Origin IGS: taaagcttctttcctgcaccaattaaaatgatttaagggaatgagaaaataaaacctcattccctttttctatgctatttcatttcatatctttgcgctatcaaaagaaca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgttcttttgatagcgcaaagatatgaaatgaaatagcatagaaaaagggaatgaggttttattttctcattcccttaaatcattttaattggtgcaggaaagaagcttta Mask Tandem Repeat Region ================================================ taaagcttctttcctgcaccaattaaaatgatttaagggaatgagaaaataaaacctcattccctttttctatgctatttcatttcatatctttgcgctatcaaaagaaca Find is-nt database================================================ Query_seq: TF1700:TF1701|TF1700:TF1701:conserved hypothetical protein:transcriptional regulator:->->:1821522..1821632 111 taaagcttctttcctgcaccaattaaaatgatttaagggaatgagaaaataaaacctcattccctttttctatgctatttcatttcatatctttgcgctatcaaaagaaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1700:TF1701|TF1700:TF1701:conserved hypothetical protein:transcriptional regulator:->->:1821522..1821632 111 taaagcttctttcctgcaccaattaaaatgatttaagggaatgagaaaataaaacctcattccctttttctatgctatttcatttcatatctttgcgctatcaaaagaaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1700:TF1701|TF1700:TF1701:conserved hypothetical protein:transcriptional regulator:->->:1821522..1821632 111 taaagcttctttcctgcaccaattaaaatgatttaagggaatgagaaaataaaacctcattccctttttctatgctatttcatttcatatctttgcgctatcaaaagaaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaagcttctttcctgcaccaattaaaatgatttaagggaatgagaaaataaaacctcattccctttttctatgctatttcatttcatatctttgcgctatcaaaagaaca Predict ORF larger than 30AA ================================================ taaagcttctttcctgcaccaattaaaatgatttaagggaatgagaaaataaaacctcattccctttttctatgctatttcatttcatatctttgcgctatcaaaagaaca Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taaagcttctttcctgcaccaattaaaatgatttaagggaatgagaaaataaaacctcattccctttttctatgctatttcatttcatatctttgcgctatcaaaagaaca Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 86 HP_score: -7.1 Tail_Score: -5.03405 Start: 37 End: 64 Full_Region: ATTAAAATGATTTAA GGGAATGAG AAAATAAAAC CTCATTCCC TTTTTCTATGCTATT ....................................GGGAATGAGAAAATAAAACCTCATTCCC............................................... TransTerm Strand: - Conf: 68 HP_score: -7.8 Tail_Score: -3.1944 Start: 37 End: 64 Full_Region: aatagcatagaaaaa gggaatgagg ttttattt tctcattccc ttaaatcattttaat ....................................gggaatgaggttttattttctcattccc............................................... Find igs database================================================ Query_seq: TF1700:TF1701|TF1700:TF1701:conserved hypothetical protein:transcriptional regulator:->->:1821522..1821632 111 taaagcttctttcctgcaccaattaaaatgatttaagggaatgagaaaataaaacctcattccctttttctatgctatttcatttcatatctttgcgctatcaaaagaaca Intra-Species Hit: Count: 1 Min: 1 Max: 111 Len: 111 Subject: tfor_TF1700_TF1701|conserved hypothetical protein:transcriptional regulator|POSITIVE:POSITIVE|[1821522,1821632]|111 HSP 1 e-value: 7.0E-57 bit: 220.0 Len: 111 Query Start:1 Query End:111 Subject Strand: POSITIVE Subject Start: 1 Subject End: 111 taaagcttctttcctgcaccaattaaaatgatttaagggaatgagaaaataaaacctcattccctttttctatgctatttcatttcatatctttgcgctatcaaaagaaca taaagcttctttcctgcaccaattaaaatgatttaagggaatgagaaaataaaacctcattccctttttctatgctatttcatttcatatctttgcgctatcaaaagaaca Inter-species Hit: Count: 1 Min: 1 Max: 111 Len: 111 Subject: NC_002950_PG1203_PG1205|transcriptional regulator, putative:DNA-binding protein, histone-like family|NEGATIVE:POSITIVE|[1283537,1284092]|556 HSP 1 e-value: 4.0E-40 bit: 165.0 Len: 111 Query Start:1 Query End:111 Subject Strand: NEGATIVE Subject Start: 22 Subject End: 130 taaagcttctttcctgcaccaattaaaatgatttaagggaatgagaaaataaaacctcattccctttttctatgctatttcatttcatatctttgcgctatcaaaagaaca taaagtttctttcctgcaccaattaagacgatttaagggaatg-gaaaataaa-cctcattccctttttctatgctatttcatttcatatctttgcgctatcaaaagaaca Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAGCUUCUUUCCUGCACCAAUUAAAAUGAUUUAAGGGAAUGAGAAAAUAAAACCUCAUUCCCUUUUUCUAUGCUAUUUCAUUUCAUAUCUUUGCGCUAUCAAAAGAACA ....(.((((((..((((.......((((((...(((((((((((..........))))))))))).............))))))........))))......))))))). (-20.85) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUUCUUUUGAUAGCGCAAAGAUAUGAAAUGAAAUAGCAUAGAAAAAGGGAAUGAGGUUUUAUUUUCUCAUUCCCUUAAAUCAUUUUAAUUGGUGCAGGAAAGAAGCUUUA ..(((((((....((((...(((.((((((((.............((((((((((((........))))))))))))...))))))))))).))))..)))))))...... (-30.79) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 274 96 60 227 182 tfor:TF0500|5end_hypothetical_protein_526688..526918_POSITIVE 255 99 54 84 33 tfor:TF2477|5end_phosphatase_2654229..2654459_POSITIVE 254 109 66 223 177 tfor:TF2660|5end_hypothetical_protein_2833293..2833523_POSITIVE 254 96 53 207 162 tfor:TF2605|5end_outer_membrane_protein,_TonB_dependent_receptor_2779855..2780085_POSITIVE 253 100 56 192 137 tfor:TF1291|5end_response_regulator_(fimR__protein)_1371959..1372189_POSITIVE 249 99 61 183 136 tfor:TF1984|5end_conserved_hypothetical_protein_2135278..2135508_POSITIVE 248 102 63 216 180 tfor:TF1485|5end_conserved_hypothetical_protein_1581871..1582101_POSITIVE 245 101 74 193 162 tfor:TF2127|5end_hypothetical_protein_2304038..2304268_POSITIVE 244 102 64 229 192 tfor:TF0049|5end_membrane-associated_HD_superfamily_hydrolase_55245..55475_POSITIVE 244 102 64 43 6 tfor:TF0050|5end_hypothetical_protein_55059..55289_POSITIVE 237 44 8 88 48 tfor:TF0581|5end_single_stranded_DNA-binding_protein_611406..611636_POSITIVE 237 100 56 210 159 tfor:TF0022|5end_two-component_system_sensor_histidine_kinase_17295..17525_POSITIVE 234 50 3 200 161 tfor:TF0739|5end_hypothetical_protein_789448..789678_POSITIVE 232 46 3 195 161 tfor:TF0734|5end_hypothetical_protein_786244..786474_POSITIVE 232 99 58 191 153 tfor:TF0187|5end_ferredoxin_202151..202381_POSITIVE 229 109 64 98 43 tfor:TF1934|5end_hypothetical_protein_2083787..2084017_POSITIVE 223 99 53 193 150 tfor:TF2785|5end_RNA_polymerase_sigma_factor,_ECF_subfamily_(sigma-70)_2969277..2969507_POSITIVE 220 99 72 152 132 tfor:TF1639|5end_conserved_hypothetical_protein_1747652..1747882_POSITIVE 219 76 36 111 75 tfor:TF2357|5end_collagenase_2522561..2522791_POSITIVE 219 22 5 199 179 tfor:TF1703|5end_conserved_hypothetical_protein_1822065..1822295_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 329 110 61 121 66 tfor:TF0499|3end_hypothetical_protein_526651..526801_POSITIVE 265 66 35 56 25 tfor:TF1700|3end_conserved_hypothetical_protein_1821461..1821611_POSITIVE 254 96 53 104 59 tfor:TF2604|3end_possible_membrane_transport_protein_2779832..2779982_POSITIVE 252 100 56 91 54 tfor:TF2855|3end_ATPase,_AAA_family_3042011..3042161_POSITIVE 245 101 74 71 40 tfor:TF2126|3end_S-adenosylhomocysteine_hydrolase_2303996..2304146_POSITIVE 243 97 55 60 26 tfor:TF2744|3end_methionyl-tRNA_formyltransferase_2927378..2927528_POSITIVE 232 97 55 59 18 tfor:TF1974|3end_glyoxalase_I_related_protein_(lactoylglutathione_lyase)_2121428..2121578_POSITIVE 229 109 64 112 57 tfor:TF1935|3end_ATP-dependent_RNA_helicase,_DEAD/DEAH-related_helicase_2083881..2084031_POSITIVE 223 99 53 133 90 tfor:TF2783|3end_aminotransferase,_PatB_family_2969297..2969447_POSITIVE 219 22 5 129 109 tfor:TF1702|3end_conserved_hypothetical_protein_1822075..1822225_POSITIVE 215 96 57 63 28 tfor:TF1500|3end_conserved_hypothetical_protein_1600354..1600504_POSITIVE 214 47 2 97 50 tfor:TF0811|3end_conserved_hypothetical_protein;_posible_sugar_phosphate_isomerase_870724..870874_POSITIVE 213 103 65 45 3 tfor:TF1382|3end_hypothetical_protein_1457777..1457927_POSITIVE 212 109 63 78 37 tfor:TF3122|3end_ABC_transporter,_ATP-binding_protein_3357743..3357893_POSITIVE 209 98 52 111 70 tfor:TF2184|3end_conserved_hypothetical_protein_2357043..2357193_POSITIVE 208 96 55 103 52 tfor:TF2757|3end_hypothetical_protein_2942335..2942485_POSITIVE 208 99 55 121 65 tfor:TF2288|3end_hypothetical_protein_2442598..2442748_POSITIVE 207 98 52 101 36 tfor:TF2785|3end_RNA_polymerase_sigma_factor,_ECF_subfamily_(sigma-70)_2969917..2970067_POSITIVE 207 76 36 148 105 tfor:TF0199|3end_conserved_hypothetical_protein_224064..224214_POSITIVE 206 100 60 110 70 tfor:TF1868|3end_conserved_hypothetical_protein;_possible_transposase_2023043..2023193_POSITIVE