Origin IGS: tgatgtggactccatcatgaagatgtgcgcaacgatctccgccttcatttttatcacaaagccctttccttgccgaaaaaggggctttcgttttgccgcctccgtttaatttttaatccgataaatacttttacaagacaacaataattccatatctttgcgggaaatattggtggtatgcaagacgccaccgcgaaaatcagcctgttgacagccttccgatggctttgtgcaagaagaagggacatcgggacaagaaagaatagatagataaataaacaagaagaacg .........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 cgttcttcttgtttatttatctatctattctttcttgtcccgatgtcccttcttcttgcacaaagccatcggaaggctgtcaacaggctgattttcgcggtggcgtcttgcataccaccaatatttcccgcaaagatatggaattattgttgtcttgtaaaagtatttatcggattaaaaattaaacggaggcggcaaaacgaaagcccctttttcggcaaggaaagggctttgtgataaaaatgaaggcggagatcgttgcgcacatcttcatgatggagtccacatca Mask Tandem Repeat Region ================================================ tgatgtggactccatcatgaagatgtgcgcaacgatctccgccttcatttttatcacaaagccctttccttgccgaaaaaggggctttcgttttgccgcctccgtttaatttttaatccgataaatacttttacaagacaacaataattccatatctttgcgggaaatattggtggtatgcaagacgccaccgcgaaaatcagcctgttgacagccttccgatggctttgtgcaagaagaagggacatcgggacaagaaagaatagatagataaataaacaagaagaacg Find is-nt database================================================ Query_seq: TF2179:TF2180|TF2179:TF2180:integral membrane protein, MarC family:phosphoribosylamine--glycine ligase:->->:2352430..2352719 290 tgatgtggactccatcatgaagatgtgcgcaacgatctccgccttcatttttatcacaaagccctttccttgccgaaaaaggggctttcgttttgccgcctccgtttaatttttaatccgataaatacttttacaagacaacaataattccatatctttgcgggaaatattggtggtatgcaagacgccaccgcgaaaatcagcctgttgacagccttccgatggctttgtgcaagaagaagggacatcgggacaagaaagaatagatagataaataaacaagaagaacg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2179:TF2180|TF2179:TF2180:integral membrane protein, MarC family:phosphoribosylamine--glycine ligase:->->:2352430..2352719 290 tgatgtggactccatcatgaagatgtgcgcaacgatctccgccttcatttttatcacaaagccctttccttgccgaaaaaggggctttcgttttgccgcctccgtttaatttttaatccgataaatacttttacaagacaacaataattccatatctttgcgggaaatattggtggtatgcaagacgccaccgcgaaaatcagcctgttgacagccttccgatggctttgtgcaagaagaagggacatcgggacaagaaagaatagatagataaataaacaagaagaacg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2179:TF2180|TF2179:TF2180:integral membrane protein, MarC family:phosphoribosylamine--glycine ligase:->->:2352430..2352719 290 tgatgtggactccatcatgaagatgtgcgcaacgatctccgccttcatttttatcacaaagccctttccttgccgaaaaaggggctttcgttttgccgcctccgtttaatttttaatccgataaatacttttacaagacaacaataattccatatctttgcgggaaatattggtggtatgcaagacgccaccgcgaaaatcagcctgttgacagccttccgatggctttgtgcaagaagaagggacatcgggacaagaaagaatagatagataaataaacaagaagaacg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgatgtggactccatcatgaagatgtgcgcaacgatctccgccttcatttttatcacaaagccctttccttgccgaaaaaggggctttcgttttgccgcctccgtttaatttttaatccgataaatacttttacaagacaacaataattccatatctttgcgggaaatattggtggtatgcaagacgccaccgcgaaaatcagcctgttgacagccttccgatggctttgtgcaagaagaagggacatcgggacaagaaagaatagatagataaataaacaagaagaacg Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 5 End: 106 .... M D S I M K M C A T I S A F I F I T K P F P C R K R G F R F A A S V ........................................................................................................................................................................................ Protein_Len: 40 Strand: + Start: 25 End: 144 ........................ M R N D L R L H F Y H K A L S L P K K G L S F C R L R L I F N P I N T F T R Q Q .................................................................................................................................................. Protein_Len: 40 Strand: + Start: 144 End: 263 ............................................................................................................................................... M I P Y L C G K Y W W Y A R R H R E N Q P V D S L P M A L C K K K G H R D K K E ........................... Protein_Len: 38 Strand: + Start: 154 End: 267 ......................................................................................................................................................... M F A G N I G G M Q D A T A K I S L L T A F R W L C A R R R D I G T R K N R ....................... Protein_Len: 58 Strand: - Start: 109 End: 282 ............................................................................................................ N K I R Y I S K C S L L L E M D K R S I N T T H L V G G R F D A Q Q C G E S P K T C S S P V D P C S L I S L Y I F M ........ Protein_Len: 60 Strand: - Start: 57 End: 272 ........................................................ Q R R R K I K L G I F V K V L C C Y N W I K A P F I P P I C S A V A F I L R N V A K R H S Q A L L L S M P V L F F L Y M .................. tgatgtggactccatcatgaagatgtgcgcaacgatctccgccttcatttttatcacaaagccctttccttgccgaaaaaggggctttcgttttgccgcctccgtttaatttttaatccgataaatacttttacaagacaacaataattccatatctttgcgggaaatattggtggtatgcaagacgccaccgcgaaaatcagcctgttgacagccttccgatggctttgtgcaagaagaagggacatcgggacaagaaagaatagatagataaataaacaagaagaacg 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================================================ tgatgtggactccatcatgaagatgtgcgcaacgatctccgccttcatttttatcacaaagccctttccttgccgaaaaaggggctttcgttttgccgcctccgtttaatttttaatccgataaatacttttacaagacaacaataattccatatctttgcgggaaatattggtggtatgcaagacgccaccgcgaaaatcagcctgttgacagccttccgatggctttgtgcaagaagaagggacatcgggacaagaaagaatagatagataaataaacaagaagaacg Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 55 HP_score: -2.3 Tail_Score: -4.09864 Start: 74 End: 90 Full_Region: AAGCCCTTTCCTTGC CGAAA AAGGGGC TTTCG TTTTGCCGCCTCCGT .........................................................................CGAAAAAGGGGCTTTCG........................................................................................................................................................................................................ Find igs database================================================ Query_seq: TF2179:TF2180|TF2179:TF2180:integral membrane protein, MarC family:phosphoribosylamine--glycine ligase:->->:2352430..2352719 290 tgatgtggactccatcatgaagatgtgcgcaacgatctccgccttcatttttatcacaaagccctttccttgccgaaaaaggggctttcgttttgccgcctccgtttaatttttaatccgataaatacttttacaagacaacaataattccatatctttgcgggaaatattggtggtatgcaagacgccaccgcgaaaatcagcctgttgacagccttccgatggctttgtgcaagaagaagggacatcgggacaagaaagaatagatagataaataaacaagaagaacg Intra-Species Hit: Count: 1 Min: 1 Max: 290 Len: 290 Subject: tfor_TF2179_TF2180|integral membrane protein, MarC family:phosphoribosylamine--glycine ligase|POSITIVE:POSITIVE|[2352430,2352719]|290 HSP 1 e-value: 1.0E-163 bit: 575.0 Len: 290 Query Start:1 Query End:290 Subject Strand: POSITIVE Subject Start: 1 Subject End: 290 tgatgtggactccatcatgaagatgtgcgcaacgatctccgccttcatttttatcacaaagccctttccttgccgaaaaaggggctttcgttttgccgcctccgtttaatttttaatccgataaatacttttacaagacaacaataattccatatctttgcgggaaatattggtggtatgcaagacgccaccgcgaaaatcagcctgttgacagccttccgatggctttgtgcaagaagaagggacatcgggacaagaaagaatagatagataaataaacaagaagaacg tgatgtggactccatcatgaagatgtgcgcaacgatctccgccttcatttttatcacaaagccctttccttgccgaaaaaggggctttcgttttgccgcctccgtttaatttttaatccgataaatacttttacaagacaacaataattccatatctttgcgggaaatattggtggtatgcaagacgccaccgcgaaaatcagcctgttgacagccttccgatggctttgtgcaagaagaagggacatcgggacaagaaagaatagatagataaataaacaagaagaacg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUGUGGACUCCAUCAUGAAGAUGUGCGCAACGAUCUCCGCCUUCAUUUUUAUCACAAAGCCCUUUCCUUGCCGAAAAAGGGGCUUUCGUUUUGCCGCCUCCGUUUAAUUUUUAAUCCGAUAAAUACUUUUACAAGACAACAAUAAUUCCAUAUCUUUGCGGGAAAUAUUGGUGGUAUGCAAGACGCCACCGCGAAAAUCAGCCUGUUGACAGCCUUCCGAUGGCUUUGUGCAAGAAGAAGGGACAUCGGGACAAGAAAGAAUAGAUAGAUAAAUAAACAAGAAGAACG ....((((........(((((((((.(((..........)))...))))))))).((((((((((((...........)))))))))).))....)))).((..((((.(((((..((((((.....(((((.(....((.(((((.((((...........)))).))))).))...((((.((.((((.((.((.....((.(((....))).)))))).)))).)).)))).).)))))....)))))).....))))).))))..))................... (-60.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGUUCUUCUUGUUUAUUUAUCUAUCUAUUCUUUCUUGUCCCGAUGUCCCUUCUUCUUGCACAAAGCCAUCGGAAGGCUGUCAACAGGCUGAUUUUCGCGGUGGCGUCUUGCAUACCACCAAUAUUUCCCGCAAAGAUAUGGAAUUAUUGUUGUCUUGUAAAAGUAUUUAUCGGAUUAAAAAUUAAACGGAGGCGGCAAAACGAAAGCCCCUUUUUCGGCAAGGAAAGGGCUUUGUGAUAAAAAUGAAGGCGGAGAUCGUUGCGCACAUCUUCAUGAUGGAGUCCACAUCA ...................((((((....((((((((((.(((.(.(((((.(((((((.....(((((((((((((.(((....))).).))))).)))))))...(((((...((.(((((.((((...........)))).))))).))...)))))...........................(((((.(((.........))))))))....))))))))))))).))).)))))....))))).((((((.((.....))))))))..)))))).......... (-72.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 505 220 174 47 10 tfor:TF2950|5end_chloromuconate_cycloisomerase_3157399..3157629_POSITIVE 393 219 172 66 14 tfor:TF1935|5end_ATP-dependent_RNA_helicase,_DEAD/DEAH-related_helicase_2082002..2082232_POSITIVE 384 228 187 133 82 tfor:TF2047|5end_hypothetical_protein_2210057..2210287_POSITIVE 381 120 71 172 121 tfor:TF0085|5end_ABC_transporter,_ATP-binding_protein_91517..91747_POSITIVE 376 107 61 54 10 tfor:TF2876|5end_cytosine_deaminase_3065144..3065374_POSITIVE 374 216 172 69 27 tfor:TF2013|5end_polysaccharide_deacetylase_2168650..2168880_POSITIVE 370 248 201 61 17 tfor:TF1484|5end_penicillin_binding_protein_1579559..1579789_POSITIVE 368 245 202 159 111 tfor:TF3108|5end_glutamine-hydrolyzing_carbamoyl-phosphate_synthase,_large_subunit_3338732..3338962_POSITIVE 363 237 192 63 17 tfor:TF0789|5end_preprotein_translocase,_secDF_family_841293..841523_POSITIVE 356 219 172 76 31 tfor:TF0218|5end_translation_initiation_factor_3_(IF-3)_243182..243412_POSITIVE 355 250 203 51 1 tfor:TF2267|5end_lysozyme-related_protein_2434869..2435099_POSITIVE 355 107 61 226 167 tfor:TF1929|5end_conserved_hypothetical_protein_2076049..2076279_POSITIVE 354 210 161 221 163 tfor:TF2381|5end_muramidase/hemagglutinin_2545757..2545987_POSITIVE 351 230 186 109 56 tfor:TF2246|5end_hypothetical_protein_2421288..2421518_POSITIVE 351 220 180 59 18 tfor:TF1548|5end_thiophene_and_furan_oxidation_protein_1652501..1652731_POSITIVE 351 196 159 81 49 tfor:TF1291|5end_response_regulator_(fimR__protein)_1371959..1372189_POSITIVE 348 105 61 63 4 tfor:TF2576|5end_translation_initiation_factor_IF-1_2745912..2746142_POSITIVE 348 106 64 231 192 tfor:TF0497|5end_conserved_hypothetical_protein_524058..524288_POSITIVE 346 255 213 170 130 tfor:TF0135|5end_hypothetical_protein_146322..146552_POSITIVE 341 233 191 224 177 tfor:TF2812|5end_hypothetical_protein_3002726..3002956_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 505 220 174 47 10 tfor:TF2949|3end_dihydroxynaphthoate_synthase_(naphthoate_synthase)_3157479..3157629_POSITIVE 384 228 187 148 97 tfor:TF2046|3end_polyribonucleotide_nucleotidyltransferase_2210152..2210302_POSITIVE 376 107 61 54 10 tfor:TF2874|3end_conserved_hypothetical_protein_3065224..3065374_POSITIVE 374 216 172 59 17 tfor:TF2012|3end_conserved_hypothetical_protein_2168720..2168870_POSITIVE 371 46 3 103 44 tfor:TF0001|3end_hypothetical_protein_158..308_POSITIVE 368 245 202 83 35 tfor:TF3107|3end_hypothetical_protein_3338736..3338886_POSITIVE 363 237 192 60 14 tfor:TF0788|3end_protein-export_membrane_protein_841370..841520_POSITIVE 355 250 203 51 1 tfor:TF2266|3end_transfer_region-related_protein,_TraQ_2434949..2435099_POSITIVE 353 250 202 108 63 tfor:TF0880|3end_conserved_hypothetical_protein_934371..934521_POSITIVE 350 217 173 117 49 tfor:TF2745|3end_hypothetical_protein_2927947..2928097_POSITIVE 342 229 182 63 6 tfor:TF2646|3end_conserved_hypothetical_protein_2816697..2816847_POSITIVE 338 210 167 49 1 tfor:TF1255|3end_conserved_hypothetical_protein_1338151..1338301_POSITIVE 337 42 7 123 80 tfor:TF1291|3end_response_regulator_(fimR__protein)_1372647..1372797_POSITIVE 333 217 183 68 40 tfor:TF3067|3end_conserved_hypothetical_protein_3292877..3293027_POSITIVE 331 230 184 126 68 tfor:TF1066|3end_hypothetical_protein_1136858..1137008_POSITIVE 325 220 173 92 24 tfor:TF3153|3end_conserved_hypothetical_protein_3389324..3389474_POSITIVE 325 105 61 67 23 tfor:TF1683|3end_conserved_hypothetical_protein_1796511..1796661_POSITIVE 324 63 21 67 21 tfor:TF2134|3end_conserved_hypothetical_protein_2310187..2310337_POSITIVE 324 226 182 140 81 tfor:TF0405|3end_conserved_hypothetical_protein_424308..424458_POSITIVE 323 229 186 137 89 tfor:TF2042|3end_sugar_phosphate_isomerase,_polysialic_acid_capsule_expression_protein_2202356..2202506_POSITIVE