Origin IGS: tagaccttaagccctgtgtcgtaacttaatcgacacagggcaatagtattatagtatgaacaaaaaccaaacaagctatgaaagtggataatgagcgacggcgaggtgtcagttatctgaagcgcgttgcagatgtgaacgcgacctatcagaaatgggcgcgtacaggtttgtcgaaccgggaaatctggcggaggtatatatatcctgtctacggaatatcagaacgaaccttgtataatatgctaaaagtggatgtgacagtgaggaaagacaacgcctcttcgccgcgtccacttctgttgtttgattttgaggacgaaaaatgaagaaagaagtaggaaagatactcagcaggatactcaaagatattcgcgtggag .........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 ctccacgcgaatatctttgagtatcctgctgagtatctttcctacttctttcttcatttttcgtcctcaaaatcaaacaacagaagtggacgcggcgaagaggcgttgtctttcctcactgtcacatccacttttagcatattatacaaggttcgttctgatattccgtagacaggatatatatacctccgccagatttcccggttcgacaaacctgtacgcgcccatttctgataggtcgcgttcacatctgcaacgcgcttcagataactgacacctcgccgtcgctcattatccactttcatagcttgtttggtttttgttcatactataatactattgccctgtgtcgattaagttacgacacagggcttaaggtcta Mask Tandem Repeat Region ================================================ tagaccttaagccctgtgtcgtaacttaatcgacacagggcaatagtattatagtatgaacaaaaaccaaacaagctatgaaagtggataatgagcgacggcgaggtgtcagttatctgaagcgcgttgcagatgtgaacgcgacctatcagaaatgggcgcgtacaggtttgtcgaaccgggaaatctggcggaggtatatatatcctgtctacggaatatcagaacgaaccttgtataatatgctaaaagtggatgtgacagtgaggaaagacaacgcctcttcgccgcgtccacttctgttgtttgattttgaggacgaaaaatgaagaaagaagtaggaaagatactcagcaggatactcaaagatattcgcgtggag Find is-nt database================================================ Query_seq: PI0340:PI0341|PI0340:PI0341:conserved hypothetical protein:conserved hypothetical protein:->->:316796..317177 382 tagaccttaagccctgtgtcgtaacttaatcgacacagggcaatagtattatagtatgaacaaaaaccaaacaagctatgaaagtggataatgagcgacggcgaggtgtcagttatctgaagcgcgttgcagatgtgaacgcgacctatcagaaatgggcgcgtacaggtttgtcgaaccgggaaatctggcggaggtatatatatcctgtctacggaatatcagaacgaaccttgtataatatgctaaaagtggatgtgacagtgaggaaagacaacgcctcttcgccgcgtccacttctgttgtttgattttgaggacgaaaaatgaagaaagaagtaggaaagatactcagcaggatactcaaagatattcgcgtggag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0340:PI0341|PI0340:PI0341:conserved hypothetical protein:conserved hypothetical protein:->->:316796..317177 382 tagaccttaagccctgtgtcgtaacttaatcgacacagggcaatagtattatagtatgaacaaaaaccaaacaagctatgaaagtggataatgagcgacggcgaggtgtcagttatctgaagcgcgttgcagatgtgaacgcgacctatcagaaatgggcgcgtacaggtttgtcgaaccgggaaatctggcggaggtatatatatcctgtctacggaatatcagaacgaaccttgtataatatgctaaaagtggatgtgacagtgaggaaagacaacgcctcttcgccgcgtccacttctgttgtttgattttgaggacgaaaaatgaagaaagaagtaggaaagatactcagcaggatactcaaagatattcgcgtggag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0340:PI0341|PI0340:PI0341:conserved hypothetical protein:conserved hypothetical protein:->->:316796..317177 382 tagaccttaagccctgtgtcgtaacttaatcgacacagggcaatagtattatagtatgaacaaaaaccaaacaagctatgaaagtggataatgagcgacggcgaggtgtcagttatctgaagcgcgttgcagatgtgaacgcgacctatcagaaatgggcgcgtacaggtttgtcgaaccgggaaatctggcggaggtatatatatcctgtctacggaatatcagaacgaaccttgtataatatgctaaaagtggatgtgacagtgaggaaagacaacgcctcttcgccgcgtccacttctgttgtttgattttgaggacgaaaaatgaagaaagaagtaggaaagatactcagcaggatactcaaagatattcgcgtggag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tagaccttaagccctgtgtcgtaacttaatcgacacagggcaatagtattatagtatgaacaaaaaccaaacaagctatgaaagtggataatgagcgacggcgaggtgtcagttatctgaagcgcgttgcagatgtgaacgcgacctatcagaaatgggcgcgtacaggtttgtcgaaccgggaaatctggcggaggtatatatatcctgtctacggaatatcagaacgaaccttgtataatatgctaaaagtggatgtgacagtgaggaaagacaacgcctcttcgccgcgtccacttctgttgtttgattttgaggacgaaaaatgaagaaagaagtaggaaagatactcagcaggatactcaaagatattcgcgtggag Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 148 End: 246 ................................................................................................................................................... M R N G R V Q V C R T G K S G G G I Y I L S T E Y Q N E P C I I C ........................................................................................................................................ Protein_Len: 60 Strand: + Start: 78 End: 326 ............................................................................. M K V D N E R R R G V S Y L K R V A D V N A T Y Q K W A R T G L S N R E I W R R Y I Y P V Y G I S E R T L Y N M L K V D ........................................................ Protein_Len: 52 Strand: - Start: 215 End: 370 ...................................................................................................................................................................................................................... P I D S R V K Y L I S F T S T V T L F S L A E E G R G S R N N S K S S S F H L F F Y S L Y E A P Y E F M ............ Protein_Len: 60 Strand: - Start: 112 End: 372 ............................................................................................................... S T Y I D Q R R F I L V F R T Y Y A L L P H S L S S L C R R K A A D V E T T Q N Q P R F I F F S T P F I S L L I S L S M .......... Protein_Len: 60 Strand: - Start: 3 End: 206 .. L R C L A I T N Y Y S C F G F L S H F H I I L S P S T D T I Q L A N C I H V R G I L F P R T C T Q R V P F D P P P I Y M ................................................................................................................................................................................ tagaccttaagccctgtgtcgtaacttaatcgacacagggcaatagtattatagtatgaacaaaaaccaaacaagctatgaaagtggataatgagcgacggcgaggtgtcagttatctgaagcgcgttgcagatgtgaacgcgacctatcagaaatgggcgcgtacaggtttgtcgaaccgggaaatctggcggaggtatatatatcctgtctacggaatatcagaacgaaccttgtataatatgctaaaagtggatgtgacagtgaggaaagacaacgcctcttcgccgcgtccacttctgttgtttgattttgaggacgaaaaatgaagaaagaagtaggaaagatactcagcaggatactcaaagatattcgcgtggag 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================================================ tagaccttaagccctgtgtcgtaacttaatcgacacagggcaatagtattatagtatgaacaaaaaccaaacaagctatgaaagtggataatgagcgacggcgaggtgtcagttatctgaagcgcgttgcagatgtgaacgcgacctatcagaaatgggcgcgtacaggtttgtcgaaccgggaaatctggcggaggtatatatatcctgtctacggaatatcagaacgaaccttgtataatatgctaaaagtggatgtgacagtgaggaaagacaacgcctcttcgccgcgtccacttctgttgtttgattttgaggacgaaaaatgaagaaagaagtaggaaagatactcagcaggatactcaaagatattcgcgtggag Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 41 HP_score: -2.4 Tail_Score: -2.91276 Start: 135 End: 168 Full_Region: AAGCGCGTTGCAGAT GTGAACGCGACCTAT CAGAA ATGGGCGCGTACAG GTTTGTCGAACCGGG ......................................................................................................................................GTGAACGCGACCTATCAGAAATGGGCGCGTACAG...................................................................................................................................................................................................................... Find igs database================================================ Query_seq: PI0340:PI0341|PI0340:PI0341:conserved hypothetical protein:conserved hypothetical protein:->->:316796..317177 382 tagaccttaagccctgtgtcgtaacttaatcgacacagggcaatagtattatagtatgaacaaaaaccaaacaagctatgaaagtggataatgagcgacggcgaggtgtcagttatctgaagcgcgttgcagatgtgaacgcgacctatcagaaatgggcgcgtacaggtttgtcgaaccgggaaatctggcggaggtatatatatcctgtctacggaatatcagaacgaaccttgtataatatgctaaaagtggatgtgacagtgaggaaagacaacgcctcttcgccgcgtccacttctgttgtttgattttgaggacgaaaaatgaagaaagaagtaggaaagatactcagcaggatactcaaagatattcgcgtggag Intra-Species Hit: Count: 1 Min: 1 Max: 382 Len: 382 Subject: pint_PI0340_PI0341|conserved hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[316796,317177]|382 HSP 1 e-value: 0.0 bit: 757.0 Len: 382 Query Start:1 Query End:382 Subject Strand: POSITIVE Subject Start: 1 Subject End: 382 tagaccttaagccctgtgtcgtaacttaatcgacacagggcaatagtattatagtatgaacaaaaaccaaacaagctatgaaagtggataatgagcgacggcgaggtgtcagttatctgaagcgcgttgcagatgtgaacgcgacctatcagaaatgggcgcgtacaggtttgtcgaaccgggaaatctggcggaggtatatatatcctgtctacggaatatcagaacgaaccttgtataatatgctaaaagtggatgtgacagtgaggaaagacaacgcctcttcgccgcgtccacttctgttgtttgattttgaggacgaaaaatgaagaaagaagtaggaaagatactcagcaggatactcaaagatattcgcgtggag tagaccttaagccctgtgtcgtaacttaatcgacacagggcaatagtattatagtatgaacaaaaaccaaacaagctatgaaagtggataatgagcgacggcgaggtgtcagttatctgaagcgcgttgcagatgtgaacgcgacctatcagaaatgggcgcgtacaggtttgtcgaaccgggaaatctggcggaggtatatatatcctgtctacggaatatcagaacgaaccttgtataatatgctaaaagtggatgtgacagtgaggaaagacaacgcctcttcgccgcgtccacttctgttgtttgattttgaggacgaaaaatgaagaaagaagtaggaaagatactcagcaggatactcaaagatattcgcgtggag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGACCUUAAGCCCUGUGUCGUAACUUAAUCGACACAGGGCAAUAGUAUUAUAGUAUGAACAAAAACCAAACAAGCUAUGAAAGUGGAUAAUGAGCGACGGCGAGGUGUCAGUUAUCUGAAGCGCGUUGCAGAUGUGAACGCGACCUAUCAGAAAUGGGCGCGUACAGGUUUGUCGAACCGGGAAAUCUGGCGGAGGUAUAUAUAUCCUGUCUACGGAAUAUCAGAACGAACCUUGUAUAAUAUGCUAAAAGUGGAUGUGACAGUGAGGAAAGACAACGCCUCUUCGCCGCGUCCACUUCUGUUGUUUGAUUUUGAGGACGAAAAAUGAAGAAAGAAGUAGGAAAGAUACUCAGCAGGAUACUCAAAGAUAUUCGCGUGGAG ..........(((((((((((.........))))))))))).......(((((((.((.............)).)))))))....(((((....((((((.((.....((((....))))..))))))))..(((((.(((((.(((((.....)))))))))).(((((((.(((...))).))))))).......))))).)))))..(((((((((((((..........................(((((((((((...(((((((...........))))))))))))))))))((((((....(((((....((.................))....)))))...))))))..........))))))).)))))). (-116.15) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUCCACGCGAAUAUCUUUGAGUAUCCUGCUGAGUAUCUUUCCUACUUCUUUCUUCAUUUUUCGUCCUCAAAAUCAAACAACAGAAGUGGACGCGGCGAAGAGGCGUUGUCUUUCCUCACUGUCACAUCCACUUUUAGCAUAUUAUACAAGGUUCGUUCUGAUAUUCCGUAGACAGGAUAUAUAUACCUCCGCCAGAUUUCCCGGUUCGACAAACCUGUACGCGCCCAUUUCUGAUAGGUCGCGUUCACAUCUGCAACGCGCUUCAGAUAACUGACACCUCGCCGUCGCUCAUUAUCCACUUUCAUAGCUUGUUUGGUUUUUGUUCAUACUAUAAUACUAUUGCCCUGUGUCGAUUAAGUUACGACACAGGGCUUAAGGUCUA ..((...............(((((...((.(((((.......))))).....................(((((((((((((.((((((((((((((((.((((.(......).))))..(((((....................((((.((((.(((...(((((((.......))).))))........(((.(.....).)))..))).))))))))..........(((((..((.((((((((....)).)))))))))))))....)))))..)))))).)).......))))))))....).)))))))))))).))..)))))...........(((((((((((.........)))))))))))....)).... (-91.91) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 381 300 252 174 121 pint:PI0257|5end_conjugative_transposon_protein,_TraF_249348..249578_POSITIVE 380 129 86 149 99 pint:PI1884|5end_conserved_hypothetical_protein_1826883..1827113_POSITIVE 380 170 122 164 101 pint:PI1547|5end_hypothetical_protein_1465808..1466038_POSITIVE 372 177 137 103 64 pint:PI1909|5end_DNA_gyrase,_B_subunit_1853223..1853453_POSITIVE 359 380 336 73 23 pint:PI1150|5end_30S_ribosomal_protein_S6_1075683..1075913_POSITIVE 356 109 63 185 119 pint:PI0316|5end_conserved_hypothetical_protein_298379..298609_POSITIVE 355 197 151 120 71 pint:PI1439|5end_hypothetical_protein_1360009..1360239_POSITIVE 354 169 127 188 141 pint:PI0093|5end_riboflavin_biosynthesis_protein_90489..90719_POSITIVE 353 199 156 204 154 pint:PI0733|5end_membrane_protein;_predicted_exporter_664389..664619_POSITIVE 348 139 93 91 38 pint:PI0161|5end_possible_TonB_receptor_153364..153594_POSITIVE 345 143 101 195 158 pint:PI2008|5end__ABC_transporter,_ATP-binding_protein_1967123..1967353_POSITIVE 344 169 122 108 55 pint:PI1617|5end_hypothetical_protein_1542923..1543153_POSITIVE 341 137 91 50 3 pint:PI0736|5end_transcriptional_regulator,_TetR_family_670580..670810_POSITIVE 339 167 121 67 17 pint:PI1497|5end_LuxS_protein,_autoinducer_AI-2_production_protein_1417571..1417801_POSITIVE 337 307 262 231 176 pint:PI2094|5end_hypothetical_protein_2049540..2049770_POSITIVE 337 169 122 70 32 pint:PI2053|5end_conserved_hypothetical_protein;_possible_outer_membrane_receptor_protein_2010673..2010903_POSITIVE 336 190 151 177 136 pint:PI1429|5end_L-aspartate_oxidase_1347650..1347880_POSITIVE 335 150 101 146 94 pint:PI1642|5end_conserved_hypothetical_protein_1558800..1559030_POSITIVE 335 170 124 72 2 pint:PI0029|5end_glutamine_amidotransferase_(GMP_synthase_(glutamine-hydrolyzing))_32593..32823_POSITIVE 334 139 92 200 150 pint:PI0952|5end_conserved_hypothetical_protein_883718..883948_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 407 41 11 80 50 pint:PI0340|3end_conserved_hypothetical_protein_316735..316885_POSITIVE 380 148 101 88 40 pint:PI1466|3end_GTP-binding_protein,_possible_GTP1/OBG_family_1393133..1393283_POSITIVE 374 145 101 79 24 pint:PI0028|3end_aminopeptidase_32727..32877_POSITIVE 359 41 4 58 18 pint:PI1634|3end_conserved_hypothetical_protein_1553819..1553969_POSITIVE 359 380 336 67 17 pint:PI1149|3end_30S_ribosomal_protein_S18_1075757..1075907_POSITIVE 356 143 103 133 77 pint:PI0531|3end_ABC_transporter,_ATP-binding_protein;_possible_gliding_motility_related_486239..486389_POSITIVE 354 169 127 130 83 pint:PI0094|3end_protoporphyrinogen_oxidase_90511..90661_POSITIVE 353 199 156 102 52 pint:PI0732|3end_conserved_hypothetical_protein_664367..664517_POSITIVE 353 130 85 116 68 pint:PI0578|3end_methyltransferase_523253..523403_POSITIVE 336 190 151 142 101 pint:PI1428|3end_quinolinate_synthetase_A_1347695..1347845_POSITIVE 335 150 101 149 97 pint:PI1641|3end_hypothetical_protein_1558883..1559033_POSITIVE 334 294 251 126 84 pint:PI1240|3end_probable_Xaa-Pro_dipeptidase_(aminopeptidase_P)_1166272..1166422_POSITIVE 334 139 92 57 7 pint:PI0950|3end_50S_ribosomal_protein_L31_883655..883805_POSITIVE 333 170 121 129 74 pint:PI0020|3end_conserved_hypothetical_protein_24955..25105_POSITIVE 330 148 102 137 94 pint:PI0998|3end_possible_flavin_reductase_domain_protein_923336..923486_POSITIVE 324 170 121 123 73 pint:PI0595|3end_conserved_hypothetical_protein_546406..546556_POSITIVE 320 306 262 120 71 pint:PI0704|3end_conserved_hypothetical_protein_641364..641514_POSITIVE 319 289 247 149 106 pint:PI0256|3end_conjugative_transposon_protein,_TraE_249420..249570_POSITIVE 318 197 160 42 1 pint:PI1781|3end_membrane-associated_zinc_metalloprotease_1714551..1714701_POSITIVE 316 196 151 118 63 pint:PI1487|3end_hypothetical_protein_1407940..1408090_POSITIVE