Origin IGS: ttatattccttaaaatggaacagttgagagaatatcaattctcgaaaactgttgcattggtgcgcgtaacgcgcacattgtaatatgcgatgtttgcggtcagcaaactcgacggttaacgaggcaatc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gattgcctcgttaaccgtcgagtttgctgaccgcaaacatcgcatattacaatgtgcgcgttacgcgcaccaatgcaacagttttcgagaattgatattctctcaactgttccattttaaggaatataa Mask Tandem Repeat Region ================================================ ttatattccttaaaatggaacagttgagagaatatcaattctcgaaaactgttgcattggtgcgcgtaacgcgcacattgtaatatgcgatgtttgcggtcagcaaactcgacggttaacgaggcaatc Find is-nt database================================================ Query_seq: TDE0495:TDE0496|TDE0495:TDE0496:hypothetical protein:DNA-binding protein, putative:<-<-:550932..551060 129 ttatattccttaaaatggaacagttgagagaatatcaattctcgaaaactgttgcattggtgcgcgtaacgcgcacattgtaatatgcgatgtttgcggtcagcaaactcgacggttaacgaggcaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0495:TDE0496|TDE0495:TDE0496:hypothetical protein:DNA-binding protein, putative:<-<-:550932..551060 129 ttatattccttaaaatggaacagttgagagaatatcaattctcgaaaactgttgcattggtgcgcgtaacgcgcacattgtaatatgcgatgtttgcggtcagcaaactcgacggttaacgaggcaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0495:TDE0496|TDE0495:TDE0496:hypothetical protein:DNA-binding protein, putative:<-<-:550932..551060 129 ttatattccttaaaatggaacagttgagagaatatcaattctcgaaaactgttgcattggtgcgcgtaacgcgcacattgtaatatgcgatgtttgcggtcagcaaactcgacggttaacgaggcaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttatattccttaaaatggaacagttgagagaatatcaattctcgaaaactgttgcattggtgcgcgtaacgcgcacattgtaatatgcgatgtttgcggtcagcaaactcgacggttaacgaggcaatc Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 32 End: 127 ............................... M S I L E N C C I G A R N A H I V I C D V C G Q Q T R R L T R Q .. Protein_Len: 42 Strand: - Start: 3 End: 128 .. Y E K F H F L Q S F I L E R F S N C Q H A Y R A C Q L I R H K R D A F E V T L S A M . ttatattccttaaaatggaacagttgagagaatatcaattctcgaaaactgttgcattggtgcgcgtaacgcgcacattgtaatatgcgatgtttgcggtcagcaaactcgacggttaacgaggcaatc 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================================================ ttatattccttaaaatggaacagttgagagaatatcaattctcgaaaactgttgcattggtgcgcgtaacgcgcacattgtaatatgcgatgtttgcggtcagcaaactcgacggttaacgaggcaatc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 79 HP_score: -10.2 Tail_Score: -3.47078 Start: 59 End: 77 Full_Region: GAAAACTGTTGCATT GGTGCGCG TAA CGCGCACA TTGTAATATGCGATG ..........................................................GGTGCGCGTAACGCGCACA.................................................... TransTerm Strand: + Conf: 91 HP_score: -13.7 Tail_Score: -2.67925 Start: 60 End: 76 Full_Region: AAAACTGTTGCATTG GTGCGCG TAA CGCGCAC ATTGTAATATGCGAT ...........................................................GTGCGCGTAACGCGCAC..................................................... Find igs database================================================ Query_seq: TDE0495:TDE0496|TDE0495:TDE0496:hypothetical protein:DNA-binding protein, putative:<-<-:550932..551060 129 ttatattccttaaaatggaacagttgagagaatatcaattctcgaaaactgttgcattggtgcgcgtaacgcgcacattgtaatatgcgatgtttgcggtcagcaaactcgacggttaacgaggcaatc Intra-Species Hit: Count: 1 Min: 1 Max: 129 Len: 129 Subject: NC_002967_TDE0495_TDE0496|hypothetical protein:DNA-binding protein, putative|NEGATIVE:NEGATIVE|[550932,551060]|129 HSP 1 e-value: 2.0E-67 bit: 256.0 Len: 129 Query Start:1 Query End:129 Subject Strand: POSITIVE Subject Start: 1 Subject End: 129 ttatattccttaaaatggaacagttgagagaatatcaattctcgaaaactgttgcattggtgcgcgtaacgcgcacattgtaatatgcgatgtttgcggtcagcaaactcgacggttaacgaggcaatc ttatattccttaaaatggaacagttgagagaatatcaattctcgaaaactgttgcattggtgcgcgtaacgcgcacattgtaatatgcgatgtttgcggtcagcaaactcgacggttaacgaggcaatc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAUAUUCCUUAAAAUGGAACAGUUGAGAGAAUAUCAAUUCUCGAAAACUGUUGCAUUGGUGCGCGUAACGCGCACAUUGUAAUAUGCGAUGUUUGCGGUCAGCAAACUCGACGGUUAACGAGGCAAUC .......((((..((((.(((((((..((((((....))))))...))))))).)))).(((((((...)))))))....((((...(((.((((((.....)))))))))...))))..))))..... (-46.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUUGCCUCGUUAACCGUCGAGUUUGCUGACCGCAAACAUCGCAUAUUACAAUGUGCGCGUUACGCGCACCAAUGCAACAGUUUUCGAGAAUUGAUAUUCUCUCAACUGUUCCAUUUUAAGGAAUAUAA .......((.((((..(.(((((((((.....)))))).))))..........(((((((...))))))).((((.(((((((...((((((....))))))..))))))).)))))))).))...... (-36.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 992 110 61 201 152 NC_002967:TDE0495|5end_hypothetical_protein_550841..551071_NEGATIVE 443 119 72 214 168 NC_002967:TDE1514|5end_permease_domain_protein_1560652..1560882_POSITIVE 430 115 73 51 8 NC_002967:TDE2019|5end_hypothetical_protein_2040719..2040949_NEGATIVE 430 115 73 220 177 NC_002967:TDE2018|5end_lipoprotein,_putative_2040550..2040780_NEGATIVE 409 119 73 46 1 NC_002967:TDE1513|5end_hypothetical_protein_1560484..1560714_POSITIVE 402 120 73 225 176 NC_002967:TDE2395|5end_Jag_protein,_putative_2423454..2423684_NEGATIVE 401 115 72 229 187 NC_002967:TDE2093|5end_hypothetical_protein_2121003..2121233_NEGATIVE 396 115 73 228 187 NC_002967:TDE2418|5end_hypothetical_protein_2443833..2444063_NEGATIVE 382 115 71 217 167 NC_002967:TDE0522|5end_hypothetical_protein_568499..568729_POSITIVE 375 115 79 219 180 NC_002967:TDE0259|5end_transcriptional_regulator,_MarR_family_293257..293487_POSITIVE 367 115 73 151 110 NC_002967:TDE2497|5end_hypothetical_protein_2522083..2522313_NEGATIVE 367 115 73 129 88 NC_002967:TDE2394|5end_hypothetical_protein_2422612..2422842_NEGATIVE 367 115 73 212 171 NC_002967:TDE1903|5end_hypothetical_protein_1922417..1922647_POSITIVE 367 115 73 72 31 NC_002967:TDE1694|5end_hypothetical_protein_1749366..1749596_NEGATIVE 367 115 73 212 171 NC_002967:TDE1693|5end_hypothetical_protein_1749226..1749456_NEGATIVE 362 115 73 152 110 NC_002967:TDE2224|5end_hypothetical_protein_2264743..2264973_POSITIVE 362 115 73 51 9 NC_002967:TDE2223|5end_hypothetical_protein_2264642..2264872_POSITIVE 357 100 56 216 169 NC_002967:TDE0609|5end_hypothetical_protein_646166..646396_NEGATIVE 356 115 71 218 165 NC_002967:TDE2484|5end_hypothetical_protein_2507720..2507950_NEGATIVE 320 111 71 180 133 NC_002967:TDE2522|5end_ABC_transporter,_ATP-binding_protein_2548098..2548328_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 374 111 72 151 113 NC_002967:TDE2094|3end_hypothetical_protein_2121077..2121227_NEGATIVE 356 102 62 109 67 NC_002967:TDE0937|3end_RNA_polymerase_sigma-70_factor_family_protein_960891..961041_POSITIVE 352 115 87 38 9 NC_002967:TDE2419|3end_hypothetical_protein_2444023..2444173_NEGATIVE 345 115 79 40 2 NC_002967:TDE2498|3end_metallo-beta-lactamase_family_protein_2522194..2522344_NEGATIVE 338 110 61 99 52 NC_002967:TDE2714|3end_hypothetical_protein_2770627..2770777_NEGATIVE 335 111 73 151 113 NC_002967:TDE2223|3end_hypothetical_protein_2264826..2264976_POSITIVE 327 115 85 36 5 NC_002967:TDE2020|3end_YD_repeat_protein_2040734..2040884_NEGATIVE 327 115 85 34 3 NC_002967:TDE1901|3end_ABC_transporter,_ATP-binding_protein_1922319..1922469_POSITIVE 305 119 88 33 1 NC_002967:TDE1512|3end_hypothetical_protein_1560551..1560701_POSITIVE 298 114 86 51 17 NC_002967:TDE2735|3end_surface_antigen,_putative_2791616..2791766_POSITIVE 292 115 87 31 1 NC_002967:TDE2222|3end_hypothetical_protein_2264702..2264852_POSITIVE 291 100 51 67 10 NC_002967:TDE1806|3end_hypothetical_protein_1843190..1843340_NEGATIVE 291 100 51 63 9 NC_002967:TDE1789|3end_hypothetical_protein_1827338..1827488_NEGATIVE 283 100 53 87 16 NC_002967:TDE0063|3end_hypothetical_protein_71329..71479_POSITIVE 280 119 71 54 4 NC_002967:TDE1904|3end_hypothetical_protein_1923197..1923347_NEGATIVE 276 80 41 130 94 NC_002967:TDE2407|3end_amidophosphoribosyltransferase_2433644..2433794_NEGATIVE 276 77 38 37 2 NC_002967:TDE2397|3end_hypothetical_protein_2425433..2425583_NEGATIVE 276 99 56 59 7 NC_002967:TDE0263|3end_spermidine_N1-acetyltransferase,_putative_296400..296550_NEGATIVE 275 69 33 147 108 NC_002967:TDE2742|3end_site-specific_recombinase,_phage_integrase_family_2796850..2797000_NEGATIVE 274 98 51 97 56 NC_002967:TDE1770|3end_hypothetical_protein_1814468..1814618_POSITIVE