Origin IGS: atagcctgtttctttttccttacctttgagataacggacaacaaagccnnnnnttaattaattaannnnntgctggaagagctgctgaattggatggawtctcaaatgggctcagtttcgttatatcacgatgcccctactaaaaccaacagcactgtttgtattgttaacaactttaatttctgcttttaagctgattgtacaaccaatggttatgacgcaaggtgggccattaaactcaacaattactatggtgtactatatttatcaacaaggttttactgatcgtcttgtaggatattctagctcaatcgctttagtatttacaacgttaattggtatgattagcttagtacaacgtcgagttctgaaggaggatgactaag .........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 cttagtcatcctccttcagaactcgacgttgtactaagctaatcataccaattaacgttgtaaatactaaagcgattgagctagaatatcctacaagacgatcagtaaaaccttgttgataaatatagtacaccatagtaattgttgagtttaatggcccaccttgcgtcataaccattggttgtacaatcagcttaaaagcagaaattaaagttgttaacaatacaaacagtgctgttggttttagtaggggcatcgtgatataacgaaactgagcccatttgagawtccatccaattcagcagctcttccagcannnnnttaattaattaannnnnggctttgttgtccgttatctcaaaggtaaggaaaaagaaacaggctat Mask Tandem Repeat Region ================================================ atagcctgtttctttttccttacctttgagataacggacaacaaagccnnnnnttaattaattaannnnntgctggaagagctgctgaattggatggawtctcaaatgggctcagtttcgttatatcacgatgcccctactaaaaccaacagcactgtttgtattgttaacaactttaatttctgcttttaagctgattgtacaaccaatggttatgacgcaaggtgggccattaaactcaacaattactatggtgtactatatttatcaacaaggttttactgatcgtcttgtaggatattctagctcaatcgctttagtatttacaacgttaattggtatgattagcttagtacaacgtcgagttctgaaggaggatgactaag Find is-nt database================================================ Query_seq: SMT_1912:SMT_1913|SMT_1912:SMT_1913:D-alanyl-D-alanine carboxypeptidase:RBL02035:<-->:1858011..1858396 386 atagcctgtttctttttccttacctttgagataacggacaacaaagccnnnnnttaattaattaannnnntgctggaagagctgctgaattggatggawtctcaaatgggctcagtttcgttatatcacgatgcccctactaaaaccaacagcactgtttgtattgttaacaactttaatttctgcttttaagctgattgtacaaccaatggttatgacgcaaggtgggccattaaactcaacaattactatggtgtactatatttatcaacaaggttttactgatcgtcttgtaggatattctagctcaatcgctttagtatttacaacgttaattggtatgattagcttagtacaacgtcgagttctgaaggaggatgactaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1912:SMT_1913|SMT_1912:SMT_1913:D-alanyl-D-alanine carboxypeptidase:RBL02035:<-->:1858011..1858396 386 atagcctgtttctttttccttacctttgagataacggacaacaaagccnnnnnttaattaattaannnnntgctggaagagctgctgaattggatggawtctcaaatgggctcagtttcgttatatcacgatgcccctactaaaaccaacagcactgtttgtattgttaacaactttaatttctgcttttaagctgattgtacaaccaatggttatgacgcaaggtgggccattaaactcaacaattactatggtgtactatatttatcaacaaggttttactgatcgtcttgtaggatattctagctcaatcgctttagtatttacaacgttaattggtatgattagcttagtacaacgtcgagttctgaaggaggatgactaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 1 Min: 113 Max: 373 Len: 261 Subject: gi|89110560|ref|AP_004340.1| glycerol-3-phosphate transporter subunit [Escherichia coli W3110] HSP 1 e-value: 3.0E-8 bit: 53.9 Len: 261 Query Start:113 Query End:373 Subject Strand: null Subject Start: 202 Subject End: 289 ................................................................................................................ Q F R Y I T M P L L K P T A L F V L L T T L I S A F K L I V Q P M V - - M T Q G G P L N S T I T M V Y Y I Y Q Q G F T D R L V G Y S S S I A L V F T T L I G M I S L V Q R R V L K ............. ................................................................................................................ R F F K I A L P L I A P V S F F L L V V N L V Y A F - F D T F P V I D A A T S G G P V Q A T T T L I Y K I Y R E G F T G L D L A S S A A Q S V V L M F L V I V L T V V Q F R Y V E ............. Find nr database================================================ Query_seq: SMT_1912:SMT_1913|SMT_1912:SMT_1913:D-alanyl-D-alanine carboxypeptidase:RBL02035:<-->:1858011..1858396 386 atagcctgtttctttttccttacctttgagataacggacaacaaagccnnnnnttaattaattaannnnntgctggaagagctgctgaattggatggawtctcaaatgggctnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngaggatgactaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atagcctgtttctttttccttacctttgagataacggacaacaaagccnnnnnttaattaattaannnnntgctggaagagctgctgaattggatggawtctcaaatgggctnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngaggatgactaag Predict ORF larger than 30AA ================================================ Protein_Len: 43 Strand: + Start: 61 End: 189 ............................................................ M X X X L E E L L N W M X S Q M G S V S L Y H D A P T K T N S T V C I V N N F N F C F ..................................................................................................................................................................................................... Protein_Len: 60 Strand: + Start: 89 End: 382 ........................................................................................ M G W X L K W A Q F R Y I T M P L L K P T A L F V L L T T L I S A F K L I V Q P M V M T Q G G P L N S T I T M V Y Y I Y .... Protein_Len: 43 Strand: - Start: 124 End: 252 ........................................................................................................................... I V I G R S F G V A S N T N N V V K I E A K L S I T C G I T I V C P P G N F E V I V M ...................................................................................................................................... atagcctgtttctttttccttacctttgagataacggacaacaaagccnnnnnttaattaattaannnnntgctggaagagctgctgaattggatggawtctcaaatgggctnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngaggatgactaag 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================================================ atagcctgtttctttttccttacctttgagataacggacaacaaagccnnnnnttaattaattaannnnntgctggaagagctgctgaattggatggawtctcaaatgggctnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngaggatgactaag Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1912:SMT_1913|SMT_1912:SMT_1913:D-alanyl-D-alanine carboxypeptidase:RBL02035:<-->:1858011..1858396 386 atagcctgtttctttttccttacctttgagataacggacaacaaagccnnnnnttaattaattaannnnntgctggaagagctgctgaattggatggawtctcaaatgggctnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngaggatgactaag Intra-Species Hit: Count: 1 Min: 1 Max: 112 Len: 112 Subject: smit_SMT_1912_SMT_1913|D-alanyl-D-alanine carboxypeptidase:RBL02035|NEGATIVE:POSITIVE|[1858011, 1858396]|386 HSP 1 e-value: 5.0E-38 bit: 160.0 Len: 112 Query Start:1 Query End:112 Subject Strand: POSITIVE Subject Start: 1 Subject End: 112 atagcctgtttctttttccttacctttgagataacggacaacaaagccnnnnnttaattaattaannnnntgctggaagagctgctgaattggatggawtctcaaatgggct.................................................................................................................................................................................................................................................................................. atagcctgtttctttttccttacctttgagataacggacaacaaagccnnnnnttaattaattaannnnntgctggaagagctgctgaattggatggawtctcaaatgggct.................................................................................................................................................................................................................................................................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAGCCUGUUUCUUUUUCCUUACCUUUGAGAUAACGGACAACAAAGCCNNNNNUUAAUUAAUUAANNNNNUGCUGGAAGAGCUGCUGAAUUGGAUGGAWUCUCAAAUGGGCU ..((((((((................(((((...((..(((...(((.......(((....))).......(((.....))).)))...)))..))...))))))))))))) (-18.39) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCCCAUUUGAGAWUCCAUCCAAUUCAGCAGCUCUUCCAGCANNNNNUUAAUUAAUUAANNNNNGGCUUUGUUGUCCGUUAUCUCAAAGGUAAGGAAAAAGAAACAGGCUAU ((((..(((((((.......((((..(((.(((.....))).......(((....))).......)))..)))).......))))))).....(..........).)))).. (-15.74) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 822 48 1 139 92 smit:SMT_1912|5end_D-alanyl-D-alanine_carboxypeptidase_1857920..1858150_NEGATIVE 278 96 54 218 178 smit:SMT_1948|5end_IS1381_transposase_protein_A_1883184..1883414_POSITIVE 278 95 54 167 130 smit:SMT_1825|5end_ATP_synthase_F1,_gamma_subunit_1796927..1797157_POSITIVE 266 87 54 170 136 smit:SMT_464|5end_ribonuclease_Z_402867..403097_POSITIVE 257 47 13 132 96 smit:SMT_1689|5end_PTS_enzyme,_maltose-and_glucose-specific,_factor_II_homologue_1671542..1671772_POSITIVE 251 33 2 147 113 smit:SMT_1411|5end_ATP-dependent_nuclease_subunit_B_1395478..1395708_NEGATIVE 249 87 54 201 165 smit:SMT_1254|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1220882..1221112_NEGATIVE 242 33 3 83 49 smit:SMT_807|5end_hypothetical_protein_predicted_by_Glimmer/Critica_716815..717045_NEGATIVE 241 98 71 68 41 smit:SMT_1907|5end_phosphate-binding_protein_1854105..1854335_POSITIVE 241 47 3 94 55 smit:SMT_1127|5end_transcriptional_regulator,_MarR_family_1061556..1061786_NEGATIVE 240 98 54 169 109 smit:SMT_1974|5end_high-affinity_zinc_uptake_system_protein_ZnuA_precursor_/_hypothetical_exported_protein_1905506..1905736_POSITIVE 237 92 54 224 185 smit:SMT_1842|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1807858..1808088_NEGATIVE 235 36 3 112 79 smit:SMT_2078|5end_acetyl_xylan_esterase,_putative_1979571..1979801_POSITIVE 230 98 80 128 110 smit:SMT_1722|5end_x-prolyl-dipeptidyl_aminopeptidase_1707529..1707759_POSITIVE 230 48 1 76 27 smit:SMT_181|5end_50S_ribosomal_protein_L24_120125..120355_POSITIVE 229 48 4 222 181 smit:SMT_1608|5end_hypothetical_protein_1597595..1597825_POSITIVE 229 47 3 54 13 smit:SMT_631|5end_glycerate_kinase_536112..536342_POSITIVE 228 97 54 158 119 smit:SMT_1678|5end_inorganic_pyrophosphatase_1662126..1662356_POSITIVE 228 48 1 141 90 smit:SMT_434|5end_orotidine_5'-phosphate_decarboxylase_376107..376337_POSITIVE 228 43 1 62 18 smit:SMT_277|5end_capsular_polysaccharide_biosynthesis_homolog_YwqC_219561..219791_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 278 97 54 139 91 smit:SMT_2017|3end_exonuclease_RexA_1935862..1936012_NEGATIVE 278 95 54 124 87 smit:SMT_1824|3end_hypothetical_protein_1796964..1797114_POSITIVE 266 87 54 62 28 smit:SMT_463|3end_para-aminobenzoate_synthetase_component_I_/_4-amino-4-deoxychorismate_lyase_402839..402989_POSITIVE 257 47 13 113 77 smit:SMT_1688|3end_putative_N-acylglucosamine-6-phosphate_2-epimerase_1671603..1671753_POSITIVE 250 97 54 134 87 smit:SMT_1970|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1903032..1903182_POSITIVE 249 87 54 96 60 smit:SMT_1255|3end_cell_division_protein_FtsH_1220987..1221137_NEGATIVE 243 96 54 137 91 smit:SMT_1807|3end_putative_mucus_binding_protein_1781740..1781890_NEGATIVE 242 85 54 129 91 smit:SMT_1941|3end_hypothetical_protein_1877663..1877813_POSITIVE 230 98 80 104 86 smit:SMT_1721|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1707585..1707735_POSITIVE 229 47 3 45 4 smit:SMT_630|3end_phosphoserine_phosphatase_536183..536333_POSITIVE 228 43 1 53 9 smit:SMT_276|3end_exopolysaccharide_biosynthesis_protein_219632..219782_POSITIVE 227 96 54 136 91 smit:SMT_2028|3end_leader_peptidase_(prepilin_peptidase)_/_N-methyltransferase_1943367..1943517_NEGATIVE 227 48 11 47 3 smit:SMT_826|3end_hypothetical_protein_749591..749741_NEGATIVE 222 47 2 41 2 smit:SMT_1486|3end_hypothetical_protein_1466444..1466594_POSITIVE 220 103 72 36 9 smit:SMT_762|3end_cation-transporting_ATPase,_E1-E2_family_protein_667368..667518_NEGATIVE 218 98 71 65 35 smit:SMT_2152|3end_cell_division_protein_2026967..2027117_POSITIVE 218 93 54 130 91 smit:SMT_1798|3end_exonuclease_RexA_1772818..1772968_NEGATIVE 211 48 2 120 71 smit:SMT_603|3end_hypothetical_protein_518532..518682_POSITIVE 208 96 54 138 87 smit:SMT_1914|3end_K03696_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpC_1860324..1860474_POSITIVE 207 47 2 137 92 smit:SMT_1407|3end_ribonuclease_HII_1385530..1385680_NEGATIVE