Origin IGS: tgctaaccaaccttcttgctctaagtcatgtatcttagccggttggtatttaggttgatcctaaatacaatcttgcaggacgtgtgaggacacgtcctgcttttttttatgtaattc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gaattacataaaaaaaagcaggacgtgtcctcacacgtcctgcaagattgtatttaggatcaacctaaataccaaccggctaagatacatgacttagagcaagaaggttggttagca Mask Tandem Repeat Region ================================================ tgctaaccaaccttcttgctctaagtcatgtatcttagccggttggtatttaggttgatcctaaatacaatcttgcaggacgtgtgaggacacgtcctgcttttttttatgtaattc Find is-nt database================================================ Query_seq: TDE2752:TDE2753|TDE2752:TDE2753:hypothetical protein:LysM domain/M23/M37 peptidase domain protein:-><-:2809531..2809647 117 tgctaaccaaccttcttgctctaagtcatgtatcttagccggttggtatttaggttgatcctaaatacaatcttgcaggacgtgtgaggacacgtcctgcttttttttatgtaattc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2752:TDE2753|TDE2752:TDE2753:hypothetical protein:LysM domain/M23/M37 peptidase domain protein:-><-:2809531..2809647 117 tgctaaccaaccttcttgctctaagtcatgtatcttagccggttggtatttaggttgatcctaaatacaatcttgcaggacgtgtgaggacacgtcctgcttttttttatgtaattc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2752:TDE2753|TDE2752:TDE2753:hypothetical protein:LysM domain/M23/M37 peptidase domain protein:-><-:2809531..2809647 117 tgctaaccaaccttcttgctctaagtcatgtatcttagccggttggtatttaggttgatcctaaatacaatcttgcaggacgtgtgaggacacgtcctgcttttttttatgtaattc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgctaaccaaccttcttgctctaagtcatgtatcttagccggttggtatttaggttgatcctaaatacaatcttgcaggacgtgtgaggacacgtcctgcttttttttatgtaattc Predict ORF larger than 30AA ================================================ tgctaaccaaccttcttgctctaagtcatgtatcttagccggttggtatttaggttgatcctaaatacaatcttgcaggacgtgtgaggacacgtcctgcttttttttatgtaattc 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: 81 Start: 42 End: 71 .........................................GTTGGTATTTAGGTTGATCCTAAATACAAT.............................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tgctaaccaaccttcttgctctaagtcatgtatcttagccggttggtatttaggttgatcctaaatacaatcttgcaggacgtgtgaggacacgtcctgcttttttttatgtaattc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 58 HP_score: -6.7 Tail_Score: -3.02263 Start: 44 End: 70 Full_Region: TGTATCTTAGCCGGT TGGTATTTAGG TTGAT CCTAAATACAA TCTTGCAGGACGTGT ...........................................TGGTATTTAGGTTGATCCTAAATACAA............................................... TransTerm Strand: + Conf: 100 HP_score: -17.7 Tail_Score: -6.0427 Start: 75 End: 100 Full_Region: CCTAAATACAATCTT GCAGGACGTGT GAGG ACACGTCCTGC TTTTTTTTATGTAAT ..........................................................................GCAGGACGTGTGAGGACACGTCCTGC................. Find igs database================================================ Query_seq: TDE2752:TDE2753|TDE2752:TDE2753:hypothetical protein:LysM domain/M23/M37 peptidase domain protein:-><-:2809531..2809647 117 tgctaaccaaccttcttgctctaagtcatgtatcttagccggttggtatttaggttgatcctaaatacaatcttgcaggacgtgtgaggacacgtcctgcttttttttatgtaattc Intra-Species Hit: Count: 1 Min: 1 Max: 100 Len: 100 Subject: NC_002967_TDE2752_TDE2753|hypothetical protein:LysM domain/M23/M37 peptidase domain protein|POSITIVE:NEGATIVE|[2809531,2809647]|117 HSP 1 e-value: 3.0E-50 bit: 198.0 Len: 100 Query Start:1 Query End:100 Subject Strand: POSITIVE Subject Start: 1 Subject End: 100 tgctaaccaaccttcttgctctaagtcatgtatcttagccggttggtatttaggttgatcctaaatacaatcttgcaggacgtgtgaggacacgtcctgc................. tgctaaccaaccttcttgctctaagtcatgtatcttagccggttggtatttaggttgatcctaaatacaatcttgcaggacgtgtgaggacacgtcctgc................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGCUAACCAACCUUCUUGCUCUAAGUCAUGUAUCUUAGCCGGUUGGUAUUUAGGUUGAUCCUAAAUACAAUCUUGCAGGACGUGUGAGGACACGUCCUGC .....(((((((........(((((........)))))..)))))))(((((((.....)))))))........(((((((((((....))))))))))) (-35.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCAGGACGUGUCCUCACACGUCCUGCAAGAUUGUAUUUAGGAUCAACCUAAAUACCAACCGGCUAAGAUACAUGACUUAGAGCAAGAAGGUUGGUUAGCA (((((((((((....))))))))))).......((((((((.....))))))))((((((..(((((........)))))........))))))...... (-37.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 338 80 34 127 73 NC_002967:TDE1137|5end_hypothetical_protein_1166749..1166979_NEGATIVE 287 60 12 73 22 NC_002967:TDE2681|5end_hypothetical_protein_2721407..2721637_NEGATIVE 287 99 54 197 153 NC_002967:TDE2353|5end_flagellar_hook-associated_protein_2389129..2389359_POSITIVE 274 100 76 26 1 NC_002967:TDE2734|5end_hypothetical_protein_2789071..2789301_POSITIVE 268 87 43 74 21 NC_002967:TDE0527|5end_hypothetical_protein_572287..572517_POSITIVE 266 79 38 217 176 NC_002967:TDE0555|5end_hypothetical_protein_591522..591752_NEGATIVE 263 42 6 56 11 NC_002967:TDE2637|5end_hypothetical_protein_2677316..2677546_NEGATIVE 257 44 1 68 26 NC_002967:TDE1041|5end_polyribonucleotide_nucleotidyltransferase_1068324..1068554_POSITIVE 256 89 44 220 179 NC_002967:TDE1269|5end_hypothetical_protein_1304522..1304752_NEGATIVE 251 88 52 218 182 NC_002967:TDE1447|5end_tRNA_delta(2)-isopentenylpyrophosphate_transferase_1492612..1492842_POSITIVE 250 58 11 45 1 NC_002967:TDE1697|5end_phosphoglycerate_mutase_1756259..1756489_NEGATIVE 249 47 2 61 18 NC_002967:TDE2605|5end_phosphoglycerate_mutase_family_protein_2645818..2646048_POSITIVE 249 78 33 141 99 NC_002967:TDE0430|5end_TPR_domain_protein_486455..486685_NEGATIVE 249 98 60 229 195 NC_002967:TDE0210|5end_cob(I)yrinic_acid_a,c-diamide_adenosyltransferase_245551..245781_POSITIVE 249 100 71 58 32 NC_002967:TDE0153|5end_coenzyme_A_disulfide_reductase,_putative_176185..176415_NEGATIVE 242 100 53 89 38 NC_002967:TDE2349|5end_hypothetical_protein_2385940..2386170_NEGATIVE 242 61 21 127 88 NC_002967:TDE2268|5end_hypothetical_protein_2304959..2305189_NEGATIVE 241 100 51 100 31 NC_002967:TDE0759|5end_hypothetical_protein_799499..799729_NEGATIVE 240 56 16 209 173 NC_002967:TDE2677|5end_hypothetical_protein_2715604..2715834_POSITIVE 238 100 58 75 32 NC_002967:TDE1657|5end_transcription_antitermination_protein_NusB_1707640..1707870_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 336 58 11 143 104 NC_002967:TDE1914|3end_Holliday_junction_DNA_helicase_RuvB_1930889..1931039_NEGATIVE 287 60 12 92 41 NC_002967:TDE2682|3end_hypothetical_protein_2721388..2721538_NEGATIVE 267 79 32 66 21 NC_002967:TDE1931|3end_cytidine_deaminase_1949020..1949170_POSITIVE 262 61 23 51 15 NC_002967:TDE0940|3end_hypothetical_protein_963635..963785_POSITIVE 257 84 41 64 19 NC_002967:TDE2752|3end_hypothetical_protein_2809470..2809620_POSITIVE 256 79 37 137 95 NC_002967:TDE2074|3end_radical_SAM_enzyme,_Cfr_family_2101537..2101687_POSITIVE 249 78 33 126 84 NC_002967:TDE0431|3end_LysM_domain_protein_486470..486620_NEGATIVE 249 100 71 35 9 NC_002967:TDE0154|3end_adenylate/guanylate_cyclase_catalytic_domain_protein_176208..176358_NEGATIVE 247 96 52 50 2 NC_002967:TDE1081|3end_hypothetical_protein_1113228..1113378_POSITIVE 238 100 58 60 17 NC_002967:TDE1658|3end_basic_membrane_protein,_putative_1707655..1707805_NEGATIVE 235 49 1 105 64 NC_002967:TDE2250|3end_hypothetical_protein_2289409..2289559_POSITIVE 234 58 14 99 51 NC_002967:TDE1363|3end_nitroreductase_family_protein_1404126..1404276_NEGATIVE 233 100 70 126 101 NC_002967:TDE1091|3end_hypothetical_protein_1123017..1123167_NEGATIVE 232 57 13 139 105 NC_002967:TDE1847|3end_hypothetical_protein_1875845..1875995_POSITIVE 232 96 54 63 18 NC_002967:TDE0387|3end_(R)-hydroxyglutaryl-CoA_dehydratase_activator_439256..439406_POSITIVE 229 99 51 146 92 NC_002967:TDE2205|3end_enoate_reductase,_putative_2242575..2242725_NEGATIVE 225 60 11 142 96 NC_002967:TDE0293|3end_MATE_efflux_family_protein_322018..322168_NEGATIVE 224 98 51 118 70 NC_002967:TDE0091|3end_RNA_polymerase_sigma-24_factor,_putative_109190..109340_NEGATIVE 223 97 59 41 12 NC_002967:TDE1589|3end_purine-binding_chemotaxis_protein_1637590..1637740_POSITIVE 223 62 23 114 63 NC_002967:TDE0299|3end_mutator_mutT_protein_330579..330729_POSITIVE