Origin IGS: tttgaactcctcaaaaaataagaaacagccccctttctttagaaaggcactttctttcggaagatatctttctacagaaagagtctttctgtagaaagagggctttgtaaacttctttaagtt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aacttaaagaagtttacaaagccctctttctacagaaagactctttctgtagaaagatatcttccgaaagaaagtgcctttctaaagaaagggggctgtttcttattttttgaggagttcaaa Mask Tandem Repeat Region ================================================ tttgaactcctcaaaaaataagaaacagccccctttctttagaaaggcactttctttcggaagatannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnggctttgtaaacttctttaagtt Find is-nt database================================================ Query_seq: TDE1949:TDE1950|TDE1949:TDE1950:ABC transporter, ATP-binding protein:membrane lipoprotein TmpC, putative:<-<-:1966158..1966280 123 tttgaactcctcaaaaaataagaaacagccccctttctttagaaaggcactttctttcggaagatatctttctacagaaagagtctttctgtagaaagagggctttgtaaacttctttaagtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1949:TDE1950|TDE1949:TDE1950:ABC transporter, ATP-binding protein:membrane lipoprotein TmpC, putative:<-<-:1966158..1966280 123 tttgaactcctcaaaaaataagaaacagccccctttctttagaaaggcactttctttcggaagatatctttctacagaaagagtctttctgtagaaagagggctttgtaaacttctttaagtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1949:TDE1950|TDE1949:TDE1950:ABC transporter, ATP-binding protein:membrane lipoprotein TmpC, putative:<-<-:1966158..1966280 123 tttgaactcctcaaaaaataagaaacagccccctttctttagaaaggcactttctttcggaagatatctttctacagaaagagtctttctgtagaaagagggctttgtaaacttctttaagtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttgaactcctcaaaaaataagaaacagccccctttctttagaaaggcactttctttcggaagatatctttctacagaaagagtctttctgtagaaagagggctttgtaaacttctttaagtt Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 2 End: 91 . M N S S K N K K Q P P F F R K A L S F G R Y L S T E R V F L ................................ Protein_Len: 30 Strand: + Start: 18 End: 107 ................. M R N S P L S L E R H F L S E D I F L Q K E S F C R K R A L ................ tttgaactcctcaaaaaataagaaacagccccctttctttagaaaggcactttctttcggaagatatctttctacagaaagagtctttctgtagaaagagggctttgtaaacttctttaagtt 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================================================ tttgaactcctcaaaaaataagaaacagccccctttctttagaaaggcactttctttcggaagatatctttctacagaaagagtctttctgtagaaagagggctttgtaaacttctttaagtt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -13.5 Tail_Score: -3.95653 Start: 63 End: 103 Full_Region: CACTTTCTTTCGGAA GATATCTTTCTACAGAAAG AGT CTTTCTGTAGAAAGAGGGC TTTGTAAACTTCTTT ..............................................................GATATCTTTCTACAGAAAGAGTCTTTCTGTAGAAAGAGGGC.................... Find igs database================================================ Query_seq: TDE1949:TDE1950|TDE1949:TDE1950:ABC transporter, ATP-binding protein:membrane lipoprotein TmpC, putative:<-<-:1966158..1966280 123 tttgaactcctcaaaaaataagaaacagccccctttctttagaaaggcactttctttcggaagatatctttctacagaaagagtctttctgtagaaagagggctttgtaaacttctttaagtt Intra-Species Hit: Count: 1 Min: 1 Max: 123 Len: 123 Subject: NC_002967_TDE1949_TDE1950|ABC transporter, ATP-binding protein:membrane lipoprotein TmpC, putative|NEGATIVE:NEGATIVE|[1966158,1966280]|123 HSP 1 e-value: 6.0E-64 bit: 244.0 Len: 123 Query Start:1 Query End:123 Subject Strand: POSITIVE Subject Start: 1 Subject End: 123 tttgaactcctcaaaaaataagaaacagccccctttctttagaaaggcactttctttcggaagatatctttctacagaaagagtctttctgtagaaagagggctttgtaaacttctttaagtt tttgaactcctcaaaaaataagaaacagccccctttctttagaaaggcactttctttcggaagatatctttctacagaaagagtctttctgtagaaagagggctttgtaaacttctttaagtt HSP 2 e-value: 7.0E-8 bit: 58.0 Len: 33 Query Start:67 Query End:99 Subject Strand: NEGATIVE Subject Start: 67 Subject End: 99 ..................................................................tctttctacagaaagagtctttctgtagaaaga........................ ..................................................................tctttctacagaaagactctttctgtagaaaga........................ Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUGAACUCCUCAAAAAAUAAGAAACAGCCCCCUUUCUUUAGAAAGGCACUUUCUUUCGGAAGAUAUCUUUCUACAGAAAGAGUCUUUCUGUAGAAAGAGGGCUUUGUAAACUUCUUUAAGUU (((((.....)))))....((((((((((((.((((((.(((((((((.((((((...(((((....)))))...)))))).))))))))).)))))).))))..)))....)))))...... (-41.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACUUAAAGAAGUUUACAAAGCCCUCUUUCUACAGAAAGACUCUUUCUGUAGAAAGAUAUCUUCCGAAAGAAAGUGCCUUUCUAAAGAAAGGGGGCUGUUUCUUAUUUUUUGAGGAGUUCAAA ..(((((((((........((((((((((((..((((((.(.((((((...(.(((....))).)...)))))).).))))))..))))))))))))........)))))))))......... (-44.49) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 876 70 21 161 112 NC_002967:TDE1949|5end_ABC_transporter,_ATP-binding_protein_1966067..1966297_NEGATIVE 316 90 43 220 161 NC_002967:TDE0730|5end_hypothetical_protein_770587..770817_NEGATIVE 293 48 18 196 169 NC_002967:TDE2118|5end_DNA_topoisomerase_IV_subunit_A_2151265..2151495_NEGATIVE 279 114 71 194 145 NC_002967:TDE2407|5end_amidophosphoribosyltransferase_2435107..2435337_NEGATIVE 276 85 49 135 96 NC_002967:TDE1108|5end_hypothetical_protein_1142859..1143089_NEGATIVE 275 89 42 194 145 NC_002967:TDE2097|5end_hypothetical_protein_2124741..2124971_NEGATIVE 274 115 71 52 3 NC_002967:TDE1910|5end_1-deoxy-D-xylulose-5-phosphate_synthase_1928837..1929067_NEGATIVE 265 109 61 142 90 NC_002967:TDE2335|5end_ATP-dependent_DNA_helicase,_UvrD/Rep_family_2369641..2369871_POSITIVE 258 90 45 153 107 NC_002967:TDE0957|5end_glycerophosphoryl_diester_phosphodiesterase_family_protein_980252..980482_POSITIVE 255 86 44 146 92 NC_002967:TDE0928|5end_phosphonate_ABC_transporter,_ATP-binding_protein,_putative_951640..951870_NEGATIVE 254 60 27 31 3 NC_002967:TDE0832|5end_hypothetical_protein_852549..852779_POSITIVE 251 49 1 208 156 NC_002967:TDE1040|5end_ribosomal_protein_S15_1067939..1068169_POSITIVE 251 84 45 41 1 NC_002967:TDE0321|5end_CBS_domain_protein_355094..355324_NEGATIVE 251 77 31 214 160 NC_002967:TDE0314|5end_hypothetical_protein_346077..346307_POSITIVE 249 69 28 101 52 NC_002967:TDE2637|5end_hypothetical_protein_2677316..2677546_NEGATIVE 249 118 85 46 6 NC_002967:TDE1751|5end_ribosomal_protein_L21_1804142..1804372_NEGATIVE 248 68 28 65 21 NC_002967:TDE1331|5end_anaerobic_ribonucleoside_triphosphate_reductase_1365868..1366098_POSITIVE 247 73 31 141 95 NC_002967:TDE0954|5end_branched-chain_amino_acid_ABC_transporter,_permease_protein_977924..978154_POSITIVE 245 120 75 161 103 NC_002967:TDE1459|5end_hypothetical_protein_1508707..1508937_NEGATIVE 244 89 41 71 14 NC_002967:TDE1057|5end_hypothetical_protein_1086245..1086475_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 316 90 43 116 57 NC_002967:TDE0731|3end_hypothetical_protein_770691..770841_NEGATIVE 293 48 18 63 36 NC_002967:TDE2119|3end_glycine_reductase_complex_selenoprotein_GrdB2_2151398..2151548_NEGATIVE 288 99 58 51 8 NC_002967:TDE0964|3end_hypothetical_protein_990578..990728_POSITIVE 280 73 31 151 113 NC_002967:TDE2527|3end_hypothetical_protein_2555449..2555599_NEGATIVE 279 114 71 84 35 NC_002967:TDE2408|3end_hypothetical_protein_2435217..2435367_NEGATIVE 277 67 30 145 88 NC_002967:TDE2550|3end_hypothetical_protein_2575520..2575670_NEGATIVE 277 60 21 45 2 NC_002967:TDE2196|3end_hypothetical_protein_2231883..2232033_NEGATIVE 267 69 26 118 68 NC_002967:TDE0157|3end_KHG/KDPG_family_aldolase/carbohydrate_kinase,_PfkB_family_185711..185861_POSITIVE 263 117 76 81 33 NC_002967:TDE1188|3end_NAD(P)_transhydrogenase,_beta_subunit_1214574..1214724_NEGATIVE 261 120 79 90 53 NC_002967:TDE1344|3end_hypothetical_protein_1383350..1383500_POSITIVE 258 90 45 151 105 NC_002967:TDE0956|3end_hypothetical_protein_980330..980480_POSITIVE 255 86 44 67 13 NC_002967:TDE0929|3end_ornithine_carbamoyltransferase_951719..951869_NEGATIVE 253 84 43 46 8 NC_002967:TDE0488|3end_lipoprotein,_putative_545145..545295_POSITIVE 249 88 41 132 61 NC_002967:TDE2514|3end_serine/threonine_protein_phosphatase_family_protein_2539855..2540005_NEGATIVE 247 73 31 144 98 NC_002967:TDE0953|3end_branched-chain_amino_acid_ABC_transporter,_permease_protein_978007..978157_POSITIVE 247 57 18 136 97 NC_002967:TDE0461|3end_hypothetical_protein_516125..516275_POSITIVE 246 73 31 109 63 NC_002967:TDE1914|3end_Holliday_junction_DNA_helicase_RuvB_1930889..1931039_NEGATIVE 244 89 41 84 27 NC_002967:TDE1058|3end_hypothetical_protein_1086232..1086382_NEGATIVE 242 69 22 68 12 NC_002967:TDE0666|3end_FeS_assembly_ATPase_SufC_704373..704523_POSITIVE 242 120 73 78 28 NC_002967:TDE0615|3end_cobalamin_biosynthesis_protein_CbiG_649856..650006_POSITIVE