Origin IGS: taaatttaaaaattaagttaatatagtataaggcttagtgaaccaatatccatttttcgcctttcaacaaggcttatagcatcgcaaatgatatttatcttatcaggatttattcggcagttctcgttagactcataccttaaaatccttaaaatatgcatcacggttgagttctgaaactataaaaacatggtattctactaatttttgcttttaaatagcaagatagcatattatttacagttacctttattcctcttacttatttgtactttttcataatatcgcaaagataagaaaaaaaattaaaccccaaaaactttttgtttattttttctaaattttgtaacttttgcgtctttatgggcaaagattattgttttgttggcagtaaaataaaagagggtgtgctgtttagaacacaccctctaatactattctattttatttataaggttta .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaaccttataaataaaatagaatagtattagagggtgtgttctaaacagcacaccctcttttattttactgccaacaaaacaataatctttgcccataaagacgcaaaagttacaaaatttagaaaaaataaacaaaaagtttttggggtttaattttttttcttatctttgcgatattatgaaaaagtacaaataagtaagaggaataaaggtaactgtaaataatatgctatcttgctatttaaaagcaaaaattagtagaataccatgtttttatagtttcagaactcaaccgtgatgcatattttaaggattttaaggtatgagtctaacgagaactgccgaataaatcctgataagataaatatcatttgcgatgctataagccttgttgaaaggcgaaaaatggatattggttcactaagccttatactatattaacttaatttttaaattta Mask Tandem Repeat Region ================================================ taaatttaaaaattaagttaatatagtataaggcttagtgaaccaatatccatttttcgcctttcaacaaggcttatagcatcgcaaatgatatttatcttatcaggatttattcggcagttctcgttagactcataccttaaaatccttaaaatatgcatcacggttgagttctgaaactataaaaacatggtattctactaatttttgcttttaaatagcaagatagcatattatttacagttacctttattcctcttacttatttgtactttttcataatatcgcaaagataagaaaaaaaattaaaccccaaaaactttttgtttattttttctaaattttgtaacttttgcgtctttatgggcaaagattattgttttgttggcagtaaaataaaagagggtgtgctgtttagaacacaccctctaatactattctattttatttataaggttta Find is-nt database================================================ Query_seq: PI1074:PI1075|PI1074:PI1075:hypothetical protein:pyruvate phosphate dikinase:->->:995508..995967 460 taaatttaaaaattaagttaatatagtataaggcttagtgaaccaatatccatttttcgcctttcaacaaggcttatagcatcgcaaatgatatttatcttatcaggatttattcggcagttctcgttagactcataccttaaaatccttaaaatatgcatcacggttgagttctgaaactataaaaacatggtattctactaatttttgcttttaaatagcaagatagcatattatttacagttacctttattcctcttacttatttgtactttttcataatatcgcaaagataagaaaaaaaattaaaccccaaaaactttttgtttattttttctaaattttgtaacttttgcgtctttatgggcaaagattattgttttgttggcagtaaaataaaagagggtgtgctgtttagaacacaccctctaatactattctattttatttataaggttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1074:PI1075|PI1074:PI1075:hypothetical protein:pyruvate phosphate dikinase:->->:995508..995967 460 taaatttaaaaattaagttaatatagtataaggcttagtgaaccaatatccatttttcgcctttcaacaaggcttatagcatcgcaaatgatatttatcttatcaggatttattcggcagttctcgttagactcataccttaaaatccttaaaatatgcatcacggttgagttctgaaactataaaaacatggtattctactaatttttgcttttaaatagcaagatagcatattatttacagttacctttattcctcttacttatttgtactttttcataatatcgcaaagataagaaaaaaaattaaaccccaaaaactttttgtttattttttctaaattttgtaacttttgcgtctttatgggcaaagattattgttttgttggcagtaaaataaaagagggtgtgctgtttagaacacaccctctaatactattctattttatttataaggttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1074:PI1075|PI1074:PI1075:hypothetical protein:pyruvate phosphate dikinase:->->:995508..995967 460 taaatttaaaaattaagttaatatagtataaggcttagtgaaccaatatccatttttcgcctttcaacaaggcttatagcatcgcaaatgatatttatcttatcaggatttattcggcagttctcgttagactcataccttaaaatccttaaaatatgcatcacggttgagttctgaaactataaaaacatggtattctactaatttttgcttttaaatagcaagatagcatattatttacagttacctttattcctcttacttatttgtactttttcataatatcgcaaagataagaaaaaaaattaaaccccaaaaactttttgtttattttttctaaattttgtaacttttgcgtctttatgggcaaagattattgttttgttggcagtaaaataaaagagggtgtgctgtttagaacacaccctctaatactattctattttatttataaggttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaatttaaaaattaagttaatatagtataaggcttagtgaaccaatatccatttttcgcctttcaacaaggcttatagcatcgcaaatgatatttatcttatcaggatttattcggcagttctcgttagactcataccttaaaatccttaaaatatgcatcacggttgagttctgaaactataaaaacatggtattctactaatttttgcttttaaatagcaagatagcatattatttacagttacctttattcctcttacttatttgtactttttcataatatcgcaaagataagaaaaaaaattaaaccccaaaaactttttgtttattttttctaaattttgtaacttttgcgtctttatgggcaaagattattgttttgttggcagtaaaataaaagagggtgtgctgtttagaacacaccctctaatactattctattttatttataaggttta Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 48 End: 140 ............................................... M H F S P F N K A Y S I A N D I Y L I R I Y S A V L V R L I P ................................................................................................................................................................................................................................................................................................................................ Protein_Len: 49 Strand: + Start: 28 End: 174 ........................... M R L S E P I S I F R L S T R L I A S Q M I F I L S G F I R Q F S L D S Y L K I L K I C I T V E F .............................................................................................................................................................................................................................................................................................. Protein_Len: 35 Strand: + Start: 233 End: 337 ........................................................................................................................................................................................................................................ M I Y S Y L Y S S Y L F V L F H N I A K I R K K I K P Q K L F V Y F F ........................................................................................................................... Protein_Len: 45 Strand: + Start: 324 End: 458 ................................................................................................................................................................................................................................................................................................................................... M F I F S K F C N F C V F M G K D Y C F V G S K I K E G V L F R T H P L I L F Y F I Y K V .. Protein_Len: 39 Strand: - Start: 309 End: 425 .................................................................................................................................................................................................................................................................................................................... V G F V K Q K N K R F K T V K A D K H A F I I T K N A T F Y F L T H Q K S C M ................................... Protein_Len: 35 Strand: - Start: 266 End: 370 ......................................................................................................................................................................................................................................................................... K Y K K M I D C L Y S F F N F G L F K K N I K E L N Q L K Q T K I P M .......................................................................................... Protein_Len: 30 Strand: - Start: 164 End: 253 ................................................................................................................................................................... P Q T R F S Y F C P I R S I K A K L Y C S L M N N V T V K M ............................................................................................................................................................................................................... Protein_Len: 48 Strand: - Start: 21 End: 164 .................... Y L I L S L S G I D M K R R E V L S I A D C I I N I K D P N I R C N E N S E Y R L I R L I H M M ........................................................................................................................................................................................................................................................................................................ taaatttaaaaattaagttaatatagtataaggcttagtgaaccaatatccatttttcgcctttcaacaaggcttatagcatcgcaaatgatatttatcttatcaggatttattcggcagttctcgttagactcataccttaaaatccttaaaatatgcatcacggttgagttctgaaactataaaaacatggtattctactaatttttgcttttaaatagcaagatagcatattatttacagttacctttattcctcttacttatttgtactttttcataatatcgcaaagataagaaaaaaaattaaaccccaaaaactttttgtttattttttctaaattttgtaacttttgcgtctttatgggcaaagattattgttttgttggcagtaaaataaaagagggtgtgctgtttagaacacaccctctaatactattctattttatttataaggttta 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================================================ taaatttaaaaattaagttaatatagtataaggcttagtgaaccaatatccatttttcgcctttcaacaaggcttatagcatcgcaaatgatatttatcttatcaggatttattcggcagttctcgttagactcataccttaaaatccttaaaatatgcatcacggttgagttctgaaactataaaaacatggtattctactaatttttgcttttaaatagcaagatagcatattatttacagttacctttattcctcttacttatttgtactttttcataatatcgcaaagataagaaaaaaaattaaaccccaaaaactttttgtttattttttctaaattttgtaacttttgcgtctttatgggcaaagattattgttttgttggcagtaaaataaaagagggtgtgctgtttagaacacaccctctaatactattctattttatttataaggttta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 74 HP_score: -4.9 Tail_Score: -5.13354 Start: 314 End: 326 Full_Region: AAAAAAATTAAACCC CAAAA ACT TTTTG TTTATTTTTTCTAAA .........................................................................................................................................................................................................................................................................................................................CAAAAACTTTTTG...................................................................................................................................... TransTerm Strand: + Conf: 46 HP_score: -2.1 Tail_Score: -3.63424 Start: 396 End: 435 Full_Region: TTTGTTGGCAGTAAA ATAAAAGAGGGTGTGCT GTTTAG AACACACCCTCTAATAC TATTCTATTTTATTT ...........................................................................................................................................................................................................................................................................................................................................................................................................ATAAAAGAGGGTGTGCTGTTTAGAACACACCCTCTAATAC......................... TransTerm Strand: - Conf: 77 HP_score: -7.8 Tail_Score: -4.25104 Start: 397 End: 434 Full_Region: aataaaatagaatag tattagagggtgtgtt ctaaac agcacaccctctttta ttttactgccaacaa ............................................................................................................................................................................................................................................................................................................................................................................................................tattagagggtgtgttctaaacagcacaccctctttta.......................... Find igs database================================================ Query_seq: PI1074:PI1075|PI1074:PI1075:hypothetical protein:pyruvate phosphate dikinase:->->:995508..995967 460 taaatttaaaaattaagttaatatagtataaggcttagtgaaccaatatccatttttcgcctttcaacaaggcttatagcatcgcaaatgatatttatcttatcaggatttattcggcagttctcgttagactcataccttaaaatccttaaaatatgcatcacggttgagttctgaaactataaaaacatggtattctactaatttttgcttttaaatagcaagatagcatattatttacagttacctttattcctcttacttatttgtactttttcataatatcgcaaagataagaaaaaaaattaaaccccaaaaactttttgtttattttttctaaattttgtaacttttgcgtctttatgggcaaagattattgttttgttggcagtaaaataaaagagggtgtgctgtttagaacacaccctctaatactattctattttatttataaggttta Intra-Species Hit: Count: 1 Min: 1 Max: 460 Len: 460 Subject: pint_PI1074_PI1075|hypothetical protein:pyruvate phosphate dikinase|POSITIVE:POSITIVE|[995508,995967]|460 HSP 1 e-value: 1.0E-167 bit: 589.0 Len: 297 Query Start:1 Query End:297 Subject Strand: POSITIVE Subject Start: 1 Subject End: 297 taaatttaaaaattaagttaatatagtataaggcttagtgaaccaatatccatttttcgcctttcaacaaggcttatagcatcgcaaatgatatttatcttatcaggatttattcggcagttctcgttagactcataccttaaaatccttaaaatatgcatcacggttgagttctgaaactataaaaacatggtattctactaatttttgcttttaaatagcaagatagcatattatttacagttacctttattcctcttacttatttgtactttttcataatatcgcaaagataag................................................................................................................................................................... taaatttaaaaattaagttaatatagtataaggcttagtgaaccaatatccatttttcgcctttcaacaaggcttatagcatcgcaaatgatatttatcttatcaggatttattcggcagttctcgttagactcataccttaaaatccttaaaatatgcatcacggttgagttctgaaactataaaaacatggtattctactaatttttgcttttaaatagcaagatagcatattatttacagttacctttattcctcttacttatttgtactttttcataatatcgcaaagataag................................................................................................................................................................... HSP 2 e-value: 1.0E-34 bit: 149.0 Len: 75 Query Start:386 Query End:460 Subject Strand: POSITIVE Subject Start: 386 Subject End: 460 .................................................................................................................................................................................................................................................................................................................................................................................................tggcagtaaaataaaagagggtgtgctgtttagaacacaccctctaatactattctattttatttataaggttta .................................................................................................................................................................................................................................................................................................................................................................................................tggcagtaaaataaaagagggtgtgctgtttagaacacaccctctaatactattctattttatttataaggttta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAUUUAAAAAUUAAGUUAAUAUAGUAUAAGGCUUAGUGAACCAAUAUCCAUUUUUCGCCUUUCAACAAGGCUUAUAGCAUCGCAAAUGAUAUUUAUCUUAUCAGGAUUUAUUCGGCAGUUCUCGUUAGACUCAUACCUUAAAAUCCUUAAAAUAUGCAUCACGGUUGAGUUCUGAAACUAUAAAAACAUGGUAUUCUACUAAUUUUUGCUUUUAAAUAGCAAGAUAGCAUAUUAUUUACAGUUACCUUUAUUCCUCUUACUUAUUUGUACUUUUUCAUAAUAUCGCAAAGAUAAGAAAAAAAAUUAAACCCCAAAAACUUUUUGUUUAUUUUUUCUAAAUUUUGUAACUUUUGCGUCUUUAUGGGCAAAGAUUAUUGUUUUGUUGGCAGUAAAAUAAAAGAGGGUGUGCUGUUUAGAACACACCCUCUAAUACUAUUCUAUUUUAUUUAUAAGGUUUA ....((((.((((.((((....(((((((...(((.((..((.(((((..(.......(((((.....))))).....((...((((((((.............(((((((....((.((((.......))))....))...)))))))...(((((((..........(((...((((((((......))))).))).)))...(((((((.......)))))))..)))))))...........................)))))))).......(((((...(((((((((((((..(((((.(((((..............))))).))))).....))))))...)))))))...))))).))...)..))))).))..)))))...........((((((((((..........)))))))))).)))))))...)))).)))).))))..... (-85.54) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAACCUUAUAAAUAAAAUAGAAUAGUAUUAGAGGGUGUGUUCUAAACAGCACACCCUCUUUUAUUUUACUGCCAACAAAACAAUAAUCUUUGCCCAUAAAGACGCAAAAGUUACAAAAUUUAGAAAAAAUAAACAAAAAGUUUUUGGGGUUUAAUUUUUUUUCUUAUCUUUGCGAUAUUAUGAAAAAGUACAAAUAAGUAAGAGGAAUAAAGGUAACUGUAAAUAAUAUGCUAUCUUGCUAUUUAAAAGCAAAAAUUAGUAGAAUACCAUGUUUUUAUAGUUUCAGAACUCAACCGUGAUGCAUAUUUUAAGGAUUUUAAGGUAUGAGUCUAACGAGAACUGCCGAAUAAAUCCUGAUAAGAUAAAUAUCAUUUGCGAUGCUAUAAGCCUUGUUGAAAGGCGAAAAAUGGAUAUUGGUUCACUAAGCCUUAUACUAUAUUAACUUAAUUUUUAAAUUUA (((((((((.((((....((((((((....((((((((((((......)))))))))))).))))))))...............(((..(((((..........)))))..)))..........................)))).)))))))))...(((((((.((((.....))))....)))))))....((((((((.((((......((.(((((((((.((((((.(((..(((((...............)))))..))).))))))))))))))))).((((......((((((..((((((((((((((...((((....((....))....))))....)))))))..)))))))..))))))...(((((((((..(((((.....))))).....)))).)))))))))......)))).)))).))))................... (-101.96) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 373 298 256 154 103 pint:PI0451|5end_serine_proteases,__S51_group_424343..424573_POSITIVE 323 429 396 188 154 pint:PI1940|5end_conserved_hypothetical_protein;_possible_outer_membrane_protein_1895730..1895960_POSITIVE 283 430 390 178 128 pint:PI0426|5end_conserved_hypothetical_protein_389345..389575_POSITIVE 278 394 353 47 1 pint:PI0666|5end_chorismate_synthase_609006..609236_POSITIVE 270 85 51 213 164 pint:PI0463|5end_50S_ribosomal_protein_L2_434158..434388_POSITIVE 268 409 361 215 163 pint:PI0700|5end_UDP-glucose_4-epimerase_637299..637529_POSITIVE 263 392 353 214 176 pint:PI0228|5end_outer_membrane_cobalamin_receptor_protein_225752..225982_POSITIVE 261 438 392 167 110 pint:PI1086|5end_pyruvate:ferredoxin_oxidoreductase_1006602..1006832_POSITIVE 260 80 31 153 93 pint:PI1265|5end_hypothetical_protein_1185016..1185246_POSITIVE 259 404 361 171 125 pint:PI1370|5end_alkyl_hydroperoxide_reductase,_subunit_F_1290540..1290770_POSITIVE 259 446 403 39 3 pint:PI0853|5end_glycosyl_transferase,_group_2_family_protein_785515..785745_POSITIVE 257 70 25 64 6 pint:PI0988|5end_hypothetical_protein_912347..912577_POSITIVE 253 140 97 175 125 pint:PI0475|5end_50S_ribosomal_protein_L6_439453..439683_POSITIVE 251 392 353 41 9 pint:PI1415|5end_cation_transporting_ATPase/E1-E2_ATPase_1333939..1334169_POSITIVE 249 419 377 218 164 pint:PI2002|5end_hypothetical_protein_1960662..1960892_POSITIVE 248 420 387 90 56 pint:PI0982|5end_hypothetical_protein_909432..909662_POSITIVE 247 430 383 98 46 pint:PI1314|5end_hypothetical_protein_1231188..1231418_POSITIVE 246 446 401 173 120 pint:PI1505|5end_2-amino-4-hydroxy-6-hydroxymethyldihydropteridine_pyrophosphokinase_1424922..1425152_POSITIVE 246 387 351 208 171 pint:PI0544|5end_hypoxanthine-guanine_phosphoribosyltransferase_(hypoxanthine_phosphoribosyltransferase)_495645..495875_POSITIVE 246 387 351 117 80 pint:PI0542|5end_hypothetical_protein_495554..495784_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 260 80 31 131 71 pint:PI1264|3end_hypothetical_protein_1185074..1185224_POSITIVE 256 416 375 128 78 pint:PI2001|3end_hypothetical_protein_1960478..1960628_POSITIVE 247 393 357 41 12 pint:PI1689|3end_conserved_hypothetical_protein_1605202..1605352_POSITIVE 247 430 383 71 19 pint:PI1313|3end_possible_POT_family_(proton-dependent_oligopeptide_transport_family)_1231241..1231391_POSITIVE 246 446 401 75 22 pint:PI1504|3end_non-specific_DNA-binding_protein_1424904..1425054_POSITIVE 245 90 49 91 45 pint:PI1732|3end_hypothetical_protein_1652098..1652248_POSITIVE 241 410 362 95 41 pint:PI1488|3end_hypothetical_protein_1407829..1407979_POSITIVE 241 409 364 125 96 pint:PI1298|3end_glycosyltransferase_1212316..1212466_POSITIVE 239 126 87 37 5 pint:PI0220|3end_conserved_hypothetical_protein_212341..212491_POSITIVE 239 87 51 74 34 pint:PI0042|3end_hypothetical_protein_43444..43594_POSITIVE 238 428 386 51 1 pint:PI0647|3end_potassium_uptake_protein_589276..589426_POSITIVE 237 430 383 81 30 pint:PI0748|3end_possible_mobilization_protein_677214..677364_POSITIVE 237 418 386 77 41 pint:PI0410|3end_glutamyl-tRNA_synthetase_(glutamate--tRNA_ligase)_377490..377640_POSITIVE 236 407 365 56 15 pint:PI2153|3end_hypothetical_protein_2099630..2099780_POSITIVE 236 290 247 134 85 pint:PI0962|3end_phosphoglycerate_mutase_892702..892852_POSITIVE 235 124 84 62 19 pint:PI2136|3end_hypothetical_protein_2082840..2082990_POSITIVE 235 120 71 79 22 pint:PI0947|3end_conserved_hypothetical_protein_880709..880859_POSITIVE 235 80 33 85 45 pint:PI0380|3end_conserved_hypothetical_protein_350541..350691_POSITIVE 235 388 349 42 6 pint:PI0005|3end_hypothetical_protein_7450..7600_POSITIVE 233 77 31 62 9 pint:PI1622|3end_hypothetical_protein_1547230..1547380_POSITIVE