Origin IGS: tataatctccttataaatgtttttttcatgcgtaattgaattaccggttacacatgcattactatacagtataccccgtttccccgcaaatttcaatctttcgtggagtttttttgtttctttgctttttggagtatttattttaagcggtgtaaatagcactgt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 acagtgctatttacaccgcttaaaataaatactccaaaaagcaaagaaacaaaaaaactccacgaaagattgaaatttgcggggaaacggggtatactgtatagtaatgcatgtgtaaccggtaattcaattacgcatgaaaaaaacatttataaggagattata Mask Tandem Repeat Region ================================================ tataatctccttataaatgtttttttcatgcgtaattgaattaccggttacacatgcattactatacagtataccccgtttccccgcaaatttcaatctttcgtggagtttttttgtttctttgctttttggagtatttattttaagcggtgtaaatagcactgt Find is-nt database================================================ Query_seq: TDE2211:TDE2212|TDE2211:TDE2212:hypothetical protein:galactokinase:<-<-:2251407..2251571 165 tataatctccttataaatgtttttttcatgcgtaattgaattaccggttacacatgcattactatacagtataccccgtttccccgcaaatttcaatctttcgtggagtttttttgtttctttgctttttggagtatttattttaagcggtgtaaatagcactgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2211:TDE2212|TDE2211:TDE2212:hypothetical protein:galactokinase:<-<-:2251407..2251571 165 tataatctccttataaatgtttttttcatgcgtaattgaattaccggttacacatgcattactatacagtataccccgtttccccgcaaatttcaatctttcgtggagtttttttgtttctttgctttttggagtatttattttaagcggtgtaaatagcactgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2211:TDE2212|TDE2211:TDE2212:hypothetical protein:galactokinase:<-<-:2251407..2251571 165 tataatctccttataaatgtttttttcatgcgtaattgaattaccggttacacatgcattactatacagtataccccgtttccccgcaaatttcaatctttcgtggagtttttttgtttctttgctttttggagtatttattttaagcggtgtaaatagcactgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tataatctccttataaatgtttttttcatgcgtaattgaattaccggttacacatgcattactatacagtataccccgtttccccgcaaatttcaatctttcgtggagtttttttgtttctttgctttttggagtatttattttaagcggtgtaaatagcactgt Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 36 End: 143 ................................... M N Y R L H M H Y Y T V Y P V S P Q I S I F R G V F L F L C F L E Y L F ...................... Protein_Len: 39 Strand: + Start: 40 End: 156 ....................................... M T G Y T C I T I Q Y T P F P R K F Q S F V E F F C F F A F W S I Y F K R C K ......... Protein_Len: 49 Strand: + Start: 17 End: 163 ................ M F F S C V I E L P V T H A L L Y S I P R F P A N F N L S W S F F V S L L F G V F I L S G V N S T .. Protein_Len: 54 Strand: - Start: 1 End: 162 I I E K Y I N K E H T I S N G T V C A N S Y L I G R K G A F K L R E H L K K T E K S K P T N I K L P T F L M ... tataatctccttataaatgtttttttcatgcgtaattgaattaccggttacacatgcattactatacagtataccccgtttccccgcaaatttcaatctttcgtggagtttttttgtttctttgctttttggagtatttattttaagcggtgtaaatagcactgt 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: 68 End: 97 ...................................................................ATTGAAATTTGCGGGGAAACGGGGTATACT.................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tataatctccttataaatgtttttttcatgcgtaattgaattaccggttacacatgcattactatacagtataccccgtttccccgcaaatttcaatctttcgtggagtttttttgtttctttgctttttggagtatttattttaagcggtgtaaatagcactgt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2211:TDE2212|TDE2211:TDE2212:hypothetical protein:galactokinase:<-<-:2251407..2251571 165 tataatctccttataaatgtttttttcatgcgtaattgaattaccggttacacatgcattactatacagtataccccgtttccccgcaaatttcaatctttcgtggagtttttttgtttctttgctttttggagtatttattttaagcggtgtaaatagcactgt Intra-Species Hit: Count: 1 Min: 1 Max: 108 Len: 108 Subject: NC_002967_TDE2211_TDE2212|hypothetical protein:galactokinase|NEGATIVE:NEGATIVE|[2251407, 2251571]|165 HSP 1 e-value: 2.0E-42 bit: 172.0 Len: 108 Query Start:1 Query End:108 Subject Strand: POSITIVE Subject Start: 1 Subject End: 108 tataatctccttataaatgnnnnnnncatgcgtaattgaattaccggttacacatgcattactatacagtataccccgtttccccgcaaatttcaatctttcgtggag......................................................... tataatctccttataaatgtttttttcatgcgtaattgaattaccggttacacatgcattactatacagtataccccgtttccccgcaaatttcaatctttcgtggag......................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUAAUCUCCUUAUAAAUGUUUUUUUCAUGCGUAAUUGAAUUACCGGUUACACAUGCAUUACUAUACAGUAUACCCCGUUUCCCCGCAAAUUUCAAUCUUUCGUGGAG ......((((................((((.(((((((......))))))).))))...((((....)))).................................)))) (-15.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUCCACGAAAGAUUGAAAUUUGCGGGGAAACGGGGUAUACUGUAUAGUAAUGCAUGUGUAACCGGUAAUUCAAUUACGCAUGAAAAAAACAUUUAUAAGGAGAUUAUA ((((.(....).........((((..(((((.((.((((((((((....))))).))))).)).))..))).....))))..................))))...... (-24.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 924 90 41 181 132 NC_002967:TDE2211|5end_hypothetical_protein_2251316..2251546_NEGATIVE 317 50 6 148 97 NC_002967:TDE1148|5end_hypothetical_protein_1186357..1186587_NEGATIVE 263 89 44 190 148 NC_002967:TDE1621|5end_hypothetical_protein_1670743..1670973_NEGATIVE 259 100 54 207 163 NC_002967:TDE0016|5end_ATPase,_AAA_family_20457..20687_POSITIVE 255 87 44 140 96 NC_002967:TDE1978|5end_hypothetical_protein_1991758..1991988_NEGATIVE 251 87 44 111 64 NC_002967:TDE0999|5end_formate/nitrite_transporter_1025870..1026100_POSITIVE 250 87 44 178 138 NC_002967:TDE0283|5end_transporter,_putative_312825..313055_NEGATIVE 248 87 44 45 9 NC_002967:TDE0793|5end_hypothetical_protein_818910..819140_POSITIVE 246 89 54 59 28 NC_002967:TDE0719|5end_bacteriocin_ABC_transporter,_ATP-binding/permease_protein,_putative_753462..753692_POSITIVE 242 78 35 204 162 NC_002967:TDE0167|5end_ABC_transporter,_ATP-binding_protein_196574..196804_NEGATIVE 240 34 6 164 133 NC_002967:TDE1701|5end_hypothetical_protein_1758140..1758370_POSITIVE 240 34 6 64 33 NC_002967:TDE1700|5end_hypothetical_protein_1758040..1758270_POSITIVE 237 99 55 67 27 NC_002967:TDE0452|5end_hypothetical_protein_510143..510373_NEGATIVE 233 87 45 184 136 NC_002967:TDE2683|5end_sigma_factor_WhiG_2724155..2724385_NEGATIVE 233 88 43 166 121 NC_002967:TDE2596|5end_hypothetical_protein_2632039..2632269_NEGATIVE 233 85 44 100 52 NC_002967:TDE0248|5end_hypothetical_protein_282068..282298_POSITIVE 230 60 18 141 92 NC_002967:TDE1803|5end_hypothetical_protein_1839270..1839500_NEGATIVE 228 89 45 155 114 NC_002967:TDE0858|5end_hypothetical_protein_879518..879748_POSITIVE 228 100 57 102 59 NC_002967:TDE0179|5end_hypothetical_protein_212881..213111_NEGATIVE 227 96 57 124 86 NC_002967:TDE0742|5end_hypothetical_protein_778635..778865_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 317 50 6 79 28 NC_002967:TDE1149|3end_hypothetical_protein_1186426..1186576_NEGATIVE 263 89 44 113 71 NC_002967:TDE1622|3end_hypothetical_protein_1670820..1670970_NEGATIVE 255 87 44 143 99 NC_002967:TDE1979|3end_hypothetical_protein_1991755..1991905_NEGATIVE 250 78 31 111 56 NC_002967:TDE0711|3end_hypothetical_protein_745690..745840_NEGATIVE 248 87 44 61 25 NC_002967:TDE0792|3end_ribosomal_protein_L17_819006..819156_POSITIVE 247 75 32 85 31 NC_002967:TDE1185|3end_lipoprotein,_putative_1211597..1211747_NEGATIVE 242 78 35 111 69 NC_002967:TDE0168|3end_transcriptional_regulator,_GntR_family_196667..196817_NEGATIVE 237 99 55 67 27 NC_002967:TDE0453|3end_hypothetical_protein_510143..510293_NEGATIVE 228 87 42 69 28 NC_002967:TDE1131|3end_hypothetical_protein_1163531..1163681_POSITIVE 228 100 57 129 86 NC_002967:TDE0180|3end_hypothetical_protein_212854..213004_NEGATIVE 225 95 51 112 74 NC_002967:TDE1415|3end_nucleotidyl_transferase/aminotransferase,_class_V_1459871..1460021_POSITIVE 221 87 41 131 91 NC_002967:TDE2742|3end_site-specific_recombinase,_phage_integrase_family_2796850..2797000_NEGATIVE 221 99 61 51 6 NC_002967:TDE1160|3end_hypothetical_protein_1194417..1194567_NEGATIVE 218 85 72 73 60 NC_002967:TDE2170|3end_hypothetical_protein_2201606..2201756_NEGATIVE 217 85 49 52 17 NC_002967:TDE2614|3end_ApbE_family_protein_2656018..2656168_NEGATIVE 215 87 42 69 18 NC_002967:TDE1213|3end_flagellar_basal_body_rod_protein_1246352..1246502_POSITIVE 214 89 44 74 17 NC_002967:TDE2544|3end_hypothetical_protein_2570935..2571085_NEGATIVE 211 96 71 94 67 NC_002967:TDE0569|3end_hypothetical_protein_600162..600312_POSITIVE 210 88 71 144 127 NC_002967:TDE1692|3end_hypothetical_protein_1748471..1748621_POSITIVE 207 98 63 64 32 NC_002967:TDE2548|3end_hypothetical_protein_2573064..2573214_NEGATIVE