Origin IGS: tgttattaaattagattaaccgcatagcttccactaccgattttgtttgcaaagctacaaaaaataatccaactgctaaaagctattggattatttttctgtgggttttgcta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tagcaaaacccacagaaaaataatccaatagcttttagcagttggattattttttgtagctttgcaaacaaaatcggtagtggaagctatgcggttaatctaatttaataaca Mask Tandem Repeat Region ================================================ tgttattaaattagattaaccgcatagcttccactaccgattttgtttgcaaagctacaaaaaataatccaactgctaaaagctattggattatttttctgtgggttttgcta Find is-nt database================================================ Query_seq: PI0690:PI0692|PI0690:PI0692:uracil permease:iron compound ABC transporter, permease protein:->->:627377..627489 113 tgttattaaattagattaaccgcatagcttccactaccgattttgtttgcaaagctacaaaaaataatccaactgctaaaagctattggattatttttctgtgggttttgcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0690:PI0692|PI0690:PI0692:uracil permease:iron compound ABC transporter, permease protein:->->:627377..627489 113 tgttattaaattagattaaccgcatagcttccactaccgattttgtttgcaaagctacaaaaaataatccaactgctaaaagctattggattatttttctgtgggttttgcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0690:PI0692|PI0690:PI0692:uracil permease:iron compound ABC transporter, permease protein:->->:627377..627489 113 tgttattaaattagattaaccgcatagcttccactaccgattttgtttgcaaagctacaaaaaataatccaactgctaaaagctattggattatttttctgtgggttttgcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgttattaaattagattaaccgcatagcttccactaccgattttgtttgcaaagctacaaaaaataatccaactgctaaaagctattggattatttttctgtgggttttgcta Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 15 End: 113 .............. M N R I A S T T D F V C K A T K N N P T A K S Y W I I F L W V L L tgttattaaattagattaaccgcatagcttccactaccgattttgtttgcaaagctacaaaaaataatccaactgctaaaagctattggattatttttctgtgggttttgcta 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================================================ tgttattaaattagattaaccgcatagcttccactaccgattttgtttgcaaagctacaaaaaataatccaactgctaaaagctattggattatttttctgtgggttttgcta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 71 HP_score: -7.6 Tail_Score: -3.53224 Start: 54 End: 105 Full_Region: tagcaaaa cccacagaaaaataatccaatagct ttt agcagttggattattttttgtagc tttgcaaacaaaatc .....................................................cccacagaaaaataatccaatagcttttagcagttggattattttttgtagc........ TransTerm Strand: + Conf: 89 HP_score: -7.5 Tail_Score: -5.01546 Start: 65 End: 93 Full_Region: CAAAGCTACAAAAAA TAATCCAACTGCT AAA AGCTATTGGATTA TTTTTCTGTGGGTTT ................................................................TAATCCAACTGCTAAAAGCTATTGGATTA.................... Find igs database================================================ Query_seq: PI0690:PI0692|PI0690:PI0692:uracil permease:iron compound ABC transporter, permease protein:->->:627377..627489 113 tgttattaaattagattaaccgcatagcttccactaccgattttgtttgcaaagctacaaaaaataatccaactgctaaaagctattggattatttttctgtgggttttgcta Intra-Species Hit: Count: 1 Min: 1 Max: 113 Len: 113 Subject: pint_PI0690_PI0692|uracil permease:iron compound ABC transporter, permease protein|POSITIVE:POSITIVE|[627377,627489]|113 HSP 1 e-value: 5.0E-58 bit: 224.0 Len: 113 Query Start:1 Query End:113 Subject Strand: POSITIVE Subject Start: 1 Subject End: 113 tgttattaaattagattaaccgcatagcttccactaccgattttgtttgcaaagctacaaaaaataatccaactgctaaaagctattggattatttttctgtgggttttgcta tgttattaaattagattaaccgcatagcttccactaccgattttgtttgcaaagctacaaaaaataatccaactgctaaaagctattggattatttttctgtgggttttgcta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUUAUUAAAUUAGAUUAACCGCAUAGCUUCCACUACCGAUUUUGUUUGCAAAGCUACAAAAAAUAAUCCAACUGCUAAAAGCUAUUGGAUUAUUUUUCUGUGGGUUUUGCUA (((..((((......))))..)))........................((((((((((((((((((((((((..((.....))..))))))))))))).))).)))))))).. (-27.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGCAAAACCCACAGAAAAAUAAUCCAAUAGCUUUUAGCAGUUGGAUUAUUUUUUGUAGCUUUGCAAACAAAAUCGGUAGUGGAAGCUAUGCGGUUAAUCUAAUUUAAUAACA ..(((((.(..((((((((.(((((((((.((.....)).))))))))))))))))).).)))))......((((((((((....))))).)))))................. (-30.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 323 56 19 135 94 pint:PI1575|5end_LemA_protein_1501143..1501373_POSITIVE 262 56 15 218 169 pint:PI0037|5end_hypothetical_protein_39354..39584_POSITIVE 257 54 21 172 140 pint:PI2099|5end_D-alanyl-D-alanine_dipeptidase_2052409..2052639_POSITIVE 256 57 19 197 161 pint:PI0006|5end_hypothetical_protein_7199..7429_POSITIVE 249 77 31 77 33 pint:PI0869|5end_possible_exodeoxyribonuclease_VII_(small_subunit)_805518..805748_POSITIVE 244 56 13 210 157 pint:PI1700|5end_hypothetical_protein_1617607..1617837_POSITIVE 243 60 13 183 131 pint:PI1279|5end_RNA_polymerase_sigma_factor/ECF_subfamily_(sigma-70)_1195215..1195445_POSITIVE 242 90 42 165 116 pint:PI1243|5end_conserved_hypothetical_protein_1167934..1168164_POSITIVE 234 106 66 159 121 pint:PI1461|5end_conserved_hypothetical_protein_1384364..1384594_POSITIVE 231 59 20 217 163 pint:PI0250|5end_hypothetical_protein_246946..247176_POSITIVE 230 55 11 57 1 pint:PI0604|5end_O-succinylbenzoic_acid--CoA_ligase_550825..551055_POSITIVE 228 57 15 193 155 pint:PI0216|5end_transposase/integrase_209176..209406_POSITIVE 225 59 21 210 164 pint:PI0581|5end_conserved_hypothetical_protein_525055..525285_POSITIVE 224 52 20 89 59 pint:PI1769|5end_hypothetical_protein_1696507..1696737_POSITIVE 223 50 13 204 171 pint:PI0720|5end_conserved_hypothetical_protein_653949..654179_POSITIVE 220 110 68 146 108 pint:PI0746|5end_hypothetical_protein_675971..676201_POSITIVE 220 58 19 221 184 pint:PI0284|5end_flavoprotein_A_268848..269078_POSITIVE 216 59 19 140 92 pint:PI2104|5end_carboxyl-terminal_protease_2057910..2058140_POSITIVE 216 55 21 45 11 pint:PI0867|5end_hypothetical_protein_803859..804089_POSITIVE 216 59 14 227 178 pint:PI0288|5end_hypothetical_protein_(possible_ISPg3-related_transposase)_272272..272502_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 323 56 19 138 97 pint:PI1574|3end_conserved_hypothetical_protein_1501226..1501376_POSITIVE 262 56 15 73 24 pint:PI0036|3end_glutathione_peroxidase_39289..39439_POSITIVE 249 77 31 55 11 pint:PI0868|3end_exodeoxyribonuclease_VII,_large_subunit_805576..805726_POSITIVE 242 110 68 41 1 pint:PI0690|3end_uracil_permease_627316..627466_POSITIVE 241 50 21 150 124 pint:PI2098|3end_hypothetical_protein_2052473..2052623_POSITIVE 240 60 13 81 21 pint:PI0683|3end_hypothetical_protein_619797..619947_POSITIVE 234 106 66 151 113 pint:PI1460|3end_ribonucleotide_reductase,_alpha_subunit,_N-terminal_region_1384436..1384586_POSITIVE 229 54 14 40 5 pint:PI0825|3end_hypothetical_protein_764196..764346_POSITIVE 226 59 20 151 113 pint:PI0113|3end_arginyl-tRNA_synthetase_110082..110232_POSITIVE 225 55 22 111 74 pint:PI1983|3end_possible_xylanase_1940004..1940154_POSITIVE 224 52 20 141 111 pint:PI1768|3end_conserved_hypothetical_protein_1696639..1696789_POSITIVE 223 58 13 117 73 pint:PI0492|3end_hypothetical_protein_452458..452608_POSITIVE 216 59 19 84 36 pint:PI2103|3end_hypothetical_protein_2057934..2058084_POSITIVE 216 55 21 99 65 pint:PI0866|3end_hypothetical_protein_803993..804143_POSITIVE 214 77 34 107 62 pint:PI0953|3end_hypothetical_protein_885390..885540_POSITIVE 214 56 22 136 100 pint:PI0474|3end_30S_ribosomal_protein_S8_439515..439665_POSITIVE 213 59 15 49 16 pint:PI0290|3end_conserved_hypothetical_protein_274131..274281_POSITIVE 209 57 20 70 28 pint:PI1848|3end_hypothetical_protein_1795015..1795165_POSITIVE 207 51 19 135 100 pint:PI1121|3end_glycosyltransferase_1046707..1046857_POSITIVE 203 52 22 107 59 pint:PI0928|3end_hypothetical_protein_860272..860422_POSITIVE