Origin IGS: ttctttaatcgaaaagatgcctaaactatgtaatctcttctaccaaggcctctgtattttcccaacctagacaaggatcggtaatggagcaaccaaagacctctgnnnnn .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 nnnnncagaggtctttggttgctccattaccgatccttgtctaggttgggaaaatacagaggccttggtagaagagattacatagtttaggcatcttttcgattaaagaa Mask Tandem Repeat Region ================================================ ttctttaatcgaaaagatgcctaaactatgtaatctcttctaccaaggcctctgtattttcccaacctagacaaggatcggtaatggagcaaccaaagacctctgnnnnn Find is-nt database================================================ Query_seq: SMT_1794:SMT_1795|SMT_1794:SMT_1795:SOS responce UmuC protein:DNA polymerase III, delta subunit:<-<-:1769165..1769274 110 ttctttaatcgaaaagatgcctaaactatgtaatctcttctaccaaggcctctgtattttcccaacctagacaaggatcggtaatggagcaaccaaagacctctgnnnnn Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1794:SMT_1795|SMT_1794:SMT_1795:SOS responce UmuC protein:DNA polymerase III, delta subunit:<-<-:1769165..1769274 110 ttctttaatcgaaaagatgcctaaactatgtaatctcttctaccaaggcctctgtattttcccaacctagacaaggatcggtaatggagcaaccaaagacctctgnnnnn Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1794:SMT_1795|SMT_1794:SMT_1795:SOS responce UmuC protein:DNA polymerase III, delta subunit:<-<-:1769165..1769274 110 ttctttaatcgaaaagatgcctaaactatgtaatctcttctaccaaggcctctgtattttcccaacctagacaaggatcggtaatggagcaaccaaagacctctgnnnnn Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttctttaatcgaaaagatgcctaaactatgtaatctcttctaccaaggcctctgtattttcccaacctagacaaggatcggtaatggagcaaccaaagacctctgnnnnn Predict ORF larger than 30AA ================================================ ttctttaatcgaaaagatgcctaaactatgtaatctcttctaccaaggcctctgtattttcccaacctagacaaggatcggtaatggagcaaccaaagacctctgnnnnn 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================================================ ttctttaatcgaaaagatgcctaaactatgtaatctcttctaccaaggcctctgtattttcccaacctagacaaggatcggtaatggagcaaccaaagacctctgnnnnn Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1794:SMT_1795|SMT_1794:SMT_1795:SOS responce UmuC protein:DNA polymerase III, delta subunit:<-<-:1769165..1769274 110 ttctttaatcgaaaagatgcctaaactatgtaatctcttctaccaaggcctctgtattttcccaacctagacaaggatcggtaatggagcaaccaaagacctctgnnnnn Intra-Species Hit: Count: 1 Min: 1 Max: 105 Len: 105 Subject: smit_SMT_1794_SMT_1795|SOS responce UmuC protein:DNA polymerase III, delta subunit|NEGATIVE:NEGATIVE|[1769165,1769274]|110 HSP 1 e-value: 3.0E-53 bit: 208.0 Len: 105 Query Start:1 Query End:105 Subject Strand: POSITIVE Subject Start: 1 Subject End: 105 ttctttaatcgaaaagatgcctaaactatgtaatctcttctaccaaggcctctgtattttcccaacctagacaaggatcggtaatggagcaaccaaagacctctg..... ttctttaatcgaaaagatgcctaaactatgtaatctcttctaccaaggcctctgtattttcccaacctagacaaggatcggtaatggagcaaccaaagacctctg..... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCUUUAAUCGAAAAGAUGCCUAAACUAUGUAAUCUCUUCUACCAAGGCCUCUGUAUUUUCCCAACCUAGACAAGGAUCGGUAAUGGAGCAACCAAAGACCUCUG .(((((......)))))........((.((....((((..((((....(((.(((...............))))))...))))..))))....)).))....... (-13.96) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAGAGGUCUUUGGUUGCUCCAUUACCGAUCCUUGUCUAGGUUGGGAAAAUACAGAGGCCUUGGUAGAAGAGAUUACAUAGUUUAGGCAUCUUUUCGAUUAAAGAA ..(((((((((((((..(((...(((............)))..))).))).))))))))))....((((((((..(........)..)))))))).......... (-28.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 967 90 41 181 132 smit:SMT_1794|5end_SOS_responce_UmuC_protein_1769074..1769304_NEGATIVE 967 90 41 209 160 smit:SMT_1066|5end_holo-(acyl_carrier_protein)_synthase_1005411..1005641_POSITIVE 376 89 42 217 166 smit:SMT_792|5end_hypothetical_protein_predicted_by_Glimmer/Critica_702571..702801_NEGATIVE 349 90 47 175 129 smit:SMT_1065|5end_phospho-2-dehydro-3-deoxyheptonate_aldolase_1004341..1004571_POSITIVE 338 90 41 150 105 smit:SMT_918|5end_hypothetical_protein_871739..871969_NEGATIVE 290 89 42 192 134 smit:SMT_1929|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1869785..1870015_NEGATIVE 290 88 45 223 171 smit:SMT_1174|5end_acylneuraminate_cytidylyltransferase_1126321..1126551_NEGATIVE 283 97 63 92 49 smit:SMT_1045|5end_cochaperonin_GroES_987582..987812_NEGATIVE 280 79 31 61 4 smit:SMT_1398|5end_dihydroorotase_1373204..1373434_POSITIVE 274 96 63 52 10 smit:SMT_1047|5end_chaperonin,_10_kDa_988090..988320_NEGATIVE 262 87 41 72 31 smit:SMT_2018|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1936760..1936990_POSITIVE 262 78 34 139 94 smit:SMT_565|5end_polypeptide_deformylase_483373..483603_NEGATIVE 260 85 44 43 1 smit:SMT_1912|5end_D-alanyl-D-alanine_carboxypeptidase_1857920..1858150_NEGATIVE 259 88 42 189 146 smit:SMT_1234|5end_cadmium_efflux_system_accessory_protein_1194932..1195162_POSITIVE 257 90 44 209 173 smit:SMT_2030|5end_chromosomal_replication_initiator_protein_DnaA_1945167..1945397_NEGATIVE 257 90 44 149 113 smit:SMT_2002|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1924405..1924635_NEGATIVE 257 90 44 188 152 smit:SMT_1966|5end_DNA_polymerase_III_alpha_subunit_1897934..1898164_POSITIVE 257 90 44 149 113 smit:SMT_1942|5end_zinc_metalloprotease_ZmpB,_truncated_1877882..1878112_POSITIVE 257 90 44 189 153 smit:SMT_1926|5end_mevalonate_kinase_1867692..1867922_POSITIVE 257 90 44 170 134 smit:SMT_1885|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1840057..1840287_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 709 71 32 151 112 smit:SMT_1065|3end_phospho-2-dehydro-3-deoxyheptonate_aldolase_1005452..1005602_POSITIVE 338 90 41 148 103 smit:SMT_919|3end_hypothetical_protein_871741..871891_NEGATIVE 269 79 36 48 2 smit:SMT_1397|3end_mutator_MutT_protein_1373271..1373421_POSITIVE 257 90 44 69 33 smit:SMT_1630|3end_hypothetical_protein_1618141..1618291_POSITIVE 257 55 14 103 60 smit:SMT_1362|3end_chaperone_protein_hscC_1341414..1341564_NEGATIVE 257 70 22 75 24 smit:SMT_1131|3end_threonine_synthase_1065271..1065421_NEGATIVE 255 70 28 146 98 smit:SMT_1912|3end_D-alanyl-D-alanine_carboxypeptidase_1857807..1857957_NEGATIVE 255 73 43 77 50 smit:SMT_1812|3end_K07485_transposase_1787193..1787343_POSITIVE 255 70 28 146 98 smit:SMT_868|3end_D-alanyl-D-alanine_carboxypeptidase_816509..816659_NEGATIVE 254 56 18 79 45 smit:SMT_589|3end_hypothetical_protein_506827..506977_POSITIVE 253 90 42 141 75 smit:SMT_833|3end_hypothetical_protein_predicted_by_Glimmer/Critica_775183..775333_NEGATIVE 252 90 41 149 99 smit:SMT_1216|3end_hypothetical_protein_1175969..1176119_POSITIVE 252 82 56 30 3 smit:SMT_982|3end_D-tyrosyl-tRNA(Tyr)_deacylase_929211..929361_NEGATIVE 248 68 23 149 106 smit:SMT_1737|3end_peptidyl-prolyl_cis-trans_isomerase_1720598..1720748_POSITIVE 242 50 10 138 101 smit:SMT_306|3end_3-oxoacyl-_249117..249267_POSITIVE 236 87 45 75 37 smit:SMT_605|3end_DNA-binding_protein_HU_519257..519407_POSITIVE 235 89 46 79 30 smit:SMT_1532|3end_hypothetical_protein_1515994..1516144_NEGATIVE 234 99 51 129 77 smit:SMT_704|3end_Cof_family_protein_614548..614698_POSITIVE 228 89 46 139 81 smit:SMT_1831|3end_galactose-6-phosphate_isomerase_1800507..1800657_POSITIVE 225 55 18 81 43 smit:SMT_2125|3end_3-phosphoshikimate_1-carboxyvinyltransferase_2009098..2009248_POSITIVE