Origin IGS: acattagaattttctcctacttggcgtggactgggtaggggattttatttttagacaattctcatttttaagaatcttgaaaacattcaatatttacttcgtgaagcttttttcatactcctattcatgatatactaggtcagtattttataaatatgaaggagattttc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gaaaatctccttcatatttataaaatactgacctagtatatcatgaataggagtatgaaaaaagcttcacgaagtaaatattgaatgttttcaagattcttaaaaatgagaattgtctaaaaataaaatcccctacccagtccacgccaagtaggagaaaattctaatgt Mask Tandem Repeat Region ================================================ acattagaattttctcctacttggcgtggactgggtaggggattttatttttagacaattctcatttttaagaatcttgaaaacattcaatatttacttcgtgaagcttttttcatactcctattcatgatatactaggtcagtattttataaatatgaaggagattttc Find is-nt database================================================ Query_seq: SMT_385:SMT_386|SMT_385:SMT_386:hypothetical protein:branched-chain amino acid transport system II carrier protein:->->:320323..320492 170 acattagaattttctcctacttggcgtggactgggtaggggattttatttttagacaattctcatttttaagaatcttgaaaacattcaatatttacttcgtgaagcttttttcatactcctattcatgatatactaggtcagtattttataaatatgaaggagattttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_385:SMT_386|SMT_385:SMT_386:hypothetical protein:branched-chain amino acid transport system II carrier protein:->->:320323..320492 170 acattagaattttctcctacttggcgtggactgggtaggggattttatttttagacaattctcatttttaagaatcttgaaaacattcaatatttacttcgtgaagcttttttcatactcctattcatgatatactaggtcagtattttataaatatgaaggagattttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_385:SMT_386|SMT_385:SMT_386:hypothetical protein:branched-chain amino acid transport system II carrier protein:->->:320323..320492 170 acattagaattttctcctacttggcgtggactgggtaggggattttatttttagacaattctcatttttaagaatcttgaaaacattcaatatttacttcgtgaagcttttttcatactcctattcatgatatactaggtcagtattttataaatatgaaggagattttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 acattagaattttctcctacttggcgtggactgggtaggggattttatttttagacaattctcatttttaagaatcttgaaaacattcaatatttacttcgtgaagcttttttcatactcctattcatgatatactaggtcagtattttataaatatgaaggagattttc Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 26 End: 127 ......................... M D W V G D F I F R Q F S F L R I L K T F N I Y F V K L F S Y S Y S ........................................... acattagaattttctcctacttggcgtggactgggtaggggattttatttttagacaattctcatttttaagaatcttgaaaacattcaatatttacttcgtgaagcttttttcatactcctattcatgatatactaggtcagtattttataaatatgaaggagattttc 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================================================ acattagaattttctcctacttggcgtggactgggtaggggattttatttttagacaattctcatttttaagaatcttgaaaacattcaatatttacttcgtgaagcttttttcatactcctattcatgatatactaggtcagtattttataaatatgaaggagattttc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_385:SMT_386|SMT_385:SMT_386:hypothetical protein:branched-chain amino acid transport system II carrier protein:->->:320323..320492 170 acattagaattttctcctacttggcgtggactgggtaggggattttatttttagacaattctcatttttaagaatcttgaaaacattcaatatttacttcgtgaagcttttttcatactcctattcatgatatactaggtcagtattttataaatatgaaggagattttc Intra-Species Hit: Count: 2 Min: 1 Max: 170 Len: 170 Subject: smit_SMT_871_SMT_872|K03311 branched-chain amino acid:cation transporter, LIVCS family:hypothetical protein|NEGATIVE:NEGATIVE|[820251,820420]|170 HSP 1 e-value: 7.0E-92 bit: 337.0 Len: 170 Query Start:1 Query End:170 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 170 acattagaattttctcctacttggcgtggactgggtaggggattttatttttagacaattctcatttttaagaatcttgaaaacattcaatatttacttcgtgaagcttttttcatactcctattcatgatatactaggtcagtattttataaatatgaaggagattttc acattagaattttctcctacttggcgtggactgggtaggggattttatttttagacaattctcatttttaagaatcttgaaaacattcaatatttacttcgtgaagcttttttcatactcctattcatgatatactaggtcagtattttataaatatgaaggagattttc Subject: smit_SMT_385_SMT_386|hypothetical protein:branched-chain amino acid transport system II carrier protein|POSITIVE:POSITIVE|[320323,320492]|170 HSP 1 e-value: 7.0E-92 bit: 337.0 Len: 170 Query Start:1 Query End:170 Subject Strand: POSITIVE Subject Start: 1 Subject End: 170 acattagaattttctcctacttggcgtggactgggtaggggattttatttttagacaattctcatttttaagaatcttgaaaacattcaatatttacttcgtgaagcttttttcatactcctattcatgatatactaggtcagtattttataaatatgaaggagattttc acattagaattttctcctacttggcgtggactgggtaggggattttatttttagacaattctcatttttaagaatcttgaaaacattcaatatttacttcgtgaagcttttttcatactcctattcatgatatactaggtcagtattttataaatatgaaggagattttc Inter-species Hit: Count: 3 Min: 11 Max: 169 Len: 159 Subject: NC_008533_SPD_0545_SPD_0546|hypothetical protein:branched-chain amino acid transport system II carrier protein|POSITIVE:POSITIVE|[558043,558212]|170 HSP 1 e-value: 1.0E-47 bit: 190.0 Len: 159 Query Start:11 Query End:169 Subject Strand: POSITIVE Subject Start: 10 Subject End: 169 ..........tttctcctacttggcgtggactgggtagggga-ttttatttttagacaattctcatttttaagaatcttgaaaacattcaatatttacttcgtgaagcttttttcatactcctattcatgatatactaggtcagtattttataaatatgaaggagatttt. ..........tttctcctacttggtgtggactgggtaggagagttttatttttagataattcttatttttaagaaagttgaaaacatttaatatttgcatcgtgatgcttttttcagactcctaatcgtggtatactaggtcagtattttataaatatgaaggagatttt. Subject: NC_003098_spr0550_spr0551|hypothetical protein:Branched-chain amino acid transport system carrier protein|POSITIVE:POSITIVE|[550513,550667]|155 HSP 1 e-value: 2.0E-39 bit: 163.0 Len: 145 Query Start:11 Query End:155 Subject Strand: POSITIVE Subject Start: 10 Subject End: 155 ..........tttctcctacttggcgtggactgggtagggga-ttttatttttagacaattctcatttttaagaatcttgaaaacattcaatatttacttcgtgaagcttttttcatactcctattcatgatatactaggtcagtattttataaat............... ..........tttctcctacttggtgtggactgggtaggagagttttatttttagataattcttatttttaagaaagttgaaaacatttaatatttgcatcgtgatgcttttttcagactcctaatcgtggtatactaggtcagtattttataaat............... Subject: NC_003028_SP_0624_SP_0626|hypothetical protein:branched-chain amino acid transport system II carrier protein|POSITIVE:POSITIVE|[592218,592819]|602 HSP 1 e-value: 2.0E-39 bit: 163.0 Len: 145 Query Start:11 Query End:155 Subject Strand: POSITIVE Subject Start: 457 Subject End: 602 ..........tttctcctacttggcgtggactgggtagggga-ttttatttttagacaattctcatttttaagaatcttgaaaacattcaatatttacttcgtgaagcttttttcatactcctattcatgatatactaggtcagtattttataaat............... ..........tttctcctacttggtgtggactgggtaggagagttttatttttagataattcttatttttaagaaaattgaaaacatttaatatttgcctcgtgatgcttttttcagactcctaatcgtggtatactaggtcagtattttataaat............... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUCUCCUACUUGGCGUGGACUGGGUAGGGGAUUUUAUUUUUAGACAAUUCUCAUUUUUAAGAAUCUUGAAAACAUUCAAUAUUUACUUCGUGAAGCUUUUUUCAUACUCCUAUUCAUGAUAUACUAGGUCAGUAUUUUAUAAAUAUGAAGGAGAUUUU ..(((((((((..(......)..))))))))).................((((.((((((((...))))))))..((((.((((((..(((((((..................))))))).(((((.....)))))....)))))))))).)))).... (-33.47) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAUCUCCUUCAUAUUUAUAAAAUACUGACCUAGUAUAUCAUGAAUAGGAGUAUGAAAAAAGCUUCACGAAGUAAAUAUUGAAUGUUUUCAAGAUUCUUAAAAAUGAGAAUUGUCUAAAAAUAAAAUCCCCUACCCAGUCCACGCCAAGUAGGAGAAA ....((((((.(.(((((((.(.((((((...)))))).).)))))))((.(((.(......((((....))))..........((((((...((((((((....)))))))).....))))))......).)))))............).)))))).. (-25.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 280 31 4 226 192 smit:SMT_1058|5end_primosomal_protein_DnaI_996486..996716_POSITIVE 279 44 3 129 92 smit:SMT_1788|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1765029..1765259_NEGATIVE 279 44 3 129 92 smit:SMT_1197|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1158751..1158981_NEGATIVE 279 45 1 59 5 smit:SMT_1007|5end_radical_SAM_domain_protein_947035..947265_POSITIVE 275 59 13 209 170 smit:SMT_1295|5end_transcriptional_regulator_CtsR_1256830..1257060_POSITIVE 269 50 3 59 1 smit:SMT_1505|5end_purine-nucleoside_phosphorylase_1488515..1488745_NEGATIVE 269 130 89 78 30 smit:SMT_647|5end_DNA_gyrase,_A_subunit_554170..554400_NEGATIVE 265 42 3 83 27 smit:SMT_110|5end_alpha-L-fucosidase_57445..57675_POSITIVE 264 69 21 100 58 smit:SMT_1924|5end_isoleucyl-tRNA_synthetase_1866188..1866418_POSITIVE 252 123 83 115 62 smit:SMT_1877|5end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_1834039..1834269_POSITIVE 251 136 96 231 196 smit:SMT_1448|5end_serine_hydroxymethyltransferase_1431848..1432078_NEGATIVE 250 66 21 186 128 smit:SMT_1655|5end_glucose-6-phosphate_1-dehydrogenase_1645021..1645251_NEGATIVE 247 50 1 88 28 smit:SMT_2001|5end_membrane_protease_protein_family_1923387..1923617_POSITIVE 247 31 6 32 4 smit:SMT_847|5end_thioredoxin_reductase_792800..793030_POSITIVE 245 26 1 75 44 smit:SMT_1879|5end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_1836806..1837036_NEGATIVE 245 33 1 46 23 smit:SMT_998|5end_peptide_chain_release_factor_3_941243..941473_NEGATIVE 244 31 3 83 42 smit:SMT_1974|5end_high-affinity_zinc_uptake_system_protein_ZnuA_precursor_/_hypothetical_exported_protein_1905506..1905736_POSITIVE 244 48 5 69 29 smit:SMT_222|5end_beta-glucosidase_154971..155201_POSITIVE 242 31 5 120 87 smit:SMT_1156|5end_K07485_transposase_1099938..1100168_POSITIVE 241 30 3 215 181 smit:SMT_2110|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1999163..1999393_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 290 41 7 38 3 smit:SMT_1534|3end_signal_peptidase_I_1517912..1518062_POSITIVE 279 44 3 43 6 smit:SMT_1198|3end_phosphoribosylaminoimidazole-succinocarboxamide_synthase_1158837..1158987_NEGATIVE 279 45 1 66 12 smit:SMT_1006|3end_6-pyruvoyl_tetrahydrobiopterin_synthase,_putative_947122..947272_POSITIVE 275 59 13 90 51 smit:SMT_1294|3end_K02049_sulfonate/nitrate/taurine_transport_system_ATP-binding_protein_1256791..1256941_POSITIVE 265 42 3 81 25 smit:SMT_109|3end_beta-galactosidase_57523..57673_POSITIVE 264 69 21 76 34 smit:SMT_1923|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1866244..1866394_POSITIVE 261 41 2 73 27 smit:SMT_123|3end_hypothetical_protein_75623..75773_POSITIVE 260 45 3 95 49 smit:SMT_872|3end_hypothetical_protein_820331..820481_NEGATIVE 260 45 3 95 49 smit:SMT_385|3end_hypothetical_protein_320262..320412_POSITIVE 255 49 3 57 16 smit:SMT_228|3end_hypothetical_protein_165093..165243_POSITIVE 255 49 3 57 16 smit:SMT_224|3end_hypothetical_protein_159599..159749_POSITIVE 252 123 83 131 78 smit:SMT_1876|3end_transcriptional_regulator,_MarR_family_1834135..1834285_POSITIVE 244 47 6 39 3 smit:SMT_1427|3end_S1_RNA_binding_domain_protein_1411300..1411450_NEGATIVE 234 33 9 108 87 smit:SMT_1721|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1707585..1707735_POSITIVE 233 149 101 83 37 smit:SMT_792|3end_hypothetical_protein_predicted_by_Glimmer/Critica_702458..702608_NEGATIVE 229 42 10 49 3 smit:SMT_821|3end_UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-_diaminopimelate_ligase_734060..734210_POSITIVE 223 50 10 53 7 smit:SMT_668|3end_hypothetical_protein_predicted_by_Glimmer/Critica_578057..578207_NEGATIVE 223 45 5 139 98 smit:SMT_506|3end_K07729_putative_transcriptional_regulator_437411..437561_NEGATIVE 223 45 5 139 98 smit:SMT_503|3end_K07729_putative_transcriptional_regulator_435980..436130_NEGATIVE 222 50 5 140 101 smit:SMT_2014|3end_tryptophan_synthase_beta_chain_1932727..1932877_POSITIVE