Origin IGS: aagaacctctcatattttaggcatattaccacaataaaccataaaattcaattatagtcttgacaactccggaataaaaggataacctattcaatatgaatgaggcctt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaggcctcattcatattgaataggttatccttttattccggagttgtcaagactataattgaattttatggtttattgtggtaatatgcctaaaatatgagaggttctt Mask Tandem Repeat Region ================================================ aagaacctctcatattttaggcatattaccacaataaaccataaaattcaattatagtcttgacaactccggaataaaaggataacctattcaatatgaatgaggcctt Find is-nt database================================================ Query_seq: TDE1234:TDE1235|TDE1234:TDE1235:hypothetical protein:hypothetical protein:<-->:1269407..1269515 109 aagaacctctcatattttaggcatattaccacaataaaccataaaattcaattatagtcttgacaactccggaataaaaggataacctattcaatatgaatgaggcctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1234:TDE1235|TDE1234:TDE1235:hypothetical protein:hypothetical protein:<-->:1269407..1269515 109 aagaacctctcatattttaggcatattaccacaataaaccataaaattcaattatagtcttgacaactccggaataaaaggataacctattcaatatgaatgaggcctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1234:TDE1235|TDE1234:TDE1235:hypothetical protein:hypothetical protein:<-->:1269407..1269515 109 aagaacctctcatattttaggcatattaccacaataaaccataaaattcaattatagtcttgacaactccggaataaaaggataacctattcaatatgaatgaggcctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aagaacctctcatattttaggcatattaccacaataaaccataaaattcaattatagtcttgacaactccggaataaaaggataacctattcaatatgaatgaggcctt Predict ORF larger than 30AA ================================================ aagaacctctcatattttaggcatattaccacaataaaccataaaattcaattatagtcttgacaactccggaataaaaggataacctattcaatatgaatgaggcctt 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: 84 Start: 23 End: 52 ......................ATTGAATTTTATGGTTTATTGTGGTAATAT......................................................... PromScan Matrix: RpoD-17 Strand: + Score: 83 Start: 59 End: 88 ..........................................................CTTGACAACTCCGGAATAAAAGGATAACCT..................... PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 38 End: 67 .....................................GTTGTCAAGACTATAATTGAATTTTATGGT.......................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aagaacctctcatattttaggcatattaccacaataaaccataaaattcaattatagtcttgacaactccggaataaaaggataacctattcaatatgaatgaggcctt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1234:TDE1235|TDE1234:TDE1235:hypothetical protein:hypothetical protein:<-->:1269407..1269515 109 aagaacctctcatattttaggcatattaccacaataaaccataaaattcaattatagtcttgacaactccggaataaaaggataacctattcaatatgaatgaggcctt Intra-Species Hit: Count: 1 Min: 1 Max: 109 Len: 109 Subject: NC_002967_TDE1234_TDE1235|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[1269407,1269515]|109 HSP 1 e-value: 1.0E-55 bit: 216.0 Len: 109 Query Start:1 Query End:109 Subject Strand: POSITIVE Subject Start: 1 Subject End: 109 aagaacctctcatattttaggcatattaccacaataaaccataaaattcaattatagtcttgacaactccggaataaaaggataacctattcaatatgaatgaggcctt aagaacctctcatattttaggcatattaccacaataaaccataaaattcaattatagtcttgacaactccggaataaaaggataacctattcaatatgaatgaggcctt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGAACCUCUCAUAUUUUAGGCAUAUUACCACAAUAAACCAUAAAAUUCAAUUAUAGUCUUGACAACUCCGGAAUAAAAGGAUAACCUAUUCAAUAUGAAUGAGGCCUU .....(((((((((((.((((..........................((((........))))....(((.........)))...))))...)))))))..)))).... (-15.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGGCCUCAUUCAUAUUGAAUAGGUUAUCCUUUUAUUCCGGAGUUGUCAAGACUAUAAUUGAAUUUUAUGGUUUAUUGUGGUAAUAUGCCUAAAAUAUGAGAGGUUCUU ..((((((..(((((((...(((((........(((((((.(((.....(((((((((.......)))))))))))).))).)))).))))).)))))))))))))... (-26.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 769 100 51 191 142 NC_002967:TDE1234|5end_hypothetical_protein_1269316..1269546_NEGATIVE 245 84 50 230 185 NC_002967:TDE2130|5end_hypothetical_protein_2162059..2162289_NEGATIVE 226 89 48 66 33 NC_002967:TDE1096|5end_hydroxymethylbutenyl_pyrophosphate_reductase_1130989..1131219_POSITIVE 212 49 6 73 30 NC_002967:TDE0369|5end_type_I_restriction-modification_system,_M_subunit_420971..421201_NEGATIVE 207 50 6 145 103 NC_002967:TDE1589|5end_purine-binding_chemotaxis_protein_1637004..1637234_POSITIVE 202 90 49 199 158 NC_002967:TDE0210|5end_cob(I)yrinic_acid_a,c-diamide_adenosyltransferase_245551..245781_POSITIVE 201 81 45 206 161 NC_002967:TDE2438|5end_hypothetical_protein_2469257..2469487_NEGATIVE 200 70 21 150 95 NC_002967:TDE0229|5end_ATPase_family_protein_262746..262976_NEGATIVE 198 88 57 144 112 NC_002967:TDE1057|5end_hypothetical_protein_1086245..1086475_NEGATIVE 197 85 56 165 132 NC_002967:TDE1108|5end_hypothetical_protein_1142859..1143089_NEGATIVE 195 82 56 50 12 NC_002967:TDE2760|5end_flagellar_biosynthesis_protein_2815881..2816111_NEGATIVE 193 33 8 188 159 NC_002967:TDE0722|5end_lipoprotein,_putative_758519..758749_POSITIVE 191 92 66 127 97 NC_002967:TDE2353|5end_flagellar_hook-associated_protein_2389129..2389359_POSITIVE 191 40 8 215 186 NC_002967:TDE0368|5end_type_I_restriction-modification_system,_S_subunit,_putative_418245..418475_NEGATIVE 191 87 56 150 118 NC_002967:TDE0321|5end_CBS_domain_protein_355094..355324_NEGATIVE 189 81 50 229 197 NC_002967:TDE2308|5end_hypothetical_protein_2345604..2345834_POSITIVE 187 89 43 190 154 NC_002967:TDE0295|5end_DNA_gyrase,_A_subunit_326667..326897_NEGATIVE 186 50 2 90 45 NC_002967:TDE0519|5end_hypothetical_protein_565989..566219_NEGATIVE 185 87 46 77 31 NC_002967:TDE0459|5end_hypothetical_protein_514382..514612_POSITIVE 184 83 52 194 164 NC_002967:TDE1203|5end_cell_division_protein_FtsA_1235033..1235263_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 438 100 54 54 5 NC_002967:TDE1234|3end_hypothetical_protein_1267631..1267781_NEGATIVE 226 89 48 42 9 NC_002967:TDE1095|3end_alanine_racemase_1131045..1131195_POSITIVE 221 100 69 36 5 NC_002967:TDE1864|3end_crossover_junction_endodeoxyribonuclease_RuvC_1888572..1888722_NEGATIVE 212 96 68 101 73 NC_002967:TDE0875|3end_ribosomal_large_subunit_pseudouridine_synthase_B_898273..898423_POSITIVE 202 90 49 129 88 NC_002967:TDE0209|3end_arsenical_pump_membrane_protein,_putative_245561..245711_POSITIVE 200 70 21 97 42 NC_002967:TDE0230|3end_DNA_replication_and_repair_protein_RecF_262799..262949_NEGATIVE 199 88 42 134 92 NC_002967:TDE2627|3end_transcriptional_regulator,_TetR_family_2668532..2668682_NEGATIVE 195 82 56 53 15 NC_002967:TDE2761|3end_hypothetical_protein_2815878..2816028_NEGATIVE 195 92 51 121 83 NC_002967:TDE1667|3end_translation_initiation_factor_IF-2B_subunit_alpha_1719993..1720143_NEGATIVE 192 79 33 73 21 NC_002967:TDE2016|3end_hypothetical_protein_2037824..2037974_NEGATIVE 191 92 66 104 74 NC_002967:TDE2352|3end_flagellar_hook-associated_protein_2389186..2389336_POSITIVE 191 40 8 104 75 NC_002967:TDE0369|3end_type_I_restriction-modification_system,_M_subunit_418356..418506_NEGATIVE 191 87 56 138 106 NC_002967:TDE0322|3end_regulatory_protein,_P-II_family_355106..355256_NEGATIVE 183 72 32 129 97 NC_002967:TDE2306|3end_hypothetical_protein_2344138..2344288_NEGATIVE 179 51 19 80 48 NC_002967:TDE2511|3end_ABC_transporter,_ATP-binding/permease_protein_2537664..2537814_POSITIVE 179 25 1 125 102 NC_002967:TDE1396|3end_hypothetical_protein_1436127..1436277_POSITIVE 178 27 5 117 93 NC_002967:TDE2676|3end_threonine_synthase_2715678..2715828_POSITIVE 178 77 45 71 47 NC_002967:TDE0889|3end_hypothetical_protein_905814..905964_POSITIVE 174 47 6 49 17 NC_002967:TDE1990|3end_ATP-dependent_helicase,_DinG_family_2006367..2006517_NEGATIVE 171 87 54 69 31 NC_002967:TDE0728|3end_FAD-binding_protein,_putative_768131..768281_POSITIVE