Origin IGS: taagacttctttaaatttatcaattagaatattcataactgaataatattattgactaaattttgattttggtcaataggaagaaattatttatgtctaagcaataaaaatacggttttagatacaatttttcgatttaattatccaattagtaattgacaaagaatatatttatgcctaaaatatagtgtataagctaagcagacattatatctatgtatcggttcatttaagcttttcttataaagaaatttattttatttaaattataaactttagttttaaggaagaaattttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaaaatttcttccttaaaactaaagtttataatttaaataaaataaatttctttataagaaaagcttaaatgaaccgatacatagatataatgtctgcttagcttatacactatattttaggcataaatatattctttgtcaattactaattggataattaaatcgaaaaattgtatctaaaaccgtatttttattgcttagacataaataatttcttcctattgaccaaaatcaaaatttagtcaataatattattcagttatgaatattctaattgataaatttaaagaagtctta Mask Tandem Repeat Region ================================================ taagacttctttaaatttatcaattagaatattcataactgaataatattattgactaaattttgattttggtcaataggaagaaattatttatgtctaagcaataaaaatacggttttagatacaatttttcgatttaattatccaattagtaattgacaaagaatatatttatgcctaaaatatagtgtataagctaagcagacattatatctatgtatcggttcatttaagcttttcttataaagaaatttattttatttaaattataaactttagttttaaggaagaaattttt Find is-nt database================================================ Query_seq: TDE0323:TDE0324|TDE0323:TDE0324:hypothetical protein:hypothetical protein:<-->:357286..357583 298 taagacttctttaaatttatcaattagaatattcataactgaataatattattgactaaattttgattttggtcaataggaagaaattatttatgtctaagcaataaaaatacggttttagatacaatttttcgatttaattatccaattagtaattgacaaagaatatatttatgcctaaaatatagtgtataagctaagcagacattatatctatgtatcggttcatttaagcttttcttataaagaaatttattttatttaaattataaactttagttttaaggaagaaattttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0323:TDE0324|TDE0323:TDE0324:hypothetical protein:hypothetical protein:<-->:357286..357583 298 taagacttctttaaatttatcaattagaatattcataactgaataatattattgactaaattttgattttggtcaataggaagaaattatttatgtctaagcaataaaaatacggttttagatacaatttttcgatttaattatccaattagtaattgacaaagaatatatttatgcctaaaatatagtgtataagctaagcagacattatatctatgtatcggttcatttaagcttttcttataaagaaatttattttatttaaattataaactttagttttaaggaagaaattttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0323:TDE0324|TDE0323:TDE0324:hypothetical protein:hypothetical protein:<-->:357286..357583 298 taagacttctttaaatttatcaattagaatattcataactgaataatattattgactaaattttgattttggtcaataggaagaaattatttatgtctaagcaataaaaatacggttttagatacaatttttcgatttaattatccaattagtaattgacaaagaatatatttatgcctaaaatatagtgtataagctaagcagacattatatctatgtatcggttcatttaagcttttcttataaagaaatttattttatttaaattataaactttagttttaaggaagaaattttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taagacttctttaaatttatcaattagaatattcataactgaataatattattgactaaattttgattttggtcaataggaagaaattatttatgtctaagcaataaaaatacggttttagatacaatttttcgatttaattatccaattagtaattgacaaagaatatatttatgcctaaaatatagtgtataagctaagcagacattatatctatgtatcggttcatttaagcttttcttataaagaaatttattttatttaaattataaactttagttttaaggaagaaattttt Predict ORF larger than 30AA ================================================ taagacttctttaaatttatcaattagaatattcataactgaataatattattgactaaattttgattttggtcaataggaagaaattatttatgtctaagcaataaaaatacggttttagatacaatttttcgatttaattatccaattagtaattgacaaagaatatatttatgcctaaaatatagtgtataagctaagcagacattatatctatgtatcggttcatttaagcttttcttataaagaaatttattttatttaaattataaactttagttttaaggaagaaattttt 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: 91 Start: 155 End: 184 ..........................................................................................................................................................ATTGACAAAGAATATATTTATGCCTAAAAT.................................................................................................................. PromScan Matrix: RpoD-17 Strand: - Score: 86 Start: 48 End: 77 ...............................................ATTGACCAAAATCAAAATTTAGTCAATAAT............................................................................................................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taagacttctttaaatttatcaattagaatattcataactgaataatattattgactaaattttgattttggtcaataggaagaaattatttatgtctaagcaataaaaatacggttttagatacaatttttcgatttaattatccaattagtaattgacaaagaatatatttatgcctaaaatatagtgtataagctaagcagacattatatctatgtatcggttcatttaagcttttcttataaagaaatttattttatttaaattataaactttagttttaaggaagaaattttt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 76 HP_score: -5.8 Tail_Score: -4.96996 Start: 237 End: 251 Full_Region: CGGTTCATTTAAGCT TTTCTT ATA AAGAAA TTTATTTTATTTAAA ............................................................................................................................................................................................................................................TTTCTTATAAAGAAA............................................... Find igs database================================================ Query_seq: TDE0323:TDE0324|TDE0323:TDE0324:hypothetical protein:hypothetical protein:<-->:357286..357583 298 taagacttctttaaatttatcaattagaatattcataactgaataatattattgactaaattttgattttggtcaataggaagaaattatttatgtctaagcaataaaaatacggttttagatacaatttttcgatttaattatccaattagtaattgacaaagaatatatttatgcctaaaatatagtgtataagctaagcagacattatatctatgtatcggttcatttaagcttttcttataaagaaatttattttatttaaattataaactttagttttaaggaagaaattttt Intra-Species Hit: Count: 1 Min: 1 Max: 227 Len: 227 Subject: NC_002967_TDE0323_TDE0324|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[357286,357583]|298 HSP 1 e-value: 1.0E-125 bit: 450.0 Len: 227 Query Start:1 Query End:227 Subject Strand: POSITIVE Subject Start: 1 Subject End: 227 taagacttctttaaatttatcaattagaatattcataactgaataatattattgactaaattttgattttggtcaataggaagaaattatttatgtctaagcaataaaaatacggttttagatacaatttttcgatttaattatccaattagtaattgacaaagaatatatttatgcctaaaatatagtgtataagctaagcagacattatatctatgtatcggttc....................................................................... taagacttctttaaatttatcaattagaatattcataactgaataatattattgactaaattttgattttggtcaataggaagaaattatttatgtctaagcaataaaaatacggttttagatacaatttttcgatttaattatccaattagtaattgacaaagaatatatttatgcctaaaatatagtgtataagctaagcagacattatatctatgtatcggttc....................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGACUUCUUUAAAUUUAUCAAUUAGAAUAUUCAUAACUGAAUAAUAUUAUUGACUAAAUUUUGAUUUUGGUCAAUAGGAAGAAAUUAUUUAUGUCUAAGCAAUAAAAAUACGGUUUUAGAUACAAUUUUUCGAUUUAAUUAUCCAAUUAGUAAUUGACAAAGAAUAUAUUUAUGCCUAAAAUAUAGUGUAUAAGCUAAGCAGACAUUAUAUCUAUGUAUCGGUUC (((((((........(((((...(((((.((((((....))))))...((((((((((((.......))))))))))))................)))))...))))).....)))))))((((((....(((...((((((((.......))))))))....)))................(((((((((....((...))..)))))))))...))))))..... (-37.22) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAACCGAUACAUAGAUAUAAUGUCUGCUUAGCUUAUACACUAUAUUUUAGGCAUAAAUAUAUUCUUUGUCAAUUACUAAUUGGAUAAUUAAAUCGAAAAAUUGUAUCUAAAACCGUAUUUUUAUUGCUUAGACAUAAAUAAUUUCUUCCUAUUGACCAAAAUCAAAAUUUAGUCAAUAAUAUUAUUCAGUUAUGAAUAUUCUAAUUGAUAAAUUUAAAGAAGUCUUA .....(((...((((((((((.((.((((((..((((...))))..)))))).............((((((((.....))).))))).......))...))))))))))...(..((..((((((..(((((.................(((((((.(((.......))).)))))))....((((((....)))))).)))))..))))))..))..)..)))... (-35.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 709 120 71 211 162 NC_002967:TDE0323|5end_hypothetical_protein_357195..357425_NEGATIVE 253 98 70 116 85 NC_002967:TDE1684|5end_adenine_phosphoribosyltransferase_1737327..1737557_NEGATIVE 241 193 152 54 14 NC_002967:TDE1035|5end_transcriptional_regulator,_PadR_family_1063454..1063684_POSITIVE 234 130 89 226 180 NC_002967:TDE1029|5end_Hsp20/alpha_crystallin_family_protein_1058574..1058804_POSITIVE 234 130 89 96 50 NC_002967:TDE1028|5end_hypothetical_protein_1058444..1058674_POSITIVE 217 56 22 174 140 NC_002967:TDE2485|5end_hypothetical_protein_2509123..2509353_NEGATIVE 212 150 101 122 68 NC_002967:TDE1217|5end_flagellar_assembly_protein_1249511..1249741_POSITIVE 212 147 102 88 41 NC_002967:TDE0180|5end_hypothetical_protein_213018..213248_NEGATIVE 212 147 102 225 178 NC_002967:TDE0179|5end_hypothetical_protein_212881..213111_NEGATIVE 203 98 60 146 107 NC_002967:TDE1452|5end_hypothetical_protein_1498891..1499121_POSITIVE 203 189 141 169 121 NC_002967:TDE0384|5end_hypothetical_protein_435048..435278_POSITIVE 200 140 95 52 7 NC_002967:TDE1610|5end_DNA-binding_protein_1659496..1659726_NEGATIVE 196 216 189 195 170 NC_002967:TDE2451|5end_S-adenosylmethionine:tRNA_ribosyltransferase-isomerase_2479832..2480062_POSITIVE 191 220 174 119 64 NC_002967:TDE1396|5end_hypothetical_protein_1435661..1435891_POSITIVE 190 119 75 196 152 NC_002967:TDE0079|5end_DNA-binding_protein_90670..90900_NEGATIVE 189 219 188 36 5 NC_002967:TDE2410|5end_hemolysin_2437247..2437477_NEGATIVE 189 138 94 173 118 NC_002967:TDE0437|5end_PBS_lyase_HEAT-like_repeat_domain_protein_493605..493835_NEGATIVE 188 81 43 231 190 NC_002967:TDE2337|5end_aminopeptidase_2373295..2373525_POSITIVE 188 102 61 163 112 NC_002967:TDE1038|5end_hypothetical_protein_1066976..1067206_NEGATIVE 186 129 81 112 62 NC_002967:TDE0581|5end_transglutaminase-like_domain_protein_616620..616850_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 253 98 70 91 60 NC_002967:TDE1685|3end_GGDEF_domain_protein_1737352..1737502_NEGATIVE 212 150 101 101 47 NC_002967:TDE1216|3end_flagellar_motor_protein_1249570..1249720_POSITIVE 212 147 102 119 72 NC_002967:TDE0181|3end_methyl-accepting_chemotaxis_protein_212987..213137_NEGATIVE 191 220 174 56 1 NC_002967:TDE1395|3end_glycosyl_hydrolase,_family_57_1435678..1435828_POSITIVE 190 119 75 138 94 NC_002967:TDE0080|3end_betaine_aldehyde_dehydrogenase_90728..90878_NEGATIVE 189 219 188 49 18 NC_002967:TDE2411|3end_glycogen_phosphorylase_2437234..2437384_NEGATIVE 189 138 94 106 51 NC_002967:TDE0438|3end_queuine_tRNA-ribosyltransferase_493672..493822_NEGATIVE 186 129 81 128 78 NC_002967:TDE0580|3end_hypothetical_protein_616716..616866_POSITIVE 183 92 61 111 80 NC_002967:TDE0034|3end_hypothetical_protein_40713..40863_NEGATIVE 182 149 113 99 67 NC_002967:TDE2533|3end_hypothetical_protein_2560240..2560390_POSITIVE 181 209 169 138 92 NC_002967:TDE1703|3end_hypothetical_protein_1760638..1760788_POSITIVE 181 212 176 95 56 NC_002967:TDE0745|3end_glycine_reductase_complex_selenoprotein_GrdA_780840..780990_POSITIVE 177 207 177 126 90 NC_002967:TDE0269|3end_hypothetical_protein_300196..300346_NEGATIVE 175 206 177 86 53 NC_002967:TDE2470|3end_S-adenosylmethionine_synthetase_2492599..2492749_NEGATIVE 175 212 177 50 19 NC_002967:TDE1329|3end_ATPase,_AAA_family_1365346..1365496_POSITIVE 171 115 71 66 18 NC_002967:TDE1932|3end_hypothetical_protein_1949131..1949281_NEGATIVE 170 113 71 106 64 NC_002967:TDE0946|3end_hypothetical_protein_968735..968885_POSITIVE 170 218 184 123 92 NC_002967:TDE0493|3end_hypothetical_protein_548581..548731_NEGATIVE 170 67 38 79 54 NC_002967:TDE0470|3end_cell_division_protein_FtsH_526557..526707_POSITIVE 169 118 71 140 94 NC_002967:TDE2728|3end_hypothetical_protein_2785815..2785965_POSITIVE