Origin IGS: ttagggggaagctctgttggagcacagctataaaatatcatcccatgtcggatgtatatatttttcttccgtgctcataacaaagcttcccgttttgatcggtattt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaataccgatcaaaacgggaagctttgttatgagcacggaagaaaaatatatacatccgacatgggatgatattttatagctgtgctccaacagagcttccccctaa Mask Tandem Repeat Region ================================================ ttagggggaagctctgttggagcacagctataaaatatcatcccatgtcggatgtatatatttttcttccgtgctcataacaaagcttcccgttttgatcggtattt Find is-nt database================================================ Query_seq: TDE1584:TDE1585|TDE1584:TDE1585:lipoprotein, putative:hypothetical protein:-><-:1632915..1633021 107 ttagggggaagctctgttggagcacagctataaaatatcatcccatgtcggatgtatatatttttcttccgtgctcataacaaagcttcccgttttgatcggtattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1584:TDE1585|TDE1584:TDE1585:lipoprotein, putative:hypothetical protein:-><-:1632915..1633021 107 ttagggggaagctctgttggagcacagctataaaatatcatcccatgtcggatgtatatatttttcttccgtgctcataacaaagcttcccgttttgatcggtattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1584:TDE1585|TDE1584:TDE1585:lipoprotein, putative:hypothetical protein:-><-:1632915..1633021 107 ttagggggaagctctgttggagcacagctataaaatatcatcccatgtcggatgtatatatttttcttccgtgctcataacaaagcttcccgttttgatcggtattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttagggggaagctctgttggagcacagctataaaatatcatcccatgtcggatgtatatatttttcttccgtgctcataacaaagcttcccgttttgatcggtattt Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 14 End: 106 ............. M L E H S Y K I S S H V G C I Y F S S V L I T K L P V L I G I . ttagggggaagctctgttggagcacagctataaaatatcatcccatgtcggatgtatatatttttcttccgtgctcataacaaagcttcccgttttgatcggtattt 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================================================ ttagggggaagctctgttggagcacagctataaaatatcatcccatgtcggatgtatatatttttcttccgtgctcataacaaagcttcccgttttgatcggtattt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1584:TDE1585|TDE1584:TDE1585:lipoprotein, putative:hypothetical protein:-><-:1632915..1633021 107 ttagggggaagctctgttggagcacagctataaaatatcatcccatgtcggatgtatatatttttcttccgtgctcataacaaagcttcccgttttgatcggtattt Intra-Species Hit: Count: 1 Min: 1 Max: 107 Len: 107 Subject: NC_002967_TDE1584_TDE1585|lipoprotein, putative:hypothetical protein|POSITIVE:NEGATIVE|[1632915,1633021]|107 HSP 1 e-value: 2.0E-54 bit: 212.0 Len: 107 Query Start:1 Query End:107 Subject Strand: POSITIVE Subject Start: 1 Subject End: 107 ttagggggaagctctgttggagcacagctataaaatatcatcccatgtcggatgtatatatttttcttccgtgctcataacaaagcttcccgttttgatcggtattt ttagggggaagctctgttggagcacagctataaaatatcatcccatgtcggatgtatatatttttcttccgtgctcataacaaagcttcccgttttgatcggtattt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAGGGGGAAGCUCUGUUGGAGCACAGCUAUAAAAUAUCAUCCCAUGUCGGAUGUAUAUAUUUUUCUUCCGUGCUCAUAACAAAGCUUCCCGUUUUGAUCGGUAUUU .....((((((((.(((((((((((.(....((((((((((((......)))))...)))))))....).)))))).))))).))))))))................ (-38.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUACCGAUCAAAACGGGAAGCUUUGUUAUGAGCACGGAAGAAAAAUAUAUACAUCCGACAUGGGAUGAUAUUUUAUAGCUGUGCUCCAACAGAGCUUCCCCCUAA ................(((((((((((((..((((((((....(((((((...(((((......))))))))))))....)))))))).)))))))))))))..... (-44.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 306 90 41 175 128 NC_002967:TDE1261|5end_choline/carnitine/betaine_transporter_family_protein_1295593..1295823_POSITIVE 297 50 3 206 161 NC_002967:TDE2516|5end_hypothetical_protein_2542021..2542251_POSITIVE 295 89 41 102 57 NC_002967:TDE2236|5end_methylaspartate_mutase,_E_subunit_2276117..2276347_NEGATIVE 294 28 1 31 6 NC_002967:TDE2685|5end_flagellar_synthesis_regulator_FleN_2725783..2726013_NEGATIVE 282 50 4 194 152 NC_002967:TDE1714|5end_N-acetylmuramoyl-L-alanine_amidase,_family_3_1769496..1769726_NEGATIVE 276 49 3 86 44 NC_002967:TDE0158|5end_hypothetical_protein_185948..186178_NEGATIVE 261 36 3 54 14 NC_002967:TDE2773|5end_hypothetical_protein_2825963..2826193_NEGATIVE 261 58 11 127 76 NC_002967:TDE0132|5end_hypothetical_protein_152046..152276_POSITIVE 259 50 6 197 154 NC_002967:TDE0633|5end_D-alanyl-D-alanine_carboxypeptidase,_putative_667778..668008_POSITIVE 253 50 3 186 132 NC_002967:TDE2697|5end_3-oxo-5-alpha-steroid_4-dehydrogenase_family_protein_2740260..2740490_POSITIVE 251 98 51 71 18 NC_002967:TDE2762|5end_flagellar_motor_switch_protein_FliY_2817744..2817974_NEGATIVE 251 59 11 84 27 NC_002967:TDE2420|5end_DNA-directed_RNA_polymerase_beta'_subunit_2449234..2449464_NEGATIVE 249 50 3 217 167 NC_002967:TDE1182|5end_hypothetical_protein_1210458..1210688_POSITIVE 248 68 22 78 29 NC_002967:TDE2193|5end_deoxycytidylate_deaminase,_putative_2229760..2229990_NEGATIVE 248 44 2 175 122 NC_002967:TDE1058|5end_hypothetical_protein_1086366..1086596_NEGATIVE 247 23 3 55 32 NC_002967:TDE2251|5end_uracil_permease_2289440..2289670_POSITIVE 247 54 15 203 158 NC_002967:TDE1520|5end_fumarate_hydratase_1566351..1566581_POSITIVE 247 75 41 225 187 NC_002967:TDE1298|5end_cyclic_nucleotide_binding_domain_protein_1335315..1335545_NEGATIVE 246 50 11 196 156 NC_002967:TDE1969|5end_sigma-54_dependent_transcriptional_regulator/response_regulator_1984500..1984730_NEGATIVE 246 29 3 179 153 NC_002967:TDE0438|5end_queuine_tRNA-ribosyltransferase_494811..495041_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 323 90 41 84 39 NC_002967:TDE1584|3end_lipoprotein,_putative_1632854..1633004_POSITIVE 313 95 64 51 13 NC_002967:TDE0435|3end_ATP-dependent_DNA_helicase,_RecQ_family_489558..489708_NEGATIVE 294 28 1 29 4 NC_002967:TDE2686|3end_flagellar_biosynthetic_protein_FlhF_2725785..2725935_NEGATIVE 273 50 4 82 26 NC_002967:TDE0166|3end_hypothetical_protein_195050..195200_NEGATIVE 265 89 41 129 78 NC_002967:TDE2485|3end_hypothetical_protein_2507903..2508053_NEGATIVE 262 50 1 56 3 NC_002967:TDE2317|3end_hemolysin_III_2354118..2354268_NEGATIVE 261 58 11 102 51 NC_002967:TDE0131|3end_hypothetical_protein_152101..152251_POSITIVE 259 50 1 112 65 NC_002967:TDE1808|3end_hypothetical_protein_1844084..1844234_NEGATIVE 256 50 1 131 81 NC_002967:TDE2460|3end_aminotransferase,_class_V_2487229..2487379_POSITIVE 251 98 51 78 25 NC_002967:TDE2763|3end_flagellar_motor_switch_protein_2817737..2817887_NEGATIVE 251 59 11 59 2 NC_002967:TDE2421|3end_DNA-directed_RNA_polymerase_beta_subunit_2449259..2449409_NEGATIVE 248 24 1 120 91 NC_002967:TDE1892|3end_hypothetical_protein_1912237..1912387_POSITIVE 247 54 15 124 79 NC_002967:TDE1519|3end_hypothetical_protein_1566352..1566502_POSITIVE 247 75 41 123 85 NC_002967:TDE1299|3end_hypothetical_protein_1335417..1335567_NEGATIVE 240 46 4 117 61 NC_002967:TDE2780|3end_hypothetical_protein_2830508..2830658_NEGATIVE 234 80 41 150 106 NC_002967:TDE2630|3end_peptide_ABC_transporter,_permease_protein,_putative_2671912..2672062_POSITIVE 232 93 52 103 66 NC_002967:TDE2297|3end_TPR_domain_protein_2336339..2336489_NEGATIVE 231 94 59 86 55 NC_002967:TDE0908|3end_ABC_transporter,_ATP-binding/permease_protein_927085..927235_POSITIVE 227 44 1 85 54 NC_002967:TDE2265|3end_hypothetical_protein_2302634..2302784_POSITIVE 227 49 5 111 58 NC_002967:TDE0104|3end_3-dehydroquinate_synthase_123683..123833_NEGATIVE