Origin IGS: gcatttacgcgacgttcagatccaaggtcagcaatcagttcgttcttattgtcataaatcttgctagaagttgtcggaattagtttacttcagataaggccttccagcannnnnttaattaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttaattaannnnntgctggaaggccttatctgaagtaaactaattccgacaacttctagcaagatttatgacaataagaacgaactgattgctgaccttggatctgaacgtcgcgtaaatgc Mask Tandem Repeat Region ================================================ gcatttacgcgacgttcagatccaaggtcagcaatcagttcgttcttattgtcataaatcttgctagaagttgtcggaattagtttacttcagataaggccttccagcannnnnttaattaa Find is-nt database================================================ Query_seq: SMT_1990:SMT_1991|SMT_1990:SMT_1991:hypothetical protein predicted by Glimmer/Critica:K03706 transcriptional pleiotropic repressor:-><-:1917738..1917859 122 gcatttacgcgacgttcagatccaaggtcagcaatcagttcgttcttattgtcataaatcttgctagaagttgtcggaattagtttacttcagataaggccttccagcannnnnttaattaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1990:SMT_1991|SMT_1990:SMT_1991:hypothetical protein predicted by Glimmer/Critica:K03706 transcriptional pleiotropic repressor:-><-:1917738..1917859 122 gcatttacgcgacgttcagatccaaggtcagcaatcagttcgttcttattgtcataaatcttgctagaagttgtcggaattagtttacttcagataaggccttccagcannnnnttaattaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1990:SMT_1991|SMT_1990:SMT_1991:hypothetical protein predicted by Glimmer/Critica:K03706 transcriptional pleiotropic repressor:-><-:1917738..1917859 122 gcatttacgcgacgttcagatccaaggtcagcaatcagttcgttcttattgtcataaatcttgctagaagttgtcggaattagtttacttcagataaggccttccagcannnnnttaattaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gcatttacgcgacgttcagatccaaggtcagcaatcagttcgttcttattgtcataaatcttgctagaagttgtcggaattagtttacttcagataaggccttccagcannnnnttaattaa Predict ORF larger than 30AA ================================================ gcatttacgcgacgttcagatccaaggtcagcaatcagttcgttcttattgtcataaatcttgctagaagttgtcggaattagtttacttcagataaggccttccagcannnnnttaattaa 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================================================ gcatttacgcgacgttcagatccaaggtcagcaatcagttcgttcttattgtcataaatcttgctagaagttgtcggaattagtttacttcagataaggccttccagcannnnnttaattaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1990:SMT_1991|SMT_1990:SMT_1991:hypothetical protein predicted by Glimmer/Critica:K03706 transcriptional pleiotropic repressor:-><-:1917738..1917859 122 gcatttacgcgacgttcagatccaaggtcagcaatcagttcgttcttattgtcataaatcttgctagaagttgtcggaattagtttacttcagataaggccttccagcannnnnttaattaa Intra-Species Hit: Count: 1 Min: 1 Max: 109 Len: 109 Subject: smit_SMT_1990_SMT_1991|hypothetical protein predicted by Glimmer/Critica:K03706 transcriptional pleiotropic repressor|POSITIVE:NEGATIVE|[1917738,1917859]|122 HSP 1 e-value: 1.0E-55 bit: 216.0 Len: 109 Query Start:1 Query End:109 Subject Strand: POSITIVE Subject Start: 1 Subject End: 109 gcatttacgcgacgttcagatccaaggtcagcaatcagttcgttcttattgtcataaatcttgctagaagttgtcggaattagtttacttcagataaggccttccagca............. gcatttacgcgacgttcagatccaaggtcagcaatcagttcgttcttattgtcataaatcttgctagaagttgtcggaattagtttacttcagataaggccttccagca............. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCAUUUACGCGACGUUCAGAUCCAAGGUCAGCAAUCAGUUCGUUCUUAUUGUCAUAAAUCUUGCUAGAAGUUGUCGGAAUUAGUUUACUUCAGAUAAGGCCUUCCAGCA ((......(((((.(((((...((((((..(((((.((......)).))))).....)))))))).)))))))).((((...((((..........)))).)))).)). (-17.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGCUGGAAGGCCUUAUCUGAAGUAAACUAAUUCCGACAACUUCUAGCAAGAUUUAUGACAAUAAGAACGAACUGAUUGCUGACCUUGGAUCUGAACGUCGCGUAAAUGC (((((((((......((.(((.........))).))...)))))))))..(((((((.((((.((......)).))))..(((.((.......)).))).))))))).. (-18.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 918 50 1 181 132 smit:SMT_1989|5end_multimodular_transpeptidase-transglycosylase_1917607..1917837_NEGATIVE 317 50 18 200 161 smit:SMT_1259|5end_hypothetical_protein_1225139..1225369_POSITIVE 277 85 41 161 111 smit:SMT_1205|5end_response_regulator_1165700..1165930_NEGATIVE 266 68 24 71 9 smit:SMT_1570|5end_hypothetical_protein_1563504..1563734_NEGATIVE 265 41 9 177 144 smit:SMT_1088|5end_hypothetical_protein_1024346..1024576_NEGATIVE 257 45 10 214 169 smit:SMT_1199|5end_lactococcin_A_ABC_transporter_permease_protein_1161063..1161293_NEGATIVE 256 78 31 213 162 smit:SMT_1738|5end_peptidyl-prolyl_cis-trans_isomerase_1720497..1720727_POSITIVE 255 66 21 231 187 smit:SMT_1694|5end_GTPase_1676674..1676904_POSITIVE 254 45 8 206 168 smit:SMT_1945|5end_putative_dihydrolipoamide_S-acetyltransferase_1879961..1880191_POSITIVE 253 67 21 195 138 smit:SMT_794|5end_hypothetical_protein_703487..703717_NEGATIVE 248 99 52 194 147 smit:SMT_1425|5end_hypothetical_protein_1410805..1411035_NEGATIVE 248 47 1 230 195 smit:SMT_1254|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1220882..1221112_NEGATIVE 247 48 5 57 10 smit:SMT_236|5end_ribosomal_small_subunit_pseudouridine_synthase_A_174625..174855_POSITIVE 244 46 1 223 173 smit:SMT_629|5end_glycogen_synthase_533967..534197_POSITIVE 243 54 12 165 117 smit:SMT_922|5end_RNA-binding_protein_876566..876796_NEGATIVE 243 54 21 163 127 smit:SMT_183|5end_30S_ribosomal_protein_S14_121014..121244_POSITIVE 242 48 3 48 3 smit:SMT_1177|5end_immunoglobulin_A1_protease_1135129..1135359_NEGATIVE 241 43 1 84 45 smit:SMT_1382|5end_glutamate_5-kinase_1360744..1360974_NEGATIVE 240 78 35 71 30 smit:SMT_1695|5end_ribulose-phosphate_3-epimerase_1677563..1677793_POSITIVE 240 48 7 201 158 smit:SMT_1471|5end_hypothetical_protein_1453933..1454163_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 264 56 13 130 95 smit:SMT_1255|3end_cell_division_protein_FtsH_1220987..1221137_NEGATIVE 254 46 8 149 123 smit:SMT_1802|3end_tyrosyl-tRNA_synthetase_1775456..1775606_NEGATIVE 248 99 52 135 88 smit:SMT_1426|3end_K03095_SprT-like_protein_1410864..1411014_NEGATIVE 243 54 21 145 109 smit:SMT_182|3end_50S_ribosomal_protein_L5_121076..121226_POSITIVE 240 78 35 60 19 smit:SMT_1694|3end_GTPase_1677632..1677782_POSITIVE 239 100 55 114 51 smit:SMT_602|3end_5'-methylthioadenosine_nucleosidase_/_S-adenosylhomocysteine_nucleosidase_517964..518114_POSITIVE 226 46 1 71 24 smit:SMT_826|3end_hypothetical_protein_749591..749741_NEGATIVE 224 99 57 151 107 smit:SMT_261|3end_ImpB/MucB/SamB_family_protein_201655..201805_POSITIVE 222 42 8 151 108 smit:SMT_1704|3end_D-alanine-D-alanine_ligase_1688554..1688704_POSITIVE 222 53 11 140 99 smit:SMT_788|3end_hypothetical_protein_699153..699303_NEGATIVE 220 47 1 64 16 smit:SMT_378|3end_hypothetical_protein_predicted_by_Glimmer/Critica_316083..316233_POSITIVE 219 65 26 76 43 smit:SMT_1902|3end_proton-translocating_NADH-quinone_oxidoreductase,_chain_L_1852028..1852178_NEGATIVE 218 100 58 110 76 smit:SMT_1734|3end_serine/threonine_protein_phosphatase_1719366..1719516_POSITIVE 218 50 14 95 49 smit:SMT_1718|3end_Holliday_junction_DNA_helicase_RuvA_1704284..1704434_NEGATIVE 215 36 9 150 121 smit:SMT_2028|3end_leader_peptidase_(prepilin_peptidase)_/_N-methyltransferase_1943367..1943517_NEGATIVE 214 79 34 141 98 smit:SMT_2135|3end_dipeptidase_2014754..2014904_NEGATIVE 214 69 31 43 4 smit:SMT_1654|3end_K03110_signal_recognition_particle_receptor_1643519..1643669_POSITIVE 214 79 34 141 98 smit:SMT_874|3end_dipeptidase_821365..821515_NEGATIVE 213 43 19 149 126 smit:SMT_360|3end_K07742_hypothetical_protein_296001..296151_POSITIVE 211 40 9 78 46 smit:SMT_1652|3end_Cof_family_protein_1641408..1641558_POSITIVE