Origin IGS: agagctatgcaagaaaacgacctcagaataccgtgttattgcctattgaaggaggtatcgaaaagccattatcctttaatcgcacataaaaaaaacaacgaggtggaatgatttttatcaggtttgggcgaaaacatctgcaaaagacaataagatgaccaacaaatggcaaatccctgaagagaatctttggaatatcaaaaaaaatcatgaatattgcagctgaatatgcatattgcgatcaacaaaccgcatgcttacccagaatatcaatcaaatgaaatagattcacataggaattacaatcaataatatttgaagctattaatactacaaatagccttg .........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 caaggctatttgtagtattaatagcttcaaatattattgattgtaattcctatgtgaatctatttcatttgattgatattctgggtaagcatgcggtttgttgatcgcaatatgcatattcagctgcaatattcatgattttttttgatattccaaagattctcttcagggatttgccatttgttggtcatcttattgtcttttgcagatgttttcgcccaaacctgataaaaatcattccacctcgttgttttttttatgtgcgattaaaggataatggcttttcgatacctccttcaataggcaataacacggtattctgaggtcgttttcttgcatagctct Mask Tandem Repeat Region ================================================ agagctatgcaagaaaacgacctcagaataccgtgttattgcctattgaaggaggtatcgaaaagccattatcctttaatcgcacataaaaaaaacaacgaggtggaatgatttttatcaggtttgggcgaaaacatctgcaaaagacaataagatgaccaacaaatggcaaatccctgaagagaatctttggaatatcaaaaaaaatcatgaatattgcagctgaatatgcatattgcgatcaacaaaccgcatgcttacccagaatatcaatcaaatgaaatagattcacataggaattacaatcaataatatttgaagctattaatactacaaatagccttg Find is-nt database================================================ Query_seq: PG1148:PG1149|PG1148:PG1149:hypothetical protein:glycosyl transferase, group 1 family protein:->->:1231437..1231781 345 agagctatgcaagaaaacgacctcagaataccgtgttattgcctattgaaggaggtatcgaaaagccattatcctttaatcgcacataaaaaaaacaacgaggtggaatgatttttatcaggtttgggcgaaaacatctgcaaaagacaataagatgaccaacaaatggcaaatccctgaagagaatctttggaatatcaaaaaaaatcatgaatattgcagctgaatatgcatattgcgatcaacaaaccgcatgcttacccagaatatcaatcaaatgaaatagattcacataggaattacaatcaataatatttgaagctattaatactacaaatagccttg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1148:PG1149|PG1148:PG1149:hypothetical protein:glycosyl transferase, group 1 family protein:->->:1231437..1231781 345 agagctatgcaagaaaacgacctcagaataccgtgttattgcctattgaaggaggtatcgaaaagccattatcctttaatcgcacataaaaaaaacaacgaggtggaatgatttttatcaggtttgggcgaaaacatctgcaaaagacaataagatgaccaacaaatggcaaatccctgaagagaatctttggaatatcaaaaaaaatcatgaatattgcagctgaatatgcatattgcgatcaacaaaccgcatgcttacccagaatatcaatcaaatgaaatagattcacataggaattacaatcaataatatttgaagctattaatactacaaatagccttg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1148:PG1149|PG1148:PG1149:hypothetical protein:glycosyl transferase, group 1 family protein:->->:1231437..1231781 345 agagctatgcaagaaaacgacctcagaataccgtgttattgcctattgaaggaggtatcgaaaagccattatcctttaatcgcacataaaaaaaacaacgaggtggaatgatttttatcaggtttgggcgaaaacatctgcaaaagacaataagatgaccaacaaatggcaaatccctgaagagaatctttggaatatcaaaaaaaatcatgaatattgcagctgaatatgcatattgcgatcaacaaaccgcatgcttacccagaatatcaatcaaatgaaatagattcacataggaattacaatcaataatatttgaagctattaatactacaaatagccttg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agagctatgcaagaaaacgacctcagaataccgtgttattgcctattgaaggaggtatcgaaaagccattatcctttaatcgcacataaaaaaaacaacgaggtggaatgatttttatcaggtttgggcgaaaacatctgcaaaagacaataagatgaccaacaaatggcaaatccctgaagagaatctttggaatatcaaaaaaaatcatgaatattgcagctgaatatgcatattgcgatcaacaaaccgcatgcttacccagaatatcaatcaaatgaaatagattcacataggaattacaatcaataatatttgaagctattaatactacaaatagccttg Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 7 End: 108 ...... M Q E N D L R I P C Y C L L K E V S K S H Y P L I A H K K N N E V E ............................................................................................................................................................................................................................................. Protein_Len: 46 Strand: + Start: 86 End: 223 ..................................................................................... M K K T T R W N D F Y Q V W A K T S A K D N K M T N K W Q I P E E N L W N I K K N H E Y C S .......................................................................................................................... Protein_Len: 34 Strand: + Start: 177 End: 278 ................................................................................................................................................................................ M K R I F G I S K K I M N I A A E Y A Y C D Q Q T A C L P R I S I K ................................................................... Protein_Len: 32 Strand: + Start: 214 End: 309 ..................................................................................................................................................................................................................... M L Q L N M H I A I N K P H A Y P E Y Q S N E I D S H R N Y N Q .................................... Protein_Len: 32 Strand: - Start: 72 End: 167 ....................................................................... G K I A C L F F L S T S H N K D P K P S F M Q L L C Y S S W C M .................................................................................................................................................................................. Protein_Len: 60 Strand: - Start: 26 End: 217 ......................... N G I S P P I S F G N D K L R V Y F F C R P P I I K I L N P R F C R C F V I L H G V F P L D R F L I K P I D F F I M F M ................................................................................................................................ agagctatgcaagaaaacgacctcagaataccgtgttattgcctattgaaggaggtatcgaaaagccattatcctttaatcgcacataaaaaaaacaacgaggtggaatgatttttatcaggtttgggcgaaaacatctgcaaaagacaataagatgaccaacaaatggcaaatccctgaagagaatctttggaatatcaaaaaaaatcatgaatattgcagctgaatatgcatattgcgatcaacaaaccgcatgcttacccagaatatcaatcaaatgaaatagattcacataggaattacaatcaataatatttgaagctattaatactacaaatagccttg 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================================================ agagctatgcaagaaaacgacctcagaataccgtgttattgcctattgaaggaggtatcgaaaagccattatcctttaatcgcacataaaaaaaacaacgaggtggaatgatttttatcaggtttgggcgaaaacatctgcaaaagacaataagatgaccaacaaatggcaaatccctgaagagaatctttggaatatcaaaaaaaatcatgaatattgcagctgaatatgcatattgcgatcaacaaaccgcatgcttacccagaatatcaatcaaatgaaatagattcacataggaattacaatcaataatatttgaagctattaatactacaaatagccttg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG1148:PG1149|PG1148:PG1149:hypothetical protein:glycosyl transferase, group 1 family protein:->->:1231437..1231781 345 agagctatgcaagaaaacgacctcagaataccgtgttattgcctattgaaggaggtatcgaaaagccattatcctttaatcgcacataaaaaaaacaacgaggtggaatgatttttatcaggtttgggcgaaaacatctgcaaaagacaataagatgaccaacaaatggcaaatccctgaagagaatctttggaatatcaaaaaaaatcatgaatattgcagctgaatatgcatattgcgatcaacaaaccgcatgcttacccagaatatcaatcaaatgaaatagattcacataggaattacaatcaataatatttgaagctattaatactacaaatagccttg Intra-Species Hit: Count: 1 Min: 1 Max: 345 Len: 345 Subject: NC_002950_PG1148_PG1149|hypothetical protein:glycosyl transferase, group 1 family protein|POSITIVE:POSITIVE|[1231437,1231781]|345 HSP 1 e-value: 1.0E-167 bit: 589.0 Len: 345 Query Start:1 Query End:345 Subject Strand: POSITIVE Subject Start: 1 Subject End: 345 agagctatgcaagaaaacgacctcagaataccgtgttattgcctattgaaggaggtatcgaaaagccattatcctttaatcgcacatnnnnnnnncaacgaggtggaatgatttttatcaggtttgggcgaaaacatctgcaaaagacaataagatgaccaacaaatggcaaatccctgaagagaatctttggaatatcnnnnnnnntcatgaatattgcagctgaatatgcatattgcgatcaacaaaccgcatgcttacccagaatatcaatcaaatgaaatagattcacataggaattacaatcaataatatttgaagctattaatactacaaatagccttg agagctatgcaagaaaacgacctcagaataccgtgttattgcctattgaaggaggtatcgaaaagccattatcctttaatcgcacataaaaaaaacaacgaggtggaatgatttttatcaggtttgggcgaaaacatctgcaaaagacaataagatgaccaacaaatggcaaatccctgaagagaatctttggaatatcaaaaaaaatcatgaatattgcagctgaatatgcatattgcgatcaacaaaccgcatgcttacccagaatatcaatcaaatgaaatagattcacataggaattacaatcaataatatttgaagctattaatactacaaatagccttg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAGCUAUGCAAGAAAACGACCUCAGAAUACCGUGUUAUUGCCUAUUGAAGGAGGUAUCGAAAAGCCAUUAUCCUUUAAUCGCACAUAAAAAAAACAACGAGGUGGAAUGAUUUUUAUCAGGUUUGGGCGAAAACAUCUGCAAAAGACAAUAAGAUGACCAACAAAUGGCAAAUCCCUGAAGAGAAUCUUUGGAAUAUCAAAAAAAAUCAUGAAUAUUGCAGCUGAAUAUGCAUAUUGCGAUCAACAAACCGCAUGCUUACCCAGAAUAUCAAUCAAAUGAAAUAGAUUCACAUAGGAAUUACAAUCAAUAAUAUUUGAAGCUAUUAAUACUACAAAUAGCCUUG ....(((((...(((..(.(((((...........(((((((..((((((((((((........)))....))))))))).))).))))..........))))).)..(((((..(((....((((((......((.((((((............((.(((.....))))).....(..(((.....)))..).......................)))))).)).....(((...((((..........)))))))...)))))))))..)))))...........))).))))).........((((......)))).((((((.........)))))).... (-63.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAAGGCUAUUUGUAGUAUUAAUAGCUUCAAAUAUUAUUGAUUGUAAUUCCUAUGUGAAUCUAUUUCAUUUGAUUGAUAUUCUGGGUAAGCAUGCGGUUUGUUGAUCGCAAUAUGCAUAUUCAGCUGCAAUAUUCAUGAUUUUUUUUGAUAUUCCAAAGAUUCUCUUCAGGGAUUUGCCAUUUGUUGGUCAUCUUAUUGUCUUUUGCAGAUGUUUUCGCCCAAACCUGAUAAAAAUCAUUCCACCUCGUUGUUUUUUUUAUGUGCGAUUAAAGGAUAAUGGCUUUUCGAUACCUCCUUCAAUAGGCAAUAACACGGUAUUCUGAGGUCGUUUUCUUGCAUAGCUCU ...((((((((((((((..((((((.(((((.(((((..((((((......((((.((((..........)))).)))).(((((((.((((((((((....)))))))...))).))))))).))))))....)))))....))))).........((((.(..(((((.....(((((((((.((.((......)).))...))))))).....)).....)))))..).))))..........)))))).....))).)))))....((((.(((((((((..((((((.(((.....))).........))))))..))))))))).))))..)))))).. (-75.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 302 258 217 68 34 NC_002950:PG0694|5end_immunoreactive_42_kDa_antigen_PG33_750845..751075_NEGATIVE 289 68 21 71 28 NC_002950:PG1824|5end_phosphopyruvate_hydratase_1919430..1919660_NEGATIVE 279 87 41 125 65 NC_002950:PG1273|5end_hypothetical_protein_1351837..1352067_NEGATIVE 276 60 21 77 36 NC_002950:PG0771|5end_hypothetical_protein_824524..824754_POSITIVE 273 138 95 108 69 NC_002950:PG2087|5end_hypothetical_protein_2186990..2187220_POSITIVE 273 164 121 69 9 NC_002950:PG1553|5end_CobN/magnesium_chelatase_family_protein_1630858..1631088_POSITIVE 270 78 31 84 36 NC_002950:PG0065|5end_efflux_transporter,_RND_family,_MFP_subunit_81187..81417_NEGATIVE 269 149 109 71 22 NC_002950:PG1262|5end_ISPg3,_transposase_1340634..1340864_NEGATIVE 269 149 109 71 22 NC_002950:PG1032|5end_ISPg3,_transposase_1094333..1094563_POSITIVE 269 115 81 227 181 NC_002950:PG0996|5end_conserved_hypothetical_protein_TIGR01777_1055592..1055822_POSITIVE 269 149 109 71 22 NC_002950:PG0798|5end_ISPg3,_transposase_852845..853075_POSITIVE 269 149 109 71 22 NC_002950:PG0261|5end_ISPg3,_transposase_294764..294994_NEGATIVE 269 149 109 71 22 NC_002950:PG0194|5end_ISPg3,_transposase_230928..231158_POSITIVE 267 64 21 175 112 NC_002950:PG1282|5end_hypothetical_protein_1360035..1360265_POSITIVE 266 259 219 167 122 NC_002950:PG2112|5end_hypothetical_protein_2221471..2221701_POSITIVE 266 60 11 108 63 NC_002950:PG1302|5end_hypothetical_protein_1380637..1380867_NEGATIVE 262 59 20 168 124 NC_002950:PG1312|5end_capA_protein,_putative_1390286..1390516_POSITIVE 261 86 41 108 63 NC_002950:PG2146|5end_hypothetical_protein_2253815..2254045_POSITIVE 261 78 31 201 151 NC_002950:PG0185|5end_ragA_protein_218329..218559_POSITIVE 258 145 101 208 170 NC_002950:PG1823|5end_hypothetical_protein_1917317..1917547_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 343 60 11 130 75 NC_002950:PG1860|3end_hypothetical_protein_1958574..1958724_NEGATIVE 273 138 95 108 69 NC_002950:PG2086|3end_hypothetical_protein_2187070..2187220_POSITIVE 270 86 41 109 65 NC_002950:PG0384|3end_MutS2_family_protein_418697..418847_POSITIVE 267 64 21 151 88 NC_002950:PG1281|3end_hypothetical_protein_1360091..1360241_POSITIVE 261 86 41 151 106 NC_002950:PG2145|3end_polysaccharide_deacetylase_2253938..2254088_POSITIVE 261 131 96 104 75 NC_002950:PG1286|3end_ferritin_1365019..1365169_NEGATIVE 259 77 31 42 3 NC_002950:PG1959|3end_ribosomal_protein_L33_2048217..2048367_NEGATIVE 259 68 21 132 72 NC_002950:PG0814|3end_hypothetical_protein_875904..876054_NEGATIVE 258 88 41 106 56 NC_002950:PG0229|3end_hypothetical_protein_265350..265500_POSITIVE 248 48 4 110 67 NC_002950:PG0980|3end_hypothetical_protein_1043214..1043364_POSITIVE 247 88 41 132 88 NC_002950:PG1340|3end_L-lactate_permease_1420298..1420448_NEGATIVE 247 255 217 83 37 NC_002950:PG0338|3end_hypothetical_protein_375137..375287_POSITIVE 245 44 3 66 27 NC_002950:PG1493|3end_hypothetical_protein_1569538..1569688_POSITIVE 245 140 100 50 17 NC_002950:PG0245|3end_universal_stress_protein_family_279773..279923_NEGATIVE 243 55 18 83 47 NC_002950:PG0164|3end_hypothetical_protein_187081..187231_NEGATIVE 242 69 23 50 10 NC_002950:PG1465|3end_hypothetical_protein_1542706..1542856_POSITIVE 241 162 122 46 2 NC_002950:PG1145|3end_long-chain-fatty-acid--CoA_ligase,_putative_1228482..1228632_NEGATIVE 240 67 21 142 89 NC_002950:PG2106|3end_hypothetical_protein_2215457..2215607_POSITIVE 240 142 109 47 1 NC_002950:PG0399|3end_lipoprotein,_putative_435707..435857_NEGATIVE 239 86 42 141 96 NC_002950:PG2142|3end_GTP-binding_protein_Era_2248564..2248714_POSITIVE