Origin IGS: aaggacttcttggtctttgattttttcgtccatattacaatgtatttaataacaccaacagcggtgcacggacaaaagtaaatcaaagaaacagtgtatgttaggggtttgagataactgcgtacttgtggcttcgat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atcgaagccacaagtacgcagttatctcaaacccctaacatacactgtttctttgatttacttttgtccgtgcaccgctgttggtgttattaaatacattgtaatatggacgaaaaaatcaaagaccaagaagtcctt Mask Tandem Repeat Region ================================================ aaggacttcttggtctttgattttttcgtccatattacaatgtatttaataacaccaacagcggtgcacggacaaaagtaaatcaaagaaacagtgtatgttaggggtttgagataactgcgtacttgtggcttcgat Find is-nt database================================================ Query_seq: PI0224:PI0225|PI0224:PI0225:conserved hypothetical protein:conserved hypothetical protein:->->:222040..222177 138 aaggacttcttggtctttgattttttcgtccatattacaatgtatttaataacaccaacagcggtgcacggacaaaagtaaatcaaagaaacagtgtatgttaggggtttgagataactgcgtacttgtggcttcgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0224:PI0225|PI0224:PI0225:conserved hypothetical protein:conserved hypothetical protein:->->:222040..222177 138 aaggacttcttggtctttgattttttcgtccatattacaatgtatttaataacaccaacagcggtgcacggacaaaagtaaatcaaagaaacagtgtatgttaggggtttgagataactgcgtacttgtggcttcgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0224:PI0225|PI0224:PI0225:conserved hypothetical protein:conserved hypothetical protein:->->:222040..222177 138 aaggacttcttggtctttgattttttcgtccatattacaatgtatttaataacaccaacagcggtgcacggacaaaagtaaatcaaagaaacagtgtatgttaggggtttgagataactgcgtacttgtggcttcgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaggacttcttggtctttgattttttcgtccatattacaatgtatttaataacaccaacagcggtgcacggacaaaagtaaatcaaagaaacagtgtatgttaggggtttgagataactgcgtacttgtggcttcgat Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: - Start: 49 End: 138 ................................................ Y C W C R H V S L L L D F F C H I N P T Q S L Q T S T A E M aaggacttcttggtctttgattttttcgtccatattacaatgtatttaataacaccaacagcggtgcacggacaaaagtaaatcaaagaaacagtgtatgttaggggtttgagataactgcgtacttgtggcttcgat 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================================================ aaggacttcttggtctttgattttttcgtccatattacaatgtatttaataacaccaacagcggtgcacggacaaaagtaaatcaaagaaacagtgtatgttaggggtttgagataactgcgtacttgtggcttcgat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI0224:PI0225|PI0224:PI0225:conserved hypothetical protein:conserved hypothetical protein:->->:222040..222177 138 aaggacttcttggtctttgattttttcgtccatattacaatgtatttaataacaccaacagcggtgcacggacaaaagtaaatcaaagaaacagtgtatgttaggggtttgagataactgcgtacttgtggcttcgat Intra-Species Hit: Count: 1 Min: 1 Max: 138 Len: 138 Subject: pint_PI0224_PI0225|conserved hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[222040,222177]|138 HSP 1 e-value: 7.0E-73 bit: 274.0 Len: 138 Query Start:1 Query End:138 Subject Strand: POSITIVE Subject Start: 1 Subject End: 138 aaggacttcttggtctttgattttttcgtccatattacaatgtatttaataacaccaacagcggtgcacggacaaaagtaaatcaaagaaacagtgtatgttaggggtttgagataactgcgtacttgtggcttcgat aaggacttcttggtctttgattttttcgtccatattacaatgtatttaataacaccaacagcggtgcacggacaaaagtaaatcaaagaaacagtgtatgttaggggtttgagataactgcgtacttgtggcttcgat Inter-species Hit: Count: 1 Min: 32 Max: 138 Len: 107 Subject: tfor_TF0021_TF0022|outer membrane phospholipase A:two-component system sensor histidine kinase|POSITIVE:POSITIVE|[16980,17434]|455 HSP 1 e-value: 2.0E-23 bit: 109.0 Len: 107 Query Start:32 Query End:138 Subject Strand: POSITIVE Subject Start: 240 Subject End: 346 ...............................atattacaatgtatttaataacaccaacagcggtgcacggacaaaagtaaatcaaagaaacagtgtatgttaggggtttgagataactgcgtacttgtggcttcgat ...............................atattactatgtatttaatgacaccaacagcggtgtatggataaaggtaaaccaaagaaactgtgtgtattacaggtttgagataactgcgtacttgtggcgtcgat Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAUUACAAUGUAUUUAAUAACACCAACAGCGGUGCACGGACAAAAGUAAAUCAAAGAAACAGUGUAUGUUAGGGGUUUGAGAUAACUGCGUACUUGUGGCUUCGAU ...((((..(((.........((((......)))).....)))...)))).((.(((..((((.((((((.((..(((...)))..))))))))))))..))).)). (-18.94) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCGAAGCCACAAGUACGCAGUUAUCUCAAACCCCUAACAUACACUGUUUCUUUGAUUUACUUUUGUCCGUGCACCGCUGUUGGUGUUAUUAAAUACAUUGUAAUAU (((((((..(((.((.....((((...........))))....)))))..)))))))((((...(((....((((((....))))))........)))..))))... (-14.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 307 45 12 220 187 pint:PI2138|5end_nicotinate_phosphoribosyltransferase_2083836..2084066_POSITIVE 267 98 60 138 88 pint:PI1496|5end_nucleoside_phosphorylase_1417116..1417346_POSITIVE 261 99 51 212 148 pint:PI0440|5end_transcription_antiterminator_410582..410812_POSITIVE 257 69 31 215 172 pint:PI1603|5end_hypothetical_protein_1533779..1534009_POSITIVE 255 99 66 220 189 pint:PI2123|5end_adenine_phosphoribosyltransferase_2071711..2071941_POSITIVE 255 69 26 93 45 pint:PI0739|5end_conserved_hypothetical_protein_671794..672024_POSITIVE 253 100 56 138 101 pint:PI2111|5end_conserved_hypothetical_protein_2062771..2063001_POSITIVE 251 66 28 112 69 pint:PI1985|5end_hypothetical_protein_1940291..1940521_POSITIVE 250 69 27 108 67 pint:PI0029|5end_glutamine_amidotransferase_(GMP_synthase_(glutamine-hydrolyzing))_32593..32823_POSITIVE 246 100 56 143 98 pint:PI1952|5end_hypothetical_protein_1906588..1906818_POSITIVE 245 99 71 169 137 pint:PI0185|5end_conserved_hypothetical_protein_176992..177222_POSITIVE 243 64 23 72 28 pint:PI1887|5end_cell_division_protein_1829115..1829345_POSITIVE 242 80 33 224 173 pint:PI1507|5end_tRNA_pseudouridine_synthase_B_1426554..1426784_POSITIVE 238 47 2 182 128 pint:PI2046|5end_hypothetical_protein_1999030..1999260_POSITIVE 238 67 24 214 168 pint:PI0887|5end_hypothetical_protein_817536..817766_POSITIVE 238 67 24 107 61 pint:PI0867|5end_hypothetical_protein_803859..804089_POSITIVE 238 67 24 107 61 pint:PI0119|5end_hypothetical_protein_111506..111736_POSITIVE 238 67 24 48 2 pint:PI0089|5end_hypothetical_protein_88162..88392_POSITIVE 236 100 73 176 141 pint:PI1303|5end_ISPg3-related_transposase_1215135..1215365_POSITIVE 233 80 32 192 150 pint:PI0777|5end_predicted_TPR-repeat-containing_protein_713285..713515_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 307 45 12 111 78 pint:PI2137|3end_RNA_methylase_SpoU_family_2083807..2083957_POSITIVE 296 41 6 119 80 pint:PI1723|3end_conserved_hypothetical_protein_1642133..1642283_POSITIVE 261 91 55 79 43 pint:PI0578|3end_methyltransferase_523253..523403_POSITIVE 261 49 2 133 77 pint:PI0081|3end_hypothetical_protein_80700..80850_POSITIVE 258 47 24 143 115 pint:PI1041|3end_hypothetical_protein_960675..960825_POSITIVE 258 47 24 131 103 pint:PI0638|3end_hypothetical_protein_582402..582552_POSITIVE 258 47 24 126 98 pint:PI0637|3end_hypothetical_protein_582397..582547_POSITIVE 255 69 26 90 42 pint:PI0738|3end_conserved_hypothetical_protein_671871..672021_POSITIVE 251 45 20 47 21 pint:PI2166|3end_hypothetical_protein_2112073..2112223_POSITIVE 246 100 56 127 82 pint:PI1951|3end_ABC_transporter,_ATP-binding_protein_1906652..1906802_POSITIVE 246 99 69 90 56 pint:PI1541|3end_hypothetical_protein_1461884..1462034_POSITIVE 238 67 24 100 54 pint:PI0819|3end_hypothetical_protein_759919..760069_POSITIVE 236 100 73 128 93 pint:PI1302|3end_hypothetical_protein_1215167..1215317_POSITIVE 233 80 32 150 108 pint:PI0776|3end_predicted_TPR-repeat-containing_protein_713323..713473_POSITIVE 228 69 21 151 106 pint:PI0428|3end_hypothetical_protein_396321..396471_POSITIVE 226 100 53 94 34 pint:PI0158|3end_hypothetical_protein_151298..151448_POSITIVE 225 99 61 127 87 pint:PI0850|3end_conserved_hypothetical_protein_783835..783985_POSITIVE 224 100 52 125 63 pint:PI0723|3end_conserved_hypothetical_protein_657379..657529_POSITIVE 223 93 58 94 52 pint:PI2068|3end_hypothetical_protein_2028800..2028950_POSITIVE 223 100 62 82 44 pint:PI1222|3end_hypothetical_protein_1143378..1143528_POSITIVE