Origin IGS: ttaannnnnagatgtaacttgacaaatgtgactgtagatatgagagaaataggattagtctatatatgactagaaagaccccaagctaactccacattaagctagggtcttttttgacactatctatcttcgtttagccatttatcgactaagcgaaggatgacaccgaccacaatcggtccgatgatagttttaaggattagttccatcatgagctatctcacctcctttcgtaggcggtgtagtagtgccgtataatattattccacataagtgttaaactcgggagtcacccaatcgggtggcttttttgtttgtggcttggttttttgatataatagagca .........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 tgctctattatatcaaaaaaccaagccacaaacaaaaaagccacccgattgggtgactcccgagtttaacacttatgtggaataatattatacggcactactacaccgcctacgaaaggaggtgagatagctcatgatggaactaatccttaaaactatcatcggaccgattgtggtcggtgtcatccttcgcttagtcgataaatggctaaacgaagatagatagtgtcaaaaaagaccctagcttaatgtggagttagcttggggtctttctagtcatatatagactaatcctatttctctcatatctacagtcacatttgtcaagttacatctnnnnnttaa Mask Tandem Repeat Region ================================================ ttaannnnnagatgtaacttgacaaatgtgactgtagatatgagagaaataggattagtctatatatgactagaaagaccccaagctaactccacattaagctagggtcttttttgacactatctatcttcgtttagccatttatcgactaagcgaaggatgacaccgaccacaatcggtccgatgatagttttaaggattagttccatcatgagctatctcacctcctttcgtaggcggtgtagtagtgccgtataatattattccacataagtgttaaactcgggagtcacccaatcgggtggcttttttgtttgtggcttggttttttgatataatagagca Find is-nt database================================================ Query_seq: SMT_215:SMT_216|SMT_215:SMT_216:leucyl-tRNA synthetase:Holliday junction DNA helicase RuvB:->->:148052..148396 345 ttaannnnnagatgtaacttgacaaatgtgactgtagatatgagagaaataggattagtctatatatgactagaaagaccccaagctaactccacattaagctagggtcttttttgacactatctatcttcgtttagccatttatcgactaagcgaaggatgacaccgaccacaatcggtccgatgatagttttaaggattagttccatcatgagctatctcacctcctttcgtaggcggtgtagtagtgccgtataatattattccacataagtgttaaactcgggagtcacccaatcgggtggcttttttgtttgtggcttggttttttgatataatagagca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_215:SMT_216|SMT_215:SMT_216:leucyl-tRNA synthetase:Holliday junction DNA helicase RuvB:->->:148052..148396 345 ttaannnnnagatgtaacttgacaaatgtgactgtagatatgagagaaataggattagtctatatatgactagaaagaccccaagctaactccacattaagctagggtcttttttgacactatctatcttcgtttagccatttatcgactaagcgaaggatgacaccgaccacaatcggtccgatgatagttttaaggattagttccatcatgagctatctcacctcctttcgtaggcggtgtagtagtgccgtataatattattccacataagtgttaaactcgggagtcacccaatcgggtggcttttttgtttgtggcttggttttttgatataatagagca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_215:SMT_216|SMT_215:SMT_216:leucyl-tRNA synthetase:Holliday junction DNA helicase RuvB:->->:148052..148396 345 ttaannnnnagatgtaacttgacaaatgtgactgtagatatgagagaaataggattagtctatatatgactagaaagaccccaagctaactccacattaagctagggtcttttttgacactatctatcttcgtttagccatttatcgactaagcgaaggatgacaccgaccacaatcggtccgatgatagttttaaggattagttccatcatgagctatctcacctcctttcgtaggcggtgtagtagtgccgtataatattattccacataagtgttaaactcgggagtcacccaatcgggtggcttttttgtttgtggcttggttttttgatataatagagca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttaannnnnagatgtaacttgacaaatgtgactgtagatatgagagaaataggattagtctatatatgactagaaagaccccaagctaactccacattaagctagggtcttttttgacactatctatcttcgtttagccatttatcgactaagcgaaggatgacaccgaccacaatcggtccgatgatagttttaaggattagttccatcatgagctatctcacctcctttcgtaggcggtgtagtagtgccgtataatattattccacataagtgttaaactcgggagtcacccaatcgggtggcttttttgtttgtggcttggttttttgatataatagagca Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 160 End: 255 ............................................................................................................................................................... M T P T T I G P M I V L R I S S I M S Y L T S F R R R C S S A V .......................................................................................... Protein_Len: 30 Strand: - Start: 123 End: 212 .......................................................................................................................... R D E N L W K D V L R L I V G V V I P G I I T K L I L E M M ..................................................................................................................................... ttaannnnnagatgtaacttgacaaatgtgactgtagatatgagagaaataggattagtctatatatgactagaaagaccccaagctaactccacattaagctagggtcttttttgacactatctatcttcgtttagccatttatcgactaagcgaaggatgacaccgaccacaatcggtccgatgatagttttaaggattagttccatcatgagctatctcacctcctttcgtaggcggtgtagtagtgccgtataatattattccacataagtgttaaactcgggagtcacccaatcgggtggcttttttgtttgtggcttggttttttgatataatagagca 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: 83 Start: 310 End: 339 .....................................................................................................................................................................................................................................................................................................................TTTGTTTGTGGCTTGGTTTTTTGATATAAT...... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttaannnnnagatgtaacttgacaaatgtgactgtagatatgagagaaataggattagtctatatatgactagaaagaccccaagctaactccacattaagctagggtcttttttgacactatctatcttcgtttagccatttatcgactaagcgaaggatgacaccgaccacaatcggtccgatgatagttttaaggattagttccatcatgagctatctcacctcctttcgtaggcggtgtagtagtgccgtataatattattccacataagtgttaaactcgggagtcacccaatcgggtggcttttttgtttgtggcttggttttttgatataatagagca Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -9.1 Tail_Score: -5.72622 Start: 289 End: 306 Full_Region: GTGTTAAACTCGGGA GTCACCC AATC GGGTGGC TTTTTTGTTTGTGGC ................................................................................................................................................................................................................................................................................................GTCACCCAATCGGGTGGC....................................... Find igs database================================================ Query_seq: SMT_215:SMT_216|SMT_215:SMT_216:leucyl-tRNA synthetase:Holliday junction DNA helicase RuvB:->->:148052..148396 345 ttaannnnnagatgtaacttgacaaatgtgactgtagatatgagagaaataggattagtctatatatgactagaaagaccccaagctaactccacattaagctagggtcttttttgacactatctatcttcgtttagccatttatcgactaagcgaaggatgacaccgaccacaatcggtccgatgatagttttaaggattagttccatcatgagctatctcacctcctttcgtaggcggtgtagtagtgccgtataatattattccacataagtgttaaactcgggagtcacccaatcgggtggcttttttgtttgtggcttggttttttgatataatagagca Intra-Species Hit: Count: 2 Min: 10 Max: 345 Len: 336 Subject: smit_SMT_215_SMT_216|leucyl-tRNA synthetase:Holliday junction DNA helicase RuvB|POSITIVE:POSITIVE|[148052,148396]|345 HSP 1 e-value: 0.0 bit: 666.0 Len: 336 Query Start:10 Query End:345 Subject Strand: POSITIVE Subject Start: 10 Subject End: 345 .........agatgtaacttgacaaatgtgactgtagatatgagagaaataggattagtctatatatgactagaaagaccccaagctaactccacattaagctagggtcttttttgacactatctatcttcgtttagccatttatcgactaagcgaaggatgacaccgaccacaatcggtccgatgatagttttaaggattagttccatcatgagctatctcacctcctttcgtaggcggtgtagtagtgccgtataatattattccacataagtgttaaactcgggagtcacccaatcgggtggcttttttgtttgtggcttggttttttgatataatagagca .........agatgtaacttgacaaatgtgactgtagatatgagagaaataggattagtctatatatgactagaaagaccccaagctaactccacattaagctagggtcttttttgacactatctatcttcgtttagccatttatcgactaagcgaaggatgacaccgaccacaatcggtccgatgatagttttaaggattagttccatcatgagctatctcacctcctttcgtaggcggtgtagtagtgccgtataatattattccacataagtgttaaactcgggagtcacccaatcgggtggcttttttgtttgtggcttggttttttgatataatagagca Subject: smit_SMT_211_SMT_212|hypothetical protein predicted by Glimmer/Critica:Holliday junction DNA helicase RuvB|POSITIVE:POSITIVE|[144377,144969]|593 HSP 1 e-value: 1.0E-144 bit: 511.0 Len: 272 Query Start:74 Query End:345 Subject Strand: POSITIVE Subject Start: 320 Subject End: 593 .........................................................................aaagaccccaagctaact-ccacattaagct-agggtcttttttgacactatctatcttcgtttagccatttatcgactaagcgaaggatgacaccgaccacaatcggtccgatgatagttttaaggattagttccatcatgagctatctcacctcctttcgtaggcggtgtagtagtgccgtataatattattccacataagtgttaaactcgggagtcacccaatcgggtggcttttttgtttgtggcttggttttttgatataatagagca .........................................................................aaagaccccaagctaacttccacattaagcttagggtcttttttgacactatctatcttcgtttagccatttatcgactaagcgaaggatgacaccgaccacaatcggtccgatgatagttttaaggattagttccatcatgagctatctcacctcctttcgtaggcggtgtagtagtgccgtataatattattccacataagtgttaaactcgggagtcacccaatcgggtggcttttttgtttgtggcttggttttttgatataatagagca Inter-species Hit: Count: 3 Min: 106 Max: 344 Len: 239 Subject: NC_008533_SPD_0240_SPD_0241|acetyltransferase, GNAT family protein:Holliday junction DNA helicase RuvB|POSITIVE:POSITIVE|[231089,232128]|1040 HSP 1 e-value: 1.0E-82 bit: 307.0 Len: 239 Query Start:106 Query End:344 Subject Strand: POSITIVE Subject Start: 801 Subject End: 1039 .........................................................................................................ggtcttttttgacactatctatcttcgtttagccatttatcgactaagcgaaggatgacaccgaccacaatcggtccgatgatagttttaaggattagttccatcatgagctatctcacctcctttcgtaggcggtgtagtagtgccgtataatattattccacataagtgttaaactcgggagtcacccaatcgggtggcttttttgtttgtggcttggttttttgatataatagagc. .........................................................................................................ggtcttttttgacactatttgtccttgtttagccatttatcgactatacgaagaacgacaccgaccacaattggtccgatgatagttttgagtactaattccatcatgggctatctcacctcctttcgtaggcggtgtagcagtgtcgtataatattataccacataagtgctaaacttaggagtcacccaatcaggtggcttttttgtttgtggcttggttttttgatataatagagc. Subject: NC_003098_spr0237_spr0238|hypothetical protein:Holliday junction DNA helicase RuvB|POSITIVE:POSITIVE|[231088,232127]|1040 HSP 1 e-value: 1.0E-82 bit: 307.0 Len: 239 Query Start:106 Query End:344 Subject Strand: POSITIVE Subject Start: 801 Subject End: 1039 .........................................................................................................ggtcttttttgacactatctatcttcgtttagccatttatcgactaagcgaaggatgacaccgaccacaatcggtccgatgatagttttaaggattagttccatcatgagctatctcacctcctttcgtaggcggtgtagtagtgccgtataatattattccacataagtgttaaactcgggagtcacccaatcgggtggcttttttgtttgtggcttggttttttgatataatagagc. .........................................................................................................ggtcttttttgacactatttgtccttgtttagccatttatcgactatacgaagaacgacaccgaccacaattggtccgatgatagttttgagtactaattccatcatgggctatctcacctcctttcgtaggcggtgtagcagtgtcgtataatattataccacataagtgctaaacttaggagtcacccaatcaggtggcttttttgtttgtggcttggttttttgatataatagagc. Subject: NC_003028_SP_0258_SP_0259|hypothetical protein:Holliday junction DNA helicase RuvB|NEGATIVE:POSITIVE|[231466,231599]|134 HSP 1 e-value: 9.0E-47 bit: 188.0 Len: 130 Query Start:215 Query End:344 Subject Strand: POSITIVE Subject Start: 3 Subject End: 133 ......................................................................................................................................................................................................................gctatctcacctcctttcgtaggcggtgtagtagtgccgtataatattattccacataagtgttaaactcgggagtcacccaatcgggtggcttttttgtttgtggcttg-gttttttgatataatagagc. ......................................................................................................................................................................................................................gctatctcacctcctttcgtaggcggtgtagaagtgccgtataatattataccacataagtgctaaacttaggagtcacccaatcaggtggcttttttgtttgtggcttgttttttttgatataatagagc. Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGUCUUUUUUGACACUAUCUAUCUUCGUUUAGCCAUUUAUCGACUAAGCGAAGGAUGACACCGACCACAAUCGGUCCGAUGAUAGUUUUAAGGAUUAGUUCCAUCAUGAGCUAUCUCACCUCCUUUCGUAGGCGGUGUAGUAGUGCCGUAUAAUAUUAUUCCACAUAAGUGUUAAACUCGGGAGUCACCCAAUCGGGUGGCUUUUUUGUUUGUGGCUUGGUUUUUUGAUAUAAUAGAGC ((.(((((((((.((((((..(((((((((((.(.......).)))))))))))......(.((((......)))).)..)))))).)))))))..))..)).......(((((..((((.(((.....))).))))..)))))((..(((.((((((....((.(((((..(((((..(((((((((((....)))))))))))..)))))..)))))))....)))))).)))..)) (-73.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCUCUAUUAUAUCAAAAAACCAAGCCACAAACAAAAAAGCCACCCGAUUGGGUGACUCCCGAGUUUAACACUUAUGUGGAAUAAUAUUAUACGGCACUACUACACCGCCUACGAAAGGAGGUGAGAUAGCUCAUGAUGGAACUAAUCCUUAAAACUAUCAUCGGACCGAUUGUGGUCGGUGUCAUCCUUCGCUUAGUCGAUAAAUGGCUAAACGAAGAUAGAUAGUGUCAAAAAAGACC ..(((...................(((((........((.(((((....))))).))...((((.....)))).))))).............(((((((..((((((.((((((..((...((((((((....(((.(((.....))))))...))))).)))..))..)))))).))))))....(((((.(((((((.....))))))).))))).....))))))).....))).. (-62.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 375 140 100 132 87 smit:SMT_962|5end_putative_hemin_transport_system_ATP-binding_protein_fecE_908584..908814_NEGATIVE 326 90 41 90 35 smit:SMT_1191|5end_phosphoribosylamine--glycine_ligase_1149737..1149967_NEGATIVE 323 221 188 40 7 smit:SMT_91|5end_hypothetical_protein_22578..22808_POSITIVE 320 205 179 161 135 smit:SMT_2062|5end_phosphoglycerate_mutase_1971425..1971655_NEGATIVE 320 205 179 161 135 smit:SMT_1995|5end_phosphoglycerate_mutase_1920750..1920980_NEGATIVE 320 205 179 161 135 smit:SMT_201|5end_phosphoglycerate_mutase_131329..131559_POSITIVE 316 79 42 226 186 smit:SMT_125|5end_hypothetical_protein_77664..77894_NEGATIVE 313 116 71 101 48 smit:SMT_1660|5end_serine_protease_1650634..1650864_NEGATIVE 310 152 115 185 148 smit:SMT_1202|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1164097..1164327_NEGATIVE 306 80 31 73 32 smit:SMT_1189|5end_phosphoribosylaminoimidazole_carboxylase_ATPase_subunit_1147754..1147984_NEGATIVE 297 136 97 71 15 smit:SMT_725|5end_hypothetical_protein_630415..630645_NEGATIVE 293 90 41 90 35 smit:SMT_2076|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1978592..1978822_NEGATIVE 293 90 41 197 142 smit:SMT_2075|5end_phosphoribosylamine--glycine_ligase_1978485..1978715_NEGATIVE 293 63 21 212 165 smit:SMT_233|5end_hypothetical_protein_172656..172886_POSITIVE 292 137 91 50 4 smit:SMT_1813|5end_amino_acid_transporter_1787142..1787372_POSITIVE 291 106 61 171 123 smit:SMT_1541|5end_isopentenyl-diphosphate_delta-isomerase_1526093..1526323_NEGATIVE 290 150 106 174 129 smit:SMT_568|5end_hypothetical_protein_485674..485904_POSITIVE 289 220 174 163 112 smit:SMT_1130|5end_MATE_efflux_family_protein_1065210..1065440_NEGATIVE 287 80 31 56 1 smit:SMT_1627|5end_hypothetical_protein_1616415..1616645_NEGATIVE 284 149 107 135 85 smit:SMT_1322|5end_K02075_zinc/manganese_transport_system_permease_protein_1291371..1291601_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 375 140 100 130 85 smit:SMT_963|3end_K02015_iron_complex_transport_system_permease_protein_908586..908736_NEGATIVE 310 152 115 61 24 smit:SMT_1203|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1164221..1164371_NEGATIVE 307 138 91 148 103 smit:SMT_302|3end_K07444_putative_N6-adenine-specific_DNA_methylase_245319..245469_POSITIVE 306 80 31 86 45 smit:SMT_1190|3end_phosphoribosylaminoimidazole_carboxylase,_catalytic_subunit_1147741..1147891_NEGATIVE 305 83 44 58 6 smit:SMT_1695|3end_ribulose-phosphate_3-epimerase_1678299..1678449_POSITIVE 297 136 97 74 18 smit:SMT_726|3end_ImpB/MucB/SamB_family_protein_630412..630562_NEGATIVE 293 140 95 75 25 smit:SMT_1348|3end_exoribonuclease_II_1325148..1325298_NEGATIVE 289 220 174 102 51 smit:SMT_1131|3end_threonine_synthase_1065271..1065421_NEGATIVE 284 149 107 142 92 smit:SMT_1321|3end_K02074_zinc/manganese_transport_system_ATP-binding_protein_1291458..1291608_POSITIVE 283 55 11 129 81 smit:SMT_1006|3end_6-pyruvoyl_tetrahydrobiopterin_synthase,_putative_947122..947272_POSITIVE 282 215 181 74 37 smit:SMT_1802|3end_tyrosyl-tRNA_synthetase_1775456..1775606_NEGATIVE 282 118 71 145 109 smit:SMT_378|3end_hypothetical_protein_predicted_by_Glimmer/Critica_316083..316233_POSITIVE 269 143 106 72 34 smit:SMT_773|3end_UDP-N-acetylenolpyruvoylglucosamine_reductase_683460..683610_NEGATIVE 267 222 181 73 31 smit:SMT_2013|3end_alpha-glycerophosphate_oxidase_1932521..1932671_POSITIVE 267 150 101 66 14 smit:SMT_1826|3end_ATP_synthase_beta_chain_1797622..1797772_POSITIVE 267 148 101 76 1 smit:SMT_987|3end_N-acetylmannosamine_kinase_/_transcriptional_regulator_931655..931805_NEGATIVE 265 167 122 68 16 smit:SMT_2040|3end_transcription-repair_coupling_factor_1950463..1950613_NEGATIVE 265 137 95 148 91 smit:SMT_1088|3end_hypothetical_protein_1024152..1024302_NEGATIVE 262 77 31 148 93 smit:SMT_260|3end_phage_transcriptional_repressor_200236..200386_POSITIVE 258 220 174 66 5 smit:SMT_625|3end_50S_ribosomal_protein_L27_530400..530550_POSITIVE