Origin IGS: gaaacaagaacaccgtgccttgggcagagtgtttctcgtgaaacatccctttcttaaaaaagtactccacataaaataatttgtggagttttttctataattagtagtttaacctaaccttcaaataggagtatactaataatgtaatcgttatcaaaaatctaaaaaggaatttttagatggatatcaaaataaaaaagggaggaaatt .........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 aatttcctcccttttttattttgatatccatctaaaaattcctttttagatttttgataacgattacattattagtatactcctatttgaaggttaggttaaactactaattatagaaaaaactccacaaattattttatgtggagtacttttttaagaaagggatgtttcacgagaaacactctgcccaaggcacggtgttcttgtttc Mask Tandem Repeat Region ================================================ gaaacaagaacaccgtgccttgggcagagtgtttctcgtgaaacatccctttcttaaaaaagtactccacataaaataatttgtggagttttttctataattagtagtttaacctaaccttcaaataggagtatactaataatgtaatcgttatcaaaaatctaaaaaggaatttttagatggatatcaaaataaaaaagggaggaaatt Find is-nt database================================================ Query_seq: SMT_116:SMT_117|SMT_116:SMT_117:beta-N-acetylhexosaminidase:K02025 multiple sugar transport system permease protein:->->:68417..68626 210 gaaacaagaacaccgtgccttgggcagagtgtttctcgtgaaacatccctttcttaaaaaagtactccacataaaataatttgtggagttttttctataattagtagtttaacctaaccttcaaataggagtatactaataatgtaatcgttatcaaaaatctaaaaaggaatttttagatggatatcaaaataaaaaagggaggaaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_116:SMT_117|SMT_116:SMT_117:beta-N-acetylhexosaminidase:K02025 multiple sugar transport system permease protein:->->:68417..68626 210 gaaacaagaacaccgtgccttgggcagagtgtttctcgtgaaacatccctttcttaaaaaagtactccacataaaataatttgtggagttttttctataattagtagtttaacctaaccttcaaataggagtatactaataatgtaatcgttatcaaaaatctaaaaaggaatttttagatggatatcaaaataaaaaagggaggaaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_116:SMT_117|SMT_116:SMT_117:beta-N-acetylhexosaminidase:K02025 multiple sugar transport system permease protein:->->:68417..68626 210 gaaacaagaacaccgtgccttgggcagagtgtttctcgtgaaacatccctttcttaaaaaagtactccacataaaataatttgtggagttttttctataattagtagtttaacctaaccttcaaataggagtatactaataatgtaatcgttatcaaaaatctaaaaaggaatttttagatggatatcaaaataaaaaagggaggaaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gaaacaagaacaccgtgccttgggcagagtgtttctcgtgaaacatccctttcttaaaaaagtactccacataaaataatttgtggagttttttctataattagtagtttaacctaaccttcaaataggagtatactaataatgtaatcgttatcaaaaatctaaaaaggaatttttagatggatatcaaaataaaaaagggaggaaatt Predict ORF larger than 30AA ================================================ gaaacaagaacaccgtgccttgggcagagtgtttctcgtgaaacatccctttcttaaaaaagtactccacataaaataatttgtggagttttttctataattagtagtttaacctaaccttcaaataggagtatactaataatgtaatcgttatcaaaaatctaaaaaggaatttttagatggatatcaaaataaaaaagggaggaaatt 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: 81 Start: 108 End: 137 ...........................................................................................................TTTAACCTAACCTTCAAATAGGAGTATACT......................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gaaacaagaacaccgtgccttgggcagagtgtttctcgtgaaacatccctttcttaaaaaagtactccacataaaataatttgtggagttttttctataattagtagtttaacctaaccttcaaataggagtatactaataatgtaatcgttatcaaaaatctaaaaaggaatttttagatggatatcaaaataaaaaagggaggaaatt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 82 HP_score: -5.3 Tail_Score: -5.42131 Start: 65 End: 88 Full_Region: TTTCTTAAAAAAGTA CTCCACATA AAATAA TTTGTGGAG TTTTTTCTATAATTA ................................................................CTCCACATAAAATAATTTGTGGAG.......................................................................................................................... TransTerm Strand: - Conf: 56 HP_score: -5.3 Tail_Score: -3.37655 Start: 65 End: 88 Full_Region: taattatagaaaaaa ctccacaaa ttattt tatgtggag tacttttttaagaaa ................................................................ctccacaaattattttatgtggag.......................................................................................................................... Find igs database================================================ Query_seq: SMT_116:SMT_117|SMT_116:SMT_117:beta-N-acetylhexosaminidase:K02025 multiple sugar transport system permease protein:->->:68417..68626 210 gaaacaagaacaccgtgccttgggcagagtgtttctcgtgaaacatccctttcttaaaaaagtactccacataaaataatttgtggagttttttctataattagtagtttaacctaaccttcaaataggagtatactaataatgtaatcgttatcaaaaatctaaaaaggaatttttagatggatatcaaaataaaaaagggaggaaatt Intra-Species Hit: Count: 1 Min: 1 Max: 210 Len: 210 Subject: smit_SMT_116_SMT_117|beta-N-acetylhexosaminidase:K02025 multiple sugar transport system permease protein|POSITIVE:POSITIVE|[68417,68626]|210 HSP 1 e-value: 1.0E-115 bit: 416.0 Len: 210 Query Start:1 Query End:210 Subject Strand: POSITIVE Subject Start: 1 Subject End: 210 gaaacaagaacaccgtgccttgggcagagtgtttctcgtgaaacatccctttcttaaaaaagtactccacataaaataatttgtggagttttttctataattagtagtttaacctaaccttcaaataggagtatactaataatgtaatcgttatcaaaaatctaaaaaggaatttttagatggatatcaaaataaaaaagggaggaaatt gaaacaagaacaccgtgccttgggcagagtgtttctcgtgaaacatccctttcttaaaaaagtactccacataaaataatttgtggagttttttctataattagtagtttaacctaaccttcaaataggagtatactaataatgtaatcgttatcaaaaatctaaaaaggaatttttagatggatatcaaaataaaaaagggaggaaatt Inter-species Hit: Count: 3 Min: 76 Max: 210 Len: 135 Subject: NC_008533_SPD_0087_SPD_0088|hypothetical protein:ABC transporter, permease protein|POSITIVE:POSITIVE|[87489,87806]|318 HSP 1 e-value: 1.0E-56 bit: 220.0 Len: 135 Query Start:76 Query End:210 Subject Strand: POSITIVE Subject Start: 185 Subject End: 318 ...........................................................................ataatttgtggagttttttctataattagtagtttaacctaaccttcaaataggagtatactaataatgtaatcgttatcaaaaatctaaaaaggaatttttagatggatatcaaaataaaaaagggaggaaatt ...........................................................................ataatttgtggagttttttctataattaggagtttaacctaacctgcaaataggagtatactaataatgtaatcgttatcaaaagtctaaaaaagaatttttagatggatatcaaaat-aaaaagggaggaaatt Subject: NC_003098_spr0080_spr0081|hypothetical protein:ABC transporter membrane-spanning permease - sugar transport|POSITIVE:POSITIVE|[87314,87776]|463 HSP 1 e-value: 8.0E-43 bit: 174.0 Len: 104 Query Start:76 Query End:179 Subject Strand: POSITIVE Subject Start: 360 Subject End: 463 ...........................................................................ataatttgtggagttttttctataattagtagtttaacctaaccttcaaataggagtatactaataatgtaatcgttatcaaaaatctaaaaaggaatttttag............................... ...........................................................................ataatttgtggagttttttctataattaggagtttaacctaacctgcaaataggagtatactaataatgtaatcgttatcaaaagtctaaaaaagaatttttag............................... Subject: NC_003028_SP_0089_SP_0090|hypothetical protein:ABC transporter, permease protein|POSITIVE:POSITIVE|[92681,92968]|288 HSP 1 e-value: 8.0E-43 bit: 174.0 Len: 104 Query Start:76 Query End:179 Subject Strand: POSITIVE Subject Start: 185 Subject End: 288 ...........................................................................ataatttgtggagttttttctataattagtagtttaacctaaccttcaaataggagtatactaataatgtaatcgttatcaaaaatctaaaaaggaatttttag............................... ...........................................................................ataatttgtggagttttttctataattaggagtttaacctaacctgcaaataggagtatactaataatgtaatcgttatcaaaagtctaaaaaagaatttttag............................... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAAUUUGUGGAGUUUUUUCUAUAAUUAGUAGUUUAACCUAACCUUCAAAUAGGAGUAUACUAAUAAUGUAAUCGUUAUCAAAAAUCUAAAAAGGAAUUUUUAGAUGGAUAUCAAAAUAAAAAAGGGAGGAAAUU ...........((((((((((...(((((((......((((.........))))....))))))).........(.((((....(((((((((....))))))))).)))).)............)))))))))) (-23.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUUCCUCCCUUUUUUAUUUUGAUAUCCAUCUAAAAAUUCCUUUUUAGAUUUUUGAUAACGAUUACAUUAUUAGUAUACUCCUAUUUGAAGGUUAGGUUAAACUACUAAUUAUAGAAAAAACUCCACAAAUUAU ...........((((((((.(((.((((.(((((((((....)))))))))....)))).))).......(((((((....((((.........))))......))))))).))))))))............... (-16.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 264 56 11 176 122 smit:SMT_162|5end_hypothetical_protein_106593..106823_POSITIVE 209 77 43 188 154 smit:SMT_2047|5end_choline_binding_protein_F_1957818..1958048_NEGATIVE 206 64 25 66 20 smit:SMT_680|5end_choline_transport_protein_589962..590192_NEGATIVE 196 39 7 31 2 smit:SMT_961|5end_K02016_iron_complex_transport_system_substrate-binding_protein_907809..908039_NEGATIVE 195 59 14 118 83 smit:SMT_1637|5end_hypothetical_protein_1623091..1623321_POSITIVE 194 35 7 51 22 smit:SMT_1119|5end_alcohol_dehydrogenase,_zinc-containing_1056292..1056522_NEGATIVE 187 40 5 153 104 smit:SMT_1979|5end_possible_cell_surface_protein_1911052..1911282_NEGATIVE 187 40 5 153 104 smit:SMT_1956|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1889710..1889940_NEGATIVE 186 88 43 152 116 smit:SMT_909|5end_type_I_restriction_enzyme_M_protein_858827..859057_NEGATIVE 184 70 25 63 17 smit:SMT_308|5end_trans-2-enoyl-ACP_reductase_II_249439..249669_POSITIVE 183 89 43 139 100 smit:SMT_2134|5end_hypothetical_protein_2014700..2014930_NEGATIVE 183 45 1 60 24 smit:SMT_1016|5end_alcohol_dehydrogenase,_zinc-containing_954094..954324_NEGATIVE 183 89 43 139 100 smit:SMT_873|5end_hypothetical_protein_821311..821541_NEGATIVE 182 89 44 186 149 smit:SMT_905|5end_hypothetical_protein_predicted_by_Glimmer/Critica_853467..853697_NEGATIVE 181 87 42 147 97 smit:SMT_1646|5end_3-isopropylmalate_dehydratase_large_subunit_1632011..1632241_POSITIVE 181 46 1 109 68 smit:SMT_130|5end_capsular_polysaccharide_biosynthesis_protein_80995..81225_POSITIVE 179 40 5 192 160 smit:SMT_1433|5end_hypothetical_protein_1417783..1418013_NEGATIVE 177 66 25 45 1 smit:SMT_1790|5end_hypothetical_protein_1765644..1765874_POSITIVE 177 75 31 51 11 smit:SMT_1761|5end_transcriptional_activator,_putative_1736458..1736688_POSITIVE 177 130 100 176 149 smit:SMT_1042|5end_hypothetical_cytosolic_protein_984972..985202_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 264 56 11 89 35 smit:SMT_161|3end_putative_folyl-polyglutamate_synthetase_106586..106736_POSITIVE 213 32 4 104 75 smit:SMT_847|3end_thioredoxin_reductase_793848..793998_POSITIVE 209 77 43 45 11 smit:SMT_2048|3end_competence-specific_global_transcription_modulator_1957961..1958111_NEGATIVE 206 64 25 76 30 smit:SMT_681|3end_choline_kinase_589952..590102_NEGATIVE 195 59 14 134 99 smit:SMT_1636|3end_5-formyltetrahydrofolate_cyclo-ligase_family_protein_1623187..1623337_POSITIVE 187 107 68 52 10 smit:SMT_1083|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1021001..1021151_POSITIVE 184 50 5 126 71 smit:SMT_1476|3end_thiol_peroxidase_1458728..1458878_NEGATIVE 183 89 43 85 46 smit:SMT_2135|3end_dipeptidase_2014754..2014904_NEGATIVE 183 45 1 59 23 smit:SMT_1017|3end_transcriptional_regulator,_MerR_family_954095..954245_NEGATIVE 183 89 43 85 46 smit:SMT_874|3end_dipeptidase_821365..821515_NEGATIVE 182 89 44 51 14 smit:SMT_906|3end_hypothetical_protein_853602..853752_NEGATIVE 181 87 42 143 93 smit:SMT_1645|3end_hypothetical_protein_1632087..1632237_POSITIVE 180 44 8 108 73 smit:SMT_2042|3end_K04077_chaperonin_GroEL_(Hsp60)_1952960..1953110_NEGATIVE 179 129 93 59 17 smit:SMT_2061|3end_K02011_iron(III)_transport_system_permease_protein_1970802..1970952_POSITIVE 179 40 5 72 40 smit:SMT_1434|3end_neopullulanase_1417903..1418053_NEGATIVE 179 129 93 59 17 smit:SMT_202|3end_K02011_iron(III)_transport_system_permease_protein_132173..132323_NEGATIVE 177 130 100 38 11 smit:SMT_1043|3end_chaperonin_GroEL_985110..985260_NEGATIVE 172 48 4 101 52 smit:SMT_260|3end_phage_transcriptional_repressor_200236..200386_POSITIVE 171 130 91 118 79 smit:SMT_1950|3end_Mn2+_and_Fe2+_transporter_of_the_NRAMP_family_1885069..1885219_POSITIVE 167 87 43 151 116 smit:SMT_910|3end_type_I_restriction_enzyme_R_protein_858827..858977_NEGATIVE