Origin IGS: tctttcttgtgccttgcatttccgtcaaaatcttgctacaatagagacattagaggtgttttgaatcccgcattttacagaaagtggcggagctgagaagtccacaaatgtgtcaaaactagttgctaatggatgaaaaattgaaataaaagtgtctttttgttttaaagacgagagttgcgggcaactgcccgaaattgggtggtaccgcggataaatacattcgtccctgtcatgtagatggcaggggcgattttttgtagaaagtgaggtgagaaga .........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 tcttctcacctcactttctacaaaaaatcgcccctgccatctacatgacagggacgaatgtatttatccgcggtaccacccaatttcgggcagttgcccgcaactctcgtctttaaaacaaaaagacacttttatttcaatttttcatccattagcaactagttttgacacatttgtggacttctcagctccgccactttctgtaaaatgcgggattcaaaacacctctaatgtctctattgtagcaagattttgacggaaatgcaaggcacaagaaaga Mask Tandem Repeat Region ================================================ tctttcttgtgccttgcatttccgtcaaaatcttgctacaatagagacattagaggtgttttgaatcccgcattttacagaaagtggcggagctgagaagtccacaaatgtgtcaaaactagttgctaatggatgaaaaattgaaataaaagtgtctttttgttttaaagacgagagttgcgggcaactgcccgaaattgggtggtaccgcggataaatacattcgtccctgtcatgtagatggcaggggcgattttttgtagaaagtgaggtgagaaga Find is-nt database================================================ Query_seq: SMT_369:SMT_370|SMT_369:SMT_370:hypothetical cytosolic protein:acetyltransferase, GNAT family:->->:304548..304827 280 tctttcttgtgccttgcatttccgtcaaaatcttgctacaatagagacattagaggtgttttgaatcccgcattttacagaaagtggcggagctgagaagtccacaaatgtgtcaaaactagttgctaatggatgaaaaattgaaataaaagtgtctttttgttttaaagacgagagttgcgggcaactgcccgaaattgggtggtaccgcggataaatacattcgtccctgtcatgtagatggcaggggcgattttttgtagaaagtgaggtgagaaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_369:SMT_370|SMT_369:SMT_370:hypothetical cytosolic protein:acetyltransferase, GNAT family:->->:304548..304827 280 tctttcttgtgccttgcatttccgtcaaaatcttgctacaatagagacattagaggtgttttgaatcccgcattttacagaaagtggcggagctgagaagtccacaaatgtgtcaaaactagttgctaatggatgaaaaattgaaataaaagtgtctttttgttttaaagacgagagttgcgggcaactgcccgaaattgggtggtaccgcggataaatacattcgtccctgtcatgtagatggcaggggcgattttttgtagaaagtgaggtgagaaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_369:SMT_370|SMT_369:SMT_370:hypothetical cytosolic protein:acetyltransferase, GNAT family:->->:304548..304827 280 tctttcttgtgccttgcatttccgtcaaaatcttgctacaatagagacattagaggtgttttgaatcccgcattttacagaaagtggcggagctgagaagtccacaaatgtgtcaaaactagttgctaatggatgaaaaattgaaataaaagtgtctttttgttttaaagacgagagttgcgggcaactgcccgaaattgggtggtaccgcggataaatacattcgtccctgtcatgtagatggcaggggcgattttttgtagaaagtgaggtgagaaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tctttcttgtgccttgcatttccgtcaaaatcttgctacaatagagacattagaggtgttttgaatcccgcattttacagaaagtggcggagctgagaagtccacaaatgtgtcaaaactagttgctaatggatgaaaaattgaaataaaagtgtctttttgttttaaagacgagagttgcgggcaactgcccgaaattgggtggtaccgcggataaatacattcgtccctgtcatgtagatggcaggggcgattttttgtagaaagtgaggtgagaaga Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: - Start: 122 End: 223 ......................................................................................................................... N S I S S F N F Y F H R K T K F V L T A P L Q G F N P P V A S L Y M ......................................................... Protein_Len: 60 Strand: - Start: 28 End: 219 ........................... I S V N S T N Q I G C K V S L P P A S F D V F T D F S T A L P H F I S I F T D K Q K L S S L Q P C S G S I P H Y R P Y M ............................................................. tctttcttgtgccttgcatttccgtcaaaatcttgctacaatagagacattagaggtgttttgaatcccgcattttacagaaagtggcggagctgagaagtccacaaatgtgtcaaaactagttgctaatggatgaaaaattgaaataaaagtgtctttttgttttaaagacgagagttgcgggcaactgcccgaaattgggtggtaccgcggataaatacattcgtccctgtcatgtagatggcaggggcgattttttgtagaaagtgaggtgagaaga 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: 13 End: 42 ............CTTGCATTTCCGTCAAAATCTTGCTACAAT.............................................................................................................................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tctttcttgtgccttgcatttccgtcaaaatcttgctacaatagagacattagaggtgttttgaatcccgcattttacagaaagtggcggagctgagaagtccacaaatgtgtcaaaactagttgctaatggatgaaaaattgaaataaaagtgtctttttgttttaaagacgagagttgcgggcaactgcccgaaattgggtggtaccgcggataaatacattcgtccctgtcatgtagatggcaggggcgattttttgtagaaagtgaggtgagaaga Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -15.1 Tail_Score: -5.24531 Start: 224 End: 253 Full_Region: CGCGGATAAATACAT TCGTCCCTGTCAT GTAG ATGGCAGGGGCGA TTTTTTGTAGAAAGT ...............................................................................................................................................................................................................................TCGTCCCTGTCATGTAGATGGCAGGGGCGA........................... Find igs database================================================ Query_seq: SMT_369:SMT_370|SMT_369:SMT_370:hypothetical cytosolic protein:acetyltransferase, GNAT family:->->:304548..304827 280 tctttcttgtgccttgcatttccgtcaaaatcttgctacaatagagacattagaggtgttttgaatcccgcattttacagaaagtggcggagctgagaagtccacaaatgtgtcaaaactagttgctaatggatgaaaaattgaaataaaagtgtctttttgttttaaagacgagagttgcgggcaactgcccgaaattgggtggtaccgcggataaatacattcgtccctgtcatgtagatggcaggggcgattttttgtagaaagtgaggtgagaaga Intra-Species Hit: Count: 1 Min: 1 Max: 280 Len: 280 Subject: smit_SMT_369_SMT_370|hypothetical cytosolic protein:acetyltransferase, GNAT family|POSITIVE:POSITIVE|[304548,304827]|280 HSP 1 e-value: 1.0E-157 bit: 555.0 Len: 280 Query Start:1 Query End:280 Subject Strand: POSITIVE Subject Start: 1 Subject End: 280 tctttcttgtgccttgcatttccgtcaaaatcttgctacaatagagacattagaggtgttttgaatcccgcattttacagaaagtggcggagctgagaagtccacaaatgtgtcaaaactagttgctaatggatgaaaaattgaaataaaagtgtctttttgttttaaagacgagagttgcgggcaactgcccgaaattgggtggtaccgcggataaatacattcgtccctgtcatgtagatggcaggggcgattttttgtagaaagtgaggtgagaaga tctttcttgtgccttgcatttccgtcaaaatcttgctacaatagagacattagaggtgttttgaatcccgcattttacagaaagtggcggagctgagaagtccacaaatgtgtcaaaactagttgctaatggatgaaaaattgaaataaaagtgtctttttgttttaaagacgagagttgcgggcaactgcccgaaattgggtggtaccgcggataaatacattcgtccctgtcatgtagatggcaggggcgattttttgtagaaagtgaggtgagaaga Inter-species Hit: Count: 4 Min: 3 Max: 273 Len: 271 Subject: NC_003028_SP_0564_SP_0565|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[530626,531037]|412 HSP 1 e-value: 1.0E-116 bit: 418.0 Len: 247 Query Start:3 Query End:249 Subject Strand: POSITIVE Subject Start: 3 Subject End: 249 ..tttcttgtgccttgcatttccgtcaaaatcttgctacaatagagacattagaggtgttttgaatcccgcattttacagaaagtggcggagctgagaagtccacaaatgtgtcaaaactagttgctaatggatgaaaaattgaaataaaagtgtctttttgttttaaagacgagagttgcgggcaactgcccgaaattgggtggtaccgcggataaatacattcgtccctgtcatgtagatggcaggg............................... ..tttcttgagccttgcatttccgaaaaaatcttgctacaatagagccattagaggtgttttgaatcccacattttacagaaagtggcggcgctgagaagtccacaaatgtgtcaaaactggttgctaatggatgaaaaattgaaataaaagtgtctttttgctttaaagacgagagttgcgggcaactgcccgaaattgggtggtaccgcggataaacacattcgtccctgtcatgtagatggcaggg............................... Subject: NC_008533_SPD_0490_SPD_0491|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[496851,497261]|411 HSP 1 e-value: 6.0E-78 bit: 291.0 Len: 247 Query Start:3 Query End:249 Subject Strand: POSITIVE Subject Start: 3 Subject End: 248 ..tttcttgtgccttgcatttccgtcaaaatcttgctacaatagagacattagaggtgttttgaatcccgcattttacagaaagtggcggagctgagaagtccacaaatgtgtcaaaactagttgctaatggatgaaaaattgaaataaaagtgtctttttgttttaaagacgagagttgcgggcaactgcccgaaattgggtggtaccgcggataaatacattcgtccctgtcatgtagatggcaggg............................... ..tttcttgagccttgcatttccgagaaaaacttgctacaatagagccattagaggtgttttgaatcccacattttacagaaagtggcggcgctgagaagtccacaaatgtgtcaaaactggttgctaatgactgaaaaaatgaaatatttctgtctttttattttaaagactaaagatgcgggc-ttggcccgaaattgggtggtaccgcggataaacacattcgtccctgtcatgtagatggcaggg............................... Subject: NC_003098_spr0488_spr0489|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[489321,489731]|411 HSP 1 e-value: 6.0E-78 bit: 291.0 Len: 247 Query Start:3 Query End:249 Subject Strand: POSITIVE Subject Start: 3 Subject End: 248 ..tttcttgtgccttgcatttccgtcaaaatcttgctacaatagagacattagaggtgttttgaatcccgcattttacagaaagtggcggagctgagaagtccacaaatgtgtcaaaactagttgctaatggatgaaaaattgaaataaaagtgtctttttgttttaaagacgagagttgcgggcaactgcccgaaattgggtggtaccgcggataaatacattcgtccctgtcatgtagatggcaggg............................... ..tttcttgagccttgcatttccgagaaaaacttgctacaatagagccattagaggtgttttgaatcccacattttacagaaagtggcggcgctgagaagtccacaaatgtgtcaaaactggttgctaatgactgaaaaaatgaaatatttctgtctttttattttaaagactaaagatgcgggc-ttggcccgaaattgggtggtaccgcggataaacacattcgtccctgtcatgtagatggcaggg............................... Subject: NC_009009_SSA_1821_SSA_1822|Acetyltransferase (N-acetylase of ribosomal proteins), putative:hypothetical protein|NEGATIVE:NEGATIVE|[1810701,1810960]|260 HSP 1 e-value: 4.0E-45 bit: 182.0 Len: 222 Query Start:52 Query End:273 Subject Strand: NEGATIVE Subject Start: 7 Subject End: 226 ...................................................agaggtgttttgaatcccgcattttacagaaagtggcggagctgagaagtccacaaatgtgtcaaaactagttgctaatggatgaaaaattgaaataaaagtgtctt----tttgttttaaagacgagagttgcgggcaactgcccgaaattgggtggtaccgcggataaatacattcgtccctgtcatgtagatggcaggggcgattttttgtagaaagtgaggt....... ...................................................agaggtgttttgagtcaagcattttacagaaagtggcggtgctgagaagtccacaaatgtgtcaagactggttgctgatggtt--aaaaatgaaataaaagtgtctttgtatttacttcaaagacgagagttgcgggcgcctgcccgaaattgggtggtaccgcggat--attgattcgtccctgtcatggatatggcagggac--ttttttatggaaagtgaggt....... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUCUUGUGCCUUGCAUUUCCGUCAAAAUCUUGCUACAAUAGAGACAUUAGAGGUGUUUUGAAUCCCGCAUUUUACAGAAAGUGGCGGAGCUGAGAAGUCCACAAAUGUGUCAAAACUAGUUGCUAAUGGAUGAAAAAUUGAAAUAAAAGUGUCUUUUUGUUUUAAAGACGAGAGUUGCGGGCAACUGCCCGAAAUUGGGUGGUACCGCGGAUAAAUACAUUCGUCCCUGUCAUGUAGAUGGCAGGGGCGAUUUUUUGUAGAAAGUGAGGU ........((((..(...((((((.....................((((((....(((((((...(((((((((....))))).))))............(((....))))))))))......)))))).........((((((((((((....)))))))))))).)))).)).((((((...((..((((....))))..)).)))))).....((((.(((((((((((((....))))))))))))).....))))....)..)))) (-84.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACCUCACUUUCUACAAAAAAUCGCCCCUGCCAUCUACAUGACAGGGACGAAUGUAUUUAUCCGCGGUACCACCCAAUUUCGGGCAGUUGCCCGCAACUCUCGUCUUUAAAACAAAAAGACACUUUUAUUUCAAUUUUUCAUCCAUUAGCAACUAGUUUUGACACAUUUGUGGACUUCUCAGCUCCGCCACUUUCUGUAAAAUGCGGGAUUCAAAACACCUCUAAUGUCUCUAUUGUAGCAAGAUUUUGACGGAAAUGCAAGGCACAAGAAA .((((((((.((((((....(((.(((((.(((....))).))))).)))............((((.((..(((......)))..))...)))).......((((((.......))))))......................((((((......(((((((.......(((((((....)).)))))....((((((.....)))))).)))))))....))))))......)))))).)))....))).))...(((...)))....... (-59.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 358 215 172 164 112 smit:SMT_1610|5end_tyrosine_recombinase_1598565..1598795_POSITIVE 341 209 166 192 136 smit:SMT_104|5end_DNA_repair_protein_49623..49853_POSITIVE 332 100 51 61 6 smit:SMT_327|5end_hypothetical_protein_263953..264183_POSITIVE 331 209 168 182 145 smit:SMT_169|5end_30S_ribosomal_protein_S10_114515..114745_POSITIVE 324 229 186 59 5 smit:SMT_138|5end_tRNA_(5-methylaminomethyl-2-thiouridylate)-methyltransferase_89262..89492_POSITIVE 319 191 153 131 98 smit:SMT_1352|5end_formamidopyrimidine-DNA_glycosylase_1330641..1330871_NEGATIVE 318 214 173 142 107 smit:SMT_1684|5end_acetyltransferase,_GNAT_family_1667757..1667987_NEGATIVE 318 214 174 205 159 smit:SMT_1256|5end_ketol-acid_reductoisomerase_1222631..1222861_NEGATIVE 318 89 50 201 154 smit:SMT_121|5end_hypothetical_protein_73303..73533_POSITIVE 317 254 211 160 114 smit:SMT_1006|5end_6-pyruvoyl_tetrahydrobiopterin_synthase,_putative_946599..946829_POSITIVE 304 249 201 170 113 smit:SMT_1454|5end_cytidine_deaminase_1437886..1438116_NEGATIVE 303 211 178 192 163 smit:SMT_1887|5end_LicC_protein_1841445..1841675_POSITIVE 303 213 174 48 1 smit:SMT_1169|5end_phosphorylase,_Pnp/UDP_family_1117350..1117580_NEGATIVE 303 210 167 55 14 smit:SMT_838|5end_cation_efflux_family_protein_782924..783154_POSITIVE 300 249 201 56 1 smit:SMT_1888|5end_K02026_multiple_sugar_transport_system_permease_protein_1842088..1842318_POSITIVE 300 214 171 80 32 smit:SMT_1800|5end_exonuclease_RexA_1773788..1774018_NEGATIVE 300 212 176 163 118 smit:SMT_335|5end_glutamine_synthetase_273753..273983_POSITIVE 299 96 53 123 72 smit:SMT_2096|5end_ATP-dependent_exonuclease_RexB_1990380..1990610_NEGATIVE 298 234 191 91 41 smit:SMT_2078|5end_acetyl_xylan_esterase,_putative_1979571..1979801_POSITIVE 295 210 170 95 60 smit:SMT_2052|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1961591..1961821_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 319 191 153 82 49 smit:SMT_1353|3end_GTP-binding_protein_1330690..1330840_NEGATIVE 318 214 173 142 107 smit:SMT_1685|3end_phenylalanyl-tRNA_synthetase_alpha_chain_1667757..1667907_NEGATIVE 318 214 174 139 93 smit:SMT_1257|3end_acetolactate_synthase_small_subunit_1222697..1222847_NEGATIVE 309 249 202 47 1 smit:SMT_1190|3end_phosphoribosylaminoimidazole_carboxylase,_catalytic_subunit_1147741..1147891_NEGATIVE 300 212 176 126 81 smit:SMT_334|3end_K03713_MerR_family_transcriptional_regulator,_glutamine_synthetase_repressor_273796..273946_POSITIVE 293 216 176 63 20 smit:SMT_887|3end_ABC-type_polar_amino_acid_transport_system,_ATPase_component_835528..835678_POSITIVE 292 216 171 57 8 smit:SMT_1489|3end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_1470714..1470864_POSITIVE 291 204 161 75 30 smit:SMT_1278|3end_30S_ribosomal_protein_S2_1242332..1242482_POSITIVE 286 190 146 119 63 smit:SMT_1529|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1512776..1512926_NEGATIVE 286 211 171 44 8 smit:SMT_478|3end_hypothetical_protein_predicted_by_Glimmer/Critica_415257..415407_POSITIVE 283 211 172 45 10 smit:SMT_2001|3end_membrane_protease_protein_family_1923889..1924039_POSITIVE 281 259 224 45 14 smit:SMT_677|3end_DNA_topoisomerase_I_585303..585453_NEGATIVE 277 211 175 35 2 smit:SMT_2044|3end_transcriptional_activator_TipA,_putative_1955274..1955424_NEGATIVE 277 211 175 35 2 smit:SMT_2016|3end_tyrosine_recombinase_1933021..1933171_NEGATIVE 277 211 175 35 2 smit:SMT_2006|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1926803..1926953_POSITIVE 277 211 175 35 2 smit:SMT_1957|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1890829..1890979_POSITIVE 277 211 175 35 2 smit:SMT_1886|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1841198..1841348_POSITIVE 277 211 175 35 2 smit:SMT_1658|3end_hypothetical_protein_1648937..1649087_POSITIVE 277 211 175 35 2 smit:SMT_1558|3end_hypothetical_protein_1543855..1544005_NEGATIVE 277 211 175 35 2 smit:SMT_1155|3end_ABC-type_oligopeptide_transport_system,_periplasmic_component_1099183..1099333_NEGATIVE