Origin IGS: gtaaccgtgagctcctacggcttatattataccataaaaggccgaatatgtgtatggatgcaggtttaaacgacaattgttttatttactccaaatatgttataatggcaaggaaaagaaggcgaat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 attcgccttcttttccttgccattataacatatttggagtaaataaaacaattgtcgtttaaacctgcatccatacacatattcggccttttatggtataatataagccgtaggagctcacggttac Mask Tandem Repeat Region ================================================ gtaaccgtgagctcctacggcttatattataccataaaaggccgaatatgtgtatggatgcaggtttaaacgacaattgttttatttactccaaatatgttataatggcaaggaaaagaaggcgaat Find is-nt database================================================ Query_seq: TDE2333:TDE2334|TDE2333:TDE2334:sanA protein, putative:hypothetical protein:<-->:2368642..2368768 127 gtaaccgtgagctcctacggcttatattataccataaaaggccgaatatgtgtatggatgcaggtttaaacgacaattgttttatttactccaaatatgttataatggcaaggaaaagaaggcgaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2333:TDE2334|TDE2333:TDE2334:sanA protein, putative:hypothetical protein:<-->:2368642..2368768 127 gtaaccgtgagctcctacggcttatattataccataaaaggccgaatatgtgtatggatgcaggtttaaacgacaattgttttatttactccaaatatgttataatggcaaggaaaagaaggcgaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2333:TDE2334|TDE2333:TDE2334:sanA protein, putative:hypothetical protein:<-->:2368642..2368768 127 gtaaccgtgagctcctacggcttatattataccataaaaggccgaatatgtgtatggatgcaggtttaaacgacaattgttttatttactccaaatatgttataatggcaaggaaaagaaggcgaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtaaccgtgagctcctacggcttatattataccataaaaggccgaatatgtgtatggatgcaggtttaaacgacaattgttttatttactccaaatatgttataatggcaaggaaaagaaggcgaat Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 24 End: 125 ....................... M L Y H K R P N M C M D A G L N D N C F I Y S K Y V I M A R K R R R .. gtaaccgtgagctcctacggcttatattataccataaaaggccgaatatgtgtatggatgcaggtttaaacgacaattgttttatttactccaaatatgttataatggcaaggaaaagaaggcgaat 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: 86 Start: 26 End: 55 .........................ATACACATATTCGGCCTTTTATGGTATAAT........................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gtaaccgtgagctcctacggcttatattataccataaaaggccgaatatgtgtatggatgcaggtttaaacgacaattgttttatttactccaaatatgttataatggcaaggaaaagaaggcgaat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2333:TDE2334|TDE2333:TDE2334:sanA protein, putative:hypothetical protein:<-->:2368642..2368768 127 gtaaccgtgagctcctacggcttatattataccataaaaggccgaatatgtgtatggatgcaggtttaaacgacaattgttttatttactccaaatatgttataatggcaaggaaaagaaggcgaat Intra-Species Hit: Count: 1 Min: 1 Max: 127 Len: 127 Subject: NC_002967_TDE2333_TDE2334|sanA protein, putative:hypothetical protein|NEGATIVE:POSITIVE|[2368642,2368768]|127 HSP 1 e-value: 2.0E-66 bit: 252.0 Len: 127 Query Start:1 Query End:127 Subject Strand: POSITIVE Subject Start: 1 Subject End: 127 gtaaccgtgagctcctacggcttatattataccataaaaggccgaatatgtgtatggatgcaggtttaaacgacaattgttttatttactccaaatatgttataatggcaaggaaaagaaggcgaat gtaaccgtgagctcctacggcttatattataccataaaaggccgaatatgtgtatggatgcaggtttaaacgacaattgttttatttactccaaatatgttataatggcaaggaaaagaaggcgaat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUAACCGUGAGCUCCUACGGCUUAUAUUAUACCAUAAAAGGCCGAAUAUGUGUAUGGAUGCAGGUUUAAACGACAAUUGUUUUAUUUACUCCAAAUAUGUUAUAAUGGCAAGGAAAAGAAGGCGAAU (((.(((((.((.....((((((...............)))))).....)).))))).)))...............(((((((.(((..(((...(((......)))....)))))).))))))).. (-21.16) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUCGCCUUCUUUUCCUUGCCAUUAUAACAUAUUUGGAGUAAAUAAAACAAUUGUCGUUUAAACCUGCAUCCAUACACAUAUUCGGCCUUUUAUGGUAUAAUAUAAGCCGUAGGAGCUCACGGUUAC ....(((...........(((...(((.......(((((((....((((.......)))).....))).))))......)))..)))((((((((((.........)))))))))).....)))... (-19.22) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 903 50 1 141 92 NC_002967:TDE2333|5end_sanA_protein,_putative_2368551..2368781_NEGATIVE 285 47 5 56 16 NC_002967:TDE2538|5end_hypothetical_protein_2563785..2564015_POSITIVE 285 43 6 99 57 NC_002967:TDE2246|5end_hypothetical_protein_2286132..2286362_POSITIVE 273 71 39 66 34 NC_002967:TDE1540|5end_hypothetical_protein_1584422..1584652_POSITIVE 269 58 12 116 73 NC_002967:TDE2740|5end_type_I_restriction-modification_system,_S_subunit,_truncation_2795202..2795432_POSITIVE 269 49 2 229 188 NC_002967:TDE2585|5end_methyl-accepting_chemotaxis_domain/unknown_domain_protein_2620303..2620533_NEGATIVE 269 46 1 70 35 NC_002967:TDE1454|5end_sugar_transporter_1501438..1501668_POSITIVE 256 45 5 231 179 NC_002967:TDE0255|5end_ABC_transporter,_ATP-binding_protein_290742..290972_NEGATIVE 253 58 18 55 18 NC_002967:TDE2419|5end_hypothetical_protein_2444769..2444999_NEGATIVE 252 41 6 78 43 NC_002967:TDE0828|5end_glucose-inhibited_division_protein_A_850169..850399_NEGATIVE 252 64 22 53 13 NC_002967:TDE0617|5end_hypothetical_protein_650227..650457_NEGATIVE 251 43 6 118 82 NC_002967:TDE2786|5end_DNA_polymerase_III_subunit_alpha_2842672..2842902_NEGATIVE 251 25 8 180 161 NC_002967:TDE0857|5end_lipoprotein,_putative_878313..878543_POSITIVE 245 57 11 152 106 NC_002967:TDE0833|5end_lipoprotein,_putative_852992..853222_POSITIVE 243 66 30 187 149 NC_002967:TDE1580|5end_hypothetical_protein_1629726..1629956_NEGATIVE 243 67 22 191 144 NC_002967:TDE1521|5end_fumarate_hydratase_1567211..1567441_POSITIVE 241 42 3 220 182 NC_002967:TDE2347|5end_30S_ribosomal_protein_S2_2384378..2384608_NEGATIVE 241 40 3 117 68 NC_002967:TDE0580|5end_hypothetical_protein_615338..615568_POSITIVE 239 43 4 220 181 NC_002967:TDE2545|5end_hypothetical_protein_2571814..2572044_NEGATIVE 234 68 30 170 134 NC_002967:TDE1165|5end_hypothetical_protein_1198390..1198620_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 285 47 5 49 9 NC_002967:TDE2537|3end_hypothetical_protein_2563858..2564008_POSITIVE 272 59 14 67 33 NC_002967:TDE0894|3end_hypothetical_protein_911239..911389_POSITIVE 269 46 1 68 33 NC_002967:TDE1453|3end_alpha-galactosidase_1501516..1501666_POSITIVE 252 41 6 62 27 NC_002967:TDE0829|3end_putative_aminopeptidase_2_850185..850335_NEGATIVE 241 50 5 151 107 NC_002967:TDE0832|3end_hypothetical_protein_853075..853225_POSITIVE 235 43 7 121 82 NC_002967:TDE2180|3end_tRNA_modification_GTPase_2210590..2210740_NEGATIVE 233 44 3 42 1 NC_002967:TDE0744|3end_thioredoxin_780241..780391_POSITIVE 230 43 19 90 65 NC_002967:TDE1660|3end_leucine_Rich_Repeat_domain_protein_1710710..1710860_NEGATIVE 229 46 5 109 49 NC_002967:TDE2573|3end_glucose-6-phosphate_isomerase_2600459..2600609_POSITIVE 224 72 38 150 112 NC_002967:TDE1695|3end_CoA-substrate-specific_enzyme_activase_domain_protein_1749498..1749648_NEGATIVE 223 70 38 95 60 NC_002967:TDE1197|3end_conserved_hypothetical_protein_TIGR00242_1230466..1230616_POSITIVE 219 64 25 38 1 NC_002967:TDE0618|3end_hypothetical_protein_650242..650392_NEGATIVE 218 50 8 90 36 NC_002967:TDE2696|3end_TPR_domain_protein_2739098..2739248_NEGATIVE 218 71 31 96 58 NC_002967:TDE0466|3end_hypothetical_protein_518645..518795_NEGATIVE 213 67 32 127 97 NC_002967:TDE0490|3end_hypothetical_protein_546272..546422_NEGATIVE 212 43 5 44 4 NC_002967:TDE1082|3end_ribosomal_large_subunit_pseudouridine_synthase,_RluD_subfamily_1114252..1114402_POSITIVE 211 44 5 99 55 NC_002967:TDE2515|3end_hypothetical_protein_2540972..2541122_NEGATIVE 208 84 56 144 110 NC_002967:TDE2182|3end_hypothetical_protein_2213035..2213185_NEGATIVE 208 21 6 85 68 NC_002967:TDE1533|3end_hypothetical_protein_1578657..1578807_POSITIVE 206 46 6 44 4 NC_002967:TDE1751|3end_ribosomal_protein_L21_1803831..1803981_NEGATIVE