Origin IGS: gaatggaaccaccggacatcctgtccggcttatgatcggacatccgtgtacatttttcagcttcgagttttgccttacggcaaaacatcgcgagaatggaaccaccggacatcctgtccggcttatgatcggacatccgtgtacatttttcagcttcgagtttgcgttgcaaactcgtaaggagtggaaccagcggcatccgtgccgctgaaggattgtacatcagtgtccgattttgaacttcgagttttgccttacggcaaaacatc .........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 gatgttttgccgtaaggcaaaactcgaagttcaaaatcggacactgatgtacaatccttcagcggcacggatgccgctggttccactccttacgagtttgcaacgcaaactcgaagctgaaaaatgtacacggatgtccgatcataagccggacaggatgtccggtggttccattctcgcgatgttttgccgtaaggcaaaactcgaagctgaaaaatgtacacggatgtccgatcataagccggacaggatgtccggtggttccattc Mask Tandem Repeat Region ================================================ gaatggaaccaccggacatcctgtccggcttatgatcggacatccgtgtacatttttcagcttcgagttttgccttacggcaaaacatcgcgagaatggaaccaccggacatcctgtccggcttatgatcggacatccgtgtacatttttcagcttcgagtttgcgttgcaaactcgtaaggagtggaaccagcggcatccgtgccgctgaaggattgtacatcagtgtccgattttgaacttcgagttttgccttacggcaaaacatc Find is-nt database================================================ Query_seq: TDE1934:TDE1935|TDE1934:TDE1935:hypothetical protein:hypothetical protein:->->:1952865..1953133 269 gaatggaaccaccggacatcctgtccggcttatgatcggacatccgtgtacatttttcagcttcgagttttgccttacggcaaaacatcgcgagaatggaaccaccggacatcctgtccggcttatgatcggacatccgtgtacatttttcagcttcgagtttgcgttgcaaactcgtaaggagtggaaccagcggcatccgtgccgctgaaggattgtacatcagtgtccgattttgaacttcgagttttgccttacggcaaaacatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1934:TDE1935|TDE1934:TDE1935:hypothetical protein:hypothetical protein:->->:1952865..1953133 269 gaatggaaccaccggacatcctgtccggcttatgatcggacatccgtgtacatttttcagcttcgagttttgccttacggcaaaacatcgcgagaatggaaccaccggacatcctgtccggcttatgatcggacatccgtgtacatttttcagcttcgagtttgcgttgcaaactcgtaaggagtggaaccagcggcatccgtgccgctgaaggattgtacatcagtgtccgattttgaacttcgagttttgccttacggcaaaacatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1934:TDE1935|TDE1934:TDE1935:hypothetical protein:hypothetical protein:->->:1952865..1953133 269 gaatggaaccaccggacatcctgtccggcttatgatcggacatccgtgtacatttttcagcttcgagttttgccttacggcaaaacatcgcgagaatggaaccaccggacatcctgtccggcttatgatcggacatccgtgtacatttttcagcttcgagtttgcgttgcaaactcgtaaggagtggaaccagcggcatccgtgccgctgaaggattgtacatcagtgtccgattttgaacttcgagttttgccttacggcaaaacatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gaatggaaccaccggacatcctgtccggcttatgatcggacatccgtgtacatttttcagcttcgagttttgccttacggcaaaacatcgcgagaatggaaccaccggacatcctgtccggcttatgatcggacatccgtgtacatttttcagcttcgagtttgcgttgcaaactcgtaaggagtggaaccagcggcatccgtgccgctgaaggattgtacatcagtgtccgattttgaacttcgagttttgccttacggcaaaacatc Predict ORF larger than 30AA ================================================ Protein_Len: 44 Strand: + Start: 46 End: 177 ............................................. M Y I F Q L R V L P Y G K T S R E W N H R T S C P A Y D R T S V Y I F Q L R V C V A N S ............................................................................................ Protein_Len: 59 Strand: + Start: 32 End: 208 ............................... M I G H P C T F F S F E F C L T A K H R E N G T T G H P V R L M I G H P C T F F S F E F A L Q T R K E W N Q R H P C R ............................................................. Protein_Len: 34 Strand: + Start: 135 End: 236 ...................................................................................................................................... M R V H F S A S S L R C K L V R S G T S G I R A A E G L Y I S V R F ................................. Protein_Len: 60 Strand: - Start: 2 End: 268 . A L I S G G S M R D P K H D S M R T C K E A E L K R Q L S T L L P V L P M R A A S P N Y M L T R N Q V E L K A K R C F M . Protein_Len: 60 Strand: - Start: 1 End: 216 P C G H V N K L K S N Q R V A F C R S F P V V P C G T R S I I P C G H V N K L K S N A N C V R L S H F W R C G H R Q L M ..................................................... gaatggaaccaccggacatcctgtccggcttatgatcggacatccgtgtacatttttcagcttcgagttttgccttacggcaaaacatcgcgagaatggaaccaccggacatcctgtccggcttatgatcggacatccgtgtacatttttcagcttcgagtttgcgttgcaaactcgtaaggagtggaaccagcggcatccgtgccgctgaaggattgtacatcagtgtccgattttgaacttcgagttttgccttacggcaaaacatc 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================================================ gaatggaaccaccggacatcctgtccggcttatgatcggacatccgtgtacatttttcagcttcgagttttgccttacggcaaaacatcgcgagaatggaaccaccggacatcctgtccggcttatgatcggacatccgtgtacatttttcagcttcgagtttgcgttgcaaactcgtaaggagtggaaccagcggcatccgtgccgctgaaggattgtacatcagtgtccgattttgaacttcgagttttgccttacggcaaaacatc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 73 HP_score: -12.3 Tail_Score: -2.64218 Start: 105 End: 121 Full_Region: GCGAGAATGGAACCA CCGGACA TCC TGTCCGG CTTATGATCGGACAT ........................................................................................................CCGGACATCCTGTCCGG.................................................................................................................................................... TransTerm Strand: - Conf: 74 HP_score: -12.3 Tail_Score: -2.80511 Start: 105 End: 121 Full_Region: atgtccgatcataag ccggaca gga tgtccgg tggttccattctcgc ........................................................................................................ccggacaggatgtccgg.................................................................................................................................................... Find igs database================================================ Query_seq: TDE1934:TDE1935|TDE1934:TDE1935:hypothetical protein:hypothetical protein:->->:1952865..1953133 269 gaatggaaccaccggacatcctgtccggcttatgatcggacatccgtgtacatttttcagcttcgagttttgccttacggcaaaacatcgcgagaatggaaccaccggacatcctgtccggcttatgatcggacatccgtgtacatttttcagcttcgagtttgcgttgcaaactcgtaaggagtggaaccagcggcatccgtgccgctgaaggattgtacatcagtgtccgattttgaacttcgagttttgccttacggcaaaacatc Intra-Species Hit: Count: 3 Min: 1 Max: 269 Len: 269 Subject: NC_002967_TDE1934_TDE1935|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[1952865,1953133]|269 HSP 1 e-value: 1.0E-150 bit: 533.0 Len: 269 Query Start:1 Query End:269 Subject Strand: POSITIVE Subject Start: 1 Subject End: 269 gaatggaaccaccggacatcctgtccggcttatgatcggacatccgtgtacatttttcagcttcgagttttgccttacggcaaaacatcgcgagaatggaaccaccggacatcctgtccggcttatgatcggacatccgtgtacatttttcagcttcgagtttgcgttgcaaactcgtaaggagtggaaccagcggcatccgtgccgctgaaggattgtacatcagtgtccgattttgaacttcgagttttgccttacggcaaaacatc gaatggaaccaccggacatcctgtccggcttatgatcggacatccgtgtacatttttcagcttcgagttttgccttacggcaaaacatcgcgagaatggaaccaccggacatcctgtccggcttatgatcggacatccgtgtacatttttcagcttcgagtttgcgttgcaaactcgtaaggagtggaaccagcggcatccgtgccgctgaaggattgtacatcagtgtccgattttgaacttcgagttttgccttacggcaaaacatc Subject: NC_002967_TDE2514_TDE2515|serine/threonine protein phosphatase family protein:hypothetical protein|NEGATIVE:NEGATIVE|[2540623,2541061]|439 HSP 1 e-value: 1.0E-14 bit: 81.8 Len: 73 Query Start:35 Query End:107 Subject Strand: NEGATIVE Subject Start: 336 Subject End: 408 ..................................atcggacatccgtgtacatttttcagcttcgagttttgccttacggcaaaacatcgcgagaatggaaccaccg.................................................................................................................................................................. ..................................atcggacatctgtgtccgattttgagtttcgagttttgcctcacggcaaaacatcgcaagaatggaaccaccg.................................................................................................................................................................. HSP 2 e-value: 2.0E-10 bit: 67.9 Len: 50 Query Start:220 Query End:269 Subject Strand: NEGATIVE Subject Start: 354 Subject End: 403 ...........................................................................................................................................................................................................................acatcagtgtccgattttgaacttcgagttttgccttacggcaaaacatc ...........................................................................................................................................................................................................................acatctgtgtccgattttgagtttcgagttttgcctcacggcaaaacatc Subject: NC_002967_TDE2492_TDE2493|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[2516505,2516834]|330 HSP 1 e-value: 4.0E-8 bit: 60.0 Len: 34 Query Start:236 Query End:269 Subject Strand: POSITIVE Subject Start: 113 Subject End: 146 ...........................................................................................................................................................................................................................................ttgaacttcgagttttgccttacggcaaaacatc ...........................................................................................................................................................................................................................................ttgaacttcgagttttgcctgacggcaaaacatc HSP 2 e-value: 6.0E-7 bit: 56.0 Len: 32 Query Start:61 Query End:92 Subject Strand: POSITIVE Subject Start: 118 Subject End: 149 ............................................................cttcgagttttgccttacggcaaaacatcgcg................................................................................................................................................................................. ............................................................cttcgagttttgcctgacggcaaaacatcgcg................................................................................................................................................................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAUGGAACCACCGGACAUCCUGUCCGGCUUAUGAUCGGACAUCCGUGUACAUUUUUCAGCUUCGAGUUUUGCCUUACGGCAAAACAUCGCGAGAAUGGAACCACCGGACAUCCUGUCCGGCUUAUGAUCGGACAUCCGUGUACAUUUUUCAGCUUCGAGUUUGCGUUGCAAACUCGUAAGGAGUGGAACCAGCGGCAUCCGUGCCGCUGAAGGAUUGUACAUCAGUGUCCGAUUUUGAACUUCGAGUUUUGCCUUACGGCAAAACAUC (((........(((((((...(((((((........(((....)))........(((((..((((.((((((((....))))))))....))))..)))))...)))))))...))))))).(((.((((((((((..(((((((...(((..((((((((((((...))))))))).))).........((((((((....))))))))..))).)))))))..)))))))))).)))..)))..((((((((....))))))))... (-112.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUGUUUUGCCGUAAGGCAAAACUCGAAGUUCAAAAUCGGACACUGAUGUACAAUCCUUCAGCGGCACGGAUGCCGCUGGUUCCACUCCUUACGAGUUUGCAACGCAAACUCGAAGCUGAAAAAUGUACACGGAUGUCCGAUCAUAAGCCGGACAGGAUGUCCGGUGGUUCCAUUCUCGCGAUGUUUUGCCGUAAGGCAAAACUCGAAGCUGAAAAAUGUACACGGAUGUCCGAUCAUAAGCCGGACAGGAUGUCCGGUGGUUCCAUUC ((.((((((((....))))))))))..........(((((((((((.((((((.....(((((((((....))))))))).....(..(((.(((((((((...))))))))))))..).....))))))))).)))))))).....((((((((...((((((((.......(((...(((.((((((((....))))))))))).....))).........(((....))).......))))))))...)))))))).......... (-118.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 700 108 61 229 182 NC_002967:TDE2489|5end_peptide_chain_release_factor_1_2512476..2512706_NEGATIVE 603 207 161 59 11 NC_002967:TDE2100|5end_hypothetical_protein_2125370..2125600_POSITIVE 492 70 40 231 201 NC_002967:TDE1933|5end_hypothetical_protein_1952611..1952841_NEGATIVE 478 90 41 192 144 NC_002967:TDE1095|5end_alanine_racemase_1129826..1130056_POSITIVE 470 176 131 213 164 NC_002967:TDE1612|5end_phosphoribosyl_transferase_domain_protein_1660549..1660779_POSITIVE 446 207 161 172 125 NC_002967:TDE2133|5end_cobalt_transport_protein,_putative_2164323..2164553_NEGATIVE 401 176 133 219 169 NC_002967:TDE2549|5end_methyl-accepting_chemotaxis_protein_2573285..2573515_POSITIVE 394 144 101 53 3 NC_002967:TDE0908|5end_ABC_transporter,_ATP-binding/permease_protein_925254..925484_POSITIVE 389 83 44 231 192 NC_002967:TDE2492|5end_hypothetical_protein_2516414..2516644_NEGATIVE 383 220 171 227 167 NC_002967:TDE2516|5end_hypothetical_protein_2542021..2542251_POSITIVE 371 180 136 228 188 NC_002967:TDE1889|5end_branched-chain_amino_acid_transport_system_II_carrier_protein_1910888..1911118_NEGATIVE 361 120 72 62 7 NC_002967:TDE2766|5end_motility_protein_A_2820874..2821104_NEGATIVE 357 246 203 170 128 NC_002967:TDE0803|5end_hypothetical_protein_825317..825547_POSITIVE 349 210 162 57 14 NC_002967:TDE1246|5end_lipoprotein,_putative_1279039..1279269_POSITIVE 347 250 203 81 35 NC_002967:TDE1294|5end_phosphocarrier_protein_HPr_1332321..1332551_NEGATIVE 346 208 161 223 163 NC_002967:TDE1051|5end_hypothetical_protein_1078496..1078726_NEGATIVE 343 210 161 83 28 NC_002967:TDE2019|5end_hypothetical_protein_2040719..2040949_NEGATIVE 340 210 163 134 82 NC_002967:TDE1325|5end_hypothetical_protein_1361721..1361951_NEGATIVE 340 235 193 65 36 NC_002967:TDE0743|5end_thioredoxin_reductase_778718..778948_POSITIVE 339 64 24 231 202 NC_002967:TDE0701|5end_hypothetical_protein_737247..737477_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 564 207 161 53 6 NC_002967:TDE0833|3end_lipoprotein,_putative_854097..854247_POSITIVE 544 50 1 70 21 NC_002967:TDE1611|3end_hypothetical_protein_1660434..1660584_POSITIVE 540 207 161 70 24 NC_002967:TDE2547|3end_hypothetical_protein_2573184..2573334_POSITIVE 454 176 133 151 101 NC_002967:TDE2100|3end_hypothetical_protein_2125572..2125722_POSITIVE 403 120 71 59 7 NC_002967:TDE1062|3end_ABC_transporter,_ATP-binding_protein,_HlyB_family_1090387..1090537_POSITIVE 381 210 162 55 1 NC_002967:TDE2396|3end_putative_inner_membrane_protein_translocase_component_YidC_2423650..2423800_NEGATIVE 381 50 3 60 13 NC_002967:TDE1094|3end_hypothetical_protein_1129722..1129872_POSITIVE 356 220 172 147 88 NC_002967:TDE0977|3end_hypothetical_protein_1001640..1001790_POSITIVE 353 100 53 117 60 NC_002967:TDE2272|3end_hypothetical_protein_2308980..2309130_NEGATIVE 350 122 82 78 39 NC_002967:TDE2736|3end_hypothetical_protein_2791702..2791852_NEGATIVE 347 237 191 77 31 NC_002967:TDE2493|3end_hypothetical_protein_2516745..2516895_NEGATIVE 346 210 161 69 20 NC_002967:TDE1916|3end_glycerol_kinase_1933277..1933427_NEGATIVE 343 210 161 68 13 NC_002967:TDE2020|3end_YD_repeat_protein_2040734..2040884_NEGATIVE 340 210 163 66 14 NC_002967:TDE1327|3end_hypothetical_protein_1361789..1361939_NEGATIVE 340 51 12 39 1 NC_002967:TDE0907|3end_hypothetical_protein_925320..925470_POSITIVE 339 59 13 64 13 NC_002967:TDE2714|3end_hypothetical_protein_2770627..2770777_NEGATIVE 339 215 184 151 110 NC_002967:TDE2057|3end_hypothetical_protein_2085158..2085308_NEGATIVE 339 69 23 92 40 NC_002967:TDE0459|3end_hypothetical_protein_515241..515391_POSITIVE 333 197 151 91 37 NC_002967:TDE2642|3end_hypothetical_protein_2682111..2682261_NEGATIVE 329 219 174 70 26 NC_002967:TDE2766|3end_motility_protein_A_2820095..2820245_NEGATIVE