Origin IGS: attttcgcacctccttctatctcaaagcaacggcaatgcctgtaattaaaaaaagtaacccaattccgcaaaatattactaacagtaaaatctttagaattgtaataatcttttctgtaatgttgtaaaactcatagtctgtcatttttcatcttctcctccact .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agtggaggagaagatgaaaaatgacagactatgagttttacaacattacagaaaagattattacaattctaaagattttactgttagtaatattttgcggaattgggttactttttttaattacaggcattgccgttgctttgagatagaaggaggtgcgaaaat Mask Tandem Repeat Region ================================================ attttcgcacctccttctatctcaaagcaacggcaatgcctgtaattaaaaaaagtaacccaattccgcaaaatattactaacagtaaaatctttagaattgtaataatcttttctgtaatgttgtaaaactcatagtctgtcatttttcatcttctcctccact Find is-nt database================================================ Query_seq: TDE1155:TDE1156|TDE1155:TDE1156:hypothetical protein:hypothetical protein:<-<-:1191546..1191710 165 attttcgcacctccttctatctcaaagcaacggcaatgcctgtaattaaaaaaagtaacccaattccgcaaaatattactaacagtaaaatctttagaattgtaataatcttttctgtaatgttgtaaaactcatagtctgtcatttttcatcttctcctccact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1155:TDE1156|TDE1155:TDE1156:hypothetical protein:hypothetical protein:<-<-:1191546..1191710 165 attttcgcacctccttctatctcaaagcaacggcaatgcctgtaattaaaaaaagtaacccaattccgcaaaatattactaacagtaaaatctttagaattgtaataatcttttctgtaatgttgtaaaactcatagtctgtcatttttcatcttctcctccact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1155:TDE1156|TDE1155:TDE1156:hypothetical protein:hypothetical protein:<-<-:1191546..1191710 165 attttcgcacctccttctatctcaaagcaacggcaatgcctgtaattaaaaaaagtaacccaattccgcaaaatattactaacagtaaaatctttagaattgtaataatcttttctgtaatgttgtaaaactcatagtctgtcatttttcatcttctcctccact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 attttcgcacctccttctatctcaaagcaacggcaatgcctgtaattaaaaaaagtaacccaattccgcaaaatattactaacagtaaaatctttagaattgtaataatcttttctgtaatgttgtaaaactcatagtctgtcatttttcatcttctcctccact Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 36 End: 125 ................................... M P V I K K S N P I P Q N I T N S K I F R I V I I F S V M L ........................................ Protein_Len: 42 Strand: - Start: 20 End: 145 ................... R L A V A I G T I L F L L G I G C F I V L L L I K L I T I I K E T I N Y F E Y D T M .................... attttcgcacctccttctatctcaaagcaacggcaatgcctgtaattaaaaaaagtaacccaattccgcaaaatattactaacagtaaaatctttagaattgtaataatcttttctgtaatgttgtaaaactcatagtctgtcatttttcatcttctcctccact 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================================================ PromScan Matrix: RpoN Strand: - Score: 82 Start: 26 End: 42 .........................CAGGCATTGCCGTTGCT........................................................................................................................... attttcgcacctccttctatctcaaagcaacggcaatgcctgtaattaaaaaaagtaacccaattccgcaaaatattactaacagtaaaatctttagaattgtaataatcttttctgtaatgttgtaaaactcatagtctgtcatttttcatcttctcctccact Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1155:TDE1156|TDE1155:TDE1156:hypothetical protein:hypothetical protein:<-<-:1191546..1191710 165 attttcgcacctccttctatctcaaagcaacggcaatgcctgtaattaaaaaaagtaacccaattccgcaaaatattactaacagtaaaatctttagaattgtaataatcttttctgtaatgttgtaaaactcatagtctgtcatttttcatcttctcctccact Intra-Species Hit: Count: 1 Min: 1 Max: 165 Len: 165 Subject: NC_002967_TDE1155_TDE1156|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[1191546,1191710]|165 HSP 1 e-value: 2.0E-76 bit: 285.0 Len: 165 Query Start:1 Query End:165 Subject Strand: POSITIVE Subject Start: 1 Subject End: 165 attttcgcacctccttctatctcaaagcaacggcaatgcctgtaattnnnnnnngtaacccaattccgcaaaatattactaacagtaaaatctttagaattgtaataatcttttctgtaatgttgtaaaactcatagtctgtcatttttcatcttctcctccact attttcgcacctccttctatctcaaagcaacggcaatgcctgtaattaaaaaaagtaacccaattccgcaaaatattactaacagtaaaatctttagaattgtaataatcttttctgtaatgttgtaaaactcatagtctgtcatttttcatcttctcctccact Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUUCGCACCUCCUUCUAUCUCAAAGCAACGGCAAUGCCUGUAAUUAAAAAAAGUAACCCAAUUCCGCAAAAUAUUACUAACAGUAAAAUCUUUAGAAUUGUAAUAAUCUUUUCUGUAAUGUUGUAAAACUCAUAGUCUGUCAUUUUUCAUCUUCUCCUCCACU ................((((......((((((((...)))....((((..(((((.....((((((.........((((.....))))........)))))).......)))))...))))))))).......))))............................ (-11.75) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUGGAGGAGAAGAUGAAAAAUGACAGACUAUGAGUUUUACAACAUUACAGAAAAGAUUAUUACAAUUCUAAAGAUUUUACUGUUAGUAAUAUUUUGCGGAAUUGGGUUACUUUUUUUAAUUACAGGCAUUGCCGUUGCUUUGAGAUAGAAGGAGGUGCGAAAAU .(((.((((((((.((.(((((..((.....)).))))).)).....................(((((((.(((((.((((.....)))).)))))..))))))).....))))))))...)))..((((..((....((.......))..))..))))...... (-28.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 881 50 1 141 92 NC_002967:TDE1155|5end_hypothetical_protein_1191455..1191685_NEGATIVE 298 50 5 228 172 NC_002967:TDE1287|5end_transcription-repair_coupling_factor_1322738..1322968_POSITIVE 293 160 112 117 70 NC_002967:TDE1863|5end_Holliday_junction_DNA_helicase_RuvA_1888579..1888809_NEGATIVE 290 44 7 58 21 NC_002967:TDE0169|5end_methyl-accepting_chemotaxis_domain_protein_198792..199022_NEGATIVE 287 48 5 189 144 NC_002967:TDE2130|5end_hypothetical_protein_2162059..2162289_NEGATIVE 275 159 113 104 52 NC_002967:TDE0554|5end_hypothetical_protein_590968..591198_NEGATIVE 263 44 10 44 4 NC_002967:TDE0828|5end_glucose-inhibited_division_protein_A_850169..850399_NEGATIVE 259 110 64 51 11 NC_002967:TDE0586|5end_hypothetical_protein_625246..625476_POSITIVE 258 69 21 66 15 NC_002967:TDE1974|5end_UDP-N-acetylglucosamine--N-acetylmuramyl-_(pentapeptide)_pyrophosphoryl-undecaprenol_N-acetylglucosamine_transferase_1988910..1989140_NEGATIVE 257 159 116 185 138 NC_002967:TDE0343|5end_hydrolase,_alpha/beta_fold_family_385365..385595_NEGATIVE 254 70 26 176 134 NC_002967:TDE2391|5end_peptidyl-prolyl_cis-trans_isomerase_2421550..2421780_NEGATIVE 252 43 7 144 113 NC_002967:TDE2057|5end_hypothetical_protein_2085343..2085573_NEGATIVE 246 156 111 100 53 NC_002967:TDE0643|5end_peptidyl-tRNA_hydrolase_679827..680057_NEGATIVE 245 42 7 132 94 NC_002967:TDE1655|5end_hypothetical_protein_1704958..1705188_POSITIVE 245 44 7 53 21 NC_002967:TDE0982|5end_dihydroorotate_dehydrogenase/oxidoreductase,_FAD-binding_1006477..1006707_POSITIVE 244 154 111 218 183 NC_002967:TDE1904|5end_hypothetical_protein_1923613..1923843_NEGATIVE 243 47 4 170 118 NC_002967:TDE1926|5end_hypothetical_protein_1942495..1942725_POSITIVE 241 66 21 89 34 NC_002967:TDE1814|5end_hypothetical_protein_1849313..1849543_NEGATIVE 241 66 21 89 34 NC_002967:TDE1792|5end_hypothetical_protein_1829795..1830025_NEGATIVE 239 160 111 154 96 NC_002967:TDE1281|5end_hypothetical_protein_1316500..1316730_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 293 160 112 124 77 NC_002967:TDE1864|3end_crossover_junction_endodeoxyribonuclease_RuvC_1888572..1888722_NEGATIVE 288 40 5 32 2 NC_002967:TDE2181|3end_PAP2_family_protein_2211995..2212145_NEGATIVE 275 159 113 89 37 NC_002967:TDE0555|3end_hypothetical_protein_590983..591133_NEGATIVE 267 44 2 82 33 NC_002967:TDE1692|3end_hypothetical_protein_1748471..1748621_POSITIVE 255 44 2 112 71 NC_002967:TDE0455|3end_kinase,_GHMP_family_512477..512627_POSITIVE 254 70 26 53 11 NC_002967:TDE2392|3end_hypothetical_protein_2421673..2421823_NEGATIVE 252 43 7 133 102 NC_002967:TDE2058|3end_hypothetical_protein_2085354..2085504_NEGATIVE 246 156 111 88 41 NC_002967:TDE0644|3end_ABC_transporter,_ATP-binding_protein_679839..679989_NEGATIVE 244 154 111 109 74 NC_002967:TDE1905|3end_hypothetical_protein_1923722..1923872_NEGATIVE 239 44 3 51 7 NC_002967:TDE2196|3end_hypothetical_protein_2231883..2232033_NEGATIVE 238 29 3 63 32 NC_002967:TDE2763|3end_flagellar_motor_switch_protein_2817737..2817887_NEGATIVE 232 43 7 53 6 NC_002967:TDE1658|3end_basic_membrane_protein,_putative_1707655..1707805_NEGATIVE 231 40 5 150 113 NC_002967:TDE2131|3end_cobalamin_biosynthesis_protein_CbiM,_putative_2162090..2162240_NEGATIVE 231 44 9 31 3 NC_002967:TDE0981|3end_hypothetical_protein_1006535..1006685_POSITIVE 230 44 6 130 87 NC_002967:TDE0625|3end_ABC_transporter,_ATP-binding_protein_658103..658253_POSITIVE 228 41 2 121 86 NC_002967:TDE1622|3end_hypothetical_protein_1670820..1670970_NEGATIVE 227 44 7 124 79 NC_002967:TDE1584|3end_lipoprotein,_putative_1632854..1633004_POSITIVE 226 45 7 131 96 NC_002967:TDE2325|3end_hypothetical_protein_2361177..2361327_POSITIVE 226 43 7 131 95 NC_002967:TDE1577|3end_lipoprotein,_putative_1625446..1625596_POSITIVE 222 39 7 148 121 NC_002967:TDE0164|3end_hypothetical_protein_193417..193567_NEGATIVE