Origin IGS: gaaaagtaaactggtgtgtcaagattgcggaagtggtcttgacatgctatggaaatatagatgttataagtgtctacaaaatgttgggtatttgcttaccttagagattctgttagacacttataaacttaatttatgattttagttaactatcagaaacgaaggaaagagt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 actctttccttcgtttctgatagttaactaaaatcataaattaagtttataagtgtctaacagaatctctaaggtaagcaaatacccaacattttgtagacacttataacatctatatttccatagcatgtcaagaccacttccgcaatcttgacacaccagtttacttttc Mask Tandem Repeat Region ================================================ gaaaagtaaactggtgtgtcaagattgcggaagtggtcttgacatgctatggaaatatagatgttataagtgtctacaaaatgttgggtatttgcttaccttagagattctgttagacacttataaacttaatttatgattttagttaactatcagaaacgaaggaaagagt Find is-nt database================================================ Query_seq: SMT_1888:SMT_1889|SMT_1888:SMT_1889:K02026 multiple sugar transport system permease protein:hypothetical protein:->->:1842903..1843074 172 gaaaagtaaactggtgtgtcaagattgcggaagtggtcttgacatgctatggaaatatagatgttataagtgtctacaaaatgttgggtatttgcttaccttagagattctgttagacacttataaacttaatttatgattttagttaactatcagaaacgaaggaaagagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1888:SMT_1889|SMT_1888:SMT_1889:K02026 multiple sugar transport system permease protein:hypothetical protein:->->:1842903..1843074 172 gaaaagtaaactggtgtgtcaagattgcggaagtggtcttgacatgctatggaaatatagatgttataagtgtctacaaaatgttgggtatttgcttaccttagagattctgttagacacttataaacttaatttatgattttagttaactatcagaaacgaaggaaagagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1888:SMT_1889|SMT_1888:SMT_1889:K02026 multiple sugar transport system permease protein:hypothetical protein:->->:1842903..1843074 172 gaaaagtaaactggtgtgtcaagattgcggaagtggtcttgacatgctatggaaatatagatgttataagtgtctacaaaatgttgggtatttgcttaccttagagattctgttagacacttataaacttaatttatgattttagttaactatcagaaacgaaggaaagagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gaaaagtaaactggtgtgtcaagattgcggaagtggtcttgacatgctatggaaatatagatgttataagtgtctacaaaatgttgggtatttgcttaccttagagattctgttagacacttataaacttaatttatgattttagttaactatcagaaacgaaggaaagagt Predict ORF larger than 30AA ================================================ Protein_Len: 42 Strand: + Start: 11 End: 136 .......... M V C Q D C G S G L D M L W K Y R C Y K C L Q N V G Y L L T L E I L L D T Y K L N L .................................... gaaaagtaaactggtgtgtcaagattgcggaagtggtcttgacatgctatggaaatatagatgttataagtgtctacaaaatgttgggtatttgcttaccttagagattctgttagacacttataaacttaatttatgattttagttaactatcagaaacgaaggaaagagt 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================================================ gaaaagtaaactggtgtgtcaagattgcggaagtggtcttgacatgctatggaaatatagatgttataagtgtctacaaaatgttgggtatttgcttaccttagagattctgttagacacttataaacttaatttatgattttagttaactatcagaaacgaaggaaagagt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1888:SMT_1889|SMT_1888:SMT_1889:K02026 multiple sugar transport system permease protein:hypothetical protein:->->:1842903..1843074 172 gaaaagtaaactggtgtgtcaagattgcggaagtggtcttgacatgctatggaaatatagatgttataagtgtctacaaaatgttgggtatttgcttaccttagagattctgttagacacttataaacttaatttatgattttagttaactatcagaaacgaaggaaagagt Intra-Species Hit: Count: 1 Min: 1 Max: 172 Len: 172 Subject: smit_SMT_1888_SMT_1889|K02026 multiple sugar transport system permease protein:hypothetical protein|POSITIVE:POSITIVE|[1842903,1843074]|172 HSP 1 e-value: 5.0E-93 bit: 341.0 Len: 172 Query Start:1 Query End:172 Subject Strand: POSITIVE Subject Start: 1 Subject End: 172 gaaaagtaaactggtgtgtcaagattgcggaagtggtcttgacatgctatggaaatatagatgttataagtgtctacaaaatgttgggtatttgcttaccttagagattctgttagacacttataaacttaatttatgattttagttaactatcagaaacgaaggaaagagt gaaaagtaaactggtgtgtcaagattgcggaagtggtcttgacatgctatggaaatatagatgttataagtgtctacaaaatgttgggtatttgcttaccttagagattctgttagacacttataaacttaatttatgattttagttaactatcagaaacgaaggaaagagt Inter-species Hit: Count: 3 Min: 54 Max: 172 Len: 119 Subject: NC_008533_SPD_1492_SPD_1493|hypothetical protein:sugar ABC transporter, permease protein|NEGATIVE:NEGATIVE|[1508518,1508789]|272 HSP 1 e-value: 1.0E-16 bit: 87.7 Len: 119 Query Start:54 Query End:172 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 119 .....................................................aatatagatgttataagtgtctacaaaatgttgggtatttgcttacctta-gagattctgttagacacttataaacttaatttatgattttagttaactatcagaaacgaaggaaagagt .....................................................aatatagaggttataagtgtctacaaaatggagggtatgcagttactttatgaagttttgtcagacacttataaacttaaga-atggttttagttaactatcagaaacgaaggaaagagt Subject: NC_003098_spr1524_spr1525|hypothetical protein:ABC transporter membrane-spanning permease - sugar transport|NEGATIVE:NEGATIVE|[1500987,1501258]|272 HSP 1 e-value: 1.0E-16 bit: 87.7 Len: 119 Query Start:54 Query End:172 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 119 .....................................................aatatagatgttataagtgtctacaaaatgttgggtatttgcttacctta-gagattctgttagacacttataaacttaatttatgattttagttaactatcagaaacgaaggaaagagt .....................................................aatatagaggttataagtgtctacaaaatggagggtatgcagttactttatgaagttttgtcagacacttataaacttaaga-atggttttagttaactatcagaaacgaaggaaagagt Subject: NC_003028_SP_1680_SP_1681|hypothetical protein:sugar ABC transporter, permease protein|NEGATIVE:NEGATIVE|[1579923,1580193]|271 HSP 1 e-value: 1.0E-16 bit: 87.7 Len: 119 Query Start:54 Query End:172 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 119 .....................................................aatatagatgttataagtgtctacaaaatgttgggtatttgcttacctta-gagattctgttagacacttataaacttaatttatgattttagttaactatcagaaacgaaggaaagagt .....................................................aatatagaggttataagtgtctacaaaatggagggtatgcagttactttatgaagttttgtcagacacttataaacttaaga-atggttttagttaactatcagaaacgaaggaaagagt Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUAUAGAUGUUAUAAGUGUCUACAAAAUGUUGGGUAUUUGCUUACCUUAGAGAUUCUGUUAGACACUUAUAAACUUAAUUUAUGAUUUUAGUUAACUAUCAGAAACGAAGGAAAGAGU ..(((((((.(((((((((((((((.(((.(((((((......)))))..)).))).)).))))))))))))).....)))))))...........((.((......)).))....... (-27.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUCUUUCCUUCGUUUCUGAUAGUUAACUAAAAUCAUAAAUUAAGUUUAUAAGUGUCUAACAGAAUCUCUAAGGUAAGCAAAUACCCAACAUUUUGUAGACACUUAUAACAUCUAUAUU ........(((.((((.((((((....)))...))).)))).))).(((((((((((((.((((((......((((......))))....))))))))))))))))))).......... (-25.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 261 68 28 165 125 smit:SMT_522|5end_K02003_446719..446949_POSITIVE 235 69 21 122 67 smit:SMT_924|5end_primosomal_protein_N'_879903..880133_NEGATIVE 229 60 21 64 31 smit:SMT_357|5end_tRNA_(guanine-N7-)-methyltransferase_293185..293415_POSITIVE 218 58 39 204 182 smit:SMT_1357|5end_endo-beta-N-acetylglucosaminidase_1336156..1336386_NEGATIVE 217 61 21 47 5 smit:SMT_1491|5end_capsular_polysaccharide_biosynthesis_protein,_putative_1471588..1471818_POSITIVE 217 60 15 213 168 smit:SMT_1026|5end_sucrose_phosphorylase_962324..962554_NEGATIVE 214 60 13 180 138 smit:SMT_704|5end_Cof_family_protein_613662..613892_POSITIVE 207 60 17 112 58 smit:SMT_1381|5end_gamma-glutamyl_phosphate_reductase_1359730..1359960_NEGATIVE 206 60 16 70 26 smit:SMT_1793|5end_inosine-5'-monophosphate_dehydrogenase_1767985..1768215_POSITIVE 205 67 28 58 23 smit:SMT_596|5end_K03976_putative_transcription_regulator_513075..513305_NEGATIVE 201 64 30 79 46 smit:SMT_2029|5end_acetyltransferase,_GNAT_family_1943749..1943979_POSITIVE 201 64 30 79 46 smit:SMT_1755|5end_acetyltransferase,_GNAT_family_1733042..1733272_POSITIVE 201 67 30 84 46 smit:SMT_265|5end_DNA-binding_protein_204073..204303_NEGATIVE 199 69 22 186 141 smit:SMT_1126|5end_K08987_putative_membrane_protein_1061342..1061572_NEGATIVE 199 58 16 209 160 smit:SMT_316|5end_acetyl-CoA_carboxylase_carboxyl_transferase_subunit_alpha_256544..256774_POSITIVE 196 69 32 125 85 smit:SMT_465|5end_oxidoreductase,_short_chain_dehydrogenase/reductase_family_protein_403244..403474_POSITIVE 196 69 32 125 85 smit:SMT_417|5end_short_chain_dehydrogenase_360373..360603_POSITIVE 194 58 25 176 143 smit:SMT_1676|5end_S4_domain_protein_1661764..1661994_NEGATIVE 194 58 25 176 143 smit:SMT_95|5end_S4_domain_protein_28177..28407_POSITIVE 193 64 27 34 2 smit:SMT_1060|5end_K03977_GTP-binding_protein_998106..998336_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 235 69 21 56 1 smit:SMT_925|3end_DNA-directed_RNA_polymerase_omega_chain_879969..880119_NEGATIVE 229 60 21 67 34 smit:SMT_356|3end_hypothetical_protein_293268..293418_POSITIVE 225 67 21 52 10 smit:SMT_1854|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1818952..1819102_POSITIVE 218 58 39 106 84 smit:SMT_1358|3end_dihydroorotate_dehydrogenase_B_1336254..1336404_NEGATIVE 208 60 16 103 56 smit:SMT_1895|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1847402..1847552_POSITIVE 207 60 17 102 48 smit:SMT_1382|3end_glutamate_5-kinase_1359740..1359890_NEGATIVE 205 67 28 58 23 smit:SMT_597|3end_K08974_putative_membrane_protein_513075..513225_NEGATIVE 196 69 32 104 64 smit:SMT_464|3end_ribonuclease_Z_403303..403453_POSITIVE 196 69 32 104 64 smit:SMT_416|3end_ribonuclease_Z_360432..360582_POSITIVE 194 58 25 118 85 smit:SMT_1969|3end_transcription-repair_coupling_factor_1900816..1900966_NEGATIVE 194 58 25 118 85 smit:SMT_1677|3end_transcription-repair_coupling_factor_1661822..1661972_NEGATIVE 194 60 19 143 101 smit:SMT_1129|3end_hypothetical_protein_1063303..1063453_NEGATIVE 194 58 25 118 85 smit:SMT_94|3end_transcription-repair_coupling_factor_28199..28349_POSITIVE 192 63 21 54 17 smit:SMT_234|3end_aminopeptidase_PepS_174151..174301_POSITIVE 191 65 29 59 26 smit:SMT_1946|3end_sucrose-6-phosphate_hydrolase_1881205..1881355_POSITIVE 191 60 19 39 1 smit:SMT_1645|3end_hypothetical_protein_1632087..1632237_POSITIVE 186 50 7 93 42 smit:SMT_467|3end_UDP-N-acetylglucosamine--N-acetylmuramyl-_(pentapeptide)_pyrophosphoryl-undecaprenol_N-acetylglucosamine_transferase_404780..404930_POSITIVE 185 68 22 142 101 smit:SMT_269|3end_phospho-N-acetylmuramoyl-pentapeptide-transferas_e_208785..208935_POSITIVE 184 69 28 78 30 smit:SMT_480|3end_K03308_neurotransmitter:Na+_symporter,_NSS_family_416765..416915_NEGATIVE 184 60 28 31 1 smit:SMT_451|3end_thiamine-phosphate_pyrophosphorylase_389647..389797_POSITIVE