Origin IGS: gttcacgcatttgtgcgtaggcgggtaagcagtggagggcgcagcgtaagccgcccgtaacggcgcacctgccaaagcacaaatgcgtagatgcggtgcagtacatttttgagacaaagtttgacctgcaccgtgtagccgctttagaggctcgaaaattttttggctaaaaacgacggtcgcatccgataatgcctacctttcttcccaagacggcgttatctttaccaaagataaaaccgaactcctctggtacccgaaaggcaaaccgggtgcttcttacaccgttccttcaggcgtaatagaa .........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 ttctattacgcctgaaggaacggtgtaagaagcacccggtttgcctttcgggtaccagaggagttcggttttatctttggtaaagataacgccgtcttgggaagaaaggtaggcattatcggatgcgaccgtcgtttttagccaaaaaattttcgagcctctaaagcggctacacggtgcaggtcaaactttgtctcaaaaatgtactgcaccgcatctacgcatttgtgctttggcaggtgcgccgttacgggcggcttacgctgcgccctccactgcttacccgcctacgcacaaatgcgtgaac Mask Tandem Repeat Region ================================================ gttcacgcatttgtgcgtaggcgggtaagcagtggagggcgcagcgtaagccgcccgtaacggcgcacctgccaaagcacaaatgcgtagatgcggtgcagtacatttttgagacaaagtttgacctgcaccgtgtagccgctttagaggctcgaaaattttttggctaaaaacgacggtcgcatccgataatgcctacctttcttcccaagacggcgttatctttaccaaagataaaaccgaactcctctggtacccgaaaggcaaaccgggtgcttcttacaccgttccttcaggcgtaatagaa Find is-nt database================================================ Query_seq: TDE0977:TDE0978|TDE0977:TDE0978:hypothetical protein:hypothetical protein:->->:1001701..1002007 307 gttcacgcatttgtgcgtaggcgggtaagcagtggagggcgcagcgtaagccgcccgtaacggcgcacctgccaaagcacaaatgcgtagatgcggtgcagtacatttttgagacaaagtttgacctgcaccgtgtagccgctttagaggctcgaaaattttttggctaaaaacgacggtcgcatccgataatgcctacctttcttcccaagacggcgttatctttaccaaagataaaaccgaactcctctggtacccgaaaggcaaaccgggtgcttcttacaccgttccttcaggcgtaatagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0977:TDE0978|TDE0977:TDE0978:hypothetical protein:hypothetical protein:->->:1001701..1002007 307 gttcacgcatttgtgcgtaggcgggtaagcagtggagggcgcagcgtaagccgcccgtaacggcgcacctgccaaagcacaaatgcgtagatgcggtgcagtacatttttgagacaaagtttgacctgcaccgtgtagccgctttagaggctcgaaaattttttggctaaaaacgacggtcgcatccgataatgcctacctttcttcccaagacggcgttatctttaccaaagataaaaccgaactcctctggtacccgaaaggcaaaccgggtgcttcttacaccgttccttcaggcgtaatagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0977:TDE0978|TDE0977:TDE0978:hypothetical protein:hypothetical protein:->->:1001701..1002007 307 gttcacgcatttgtgcgtaggcgggtaagcagtggagggcgcagcgtaagccgcccgtaacggcgcacctgccaaagcacaaatgcgtagatgcggtgcagtacatttttgagacaaagtttgacctgcaccgtgtagccgctttagaggctcgaaaattttttggctaaaaacgacggtcgcatccgataatgcctacctttcttcccaagacggcgttatctttaccaaagataaaaccgaactcctctggtacccgaaaggcaaaccgggtgcttcttacaccgttccttcaggcgtaatagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 1 Min: 176 Max: 304 Len: 129 Subject: UniRef90_Q73PQ6 Cluster: Hypothetical protein; n=1; Treponema denticola|Rep: Hypothetical protein - Treponema denticola HSP 1 e-value: 3.0E-7 bit: 56.2 Len: 129 Query Start:176 Query End:304 Subject Strand: null Subject Start: 458 Subject End: 500 ............................................................................................................................................................................... T V A S D N A Y L S S Q D G V I F T K D K T E L L W Y P K G K P G A S Y T V P S G V I ... ............................................................................................................................................................................... T V A S D N A Y L L A E N G V I F N K D K T V L L G Y L P D K P D V F Y T V P A S V I ... gttcacgcatttgtgcgtaggcgggtaagcagtggagggcgcagcgtaagccgcccgtaacggcgcacctgccaaagcacaaatgcgtagatgcggtgcagtacatttttgagacaaagtttgacctgcaccgtgtagccgctttagaggctcgaaaattttttggctaaaaacgnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngaa Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 69 End: 167 .................................................................... M P K H K C V D A V Q Y I F E T K F D L H R V A A L E A R K F F G ............................................................................................................................................ Protein_Len: 37 Strand: + Start: 189 End: 299 ............................................................................................................................................................................................ M M P T F L P K T A L S L P K I K P N S S G T R K A N R V L L T P F L Q A ........ Protein_Len: 50 Strand: + Start: 158 End: 307 ............................................................................................................................................................. M F W L K T T V A S D N A Y L S S Q D G V I F T K D K T E L L W Y P K G K P G A S Y T V P S G V I E Protein_Len: 43 Strand: - Start: 6 End: 131 ..... * A N T R L R T L L P P R L T L R G Y R R V Q W L V F A Y I R H L V N K L C L K V Q M ................................................................................................................................................................................ Protein_Len: 35 Strand: - Start: 2 End: 106 . E R M Q A Y A P L C H L A C R L G G T V A C R G F C L H T S A T C Y M ......................................................................................................................................................................................................... Protein_Len: 53 Strand: - Start: 1 End: 159 N V C K H T P P Y A T S P A A Y A A R L P A G A L A C I R L H P A T C K Q S L T Q G A G H L R K L P E F M .................................................................................................................................................... gttcacgcatttgtgcgtaggcgggtaagcagtggagggcgcagcgtaagccgcccgtaacggcgcacctgccaaagcacaaatgcgtagatgcggtgcagtacatttttgagacaaagtttgacctgcaccgtgtagccgctttagaggctcgaaaattttttggctaaaaacgnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngaa 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================================================ gttcacgcatttgtgcgtaggcgggtaagcagtggagggcgcagcgtaagccgcccgtaacggcgcacctgccaaagcacaaatgcgtagatgcggtgcagtacatttttgagacaaagtttgacctgcaccgtgtagccgctttagaggctcgaaaattttttggctaaaaacgnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0977:TDE0978|TDE0977:TDE0978:hypothetical protein:hypothetical protein:->->:1001701..1002007 307 gttcacgcatttgtgcgtaggcgggtaagcagtggagggcgcagcgtaagccgcccgtaacggcgcacctgccaaagcacaaatgcgtagatgcggtgcagtacatttttgagacaaagtttgacctgcaccgtgtagccgctttagaggctcgaaaattttttggctaaaaacgnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngaa Intra-Species Hit: Count: 1 Min: 1 Max: 174 Len: 174 Subject: NC_002967_TDE0977_TDE0978|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[1001701,1002007]|307 HSP 1 e-value: 6.0E-94 bit: 345.0 Len: 174 Query Start:1 Query End:174 Subject Strand: POSITIVE Subject Start: 1 Subject End: 174 gttcacgcatttgtgcgtaggcgggtaagcagtggagggcgcagcgtaagccgcccgtaacggcgcacctgccaaagcacaaatgcgtagatgcggtgcagtacatttttgagacaaagtttgacctgcaccgtgtagccgctttagaggctcgaaaattttttggctaaaaac..................................................................................................................................... gttcacgcatttgtgcgtaggcgggtaagcagtggagggcgcagcgtaagccgcccgtaacggcgcacctgccaaagcacaaatgcgtagatgcggtgcagtacatttttgagacaaagtttgacctgcaccgtgtagccgctttagaggctcgaaaattttttggctaaaaac..................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUCACGCAUUUGUGCGUAGGCGGGUAAGCAGUGGAGGGCGCAGCGUAAGCCGCCCGUAACGGCGCACCUGCCAAAGCACAAAUGCGUAGAUGCGGUGCAGUACAUUUUUGAGACAAAGUUUGACCUGCACCGUGUAGCCGCUUUAGAGGCUCGAAAAUUUUUUGGCUAAAAAC ..((((((((((((((...(((((((..((.((...(((((..((....)))))))...)).))..)))))))...)))))))))))).)).(((((((((..((..(((......)))..))..))))))))).((((((((.....))).............)))))..... (-78.11) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUUUUAGCCAAAAAAUUUUCGAGCCUCUAAAGCGGCUACACGGUGCAGGUCAAACUUUGUCUCAAAAAUGUACUGCACCGCAUCUACGCAUUUGUGCUUUGGCAGGUGCGCCGUUACGGGCGGCUUACGCUGCGCCCUCCACUGCUUACCCGCCUACGCACAAAUGCGUGAAC ......................((((.(....).))))...((((((((..((...((((...))))..))..))))))))....(((((((((((((...(((.((((.((.((...(((((((....))..)))))...)).)).)))).)))...)))))))))))))... (-66.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 521 79 38 77 41 NC_002967:TDE1629|5end_dihydrolipoamide_dehydrogenase_1678514..1678744_NEGATIVE 421 59 15 212 148 NC_002967:TDE2516|5end_hypothetical_protein_2542021..2542251_POSITIVE 420 60 13 77 30 NC_002967:TDE2715|5end_hypothetical_protein_2772668..2772898_POSITIVE 415 60 20 66 8 NC_002967:TDE2542|5end_antigen,_putative_2570826..2571056_NEGATIVE 404 69 21 64 5 NC_002967:TDE1782|5end_hypothetical_protein_1823417..1823647_NEGATIVE 404 69 21 221 162 NC_002967:TDE1781|5end_hypothetical_protein_1823260..1823490_NEGATIVE 401 89 45 90 49 NC_002967:TDE2280|5end_transglycosylase,_SLT_family_2317358..2317588_NEGATIVE 400 46 1 220 161 NC_002967:TDE1846|5end_hypothetical_protein_1875426..1875656_NEGATIVE 397 65 21 172 130 NC_002967:TDE2632|5end_peptide_ABC_transporter,_ATP-binding_protein,_putative_2672650..2672880_POSITIVE 392 70 29 195 141 NC_002967:TDE2268|5end_hypothetical_protein_2304959..2305189_NEGATIVE 392 67 23 53 4 NC_002967:TDE1247|5end_hypothetical_protein_1281623..1281853_POSITIVE 389 69 29 56 9 NC_002967:TDE2418|5end_hypothetical_protein_2443833..2444063_NEGATIVE 383 70 24 123 59 NC_002967:TDE2103|5end_glycosyl_transferase,_group_2_family_protein_2128393..2128623_NEGATIVE 381 75 35 77 35 NC_002967:TDE1999|5end_DNA_polymerase_III_domain_protein_2017063..2017293_POSITIVE 376 69 21 203 141 NC_002967:TDE0946|5end_hypothetical_protein_968212..968442_POSITIVE 375 67 29 98 59 NC_002967:TDE0970|5end_hypothetical_protein_994769..994999_POSITIVE 369 53 15 211 154 NC_002967:TDE2309|5end_sigma-54_dependent_transcriptional_regulator,_putative_2348099..2348329_NEGATIVE 367 77 31 66 2 NC_002967:TDE1515|5end_permease_domain_protein_1561978..1562208_POSITIVE 365 77 33 55 17 NC_002967:TDE1547|5end_ribonuclease_HII_1591124..1591354_POSITIVE 363 59 11 74 12 NC_002967:TDE1858|5end_transcriptional_regulator,_PadR_family_1884632..1884862_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 463 99 52 100 50 NC_002967:TDE0977|3end_hypothetical_protein_1001640..1001790_POSITIVE 435 60 16 139 71 NC_002967:TDE2543|3end_hypothetical_protein_2570753..2570903_NEGATIVE 408 98 54 131 81 NC_002967:TDE0908|3end_ABC_transporter,_ATP-binding/permease_protein_927085..927235_POSITIVE 388 71 31 50 6 NC_002967:TDE2210|3end_hypothetical_protein_2249394..2249544_NEGATIVE 381 79 36 117 63 NC_002967:TDE2622|3end_ABC_transporter,_ATP-binding_protein_2662178..2662328_NEGATIVE 381 75 35 77 35 NC_002967:TDE1998|3end_phosphohexose_mutase_family_protein_2017143..2017293_POSITIVE 377 66 23 63 5 NC_002967:TDE2104|3end_hypothetical_protein_2128525..2128675_NEGATIVE 372 69 29 41 5 NC_002967:TDE2118|3end_DNA_topoisomerase_IV_subunit_A_2149154..2149304_NEGATIVE 365 77 33 55 17 NC_002967:TDE1546|3end_hypothetical_protein_1591204..1591354_POSITIVE 361 69 21 81 21 NC_002967:TDE2181|3end_PAP2_family_protein_2211995..2212145_NEGATIVE 361 60 20 139 95 NC_002967:TDE0833|3end_lipoprotein,_putative_854097..854247_POSITIVE 360 54 13 72 33 NC_002967:TDE2544|3end_hypothetical_protein_2570935..2571085_NEGATIVE 359 77 35 50 3 NC_002967:TDE1277|3end_Fe-hydrogenase_large_subunit_family_protein_1312242..1312392_POSITIVE 357 60 13 110 39 NC_002967:TDE0493|3end_hypothetical_protein_548581..548731_NEGATIVE 356 66 24 68 3 NC_002967:TDE1980|3end_hypothetical_protein_1991960..1992110_NEGATIVE 355 56 15 78 40 NC_002967:TDE2293|3end_hypothetical_protein_2329325..2329475_NEGATIVE 354 78 32 88 51 NC_002967:TDE0352|3end_ribose_5-phosphate_isomerase_B_396739..396889_POSITIVE 352 66 21 143 110 NC_002967:TDE2057|3end_hypothetical_protein_2085158..2085308_NEGATIVE 351 60 19 40 2 NC_002967:TDE2567|3end_hypothetical_protein_2594198..2594348_NEGATIVE 350 56 11 44 2 NC_002967:TDE1540|3end_hypothetical_protein_1584948..1585098_POSITIVE