Origin IGS: tatatattgtttttatttttttcaagcatgcagtaacagaatgaacgatgatcgctacatagtgcgacaggttcagaaaattactattggctgtaaaaatacaacgaataaatgacataacatggtcatcgccgaaaaaataaaacggcgcacatttgttttttgaaaaaaaaagatttgtttctcttttttgcagtcgatcgaaaaagaaaacgaacgtgcaaaagaaatca .........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 tgatttcttttgcacgttcgttttctttttcgatcgactgcaaaaaagagaaacaaatctttttttttcaaaaaacaaatgtgcgccgttttattttttcggcgatgaccatgttatgtcatttattcgttgtatttttacagccaatagtaattttctgaacctgtcgcactatgtagcgatcatcgttcattctgttactgcatgcttgaaaaaaataaaaacaatatata Mask Tandem Repeat Region ================================================ tatatattgtttttatttttttcaagcatgcagtaacagaatgaacgatgatcgctacatagtgcgacaggttcagaaaattactattggctgtaaaaatacaacgaataaatgacataacatggtcatcgccgaaaaaataaaacggcgcacatttgttttttgaaaaaaaaagatttgtttctcttttttgcagtcgatcgaaaaagaaaacgaacgtgcaaaagaaatca Find is-nt database================================================ Query_seq: TF2742:TF2743|TF2742:TF2743:single-strand DNA-specific exonuclease:conserved hypothetical protein:->->:2925664..2925896 233 tatatattgtttttatttttttcaagcatgcagtaacagaatgaacgatgatcgctacatagtgcgacaggttcagaaaattactattggctgtaaaaatacaacgaataaatgacataacatggtcatcgccgaaaaaataaaacggcgcacatttgttttttgaaaaaaaaagatttgtttctcttttttgcagtcgatcgaaaaagaaaacgaacgtgcaaaagaaatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2742:TF2743|TF2742:TF2743:single-strand DNA-specific exonuclease:conserved hypothetical protein:->->:2925664..2925896 233 tatatattgtttttatttttttcaagcatgcagtaacagaatgaacgatgatcgctacatagtgcgacaggttcagaaaattactattggctgtaaaaatacaacgaataaatgacataacatggtcatcgccgaaaaaataaaacggcgcacatttgttttttgaaaaaaaaagatttgtttctcttttttgcagtcgatcgaaaaagaaaacgaacgtgcaaaagaaatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2742:TF2743|TF2742:TF2743:single-strand DNA-specific exonuclease:conserved hypothetical protein:->->:2925664..2925896 233 tatatattgtttttatttttttcaagcatgcagtaacagaatgaacgatgatcgctacatagtgcgacaggttcagaaaattactattggctgtaaaaatacaacgaataaatgacataacatggtcatcgccgaaaaaataaaacggcgcacatttgttttttgaaaaaaaaagatttgtttctcttttttgcagtcgatcgaaaaagaaaacgaacgtgcaaaagaaatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tatatattgtttttatttttttcaagcatgcagtaacagaatgaacgatgatcgctacatagtgcgacaggttcagaaaattactattggctgtaaaaatacaacgaataaatgacataacatggtcatcgccgaaaaaataaaacggcgcacatttgttttttgaaaaaaaaagatttgtttctcttttttgcagtcgatcgaaaaagaaaacgaacgtgcaaaagaaatca Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: + Start: 2 End: 112 . M Y C F Y F F Q A C S N R M N D D R Y I V R Q V Q K I T I G C K N T T N K ......................................................................................................................... Protein_Len: 32 Strand: - Start: 129 End: 224 ................................................................................................................................ R R F F L V A C M Q K K F F F S K N R K K A T S R F L F R V H M ......... Protein_Len: 52 Strand: - Start: 76 End: 231 ........................................................................... F I V I P Q L F V V F L H C L M T M A S F I F R R V N T K Q F F F I Q K E K K C D I S F S F S R A F S M .. Protein_Len: 60 Strand: - Start: 2 End: 196 . K K L C A T V S H V I I A V Y H S L N L F N S N A T F I C R I F S M V H D D G F F Y F P A C K N K S F F L N T E R K Q M ..................................... tatatattgtttttatttttttcaagcatgcagtaacagaatgaacgatgatcgctacatagtgcgacaggttcagaaaattactattggctgtaaaaatacaacgaataaatgacataacatggtcatcgccgaaaaaataaaacggcgcacatttgttttttgaaaaaaaaagatttgtttctcttttttgcagtcgatcgaaaaagaaaacgaacgtgcaaaagaaatca 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================================================ tatatattgtttttatttttttcaagcatgcagtaacagaatgaacgatgatcgctacatagtgcgacaggttcagaaaattactattggctgtaaaaatacaacgaataaatgacataacatggtcatcgccgaaaaaataaaacggcgcacatttgttttttgaaaaaaaaagatttgtttctcttttttgcagtcgatcgaaaaagaaaacgaacgtgcaaaagaaatca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF2742:TF2743|TF2742:TF2743:single-strand DNA-specific exonuclease:conserved hypothetical protein:->->:2925664..2925896 233 tatatattgtttttatttttttcaagcatgcagtaacagaatgaacgatgatcgctacatagtgcgacaggttcagaaaattactattggctgtaaaaatacaacgaataaatgacataacatggtcatcgccgaaaaaataaaacggcgcacatttgttttttgaaaaaaaaagatttgtttctcttttttgcagtcgatcgaaaaagaaaacgaacgtgcaaaagaaatca Intra-Species Hit: Count: 1 Min: 23 Max: 233 Len: 211 Subject: tfor_TF2742_TF2743|single-strand DNA-specific exonuclease:conserved hypothetical protein|POSITIVE:POSITIVE|[2925664,2925896]|233 HSP 1 e-value: 1.0E-100 bit: 365.0 Len: 211 Query Start:23 Query End:233 Subject Strand: POSITIVE Subject Start: 23 Subject End: 233 ......................caagcatgcagtaacagaatgaacgatgatcgctacatagtgcgacaggttcagaaaattactattggctgtaaaaatacaacgaataaatgacataacatggtcatcgccgaaaaaataaaacggcgcacatttgttttttgnnnnnnnnngatttgtttctcttttttgcagtcgatcgaaaaagaaaacgaacgtgcaaaagaaatca ......................caagcatgcagtaacagaatgaacgatgatcgctacatagtgcgacaggttcagaaaattactattggctgtaaaaatacaacgaataaatgacataacatggtcatcgccgaaaaaataaaacggcgcacatttgttttttgaaaaaaaaagatttgtttctcttttttgcagtcgatcgaaaaagaaaacgaacgtgcaaaagaaatca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAAGCAUGCAGUAACAGAAUGAACGAUGAUCGCUACAUAGUGCGACAGGUUCAGAAAAUUACUAUUGGCUGUAAAAAUACAACGAAUAAAUGACAUAACAUGGUCAUCGCCGAAAAAAUAAAACGGCGCACAUUUGUUUUUUGAAAAAAAAAGAUUUGUUUCUCUUUUUUGCAGUCGAUCGAAAAAGAAAACGAACGUGCAAAAGAAAUCA ...(((((.(((((.....(((((..((.((((........)))))).))))).....))))).(((((((((((((...(((((((..(((((........)))))(((((...........)))))........((((((....)))))).))))))).....))))))))))))).................)))))........... (-50.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUUUCUUUUGCACGUUCGUUUUCUUUUUCGAUCGACUGCAAAAAAGAGAAACAAAUCUUUUUUUUUCAAAAAACAAAUGUGCGCCGUUUUAUUUUUUCGGCGAUGACCAUGUUAUGUCAUUUAUUCGUUGUAUUUUUACAGCCAAUAGUAAUUUUCUGAACCUGUCGCACUAUGUAGCGAUCAUCGUUCAUUCUGUUACUGCAUGCUUG ...........(((((((.(((((.....((....)).((.((((((((((......)))))))))).)).))))).)))))))((((...........)))).(((((........)))))......((((((....))))))...(((((((....(((((.((((((........)))).))..)))))....)))))))........ (-45.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 329 130 83 55 13 tfor:TF1958|5end_cytidylate_kinase_2108659..2108889_POSITIVE 325 130 83 130 88 tfor:TF2205|5end_conserved_hypothetical_protein;_possible_transcriptional_regulator_2379055..2379285_POSITIVE 319 50 10 70 27 tfor:TF2643|5end_possible_O-antigen_transporter_2811744..2811974_POSITIVE 302 138 100 89 51 tfor:TF0241|5end_UDP-N-acetyl_glucosamine_-2-epimerase_271321..271551_POSITIVE 297 145 101 77 28 tfor:TF3001|5end_transposase_3216491..3216721_POSITIVE 292 49 2 197 144 tfor:TF1068|5end_conserved_hypothetical_protein;_possible_N-acetylglucosamine_kinase_1138036..1138266_POSITIVE 291 55 17 62 17 tfor:TF2926|5end_glycine_hydroxymethyltransferase_3128070..3128300_POSITIVE 284 47 4 180 134 tfor:TF3098|5end_conserved_hypothetical_protein_3329913..3330143_POSITIVE 272 69 23 56 6 tfor:TF1624|5end_carboxyl-terminal_protease_1737252..1737482_POSITIVE 269 50 4 84 43 tfor:TF1031|5end_conserved_hypothetical_protein_1089560..1089790_POSITIVE 268 55 21 71 35 tfor:TF0014|5end_beta-glucosidase_(beta-D-glucoside_glucohydrolase),_periplasmic_7233..7463_POSITIVE 267 49 1 62 10 tfor:TF2276|5end_conserved_hypothetical_protein_2438226..2438456_POSITIVE 267 36 4 82 45 tfor:TF0783|5end_periplasmic_TonB_membrane-linking_protein_836552..836782_POSITIVE 264 126 83 97 56 tfor:TF2774|5end_2-amino-4-hydroxy-6-hydroxymethyldihydropteridine_pyrophosphokinase_2959133..2959363_POSITIVE 263 50 1 55 10 tfor:TF2834|5end_cardiolipin_synthase_3025986..3026216_POSITIVE 260 168 123 83 35 tfor:TF2042|5end_sugar_phosphate_isomerase,_polysialic_acid_capsule_expression_protein_2201647..2201877_POSITIVE 259 49 1 88 43 tfor:TF0056|5end_integrase_frangment,_C-terminal_59074..59304_POSITIVE 257 207 166 186 141 tfor:TF3146|5end_GTP-binding_protein_Obg_3381852..3382082_POSITIVE 255 129 83 160 119 tfor:TF2689|5end_hypothetical_protein_2864824..2865054_POSITIVE 255 72 31 168 130 tfor:TF2670|5end_hypothetical_protein_2842779..2843009_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 329 130 83 48 6 tfor:TF1957|3end_penicillin_tolerance_protein;_possible_isoprene_biosynthesis_related_protein_2108732..2108882_POSITIVE 325 130 83 117 75 tfor:TF2204|3end_conserved_hypothetical_protein_2379122..2379272_POSITIVE 319 50 10 73 30 tfor:TF2642|3end_acetylornithine_deacetylase_2811827..2811977_POSITIVE 302 138 100 95 57 tfor:TF0240|3end_conserved_hypothetical_protein;_possible_gycosyltransferase_I_family_protein_271407..271557_POSITIVE 284 47 4 148 102 tfor:TF3097|3end_conserved_hypothetical_protein_3329961..3330111_POSITIVE 276 52 20 125 85 tfor:TF1049|3end_cobyrinic_acid_a,c-diamide_synthase_1111539..1111689_POSITIVE 272 69 23 56 6 tfor:TF1623|3end_5-formyltetrahydrofolate_cyclo-ligase_1737332..1737482_POSITIVE 268 55 21 43 7 tfor:TF0013|3end_conserved_hypothetical_protein;_possible_TPR-repeat-containing_protein_7285..7435_POSITIVE 267 49 1 56 4 tfor:TF2275|3end_conserved_hypothetical_protein_2438300..2438450_POSITIVE 267 36 4 42 5 tfor:TF0782|3end_ThiJ/PfpI_family_protein_836592..836742_POSITIVE 264 126 83 127 86 tfor:TF2773|3end_S-adenosylmethionine_tRNA_ribosyltransferase_2959243..2959393_POSITIVE 263 49 5 146 97 tfor:TF0531|3end_hypothetical_protein_557469..557619_POSITIVE 257 207 166 76 31 tfor:TF3145|3end_conserved_hypothetical_protein;_possible_GTP_cyclohydrolase_I_family_3381822..3381972_POSITIVE 255 72 31 42 4 tfor:TF2668|3end_hypothetical_protein_2842733..2842883_POSITIVE 255 54 17 48 3 tfor:TF1490|3end_hypothetical_protein_1590782..1590932_POSITIVE 252 49 1 136 68 tfor:TF2336|3end_conserved_hypothetical_protein_2498159..2498309_POSITIVE 251 200 155 72 30 tfor:TF2335|3end_conserved_hypothetical_protein_2496177..2496327_POSITIVE 251 50 4 71 35 tfor:TF0731|3end_conserved_hypothetical_protein_784796..784946_POSITIVE 251 47 10 132 83 tfor:TF0543|3end_glycine_cleavage_system_p-protein_575180..575330_POSITIVE 250 49 16 69 26 tfor:TF2628|3end_conserved_hypothetical_protein_2801376..2801526_POSITIVE