Origin IGS: attttcattatacaatatgtattactttttgtcaacttatatagttcgattttataattcagttgccctgatccccactcccccattgctggacaaaaggcttatttttatgtaaaataaagagaaatgcggctttaaggagcatagaaatag .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ctatttctatgctccttaaagccgcatttctctttattttacataaaaataagccttttgtccagcaatgggggagtggggatcagggcaactgaattataaaatcgaactatataagttgacaaaaagtaatacatattgtataatgaaaat Mask Tandem Repeat Region ================================================ attttcattatacaatatgtattactttttgtcaacttatatagttcgattttataattcagttgccctgatccccactcccccattgctggacaaaaggcttatttttatgtaaaataaagagaaatgcggctttaaggagcatagaaatag Find is-nt database================================================ Query_seq: TDE2051:TDE2052|TDE2051:TDE2052:hypothetical protein:aminotransferase, class V:<-->:2080389..2080541 153 attttcattatacaatatgtattactttttgtcaacttatatagttcgattttataattcagttgccctgatccccactcccccattgctggacaaaaggcttatttttatgtaaaataaagagaaatgcggctttaaggagcatagaaatag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2051:TDE2052|TDE2051:TDE2052:hypothetical protein:aminotransferase, class V:<-->:2080389..2080541 153 attttcattatacaatatgtattactttttgtcaacttatatagttcgattttataattcagttgccctgatccccactcccccattgctggacaaaaggcttatttttatgtaaaataaagagaaatgcggctttaaggagcatagaaatag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2051:TDE2052|TDE2051:TDE2052:hypothetical protein:aminotransferase, class V:<-->:2080389..2080541 153 attttcattatacaatatgtattactttttgtcaacttatatagttcgattttataattcagttgccctgatccccactcccccattgctggacaaaaggcttatttttatgtaaaataaagagaaatgcggctttaaggagcatagaaatag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 attttcattatacaatatgtattactttttgtcaacttatatagttcgattttataattcagttgccctgatccccactcccccattgctggacaaaaggcttatttttatgtaaaataaagagaaatgcggctttaaggagcatagaaatag Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 17 End: 112 ................ M Y Y F L S T Y I V R F Y N S V A L I P T P P L L D K R L I F M ......................................... Protein_Len: 30 Strand: - Start: 62 End: 151 ............................................................. N G Q D G S G W Q Q V F P K N K H L I F L F A A K L L M S M .. attttcattatacaatatgtattactttttgtcaacttatatagttcgattttataattcagttgccctgatccccactcccccattgctggacaaaaggcttatttttatgtaaaataaagagaaatgcggctttaaggagcatagaaatag Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: - Score: 92 Start: 7 End: 36 ......GTTGACAAAAAGTAATACATATTGTATAAT..................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 85 Start: 89 End: 118 ........................................................................................CTGGACAAAAGGCTTATTTTTATGTAAAAT................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ attttcattatacaatatgtattactttttgtcaacttatatagttcgattttataattcagttgccctgatccccactcccccattgctggacaaaaggcttatttttatgtaaaataaagagaaatgcggctttaaggagcatagaaatag Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2051:TDE2052|TDE2051:TDE2052:hypothetical protein:aminotransferase, class V:<-->:2080389..2080541 153 attttcattatacaatatgtattactttttgtcaacttatatagttcgattttataattcagttgccctgatccccactcccccattgctggacaaaaggcttatttttatgtaaaataaagagaaatgcggctttaaggagcatagaaatag Intra-Species Hit: Count: 1 Min: 1 Max: 153 Len: 153 Subject: NC_002967_TDE2051_TDE2052|hypothetical protein:aminotransferase, class V|NEGATIVE:POSITIVE|[2080389,2080541]|153 HSP 1 e-value: 9.0E-82 bit: 303.0 Len: 153 Query Start:1 Query End:153 Subject Strand: POSITIVE Subject Start: 1 Subject End: 153 attttcattatacaatatgtattactttttgtcaacttatatagttcgattttataattcagttgccctgatccccactcccccattgctggacaaaaggcttatttttatgtaaaataaagagaaatgcggctttaaggagcatagaaatag attttcattatacaatatgtattactttttgtcaacttatatagttcgattttataattcagttgccctgatccccactcccccattgctggacaaaaggcttatttttatgtaaaataaagagaaatgcggctttaaggagcatagaaatag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUUCAUUAUACAAUAUGUAUUACUUUUUGUCAACUUAUAUAGUUCGAUUUUAUAAUUCAGUUGCCCUGAUCCCCACUCCCCCAUUGCUGGACAAAAGGCUUAUUUUUAUGUAAAAUAAAGAGAAAUGCGGCUUUAAGGAGCAUAGAAAUAG .........((((.....))))..(((((((((......(((((.......)))))..((((.....))))....................)))))))))..(((((((((((....(((((.(.....)..)))))....))))))))))). (-23.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUAUUUCUAUGCUCCUUAAAGCCGCAUUUCUCUUUAUUUUACAUAAAAAUAAGCCUUUUGUCCAGCAAUGGGGGAGUGGGGAUCAGGGCAACUGAAUUAUAAAAUCGAACUAUAUAAGUUGACAAAAAGUAAUACAUAUUGUAUAAUGAAAAU ...((((..(((.(((.....((.((((((..((((((((.....))))))))........(((....))).)))))).))...))))))....................(((((((((..((.....))...))...)))))))..)))).. (-25.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 969 110 61 201 152 NC_002967:TDE2051|5end_hypothetical_protein_2080298..2080528_NEGATIVE 327 101 62 68 22 NC_002967:TDE2564|5end_PemK_family_protein_2589975..2590205_POSITIVE 309 109 61 173 123 NC_002967:TDE1926|5end_hypothetical_protein_1942495..1942725_POSITIVE 301 140 92 231 177 NC_002967:TDE2737|5end_hypothetical_protein_2791870..2792100_POSITIVE 294 91 61 161 126 NC_002967:TDE0863|5end_MgtC_family_protein_884526..884756_POSITIVE 293 103 64 47 1 NC_002967:TDE0107|5end_alpha-amylase_family_protein_128266..128496_NEGATIVE 292 105 61 91 49 NC_002967:TDE2485|5end_hypothetical_protein_2509123..2509353_NEGATIVE 292 101 61 137 82 NC_002967:TDE0573|5end_hypothetical_protein_604681..604911_POSITIVE 290 80 36 201 169 NC_002967:TDE0587|5end_hypothetical_protein_625749..625979_POSITIVE 283 128 85 229 189 NC_002967:TDE0061|5end_fic_family_protein_68944..69174_NEGATIVE 277 105 61 46 11 NC_002967:TDE0370|5end_UDP-N-acetylmuramoylalanine--D-glutamate_ligase_421084..421314_POSITIVE 275 104 61 153 105 NC_002967:TDE2103|5end_glycosyl_transferase,_group_2_family_protein_2128393..2128623_NEGATIVE 271 89 42 79 15 NC_002967:TDE0294|5end_TrkA_domain_protein_324210..324440_NEGATIVE 269 100 62 100 53 NC_002967:TDE1892|5end_hypothetical_protein_1912065..1912295_POSITIVE 267 103 61 46 1 NC_002967:TDE1731|5end_hypothetical_protein_1786935..1787165_NEGATIVE 266 109 66 208 164 NC_002967:TDE1058|5end_hypothetical_protein_1086366..1086596_NEGATIVE 264 105 61 231 187 NC_002967:TDE1144|5end_hypothetical_protein_1182855..1183085_NEGATIVE 258 90 42 184 129 NC_002967:TDE1304|5end_hypothetical_protein_1339716..1339946_POSITIVE 255 109 66 125 72 NC_002967:TDE2265|5end_hypothetical_protein_2302165..2302395_POSITIVE 254 100 65 221 187 NC_002967:TDE0833|5end_lipoprotein,_putative_852992..853222_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 327 101 62 81 35 NC_002967:TDE2563|3end_hypothetical_protein_2590068..2590218_POSITIVE 323 110 61 57 11 NC_002967:TDE2086|3end_DnaJ_domain_protein_2115475..2115625_POSITIVE 306 104 73 34 5 NC_002967:TDE2181|3end_PAP2_family_protein_2211995..2212145_NEGATIVE 301 102 61 55 5 NC_002967:TDE2604|3end_hypothetical_protein_2644224..2644374_NEGATIVE 296 103 65 48 12 NC_002967:TDE2196|3end_hypothetical_protein_2231883..2232033_NEGATIVE 292 101 61 110 55 NC_002967:TDE0572|3end_hypothetical_protein_604734..604884_POSITIVE 271 89 42 69 5 NC_002967:TDE0295|3end_DNA_gyrase,_A_subunit_324220..324370_NEGATIVE 267 103 62 142 111 NC_002967:TDE2545|3end_hypothetical_protein_2571170..2571320_NEGATIVE 266 109 66 76 32 NC_002967:TDE1059|3end_hypothetical_protein_1086498..1086648_NEGATIVE 259 89 43 126 74 NC_002967:TDE2103|3end_glycosyl_transferase,_group_2_family_protein_2127527..2127677_NEGATIVE 258 98 51 115 64 NC_002967:TDE0241|3end_hypothetical_protein_274701..274851_NEGATIVE 255 100 62 111 63 NC_002967:TDE1564|3end_hypothetical_protein_1616704..1616854_POSITIVE 250 103 65 63 13 NC_002967:TDE1857|3end_hypothetical_protein_1883929..1884079_NEGATIVE 245 101 66 130 88 NC_002967:TDE1914|3end_Holliday_junction_DNA_helicase_RuvB_1930889..1931039_NEGATIVE 242 101 61 66 20 NC_002967:TDE2345|3end_ribosome_recycling_factor_2381946..2382096_NEGATIVE 240 83 58 150 118 NC_002967:TDE2527|3end_hypothetical_protein_2555449..2555599_NEGATIVE 240 102 64 48 7 NC_002967:TDE0740|3end_hypothetical_protein_776204..776354_POSITIVE 239 103 61 73 33 NC_002967:TDE0559|3end_hypothetical_protein_594126..594276_POSITIVE 238 107 63 96 57 NC_002967:TDE1396|3end_hypothetical_protein_1436127..1436277_POSITIVE 237 110 61 86 33 NC_002967:TDE0664|3end_OmpA_family_protein_699728..699878_POSITIVE