Origin IGS: ggtcagtactaaaaaacttgttgttttttagcggtaaccgtgatcctttgaaaaaaaattattggaggttcgataaacagttcggcaggaattctgccttgctgtttatcggtattggaggtgctt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aagcacctccaataccgataaacagcaaggcagaattcctgccgaactgtttatcgaacctccaataattttttttcaaaggatcacggttaccgctaaaaaacaacaagttttttagtactgacc Mask Tandem Repeat Region ================================================ ggtcagtactaaaaaacttgttgttttttagcggtaaccgtgatcctttgaaaaaaaattattggaggttcgataaacagttcggcaggaattctgccttgctgtttatcggtattggaggtgctt Find is-nt database================================================ Query_seq: TDE1654:TDE1655|TDE1654:TDE1655:ATP-dependent helicase HrpA, putative:hypothetical protein:->->:1704972..1705097 126 ggtcagtactaaaaaacttgttgttttttagcggtaaccgtgatcctttgaaaaaaaattattggaggttcgataaacagttcggcaggaattctgccttgctgtttatcggtattggaggtgctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1654:TDE1655|TDE1654:TDE1655:ATP-dependent helicase HrpA, putative:hypothetical protein:->->:1704972..1705097 126 ggtcagtactaaaaaacttgttgttttttagcggtaaccgtgatcctttgaaaaaaaattattggaggttcgataaacagttcggcaggaattctgccttgctgtttatcggtattggaggtgctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1654:TDE1655|TDE1654:TDE1655:ATP-dependent helicase HrpA, putative:hypothetical protein:->->:1704972..1705097 126 ggtcagtactaaaaaacttgttgttttttagcggtaaccgtgatcctttgaaaaaaaattattggaggttcgataaacagttcggcaggaattctgccttgctgtttatcggtattggaggtgctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ggtcagtactaaaaaacttgttgttttttagcggtaaccgtgatcctttgaaaaaaaattattggaggttcgataaacagttcggcaggaattctgccttgctgtttatcggtattggaggtgctt Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 18 End: 125 ................. M L F F S G N R D P L K K N Y W R F D K Q F G R N S A L L F I G I G G A . ggtcagtactaaaaaacttgttgttttttagcggtaaccgtgatcctttgaaaaaaaattattggaggttcgataaacagttcggcaggaattctgccttgctgtttatcggtattggaggtgctt 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================================================ ggtcagtactaaaaaacttgttgttttttagcggtaaccgtgatcctttgaaaaaaaattattggaggttcgataaacagttcggcaggaattctgccttgctgtttatcggtattggaggtgctt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1654:TDE1655|TDE1654:TDE1655:ATP-dependent helicase HrpA, putative:hypothetical protein:->->:1704972..1705097 126 ggtcagtactaaaaaacttgttgttttttagcggtaaccgtgatcctttgaaaaaaaattattggaggttcgataaacagttcggcaggaattctgccttgctgtttatcggtattggaggtgctt Intra-Species Hit: Count: 1 Min: 1 Max: 126 Len: 126 Subject: NC_002967_TDE1654_TDE1655|ATP-dependent helicase HrpA, putative:hypothetical protein|POSITIVE:POSITIVE|[1704972,1705097]|126 HSP 1 e-value: 2.0E-51 bit: 202.0 Len: 126 Query Start:1 Query End:126 Subject Strand: POSITIVE Subject Start: 1 Subject End: 126 ggtcagtactaaaaaacttgttgttttttagcggtaaccgtgatcctttgnnnnnnnnttattggaggttcgataaacagttcggcaggaattctgccttgctgtttatcggtattggaggtgctt ggtcagtactaaaaaacttgttgttttttagcggtaaccgtgatcctttgaaaaaaaattattggaggttcgataaacagttcggcaggaattctgccttgctgtttatcggtattggaggtgctt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGUCAGUACUAAAAAACUUGUUGUUUUUUAGCGGUAACCGUGAUCCUUUGAAAAAAAAUUAUUGGAGGUUCGAUAAACAGUUCGGCAGGAAUUCUGCCUUGCUGUUUAUCGGUAUUGGAGGUGCUU ........(((((((((.....))))))))).((((.((.....((((..(.((....)).)..)))).((((((((((((..(((((.....)))))..)))))))))))).......)))))). (-40.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGCACCUCCAAUACCGAUAAACAGCAAGGCAGAAUUCCUGCCGAACUGUUUAUCGAACCUCCAAUAAUUUUUUUUCAAAGGAUCACGGUUACCGCUAAAAAACAACAAGUUUUUUAGUACUGACC ...............((((((((((...(((((.....)))))...))))))))))....(((.................)))....(((((..((((((((((.....))))))))))..))))) (-37.13) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 683 110 63 68 21 NC_002967:TDE1583|5end_hypothetical_protein_1631808..1632038_POSITIVE 673 110 64 221 175 NC_002967:TDE1980|5end_hypothetical_protein_1992061..1992291_NEGATIVE 673 110 64 70 24 NC_002967:TDE1326|5end_hypothetical_protein_1361661..1361891_POSITIVE 672 110 63 99 52 NC_002967:TDE2667|5end_hypothetical_protein_2704374..2704604_POSITIVE 484 111 71 129 89 NC_002967:TDE1334|5end_hypothetical_protein_1370144..1370374_POSITIVE 477 111 72 149 110 NC_002967:TDE2220|5end_prolyl-tRNA_synthetase_2260885..2261115_POSITIVE 447 108 63 148 108 NC_002967:TDE2479|5end_hypothetical_protein_2503290..2503520_NEGATIVE 437 110 62 140 97 NC_002967:TDE1325|5end_hypothetical_protein_1361721..1361951_NEGATIVE 413 116 72 187 143 NC_002967:TDE1298|5end_cyclic_nucleotide_binding_domain_protein_1335315..1335545_NEGATIVE 401 110 69 146 105 NC_002967:TDE1210|5end_ATP-dependent_protease_peptidase_subunit_1243329..1243559_POSITIVE 401 110 62 180 137 NC_002967:TDE0466|5end_hypothetical_protein_518854..519084_NEGATIVE 385 110 72 149 111 NC_002967:TDE2131|5end_cobalamin_biosynthesis_protein_CbiM,_putative_2162683..2162913_NEGATIVE 383 110 64 189 138 NC_002967:TDE2497|5end_hypothetical_protein_2522083..2522313_NEGATIVE 383 110 64 167 116 NC_002967:TDE2394|5end_hypothetical_protein_2422612..2422842_NEGATIVE 383 110 64 190 139 NC_002967:TDE2224|5end_hypothetical_protein_2264743..2264973_POSITIVE 383 110 64 89 38 NC_002967:TDE2223|5end_hypothetical_protein_2264642..2264872_POSITIVE 379 111 72 178 139 NC_002967:TDE1849|5end_hypothetical_protein_1878123..1878353_NEGATIVE 379 110 71 151 112 NC_002967:TDE1006|5end_flagellar_basal-body_rod_protein_FlgG_1030427..1030657_POSITIVE 376 110 71 151 112 NC_002967:TDE2666|5end_hydrolase,_carbon-nitrogen_family_2704394..2704624_NEGATIVE 376 111 72 179 140 NC_002967:TDE1236|5end_triosephosphate_isomerase_1269486..1269716_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 646 110 64 60 14 NC_002967:TDE1902|3end_hypothetical_protein_1922377..1922527_NEGATIVE 484 111 71 53 13 NC_002967:TDE1333|3end_hflC_protein,_putative_1370148..1370298_POSITIVE 447 108 63 72 32 NC_002967:TDE2480|3end_heat_shock_protein_90_2503366..2503516_NEGATIVE 437 110 62 72 29 NC_002967:TDE1327|3end_hypothetical_protein_1361789..1361939_NEGATIVE 426 110 64 61 11 NC_002967:TDE2396|3end_putative_inner_membrane_protein_translocase_component_YidC_2423650..2423800_NEGATIVE 415 111 72 76 37 NC_002967:TDE1916|3end_glycerol_kinase_1933277..1933427_NEGATIVE 413 116 72 85 41 NC_002967:TDE1299|3end_hypothetical_protein_1335417..1335567_NEGATIVE 401 110 69 79 38 NC_002967:TDE1209|3end_site-specific_recombinase,_phage_integrase_family_1243342..1243492_POSITIVE 389 110 62 82 26 NC_002967:TDE0743|3end_thioredoxin_reductase_779751..779901_POSITIVE 385 110 72 76 38 NC_002967:TDE2132|3end_cobalt_ABC_transporter,_ATP-binding_protein,_putative_2162756..2162906_NEGATIVE 383 110 64 78 27 NC_002967:TDE2498|3end_metallo-beta-lactamase_family_protein_2522194..2522344_NEGATIVE 383 110 64 69 18 NC_002967:TDE2222|3end_hypothetical_protein_2264702..2264852_POSITIVE 383 110 64 72 21 NC_002967:TDE1901|3end_ABC_transporter,_ATP-binding_protein_1922319..1922469_POSITIVE 382 90 59 151 120 NC_002967:TDE1326|3end_hypothetical_protein_1361842..1361992_POSITIVE 379 111 72 74 35 NC_002967:TDE1850|3end_ABC_transporter,_permease_protein,_putative_1878227..1878377_NEGATIVE 379 110 71 139 100 NC_002967:TDE1005|3end_hypothetical_protein_1030495..1030645_POSITIVE 360 110 62 79 36 NC_002967:TDE0065|3end_hypothetical_protein_72822..72972_NEGATIVE 358 110 61 73 16 NC_002967:TDE2485|3end_hypothetical_protein_2507903..2508053_NEGATIVE 358 110 62 50 6 NC_002967:TDE1973|3end_CvpA_family_protein_1987239..1987389_NEGATIVE 356 110 63 76 35 NC_002967:TDE1626|3end_glycine_cleavage_system_H_protein_1674911..1675061_NEGATIVE