Origin IGS: atcatacctccaataaaagtgggatttcccaccgatattttagcacacataatcaaaaaaaacaagccagaaccacggacatccgtggccgaaccaagccggcaataggcgagtcgaggacgcgaagcgaataaaaataaaccagtaaaaccaagccgtaaatagagggtacagatactcgatcaaaaatatacatccttatatatttttgatcttcgagtttgtgacaagcacaaactctttaagctgaaaccacccgccatccgtggcgggcgcaggcgtgcttt .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaagcacgcctgcgcccgccacggatggcgggtggtttcagcttaaagagtttgtgcttgtcacaaactcgaagatcaaaaatatataaggatgtatatttttgatcgagtatctgtaccctctatttacggcttggttttactggtttatttttattcgcttcgcgtcctcgactcgcctattgccggcttggttcggccacggatgtccgtggttctggcttgttttttttgattatgtgtgctaaaatatcggtgggaaatcccacttttattggaggtatgat Mask Tandem Repeat Region ================================================ atcatacctccaataaaagtgggatttcccaccgatattttagcacacataatcaaaaaaaacaagccagaaccacggacatccgtggccgaaccaagccggcaataggcgagtcgaggacgcgaagcgaataaaaataaaccagtaaaaccaagccgtaaatagagggtacagatactcgatcaaaaatatacatccttatatatttttgatcttcgagtttgtgacaagcacaaactctttaagctgaaaccacccgccatccgtggcgggcgcaggcgtgcttt Find is-nt database================================================ Query_seq: TDE1846:TDE1847|TDE1846:TDE1847:hypothetical protein:hypothetical protein:<-->:1875517..1875803 287 atcatacctccaataaaagtgggatttcccaccgatattttagcacacataatcaaaaaaaacaagccagaaccacggacatccgtggccgaaccaagccggcaataggcgagtcgaggacgcgaagcgaataaaaataaaccagtaaaaccaagccgtaaatagagggtacagatactcgatcaaaaatatacatccttatatatttttgatcttcgagtttgtgacaagcacaaactctttaagctgaaaccacccgccatccgtggcgggcgcaggcgtgcttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1846:TDE1847|TDE1846:TDE1847:hypothetical protein:hypothetical protein:<-->:1875517..1875803 287 atcatacctccaataaaagtgggatttcccaccgatattttagcacacataatcaaaaaaaacaagccagaaccacggacatccgtggccgaaccaagccggcaataggcgagtcgaggacgcgaagcgaataaaaataaaccagtaaaaccaagccgtaaatagagggtacagatactcgatcaaaaatatacatccttatatatttttgatcttcgagtttgtgacaagcacaaactctttaagctgaaaccacccgccatccgtggcgggcgcaggcgtgcttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1846:TDE1847|TDE1846:TDE1847:hypothetical protein:hypothetical protein:<-->:1875517..1875803 287 atcatacctccaataaaagtgggatttcccaccgatattttagcacacataatcaaaaaaaacaagccagaaccacggacatccgtggccgaaccaagccggcaataggcgagtcgaggacgcgaagcgaataaaaataaaccagtaaaaccaagccgtaaatagagggtacagatactcgatcaaaaatatacatccttatatatttttgatcttcgagtttgtgacaagcacaaactctttaagctgaaaccacccgccatccgtggcgggcgcaggcgtgcttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atcatacctccaataaaagtgggatttcccaccgatattttagcacacataatcaaaaaaaacaagccagaaccacggacatccgtggccgaaccaagccggcaataggcgagtcgaggacgcgaagcgaataaaaataaaccagtaaaaccaagccgtaaatagagggtacagatactcgatcaaaaatatacatccttatatatttttgatcttcgagtttgtgacaagcacaaactctttaagctgaaaccacccgccatccgtggcgggcgcaggcgtgcttt Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 1 End: 105 M I P P I K V G F P T D I L A H I I K K N K P E P R T S V A E P S R Q ...................................................................................................................................................................................... Protein_Len: 36 Strand: + Start: 24 End: 131 ....................... M S H R Y F S T H N Q K K Q A R T T D I R G R T K P A I G E S R T R S E ............................................................................................................................................................ Protein_Len: 37 Strand: + Start: 175 End: 285 .............................................................................................................................................................................. M L D Q K Y T S L Y I F D L R V C D K H K L F K L K P P A I R G G R R R A .. Protein_Len: 31 Strand: - Start: 186 End: 278 ......................................................................................................................................................................................... F Y V D K Y I K S R R T Q S L C L S K L S F G G A M R P P R M ......... Protein_Len: 49 Strand: - Start: 56 End: 202 ....................................................... F F C A L V V S M R P R V L G A I P S D L V R L S Y F Y V L L V L G Y I S P V S V R D F I Y M R M ..................................................................................... Protein_Len: 50 Strand: - Start: 43 End: 192 .......................................... C V Y D F F V L W F W P C G H G F W A P L L R T S S A F R I F I F W Y F W A T F L P Y L Y E I L F M ............................................................................................... Protein_Len: 58 Strand: - Start: 3 End: 176 .. M G G I F T P N G V S I K A C M I L F F L G S G R V D T A S G L R C Y A L R P R S A F L F L G T F G L R L Y L T C M ............................................................................................................... atcatacctccaataaaagtgggatttcccaccgatattttagcacacataatcaaaaaaaacaagccagaaccacggacatccgtggccgaaccaagccggcaataggcgagtcgaggacgcgaagcgaataaaaataaaccagtaaaaccaagccgtaaatagagggtacagatactcgatcaaaaatatacatccttatatatttttgatcttcgagtttgtgacaagcacaaactctttaagctgaaaccacccgccatccgtggcgggcgcaggcgtgcttt Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: - Score: 84 Start: 37 End: 66 ....................................CTTGTTTTTTTTGATTATGTGTGCTAAAAT............................................................................................................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atcatacctccaataaaagtgggatttcccaccgatattttagcacacataatcaaaaaaaacaagccagaaccacggacatccgtggccgaaccaagccggcaataggcgagtcgaggacgcgaagcgaataaaaataaaccagtaaaaccaagccgtaaatagagggtacagatactcgatcaaaaatatacatccttatatatttttgatcttcgagtttgtgacaagcacaaactctttaagctgaaaccacccgccatccgtggcgggcgcaggcgtgcttt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 86 HP_score: -8.1 Tail_Score: -4.65078 Start: 19 End: 32 Full_Region: tgtgctaaaatatcg gtggg aaat cccac ttttattggaggtat ..................gtgggaaatcccac............................................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 80 HP_score: -10.4 Tail_Score: -3.52449 Start: 73 End: 88 Full_Region: gccggcttggttcgg ccacgg atgt ccgtgg ttctggcttgttttt ........................................................................ccacggatgtccgtgg....................................................................................................................................................................................................... TransTerm Strand: + Conf: 84 HP_score: -10.7 Tail_Score: -3.59979 Start: 218 End: 240 Full_Region: ATATTTTTGATCTTC GAGTTTGTG ACAAG CACAAACTC TTTAAGCTGAAACCA .........................................................................................................................................................................................................................GAGTTTGTGACAAGCACAAACTC............................................... Find igs database================================================ Query_seq: TDE1846:TDE1847|TDE1846:TDE1847:hypothetical protein:hypothetical protein:<-->:1875517..1875803 287 atcatacctccaataaaagtgggatttcccaccgatattttagcacacataatcaaaaaaaacaagccagaaccacggacatccgtggccgaaccaagccggcaataggcgagtcgaggacgcgaagcgaataaaaataaaccagtaaaaccaagccgtaaatagagggtacagatactcgatcaaaaatatacatccttatatatttttgatcttcgagtttgtgacaagcacaaactctttaagctgaaaccacccgccatccgtggcgggcgcaggcgtgcttt Intra-Species Hit: Count: 1 Min: 1 Max: 287 Len: 287 Subject: NC_002967_TDE1846_TDE1847|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[1875517,1875803]|287 HSP 1 e-value: 1.0E-147 bit: 521.0 Len: 287 Query Start:1 Query End:287 Subject Strand: POSITIVE Subject Start: 1 Subject End: 287 atcatacctccaataaaagtgggatttcccaccgatattttagcacacataatcnnnnnnnncaagccagaaccacggacatccgtggccgaaccaagccggcaataggcgagtcgaggacgcgaagcgaataaaaataaaccagtaaaaccaagccgtaaatagagggtacagatactcgatcaaaaatatacatccttatatatttttgatcttcgagtttgtgacaagcacaaactctttaagctgaaaccacccgccatccgtggcgggcgcaggcgtgcttt atcatacctccaataaaagtgggatttcccaccgatattttagcacacataatcaaaaaaaacaagccagaaccacggacatccgtggccgaaccaagccggcaataggcgagtcgaggacgcgaagcgaataaaaataaaccagtaaaaccaagccgtaaatagagggtacagatactcgatcaaaaatatacatccttatatatttttgatcttcgagtttgtgacaagcacaaactctttaagctgaaaccacccgccatccgtggcgggcgcaggcgtgcttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCAUACCUCCAAUAAAAGUGGGAUUUCCCACCGAUAUUUUAGCACACAUAAUCAAAAAAAACAAGCCAGAACCACGGACAUCCGUGGCCGAACCAAGCCGGCAAUAGGCGAGUCGAGGACGCGAAGCGAAUAAAAAUAAACCAGUAAAACCAAGCCGUAAAUAGAGGGUACAGAUACUCGAUCAAAAAUAUACAUCCUUAUAUAUUUUUGAUCUUCGAGUUUGUGACAAGCACAAACUCUUUAAGCUGAAACCACCCGCCAUCCGUGGCGGGCGCAGGCGUGCUUU ......((((........(((((....))))).................................(((.....(((((....)))))((((........))))....))).....)))).((((..(((.............((((........(((.(......).)))..........(((((((((((((........)))))))))))))...(((((((((.....))))))))).....))))......(((((((....))))))))))...)))).... (-85.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAGCACGCCUGCGCCCGCCACGGAUGGCGGGUGGUUUCAGCUUAAAGAGUUUGUGCUUGUCACAAACUCGAAGAUCAAAAAUAUAUAAGGAUGUAUAUUUUUGAUCGAGUAUCUGUACCCUCUAUUUACGGCUUGGUUUUACUGGUUUAUUUUUAUUCGCUUCGCGUCCUCGACUCGCCUAUUGCCGGCUUGGUUCGGCCACGGAUGUCCGUGGUUCUGGCUUGUUUUUUUUGAUUAUGUGUGCUAAAAUAUCGGUGGGAAAUCCCACUUUUAUUGGAGGUAUGAU ((((((.(((...((((((((....))))))))(((..(((......(((((((((.....)))))))))...(((((((((((((((....)))))))))))))))......))).)))..(((....((((..(((......((............(((...))).)).......)))....))))...)))...((((((((....))))))))..))).))))))............(((((..((((..((((((....))))))..))))...)))))... (-93.94) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1159 130 81 221 172 NC_002967:TDE1846|5end_hypothetical_protein_1875426..1875656_NEGATIVE 468 128 82 205 148 NC_002967:TDE2268|5end_hypothetical_protein_2304959..2305189_NEGATIVE 444 272 231 221 181 NC_002967:TDE1095|5end_alanine_racemase_1129826..1130056_POSITIVE 425 130 82 80 21 NC_002967:TDE0570|5end_hypothetical_protein_600169..600399_POSITIVE 415 280 235 177 116 NC_002967:TDE2100|5end_hypothetical_protein_2125370..2125600_POSITIVE 397 280 248 38 1 NC_002967:TDE2238|5end_hypothetical_protein_2276337..2276567_POSITIVE 381 128 82 100 44 NC_002967:TDE0946|5end_hypothetical_protein_968212..968442_POSITIVE 374 91 70 172 151 NC_002967:TDE2133|5end_cobalt_transport_protein,_putative_2164323..2164553_NEGATIVE 374 124 83 67 12 NC_002967:TDE1035|5end_transcriptional_regulator,_PadR_family_1063454..1063684_POSITIVE 374 278 245 33 3 NC_002967:TDE0588|5end_histidine_ammonia-lyase_626450..626680_POSITIVE 372 128 81 187 122 NC_002967:TDE2632|5end_peptide_ABC_transporter,_ATP-binding_protein,_putative_2672650..2672880_POSITIVE 371 256 214 229 187 NC_002967:TDE1612|5end_phosphoribosyl_transferase_domain_protein_1660549..1660779_POSITIVE 370 129 84 60 10 NC_002967:TDE0852|5end_50S_ribosomal_protein_L13_875019..875249_POSITIVE 367 128 83 120 79 NC_002967:TDE2516|5end_hypothetical_protein_2542021..2542251_POSITIVE 365 112 75 156 123 NC_002967:TDE1390|5end_hypothetical_protein_1429692..1429922_POSITIVE 363 128 83 184 138 NC_002967:TDE2251|5end_uracil_permease_2289440..2289670_POSITIVE 362 129 81 169 124 NC_002967:TDE0268|5end_hypothetical_protein_300049..300279_NEGATIVE 359 120 75 51 9 NC_002967:TDE1737|5end_hypothetical_protein_1790133..1790363_POSITIVE 358 239 196 231 188 NC_002967:TDE1889|5end_branched-chain_amino_acid_transport_system_II_carrier_protein_1910888..1911118_NEGATIVE 358 119 73 218 160 NC_002967:TDE1354|5end_hypothetical_protein_1394886..1395116_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 403 272 236 37 1 NC_002967:TDE1094|3end_hypothetical_protein_1129722..1129872_POSITIVE 394 270 223 50 1 NC_002967:TDE1611|3end_hypothetical_protein_1660434..1660584_POSITIVE 386 280 235 88 41 NC_002967:TDE2482|3end_hypothetical_protein_2505822..2505972_POSITIVE 386 118 76 120 86 NC_002967:TDE2101|3end_hypothetical_protein_2125549..2125699_NEGATIVE 383 271 235 151 114 NC_002967:TDE2238|3end_hypothetical_protein_2276545..2276695_POSITIVE 381 128 82 128 72 NC_002967:TDE0945|3end_hypothetical_protein_968320..968470_POSITIVE 377 110 65 77 30 NC_002967:TDE2317|3end_hemolysin_III_2354118..2354268_NEGATIVE 376 128 82 128 72 NC_002967:TDE2269|3end_hypothetical_protein_2304931..2305081_NEGATIVE 363 128 83 73 27 NC_002967:TDE2250|3end_hypothetical_protein_2289409..2289559_POSITIVE 359 129 81 72 16 NC_002967:TDE1839|3end_hypothetical_protein_1870391..1870541_NEGATIVE 355 280 240 66 29 NC_002967:TDE2104|3end_hypothetical_protein_2128525..2128675_NEGATIVE 354 124 87 147 95 NC_002967:TDE1056|3end_hypothetical_protein_1085895..1086045_POSITIVE 353 130 84 120 70 NC_002967:TDE1848|3end_hypothetical_protein_1875897..1876047_NEGATIVE 350 280 252 59 19 NC_002967:TDE0562|3end_hypothetical_protein_595581..595731_POSITIVE 348 272 231 54 14 NC_002967:TDE0833|3end_lipoprotein,_putative_854097..854247_POSITIVE 342 127 89 70 36 NC_002967:TDE2481|3end_hypothetical_protein_2505352..2505502_NEGATIVE 340 129 81 89 27 NC_002967:TDE2621|3end_hypothetical_protein_2662197..2662347_POSITIVE 339 120 72 122 67 NC_002967:TDE2515|3end_hypothetical_protein_2540972..2541122_NEGATIVE 334 130 84 104 59 NC_002967:TDE0353|3end_lipase/acylhydrolase,_GDSL_family_396743..396893_NEGATIVE 332 272 235 71 33 NC_002967:TDE2547|3end_hypothetical_protein_2573184..2573334_POSITIVE