Origin IGS: aatttgttcaaaattttaatgagtttctagttataaattctagacctcttgagtgaggtaaagtatgtatttggagaagacttttctcttctccattttatatataatttgaataaaaagtgttgtgtcttctaaaatagaattagatactgggcaacttatgatggagatgtcaaggcatttcaatagatcataatatagaagagttcaagaatgaaactggttttcacgttttttcttgactctttttttggttgtgatataattaaccagtaaataatttcaaagaatagtatttttctcttaaaaaagagaagttcaaaaggaaaggagtcagat .........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 atctgactcctttccttttgaacttctcttttttaagagaaaaatactattctttgaaattatttactggttaattatatcacaaccaaaaaaagagtcaagaaaaaacgtgaaaaccagtttcattcttgaactcttctatattatgatctattgaaatgccttgacatctccatcataagttgcccagtatctaattctattttagaagacacaacactttttattcaaattatatataaaatggagaagagaaaagtcttctccaaatacatactttacctcactcaagaggtctagaatttataactagaaactcattaaaattttgaacaaatt Mask Tandem Repeat Region ================================================ aatttgttcaaaattttaatgagtttctagttataaattctagacctcttgagtgaggtaaagtatgtatttggagaagacttttctcttctccattttatatataatttgaataaaaagtgttgtgtcttctaaaatagaattagatactgggcaacttatgatggagatgtcaaggcatttcaatagatcataatatagaagagttcaagaatgaaactggttttcacgttttttcttgactctttttttggttgtgatataattaaccagtaaataatttcaaagaatagtatttttctcttaaaaaagagaagttcaaaaggaaaggagtcagat Find is-nt database================================================ Query_seq: SMT_1319:SMT_1320|SMT_1319:SMT_1320:muscus binding protein:transcriptional regulator, MarR family:->->:1290035..1290373 339 aatttgttcaaaattttaatgagtttctagttataaattctagacctcttgagtgaggtaaagtatgtatttggagaagacttttctcttctccattttatatataatttgaataaaaagtgttgtgtcttctaaaatagaattagatactgggcaacttatgatggagatgtcaaggcatttcaatagatcataatatagaagagttcaagaatgaaactggttttcacgttttttcttgactctttttttggttgtgatataattaaccagtaaataatttcaaagaatagtatttttctcttaaaaaagagaagttcaaaaggaaaggagtcagat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1319:SMT_1320|SMT_1319:SMT_1320:muscus binding protein:transcriptional regulator, MarR family:->->:1290035..1290373 339 aatttgttcaaaattttaatgagtttctagttataaattctagacctcttgagtgaggtaaagtatgtatttggagaagacttttctcttctccattttatatataatttgaataaaaagtgttgtgtcttctaaaatagaattagatactgggcaacttatgatggagatgtcaaggcatttcaatagatcataatatagaagagttcaagaatgaaactggttttcacgttttttcttgactctttttttggttgtgatataattaaccagtaaataatttcaaagaatagtatttttctcttaaaaaagagaagttcaaaaggaaaggagtcagat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1319:SMT_1320|SMT_1319:SMT_1320:muscus binding protein:transcriptional regulator, MarR family:->->:1290035..1290373 339 aatttgttcaaaattttaatgagtttctagttataaattctagacctcttgagtgaggtaaagtatgtatttggagaagacttttctcttctccattttatatataatttgaataaaaagtgttgtgtcttctaaaatagaattagatactgggcaacttatgatggagatgtcaaggcatttcaatagatcataatatagaagagttcaagaatgaaactggttttcacgttttttcttgactctttttttggttgtgatataattaaccagtaaataatttcaaagaatagtatttttctcttaaaaaagagaagttcaaaaggaaaggagtcagat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatttgttcaaaattttaatgagtttctagttataaattctagacctcttgagtgaggtaaagtatgtatttggagaagacttttctcttctccattttatatataatttgaataaaaagtgttgtgtcttctaaaatagaattagatactgggcaacttatgatggagatgtcaaggcatttcaatagatcataatatagaagagttcaagaatgaaactggttttcacgttttttcttgactctttttttggttgtgatataattaaccagtaaataatttcaaagaatagtatttttctcttaaaaaagagaagttcaaaaggaaaggagtcagat Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 37 End: 132 .................................... M L D L L S E V K Y V F G E D F S L L H F I Y N L N K K C C V F ............................................................................................................................................................................................................... Protein_Len: 37 Strand: - Start: 186 End: 296 ......................................................................................................................................................................................... Y I M I Y F L E L I F S T K V N K R S E K K P Q S I I L W Y I I E F F L M ........................................... Protein_Len: 48 Strand: - Start: 43 End: 186 .......................................... V E Q T L Y L I Y K S F V K R K E M K Y I I Q I F L T T D E L I S N S V P C S I I S I D L C K M ......................................................................................................................................................... aatttgttcaaaattttaatgagtttctagttataaattctagacctcttgagtgaggtaaagtatgtatttggagaagacttttctcttctccattttatatataatttgaataaaaagtgttgtgtcttctaaaatagaattagatactgggcaacttatgatggagatgtcaaggcatttcaatagatcataatatagaagagttcaagaatgaaactggttttcacgttttttcttgactctttttttggttgtgatataattaaccagtaaataatttcaaagaatagtatttttctcttaaaaaagagaagttcaaaaggaaaggagtcagat 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: 81 Start: 190 End: 219 .............................................................................................................................................................................................TTTCATTCTTGAACTCTTCTATATTATGAT........................................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aatttgttcaaaattttaatgagtttctagttataaattctagacctcttgagtgaggtaaagtatgtatttggagaagacttttctcttctccattttatatataatttgaataaaaagtgttgtgtcttctaaaatagaattagatactgggcaacttatgatggagatgtcaaggcatttcaatagatcataatatagaagagttcaagaatgaaactggttttcacgttttttcttgactctttttttggttgtgatataattaaccagtaaataatttcaaagaatagtatttttctcttaaaaaagagaagttcaaaaggaaaggagtcagat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -9.7 Tail_Score: -4.65494 Start: 72 End: 95 Full_Region: GGTAAAGTATGTATT TGGAGAAGA CTTTTC TCTTCTCCA TTTTATATATAATTT .......................................................................TGGAGAAGACTTTTCTCTTCTCCA.................................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 49 HP_score: -2.9 Tail_Score: -3.68704 Start: 215 End: 229 Full_Region: agtcaagaaaaaacg tgaaa accag tttca ttcttgaactcttct ......................................................................................................................................................................................................................tgaaaaccagtttca.............................................................................................................. Find igs database================================================ Query_seq: SMT_1319:SMT_1320|SMT_1319:SMT_1320:muscus binding protein:transcriptional regulator, MarR family:->->:1290035..1290373 339 aatttgttcaaaattttaatgagtttctagttataaattctagacctcttgagtgaggtaaagtatgtatttggagaagacttttctcttctccattttatatataatttgaataaaaagtgttgtgtcttctaaaatagaattagatactgggcaacttatgatggagatgtcaaggcatttcaatagatcataatatagaagagttcaagaatgaaactggttttcacgttttttcttgactctttttttggttgtgatataattaaccagtaaataatttcaaagaatagtatttttctcttaaaaaagagaagttcaaaaggaaaggagtcagat Intra-Species Hit: Count: 2 Min: 1 Max: 339 Len: 339 Subject: smit_SMT_1319_SMT_1320|muscus binding protein:transcriptional regulator, MarR family|POSITIVE:POSITIVE|[1290035,1290373]|339 HSP 1 e-value: 1.0E-180 bit: 630.0 Len: 339 Query Start:1 Query End:339 Subject Strand: POSITIVE Subject Start: 1 Subject End: 339 aatttgttcaaaattttaatgagtttctagttataaattctagacctcttgagtgaggtaaagtatgtatttggagaagacttttctcttctccattttatatataatttgaataaaaagtgttgtgtcttctaaaatagaattagatactgggcaacttatgatggagatgtcaaggcatttcaatagatcataatatagaagagttcaagaatgaaactggttttcacgttttttcttgactcnnnnnnnggttgtgatataattaaccagtaaataatttcaaagaatagtatttttctcttaaaaaagagaagttcaaaaggaaaggagtcagat aatttgttcaaaattttaatgagtttctagttataaattctagacctcttgagtgaggtaaagtatgtatttggagaagacttttctcttctccattttatatataatttgaataaaaagtgttgtgtcttctaaaatagaattagatactgggcaacttatgatggagatgtcaaggcatttcaatagatcataatatagaagagttcaagaatgaaactggttttcacgttttttcttgactctttttttggttgtgatataattaaccagtaaataatttcaaagaatagtatttttctcttaaaaaagagaagttcaaaaggaaaggagtcagat Subject: smit_SMT_2064_SMT_2065|amino acid ABC transporter, ATP-binding protein:transcriptional regulator, MarR family|POSITIVE:POSITIVE|[1972502,1972804]|303 HSP 1 e-value: 1.0E-134 bit: 480.0 Len: 303 Query Start:37 Query End:339 Subject Strand: POSITIVE Subject Start: 6 Subject End: 303 ....................................attctagacctcttgagtgaggtaaagtatgtatttggagaagacttttctcttctccattttatatataatttgaataaaaagtgttgtgtcttctaaaatagaattagatactgggcaacttatgatggagatgtcaaggcatttcaatagatcataatatagaagagttcaagaatgaaactggttttcacgttttttcttgactcnnnnnnnggttgtgatataattaaccagtaaataatttcaaagaatagtatttttctcttaaaaaagagaagttcaaaaggaaaggagtcagat ....................................attctagacctcttgagtgaggtaaagtatgtatt-ggagaagacttt-ctct-ctccattttatatataatt-gaataaaaagtgttgt-tcttctaaaatagaattagatactgggcaacttatgatggagatgtcaaggcatttcaatagatcataatatagaagagttcaagaatgaaactggttttcacgttttttcttgactctttttttggttgtgatataattaaccagtaaataatttcaaagaatagtatttttctcttaaaaaagagaagttcaaaaggaaaggagtcagat Inter-species Hit: Count: 1 Min: 193 Max: 339 Len: 147 Subject: NC_003028_SP_2172_SP_2173|adc operon repressor AdcR:dltD protein|NEGATIVE:NEGATIVE|[2090276,2090429]|154 HSP 1 e-value: 8.0E-41 bit: 168.0 Len: 147 Query Start:193 Query End:339 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 149 ................................................................................................................................................................................................ataatatagaagagttcaagaatgaaactggttttcacgttttttcttgactcnnnnnnnggttgtgatataattaaccagtaaataa--tttcaaagaatagtatttttctcttaaaaaagagaagttcaaaaggaaaggagtcagat ................................................................................................................................................................................................ataatatagaagagttcaagaatgaaactagttttcacgttttttcttgactctttttttgcttgtgatataattaactggtaaacaaaatgtcaaagaatagtatttttctcttaaaaaagagaagtctaaaaggaaaggagtcagat Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAAUAUAGAAGAGUUCAAGAAUGAAACUGGUUUUCACGUUUUUUCUUGACUCUUUUUUUGGUUGUGAUAUAAUUAACCAGUAAAUAAUUUCAAAGAAUAGUAUUUUUCUCUUAAAAAAGAGAAGUUCAAAAGGAAAGGAGUCAGAU .......((((((((.((((((.(((((((.....)).))))))))))))))))))).(((((((.........))))))).......((((...((((.......(((((((....))))))))))).....)))).......... (-28.91) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCUGACUCCUUUCCUUUUGAACUUCUCUUUUUUAAGAGAAAAAUACUAUUCUUUGAAAUUAUUUACUGGUUAAUUAUAUCACAACCAAAAAAAGAGUCAAGAAAAAACGUGAAAACCAGUUUCAUUCUUGAACUCUUCUAUAUUAU .......................(((((((....)))))))..........................(((((...........)))))....((((((((((((.((((((....))..))))..)))))).))))))......... (-22.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 268 59 11 87 32 smit:SMT_566|5end_K07282_poly-gamma-glutamate_synthesis_protein_(capsule_biosynthesis_protein)_483498..483728_POSITIVE 256 58 15 135 87 smit:SMT_884|5end_hypothetical_protein_predicted_by_Glimmer/Critica_832306..832536_NEGATIVE 247 67 27 153 116 smit:SMT_635|5end_ribonucleoside-diphosphate_reductase_alpha_chain_540658..540888_POSITIVE 245 48 4 166 126 smit:SMT_222|5end_beta-glucosidase_154971..155201_POSITIVE 243 59 11 201 142 smit:SMT_895|5end_cysteinyl-tRNA_synthetase_843037..843267_NEGATIVE 242 68 37 111 79 smit:SMT_1018|5end_hypothetical_protein_predicted_by_Glimmer/Critica_954564..954794_POSITIVE 241 57 11 231 185 smit:SMT_2065|5end_transcriptional_regulator,_MarR_family_1972665..1972895_POSITIVE 241 68 38 194 161 smit:SMT_976|5end_hypothetical_protein_925183..925413_NEGATIVE 238 64 31 210 167 smit:SMT_1834|5end_cell_division_protein_1803695..1803925_NEGATIVE 235 66 27 123 84 smit:SMT_1512|5end_hypothetical_protein_1494747..1494977_NEGATIVE 232 60 25 112 75 smit:SMT_1258|5end_acetolactate_synthase_large_subunit_1224866..1225096_NEGATIVE 226 80 35 87 51 smit:SMT_2016|5end_tyrosine_recombinase_1933425..1933655_NEGATIVE 224 80 38 90 54 smit:SMT_1973|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1905438..1905668_NEGATIVE 223 68 26 76 29 smit:SMT_1972|5end_uncharacterized_conserved_phage_related_protein_1903662..1903892_POSITIVE 223 66 23 111 74 smit:SMT_1199|5end_lactococcin_A_ABC_transporter_permease_protein_1161063..1161293_NEGATIVE 221 68 27 64 14 smit:SMT_675|5end_DNA_repair_protein_582977..583207_NEGATIVE 218 137 98 52 11 smit:SMT_1210|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1171051..1171281_NEGATIVE 218 137 98 131 90 smit:SMT_1209|5end_choline_binding_protein_PcpA_1170972..1171202_NEGATIVE 217 45 1 186 149 smit:SMT_1132|5end_glutamate--cysteine_ligase,_putative,_truncated_1068108..1068338_NEGATIVE 213 65 22 197 157 smit:SMT_1572|5end_excinuclease_ABC_subunit_B_1564402..1564632_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 256 58 15 101 53 smit:SMT_885|3end_single-stranded-DNA-specific_exonuclease_RecJ_832340..832490_NEGATIVE 245 48 4 67 27 smit:SMT_221|3end_prolyl-tRNA_synthetase_154952..155102_POSITIVE 243 59 11 119 60 smit:SMT_896|3end_hypothetical_protein_843119..843269_NEGATIVE 241 68 38 125 92 smit:SMT_977|3end_conserved_hypothetical_protein,_Rrf2_family_protein_925252..925402_NEGATIVE 235 66 27 109 70 smit:SMT_1513|3end_hypothetical_protein_1494761..1494911_NEGATIVE 231 70 22 130 75 smit:SMT_516|3end_hypothetical_protein_442527..442677_NEGATIVE 223 66 23 98 61 smit:SMT_1200|3end_K06148_ATP-binding_cassette,_subfamily_C,_bacterial_1161076..1161226_NEGATIVE 222 66 23 149 96 smit:SMT_1195|3end_amidophosphoribosyltransferase_1153376..1153526_NEGATIVE 218 137 98 144 103 smit:SMT_1210|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1170959..1171109_NEGATIVE 217 43 4 92 56 smit:SMT_1449|3end_K08591_putative_membrane_protein_1432658..1432808_POSITIVE 213 65 22 120 80 smit:SMT_1571|3end_CAAX_amino_terminal_protease_family_protein_1564405..1564555_POSITIVE 212 62 27 120 85 smit:SMT_998|3end_peptide_chain_release_factor_3_939699..939849_NEGATIVE 211 64 22 148 103 smit:SMT_1348|3end_exoribonuclease_II_1325148..1325298_NEGATIVE 209 44 8 92 56 smit:SMT_1296|3end_K03696_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpC_1259802..1259952_POSITIVE 207 68 29 129 84 smit:SMT_203|3end_putative_ABC_transporter_BitD_133821..133971_NEGATIVE 202 63 29 114 79 smit:SMT_771|3end_spermidine/putrescine_transport_system_permease_protein_PotB_681356..681506_NEGATIVE 201 60 29 30 2 smit:SMT_1800|3end_exonuclease_RexA_1773540..1773690_NEGATIVE 200 58 12 143 88 smit:SMT_576|3end_transcriptional_regulator,_LysR_family_495407..495557_POSITIVE 198 45 6 90 52 smit:SMT_459|3end_hypothetical_protein_397690..397840_POSITIVE 197 49 6 123 73 smit:SMT_1532|3end_hypothetical_protein_1515994..1516144_NEGATIVE