Origin IGS: tagacccatcccccatagctgaatgtagcaaatacaaaatcgcaggtcaatatatagaacacccctcaaaaaaagcagttacataactgcaaccgcttttctattcttgcagggtgtaaccgacaccacnnnnnttaattaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttaattaannnnngtggtgtcggttacaccctgcaagaatagaaaagcggttgcagttatgtaactgctttttttgaggggtgttctatatattgacctgcgattttgtatttgctacattcagctatgggggatgggtcta Mask Tandem Repeat Region ================================================ tagacccatcccccatagctgaatgtagcaaatacaaaatcgcaggtcaatatatagaacacccctcaaaaaaagcagttacataactgcaaccgcttttctattcttgcagggtgtaaccgacaccacnnnnnttaattaa Find is-nt database================================================ Query_seq: SMT_2047:SMT_2048|SMT_2047:SMT_2048:choline binding protein F:competence-specific global transcription modulator:<-<-:1957909..1958050 142 tagacccatcccccatagctgaatgtagcaaatacaaaatcgcaggtcaatatatagaacacccctcaaaaaaagcagttacataactgcaaccgcttttctattcttgcagggtgtaaccgacaccacnnnnnttaattaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_2047:SMT_2048|SMT_2047:SMT_2048:choline binding protein F:competence-specific global transcription modulator:<-<-:1957909..1958050 142 tagacccatcccccatagctgaatgtagcaaatacaaaatcgcaggtcaatatatagaacacccctcaaaaaaagcagttacataactgcaaccgcttttctattcttgcagggtgtaaccgacaccacnnnnnttaattaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_2047:SMT_2048|SMT_2047:SMT_2048:choline binding protein F:competence-specific global transcription modulator:<-<-:1957909..1958050 142 tagacccatcccccatagctgaatgtagcaaatacaaaatcgcaggtcaatatatagaacacccctcaaaaaaagcagttacataactgcaaccgcttttctattcttgcagggtgtaaccgacaccacnnnnnttaattaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tagacccatcccccatagctgaatgtagcaaatacaaaatcgcaggtcaatatatagaacacccctcaaaaaaagcagttacataactgcaaccgcttttctattcttgcagggtgtaaccgacaccacnnnnnttaattaa Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: + Start: 32 End: 139 ............................... M Q N R R S I Y R T P L K K S S Y I T A T A F L F L Q G V T D T T X X N * ... tagacccatcccccatagctgaatgtagcaaatacaaaatcgcaggtcaatatatagaacacccctcaaaaaaagcagttacataactgcaaccgcttttctattcttgcagggtgtaaccgacaccacnnnnnttaattaa 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: 82 Start: 22 End: 51 .....................ATTGACCTGCGATTTTGTATTTGCTACATT........................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tagacccatcccccatagctgaatgtagcaaatacaaaatcgcaggtcaatatatagaacacccctcaaaaaaagcagttacataactgcaaccgcttttctattcttgcagggtgtaaccgacaccacnnnnnttaattaa Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -7.6 Tail_Score: -5.41143 Start: 75 End: 90 Full_Region: aatagaaaagcggtt gcagtt atgt aactgc tttttttgaggggtg ..........................................................................gcagttatgtaactgc.................................................... Find igs database================================================ Query_seq: SMT_2047:SMT_2048|SMT_2047:SMT_2048:choline binding protein F:competence-specific global transcription modulator:<-<-:1957909..1958050 142 tagacccatcccccatagctgaatgtagcaaatacaaaatcgcaggtcaatatatagaacacccctcaaaaaaagcagttacataactgcaaccgcttttctattcttgcagggtgtaaccgacaccacnnnnnttaattaa Intra-Species Hit: Count: 1 Min: 1 Max: 129 Len: 129 Subject: smit_SMT_2047_SMT_2048|choline binding protein F:competence-specific global transcription modulator|NEGATIVE:NEGATIVE|[1957909,1958050]|142 HSP 1 e-value: 6.0E-55 bit: 214.0 Len: 129 Query Start:1 Query End:129 Subject Strand: POSITIVE Subject Start: 1 Subject End: 129 tagacccatcccccatagctgaatgtagcaaatacaaaatcgcaggtcaatatatagaacacccctcnnnnnnngcagttacataactgcaaccgcttttctattcttgcagggtgtaaccgacaccac............. tagacccatcccccatagctgaatgtagcaaatacaaaatcgcaggtcaatatatagaacacccctcaaaaaaagcagttacataactgcaaccgcttttctattcttgcagggtgtaaccgacaccac............. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGACCCAUCCCCCAUAGCUGAAUGUAGCAAAUACAAAAUCGCAGGUCAAUAUAUAGAACACCCCUCAAAAAAAGCAGUUACAUAACUGCAACCGCUUUUCUAUUCUUGCAGGGUGUAACCGACACCAC ..((((...........((((....)))).....(......)..))))..........((((((..........((((((....))))))....((............)).))))))............ (-24.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUGGUGUCGGUUACACCCUGCAAGAAUAGAAAAGCGGUUGCAGUUAUGUAACUGCUUUUUUUGAGGGGUGUUCUAUAUAUUGACCUGCGAUUUUGUAUUUGCUACAUUCAGCUAUGGGGGAUGGGUCUA ...((((.((..(((((((.(((.....((((((((((((((....))))))))))))))))).))))))).))))))...(((((...(((((.(((..(((......))).))).)))))))))).. (-42.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 932 50 1 141 92 smit:SMT_2047|5end_choline_binding_protein_F_1957818..1958048_NEGATIVE 311 116 74 57 2 smit:SMT_780|5end_peptidase_family_U32_689321..689551_NEGATIVE 266 32 1 67 29 smit:SMT_680|5end_choline_transport_protein_589962..590192_NEGATIVE 264 102 62 205 169 smit:SMT_534|5end_hypothetical_protein_predicted_by_Glimmer/Critica_453571..453801_POSITIVE 264 102 62 205 169 smit:SMT_531|5end_hypothetical_protein_predicted_by_Glimmer/Critica_452672..452902_POSITIVE 264 102 62 205 169 smit:SMT_527|5end_hypothetical_protein_predicted_by_Glimmer/Critica_451502..451732_POSITIVE 264 102 62 205 169 smit:SMT_511|5end_hypothetical_protein_predicted_by_Glimmer/Critica_439391..439621_POSITIVE 259 120 87 214 187 smit:SMT_739|5end_50S_ribosomal_protein_L7/L12_643642..643872_NEGATIVE 251 116 86 227 198 smit:SMT_2045|5end_K+_transport_system,_NAD-binding_component_1956139..1956369_POSITIVE 245 99 61 139 99 smit:SMT_2162|5end_hypothetical_protein_2036931..2037161_POSITIVE 244 47 2 80 18 smit:SMT_1017|5end_transcriptional_regulator,_MerR_family_954448..954678_NEGATIVE 243 118 75 202 146 smit:SMT_629|5end_glycogen_synthase_533967..534197_POSITIVE 242 30 3 62 35 smit:SMT_1046|5end_chaperonin_GroEL_987904..988134_NEGATIVE 242 30 3 62 35 smit:SMT_1044|5end_chaperonin_GroEL_(HSP60_family)_987435..987665_NEGATIVE 240 117 75 183 130 smit:SMT_1508|5end_hypothetical_protein_1491568..1491798_NEGATIVE 236 110 64 77 31 smit:SMT_1494|5end_nucleoside_diphosphate_kinase_1479500..1479730_POSITIVE 235 119 87 60 23 smit:SMT_1991|5end_K03706_transcriptional_pleiotropic_repressor_1918264..1918494_NEGATIVE 234 30 3 101 68 smit:SMT_543|5end_topoisomerase_IV_subunit_B_458372..458602_POSITIVE 233 119 74 117 70 smit:SMT_1872|5end_K03217_preprotein_translocase_YidC_subunit_1831764..1831994_NEGATIVE 233 49 1 145 80 smit:SMT_1697|5end_hypothetical_protein_1678846..1679076_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 266 32 1 77 39 smit:SMT_681|3end_choline_kinase_589952..590102_NEGATIVE 264 102 62 91 55 smit:SMT_533|3end_RNA_binding_protein_453537..453687_POSITIVE 264 102 62 91 55 smit:SMT_530|3end_RNA_binding_protein_452638..452788_POSITIVE 264 102 62 91 55 smit:SMT_526|3end_RNA_binding_protein_451468..451618_POSITIVE 264 102 62 91 55 smit:SMT_510|3end_hypothetical_protein_439357..439507_POSITIVE 259 120 87 141 114 smit:SMT_740|3end_50S_ribosomal_protein_L10_643715..643865_NEGATIVE 258 106 65 111 64 smit:SMT_1717|3end_DNA-3-methyladenine_glycosylase_I_1703711..1703861_NEGATIVE 258 110 62 98 49 smit:SMT_773|3end_UDP-N-acetylenolpyruvoylglucosamine_reductase_683460..683610_NEGATIVE 258 118 74 150 112 smit:SMT_468|3end_ABC-type_oligopeptide_transport_system,_periplasmic_component_404903..405053_POSITIVE 242 30 3 46 19 smit:SMT_1047|3end_chaperonin,_10_kDa_987920..988070_NEGATIVE 242 30 3 46 19 smit:SMT_1045|3end_cochaperonin_GroES_987451..987601_NEGATIVE 234 30 3 49 16 smit:SMT_542|3end_hypothetical_protein_458400..458550_POSITIVE 233 49 1 143 78 smit:SMT_1696|3end_hypothetical_protein_1678924..1679074_POSITIVE 232 112 76 70 36 smit:SMT_2081|3end_glycosyltransferase_1981336..1981486_POSITIVE 227 47 2 85 37 smit:SMT_425|3end_hypothetical_cytosolic_protein_368424..368574_POSITIVE 225 95 51 75 31 smit:SMT_895|3end_cysteinyl-tRNA_synthetase_841694..841844_NEGATIVE 217 120 71 63 5 smit:SMT_1806|3end_aminoacylase/N-acyl-L-amino_acid_amidohydrolase/hippurate_hydrolase_1781644..1781794_POSITIVE 213 116 74 109 61 smit:SMT_1787|3end_phosphoribosylformylglycinamidine_synthase_1763668..1763818_NEGATIVE 212 120 87 37 7 smit:SMT_904|3end_hypothetical_protein_852294..852444_NEGATIVE 212 70 29 149 97 smit:SMT_269|3end_phospho-N-acetylmuramoyl-pentapeptide-transferas_e_208785..208935_POSITIVE