Origin IGS: acgaatgacaaaataataaacgatttaactctaaaagttagacaatcagtctgatttttagggtttttctttatgctaataaaaatgtgtatttatagatatgagtgtttaaaaagaatgaccttcatctggctagagaactcatatagtggtataatttaagaaacataatgaaaatagctttagtgtggatgcattacaatatagaggggaaaag .........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 cttttcccctctatattgtaatgcatccacactaaagctattttcattatgtttcttaaattataccactatatgagttctctagccagatgaaggtcattctttttaaacactcatatctataaatacacatttttattagcataaagaaaaaccctaaaaatcagactgattgtctaacttttagagttaaatcgtttattattttgtcattcgt Mask Tandem Repeat Region ================================================ acgaatgacaaaataataaacgatttaactctaaaagttagacaatcagtctgatttttagggtttttctttatgctaataaaaatgtgtatttatagatatgagtgtttaaaaagaatgaccttcatctggctagagaactcatatagtggtataatttaagaaacataatgaaaatagctttagtgtggatgcattacaatatagaggggaaaag Find is-nt database================================================ Query_seq: SMT_1313:SMT_1314|SMT_1313:SMT_1314:extramembranal protein:dTDP-4-dehydrorhamnose 3,5-epimerase related enzyme:->->:1278683..1278899 217 acgaatgacaaaataataaacgatttaactctaaaagttagacaatcagtctgatttttagggtttttctttatgctaataaaaatgtgtatttatagatatgagtgtttaaaaagaatgaccttcatctggctagagaactcatatagtggtataatttaagaaacataatgaaaatagctttagtgtggatgcattacaatatagaggggaaaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1313:SMT_1314|SMT_1313:SMT_1314:extramembranal protein:dTDP-4-dehydrorhamnose 3,5-epimerase related enzyme:->->:1278683..1278899 217 acgaatgacaaaataataaacgatttaactctaaaagttagacaatcagtctgatttttagggtttttctttatgctaataaaaatgtgtatttatagatatgagtgtttaaaaagaatgaccttcatctggctagagaactcatatagtggtataatttaagaaacataatgaaaatagctttagtgtggatgcattacaatatagaggggaaaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1313:SMT_1314|SMT_1313:SMT_1314:extramembranal protein:dTDP-4-dehydrorhamnose 3,5-epimerase related enzyme:->->:1278683..1278899 217 acgaatgacaaaataataaacgatttaactctaaaagttagacaatcagtctgatttttagggtttttctttatgctaataaaaatgtgtatttatagatatgagtgtttaaaaagaatgaccttcatctggctagagaactcatatagtggtataatttaagaaacataatgaaaatagctttagtgtggatgcattacaatatagaggggaaaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 acgaatgacaaaataataaacgatttaactctaaaagttagacaatcagtctgatttttagggtttttctttatgctaataaaaatgtgtatttatagatatgagtgtttaaaaagaatgaccttcatctggctagagaactcatatagtggtataatttaagaaacataatgaaaatagctttagtgtggatgcattacaatatagaggggaaaag Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: - Start: 3 End: 92 .. F S L I I F S K V R F T L C D T Q N K P N K K I S I F I H M ............................................................................................................................. acgaatgacaaaataataaacgatttaactctaaaagttagacaatcagtctgatttttagggtttttctttatgctaataaaaatgtgtatttatagatatgagtgtttaaaaagaatgaccttcatctggctagagaactcatatagtggtataatttaagaaacataatgaaaatagctttagtgtggatgcattacaatatagaggggaaaag 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: 82 Start: 129 End: 158 ................................................................................................................................CTGGCTAGAGAACTCATATAGTGGTATAAT........................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ acgaatgacaaaataataaacgatttaactctaaaagttagacaatcagtctgatttttagggtttttctttatgctaataaaaatgtgtatttatagatatgagtgtttaaaaagaatgaccttcatctggctagagaactcatatagtggtataatttaagaaacataatgaaaatagctttagtgtggatgcattacaatatagaggggaaaag Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -9.5 Tail_Score: -5.40464 Start: 29 End: 63 Full_Region: TAATAAACGATTTAA CTCTAAAAGTTAGAC AATCA GTCTGATTTTTAGGG TTTTTCTTTATGCTA ............................CTCTAAAAGTTAGACAATCAGTCTGATTTTTAGGG.......................................................................................................................................................... Find igs database================================================ Query_seq: SMT_1313:SMT_1314|SMT_1313:SMT_1314:extramembranal protein:dTDP-4-dehydrorhamnose 3,5-epimerase related enzyme:->->:1278683..1278899 217 acgaatgacaaaataataaacgatttaactctaaaagttagacaatcagtctgatttttagggtttttctttatgctaataaaaatgtgtatttatagatatgagtgtttaaaaagaatgaccttcatctggctagagaactcatatagtggtataatttaagaaacataatgaaaatagctttagtgtggatgcattacaatatagaggggaaaag Intra-Species Hit: Count: 1 Min: 1 Max: 217 Len: 217 Subject: smit_SMT_1313_SMT_1314|extramembranal protein:dTDP-4-dehydrorhamnose 3,5-epimerase related enzyme|POSITIVE:POSITIVE|[1278683,1278899]|217 HSP 1 e-value: 1.0E-120 bit: 430.0 Len: 217 Query Start:1 Query End:217 Subject Strand: POSITIVE Subject Start: 1 Subject End: 217 acgaatgacaaaataataaacgatttaactctaaaagttagacaatcagtctgatttttagggtttttctttatgctaataaaaatgtgtatttatagatatgagtgtttaaaaagaatgaccttcatctggctagagaactcatatagtggtataatttaagaaacataatgaaaatagctttagtgtggatgcattacaatatagaggggaaaag acgaatgacaaaataataaacgatttaactctaaaagttagacaatcagtctgatttttagggtttttctttatgctaataaaaatgtgtatttatagatatgagtgtttaaaaagaatgaccttcatctggctagagaactcatatagtggtataatttaagaaacataatgaaaatagctttagtgtggatgcattacaatatagaggggaaaag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACGAAUGACAAAAUAAUAAACGAUUUAACUCUAAAAGUUAGACAAUCAGUCUGAUUUUUAGGGUUUUUCUUUAUGCUAAUAAAAAUGUGUAUUUAUAGAUAUGAGUGUUUAAAAAGAAUGACCUUCAUCUGGCUAGAGAACUCAUAUAGUGGUAUAAUUUAAGAAACAUAAUGAAAAUAGCUUUAGUGUGGAUGCAUUACAAUAUAGAGGGGAAAAG ...........................((((((((((((((((.....))))))))))))))))((..((((((((((.........((((((.....((((((((.((((...(((.((.....)))))...))))..))))))))...))))))..........(.....)....))))..((((((....))))))....))))))..)).... (-44.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUUUCCCCUCUAUAUUGUAAUGCAUCCACACUAAAGCUAUUUUCAUUAUGUUUCUUAAAUUAUACCACUAUAUGAGUUCUCUAGCCAGAUGAAGGUCAUUCUUUUUAAACACUCAUAUCUAUAAAUACACAUUUUUAUUAGCAUAAAGAAAAACCCUAAAAAUCAGACUGAUUGUCUAACUUUUAGAGUUAAAUCGUUUAUUAUUUUGUCAUUCGU ............(((..((((((.................(((((.(((((((.................((((((((..........((((.....))))..........))))))))..(((((........))))).))))))).)))))...((((((.(.((((.....)))).).))))))............))))))..)))....... (-26.05) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 319 64 28 230 192 smit:SMT_541|5end_K03697_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpE_457842..458072_NEGATIVE 306 150 114 159 119 smit:SMT_1843|5end_transposase,_TnpA_1808100..1808330_POSITIVE 306 150 114 159 119 smit:SMT_1238|5end_transposase,_TnpA_1198738..1198968_POSITIVE 282 64 28 139 101 smit:SMT_734|5end_hypothetical_protein_639967..640197_POSITIVE 282 64 28 138 100 smit:SMT_570|5end_hypothetical_protein_488581..488811_POSITIVE 282 64 28 138 100 smit:SMT_542|5end_hypothetical_protein_457940..458170_POSITIVE 277 208 177 59 30 smit:SMT_809|5end_sensor_histidine_kinase_(homolog_to_BlpH_Spn)_719745..719975_NEGATIVE 255 147 103 214 167 smit:SMT_1454|5end_cytidine_deaminase_1437886..1438116_NEGATIVE 243 75 35 92 42 smit:SMT_347|5end_hypothetical_protein_286210..286440_NEGATIVE 240 165 123 72 36 smit:SMT_505|5end_peptidyl-prolyl_cis-trans_isomerase,_cyclophilin-type_437106..437336_NEGATIVE 240 165 123 72 36 smit:SMT_502|5end_peptidyl-prolyl_cis-trans_isomerase,_cyclophilin-type_435675..435905_NEGATIVE 238 78 41 182 147 smit:SMT_1433|5end_hypothetical_protein_1417783..1418013_NEGATIVE 232 56 33 231 210 smit:SMT_399|5end_cytochrome_c-type_biogenesis_protein_CcdA_328366..328596_POSITIVE 226 68 22 50 11 smit:SMT_874|5end_dipeptidase_822765..822995_NEGATIVE 221 142 101 120 76 smit:SMT_354|5end_hypothetical_protein_291343..291573_POSITIVE 216 147 103 174 140 smit:SMT_1303|5end_tRNA-dihydrouridine_synthase_1265731..1265961_NEGATIVE 212 168 122 206 156 smit:SMT_1803|5end_K03693_penicillin_binding_protein_1776804..1777034_POSITIVE 209 137 91 218 173 smit:SMT_1566|5end_K03475_PTS_system,_unknown_pentitol_phosphotransferase_enzyme_IIC_component_1557918..1558148_POSITIVE 209 152 111 97 60 smit:SMT_479|5end_K03308_neurotransmitter:Na+_symporter,_NSS_family_416656..416886_NEGATIVE 209 152 111 97 60 smit:SMT_462|5end_K03308_neurotransmitter:Na+_symporter,_NSS_family_401658..401888_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 349 65 27 64 26 smit:SMT_1313|3end_extramembranal_protein_1278622..1278772_POSITIVE 257 63 33 71 43 smit:SMT_398|3end_hypothetical_protein_328279..328429_POSITIVE 238 78 41 62 27 smit:SMT_1434|3end_neopullulanase_1417903..1418053_NEGATIVE 227 62 28 49 12 smit:SMT_1761|3end_transcriptional_activator,_putative_1737185..1737335_POSITIVE 225 76 31 40 2 smit:SMT_875|3end_nitroreductase_family_protein_822779..822929_NEGATIVE 221 142 101 61 17 smit:SMT_353|3end_immunity_protein_BlpL_291364..291514_POSITIVE 218 70 23 123 73 smit:SMT_1205|3end_response_regulator_1164969..1165119_NEGATIVE 215 70 28 111 67 smit:SMT_571|3end_putative_transposase,_ISSmu1_490009..490159_POSITIVE 211 78 31 116 67 smit:SMT_1945|3end_putative_dihydrolipoamide_S-acetyltransferase_1880646..1880796_POSITIVE 208 137 91 151 102 smit:SMT_1280|3end_cysteine_synthase_1243543..1243693_NEGATIVE 206 155 113 50 1 smit:SMT_1085|3end_sensor_histidine_kinase_(homolog_to_HK11_Spn)_1021926..1022076_NEGATIVE 205 152 123 52 15 smit:SMT_1321|3end_K02074_zinc/manganese_transport_system_ATP-binding_protein_1291458..1291608_POSITIVE 204 74 36 90 51 smit:SMT_1605|3end_hypothetical_protein_1595737..1595887_POSITIVE 203 69 33 97 59 smit:SMT_1102|3end_transketolase_1043029..1043179_NEGATIVE 201 155 117 61 21 smit:SMT_213|3end_leucyl-tRNA_synthetase_146167..146317_POSITIVE 200 166 121 60 7 smit:SMT_930|3end_ATP-dependent_RNA_helicase_883389..883539_NEGATIVE 197 152 112 59 8 smit:SMT_1845|3end_K01191_alpha-mannosidase_1810435..1810585_POSITIVE 195 198 179 145 121 smit:SMT_1785|3end_phenylalanyl-tRNA_synthetase_beta_chain_1762327..1762477_NEGATIVE 195 63 21 121 79 smit:SMT_518|3end_biotin_synthase_443215..443365_NEGATIVE 194 77 31 88 41 smit:SMT_1354|3end_diacylglycerol_kinase_1331606..1331756_NEGATIVE