Origin IGS: cctcttttgaaaatatacacgctgtctgctgcgtcgcttcaaaaaaattaatcctcaacgtacataaagtacgcctgcggttaattttttctcgctccttgcatccaacatgtctattttcaaaagtcctgtcagtgaggatttcagatagtgatagctttttgcttaagtagctttgagcggcggactgctgacacttgtttatcattataatataaaagtaaacaagtatcggctccgtgcttttcaaggttccgctatcgctgtccgagggagataaatataaaactgtttatatttataatctagcataatttttctttagcactccaactattcataataat .........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 attattatgaatagttggagtgctaaagaaaaattatgctagattataaatataaacagttttatatttatctccctcggacagcgatagcggaaccttgaaaagcacggagccgatacttgtttacttttatattataatgataaacaagtgtcagcagtccgccgctcaaagctacttaagcaaaaagctatcactatctgaaatcctcactgacaggacttttgaaaatagacatgttggatgcaaggagcgagaaaaaattaaccgcaggcgtactttatgtacgttgaggattaatttttttgaagcgacgcagcagacagcgtgtatattttcaaaagagg Mask Tandem Repeat Region ================================================ cctcttttgaaaatatacacgctgtctgctgcgtcgcttcaaaaaaattaatcctcaacgtacataaagtacgcctgcggttaattttttctcgctccttgcatccaacatgtctattttcaaaagtcctgtcagtgaggatttcagatagtgatagctttttgcttaagtagctttgagcggcggactgctgacacttgtttatcattataatataaaagtaaacaagtatcggctccgtgcttttcaaggttccgctatcgctgtccgagggagataaatataaaactgtttatatttataatctagcataatttttctttagcactccaactattcataataat Find is-nt database================================================ Query_seq: TDE2011:TDE2012|TDE2011:TDE2012:hypothetical protein:hypothetical protein:-><-:2033543..2033889 347 cctcttttgaaaatatacacgctgtctgctgcgtcgcttcaaaaaaattaatcctcaacgtacataaagtacgcctgcggttaattttttctcgctccttgcatccaacatgtctattttcaaaagtcctgtcagtgaggatttcagatagtgatagctttttgcttaagtagctttgagcggcggactgctgacacttgtttatcattataatataaaagtaaacaagtatcggctccgtgcttttcaaggttccgctatcgctgtccgagggagataaatataaaactgtttatatttataatctagcataatttttctttagcactccaactattcataataat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2011:TDE2012|TDE2011:TDE2012:hypothetical protein:hypothetical protein:-><-:2033543..2033889 347 cctcttttgaaaatatacacgctgtctgctgcgtcgcttcaaaaaaattaatcctcaacgtacataaagtacgcctgcggttaattttttctcgctccttgcatccaacatgtctattttcaaaagtcctgtcagtgaggatttcagatagtgatagctttttgcttaagtagctttgagcggcggactgctgacacttgtttatcattataatataaaagtaaacaagtatcggctccgtgcttttcaaggttccgctatcgctgtccgagggagataaatataaaactgtttatatttataatctagcataatttttctttagcactccaactattcataataat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2011:TDE2012|TDE2011:TDE2012:hypothetical protein:hypothetical protein:-><-:2033543..2033889 347 cctcttttgaaaatatacacgctgtctgctgcgtcgcttcaaaaaaattaatcctcaacgtacataaagtacgcctgcggttaattttttctcgctccttgcatccaacatgtctattttcaaaagtcctgtcagtgaggatttcagatagtgatagctttttgcttaagtagctttgagcggcggactgctgacacttgtttatcattataatataaaagtaaacaagtatcggctccgtgcttttcaaggttccgctatcgctgtccgagggagataaatataaaactgtttatatttataatctagcataatttttctttagcactccaactattcataataat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cctcttttgaaaatatacacgctgtctgctgcgtcgcttcaaaaaaattaatcctcaacgtacataaagtacgcctgcggttaattttttctcgctccttgcatccaacatgtctattttcaaaagtcctgtcagtgaggatttcagatagtgatagctttttgcttaagtagctttgagcggcggactgctgacacttgtttatcattataatataaaagtaaacaagtatcggctccgtgcttttcaaggttccgctatcgctgtccgagggagataaatataaaactgtttatatttataatctagcataatttttctttagcactccaactattcataataat Predict ORF larger than 30AA ================================================ Protein_Len: 52 Strand: + Start: 15 End: 170 .............. M H A V C C V A S K K L I L N V H K V R L R L I F S R S L H P T C L F S K V L S V R I S D S D S F L L K ................................................................................................................................................................................. Protein_Len: 34 Strand: + Start: 176 End: 277 ............................................................................................................................................................................... M S G G L L T L V Y H Y N I K V N K Y R L R A F Q G S A I A V R G R ...................................................................... Protein_Len: 30 Strand: - Start: 58 End: 147 ......................................................... R V Y L V G A T L K K E S R A D L M D I K L L G T L S S K M ........................................................................................................................................................................................................ Protein_Len: 60 Strand: - Start: 2 End: 250 . R R R N I K E R E K C G V H R N E F T R D T L I E S L S L K K S L Y S Q A A S Q Q C K N I M I I Y F Y V L I P E T S K M ................................................................................................. cctcttttgaaaatatacacgctgtctgctgcgtcgcttcaaaaaaattaatcctcaacgtacataaagtacgcctgcggttaattttttctcgctccttgcatccaacatgtctattttcaaaagtcctgtcagtgaggatttcagatagtgatagctttttgcttaagtagctttgagcggcggactgctgacacttgtttatcattataatataaaagtaaacaagtatcggctccgtgcttttcaaggttccgctatcgctgtccgagggagataaatataaaactgtttatatttataatctagcataatttttctttagcactccaactattcataataat 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================================================ cctcttttgaaaatatacacgctgtctgctgcgtcgcttcaaaaaaattaatcctcaacgtacataaagtacgcctgcggttaattttttctcgctccttgcatccaacatgtctattttcaaaagtcctgtcagtgaggatttcagatagtgatagctttttgcttaagtagctttgagcggcggactgctgacacttgtttatcattataatataaaagtaaacaagtatcggctccgtgcttttcaaggttccgctatcgctgtccgagggagataaatataaaactgtttatatttataatctagcataatttttctttagcactccaactattcataataat Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 43 HP_score: -2.7 Tail_Score: -3.01247 Start: 53 End: 80 Full_Region: gcgagaaaaaattaa ccgcaggcgtac tttat gtacgttgagg attaatttttttgaa ....................................................ccgcaggcgtactttatgtacgttgagg........................................................................................................................................................................................................................................................................... Find igs database================================================ Query_seq: TDE2011:TDE2012|TDE2011:TDE2012:hypothetical protein:hypothetical protein:-><-:2033543..2033889 347 cctcttttgaaaatatacacgctgtctgctgcgtcgcttcaaaaaaattaatcctcaacgtacataaagtacgcctgcggttaattttttctcgctccttgcatccaacatgtctattttcaaaagtcctgtcagtgaggatttcagatagtgatagctttttgcttaagtagctttgagcggcggactgctgacacttgtttatcattataatataaaagtaaacaagtatcggctccgtgcttttcaaggttccgctatcgctgtccgagggagataaatataaaactgtttatatttataatctagcataatttttctttagcactccaactattcataataat Intra-Species Hit: Count: 1 Min: 1 Max: 347 Len: 347 Subject: NC_002967_TDE2011_TDE2012|hypothetical protein:hypothetical protein|POSITIVE:NEGATIVE|[2033543,2033889]|347 HSP 1 e-value: 0.0 bit: 646.0 Len: 347 Query Start:1 Query End:347 Subject Strand: POSITIVE Subject Start: 1 Subject End: 347 cctcttttgaaaatatacacgctgtctgctgcgtcgcttcnnnnnnnttaatcctcaacgtacataaagtacgcctgcggttaattttttctcgctccttgcatccaacatgtctattttcaaaagtcctgtcagtgaggatttcagatagtgatagctttttgcttaagtagctttgagcggcggactgctgacacttgtttatcattataatataaaagtaaacaagtatcggctccgtgcttttcaaggttccgctatcgctgtccgagggagataaatataaaactgtttatatttataatctagcataatttttctttagcactccaactattcataataat cctcttttgaaaatatacacgctgtctgctgcgtcgcttcaaaaaaattaatcctcaacgtacataaagtacgcctgcggttaattttttctcgctccttgcatccaacatgtctattttcaaaagtcctgtcagtgaggatttcagatagtgatagctttttgcttaagtagctttgagcggcggactgctgacacttgtttatcattataatataaaagtaaacaagtatcggctccgtgcttttcaaggttccgctatcgctgtccgagggagataaatataaaactgtttatatttataatctagcataatttttctttagcactccaactattcataataat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCUCUUUUGAAAAUAUACACGCUGUCUGCUGCGUCGCUUCAAAAAAAUUAAUCCUCAACGUACAUAAAGUACGCCUGCGGUUAAUUUUUUCUCGCUCCUUGCAUCCAACAUGUCUAUUUUCAAAAGUCCUGUCAGUGAGGAUUUCAGAUAGUGAUAGCUUUUUGCUUAAGUAGCUUUGAGCGGCGGACUGCUGACACUUGUUUAUCAUUAUAAUAUAAAAGUAAACAAGUAUCGGCUCCGUGCUUUUCAAGGUUCCGCUAUCGCUGUCCGAGGGAGAUAAAUAUAAAACUGUUUAUAUUUAUAAUCUAGCAUAAUUUUUCUUUAGCACUCCAACUAUUCAUAAUAAU ...((((((((((((.(((.(.((..(((...(..((....((((((((((.((.((.(((((.....)))))..)).))))))))))))...))..)..)))..)).).))).))))))))))))........(((((....((.((((((((((((....(((....)))((((((((((.((((..(((((.((((((((((..((((...))))..)))))))))).))))))))))))...)))))))...)))))))))))).)).(((((((((((((((....)))))))))))......((.(((.......))))).)))).....)))))...... (-100.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUAUUAUGAAUAGUUGGAGUGCUAAAGAAAAAUUAUGCUAGAUUAUAAAUAUAAACAGUUUUAUAUUUAUCUCCCUCGGACAGCGAUAGCGGAACCUUGAAAAGCACGGAGCCGAUACUUGUUUACUUUUAUAUUAUAAUGAUAAACAAGUGUCAGCAGUCCGCCGCUCAAAGCUACUUAAGCAAAAAGCUAUCACUAUCUGAAAUCCUCACUGACAGGACUUUUGAAAAUAGACAUGUUGGAUGCAAGGAGCGAGAAAAAAUUAACCGCAGGCGUACUUUAUGUACGUUGAGGAUUAAUUUUUUUGAAGCGACGCAGCAGACAGCGUGUAUAUUUUCAAAAGAGG ................((((.((..............))......(((((((((((....))))))))))))))).(((((.((.((((((.....(((((..(((...((((.((((((((((((...((((...))))...)))))))))))).((.....)).))))...)))..)))))......)))))).)).)))))..((((.......))))((((((((((((.((((((((..(((..(..((..(((((((((((((...(((((((.....)))))))..)).)))))))))))...))..)...)))..)))))))).))))))))))))... (-108.14) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 520 79 31 105 57 NC_002967:TDE1847|5end_hypothetical_protein_1875664..1875894_POSITIVE 516 279 235 55 10 NC_002967:TDE2025|5end_hypothetical_protein_2051440..2051670_NEGATIVE 509 279 235 58 1 NC_002967:TDE1568|5end_hypothetical_protein_1619544..1619774_POSITIVE 506 140 94 228 179 NC_002967:TDE1566|5end_hypothetical_protein_1617822..1618052_POSITIVE 466 79 31 225 177 NC_002967:TDE0048|5end_hypothetical_protein_57822..58052_NEGATIVE 432 60 11 205 155 NC_002967:TDE0569|5end_hypothetical_protein_599636..599866_POSITIVE 399 279 241 58 18 NC_002967:TDE2020|5end_YD_repeat_protein_2044156..2044386_NEGATIVE 398 47 1 158 111 NC_002967:TDE0976|5end_hypothetical_protein_1000026..1000256_POSITIVE 370 110 71 140 101 NC_002967:TDE1886|5end_MiaB-like_tRNA_modifying_enzyme_1908488..1908718_NEGATIVE 349 276 232 97 39 NC_002967:TDE2102|5end_hypothetical_protein_2127347..2127577_NEGATIVE 348 279 238 55 10 NC_002967:TDE1560|5end_YD_repeat_protein_1611450..1611680_POSITIVE 345 154 111 133 85 NC_002967:TDE1662|5end_replicative_DNA_helicase_1715898..1716128_POSITIVE 338 273 232 227 183 NC_002967:TDE1011|5end_hypothetical_protein_1038101..1038331_POSITIVE 338 274 232 150 94 NC_002967:TDE0243|5end_ABC_transporter,_ATP-binding_protein_277501..277731_NEGATIVE 336 198 158 62 13 NC_002967:TDE2485|5end_hypothetical_protein_2509123..2509353_NEGATIVE 336 269 228 133 81 NC_002967:TDE1878|5end_hydrolase,_haloacid_dehalogenase-like_family_1900745..1900975_NEGATIVE 333 279 234 59 14 NC_002967:TDE1139|5end_hypothetical_protein_1168615..1168845_NEGATIVE 329 276 233 51 1 NC_002967:TDE2478|5end_excinuclease_ABC,_C_subunit_2500873..2501103_POSITIVE 328 271 233 180 134 NC_002967:TDE2624|5end_hypothetical_protein_2664905..2665135_NEGATIVE 324 271 233 61 22 NC_002967:TDE2618|5end_PHP_domain_protein_2659392..2659622_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 591 80 33 83 36 NC_002967:TDE1847|3end_hypothetical_protein_1875845..1875995_POSITIVE 411 200 157 130 86 NC_002967:TDE2407|3end_amidophosphoribosyltransferase_2433644..2433794_NEGATIVE 399 279 241 57 17 NC_002967:TDE2021|3end_hypothetical_protein_2044157..2044307_NEGATIVE 379 62 21 51 6 NC_002967:TDE0049|3end_hypothetical_protein_58199..58349_NEGATIVE 370 110 71 136 97 NC_002967:TDE1887|3end_TPR_domain_protein_1908492..1908642_NEGATIVE 363 276 232 113 67 NC_002967:TDE0157|3end_KHG/KDPG_family_aldolase/carbohydrate_kinase,_PfkB_family_185711..185861_POSITIVE 345 195 156 139 101 NC_002967:TDE2195|3end_RNA_pseudouridylate_synthase_family_protein_2231911..2232061_POSITIVE 345 154 111 65 17 NC_002967:TDE1661|3end_hypothetical_protein_1715910..1716060_POSITIVE 337 273 232 124 81 NC_002967:TDE2527|3end_hypothetical_protein_2555449..2555599_NEGATIVE 326 269 228 151 99 NC_002967:TDE0244|3end_ABC_transporter,_ATP-binding/permease_protein_277489..277639_NEGATIVE 323 207 167 77 40 NC_002967:TDE2132|3end_cobalt_ABC_transporter,_ATP-binding_protein,_putative_2162756..2162906_NEGATIVE 318 277 236 147 96 NC_002967:TDE1515|3end_permease_domain_protein_1563179..1563329_POSITIVE 317 274 232 143 86 NC_002967:TDE0362|3end_bacterial_Ig-like_domain_protein_407501..407651_NEGATIVE 312 270 228 65 15 NC_002967:TDE0919|3end_hypothetical_protein_939125..939275_POSITIVE 310 277 231 81 26 NC_002967:TDE2263|3end_acetyl_hydrolase,_putative_2299277..2299427_NEGATIVE 309 274 231 113 72 NC_002967:TDE1041|3end_polyribonucleotide_nucleotidyltransferase_1070500..1070650_POSITIVE 304 119 75 146 98 NC_002967:TDE1937|3end_hypothetical_protein_1953448..1953598_POSITIVE 304 119 75 52 4 NC_002967:TDE1936|3end_hypothetical_protein_1953354..1953504_POSITIVE 303 275 234 71 26 NC_002967:TDE1028|3end_hypothetical_protein_1058661..1058811_POSITIVE 301 268 232 43 3 NC_002967:TDE1406|3end_hypothetical_protein_1448677..1448827_NEGATIVE