Origin IGS: aaaaagaaccacgagtcacataggattcgtggttttatagttcatcggctaatttgttagctcatatttcccccttctttaacaaaaataaaaatgcctatcaaactgataaaacatgtgatataatagggacggcactaacaatacgccttggaaaaggaggtattacagatgctagaacttctcaaaatagtacttatcgcagtcatcgagagtatcatctcatggctggtgactcgttggttagacgatcacttcgacaagtaaccttcctggttagtgctatctaacctagaaaaaaatcccctcagtattgcagtaccgaggggatttctgttagcactaaaatgctagaacttctcaattcccctttattatctcacatactctatttaattgtcaagaaagaggtgttttatatct .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 agatataaaacacctctttcttgacaattaaatagagtatgtgagataataaaggggaattgagaagttctagcattttagtgctaacagaaatcccctcggtactgcaatactgaggggatttttttctaggttagatagcactaaccaggaaggttacttgtcgaagtgatcgtctaaccaacgagtcaccagccatgagatgatactctcgatgactgcgataagtactattttgagaagttctagcatctgtaatacctccttttccaaggcgtattgttagtgccgtccctattatatcacatgttttatcagtttgataggcatttttatttttgttaaagaagggggaaatatgagctaacaaattagccgatgaactataaaaccacgaatcctatgtgactcgtggttcttttt Mask Tandem Repeat Region ================================================ aaaaagaaccacgagtcacataggattcgtggttttatagttcatcggctaatttgttagctcatatttcccccttctttaacaaaaataaaaatgcctatcaaactgataaaacatgtgatataatagggacggcactaacaatacgccttggaaaaggaggtattacagatgctagaacttctcaaaatagtacttatcgcagtcatcgagagtatcatctcatggctggtgactcgttggttagacgatcacttcgacaagtaaccttcctggttagtgctatctaacctagaaaaaaatcccctcagtattgcagtaccgaggggatttctgttagcactaaaatgctagaacttctcaattcccctttattatctcacatactctatttaattgtcaagaaagaggtgttttatatct Find is-nt database================================================ Query_seq: SMT_847:SMT_848|SMT_847:SMT_848:thioredoxin reductase:hypothetical protein:-><-:793909..794331 423 aaaaagaaccacgagtcacataggattcgtggttttatagttcatcggctaatttgttagctcatatttcccccttctttaacaaaaataaaaatgcctatcaaactgataaaacatgtgatataatagggacggcactaacaatacgccttggaaaaggaggtattacagatgctagaacttctcaaaatagtacttatcgcagtcatcgagagtatcatctcatggctggtgactcgttggttagacgatcacttcgacaagtaaccttcctggttagtgctatctaacctagaaaaaaatcccctcagtattgcagtaccgaggggatttctgttagcactaaaatgctagaacttctcaattcccctttattatctcacatactctatttaattgtcaagaaagaggtgttttatatct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_847:SMT_848|SMT_847:SMT_848:thioredoxin reductase:hypothetical protein:-><-:793909..794331 423 aaaaagaaccacgagtcacataggattcgtggttttatagttcatcggctaatttgttagctcatatttcccccttctttaacaaaaataaaaatgcctatcaaactgataaaacatgtgatataatagggacggcactaacaatacgccttggaaaaggaggtattacagatgctagaacttctcaaaatagtacttatcgcagtcatcgagagtatcatctcatggctggtgactcgttggttagacgatcacttcgacaagtaaccttcctggttagtgctatctaacctagaaaaaaatcccctcagtattgcagtaccgaggggatttctgttagcactaaaatgctagaacttctcaattcccctttattatctcacatactctatttaattgtcaagaaagaggtgttttatatct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_847:SMT_848|SMT_847:SMT_848:thioredoxin reductase:hypothetical protein:-><-:793909..794331 423 aaaaagaaccacgagtcacataggattcgtggttttatagttcatcggctaatttgttagctcatatttcccccttctttaacaaaaataaaaatgcctatcaaactgataaaacatgtgatataatagggacggcactaacaatacgccttggaaaaggaggtattacagatgctagaacttctcaaaatagtacttatcgcagtcatcgagagtatcatctcatggctggtgactcgttggttagacgatcacttcgacaagtaaccttcctggttagtgctatctaacctagaaaaaaatcccctcagtattgcagtaccgaggggatttctgttagcactaaaatgctagaacttctcaattcccctttattatctcacatactctatttaattgtcaagaaagaggtgttttatatct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaaagaaccacgagtcacataggattcgtggttttatagttcatcggctaatttgttagctcatatttcccccttctttaacaaaaataaaaatgcctatcaaactgataaaacatgtgatataatagggacggcactaacaatacgccttggaaaaggaggtattacagatgctagaacttctcaaaatagtacttatcgcagtcatcgagagtatcatctcatggctggtgactcgttggttagacgatcacttcgacaagtaaccttcctggttagtgctatctaacctagaaaaaaatcccctcagtattgcagtaccgaggggatttctgttagcactaaaatgctagaacttctcaattcccctttattatctcacatactctatttaattgtcaagaaagaggtgttttatatct Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 151 End: 264 ...................................................................................................................................................... M E K E V L Q M L E L L K I V L I A V I E S I I S W L V T R W L D D H F D K ............................................................................................................................................................... Protein_Len: 60 Strand: + Start: 54 End: 287 ..................................................... M L A H I S P F F N K N K N A Y Q T D K T C D I I G T A L T I R L G K G G I T D A R T S Q N S T Y R S H R E Y H L M A G ........................................................................................................................................ Protein_Len: 31 Strand: + Start: 330 End: 422 ......................................................................................................................................................................................................................................................................................................................................... M S V S T K M L E L L N S P L L S H I L Y L I V K K E V F Y I . aaaaagaaccacgagtcacataggattcgtggttttatagttcatcggctaatttgttagctcatatttcccccttctttaacaaaaataaaaatgcctatcaaactgataaaacatgtgatataatagggacggcactaacaatacgccttggaaaaggaggtattacagatgctagaacttctcaaaatagtacttatcgcagtcatcgagagtatcatctcatggctggtgactcgttggttagacgatcacttcgacaagtaaccttcctggttagtgctatctaacctagaaaaaaatcccctcagtattgcagtaccgaggggatttctgttagcactaaaatgctagaacttctcaattcccctttattatctcacatactctatttaattgtcaagaaagaggtgttttatatct 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================================================ aaaaagaaccacgagtcacataggattcgtggttttatagttcatcggctaatttgttagctcatatttcccccttctttaacaaaaataaaaatgcctatcaaactgataaaacatgtgatataatagggacggcactaacaatacgccttggaaaaggaggtattacagatgctagaacttctcaaaatagtacttatcgcagtcatcgagagtatcatctcatggctggtgactcgttggttagacgatcacttcgacaagtaaccttcctggttagtgctatctaacctagaaaaaaatcccctcagtattgcagtaccgaggggatttctgttagcactaaaatgctagaacttctcaattcccctttattatctcacatactctatttaattgtcaagaaagaggtgttttatatct Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 47 HP_score: -4.3 Tail_Score: -2.58861 Start: 265 End: 279 Full_Region: taggttagatagcac taacc aggaa ggtta cttgtcgaagtgatc ........................................................................................................................................................................................................................................................................taaccaggaaggtta................................................................................................................................................ TransTerm Strand: - Conf: 46 HP_score: -2.3 Tail_Score: -3.44622 Start: 268 End: 299 Full_Region: atactgaggggattt ttttctaggttag atagca ctaaccaggaagg ttacttgtcgaagtg ...........................................................................................................................................................................................................................................................................ttttctaggttagatagcactaaccaggaagg............................................................................................................................ TransTerm Strand: - Conf: 45 HP_score: -3.6 Tail_Score: -2.66452 Start: 269 End: 298 Full_Region: tactgaggggatttt tttctaggttag atagca ctaaccaggaag gttacttgtcgaagt ............................................................................................................................................................................................................................................................................tttctaggttagatagcactaaccaggaag............................................................................................................................. TransTerm Strand: - Conf: 100 HP_score: -12.1 Tail_Score: -5.66684 Start: 303 End: 330 Full_Region: tagtgctaacagaaa tcccctcggta ctgcaa tactgagggga tttttttctaggtta ..............................................................................................................................................................................................................................................................................................................tcccctcggtactgcaatactgagggga............................................................................................. Find igs database================================================ Query_seq: SMT_847:SMT_848|SMT_847:SMT_848:thioredoxin reductase:hypothetical protein:-><-:793909..794331 423 aaaaagaaccacgagtcacataggattcgtggttttatagttcatcggctaatttgttagctcatatttcccccttctttaacaaaaataaaaatgcctatcaaactgataaaacatgtgatataatagggacggcactaacaatacgccttggaaaaggaggtattacagatgctagaacttctcaaaatagtacttatcgcagtcatcgagagtatcatctcatggctggtgactcgttggttagacgatcacttcgacaagtaaccttcctggttagtgctatctaacctagaaaaaaatcccctcagtattgcagtaccgaggggatttctgttagcactaaaatgctagaacttctcaattcccctttattatctcacatactctatttaattgtcaagaaagaggtgttttatatct Intra-Species Hit: Count: 1 Min: 1 Max: 423 Len: 423 Subject: smit_SMT_847_SMT_848|thioredoxin reductase:hypothetical protein|POSITIVE:NEGATIVE|[793909,794331]|423 HSP 1 e-value: 0.0 bit: 797.0 Len: 423 Query Start:1 Query End:423 Subject Strand: POSITIVE Subject Start: 1 Subject End: 423 aaaaagaaccacgagtcacataggattcgtggttttatagttcatcggctaatttgttagctcatatttcccccttctttaacaaaaataaaaatgcctatcaaactgataaaacatgtgatataatagggacggcactaacaatacgccttggaaaaggaggtattacagatgctagaacttctcaaaatagtacttatcgcagtcatcgagagtatcatctcatggctggtgactcgttggttagacgatcacttcgacaagtaaccttcctggttagtgctatctaacctagnnnnnnntcccctcagtattgcagtaccgaggggatttctgttagcactaaaatgctagaacttctcaattcccctttattatctcacatactctatttaattgtcaagaaagaggtgttttatatct aaaaagaaccacgagtcacataggattcgtggttttatagttcatcggctaatttgttagctcatatttcccccttctttaacaaaaataaaaatgcctatcaaactgataaaacatgtgatataatagggacggcactaacaatacgccttggaaaaggaggtattacagatgctagaacttctcaaaatagtacttatcgcagtcatcgagagtatcatctcatggctggtgactcgttggttagacgatcacttcgacaagtaaccttcctggttagtgctatctaacctagaaaaaaatcccctcagtattgcagtaccgaggggatttctgttagcactaaaatgctagaacttctcaattcccctttattatctcacatactctatttaattgtcaagaaagaggtgttttatatct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAAGAACCACGAGUCACAUAGGAUUCGUGGUUUUAUAGUUCAUCGGCUAAUUUGUUAGCUCAUAUUUCCCCCUUCUUUAACAAAAAUAAAAAUGCCUAUCAAACUGAUAAAACAUGUGAUAUAAUAGGGACGGCACUAACAAUACGCCUUGGAAAAGGAGGUAUUACAGAUGCUAGAACUUCUCAAAAUAGUACUUAUCGCAGUCAUCGAGAGUAUCAUCUCAUGGCUGGUGACUCGUUGGUUAGACGAUCACUUCGACAAGUAACCUUCCUGGUUAGUGCUAUCUAACCUAGAAAAAAAUCCCCUCAGUAUUGCAGUACCGAGGGGAUUUCUGUUAGCACUAAAAUGCUAGAACUUCUCAAUUCCCCUUUAUUAUCUCACAUACUCUAUUUAAUUGUCAAGAAAGAGGUGUUUUAUAUCU .....((((((((((((......))))))))))))(((((..((((.(((((....))))).............(((((..(((((((((........((((.....))))....((((((.((((((((((.((((((...(((((.((((....))))..)))))..)).)))).(((.((((...((((((((((.((((((((((.((((......)))))))))))((((.(((((.....)))))))))..))).)))))...(((..((((((......))))))..)))..((((((((((.((((....)))).))))))))))))))).(((......))).)))).))).....))))...)))))).))))))....)))))..)))).)))))...))))..)))))... (-121.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAUAUAAAACACCUCUUUCUUGACAAUUAAAUAGAGUAUGUGAGAUAAUAAAGGGGAAUUGAGAAGUUCUAGCAUUUUAGUGCUAACAGAAAUCCCCUCGGUACUGCAAUACUGAGGGGAUUUUUUUCUAGGUUAGAUAGCACUAACCAGGAAGGUUACUUGUCGAAGUGAUCGUCUAACCAACGAGUCACCAGCCAUGAGAUGAUACUCUCGAUGACUGCGAUAAGUACUAUUUUGAGAAGUUCUAGCAUCUGUAAUACCUCCUUUUCCAAGGCGUAUUGUUAGUGCCGUCCCUAUUAUAUCACAUGUUUUAUCAGUUUGAUAGGCAUUUUUAUUUUUGUUAAAGAAGGGGGAAAUAUGAGCUAACAAAUUAGCCGAUGAACUAUAAAACCACGAAUCCUAUGUGACUCGUGGUUCUUUUU ............(((((((((((((((..(((((((.(((((((.(((((...(((((....((((.((((......(((((((((..((((((((((((((((......)))))))))))))))).((((...))))))))))))).(((((.(((.((((((((..((((((((.......)))).))))(((.(((((((......)))).))).)))))))))))))).))))))))).)))).((((..(((((((..((((....)))).)))))))..))))..)))))))))).)))))))..(((((.....))))).....)))))))))))).)))))))))).....((.(((((....)))))))...........((((((((.((......)).))))))))...... (-130.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 358 176 132 223 183 smit:SMT_216|5end_Holliday_junction_DNA_helicase_RuvB_148257..148487_POSITIVE 358 176 132 223 183 smit:SMT_212|5end_Holliday_junction_DNA_helicase_RuvB_144830..145060_POSITIVE 342 80 44 201 169 smit:SMT_1681|5end_D-alanine-activating_enzyme_1664184..1664414_POSITIVE 335 164 121 215 164 smit:SMT_1532|5end_hypothetical_protein_1516296..1516526_NEGATIVE 318 229 181 152 99 smit:SMT_1984|5end_phosphinothricin_N-acetyltransferase_1914028..1914258_NEGATIVE 318 229 181 152 99 smit:SMT_1869|5end_phosphinothricin_N-acetyltransferase_1829215..1829445_NEGATIVE 317 258 214 208 162 smit:SMT_2089|5end_dTDP-4-dehydrorhamnose_3,5-epimerase_related_enzyme_1984987..1985217_POSITIVE 317 258 214 208 162 smit:SMT_291|5end_dTDP-4-dehydrorhamnose_3,5-epimerase_234197..234427_POSITIVE 313 260 216 63 25 smit:SMT_899|5end_5,10-methylenetetrahydrofolate_reductase_848263..848493_NEGATIVE 311 140 95 98 50 smit:SMT_1375|5end_putative_glucose-inhibited_division_protein_1354438..1354668_NEGATIVE 309 267 226 201 141 smit:SMT_1478|5end_manganese_transport_system_membrane_protein_1461256..1461486_NEGATIVE 300 249 201 89 40 smit:SMT_1564|5end_transcriptional_antiterminator,_BglG_family_1555587..1555817_POSITIVE 292 370 322 204 154 smit:SMT_1116|5end_K02244_competence_protein_ComGB_1053841..1054071_NEGATIVE 289 270 227 84 34 smit:SMT_1085|5end_sensor_histidine_kinase_(homolog_to_HK11_Spn)_1022267..1022497_NEGATIVE 288 245 202 194 144 smit:SMT_221|5end_prolyl-tRNA_synthetase_153019..153249_POSITIVE 284 179 133 197 148 smit:SMT_1620|5end_hypothetical_protein_1607240..1607470_NEGATIVE 283 239 196 50 6 smit:SMT_492|5end_branched-chain_amino_acid_ABC_transporter,_ATP-binding_protein_426373..426603_POSITIVE 282 250 204 48 13 smit:SMT_2141|5end_hypothetical_protein_2019976..2020206_NEGATIVE 282 250 204 48 13 smit:SMT_870|5end_hypothetical_protein_818737..818967_NEGATIVE 282 290 242 87 41 smit:SMT_228|5end_hypothetical_protein_164384..164614_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 342 80 44 110 78 smit:SMT_1680|3end_hypothetical_protein_1664173..1664323_POSITIVE 318 229 181 150 97 smit:SMT_1870|3end_K07566_putative_translation_factor_1829217..1829367_NEGATIVE 318 36 5 86 55 smit:SMT_847|3end_thioredoxin_reductase_793848..793998_POSITIVE 301 335 292 68 31 smit:SMT_1624|3end_formate_acetyltransferase_1611421..1611571_NEGATIVE 298 250 201 150 98 smit:SMT_969|3end_30S_ribosomal_protein_S15_914653..914803_NEGATIVE 283 239 196 50 6 smit:SMT_491|3end_K01998_branched-chain_amino_acid_transport_system_permease_protein_426453..426603_POSITIVE 281 170 121 60 19 smit:SMT_1585|3end_phosphopantetheine_adenylyltransferase_1575810..1575960_POSITIVE 279 335 292 85 37 smit:SMT_872|3end_hypothetical_protein_820331..820481_NEGATIVE 279 335 292 85 37 smit:SMT_385|3end_hypothetical_protein_320262..320412_POSITIVE 274 364 322 146 104 smit:SMT_1470|3end_K06188_aquaporin_Z_1453266..1453416_POSITIVE 274 310 267 87 32 smit:SMT_925|3end_DNA-directed_RNA_polymerase_omega_chain_879969..880119_NEGATIVE 269 370 323 65 20 smit:SMT_2040|3end_transcription-repair_coupling_factor_1950463..1950613_NEGATIVE 266 269 221 117 73 smit:SMT_1608|3end_hypothetical_protein_1598196..1598346_POSITIVE 263 74 31 69 22 smit:SMT_1381|3end_gamma-glutamyl_phosphate_reductase_1358468..1358618_NEGATIVE 263 270 230 137 98 smit:SMT_962|3end_putative_hemin_transport_system_ATP-binding_protein_fecE_907829..907979_NEGATIVE 263 369 323 52 15 smit:SMT_681|3end_choline_kinase_589952..590102_NEGATIVE 262 258 213 90 39 smit:SMT_586|3end_ATP_synthase_F1,_beta_subunit_504019..504169_POSITIVE 260 50 13 91 40 smit:SMT_1455|3end_deoxyribose-phosphate_aldolase_1437873..1438023_NEGATIVE 260 260 214 84 32 smit:SMT_678|3end_K04096_DNA_processing_protein_587447..587597_NEGATIVE 259 84 42 148 102 smit:SMT_1977|3end_endopeptidase_O_1908454..1908604_POSITIVE