Origin IGS: cgatcatcctcctatcatttaatcaaaatcacctacttagtttaaagcaattttcaagtaactataatataaaagggggagaccccctttttatattatagcat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atgctataatataaaaagggggtctcccccttttatattatagttacttgaaaattgctttaaactaagtaggtgattttgattaaatgataggaggatgatcg Mask Tandem Repeat Region ================================================ cgatcatcctcctatcatttaatcaaaatcacctacttagtttaaagcaattttcaagtaactataatataaaagggggagaccccctttttatattatagcat Find is-nt database================================================ Query_seq: SMT_1080:SMT_1081|SMT_1080:SMT_1081:CAAX amino terminal protease family protein:K06901 putative MFS transporter, AGZA family, xanthine/uracil permease:<-<-:1018581..1018684 104 cgatcatcctcctatcatttaatcaaaatcacctacttagtttaaagcaattttcaagtaactataatataaaagggggagaccccctttttatattatagcat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1080:SMT_1081|SMT_1080:SMT_1081:CAAX amino terminal protease family protein:K06901 putative MFS transporter, AGZA family, xanthine/uracil permease:<-<-:1018581..1018684 104 cgatcatcctcctatcatttaatcaaaatcacctacttagtttaaagcaattttcaagtaactataatataaaagggggagaccccctttttatattatagcat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1080:SMT_1081|SMT_1080:SMT_1081:CAAX amino terminal protease family protein:K06901 putative MFS transporter, AGZA family, xanthine/uracil permease:<-<-:1018581..1018684 104 cgatcatcctcctatcatttaatcaaaatcacctacttagtttaaagcaattttcaagtaactataatataaaagggggagaccccctttttatattatagcat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cgatcatcctcctatcatttaatcaaaatcacctacttagtttaaagcaattttcaagtaactataatataaaagggggagaccccctttttatattatagcat Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 3 End: 98 .. M I L L S F N Q N H L L S L K Q F S S N Y N I K G G D P L F I L ...... cgatcatcctcctatcatttaatcaaaatcacctacttagtttaaagcaattttcaagtaactataatataaaagggggagaccccctttttatattatagcat 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================================================ cgatcatcctcctatcatttaatcaaaatcacctacttagtttaaagcaattttcaagtaactataatataaaagggggagaccccctttttatattatagcat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -10.5 Tail_Score: -5.1523 Start: 75 End: 87 Full_Region: AACTATAATATAAAA GGGGG AGA CCCCC TTTTTATATTATAGC ..........................................................................GGGGGAGACCCCC................. Find igs database================================================ Query_seq: SMT_1080:SMT_1081|SMT_1080:SMT_1081:CAAX amino terminal protease family protein:K06901 putative MFS transporter, AGZA family, xanthine/uracil permease:<-<-:1018581..1018684 104 cgatcatcctcctatcatttaatcaaaatcacctacttagtttaaagcaattttcaagtaactataatataaaagggggagaccccctttttatattatagcat Intra-Species Hit: Count: 1 Min: 1 Max: 104 Len: 104 Subject: smit_SMT_1080_SMT_1081|CAAX amino terminal protease family protein:K06901 putative MFS transporter, AGZA family, xanthine/uracil permease|NEGATIVE:NEGATIVE|[1018581,1018684]|104 HSP 1 e-value: 1.0E-52 bit: 206.0 Len: 104 Query Start:1 Query End:104 Subject Strand: POSITIVE Subject Start: 1 Subject End: 104 cgatcatcctcctatcatttaatcaaaatcacctacttagtttaaagcaattttcaagtaactataatataaaagggggagaccccctttttatattatagcat cgatcatcctcctatcatttaatcaaaatcacctacttagtttaaagcaattttcaagtaactataatataaaagggggagaccccctttttatattatagcat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGAUCAUCCUCCUAUCAUUUAAUCAAAAUCACCUACUUAGUUUAAAGCAAUUUUCAAGUAACUAUAAUAUAAAAGGGGGAGACCCCCUUUUUAUAUUAUAGCAU .................................(((((.(...(((....))).)))))).((((((((((((((((((....))))))))))))))))))... (-25.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUGCUAUAAUAUAAAAAGGGGGUCUCCCCCUUUUAUAUUAUAGUUACUUGAAAAUUGCUUUAAACUAAGUAGGUGAUUUUGAUUAAAUGAUAGGAGGAUGAUCG ..((((((((((((((.(((((...)))))))))))))))))))......(((((..(((..........)))..)))))(((((.............))))). (-27.92) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 785 50 1 141 92 smit:SMT_1080|5end_CAAX_amino_terminal_protease_family_protein_1018490..1018720_NEGATIVE 307 94 61 179 147 smit:SMT_1217|5end_hypothetical_protein_1176603..1176833_NEGATIVE 290 93 56 140 95 smit:SMT_1045|5end_cochaperonin_GroES_987582..987812_NEGATIVE 264 90 48 163 117 smit:SMT_92|5end_GTP-binding_protein,_probable_translation_factor_22857..23087_POSITIVE 262 94 71 136 108 smit:SMT_1423|5end_hypothetical_protein_1407737..1407967_POSITIVE 248 93 71 149 127 smit:SMT_1667|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1657567..1657797_NEGATIVE 245 60 11 230 176 smit:SMT_1500|5end_K03742_competence/damage-inducible_protein_CinA_N-terminal_domain_1483384..1483614_POSITIVE 223 47 1 82 37 smit:SMT_1927|5end_cell_division_protein_FtsH_1868779..1869009_NEGATIVE 218 100 62 210 170 smit:SMT_863|5end_K07485_transposase_813585..813815_POSITIVE 217 47 2 196 144 smit:SMT_1442|5end_hypothetical_protein_1426328..1426558_NEGATIVE 216 90 72 190 163 smit:SMT_1143|5end_K02025_multiple_sugar_transport_system_permease_protein_1086928..1087158_POSITIVE 213 84 46 80 35 smit:SMT_2119|5end_mercuric_reductase_2005583..2005813_POSITIVE 212 49 1 223 179 smit:SMT_1553|5end_K04074_cell_division_initiation_protein_1535913..1536143_POSITIVE 211 88 43 179 127 smit:SMT_1348|5end_exoribonuclease_II_1327502..1327732_NEGATIVE 210 87 48 112 64 smit:SMT_1066|5end_holo-(acyl_carrier_protein)_synthase_1005411..1005641_POSITIVE 206 42 1 191 144 smit:SMT_806|5end_hypothetical_protein_716166..716396_NEGATIVE 205 92 66 203 177 smit:SMT_773|5end_UDP-N-acetylenolpyruvoylglucosamine_reductase_684365..684595_NEGATIVE 203 100 56 147 108 smit:SMT_352|5end_hypothetical_protein_290531..290761_POSITIVE 200 94 72 197 167 smit:SMT_1530|5end_K07456_DNA_mismatch_repair_protein_MutS2_1515346..1515576_NEGATIVE 200 90 45 182 123 smit:SMT_191|5end_adenylate_kinase_125745..125975_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 307 94 61 94 62 smit:SMT_1218|3end_DNA_polymerase_I_1176688..1176838_NEGATIVE 290 93 56 84 39 smit:SMT_1046|3end_chaperonin_GroEL_987638..987788_NEGATIVE 264 90 48 78 32 smit:SMT_91|3end_hypothetical_protein_22852..23002_POSITIVE 248 93 71 93 71 smit:SMT_2045|3end_K+_transport_system,_NAD-binding_component_1956758..1956908_POSITIVE 248 93 71 93 71 smit:SMT_1668|3end_K+_transport_system,_NAD-binding_component_1657623..1657773_NEGATIVE 218 93 62 93 63 smit:SMT_364|3end_ribosome-binding_factor_A_301353..301503_POSITIVE 216 90 72 79 52 smit:SMT_1142|3end_K02027_multiple_sugar_transport_system_substrate-binding_protein_1086897..1087047_POSITIVE 211 88 43 77 25 smit:SMT_1349|3end_K03075_preprotein_translocase_SecG_subunit_1327604..1327754_NEGATIVE 210 87 48 73 25 smit:SMT_1065|3end_phospho-2-dehydro-3-deoxyheptonate_aldolase_1005452..1005602_POSITIVE 208 90 43 54 12 smit:SMT_950|3end_UDP-glucose_4-epimerase_897677..897827_NEGATIVE 205 93 71 24 1 smit:SMT_1084|3end_hypothetical_protein_1021326..1021476_NEGATIVE 205 92 66 89 63 smit:SMT_774|3end_hypothetical_protein_684479..684629_NEGATIVE 203 100 56 132 93 smit:SMT_351|3end_hypothetical_protein_290596..290746_POSITIVE 201 60 25 73 45 smit:SMT_872|3end_hypothetical_protein_820331..820481_NEGATIVE 201 60 25 73 45 smit:SMT_385|3end_hypothetical_protein_320262..320412_POSITIVE 200 94 72 94 64 smit:SMT_1531|3end_hypothetical_protein_1515449..1515599_NEGATIVE 198 51 11 44 3 smit:SMT_1667|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1657439..1657589_NEGATIVE 197 68 28 111 64 smit:SMT_749|3end_shikimate_kinase_653495..653645_NEGATIVE 196 92 54 54 8 smit:SMT_405|3end_zinc_metalloprotease_ZmpB,_truncated_339938..340088_POSITIVE 194 92 57 91 60 smit:SMT_1504|3end_topology_modulation_protein_1487808..1487958_POSITIVE