Origin IGS: ggtcaaactcctaaaaatttctgttagttaatagtgacaaaataggggcgtaaatatgccgatttcttatacttttgtcaacgggaattttgtgttgatttcggtgagacacaaccgaaagaaagcatcgttatatttaacaagcactttcaaaccggctcacgaaacgatgtgcgcgagattttaacagttttttcccttagaatatagcgtaaaaacgaaatttctatacaattaggcaaattttatcgttcagagtaatccgtt .........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 aacggattactctgaacgataaaatttgcctaattgtatagaaatttcgtttttacgctatattctaagggaaaaaactgttaaaatctcgcgcacatcgtttcgtgagccggtttgaaagtgcttgttaaatataacgatgctttctttcggttgtgtctcaccgaaatcaacacaaaattcccgttgacaaaagtataagaaatcggcatatttacgcccctattttgtcactattaactaacagaaatttttaggagtttgacc Mask Tandem Repeat Region ================================================ ggtcaaactcctaaaaatttctgttagttaatagtgacaaaataggggcgtaaatatgccgatttcttatacttttgtcaacgggaattttgtgttgatttcggtgagacacaaccgaaagaaagcatcgttatatttaacaagcactttcaaaccggctcacgaaacgatgtgcgcgagattttaacagttttttcccttagaatatagcgtaaaaacgaaatttctatacaattaggcaaattttatcgttcagagtaatccgtt Find is-nt database================================================ Query_seq: AA02944:AA02946|AA02944:AA02946:30S ribosomal protein S20:virulence factor protein:->->:2059089..2059355 267 ggtcaaactcctaaaaatttctgttagttaatagtgacaaaataggggcgtaaatatgccgatttcttatacttttgtcaacgggaattttgtgttgatttcggtgagacacaaccgaaagaaagcatcgttatatttaacaagcactttcaaaccggctcacgaaacgatgtgcgcgagattttaacagttttttcccttagaatatagcgtaaaaacgaaatttctatacaattaggcaaattttatcgttcagagtaatccgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA02944:AA02946|AA02944:AA02946:30S ribosomal protein S20:virulence factor protein:->->:2059089..2059355 267 ggtcaaactcctaaaaatttctgttagttaatagtgacaaaataggggcgtaaatatgccgatttcttatacttttgtcaacgggaattttgtgttgatttcggtgagacacaaccgaaagaaagcatcgttatatttaacaagcactttcaaaccggctcacgaaacgatgtgcgcgagattttaacagttttttcccttagaatatagcgtaaaaacgaaatttctatacaattaggcaaattttatcgttcagagtaatccgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA02944:AA02946|AA02944:AA02946:30S ribosomal protein S20:virulence factor protein:->->:2059089..2059355 267 ggtcaaactcctaaaaatttctgttagttaatagtgacaaaataggggcgtaaatatgccgatttcttatacttttgtcaacgggaattttgtgttgatttcggtgagacacaaccgaaagaaagcatcgttatatttaacaagcactttcaaaccggctcacgaaacgatgtgcgcgagattttaacagttttttcccttagaatatagcgtaaaaacgaaatttctatacaattaggcaaattttatcgttcagagtaatccgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ggtcaaactcctaaaaatttctgttagttaatagtgacaaaataggggcgtaaatatgccgatttcttatacttttgtcaacgggaattttgtgttgatttcggtgagacacaaccgaaagaaagcatcgttatatttaacaagcactttcaaaccggctcacgaaacgatgtgcgcgagattttaacagttttttcccttagaatatagcgtaaaaacgaaatttctatacaattaggcaaattttatcgttcagagtaatccgtt Predict ORF larger than 30AA ================================================ Protein_Len: 43 Strand: + Start: 56 End: 184 ....................................................... M P I S Y T F V N G N F V L I S V R H N R K K A S L Y L T S T F K P A H E T M C A R F ................................................................................... Protein_Len: 30 Strand: - Start: 153 End: 242 ........................................................................................................................................................ V P E R F S T R S I K V T K E R L I Y R L F S I E I C N P M ......................... Protein_Len: 33 Strand: - Start: 14 End: 112 ............. F N R N T L L S L I P A Y I H R N R I S K D V P I K H Q N R H S M ........................................................................................................................................................... ggtcaaactcctaaaaatttctgttagttaatagtgacaaaataggggcgtaaatatgccgatttcttatacttttgtcaacgggaattttgtgttgatttcggtgagacacaaccgaaagaaagcatcgttatatttaacaagcactttcaaaccggctcacgaaacgatgtgcgcgagattttaacagttttttcccttagaatatagcgtaaaaacgaaatttctatacaattaggcaaattttatcgttcagagtaatccgtt Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: - Score: 84 Start: 53 End: 82 ....................................................GTTGACAAAAGTATAAGAAATCGGCATATT......................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ggtcaaactcctaaaaatttctgttagttaatagtgacaaaataggggcgtaaatatgccgatttcttatacttttgtcaacgggaattttgtgttgatttcggtgagacacaaccgaaagaaagcatcgttatatttaacaagcactttcaaaccggctcacgaaacgatgtgcgcgagattttaacagttttttcccttagaatatagcgtaaaaacgaaatttctatacaattaggcaaattttatcgttcagagtaatccgtt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: AA02944:AA02946|AA02944:AA02946:30S ribosomal protein S20:virulence factor protein:->->:2059089..2059355 267 ggtcaaactcctaaaaatttctgttagttaatagtgacaaaataggggcgtaaatatgccgatttcttatacttttgtcaacgggaattttgtgttgatttcggtgagacacaaccgaaagaaagcatcgttatatttaacaagcactttcaaaccggctcacgaaacgatgtgcgcgagattttaacagttttttcccttagaatatagcgtaaaaacgaaatttctatacaattaggcaaattttatcgttcagagtaatccgtt Intra-Species Hit: Count: 1 Min: 1 Max: 267 Len: 267 Subject: aact_AA02944_AA02946|30S ribosomal protein S20:virulence factor protein|POSITIVE:POSITIVE|[2059089,2059355]|267 HSP 1 e-value: 1.0E-149 bit: 529.0 Len: 267 Query Start:1 Query End:267 Subject Strand: POSITIVE Subject Start: 1 Subject End: 267 ggtcaaactcctaaaaatttctgttagttaatagtgacaaaataggggcgtaaatatgccgatttcttatacttttgtcaacgggaattttgtgttgatttcggtgagacacaaccgaaagaaagcatcgttatatttaacaagcactttcaaaccggctcacgaaacgatgtgcgcgagattttaacagttttttcccttagaatatagcgtaaaaacgaaatttctatacaattaggcaaattttatcgttcagagtaatccgtt ggtcaaactcctaaaaatttctgttagttaatagtgacaaaataggggcgtaaatatgccgatttcttatacttttgtcaacgggaattttgtgttgatttcggtgagacacaaccgaaagaaagcatcgttatatttaacaagcactttcaaaccggctcacgaaacgatgtgcgcgagattttaacagttttttcccttagaatatagcgtaaaaacgaaatttctatacaattaggcaaattttatcgttcagagtaatccgtt Inter-species Hit: Count: 3 Min: 1 Max: 247 Len: 247 Subject: NC_007146_NTHI1137_NTHI1139|putative virulence factor MviN:30S ribosomal protein S20|NEGATIVE:POSITIVE|[1082802,1083103]|302 HSP 1 e-value: 2.0E-40 bit: 167.0 Len: 198 Query Start:46 Query End:243 Subject Strand: NEGATIVE Subject Start: 67 Subject End: 265 .............................................gggcgtaaatatgccgatttcttatacttttgtcaacgggaattttgtgttgatttcggtgagacacaaccgaaagaaagcatcgttatatttaacaagcactttcaa-accggctcac-gaaacgatgtgcgcgagattttaacagttttttcccttagaatatagcgtaaaaacgaaatttctatacaattaggcaaa........................ .............................................gggcgtcaatatgccgattttttatacttttgtcaatggaaaatttgtgttgatttcggtgagacacaaccgaaagtaagtatcgttat-ttttacaagctctttcaatatgggctcacacaaacgatgtgtggcggattttatcagttttttttcacggaatatagcgtaaaaacaaaatttctatacaattaggcaaa........................ Subject: NC_002663_PM1659_PM1660|30S ribosomal protein S20:MviN|NEGATIVE:POSITIVE|[1866354,1866700]|347 HSP 1 e-value: 1.0E-39 bit: 165.0 Len: 153 Query Start:95 Query End:247 Subject Strand: POSITIVE Subject Start: 110 Subject End: 264 ..............................................................................................ttgatttcggtgagacacaaccgaaaga-aagcatcgttatatttaacaagcactttcaa-accggctcacgaaacgatgtgcgcgagattttaacagttttttcccttagaatatagcgtaaaaacgaaatttctatacaattaggcaaatttt.................... ..............................................................................................ttgatttcggtgagacacaaccgaaagttaagcatcgttatatcaatcaagcgctttcaagataggctcaccaaacgatgtgggcgagattttagcagttttttcacgtagaatatagcgtaaaaacaaaatttctatacaattaagcaaatttt.................... Subject: NC_000907_HI0964_HI0965|virulence factor:30S ribosomal protein S20|NEGATIVE:POSITIVE|[1024206,1024513]|308 HSP 1 e-value: 1.0E-39 bit: 165.0 Len: 243 Query Start:1 Query End:243 Subject Strand: NEGATIVE Subject Start: 67 Subject End: 308 ggtcaaactcctaaaaatttctgttagttaatagtgacaaaatag-gggcgtaaatatgccgatttcttatacttttgtcaacgggaattttgtgttgatttcggtgagacacaaccgaaagaaagcatcgttatatttaacaagcactttcaa-accggctcac-gaaacgatgtgcgcgagattttaacagttttttcccttagaatatagcgtaaaaacgaaatttctatacaattaggcaaa........................ ggtcaaactcctaaaa-tttctgttgattgatag--acaaaataaagggcatcaatatgccgattttttatacttttgtcaatggaaaatttgtgttgatttcggtgagacacaaccgaaagtaagtatcgttat-ttttacaagctctttcaatatgggctcacacaaacgatgtgtggcggattttatcagttttttttcacggaatatagcgtaaaaacaaaatttctatacaattaggcaaa........................ Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGUCAAACUCCUAAAAAUUUCUGUUAGUUAAUAGUGACAAAAUAGGGGCGUAAAUAUGCCGAUUUCUUAUACUUUUGUCAACGGGAAUUUUGUGUUGAUUUCGGUGAGACACAACCGAAAGAAAGCAUCGUUAUAUUUAACAAGCACUUUCAAACCGGCUCACGAAACGAUGUGCGCGAGAUUUUAACAGUUUUUUCCCUUAGAAUAUAGCGUAAAAACGAAAUUUCUAUACAAUUAGGCAAAUUUU .(((.........(((((((((((..........(((((((((((((((((....))))).....)))))...))))))))))))))))))((((.((((((((((((.(......(((((...((...((((....))))..)).)))))......)))))).........(((((...(((((((..(......)..)))))))...)))))....)))))))...)))).....)))....... (-53.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAUUUGCCUAAUUGUAUAGAAAUUUCGUUUUUACGCUAUAUUCUAAGGGAAAAAACUGUUAAAAUCUCGCGCACAUCGUUUCGUGAGCCGGUUUGAAAGUGCUUGUUAAAUAUAACGAUGCUUUCUUUCGGUUGUGUCUCACCGAAAUCAACACAAAAUUCCCGUUGACAAAAGUAUAAGAAAUCGGCAUAUUUACGCCCCUAUUUUGUCACUAUUAACUAACAGAAAUUUUUAGGAGUUUGACC ....(((.(((....((((((......(((....)))))))))....))).)))(((((.((((((....((((((........))).(((((((((((((((.((((((....))))))))))))).((((((........)))))).(((((...........)))))............)))))))).......))).....((((((............))))))..)))))).))))).... (-47.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 359 120 79 216 170 aact:AA00575|5end_shikimate_5-dehydrogenase_393216..393446_POSITIVE 323 87 41 183 142 aact:AA02925|5end_conserved_hypothetical_protein_2047493..2047723_POSITIVE 306 129 81 82 39 aact:AA02232|5end_NagC-like_transcriptional_regulator_1518455..1518685_POSITIVE 305 179 135 216 162 aact:AA00923|5end_diaminopimelate_decarboxylase_633993..634223_POSITIVE 300 159 116 114 67 aact:AA01019|5end_conserved_hypothetical_protein_712223..712453_POSITIVE 295 195 155 87 48 aact:AA01431|5end_conserved_hypothetical_protein_(possible_hydrolase)_959856..960086_POSITIVE 288 198 155 100 58 aact:AA01360|5end_XAA-pro_aminopeptidase_(X-pro_aminopeptidase)_921047..921277_POSITIVE 284 180 136 164 128 aact:AA00126|5end_conserved_hypothetical_protein_91053..91283_POSITIVE 282 87 41 176 117 aact:AA01398|5end_KDO_kinase_944889..945119_POSITIVE 278 159 115 65 19 aact:AA01517|5end_peptidyl-prolyl_cis-trans_isomerase;_macrophage_infectivity_protein_1020989..1021219_POSITIVE 277 180 144 165 129 aact:AA00993|5end_possible_D-tyrosyl-tRNA(Tyr)_deacylase_694488..694718_POSITIVE 275 84 41 141 90 aact:AA02132|5end_dihydroorotate_dehydrogenase_1455089..1455319_POSITIVE 272 130 84 179 131 aact:AA02585|5end_hypothetical_protein_1798798..1799028_POSITIVE 272 200 151 162 106 aact:AA00529|5end_outer_membrane_protein,_Omp_18/16_361730..361960_POSITIVE 271 185 145 70 20 aact:AA02374|5end_ribose_5-phosphate_isomerase_A_1625839..1626069_POSITIVE 269 178 134 100 46 aact:AA00425|5end_N-terminal_region_of_competence_protein_M_287295..287525_POSITIVE 268 74 34 76 26 aact:AA02384|5end_2-dehydro-3-deoxygluconokinase_1632112..1632342_POSITIVE 267 78 33 212 163 aact:AA00423|5end_GTP-binding_protein_286533..286763_POSITIVE 266 135 91 70 28 aact:AA01747|5end_single-stranded-DNA-specific_exonuclease_1181359..1181589_POSITIVE 266 185 148 218 175 aact:AA01688|5end_conserved_hypothetical_protein;_possible_membrane_protein_1139635..1139865_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 323 87 41 51 10 aact:AA02922|3end_gamma-glutamylphosphate_reductase_2047441..2047591_POSITIVE 303 178 135 147 103 aact:AA00921|3end_conserved_hypothetical_protein_634014..634164_POSITIVE 300 159 116 111 64 aact:AA01018|3end_conserved_hypothetical_protein_(possible_transcriptional_regulator)_712300..712450_POSITIVE 300 60 20 63 18 aact:AA00657|3end_heat_shock_protein_70_451466..451616_POSITIVE 288 198 155 82 40 aact:AA01359|3end_conserved_hypothetical_protein_921109..921259_POSITIVE 284 180 136 44 8 aact:AA00125|3end_conserved_hypothetical_protein_(possible_phage-related_protein)_91013..91163_POSITIVE 282 87 41 87 28 aact:AA01396|3end_saccharide_biosynthesis_regulatory_protein_944880..945030_POSITIVE 275 84 41 124 73 aact:AA02131|3end_conserved_hypothetical_protein_(possible_TrpH_protein)_1455152..1455302_POSITIVE 269 178 134 128 74 aact:AA00424|3end_hypothetical_protein_287403..287553_POSITIVE 268 80 35 56 11 aact:AA02944|3end_30S_ribosomal_protein_S20_2059028..2059178_POSITIVE 268 74 34 61 11 aact:AA02383|3end_oxidoreductase_1632177..1632327_POSITIVE 267 78 33 79 30 aact:AA00422|3end_LapB_membrane_protein_286480..286630_POSITIVE 266 177 156 149 117 aact:AA00221|3end_NADP-specific_glutamate_dehydrogenase_153865..154015_POSITIVE 265 200 154 55 3 aact:AA00528|3end_conserved_hypothetical_protein_361703..361853_POSITIVE 263 179 136 145 94 aact:AA02046|3end_PTS_system_galactitol-specific_enzyme_IIC_1393687..1393837_POSITIVE 263 120 74 148 91 aact:AA00927|3end_ATP-dependent_DNA_helicase_637777..637927_POSITIVE 259 177 148 132 100 aact:AA00198|3end_conserved_hypothetical_protein_(Cytosine_deaminase-related_enzyme)_138643..138793_POSITIVE 256 183 145 85 48 aact:AA00507|3end_hypothetical_protein_353201..353351_POSITIVE 254 188 144 74 32 aact:AA02001|3end_conserved_hypothetical_protein_1360239..1360389_POSITIVE 254 89 46 119 69 aact:AA01021|3end_hypothetical_protein_714276..714426_POSITIVE