Origin IGS: ttaattaannnnncatttacctgattctacctttatctgctacttcttttgcgactgtacgacgctgataaattcttgatacttttaaatattggtctaatctcatttttataccctcaaattattattgtaccatttttatccytttatagaagaaaaatg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 catttttcttctataaarggataaaaatggtacaataataatttgagggtataaaaatgagattagaccaatatttaaaagtatcaagaatttatcagcgtcgtacagtcgcaaaagaagtagcagataaaggtagaatcaggtaaatgnnnnnttaattaa Mask Tandem Repeat Region ================================================ ttaattaannnnncatttacctgattctacctttatctgctacttcttttgcgactgtacgacgctgataaattcttgatacttttaaatattggtctaatctcatttttataccctcaaattattattgtaccatttttatccytttatagaagaaaaatg Find is-nt database================================================ Query_seq: SMT_2116:SMT_2117|SMT_2116:SMT_2117:extramembranal protein:transcription-repair coupling factor:-><-:2003835..2003996 162 ttaattaannnnncatttacctgattctacctttatctgctacttcttttgcgactgtacgacgctgataaattcttgatacttttaaatattggtctaatctcatttttataccctcaaattattattgtaccatttttatccytttatagaagaaaaatg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_2116:SMT_2117|SMT_2116:SMT_2117:extramembranal protein:transcription-repair coupling factor:-><-:2003835..2003996 162 ttaattaannnnncatttacctgattctacctttatctgctacttcttttgcgactgtacgacgctgataaattcttgatacttttaaatattggtctaatctcatttttataccctcaaattattattgtaccatttttatccytttatagaagaaaaatg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_2116:SMT_2117|SMT_2116:SMT_2117:extramembranal protein:transcription-repair coupling factor:-><-:2003835..2003996 162 ttaattaannnnncatttacctgattctacctttatctgctacttcttttgcgactgtacgacgctgataaattcttgatacttttaaatattggtctaatctcatttttataccctcaaattattattgtaccatttttatccytttatagaagaaaaatg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttaattaannnnncatttacctgattctacctttatctgctacttcttttgcgactgtacgacgctgataaattcttgatacttttaaatattggtctaatctcatttttataccctcaaattattattgtaccatttttatccytttatagaagaaaaatg Predict ORF larger than 30AA ================================================ Protein_Len: 42 Strand: + Start: 37 End: 162 .................................... M L L L L R L Y D A D K F L I L L N I G L I S F L Y P Q I I I V P F L S X Y R R K M Protein_Len: 31 Strand: - Start: 20 End: 112 ................... R I R G K D A V E K A V T R R Q Y I R S V K L Y Q D L R M K M .................................................. ttaattaannnnncatttacctgattctacctttatctgctacttcttttgcgactgtacgacgctgataaattcttgatacttttaaatattggtctaatctcatttttataccctcaaattattattgtaccatttttatccytttatagaagaaaaatg 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================================================ ttaattaannnnncatttacctgattctacctttatctgctacttcttttgcgactgtacgacgctgataaattcttgatacttttaaatattggtctaatctcatttttataccctcaaattattattgtaccatttttatccytttatagaagaaaaatg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_2116:SMT_2117|SMT_2116:SMT_2117:extramembranal protein:transcription-repair coupling factor:-><-:2003835..2003996 162 ttaattaannnnncatttacctgattctacctttatctgctacttcttttgcgactgtacgacgctgataaattcttgatacttttaaatattggtctaatctcatttttataccctcaaattattattgtaccatttttatccytttatagaagaaaaatg Intra-Species Hit: Count: 1 Min: 14 Max: 162 Len: 149 Subject: smit_SMT_2116_SMT_2117|extramembranal protein:transcription-repair coupling factor|POSITIVE:NEGATIVE|[2003835,2003996]|162 HSP 1 e-value: 2.0E-78 bit: 293.0 Len: 149 Query Start:14 Query End:162 Subject Strand: POSITIVE Subject Start: 14 Subject End: 162 .............catttacctgattctacctttatctgctacttcttttgcgactgtacgacgctgataaattcttgatacttttaaatattggtctaatctcatttttataccctcaaattattattgtaccatttttatccytttatagaagaaaaatg .............catttacctgattctacctttatctgctacttcttttgcgactgtacgacgctgataaattcttgatacttttaaatattggtctaatctcatttttataccctcaaattattattgtaccatttttatccytttatagaagaaaaatg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAUUUACCUGAUUCUACCUUUAUCUGCUACUUCUUUUGCGACUGUACGACGCUGAUAAAUUCUUGAUACUUUUAAAUAUUGGUCUAAUCUCAUUUUUAUACCCUCAAAUUAUUAUUGUACCAUUUUUAUCCYUUUAUAGAAGAAAAAUG .............................(((((...(((.(.....).))).((((((....((.(((...(((.....(((.(((........))).)))......))).....))).))..)))))).......)))))....... (-12.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAUUUUUCUUCUAUAAARGGAUAAAAAUGGUACAAUAAUAAUUUGAGGGUAUAAAAAUGAGAUUAGACCAAUAUUUAAAAGUAUCAAGAAUUUAUCAGCGUCGUACAGUCGCAAAAGAAGUAGCAGAUAAAGGUAGAAUCAGGUAAAUG (((((.((((((((.....((((((..((((((..(((....)))..(((.(((........))).)))...........))))))....)))))).(((.(.....).)))....................)))))...))).))))) (-20.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 800 58 11 57 9 smit:SMT_1676|5end_S4_domain_protein_1661764..1661994_NEGATIVE 800 58 11 57 9 smit:SMT_95|5end_S4_domain_protein_28177..28407_POSITIVE 482 110 61 226 178 smit:SMT_1968|5end_transcription-repair_coupling_factor_1900640..1900870_NEGATIVE 303 49 7 169 118 smit:SMT_1711|5end_Xaa-Pro_dipeptidase_1697494..1697724_NEGATIVE 302 49 7 211 169 smit:SMT_109|5end_beta-galactosidase_53925..54155_POSITIVE 284 54 17 146 101 smit:SMT_908|5end_hypothetical_protein_857230..857460_NEGATIVE 264 58 12 78 14 smit:SMT_1191|5end_phosphoribosylamine--glycine_ligase_1149737..1149967_NEGATIVE 264 51 12 231 178 smit:SMT_540|5end_DNA_gyrase,_B_subunit_456358..456588_POSITIVE 261 64 26 231 198 smit:SMT_850|5end_hypothetical_protein_797014..797244_NEGATIVE 261 47 3 134 87 smit:SMT_628|5end_glucose-1-phosphate_adenylyltransferase,_GlgD_subunit_532831..533061_POSITIVE 261 67 21 51 11 smit:SMT_107|5end_ribose-phosphate_pyrophosphokinase_52402..52632_POSITIVE 259 75 33 87 46 smit:SMT_1386|5end_phosphoenolpyruvate-protein_phosphotransferase_1362806..1363036_POSITIVE 259 50 1 191 132 smit:SMT_877|5end_hypothetical_protein_824412..824642_NEGATIVE 259 69 24 57 22 smit:SMT_412|5end_hypothetical_protein_predicted_by_Glimmer/Critica_356606..356836_NEGATIVE 258 54 23 175 145 smit:SMT_2035|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1947167..1947397_POSITIVE 255 54 14 142 99 smit:SMT_1752|5end_N-(5'-phosphoribosyl)-anthranilate_isomerase_1729772..1730002_POSITIVE 254 39 7 88 49 smit:SMT_946|5end_hypothetical_protein_896409..896639_NEGATIVE 249 45 6 73 30 smit:SMT_1612|5end_K06024_segregation_and_condensation_protein_B_1600052..1600282_POSITIVE 241 57 17 68 33 smit:SMT_1872|5end_K03217_preprotein_translocase_YidC_subunit_1831764..1831994_NEGATIVE 241 70 25 138 91 smit:SMT_422|5end_K02004_363781..364011_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 582 130 82 70 22 smit:SMT_1969|3end_transcription-repair_coupling_factor_1900816..1900966_NEGATIVE 582 130 82 70 22 smit:SMT_1677|3end_transcription-repair_coupling_factor_1661822..1661972_NEGATIVE 582 130 82 70 22 smit:SMT_94|3end_transcription-repair_coupling_factor_28199..28349_POSITIVE 302 49 7 79 37 smit:SMT_108|3end_hypothetical_protein_53873..54023_POSITIVE 292 53 12 147 95 smit:SMT_1554|3end_isoleucyl-tRNA_synthetase_1539912..1540062_POSITIVE 278 57 16 68 26 smit:SMT_717|3end_Mn2+_and_Fe2+_transporter_of_the_NRAMP_family_622815..622965_NEGATIVE 261 47 3 144 97 smit:SMT_627|3end_glucose-1-phosphate_adenylyltransferase_532921..533071_POSITIVE 259 75 33 72 31 smit:SMT_1385|3end_phosphocarrier_protein_HPr_1362871..1363021_POSITIVE 249 45 6 54 11 smit:SMT_1611|3end_K05896_segregation_and_condensation_protein_A_1600113..1600263_POSITIVE 244 57 13 128 84 smit:SMT_1443|3end_23S_rRNA_m(5)U_1939_methyltransferase_1426503..1426653_NEGATIVE 241 70 25 125 78 smit:SMT_421|3end_K02003_363848..363998_POSITIVE 239 53 24 43 12 smit:SMT_773|3end_UDP-N-acetylenolpyruvoylglucosamine_reductase_683460..683610_NEGATIVE 238 52 17 151 108 smit:SMT_909|3end_type_I_restriction_enzyme_M_protein_857223..857373_NEGATIVE 238 68 23 150 110 smit:SMT_639|3end_6-phospho-beta-galactosidase_543479..543629_NEGATIVE 234 69 23 136 90 smit:SMT_1842|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1807784..1807934_NEGATIVE 230 49 1 63 22 smit:SMT_101|3end_cell_division_protein_34067..34217_POSITIVE 229 52 23 48 16 smit:SMT_2041|3end_transcription-repair_coupling_factor_1951487..1951637_NEGATIVE 227 53 18 55 8 smit:SMT_451|3end_thiamine-phosphate_pyrophosphorylase_389647..389797_POSITIVE 224 46 8 146 106 smit:SMT_1751|3end_indole-3-glycerol_phosphate_synthase_1729865..1730015_POSITIVE 224 50 1 131 85 smit:SMT_264|3end_hypothetical_protein_203321..203471_NEGATIVE