Origin IGS: gataaaaagaagttagttgttagctaacttcttttggttttgagaaaatagattgatgcctatcctcatgttttagatgtcaatgagtctattgaattgtagaaaaaatcctgagttttgcttctcaggattttctttcatc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gatgaaagaaaatcctgagaagcaaaactcaggattttttctacaattcaatagactcattgacatctaaaacatgaggataggcatcaatctattttctcaaaaccaaaagaagttagctaacaactaacttctttttatc Mask Tandem Repeat Region ================================================ gataaaaagaagttagttgttagctaacttcttttggttttgagaaaatagattgatgcctatcctcatgttttagatgtcaatgagtctattgaattgtagaaaaaatcctgagttttgcttctcaggattttctttcatc Find is-nt database================================================ Query_seq: SMT_297:SMT_298|SMT_297:SMT_298:ABC transporter substrate-binding protein - oligopeptide transport:penicillin-binding protein 1A:-><-:240667..240808 142 gataaaaagaagttagttgttagctaacttcttttggttttgagaaaatagattgatgcctatcctcatgttttagatgtcaatgagtctattgaattgtagaaaaaatcctgagttttgcttctcaggattttctttcatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_297:SMT_298|SMT_297:SMT_298:ABC transporter substrate-binding protein - oligopeptide transport:penicillin-binding protein 1A:-><-:240667..240808 142 gataaaaagaagttagttgttagctaacttcttttggttttgagaaaatagattgatgcctatcctcatgttttagatgtcaatgagtctattgaattgtagaaaaaatcctgagttttgcttctcaggattttctttcatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_297:SMT_298|SMT_297:SMT_298:ABC transporter substrate-binding protein - oligopeptide transport:penicillin-binding protein 1A:-><-:240667..240808 142 gataaaaagaagttagttgttagctaacttcttttggttttgagaaaatagattgatgcctatcctcatgttttagatgtcaatgagtctattgaattgtagaaaaaatcctgagttttgcttctcaggattttctttcatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gataaaaagaagttagttgttagctaacttcttttggttttgagaaaatagattgatgcctatcctcatgttttagatgtcaatgagtctattgaattgtagaaaaaatcctgagttttgcttctcaggattttctttcatc Predict ORF larger than 30AA ================================================ gataaaaagaagttagttgttagctaacttcttttggttttgagaaaatagattgatgcctatcctcatgttttagatgtcaatgagtctattgaattgtagaaaaaatcctgagttttgcttctcaggattttctttcatc 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================================================ gataaaaagaagttagttgttagctaacttcttttggttttgagaaaatagattgatgcctatcctcatgttttagatgtcaatgagtctattgaattgtagaaaaaatcctgagttttgcttctcaggattttctttcatc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_297:SMT_298|SMT_297:SMT_298:ABC transporter substrate-binding protein - oligopeptide transport:penicillin-binding protein 1A:-><-:240667..240808 142 gataaaaagaagttagttgttagctaacttcttttggttttgagaaaatagattgatgcctatcctcatgttttagatgtcaatgagtctattgaattgtagaaaaaatcctgagttttgcttctcaggattttctttcatc Intra-Species Hit: Count: 1 Min: 1 Max: 142 Len: 142 Subject: smit_SMT_297_SMT_298|ABC transporter substrate-binding protein - oligopeptide transport:penicillin-binding protein 1A|POSITIVE:NEGATIVE|[240667,240808]|142 HSP 1 e-value: 3.0E-75 bit: 281.0 Len: 142 Query Start:1 Query End:142 Subject Strand: POSITIVE Subject Start: 1 Subject End: 142 gataaaaagaagttagttgttagctaacttcttttggttttgagaaaatagattgatgcctatcctcatgttttagatgtcaatgagtctattgaattgtagaaaaaatcctgagttttgcttctcaggattttctttcatc gataaaaagaagttagttgttagctaacttcttttggttttgagaaaatagattgatgcctatcctcatgttttagatgtcaatgagtctattgaattgtagaaaaaatcctgagttttgcttctcaggattttctttcatc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUAAAAAGAAGUUAGUUGUUAGCUAACUUCUUUUGGUUUUGAGAAAAUAGAUUGAUGCCUAUCCUCAUGUUUUAGAUGUCAAUGAGUCUAUUGAAUUGUAGAAAAAAUCCUGAGUUUUGCUUCUCAGGAUUUUCUUUCAUC ....(((((((((((((.....))))))))))))).....(((((......((((((..(((...........)))..))))))...(((((......))))).(((((((((((........))))))))))).))))).. (-39.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUGAAAGAAAAUCCUGAGAAGCAAAACUCAGGAUUUUUUCUACAAUUCAAUAGACUCAUUGACAUCUAAAACAUGAGGAUAGGCAUCAAUCUAUUUUCUCAAAACCAAAAGAAGUUAGCUAACAACUAACUUCUUUUUAUC ((((..(((((((((((((........))))))))))))).......(((((......)))))))))........(((((((((......)))))))))........((((((((((((.......)))))))))))).... (-38.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 254 41 4 227 190 smit:SMT_1063|5end_preprotein_translocase_SecA_subunit_1000714..1000944_POSITIVE 253 86 46 208 158 smit:SMT_1255|5end_cell_division_protein_FtsH_1221811..1222041_NEGATIVE 253 139 91 118 73 smit:SMT_702|5end_hypothetical_protein_612311..612541_NEGATIVE 242 129 87 209 169 smit:SMT_1091|5end_competence-specific_global_transcription_modulator_1033040..1033270_NEGATIVE 239 70 22 208 169 smit:SMT_482|5end_hypothetical_protein_predicted_by_Glimmer/Critica_418536..418766_NEGATIVE 239 95 56 176 137 smit:SMT_235|5end_hypothetical_protein_174081..174311_POSITIVE 232 79 31 51 3 smit:SMT_1515|5end_amino_acid_ABC_transporter,_ATP-binding_protein_1497489..1497719_NEGATIVE 226 79 34 56 9 smit:SMT_931|5end_cobyric_acid_synthase_884491..884721_POSITIVE 221 131 109 86 64 smit:SMT_2034|5end_hydrolase,_haloacid_dehalogenase-like_family_1946671..1946901_POSITIVE 220 90 57 200 164 smit:SMT_555|5end_K09015_Fe-S_cluster_assembly_protein_SufD_472271..472501_POSITIVE 219 130 84 65 5 smit:SMT_1891|5end_putative_dihydrolipoamide_S-acetyltransferase_1844373..1844603_POSITIVE 219 130 84 65 5 smit:SMT_1402|5end_pyruvate_dehydrogenase_E2_component_(dihydrolipoamide_acetyltransferase)_1378115..1378345_POSITIVE 219 54 17 170 133 smit:SMT_98|5end_hypothetical_protein_28924..29154_POSITIVE 219 54 17 55 18 smit:SMT_97|5end_hypothetical_protein_28809..29039_POSITIVE 218 99 55 180 113 smit:SMT_893|5end_leucine_rich_protein_841311..841541_NEGATIVE 218 69 31 48 10 smit:SMT_535|5end_hypothetical_protein_454215..454445_POSITIVE 218 91 53 43 1 smit:SMT_208|5end_leucyl-tRNA_synthetase_139977..140207_POSITIVE 216 138 108 221 192 smit:SMT_1366|5end_K02238_competence_protein_ComEC_1346888..1347118_NEGATIVE 214 42 8 81 50 smit:SMT_1388|5end_hypothetical_protein_1365214..1365444_POSITIVE 212 65 24 129 88 smit:SMT_1500|5end_K03742_competence/damage-inducible_protein_CinA_N-terminal_domain_1483384..1483614_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 307 137 94 86 41 smit:SMT_1654|3end_K03110_signal_recognition_particle_receptor_1643519..1643669_POSITIVE 263 35 5 86 56 smit:SMT_297|3end_ABC_transporter_substrate-binding_protein_-_oligopeptide_transport_240606..240756_POSITIVE 262 65 22 130 73 smit:SMT_162|3end_hypothetical_protein_107134..107284_POSITIVE 254 41 4 81 44 smit:SMT_1062|3end_hypothetical_protein_1000648..1000798_POSITIVE 250 138 103 89 44 smit:SMT_1016|3end_alcohol_dehydrogenase,_zinc-containing_953057..953207_NEGATIVE 245 139 91 151 93 smit:SMT_1815|3end_K02035_peptide/nickel_transport_system_substrate-binding_protein_1788899..1789049_NEGATIVE 242 129 87 89 49 smit:SMT_1092|3end_transcription_antitermination_factor_1033160..1033310_NEGATIVE 240 90 46 134 97 smit:SMT_1094|3end_membrane_carboxypeptidase_(penicillin-binding_protein)_1034141..1034291_NEGATIVE 235 66 21 79 25 smit:SMT_1620|3end_hypothetical_protein_1606695..1606845_NEGATIVE 232 79 31 51 3 smit:SMT_1516|3end_K02029_polar_amino_acid_transport_system_permease_protein_1497489..1497639_NEGATIVE 224 136 102 87 49 smit:SMT_1307|3end_glycerol_uptake_facilitator_protein_1272448..1272598_POSITIVE 221 131 109 74 52 smit:SMT_2033|3end_hydrolase,_haloacid_dehalogenase-like_family_1946739..1946889_POSITIVE 221 140 94 101 49 smit:SMT_1073|3end_L-asparaginase_1012251..1012401_POSITIVE 219 40 4 92 54 smit:SMT_1404|3end_lipoate-protein_ligase_A_1382036..1382186_POSITIVE 219 54 17 50 13 smit:SMT_96|3end_hypothetical_protein_28884..29034_POSITIVE 218 70 29 74 34 smit:SMT_540|3end_DNA_gyrase,_B_subunit_457157..457307_POSITIVE 213 140 93 106 60 smit:SMT_1701|3end_transcriptional_regulator,_RpiR_family_1683599..1683749_NEGATIVE 212 65 24 90 49 smit:SMT_1499|3end_K03742_competence/damage-inducible_protein_CinA_N-terminal_domain_1483425..1483575_POSITIVE 209 88 58 99 71 smit:SMT_1124|3end_pyrrolidone-carboxylate_peptidase_1060225..1060375_NEGATIVE 208 134 98 75 41 smit:SMT_694|3end_putative_ATP-binding_component_of_a_transport_system_605968..606118_POSITIVE