Origin IGS: taaagcgttttgcttgtaatctgaaacattcaaagaacgctgtataccagtattttatatgctttcggtataggttatgaaggaacgagttgctcttgacctatcaaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tttgataggtcaagagcaactcgttccttcataacctataccgaaagcatataaaatactggtatacagcgttctttgaatgtttcagattacaagcaaaacgcttta Mask Tandem Repeat Region ================================================ taaagcgttttgcttgtaatctgaaacattcaaagaacgctgtataccagtattttatatgctttcggtataggttatgaaggaacgagttgctcttgacctatcaaa Find is-nt database================================================ Query_seq: PI1514:PI1515|PI1514:PI1515:tRNA nucleotidyltransferase/poly(A) polymerase:hypothetical protein:->->:1434133..1434240 108 taaagcgttttgcttgtaatctgaaacattcaaagaacgctgtataccagtattttatatgctttcggtataggttatgaaggaacgagttgctcttgacctatcaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1514:PI1515|PI1514:PI1515:tRNA nucleotidyltransferase/poly(A) polymerase:hypothetical protein:->->:1434133..1434240 108 taaagcgttttgcttgtaatctgaaacattcaaagaacgctgtataccagtattttatatgctttcggtataggttatgaaggaacgagttgctcttgacctatcaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1514:PI1515|PI1514:PI1515:tRNA nucleotidyltransferase/poly(A) polymerase:hypothetical protein:->->:1434133..1434240 108 taaagcgttttgcttgtaatctgaaacattcaaagaacgctgtataccagtattttatatgctttcggtataggttatgaaggaacgagttgctcttgacctatcaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaagcgttttgcttgtaatctgaaacattcaaagaacgctgtataccagtattttatatgctttcggtataggttatgaaggaacgagttgctcttgacctatcaaa Predict ORF larger than 30AA ================================================ taaagcgttttgcttgtaatctgaaacattcaaagaacgctgtataccagtattttatatgctttcggtataggttatgaaggaacgagttgctcttgacctatcaaa 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================================================ taaagcgttttgcttgtaatctgaaacattcaaagaacgctgtataccagtattttatatgctttcggtataggttatgaaggaacgagttgctcttgacctatcaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1514:PI1515|PI1514:PI1515:tRNA nucleotidyltransferase/poly(A) polymerase:hypothetical protein:->->:1434133..1434240 108 taaagcgttttgcttgtaatctgaaacattcaaagaacgctgtataccagtattttatatgctttcggtataggttatgaaggaacgagttgctcttgacctatcaaa Intra-Species Hit: Count: 1 Min: 1 Max: 108 Len: 108 Subject: pint_PI1514_PI1515|tRNA nucleotidyltransferase/poly(A) polymerase:hypothetical protein|POSITIVE:POSITIVE|[1434133,1434240]|108 HSP 1 e-value: 4.0E-55 bit: 214.0 Len: 108 Query Start:1 Query End:108 Subject Strand: POSITIVE Subject Start: 1 Subject End: 108 taaagcgttttgcttgtaatctgaaacattcaaagaacgctgtataccagtattttatatgctttcggtataggttatgaaggaacgagttgctcttgacctatcaaa taaagcgttttgcttgtaatctgaaacattcaaagaacgctgtataccagtattttatatgctttcggtataggttatgaaggaacgagttgctcttgacctatcaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAGCGUUUUGCUUGUAAUCUGAAACAUUCAAAGAACGCUGUAUACCAGUAUUUUAUAUGCUUUCGGUAUAGGUUAUGAAGGAACGAGUUGCUCUUGACCUAUCAAA ...((((((((...(((........))).....)))))))).(((((((((((.....)))))...)))))).....((((((..((((.....)))).))).))).. (-23.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUGAUAGGUCAAGAGCAACUCGUUCCUUCAUAACCUAUACCGAAAGCAUAUAAAAUACUGGUAUACAGCGUUCUUUGAAUGUUUCAGAUUACAAGCAAAACGCUUUA ..(((.(((....(((...)))...)))))).....(((((((................))))))).((((((..(((..(((........)))..)))))))))... (-17.99) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 331 88 48 182 134 pint:PI0681|5end_hypothetical_protein_619000..619230_POSITIVE 331 88 48 154 106 pint:PI0682|5end_hypothetical_protein_618972..619202_POSITIVE 281 94 61 81 40 pint:PI1510|5end_cell_division_protein_1428412..1428642_POSITIVE 278 41 10 99 66 pint:PI1216|5end_probable_phosphohydrolase_1134814..1135044_POSITIVE 269 79 33 146 107 pint:PI1711|5end_ABC_transporter,_ATP-binding_protein_1627597..1627827_POSITIVE 269 79 33 46 7 pint:PI1712|5end_hypothetical_protein_1627497..1627727_POSITIVE 265 88 44 82 33 pint:PI0951|5end_hypothetical_protein_884526..884756_POSITIVE 263 94 62 215 187 pint:PI1947|5end_hypothetical_protein_1902534..1902764_POSITIVE 262 93 51 209 152 pint:PI1690|5end_transcription_regulator;_possible_Fe2+/Zn2+_uptake_regulation_proteins_1604984..1605214_POSITIVE 255 90 44 214 171 pint:PI0476|5end_50S_ribosomal_protein_L18_440041..440271_POSITIVE 251 92 60 47 15 pint:PI1768|5end_conserved_hypothetical_protein_1695456..1695686_POSITIVE 251 95 61 215 187 pint:PI0491|5end_hypothetical_protein_451010..451240_POSITIVE 249 89 44 72 20 pint:PI2146|5end_prolipoprotein_diacylglyceryl_transferase_2092402..2092632_POSITIVE 248 98 59 207 165 pint:PI2045|5end_hypothetical_protein_1998494..1998724_POSITIVE 246 95 59 175 125 pint:PI1671|5end_hypothetical_protein_1586397..1586627_POSITIVE 244 77 38 174 136 pint:PI0926|5end_hypothetical_protein_856824..857054_POSITIVE 244 98 59 165 127 pint:PI0847|5end_thiamine_biosynthesis_lipoprotein,_ApbE_781130..781360_POSITIVE 243 97 65 84 54 pint:PI2104|5end_carboxyl-terminal_protease_2057910..2058140_POSITIVE 242 85 42 178 135 pint:PI0179|5end_hypothetical_protein_171757..171987_POSITIVE 239 95 73 22 1 pint:PI0175|5end_succinyl-CoA_synthetase_beta_subunit_167023..167253_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 293 96 51 112 75 pint:PI1683|3end_integral_membrane_protein_1600898..1601048_POSITIVE 291 99 52 101 45 pint:PI0391|3end_conserved_hypothetical_protein_358216..358366_POSITIVE 278 41 10 76 43 pint:PI1215|3end_orotidine_5'-phosphate_decarboxylase_1134871..1135021_POSITIVE 264 100 52 127 75 pint:PI0005|3end_hypothetical_protein_7450..7600_POSITIVE 252 72 32 47 5 pint:PI0708|3end_conserved_hypothetical_protein_646234..646384_POSITIVE 237 92 58 88 52 pint:PI1075|3end_pyruvate_phosphate_dikinase_998571..998721_POSITIVE 236 95 61 150 117 pint:PI0654|3end_K+-dependent_Na+/Ca+_exchanger_related-protein_597223..597373_POSITIVE 236 69 23 108 60 pint:PI0168|3end_methionyl-tRNA_synthetase_(methionine--tRNA_ligase)_163279..163429_POSITIVE 234 100 61 85 41 pint:PI1694|3end_hypothetical_protein_1609946..1610096_POSITIVE 233 58 12 114 67 pint:PI0425|3end_hypothetical_protein_389722..389872_POSITIVE 227 80 35 86 33 pint:PI1646|3end_hypothetical_protein_1563128..1563278_POSITIVE 227 68 28 150 101 pint:PI1077|3end_hypothetical_protein_999569..999719_POSITIVE 224 99 61 58 25 pint:PI0428|3end_hypothetical_protein_396321..396471_POSITIVE 223 92 53 141 108 pint:PI2046|3end_hypothetical_protein_1999205..1999355_POSITIVE 221 94 61 46 15 pint:PI0743|3end_hypothetical_protein_673026..673176_POSITIVE 214 98 56 121 69 pint:PI0543|3end_adenylate_kinase_495722..495872_POSITIVE 213 67 26 48 3 pint:PI0358|3end_hypothetical_protein_328105..328255_POSITIVE 212 99 58 113 72 pint:PI1503|3end_30S_ribosomal_protein_S15_1423780..1423930_POSITIVE 212 68 32 146 109 pint:PI1099|3end_low_molecular_weight_protein-tyrosine-phosphatase_1023636..1023786_POSITIVE 211 87 60 150 120 pint:PI0213|3end_conserved_hypothetical_protein_208509..208659_POSITIVE