Origin IGS: ttttttctccttttatcctttagataggacaggtattttcaatattaaattatatcatattttcctattctttgcccatttctactaatgttataaggtaaatactattcccaaaaaagtagaaattcctatcctt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaggataggaatttctacttttttgggaatagtatttaccttataacattagtagaaatgggcaaagaataggaaaatatgatataatttaatattgaaaatacctgtcctatctaaaggataaaaggagaaaaaa Mask Tandem Repeat Region ================================================ ttttttctccttttatcctttagataggacaggtattttcaatattaaattatatcatattttcctattctttgcccatttctactaatgttataaggtaaatactattcccaaaaaagtagaaattcctatcctt Find is-nt database================================================ Query_seq: SMT_1178:SMT_1179|SMT_1178:SMT_1179:choline binding protein A:aldose 1-epimerase:<-<-:1136729..1136864 136 ttttttctccttttatcctttagataggacaggtattttcaatattaaattatatcatattttcctattctttgcccatttctactaatgttataaggtaaatactattcccaaaaaagtagaaattcctatcctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1178:SMT_1179|SMT_1178:SMT_1179:choline binding protein A:aldose 1-epimerase:<-<-:1136729..1136864 136 ttttttctccttttatcctttagataggacaggtattttcaatattaaattatatcatattttcctattctttgcccatttctactaatgttataaggtaaatactattcccaaaaaagtagaaattcctatcctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1178:SMT_1179|SMT_1178:SMT_1179:choline binding protein A:aldose 1-epimerase:<-<-:1136729..1136864 136 ttttttctccttttatcctttagataggacaggtattttcaatattaaattatatcatattttcctattctttgcccatttctactaatgttataaggtaaatactattcccaaaaaagtagaaattcctatcctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttttttctccttttatcctttagataggacaggtattttcaatattaaattatatcatattttcctattctttgcccatttctactaatgttataaggtaaatactattcccaaaaaagtagaaattcctatcctt Predict ORF larger than 30AA ================================================ ttttttctccttttatcctttagataggacaggtattttcaatattaaattatatcatattttcctattctttgcccatttctactaatgttataaggtaaatactattcccaaaaaagtagaaattcctatcctt 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================================================ ttttttctccttttatcctttagataggacaggtattttcaatattaaattatatcatattttcctattctttgcccatttctactaatgttataaggtaaatactattcccaaaaaagtagaaattcctatcctt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1178:SMT_1179|SMT_1178:SMT_1179:choline binding protein A:aldose 1-epimerase:<-<-:1136729..1136864 136 ttttttctccttttatcctttagataggacaggtattttcaatattaaattatatcatattttcctattctttgcccatttctactaatgttataaggtaaatactattcccaaaaaagtagaaattcctatcctt Intra-Species Hit: Count: 1 Min: 1 Max: 136 Len: 136 Subject: smit_SMT_1178_SMT_1179|choline binding protein A:aldose 1-epimerase|NEGATIVE:NEGATIVE|[1136729,1136864]|136 HSP 1 e-value: 1.0E-71 bit: 270.0 Len: 136 Query Start:1 Query End:136 Subject Strand: POSITIVE Subject Start: 1 Subject End: 136 ttttttctccttttatcctttagataggacaggtattttcaatattaaattatatcatattttcctattctttgcccatttctactaatgttataaggtaaatactattcccaaaaaagtagaaattcctatcctt ttttttctccttttatcctttagataggacaggtattttcaatattaaattatatcatattttcctattctttgcccatttctactaatgttataaggtaaatactattcccaaaaaagtagaaattcctatcctt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUUUCUCCUUUUAUCCUUUAGAUAGGACAGGUAUUUUCAAUAUUAAAUUAUAUCAUAUUUUCCUAUUCUUUGCCCAUUUCUACUAAUGUUAUAAGGUAAAUACUAUUCCCAAAAAAGUAGAAAUUCCUAUCCUU ......................(((((((..((((.....((((..((((........))))...))))...)))).(((((((((..........(((....)))...........))))))))))))))))... (-17.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGGAUAGGAAUUUCUACUUUUUUGGGAAUAGUAUUUACCUUAUAACAUUAGUAGAAAUGGGCAAAGAAUAGGAAAAUAUGAUAUAAUUUAAUAUUGAAAAUACCUGUCCUAUCUAAAGGAUAAAAGGAGAAAAAA .((((((((.(((((((((.....(((((......)).))).........))))))))).....................(((((......))))).......))))))))......................... (-22.34) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 740 110 61 201 152 smit:SMT_1178|5end_choline_binding_protein_A_1136638..1136868_NEGATIVE 258 93 55 133 93 smit:SMT_2145|5end_K05832_putative_ABC_transport_system_permease_protein_2022019..2022249_NEGATIVE 246 41 2 127 91 smit:SMT_1590|5end_DNA-entry_nuclease_1578565..1578795_POSITIVE 243 100 52 132 88 smit:SMT_1451|5end_K02057_simple_sugar_transport_system_permease_protein_1434683..1434913_NEGATIVE 242 99 55 134 88 smit:SMT_498|5end_hypothetical_protein_431751..431981_POSITIVE 238 56 11 112 67 smit:SMT_1801|5end_heavy_metal_translocating_P-type_ATPase_1773916..1774146_POSITIVE 232 93 55 133 93 smit:SMT_1603|5end_K05832_putative_ABC_transport_system_permease_protein_1593374..1593604_POSITIVE 231 47 6 187 143 smit:SMT_1414|5end_hypothetical_protein_1398446..1398676_NEGATIVE 225 112 72 126 79 smit:SMT_991|5end_hypothetical_protein_934425..934655_NEGATIVE 212 31 1 126 91 smit:SMT_565|5end_polypeptide_deformylase_483373..483603_NEGATIVE 210 41 10 220 191 smit:SMT_1341|5end_putative_cell_division_protein_1319115..1319345_NEGATIVE 210 36 8 140 104 smit:SMT_909|5end_type_I_restriction_enzyme_M_protein_858827..859057_NEGATIVE 210 78 31 67 24 smit:SMT_855|5end_dihydrofolate_reductase_799998..800228_NEGATIVE 210 80 49 157 124 smit:SMT_218|5end_undecaprenyl_pyrophosphate_synthetase_150155..150385_POSITIVE 210 98 55 195 140 smit:SMT_129|5end_putative_glycosyltransferase_79973..80203_POSITIVE 206 126 89 222 186 smit:SMT_1622|5end_K03499_trk_system_potassium_uptake_protein_TrkA_1608243..1608473_POSITIVE 203 102 63 137 96 smit:SMT_558|5end_K09014_Fe-S_cluster_assembly_protein_SufB_475255..475485_POSITIVE 202 44 4 137 96 smit:SMT_1339|5end_hypothetical_protein_1314746..1314976_NEGATIVE 200 99 56 140 89 smit:SMT_2027|5end_competence-specific_global_transcription_modulator_1943204..1943434_NEGATIVE 198 95 56 136 89 smit:SMT_1954|5end_6-phospho-beta-glucosidase_1888548..1888778_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 249 114 79 61 26 smit:SMT_2089|3end_dTDP-4-dehydrorhamnose_3,5-epimerase_related_enzyme_1985270..1985420_POSITIVE 246 41 2 88 52 smit:SMT_1589|3end_hypothetical_protein_1578606..1578756_POSITIVE 243 100 52 139 95 smit:SMT_1452|3end_ABC-type_uncharacterized_transport_system,_ATPase_component_1434676..1434826_NEGATIVE 242 99 55 113 67 smit:SMT_497|3end_hypothetical_protein_431810..431960_POSITIVE 232 93 55 121 81 smit:SMT_1602|3end_hypothetical_protein_1593442..1593592_POSITIVE 221 40 8 67 42 smit:SMT_1982|3end_conserved_hypothetical_protein_1913412..1913562_POSITIVE 210 100 65 128 91 smit:SMT_1964|3end_sodium/hydrogen_exchanger_family_protein_1896596..1896746_NEGATIVE 210 41 10 59 30 smit:SMT_1342|3end_protease_maturation_protein,_putative_1319276..1319426_NEGATIVE 210 36 8 140 104 smit:SMT_910|3end_type_I_restriction_enzyme_R_protein_858827..858977_NEGATIVE 203 102 63 79 38 smit:SMT_557|3end_K04488_nitrogen_fixation_protein_NifU_and_related_proteins_475277..475427_POSITIVE 190 108 65 122 64 smit:SMT_1772|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1749370..1749520_POSITIVE 190 41 8 151 108 smit:SMT_434|3end_orotidine_5'-phosphate_decarboxylase_376888..377038_POSITIVE 190 112 76 62 24 smit:SMT_190|3end_preprotein_translocase,_SecY_subunit_125675..125825_POSITIVE 185 91 52 107 74 smit:SMT_1669|3end_potassium_uptake_protein_KtrB_1658302..1658452_NEGATIVE 185 107 64 131 69 smit:SMT_1349|3end_K03075_preprotein_translocase_SecG_subunit_1327604..1327754_NEGATIVE 185 91 52 107 74 smit:SMT_1168|3end_potassium_uptake_protein_KtrB_1115173..1115323_NEGATIVE 185 105 61 59 16 smit:SMT_905|3end_hypothetical_protein_predicted_by_Glimmer/Critica_852766..852916_NEGATIVE 184 110 76 96 46 smit:SMT_940|3end_tRNA_pseudouridine_synthase_A_892015..892165_NEGATIVE 183 85 50 110 78 smit:SMT_454|3end_hypothetical_protein_391740..391890_POSITIVE 183 96 54 49 1 smit:SMT_91|3end_hypothetical_protein_22852..23002_POSITIVE