Origin IGS: tactggtttgtaaattcattaaatctccgactattttctgctgcttcctccctcttgacttcataaatatttttttatatatatttaatgtgccgtcttttaggggagagt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 actctcccctaaaagacggcacattaaatatatataaaaaaatatttatgaagtcaagagggaggaagcagcagaaaatagtcggagatttaatgaatttacaaaccagta Mask Tandem Repeat Region ================================================ tactggtttgtaaattcattaaatctccgactattttctgctgcttcctccctcttgacttcataaatatttttttatatatatttaatgtgccgtcttttaggggagagt Find is-nt database================================================ Query_seq: TDE1276:TDE1277|TDE1276:TDE1277:hypothetical protein:Fe-hydrogenase large subunit family protein:<-->:1310710..1310820 111 tactggtttgtaaattcattaaatctccgactattttctgctgcttcctccctcttgacttcataaatatttttttatatatatttaatgtgccgtcttttaggggagagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1276:TDE1277|TDE1276:TDE1277:hypothetical protein:Fe-hydrogenase large subunit family protein:<-->:1310710..1310820 111 tactggtttgtaaattcattaaatctccgactattttctgctgcttcctccctcttgacttcataaatatttttttatatatatttaatgtgccgtcttttaggggagagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1276:TDE1277|TDE1276:TDE1277:hypothetical protein:Fe-hydrogenase large subunit family protein:<-->:1310710..1310820 111 tactggtttgtaaattcattaaatctccgactattttctgctgcttcctccctcttgacttcataaatatttttttatatatatttaatgtgccgtcttttaggggagagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tactggtttgtaaattcattaaatctccgactattttctgctgcttcctccctcttgacttcataaatatttttttatatatatttaatgtgccgtcttttaggggagagt Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 3 End: 110 .. M V C K F I K S P T I F C C F L P L D F I N I F L Y I F N V P S F R G E . tactggtttgtaaattcattaaatctccgactattttctgctgcttcctccctcttgacttcataaatatttttttatatatatttaatgtgccgtcttttaggggagagt 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================================================ tactggtttgtaaattcattaaatctccgactattttctgctgcttcctccctcttgacttcataaatatttttttatatatatttaatgtgccgtcttttaggggagagt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1276:TDE1277|TDE1276:TDE1277:hypothetical protein:Fe-hydrogenase large subunit family protein:<-->:1310710..1310820 111 tactggtttgtaaattcattaaatctccgactattttctgctgcttcctccctcttgacttcataaatatttttttatatatatttaatgtgccgtcttttaggggagagt Intra-Species Hit: Count: 1 Min: 1 Max: 111 Len: 111 Subject: NC_002967_TDE1276_TDE1277|hypothetical protein:Fe-hydrogenase large subunit family protein|NEGATIVE:POSITIVE|[1310710,1310820]|111 HSP 1 e-value: 2.0E-44 bit: 178.0 Len: 111 Query Start:1 Query End:111 Subject Strand: POSITIVE Subject Start: 1 Subject End: 111 tactggtttgtaaattcattaaatctccgactattttctgctgcttcctccctcttgacttcataaatannnnnnnatatatatttaatgtgccgtcttttaggggagagt tactggtttgtaaattcattaaatctccgactattttctgctgcttcctccctcttgacttcataaatatttttttatatatatttaatgtgccgtcttttaggggagagt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UACUGGUUUGUAAAUUCAUUAAAUCUCCGACUAUUUUCUGCUGCUUCCUCCCUCUUGACUUCAUAAAUAUUUUUUUAUAUAUAUUUAAUGUGCCGUCUUUUAGGGGAGAGU ....((((((.........))))))......................(((((.((.(((..(((((((((..........)))))).)))....)))....)))))))... (-15.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUCUCCCCUAAAAGACGGCACAUUAAAUAUAUAUAAAAAAAUAUUUAUGAAGUCAAGAGGGAGGAAGCAGCAGAAAAUAGUCGGAGAUUUAAUGAAUUUACAAACCAGUA ..((..((((....(((..((...(((((((..........)))))))))..)))...))))..))..............((..(((((((...)))))).)..))..... (-14.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 865 70 21 161 112 NC_002967:TDE1276|5end_hypothetical_protein_1310619..1310849_NEGATIVE 695 44 1 231 188 NC_002967:TDE1275|5end_oligopeptide/dipeptide_ABC_transporter,_permease_protein_1310523..1310753_NEGATIVE 337 58 15 131 87 NC_002967:TDE2097|5end_hypothetical_protein_2124741..2124971_NEGATIVE 284 50 2 129 74 NC_002967:TDE1157|5end_phage_terminase,_large_subunit,_putative_1193293..1193523_NEGATIVE 279 62 23 151 111 NC_002967:TDE0957|5end_glycerophosphoryl_diester_phosphodiesterase_family_protein_980252..980482_POSITIVE 273 57 26 82 49 NC_002967:TDE0612|5end_hypothetical_protein_647471..647701_NEGATIVE 273 57 26 164 131 NC_002967:TDE0611|5end_hypothetical_protein_647389..647619_NEGATIVE 264 67 24 118 76 NC_002967:TDE2175|5end_hypothetical_protein_2204320..2204550_NEGATIVE 262 58 27 46 16 NC_002967:TDE2762|5end_flagellar_motor_switch_protein_FliY_2817744..2817974_NEGATIVE 262 66 34 110 78 NC_002967:TDE1329|5end_ATPase,_AAA_family_1363503..1363733_POSITIVE 260 108 87 36 11 NC_002967:TDE2619|5end_RNA_methyltransferase,_TrmA_family,_putative_2660280..2660510_POSITIVE 260 54 15 231 192 NC_002967:TDE1143|5end_hypothetical_protein_1181834..1182064_NEGATIVE 252 76 33 223 175 NC_002967:TDE0214|5end_hypothetical_protein_250449..250679_NEGATIVE 244 62 23 120 81 NC_002967:TDE1521|5end_fumarate_hydratase_1567211..1567441_POSITIVE 240 61 26 49 10 NC_002967:TDE0578|5end_hypothetical_protein_609493..609723_POSITIVE 240 48 4 71 25 NC_002967:TDE0355|5end_hypothetical_protein_399005..399235_POSITIVE 238 53 25 48 18 NC_002967:TDE0002|5end_DNA_gyrase,_B_subunit_1544..1774_POSITIVE 237 62 28 186 154 NC_002967:TDE1621|5end_hypothetical_protein_1670743..1670973_NEGATIVE 233 44 5 161 125 NC_002967:TDE2352|5end_flagellar_hook-associated_protein_2387235..2387465_POSITIVE 233 79 38 223 190 NC_002967:TDE0815|5end_hypothetical_protein_837365..837595_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 279 62 23 149 109 NC_002967:TDE0956|3end_hypothetical_protein_980330..980480_POSITIVE 278 62 24 137 100 NC_002967:TDE2527|3end_hypothetical_protein_2555449..2555599_NEGATIVE 262 58 27 53 23 NC_002967:TDE2763|3end_flagellar_motor_switch_protein_2817737..2817887_NEGATIVE 252 108 91 23 6 NC_002967:TDE2618|3end_PHP_domain_protein_2660347..2660497_POSITIVE 244 62 23 105 66 NC_002967:TDE1520|3end_fumarate_hydratase_1567276..1567426_POSITIVE 237 62 28 109 77 NC_002967:TDE1622|3end_hypothetical_protein_1670820..1670970_NEGATIVE 233 44 5 150 114 NC_002967:TDE2351|3end_hypothetical_protein_2387304..2387454_POSITIVE 232 57 28 102 67 NC_002967:TDE2297|3end_TPR_domain_protein_2336339..2336489_NEGATIVE 232 58 27 138 98 NC_002967:TDE0448|3end_deoxyribose-phosphate_aldolase_506526..506676_POSITIVE 226 62 24 102 67 NC_002967:TDE1092|3end_hypothetical_protein_1123806..1123956_NEGATIVE 226 53 34 148 123 NC_002967:TDE0059|3end_hypothetical_protein_67481..67631_POSITIVE 226 53 34 65 40 NC_002967:TDE0058|3end_hypothetical_protein_67398..67548_POSITIVE 225 63 27 148 99 NC_002967:TDE2174|3end_hypothetical_protein_2203099..2203249_NEGATIVE 225 50 7 111 71 NC_002967:TDE1186|3end_hypothetical_protein_1212985..1213135_NEGATIVE 224 57 15 131 87 NC_002967:TDE1309|3end_modulator_of_DNA_gyrase_family_protein_1346042..1346192_POSITIVE 223 71 31 126 82 NC_002967:TDE1206|3end_TPR_domain_protein_1239312..1239462_POSITIVE 222 68 24 87 47 NC_002967:TDE1563|3end_hypothetical_protein_1616513..1616663_POSITIVE 221 106 61 128 68 NC_002967:TDE1549|3end_recombination_protein_RecR_1592807..1592957_POSITIVE 221 57 14 145 93 NC_002967:TDE0884|3end_tRNA_(guanine-N(1)-)-methyltransferase_903032..903182_POSITIVE 221 50 4 145 92 NC_002967:TDE0882|3end_hypothetical_protein_901762..901912_POSITIVE