Origin IGS: ttgttctcctttctgatttgtgtcgtatatatttgactatattatattcttctaagaaatagatgtcaagcatatttgacatatttcttaaagaaatcttacttgtttttgccctatttgtctgactagtgcaagctggtcggatttatggtaaaatagataggat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atcctatctattttaccataaatccgaccagcttgcactagtcagacaaatagggcaaaaacaagtaagatttctttaagaaatatgtcaaatatgcttgacatctatttcttagaagaatataatatagtcaaatatatacgacacaaatcagaaaggagaacaa Mask Tandem Repeat Region ================================================ ttgttctcctttctgatttgtgtcgtatatatttgactatattatattcttctaagaaatagatgtcaagcatatttgacatatttcttaaagaaatcttacttgtttttgccctatttgtctgactagtgcaagctggtcggatttatggtaaaatagataggat Find is-nt database================================================ Query_seq: SMT_265:SMT_266|SMT_265:SMT_266:DNA-binding protein:S-adenosyl-methyltransferase:<-->:204164..204329 166 ttgttctcctttctgatttgtgtcgtatatatttgactatattatattcttctaagaaatagatgtcaagcatatttgacatatttcttaaagaaatcttacttgtttttgccctatttgtctgactagtgcaagctggtcggatttatggtaaaatagataggat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_265:SMT_266|SMT_265:SMT_266:DNA-binding protein:S-adenosyl-methyltransferase:<-->:204164..204329 166 ttgttctcctttctgatttgtgtcgtatatatttgactatattatattcttctaagaaatagatgtcaagcatatttgacatatttcttaaagaaatcttacttgtttttgccctatttgtctgactagtgcaagctggtcggatttatggtaaaatagataggat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_265:SMT_266|SMT_265:SMT_266:DNA-binding protein:S-adenosyl-methyltransferase:<-->:204164..204329 166 ttgttctcctttctgatttgtgtcgtatatatttgactatattatattcttctaagaaatagatgtcaagcatatttgacatatttcttaaagaaatcttacttgtttttgccctatttgtctgactagtgcaagctggtcggatttatggtaaaatagataggat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttgttctcctttctgatttgtgtcgtatatatttgactatattatattcttctaagaaatagatgtcaagcatatttgacatatttcttaaagaaatcttacttgtttttgccctatttgtctgactagtgcaagctggtcggatttatggtaaaatagataggat Predict ORF larger than 30AA ================================================ Protein_Len: 48 Strand: - Start: 2 End: 145 . T R R E S K H R I Y K V I N Y E E L F Y I D L M N S M N R L S I K S T K A R N T Q S T C A P R M ..................... ttgttctcctttctgatttgtgtcgtatatatttgactatattatattcttctaagaaatagatgtcaagcatatttgacatatttcttaaagaaatcttacttgtttttgccctatttgtctgactagtgcaagctggtcggatttatggtaaaatagataggat 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: 90 Start: 41 End: 70 ........................................CTTGACATCTATTTCTTAGAAGAATATAAT................................................................................................ PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 128 End: 157 ...............................................................................................................................AGTGCAAGCTGGTCGGATTTATGGTAAAAT......... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttgttctcctttctgatttgtgtcgtatatatttgactatattatattcttctaagaaatagatgtcaagcatatttgacatatttcttaaagaaatcttacttgtttttgccctatttgtctgactagtgcaagctggtcggatttatggtaaaatagataggat Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 52 HP_score: -4.2 Tail_Score: -3.41738 Start: 64 End: 81 Full_Region: tttctttaagaaata tgtcaa atatgc ttgaca tctatttcttagaag ...............................................................tgtcaaatatgcttgaca..................................................................................... Find igs database================================================ Query_seq: SMT_265:SMT_266|SMT_265:SMT_266:DNA-binding protein:S-adenosyl-methyltransferase:<-->:204164..204329 166 ttgttctcctttctgatttgtgtcgtatatatttgactatattatattcttctaagaaatagatgtcaagcatatttgacatatttcttaaagaaatcttacttgtttttgccctatttgtctgactagtgcaagctggtcggatttatggtaaaatagataggat Intra-Species Hit: Count: 1 Min: 1 Max: 166 Len: 166 Subject: smit_SMT_265_SMT_266|DNA-binding protein:S-adenosyl- methyltransferase|NEGATIVE:POSITIVE|[204164,204329]|166 HSP 1 e-value: 2.0E-89 bit: 329.0 Len: 166 Query Start:1 Query End:166 Subject Strand: POSITIVE Subject Start: 1 Subject End: 166 ttgttctcctttctgatttgtgtcgtatatatttgactatattatattcttctaagaaatagatgtcaagcatatttgacatatttcttaaagaaatcttacttgtttttgccctatttgtctgactagtgcaagctggtcggatttatggtaaaatagataggat ttgttctcctttctgatttgtgtcgtatatatttgactatattatattcttctaagaaatagatgtcaagcatatttgacatatttcttaaagaaatcttacttgtttttgccctatttgtctgactagtgcaagctggtcggatttatggtaaaatagataggat Inter-species Hit: Count: 3 Min: 2 Max: 162 Len: 161 Subject: NC_003028_SP_0333_SP_0334|transcriptional regulator, putative:S-adenosyl-methyltransferase MraW|NEGATIVE:POSITIVE|[305432,305596]|165 HSP 1 e-value: 8.0E-30 bit: 131.0 Len: 161 Query Start:2 Query End:162 Subject Strand: POSITIVE Subject Start: 2 Subject End: 161 .tgttctcctttctgatttgtgtcgtatatatttgactatattatattcttctaagaaataga-tgtcaagcatatttgacatatttcttaaagaaatcttacttgtttttgccctatttgtctgactagtgcaagctggtcggatttatggtaaaatagata.... .tgttctcctttctgatttatgtcgtatatatttgactatattatagtcttttaa-acataaagtgtcaagtatttttgacatattttttgaagaaatagta-gtctccttgtcctatttgtctgacaagtgcaagctggtcggatttgtggtaaaatagata.... Subject: NC_008533_SPD_0303_SPD_0304|transcriptional regulator, putative:S-adenosyl-methyltransferase MraW|NEGATIVE:POSITIVE|[300862,301026]|165 HSP 1 e-value: 5.0E-28 bit: 125.0 Len: 158 Query Start:5 Query End:162 Subject Strand: POSITIVE Subject Start: 5 Subject End: 161 ....tctcctttctgatttgtgtcgtatatatttgactatattatattcttctaagaaataga-tgtcaagcatatttgacatatttcttaaagaaatcttacttgtttttgccctatttgtctgactagtgcaagctggtcggatttatggtaaaatagata.... ....tctcctttctgatttatgtcgtatatatttgactatattatagtcttttaa-acataaagtgtcaagtatttttgacatattttttgaagaaatagta-gtctccttgtcctatttgtctgacaagtgcaagctggtcggatttgtggtaaaatagata.... Subject: NC_003098_spr0301_spr0302|Transcription regulator:S-adenosyl-methyltransferase MraW|NEGATIVE:POSITIVE|[300813,300977]|165 HSP 1 e-value: 5.0E-28 bit: 125.0 Len: 158 Query Start:5 Query End:162 Subject Strand: POSITIVE Subject Start: 5 Subject End: 161 ....tctcctttctgatttgtgtcgtatatatttgactatattatattcttctaagaaataga-tgtcaagcatatttgacatatttcttaaagaaatcttacttgtttttgccctatttgtctgactagtgcaagctggtcggatttatggtaaaatagata.... ....tctcctttctgatttatgtcgtatatatttgactatattatagtcttttaa-acataaagtgtcaagtatttttgacatattttttgaagaaatagta-gtctccttgtcctatttgtctgacaagtgcaagctggtcggatttgtggtaaaatagata.... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUUCUCCUUUCUGAUUUGUGUCGUAUAUAUUUGACUAUAUUAUAUUCUUCUAAGAAAUAGAUGUCAAGCAUAUUUGACAUAUUUCUUAAAGAAAUCUUACUUGUUUUUGCCCUAUUUGUCUGACUAGUGCAAGCUGGUCGGAUUUAUGGUAAAAUAGAUA .......((((..((..(((((((.((((.((((((....((((.((((....))))))))..)))))).)))).)))))))..))..))))........((...(((((((.((...(((((((((((....))))))))))).)).))))))).))... (-45.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUCUAUUUUACCAUAAAUCCGACCAGCUUGCACUAGUCAGACAAAUAGGGCAAAAACAAGUAAGAUUUCUUUAAGAAAUAUGUCAAAUAUGCUUGACAUCUAUUUCUUAGAAGAAUAUAAUAUAGUCAAAUAUAUACGACACAAAUCAGAAAGGAGAACA ..................(((.....(((((.....(((..........))).....)))))..(((((.(((((((((((((((((......))))))..))))))))))).............(((..........)))..))))).....)))..... (-26.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 847 139 91 231 183 smit:SMT_265|5end_DNA-binding_protein_204073..204303_NEGATIVE 311 150 101 87 33 smit:SMT_719|5end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_625647..625877_NEGATIVE 304 144 101 123 73 smit:SMT_446|5end_ABC-type_cobalt_transport_system,_ATPase_component_384870..385100_POSITIVE 295 140 95 141 90 smit:SMT_1694|5end_GTPase_1676674..1676904_POSITIVE 273 143 101 62 24 smit:SMT_818|5end_cystathionine_gamma-synthase_729801..730031_NEGATIVE 272 151 123 203 177 smit:SMT_1115|5end_K02245_competence_protein_ComGC_1052796..1053026_NEGATIVE 269 140 94 143 83 smit:SMT_1380|5end_pyrroline-5-carboxylate_reductase_1358464..1358694_NEGATIVE 269 146 101 196 147 smit:SMT_661|5end_two-component_response_regulator_572596..572826_NEGATIVE 267 143 114 32 1 smit:SMT_1602|5end_hypothetical_protein_1592385..1592615_POSITIVE 267 140 95 97 51 smit:SMT_1481|5end_endopeptidase_O_1462229..1462459_POSITIVE 266 140 97 128 92 smit:SMT_1842|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1807858..1808088_NEGATIVE 266 140 97 216 180 smit:SMT_1841|5end_hypothetical_protein_1807770..1808000_NEGATIVE 264 143 101 228 187 smit:SMT_1619|5end_K02006_cobalt_transport_system_ATP-binding_protein_1606526..1606756_NEGATIVE 262 145 108 220 180 smit:SMT_2018|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1936760..1936990_POSITIVE 262 145 108 220 180 smit:SMT_1799|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1773416..1773646_POSITIVE 258 143 102 45 3 smit:SMT_161|5end_putative_folyl-polyglutamate_synthetase_105358..105588_POSITIVE 256 148 116 91 53 smit:SMT_1522|5end_K02004_1503177..1503407_NEGATIVE 255 152 112 224 175 smit:SMT_228|5end_hypothetical_protein_164384..164614_POSITIVE 254 150 112 171 138 smit:SMT_1994|5end_phosphoglycerate_mutase_1920501..1920731_NEGATIVE 253 139 94 169 130 smit:SMT_638|5end_hypothetical_protein_543449..543679_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 304 144 101 122 72 smit:SMT_445|3end_hypothetical_protein_384949..385099_POSITIVE 297 140 91 138 81 smit:SMT_398|3end_hypothetical_protein_328279..328429_POSITIVE 295 140 95 139 88 smit:SMT_1693|3end_dimethyladenosine_transferase_1676752..1676902_POSITIVE 269 140 94 139 79 smit:SMT_1381|3end_gamma-glutamyl_phosphate_reductase_1358468..1358618_NEGATIVE 269 146 101 140 91 smit:SMT_662|3end_A/G-specific_adenine_glycosylase_572652..572802_NEGATIVE 267 140 95 54 8 smit:SMT_1480|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1462266..1462416_POSITIVE 264 143 101 59 18 smit:SMT_1620|3end_hypothetical_protein_1606695..1606845_NEGATIVE 254 150 112 137 104 smit:SMT_1995|3end_phosphoglycerate_mutase_1920535..1920685_NEGATIVE 253 139 94 139 100 smit:SMT_639|3end_6-phospho-beta-galactosidase_543479..543629_NEGATIVE 244 125 82 151 108 smit:SMT_1796|3end_dihydroorotate_dehydrogenase_A_1769881..1770031_NEGATIVE 243 140 92 106 57 smit:SMT_2126|3end_indole-3-glycerol_phosphate_synthase_2009366..2009516_POSITIVE 243 150 101 137 84 smit:SMT_455|3end_cation_transport_ATPase_393993..394143_POSITIVE 237 139 95 141 95 smit:SMT_1847|3end_hypothetical_protein_1812697..1812847_POSITIVE 234 158 116 141 98 smit:SMT_810|3end_oxidoreductase_721108..721258_POSITIVE 229 150 110 138 97 smit:SMT_826|3end_hypothetical_protein_749591..749741_NEGATIVE 226 144 104 81 36 smit:SMT_108|3end_hypothetical_protein_53873..54023_POSITIVE 225 160 122 41 7 smit:SMT_1928|3end_O-methyltransferase_family_protein_1869158..1869308_NEGATIVE 225 138 91 135 84 smit:SMT_1043|3end_chaperonin_GroEL_985110..985260_NEGATIVE 225 139 94 148 104 smit:SMT_909|3end_type_I_restriction_enzyme_M_protein_857223..857373_NEGATIVE 220 146 102 137 71 smit:SMT_1856|3end_polypeptide_deformylase_1820999..1821149_POSITIVE