Origin IGS: tgatatgtcagcatcacaaaacctgtctgagttgtcgtaatagaatttttacctatcaacttcactgtaatattgtcagttgggcaataaaaacggaaagtaccgataactggataccaatctccactttctgatttatactgaggacagttctctttagtaacaacaatctcagcattttctaatgtaatagtacgagtatcagcatcgaatttcacagttccagacttaacccacttacgttcagagtcaagtttgttaccattttctttagtcatcttctgaccaagaaaaacaagttgttcgtcaagatcattgtcagcgaaactgttagacactccaaaaacggcagtaagcactgccaccaatactctcaatcgtaaaaaattcttcataatttaaaattgtttgttgttaaattgtttgtagttaaatttgcaaagaatctaatattcttcttttccgatgggcaaagataaactaaataataatactatgcaagaaaaaataaaaaaaacaaccaacaaacacagcaattaacaattacgc .........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 gcgtaattgttaattgctgtgtttgttggttgttttttttattttttcttgcatagtattattatttagtttatctttgcccatcggaaaagaagaatattagattctttgcaaatttaactacaaacaatttaacaacaaacaattttaaattatgaagaattttttacgattgagagtattggtggcagtgcttactgccgtttttggagtgtctaacagtttcgctgacaatgatcttgacgaacaacttgtttttcttggtcagaagatgactaaagaaaatggtaacaaacttgactctgaacgtaagtgggttaagtctggaactgtgaaattcgatgctgatactcgtactattacattagaaaatgctgagattgttgttactaaagagaactgtcctcagtataaatcagaaagtggagattggtatccagttatcggtactttccgtttttattgcccaactgacaatattacagtgaagttgataggtaaaaattctattacgacaactcagacaggttttgtgatgctgacatatca Mask Tandem Repeat Region ================================================ tgatatgtcagcatcacaaaacctgtctgagttgtcgtaatagaatttttacctatcaacttcactgtaatattgtcagttgggcaataaaaacggaaagtaccgataactggataccaatctccactttctgatttatactgaggacagttctctttagtaacaacaatctcagcattttctaatgtaatagtacgagtatcagcatcgaatttcacagttccagacttaacccacttacgttcagagtcaagtttgttaccattttctttagtcatcttctgaccaagaaaaacaagttgttcgtcaagatcattgtcagcgaaactgttagacactccaaaaacggcagtaagcactgccaccaatactctcaatcgtaaaaaattcttcataatttannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntgcaaagaatctaatattcttcttttccgatgggcaaagataaactaaataataatactatgcaagaaaaaataaaaaaaacaaccaacaaacacagcaattaacaattacgc Find is-nt database================================================ Query_seq: PI1994:PI1996|PI1994:PI1996:hypothetical protein:hypothetical protein:->->:1949905..1950453 549 tgatatgtcagcatcacaaaacctgtctgagttgtcgtaatagaatttttacctatcaacttcactgtaatattgtcagttgggcaataaaaacggaaagtaccgataactggataccaatctccactttctgatttatactgaggacagttctctttagtaacaacaatctcagcattttctaatgtaatagtacgagtatcagcatcgaatttcacagttccagacttaacccacttacgttcagagtcaagtttgttaccattttctttagtcatcttctgaccaagaaaaacaagttgttcgtcaagatcattgtcagcgaaactgttagacactccaaaaacggcagtaagcactgccaccaatactctcaatcgtaaaaaattcttcataatttaaaattgtttgttgttaaattgtttgtagttaaatttgcaaagaatctaatattcttcttttccgatgggcaaagataaactaaataataatactatgcaagaaaaaataaaaaaaacaaccaacaaacacagcaattaacaattacgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1994:PI1996|PI1994:PI1996:hypothetical protein:hypothetical protein:->->:1949905..1950453 549 tgatatgtcagcatcacaaaacctgtctgagttgtcgtaatagaatttttacctatcaacttcactgtaatattgtcagttgggcaataaaaacggaaagtaccgataactggataccaatctccactttctgatttatactgaggacagttctctttagtaacaacaatctcagcattttctaatgtaatagtacgagtatcagcatcgaatttcacagttccagacttaacccacttacgttcagagtcaagtttgttaccattttctttagtcatcttctgaccaagaaaaacaagttgttcgtcaagatcattgtcagcgaaactgttagacactccaaaaacggcagtaagcactgccaccaatactctcaatcgtaaaaaattcttcataatttaaaattgtttgttgttaaattgtttgtagttaaatttgcaaagaatctaatattcttcttttccgatgggcaaagataaactaaataataatactatgcaagaaaaaataaaaaaaacaaccaacaaacacagcaattaacaattacgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1994:PI1996|PI1994:PI1996:hypothetical protein:hypothetical protein:->->:1949905..1950453 549 tgatatgtcagcatcacaaaacctgtctgagttgtcgtaatagaatttttacctatcaacttcactgtaatattgtcagttgggcaataaaaacggaaagtaccgataactggataccaatctccactttctgatttatactgaggacagttctctttagtaacaacaatctcagcattttctaatgtaatagtacgagtatcagcatcgaatttcacagttccagacttaacccacttacgttcagagtcaagtttgttaccattttctttagtcatcttctgaccaagaaaaacaagttgttcgtcaagatcattgtcagcgaaactgttagacactccaaaaacggcagtaagcactgccaccaatactctcaatcgtaaaaaattcttcataatttaaaattgtttgttgttaaattgtttgtagttaaatttgcaaagaatctaatattcttcttttccgatgggcaaagataaactaaataataatactatgcaagaaaaaataaaaaaaacaaccaacaaacacagcaattaacaattacgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgatatgtcagcatcacaaaacctgtctgagttgtcgtaatagaatttttacctatcaacttcactgtaatattgtcagttgggcaataaaaacggaaagtaccgataactggataccaatctccactttctgatttatactgaggacagttctctttagtaacaacaatctcagcattttctaatgtaatagtacgagtatcagcatcgaatttcacagttccagacttaacccacttacgttcagagtcaagtttgttaccattttctttagtcatcttctgaccaagaaaaacaagttgttcgtcaagatcattgtcagcgaaactgttagacactccaaaaacggcagtaagcactgccaccaatactctcaatcgtaaaaaattcttcataatttaaaattgtttgttgttaaattgtttgtagttaaatttgcaaagaatctaatattcttcttttccgatgggcaaagataaactaaataataatactatgcaagaaaaaataaaaaaaacaaccaacaaacacagcaattaacaattacgc Predict ORF larger than 30AA ================================================ Protein_Len: 43 Strand: + Start: 3 End: 131 .. M C Q H H K T C L S C R N R I F T Y Q L H C N I V S W A I K T E S T D N W I P I S T F .................................................................................................................................................................................................................................................................................................................................................................................................................................. Protein_Len: 38 Strand: + Start: 169 End: 282 ........................................................................................................................................................................ M S A F S N V I V R V S A S N F T V P D L T H L R S E S S L L P F S L V I F ........................................................................................................................................................................................................................................................................... Protein_Len: 60 Strand: + Start: 201 End: 380 ........................................................................................................................................................................................................ M S I E F H S S R L N P L T F R V K F V T I F F S H L L T K K N K L F V K I I V S E T V R H S K N G S K H C H Q Y S Q S ......................................................................................................................................................................... Protein_Len: 30 Strand: + Start: 387 End: 476 .................................................................................................................................................................................................................................................................................................................................................................................................. M L H N L K L F V V K L F V V K F A K N L I F F F S D G Q R ......................................................................... Protein_Len: 38 Strand: - Start: 65 End: 178 ................................................................ Q L I T L Q A I F V S L V S L Q I G I E V K Q N I S L V T R K L L L L R L M ................................................................................................................................................................................................................................................................................................................................................................................... Protein_Len: 60 Strand: - Start: 3 End: 398 .. T G S K V W K R E S D L K N G N E K T M K Q G L F V L Q E D L D N D A F S N S V G F V A T L V A V L V R L R L F N K M M ....................................................................................................................................................... tgatatgtcagcatcacaaaacctgtctgagttgtcgtaatagaatttttacctatcaacttcactgtaatattgtcagttgggcaataaaaacggaaagtaccgataactggataccaatctccactttctgatttatactgaggacagttctctttagtaacaacaatctcagcattttctaatgtaatagtacgagtatcagcatcgaatttcacagttccagacttaacccacttacgttcagagtcaagtttgttaccattttctttagtcatcttctgaccaagaaaaacaagttgttcgtcaagatcattgtcagcgaaactgttagacactccaaaaacggcagtaagcactgccaccaatactctcaatcgtaaaaaattcttcataatttaaaattgtttgttgttaaattgtttgtagttaaatttgcaaagaatctaatattcttcttttccgatgggcaaagataaactaaataataatactatgcaagaaaaaataaaaaaaacaaccaacaaacacagcaattaacaattacgc 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================================================ tgatatgtcagcatcacaaaacctgtctgagttgtcgtaatagaatttttacctatcaacttcactgtaatattgtcagttgggcaataaaaacggaaagtaccgataactggataccaatctccactttctgatttatactgaggacagttctctttagtaacaacaatctcagcattttctaatgtaatagtacgagtatcagcatcgaatttcacagttccagacttaacccacttacgttcagagtcaagtttgttaccattttctttagtcatcttctgaccaagaaaaacaagttgttcgtcaagatcattgtcagcgaaactgttagacactccaaaaacggcagtaagcactgccaccaatactctcaatcgtaaaaaattcttcataatttaaaattgtttgttgttaaattgtttgtagttaaatttgcaaagaatctaatattcttcttttccgatgggcaaagataaactaaataataatactatgcaagaaaaaataaaaaaaacaaccaacaaacacagcaattaacaattacgc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 83 HP_score: -7.7 Tail_Score: -4.65838 Start: 347 End: 364 Full_Region: gattgagagtattgg tggcagt gctt actgccg tttttggagtgtcta ..........................................................................................................................................................................................................................................................................................................................................................tggcagtgcttactgccg......................................................................................................................................................................................... TransTerm Strand: - Conf: 75 HP_score: -9.0 Tail_Score: -3.3878 Start: 348 End: 363 Full_Region: attgagagtattggt ggcagt gctt actgcc gtttttggagtgtct ...........................................................................................................................................................................................................................................................................................................................................................ggcagtgcttactgcc.......................................................................................................................................................................................... Find igs database================================================ Query_seq: PI1994:PI1996|PI1994:PI1996:hypothetical protein:hypothetical protein:->->:1949905..1950453 549 tgatatgtcagcatcacaaaacctgtctgagttgtcgtaatagaatttttacctatcaacttcactgtaatattgtcagttgggcaataaaaacggaaagtaccgataactggataccaatctccactttctgatttatactgaggacagttctctttagtaacaacaatctcagcattttctaatgtaatagtacgagtatcagcatcgaatttcacagttccagacttaacccacttacgttcagagtcaagtttgttaccattttctttagtcatcttctgaccaagaaaaacaagttgttcgtcaagatcattgtcagcgaaactgttagacactccaaaaacggcagtaagcactgccaccaatactctcaatcgtaaaaaattcttcataatttaaaattgtttgttgttaaattgtttgtagttaaatttgcaaagaatctaatattcttcttttccgatgggcaaagataaactaaataataatactatgcaagaaaaaataaaaaaaacaaccaacaaacacagcaattaacaattacgc Intra-Species Hit: Count: 1 Min: 1 Max: 549 Len: 549 Subject: pint_PI1994_PI1996|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[1949905,1950453]|549 HSP 1 e-value: 0.0 bit: 995.0 Len: 502 Query Start:1 Query End:502 Subject Strand: POSITIVE Subject Start: 1 Subject End: 502 tgatatgtcagcatcacaaaacctgtctgagttgtcgtaatagaatttttacctatcaacttcactgtaatattgtcagttgggcaataaaaacggaaagtaccgataactggataccaatctccactttctgatttatactgaggacagttctctttagtaacaacaatctcagcattttctaatgtaatagtacgagtatcagcatcgaatttcacagttccagacttaacccacttacgttcagagtcaagtttgttaccattttctttagtcatcttctgaccaagaaaaacaagttgttcgtcaagatcattgtcagcgaaactgttagacactccaaaaacggcagtaagcactgccaccaatactctcaatcgtaaaaaattcttcataatttaaaattgtttgttgttaaattgtttgtagttaaatttgcaaagaatctaatattcttcttttccgatgggcaaagataaactaaataataatactatgcaag............................................... tgatatgtcagcatcacaaaacctgtctgagttgtcgtaatagaatttttacctatcaacttcactgtaatattgtcagttgggcaataaaaacggaaagtaccgataactggataccaatctccactttctgatttatactgaggacagttctctttagtaacaacaatctcagcattttctaatgtaatagtacgagtatcagcatcgaatttcacagttccagacttaacccacttacgttcagagtcaagtttgttaccattttctttagtcatcttctgaccaagaaaaacaagttgttcgtcaagatcattgtcagcgaaactgttagacactccaaaaacggcagtaagcactgccaccaatactctcaatcgtaaaaaattcttcataatttaaaattgtttgttgttaaattgtttgtagttaaatttgcaaagaatctaatattcttcttttccgatgggcaaagataaactaaataataatactatgcaag............................................... HSP 2 e-value: 6.0E-9 bit: 63.9 Len: 32 Query Start:518 Query End:549 Subject Strand: POSITIVE Subject Start: 518 Subject End: 549 .....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................caaccaacaaacacagcaattaacaattacgc .....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................caaccaacaaacacagcaattaacaattacgc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUAUGUCAGCAUCACAAAACCUGUCUGAGUUGUCGUAAUAGAAUUUUUACCUAUCAACUUCACUGUAAUAUUGUCAGUUGGGCAAUAAAAACGGAAAGUACCGAUAACUGGAUACCAAUCUCCACUUUCUGAUUUAUACUGAGGACAGUUCUCUUUAGUAACAACAAUCUCAGCAUUUUCUAAUGUAAUAGUACGAGUAUCAGCAUCGAAUUUCACAGUUCCAGACUUAACCCACUUACGUUCAGAGUCAAGUUUGUUACCAUUUUCUUUAGUCAUCUUCUGACCAAGAAAAACAAGUUGUUCGUCAAGAUCAUUGUCAGCGAAACUGUUAGACACUCCAAAAACGGCAGUAAGCACUGCCACCAAUACUCUCAAUCGUAAAAAAUUCUUCAUAAUUUAAAAUUGUUUGUUGUUAAAUUGUUUGUAGUUAAAUUUGCAAAGAAUCUAAUAUUCUUCUUUUCCGAUGGGCAAAGAUAAACUAAAUAAUAAUACUAUGCAAGAAAAAAUAAAAAAAACAACCAACAAACACAGCAAUUAACAAUUACGC ...((((.((((.(((((.....)))..)))))).))))..(((((((((((...........(((((.((((((...((((((.........((((((((...(((...(((...))))))...)))))))).....(((((((((......)))))))))........))))))......)))))).)))))..((((((......(((((..(...((..(((((((.((.(...........).)).)))))))..))..(((((((..((((.....)))).)))))))....)..)))))..........((((((((....)))).))))..........((((((....))))))....))))))......)).)))))))))...........(((((((.((((((....(((((((.(((...((((((.(((((.....)))))(((((.((....)).)))))....................))))))................)))..))))))).)))))).))))))).... (-104.41) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCGUAAUUGUUAAUUGCUGUGUUUGUUGGUUGUUUUUUUUAUUUUUUCUUGCAUAGUAUUAUUAUUUAGUUUAUCUUUGCCCAUCGGAAAAGAAGAAUAUUAGAUUCUUUGCAAAUUUAACUACAAACAAUUUAACAACAAACAAUUUUAAAUUAUGAAGAAUUUUUUACGAUUGAGAGUAUUGGUGGCAGUGCUUACUGCCGUUUUUGGAGUGUCUAACAGUUUCGCUGACAAUGAUCUUGACGAACAACUUGUUUUUCUUGGUCAGAAGAUGACUAAAGAAAAUGGUAACAAACUUGACUCUGAACGUAAGUGGGUUAAGUCUGGAACUGUGAAAUUCGAUGCUGAUACUCGUACUAUUACAUUAGAAAAUGCUGAGAUUGUUGUUACUAAAGAGAACUGUCCUCAGUAUAAAUCAGAAAGUGGAGAUUGGUAUCCAGUUAUCGGUACUUUCCGUUUUUAUUGCCCAACUGACAAUAUUACAGUGAAGUUGAUAGGUAAAAAUUCUAUUACGACAACUCAGACAGGUUUUGUGAUGCUGACAUAUCA ((....(((((((((((((((.((((..((((.............(((((.((((((...........((((.(((((.((....)).))))).)))).(((((((.((((............)))).)))))))................)))))))))))........(((.(((((((((((((((.....((((.(((((((((..(((((((..(((.....)))....(((((..((.((((.....)))).))..)))))..)))).)))...)))))))))..((.(((((((((...((....))))))))))).)).....)))).....(((((..((.(((...(((......)))...((((((((((.(((.((......)).))).)).)))))))).............)))))..)))))..))))))))))))))).))).........))))..))))...))))))..)))))))))...........(((((((.((((......))))))))))))).......... (-131.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 326 367 323 39 7 pint:PI1697|5end_conserved_hypothetical_protein_1612217..1612447_POSITIVE 313 38 2 172 135 pint:PI0533|5end_ABC_transporter,_permease_protein_487259..487489_POSITIVE 312 359 313 188 130 pint:PI0887|5end_hypothetical_protein_817536..817766_POSITIVE 306 359 322 201 159 pint:PI1333|5end_conserved_hypothetical_protein_1250777..1251007_POSITIVE 303 372 336 162 126 pint:PI0307|5end_RNA_polymerase_sigma-70_factor,_ECF_subfamily_290042..290272_POSITIVE 300 325 285 179 140 pint:PI2079|5end_conserved_hypothetical_protein;_possible_ATPase_2036715..2036945_POSITIVE 281 160 111 178 131 pint:PI0197|5end_acetate_kinase_188602..188832_POSITIVE 274 472 435 166 123 pint:PI1666|5end_conserved_hypothetical_protein_1579231..1579461_POSITIVE 274 350 308 176 129 pint:PI0454|5end_hypothetical_protein_426653..426883_POSITIVE 271 236 201 199 162 pint:PI2126|5end_conserved_hypothetical_protein_2074907..2075137_POSITIVE 271 338 301 66 27 pint:PI1256|5end_conserved_hypothetical_protein_1177481..1177711_POSITIVE 271 358 311 172 113 pint:PI0088|5end_S-adenosylmethionine_synthetase_86663..86893_POSITIVE 270 363 322 158 125 pint:PI0670|5end_hypothetical_protein_611000..611230_POSITIVE 270 363 322 82 49 pint:PI0669|5end_hypothetical_protein_610924..611154_POSITIVE 270 350 305 76 26 pint:PI0202|5end_DNA_helicase_191753..191983_POSITIVE 269 380 345 200 156 pint:PI1789|5end_hypothetical_protein_1718727..1718957_POSITIVE 269 382 341 104 63 pint:PI0267|5end_conjugative_transposon_protein,_TraQ_258786..259016_POSITIVE 268 367 321 162 119 pint:PI0992|5end_RNA_polymerase_sigma-70_factor_916456..916686_POSITIVE 261 364 321 84 45 pint:PI0953|5end_hypothetical_protein_885119..885349_POSITIVE 260 369 322 177 129 pint:PI0701|5end_hypothetical_protein_638356..638586_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 312 359 313 135 77 pint:PI0885|3end_hypothetical_protein_817563..817713_POSITIVE 294 380 337 148 102 pint:PI0797|3end_tRNA_pseudouridine_synthase_A_(pseudouridylate_synthase)_735752..735902_POSITIVE 281 160 111 139 92 pint:PI0196|3end_hypothetical_protein_188643..188793_POSITIVE 275 360 315 117 54 pint:PI0879|3end_hypothetical_protein_814051..814201_POSITIVE 273 480 435 79 33 pint:PI0010|3end_conserved_hypothetical_protein_11679..11829_POSITIVE 269 380 345 100 56 pint:PI1788|3end_hypothetical_protein_1718707..1718857_POSITIVE 268 367 321 85 42 pint:PI0991|3end_conserved_hypothetical_protein_916459..916609_POSITIVE 268 379 335 61 12 pint:PI0042|3end_hypothetical_protein_43444..43594_POSITIVE 267 230 185 129 78 pint:PI1730|3end_hypothetical_protein_1650367..1650517_POSITIVE 265 323 282 80 34 pint:PI2166|3end_hypothetical_protein_2112073..2112223_POSITIVE 258 49 6 48 5 pint:PI0944|3end_hypothetical_protein_875249..875399_POSITIVE 257 353 321 56 18 pint:PI1954|3end_translation_initiation_factor_IF-2_1911647..1911797_POSITIVE 257 367 332 58 19 pint:PI0832|3end_sigma-54-dependent_transcriptional_regulator_770155..770305_POSITIVE 257 288 247 86 43 pint:PI0827|3end_hypothetical_protein_764163..764313_POSITIVE 257 288 247 119 76 pint:PI0825|3end_hypothetical_protein_764196..764346_POSITIVE 252 359 315 135 79 pint:PI1797|3end_hypothetical_protein_1731559..1731709_POSITIVE 250 258 211 79 32 pint:PI1023|3end_hypothetical_protein_940195..940345_POSITIVE 249 369 321 146 109 pint:PI1448|3end_hypothetical_protein_1371832..1371982_POSITIVE 248 113 73 133 91 pint:PI2025|3end_conserved_hypothetical_protein_1979452..1979602_POSITIVE 247 384 341 39 3 pint:PI0645|3end_hypothetical_protein_586807..586957_POSITIVE