Origin IGS: aaaatgggagtaggaaaatttcytactcttttctgtaagcagtttccttgacattttttttattttgcgctatcatatgtccatataatatatgggagtctgtgtacagtctgagaggaagtgttaaacttcgaccgcacctgatctgggtaatgccagcgtagggaacgatacttagtctattcttgaccttttccatat .........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 atatggaaaaggtcaagaatagactaagtatcgttccctacgctggcattacccagatcaggtgcggtcgaagtttaacacttcctctcagactgtacacagactcccatatattatatggacatatgatagcgcaaaataaaaaaaatgtcaaggaaactgcttacagaaaagagtargaaattttcctactcccatttt Mask Tandem Repeat Region ================================================ aaaatgggagtaggaaaatttcytactcttttctgtaagcagtttccttgacattttttttattttgcgctatcatatgtccatataatatatgggagtctgtgtacagtctgagaggaagtgttaaacttcgaccgcacctgatctgggtaatgccagcgtagggaacgatacttagtctattcttgaccttttccatat Find is-nt database================================================ Query_seq: SMT_1290:SMT_1291|SMT_1290:SMT_1291:autolysin:hypothetical protein:->->:1253814..1254014 201 aaaatgggagtaggaaaatttcytactcttttctgtaagcagtttccttgacattttttttattttgcgctatcatatgtccatataatatatgggagtctgtgtacagtctgagaggaagtgttaaacttcgaccgcacctgatctgggtaatgccagcgtagggaacgatacttagtctattcttgaccttttccatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1290:SMT_1291|SMT_1290:SMT_1291:autolysin:hypothetical protein:->->:1253814..1254014 201 aaaatgggagtaggaaaatttcytactcttttctgtaagcagtttccttgacattttttttattttgcgctatcatatgtccatataatatatgggagtctgtgtacagtctgagaggaagtgttaaacttcgaccgcacctgatctgggtaatgccagcgtagggaacgatacttagtctattcttgaccttttccatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1290:SMT_1291|SMT_1290:SMT_1291:autolysin:hypothetical protein:->->:1253814..1254014 201 aaaatgggagtaggaaaatttcytactcttttctgtaagcagtttccttgacattttttttattttgcgctatcatatgtccatataatatatgggagtctgtgtacagtctgagaggaagtgttaaacttcgaccgcacctgatctgggtaatgccagcgtagggaacgatacttagtctattcttgaccttttccatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaatgggagtaggaaaatttcytactcttttctgtaagcagtttccttgacattttttttattttgcgctatcatatgtccatataatatatgggagtctgtgtacagtctgagaggaagtgttaaacttcgaccgcacctgatctgggtaatgccagcgtagggaacgatacttagtctattcttgaccttttccatat Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 48 End: 161 ............................................... M T F F L F C A I I C P Y N I W E S V Y S L R G S V K L R P H L I W V M P A ........................................ Protein_Len: 58 Strand: - Start: 26 End: 199 ......................... E K R Y A T E K V N K K N Q A I M H G Y L I H S D T Y L R L P L T L S R G C R I Q T I G A Y P V I S L R N K V K E M .. aaaatgggagtaggaaaatttcytactcttttctgtaagcagtttccttgacattttttttattttgcgctatcatatgtccatataatatatgggagtctgtgtacagtctgagaggaagtgttaaacttcgaccgcacctgatctgggtaatgccagcgtagggaacgatacttagtctattcttgaccttttccatat 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: 94 Start: 46 End: 75 .............................................CTTGACATTTTTTTTATTTTGCGCTATCAT.............................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaaatgggagtaggaaaatttcytactcttttctgtaagcagtttccttgacattttttttattttgcgctatcatatgtccatataatatatgggagtctgtgtacagtctgagaggaagtgttaaacttcgaccgcacctgatctgggtaatgccagcgtagggaacgatacttagtctattcttgaccttttccatat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1290:SMT_1291|SMT_1290:SMT_1291:autolysin:hypothetical protein:->->:1253814..1254014 201 aaaatgggagtaggaaaatttcytactcttttctgtaagcagtttccttgacattttttttattttgcgctatcatatgtccatataatatatgggagtctgtgtacagtctgagaggaagtgttaaacttcgaccgcacctgatctgggtaatgccagcgtagggaacgatacttagtctattcttgaccttttccatat Intra-Species Hit: Count: 1 Min: 1 Max: 201 Len: 201 Subject: smit_SMT_1290_SMT_1291|autolysin:hypothetical protein|POSITIVE:POSITIVE|[1253814,1254014]|201 HSP 1 e-value: 4.0E-95 bit: 348.0 Len: 201 Query Start:1 Query End:201 Subject Strand: POSITIVE Subject Start: 1 Subject End: 201 aaaatgggagtaggaaaatttcytactcttttctgtaagcagtttccttgacannnnnnnnattttgcgctatcatatgtccatataatatatgggagtctgtgtacagtctgagaggaagtgttaaacttcgaccgcacctgatctgggtaatgccagcgtagggaacgatacttagtctattcttgaccttttccatat aaaatgggagtaggaaaatttcytactcttttctgtaagcagtttccttgacattttttttattttgcgctatcatatgtccatataatatatgggagtctgtgtacagtctgagaggaagtgttaaacttcgaccgcacctgatctgggtaatgccagcgtagggaacgatacttagtctattcttgaccttttccatat Inter-species Hit: Count: 3 Min: 1 Max: 199 Len: 199 Subject: NC_008533_SPD_2027_SPD_2028|hypothetical protein:choline binding protein D|NEGATIVE:NEGATIVE|[2006257,2006511]|255 HSP 1 e-value: 9.0E-69 bit: 261.0 Len: 199 Query Start:1 Query End:199 Subject Strand: NEGATIVE Subject Start: 55 Subject End: 255 aaaatgggagtagga-aaatttcytactcttttctgtaagcagtttccttgacannnnnnnnattttgcgctatcatatgtccatataatatatgggagtctgtgtacagtctgagaggaagtgttaaacttcgaccgcacctgatctgggtaatgccagcgtagggaacgatacttagtctattcttg-accttttccat.. aaaattggagtaggagaaatttcctgctcttttctgtaagcagtttccttgacatttttcttattttgcgctatcatatatacatataatatatgggagtctgtgtacagtctgagaggaagtgttaaacttcgaccgcacctgatctgggtaatgccagcggagggaacgatacttagtctaattttgcaccttttccat.. Subject: NC_003098_spr2005_spr2006|hypothetical protein:Choline binding protein D|NEGATIVE:NEGATIVE|[1998757,1999011]|255 HSP 1 e-value: 9.0E-69 bit: 261.0 Len: 199 Query Start:1 Query End:199 Subject Strand: NEGATIVE Subject Start: 55 Subject End: 255 aaaatgggagtagga-aaatttcytactcttttctgtaagcagtttccttgacannnnnnnnattttgcgctatcatatgtccatataatatatgggagtctgtgtacagtctgagaggaagtgttaaacttcgaccgcacctgatctgggtaatgccagcgtagggaacgatacttagtctattcttg-accttttccat.. aaaattggagtaggagaaatttcctgctcttttctgtaagcagtttccttgacatttttcttattttgcgctatcatatatacatataatatatgggagtctgtgtacagtctgagaggaagtgttaaacttcgaccgcacctgatctgggtaatgccagcggagggaacgatacttagtctaattttgcaccttttccat.. Subject: NC_003028_SP_2199_SP_2200|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[2121205,2121382]|178 HSP 1 e-value: 1.0E-49 bit: 197.0 Len: 118 Query Start:82 Query End:199 Subject Strand: NEGATIVE Subject Start: 55 Subject End: 173 .................................................................................catataatatatgggagtctgtgtacagtctgagaggaagtgttaaacttcgaccgcacctgatctgggtaatgccagcgtagggaacgatacttagtctattcttg-accttttccat.. .................................................................................catataatatatgggagtctgtgtacagtctgagaggaagtgttaaacttcgaccgcacctgatctgggtaatgccagcggagggaacgatacttagtctaattttgcaccttttccat.. Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAUGGGAGUAGGAAAAUUUCYUACUCUUUUCUGUAAGCAGUUUCCUUGACAUUUUUUUUAUUUUGCGCUAUCAUAUGUCCAUAUAAUAUAUGGGAGUCUGUGUACAGUCUGAGAGGAAGUGUUAAACUUCGACCGCACCUGAUCUGGGUAAUGCCAGCGUAGGGAACGAUACUUAGUCUAUUCUUGACCUUUUCCAU ...(((((((.(((...........(((((..(((((.((((.(((((.(((((......................)))))............))))).)))).)))))...)))))(((((.....)))))...((..((((..((((......))))..))))...))...................)))))))))) (-47.37) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUGGAAAAGGUCAAGAAUAGACUAAGUAUCGUUCCCUACGCUGGCAUUACCCAGAUCAGGUGCGGUCGAAGUUUAACACUUCCUCUCAGACUGUACACAGACUCCCAUAUAUUAUAUGGACAUAUGAUAGCGCAAAAUAAAAAAAAUGUCAAGGAAACUGCUUACAGAAAAGAGUARGAAAUUUUCCUACUCCCAUUUU ..((((((..((.....((((((..(.(((((..(((...((((......))))...))).))))))..)))))).......((((....(((((..(((....((((((...)))))).....(((((.................)))))......)))..)))))...))))...))..))))))............ (-43.43) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 348 180 133 221 174 smit:SMT_1636|5end_5-formyltetrahydrofolate_cyclo-ligase_family_protein_1622568..1622798_POSITIVE 346 160 111 160 102 smit:SMT_954|5end_cation-transporting_ATPase,_E1-E2_family_904025..904255_NEGATIVE 339 180 140 118 75 smit:SMT_304|5end_hypothetical_protein_246580..246810_POSITIVE 338 174 132 48 6 smit:SMT_1369|5end_alanine_dehydrogenase_1348280..1348510_POSITIVE 332 149 101 216 148 smit:SMT_2034|5end_hydrolase,_haloacid_dehalogenase-like_family_1946671..1946901_POSITIVE 329 180 140 223 179 smit:SMT_2044|5end_transcriptional_activator_TipA,_putative_1955885..1956115_NEGATIVE 329 180 140 208 164 smit:SMT_2016|5end_tyrosine_recombinase_1933425..1933655_NEGATIVE 329 180 140 181 137 smit:SMT_2008|5end_K07485_transposase_1928662..1928892_NEGATIVE 329 180 140 50 6 smit:SMT_2005|5end_pullulanase,_type_I_1926289..1926519_NEGATIVE 329 180 140 199 155 smit:SMT_2001|5end_membrane_protease_protein_family_1923387..1923617_POSITIVE 329 180 140 144 100 smit:SMT_1967|5end_dicarboxylate/amino_acid:cation_(Na+_or_H+)_symporter_(DAACS)_family_protein_1899683..1899913_NEGATIVE 329 180 140 144 100 smit:SMT_1961|5end_K07485_transposase_1894206..1894436_POSITIVE 329 180 140 144 100 smit:SMT_1955|5end_carbamoyl-phosphate_synthase_small_chain_1889408..1889638_NEGATIVE 329 180 140 188 144 smit:SMT_1954|5end_6-phospho-beta-glucosidase_1888548..1888778_POSITIVE 329 180 140 179 135 smit:SMT_1944|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1879494..1879724_NEGATIVE 329 180 140 144 100 smit:SMT_1690|5end_K06148_ATP-binding_cassette,_subfamily_C,_bacterial_1674779..1675009_NEGATIVE 329 180 140 220 176 smit:SMT_1686|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1670175..1670405_POSITIVE 329 180 140 193 149 smit:SMT_1155|5end_ABC-type_oligopeptide_transport_system,_periplasmic_component_1099665..1099895_NEGATIVE 329 180 140 144 100 smit:SMT_779|5end_ribonuclease_BN,_putative_688530..688760_NEGATIVE 329 180 140 144 100 smit:SMT_388|5end_branched-chain_amino_acid_transport_system_II_carrier_protein_321172..321402_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 315 157 111 88 56 smit:SMT_1636|3end_5-formyltetrahydrofolate_cyclo-ligase_family_protein_1623187..1623337_POSITIVE 301 176 131 59 6 smit:SMT_1914|3end_K03696_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpC_1860324..1860474_POSITIVE 300 136 91 76 26 smit:SMT_1851|3end_ABC_transporter,_permease_protein,_putative_1815578..1815728_NEGATIVE 300 136 91 76 26 smit:SMT_80|3end_ABC_transporter,_permease_protein,_putative_10992..11142_POSITIVE 296 167 123 143 101 smit:SMT_1487|3end_hypothetical_protein_1467076..1467226_POSITIVE 277 146 108 145 99 smit:SMT_1454|3end_cytidine_deaminase_1437497..1437647_NEGATIVE 270 180 135 96 39 smit:SMT_308|3end_trans-2-enoyl-ACP_reductase_II_250493..250643_POSITIVE 268 159 116 137 93 smit:SMT_942|3end_hypothetical_protein_893528..893678_NEGATIVE 266 138 91 77 25 smit:SMT_1275|3end_rod_shape-determining_protein_MreC_1239492..1239642_POSITIVE 265 165 129 55 20 smit:SMT_1010|3end_hypothetical_protein_948761..948911_POSITIVE 263 178 132 66 23 smit:SMT_213|3end_leucyl-tRNA_synthetase_146167..146317_POSITIVE 260 175 137 40 9 smit:SMT_904|3end_hypothetical_protein_852294..852444_NEGATIVE 254 170 132 151 120 smit:SMT_1814|3end_amino_acid_transporter_1788640..1788790_POSITIVE 248 161 132 146 117 smit:SMT_1696|3end_hypothetical_protein_1678924..1679074_POSITIVE 246 166 123 69 25 smit:SMT_1941|3end_hypothetical_protein_1877663..1877813_POSITIVE 246 156 116 145 100 smit:SMT_537|3end_oxidoreductase,_aldo/keto_reductase_family_455368..455518_POSITIVE 246 160 112 62 22 smit:SMT_447|3end_ABC-type_cobalt_transport_system,_permease_component_CbiQ_related_transporter_386987..387137_POSITIVE 245 158 111 53 8 smit:SMT_547|3end_branched-chain_amino_acid_aminotransferase_465049..465199_POSITIVE 244 165 130 151 120 smit:SMT_919|3end_hypothetical_protein_871741..871891_NEGATIVE 243 184 142 60 11 smit:SMT_2093|3end_hypothetical_protein_LOC618557_1989186..1989336_POSITIVE