Origin IGS: taaaagaaaaacaatacgaaaacaatgcggtggctttgcagtaagaatgcagagccgctgcatcgcttttatcgcataggttcagagaaaagaaagccgtgca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgcacggctttcttttctctgaacctatgcgataaaagcgatgcagcggctctgcattcttactgcaaagccaccgcattgttttcgtattgtttttctttta Mask Tandem Repeat Region ================================================ taaaagaaaaacaatacgaaaacaatgcggtggctttgcagtaagaatgcagagccgctgcatcgcttttatcgcataggttcagagaaaagaaagccgtgca Find is-nt database================================================ Query_seq: PI1812:PI1813|PI1812:PI1813:possible alpha-amylase:hypothetical protein:->->:1752915..1753017 103 taaaagaaaaacaatacgaaaacaatgcggtggctttgcagtaagaatgcagagccgctgcatcgcttttatcgcataggttcagagaaaagaaagccgtgca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1812:PI1813|PI1812:PI1813:possible alpha-amylase:hypothetical protein:->->:1752915..1753017 103 taaaagaaaaacaatacgaaaacaatgcggtggctttgcagtaagaatgcagagccgctgcatcgcttttatcgcataggttcagagaaaagaaagccgtgca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1812:PI1813|PI1812:PI1813:possible alpha-amylase:hypothetical protein:->->:1752915..1753017 103 taaaagaaaaacaatacgaaaacaatgcggtggctttgcagtaagaatgcagagccgctgcatcgcttttatcgcataggttcagagaaaagaaagccgtgca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaaagaaaaacaatacgaaaacaatgcggtggctttgcagtaagaatgcagagccgctgcatcgcttttatcgcataggttcagagaaaagaaagccgtgca Predict ORF larger than 30AA ================================================ taaaagaaaaacaatacgaaaacaatgcggtggctttgcagtaagaatgcagagccgctgcatcgcttttatcgcataggttcagagaaaagaaagccgtgca 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================================================ taaaagaaaaacaatacgaaaacaatgcggtggctttgcagtaagaatgcagagccgctgcatcgcttttatcgcataggttcagagaaaagaaagccgtgca Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -10.7 Tail_Score: -4.40358 Start: 22 End: 66 Full_Region: AAAAACAATACGAAA ACAATGCGGTGGCTTTGCAGT AAG AATGCAGAGCCGCTGCATCGC TTTTATCGCATAGGT .....................ACAATGCGGTGGCTTTGCAGTAAGAATGCAGAGCCGCTGCATCGC..................................... TransTerm Strand: + Conf: 100 HP_score: -14.2 Tail_Score: -3.23733 Start: 23 End: 65 Full_Region: AAAACAATACGAAAA CAATGCGGTGGCTTTGCAGT AAG AATGCAGAGCCGCTGCATCG CTTTTATCGCATAGG ......................CAATGCGGTGGCTTTGCAGTAAGAATGCAGAGCCGCTGCATCG...................................... TransTerm Strand: - Conf: 100 HP_score: -9.8 Tail_Score: -4.53703 Start: 23 End: 65 Full_Region: cctatgcgataaaag cgatgcagcggctctgcatt ctt actgcaaagccaccgcattg ttttcgtattgtttt ......................cgatgcagcggctctgcattcttactgcaaagccaccgcattg...................................... TransTerm Strand: + Conf: 100 HP_score: -14.5 Tail_Score: -2.80345 Start: 26 End: 62 Full_Region: ACAATACGAAAACAA TGCGGTGGCTTTGCAGT AAG AATGCAGAGCCGCTGCA TCGCTTTTATCGCAT .........................TGCGGTGGCTTTGCAGTAAGAATGCAGAGCCGCTGCA......................................... Find igs database================================================ Query_seq: PI1812:PI1813|PI1812:PI1813:possible alpha-amylase:hypothetical protein:->->:1752915..1753017 103 taaaagaaaaacaatacgaaaacaatgcggtggctttgcagtaagaatgcagagccgctgcatcgcttttatcgcataggttcagagaaaagaaagccgtgca Intra-Species Hit: Count: 1 Min: 1 Max: 103 Len: 103 Subject: pint_PI1812_PI1813|possible alpha-amylase:hypothetical protein|POSITIVE:POSITIVE|[1752915,1753017]|103 HSP 1 e-value: 4.0E-52 bit: 204.0 Len: 103 Query Start:1 Query End:103 Subject Strand: POSITIVE Subject Start: 1 Subject End: 103 taaaagaaaaacaatacgaaaacaatgcggtggctttgcagtaagaatgcagagccgctgcatcgcttttatcgcataggttcagagaaaagaaagccgtgca taaaagaaaaacaatacgaaaacaatgcggtggctttgcagtaagaatgcagagccgctgcatcgcttttatcgcataggttcagagaaaagaaagccgtgca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAGAAAAACAAUACGAAAACAAUGCGGUGGCUUUGCAGUAAGAAUGCAGAGCCGCUGCAUCGCUUUUAUCGCAUAGGUUCAGAGAAAAGAAAGCCGUGCA .................((((.(.((((((((((((((((.......)))))))))))))))).).))))...((((.(((((........))..))))))). (-35.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGCACGGCUUUCUUUUCUCUGAACCUAUGCGAUAAAAGCGAUGCAGCGGCUCUGCAUUCUUACUGCAAAGCCACCGCAUUGUUUUCGUAUUGUUUUUCUUUUA ....................((((..((((((...(((((((((.(.((((.((((.......)))).)))).).))))))))))))))).))))........ (-29.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 472 60 14 159 107 pint:PI2146|5end_prolipoprotein_diacylglyceryl_transferase_2092402..2092632_POSITIVE 367 65 21 74 14 pint:PI1568|5end_OmpA_family_protein_1489584..1489814_POSITIVE 365 66 21 190 148 pint:PI1099|5end_low_molecular_weight_protein-tyrosine-phosphatase_1023059..1023289_POSITIVE 362 65 27 220 182 pint:PI2046|5end_hypothetical_protein_1999030..1999260_POSITIVE 351 70 25 171 129 pint:PI0029|5end_glutamine_amidotransferase_(GMP_synthase_(glutamine-hydrolyzing))_32593..32823_POSITIVE 350 66 26 51 2 pint:PI0545|5end_sugar_kinase_496411..496641_POSITIVE 349 68 25 75 16 pint:PI1801|5end_30S_ribosomal_protein_S9_1733949..1734179_POSITIVE 347 70 22 197 154 pint:PI1486|5end_alginate_O-acetylation_protein_1405507..1405737_POSITIVE 346 65 26 185 142 pint:PI2111|5end_conserved_hypothetical_protein_2062771..2063001_POSITIVE 343 65 26 196 153 pint:PI0159|5end_hypothetical_protein_151273..151503_POSITIVE 343 65 26 108 65 pint:PI0157|5end_hypothetical_protein_151185..151415_POSITIVE 340 80 31 133 75 pint:PI0734|5end_ABC_transporter,_ATP-binding_/_permease_667052..667282_POSITIVE 339 70 26 55 16 pint:PI1601|5end_hypothetical_protein_1530282..1530512_POSITIVE 338 64 27 209 168 pint:PI1888|5end_UDP-N-acetylmuramate--L-alanine_ligase_1829980..1830210_POSITIVE 336 60 12 56 14 pint:PI1589|5end_conserved_hypothetical_protein_1517358..1517588_POSITIVE 333 70 26 55 16 pint:PI2153|5end_hypothetical_protein_2099392..2099622_POSITIVE 333 70 26 55 16 pint:PI1567|5end_hypothetical_protein_1489229..1489459_POSITIVE 333 80 31 208 158 pint:PI0831|5end_hypothetical_protein_768129..768359_POSITIVE 333 70 26 181 142 pint:PI0788|5end_3-methyladenine_DNA_glycosylase_(DNA-3-methyladenine_glycosylase_I)_726152..726382_POSITIVE 333 70 26 186 147 pint:PI0771|5end_conserved_hypothetical_protein_706524..706754_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 502 63 25 66 28 pint:PI1812|3end_possible_alpha-amylase_1752854..1753004_POSITIVE 374 100 52 86 19 pint:PI0684|3end_coproporphyrinogen_III_oxidase_620507..620657_POSITIVE 369 65 26 135 92 pint:PI0182|3end_hypothetical_protein_174277..174427_POSITIVE 347 65 26 141 98 pint:PI0200|3end_hypothetical_protein_191735..191885_POSITIVE 343 65 26 141 98 pint:PI0158|3end_hypothetical_protein_151298..151448_POSITIVE 339 70 26 147 108 pint:PI1601|3end_hypothetical_protein_1530454..1530604_POSITIVE 338 64 27 135 94 pint:PI1887|3end_cell_division_protein_1829986..1830136_POSITIVE 336 77 32 88 39 pint:PI0778|3end_hypothetical_protein_714885..715035_POSITIVE 333 70 26 137 98 pint:PI1814|3end_hypothetical_protein_1753233..1753383_POSITIVE 333 70 26 137 98 pint:PI0689|3end_hypothetical_protein_625877..626027_POSITIVE 329 70 22 137 94 pint:PI0004|3end_hypothetical_protein_6389..6539_POSITIVE 328 66 27 89 55 pint:PI0567|3end_hypothetical_protein_513055..513205_POSITIVE 325 100 51 85 49 pint:PI0719|3end_conserved_hypothetical_protein_654010..654160_POSITIVE 325 70 22 137 94 pint:PI0061|3end_hypothetical_protein_60690..60840_POSITIVE 324 70 26 147 108 pint:PI1076|3end_hypothetical_protein_999065..999215_POSITIVE 322 66 26 91 47 pint:PI2048|3end_possible_two-component_system_sensor_histidine_kinase_2002566..2002716_POSITIVE 322 65 26 141 98 pint:PI2011|3end_hypothetical_protein_1970730..1970880_POSITIVE 321 66 26 138 94 pint:PI1521|3end_hypothetical_protein_1441461..1441611_POSITIVE 321 66 26 47 3 pint:PI1520|3end_hypothetical_protein_1441370..1441520_POSITIVE 318 67 23 131 89 pint:PI1641|3end_hypothetical_protein_1558883..1559033_POSITIVE