Origin IGS: aaagattcgcttacgcaaaagtacttaaatttggctaatttcagccttttttagggcttaaaattcatctatatgcgtataattcattatttttgcacattattataattatatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aatataattataataatgtgcaaaaataatgaattatacgcatatagatgaattttaagccctaaaaaaggctgaaattagccaaatttaagtacttttgcgtaagcgaatcttt Mask Tandem Repeat Region ================================================ aaagattcgcttacgcaaaagtacttaaatttggctaatttcagccttttttagggcttaaaattcatctatatgcgtataattcattatttttgcacattattataattatatt Find is-nt database================================================ Query_seq: PI0204:PI0205|PI0204:PI0205:dGTP triphosphohydrolase (deoxyguanosinetriphosphate triphosphohydrolase):deoxyuridine 5'-triphosphate nucleotidohydrolase:->->:197606..197720 115 aaagattcgcttacgcaaaagtacttaaatttggctaatttcagccttttttagggcttaaaattcatctatatgcgtataattcattatttttgcacattattataattatatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0204:PI0205|PI0204:PI0205:dGTP triphosphohydrolase (deoxyguanosinetriphosphate triphosphohydrolase):deoxyuridine 5'-triphosphate nucleotidohydrolase:->->:197606..197720 115 aaagattcgcttacgcaaaagtacttaaatttggctaatttcagccttttttagggcttaaaattcatctatatgcgtataattcattatttttgcacattattataattatatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0204:PI0205|PI0204:PI0205:dGTP triphosphohydrolase (deoxyguanosinetriphosphate triphosphohydrolase):deoxyuridine 5'-triphosphate nucleotidohydrolase:->->:197606..197720 115 aaagattcgcttacgcaaaagtacttaaatttggctaatttcagccttttttagggcttaaaattcatctatatgcgtataattcattatttttgcacattattataattatatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaagattcgcttacgcaaaagtacttaaatttggctaatttcagccttttttagggcttaaaattcatctatatgcgtataattcattatttttgcacattattataattatatt Predict ORF larger than 30AA ================================================ aaagattcgcttacgcaaaagtacttaaatttggctaatttcagccttttttagggcttaaaattcatctatatgcgtataattcattatttttgcacattattataattatatt 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================================================ aaagattcgcttacgcaaaagtacttaaatttggctaatttcagccttttttagggcttaaaattcatctatatgcgtataattcattatttttgcacattattataattatatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI0204:PI0205|PI0204:PI0205:dGTP triphosphohydrolase (deoxyguanosinetriphosphate triphosphohydrolase):deoxyuridine 5'-triphosphate nucleotidohydrolase:->->:197606..197720 115 aaagattcgcttacgcaaaagtacttaaatttggctaatttcagccttttttagggcttaaaattcatctatatgcgtataattcattatttttgcacattattataattatatt Intra-Species Hit: Count: 1 Min: 1 Max: 115 Len: 115 Subject: pint_PI0204_PI0205|dGTP triphosphohydrolase (deoxyguanosinetriphosphate triphosphohydrolase):deoxyuridine 5'-triphosphate nucleotidohydrolase|POSITIVE:POSITIVE|[197606, 197720]|115 HSP 1 e-value: 3.0E-59 bit: 228.0 Len: 115 Query Start:1 Query End:115 Subject Strand: POSITIVE Subject Start: 1 Subject End: 115 aaagattcgcttacgcaaaagtacttaaatttggctaatttcagccttttttagggcttaaaattcatctatatgcgtataattcattatttttgcacattattataattatatt aaagattcgcttacgcaaaagtacttaaatttggctaatttcagccttttttagggcttaaaattcatctatatgcgtataattcattatttttgcacattattataattatatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAGAUUCGCUUACGCAAAAGUACUUAAAUUUGGCUAAUUUCAGCCUUUUUUAGGGCUUAAAAUUCAUCUAUAUGCGUAUAAUUCAUUAUUUUUGCACAUUAUUAUAAUUAUAUU ..............(((((((((((((((...((((......))))...))))))..............((((....))))......)))))))))................... (-17.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUAUAAUUAUAAUAAUGUGCAAAAAUAAUGAAUUAUACGCAUAUAGAUGAAUUUUAAGCCCUAAAAAAGGCUGAAAUUAGCCAAAUUUAAGUACUUUUGCGUAAGCGAAUCUUU ...............((((((..................)))))).....(((((((.(((........)))))))))).................(((((....)))))..... (-16.87) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 334 50 5 103 59 pint:PI2100|5end_conserved_hypothetical_protein_2053351..2053581_POSITIVE 291 70 29 199 161 pint:PI0285|5end_succinyltransferase_protein_270097..270327_POSITIVE 265 72 33 215 170 pint:PI0535|5end_hypothetical_protein_489508..489738_POSITIVE 234 59 20 184 137 pint:PI2178|5end_1-hydroxy-2-methyl-2-(E)-butenyl_4-diphosphate_synthase,_GcpE_2117677..2117907_POSITIVE 233 79 32 169 118 pint:PI0932|5end_conserved_hypothetical_protein;_possible_hemin_receptor_863854..864084_POSITIVE 231 60 14 168 114 pint:PI0331|5end_hypothetical_protein_311656..311886_POSITIVE 227 49 8 200 155 pint:PI0634|5end_conserved_hypothetical_protein_580082..580312_POSITIVE 226 88 44 184 137 pint:PI0869|5end_possible_exodeoxyribonuclease_VII_(small_subunit)_805518..805748_POSITIVE 220 78 38 227 188 pint:PI0460|5end_50S_ribosomal_protein_L3_432471..432701_POSITIVE 220 76 42 53 18 pint:PI0379|5end_conserved_hypothetical_protein_349872..350102_POSITIVE 219 58 14 125 81 pint:PI0141|5end_glutamine_amidotransferase_involved_in_pyridoxine_biosynthesis_132710..132940_POSITIVE 216 59 15 157 95 pint:PI0812|5end_conserved_hypothetical_protein;_possible_ferredoxin_750185..750415_POSITIVE 215 110 66 95 58 pint:PI0333|5end_hypothetical_protein_313478..313708_POSITIVE 213 47 1 203 157 pint:PI0477|5end_30S_ribosomal_protein_S5_440392..440622_POSITIVE 210 57 15 172 129 pint:PI0651|5end_HD_superfamily_hydrolase_592270..592500_POSITIVE 208 57 14 49 7 pint:PI2096|5end_conserved_hypothetical_protein;_possible_phosphoesterase_2050268..2050498_POSITIVE 208 72 34 189 145 pint:PI1242|5end_tRNA_(guanine-N1-)-methyltransferase_1167162..1167392_POSITIVE 206 50 4 120 62 pint:PI1629|5end_hypothetical_protein_1551707..1551937_POSITIVE 206 79 40 47 6 pint:PI0642|5end_thioredoxin_family_protein_584672..584902_POSITIVE 205 97 55 143 104 pint:PI0531|5end_ABC_transporter,_ATP-binding_protein;_possible_gliding_motility_related_484696..484926_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 265 72 33 117 72 pint:PI1533|3end_conserved_hypothetical_protein;_possible_transposase_1453589..1453739_POSITIVE 265 72 33 117 72 pint:PI0534|3end_conserved_hypothetical_protein;_possible_transposase_489490..489640_POSITIVE 251 58 11 116 67 pint:PI0340|3end_conserved_hypothetical_protein_316735..316885_POSITIVE 234 59 20 137 90 pint:PI2177|3end_phosphoribosylaminoimidazole_carboxylase_2117710..2117860_POSITIVE 227 49 8 118 73 pint:PI0633|3end_possible_preprotein_translocase,_YajC_subunit_580080..580230_POSITIVE 220 78 38 143 104 pint:PI0459|3end_30S_ribosomal_protein_S10_432467..432617_POSITIVE 219 58 14 59 15 pint:PI0139|3end_pyridoxine_biosynthesis_protein_132724..132874_POSITIVE 215 110 66 135 98 pint:PI0334|3end_hypothetical_protein_313598..313748_POSITIVE 215 110 66 89 52 pint:PI0332|3end_conserved_hypothetical_protein_313552..313702_POSITIVE 210 69 24 127 76 pint:PI1653|3end_hypothetical_protein_1565714..1565864_POSITIVE 206 79 34 107 67 pint:PI2025|3end_conserved_hypothetical_protein_1979452..1979602_POSITIVE 206 72 33 117 72 pint:PI1971|3end_possible_IS1249-related_transposase_1928949..1929099_POSITIVE 206 50 4 115 57 pint:PI1628|3end_hypothetical_protein_1551782..1551932_POSITIVE 205 97 55 124 85 pint:PI0530|3end_possible_membrane-fusion_protein_484757..484907_POSITIVE 202 80 31 125 71 pint:PI0683|3end_hypothetical_protein_619797..619947_POSITIVE 201 59 15 57 2 pint:PI2142|3end_conserved_hypothetical_protein_2089176..2089326_POSITIVE 195 58 30 35 3 pint:PI1651|3end_hypothetical_protein_1564512..1564662_POSITIVE 195 60 14 119 75 pint:PI0778|3end_hypothetical_protein_714885..715035_POSITIVE 194 80 31 111 57 pint:PI0166|3end_hypothetical_protein_161258..161408_POSITIVE 192 52 29 109 89 pint:PI1293|3end_ISPg4-related_transposase_(IS5_family)_1208447..1208597_POSITIVE