Origin IGS: gacccacctcctctaattttgtactattgtatcaaaagctgactgagtgtcaaggaggaggctgataaattgaggagaaaaaagcatcccagttacgagatgcttttaaattaatcaatgaagcaaactttctaagagatagagtaggtaaatgtagtctgagtaaaagatgatgaaacctacaaaaaagaaacaacctccgctgttcctttttactt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aagtaaaaaggaacagcggaggttgtttcttttttgtaggtttcatcatcttttactcagactacatttacctactctatctcttagaaagtttgcttcattgattaatttaaaagcatctcgtaactgggatgcttttttctcctcaatttatcagcctcctccttgacactcagtcagcttttgatacaatagtacaaaattagaggaggtgggtc Mask Tandem Repeat Region ================================================ gacccacctcctctaattttgtactattgtatcaaaagctgactgagtgtcaaggaggaggctgataaattgaggagaaaaaagcatcccagttacgagatgcttttaaattaatcaatgaagcaaactttctaagagatagagtaggtaaatgtagtctgagtaaaagatgatgaaacctacaaaaaagaaacaacctccgctgttcctttttactt Find is-nt database================================================ Query_seq: SMT_1169:SMT_1170|SMT_1169:SMT_1170:phosphorylase, Pnp/UDP family:acetyltransferase, CysE/LacA/LpxA/NodL family:<-<-:1117441..1117658 218 gacccacctcctctaattttgtactattgtatcaaaagctgactgagtgtcaaggaggaggctgataaattgaggagaaaaaagcatcccagttacgagatgcttttaaattaatcaatgaagcaaactttctaagagatagagtaggtaaatgtagtctgagtaaaagatgatgaaacctacaaaaaagaaacaacctccgctgttcctttttactt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1169:SMT_1170|SMT_1169:SMT_1170:phosphorylase, Pnp/UDP family:acetyltransferase, CysE/LacA/LpxA/NodL family:<-<-:1117441..1117658 218 gacccacctcctctaattttgtactattgtatcaaaagctgactgagtgtcaaggaggaggctgataaattgaggagaaaaaagcatcccagttacgagatgcttttaaattaatcaatgaagcaaactttctaagagatagagtaggtaaatgtagtctgagtaaaagatgatgaaacctacaaaaaagaaacaacctccgctgttcctttttactt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1169:SMT_1170|SMT_1169:SMT_1170:phosphorylase, Pnp/UDP family:acetyltransferase, CysE/LacA/LpxA/NodL family:<-<-:1117441..1117658 218 gacccacctcctctaattttgtactattgtatcaaaagctgactgagtgtcaaggaggaggctgataaattgaggagaaaaaagcatcccagttacgagatgcttttaaattaatcaatgaagcaaactttctaagagatagagtaggtaaatgtagtctgagtaaaagatgatgaaacctacaaaaaagaaacaacctccgctgttcctttttactt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gacccacctcctctaattttgtactattgtatcaaaagctgactgagtgtcaaggaggaggctgataaattgaggagaaaaaagcatcccagttacgagatgcttttaaattaatcaatgaagcaaactttctaagagatagagtaggtaaatgtagtctgagtaaaagatgatgaaacctacaaaaaagaaacaacctccgctgttcctttttactt Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 69 End: 170 .................................................................... M E E K K A S Q L R D A F K L I N E A N F L R D R V G K C S L S K R ................................................ Protein_Len: 48 Strand: - Start: 53 End: 196 .................................................... P P P Q Y I S S F F A D W N R S A K L N I L S A F K R L S L T P L H L R L L L H H F R C F L F M ...................... gacccacctcctctaattttgtactattgtatcaaaagctgactgagtgtcaaggaggaggctgataaattgaggagaaaaaagcatcccagttacgagatgcttttaaattaatcaatgaagcaaactttctaagagatagagtaggtaaatgtagtctgagtaaaagatgatgaaacctacaaaaaagaaacaacctccgctgttcctttttactt 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================================================ gacccacctcctctaattttgtactattgtatcaaaagctgactgagtgtcaaggaggaggctgataaattgaggagaaaaaagcatcccagttacgagatgcttttaaattaatcaatgaagcaaactttctaagagatagagtaggtaaatgtagtctgagtaaaagatgatgaaacctacaaaaaagaaacaacctccgctgttcctttttactt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 91 HP_score: -6.4 Tail_Score: -5.31877 Start: 84 End: 103 Full_Region: ttgattaatttaaaa gcatctcg taac tgggatgc ttttttctcctcaat ...................................................................................gcatctcgtaactgggatgc................................................................................................................... Find igs database================================================ Query_seq: SMT_1169:SMT_1170|SMT_1169:SMT_1170:phosphorylase, Pnp/UDP family:acetyltransferase, CysE/LacA/LpxA/NodL family:<-<-:1117441..1117658 218 gacccacctcctctaattttgtactattgtatcaaaagctgactgagtgtcaaggaggaggctgataaattgaggagaaaaaagcatcccagttacgagatgcttttaaattaatcaatgaagcaaactttctaagagatagagtaggtaaatgtagtctgagtaaaagatgatgaaacctacaaaaaagaaacaacctccgctgttcctttttactt Intra-Species Hit: Count: 1 Min: 1 Max: 218 Len: 218 Subject: smit_SMT_1169_SMT_1170|phosphorylase, Pnp/UDP family:acetyltransferase, CysE/LacA/LpxA/NodL family|NEGATIVE:NEGATIVE|[1117441,1117658]|218 HSP 1 e-value: 1.0E-120 bit: 432.0 Len: 218 Query Start:1 Query End:218 Subject Strand: POSITIVE Subject Start: 1 Subject End: 218 gacccacctcctctaattttgtactattgtatcaaaagctgactgagtgtcaaggaggaggctgataaattgaggagaaaaaagcatcccagttacgagatgcttttaaattaatcaatgaagcaaactttctaagagatagagtaggtaaatgtagtctgagtaaaagatgatgaaacctacaaaaaagaaacaacctccgctgttcctttttactt gacccacctcctctaattttgtactattgtatcaaaagctgactgagtgtcaaggaggaggctgataaattgaggagaaaaaagcatcccagttacgagatgcttttaaattaatcaatgaagcaaactttctaagagatagagtaggtaaatgtagtctgagtaaaagatgatgaaacctacaaaaaagaaacaacctccgctgttcctttttactt Inter-species Hit: Count: 1 Min: 7 Max: 218 Len: 212 Subject: NC_003028_SP_0074_SP_0075|acetyltransferase, CysE/LacA/LpxA/NodL family:phosphorylase, Pnp/Udp family|POSITIVE:POSITIVE|[81205,81480]|276 HSP 1 e-value: 4.0E-60 bit: 232.0 Len: 212 Query Start:7 Query End:218 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 210 ......cctcctctaattttgtactattgtatcaaaagctgactgagtgtcaaggaggaggctgataaattgaggagaaaaaagcatcccagttacgagatgcttttaaattaatcaatgaagcaaactttctaagagatagagtaggtaaatgtagtctgagtaaaagatgatgaaacctacaaaaaagaaacaacctccgctgttcctttttactt ......cctcctctaattttgtactattgtatcaaaatctgaccgagtgtcaaggaggaagctgatgaactgaggagaaaaa--catcccacttacgagatgctttgaacttgcttaatgaaacagacttgctaagagatagagtaggtaaatgtgaactgggtaaaaaatgatgaaacctacaaaaaagaaacaaccccagctgttcctttttactt Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCUCCUCUAAUUUUGUACUAUUGUAUCAAAAGCUGACUGAGUGUCAAGGAGGAGGCUGAUAAAUUGAGGAGAAAAAAGCAUCCCAGUUACGAGAUGCUUUUAAAUUAAUCAAUGAAGCAAACUUUCUAAGAGAUAGAGUAGGUAAAUGUAGUCUGAGUAAAAGAUGAUGAAACCUACAAAAAAGAAACAACCUCCGCUGUUCCUUUUUACUU ((((((((..((((((((....))).)))))..((((.....)))).)))))))).((....(((((......(((((((((.(......).))))))))).......)))))....))..((.((.....)).)).((((((.......((((.......))))......)))))).((((((.((((........)))).)))))).... (-51.24) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGUAAAAAGGAACAGCGGAGGUUGUUUCUUUUUUGUAGGUUUCAUCAUCUUUUACUCAGACUACAUUUACCUACUCUAUCUCUUAGAAAGUUUGCUUCAUUGAUUAAUUUAAAAGCAUCUCGUAACUGGGAUGCUUUUUUCUCCUCAAUUUAUCAGCCUCCUCCUUGACACUCAGUCAGCUUUUGAUACAAUAGUACAAAAUUAGAGGAGG ....(((((((((((((....))))))))))))).((((((.......(((.......)))........))))))((((.....))))...........(((((.......((((((((((((....))))))))))))......))))).......(((((((..((((.....))))..(((((.(((....))))))))...))))))) (-53.88) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 930 80 31 177 128 smit:SMT_1169|5end_phosphorylase,_Pnp/UDP_family_1117350..1117580_NEGATIVE 325 74 39 79 47 smit:SMT_1423|5end_hypothetical_protein_1407737..1407967_POSITIVE 320 79 36 54 1 smit:SMT_1489|5end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_1468892..1469122_POSITIVE 315 42 2 140 97 smit:SMT_652|5end_transporter,_putative_563215..563445_NEGATIVE 299 60 28 195 161 smit:SMT_778|5end_S-adenosylmethionine:tRNA_ribosyltransferase-isomerase_686870..687100_POSITIVE 286 85 46 157 113 smit:SMT_935|5end_UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-_diaminopimelate_ligase_887326..887556_POSITIVE 277 80 31 86 26 smit:SMT_729|5end_K07707_two-component_system,_AgrA_family,_response_regulator_AgrA_635068..635298_NEGATIVE 275 57 34 229 203 smit:SMT_1472|5end_hypothetical_protein,_coenzyme_PQQ_synthesis_homologue_1454262..1454492_NEGATIVE 274 50 1 83 24 smit:SMT_2139|5end_cell_division_protein_FtsZ_2017083..2017313_POSITIVE 274 50 1 83 24 smit:SMT_2137|5end_cell_division_protein_FtsZ_2015797..2016027_POSITIVE 274 50 1 83 24 smit:SMT_2129|5end_cell_division_protein_FtsZ_2010090..2010320_POSITIVE 274 50 1 83 24 smit:SMT_1548|5end_cell_division_protein_FtsZ_1532384..1532614_POSITIVE 268 89 42 178 126 smit:SMT_1471|5end_hypothetical_protein_1453933..1454163_NEGATIVE 264 57 11 178 113 smit:SMT_966|5end_transcriptional_regulator,_TetR_family_912191..912421_NEGATIVE 263 69 24 97 49 smit:SMT_999|5end_hypothetical_protein_predicted_by_Glimmer/Critica_941642..941872_NEGATIVE 259 58 12 126 75 smit:SMT_1879|5end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_1836806..1837036_NEGATIVE 257 57 12 53 15 smit:SMT_1615|5end_K02016_iron_complex_transport_system_substrate-binding_protein_1602699..1602929_NEGATIVE 255 74 31 220 166 smit:SMT_1980|5end_glycosyltransferase_1911161..1911391_POSITIVE 254 60 17 197 148 smit:SMT_944|5end_PhnA_protein_895106..895336_NEGATIVE 252 56 18 160 122 smit:SMT_1898|5end_aminotransferase_(class_V),_putative_1849929..1850159_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 358 79 32 64 1 smit:SMT_1488|3end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_1468982..1469132_POSITIVE 320 72 32 74 29 smit:SMT_799|3end_hypothetical_protein_707296..707446_NEGATIVE 315 42 2 63 20 smit:SMT_653|3end_positive_transcriptional_regulator_MutR_family_563292..563442_NEGATIVE 286 85 46 58 14 smit:SMT_934|3end_pyridine_nucleotide-disulfide_oxidoreductase_887307..887457_POSITIVE 284 79 31 76 35 smit:SMT_455|3end_cation_transport_ATPase_393993..394143_POSITIVE 277 207 173 92 46 smit:SMT_459|3end_hypothetical_protein_397690..397840_POSITIVE 274 50 1 65 6 smit:SMT_2138|3end_cell_division_protein_FtsA_2017145..2017295_POSITIVE 274 50 1 65 6 smit:SMT_2136|3end_cell_division_protein_FtsA_2015859..2016009_POSITIVE 274 50 1 65 6 smit:SMT_2128|3end_cell_division_protein_FtsA_2010152..2010302_POSITIVE 274 50 1 65 6 smit:SMT_1547|3end_cell_division_protein_FtsA_1532446..1532596_POSITIVE 273 88 41 71 3 smit:SMT_728|3end_hypothetical_protein_633203..633353_NEGATIVE 272 80 32 68 1 smit:SMT_1618|3end_K02015_iron_complex_transport_system_permease_protein_1604490..1604640_NEGATIVE 268 72 31 72 26 smit:SMT_1536|3end_trigger_factor_1520636..1520786_NEGATIVE 268 72 31 77 31 smit:SMT_915|3end_sucrose_operon_repressor_868619..868769_POSITIVE 262 80 31 76 19 smit:SMT_2008|3end_K07485_transposase_1928165..1928315_NEGATIVE 256 72 32 77 32 smit:SMT_1477|3end_K02077_zinc/manganese_transport_system_substrate-binding_protein_1459447..1459597_NEGATIVE 256 55 11 151 89 smit:SMT_967|3end_K01992_ABC-2_type_transport_system_permease_protein_912215..912365_NEGATIVE 254 60 17 66 17 smit:SMT_945|3end_cytidylate_kinase_895237..895387_NEGATIVE 252 70 21 142 96 smit:SMT_82|3end_transcriptional_regulator,_TetR_family_14330..14480_POSITIVE 251 50 1 61 6 smit:SMT_2152|3end_cell_division_protein_2026967..2027117_POSITIVE