Origin IGS: atattttagattaaaccgcataaaaatgcaataaaatgaataaaaatacatatttttcttaaaaacacttgacaatttttatttaatttgataaattatgactacacacagaaaagatacacatactacttcaaaagaacccccgtatcctcctttcgggggttcttttctttttttgagcgaaatttaat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 attaaatttcgctcaaaaaaagaaaagaacccccgaaaggaggatacgggggttcttttgaagtagtatgtgtatcttttctgtgtgtagtcataatttatcaaattaaataaaaattgtcaagtgtttttaagaaaaatatgtatttttattcattttattgcatttttatgcggtttaatctaaaatat Mask Tandem Repeat Region ================================================ atattttagattaaaccgcataaaaatgcaataaaatgaataaaaatacatatttttcttaaaaacacttgacaatttttatttaatttgataaattatgactacacacagaaaagatacacatactacttcaaaagaacccccgtatcctcctttcgggggttcttttctttttttgagcgaaatttaat Find is-nt database================================================ Query_seq: TDE2613:TDE2614|TDE2613:TDE2614:hypothetical protein:ApbE family protein:-><-:2655917..2656107 191 atattttagattaaaccgcataaaaatgcaataaaatgaataaaaatacatatttttcttaaaaacacttgacaatttttatttaatttgataaattatgactacacacagaaaagatacacatactacttcaaaagaacccccgtatcctcctttcgggggttcttttctttttttgagcgaaatttaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2613:TDE2614|TDE2613:TDE2614:hypothetical protein:ApbE family protein:-><-:2655917..2656107 191 atattttagattaaaccgcataaaaatgcaataaaatgaataaaaatacatatttttcttaaaaacacttgacaatttttatttaatttgataaattatgactacacacagaaaagatacacatactacttcaaaagaacccccgtatcctcctttcgggggttcttttctttttttgagcgaaatttaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2613:TDE2614|TDE2613:TDE2614:hypothetical protein:ApbE family protein:-><-:2655917..2656107 191 atattttagattaaaccgcataaaaatgcaataaaatgaataaaaatacatatttttcttaaaaacacttgacaatttttatttaatttgataaattatgactacacacagaaaagatacacatactacttcaaaagaacccccgtatcctcctttcgggggttcttttctttttttgagcgaaatttaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atattttagattaaaccgcataaaaatgcaataaaatgaataaaaatacatatttttcttaaaaacacttgacaatttttatttaatttgataaattatgactacacacagaaaagatacacatactacttcaaaagaacccccgtatcctcctttcgggggttcttttctttttttgagcgaaatttaat Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 88 End: 189 ....................................................................................... M I N Y D Y T Q K R Y T Y Y F K R T P V S S F R G F F S F F E R N L .. Protein_Len: 32 Strand: + Start: 95 End: 187 .............................................................................................. M M T T H R K D T H T T S K E P P Y P P F G G S F L F L S E I * .... Protein_Len: 35 Strand: - Start: 82 End: 186 ................................................................................. K I Q Y I I V V C L F S V C V V E F S G G Y G G K P P E K R K K L S M ..... atattttagattaaaccgcataaaaatgcaataaaatgaataaaaatacatatttttcttaaaaacacttgacaatttttatttaatttgataaattatgactacacacagaaaagatacacatactacttcaaaagaacccccgtatcctcctttcgggggttcttttctttttttgagcgaaatttaat 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: 86 Start: 68 End: 97 ...................................................................CTTGACAATTTTTATTTAATTTGATAAATT.............................................................................................. PromScan Matrix: RpoD-17 Strand: - Score: 84 Start: 3 End: 32 ..ATTGCATTTTTATGCGGTTTAATCTAAAAT............................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atattttagattaaaccgcataaaaatgcaataaaatgaataaaaatacatatttttcttaaaaacacttgacaatttttatttaatttgataaattatgactacacacagaaaagatacacatactacttcaaaagaacccccgtatcctcctttcgggggttcttttctttttttgagcgaaatttaat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -10.4 Tail_Score: -5.40072 Start: 132 End: 170 Full_Region: ATACACATACTACTT CAAAAGAACCCCCGTA TCCTCCT TTCGGGGGTTCTTTTC TTTTTTTGAGCGAAA ...................................................................................................................................CAAAAGAACCCCCGTATCCTCCTTTCGGGGGTTCTTTTC..................... TransTerm Strand: + Conf: 100 HP_score: -10.3 Tail_Score: -5.55855 Start: 137 End: 165 Full_Region: CATACTACTTCAAAA GAACCCCCGTA TCCTCCT TTCGGGGGTTC TTTTCTTTTTTTGAG ........................................................................................................................................GAACCCCCGTATCCTCCTTTCGGGGGTTC.......................... Find igs database================================================ Query_seq: TDE2613:TDE2614|TDE2613:TDE2614:hypothetical protein:ApbE family protein:-><-:2655917..2656107 191 atattttagattaaaccgcataaaaatgcaataaaatgaataaaaatacatatttttcttaaaaacacttgacaatttttatttaatttgataaattatgactacacacagaaaagatacacatactacttcaaaagaacccccgtatcctcctttcgggggttcttttctttttttgagcgaaatttaat Intra-Species Hit: Count: 1 Min: 1 Max: 170 Len: 170 Subject: NC_002967_TDE2613_TDE2614|hypothetical protein:ApbE family protein|POSITIVE:NEGATIVE|[2655917,2656107]|191 HSP 1 e-value: 8.0E-92 bit: 337.0 Len: 170 Query Start:1 Query End:170 Subject Strand: POSITIVE Subject Start: 1 Subject End: 170 atattttagattaaaccgcataaaaatgcaataaaatgaataaaaatacatatttttcttaaaaacacttgacaatttttatttaatttgataaattatgactacacacagaaaagatacacatactacttcaaaagaacccccgtatcctcctttcgggggttcttttc..................... atattttagattaaaccgcataaaaatgcaataaaatgaataaaaatacatatttttcttaaaaacacttgacaatttttatttaatttgataaattatgactacacacagaaaagatacacatactacttcaaaagaacccccgtatcctcctttcgggggttcttttc..................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAUUUUAGAUUAAACCGCAUAAAAAUGCAAUAAAAUGAAUAAAAAUACAUAUUUUUCUUAAAAACACUUGACAAUUUUUAUUUAAUUUGAUAAAUUAUGACUACACACAGAAAAGAUACACAUACUACUUCAAAAGAACCCCCGUAUCCUCCUUUCGGGGGUUCUUUUC .((((((..........((((....))))..((((.(((((((((((...........................))))))))))).)))).......................)))))).............(((((((((((((...........))))))))))))). (-30.53) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAAAGAACCCCCGAAAGGAGGAUACGGGGGUUCUUUUGAAGUAGUAUGUGUAUCUUUUCUGUGUGUAGUCAUAAUUUAUCAAAUUAAAUAAAAAUUGUCAAGUGUUUUUAAGAAAAAUAUGUAUUUUUAUUCAUUUUAUUGCAUUUUUAUGCGGUUUAAUCUAAAAUAU .(((((((((((((...........)))))))))))))(((.....(((..(((.((((((.((((....))))...............(((((((........))))))))))))))))..))).....))).((..(((((((....)))))))..)).......... (-36.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 331 170 122 145 89 NC_002967:TDE2259|5end_hypothetical_protein_2297237..2297467_NEGATIVE 299 170 136 196 168 NC_002967:TDE0469|5end_hypothetical_protein_523987..524217_NEGATIVE 297 162 121 139 91 NC_002967:TDE2103|5end_glycosyl_transferase,_group_2_family_protein_2128393..2128623_NEGATIVE 291 164 132 227 193 NC_002967:TDE2705|5end_ISTde3,_transposase_2751765..2751995_NEGATIVE 279 164 125 82 36 NC_002967:TDE2690|5end_hypothetical_protein_2728898..2729128_NEGATIVE 273 170 122 139 89 NC_002967:TDE0957|5end_glycerophosphoryl_diester_phosphodiesterase_family_protein_980252..980482_POSITIVE 273 170 136 179 151 NC_002967:TDE0570|5end_hypothetical_protein_600169..600399_POSITIVE 270 169 124 112 65 NC_002967:TDE1885|5end_hypothetical_protein_1906857..1907087_POSITIVE 257 163 138 109 78 NC_002967:TDE2740|5end_type_I_restriction-modification_system,_S_subunit,_truncation_2795202..2795432_POSITIVE 257 170 128 219 184 NC_002967:TDE2260|5end_hypothetical_protein_2297338..2297568_POSITIVE 254 167 143 142 122 NC_002967:TDE1310|5end_modulator_of_DNA_gyrase_family_protein_1345962..1346192_POSITIVE 254 164 137 65 19 NC_002967:TDE0980|5end_asparaginyl-tRNA_synthetase_1005400..1005630_NEGATIVE 253 170 136 163 131 NC_002967:TDE1058|5end_hypothetical_protein_1086366..1086596_NEGATIVE 252 162 142 215 197 NC_002967:TDE1027|5end_ribonuclease_III_1057562..1057792_POSITIVE 246 167 129 97 64 NC_002967:TDE2239|5end_hypothetical_protein_2277546..2277776_NEGATIVE 246 165 136 231 199 NC_002967:TDE1152|5end_head-to-tail_joining_protein,_putative_1190209..1190439_NEGATIVE 245 159 130 102 60 NC_002967:TDE2199|5end_racemase,_Asp/Glu/Hydantoin_family_2237150..2237380_NEGATIVE 244 165 136 186 150 NC_002967:TDE2326|5end_cobyric_acid_synthase_CobQ,_putative_2361087..2361317_POSITIVE 244 170 143 195 162 NC_002967:TDE1316|5end_hypothetical_protein_1354741..1354971_POSITIVE 244 166 144 119 95 NC_002967:TDE0514|5end_hypothetical_protein_562743..562973_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 346 160 114 125 73 NC_002967:TDE0461|3end_hypothetical_protein_516125..516275_POSITIVE 315 170 132 81 42 NC_002967:TDE2706|3end_hypothetical_protein_2751916..2752066_NEGATIVE 300 170 139 74 45 NC_002967:TDE2205|3end_enoate_reductase,_putative_2242575..2242725_NEGATIVE 284 163 127 82 43 NC_002967:TDE2204|3end_Na+/H+_antiporter_family_protein_2242550..2242700_POSITIVE 274 168 140 49 15 NC_002967:TDE2028|3end_OmpA_family_protein_2057019..2057169_POSITIVE 273 170 122 137 87 NC_002967:TDE0956|3end_hypothetical_protein_980330..980480_POSITIVE 273 170 136 92 64 NC_002967:TDE0569|3end_hypothetical_protein_600162..600312_POSITIVE 272 170 129 150 117 NC_002967:TDE2527|3end_hypothetical_protein_2555449..2555599_NEGATIVE 264 167 136 43 10 NC_002967:TDE1857|3end_hypothetical_protein_1883929..1884079_NEGATIVE 254 167 143 142 122 NC_002967:TDE1309|3end_modulator_of_DNA_gyrase_family_protein_1346042..1346192_POSITIVE 254 170 121 72 4 NC_002967:TDE0210|3end_cob(I)yrinic_acid_a,c-diamide_adenosyltransferase_246146..246296_POSITIVE 251 170 129 80 41 NC_002967:TDE1893|3end_GTP-binding_protein_LepA_1912212..1912362_NEGATIVE 251 169 141 124 88 NC_002967:TDE0157|3end_KHG/KDPG_family_aldolase/carbohydrate_kinase,_PfkB_family_185711..185861_POSITIVE 250 164 125 131 85 NC_002967:TDE0711|3end_hypothetical_protein_745690..745840_NEGATIVE 244 166 144 92 68 NC_002967:TDE0515|3end_hypothetical_protein_562770..562920_NEGATIVE 241 161 148 38 25 NC_002967:TDE2695|3end_transcript_cleavage_factor/unknown_domain_fusion_protein_2736374..2736524_NEGATIVE 239 167 139 131 93 NC_002967:TDE2246|3end_hypothetical_protein_2286454..2286604_POSITIVE 239 170 143 139 105 NC_002967:TDE2086|3end_DnaJ_domain_protein_2115475..2115625_POSITIVE 235 170 130 126 86 NC_002967:TDE1930|3end_hypothetical_protein_1947432..1947582_NEGATIVE 235 164 127 132 87 NC_002967:TDE0168|3end_transcriptional_regulator,_GntR_family_196667..196817_NEGATIVE