Origin IGS: attattttggcataaagtattgttccggtgtaaagacttgaattcttgccgatttaaaatcgcctaaatttcttgatggtgctttcatacttgttttttttctttttttgctatattattaagctatgatttttgactaaaatcggcggcttttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaaaagccgccgattttagtcaaaaatcatagcttaataatatagcaaaaaaagaaaaaaaacaagtatgaaagcaccatcaagaaatttaggcgattttaaatcggcaagaattcaagtctttacaccggaacaatactttatgccaaaataat Mask Tandem Repeat Region ================================================ attattttggcataaagtattgttccggtgtaaagacttgaattcttgccgatttaaaatcgcctaaatttcttgatggtgctttcatacttgttttttttctttttttgctatattattaagctatgatttttgactaaaatcggcggcttttt Find is-nt database================================================ Query_seq: TDE0889:TDE0890|TDE0889:TDE0890:hypothetical protein:hypothetical protein:->->:905875..906029 155 attattttggcataaagtattgttccggtgtaaagacttgaattcttgccgatttaaaatcgcctaaatttcttgatggtgctttcatacttgttttttttctttttttgctatattattaagctatgatttttgactaaaatcggcggcttttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0889:TDE0890|TDE0889:TDE0890:hypothetical protein:hypothetical protein:->->:905875..906029 155 attattttggcataaagtattgttccggtgtaaagacttgaattcttgccgatttaaaatcgcctaaatttcttgatggtgctttcatacttgttttttttctttttttgctatattattaagctatgatttttgactaaaatcggcggcttttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0889:TDE0890|TDE0889:TDE0890:hypothetical protein:hypothetical protein:->->:905875..906029 155 attattttggcataaagtattgttccggtgtaaagacttgaattcttgccgatttaaaatcgcctaaatttcttgatggtgctttcatacttgttttttttctttttttgctatattattaagctatgatttttgactaaaatcggcggcttttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 attattttggcataaagtattgttccggtgtaaagacttgaattcttgccgatttaaaatcgcctaaatttcttgatggtgctttcatacttgttttttttctttttttgctatattattaagctatgatttttgactaaaatcggcggcttttt Predict ORF larger than 30AA ================================================ attattttggcataaagtattgttccggtgtaaagacttgaattcttgccgatttaaaatcgcctaaatttcttgatggtgctttcatacttgttttttttctttttttgctatattattaagctatgatttttgactaaaatcggcggcttttt 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: 82 Start: 90 End: 119 .........................................................................................CTTGTTTTTTTTCTTTTTTTGCTATATTAT.................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ attattttggcataaagtattgttccggtgtaaagacttgaattcttgccgatttaaaatcgcctaaatttcttgatggtgctttcatacttgttttttttctttttttgctatattattaagctatgatttttgactaaaatcggcggcttttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0889:TDE0890|TDE0889:TDE0890:hypothetical protein:hypothetical protein:->->:905875..906029 155 attattttggcataaagtattgttccggtgtaaagacttgaattcttgccgatttaaaatcgcctaaatttcttgatggtgctttcatacttgttttttttctttttttgctatattattaagctatgatttttgactaaaatcggcggcttttt Intra-Species Hit: Count: 1 Min: 1 Max: 155 Len: 155 Subject: NC_002967_TDE0889_TDE0890|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[905875,906029]|155 HSP 1 e-value: 6.0E-46 bit: 184.0 Len: 93 Query Start:1 Query End:93 Subject Strand: POSITIVE Subject Start: 1 Subject End: 93 attattttggcataaagtattgttccggtgtaaagacttgaattcttgccgatttaaaatcgcctaaatttcttgatggtgctttcatacttg.............................................................. attattttggcataaagtattgttccggtgtaaagacttgaattcttgccgatttaaaatcgcctaaatttcttgatggtgctttcatacttg.............................................................. HSP 2 e-value: 6.0E-18 bit: 91.7 Len: 46 Query Start:110 Query End:155 Subject Strand: POSITIVE Subject Start: 110 Subject End: 155 .............................................................................................................gctatattattaagctatgatttttgactaaaatcggcggcttttt .............................................................................................................gctatattattaagctatgatttttgactaaaatcggcggcttttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUAUUUUGGCAUAAAGUAUUGUUCCGGUGUAAAGACUUGAAUUCUUGCCGAUUUAAAAUCGCCUAAAUUUCUUGAUGGUGCUUUCAUACUUGUUUUUUUUCUUUUUUUGCUAUAUUAUUAAGCUAUGAUUUUUGACUAAAAUCGGCGGCUUUUU .......(((((.((((.......(.((((((((((((.(((.....(.((((.....)))).).....))).....))).)))).))))).)........))))...))))).......(((((.(((((((.....)))))))..)))))... (-25.36) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAAGCCGCCGAUUUUAGUCAAAAAUCAUAGCUUAAUAAUAUAGCAAAAAAAGAAAAAAAACAAGUAUGAAAGCACCAUCAAGAAAUUUAGGCGAUUUUAAAUCGGCAAGAAUUCAAGUCUUUACACCGGAACAAUACUUUAUGCCAAAAUAAU ..((((..((((((((.((((..........(((.........)))......................(((........)))............))))..)))))))).....(((..((......))..))).....))))............. (-18.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 322 129 83 93 47 NC_002967:TDE0950|5end_hypothetical_protein_974312..974542_NEGATIVE 285 64 22 159 127 NC_002967:TDE2493|5end_hypothetical_protein_2518364..2518594_NEGATIVE 274 100 60 133 101 NC_002967:TDE1947|5end_ABC_transporter,_permease_protein_1963449..1963679_NEGATIVE 268 65 26 184 146 NC_002967:TDE1236|5end_triosephosphate_isomerase_1269486..1269716_POSITIVE 268 65 26 74 36 NC_002967:TDE1235|5end_hypothetical_protein_1269376..1269606_POSITIVE 265 68 21 44 8 NC_002967:TDE1052|5end_rubredoxin_1078870..1079100_NEGATIVE 254 63 23 136 103 NC_002967:TDE0877|5end_hypothetical_protein_898589..898819_POSITIVE 249 65 25 152 106 NC_002967:TDE1655|5end_hypothetical_protein_1704958..1705188_POSITIVE 244 59 17 112 72 NC_002967:TDE0886|5end_hypothetical_protein_903341..903571_POSITIVE 243 65 26 134 96 NC_002967:TDE1334|5end_hypothetical_protein_1370144..1370374_POSITIVE 239 60 11 72 31 NC_002967:TDE2634|5end_hypothetical_protein_2674625..2674855_POSITIVE 238 63 21 153 117 NC_002967:TDE0546|5end_hypothetical_protein_584909..585139_POSITIVE 237 77 31 181 131 NC_002967:TDE2275|5end_tRNA_pseudouridine_synthase_A_2311076..2311306_POSITIVE 235 85 41 178 119 NC_002967:TDE1325|5end_hypothetical_protein_1361721..1361951_NEGATIVE 234 57 20 228 190 NC_002967:TDE2250|5end_hypothetical_protein_2288568..2288798_POSITIVE 234 52 16 208 178 NC_002967:TDE0350|5end_MATE_efflux_family_protein_393572..393802_POSITIVE 232 88 45 78 33 NC_002967:TDE2131|5end_cobalamin_biosynthesis_protein_CbiM,_putative_2162683..2162913_NEGATIVE 231 83 43 59 12 NC_002967:TDE0186|5end_hypothetical_protein_223698..223928_NEGATIVE 230 49 16 197 159 NC_002967:TDE1991|5end_hypothetical_protein_2009398..2009628_NEGATIVE 230 114 71 144 103 NC_002967:TDE1517|5end_hypothetical_protein_1563816..1564046_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 622 53 12 151 110 NC_002967:TDE0887|3end_PIN_domain_protein_904333..904483_NEGATIVE 280 68 26 87 43 NC_002967:TDE1916|3end_glycerol_kinase_1933277..1933427_NEGATIVE 274 100 60 128 96 NC_002967:TDE1948|3end_ABC_transporter,_permease_protein_1963454..1963604_NEGATIVE 269 90 46 143 99 NC_002967:TDE0496|3end_DNA-binding_protein,_putative_550971..551121_NEGATIVE 253 82 45 49 15 NC_002967:TDE2646|3end_ABC_transporter,_ATP-binding_protein,_putative_2686030..2686180_POSITIVE 251 65 26 91 50 NC_002967:TDE0743|3end_thioredoxin_reductase_779751..779901_POSITIVE 244 59 17 75 35 NC_002967:TDE0885|3end_50S_ribosomal_protein_L19_903384..903534_POSITIVE 243 65 26 58 20 NC_002967:TDE1333|3end_hflC_protein,_putative_1370148..1370298_POSITIVE 239 60 11 69 28 NC_002967:TDE2633|3end_hypothetical_protein_2674702..2674852_POSITIVE 238 63 21 134 98 NC_002967:TDE0545|3end_hypothetical_protein_584970..585120_POSITIVE 237 66 26 71 29 NC_002967:TDE2396|3end_putative_inner_membrane_protein_translocase_component_YidC_2423650..2423800_NEGATIVE 236 65 23 122 84 NC_002967:TDE1403|3end_ABC_transporter,_ATP-binding_protein_1444500..1444650_NEGATIVE 235 85 41 110 51 NC_002967:TDE1327|3end_hypothetical_protein_1361789..1361939_NEGATIVE 234 65 22 60 17 NC_002967:TDE2312|3end_hypothetical_protein_2349049..2349199_POSITIVE 230 114 71 147 106 NC_002967:TDE1516|3end_ABC_transporter,_ATP-binding_protein,_putative_1563899..1564049_POSITIVE 230 128 81 68 20 NC_002967:TDE0789|3end_30S_ribosomal_protein_S13_817007..817157_POSITIVE 228 114 72 142 105 NC_002967:TDE1252|3end_lipoprotein,_putative_1287094..1287244_POSITIVE 227 42 5 65 34 NC_002967:TDE1961|3end_PIN_domain_protein_1974550..1974700_NEGATIVE 226 108 62 121 70 NC_002967:TDE1883|3end_hypothetical_protein_1904910..1905060_NEGATIVE 224 64 22 58 20 NC_002967:TDE1770|3end_hypothetical_protein_1814468..1814618_POSITIVE