGATIVE 306 101 64 65 27 NC_002967:TDE2344|5end_undecaprenyl_diphosphate_synthase_2381945..2382175_NEGATIVE 295 90 41 203 166 NC_002967:TDE2121|5end_hypothetical_protein_2154729..2154959_NEGATIVE 293 100 64 37 1 NC_002967:TDE1072|5end_lipoprotein,_putative_1100741..1100971_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 946 98 51 151 104 NC_002967:TDE2238|3end_hypothetical_protein_2276545..2276695_POSITIVE 837 90 41 66 13 NC_002967:TDE2547|3end_hypothetical_protein_2573184..2573334_POSITIVE 603 100 62 38 1 NC_002967:TDE1094|3end_hypothetical_protein_1129722..1129872_POSITIVE 427 101 79 51 28 NC_002967:TDE2493|3end_hypothetical_protein_2516745..2516895_NEGATIVE 412 99 51 77 29 NC_002967:TDE2736|3end_hypothetical_protein_2791702..2791852_NEGATIVE 408 122 84 102 62 NC_002967:TDE2482|3end_hypothetical_protein_2505822..2505972_POSITIVE 385 106 61 60 13 NC_002967:TDE1611|3end_hypothetical_protein_1660434..1660584_POSITIVE 353 99 82 38 20 NC_002967:TDE1048|3end_30S_ribosomal_protein_S7_1075032..1075182_POSITIVE 346 37 4 87 54 NC_002967:TDE1056|3end_hypothetical_protein_1085895..1086045_POSITIVE 339 37 4 88 55 NC_002967:TDE2316|3end_hypothetical_protein_2353978..2354128_POSITIVE 336 44 1 129 86 NC_002967:TDE2100|3end_hypothetical_protein_2125572..2125722_POSITIVE 336 120 81 148 112 NC_002967:TDE0595|3end_hypothetical_protein_634838..634988_NEGATIVE 333 100 60 55 18 NC_002967:TDE0833|3end_lipoprotein,_putative_854097..854247_POSITIVE 310 80 31 59 10 NC_002967:TDE2239|3end_hypothetical_protein_2276554..2276704_NEGATIVE 306 101 64 64 26 NC_002967:TDE2345|3end_ribosome_recycling_factor_2381946..2382096_NEGATIVE 292 100 70 143 104 NC_002967:TDE1402|3end_hypothetical_protein_1444515..1444665_POSITIVE 287 129 81 69 21 NC_002967:TDE2643|3end_oxidoreductase,_FAD-dependent_2683734..2683884_POSITIVE 285 101 62 144 103 NC_002967:TDE1254|3end_Smr_domain_protein_1289003..1289153_POSITIVE 277 103 71 62 32 NC_002967:TDE2766|3end_motility_protein_A_2820095..2820245_NEGATIVE 276 99 64 43 6 NC_002967:TDE2572|3end_CDP-diacylglycerol--glycerol-3-phosphate_3-phosphatidyltransferase_2598145..2598295_NEGATIVE