Origin IGS: atcaaatcattgagacgttaggaacagtattttcttaaactctctgcaaagctacggaaatacgtcaagtacttcgcaaccagcataacagacttccccgtgagttgcatggtcgtgctagtgaagatatcttcagcagacttcgggctacaccataggggttgtcgggctatgctgtagagcttgtcgagccacgccgtagaggccggatcgttatactctacggcttatctcgttatgttctaaggaattcctcgttatcccttacggattatctccctacgctctatagctcatttccatacgctctaggggatagccaaaacacaccgttcagcaaggaaaagaggggcgaaaaaaactgtaaaaacggacaagtctgcttagttt .........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 aaactaagcagacttgtccgtttttacagtttttttcgcccctcttttccttgctgaacggtgtgttttggctatcccctagagcgtatggaaatgagctatagagcgtagggagataatccgtaagggataacgaggaattccttagaacataacgagataagccgtagagtataacgatccggcctctacggcgtggctcgacaagctctacagcatagcccgacaacccctatggtgtagcccgaagtctgctgaagatatcttcactagcacgaccatgcaactcacggggaagtctgttatgctggttgcgaagtacttgacgtatttccgtagctttgcagagagtttaagaaaatactgttcctaacgtctcaatgatttgat Mask Tandem Repeat Region ================================================ atcaaatcattgagacgttaggaacagtattttcttaaactctctgcaaagctacggaaatacgtcaagtacttcgcaaccagcataacagacttccccgtgagttgcatggtcgtgctagtgaagatatcttcagcagacttcgggctacaccataggggttgtcgggctatgctgtagagcttgtcgagccacgccgtagaggccggatcgttatactctacggcttatctcgttatgttctaaggaattcctcgttatcccttacggattatctccctacgctctatagctcatttccatacgctctaggggatagccaaaacacaccgttcagcaaggaaaagaggggcgaaaaaaactgtaaaaacggacaagtctgcttagttt Find is-nt database================================================ Query_seq: PG1101:PG1102|PG1101:PG1102:sodium:solute symporter family protein:hypothetical protein:<-<-:1170560..1170949 390 atcaaatcattgagacgttaggaacagtattttcttaaactctctgcaaagctacggaaatacgtcaagtacttcgcaaccagcataacagacttccccgtgagttgcatggtcgtgctagtgaagatatcttcagcagacttcgggctacaccataggggttgtcgggctatgctgtagagcttgtcgagccacgccgtagaggccggatcgttatactctacggcttatctcgttatgttctaaggaattcctcgttatcccttacggattatctccctacgctctatagctcatttccatacgctctaggggatagccaaaacacaccgttcagcaaggaaaagaggggcgaaaaaaactgtaaaaacggacaagtctgcttagttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1101:PG1102|PG1101:PG1102:sodium:solute symporter family protein:hypothetical protein:<-<-:1170560..1170949 390 atcaaatcattgagacgttaggaacagtattttcttaaactctctgcaaagctacggaaatacgtcaagtacttcgcaaccagcataacagacttccccgtgagttgcatggtcgtgctagtgaagatatcttcagcagacttcgggctacaccataggggttgtcgggctatgctgtagagcttgtcgagccacgccgtagaggccggatcgttatactctacggcttatctcgttatgttctaaggaattcctcgttatcccttacggattatctccctacgctctatagctcatttccatacgctctaggggatagccaaaacacaccgttcagcaaggaaaagaggggcgaaaaaaactgtaaaaacggacaagtctgcttagttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1101:PG1102|PG1101:PG1102:sodium:solute symporter family protein:hypothetical protein:<-<-:1170560..1170949 390 atcaaatcattgagacgttaggaacagtattttcttaaactctctgcaaagctacggaaatacgtcaagtacttcgcaaccagcataacagacttccccgtgagttgcatggtcgtgctagtgaagatatcttcagcagacttcgggctacaccataggggttgtcgggctatgctgtagagcttgtcgagccacgccgtagaggccggatcgttatactctacggcttatctcgttatgttctaaggaattcctcgttatcccttacggattatctccctacgctctatagctcatttccatacgctctaggggatagccaaaacacaccgttcagcaaggaaaagaggggcgaaaaaaactgtaaaaacggacaagtctgcttagttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atcaaatcattgagacgttaggaacagtattttcttaaactctctgcaaagctacggaaatacgtcaagtacttcgcaaccagcataacagacttccccgtgagttgcatggtcgtgctagtgaagatatcttcagcagacttcgggctacaccataggggttgtcgggctatgctgtagagcttgtcgagccacgccgtagaggccggatcgttatactctacggcttatctcgttatgttctaaggaattcctcgttatcccttacggattatctccctacgctctatagctcatttccatacgctctaggggatagccaaaacacaccgttcagcaaggaaaagaggggcgaaaaaaactgtaaaaacggacaagtctgcttagttt Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 60 End: 155 ........................................................... M R Q V L R N Q H N R L P R E L H G R A S E D I F S R L R A T P ........................................................................................................................................................................................................................................... Protein_Len: 31 Strand: + Start: 85 End: 177 .................................................................................... M T D F P V S C M V V L V K I S S A D F G L H H R G C R A M L ..................................................................................................................................................................................................................... Protein_Len: 60 Strand: + Start: 162 End: 389 ................................................................................................................................................................. M S G Y A V E L V E P R R R G R I V I L Y G L S R Y V L R N S S L S L T D Y L P T L Y S S F P Y A L G D S Q N T P F S K . Protein_Len: 51 Strand: - Start: 21 End: 173 .................... S C Y K R L S E A F S R F Y T L Y K A V L M V S K G T L Q M T T S T F I D E A S K P S C W L P Q R A M ......................................................................................................................................................................................................................... atcaaatcattgagacgttaggaacagtattttcttaaactctctgcaaagctacggaaatacgtcaagtacttcgcaaccagcataacagacttccccgtgagttgcatggtcgtgctagtgaagatatcttcagcagacttcgggctacaccataggggttgtcgggctatgctgtagagcttgtcgagccacgccgtagaggccggatcgttatactctacggcttatctcgttatgttctaaggaattcctcgttatcccttacggattatctccctacgctctatagctcatttccatacgctctaggggatagccaaaacacaccgttcagcaaggaaaagaggggcgaaaaaaactgtaaaaacggacaagtctgcttagttt 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================================================ atcaaatcattgagacgttaggaacagtattttcttaaactctctgcaaagctacggaaatacgtcaagtacttcgcaaccagcataacagacttccccgtgagttgcatggtcgtgctagtgaagatatcttcagcagacttcgggctacaccataggggttgtcgggctatgctgtagagcttgtcgagccacgccgtagaggccggatcgttatactctacggcttatctcgttatgttctaaggaattcctcgttatcccttacggattatctccctacgctctatagctcatttccatacgctctaggggatagccaaaacacaccgttcagcaaggaaaagaggggcgaaaaaaactgtaaaaacggacaagtctgcttagttt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 49 HP_score: -3.0 Tail_Score: -3.64318 Start: 174 End: 227 Full_Region: GGGTTGTCGGGCTAT GCTGTAGAGCTTGTCGAGCCACGCC GTAGA GGCCGGATCGTTATACTCTACGGC TTATCTCGTTATGTT .............................................................................................................................................................................GCTGTAGAGCTTGTCGAGCCACGCCGTAGAGGCCGGATCGTTATACTCTACGGC................................................................................................................................................................... Find igs database================================================ Query_seq: PG1101:PG1102|PG1101:PG1102:sodium:solute symporter family protein:hypothetical protein:<-<-:1170560..1170949 390 atcaaatcattgagacgttaggaacagtattttcttaaactctctgcaaagctacggaaatacgtcaagtacttcgcaaccagcataacagacttccccgtgagttgcatggtcgtgctagtgaagatatcttcagcagacttcgggctacaccataggggttgtcgggctatgctgtagagcttgtcgagccacgccgtagaggccggatcgttatactctacggcttatctcgttatgttctaaggaattcctcgttatcccttacggattatctccctacgctctatagctcatttccatacgctctaggggatagccaaaacacaccgttcagcaaggaaaagaggggcgaaaaaaactgtaaaaacggacaagtctgcttagttt Intra-Species Hit: Count: 1 Min: 1 Max: 390 Len: 390 Subject: NC_002950_PG1101_PG1102|sodium:solute symporter family protein:hypothetical protein|NEGATIVE:NEGATIVE|[1170560,1170949]|390 HSP 1 e-value: 0.0 bit: 731.0 Len: 390 Query Start:1 Query End:390 Subject Strand: POSITIVE Subject Start: 1 Subject End: 390 atcaaatcattgagacgttaggaacagtattttcttaaactctctgcaaagctacggaaatacgtcaagtacttcgcaaccagcataacagacttccccgtgagttgcatggtcgtgctagtgaagatatcttcagcagacttcgggctacaccataggggttgtcgggctatgctgtagagcttgtcgagccacgccgtagaggccggatcgttatactctacggcttatctcgttatgttctaaggaattcctcgttatcccttacggattatctccctacgctctatagctcatttccatacgctctaggggatagccaaaacacaccgttcagcaaggaaaagaggggcgnnnnnnnctgtaaaaacggacaagtctgcttagttt atcaaatcattgagacgttaggaacagtattttcttaaactctctgcaaagctacggaaatacgtcaagtacttcgcaaccagcataacagacttccccgtgagttgcatggtcgtgctagtgaagatatcttcagcagacttcgggctacaccataggggttgtcgggctatgctgtagagcttgtcgagccacgccgtagaggccggatcgttatactctacggcttatctcgttatgttctaaggaattcctcgttatcccttacggattatctccctacgctctatagctcatttccatacgctctaggggatagccaaaacacaccgttcagcaaggaaaagaggggcgaaaaaaactgtaaaaacggacaagtctgcttagttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCAAAUCAUUGAGACGUUAGGAACAGUAUUUUCUUAAACUCUCUGCAAAGCUACGGAAAUACGUCAAGUACUUCGCAACCAGCAUAACAGACUUCCCCGUGAGUUGCAUGGUCGUGCUAGUGAAGAUAUCUUCAGCAGACUUCGGGCUACACCAUAGGGGUUGUCGGGCUAUGCUGUAGAGCUUGUCGAGCCACGCCGUAGAGGCCGGAUCGUUAUACUCUACGGCUUAUCUCGUUAUGUUCUAAGGAAUUCCUCGUUAUCCCUUACGGAUUAUCUCCCUACGCUCUAUAGCUCAUUUCCAUACGCUCUAGGGGAUAGCCAAAACACACCGUUCAGCAAGGAAAAGAGGGGCGAAAAAAACUGUAAAAACGGACAAGUCUGCUUAGUUU ...........((((..(((((((.......)))))))..))))....((((((..(((.(((.....))).))).............(((((((..((((...(((((.((((.((((...((((....))))))))))))...(((((..((.(((((((....(((....((((((((((....((((....(((((((((..............)))))))))....))))....(((((((((.((........)).))))).))))...........)))))))))).....)))..)).))))).))..))))).........(((((..(........)..)))))........)))))..))))..)))))))..)))))) (-111.84) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAACUAAGCAGACUUGUCCGUUUUUACAGUUUUUUUCGCCCCUCUUUUCCUUGCUGAACGGUGUGUUUUGGCUAUCCCCUAGAGCGUAUGGAAAUGAGCUAUAGAGCGUAGGGAGAUAAUCCGUAAGGGAUAACGAGGAAUUCCUUAGAACAUAACGAGAUAAGCCGUAGAGUAUAACGAUCCGGCCUCUACGGCGUGGCUCGACAAGCUCUACAGCAUAGCCCGACAACCCCUAUGGUGUAGCCCGAAGUCUGCUGAAGAUAUCUUCACUAGCACGACCAUGCAACUCACGGGGAAGUCUGUUAUGCUGGUUGCGAAGUACUUGACGUAUUUCCGUAGCUUUGCAGAGAGUUUAAGAAAAUACUGUUCCUAACGUCUCAAUGAUUUGAU ........((((((((..((((...(((((..(((((...((((..((((((((.((((.....)))).(..(((((((((..((.(((((.......)))))..)).))))).))))..).))))))))....)))).................((((....(((((((((..............)))))))))....))))..(((((((.(((((((((..(((..((((..(((.((.((.....(((((((((((....))))...)))).)))...)).))))).))))..))).)))))))))((((((((((((.....)))))).)))))).......)))))))..))))).)))))....))))...))).).)))).. (-121.34) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1019 120 71 211 162 NC_002950:PG1101|5end_sodium:solute_symporter_family_protein_1170469..1170699_NEGATIVE 551 209 161 200 137 NC_002950:PG1218|5end_hypothetical_protein_1295937..1296167_POSITIVE 530 190 144 213 167 NC_002950:PG1840|5end_hypothetical_protein_1937102..1937332_POSITIVE 448 210 161 213 147 NC_002950:PG2107|5end_thiamine_biosynthesis_protein_ThiH_2216658..2216888_NEGATIVE 446 149 107 131 88 NC_002950:PG1594|5end_ComEC/Rec2-related_protein_1673587..1673817_NEGATIVE 422 226 186 55 6 NC_002950:PG1022|5end_hypothetical_protein_1083537..1083767_POSITIVE 417 209 165 51 1 NC_002950:PG1576|5end_L-aspartate_oxidase_1653016..1653246_POSITIVE 417 209 163 182 129 NC_002950:PG1196|5end_hypothetical_protein_1275127..1275357_POSITIVE 416 210 163 193 136 NC_002950:PG0468|5end_mannose-6-phosphate_isomerase,_class_I_511384..511614_NEGATIVE 407 198 153 220 175 NC_002950:PG2029|5end_hypothetical_protein_2126543..2126773_POSITIVE 399 206 164 64 9 NC_002950:PG0500|5end_queuine_tRNA-ribosyltransferase_539197..539427_POSITIVE 398 210 168 74 29 NC_002950:PG1457|5end_hypothetical_protein_1538650..1538880_POSITIVE 393 210 167 70 7 NC_002950:PG1094|5end_phosphomannomutase_1158753..1158983_POSITIVE 392 199 157 219 171 NC_002950:PG1006|5end_hypothetical_protein_1066478..1066708_NEGATIVE 392 208 170 60 25 NC_002950:PG0223|5end_exonuclease_257610..257840_NEGATIVE 391 210 165 195 133 NC_002950:PG0141|5end_spoOJ_protein_164747..164977_NEGATIVE 390 170 126 209 158 NC_002950:PG2031|5end_hypothetical_protein_2130339..2130569_POSITIVE 386 210 161 59 8 NC_002950:PG0433|5end_tetrapyrrole_methylase_family_protein_471396..471626_NEGATIVE 384 210 161 207 143 NC_002950:PG0201|5end_ribonuclease_P_238770..239000_NEGATIVE 379 210 166 200 145 NC_002950:PG1225|5end_ABC_transporter,_ATP-binding_protein_1301385..1301615_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 490 208 161 148 85 NC_002950:PG1638|3end_thioredoxin_family_protein_1718664..1718814_NEGATIVE 464 320 280 61 21 NC_002950:PG0261|3end_ISPg3,_transposase_293862..294012_NEGATIVE 446 149 107 124 81 NC_002950:PG1595|3end_ribulose-phosphate_3-epimerase_1673594..1673744_NEGATIVE 407 209 162 86 36 NC_002950:PG0453|3end_hypothetical_protein_496670..496820_POSITIVE 400 207 161 141 90 NC_002950:PG0199|3end_TatD_family_protein_237424..237574_NEGATIVE 394 228 184 149 100 NC_002950:PG1715|3end_hypothetical_protein_1803393..1803543_NEGATIVE 392 199 151 130 81 NC_002950:PG1972|3end_hemagglutinin_protein_HagB_2061203..2061353_POSITIVE 392 208 170 56 21 NC_002950:PG0224|3end_hypothetical_protein_257614..257764_NEGATIVE 390 210 161 68 6 NC_002950:PG0148|3end_sigma-54-dependent_transcriptional_regulator_169654..169804_NEGATIVE 382 209 166 121 69 NC_002950:PG0746|3end_sensor_histidine_kinase_792536..792686_NEGATIVE 379 228 182 75 15 NC_002950:PG0459|3end_ISPg5,_transposase_Orf1_501517..501667_NEGATIVE 378 148 103 81 23 NC_002950:PG0333|3end_hypothetical_protein_368811..368961_POSITIVE 377 199 154 130 75 NC_002950:PG1975|3end_hemagglutinin_protein_HagC_2064350..2064500_POSITIVE 375 189 141 58 13 NC_002950:PG0733|3end_riboflavin_synthase_subunit_alpha_783856..784006_POSITIVE 375 209 168 134 96 NC_002950:PG0381|3end_cell_volume_regulation_protein_CvrA_411185..411335_NEGATIVE 375 210 162 84 27 NC_002950:PG0245|3end_universal_stress_protein_family_279773..279923_NEGATIVE 371 209 161 41 5 NC_002950:PG1006|3end_hypothetical_protein_1063794..1063944_NEGATIVE 370 206 162 61 21 NC_002950:PG2071|3end_hypothetical_protein_2167452..2167602_POSITIVE 370 200 157 55 5 NC_002950:PG0348|3end_ATP-dependent_DNA_helicase_RecG_384521..384671_POSITIVE 369 200 153 146 96 NC_002950:PG1270|3end_hypothetical_protein_1349278..1349428_NEGATIVE