Origin IGS: tagctgtttttcaacgacgatattcagcaacaacaaggaaacggtttctctaatacgcttctattgtaccgcaaaaacgtttggatacaaagccctaaaaaagcctatgcttgctcacgcatacataggccttgccacttaactaaataactcaaaaaattacttgactcaattcttgttagtgcgtcttcgtcacgaggacatactaacttacatttgtttgactattaacttactaataactattttgtctatttgtaatcaagacttatttataagtgttgcaaaggtatatataaaaaaacaaaaaaacaaactatttacggcgtttttttcttggaattatggatttttatagctacagcagcactttaacatatacttttggcttttatttccattaataacaggcaactttgttattattttcctcaacctactaacaatatgtttattttttcttaataccgttttggttgaattgttattacaaaattgctgttacatacaatgttcattggtaaacggctttgttgcaaaggagggattagcttgttta .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaacaagctaatccctcctttgcaacaaagccgtttaccaatgaacattgtatgtaacagcaattttgtaataacaattcaaccaaaacggtattaagaaaaaataaacatattgttagtaggttgaggaaaataataacaaagttgcctgttattaatggaaataaaagccaaaagtatatgttaaagtgctgctgtagctataaaaatccataattccaagaaaaaaacgccgtaaatagtttgtttttttgtttttttatatatacctttgcaacacttataaataagtcttgattacaaatagacaaaatagttattagtaagttaatagtcaaacaaatgtaagttagtatgtcctcgtgacgaagacgcactaacaagaattgagtcaagtaattttttgagttatttagttaagtggcaaggcctatgtatgcgtgagcaagcataggcttttttagggctttgtatccaaacgtttttgcggtacaatagaagcgtattagagaaaccgtttccttgttgttgctgaatatcgtcgttgaaaaacagcta Mask Tandem Repeat Region ================================================ tagctgtttttcaacgacgatattcagcaacaacaaggaaacggtttctctaatacgcttctattgtaccgcaaaaacgtttggatacaaagccctaaaaaagcctatgcttgctcacgcatacataggccttgccacttaactaaataactcaaaaaattacttgactcaattcttgttagtgcgtcttcgtcacgaggacatactaacttacatttgtttgactattaacttactaataactattttgtctatttgtaatcaagacttatttataagtgttgcaaaggtatatataaaaaaacaaaaaaacaaactatttacggcgtttttttcttggaattatggatttttatagctacagcagcactttaacatatacttttggcttttatttccattaataacaggcaactttgttattattttcctcaacctactaacaatatgtttattttttcttaataccgttttggttgaattgttattacaaaattgctgttacatacaatgttcattggtaaacggctttgttgcaaaggagggattagcttgttta Find is-nt database================================================ Query_seq: PI1866:PI1867|PI1866:PI1867:hypothetical protein:helicase related protein:->->:1811971..1812529 559 tagctgtttttcaacgacgatattcagcaacaacaaggaaacggtttctctaatacgcttctattgtaccgcaaaaacgtttggatacaaagccctaaaaaagcctatgcttgctcacgcatacataggccttgccacttaactaaataactcaaaaaattacttgactcaattcttgttagtgcgtcttcgtcacgaggacatactaacttacatttgtttgactattaacttactaataactattttgtctatttgtaatcaagacttatttataagtgttgcaaaggtatatataaaaaaacaaaaaaacaaactatttacggcgtttttttcttggaattatggatttttatagctacagcagcactttaacatatacttttggcttttatttccattaataacaggcaactttgttattattttcctcaacctactaacaatatgtttattttttcttaataccgttttggttgaattgttattacaaaattgctgttacatacaatgttcattggtaaacggctttgttgcaaaggagggattagcttgttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1866:PI1867|PI1866:PI1867:hypothetical protein:helicase related protein:->->:1811971..1812529 559 tagctgtttttcaacgacgatattcagcaacaacaaggaaacggtttctctaatacgcttctattgtaccgcaaaaacgtttggatacaaagccctaaaaaagcctatgcttgctcacgcatacataggccttgccacttaactaaataactcaaaaaattacttgactcaattcttgttagtgcgtcttcgtcacgaggacatactaacttacatttgtttgactattaacttactaataactattttgtctatttgtaatcaagacttatttataagtgttgcaaaggtatatataaaaaaacaaaaaaacaaactatttacggcgtttttttcttggaattatggatttttatagctacagcagcactttaacatatacttttggcttttatttccattaataacaggcaactttgttattattttcctcaacctactaacaatatgtttattttttcttaataccgttttggttgaattgttattacaaaattgctgttacatacaatgttcattggtaaacggctttgttgcaaaggagggattagcttgttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1866:PI1867|PI1866:PI1867:hypothetical protein:helicase related protein:->->:1811971..1812529 559 tagctgtttttcaacgacgatattcagcaacaacaaggaaacggtttctctaatacgcttctattgtaccgcaaaaacgtttggatacaaagccctaaaaaagcctatgcttgctcacgcatacataggccttgccacttaactaaataactcaaaaaattacttgactcaattcttgttagtgcgtcttcgtcacgaggacatactaacttacatttgtttgactattaacttactaataactattttgtctatttgtaatcaagacttatttataagtgttgcaaaggtatatataaaaaaacaaaaaaacaaactatttacggcgtttttttcttggaattatggatttttatagctacagcagcactttaacatatacttttggcttttatttccattaataacaggcaactttgttattattttcctcaacctactaacaatatgtttattttttcttaataccgttttggttgaattgttattacaaaattgctgttacatacaatgttcattggtaaacggctttgttgcaaaggagggattagcttgttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tagctgtttttcaacgacgatattcagcaacaacaaggaaacggtttctctaatacgcttctattgtaccgcaaaaacgtttggatacaaagccctaaaaaagcctatgcttgctcacgcatacataggccttgccacttaactaaataactcaaaaaattacttgactcaattcttgttagtgcgtcttcgtcacgaggacatactaacttacatttgtttgactattaacttactaataactattttgtctatttgtaatcaagacttatttataagtgttgcaaaggtatatataaaaaaacaaaaaaacaaactatttacggcgtttttttcttggaattatggatttttatagctacagcagcactttaacatatacttttggcttttatttccattaataacaggcaactttgttattattttcctcaacctactaacaatatgtttattttttcttaataccgttttggttgaattgttattacaaaattgctgttacatacaatgttcattggtaaacggctttgttgcaaaggagggattagcttgttta Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: + Start: 20 End: 139 ................... M F S N N K E T V S L I R F Y C T A K T F G Y K A L K K P M L A H A Y I G L A T .................................................................................................................................................................................................................................................................................................................................................................................................................................... Protein_Len: 48 Strand: + Start: 4 End: 147 ... M F F N D D I Q Q Q Q G N G F S N T L L L Y R K N V W I Q S P K K A Y A C S R I H R P C H L T K ............................................................................................................................................................................................................................................................................................................................................................................................................................ Protein_Len: 60 Strand: + Start: 164 End: 355 ................................................................................................................................................................... M T Q F L L V R L R H E D I L T Y I C L T I N L L I T I L S I C N Q D L F I S V A K V Y I K K Q K N K L F T A F F S W N ............................................................................................................................................................................................................ Protein_Len: 34 Strand: + Start: 271 End: 372 .............................................................................................................................................................................................................................................................................. M Y K C C K G I Y K K T K K Q T I Y G V F F L E L W I F I A T A A L ........................................................................................................................................................................................... Protein_Len: 60 Strand: + Start: 377 End: 559 ........................................................................................................................................................................................................................................................................................................................................................................................ M Y F W L L F P L I T G N F V I I F L N L L T I C L F F L N T V L V E L L L Q N C C Y I Q C S L V N G F V A K E G L A C Protein_Len: 34 Strand: - Start: 346 End: 447 ......................................................................................................................................................................................................................................................................................................................................................... P N K Y S C C C K L M Y K Q S K N G N I V P L K T I I K R L R S V M ................................................................................................................ tagctgtttttcaacgacgatattcagcaacaacaaggaaacggtttctctaatacgcttctattgtaccgcaaaaacgtttggatacaaagccctaaaaaagcctatgcttgctcacgcatacataggccttgccacttaactaaataactcaaaaaattacttgactcaattcttgttagtgcgtcttcgtcacgaggacatactaacttacatttgtttgactattaacttactaataactattttgtctatttgtaatcaagacttatttataagtgttgcaaaggtatatataaaaaaacaaaaaaacaaactatttacggcgtttttttcttggaattatggatttttatagctacagcagcactttaacatatacttttggcttttatttccattaataacaggcaactttgttattattttcctcaacctactaacaatatgtttattttttcttaataccgttttggttgaattgttattacaaaattgctgttacatacaatgttcattggtaaacggctttgttgcaaaggagggattagcttgttta 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: 83 Start: 131 End: 160 ..................................................................................................................................CTTGCCACTTAACTAAATAACTCAAAAAAT............................................................................................................................................................................................................................................................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 82 Start: 220 End: 249 ...........................................................................................................................................................................................................................TTTGACTATTAACTTACTAATAACTATTTT...................................................................................................................................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tagctgtttttcaacgacgatattcagcaacaacaaggaaacggtttctctaatacgcttctattgtaccgcaaaaacgtttggatacaaagccctaaaaaagcctatgcttgctcacgcatacataggccttgccacttaactaaataactcaaaaaattacttgactcaattcttgttagtgcgtcttcgtcacgaggacatactaacttacatttgtttgactattaacttactaataactattttgtctatttgtaatcaagacttatttataagtgttgcaaaggtatatataaaaaaacaaaaaaacaaactatttacggcgtttttttcttggaattatggatttttatagctacagcagcactttaacatatacttttggcttttatttccattaataacaggcaactttgttattattttcctcaacctactaacaatatgtttattttttcttaataccgttttggttgaattgttattacaaaattgctgttacatacaatgttcattggtaaacggctttgttgcaaaggagggattagcttgttta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -10.6 Tail_Score: -5.07107 Start: 103 End: 130 Full_Region: tagttaagtggcaag gcctatgtatgc gtga gcaagcataggc ttttttagggctttg ......................................................................................................gcctatgtatgcgtgagcaagcataggc............................................................................................................................................................................................................................................................................................................................................................................................................................................. TransTerm Strand: + Conf: 91 HP_score: -12.1 Tail_Score: -3.41807 Start: 178 End: 210 Full_Region: CTTGACTCAATTCTT GTTAGTGCGTCTTCG TCA CGAGGACATACTAAC TTACATTTGTTTGAC .................................................................................................................................................................................GTTAGTGCGTCTTCGTCACGAGGACATACTAAC............................................................................................................................................................................................................................................................................................................................................................. Find igs database================================================ Query_seq: PI1866:PI1867|PI1866:PI1867:hypothetical protein:helicase related protein:->->:1811971..1812529 559 tagctgtttttcaacgacgatattcagcaacaacaaggaaacggtttctctaatacgcttctattgtaccgcaaaaacgtttggatacaaagccctaaaaaagcctatgcttgctcacgcatacataggccttgccacttaactaaataactcaaaaaattacttgactcaattcttgttagtgcgtcttcgtcacgaggacatactaacttacatttgtttgactattaacttactaataactattttgtctatttgtaatcaagacttatttataagtgttgcaaaggtatatataaaaaaacaaaaaaacaaactatttacggcgtttttttcttggaattatggatttttatagctacagcagcactttaacatatacttttggcttttatttccattaataacaggcaactttgttattattttcctcaacctactaacaatatgtttattttttcttaataccgttttggttgaattgttattacaaaattgctgttacatacaatgttcattggtaaacggctttgttgcaaaggagggattagcttgttta Intra-Species Hit: Count: 1 Min: 1 Max: 559 Len: 559 Subject: pint_PI1866_PI1867|hypothetical protein:helicase related protein|POSITIVE:POSITIVE|[1811971,1812529]|559 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 tagctgtttttcaacgacgatattcagcaacaacaaggaaacggtttctctaatacgcttctattgtaccgcaaaaacgtttggatacaaagccctaaaaaagcctatgcttgctcacgcatacataggccttgccacttaactaaataactcaaaaaattacttgactcaattcttgttagtgcgtcttcgtcacgaggacatactaacttacatttgtttgactattaacttactaataactattttgtctatttgtaatcaagacttatttataagtgttgcaaaggtatatat...................................................................................................................................................................................................................................................................... tagctgtttttcaacgacgatattcagcaacaacaaggaaacggtttctctaatacgcttctattgtaccgcaaaaacgtttggatacaaagccctaaaaaagcctatgcttgctcacgcatacataggccttgccacttaactaaataactcaaaaaattacttgactcaattcttgttagtgcgtcttcgtcacgaggacatactaacttacatttgtttgactattaacttactaataactattttgtctatttgtaatcaagacttatttataagtgttgcaaaggtatatat...................................................................................................................................................................................................................................................................... HSP 2 e-value: 1.0E-124 bit: 448.0 Len: 247 Query Start:313 Query End:559 Subject Strand: POSITIVE Subject Start: 313 Subject End: 559 ........................................................................................................................................................................................................................................................................................................................caaactatttacggcgnnnnnnncttggaattatggatttttatagctacagcagcactttaacatatacttttggcttttatttccattaataacaggcaactttgttattattttcctcaacctactaacaatatgtttattttttcttaataccgttttggttgaattgttattacaaaattgctgttacatacaatgttcattggtaaacggctttgttgcaaaggagggattagcttgttta ........................................................................................................................................................................................................................................................................................................................caaactatttacggcgtttttttcttggaattatggatttttatagctacagcagcactttaacatatacttttggcttttatttccattaataacaggcaactttgttattattttcctcaacctactaacaatatgtttattttttcttaataccgttttggttgaattgttattacaaaattgctgttacatacaatgttcattggtaaacggctttgttgcaaaggagggattagcttgttta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGCUGUUUUUCAACGACGAUAUUCAGCAACAACAAGGAAACGGUUUCUCUAAUACGCUUCUAUUGUACCGCAAAAACGUUUGGAUACAAAGCCCUAAAAAAGCCUAUGCUUGCUCACGCAUACAUAGGCCUUGCCACUUAACUAAAUAACUCAAAAAAUUACUUGACUCAAUUCUUGUUAGUGCGUCUUCGUCACGAGGACAUACUAACUUACAUUUGUUUGACUAUUAACUUACUAAUAACUAUUUUGUCUAUUUGUAAUCAAGACUUAUUUAUAAGUGUUGCAAAGGUAUAUAUAAAAAAACAAAAAAACAAACUAUUUACGGCGUUUUUUUCUUGGAAUUAUGGAUUUUUAUAGCUACAGCAGCACUUUAACAUAUACUUUUGGCUUUUAUUUCCAUUAAUAACAGGCAACUUUGUUAUUAUUUUCCUCAACCUACUAACAAUAUGUUUAUUUUUUCUUAAUACCGUUUUGGUUGAAUUGUUAUUACAAAAUUGCUGUUACAUACAAUGUUCAUUGGUAAACGGCUUUGUUGCAAAGGAGGGAUUAGCUUGUUUA ..((((..(.((......)).)..))))...((((((............(((((.(.(((((.(((((..(((((..((((((((...((((((........(((((((..(((....)))..))))))).............(((((((.((.....(((((..(((..(((..(((((((((.(((((((...)))))))...(.(((........))).)..........)))))))))..)))..))).....)))))...)).))))))).(((((((((....(((..((((((((..(((((((((..............)))))))...........))..))))))))..))).)))))))))..............))))))....))).....((((((.(((.(((((...((......((((((....(((..(((...............)))..)))..)))))).....))..))))).)))))))))....((((....))))..)))))..))))))))))))))).)))))))))))).. (-117.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAACAAGCUAAUCCCUCCUUUGCAACAAAGCCGUUUACCAAUGAACAUUGUAUGUAACAGCAAUUUUGUAAUAACAAUUCAACCAAAACGGUAUUAAGAAAAAAUAAACAUAUUGUUAGUAGGUUGAGGAAAAUAAUAACAAAGUUGCCUGUUAUUAAUGGAAAUAAAAGCCAAAAGUAUAUGUUAAAGUGCUGCUGUAGCUAUAAAAAUCCAUAAUUCCAAGAAAAAAACGCCGUAAAUAGUUUGUUUUUUUGUUUUUUUAUAUAUACCUUUGCAACACUUAUAAAUAAGUCUUGAUUACAAAUAGACAAAAUAGUUAUUAGUAAGUUAAUAGUCAAACAAAUGUAAGUUAGUAUGUCCUCGUGACGAAGACGCACUAACAAGAAUUGAGUCAAGUAAUUUUUUGAGUUAUUUAGUUAAGUGGCAAGGCCUAUGUAUGCGUGAGCAAGCAUAGGCUUUUUUAGGGCUUUGUAUCCAAACGUUUUUGCGGUACAAUAGAAGCGUAUUAGAGAAACCGUUUCCUUGUUGUUGCUGAAUAUCGUCGUUGAAAAACAGCUA ......(((.............(((((((.(((((.....((((..........((((((((((((((((........(((((((..((((((((...............))))))))....)))))))..........))))))))).)))))))...((((....((((((....((((((((.((((.((((...))))..................((((((((((((..........)))).))))))))..)))).))))))))..((((..(((((((((((((.((..((((((.....(((......((((((((....))))))).)............((((((.((((.(((...))).)))).)))))).........)))..))))))....)).)))))))..)))))))))).((((((((.(((....))).))))))))........))))))...))))..))))...)))))......((((((..((....))..))))))....)))))))...........(((....))).))). (-132.83) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 334 538 491 49 9 pint:PI1921|5end_conserved_hypothetical_protein_1863917..1864147_POSITIVE 325 88 43 99 51 pint:PI0529|5end_hypothetical_protein_483026..483256_POSITIVE 315 138 91 54 10 pint:PI0545|5end_sugar_kinase_496411..496641_POSITIVE 294 137 103 170 136 pint:PI1232|5end_conserved_hypothetical_protein_1152757..1152987_POSITIVE 293 150 103 176 110 pint:PI0365|5end_hypothetical_protein_335721..335951_POSITIVE 291 288 248 110 75 pint:PI0577|5end_conserved_hypothetical_protein_521811..522041_POSITIVE 287 367 324 230 180 pint:PI1851|5end_conserved_hypothetical_protein_1796847..1797077_POSITIVE 287 137 101 209 167 pint:PI0953|5end_hypothetical_protein_885119..885349_POSITIVE 286 150 103 70 18 pint:PI0586|5end_hypothetical_protein_533757..533987_POSITIVE 283 549 501 78 21 pint:PI0774|5end_phosphoserine_aminotransferase_(phosphoserine_transaminase)_709497..709727_POSITIVE 283 138 92 61 6 pint:PI0329|5end_hypothetical_protein_310066..310296_POSITIVE 280 209 163 124 71 pint:PI1876|5end_possible_flagellar_motor_protein,_OmpA_family_1819082..1819312_POSITIVE 277 207 177 102 66 pint:PI1399|5end_hypothetical_protein_1320573..1320803_POSITIVE 276 548 506 168 113 pint:PI0408|5end_hypothetical_protein_374154..374384_POSITIVE 276 93 52 226 180 pint:PI0159|5end_hypothetical_protein_151273..151503_POSITIVE 276 93 52 138 92 pint:PI0157|5end_hypothetical_protein_151185..151415_POSITIVE 271 135 91 73 18 pint:PI0200|5end_hypothetical_protein_191545..191775_POSITIVE 270 370 324 51 14 pint:PI1871|5end_glycosyl_transferase,_group_1_family_protein_1815788..1816018_POSITIVE 269 146 103 58 13 pint:PI0796|5end_competence_protein_733324..733554_POSITIVE 267 137 103 110 74 pint:PI1854|5end_possible_glycosyl_transferase_1800925..1801155_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 388 135 91 122 80 pint:PI1715|3end_conserved_hypothetical_protein;_possible_DNA-binding_protein,_histone-like_family_1632324..1632474_POSITIVE 346 215 181 136 94 pint:PI1882|3end_hypothetical_protein_1826487..1826637_POSITIVE 325 88 43 115 67 pint:PI0528|3end_hypothetical_protein_483122..483272_POSITIVE 313 136 92 55 19 pint:PI0999|3end_hypothetical_protein_922812..922962_POSITIVE 300 140 92 145 96 pint:PI0019|3end_conserved_hypothetical_protein_24454..24604_POSITIVE 294 137 103 62 28 pint:PI1230|3end_probable_metallo-beta-lactamase_family_protein_1152729..1152879_POSITIVE 293 138 108 148 109 pint:PI2099|3end_D-alanyl-D-alanine_dipeptidase_2053277..2053427_POSITIVE 280 209 163 68 15 pint:PI1875|3end_hypothetical_protein_1819106..1819256_POSITIVE 277 207 177 121 85 pint:PI1398|3end_probable_imidazolonepropionase_1320672..1320822_POSITIVE 276 548 506 81 26 pint:PI0407|3end_tryptophanyl-tRNA_synthetase_(tryptophan--tRNA_ligase)_374147..374297_POSITIVE 267 197 151 133 95 pint:PI1780|3end_1-deoxy-D-xylulose_5-phosphate_reductoisomerase_1713097..1713247_POSITIVE 267 147 101 54 6 pint:PI0948|3end_hypothetical_protein_881978..882128_POSITIVE 267 547 505 139 87 pint:PI0056|3end_conserved_hypothetical_protein;_possible_DNA_uptake_protein_55907..56057_POSITIVE 266 375 338 135 97 pint:PI0015|3end_possible__transport_protein_20150..20300_POSITIVE 263 138 92 145 100 pint:PI1490|3end_GTP_cyclohydrolase_I_1409127..1409277_POSITIVE 261 60 13 84 37 pint:PI1806|3end_integral_membrane_transport_protein;_possible_sugar_transport_proteins_1742191..1742341_POSITIVE 260 140 108 139 114 pint:PI0890|3end_ribose_5-phosphate_isomerase_B_820931..821081_POSITIVE 260 141 101 139 101 pint:PI0600|3end_bifunctional_purine_biosynthesis_protein,_5-aminoimidazole-4-carboxamide_ribonucleotide(AICAR)_transformylase/IMP_cyclohydrolase_548797..548947_POSITIVE 260 136 102 57 24 pint:PI0354|3end_hypothetical_protein_326241..326391_POSITIVE 259 536 496 62 10 pint:PI1708|3end_hypothetical_protein_1625562..1625712_POSITIVE