Origin IGS: taaattatacgataaagaccgacattttttgttggtctttttctttacccataagggggaaatattccctcatagggataatttctccttaaattaacaaaaggagaaattattatgtttcactttattactcatcttttttctcgaccattttcacatgttgagcgatatgacagcattcgtgttgatacatgtgtaaaacaaatcattagcaatgttcatgtatcgatgatttgtgagcaatggttaactgtgtcatttacttcctgtctcaaagcaaaaatgaaataagcataataataaaattacattccctcgccccactaagcatcttgatttgaagaaataaaattatatgtaaaatatta .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 taatattttacatataattttatttcttcaaatcaagatgcttagtggggcgagggaatgtaattttattattatgcttatttcatttttgctttgagacaggaagtaaatgacacagttaaccattgctcacaaatcatcgatacatgaacattgctaatgatttgttttacacatgtatcaacacgaatgctgtcatatcgctcaacatgtgaaaatggtcgagaaaaaagatgagtaataaagtgaaacataataatttctccttttgttaatttaaggagaaattatccctatgagggaatatttcccccttatgggtaaagaaaaagaccaacaaaaaatgtcggtctttatcgtataattta Mask Tandem Repeat Region ================================================ taaattatacgataaagaccgacattttttgttggtctttttctttacccataagggggaaatattccctcatagggataatttctccttaaattaacaaaaggagaaattattatgtttcactttattactcatcttttttctcgaccattttcacatgttgagcgatatgacagcattcgtgttgatacatgtgtaaaacaaatcattagcaatgttcatgtatcgatgatttgtgagcaatggttaactgtgtcatttacttcctgtctcaaagcaaaaatgaaataagcataataataaaattacattccctcgccccactaagcatcttgatttgaagaaataaaattatatgtaaaatatta Find is-nt database================================================ Query_seq: AA00666:AA00667|AA00666:AA00667:hypothetical protein:cytolethal distending toxin protein C:->->:457715..458082 368 taaattatacgataaagaccgacattttttgttggtctttttctttacccataagggggaaatattccctcatagggataatttctccttaaattaacaaaaggagaaattattatgtttcactttattactcatcttttttctcgaccattttcacatgttgagcgatatgacagcattcgtgttgatacatgtgtaaaacaaatcattagcaatgttcatgtatcgatgatttgtgagcaatggttaactgtgtcatttacttcctgtctcaaagcaaaaatgaaataagcataataataaaattacattccctcgccccactaagcatcttgatttgaagaaataaaattatatgtaaaatatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA00666:AA00667|AA00666:AA00667:hypothetical protein:cytolethal distending toxin protein C:->->:457715..458082 368 taaattatacgataaagaccgacattttttgttggtctttttctttacccataagggggaaatattccctcatagggataatttctccttaaattaacaaaaggagaaattattatgtttcactttattactcatcttttttctcgaccattttcacatgttgagcgatatgacagcattcgtgttgatacatgtgtaaaacaaatcattagcaatgttcatgtatcgatgatttgtgagcaatggttaactgtgtcatttacttcctgtctcaaagcaaaaatgaaataagcataataataaaattacattccctcgccccactaagcatcttgatttgaagaaataaaattatatgtaaaatatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA00666:AA00667|AA00666:AA00667:hypothetical protein:cytolethal distending toxin protein C:->->:457715..458082 368 taaattatacgataaagaccgacattttttgttggtctttttctttacccataagggggaaatattccctcatagggataatttctccttaaattaacaaaaggagaaattattatgtttcactttattactcatcttttttctcgaccattttcacatgttgagcgatatgacagcattcgtgttgatacatgtgtaaaacaaatcattagcaatgttcatgtatcgatgatttgtgagcaatggttaactgtgtcatttacttcctgtctcaaagcaaaaatgaaataagcataataataaaattacattccctcgccccactaagcatcttgatttgaagaaataaaattatatgtaaaatatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaattatacgataaagaccgacattttttgttggtctttttctttacccataagggggaaatattccctcatagggataatttctccttaaattaacaaaaggagaaattattatgtttcactttattactcatcttttttctcgaccattttcacatgttgagcgatatgacagcattcgtgttgatacatgtgtaaaacaaatcattagcaatgttcatgtatcgatgatttgtgagcaatggttaactgtgtcatttacttcctgtctcaaagcaaaaatgaaataagcataataataaaattacattccctcgccccactaagcatcttgatttgaagaaataaaattatatgtaaaatatta Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 109 End: 288 ............................................................................................................ M I M F H F I T H L F S R P F S H V E R Y D S I R V D T C V K Q I I S N V H V S M I C E Q W L T V S F T S C L K A K M K ................................................................................ Protein_Len: 32 Strand: + Start: 243 End: 338 .................................................................................................................................................................................................................................................. M V N C V I Y F L S Q S K N E I S I I I K L H S L A P L S I L I .............................. Protein_Len: 30 Strand: - Start: 275 End: 364 .................................................................................................................................................................................................................................................................................. L L F S I L M I I F N C E R A G S L M K I Q L F L I I H L M .... taaattatacgataaagaccgacattttttgttggtctttttctttacccataagggggaaatattccctcatagggataatttctccttaaattaacaaaaggagaaattattatgtttcactttattactcatcttttttctcgaccattttcacatgttgagcgatatgacagcattcgtgttgatacatgtgtaaaacaaatcattagcaatgttcatgtatcgatgatttgtgagcaatggttaactgtgtcatttacttcctgtctcaaagcaaaaatgaaataagcataataataaaattacattccctcgccccactaagcatcttgatttgaagaaataaaattatatgtaaaatatta 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================================================ taaattatacgataaagaccgacattttttgttggtctttttctttacccataagggggaaatattccctcatagggataatttctccttaaattaacaaaaggagaaattattatgtttcactttattactcatcttttttctcgaccattttcacatgttgagcgatatgacagcattcgtgttgatacatgtgtaaaacaaatcattagcaatgttcatgtatcgatgatttgtgagcaatggttaactgtgtcatttacttcctgtctcaaagcaaaaatgaaataagcataataataaaattacattccctcgccccactaagcatcttgatttgaagaaataaaattatatgtaaaatatta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 64 HP_score: -5.4 Tail_Score: -4.04752 Start: 17 End: 37 Full_Region: atgggtaaagaaaaa gaccaaca aaaaa tgtcggtc tttatcgtataattt ................gaccaacaaaaaatgtcggtc........................................................................................................................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 74 HP_score: -7.3 Tail_Score: -4.07975 Start: 45 End: 81 Full_Region: TGTTGGTCTTTTTCT TTACCCATAAGGGGGAA ATA TTCCCTCATAGGGATAA TTTCTCCTTAAATTA ............................................TTACCCATAAGGGGGAAATATTCCCTCATAGGGATAA............................................................................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 81 HP_score: -9.9 Tail_Score: -3.17075 Start: 56 End: 88 Full_Region: TTCTTTACCCATAAG GGGGAAATATTCCCT CAT AGGGATAATTTCTCC TTAAATTAACAAAAG .......................................................GGGGAAATATTCCCTCATAGGGATAATTTCTCC........................................................................................................................................................................................................................................................................................ TransTerm Strand: + Conf: 69 HP_score: -7.0 Tail_Score: -3.87979 Start: 79 End: 112 Full_Region: ATTCCCTCATAGGGA TAATTTCTCCTT AAATTAACAA AAGGAGAAATTA TTATGTTTCACTTTA ..............................................................................TAATTTCTCCTTAAATTAACAAAAGGAGAAATTA................................................................................................................................................................................................................................................................ Find igs database================================================ Query_seq: AA00666:AA00667|AA00666:AA00667:hypothetical protein:cytolethal distending toxin protein C:->->:457715..458082 368 taaattatacgataaagaccgacattttttgttggtctttttctttacccataagggggaaatattccctcatagggataatttctccttaaattaacaaaaggagaaattattatgtttcactttattactcatcttttttctcgaccattttcacatgttgagcgatatgacagcattcgtgttgatacatgtgtaaaacaaatcattagcaatgttcatgtatcgatgatttgtgagcaatggttaactgtgtcatttacttcctgtctcaaagcaaaaatgaaataagcataataataaaattacattccctcgccccactaagcatcttgatttgaagaaataaaattatatgtaaaatatta Intra-Species Hit: Count: 1 Min: 1 Max: 368 Len: 368 Subject: aact_AA00666_AA00667|hypothetical protein:cytolethal distending toxin protein C|POSITIVE:POSITIVE|[457715,458082]|368 HSP 1 e-value: 0.0 bit: 729.0 Len: 368 Query Start:1 Query End:368 Subject Strand: POSITIVE Subject Start: 1 Subject End: 368 taaattatacgataaagaccgacattttttgttggtctttttctttacccataagggggaaatattccctcatagggataatttctccttaaattaacaaaaggagaaattattatgtttcactttattactcatcttttttctcgaccattttcacatgttgagcgatatgacagcattcgtgttgatacatgtgtaaaacaaatcattagcaatgttcatgtatcgatgatttgtgagcaatggttaactgtgtcatttacttcctgtctcaaagcaaaaatgaaataagcataataataaaattacattccctcgccccactaagcatcttgatttgaagaaataaaattatatgtaaaatatta taaattatacgataaagaccgacattttttgttggtctttttctttacccataagggggaaatattccctcatagggataatttctccttaaattaacaaaaggagaaattattatgtttcactttattactcatcttttttctcgaccattttcacatgttgagcgatatgacagcattcgtgttgatacatgtgtaaaacaaatcattagcaatgttcatgtatcgatgatttgtgagcaatggttaactgtgtcatttacttcctgtctcaaagcaaaaatgaaataagcataataataaaattacattccctcgccccactaagcatcttgatttgaagaaataaaattatatgtaaaatatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAUUAUACGAUAAAGACCGACAUUUUUUGUUGGUCUUUUUCUUUACCCAUAAGGGGGAAAUAUUCCCUCAUAGGGAUAAUUUCUCCUUAAAUUAACAAAAGGAGAAAUUAUUAUGUUUCACUUUAUUACUCAUCUUUUUUCUCGACCAUUUUCACAUGUUGAGCGAUAUGACAGCAUUCGUGUUGAUACAUGUGUAAAACAAAUCAUUAGCAAUGUUCAUGUAUCGAUGAUUUGUGAGCAAUGGUUAACUGUGUCAUUUACUUCCUGUCUCAAAGCAAAAAUGAAAUAAGCAUAAUAAUAAAAUUACAUUCCCUCGCCCCACUAAGCAUCUUGAUUUGAAGAAAUAAAAUUAUAUGUAAAAUAUUA ..........((.(((((((((((.....))))))))))).))...........(((((((....((((.....))))..((((((((((..........))))))))))((((((((((...((((((................(((((((..(((((((....((((((((......))))))))..)))))))....((((((((((.(((.......)))...))))))))))....)))))))...(((.......((.....))......)))..))))))..))))))))))...........)))))))..........((((..((((((.........)))))).))))......... (-88.02) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUAUUUUACAUAUAAUUUUAUUUCUUCAAAUCAAGAUGCUUAGUGGGGCGAGGGAAUGUAAUUUUAUUAUUAUGCUUAUUUCAUUUUUGCUUUGAGACAGGAAGUAAAUGACACAGUUAACCAUUGCUCACAAAUCAUCGAUACAUGAACAUUGCUAAUGAUUUGUUUUACACAUGUAUCAACACGAAUGCUGUCAUAUCGCUCAACAUGUGAAAAUGGUCGAGAAAAAAGAUGAGUAAUAAAGUGAAACAUAAUAAUUUCUCCUUUUGUUAAUUUAAGGAGAAAUUAUCCCUAUGAGGGAAUAUUUCCCCCUUAUGGGUAAAGAAAAAGACCAACAAAAAAUGUCGGUCUUUAUCGUAUAAUUUA .....((((((....((((.(((((((((...(((..(....)..)))...))))))))).))))((((((((...(((.((((...((((((((.......))))))))........(..((((((..(((((.......((((((((((((...(....)...)))).....))))))))....((((((....))).))).......))))).))))))..))))).)))...)))))))).))))))....(((((((((((((..........))))))))))))).((((((((((.........))))))))))....((.(((((((.(((.....))).))))))).)).......... (-90.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 319 260 215 102 54 aact:AA01207|5end_hypothetical_protein_826288..826518_POSITIVE 285 60 14 157 115 aact:AA00661|5end_outer_membrane_protein_453402..453632_POSITIVE 275 190 153 215 180 aact:AA02626|5end_conserved_hypothetical_protein_1828331..1828561_POSITIVE 269 217 176 79 33 aact:AA01913|5end_GMP_synthase_1288535..1288765_POSITIVE 268 190 144 51 10 aact:AA00387|5end_transcription_regulatory_protein_262305..262535_POSITIVE 264 60 18 147 101 aact:AA01837|5end_transcriptional_regulatory_protein_1235450..1235680_POSITIVE 263 187 141 205 161 aact:AA00576|5end_conserved_hypothetical_protein_(possible_translation_factor)_394020..394250_POSITIVE 262 198 153 137 95 aact:AA02961|5end_pyrroline-5-carboxylate_reductase_2070785..2071015_POSITIVE 259 250 203 137 85 aact:AA02658|5end_conserved_hypothetical_protein_1852260..1852490_POSITIVE 259 270 223 58 12 aact:AA01743|5end_lysyl-tRNA_synthetase_1177808..1178038_POSITIVE 259 64 26 53 12 aact:AA00199|5end_hypothetical_protein_138575..138805_POSITIVE 258 180 131 137 72 aact:AA02663|5end_DNA_ligase_1853564..1853794_POSITIVE 257 268 224 103 61 aact:AA00478|5end_mannose-specific_phosphotransferase_element_332492..332722_POSITIVE 252 89 48 166 122 aact:AA00702|5end_conserved_hypothetical_protein_481660..481890_POSITIVE 251 193 162 49 16 aact:AA02973|5end_tyrosine-specific_transport_protein_2077707..2077937_POSITIVE 249 80 35 173 128 aact:AA02788|5end_possible_ABC-related_substrate_binding_protein_1955402..1955632_POSITIVE 249 257 211 91 39 aact:AA00438|5end_probable_chromosomal_partitioning_protein_(ParB-like_family)_302991..303221_POSITIVE 249 285 243 133 87 aact:AA00237|5end_hypothetical_protein_170934..171164_POSITIVE 248 197 159 179 137 aact:AA01413|5end_conserved_hypothetical_protein_951773..952003_POSITIVE 248 331 313 177 157 aact:AA01335|5end_primosomal_protein_N'_901993..902223_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 321 90 54 37 1 aact:AA00666|3end_hypothetical_protein_457654..457804_POSITIVE 319 260 215 61 13 aact:AA01206|3end_phosphoribosylformylglycinamidine_cyclo-ligase_826327..826477_POSITIVE 267 60 12 127 74 aact:AA02167|3end_hypothetical_protein_1483474..1483624_POSITIVE 262 60 11 132 80 aact:AA00199|3end_hypothetical_protein_138744..138894_POSITIVE 259 250 203 137 85 aact:AA02657|3end_conserved_hypothetical_protein_1852340..1852490_POSITIVE 258 180 131 89 24 aact:AA02662|3end_hypothetical_protein_1853596..1853746_POSITIVE 251 58 17 143 110 aact:AA02184|3end_anthranilate_isomerase;_indole-3-glycerol_phosphate_synthase;_phosphoribosylanthranilate_isomerase_1492541..1492691_POSITIVE 250 64 27 41 1 aact:AA00198|3end_conserved_hypothetical_protein_(Cytosine_deaminase-related_enzyme)_138643..138793_POSITIVE 249 80 35 86 41 aact:AA02787|3end_ribose_ABC_transporter,_sugar_binding_protein_1955395..1955545_POSITIVE 249 257 211 95 43 aact:AA00437|3end_conserved_hypothetical_protein;_possible_parB-like_nuclease_303075..303225_POSITIVE 249 285 243 140 94 aact:AA00236|3end_anaerobic_ribonucleoside-triphosphate_reductase_171021..171171_POSITIVE 248 197 159 143 101 aact:AA01411|3end_stationary-phase_survival_protein_951817..951967_POSITIVE 242 268 225 55 14 aact:AA01711|3end_conserved_hypothetical_protein_1160502..1160652_POSITIVE 242 280 231 72 13 aact:AA01486|3end_ATP_synthase_F1,_subunit_alpha_1000178..1000328_POSITIVE 240 345 308 49 10 aact:AA02560|3end_integral_membrane_protein_1783630..1783780_POSITIVE 237 200 154 65 16 aact:AA01896|3end_hypothetical_protein_1281163..1281313_POSITIVE 237 197 158 75 24 aact:AA00029|3end_type_III_restriction-modification_system:_methylase_24943..25093_POSITIVE 236 167 123 151 94 aact:AA01883|3end_recycling_protein;_permease_1271187..1271337_POSITIVE 233 188 142 69 19 aact:AA01182|3end_3-oxoacyl-(acyl-carrier-protein)_synthase_810510..810660_POSITIVE 233 268 221 88 20 aact:AA00735|3end_citrate_lyase,_beta_chain_503626..503776_POSITIVE