Origin IGS: aaattttacattttacgcaataatgatgattaaattcaaattcgattcaaagataagcgatgtttcggaagccggcaagaaatttcgtcattactcgttttttttagcaataaataggtcgcatctcaaaaaaaacagtacttttgt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 acaaaagtactgttttttttgagatgcgacctatttattgctaaaaaaaacgagtaatgacgaaatttcttgccggcttccgaaacatcgcttatctttgaatcgaatttgaatttaatcatcattattgcgtaaaatgtaaaattt Mask Tandem Repeat Region ================================================ aaattttacattttacgcaataatgatgattaaattcaaattcgattcaaagataagcgatgtttcggaagccggcaagaaatttcgtcattactcgttttttttagcaataaataggtcgcatctcaaaaaaaacagtacttttgt Find is-nt database================================================ Query_seq: TF2733:TF2734|TF2733:TF2734:DNA polymerase III, alpha subunit:conserved hypothetical protein:->->:2916034..2916180 147 aaattttacattttacgcaataatgatgattaaattcaaattcgattcaaagataagcgatgtttcggaagccggcaagaaatttcgtcattactcgttttttttagcaataaataggtcgcatctcaaaaaaaacagtacttttgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2733:TF2734|TF2733:TF2734:DNA polymerase III, alpha subunit:conserved hypothetical protein:->->:2916034..2916180 147 aaattttacattttacgcaataatgatgattaaattcaaattcgattcaaagataagcgatgtttcggaagccggcaagaaatttcgtcattactcgttttttttagcaataaataggtcgcatctcaaaaaaaacagtacttttgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2733:TF2734|TF2733:TF2734:DNA polymerase III, alpha subunit:conserved hypothetical protein:->->:2916034..2916180 147 aaattttacattttacgcaataatgatgattaaattcaaattcgattcaaagataagcgatgtttcggaagccggcaagaaatttcgtcattactcgttttttttagcaataaataggtcgcatctcaaaaaaaacagtacttttgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaattttacattttacgcaataatgatgattaaattcaaattcgattcaaagataagcgatgtttcggaagccggcaagaaatttcgtcattactcgttttttttagcaataaataggtcgcatctcaaaaaaaacagtacttttgt Predict ORF larger than 30AA ================================================ Protein_Len: 42 Strand: + Start: 20 End: 145 ................... M M M I K F K F D S K I S D V S E A G K K F R H Y S F F L A I N R S H L K K N S T F .. aaattttacattttacgcaataatgatgattaaattcaaattcgattcaaagataagcgatgtttcggaagccggcaagaaatttcgtcattactcgttttttttagcaataaataggtcgcatctcaaaaaaaacagtacttttgt 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: 50 End: 79 .................................................CTTGCCGGCTTCCGAAACATCGCTTATCTT.................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaattttacattttacgcaataatgatgattaaattcaaattcgattcaaagataagcgatgtttcggaagccggcaagaaatttcgtcattactcgttttttttagcaataaataggtcgcatctcaaaaaaaacagtacttttgt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF2733:TF2734|TF2733:TF2734:DNA polymerase III, alpha subunit:conserved hypothetical protein:->->:2916034..2916180 147 aaattttacattttacgcaataatgatgattaaattcaaattcgattcaaagataagcgatgtttcggaagccggcaagaaatttcgtcattactcgttttttttagcaataaataggtcgcatctcaaaaaaaacagtacttttgt Intra-Species Hit: Count: 1 Min: 1 Max: 127 Len: 127 Subject: tfor_TF2733_TF2734|DNA polymerase III, alpha subunit:conserved hypothetical protein|POSITIVE:POSITIVE|[2916034,2916180]|147 HSP 1 e-value: 6.0E-52 bit: 204.0 Len: 127 Query Start:1 Query End:127 Subject Strand: POSITIVE Subject Start: 1 Subject End: 127 aaattttacattttacgcaataatgatgattaaattcaaattcgattcaaagataagcgatgtttcggaagccggcaagaaatttcgtcattactcgnnnnnnnnagcaataaataggtcgcatctc.................... aaattttacattttacgcaataatgatgattaaattcaaattcgattcaaagataagcgatgtttcggaagccggcaagaaatttcgtcattactcgttttttttagcaataaataggtcgcatctc.................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUUUUACAUUUUACGCAAUAAUGAUGAUUAAAUUCAAAUUCGAUUCAAAGAUAAGCGAUGUUUCGGAAGCCGGCAAGAAAUUUCGUCAUUACUCGUUUUUUUUAGCAAUAAAUAGGUCGCAUCUC ................((..(((((((((.....(((....(((.(((..(((((.....)))))..)))..)))...)))...)))))))))...(((......)))............))..... (-16.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAGAUGCGACCUAUUUAUUGCUAAAAAAAACGAGUAAUGACGAAAUUUCUUGCCGGCUUCCGAAACAUCGCUUAUCUUUGAAUCGAAUUUGAAUUUAAUCAUCAUUAUUGCGUAAAAUGUAAAAUUU (((((((((.....((((((((..........)))))))).............(((...))).....))))..))))).............................((((((...))))))..... (-14.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 360 100 57 52 10 tfor:TF1658|5end_glycosyltranferase_1773539..1773769_POSITIVE 347 97 52 65 17 tfor:TF0797|5end_conserved_hypothetical_protein_853296..853526_POSITIVE 325 98 52 207 156 tfor:TF0233|5end_DNA_polymerase_III_gamma/tau_subunit_259355..259585_POSITIVE 307 88 41 119 73 tfor:TF0253|5end_conserved_hypothetical_protein_283707..283937_POSITIVE 300 91 59 147 111 tfor:TF2154|5end_conserved_hypothetical_protein_2329153..2329383_POSITIVE 298 77 39 62 18 tfor:TF1670|5end_ATP_synthase,_alpha_subunit_1784455..1784685_POSITIVE 297 90 41 213 156 tfor:TF0890|5end_transfer_region-related_protein,_TraQ_940014..940244_POSITIVE 295 100 52 222 171 tfor:TF1048|5end_permease_1109241..1109471_POSITIVE 294 90 57 188 159 tfor:TF1918|5end_hypothetical_protein_2069864..2070094_POSITIVE 292 100 57 157 97 tfor:TF2842|5end_methyltransferase_3032094..3032324_POSITIVE 292 100 57 171 126 tfor:TF2455|5end_conserved_hypothetical_protein;_possible_membrane_protein_2631959..2632189_POSITIVE 291 87 41 96 43 tfor:TF2806|5end_conserved_hypothetical_protein_2994475..2994705_POSITIVE 289 87 41 163 112 tfor:TF1885|5end_conserved_hypothetical_protein_2037307..2037537_POSITIVE 288 98 58 51 9 tfor:TF0364|5end_ysyl_endopeptidase_380395..380625_POSITIVE 287 99 58 153 108 tfor:TF2848|5end_cobalamin_biosynthesis_protein_3036368..3036598_POSITIVE 286 98 51 220 172 tfor:TF0608|5end_isoleucyl-tRNA_synthetase_637889..638119_POSITIVE 285 89 41 190 143 tfor:TF0951|5end_D-alanine--D-alanine_ligase_995718..995948_POSITIVE 284 96 52 97 56 tfor:TF1866|5end_conserved_hypothetical_protein;_possible_transposase_2022272..2022502_POSITIVE 283 89 57 205 171 tfor:TF2886|5end_RNA_methylase_SpoU_family_3075651..3075881_POSITIVE 283 97 58 218 167 tfor:TF1764|5end_transcriptional_regulator;_possible_MerR_family_1901409..1901639_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 307 88 41 91 45 tfor:TF0252|3end_hypothetical_protein_283759..283909_POSITIVE 300 91 59 86 50 tfor:TF2153|3end_6-phosphofructokinase_2329172..2329322_POSITIVE 292 100 57 139 79 tfor:TF2841|3end_conserved_hypothetical_protein_3032156..3032306_POSITIVE 286 98 51 149 101 tfor:TF0607|3end_DnaK_suppressor_protein_637898..638048_POSITIVE 284 96 52 151 110 tfor:TF1865|3end_conserved_hypothetical_protein;_possible_transposase_2022406..2022556_POSITIVE 282 96 58 140 107 tfor:TF0120|3end_hexouronate_transporter_132811..132961_POSITIVE 279 89 41 68 26 tfor:TF1794|3end_possible_glucose-1-phosphatase_1935816..1935966_POSITIVE 278 79 57 59 36 tfor:TF1889|3end_hypothetical_protein_2042125..2042275_POSITIVE 276 96 57 53 3 tfor:TF2770|3end_conserved_hypothetical_protein_2956639..2956789_POSITIVE 275 98 57 48 3 tfor:TF1669|3end_ATP_synthase,_gamma_subunit_1784503..1784653_POSITIVE 274 87 41 63 19 tfor:TF0746|3end_possible_DNA_polymerase_III_792910..793060_POSITIVE 271 90 41 143 83 tfor:TF0299|3end_hypothetical_protein_325365..325515_POSITIVE 269 98 58 150 108 tfor:TF0350|3end_hypothetical_protein_371101..371251_POSITIVE 266 100 57 54 2 tfor:TF1888|3end_RNA_polymerase_ECF-type_sigma_factor_2041559..2041709_POSITIVE 263 100 51 65 1 tfor:TF2800|3end_anti-sigma_factor_2986346..2986496_POSITIVE 262 77 57 52 28 tfor:TF3138|3end_Na+-translocating_quinone_reductase,_subunit_D_3372654..3372804_POSITIVE 261 97 58 50 12 tfor:TF3135|3end_hypothetical_protein_3370074..3370224_POSITIVE 261 89 55 57 20 tfor:TF2036|3end_possible_pyruvate_formate-lyase_activating_enzyme_2196837..2196987_POSITIVE 259 97 58 94 61 tfor:TF2392|3end_alpha-galactosidase_2565506..2565656_POSITIVE 259 87 43 46 7 tfor:TF1000|3end_sec-independent_protein_translocase_1054169..1054319_POSITIVE