Origin IGS: aattagtatataattacaagcgtttcgatggtgtggagttgatggaacagggtaaactacctataataaattaggcaagggaaaaaaatccctactcttcacgtaaatttaaaaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tttttaaatttacgtgaagagtagggatttttttcccttgcctaatttattataggtagtttaccctgttccatcaactccacaccatcgaaacgcttgtaattatatactaatt Mask Tandem Repeat Region ================================================ aattagtatataattacaagcgtttcgatggtgtggagttgatggaacagggtaaactacctataataaattaggcaagggaaaaaaatccctactcttcacgtaaatttaaaaa Find is-nt database================================================ Query_seq: TDE0559:TDE0560|TDE0559:TDE0560:hypothetical protein:hypothetical protein:->->:594187..594301 115 aattagtatataattacaagcgtttcgatggtgtggagttgatggaacagggtaaactacctataataaattaggcaagggaaaaaaatccctactcttcacgtaaatttaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0559:TDE0560|TDE0559:TDE0560:hypothetical protein:hypothetical protein:->->:594187..594301 115 aattagtatataattacaagcgtttcgatggtgtggagttgatggaacagggtaaactacctataataaattaggcaagggaaaaaaatccctactcttcacgtaaatttaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0559:TDE0560|TDE0559:TDE0560:hypothetical protein:hypothetical protein:->->:594187..594301 115 aattagtatataattacaagcgtttcgatggtgtggagttgatggaacagggtaaactacctataataaattaggcaagggaaaaaaatccctactcttcacgtaaatttaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aattagtatataattacaagcgtttcgatggtgtggagttgatggaacagggtaaactacctataataaattaggcaagggaaaaaaatccctactcttcacgtaaatttaaaaa Predict ORF larger than 30AA ================================================ aattagtatataattacaagcgtttcgatggtgtggagttgatggaacagggtaaactacctataataaattaggcaagggaaaaaaatccctactcttcacgtaaatttaaaaa 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: 38 End: 67 .....................................GTTGATGGAACAGGGTAAACTACCTATAAT................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aattagtatataattacaagcgtttcgatggtgtggagttgatggaacagggtaaactacctataataaattaggcaagggaaaaaaatccctactcttcacgtaaatttaaaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0559:TDE0560|TDE0559:TDE0560:hypothetical protein:hypothetical protein:->->:594187..594301 115 aattagtatataattacaagcgtttcgatggtgtggagttgatggaacagggtaaactacctataataaattaggcaagggaaaaaaatccctactcttcacgtaaatttaaaaa Intra-Species Hit: Count: 1 Min: 1 Max: 115 Len: 115 Subject: NC_002967_TDE0559_TDE0560|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[594187,594301]|115 HSP 1 e-value: 1.0E-46 bit: 186.0 Len: 115 Query Start:1 Query End:115 Subject Strand: POSITIVE Subject Start: 1 Subject End: 115 aattagtatataattacaagcgtttcgatggtgtggagttgatggaacagggtaaactacctataataaattaggcaagggnnnnnnntccctactcttcacgtaaatttaaaaa aattagtatataattacaagcgtttcgatggtgtggagttgatggaacagggtaaactacctataataaattaggcaagggaaaaaaatccctactcttcacgtaaatttaaaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUAGUAUAUAAUUACAAGCGUUUCGAUGGUGUGGAGUUGAUGGAACAGGGUAAACUACCUAUAAUAAAUUAGGCAAGGGAAAAAAAUCCCUACUCUUCACGUAAAUUUAAAAA .....(((......))).............(((.(((((..........(((((...)))))...............(((((......)))))))))).)))............. (-18.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUUAAAUUUACGUGAAGAGUAGGGAUUUUUUUCCCUUGCCUAAUUUAUUAUAGGUAGUUUACCCUGUUCCAUCAACUCCACACCAUCGAAACGCUUGUAAUUAUAUACUAAUU .............(((..((((.((((......)))).((((((........))))))..................))))..))).............................. (-17.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 287 54 19 74 29 NC_002967:TDE1167|5end_hypothetical_protein_1198938..1199168_NEGATIVE 281 58 14 48 1 NC_002967:TDE0333|5end_MATE_efflux_family_protein_371648..371878_POSITIVE 268 58 11 184 121 NC_002967:TDE0726|5end_aldehyde_oxidase_and_xanthine_dehydrogenase_family_protein_764644..764874_POSITIVE 253 84 41 214 172 NC_002967:TDE2600|5end_hypothetical_protein_2633958..2634188_POSITIVE 251 51 18 49 12 NC_002967:TDE2093|5end_hypothetical_protein_2121003..2121233_NEGATIVE 242 58 14 145 101 NC_002967:TDE2497|5end_hypothetical_protein_2522083..2522313_NEGATIVE 242 58 14 123 79 NC_002967:TDE2394|5end_hypothetical_protein_2422612..2422842_NEGATIVE 242 58 14 206 162 NC_002967:TDE1903|5end_hypothetical_protein_1922417..1922647_POSITIVE 242 52 19 50 14 NC_002967:TDE1782|5end_hypothetical_protein_1823417..1823647_NEGATIVE 242 52 19 207 171 NC_002967:TDE1781|5end_hypothetical_protein_1823260..1823490_NEGATIVE 242 58 14 66 22 NC_002967:TDE1694|5end_hypothetical_protein_1749366..1749596_NEGATIVE 242 58 14 206 162 NC_002967:TDE1693|5end_hypothetical_protein_1749226..1749456_NEGATIVE 242 58 14 204 160 NC_002967:TDE1514|5end_permease_domain_protein_1560652..1560882_POSITIVE 242 58 14 206 162 NC_002967:TDE0641|5end_UDP-N-acetylglucosamine_1-carboxyvinyltransferase_678282..678512_NEGATIVE 239 58 18 184 142 NC_002967:TDE2052|5end_aminotransferase,_class_V_2080402..2080632_POSITIVE 238 107 73 77 40 NC_002967:TDE2494|5end_hypothetical_protein_2518497..2518727_POSITIVE 238 58 13 194 138 NC_002967:TDE0400|5end_transcriptional_regulator,_LysR_family_451803..452033_NEGATIVE 237 58 14 146 101 NC_002967:TDE2224|5end_hypothetical_protein_2264743..2264973_POSITIVE 237 65 29 185 145 NC_002967:TDE2222|5end_hypothetical_protein_2263738..2263968_POSITIVE 237 54 20 170 142 NC_002967:TDE0995|5end_hypothetical_protein_1022576..1022806_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 287 54 19 63 18 NC_002967:TDE1168|3end_hypothetical_protein_1198949..1199099_NEGATIVE 254 52 18 150 113 NC_002967:TDE2504|3end_O-sialoglycoprotein_endopeptidase_2530097..2530247_POSITIVE 239 53 12 57 16 NC_002967:TDE2179|3end_voltage-gated_chloride_channel_2210614..2210764_POSITIVE 237 58 14 149 104 NC_002967:TDE2223|3end_hypothetical_protein_2264826..2264976_POSITIVE 237 58 14 149 104 NC_002967:TDE2094|3end_hypothetical_protein_2121077..2121227_NEGATIVE 237 58 15 70 23 NC_002967:TDE1988|3end_hypothetical_protein_2005590..2005740_POSITIVE 235 62 23 58 7 NC_002967:TDE2553|3end_lysyl-tRNA_synthetase_2579047..2579197_NEGATIVE 231 53 18 83 38 NC_002967:TDE1239|3end_hypothetical_protein_1271217..1271367_NEGATIVE 230 52 17 72 25 NC_002967:TDE0536|3end_hypothetical_protein_578064..578214_NEGATIVE 228 51 18 70 41 NC_002967:TDE2219|3end_hypothetical_protein_2258961..2259111_NEGATIVE 224 67 21 91 32 NC_002967:TDE0814|3end_transcriptional_regulator,_putative_835709..835859_NEGATIVE 222 52 19 41 6 NC_002967:TDE0696|3end_hypothetical_protein_734210..734360_POSITIVE 216 53 14 64 20 NC_002967:TDE2231|3end_internalin-related_protein_2270539..2270689_POSITIVE 213 96 56 92 46 NC_002967:TDE2638|3end_hypothetical_protein_2678199..2678349_POSITIVE 212 45 18 83 52 NC_002967:TDE0740|3end_hypothetical_protein_776204..776354_POSITIVE 211 41 11 148 117 NC_002967:TDE0725|3end_exopolysaccharide_biosynthesis_protein_764720..764870_POSITIVE 210 78 31 87 40 NC_002967:TDE1693|3end_hypothetical_protein_1748438..1748588_NEGATIVE 210 52 19 124 93 NC_002967:TDE1193|3end_hypothetical_protein_1219526..1219676_NEGATIVE 210 80 33 65 1 NC_002967:TDE0837|3end_Na(+)-translocating_NADH-quinone_reductase,_B_subunit_856093..856243_NEGATIVE 210 52 19 124 93 NC_002967:TDE0579|3end_hypothetical_protein_609898..610048_NEGATIVE