Origin IGS: taagtcgtattcttgttttcaatgttaatatgtggggcttgcaaaggttctgacattgtttttgttaggtttcgctttcacgagaaaccgtatataatataattttcgatgtatatttttaatttatctaagctttgagaagcatttatctaagcttagataaattattatcagagttctgataaatatttcttaaagctttgataatttatttttaacaggcataaatatctttggaactgtgctttttctccttcttaacgcttcgaaagaacatgggaacgttgcctttgcagcggtctcattacagtattgtttgtatttcctaataaataaggattgtgtagttattagcttttcactacctttgcatccactaaacgatattagattaatgcaataaagaa .........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 ttctttattgcattaatctaatatcgtttagtggatgcaaaggtagtgaaaagctaataactacacaatccttatttattaggaaatacaaacaatactgtaatgagaccgctgcaaaggcaacgttcccatgttctttcgaagcgttaagaaggagaaaaagcacagttccaaagatatttatgcctgttaaaaataaattatcaaagctttaagaaatatttatcagaactctgataataatttatctaagcttagataaatgcttctcaaagcttagataaattaaaaatatacatcgaaaattatattatatacggtttctcgtgaaagcgaaacctaacaaaaacaatgtcagaacctttgcaagccccacatattaacattgaaaacaagaatacgactta Mask Tandem Repeat Region ================================================ taagtcgtattcttgttttcaatgttaatatgtggggcttgcaaaggttctgacattgtttttgttaggtttcgctttcacgagaaaccgtatataatataattttcgatgtatatttttaatttatctaagctttgagaagcatttatctaagcttagataaattattatcagagttctgataaatatttcttaaagctttgataatttatttttaacaggcataaatatctttggaactgtgctttttctccttcttaacgcttcgaaagaacatgggaacgttgcctttgcagcggtctcattacagtattgtttgtatttcctaataaataaggattgtgtagttattagcttttcactacctttgcatccactaaacgatattagattaatgcaataaagaa Find is-nt database================================================ Query_seq: PI0938:PI0939|PI0938:PI0939:hypothetical protein:TonB-dependent outer membrane protein:->->:869602..870008 407 taagtcgtattcttgttttcaatgttaatatgtggggcttgcaaaggttctgacattgtttttgttaggtttcgctttcacgagaaaccgtatataatataattttcgatgtatatttttaatttatctaagctttgagaagcatttatctaagcttagataaattattatcagagttctgataaatatttcttaaagctttgataatttatttttaacaggcataaatatctttggaactgtgctttttctccttcttaacgcttcgaaagaacatgggaacgttgcctttgcagcggtctcattacagtattgtttgtatttcctaataaataaggattgtgtagttattagcttttcactacctttgcatccactaaacgatattagattaatgcaataaagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0938:PI0939|PI0938:PI0939:hypothetical protein:TonB-dependent outer membrane protein:->->:869602..870008 407 taagtcgtattcttgttttcaatgttaatatgtggggcttgcaaaggttctgacattgtttttgttaggtttcgctttcacgagaaaccgtatataatataattttcgatgtatatttttaatttatctaagctttgagaagcatttatctaagcttagataaattattatcagagttctgataaatatttcttaaagctttgataatttatttttaacaggcataaatatctttggaactgtgctttttctccttcttaacgcttcgaaagaacatgggaacgttgcctttgcagcggtctcattacagtattgtttgtatttcctaataaataaggattgtgtagttattagcttttcactacctttgcatccactaaacgatattagattaatgcaataaagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0938:PI0939|PI0938:PI0939:hypothetical protein:TonB-dependent outer membrane protein:->->:869602..870008 407 taagtcgtattcttgttttcaatgttaatatgtggggcttgcaaaggttctgacattgtttttgttaggtttcgctttcacgagaaaccgtatataatataattttcgatgtatatttttaatttatctaagctttgagaagcatttatctaagcttagataaattattatcagagttctgataaatatttcttaaagctttgataatttatttttaacaggcataaatatctttggaactgtgctttttctccttcttaacgcttcgaaagaacatgggaacgttgcctttgcagcggtctcattacagtattgtttgtatttcctaataaataaggattgtgtagttattagcttttcactacctttgcatccactaaacgatattagattaatgcaataaagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taagtcgtattcttgttttcaatgttaatatgtggggcttgcaaaggttctgacattgtttttgttaggtttcgctttcacgagaaaccgtatataatataattttcgatgtatatttttaatttatctaagctttgagaagcatttatctaagcttagataaattattatcagagttctgataaatatttcttaaagctttgataatttatttttaacaggcataaatatctttggaactgtgctttttctccttcttaacgcttcgaaagaacatgggaacgttgcctttgcagcggtctcattacagtattgtttgtatttcctaataaataaggattgtgtagttattagcttttcactacctttgcatccactaaacgatattagattaatgcaataaagaa Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 228 End: 326 ................................................................................................................................................................................................................................... M S L E L C F F S F L T L R K N M G T L P L Q R S H Y S I V C I S ................................................................................. Protein_Len: 59 Strand: + Start: 224 End: 400 ............................................................................................................................................................................................................................... M N I F G T V L F L L L N A S K E H G N V A F A A V S L Q Y C L Y F L I N K D C V V I S F S L P L H P L N D I R L M Q ....... Protein_Len: 60 Strand: - Start: 196 End: 396 ................................................................................................................................................................................................... V P M F I K P V T S K R R R L A E F S C P F T A K A A T E N C Y Q K Y K R I F L S Q T T I L K E S G K C G S F S I L N M ........... Protein_Len: 32 Strand: - Start: 28 End: 123 ........................... Y T P S A F T R V N N K N P K A K V L F R I Y Y L K R H I N K M ............................................................................................................................................................................................................................................................................................ taagtcgtattcttgttttcaatgttaatatgtggggcttgcaaaggttctgacattgtttttgttaggtttcgctttcacgagaaaccgtatataatataattttcgatgtatatttttaatttatctaagctttgagaagcatttatctaagcttagataaattattatcagagttctgataaatatttcttaaagctttgataatttatttttaacaggcataaatatctttggaactgtgctttttctccttcttaacgcttcgaaagaacatgggaacgttgcctttgcagcggtctcattacagtattgtttgtatttcctaataaataaggattgtgtagttattagcttttcactacctttgcatccactaaacgatattagattaatgcaataaagaa 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================================================ taagtcgtattcttgttttcaatgttaatatgtggggcttgcaaaggttctgacattgtttttgttaggtttcgctttcacgagaaaccgtatataatataattttcgatgtatatttttaatttatctaagctttgagaagcatttatctaagcttagataaattattatcagagttctgataaatatttcttaaagctttgataatttatttttaacaggcataaatatctttggaactgtgctttttctccttcttaacgcttcgaaagaacatgggaacgttgcctttgcagcggtctcattacagtattgtttgtatttcctaataaataaggattgtgtagttattagcttttcactacctttgcatccactaaacgatattagattaatgcaataaagaa Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -14.6 Tail_Score: -3.34233 Start: 120 End: 167 Full_Region: TTCGATGTATATTTT TAATTTATCTAAGCTTTGAGAA GCAT TTATCTAAGCTTAGATAAATTA TTATCAGAGTTCTGA .......................................................................................................................TAATTTATCTAAGCTTTGAGAAGCATTTATCTAAGCTTAGATAAATTA................................................................................................................................................................................................................................................ TransTerm Strand: + Conf: 95 HP_score: -11.9 Tail_Score: -3.8062 Start: 123 End: 164 Full_Region: GATGTATATTTTTAA TTTATCTAAGCTTTGAGAA GCAT TTATCTAAGCTTAGATAAA TTATTATCAGAGTTC ..........................................................................................................................TTTATCTAAGCTTTGAGAAGCATTTATCTAAGCTTAGATAAA................................................................................................................................................................................................................................................... Find igs database================================================ Query_seq: PI0938:PI0939|PI0938:PI0939:hypothetical protein:TonB-dependent outer membrane protein:->->:869602..870008 407 taagtcgtattcttgttttcaatgttaatatgtggggcttgcaaaggttctgacattgtttttgttaggtttcgctttcacgagaaaccgtatataatataattttcgatgtatatttttaatttatctaagctttgagaagcatttatctaagcttagataaattattatcagagttctgataaatatttcttaaagctttgataatttatttttaacaggcataaatatctttggaactgtgctttttctccttcttaacgcttcgaaagaacatgggaacgttgcctttgcagcggtctcattacagtattgtttgtatttcctaataaataaggattgtgtagttattagcttttcactacctttgcatccactaaacgatattagattaatgcaataaagaa Intra-Species Hit: Count: 1 Min: 1 Max: 407 Len: 407 Subject: pint_PI0938_PI0939|hypothetical protein:TonB-dependent outer membrane protein|POSITIVE:POSITIVE|[869602,870008]|407 HSP 1 e-value: 0.0 bit: 807.0 Len: 407 Query Start:1 Query End:407 Subject Strand: POSITIVE Subject Start: 1 Subject End: 407 taagtcgtattcttgttttcaatgttaatatgtggggcttgcaaaggttctgacattgtttttgttaggtttcgctttcacgagaaaccgtatataatataattttcgatgtatatttttaatttatctaagctttgagaagcatttatctaagcttagataaattattatcagagttctgataaatatttcttaaagctttgataatttatttttaacaggcataaatatctttggaactgtgctttttctccttcttaacgcttcgaaagaacatgggaacgttgcctttgcagcggtctcattacagtattgtttgtatttcctaataaataaggattgtgtagttattagcttttcactacctttgcatccactaaacgatattagattaatgcaataaagaa taagtcgtattcttgttttcaatgttaatatgtggggcttgcaaaggttctgacattgtttttgttaggtttcgctttcacgagaaaccgtatataatataattttcgatgtatatttttaatttatctaagctttgagaagcatttatctaagcttagataaattattatcagagttctgataaatatttcttaaagctttgataatttatttttaacaggcataaatatctttggaactgtgctttttctccttcttaacgcttcgaaagaacatgggaacgttgcctttgcagcggtctcattacagtattgtttgtatttcctaataaataaggattgtgtagttattagcttttcactacctttgcatccactaaacgatattagattaatgcaataaagaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGUCGUAUUCUUGUUUUCAAUGUUAAUAUGUGGGGCUUGCAAAGGUUCUGACAUUGUUUUUGUUAGGUUUCGCUUUCACGAGAAACCGUAUAUAAUAUAAUUUUCGAUGUAUAUUUUUAAUUUAUCUAAGCUUUGAGAAGCAUUUAUCUAAGCUUAGAUAAAUUAUUAUCAGAGUUCUGAUAAAUAUUUCUUAAAGCUUUGAUAAUUUAUUUUUAACAGGCAUAAAUAUCUUUGGAACUGUGCUUUUUCUCCUUCUUAACGCUUCGAAAGAACAUGGGAACGUUGCCUUUGCAGCGGUCUCAUUACAGUAUUGUUUGUAUUUCCUAAUAAAUAAGGAUUGUGUAGUUAUUAGCUUUUCACUACCUUUGCAUCCACUAAACGAUAUUAGAUUAAUGCAAUAAAGAA ......(((((...((((..((((((.....(((((...(((((((((..(((..............((((((.(......).)))))).....(((((...(((((((.((.......(((.(((((.(((((((((((((.(((((((..(((((.(((((....))))).)))))..))))))).))))))))))))).))))).)))........(((((((....((....))..)))))))...............)).)))))))...((((((.((((((....)))))).))))))((((((.((((((((........))))))))..))))))....))))).....)))..)))))))))))))).....)))))))))).)))))......... (-105.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCUUUAUUGCAUUAAUCUAAUAUCGUUUAGUGGAUGCAAAGGUAGUGAAAAGCUAAUAACUACACAAUCCUUAUUUAUUAGGAAAUACAAACAAUACUGUAAUGAGACCGCUGCAAAGGCAACGUUCCCAUGUUCUUUCGAAGCGUUAAGAAGGAGAAAAAGCACAGUUCCAAAGAUAUUUAUGCCUGUUAAAAAUAAAUUAUCAAAGCUUUAAGAAAUAUUUAUCAGAACUCUGAUAAUAAUUUAUCUAAGCUUAGAUAAAUGCUUCUCAAAGCUUAGAUAAAUUAAAAAUAUACAUCGAAAAUUAUAUUAUAUACGGUUUCUCGUGAAAGCGAAACCUAACAAAAACAAUGUCAGAACCUUUGCAAGCCCCACAUAUUAACAUUGAAAACAAGAAUACGACUUA .......................((((...((((.(((((((((..(((...((.((((.((......((((........))))............(((((.(((.((.((.(((....))).)).)).))).(((((((..........))))))).......))))).....)).))))...)).((((.....(((.(((((.(((((((.((((....(((((((....)))))))..(((((((((....)))))))))..)))).))))))).))))).)))..............................((((..((((....)))))))).......))))...)))..)))))))))....)))).........(((....)))....)))).... (-83.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 600 180 131 202 153 pint:PI1716|5end_hypothetical_protein_1631588..1631818_POSITIVE 432 158 118 231 192 pint:PI1715|5end_conserved_hypothetical_protein;_possible_DNA-binding_protein,_histone-like_family_1631639..1631869_POSITIVE 334 300 263 202 170 pint:PI0424|5end_methylated-DNA--[protein]-cysteine_S-methyltransferase_388429..388659_POSITIVE 329 308 268 63 13 pint:PI1605|5end_conserved_hypothetical_protein_1534244..1534474_POSITIVE 324 302 263 188 148 pint:PI1671|5end_hypothetical_protein_1586397..1586627_POSITIVE 321 300 260 194 143 pint:PI0736|5end_transcriptional_regulator,_TetR_family_670580..670810_POSITIVE 318 299 253 217 162 pint:PI1198|5end_acetyltransferase_1114582..1114812_POSITIVE 299 326 284 216 173 pint:PI0728|5end_integrase_660427..660657_POSITIVE 295 279 231 75 27 pint:PI0263|5end_conjugative_transposon_protein,_TraM_255256..255486_POSITIVE 294 317 278 48 13 pint:PI1692|5end_alanine_racemase_1605691..1605921_POSITIVE 293 49 7 205 158 pint:PI1132|5end_DnaJ_heat_shock_protein_(Hsp40)_1058434..1058664_POSITIVE 293 93 51 76 31 pint:PI0743|5end_hypothetical_protein_672728..672958_POSITIVE 292 282 241 180 142 pint:PI1297|5end_conserved_hypothetical_protein_1209799..1210029_POSITIVE 291 299 251 165 103 pint:PI1011|5end_cytochrome_c_biogenesis_protein_CycY_932115..932345_POSITIVE 290 298 276 35 8 pint:PI0203|5end_conserved_hypothetical_protein_195109..195339_POSITIVE 289 301 263 108 71 pint:PI0635|5end_dephospho-CoA_kinase_580954..581184_POSITIVE 287 289 242 218 158 pint:PI0975|5end_glycine_dehydrogenase_[decarboxylating]_subunit_2_900798..901028_POSITIVE 285 50 1 145 92 pint:PI1079|5end_conserved_hypothetical_protein_999863..1000093_POSITIVE 284 308 261 76 14 pint:PI1157|5end_hypothetical_protein_1081704..1081934_POSITIVE 283 299 261 208 168 pint:PI1048|5end_1,4-dihydroxy-2-naphthoate_octaprenyltransferase_966277..966507_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 334 300 263 125 93 pint:PI0423|3end_hypothetical_protein_388432..388582_POSITIVE 321 300 260 125 74 pint:PI0735|3end_ABC_transporter,_ATP-binding_/_permease_670591..670741_POSITIVE 319 300 254 79 31 pint:PI0091|3end_hypothetical_protein_89774..89924_POSITIVE 315 303 261 132 84 pint:PI0578|3end_methyltransferase_523253..523403_POSITIVE 293 299 271 44 15 pint:PI1197|3end_pseudouridylate_synthetase_1114489..1114639_POSITIVE 291 302 262 142 100 pint:PI1180|3end_ferric_uptake_regulation_protein_1102409..1102559_POSITIVE 290 79 31 135 89 pint:PI1227|3end_conserved_hypothetical_protein;_possible_DNA-binding_protein,_histone-like_family_1148974..1149124_POSITIVE 290 298 276 35 8 pint:PI0202|3end_DNA_helicase_195189..195339_POSITIVE 290 320 271 124 69 pint:PI0019|3end_conserved_hypothetical_protein_24454..24604_POSITIVE 285 50 1 132 79 pint:PI1078|3end_conserved_hypothetical_protein_999930..1000080_POSITIVE 284 308 261 73 11 pint:PI1156|3end_possible_glycerate_kinase_family_protein_1081781..1081931_POSITIVE 280 294 260 110 66 pint:PI0912|3end_conserved_hypothetical_protein_842692..842842_POSITIVE 279 326 282 133 90 pint:PI0220|3end_conserved_hypothetical_protein_212341..212491_POSITIVE 278 315 275 61 17 pint:PI0704|3end_conserved_hypothetical_protein_641364..641514_POSITIVE 276 309 262 145 98 pint:PI0911|3end_tyrosine_phenol-lyase_841209..841359_POSITIVE 274 266 230 96 62 pint:PI2177|3end_phosphoribosylaminoimidazole_carboxylase_2117710..2117860_POSITIVE 274 50 5 124 70 pint:PI0587|3end_conserved_hypothetical_protein_535347..535497_POSITIVE 267 300 253 117 74 pint:PI0955|3end_conserved_hypothetical_protein_886084..886234_POSITIVE 267 74 32 134 95 pint:PI0581|3end_conserved_hypothetical_protein_532589..532739_POSITIVE 265 79 31 149 111 pint:PI0588|3end_hypothetical_protein_535425..535575_POSITIVE