Origin IGS: cacactgtctaaaaaccgcccgacaagcccctccgtcccgtaaaggggaacgcagaggcttacgagcggcttttgctcggccgcacatccgaagcgcgcggcgcggcgttggagaaaattcatcgtacggt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 accgtacgatgaattttctccaacgccgcgccgcgcgcttcggatgtgcggccgagcaaaagccgctcgtaagcctctgcgttcccctttacgggacggaggggcttgtcgggcggtttttagacagtgtg Mask Tandem Repeat Region ================================================ cacactgtctaaaaaccgcccgacaagcccctccgtcccgtaaaggggaacgcagaggcttacgagcggcttttgctcggccgcacatccgaagcgcgcggcgcggcgttggagaaaattcatcgtacggt Find is-nt database================================================ Query_seq: TDE2103:TDE2104|TDE2103:TDE2104:glycosyl transferase, group 2 family protein:hypothetical protein:<-<-:2128484..2128614 131 cacactgtctaaaaaccgcccgacaagcccctccgtcccgtaaaggggaacgcagaggcttacgagcggcttttgctcggccgcacatccgaagcgcgcggcgcggcgttggagaaaattcatcgtacggt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2103:TDE2104|TDE2103:TDE2104:glycosyl transferase, group 2 family protein:hypothetical protein:<-<-:2128484..2128614 131 cacactgtctaaaaaccgcccgacaagcccctccgtcccgtaaaggggaacgcagaggcttacgagcggcttttgctcggccgcacatccgaagcgcgcggcgcggcgttggagaaaattcatcgtacggt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2103:TDE2104|TDE2103:TDE2104:glycosyl transferase, group 2 family protein:hypothetical protein:<-<-:2128484..2128614 131 cacactgtctaaaaaccgcccgacaagcccctccgtcccgtaaaggggaacgcagaggcttacgagcggcttttgctcggccgcacatccgaagcgcgcggcgcggcgttggagaaaattcatcgtacggt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cacactgtctaaaaaccgcccgacaagcccctccgtcccgtaaaggggaacgcagaggcttacgagcggcttttgctcggccgcacatccgaagcgcgcggcgcggcgttggagaaaattcatcgtacggt Predict ORF larger than 30AA ================================================ Protein_Len: 41 Strand: - Start: 1 End: 123 V S D L F R G V L G E T G Y L P V C L S V L P K Q E A A C G F R A A R R Q L F N M ........ cacactgtctaaaaaccgcccgacaagcccctccgtcccgtaaaggggaacgcagaggcttacgagcggcttttgctcggccgcacatccgaagcgcgcggcgcggcgttggagaaaattcatcgtacggt 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================================================ cacactgtctaaaaaccgcccgacaagcccctccgtcccgtaaaggggaacgcagaggcttacgagcggcttttgctcggccgcacatccgaagcgcgcggcgcggcgttggagaaaattcatcgtacggt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 54 HP_score: -8.1 Tail_Score: -3.14848 Start: 16 End: 69 Full_Region: CACACTGTCTAAAAA CCGCCCGACAAGCCCCTCCGTCCC GTAAAG GGGAACGCAGAGGCTTACGAGCGG CTTTTGCTCGGCCGC ...............CCGCCCGACAAGCCCCTCCGTCCCGTAAAGGGGAACGCAGAGGCTTACGAGCGG.............................................................. TransTerm Strand: - Conf: 75 HP_score: -13.8 Tail_Score: -3.34984 Start: 17 End: 68 Full_Region: cggccgagcaaaagc cgctcgtaagcctctgcgttcc cctttac gggacggaggggcttgtcgggcg gtttttagacagtgt ................cgctcgtaagcctctgcgttcccctttacgggacggaggggcttgtcgggcg............................................................... Find igs database================================================ Query_seq: TDE2103:TDE2104|TDE2103:TDE2104:glycosyl transferase, group 2 family protein:hypothetical protein:<-<-:2128484..2128614 131 cacactgtctaaaaaccgcccgacaagcccctccgtcccgtaaaggggaacgcagaggcttacgagcggcttttgctcggccgcacatccgaagcgcgcggcgcggcgttggagaaaattcatcgtacggt Intra-Species Hit: Count: 1 Min: 1 Max: 131 Len: 131 Subject: NC_002967_TDE2103_TDE2104|glycosyl transferase, group 2 family protein:hypothetical protein|NEGATIVE:NEGATIVE|[2128484,2128614]|131 HSP 1 e-value: 1.0E-68 bit: 260.0 Len: 131 Query Start:1 Query End:131 Subject Strand: POSITIVE Subject Start: 1 Subject End: 131 cacactgtctaaaaaccgcccgacaagcccctccgtcccgtaaaggggaacgcagaggcttacgagcggcttttgctcggccgcacatccgaagcgcgcggcgcggcgttggagaaaattcatcgtacggt cacactgtctaaaaaccgcccgacaagcccctccgtcccgtaaaggggaacgcagaggcttacgagcggcttttgctcggccgcacatccgaagcgcgcggcgcggcgttggagaaaattcatcgtacggt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CACACUGUCUAAAAACCGCCCGACAAGCCCCUCCGUCCCGUAAAGGGGAACGCAGAGGCUUACGAGCGGCUUUUGCUCGGCCGCACAUCCGAAGCGCGCGGCGCGGCGUUGGAGAAAAUUCAUCGUACGGU ..............((((..(((.(((((.((.((((((......))).))).)).)))))....((((((.......))))))...(((((.((.(((...))))).))))).........)))..)))) (-46.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACCGUACGAUGAAUUUUCUCCAACGCCGCGCCGCGCGCUUCGGAUGUGCGGCCGAGCAAAAGCCGCUCGUAAGCCUCUGCGUUCCCCUUUACGGGACGGAGGGGCUUGUCGGGCGGUUUUUAGACAGUGUG ....((((.((.............((((.(((((((((....).)))))))))).)).((((((((((((((((((((.((((((.......)))))).))))))))).)))))))))))....)).)))) (-65.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1232 110 61 201 152 NC_002967:TDE2103|5end_glycosyl_transferase,_group_2_family_protein_2128393..2128623_NEGATIVE 531 109 63 66 16 NC_002967:TDE0852|5end_50S_ribosomal_protein_L13_875019..875249_POSITIVE 472 120 73 58 12 NC_002967:TDE1856|5end_radical_SAM_domain_protein_1883133..1883363_POSITIVE 456 130 81 66 15 NC_002967:TDE2715|5end_hypothetical_protein_2772668..2772898_POSITIVE 435 110 67 48 3 NC_002967:TDE2543|5end_hypothetical_protein_2570950..2571180_NEGATIVE 435 110 67 172 127 NC_002967:TDE2542|5end_antigen,_putative_2570826..2571056_NEGATIVE 415 108 64 145 92 NC_002967:TDE2632|5end_peptide_ABC_transporter,_ATP-binding_protein,_putative_2672650..2672880_POSITIVE 415 109 63 64 7 NC_002967:TDE1736|5end_ferredoxin,_2(4Fe-4S)_1789908..1790138_POSITIVE 407 53 16 190 146 NC_002967:TDE0741|5end_hypothetical_protein_778158..778388_NEGATIVE 404 104 71 231 194 NC_002967:TDE2056|5end_outer_membrane_hemin-binding_protein_A_2085070..2085300_NEGATIVE 404 109 66 198 148 NC_002967:TDE1781|5end_hypothetical_protein_1823260..1823490_NEGATIVE 404 109 61 68 5 NC_002967:TDE0740|5end_hypothetical_protein_775987..776217_POSITIVE 399 108 63 83 7 NC_002967:TDE2268|5end_hypothetical_protein_2304959..2305189_NEGATIVE 386 70 21 70 11 NC_002967:TDE1260|5end_cholinephosphate_cytidylyltransferase/choline_kinase_1294028..1294258_POSITIVE 385 109 66 184 126 NC_002967:TDE1492|5end_chemotaxis_protein_CheW_1537231..1537461_POSITIVE 384 100 53 231 183 NC_002967:TDE0178|5end_methyl-accepting_chemotaxis_protein_212628..212858_NEGATIVE 382 56 16 118 85 NC_002967:TDE2181|5end_PAP2_family_protein_2213035..2213265_NEGATIVE 381 80 32 200 145 NC_002967:TDE0884|5end_tRNA_(guanine-N(1)-)-methyltransferase_902221..902451_POSITIVE 379 110 63 197 132 NC_002967:TDE2583|5end_hypothetical_protein_2616322..2616552_POSITIVE 374 100 58 231 187 NC_002967:TDE0573|5end_hypothetical_protein_604681..604911_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 472 120 73 58 12 NC_002967:TDE1855|3end_hypothetical_protein_1883213..1883363_POSITIVE 435 110 67 63 18 NC_002967:TDE2544|3end_hypothetical_protein_2570935..2571085_NEGATIVE 429 113 71 151 106 NC_002967:TDE2057|3end_hypothetical_protein_2085158..2085308_NEGATIVE 424 99 52 78 19 NC_002967:TDE0977|3end_hypothetical_protein_1001640..1001790_POSITIVE 421 109 66 80 14 NC_002967:TDE2736|3end_hypothetical_protein_2791702..2791852_NEGATIVE 415 108 64 148 95 NC_002967:TDE2631|3end_peptide_ABC_transporter,_permease_protein,_putative_2672733..2672883_POSITIVE 415 109 63 74 17 NC_002967:TDE1735|3end_hypothetical_protein_1789998..1790148_POSITIVE 404 110 66 79 33 NC_002967:TDE1770|3end_hypothetical_protein_1814468..1814618_POSITIVE 399 108 63 111 35 NC_002967:TDE2269|3end_hypothetical_protein_2304931..2305081_NEGATIVE 392 108 64 114 57 NC_002967:TDE1848|3end_hypothetical_protein_1875897..1876047_NEGATIVE 386 99 53 128 84 NC_002967:TDE0833|3end_lipoprotein,_putative_854097..854247_POSITIVE 385 107 67 44 1 NC_002967:TDE0617|3end_hypothetical_protein_650093..650243_NEGATIVE 384 100 53 88 40 NC_002967:TDE0179|3end_hypothetical_protein_212771..212921_NEGATIVE 383 60 13 55 4 NC_002967:TDE2604|3end_hypothetical_protein_2644224..2644374_NEGATIVE 382 56 16 118 85 NC_002967:TDE2182|3end_hypothetical_protein_2213035..2213185_NEGATIVE 382 53 16 61 15 NC_002967:TDE2028|3end_OmpA_family_protein_2057019..2057169_POSITIVE 382 92 51 104 59 NC_002967:TDE0353|3end_lipase/acylhydrolase,_GDSL_family_396743..396893_NEGATIVE 378 105 66 144 104 NC_002967:TDE1782|3end_hypothetical_protein_1823304..1823454_NEGATIVE 377 97 53 128 82 NC_002967:TDE2527|3end_hypothetical_protein_2555449..2555599_NEGATIVE 373 99 51 71 21 NC_002967:TDE2312|3end_hypothetical_protein_2349049..2349199_POSITIVE