Origin IGS: aaaaattccttgtattgaggggagagtataacagtttttaagaaaaatgtataccgcttaaaaaatgtacagagaggtacattttttaagcttcaagttttgcctcacggcaaaacgtcgctagcgtgaaaccaccggcagccaaaaaacaaagctatttttcgctcaagagttcttctacaaggtagtcatcactcatacagtgcatatccgaaattcctttgct .........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 agcaaaggaatttcggatatgcactgtatgagtgatgactaccttgtagaagaactcttgagcgaaaaatagctttgttttttggctgccggtggtttcacgctagcgacgttttgccgtgaggcaaaacttgaagcttaaaaaatgtacctctctgtacattttttaagcggtatacatttttcttaaaaactgttatactctcccctcaatacaaggaattttt Mask Tandem Repeat Region ================================================ aaaaattccttgtattgaggggagagtataacagtttttaagaaaaatgtataccgcttaaaaaatgtacagagaggtacattttttaagcttcaagttttgcctcacggcaaaacgtcgctagcgtgaaaccaccggcagccaaaaaacaaagctatttttcgctcaagagttcttctacaaggtagtcatcactcatacagtgcatatccgaaattcctttgct Find is-nt database================================================ Query_seq: TDE2489:TDE2490|TDE2489:TDE2490:peptide chain release factor 1:primosomal protein N':<-<-:2512567..2512792 226 aaaaattccttgtattgaggggagagtataacagtttttaagaaaaatgtataccgcttaaaaaatgtacagagaggtacattttttaagcttcaagttttgcctcacggcaaaacgtcgctagcgtgaaaccaccggcagccaaaaaacaaagctatttttcgctcaagagttcttctacaaggtagtcatcactcatacagtgcatatccgaaattcctttgct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2489:TDE2490|TDE2489:TDE2490:peptide chain release factor 1:primosomal protein N':<-<-:2512567..2512792 226 aaaaattccttgtattgaggggagagtataacagtttttaagaaaaatgtataccgcttaaaaaatgtacagagaggtacattttttaagcttcaagttttgcctcacggcaaaacgtcgctagcgtgaaaccaccggcagccaaaaaacaaagctatttttcgctcaagagttcttctacaaggtagtcatcactcatacagtgcatatccgaaattcctttgct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2489:TDE2490|TDE2489:TDE2490:peptide chain release factor 1:primosomal protein N':<-<-:2512567..2512792 226 aaaaattccttgtattgaggggagagtataacagtttttaagaaaaatgtataccgcttaaaaaatgtacagagaggtacattttttaagcttcaagttttgcctcacggcaaaacgtcgctagcgtgaaaccaccggcagccaaaaaacaaagctatttttcgctcaagagttcttctacaaggtagtcatcactcatacagtgcatatccgaaattcctttgct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaaattccttgtattgaggggagagtataacagtttttaagaaaaatgtataccgcttaaaaaatgtacagagaggtacattttttaagcttcaagttttgcctcacggcaaaacgtcgctagcgtgaaaccaccggcagccaaaaaacaaagctatttttcgctcaagagttcttctacaaggtagtcatcactcatacagtgcatatccgaaattcctttgct Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 28 End: 126 ........................... M T V F K K N V Y R L K N V Q R G T F F K L Q V L P H G K T S L A .................................................................................................... aaaaattccttgtattgaggggagagtataacagtttttaagaaaaatgtataccgcttaaaaaatgtacagagaggtacattttttaagcttcaagttttgcctcacggcaaaacgtcgctagcgtgaaaccaccggcagccaaaaaacaaagctatttttcgctcaagagttcttctacaaggtagtcatcactcatacagtgcatatccgaaattcctttgct 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: 25 End: 54 ........................GTATACATTTTTCTTAAAAACTGTTATACT............................................................................................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaaaattccttgtattgaggggagagtataacagtttttaagaaaaatgtataccgcttaaaaaatgtacagagaggtacattttttaagcttcaagttttgcctcacggcaaaacgtcgctagcgtgaaaccaccggcagccaaaaaacaaagctatttttcgctcaagagttcttctacaaggtagtcatcactcatacagtgcatatccgaaattcctttgct Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 64 HP_score: -7.7 Tail_Score: -2.92714 Start: 52 End: 95 Full_Region: ccgtgaggcaaaact tgaagcttaaaaaatgtac ctctct gtacattttttaagcggta tacatttttcttaaa ...................................................tgaagcttaaaaaatgtacctctctgtacattttttaagcggta................................................................................................................................... TransTerm Strand: + Conf: 71 HP_score: -3.3 Tail_Score: -5.09426 Start: 66 End: 81 Full_Region: ATACCGCTTAAAAAA TGTAC AGAGAG GTACA TTTTTTAAGCTTCAA .................................................................TGTACAGAGAGGTACA................................................................................................................................................. TransTerm Strand: - Conf: 71 HP_score: -3.3 Tail_Score: -5.02476 Start: 66 End: 81 Full_Region: ttgaagcttaaaaaa tgtac ctctct gtaca ttttttaagcggtat .................................................................tgtacctctctgtaca................................................................................................................................................. Find igs database================================================ Query_seq: TDE2489:TDE2490|TDE2489:TDE2490:peptide chain release factor 1:primosomal protein N':<-<-:2512567..2512792 226 aaaaattccttgtattgaggggagagtataacagtttttaagaaaaatgtataccgcttaaaaaatgtacagagaggtacattttttaagcttcaagttttgcctcacggcaaaacgtcgctagcgtgaaaccaccggcagccaaaaaacaaagctatttttcgctcaagagttcttctacaaggtagtcatcactcatacagtgcatatccgaaattcctttgct Intra-Species Hit: Count: 1 Min: 1 Max: 226 Len: 226 Subject: NC_002967_TDE2489_TDE2490|peptide chain release factor 1:primosomal protein N'|NEGATIVE:NEGATIVE|[2512567,2512792]|226 HSP 1 e-value: 1.0E-125 bit: 448.0 Len: 226 Query Start:1 Query End:226 Subject Strand: POSITIVE Subject Start: 1 Subject End: 226 aaaaattccttgtattgaggggagagtataacagtttttaagaaaaatgtataccgcttaaaaaatgtacagagaggtacattttttaagcttcaagttttgcctcacggcaaaacgtcgctagcgtgaaaccaccggcagccaaaaaacaaagctatttttcgctcaagagttcttctacaaggtagtcatcactcatacagtgcatatccgaaattcctttgct aaaaattccttgtattgaggggagagtataacagtttttaagaaaaatgtataccgcttaaaaaatgtacagagaggtacattttttaagcttcaagttttgcctcacggcaaaacgtcgctagcgtgaaaccaccggcagccaaaaaacaaagctatttttcgctcaagagttcttctacaaggtagtcatcactcatacagtgcatatccgaaattcctttgct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAAUUCCUUGUAUUGAGGGGAGAGUAUAACAGUUUUUAAGAAAAAUGUAUACCGCUUAAAAAAUGUACAGAGAGGUACAUUUUUUAAGCUUCAAGUUUUGCCUCACGGCAAAACGUCGCUAGCGUGAAACCACCGGCAGCCAAAAAACAAAGCUAUUUUUCGCUCAAGAGUUCUUCUACAAGGUAGUCAUCACUCAUACAGUGCAUAUCCGAAAUUCCUUUGCU .......((((((((((((.((((((((.....((((((................(((((((((((((((......))))))))))))))).....((((((((....))))))))...(((.(((((....)))..)))))..)))))).....)))))))).))))).........))))))).......((((.....))))..................... (-59.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCAAAGGAAUUUCGGAUAUGCACUGUAUGAGUGAUGACUACCUUGUAGAAGAACUCUUGAGCGAAAAAUAGCUUUGUUUUUUGGCUGCCGGUGGUUUCACGCUAGCGACGUUUUGCCGUGAGGCAAAACUUGAAGCUUAAAAAAUGUACCUCUCUGUACAUUUUUUAAGCGGUAUACAUUUUUCUUAAAAACUGUUAUACUCUCCCCUCAAUACAAGGAAUUUUU .....(((((((((..........(((....((((.(((((((..((.(((((((....((((........)))).))))))).))....)))))))))))....)))..((((((((....)))))))).(((.(((((((((((((((......))))))))))))))).(((((((.((((....)))).)).))))).......)))......))))))))) (-66.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1024 140 91 231 182 NC_002967:TDE2489|5end_peptide_chain_release_factor_1_2512476..2512706_NEGATIVE 364 140 92 50 1 NC_002967:TDE2100|5end_hypothetical_protein_2125370..2125600_POSITIVE 360 142 101 55 16 NC_002967:TDE2007|5end_ABC_transporter,_ATP-binding/permease_protein_2026819..2027049_POSITIVE 358 167 123 100 49 NC_002967:TDE1260|5end_cholinephosphate_cytidylyltransferase/choline_kinase_1294028..1294258_POSITIVE 357 143 101 194 155 NC_002967:TDE2268|5end_hypothetical_protein_2304959..2305189_NEGATIVE 339 145 101 221 175 NC_002967:TDE0555|5end_hypothetical_protein_591522..591752_NEGATIVE 338 100 52 231 184 NC_002967:TDE1933|5end_hypothetical_protein_1952611..1952841_NEGATIVE 333 142 109 49 8 NC_002967:TDE0665|5end_pyruvate_ferredoxin/flavodoxin_oxidoreductase_family_protein_703352..703582_NEGATIVE 326 145 101 80 38 NC_002967:TDE0946|5end_hypothetical_protein_968212..968442_POSITIVE 323 100 54 199 155 NC_002967:TDE2549|5end_methyl-accepting_chemotaxis_protein_2573285..2573515_POSITIVE 318 126 86 228 189 NC_002967:TDE2042|5end_hypothetical_protein_2072179..2072409_NEGATIVE 314 139 91 192 141 NC_002967:TDE1689|5end_ABC_transporter,_ATP-binding_protein_1746565..1746795_NEGATIVE 309 167 121 231 179 NC_002967:TDE1143|5end_hypothetical_protein_1181834..1182064_NEGATIVE 308 143 101 225 186 NC_002967:TDE0573|5end_hypothetical_protein_604681..604911_POSITIVE 308 144 103 175 137 NC_002967:TDE0180|5end_hypothetical_protein_213018..213248_NEGATIVE 307 200 151 131 66 NC_002967:TDE2058|5end_hypothetical_protein_2086172..2086402_NEGATIVE 304 147 103 51 18 NC_002967:TDE2234|5end_iron_compound_ABC_transporter,_periplasmic_iron_compound-binding_protein,_putative_2273245..2273475_NEGATIVE 303 139 91 171 118 NC_002967:TDE2632|5end_peptide_ABC_transporter,_ATP-binding_protein,_putative_2672650..2672880_POSITIVE 302 120 72 93 34 NC_002967:TDE2005|5end_hypothetical_protein_2023776..2024006_POSITIVE 301 180 132 47 3 NC_002967:TDE0537|5end_hypothetical_protein_579024..579254_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 367 98 54 129 87 NC_002967:TDE2100|3end_hypothetical_protein_2125572..2125722_POSITIVE 340 145 101 108 66 NC_002967:TDE2515|3end_hypothetical_protein_2540972..2541122_NEGATIVE 335 143 102 117 88 NC_002967:TDE0833|3end_lipoprotein,_putative_854097..854247_POSITIVE 326 139 91 75 34 NC_002967:TDE2312|3end_hypothetical_protein_2349049..2349199_POSITIVE 326 145 101 108 66 NC_002967:TDE0945|3end_hypothetical_protein_968320..968470_POSITIVE 303 148 107 62 14 NC_002967:TDE1593|3end_Fe-hydrogenase_1641209..1641359_NEGATIVE 302 120 72 82 23 NC_002967:TDE2004|3end_hypothetical_protein_2023845..2023995_POSITIVE 300 143 108 141 111 NC_002967:TDE2057|3end_hypothetical_protein_2085158..2085308_NEGATIVE 298 120 71 106 43 NC_002967:TDE2272|3end_hypothetical_protein_2308980..2309130_NEGATIVE 293 121 96 28 5 NC_002967:TDE2393|3end_hypothetical_protein_2422588..2422738_POSITIVE 293 121 96 89 66 NC_002967:TDE1902|3end_hypothetical_protein_1922377..1922527_NEGATIVE 292 140 93 78 25 NC_002967:TDE0689|3end_5-methylthioribose_kinase_726972..727122_POSITIVE 289 140 94 82 34 NC_002967:TDE1770|3end_hypothetical_protein_1814468..1814618_POSITIVE 287 141 102 87 59 NC_002967:TDE1533|3end_hypothetical_protein_1578657..1578807_POSITIVE 286 139 100 48 12 NC_002967:TDE1855|3end_hypothetical_protein_1883213..1883363_POSITIVE 281 100 54 99 55 NC_002967:TDE2238|3end_hypothetical_protein_2276545..2276695_POSITIVE 276 138 97 47 5 NC_002967:TDE1934|3end_hypothetical_protein_1952804..1952954_POSITIVE 276 139 91 143 96 NC_002967:TDE1736|3end_ferredoxin,_2(4Fe-4S)_1790158..1790308_POSITIVE 275 102 61 137 98 NC_002967:TDE1924|3end_hypothetical_protein_1941674..1941824_NEGATIVE 275 145 103 119 53 NC_002967:TDE0977|3end_hypothetical_protein_1001640..1001790_POSITIVE