Origin IGS: tcaaccttccaaaagcctattgtatcaagctttctagcttgggcagtaggctttttttgtgtataggaggcaaaaaagggccagaatctgaatgaactagtaccggaaaatatttcaagtacagactaattcaaattgcgtagcagaaatcatacaaatgaaattgattatagtaaaataggattagaattattaagaaagttggtttttta .........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 taaaaaaccaactttcttaataattctaatcctattttactataatcaatttcatttgtatgatttctgctacgcaatttgaattagtctgtacttgaaatattttccggtactagttcattcagattctggcccttttttgcctcctatacacaaaaaaagcctactgcccaagctagaaagcttgatacaataggcttttggaaggttga Mask Tandem Repeat Region ================================================ tcaaccttccaaaagcctattgtatcaagctttctagcttgggcagtaggctttttttgtgtataggaggcaaaaaagggccagaatctgaatgaactagtaccggaaaatatttcaagtacagactaattcaaattgcgtagcagaaatcatacaaatgaaattgattatagtaaaataggattagaattattaagaaagttggtttttta Find is-nt database================================================ Query_seq: SMT_605:SMT_606|SMT_605:SMT_606:DNA-binding protein HU:cytochrome c-type biogenesis protein CcdA:->->:519318..519529 212 tcaaccttccaaaagcctattgtatcaagctttctagcttgggcagtaggctttttttgtgtataggaggcaaaaaagggccagaatctgaatgaactagtaccggaaaatatttcaagtacagactaattcaaattgcgtagcagaaatcatacaaatgaaattgattatagtaaaataggattagaattattaagaaagttggtttttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_605:SMT_606|SMT_605:SMT_606:DNA-binding protein HU:cytochrome c-type biogenesis protein CcdA:->->:519318..519529 212 tcaaccttccaaaagcctattgtatcaagctttctagcttgggcagtaggctttttttgtgtataggaggcaaaaaagggccagaatctgaatgaactagtaccggaaaatatttcaagtacagactaattcaaattgcgtagcagaaatcatacaaatgaaattgattatagtaaaataggattagaattattaagaaagttggtttttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_605:SMT_606|SMT_605:SMT_606:DNA-binding protein HU:cytochrome c-type biogenesis protein CcdA:->->:519318..519529 212 tcaaccttccaaaagcctattgtatcaagctttctagcttgggcagtaggctttttttgtgtataggaggcaaaaaagggccagaatctgaatgaactagtaccggaaaatatttcaagtacagactaattcaaattgcgtagcagaaatcatacaaatgaaattgattatagtaaaataggattagaattattaagaaagttggtttttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tcaaccttccaaaagcctattgtatcaagctttctagcttgggcagtaggctttttttgtgtataggaggcaaaaaagggccagaatctgaatgaactagtaccggaaaatatttcaagtacagactaattcaaattgcgtagcagaaatcatacaaatgaaattgattatagtaaaataggattagaattattaagaaagttggtttttta Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: - Start: 20 End: 130 ................... Q I L S E L K P L L S K K H I P P L F P G S D S H V L V P F Y K L Y L S M .................................................................................. Protein_Len: 37 Strand: - Start: 3 End: 113 .. V K W F G I T D L K R A Q A T P K K Q T Y S A F F P W F R F S S T G S F M ................................................................................................... tcaaccttccaaaagcctattgtatcaagctttctagcttgggcagtaggctttttttgtgtataggaggcaaaaaagggccagaatctgaatgaactagtaccggaaaatatttcaagtacagactaattcaaattgcgtagcagaaatcatacaaatgaaattgattatagtaaaataggattagaattattaagaaagttggtttttta 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: 149 End: 178 ....................................................................................................................................................TTTTACTATAATCAATTTCATTTGTATGAT.................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tcaaccttccaaaagcctattgtatcaagctttctagcttgggcagtaggctttttttgtgtataggaggcaaaaaagggccagaatctgaatgaactagtaccggaaaatatttcaagtacagactaattcaaattgcgtagcagaaatcatacaaatgaaattgattatagtaaaataggattagaattattaagaaagttggtttttta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_605:SMT_606|SMT_605:SMT_606:DNA-binding protein HU:cytochrome c-type biogenesis protein CcdA:->->:519318..519529 212 tcaaccttccaaaagcctattgtatcaagctttctagcttgggcagtaggctttttttgtgtataggaggcaaaaaagggccagaatctgaatgaactagtaccggaaaatatttcaagtacagactaattcaaattgcgtagcagaaatcatacaaatgaaattgattatagtaaaataggattagaattattaagaaagttggtttttta Intra-Species Hit: Count: 1 Min: 1 Max: 212 Len: 212 Subject: smit_SMT_605_SMT_606|DNA-binding protein HU:cytochrome c-type biogenesis protein CcdA|POSITIVE:POSITIVE|[519318,519529]|212 HSP 1 e-value: 1.0E-104 bit: 379.0 Len: 212 Query Start:1 Query End:212 Subject Strand: POSITIVE Subject Start: 1 Subject End: 212 tcaaccttccaaaagcctattgtatcaagctttctagcttgggcagtaggcnnnnnnngtgtataggaggcaaaaaagggccagaatctgaatgaactagtaccggaaaatatttcaagtacagactaattcaaattgcgtagcagaaatcatacaaatgaaattgattatagtaaaataggattagaattattaagaaagttggtttttta tcaaccttccaaaagcctattgtatcaagctttctagcttgggcagtaggctttttttgtgtataggaggcaaaaaagggccagaatctgaatgaactagtaccggaaaatatttcaagtacagactaattcaaattgcgtagcagaaatcatacaaatgaaattgattatagtaaaataggattagaattattaagaaagttggtttttta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCAACCUUCCAAAAGCCUAUUGUAUCAAGCUUUCUAGCUUGGGCAGUAGGCUUUUUUUGUGUAUAGGAGGCAAAAAAGGGCCAGAAUCUGAAUGAACUAGUACCGGAAAAUAUUUCAAGUACAGACUAAUUCAAAUUGCGUAGCAGAAAUCAUACAAAUGAAAUUGAUUAUAGUAAAAUAGGAUUAGAAUUAUUAAGAAAGUUGGUUUUUUA .....((((((((((((((((((.(((((((....))))))))))))))))))))..........)))))....((((((((((..(((.(((((....((((..(((.....)))..))))...(((((((...(((((((((((...((((....))))..))).)))).))))....)))))))..))))).)))...)))))))))). (-57.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAAACCAACUUUCUUAAUAAUUCUAAUCCUAUUUUACUAUAAUCAAUUUCAUUUGUAUGAUUUCUGCUACGCAAUUUGAAUUAGUCUGUACUUGAAAUAUUUUCCGGUACUAGUUCAUUCAGAUUCUGGCCCUUUUUUGCCUCCUAUACACAAAAAAAGCCUACUGCCCAAGCUAGAAAGCUUGAUACAAUAGGCUUUUGGAAGGUUGA ........((((((((........................................((((((...........(.(((((((((.((.(((((((.(((.....))).))))).)))).)))))))))).(((........)))...))))))....(((((((((.((..((((((....))))))...)).))))))))).)))))))). (-48.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 427 49 3 163 116 smit:SMT_1696|5end_hypothetical_protein_1678182..1678412_POSITIVE 297 58 12 224 168 smit:SMT_945|5end_cytidylate_kinase_895908..896138_NEGATIVE 293 114 77 73 34 smit:SMT_1375|5end_putative_glucose-inhibited_division_protein_1354438..1354668_NEGATIVE 292 53 17 156 127 smit:SMT_1802|5end_tyrosyl-tRNA_synthetase_1776712..1776942_NEGATIVE 291 84 41 58 17 smit:SMT_1248|5end_Na+/H+_antiporter_1210529..1210759_NEGATIVE 288 57 16 135 96 smit:SMT_1612|5end_K06024_segregation_and_condensation_protein_B_1600052..1600282_POSITIVE 286 57 13 103 43 smit:SMT_1409|5end_hypothetical_protein_1388514..1388744_NEGATIVE 282 51 15 115 74 smit:SMT_1914|5end_K03696_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpC_1859486..1859716_POSITIVE 280 109 63 196 151 smit:SMT_1521|5end_K02003_1501887..1502117_NEGATIVE 276 63 29 75 32 smit:SMT_1992|5end_carboxynorspermidine_decarboxylase_1919207..1919437_NEGATIVE 276 63 29 75 32 smit:SMT_1415|5end_carboxynorspermidine_decarboxylase_1399570..1399800_NEGATIVE 271 105 64 194 152 smit:SMT_809|5end_sensor_histidine_kinase_(homolog_to_BlpH_Spn)_719745..719975_NEGATIVE 267 49 6 42 3 smit:SMT_825|5end_aspartate_aminotransferase_749594..749824_NEGATIVE 266 56 15 193 143 smit:SMT_2133|5end_hypothetical_protein_2014007..2014237_NEGATIVE 266 56 15 193 143 smit:SMT_872|5end_hypothetical_protein_820618..820848_NEGATIVE 266 56 15 193 143 smit:SMT_385|5end_hypothetical_protein_319895..320125_POSITIVE 265 85 42 48 13 smit:SMT_847|5end_thioredoxin_reductase_792800..793030_POSITIVE 264 49 6 61 22 smit:SMT_675|5end_DNA_repair_protein_582977..583207_NEGATIVE 263 210 169 161 122 smit:SMT_1075|5end_hypothetical_protein_1013473..1013703_POSITIVE 262 74 37 92 60 smit:SMT_2044|5end_transcriptional_activator_TipA,_putative_1955885..1956115_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 430 55 11 80 36 smit:SMT_605|3end_DNA-binding_protein_HU_519257..519407_POSITIVE 291 84 41 46 5 smit:SMT_1249|3end_hypothetical_protein_1210541..1210691_NEGATIVE 289 90 41 148 83 smit:SMT_225|3end_pullulanase_159666..159816_NEGATIVE 288 57 16 116 77 smit:SMT_1611|3end_K05896_segregation_and_condensation_protein_A_1600113..1600263_POSITIVE 286 57 13 85 25 smit:SMT_1410|3end_exonuclease_RexA_1388532..1388682_NEGATIVE 282 106 64 60 19 smit:SMT_1792|3end_K03307_solute:Na+_symporter,_SSS_family_1766575..1766725_NEGATIVE 276 63 29 75 32 smit:SMT_1993|3end_hypothetical_protein_1919207..1919357_NEGATIVE 276 63 29 75 32 smit:SMT_1416|3end_hypothetical_protein_1399570..1399720_NEGATIVE 271 56 15 75 25 smit:SMT_1670|3end_K02030_polar_amino_acid_transport_system_substrate-binding_protein_1659295..1659445_POSITIVE 271 56 15 54 4 smit:SMT_1068|3end_ATP-dependent_DNA_helicase_RecG_1008986..1009136_POSITIVE 267 49 6 45 6 smit:SMT_826|3end_hypothetical_protein_749591..749741_NEGATIVE 266 56 15 78 28 smit:SMT_2134|3end_hypothetical_protein_2014122..2014272_NEGATIVE 266 56 15 78 28 smit:SMT_873|3end_hypothetical_protein_820733..820883_NEGATIVE 266 56 15 78 28 smit:SMT_384|3end_hypothetical_protein_319860..320010_POSITIVE 252 49 1 75 23 smit:SMT_1542|3end_phosphomevalonate_kinase_1526077..1526227_NEGATIVE 248 72 36 75 43 smit:SMT_155|3end_hypothetical_protein_102492..102642_NEGATIVE 248 51 14 137 100 smit:SMT_121|3end_hypothetical_protein_74414..74564_POSITIVE 247 89 44 86 36 smit:SMT_1353|3end_GTP-binding_protein_1330690..1330840_NEGATIVE 247 43 1 141 95 smit:SMT_658|3end_hypothetical_protein_569403..569553_NEGATIVE 246 40 9 41 9 smit:SMT_730|3end_hypothetical_protein_636111..636261_NEGATIVE