Origin IGS: tatcaatctccttttaatttttacgaacaataatagaattatatcatttatcattcactttttcaacatctttgtttgatttatttaagaaattgatctaatttcattttttgtttggaatctgcttttctgcctgctttctgttataatagaaaacatcttatctgaaaagacactagaaaggtccct .........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 agggacctttctagtgtcttttcagataagatgttttctattataacagaaagcaggcagaaaagcagattccaaacaaaaaatgaaattagatcaatttcttaaataaatcaaacaaagatgttgaaaaagtgaatgataaatgatataattctattattgttcgtaaaaattaaaaggagattgata Mask Tandem Repeat Region ================================================ tatcaatctccttttaatttttacgaacaataatagaattatatcatttatcattcactttttcaacatctttgtttgatttatttaagaaattgatctaatttcattttttgtttggaatctgcttttctgcctgctttctgttataatagaaaacatcttatctgaaaagacactagaaaggtccct Find is-nt database================================================ Query_seq: SMT_1081:SMT_1082|SMT_1081:SMT_1082:K06901 putative MFS transporter, AGZA family, xanthine/uracil permease:Cof family protein:<-->:1020104..1020292 189 tatcaatctccttttaatttttacgaacaataatagaattatatcatttatcattcactttttcaacatctttgtttgatttatttaagaaattgatctaatttcattttttgtttggaatctgcttttctgcctgctttctgttataatagaaaacatcttatctgaaaagacactagaaaggtccct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1081:SMT_1082|SMT_1081:SMT_1082:K06901 putative MFS transporter, AGZA family, xanthine/uracil permease:Cof family protein:<-->:1020104..1020292 189 tatcaatctccttttaatttttacgaacaataatagaattatatcatttatcattcactttttcaacatctttgtttgatttatttaagaaattgatctaatttcattttttgtttggaatctgcttttctgcctgctttctgttataatagaaaacatcttatctgaaaagacactagaaaggtccct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1081:SMT_1082|SMT_1081:SMT_1082:K06901 putative MFS transporter, AGZA family, xanthine/uracil permease:Cof family protein:<-->:1020104..1020292 189 tatcaatctccttttaatttttacgaacaataatagaattatatcatttatcattcactttttcaacatctttgtttgatttatttaagaaattgatctaatttcattttttgtttggaatctgcttttctgcctgctttctgttataatagaaaacatcttatctgaaaagacactagaaaggtccct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tatcaatctccttttaatttttacgaacaataatagaattatatcatttatcattcactttttcaacatctttgtttgatttatttaagaaattgatctaatttcattttttgtttggaatctgcttttctgcctgctttctgttataatagaaaacatcttatctgaaaagacactagaaaggtccct Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 92 End: 187 ........................................................................................... M D L I S F F V W N L L F C L L S V I I E N I L S E K T L E R S .. tatcaatctccttttaatttttacgaacaataatagaattatatcatttatcattcactttttcaacatctttgtttgatttatttaagaaattgatctaatttcattttttgtttggaatctgcttttctgcctgctttctgttataatagaaaacatcttatctgaaaagacactagaaaggtccct 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: 89 Start: 38 End: 67 .....................................GTTGAAAAAGTGAATGATAAATGATATAAT.......................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 121 End: 150 ........................................................................................................................TCTGCTTTTCTGCCTGCTTTCTGTTATAAT....................................... PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 143 End: 172 ..............................................................................................................................................CTTTTCAGATAAGATGTTTTCTATTATAAC................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tatcaatctccttttaatttttacgaacaataatagaattatatcatttatcattcactttttcaacatctttgtttgatttatttaagaaattgatctaatttcattttttgtttggaatctgcttttctgcctgctttctgttataatagaaaacatcttatctgaaaagacactagaaaggtccct Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 46 HP_score: -3.8 Tail_Score: -3.07816 Start: 89 End: 105 Full_Region: ttccaaacaaaaaat gaaatt agatc aatttc ttaaataaatcaaac ........................................................................................gaaattagatcaatttc.................................................................................... Find igs database================================================ Query_seq: SMT_1081:SMT_1082|SMT_1081:SMT_1082:K06901 putative MFS transporter, AGZA family, xanthine/uracil permease:Cof family protein:<-->:1020104..1020292 189 tatcaatctccttttaatttttacgaacaataatagaattatatcatttatcattcactttttcaacatctttgtttgatttatttaagaaattgatctaatttcattttttgtttggaatctgcttttctgcctgctttctgttataatagaaaacatcttatctgaaaagacactagaaaggtccct Intra-Species Hit: Count: 1 Min: 1 Max: 189 Len: 189 Subject: smit_SMT_1081_SMT_1082|K06901 putative MFS transporter, AGZA family, xanthine/uracil permease:Cof family protein|NEGATIVE:POSITIVE|[1020104,1020292]|189 HSP 1 e-value: 1.0E-103 bit: 375.0 Len: 189 Query Start:1 Query End:189 Subject Strand: POSITIVE Subject Start: 1 Subject End: 189 tatcaatctccttttaatttttacgaacaataatagaattatatcatttatcattcactttttcaacatctttgtttgatttatttaagaaattgatctaatttcattttttgtttggaatctgcttttctgcctgctttctgttataatagaaaacatcttatctgaaaagacactagaaaggtccct tatcaatctccttttaatttttacgaacaataatagaattatatcatttatcattcactttttcaacatctttgtttgatttatttaagaaattgatctaatttcattttttgtttggaatctgcttttctgcctgctttctgttataatagaaaacatcttatctgaaaagacactagaaaggtccct Inter-species Hit: Count: 3 Min: 2 Max: 187 Len: 186 Subject: NC_008533_SPD_0266_SPD_0267|Cof family protein:xanthine/uracil permease family protein|NEGATIVE:POSITIVE|[265579,265767]|189 HSP 1 e-value: 1.0E-84 bit: 313.0 Len: 186 Query Start:2 Query End:187 Subject Strand: NEGATIVE Subject Start: 3 Subject End: 188 .atcaatctccttttaatttttacgaacaataatagaattatatcatttatcattcactttttcaacatctttgtttgatttatttaagaaattgatctaatttcattttttgtttggaatctgcttttctgcctgctttctgttataatagaaaacatcttatctgaaaagacactagaaaggtcc.. .atcaatctccttttaatttttacgaacaataatagaattatatcatttatcattcactttttcaatgtctttgtttgatttgtttaagaaattaatccaatttcattttttgtttggaatctgcttttctgcctgctttctgttataatagaagacatcttatctgaaaacacactagaaaggtcc.. Subject: NC_003098_spr0263_spr0264|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[265529,265663]|135 HSP 1 e-value: 5.0E-53 bit: 208.0 Len: 133 Query Start:55 Query End:187 Subject Strand: NEGATIVE Subject Start: 3 Subject End: 135 ......................................................tcactttttcaacatctttgtttgatttatttaagaaattgatctaatttcattttttgtttggaatctgcttttctgcctgctttctgttataatagaaaacatcttatctgaaaagacactagaaaggtcc.. ......................................................tcactttttcaatgtctttgtttgatttgtttaagaaattaatccaatttcattttttgtttggaatctgcttttctgcctgctttctgttataatagaagacatcttatctgaaaacacactagaaaggtcc.. Subject: NC_003028_SP_0286_SP_0287|Cof family protein:xanthine/uracil permease family protein|NEGATIVE:POSITIVE|[265079,265213]|135 HSP 1 e-value: 5.0E-53 bit: 208.0 Len: 133 Query Start:55 Query End:187 Subject Strand: NEGATIVE Subject Start: 3 Subject End: 135 ......................................................tcactttttcaacatctttgtttgatttatttaagaaattgatctaatttcattttttgtttggaatctgcttttctgcctgctttctgttataatagaaaacatcttatctgaaaagacactagaaaggtcc.. ......................................................tcactttttcaatgtctttgtttgatttgtttaagaaattaatccaatttcattttttgtttggaatctgcttttctgcctgctttctgttataatagaagacatcttatctgaaaacacactagaaaggtcc.. Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCAAUCUCCUUUUAAUUUUUACGAACAAUAAUAGAAUUAUAUCAUUUAUCAUUCACUUUUUCAACAUCUUUGUUUGAUUUAUUUAAGAAAUUGAUCUAAUUUCAUUUUUUGUUUGGAAUCUGCUUUUCUGCCUGCUUUCUGUUAUAAUAGAAAACAUCUUAUCUGAAAAGACACUAGAAAGGUCC ......................(((((((.(((..(((((.((((.((.((..........((((((....)).)))).........)))).)))).)))))..)))..)))))))......(((((((((..((.(((((((....))))))).)).....(((....)))...))))))))).. (-29.41) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGACCUUUCUAGUGUCUUUUCAGAUAAGAUGUUUUCUAUUAUAACAGAAAGCAGGCAGAAAAGCAGAUUCCAAACAAAAAAUGAAAUUAGAUCAAUUUCUUAAAUAAAUCAAACAAAGAUGUUGAAAAAGUGAAUGAUAAAUGAUAUAAUUCUAUUAUUGUUCGUAAAAAUUAAAAGGAGAUUGAU ((((((....)).))))(((((.......((((((((........)))))))).((......)).................)))))....(((((((((((.......((((.((....))))))......(((..((((..((......))..))))..)))............))))))))))) (-31.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 750 139 91 231 183 smit:SMT_1081|5end_K06901_putative_MFS_transporter,_AGZA_family,_xanthine/uracil_permease_1020013..1020243_NEGATIVE 307 136 92 132 85 smit:SMT_1752|5end_N-(5'-phosphoribosyl)-anthranilate_isomerase_1729772..1730002_POSITIVE 293 156 115 210 174 smit:SMT_1857|5end_hypothetical_protein_1820931..1821161_POSITIVE 293 156 115 210 174 smit:SMT_834|5end_hypothetical_protein_777112..777342_NEGATIVE 283 143 104 226 178 smit:SMT_2056|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1966323..1966553_POSITIVE 283 143 104 226 178 smit:SMT_1892|5end_hypothetical_protein_1845595..1845825_POSITIVE 282 146 107 59 16 smit:SMT_886|5end_single-stranded-DNA-specific_exonuclease_RecJ_834575..834805_NEGATIVE 278 140 93 135 77 smit:SMT_1267|5end_hypothetical_protein_1231658..1231888_POSITIVE 276 156 111 79 25 smit:SMT_1205|5end_response_regulator_1165700..1165930_NEGATIVE 275 140 95 151 103 smit:SMT_638|5end_hypothetical_protein_543449..543679_NEGATIVE 272 146 111 69 25 smit:SMT_1885|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1840057..1840287_NEGATIVE 271 144 101 153 98 smit:SMT_877|5end_hypothetical_protein_824412..824642_NEGATIVE 261 160 114 175 132 smit:SMT_1962|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1895639..1895869_NEGATIVE 261 160 114 175 132 smit:SMT_823|5end_putative_mucus_binding_protein_746790..747020_NEGATIVE 259 137 96 231 193 smit:SMT_381|5end_hypothetical_protein_317034..317264_POSITIVE 254 155 111 214 173 smit:SMT_155|5end_hypothetical_protein_102704..102934_NEGATIVE 253 167 122 170 118 smit:SMT_1189|5end_phosphoribosylaminoimidazole_carboxylase_ATPase_subunit_1147754..1147984_NEGATIVE 250 136 103 40 3 smit:SMT_1696|5end_hypothetical_protein_1678182..1678412_POSITIVE 243 144 113 191 149 smit:SMT_229|5end_mechanosensitive_ion_channel_165623..165853_NEGATIVE 242 138 91 203 154 smit:SMT_1611|5end_K05896_segregation_and_condensation_protein_A_1599305..1599535_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 307 136 92 145 98 smit:SMT_1751|3end_indole-3-glycerol_phosphate_synthase_1729865..1730015_POSITIVE 295 136 96 69 23 smit:SMT_380|3end_hypothetical_protein_316944..317094_POSITIVE 276 156 111 82 28 smit:SMT_1206|3end_similar_to_sensor_histidine_kinase_(AgrC_from_Staphylococcus)_1165697..1165847_NEGATIVE 275 140 95 121 73 smit:SMT_639|3end_6-phospho-beta-galactosidase_543479..543629_NEGATIVE 263 138 101 146 108 smit:SMT_878|3end_excinuclease_ABC,_subunit_C_824402..824552_NEGATIVE 250 136 103 77 40 smit:SMT_1695|3end_ribulose-phosphate_3-epimerase_1678299..1678449_POSITIVE 243 144 113 148 106 smit:SMT_230|3end_hypothetical_protein_predicted_by_Glimmer/Critica_165666..165816_NEGATIVE 234 144 101 125 82 smit:SMT_795|3end_similar_to_O6-alkylguanine-DNA-alkyltransferase_703500..703650_NEGATIVE 232 169 121 64 5 smit:SMT_805|3end_hypothetical_protein_predicted_by_Glimmer/Critica_715692..715842_NEGATIVE 229 142 116 80 48 smit:SMT_1073|3end_L-asparaginase_1012251..1012401_POSITIVE 224 137 92 65 16 smit:SMT_1612|3end_K06024_segregation_and_condensation_protein_B_1600701..1600851_POSITIVE 223 141 110 136 103 smit:SMT_788|3end_hypothetical_protein_699153..699303_NEGATIVE 220 143 101 70 30 smit:SMT_1920|3end_ABC_transporter,_ATP-binding_protein_1862736..1862886_NEGATIVE 220 143 109 122 77 smit:SMT_156|3end_hypothetical_protein_103518..103668_POSITIVE 218 140 91 151 107 smit:SMT_1939|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1876453..1876603_POSITIVE 217 139 115 38 9 smit:SMT_1256|3end_ketol-acid_reductoisomerase_1221855..1222005_NEGATIVE 217 156 116 48 4 smit:SMT_328|3end_23S_rRNA_methyltransferase_264863..265013_POSITIVE 216 136 111 144 116 smit:SMT_1889|3end_hypothetical_protein_1843467..1843617_POSITIVE 210 150 117 107 79 smit:SMT_1377|3end_hypothetical_protein_1355556..1355706_NEGATIVE 210 135 109 68 43 smit:SMT_921|3end_putative_PP2C_protein_phosphatase_874498..874648_NEGATIVE