Origin IGS: attcttaccttctgacaataaagtttacgctttcatttgttgatatagtaaatatatctcaatatcttacatttgtcaataggttttcacaatttttttcatttttcactaaattttacacaaaaaacttataaaaatcttgtaatttatagtcataacaacattttagtaccatgtataaaaatgtagatttttctatttattcctatgtaaattaaccttatagcctattattctaatttttttattcaaaaggctactattctttccagttttatggtaaaatctttaacggagaaggaaaatcgaggtgaaaat .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 attttcacctcgattttccttctccgttaaagattttaccataaaactggaaagaatagtagccttttgaataaaaaaattagaataataggctataaggttaatttacataggaataaatagaaaaatctacatttttatacatggtactaaaatgttgttatgactataaattacaagatttttataagttttttgtgtaaaatttagtgaaaaatgaaaaaaattgtgaaaacctattgacaaatgtaagatattgagatatatttactatatcaacaaatgaaagcgtaaactttattgtcagaaggtaagaat Mask Tandem Repeat Region ================================================ attcttaccttctgacaataaagtttacgctttcatttgttgatatagtaaatatatctcaatatcttacatttgtcaataggttttcacaatttttttcatttttcactaaattttacacaaaaaacttataaaaatcttgtaatttatagtcataacaacattttagtaccatgtataaaaatgtagatttttctatttattcctatgtaaattaaccttatagcctattattctaatttttttattcaaaaggctactattctttccagttttatggtaaaatctttaacggagaaggaaaatcgaggtgaaaat Find is-nt database================================================ Query_seq: SMT_1185:SMT_1186|SMT_1185:SMT_1186:beta-galactosidase:hypothetical protein:<-->:1143912..1144229 318 attcttaccttctgacaataaagtttacgctttcatttgttgatatagtaaatatatctcaatatcttacatttgtcaataggttttcacaatttttttcatttttcactaaattttacacaaaaaacttataaaaatcttgtaatttatagtcataacaacattttagtaccatgtataaaaatgtagatttttctatttattcctatgtaaattaaccttatagcctattattctaatttttttattcaaaaggctactattctttccagttttatggtaaaatctttaacggagaaggaaaatcgaggtgaaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1185:SMT_1186|SMT_1185:SMT_1186:beta-galactosidase:hypothetical protein:<-->:1143912..1144229 318 attcttaccttctgacaataaagtttacgctttcatttgttgatatagtaaatatatctcaatatcttacatttgtcaataggttttcacaatttttttcatttttcactaaattttacacaaaaaacttataaaaatcttgtaatttatagtcataacaacattttagtaccatgtataaaaatgtagatttttctatttattcctatgtaaattaaccttatagcctattattctaatttttttattcaaaaggctactattctttccagttttatggtaaaatctttaacggagaaggaaaatcgaggtgaaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1185:SMT_1186|SMT_1185:SMT_1186:beta-galactosidase:hypothetical protein:<-->:1143912..1144229 318 attcttaccttctgacaataaagtttacgctttcatttgttgatatagtaaatatatctcaatatcttacatttgtcaataggttttcacaatttttttcatttttcactaaattttacacaaaaaacttataaaaatcttgtaatttatagtcataacaacattttagtaccatgtataaaaatgtagatttttctatttattcctatgtaaattaaccttatagcctattattctaatttttttattcaaaaggctactattctttccagttttatggtaaaatctttaacggagaaggaaaatcgaggtgaaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 attcttaccttctgacaataaagtttacgctttcatttgttgatatagtaaatatatctcaatatcttacatttgtcaataggttttcacaatttttttcatttttcactaaattttacacaaaaaacttataaaaatcttgtaatttatagtcataacaacattttagtaccatgtataaaaatgtagatttttctatttattcctatgtaaattaaccttatagcctattattctaatttttttattcaaaaggctactattctttccagttttatggtaaaatctttaacggagaaggaaaatcgaggtgaaaat Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: + Start: 12 End: 131 ........... M T I K F T L S F V D I V N I S Q Y L T F V N R F S Q F F S F F T K F Y T K N L ........................................................................................................................................................................................... Protein_Len: 45 Strand: + Start: 52 End: 186 ................................................... M Y L N I L H L S I G F H N F F H F S L N F T Q K T Y K N L V I Y S H N N I L V P C I K M .................................................................................................................................... Protein_Len: 35 Strand: + Start: 214 End: 318 ..................................................................................................................................................................................................................... M N L I A Y Y S N F F I Q K A T I L S S F M V K S L T E K E N R G E N attcttaccttctgacaataaagtttacgctttcatttgttgatatagtaaatatatctcaatatcttacatttgtcaataggttttcacaatttttttcatttttcactaaattttacacaaaaaacttataaaaatcttgtaatttatagtcataacaacattttagtaccatgtataaaaatgtagatttttctatttattcctatgtaaattaaccttatagcctattattctaatttttttattcaaaaggctactattctttccagttttatggtaaaatctttaacggagaaggaaaatcgaggtgaaaat 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: 88 Start: 51 End: 80 ..................................................ATTGACAAATGTAAGATATTGAGATATATT.............................................................................................................................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ attcttaccttctgacaataaagtttacgctttcatttgttgatatagtaaatatatctcaatatcttacatttgtcaataggttttcacaatttttttcatttttcactaaattttacacaaaaaacttataaaaatcttgtaatttatagtcataacaacattttagtaccatgtataaaaatgtagatttttctatttattcctatgtaaattaaccttatagcctattattctaatttttttattcaaaaggctactattctttccagttttatggtaaaatctttaacggagaaggaaaatcgaggtgaaaat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1185:SMT_1186|SMT_1185:SMT_1186:beta-galactosidase:hypothetical protein:<-->:1143912..1144229 318 attcttaccttctgacaataaagtttacgctttcatttgttgatatagtaaatatatctcaatatcttacatttgtcaataggttttcacaatttttttcatttttcactaaattttacacaaaaaacttataaaaatcttgtaatttatagtcataacaacattttagtaccatgtataaaaatgtagatttttctatttattcctatgtaaattaaccttatagcctattattctaatttttttattcaaaaggctactattctttccagttttatggtaaaatctttaacggagaaggaaaatcgaggtgaaaat Intra-Species Hit: Count: 1 Min: 1 Max: 318 Len: 318 Subject: smit_SMT_1185_SMT_1186|beta-galactosidase:hypothetical protein|NEGATIVE:POSITIVE|[1143912,1144229]|318 HSP 1 e-value: 1.0E-104 bit: 379.0 Len: 212 Query Start:107 Query End:318 Subject Strand: POSITIVE Subject Start: 107 Subject End: 318 ..........................................................................................................cactaaattttacacaaaaaacttataaaaatcttgtaatttatagtcataacaacattttagtaccatgtataaaaatgtagatttttctatttattcctatgtaaattaaccttatagcctattattctaannnnnnnattcaaaaggctactattctttccagttttatggtaaaatctttaacggagaaggaaaatcgaggtgaaaat ..........................................................................................................cactaaattttacacaaaaaacttataaaaatcttgtaatttatagtcataacaacattttagtaccatgtataaaaatgtagatttttctatttattcctatgtaaattaaccttatagcctattattctaatttttttattcaaaaggctactattctttccagttttatggtaaaatctttaacggagaaggaaaatcgaggtgaaaat HSP 2 e-value: 5.0E-45 bit: 182.0 Len: 92 Query Start:1 Query End:92 Subject Strand: POSITIVE Subject Start: 1 Subject End: 92 attcttaccttctgacaataaagtttacgctttcatttgttgatatagtaaatatatctcaatatcttacatttgtcaataggttttcacaa.................................................................................................................................................................................................................................. attcttaccttctgacaataaagtttacgctttcatttgttgatatagtaaatatatctcaatatcttacatttgtcaataggttttcacaa.................................................................................................................................................................................................................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUCUUACCUUCUGACAAUAAAGUUUACGCUUUCAUUUGUUGAUAUAGUAAAUAUAUCUCAAUAUCUUACAUUUGUCAAUAGGUUUUCACAAUUUUUUUCAUUUUUCACUAAAUUUUACACAAAAAACUUAUAAAAAUCUUGUAAUUUAUAGUCAUAACAACAUUUUAGUACCAUGUAUAAAAAUGUAGAUUUUUCUAUUUAUUCCUAUGUAAAUUAACCUUAUAGCCUAUUAUUCUAAUUUUUUUAUUCAAAAGGCUACUAUUCUUUCCAGUUUUAUGGUAAAAUCUUUAACGGAGAAGGAAAAUCGAGGUGAAAAU ......((((..((((((.(((((....)))))...(((..((((((.....)))))).)))..........))))))..))))((((((.....(((((.((((((..((((((((((.((.((((((.............(((((((((.........(((((((.((((...)))).)))))))(((....)))...........)))))))))......((((((........................))))))...........)))))).)))))))))..)))..)))))).))))).....)))))).. (-55.36) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUUCACCUCGAUUUUCCUUCUCCGUUAAAGAUUUUACCAUAAAACUGGAAAGAAUAGUAGCCUUUUGAAUAAAAAAAUUAGAAUAAUAGGCUAUAAGGUUAAUUUACAUAGGAAUAAAUAGAAAAAUCUACAUUUUUAUACAUGGUACUAAAAUGUUGUUAUGACUAUAAAUUACAAGAUUUUUAUAAGUUUUUUGUGUAAAAUUUAGUGAAAAAUGAAAAAAAUUGUGAAAACCUAUUGACAAAUGUAAGAUAUUGAGAUAUAUUUACUAUAUCAACAAAUGAAAGCGUAAACUUUAUUGUCAGAAGGUAAGAAU .(((((((...((((((.((..(((.....(((((..(((......((....))....(((((((.(((..(((.....)))...))).)))))))..))).))))).....)))......)).)))))).....(((((((((....((((((((.((((.((........)).)))).)))))....)))....)))))))))....)))))))..................((((.(((((((..............((((((.....))))))........((((......)))).))))))).))))...... (-56.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 742 50 1 141 92 smit:SMT_1185|5end_beta-galactosidase_1143821..1144051_NEGATIVE 238 296 254 55 19 smit:SMT_1025|5end_hypothetical_protein_960557..960787_NEGATIVE 235 279 248 61 23 smit:SMT_1845|5end_K01191_alpha-mannosidase_1809663..1809893_POSITIVE 235 279 248 61 23 smit:SMT_114|5end_alpha-mannosidase_62804..63034_POSITIVE 233 280 238 71 23 smit:SMT_1434|5end_neopullulanase_1419645..1419875_NEGATIVE 230 272 241 49 11 smit:SMT_746|5end_LPS_biosynthesis_protein_651222..651452_NEGATIVE 229 173 139 101 69 smit:SMT_713|5end_heat_shock_protein_HtpX_620888..621118_NEGATIVE 229 173 139 101 69 smit:SMT_695|5end_heat_shock_protein_HtpX_606883..607113_NEGATIVE 227 103 62 186 148 smit:SMT_1734|5end_serine/threonine_protein_phosphatase_1718558..1718788_POSITIVE 214 283 255 156 130 smit:SMT_1897|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1848858..1849088_NEGATIVE 214 284 255 184 153 smit:SMT_1705|5end_UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-_diaminopimelate--D-alanyl-D-alanine_ligase_1688558..1688788_POSITIVE 213 293 254 124 93 smit:SMT_736|5end_hypothetical_protein_642270..642500_NEGATIVE 213 50 11 128 84 smit:SMT_344|5end_K02503_Hit-like_protein_involved_in_cell-cycle_regulation_283974..284204_NEGATIVE 212 279 234 62 20 smit:SMT_869|5end_hypothetical_protein_817698..817928_NEGATIVE 212 251 218 230 187 smit:SMT_830|5end_hypothetical_protein_772623..772853_NEGATIVE 210 69 21 139 94 smit:SMT_2024|5end_hypothetical_protein_1940359..1940589_POSITIVE 210 69 21 139 94 smit:SMT_724|5end_hypothetical_protein_630060..630290_NEGATIVE 209 269 224 221 173 smit:SMT_910|5end_type_I_restriction_enzyme_R_protein_861889..862119_NEGATIVE 206 109 75 137 109 smit:SMT_1738|5end_peptidyl-prolyl_cis-trans_isomerase_1720497..1720727_POSITIVE 206 298 254 41 2 smit:SMT_301|5end_hypothetical_protein_244086..244316_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 264 298 253 121 75 smit:SMT_903|3end_hypothetical_protein_851945..852095_NEGATIVE 255 301 271 135 109 smit:SMT_252|3end_K07720_two-component_system,_response_regulator_YesN_187454..187604_NEGATIVE 229 173 139 99 67 smit:SMT_714|3end_hypothetical_protein_predicted_by_Glimmer/Critica_620890..621040_NEGATIVE 229 173 139 99 67 smit:SMT_696|3end_K03744_LemA_protein_606885..607035_NEGATIVE 225 300 255 133 83 smit:SMT_146|3end_sugar_transport_system_permease_protein_97382..97532_POSITIVE 221 276 233 107 62 smit:SMT_1388|3end_hypothetical_protein_1365833..1365983_POSITIVE 214 283 255 137 111 smit:SMT_1898|3end_aminotransferase_(class_V),_putative_1848877..1849027_NEGATIVE 214 284 255 100 69 smit:SMT_1704|3end_D-alanine-D-alanine_ligase_1688554..1688704_POSITIVE 213 293 254 124 93 smit:SMT_737|3end_hypothetical_protein_642270..642420_NEGATIVE 212 279 234 60 18 smit:SMT_870|3end_hypothetical_protein_817700..817850_NEGATIVE 210 282 247 82 39 smit:SMT_739|3end_50S_ribosomal_protein_L7/L12_643274..643424_NEGATIVE 210 69 21 149 104 smit:SMT_725|3end_hypothetical_protein_630050..630200_NEGATIVE 204 288 248 127 71 smit:SMT_859|3end_K02086_DNA_replication_protein_803381..803531_NEGATIVE 201 115 75 92 50 smit:SMT_1908|3end_isochorismatase_family_protein_1855237..1855387_POSITIVE 201 110 65 84 36 smit:SMT_952|3end_hypothetical_protein_900115..900265_NEGATIVE 200 309 286 44 20 smit:SMT_972|3end_ABC-type_multidrug/protein/lipid_transport_system,_ATPase_component_919256..919406_NEGATIVE 200 50 1 68 20 smit:SMT_773|3end_UDP-N-acetylenolpyruvoylglucosamine_reductase_683460..683610_NEGATIVE 199 288 248 38 8 smit:SMT_125|3end_hypothetical_protein_76717..76867_NEGATIVE 197 244 213 35 5 smit:SMT_1935|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1873930..1874080_POSITIVE 197 244 213 35 5 smit:SMT_1314|3end_dTDP-4-dehydrorhamnose_3,5-epimerase_related_enzyme_1280192..1280342_POSITIVE