Origin IGS: aaacatagccggtctaccggcataatggtagacaccctaccaacataatggtagactgtctaccaacgtaatggtgagcagtctaccagcataatggtggacaccctaccggcataatggtgggcagtctaccagcataatggtagccggtctaccaatataatgataaagtccttttggattgggacaattcaatccaaaaaatacatgaataaaccccgaaccttgaacccgccggggtctttaggggcagcgcccctaaacagcgcgggagagagagggggttatagggggagagtacaaccaacggagtttcgaggtgaaccctgctctggacggggtgctctctccccctaaattaaggagtttctt .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 aagaaactccttaatttagggggagagagcaccccgtccagagcagggttcacctcgaaactccgttggttgtactctccccctataaccccctctctctcccgcgctgtttaggggcgctgcccctaaagaccccggcgggttcaaggttcggggtttattcatgtattttttggattgaattgtcccaatccaaaaggactttatcattatattggtagaccggctaccattatgctggtagactgcccaccattatgccggtagggtgtccaccattatgctggtagactgctcaccattacgttggtagacagtctaccattatgttggtagggtgtctaccattatgccggtagaccggctatgttt Mask Tandem Repeat Region ================================================ aaacannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnatataatgataaagtccttttggattgggacaattcaatccaaaaaatacatgaataaaccccgaaccttgaacccgccggggtctttaggggcagcgcccctaaacagcgcgggagagagagggggttatagggggagagtacaaccaacggagtttcgaggtgaaccctgctctggacggggtgctctctccccctaaattaaggagtttctt Find is-nt database================================================ Query_seq: TDE2734:TDE2735|TDE2734:TDE2735:hypothetical protein:surface antigen, putative:->->:2789922..2790293 372 aaacatagccggtctaccggcataatggtagacaccctaccaacataatggtagactgtctaccaacgtaatggtgagcagtctaccagcataatggtggacaccctaccggcataatggtgggcagtctaccagcataatggtagccggtctaccaatataatgataaagtccttttggattgggacaattcaatccaaaaaatacatgaataaaccccgaaccttgaacccgccggggtctttaggggcagcgcccctaaacagcgcgggagagagagggggttatagggggagagtacaaccaacggagtttcgaggtgaaccctgctctggacggggtgctctctccccctaaattaaggagtttctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2734:TDE2735|TDE2734:TDE2735:hypothetical protein:surface antigen, putative:->->:2789922..2790293 372 aaacatagccggtctaccggcataatggtagacaccctaccaacataatggtagactgtctaccaacgtaatggtgagcagtctaccagcataatggtggacaccctaccggcataatggtgggcagtctaccagcataatggtagccggtctaccaatataatgataaagtccttttggattgggacaattcaatccaaaaaatacatgaataaaccccgaaccttgaacccgccggggtctttaggggcagcgcccctaaacagcgcgggagagagagggggttatagggggagagtacaaccaacggagtttcgaggtgaaccctgctctggacggggtgctctctccccctaaattaaggagtttctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2734:TDE2735|TDE2734:TDE2735:hypothetical protein:surface antigen, putative:->->:2789922..2790293 372 aaacatagccggtctaccggcataatggtagacaccctaccaacataatggtagactgtctaccaacgtaatggtgagcagtctaccagcataatggtggacaccctaccggcataatggtgggcagtctaccagcataatggtagccggtctaccaatataatgataaagtccttttggattgggacaattcaatccaaaaaatacatgaataaaccccgaaccttgaacccgccggggtctttaggggcagcgcccctaaacagcgcgggagagagagggggttatagggggagagtacaaccaacggagtttcgaggtgaaccctgctctggacggggtgctctctccccctaaattaaggagtttctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaacatagccggtctaccggcataatggtagacaccctaccaacataatggtagactgtctaccaacgtaatggtgagcagtctaccagcataatggtggacaccctaccggcataatggtgggcagtctaccagcataatggtagccggtctaccaatataatgataaagtccttttggattgggacaattcaatccaaaaaatacatgaataaaccccgaaccttgaacccgccggggtctttaggggcagcgcccctaaacagcgcgggagagagagggggttatagggggagagtacaaccaacggagtttcgaggtgaaccctgctctggacggggtgctctctccccctaaattaaggagtttctt Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 160 End: 354 ............................................................................................................................................................... M M I K S F W I G T I Q S K K Y M N K P R T L N P P G S L G A A P L N S A G E R G G Y R G R V Q P T E F R G E P C S G R .................. Protein_Len: 51 Strand: - Start: 155 End: 307 .......................................................................................................................................................... W Y L S L T R K S Q S L E I W F I C S Y V G F R S G A P T K L P L A G L C R P L S L P N Y P S L V V M ................................................................. Protein_Len: 35 Strand: - Start: 109 End: 213 ............................................................................................................ R C L P P C D V L M I T A P R G I Y H Y L G K P N P C N L G F F V H M ............................................................................................................................................................... aaacatagccggtctaccggcataatggtagacaccctaccaacataatggtagactgtctaccaacgtaatggtgagcagtctaccagcataatggtggacaccctaccggcataatggtgggcagtctaccagcataatggtagccggtctaccaatataatgataaagtccttttggattgggacaattcaatccaaaaaatacatgaataaaccccgaaccttgaacccgccggggtctttaggggcagcgcccctaaacagcgcgggagagagagggggttatagggggagagtacaaccaacggagtttcgaggtgaaccctgctctggacggggtgctctctccccctaaattaaggagtttctt 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================================================ aaacatagccggtctaccggcataatggtagacaccctaccaacataatggtagactgtctaccaacgtaatggtgagcagtctaccagcataatggtggacaccctaccggcataatggtgggcagtctaccagcataatggtagccggtctaccaatataatgataaagtccttttggattgggacaattcaatccaaaaaatacatgaataaaccccgaaccttgaacccgccggggtctttaggggcagcgcccctaaacagcgcgggagagagagggggttatagggggagagtacaaccaacggagtttcgaggtgaaccctgctctggacggggtgctctctccccctaaattaaggagtttctt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 86 HP_score: -14.5 Tail_Score: -3.31144 Start: 26 End: 65 Full_Region: tgctcaccattacgt tggtagacagtctacca ttatgt tggtagggtgtctacca ttatgccggtagacc .........................tggtagacagtctaccattatgttggtagggtgtctacca................................................................................................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 77 HP_score: -10.1 Tail_Score: -3.71552 Start: 49 End: 88 Full_Region: tgtccaccattatgc tggtagactgctcacca ttacgt tggtagacagtctacca ttatgttggtagggt ................................................tggtagactgctcaccattacgttggtagacagtctacca............................................................................................................................................................................................................................................................................................ TransTerm Strand: - Conf: 46 HP_score: -2.0 Tail_Score: -3.44229 Start: 95 End: 134 Full_Region: cggctaccattatgc tggtagactgcccacc attatgcc ggtagggtgtccacca ttatgctggtagact ..............................................................................................tggtagactgcccaccattatgccggtagggtgtccacca.............................................................................................................................................................................................................................................. TransTerm Strand: + Conf: 51 HP_score: -5.8 Tail_Score: -2.82834 Start: 117 End: 158 Full_Region: CACCCTACCGGCATA ATGGTGGGCAGTCTACCA GCATAA TGGTAGCCGGTCTACCAA TATAATGATAAAGTC ....................................................................................................................ATGGTGGGCAGTCTACCAGCATAATGGTAGCCGGTCTACCAA...................................................................................................................................................................................................................... TransTerm Strand: - Conf: 50 HP_score: -4.9 Tail_Score: -3.31263 Start: 118 End: 157 Full_Region: actttatcattatat tggtagaccggctacca ttatgc tggtagactgcccacca ttatgccggtagggt .....................................................................................................................tggtagaccggctaccattatgctggtagactgcccacca....................................................................................................................................................................................................................... Find igs database================================================ Query_seq: TDE2734:TDE2735|TDE2734:TDE2735:hypothetical protein:surface antigen, putative:->->:2789922..2790293 372 aaacatagccggtctaccggcataatggtagacaccctaccaacataatggtagactgtctaccaacgtaatggtgagcagtctaccagcataatggtggacaccctaccggcataatggtgggcagtctaccagcataatggtagccggtctaccaatataatgataaagtccttttggattgggacaattcaatccaaaaaatacatgaataaaccccgaaccttgaacccgccggggtctttaggggcagcgcccctaaacagcgcgggagagagagggggttatagggggagagtacaaccaacggagtttcgaggtgaaccctgctctggacggggtgctctctccccctaaattaaggagtttctt Intra-Species Hit: Count: 1 Min: 1 Max: 372 Len: 372 Subject: NC_002967_TDE2734_TDE2735|hypothetical protein:surface antigen, putative|POSITIVE:POSITIVE|[2789922,2790293]|372 HSP 1 e-value: 0.0 bit: 737.0 Len: 372 Query Start:1 Query End:372 Subject Strand: POSITIVE Subject Start: 1 Subject End: 372 aaacatagccggtctaccggcataatggtagacaccctaccaacataatggtagactgtctaccaacgtaatggtgagcagtctaccagcataatggtggacaccctaccggcataatggtgggcagtctaccagcataatggtagccggtctaccaatataatgataaagtccttttggattgggacaattcaatccaaaaaatacatgaataaaccccgaaccttgaacccgccggggtctttaggggcagcgcccctaaacagcgcgggagagagagggggttatagggggagagtacaaccaacggagtttcgaggtgaaccctgctctggacggggtgctctctccccctaaattaaggagtttctt aaacatagccggtctaccggcataatggtagacaccctaccaacataatggtagactgtctaccaacgtaatggtgagcagtctaccagcataatggtggacaccctaccggcataatggtgggcagtctaccagcataatggtagccggtctaccaatataatgataaagtccttttggattgggacaattcaatccaaaaaatacatgaataaaccccgaaccttgaacccgccggggtctttaggggcagcgcccctaaacagcgcgggagagagagggggttatagggggagagtacaaccaacggagtttcgaggtgaaccctgctctggacggggtgctctctccccctaaattaaggagtttctt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAACAUAGCCGGUCUACCGGCAUAAUGGUAGACACCCUACCAACAUAAUGGUAGACUGUCUACCAACGUAAUGGUGAGCAGUCUACCAGCAUAAUGGUGGACACCCUACCGGCAUAAUGGUGGGCAGUCUACCAGCAUAAUGGUAGCCGGUCUACCAAUAUAAUGAUAAAGUCCUUUUGGAUUGGGACAAUUCAAUCCAAAAAAUACAUGAAUAAACCCCGAACCUUGAACCCGCCGGGGUCUUUAGGGGCAGCGCCCCUAAACAGCGCGGGAGAGAGAGGGGGUUAUAGGGGGAGAGUACAACCAACGGAGUUUCGAGGUGAACCCUGCUCUGGACGGGGUGCUCUCUCCCCCUAAAUUAAGGAGUUUCUU ...(((.(((((....)))))....((((((((...((((((......(((((((((((((((((..((..(((((.(..((((((((......))))))))..).)))))..))..)))))))))))))))))......))))))...)))))))).....)))..(((.(((((((((((((((....))))))))))).............((((((....(((...((((((...((..((((((((...)))))))))).).)))))...)))..)))))).(((((((((((..((.((..((((((...(.((....))).))))))....)).))..))))))))))).....)))).)))... (-168.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGAAACUCCUUAAUUUAGGGGGAGAGAGCACCCCGUCCAGAGCAGGGUUCACCUCGAAACUCCGUUGGUUGUACUCUCCCCCUAUAACCCCCUCUCUCUCCCGCGCUGUUUAGGGGCGCUGCCCCUAAAGACCCCGGCGGGUUCAAGGUUCGGGGUUUAUUCAUGUAUUUUUUGGAUUGAAUUGUCCCAAUCCAAAAGGACUUUAUCAUUAUAUUGGUAGACCGGCUACCAUUAUGCUGGUAGACUGCCCACCAUUAUGCCGGUAGGGUGUCCACCAUUAUGCUGGUAGACUGCUCACCAUUACGUUGGUAGACAGUCUACCAUUAUGUUGGUAGGGUGUCUACCAUUAUGCCGGUAGACCGGCUAUGUUU ..(((...........(((((((((((.((.(((.((.....)).)))...(((.((......))..))).)).))))))))))).((((((.(((....((((((.(.(((((((((...))))))))).).)...)))))....)))...))))))..)))..((.((((((((((((........))))))))))))))...............((((.(((((((((..((((.((((((((.(((((((........))).)))).(((((((.((((.((((((((((((.((((......)))))).)))))))))).)))).)))).))).)))))))).))))..))))).)))))))).... (-152.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 804 298 255 227 184 NC_002967:TDE1060|5end_hypothetical_protein_1086519..1086749_POSITIVE 743 238 195 43 1 NC_002967:TDE2736|5end_hypothetical_protein_2791812..2792042_NEGATIVE 626 286 242 228 184 NC_002967:TDE2419|5end_hypothetical_protein_2444769..2444999_NEGATIVE 623 309 263 178 119 NC_002967:TDE2260|5end_hypothetical_protein_2297338..2297568_POSITIVE 548 330 281 179 131 NC_002967:TDE2309|5end_sigma-54_dependent_transcriptional_regulator,_putative_2348099..2348329_NEGATIVE 472 284 241 51 9 NC_002967:TDE2715|5end_hypothetical_protein_2772668..2772898_POSITIVE 469 290 241 72 22 NC_002967:TDE2141|5end_hypothetical_protein_2175768..2175998_NEGATIVE 436 340 291 100 49 NC_002967:TDE1982|5end_hypothetical_protein_1992984..1993214_NEGATIVE 424 285 246 166 121 NC_002967:TDE1884|5end_hypothetical_protein_1906857..1907087_NEGATIVE 420 219 174 210 169 NC_002967:TDE2548|5end_hypothetical_protein_2573198..2573428_NEGATIVE 397 356 317 168 128 NC_002967:TDE1058|5end_hypothetical_protein_1086366..1086596_NEGATIVE 397 284 246 226 182 NC_002967:TDE0741|5end_hypothetical_protein_778158..778388_NEGATIVE 393 299 251 229 163 NC_002967:TDE2268|5end_hypothetical_protein_2304959..2305189_NEGATIVE 387 309 264 203 152 NC_002967:TDE2516|5end_hypothetical_protein_2542021..2542251_POSITIVE 384 301 268 44 2 NC_002967:TDE1057|5end_hypothetical_protein_1086245..1086475_NEGATIVE 380 256 218 67 21 NC_002967:TDE2028|5end_OmpA_family_protein_2052923..2053153_POSITIVE 379 220 175 165 126 NC_002967:TDE2314|5end_hypothetical_protein_2352054..2352284_POSITIVE 369 269 226 72 26 NC_002967:TDE1541|5end_metallo-beta-lactamase_family_protein_1584898..1585128_POSITIVE 363 219 171 113 67 NC_002967:TDE0617|5end_hypothetical_protein_650227..650457_NEGATIVE 361 273 231 217 183 NC_002967:TDE0945|5end_hypothetical_protein_967128..967358_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 839 340 291 69 19 NC_002967:TDE1893|3end_GTP-binding_protein_LepA_1912212..1912362_NEGATIVE 777 330 281 139 87 NC_002967:TDE1982|3end_hypothetical_protein_1992511..1992661_NEGATIVE 728 236 192 151 108 NC_002967:TDE2736|3end_hypothetical_protein_2791702..2791852_NEGATIVE 709 298 253 49 3 NC_002967:TDE2420|3end_DNA-directed_RNA_polymerase_beta'_subunit_2444960..2445110_NEGATIVE 505 300 253 56 2 NC_002967:TDE1058|3end_hypothetical_protein_1086232..1086382_NEGATIVE 461 296 257 44 2 NC_002967:TDE0828|3end_glucose-inhibited_division_protein_A_848283..848433_NEGATIVE 443 330 281 134 80 NC_002967:TDE2136|3end_hypothetical_protein_2165390..2165540_NEGATIVE 436 100 51 54 5 NC_002967:TDE2734|3end_hypothetical_protein_2789861..2790011_POSITIVE 417 273 236 147 116 NC_002967:TDE1057|3end_hypothetical_protein_1086105..1086255_NEGATIVE 415 297 254 52 2 NC_002967:TDE0969|3end_hypothetical_protein_994575..994725_POSITIVE 410 298 251 83 32 NC_002967:TDE1008|3end_flagellar_protein,_putative_1032806..1032956_POSITIVE 403 297 256 52 7 NC_002967:TDE0724|3end_hypothetical_protein_763237..763387_POSITIVE 403 297 256 72 27 NC_002967:TDE0723|3end_hypothetical_protein_761661..761811_POSITIVE 403 297 256 52 7 NC_002967:TDE0722|3end_lipoprotein,_putative_759864..760014_POSITIVE 403 297 256 52 7 NC_002967:TDE0715|3end_hypothetical_protein_750550..750700_POSITIVE 403 297 255 53 10 NC_002967:TDE0665|3end_pyruvate_ferredoxin/flavodoxin_oxidoreductase_family_protein_699792..699942_NEGATIVE 398 299 251 103 42 NC_002967:TDE0492|3end_sensor_histidine_kinase/response_regulator_548657..548807_POSITIVE 383 356 324 36 4 NC_002967:TDE1059|3end_hypothetical_protein_1086498..1086648_NEGATIVE 380 256 218 62 16 NC_002967:TDE2027|3end_hypothetical_protein_2052998..2053148_POSITIVE 375 336 300 45 4 NC_002967:TDE2265|3end_hypothetical_protein_2302634..2302784_POSITIVE