Origin IGS: ggctctgaaaaatataaaagggcgtaaatttcacaaccggcacggatgccggtggtttaaacttacgagttttttgcgaagcaaaaatactcgaagctgaaaaatgtacaagggcgtaaatttcacaaccggcacggatgccggtggtttaaacttacgagttttttgcgaagcaaaaatactcgaagctgaaaaatgtacaaggacgtacatttttcagcgg .........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 ccgctgaaaaatgtacgtccttgtacatttttcagcttcgagtatttttgcttcgcaaaaaactcgtaagtttaaaccaccggcatccgtgccggttgtgaaatttacgcccttgtacatttttcagcttcgagtatttttgcttcgcaaaaaactcgtaagtttaaaccaccggcatccgtgccggttgtgaaatttacgcccttttatatttttcagagcc Mask Tandem Repeat Region ================================================ ggctnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnttcagcgg Find is-nt database================================================ Query_seq: TDE0833:TDE0834|TDE0833:TDE0834:lipoprotein, putative:Na(+)-translocating NADH-quinone reductase, E subunit:-><-:854158..854380 223 ggctctgaaaaatataaaagggcgtaaatttcacaaccggcacggatgccggtggtttaaacttacgagttttttgcgaagcaaaaatactcgaagctgaaaaatgtacaagggcgtaaatttcacaaccggcacggatgccggtggtttaaacttacgagttttttgcgaagcaaaaatactcgaagctgaaaaatgtacaaggacgtacatttttcagcgg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0833:TDE0834|TDE0833:TDE0834:lipoprotein, putative:Na(+)-translocating NADH-quinone reductase, E subunit:-><-:854158..854380 223 ggctctgaaaaatataaaagggcgtaaatttcacaaccggcacggatgccggtggtttaaacttacgagttttttgcgaagcaaaaatactcgaagctgaaaaatgtacaagggcgtaaatttcacaaccggcacggatgccggtggtttaaacttacgagttttttgcgaagcaaaaatactcgaagctgaaaaatgtacaaggacgtacatttttcagcgg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0833:TDE0834|TDE0833:TDE0834:lipoprotein, putative:Na(+)-translocating NADH-quinone reductase, E subunit:-><-:854158..854380 223 ggctctgaaaaatataaaagggcgtaaatttcacaaccggcacggatgccggtggtttaaacttacgagttttttgcgaagcaaaaatactcgaagctgaaaaatgtacaagggcgtaaatttcacaaccggcacggatgccggtggtttaaacttacgagttttttgcgaagcaaaaatactcgaagctgaaaaatgtacaaggacgtacatttttcagcgg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ggctctgaaaaatataaaagggcgtaaatttcacaaccggcacggatgccggtggtttaaacttacgagttttttgcgaagcaaaaatactcgaagctgaaaaatgtacaagggcgtaaatttcacaaccggcacggatgccggtggtttaaacttacgagttttttgcgaagcaaaaatactcgaagctgaaaaatgtacaaggacgtacatttttcagcgg Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 5 End: 97 .... M K N I K G R K F H N R H G C R W F K L T S F L R S K N T R S .............................................................................................................................. Protein_Len: 31 Strand: + Start: 97 End: 189 ................................................................................................ M K N V Q G R K F H N R H G C R W F K L T S F L R S K N T R S .................................. Protein_Len: 40 Strand: + Start: 104 End: 223 ....................................................................................................... M Y K G V N F T T G T D A G G L N L R V F C E A K I L E A E K C T R T Y I F Q R Protein_Len: 60 Strand: - Start: 34 End: 213 ................................. L R C P H R H N L S V L K K R L L F V R L Q F I Y L P T F K V V P V S A P P K F K R T K Q S A F I S S A S F H V L V Y M .......... Protein_Len: 46 Strand: - Start: 2 End: 139 . S Q F I Y F P T F K V V P V S A P P K F K R T K Q S A F I S S A S F H V L A Y I E C G A R M .................................................................................... ggctctgaaaaatataaaagggcgtaaatttcacaaccggcacggatgccggtggtttaaacttacgagttttttgcgaagcaaaaatactcgaagctgaaaaatgtacaagggcgtaaatttcacaaccggcacggatgccggtggtttaaacttacgagttttttgcgaagcaaaaatactcgaagctgaaaaatgtacaaggacgtacatttttcagcgg 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================================================ ggctctgaaaaatataaaagggcgtaaatttcacaaccggcacggatgccggtggtttaaacttacgagttttttgcgaagcaaaaatactcgaagctgaaaaatgtacaagggcgtaaatttcacaaccggcacggatgccggtggtttaaacttacgagttttttgcgaagcaaaaatactcgaagctgaaaaatgtacaaggacgtacatttttcagcgg Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 78 HP_score: -10.4 Tail_Score: -3.39668 Start: 37 End: 52 Full_Region: cgtaagtttaaacca ccggca tccg tgccgg ttgtgaaatttacgc ....................................ccggcatccgtgccgg........................................................................................................................................................................... TransTerm Strand: - Conf: 73 HP_score: -8.9 Tail_Score: -3.53012 Start: 62 End: 96 Full_Region: ttgtacatttttcag cttcgagtatttttgc ttc gcaaaaaactcgtaag tttaaaccaccggca .............................................................cttcgagtatttttgcttcgcaaaaaactcgtaag............................................................................................................................... TransTerm Strand: - Conf: 76 HP_score: -10.8 Tail_Score: -2.64155 Start: 66 End: 93 Full_Region: tacatttttcagctt cgagtatttttgc ttc gcaaaaaactcg taagtttaaaccacc .................................................................cgagtatttttgcttcgcaaaaaactcg.................................................................................................................................. TransTerm Strand: + Conf: 80 HP_score: -10.1 Tail_Score: -3.66356 Start: 126 End: 147 Full_Region: AGGGCGTAAATTTCA CAACCGGCA CGGA TGCCGGTGG TTTAAACTTACGAGT .............................................................................................................................CAACCGGCACGGATGCCGGTGG............................................................................ TransTerm Strand: + Conf: 76 HP_score: -10.4 Tail_Score: -2.94412 Start: 129 End: 144 Full_Region: GCGTAAATTTCACAA CCGGCA CGGA TGCCGG TGGTTTAAACTTACG ................................................................................................................................CCGGCACGGATGCCGG............................................................................... TransTerm Strand: - Conf: 78 HP_score: -10.4 Tail_Score: -3.39668 Start: 129 End: 144 Full_Region: cgtaagtttaaacca ccggca tccg tgccgg ttgtgaaatttacgc ................................................................................................................................ccggcatccgtgccgg............................................................................... TransTerm Strand: - Conf: 73 HP_score: -8.9 Tail_Score: -3.53012 Start: 154 End: 188 Full_Region: ttgtacatttttcag cttcgagtatttttgc ttc gcaaaaaactcgtaag tttaaaccaccggca .........................................................................................................................................................cttcgagtatttttgcttcgcaaaaaactcgtaag................................... TransTerm Strand: - Conf: 76 HP_score: -10.8 Tail_Score: -2.64155 Start: 158 End: 185 Full_Region: tacatttttcagctt cgagtatttttgc ttc gcaaaaaactcg taagtttaaaccacc .............................................................................................................................................................cgagtatttttgcttcgcaaaaaactcg...................................... Find igs database================================================ Query_seq: TDE0833:TDE0834|TDE0833:TDE0834:lipoprotein, putative:Na(+)-translocating NADH-quinone reductase, E subunit:-><-:854158..854380 223 ggctctgaaaaatataaaagggcgtaaatttcacaaccggcacggatgccggtggtttaaacttacgagttttttgcgaagcaaaaatactcgaagctgaaaaatgtacaagggcgtaaatttcacaaccggcacggatgccggtggtttaaacttacgagttttttgcgaagcaaaaatactcgaagctgaaaaatgtacaaggacgtacatttttcagcgg Intra-Species Hit: Count: 2 Min: 1 Max: 223 Len: 223 Subject: NC_002967_TDE0833_TDE0834|lipoprotein, putative:Na(+)-translocating NADH-quinone reductase, E subunit|POSITIVE:NEGATIVE|[854158,854380]|223 HSP 1 e-value: 1.0E-123 bit: 442.0 Len: 223 Query Start:1 Query End:223 Subject Strand: POSITIVE Subject Start: 1 Subject End: 223 ggctctgaaaaatataaaagggcgtaaatttcacaaccggcacggatgccggtggtttaaacttacgagttttttgcgaagcaaaaatactcgaagctgaaaaatgtacaagggcgtaaatttcacaaccggcacggatgccggtggtttaaacttacgagttttttgcgaagcaaaaatactcgaagctgaaaaatgtacaaggacgtacatttttcagcgg ggctctgaaaaatataaaagggcgtaaatttcacaaccggcacggatgccggtggtttaaacttacgagttttttgcgaagcaaaaatactcgaagctgaaaaatgtacaagggcgtaaatttcacaaccggcacggatgccggtggtttaaacttacgagttttttgcgaagcaaaaatactcgaagctgaaaaatgtacaaggacgtacatttttcagcgg Subject: NC_002967_TDE2265_TDE2266|hypothetical protein:reverse transcriptase family protein|POSITIVE:NEGATIVE|[2302695,2303131]|437 HSP 1 e-value: 8.0E-9 bit: 61.9 Len: 46 Query Start:156 Query End:201 Subject Strand: NEGATIVE Subject Start: 126 Subject End: 172 ...........................................................................................................................................................tacgagttttttgcg-aagcaaaaatactcgaagctgaaaaatgtac...................... ...........................................................................................................................................................tacgagttttttgcgtaagcaaaaacactcgaagatgaaaaatgtac...................... HSP 2 e-value: 8.0E-9 bit: 61.9 Len: 46 Query Start:64 Query End:109 Subject Strand: NEGATIVE Subject Start: 126 Subject End: 172 ...............................................................tacgagttttttgcg-aagcaaaaatactcgaagctgaaaaatgtac.................................................................................................................. ...............................................................tacgagttttttgcgtaagcaaaaacactcgaagatgaaaaatgtac.................................................................................................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGCUCUGAAAAAUAUAAAAGGGCGUAAAUUUCACAACCGGCACGGAUGCCGGUGGUUUAAACUUACGAGUUUUUUGCGAAGCAAAAAUACUCGAAGCUGAAAAAUGUACAAGGGCGUAAAUUUCACAACCGGCACGGAUGCCGGUGGUUUAAACUUACGAGUUUUUUGCGAAGCAAAAAUACUCGAAGCUGAAAAAUGUACAAGGACGUACAUUUUUCAGCGG .(((((............))))).........((.(((((((....))))))).)).........((((((((((((...(((((((.((((((((.(((((.((((......))))...)))))..(((((((....)))))))........))).))))))))))))...))))))).)))))..((((((((((((((......)))))))))))))).. (-82.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCGCUGAAAAAUGUACGUCCUUGUACAUUUUUCAGCUUCGAGUAUUUUUGCUUCGCAAAAAACUCGUAAGUUUAAACCACCGGCAUCCGUGCCGGUUGUGAAAUUUACGCCCUUGUACAUUUUUCAGCUUCGAGUAUUUUUGCUUCGCAAAAAACUCGUAAGUUUAAACCACCGGCAUCCGUGCCGGUUGUGAAAUUUACGCCCUUUUAUAUUUUUCAGAGCC ..(((((((((((((((....)))))))))))))))...((((.(((((((...)))))))))))((((((((..((.((((((((..((((((((.(((((((.((((....)))).)))))..((((((((((.(((((((...)))))))))))).)))))...)).))))))))..)))))))).)).))))))))....................... (-81.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 608 170 121 111 58 NC_002967:TDE2548|5end_hypothetical_protein_2573198..2573428_NEGATIVE 557 220 173 45 1 NC_002967:TDE1934|5end_hypothetical_protein_1952614..1952844_POSITIVE 536 170 121 134 84 NC_002967:TDE2338|5end_hypothetical_protein_2374719..2374949_NEGATIVE 536 110 62 221 180 NC_002967:TDE1935|5end_hypothetical_protein_1952994..1953224_POSITIVE 476 170 121 132 84 NC_002967:TDE1890|5end_hypothetical_protein_1911012..1911242_POSITIVE 397 149 101 204 156 NC_002967:TDE2134|5end_hypothetical_protein_2164447..2164677_POSITIVE 364 220 180 221 184 NC_002967:TDE1933|5end_hypothetical_protein_1952611..1952841_NEGATIVE 361 178 132 69 23 NC_002967:TDE1923|5end_hypothetical_protein_1941692..1941922_NEGATIVE 352 79 36 190 142 NC_002967:TDE2237|5end_hypothetical_protein_2276402..2276632_NEGATIVE 349 136 94 178 146 NC_002967:TDE1808|5end_hypothetical_protein_1845049..1845279_NEGATIVE 348 77 37 148 107 NC_002967:TDE1847|5end_hypothetical_protein_1875664..1875894_POSITIVE 347 175 131 90 44 NC_002967:TDE1326|5end_hypothetical_protein_1361661..1361891_POSITIVE 331 80 31 227 174 NC_002967:TDE0976|5end_hypothetical_protein_1000026..1000256_POSITIVE 325 79 37 60 18 NC_002967:TDE1939|5end_hypothetical_protein_1954627..1954857_POSITIVE 324 137 94 226 182 NC_002967:TDE2528|5end_hypothetical_protein_2556912..2557142_NEGATIVE 320 143 103 66 32 NC_002967:TDE0256|5end_hypothetical_protein_291440..291670_NEGATIVE 315 220 188 189 157 NC_002967:TDE2549|5end_methyl-accepting_chemotaxis_protein_2573285..2573515_POSITIVE 310 147 101 139 75 NC_002967:TDE1358|5end_hypothetical_protein_1397732..1397962_POSITIVE 304 57 19 133 101 NC_002967:TDE1104|5end_tRNA_pseudouridine_synthase_B_1137786..1138016_NEGATIVE 299 80 35 203 146 NC_002967:TDE0848|5end_hypothetical_protein_871269..871499_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 799 190 141 55 5 NC_002967:TDE2101|3end_hypothetical_protein_2125549..2125699_NEGATIVE 476 216 173 151 111 NC_002967:TDE1934|3end_hypothetical_protein_1952804..1952954_POSITIVE 376 149 104 63 17 NC_002967:TDE2516|3end_hypothetical_protein_2542193..2542343_POSITIVE 363 209 164 54 9 NC_002967:TDE0945|3end_hypothetical_protein_968320..968470_POSITIVE 361 178 132 87 41 NC_002967:TDE1924|3end_hypothetical_protein_1941674..1941824_NEGATIVE 357 189 142 52 3 NC_002967:TDE2735|3end_surface_antigen,_putative_2791616..2791766_POSITIVE 357 79 37 119 70 NC_002967:TDE0049|3end_hypothetical_protein_58199..58349_NEGATIVE 333 219 181 85 47 NC_002967:TDE1056|3end_hypothetical_protein_1085895..1086045_POSITIVE 324 78 35 84 38 NC_002967:TDE2714|3end_hypothetical_protein_2770627..2770777_NEGATIVE 304 57 19 118 86 NC_002967:TDE1105|3end_ribosome-binding_factor_A_1137801..1137951_NEGATIVE 304 78 37 78 38 NC_002967:TDE0978|3end_hypothetical_protein_1002424..1002574_POSITIVE 304 67 23 68 24 NC_002967:TDE0833|3end_lipoprotein,_putative_854097..854247_POSITIVE 299 147 101 112 58 NC_002967:TDE2239|3end_hypothetical_protein_2276554..2276704_NEGATIVE 298 137 96 149 98 NC_002967:TDE1357|3end_aldose_1-epimerase_1397830..1397980_POSITIVE 294 79 35 99 57 NC_002967:TDE0353|3end_lipase/acylhydrolase,_GDSL_family_396743..396893_NEGATIVE 293 69 21 99 50 NC_002967:TDE0359|3end_ABC_transporter,_ATP-binding/permease_protein_402193..402343_NEGATIVE 291 101 64 46 9 NC_002967:TDE1299|3end_hypothetical_protein_1335417..1335567_NEGATIVE 287 76 33 66 23 NC_002967:TDE2311|3end_hypothetical_protein_2348437..2348587_POSITIVE 283 50 5 136 98 NC_002967:TDE0142|3end_hypothetical_protein_163979..164129_NEGATIVE 281 138 95 74 15 NC_002967:TDE2242|3end_antigen,_putative_2279569..2279719_NEGATIVE